CORD-19-Sentences  

CORD-19:d8454139f839889cb542b3c91009e20ceded8625 JSONTXT 8 Projects

Annnotations TAB TSV DIC JSON TextAE Lectin_function

Id Subject Object Predicate Lexical cue
TextSentencer_T1 0-16 Sentence denotes xMAP Technology:
T84490 0-16 Sentence denotes xMAP Technology:
TextSentencer_T2 17-55 Sentence denotes Applications in Detection of Pathogens
T44896 17-55 Sentence denotes Applications in Detection of Pathogens
TextSentencer_T3 57-65 Sentence denotes Abstract
T32447 57-65 Sentence denotes Abstract
TextSentencer_T4 66-441 Sentence denotes xMAP technology is applicable for high-throughput, multiplex and simultaneous detection of different analytes within a single complex sample. xMAP multiplex assays are currently available in various nucleic acid and immunoassay formats, enabling simultaneous detection and typing of pathogenic viruses, bacteria, parasites and fungi and also antigen or antibody interception.
T84424 66-441 Sentence denotes xMAP technology is applicable for high-throughput, multiplex and simultaneous detection of different analytes within a single complex sample. xMAP multiplex assays are currently available in various nucleic acid and immunoassay formats, enabling simultaneous detection and typing of pathogenic viruses, bacteria, parasites and fungi and also antigen or antibody interception.
TextSentencer_T5 442-610 Sentence denotes As an open architecture platform, the xMAP technology is beneficial to end users and therefore it is used in various pharmaceutical, clinical and research laboratories.
T4651 442-610 Sentence denotes As an open architecture platform, the xMAP technology is beneficial to end users and therefore it is used in various pharmaceutical, clinical and research laboratories.
TextSentencer_T6 611-768 Sentence denotes The main aim of this review is to summarize the latest findings and applications in the field of pathogen detection using microsphere-based multiplex assays.
T5861 611-768 Sentence denotes The main aim of this review is to summarize the latest findings and applications in the field of pathogen detection using microsphere-based multiplex assays.
TextSentencer_T7 770-1007 Sentence denotes High-throughput multiplex detection techniques are designed for the rapid, sensitive and specific testing of large numbers of analytes (nucleic acid assays, immunoassays, enzyme assays, or receptor-ligands) in a single biological sample.
T69911 770-1007 Sentence denotes High-throughput multiplex detection techniques are designed for the rapid, sensitive and specific testing of large numbers of analytes (nucleic acid assays, immunoassays, enzyme assays, or receptor-ligands) in a single biological sample.
TextSentencer_T8 1008-1069 Sentence denotes These techniques enable analysis of large numbers of samples.
T30498 1008-1069 Sentence denotes These techniques enable analysis of large numbers of samples.
TextSentencer_T9 1070-1671 Sentence denotes On the other hand, there are also classical single reaction detection methods based on determination of nucleic acids such as polymerase chain reaction (PCR) (Dunbar, 2006; Taylor et al., 2001) , quantitative real-time PCR (qPCR) (Wuyts et al., 2015; Iannone et al., 2000) , reverse transcription PCR (RT-PCR) (Weis et al., 1992) and reverse transcription quantitative PCR (RT-qPCR) (Bustin, 2000) , or antibody-based tests like enzyme-linked immunosorbent assays (ELISA) (Engvall and Perlmann, 1971; Vanweeme and Schuurs, 1971 ) represent nowadays the "gold diagnostic standard" in many laboratories.
T93536 1070-1671 Sentence denotes On the other hand, there are also classical single reaction detection methods based on determination of nucleic acids such as polymerase chain reaction (PCR) (Dunbar, 2006; Taylor et al., 2001) , quantitative real-time PCR (qPCR) (Wuyts et al., 2015; Iannone et al., 2000) , reverse transcription PCR (RT-PCR) (Weis et al., 1992) and reverse transcription quantitative PCR (RT-qPCR) (Bustin, 2000) , or antibody-based tests like enzyme-linked immunosorbent assays (ELISA) (Engvall and Perlmann, 1971; Vanweeme and Schuurs, 1971 ) represent nowadays the "gold diagnostic standard" in many laboratories.
TextSentencer_T10 1672-1938 Sentence denotes Despite the previous implementation of these methods for routine rapid, sensitive, specific and cost-effective molecular diagnostics, their ability to simultaneously detect multiple analytes in a single reaction is limited and this limitation has yet to be overcome.
T99696 1672-1938 Sentence denotes Despite the previous implementation of these methods for routine rapid, sensitive, specific and cost-effective molecular diagnostics, their ability to simultaneously detect multiple analytes in a single reaction is limited and this limitation has yet to be overcome.
TextSentencer_T11 1939-2179 Sentence denotes The increasing amount of proteomic, transcriptomic and genomic sequence data from a large number of organisms accessible in public databases represents an exceptional opportunity for the development of new, multiplex detection technologies.
T69957 1939-2179 Sentence denotes The increasing amount of proteomic, transcriptomic and genomic sequence data from a large number of organisms accessible in public databases represents an exceptional opportunity for the development of new, multiplex detection technologies.
TextSentencer_T12 2180-2398 Sentence denotes The Luminex R xMAP technology (x = analyte, MAP = Multi-Analyte Profiling) that was invented in the late 1990s represents such a platform that can benefit from all the advances in DNA research (Angeloni et al., 2014) .
T77137 2180-2398 Sentence denotes The Luminex R xMAP technology (x = analyte, MAP = Multi-Analyte Profiling) that was invented in the late 1990s represents such a platform that can benefit from all the advances in DNA research (Angeloni et al., 2014) .
TextSentencer_T13 2399-2731 Sentence denotes Although PCR allows multiplex amplification of several targets in a single run xMAP as a methodology represents a significant step forward, and was designed with the aim of creating a high-throughput bioassay platform, enabling rapid, cost-effective, and simultaneous analysis of multiple analytes within a single biological sample.
T22730 2399-2731 Sentence denotes Although PCR allows multiplex amplification of several targets in a single run xMAP as a methodology represents a significant step forward, and was designed with the aim of creating a high-throughput bioassay platform, enabling rapid, cost-effective, and simultaneous analysis of multiple analytes within a single biological sample.
TextSentencer_T14 2732-2921 Sentence denotes As an open architecture platform, the xMAP system holds many benefits for the end user and therefore it is used in pharmaceutical, clinical and research laboratories (Dunbar and Li, 2010) .
T91117 2732-2921 Sentence denotes As an open architecture platform, the xMAP system holds many benefits for the end user and therefore it is used in pharmaceutical, clinical and research laboratories (Dunbar and Li, 2010) .
TextSentencer_T15 2922-3114 Sentence denotes The main aim of this review is to summarize the state-of-the-art of xMAP technology applications in the detection of viral, bacterial, parasitical and fungal pathogens from different matrices.
T92743 2922-3114 Sentence denotes The main aim of this review is to summarize the state-of-the-art of xMAP technology applications in the detection of viral, bacterial, parasitical and fungal pathogens from different matrices.
TextSentencer_T16 3115-3203 Sentence denotes The principle of xMAP technology is based on the concept of a liquid (suspension) array.
T32488 3115-3203 Sentence denotes The principle of xMAP technology is based on the concept of a liquid (suspension) array.
TextSentencer_T17 3204-3462 Sentence denotes In contrast to the conventional microarray technology where the identity of the analyte is characterized by its position on the glass slide, the xMAP technology uses different sets of microspheres in a liquid suspension as determiners of analyte specificity.
T97034 3204-3462 Sentence denotes In contrast to the conventional microarray technology where the identity of the analyte is characterized by its position on the glass slide, the xMAP technology uses different sets of microspheres in a liquid suspension as determiners of analyte specificity.
TextSentencer_T18 3463-3543 Sentence denotes Microsphere sets are internally dyed with two spectrally different fluorophores.
T63185 3463-3543 Sentence denotes Microsphere sets are internally dyed with two spectrally different fluorophores.
TextSentencer_T19 3544-3747 Sentence denotes The spectral signature is unique for each microsphere set and is determined by different concentrations of internal dyes, producing a 100-member array of spectrally distinct microsphere sets (Figure 1 ).
T11873 3544-3747 Sentence denotes The spectral signature is unique for each microsphere set and is determined by different concentrations of internal dyes, producing a 100-member array of spectrally distinct microsphere sets (Figure 1 ).
TextSentencer_T20 3748-3870 Sentence denotes Integration of a third internal dye has allowed the expansion of up to 500-member microsphere sets (Dunbar and Li, 2010) .
T28434 3748-3870 Sentence denotes Integration of a third internal dye has allowed the expansion of up to 500-member microsphere sets (Dunbar and Li, 2010) .
TextSentencer_T21 3871-4079 Sentence denotes The surface of each microsphere set allows a simple chemical coupling of various reagents specific to a particular bioassay, such as nucleic acid assays, immunoassays, enzyme assays or receptor-ligand assays.
T50783 3871-4079 Sentence denotes The surface of each microsphere set allows a simple chemical coupling of various reagents specific to a particular bioassay, such as nucleic acid assays, immunoassays, enzyme assays or receptor-ligand assays.
TextSentencer_T22 4080-4274 Sentence denotes A further fluorescent reporter (e.g., Streptavidin-R-phycoerythrin, Alexa 532, Cy3) is coupled to a target molecule, which allows its detection after specific capture on the microsphere surface.
T42526 4080-4274 Sentence denotes A further fluorescent reporter (e.g., Streptavidin-R-phycoerythrin, Alexa 532, Cy3) is coupled to a target molecule, which allows its detection after specific capture on the microsphere surface.
TextSentencer_T23 4275-4454 Sentence denotes There are different types of commercially available microspheres (Table 1) , and their selection is generally FIGURE 1 | The xMAP Technology based on internally dyed microspheres.
T13588 4275-4454 Sentence denotes There are different types of commercially available microspheres (Table 1) , and their selection is generally FIGURE 1 | The xMAP Technology based on internally dyed microspheres.
TextSentencer_T24 4455-4563 Sentence denotes Different concentrations of red and infrared fluorophores were used to create 100 distinct microsphere sets.
T39074 4455-4563 Sentence denotes Different concentrations of red and infrared fluorophores were used to create 100 distinct microsphere sets.
TextSentencer_T25 4564-4838 Sentence denotes Each set is able to conjugate to a specific target molecule (yellow and orange lines = nucleic acid; green star = fluorescent reporter). determined by the type of instrumentation used for detection and the particular analyte of interest (Dunbar and Li, 2010; Houser, 2012) .
T50917 4564-4838 Sentence denotes Each set is able to conjugate to a specific target molecule (yellow and orange lines = nucleic acid; green star = fluorescent reporter). determined by the type of instrumentation used for detection and the particular analyte of interest (Dunbar and Li, 2010; Houser, 2012) .
TextSentencer_T26 4839-5026 Sentence denotes Basic microspheres are 5.6 µm polystyrene beads whose surface is covered by approximately 10 8 carboxyl groups (COOH) for covalent coupling of capture reagents (Tang and Stratton, 2006) .
T2 4839-5026 Sentence denotes Basic microspheres are 5.6 µm polystyrene beads whose surface is covered by approximately 10 8 carboxyl groups (COOH) for covalent coupling of capture reagents (Tang and Stratton, 2006) .
TextSentencer_T27 5027-5169 Sentence denotes Magnetic microspheres (Figure 2 ) differ in size and structure through the addition of a magnetite layer (Dunbar and Li, 2010; Houser, 2012) .
T59828 5027-5169 Sentence denotes Magnetic microspheres (Figure 2 ) differ in size and structure through the addition of a magnetite layer (Dunbar and Li, 2010; Houser, 2012) .
TextSentencer_T28 5170-5310 Sentence denotes Usage of magnetic beads improves washing efficiency as the magnetic separation step enables the elimination of unwanted sample constituents.
T36565 5170-5310 Sentence denotes Usage of magnetic beads improves washing efficiency as the magnetic separation step enables the elimination of unwanted sample constituents.
TextSentencer_T29 5311-5521 Sentence denotes Moreover, MagPlex-TAG microspheres are covalently pre-coupled with unique 24 base pair-(bp)-long anti-TAG oligonucleotides that serve as an anchor for target sequences containing the complementary TAG sequence.
T5388 5311-5521 Sentence denotes Moreover, MagPlex-TAG microspheres are covalently pre-coupled with unique 24 base pair-(bp)-long anti-TAG oligonucleotides that serve as an anchor for target sequences containing the complementary TAG sequence.
TextSentencer_T30 5522-5614 Sentence denotes This proprietary TAG system (xTAG technology) is optimized to have minimum cross-reactivity.
T96602 5522-5614 Sentence denotes This proprietary TAG system (xTAG technology) is optimized to have minimum cross-reactivity.
TextSentencer_T31 5615-5819 Sentence denotes An assay can be easily designed by adding a complementary TAG sequence into the sequence of the primer or detection probe of interest and hybridization to the anti-TAG sequence on the microsphere surface.
T91925 5615-5819 Sentence denotes An assay can be easily designed by adding a complementary TAG sequence into the sequence of the primer or detection probe of interest and hybridization to the anti-TAG sequence on the microsphere surface.
TextSentencer_T32 5820-5880 Sentence denotes The analysis of beads is in general performed by two lasers.
T37181 5820-5880 Sentence denotes The analysis of beads is in general performed by two lasers.
TextSentencer_T33 5881-6059 Sentence denotes The red classification laser/LED (635 nm) excites the inner fluorescent dyes of the microspheres, thus identifying a specific microsphere set according to its spectral signature.
T54956 5881-6059 Sentence denotes The red classification laser/LED (635 nm) excites the inner fluorescent dyes of the microspheres, thus identifying a specific microsphere set according to its spectral signature.
TextSentencer_T34 6060-6234 Sentence denotes If the analyte of interest is present, the green reporter laser/LED (525-532 nm) recognizes the fluorescent reporter bound to the captured analyte on the microsphere surface.
T92911 6060-6234 Sentence denotes If the analyte of interest is present, the green reporter laser/LED (525-532 nm) recognizes the fluorescent reporter bound to the captured analyte on the microsphere surface.
TextSentencer_T35 6235-6318 Sentence denotes There are approximately 10 4 microspheres from each set present in a single sample.
T34824 6235-6318 Sentence denotes There are approximately 10 4 microspheres from each set present in a single sample.
TextSentencer_T36 6319-6474 Sentence denotes This number represents the range in xMAP, in which it is possible to perform determination of quantity according to a calibration curve, similarly to qPCR.
T27656 6319-6474 Sentence denotes This number represents the range in xMAP, in which it is possible to perform determination of quantity according to a calibration curve, similarly to qPCR.
TextSentencer_T37 6475-6721 Sentence denotes However, one must bear in mind that inclusion of a PCR amplification step prior to xMAP analysis does not reveal the real number of DNA molecules present in the original sample, but can only be used for the approximate estimation of DNA quantity.
T33614 6475-6721 Sentence denotes However, one must bear in mind that inclusion of a PCR amplification step prior to xMAP analysis does not reveal the real number of DNA molecules present in the original sample, but can only be used for the approximate estimation of DNA quantity.
TextSentencer_T38 6722-6778 Sentence denotes Therefore, xMAP can provide only semi-quantitative data.
T94367 6722-6778 Sentence denotes Therefore, xMAP can provide only semi-quantitative data.
TextSentencer_T39 6779-6873 Sentence denotes The simultaneous reading of both spectra is performed in purpose-designed readers ( Table 2) .
T77497 6779-6873 Sentence denotes The simultaneous reading of both spectra is performed in purpose-designed readers ( Table 2) .
TextSentencer_T40 6874-6988 Sentence denotes They differ by their mechanisms of fluorescence capture and by the maximum number of samples that can be analyzed.
T23695 6874-6988 Sentence denotes They differ by their mechanisms of fluorescence capture and by the maximum number of samples that can be analyzed.
TextSentencer_T41 6989-7117 Sentence denotes The basic detection instrument, which is called MAGPIX, is compatible only with magnetic microspheres (MagPlex and MagPlex-TAG).
T98211 6989-7117 Sentence denotes The basic detection instrument, which is called MAGPIX, is compatible only with magnetic microspheres (MagPlex and MagPlex-TAG).
TextSentencer_T42 7118-7267 Sentence denotes The principle of microsphere analysis in the MAGPIX instrument is based on their immobilization in the monolayer on the magnetic surface (Figure 3) .
T94868 7118-7267 Sentence denotes The principle of microsphere analysis in the MAGPIX instrument is based on their immobilization in the monolayer on the magnetic surface (Figure 3) .
TextSentencer_T43 7268-7438 Sentence denotes Unlike flowbased instruments, the fluorescent imager of the MAGPIX system reads all the microspheres at once, while generating data that is comparable with other methods.
T53482 7268-7438 Sentence denotes Unlike flowbased instruments, the fluorescent imager of the MAGPIX system reads all the microspheres at once, while generating data that is comparable with other methods.
TextSentencer_T44 7439-7482 Sentence denotes Reading a 96-well-plate takes about 60 min.
T65228 7439-7482 Sentence denotes Reading a 96-well-plate takes about 60 min.
TextSentencer_T45 7483-7561 Sentence denotes The maximal reading capacity of MAGPIX instruments is limited to 50 bead sets.
T48985 7483-7561 Sentence denotes The maximal reading capacity of MAGPIX instruments is limited to 50 bead sets.
TextSentencer_T46 7562-7695 Sentence denotes Advanced detection instruments -the Luminex 100/200 (Bio-Plex 200) and FlexMAP (Bio-Plex) 3D -are based on flow cytometry principles.
T72751 7562-7695 Sentence denotes Advanced detection instruments -the Luminex 100/200 (Bio-Plex 200) and FlexMAP (Bio-Plex) 3D -are based on flow cytometry principles.
TextSentencer_T47 7696-7780 Sentence denotes The microspheres with bound analyte are focused into a rapidly flowing fluid stream.
T52200 7696-7780 Sentence denotes The microspheres with bound analyte are focused into a rapidly flowing fluid stream.
TextSentencer_T48 7781-7901 Sentence denotes Each microsphere is then individually detected and digitally processed as the stream passes through the imaging cuvette.
T28340 7781-7901 Sentence denotes Each microsphere is then individually detected and digitally processed as the stream passes through the imaging cuvette.
TextSentencer_T49 7902-7993 Sentence denotes Flow cytometrybased platforms are convenient for applications with samples of limited size.
T67383 7902-7993 Sentence denotes Flow cytometrybased platforms are convenient for applications with samples of limited size.
TextSentencer_T50 7994-8086 Sentence denotes The reading of a 96-well-plate is faster than in the MAGPIX system and takes 45 min or less.
T85817 7994-8086 Sentence denotes The reading of a 96-well-plate is faster than in the MAGPIX system and takes 45 min or less.
TextSentencer_T51 8087-8188 Sentence denotes The capacity of the 3D platform is further increased by the possibility of analyzing 384-well plates.
T31210 8087-8188 Sentence denotes The capacity of the 3D platform is further increased by the possibility of analyzing 384-well plates.
TextSentencer_T52 8189-8439 Sentence denotes The microsphere-based technology can be applied in various assay formats, which can be divided, according to the type of analyte, into microsphere-based multiplex nucleic acid assay formats (MBMNA) and microsphere-based multiplex immunoassays (MBMI).
T1264 8189-8439 Sentence denotes The microsphere-based technology can be applied in various assay formats, which can be divided, according to the type of analyte, into microsphere-based multiplex nucleic acid assay formats (MBMNA) and microsphere-based multiplex immunoassays (MBMI).
TextSentencer_T53 8440-8640 Sentence denotes In general, xMAP-based assay formats are in comparison to other commonly used methods very open and flexible, ensuring the result data within few hours, while requiring only minimal amounts of sample.
T45011 8440-8640 Sentence denotes In general, xMAP-based assay formats are in comparison to other commonly used methods very open and flexible, ensuring the result data within few hours, while requiring only minimal amounts of sample.
TextSentencer_T54 8641-8910 Sentence denotes Detection assays based on nucleic acids have a potential for high levels of multiplexing, approaching the levels of sensitivity achieved by target amplification methods like multiplex PCR or TaqMan chemistry assays, while using the same protocols of DNA/RNA extraction.
T67118 8641-8910 Sentence denotes Detection assays based on nucleic acids have a potential for high levels of multiplexing, approaching the levels of sensitivity achieved by target amplification methods like multiplex PCR or TaqMan chemistry assays, while using the same protocols of DNA/RNA extraction.
TextSentencer_T55 8911-9225 Sentence denotes Multiplex oligonucleotide ligation PCR assay format (MOL-PCR) is able to simultaneously perform detection and identification, strain typing, detect antibiotic resistance determination, virulence prediction, etc., thereby surpasses other methods like Multiplex Ligation-dependent Probe Amplification (MLPA) or qPCR.
T64409 8911-9225 Sentence denotes Multiplex oligonucleotide ligation PCR assay format (MOL-PCR) is able to simultaneously perform detection and identification, strain typing, detect antibiotic resistance determination, virulence prediction, etc., thereby surpasses other methods like Multiplex Ligation-dependent Probe Amplification (MLPA) or qPCR.
TextSentencer_T56 9226-9373 Sentence denotes The disadvantage of technology is that it is not capable to perform quantitative analysis like qPCR, because providing only semi-quantitative data.
T54384 9226-9373 Sentence denotes The disadvantage of technology is that it is not capable to perform quantitative analysis like qPCR, because providing only semi-quantitative data.
TextSentencer_T57 9374-9538 Sentence denotes xMAP immunoassays surpass the common enzyme immunoassays in the ability of multiple simultaneous detection, while requiring smaller amount of sample and lower cost.
T73041 9374-9538 Sentence denotes xMAP immunoassays surpass the common enzyme immunoassays in the ability of multiple simultaneous detection, while requiring smaller amount of sample and lower cost.
TextSentencer_T58 9539-9616 Sentence denotes Moreover, these assay formats produce superior dynamic range and sensitivity.
T14070 9539-9616 Sentence denotes Moreover, these assay formats produce superior dynamic range and sensitivity.
TextSentencer_T59 9617-9823 Sentence denotes xMAP technology is applicable in numerous nucleic acid assay formats such as, e.g., gene expression analysis, microRNA analysis, single nucleotide polymorphism (SNP) analysis or specific sequence detection.
T17645 9617-9823 Sentence denotes xMAP technology is applicable in numerous nucleic acid assay formats such as, e.g., gene expression analysis, microRNA analysis, single nucleotide polymorphism (SNP) analysis or specific sequence detection.
TextSentencer_T60 9824-9996 Sentence denotes Basically, nucleic acid assays can be developed by coupling sequence-specific capture oligos to magnetic microspheres or by use of xTAG technology (Angeloni et al., 2014) .
T22879 9824-9996 Sentence denotes Basically, nucleic acid assays can be developed by coupling sequence-specific capture oligos to magnetic microspheres or by use of xTAG technology (Angeloni et al., 2014) .
TextSentencer_T61 9997-10156 Sentence denotes When performing xMAP analysis of nucleic acids it is essential to include PCR amplification to enrich the number of targets in the sample to detectable levels.
T20791 9997-10156 Sentence denotes When performing xMAP analysis of nucleic acids it is essential to include PCR amplification to enrich the number of targets in the sample to detectable levels.
TextSentencer_T62 10157-10267 Sentence denotes There are two general strategies for including a PCR step in the detection of pathogens using xMAP technology.
T58460 10157-10267 Sentence denotes There are two general strategies for including a PCR step in the detection of pathogens using xMAP technology.
TextSentencer_T63 10268-10357 Sentence denotes The main difference between the two lies in which phase the PCR amplification is applied.
T18134 10268-10357 Sentence denotes The main difference between the two lies in which phase the PCR amplification is applied.
TextSentencer_T64 10358-10610 Sentence denotes In direct DNA hybridization (DDH), allele-specific primer extension (ASPE), single base chain extension (SBCE), and Oligonucleotide ligation assay (OLA) all the target DNA sequences are amplified in multiplex PCR prior to hybridization to microspheres.
T23911 10358-10610 Sentence denotes In direct DNA hybridization (DDH), allele-specific primer extension (ASPE), single base chain extension (SBCE), and Oligonucleotide ligation assay (OLA) all the target DNA sequences are amplified in multiplex PCR prior to hybridization to microspheres.
TextSentencer_T65 10611-10822 Sentence denotes The disadvantage of these methods is that in assays containing large amounts of targets multiplex PCR leads to amplification bias, which is caused by the different lengths of the amplicons (Nolan et al., 2001) .
T93986 10611-10822 Sentence denotes The disadvantage of these methods is that in assays containing large amounts of targets multiplex PCR leads to amplification bias, which is caused by the different lengths of the amplicons (Nolan et al., 2001) .
TextSentencer_T66 10823-11056 Sentence denotes In contrast, in the multiplex oligonucleotide ligation PCR assay (MOL-PCR) sequence discrimination by detection probes occurs before the amplification step, which can subsequently be run just in singleplex PCR with universal primers.
T98311 10823-11056 Sentence denotes In contrast, in the multiplex oligonucleotide ligation PCR assay (MOL-PCR) sequence discrimination by detection probes occurs before the amplification step, which can subsequently be run just in singleplex PCR with universal primers.
TextSentencer_T67 11057-11224 Sentence denotes Direct DNA hybridization is one of the basic approaches used for the selective identification of sequences of interest from heterogeneous mixtures of DNAs (Figure 4) .
T49437 11057-11224 Sentence denotes Direct DNA hybridization is one of the basic approaches used for the selective identification of sequences of interest from heterogeneous mixtures of DNAs (Figure 4) .
TextSentencer_T68 11225-11441 Sentence denotes It is often used, e.g., for identification of species (Defoort et al., 2000; Page and Kurtzman, 2005; Righter et al., 2011; Liu Y. et al., 2012) or genotyping of pathogens (Letant et al., 2007; Zubach et al., 2012) .
T74386 11225-11441 Sentence denotes It is often used, e.g., for identification of species (Defoort et al., 2000; Page and Kurtzman, 2005; Righter et al., 2011; Liu Y. et al., 2012) or genotyping of pathogens (Letant et al., 2007; Zubach et al., 2012) .
TextSentencer_T69 11442-11668 Sentence denotes In DDH, the amplification of target sequences is ensured by specific primer pairs, and one primer from each pair is fluorescently labeled at the 5 end, permitting detection of the amplicon (Christopher-Hennings et al., 2013) .
T20182 11442-11668 Sentence denotes In DDH, the amplification of target sequences is ensured by specific primer pairs, and one primer from each pair is fluorescently labeled at the 5 end, permitting detection of the amplicon (Christopher-Hennings et al., 2013) .
TextSentencer_T70 11669-11816 Sentence denotes The subsequent incubation of amplicon with microspheres leads to a direct and specific hybridization between matching capture and target sequences.
T4274 11669-11816 Sentence denotes The subsequent incubation of amplicon with microspheres leads to a direct and specific hybridization between matching capture and target sequences.
TextSentencer_T71 11817-12025 Sentence denotes Amplicon sequences should be 100-300 bp in length FIGURE 4 | Direct DNA hybridization (DDH, yellow lines = capture oligonucleotide; orange line = amplified target sequence; green star = fluorescent reporter).
T85989 11817-12025 Sentence denotes Amplicon sequences should be 100-300 bp in length FIGURE 4 | Direct DNA hybridization (DDH, yellow lines = capture oligonucleotide; orange line = amplified target sequence; green star = fluorescent reporter).
TextSentencer_T72 12026-12110 Sentence denotes Target DNA sequence is amplified, while one of the primers is fluorescently labeled.
T82643 12026-12110 Sentence denotes Target DNA sequence is amplified, while one of the primers is fluorescently labeled.
TextSentencer_T73 12111-12240 Sentence denotes Amplicons are then specifically hybridized (according to complementarity) to capture oligonucleotides on the microsphere surface.
T91869 12111-12240 Sentence denotes Amplicons are then specifically hybridized (according to complementarity) to capture oligonucleotides on the microsphere surface.
TextSentencer_T74 12241-12375 Sentence denotes to minimize steric hindrance during hybridization and the capture sequence on microspheres should be 18-20 bp in size (Dunbar, 2006) .
T4717 12241-12375 Sentence denotes to minimize steric hindrance during hybridization and the capture sequence on microspheres should be 18-20 bp in size (Dunbar, 2006) .
TextSentencer_T75 12376-12491 Sentence denotes The specificity of the capture sequences and stringency of hybridization conditions allow discrimination up to SNP.
T18428 12376-12491 Sentence denotes The specificity of the capture sequences and stringency of hybridization conditions allow discrimination up to SNP.
TextSentencer_T76 12492-12654 Sentence denotes If the SNP or mutation discrimination is intended, the presumed mismatch should be located at the center of the capture sequence (Livshits and Mirzabekov, 1996) .
T80880 12492-12654 Sentence denotes If the SNP or mutation discrimination is intended, the presumed mismatch should be located at the center of the capture sequence (Livshits and Mirzabekov, 1996) .
TextSentencer_T77 12655-12804 Sentence denotes This assay format then requires a unique capture sequence coupled to a specific microsphere set to score each SNP allele (Kellar and Iannone, 2002) .
T76293 12655-12804 Sentence denotes This assay format then requires a unique capture sequence coupled to a specific microsphere set to score each SNP allele (Kellar and Iannone, 2002) .
TextSentencer_T78 12805-13066 Sentence denotes Allele-specific primer extension ( Figure 5 ) is an approach usually used for determination of allelic variants of pathogens (Page and Allele-specific detection probes, differing in one nucleotide on the polymorphic side, hybridize to amplified target sequence.
T94131 12805-13066 Sentence denotes Allele-specific primer extension ( Figure 5 ) is an approach usually used for determination of allelic variants of pathogens (Page and Allele-specific detection probes, differing in one nucleotide on the polymorphic side, hybridize to amplified target sequence.
TextSentencer_T79 13067-13203 Sentence denotes After addition of DNA polymerase and dNTPs (one of which is fluorescently labeled), molecules are extended according to complementarity.
T28144 13067-13203 Sentence denotes After addition of DNA polymerase and dNTPs (one of which is fluorescently labeled), molecules are extended according to complementarity.
TextSentencer_T80 13204-13271 Sentence denotes Products are captured by anti-TAGs on the specific microsphere set.
T31927 13204-13271 Sentence denotes Products are captured by anti-TAGs on the specific microsphere set.
TextSentencer_T81 13272-13307 Sentence denotes Kurtzman, 2005; Lin et al., 2008) .
T20298 13272-13307 Sentence denotes Kurtzman, 2005; Lin et al., 2008) .
TextSentencer_T82 13308-13488 Sentence denotes The defining characteristic of ASPE is the extension of two allele-specific detection probes, which contain a polymorphic site at the 3 end, defining the particular allele variant.
T90775 13308-13488 Sentence denotes The defining characteristic of ASPE is the extension of two allele-specific detection probes, which contain a polymorphic site at the 3 end, defining the particular allele variant.
TextSentencer_T83 13489-13666 Sentence denotes In this arrangement, DNA polymerase can extend detection probes by incorporation of dNTPs (one nucleotide is labeled, e.g., biotin-dCTP), if the allele is present in the sample.
T2909 13489-13666 Sentence denotes In this arrangement, DNA polymerase can extend detection probes by incorporation of dNTPs (one nucleotide is labeled, e.g., biotin-dCTP), if the allele is present in the sample.
TextSentencer_T84 13667-13784 Sentence denotes Just one probe is extended in the case of a homozygous target; conversely, in heterozygotes both probes are extended.
T68127 13667-13784 Sentence denotes Just one probe is extended in the case of a homozygous target; conversely, in heterozygotes both probes are extended.
TextSentencer_T85 13785-13902 Sentence denotes The fluorescence signal is generated by a fluorophore bound to labeled dNTPs, incorporated within the extended probe.
T54709 13785-13902 Sentence denotes The fluorescence signal is generated by a fluorophore bound to labeled dNTPs, incorporated within the extended probe.
TextSentencer_T86 13903-13980 Sentence denotes The use and assay format of SBCE is similar to the previously described ASPE.
T68615 13903-13980 Sentence denotes The use and assay format of SBCE is similar to the previously described ASPE.
TextSentencer_T87 13981-14061 Sentence denotes However, there are slight differences, mainly in the design of detection probes.
T33374 13981-14061 Sentence denotes However, there are slight differences, mainly in the design of detection probes.
TextSentencer_T88 14062-14181 Sentence denotes In the case of SBCE (Figure 6) , probe sequences are terminated one base before the polymorphic site Ye et al., 2001) .
T31956 14062-14181 Sentence denotes In the case of SBCE (Figure 6) , probe sequences are terminated one base before the polymorphic site Ye et al., 2001) .
TextSentencer_T89 14182-14471 Sentence denotes Due to this design the labeled dideoxyribonucleoside triphosphate (ddNTP) terminators serve as a "query" nucleotide and are used for single base probe extension at the same time; this assay requires the setting up of separate reactions for each of the four ddNTPs (ddC, ddG, ddA, and ddT).
T37812 14182-14471 Sentence denotes Due to this design the labeled dideoxyribonucleoside triphosphate (ddNTP) terminators serve as a "query" nucleotide and are used for single base probe extension at the same time; this assay requires the setting up of separate reactions for each of the four ddNTPs (ddC, ddG, ddA, and ddT).
TextSentencer_T90 14472-14768 Sentence denotes Moreover, PCR products from the previous step of PCR amplification of the target sequence need to be treated with exonuclease I and shrimp alkaline phosphatase (ExoI/SAP) before use as a template in the SBCE reaction (Ye et al., 2001; Dunbar, 2006) to get rid of unincorporated primers and dNTPs.
T46389 14472-14768 Sentence denotes Moreover, PCR products from the previous step of PCR amplification of the target sequence need to be treated with exonuclease I and shrimp alkaline phosphatase (ExoI/SAP) before use as a template in the SBCE reaction (Ye et al., 2001; Dunbar, 2006) to get rid of unincorporated primers and dNTPs.
TextSentencer_T91 14769-14936 Sentence denotes Although SBCE has been proven to be highly specific and reliable (Chen et al., 1999; Syvanen, 1999) , it is in the process of being replaced by less laborious methods.
T33752 14769-14936 Sentence denotes Although SBCE has been proven to be highly specific and reliable (Chen et al., 1999; Syvanen, 1999) , it is in the process of being replaced by less laborious methods.
TextSentencer_T92 14937-15114 Sentence denotes Oligonucleotide ligation-based formats include a ligation step of two oligonucleotide detection probes, which occurs in the presence of a target sequence of a specific pathogen.
T54772 14937-15114 Sentence denotes Oligonucleotide ligation-based formats include a ligation step of two oligonucleotide detection probes, which occurs in the presence of a target sequence of a specific pathogen.
TextSentencer_T93 15115-15270 Sentence denotes These assays are based on the ability of detection probes to hybridize next to each other on a complementary target DNA sequence (Landegren et al., 1988) .
T7811 15115-15270 Sentence denotes These assays are based on the ability of detection probes to hybridize next to each other on a complementary target DNA sequence (Landegren et al., 1988) .
TextSentencer_T94 15271-15587 Sentence denotes If there are no mismatches near the junction site and there is a phosphate group at the 5 end of a second probe (necessary for phosphodiester bond formation), annealing occurs; DNA ligase then recognizes the nick and forms a covalent bond between adjoining nucleotides while creating a single-stranded DNA molecule .
T96216 15271-15587 Sentence denotes If there are no mismatches near the junction site and there is a phosphate group at the 5 end of a second probe (necessary for phosphodiester bond formation), annealing occurs; DNA ligase then recognizes the nick and forms a covalent bond between adjoining nucleotides while creating a single-stranded DNA molecule .
TextSentencer_T95 15588-15771 Sentence denotes The most crucial step during the multiplexing of different ligation assays is the design of suitable probes with similar melting temperatures of between 51 and 56 • C (Dunbar, 2006) .
T92470 15588-15771 Sentence denotes The most crucial step during the multiplexing of different ligation assays is the design of suitable probes with similar melting temperatures of between 51 and 56 • C (Dunbar, 2006) .
TextSentencer_T96 15772-15899 Sentence denotes In the OLA assay format, the target DNA sequence is PCRamplified prior to the ligation step of the annealed probes (Figure 7) .
T84255 15772-15899 Sentence denotes In the OLA assay format, the target DNA sequence is PCRamplified prior to the ligation step of the annealed probes (Figure 7) .
TextSentencer_T97 15900-15974 Sentence denotes OLA is suitable for SNP genotyping Taylor et al., 2001; Ye et al., 2001) .
T10694 15900-15974 Sentence denotes OLA is suitable for SNP genotyping Taylor et al., 2001; Ye et al., 2001) .
TextSentencer_T98 15975-16088 Sentence denotes The multiplex oligonucleotide ligation PCR assay represents an improved version of the previous OLA assay format.
T49726 15975-16088 Sentence denotes The multiplex oligonucleotide ligation PCR assay represents an improved version of the previous OLA assay format.
TextSentencer_T99 16089-16202 Sentence denotes One advantage is that ligation is carried out prior to the PCRamplification (Figure 8 ) (Nolan and White, 2004) .
T85247 16089-16202 Sentence denotes One advantage is that ligation is carried out prior to the PCRamplification (Figure 8 ) (Nolan and White, 2004) .
TextSentencer_T100 16203-16386 Sentence denotes Unlike in the OLA assay, one of the detection probes consists of a sequence complementary to the target sequence and an extension composed of the TAG sequence and primer binding site.
T66750 16203-16386 Sentence denotes Unlike in the OLA assay, one of the detection probes consists of a sequence complementary to the target sequence and an extension composed of the TAG sequence and primer binding site.
TextSentencer_T101 16387-16536 Sentence denotes The FIGURE 6 | Principle of Single base chain extension (SBCE) (red dot = dideoxynucleotide; green star = fluorescent reporter; red line = anti-TAG).
T38143 16387-16536 Sentence denotes The FIGURE 6 | Principle of Single base chain extension (SBCE) (red dot = dideoxynucleotide; green star = fluorescent reporter; red line = anti-TAG).
TextSentencer_T102 16537-16615 Sentence denotes Specific detection probes are terminated one base before the polymorphic site.
T97878 16537-16615 Sentence denotes Specific detection probes are terminated one base before the polymorphic site.
TextSentencer_T103 16616-16750 Sentence denotes Utilization of fluorescently labeled dideoxynucleotides necessitates a separate reaction for each nucleotide in focus (minimally two).
T86366 16616-16750 Sentence denotes Utilization of fluorescently labeled dideoxynucleotides necessitates a separate reaction for each nucleotide in focus (minimally two).
TextSentencer_T104 16751-16957 Sentence denotes Target DNA hybridizes with probes after amplification but only the mix with the proper ddNTP leads ultimately to the synthesis of a labeled product, which is captured by anti-TAG on the microsphere surface.
T18844 16751-16957 Sentence denotes Target DNA hybridizes with probes after amplification but only the mix with the proper ddNTP leads ultimately to the synthesis of a labeled product, which is captured by anti-TAG on the microsphere surface.
TextSentencer_T105 16958-17039 Sentence denotes second probe is the same as the first except for the absence of the TAG sequence.
T2230 16958-17039 Sentence denotes second probe is the same as the first except for the absence of the TAG sequence.
TextSentencer_T106 17040-17147 Sentence denotes Each probe pair is specific for a particular target sequence, but all pairs share the same primer sequence.
T25632 17040-17147 Sentence denotes Each probe pair is specific for a particular target sequence, but all pairs share the same primer sequence.
TextSentencer_T107 17148-17546 Sentence denotes Basically, these modular detection probes anneal to a target sequence, ligate into a complex single-stranded DNA molecule and only if this occurs does the molecule become a template for singleplex PCR using a universal pair of primers (one is fluorescently FIGURE 7 | Principle of Oligonucleotide ligation assay (OLA) (green star = fluorescent reporter; Pho = phosphate group; red line = anti-TAG).
T39872 17148-17546 Sentence denotes Basically, these modular detection probes anneal to a target sequence, ligate into a complex single-stranded DNA molecule and only if this occurs does the molecule become a template for singleplex PCR using a universal pair of primers (one is fluorescently FIGURE 7 | Principle of Oligonucleotide ligation assay (OLA) (green star = fluorescent reporter; Pho = phosphate group; red line = anti-TAG).
TextSentencer_T108 17547-17638 Sentence denotes The target DNA sequence is PCR-amplified prior to the ligation step of the annealed probes.
T393 17547-17638 Sentence denotes The target DNA sequence is PCR-amplified prior to the ligation step of the annealed probes.
TextSentencer_T109 17639-17832 Sentence denotes One of the detection probes consists of a sequence complementary to the target sequence (polymorphic site at the 3 end if SNP identification is needed) and also an additional TAG tail sequence.
T25169 17639-17832 Sentence denotes One of the detection probes consists of a sequence complementary to the target sequence (polymorphic site at the 3 end if SNP identification is needed) and also an additional TAG tail sequence.
TextSentencer_T110 17833-17973 Sentence denotes The second detection probe is fully complementary to the target sequence and serves as a reporter due to its fluorescent label at the 3 end.
T17298 17833-17973 Sentence denotes The second detection probe is fully complementary to the target sequence and serves as a reporter due to its fluorescent label at the 3 end.
TextSentencer_T111 17974-18064 Sentence denotes Detection probes bind next to each other, DNA ligase recognizes the nick and makes a bond.
T36958 17974-18064 Sentence denotes Detection probes bind next to each other, DNA ligase recognizes the nick and makes a bond.
TextSentencer_T112 18065-18138 Sentence denotes The product is captured by anti-TAG on the microsphere surface. labeled).
T31262 18065-18138 Sentence denotes The product is captured by anti-TAG on the microsphere surface. labeled).
TextSentencer_T113 18139-18627 Sentence denotes Additionally, all the ligation products are very similar in length (approximately 100 bp -120 bp), so the use of a universal primer pair during PCR makes the simultaneous amplification FIGURE 8 | Principle of Multiplex oligonucleotide ligation PCR assay (MOL-PCR) (orange line = detection probe 1; green line = detection probe 2; blue lines = universal PCR primers; burgundy line = amplified negative strand; green star = fluorescent reporter; Pho = phosphate group; red line = anti-TAG).
T8098 18139-18627 Sentence denotes Additionally, all the ligation products are very similar in length (approximately 100 bp -120 bp), so the use of a universal primer pair during PCR makes the simultaneous amplification FIGURE 8 | Principle of Multiplex oligonucleotide ligation PCR assay (MOL-PCR) (orange line = detection probe 1; green line = detection probe 2; blue lines = universal PCR primers; burgundy line = amplified negative strand; green star = fluorescent reporter; Pho = phosphate group; red line = anti-TAG).
TextSentencer_T114 18628-18834 Sentence denotes Specific detection probes bind next to each other to target sequence via complementary parts, while the parts including the TAG sequence and binding sites for PCR primers form tails sticking out into space.
T41182 18628-18834 Sentence denotes Specific detection probes bind next to each other to target sequence via complementary parts, while the parts including the TAG sequence and binding sites for PCR primers form tails sticking out into space.
TextSentencer_T115 18835-18883 Sentence denotes DNA ligase recognizes the nick and makes a bond.
T23254 18835-18883 Sentence denotes DNA ligase recognizes the nick and makes a bond.
TextSentencer_T116 18884-19029 Sentence denotes The complex sequence of ligated probes becomes a template for singleplex PCR with universal primers; one of the primers is fluorescently labeled.
T79026 18884-19029 Sentence denotes The complex sequence of ligated probes becomes a template for singleplex PCR with universal primers; one of the primers is fluorescently labeled.
TextSentencer_T117 19030-19159 Sentence denotes Labeled amplicon hybridizes via its TAG sequence to capture anti-TAG on the microsphere. of many short fragments highly feasible.
T26662 19030-19159 Sentence denotes Labeled amplicon hybridizes via its TAG sequence to capture anti-TAG on the microsphere. of many short fragments highly feasible.
TextSentencer_T118 19160-19313 Sentence denotes All these facts ensure that MOL-PCR is not susceptible to the amplification bias that is characteristic of multiplex PCR or previously mentioned formats.
T60735 19160-19313 Sentence denotes All these facts ensure that MOL-PCR is not susceptible to the amplification bias that is characteristic of multiplex PCR or previously mentioned formats.
TextSentencer_T119 19314-19365 Sentence denotes Only a minimal amount of target/sample is required.
T56878 19314-19365 Sentence denotes Only a minimal amount of target/sample is required.
TextSentencer_T120 19366-19751 Sentence denotes The MOL-PCR upgrade has the potential to have widespread impact on genomic assays, because not only is sequence detection and SNP identification possible, but the detection of indels (insertion/deletion), screening tests for pathogens (virus, bacteria, fungi) from various matrices or determination of antibiotic resistances is also feasible Thierry et al., 2013; Wuyts et al., 2015) .
T7953 19366-19751 Sentence denotes The MOL-PCR upgrade has the potential to have widespread impact on genomic assays, because not only is sequence detection and SNP identification possible, but the detection of indels (insertion/deletion), screening tests for pathogens (virus, bacteria, fungi) from various matrices or determination of antibiotic resistances is also feasible Thierry et al., 2013; Wuyts et al., 2015) .
TextSentencer_T121 19752-19842 Sentence denotes MOL-PCR could replace, e.g., MLPA or qPCR in certain applications in routine diagnostics .
T26862 19752-19842 Sentence denotes MOL-PCR could replace, e.g., MLPA or qPCR in certain applications in routine diagnostics .
TextSentencer_T122 19843-20094 Sentence denotes Microsphere-based multiplex immunoassay (MBMIs) are typically biochemical tests that allow the detection or measuring of the concentration of an analyte (protein) in a solution through the use of an antibody or immunoglobulin (Angeloni et al., 2014) .
T57713 19843-20094 Sentence denotes Microsphere-based multiplex immunoassay (MBMIs) are typically biochemical tests that allow the detection or measuring of the concentration of an analyte (protein) in a solution through the use of an antibody or immunoglobulin (Angeloni et al., 2014) .
TextSentencer_T123 20095-20399 Sentence denotes Single-analyte ELISA cannot support simultaneous detection of multiple specific antibody responses within a single serum sample (Bokken et al., 2012) , and has further disadvantages, such as the requirement for a relatively large amount of sample, negligible non-specific binding or increased background.
T30144 20095-20399 Sentence denotes Single-analyte ELISA cannot support simultaneous detection of multiple specific antibody responses within a single serum sample (Bokken et al., 2012) , and has further disadvantages, such as the requirement for a relatively large amount of sample, negligible non-specific binding or increased background.
TextSentencer_T124 20400-20475 Sentence denotes MBMIs represent an alternative for commonly used indirect tests like ELISA.
T86008 20400-20475 Sentence denotes MBMIs represent an alternative for commonly used indirect tests like ELISA.
TextSentencer_T125 20476-20657 Sentence denotes The conversion of an ELISA assay to the MBMI format is uncomplicated, efficient, cost-saving and produces an assay with superior dynamic range and sensitivity (Baker et al., 2012) .
T39999 20476-20657 Sentence denotes The conversion of an ELISA assay to the MBMI format is uncomplicated, efficient, cost-saving and produces an assay with superior dynamic range and sensitivity (Baker et al., 2012) .
TextSentencer_T126 20658-20839 Sentence denotes MBMIs are often used in the diagnostics of various pathogens including multicellular organisms, such as e.g., parasites, in tests where the current methods are not sensitive enough.
T79332 20658-20839 Sentence denotes MBMIs are often used in the diagnostics of various pathogens including multicellular organisms, such as e.g., parasites, in tests where the current methods are not sensitive enough.
TextSentencer_T127 20840-20945 Sentence denotes The methods of choice are usually Capture Sandwich (CS) and Indirect Serological Assay (ISA) (Figure 9) .
T11243 20840-20945 Sentence denotes The methods of choice are usually Capture Sandwich (CS) and Indirect Serological Assay (ISA) (Figure 9) .
TextSentencer_T128 20946-21276 Sentence denotes However, the problems typical for methods based on serology remain: the need for periodical testing in order to avoid false negative results resulting from a wide and inevitable lag between infection and development of a specific response against a parasite in the form of IgG antibodies (sero-positivity) (Nockler et al., 1995) .
T96547 20946-21276 Sentence denotes However, the problems typical for methods based on serology remain: the need for periodical testing in order to avoid false negative results resulting from a wide and inevitable lag between infection and development of a specific response against a parasite in the form of IgG antibodies (sero-positivity) (Nockler et al., 1995) .
TextSentencer_T129 21277-21463 Sentence denotes The CS assay utilizes microspheres covalently coupled with a capture antibody (polyclonal antibodies should be purified and mono-specific) that takes up target molecules from the sample.
T44748 21277-21463 Sentence denotes The CS assay utilizes microspheres covalently coupled with a capture antibody (polyclonal antibodies should be purified and mono-specific) that takes up target molecules from the sample.
TextSentencer_T130 21464-21568 Sentence denotes This complex is recognized by a labeled detection antibody (Baker et al., 2012; Angeloni et al., 2014) .
T63390 21464-21568 Sentence denotes This complex is recognized by a labeled detection antibody (Baker et al., 2012; Angeloni et al., 2014) .
TextSentencer_T131 21569-21716 Sentence denotes The CS format can be used in cases where, for example, confirmation of pathogen identity within the inflammatory focus or altered tissue is needed.
T13841 21569-21716 Sentence denotes The CS format can be used in cases where, for example, confirmation of pathogen identity within the inflammatory focus or altered tissue is needed.
TextSentencer_T132 21717-21821 Sentence denotes In contrast to CS, in ISA a specific antibody against an antigen coupled with a microsphere is captured.
T92813 21717-21821 Sentence denotes In contrast to CS, in ISA a specific antibody against an antigen coupled with a microsphere is captured.
TextSentencer_T133 21822-21950 Sentence denotes If the binding of serum antibody to antigen occurs, a labeled secondary antibody (antiantibody) then provides the visualization.
T44014 21822-21950 Sentence denotes If the binding of serum antibody to antigen occurs, a labeled secondary antibody (antiantibody) then provides the visualization.
TextSentencer_T134 21951-22103 Sentence denotes ISA is typically used for serological screenings (monitoring and prevention purposes) that are carried out on serum samples (van der Wal et al., 2013) .
T22858 21951-22103 Sentence denotes ISA is typically used for serological screenings (monitoring and prevention purposes) that are carried out on serum samples (van der Wal et al., 2013) .
TextSentencer_T135 22104-22163 Sentence denotes The xMAP technology is used in many different applications.
T32054 22104-22163 Sentence denotes The xMAP technology is used in many different applications.
TextSentencer_T136 22164-22438 Sentence denotes This chapter describes the use of this technology for multiplex detection of viral, bacterial, parasitical and fungal agents using the microsphere-based multiplex nucleic acid-assay formats (MBMNA) and microsphere-based multiplex immuno-assay formats (MBMI) described above.
T77409 22164-22438 Sentence denotes This chapter describes the use of this technology for multiplex detection of viral, bacterial, parasitical and fungal agents using the microsphere-based multiplex nucleic acid-assay formats (MBMNA) and microsphere-based multiplex immuno-assay formats (MBMI) described above.
TextSentencer_T137 22439-22684 Sentence denotes Viruses are a very diverse group of infectious agents and are divided into groups according to a number of properties, e.g., type of nucleic acid, the presence of the viral envelope, antigenic structure, mode of transmission, pathogenicity, etc.
T70314 22439-22684 Sentence denotes Viruses are a very diverse group of infectious agents and are divided into groups according to a number of properties, e.g., type of nucleic acid, the presence of the viral envelope, antigenic structure, mode of transmission, pathogenicity, etc.
TextSentencer_T138 22685-22885 Sentence denotes They can be classified also according to the syndromes which they cause and mode of transmission, e.g., respiratory viruses, viruses causing gastroenteritis, tumors, hepatitis, rashes or neuroviruses.
T10108 22685-22885 Sentence denotes They can be classified also according to the syndromes which they cause and mode of transmission, e.g., respiratory viruses, viruses causing gastroenteritis, tumors, hepatitis, rashes or neuroviruses.
TextSentencer_T139 22886-23069 Sentence denotes To date, the majority of applications that enable multiplex viral detection and identification are based on the capture of viral nucleic acid by adoption of various DDH modifications.
T62111 22886-23069 Sentence denotes To date, the majority of applications that enable multiplex viral detection and identification are based on the capture of viral nucleic acid by adoption of various DDH modifications.
TextSentencer_T140 23070-23368 Sentence denotes Respiratory viruses are causative agents of the most common diseases of the human upper and lower respiratory tract, which are often associated with significant patient morbidity and mortality (Berry et al., 2015) , e.g., H5N1 subtype of highly pathogenic influenza A virus (Neumann et al., 2010) .
T55706 23070-23368 Sentence denotes Respiratory viruses are causative agents of the most common diseases of the human upper and lower respiratory tract, which are often associated with significant patient morbidity and mortality (Berry et al., 2015) , e.g., H5N1 subtype of highly pathogenic influenza A virus (Neumann et al., 2010) .
TextSentencer_T141 23369-23613 Sentence denotes The MBMNA method for more effective detection and genotyping of H5N1 viral isolates from clinical samples comprising pharyngeal swabs and tracheal aspirates was developed and its efficiency was compared with RT-PCR and qPCR (Zou et al., 2007) .
T11033 23369-23613 Sentence denotes The MBMNA method for more effective detection and genotyping of H5N1 viral isolates from clinical samples comprising pharyngeal swabs and tracheal aspirates was developed and its efficiency was compared with RT-PCR and qPCR (Zou et al., 2007) .
TextSentencer_T142 23614-23775 Sentence denotes The results using the MBMNA approach showed that this assay is vulnerable to viral mutations although the primers were designed according to conserved sequences.
T25185 23614-23775 Sentence denotes The results using the MBMNA approach showed that this assay is vulnerable to viral mutations although the primers were designed according to conserved sequences.
TextSentencer_T143 23776-23963 Sentence denotes Therefore, there is a need to monitor viral mutations in order to reduce false-negative results and add new primers and probes to adapt to the mutations, which is a disadvantage of MBMNA.
T90980 23776-23963 Sentence denotes Therefore, there is a need to monitor viral mutations in order to reduce false-negative results and add new primers and probes to adapt to the mutations, which is a disadvantage of MBMNA.
TextSentencer_T144 23964-24270 Sentence denotes On the other hand, MBMNA holds a number of advantages compared to RT-qPCR and qPCR, e.g., allele-specific probes with TAG sequences can be recognized by a universal set of primers, thus potentially eliminating the problem with different primer sets (which may be incompatible) used in conventional methods.
T98461 23964-24270 Sentence denotes On the other hand, MBMNA holds a number of advantages compared to RT-qPCR and qPCR, e.g., allele-specific probes with TAG sequences can be recognized by a universal set of primers, thus potentially eliminating the problem with different primer sets (which may be incompatible) used in conventional methods.
TextSentencer_T145 24271-24452 Sentence denotes Moreover, amplification is carried out with a single set of universal primers where only one primer is labeled; therefore, the background is low and no post-PCR cleanup is required.
T68790 24271-24452 Sentence denotes Moreover, amplification is carried out with a single set of universal primers where only one primer is labeled; therefore, the background is low and no post-PCR cleanup is required.
TextSentencer_T146 24453-24560 Sentence denotes Another application of the MBMNA method was developed for the identification of human adenoviruses (HAdVs).
T42333 24453-24560 Sentence denotes Another application of the MBMNA method was developed for the identification of human adenoviruses (HAdVs).
TextSentencer_T147 24561-24648 Sentence denotes Conventional serological identification of HAdVs serotypes is a time consuming process.
T76443 24561-24648 Sentence denotes Conventional serological identification of HAdVs serotypes is a time consuming process.
TextSentencer_T148 24649-25013 Sentence denotes Target-specific extension (TSE), which is a variant of ASPE was suggested to accelerate identification through the use of MBMNA for simultaneous identification of different serotypes; this is not possible using commercially available neutralization tests, antibody studies, or antigen detection by immunofluorescence or conventional PCR (Washington et al., 2010) .
T18073 24649-25013 Sentence denotes Target-specific extension (TSE), which is a variant of ASPE was suggested to accelerate identification through the use of MBMNA for simultaneous identification of different serotypes; this is not possible using commercially available neutralization tests, antibody studies, or antigen detection by immunofluorescence or conventional PCR (Washington et al., 2010) .
TextSentencer_T149 25014-25139 Sentence denotes Universal primers were used for nonspecific PCR amplification and serotype-specific probes coupled to tags were used for TSE.
T31712 25014-25139 Sentence denotes Universal primers were used for nonspecific PCR amplification and serotype-specific probes coupled to tags were used for TSE.
TextSentencer_T150 25140-25288 Sentence denotes This MBMNA procedure is methodically simple, the cost is relatively low, and it enables diagnosis of up to five HAdV serotypes in a single reaction.
T98300 25140-25288 Sentence denotes This MBMNA procedure is methodically simple, the cost is relatively low, and it enables diagnosis of up to five HAdV serotypes in a single reaction.
TextSentencer_T151 25289-25689 Sentence denotes Besides the in-house assays described above, commercial kits have also been developed for the detection of respiratory viruses by xMAP, e.g., xTAG R Respiratory Viral Panel (xTAG RVP) (Krunic et al., 2011) . xTAG RVP is multiplex nucleic acid test designed for detection of multiple respiratory virus nucleic acids in human nasopharyngeal swabs (Selvaraju and Selvarangan, 2012; Smith et al., 2012) .
T58762 25289-25689 Sentence denotes Besides the in-house assays described above, commercial kits have also been developed for the detection of respiratory viruses by xMAP, e.g., xTAG R Respiratory Viral Panel (xTAG RVP) (Krunic et al., 2011) . xTAG RVP is multiplex nucleic acid test designed for detection of multiple respiratory virus nucleic acids in human nasopharyngeal swabs (Selvaraju and Selvarangan, 2012; Smith et al., 2012) .
TextSentencer_T152 25690-26013 Sentence denotes Qualitative detection of a panel including respiratory syncytial virus (RSV), Influenza A virus (influenza A matrix, H1 subtype, H3 subtype, H5 subtype), Influenza B (Parainfluenza 1,2,3, and 4), Metapneumovirus (hMPV), HAdV, Entero-Rhinovirus, Corona NL63, Corona HKU1, Corona 229E, Corona OC43, and Bocavirus is possible.
T61455 25690-26013 Sentence denotes Qualitative detection of a panel including respiratory syncytial virus (RSV), Influenza A virus (influenza A matrix, H1 subtype, H3 subtype, H5 subtype), Influenza B (Parainfluenza 1,2,3, and 4), Metapneumovirus (hMPV), HAdV, Entero-Rhinovirus, Corona NL63, Corona HKU1, Corona 229E, Corona OC43, and Bocavirus is possible.
TextSentencer_T153 26014-26091 Sentence denotes Bacteriophage MS2 and bacteriophage λ DNA were used as the internal controls.
T58532 26014-26091 Sentence denotes Bacteriophage MS2 and bacteriophage λ DNA were used as the internal controls.
TextSentencer_T154 26092-26299 Sentence denotes The detection of respiratory virus targets using the xTAG RVP, which detects 20 respiratory viral targets, was compared with individual qPCR nucleic acid amplification tests (NATs) (Pabbaraju et al., 2008) .
T27889 26092-26299 Sentence denotes The detection of respiratory virus targets using the xTAG RVP, which detects 20 respiratory viral targets, was compared with individual qPCR nucleic acid amplification tests (NATs) (Pabbaraju et al., 2008) .
TextSentencer_T155 26300-26556 Sentence denotes The xTAG RVP can detect all the respiratory viral targets included in the in-house NAT panel, which is used for detection of Influenza A, B viruses (IFVA, IFVB), parainfluenza virus types 1 to 4 (PIV 1-4), RSV, hMPV, and respiratory adenovirus types (ADV).
T89800 26300-26556 Sentence denotes The xTAG RVP can detect all the respiratory viral targets included in the in-house NAT panel, which is used for detection of Influenza A, B viruses (IFVA, IFVB), parainfluenza virus types 1 to 4 (PIV 1-4), RSV, hMPV, and respiratory adenovirus types (ADV).
TextSentencer_T156 26557-26659 Sentence denotes Of the 1,530 samples tested, 532 were positive by xTAG RVP and 580 by in-house NATs for these targets.
T81844 26557-26659 Sentence denotes Of the 1,530 samples tested, 532 were positive by xTAG RVP and 580 by in-house NATs for these targets.
TextSentencer_T157 26660-26902 Sentence denotes This gives the xTAG RVP a sensitivity of 91.2% and a specificity of 99.7%; in addition, xTAG RVP can detect picornaviruses (the in-house assays did not detect 88 picornaviruses) and coronaviruses and can subtype IFVA positives simultaneously.
T96638 26660-26902 Sentence denotes This gives the xTAG RVP a sensitivity of 91.2% and a specificity of 99.7%; in addition, xTAG RVP can detect picornaviruses (the in-house assays did not detect 88 picornaviruses) and coronaviruses and can subtype IFVA positives simultaneously.
TextSentencer_T158 26903-27172 Sentence denotes The xTAG RVP includes all the respiratory viral targets that are tested routinely for the diagnosis of acute respiratory tract infections; further, the technology is flexible and can easily allow for incorporation of other targets (e.g., human bocavirus) in the future.
T69323 26903-27172 Sentence denotes The xTAG RVP includes all the respiratory viral targets that are tested routinely for the diagnosis of acute respiratory tract infections; further, the technology is flexible and can easily allow for incorporation of other targets (e.g., human bocavirus) in the future.
TextSentencer_T159 27173-27535 Sentence denotes The xTAG RVP assay was subsequently modified and was marketed as the xTAG RVP Fast assay, which has a simpler protocol; the results are obtained in a shorter time and handling of the amplified product is not required (amplified DNA is mixed with TAG primers specific to each viral target), which could be a potential contamination risk (Pabbaraju et al., 2011) .
T17526 27173-27535 Sentence denotes The xTAG RVP assay was subsequently modified and was marketed as the xTAG RVP Fast assay, which has a simpler protocol; the results are obtained in a shorter time and handling of the amplified product is not required (amplified DNA is mixed with TAG primers specific to each viral target), which could be a potential contamination risk (Pabbaraju et al., 2011) .
TextSentencer_T160 27536-27657 Sentence denotes The respiratory samples were tested for a variety of respiratory viral targets by xTAG RVP and xTAG RVP Fast in parallel.
T745 27536-27657 Sentence denotes The respiratory samples were tested for a variety of respiratory viral targets by xTAG RVP and xTAG RVP Fast in parallel.
TextSentencer_T161 27658-27967 Sentence denotes The xTAG RVP was more sensitive than xTAG RVP Fast (88.6% versus 77.5%) for all the viral targets; in addition, some targets (influenza B virus, parainfluenza virus type 2, and human coronavirus 229E) were not detected using xTAG RVP Fast and, e.g., the sensitivity for detection of IFVB was very low (41.3%).
T89152 27658-27967 Sentence denotes The xTAG RVP was more sensitive than xTAG RVP Fast (88.6% versus 77.5%) for all the viral targets; in addition, some targets (influenza B virus, parainfluenza virus type 2, and human coronavirus 229E) were not detected using xTAG RVP Fast and, e.g., the sensitivity for detection of IFVB was very low (41.3%).
TextSentencer_T162 27968-28045 Sentence denotes Therefore, it is not suitable as the primary assay for the detection of IFVB.
T86445 27968-28045 Sentence denotes Therefore, it is not suitable as the primary assay for the detection of IFVB.
TextSentencer_T163 28046-28197 Sentence denotes In addition to respiratory viral diseases the MBMNA was successfully applied also for detection of viral pathogens causing acute viral gastroenteritis.
T33218 28046-28197 Sentence denotes In addition to respiratory viral diseases the MBMNA was successfully applied also for detection of viral pathogens causing acute viral gastroenteritis.
TextSentencer_T164 28198-28362 Sentence denotes Acute viral gastroenteritis is usually caused by four distinct families of viruses: rotaviruses, noroviruses, astroviruses, and adenoviruses (Liu Y. et al., 2012) .
T21164 28198-28362 Sentence denotes Acute viral gastroenteritis is usually caused by four distinct families of viruses: rotaviruses, noroviruses, astroviruses, and adenoviruses (Liu Y. et al., 2012) .
TextSentencer_T165 28363-28554 Sentence denotes The authors focused on simultaneous detection of rotavirus A (RVA), noroviruses (NoVs), sapoviruses (SaV), human astrovirus (HAstV), enteric adenoviruses (EAds) and human bocavirus 2 (HBoV2).
T42160 28363-28554 Sentence denotes The authors focused on simultaneous detection of rotavirus A (RVA), noroviruses (NoVs), sapoviruses (SaV), human astrovirus (HAstV), enteric adenoviruses (EAds) and human bocavirus 2 (HBoV2).
TextSentencer_T166 28555-28635 Sentence denotes Altogether 140 fecal samples were tested using the MBMNA and RT-PCR in parallel.
T21277 28555-28635 Sentence denotes Altogether 140 fecal samples were tested using the MBMNA and RT-PCR in parallel.
TextSentencer_T167 28636-28813 Sentence denotes The specificity of MBMNA was equal to the conventional RT-PCR (>90%), but MBMNA was faster in terms of detection of different viral pathogens in one tube (Liu Y. et al., 2012) .
T28179 28636-28813 Sentence denotes The specificity of MBMNA was equal to the conventional RT-PCR (>90%), but MBMNA was faster in terms of detection of different viral pathogens in one tube (Liu Y. et al., 2012) .
TextSentencer_T168 28814-29115 Sentence denotes The studies of (Hamza et al., 2014) were also directed to the detection of human enteric viruses (human adenovirus (HAdV), human polyomavirus (HPyV), enterovirus (EV), rotavirus (RoV), norovirus GI (NoVGI), and norovirus GII (NoVGII), but environmental water samples were tested (Hamza et al., 2014) .
T59221 28814-29115 Sentence denotes The studies of (Hamza et al., 2014) were also directed to the detection of human enteric viruses (human adenovirus (HAdV), human polyomavirus (HPyV), enterovirus (EV), rotavirus (RoV), norovirus GI (NoVGI), and norovirus GII (NoVGII), but environmental water samples were tested (Hamza et al., 2014) .
TextSentencer_T169 29116-29275 Sentence denotes MBMNA provided high specificity and no cross-reactivity, but was not as sensitive as qPCR for the identification of viral contamination in river water samples.
T58300 29116-29275 Sentence denotes MBMNA provided high specificity and no cross-reactivity, but was not as sensitive as qPCR for the identification of viral contamination in river water samples.
TextSentencer_T170 29276-29490 Sentence denotes In contrast, all wastewater samples that were positive in qPCR were also positive by the MBMNA and the detection limit was higher than qPCR; MBMNA was as sensitive as qPCR for viral detection in wastewater samples.
T19809 29276-29490 Sentence denotes In contrast, all wastewater samples that were positive in qPCR were also positive by the MBMNA and the detection limit was higher than qPCR; MBMNA was as sensitive as qPCR for viral detection in wastewater samples.
TextSentencer_T171 29491-29609 Sentence denotes Therefore, MBMNA could be a reliable method for the simultaneous detection of viral pathogens, but only in wastewater.
T52668 29491-29609 Sentence denotes Therefore, MBMNA could be a reliable method for the simultaneous detection of viral pathogens, but only in wastewater.
TextSentencer_T172 29610-29918 Sentence denotes For detection of gastrointestinal pathogens xTAG R Gastrointestinal Pathogen Panel -GPP is commercially available [multiplex detection of various viral, bacterial and parasitic nucleic acids in human stool samples (Beckmann et al., 2014; Perry et al., 2014; Wessels et al., 2014; Zboromyrska et al., 2014) ].
T82149 29610-29918 Sentence denotes For detection of gastrointestinal pathogens xTAG R Gastrointestinal Pathogen Panel -GPP is commercially available [multiplex detection of various viral, bacterial and parasitic nucleic acids in human stool samples (Beckmann et al., 2014; Perry et al., 2014; Wessels et al., 2014; Zboromyrska et al., 2014) ].
TextSentencer_T173 29919-30095 Sentence denotes In comparison to the two previous studies mentioned above only three enteric viruses (norovirus, rotavirus and adenovirus 40/41) can be identified by the GPP (See chapter 4.2).
T90408 29919-30095 Sentence denotes In comparison to the two previous studies mentioned above only three enteric viruses (norovirus, rotavirus and adenovirus 40/41) can be identified by the GPP (See chapter 4.2).
TextSentencer_T174 30096-30178 Sentence denotes Viruses such as human papillomaviruses (HPV) are also associated with oncogenesis.
T14017 30096-30178 Sentence denotes Viruses such as human papillomaviruses (HPV) are also associated with oncogenesis.
TextSentencer_T175 30179-30412 Sentence denotes HPV belong to those viruses, which require simultaneous detection and typing to identify individual HPV types because the genotype determination is necessary for the investigation of epidemiology and behavior of individual HPV types.
T59083 30179-30412 Sentence denotes HPV belong to those viruses, which require simultaneous detection and typing to identify individual HPV types because the genotype determination is necessary for the investigation of epidemiology and behavior of individual HPV types.
TextSentencer_T176 30413-30743 Sentence denotes Therefore, DDH was designed for detection and genotyping of HPV using L1 consensus (primer systems, which can detect 10 to 100 molecules of HPV targets) resulting in the establishment of a method for simultaneous detection of 26 different HPV genotypes including 18 high-risk HPV and 8 lowrisk HPV genotypes (Jiang et al., 2006) .
T93455 30413-30743 Sentence denotes Therefore, DDH was designed for detection and genotyping of HPV using L1 consensus (primer systems, which can detect 10 to 100 molecules of HPV targets) resulting in the establishment of a method for simultaneous detection of 26 different HPV genotypes including 18 high-risk HPV and 8 lowrisk HPV genotypes (Jiang et al., 2006) .
TextSentencer_T177 30744-30892 Sentence denotes Subsequent analysis of the data showed that the 26-plex method precisely discriminated all 18 high-risk HPV targets and also 8 low-risk HPV targets.
T26583 30744-30892 Sentence denotes Subsequent analysis of the data showed that the 26-plex method precisely discriminated all 18 high-risk HPV targets and also 8 low-risk HPV targets.
TextSentencer_T178 30893-31016 Sentence denotes Another study focused on genotyping HPV also used specific probes targeting a region of the L1 gene (Zubach et al., 2012) .
T96090 30893-31016 Sentence denotes Another study focused on genotyping HPV also used specific probes targeting a region of the L1 gene (Zubach et al., 2012) .
TextSentencer_T179 31017-31332 Sentence denotes DDH was optimized for the detection and genotyping of 46 mucosal HPV types, which are associated with infections of the genital, anal, and oropharyngeal mucosae and the method enables a more comprehensive coverage of HPV types compared with the previously mentioned study, where only 26 types of HPV were genotyped.
T54662 31017-31332 Sentence denotes DDH was optimized for the detection and genotyping of 46 mucosal HPV types, which are associated with infections of the genital, anal, and oropharyngeal mucosae and the method enables a more comprehensive coverage of HPV types compared with the previously mentioned study, where only 26 types of HPV were genotyped.
TextSentencer_T180 31333-31629 Sentence denotes The DDH was more sensitive than the Linear Array (a leading commercial genotyping method) in terms of distinguishing positive/negative HPV samples, but less sensitive for detection of multiple HPV types; another limitation was the inability of the PCR system to amplify certain variants of HPV68.
T76532 31333-31629 Sentence denotes The DDH was more sensitive than the Linear Array (a leading commercial genotyping method) in terms of distinguishing positive/negative HPV samples, but less sensitive for detection of multiple HPV types; another limitation was the inability of the PCR system to amplify certain variants of HPV68.
TextSentencer_T181 31630-31794 Sentence denotes HPV genotype detection was by combined whole genome amplification and xMAP technology showed that this method is highly specific and sensitive (Lowe et al., 2010) .
T81755 31630-31794 Sentence denotes HPV genotype detection was by combined whole genome amplification and xMAP technology showed that this method is highly specific and sensitive (Lowe et al., 2010) .
TextSentencer_T182 31795-31918 Sentence denotes This approach is capable to identify all high risk HPV types with the analytical limit of detection 100 copies plasmid DNA.
T33366 31795-31918 Sentence denotes This approach is capable to identify all high risk HPV types with the analytical limit of detection 100 copies plasmid DNA.
TextSentencer_T183 31919-32377 Sentence denotes Many viruses can cause infections with fatal consequences for human health, e.g., Hendra and Nipah viruses, which can infect cells of the central nervous system and may cause relapsing encephalitis (Clayton et al., 2013) , Ebola virus, which causes lethal hemorrhagic disease in humans (Takada and Kawaoka, 2001) or Menangle virus, which causes an influenzalike illness with a rash in humans (Bowden et al., 2012) ; these zoonotic viruses are linked to bats.
T58559 31919-32377 Sentence denotes Many viruses can cause infections with fatal consequences for human health, e.g., Hendra and Nipah viruses, which can infect cells of the central nervous system and may cause relapsing encephalitis (Clayton et al., 2013) , Ebola virus, which causes lethal hemorrhagic disease in humans (Takada and Kawaoka, 2001) or Menangle virus, which causes an influenzalike illness with a rash in humans (Bowden et al., 2012) ; these zoonotic viruses are linked to bats.
TextSentencer_T184 32378-32522 Sentence denotes The surveillance of zoonotic viruses in wildlife populations is necessary in order to monitor the risk of emerging infectious disease outbreaks.
T4106 32378-32522 Sentence denotes The surveillance of zoonotic viruses in wildlife populations is necessary in order to monitor the risk of emerging infectious disease outbreaks.
TextSentencer_T185 32523-32806 Sentence denotes For the complex detection and genotyping of paramyxoviruses in Australian bats two bat virus panel assays (BVPA) for detection of paramyxoviruses in Australian bats (BVPA-1) and for paramyxoviruses and filoviruses in non-Australian bats (BVPA-2) were introduced (Boyd et al., 2015) .
T69193 32523-32806 Sentence denotes For the complex detection and genotyping of paramyxoviruses in Australian bats two bat virus panel assays (BVPA) for detection of paramyxoviruses in Australian bats (BVPA-1) and for paramyxoviruses and filoviruses in non-Australian bats (BVPA-2) were introduced (Boyd et al., 2015) .
TextSentencer_T186 32807-33005 Sentence denotes Examined RNA was extracted from the urine of bats and a total of 532 samples were tested in 11-plex BVPA-1 and 540 field 8-plex BVPA-2; both developed assays were proven to be reliable and accurate.
T58624 32807-33005 Sentence denotes Examined RNA was extracted from the urine of bats and a total of 532 samples were tested in 11-plex BVPA-1 and 540 field 8-plex BVPA-2; both developed assays were proven to be reliable and accurate.
TextSentencer_T187 33006-33400 Sentence denotes A number of pathogens, including viruses, are implicated in reproductive diseases of swine. (Chen et al., 2015) combined onestep asymmetric multiplex reverse transcription PCR (RT-PCR) with DDH for simultaneous detection of respiratory syndrome virus (PRRSV), porcine circovirus type 2 (PCV-2), porcine pseudorabies virus (PRV), classical swine fever virus (CSFV), and porcine parvovirus (PPV).
T63437 33006-33400 Sentence denotes A number of pathogens, including viruses, are implicated in reproductive diseases of swine. (Chen et al., 2015) combined onestep asymmetric multiplex reverse transcription PCR (RT-PCR) with DDH for simultaneous detection of respiratory syndrome virus (PRRSV), porcine circovirus type 2 (PCV-2), porcine pseudorabies virus (PRV), classical swine fever virus (CSFV), and porcine parvovirus (PPV).
TextSentencer_T188 33401-33462 Sentence denotes All strains of these five viruses were accurately identified.
T30618 33401-33462 Sentence denotes All strains of these five viruses were accurately identified.
TextSentencer_T189 33463-33677 Sentence denotes The results showed that the combination of RT-PCR with the DDH assay is more accurate and specific than the other methods, e.g., conventional RT-PCR, and could be a useful tool in the diagnostics of swine diseases.
T96522 33463-33677 Sentence denotes The results showed that the combination of RT-PCR with the DDH assay is more accurate and specific than the other methods, e.g., conventional RT-PCR, and could be a useful tool in the diagnostics of swine diseases.
TextSentencer_T190 33678-34007 Sentence denotes MBMNAs could become very important for veterinary diagnostic testing and (Christopher-Hennings et al., 2013) reported the potential use of MBMNAs for detection of different pathogens in pigs using panels for the multiplex detection of swine pathogens (viruses and bacteria) in serum, lung, oral fluids, feces and spleen or liver.
T11751 33678-34007 Sentence denotes MBMNAs could become very important for veterinary diagnostic testing and (Christopher-Hennings et al., 2013) reported the potential use of MBMNAs for detection of different pathogens in pigs using panels for the multiplex detection of swine pathogens (viruses and bacteria) in serum, lung, oral fluids, feces and spleen or liver.
TextSentencer_T191 34008-34208 Sentence denotes Although direct diagnosis based on the detection of the nucleic acids of viral pathogens described above prevails, xMAP antibody-based tests for the detection and typing of viruses are also available.
T63063 34008-34208 Sentence denotes Although direct diagnosis based on the detection of the nucleic acids of viral pathogens described above prevails, xMAP antibody-based tests for the detection and typing of viruses are also available.
TextSentencer_T192 34209-34485 Sentence denotes MBMI was used to develop a competitive immunoassay that measures HPV type 6, 11, 16, and 18 specific neutralizing antibodies (Opalka et al., 2003) ; this was later validated for use in epidemiology studies and clinical vaccine trials (Opalka et al., 2003; Dias et al., 2005) .
T56061 34209-34485 Sentence denotes MBMI was used to develop a competitive immunoassay that measures HPV type 6, 11, 16, and 18 specific neutralizing antibodies (Opalka et al., 2003) ; this was later validated for use in epidemiology studies and clinical vaccine trials (Opalka et al., 2003; Dias et al., 2005) .
TextSentencer_T193 34486-34600 Sentence denotes MBMI was also compared with a Western blot assay for the detection of HIVspecific antibodies (Kong et al., 2016) .
T3782 34486-34600 Sentence denotes MBMI was also compared with a Western blot assay for the detection of HIVspecific antibodies (Kong et al., 2016) .
TextSentencer_T194 34601-34737 Sentence denotes The microspheres were coupled with anti-p24 monoclonal antibody and with HIV antigens: gp41, p17, p24, p31, and p66 recombinant protein.
T71519 34601-34737 Sentence denotes The microspheres were coupled with anti-p24 monoclonal antibody and with HIV antigens: gp41, p17, p24, p31, and p66 recombinant protein.
TextSentencer_T195 34738-34850 Sentence denotes The results of both methods showed that MBMI sensitivity was 82.7% and Western blot assay sensitivity was 74.7%.
T26450 34738-34850 Sentence denotes The results of both methods showed that MBMI sensitivity was 82.7% and Western blot assay sensitivity was 74.7%.
TextSentencer_T196 34851-35010 Sentence denotes The MBMI was more efficient and precise for screening several parameters and based on the acquired results it was better in HIV diagnostics than Western blots.
T31361 34851-35010 Sentence denotes The MBMI was more efficient and precise for screening several parameters and based on the acquired results it was better in HIV diagnostics than Western blots.
TextSentencer_T197 35011-35166 Sentence denotes For the determination of antibodies against HCV in patient serum samples MBMI based on the antigenic properties of four recombinant proteins was designed .
T39556 35011-35166 Sentence denotes For the determination of antibodies against HCV in patient serum samples MBMI based on the antigenic properties of four recombinant proteins was designed .
TextSentencer_T198 35167-35448 Sentence denotes Only a small number of samples was tested and that is why the specificity and sensitivity were 100%, but in spite of this the MBMI has the potential to become a viable alternative to standard tests due to its excellent specificity and it may be used for screening of HCV infection.
T8843 35167-35448 Sentence denotes Only a small number of samples was tested and that is why the specificity and sensitivity were 100%, but in spite of this the MBMI has the potential to become a viable alternative to standard tests due to its excellent specificity and it may be used for screening of HCV infection.
TextSentencer_T199 35449-35887 Sentence denotes Detection of antibodies against several Epstein-Barr virus (EBV) antigens in nasopharyngeal carcinoma patients (NPC) showed the possibility of simultaneous detection of multiple markers using MBMI, which is not possible with ELISA, and because of the distinct EBV serology spectrum in individual NPC patients, the multiplexed microsphere assay has powerful potential to allow serological diagnosis of NPC in the future (Gu et al., 2008) .
T21026 35449-35887 Sentence denotes Detection of antibodies against several Epstein-Barr virus (EBV) antigens in nasopharyngeal carcinoma patients (NPC) showed the possibility of simultaneous detection of multiple markers using MBMI, which is not possible with ELISA, and because of the distinct EBV serology spectrum in individual NPC patients, the multiplexed microsphere assay has powerful potential to allow serological diagnosis of NPC in the future (Gu et al., 2008) .
TextSentencer_T200 35888-36120 Sentence denotes MBMI showed increased sensitivity and the possibility of quantifying antibodies, antigens, as well as other substances (e.g., hormones, cytokines, tumor markers, etc.), in contrast to conventional ELISA tests (duPont et al., 2005) .
T61196 35888-36120 Sentence denotes MBMI showed increased sensitivity and the possibility of quantifying antibodies, antigens, as well as other substances (e.g., hormones, cytokines, tumor markers, etc.), in contrast to conventional ELISA tests (duPont et al., 2005) .
TextSentencer_T201 36121-36220 Sentence denotes The majority of applications for multiplex bacterial diagnostics are based on the detection of DNA.
T19576 36121-36220 Sentence denotes The majority of applications for multiplex bacterial diagnostics are based on the detection of DNA.
TextSentencer_T202 36221-36372 Sentence denotes The most widely used approaches are based on the DDH, ligation assays or ASPE, but multiplex detection of bacteria may be performed as well using MBMI.
T19366 36221-36372 Sentence denotes The most widely used approaches are based on the DDH, ligation assays or ASPE, but multiplex detection of bacteria may be performed as well using MBMI.
TextSentencer_T203 36373-36574 Sentence denotes Direct DNA hybridization was used for the detection of pathogens causing foodborne diseases such as acute gastroenteritis and diarrhea, which are usually associated with ingestion of contaminated food.
T83922 36373-36574 Sentence denotes Direct DNA hybridization was used for the detection of pathogens causing foodborne diseases such as acute gastroenteritis and diarrhea, which are usually associated with ingestion of contaminated food.
TextSentencer_T204 36575-36725 Sentence denotes DDH was applied for the typing of 500 Salmonella isolates using the genes encoding the flagellar antigens H (fliC and fljB) (McQuiston et al., 2011) .
T53676 36575-36725 Sentence denotes DDH was applied for the typing of 500 Salmonella isolates using the genes encoding the flagellar antigens H (fliC and fljB) (McQuiston et al., 2011) .
TextSentencer_T205 36726-36897 Sentence denotes Allele-specific probes for fifteen H antigens, 5 complex major antigens and 16 complex secondary antigens according to the Kauffmann-White serotyping scheme were designed.
T49823 36726-36897 Sentence denotes Allele-specific probes for fifteen H antigens, 5 complex major antigens and 16 complex secondary antigens according to the Kauffmann-White serotyping scheme were designed.
TextSentencer_T206 36898-37082 Sentence denotes Comparison of DDH with traditional serotyping methods revealed that the DDH cannot completely replace these methods because unfortunately not all flagellar antigen types were detected.
T47313 36898-37082 Sentence denotes Comparison of DDH with traditional serotyping methods revealed that the DDH cannot completely replace these methods because unfortunately not all flagellar antigen types were detected.
TextSentencer_T207 37083-37376 Sentence denotes A similar DDH assay for the typing of Salmonella focused only on the most common six serogroups of Salmonella in the United States (B, C 1 , C 2 , D, E, and O13), as well as serotype Paratyphi A, using the rfb genes required for O-antigen biosynthesis in Salmonella (Fitzgerald et al., 2007) .
T66763 37083-37376 Sentence denotes A similar DDH assay for the typing of Salmonella focused only on the most common six serogroups of Salmonella in the United States (B, C 1 , C 2 , D, E, and O13), as well as serotype Paratyphi A, using the rfb genes required for O-antigen biosynthesis in Salmonella (Fitzgerald et al., 2007) .
TextSentencer_T208 37377-37549 Sentence denotes In contrast with the previous study of McQuiston et al. (2011) , the authors showed that the DDH was more specific than traditionally used methods for typing of Salmonella.
T12590 37377-37549 Sentence denotes In contrast with the previous study of McQuiston et al. (2011) , the authors showed that the DDH was more specific than traditionally used methods for typing of Salmonella.
TextSentencer_T209 37550-37936 Sentence denotes In the previous sections, it was described how DDH can be used for typing of pathogens; however, in most cases DDH is used only for the detection of pathogens, as described below. attempted simultaneous detection of the enteric pathogens Aeromonas, Campylobacter jejuni/coli, Shigella, enteroinvasive Escherichia coli (EIEC), Vibrio, Yersinia and as well as Salmonella in fecal samples.
T2408 37550-37936 Sentence denotes In the previous sections, it was described how DDH can be used for typing of pathogens; however, in most cases DDH is used only for the detection of pathogens, as described below. attempted simultaneous detection of the enteric pathogens Aeromonas, Campylobacter jejuni/coli, Shigella, enteroinvasive Escherichia coli (EIEC), Vibrio, Yersinia and as well as Salmonella in fecal samples.
TextSentencer_T210 37937-38130 Sentence denotes However, there were some limitations to the method, which included the limited number of clinically significant pathogens or the inability to detect diarrheagenic E. coli, protozoa, or viruses.
T68805 37937-38130 Sentence denotes However, there were some limitations to the method, which included the limited number of clinically significant pathogens or the inability to detect diarrheagenic E. coli, protozoa, or viruses.
TextSentencer_T211 38131-38604 Sentence denotes The full capacity of the DDH assay was utilized when the panel was expanded to include the most common bacterial/viral enteropathogens found in stool samples, such as Salmonella, Shigella, Vibrio, toxin B producer Clostridium difficile, Campylobacter, Clostridium perfringens, Yersinia enterocolitica, Aeromonas, Escherichia coli O157:H7, verocytotoxin-producing Escherichia coli and adenovirus, Group A rotavirus, norovirus GI and GII and astrovirus (Onori et al., 2014) .
T31737 38131-38604 Sentence denotes The full capacity of the DDH assay was utilized when the panel was expanded to include the most common bacterial/viral enteropathogens found in stool samples, such as Salmonella, Shigella, Vibrio, toxin B producer Clostridium difficile, Campylobacter, Clostridium perfringens, Yersinia enterocolitica, Aeromonas, Escherichia coli O157:H7, verocytotoxin-producing Escherichia coli and adenovirus, Group A rotavirus, norovirus GI and GII and astrovirus (Onori et al., 2014) .
TextSentencer_T212 38605-38759 Sentence denotes The results showed that the assay is rapid, sensitive, specific, and reliable for screening and for exploring the etiology of gastrointestinal infections.
T17365 38605-38759 Sentence denotes The results showed that the assay is rapid, sensitive, specific, and reliable for screening and for exploring the etiology of gastrointestinal infections.
TextSentencer_T213 38760-39029 Sentence denotes The sensitivity of MBMNA was demonstrated to be greater than the routine methods (76.3% versus 66.5%), with the exception of Salmonella sp. and toxigenic C. difficile where the adoption of multiplex PCR did not always result in a significant improvement of specificity.
T13982 38760-39029 Sentence denotes The sensitivity of MBMNA was demonstrated to be greater than the routine methods (76.3% versus 66.5%), with the exception of Salmonella sp. and toxigenic C. difficile where the adoption of multiplex PCR did not always result in a significant improvement of specificity.
TextSentencer_T214 39030-39336 Sentence denotes The causative agents were not found in 44 of 245 (18%) of the presumed infectious gastroenteritis cases, but this could be due to the limitations of the detection panel, which did not include allelespecific probes for detection of parasitic enteric pathogens or emerging viruses related to gastroenteritis.
T72637 39030-39336 Sentence denotes The causative agents were not found in 44 of 245 (18%) of the presumed infectious gastroenteritis cases, but this could be due to the limitations of the detection panel, which did not include allelespecific probes for detection of parasitic enteric pathogens or emerging viruses related to gastroenteritis.
TextSentencer_T215 39337-39662 Sentence denotes Also, using DDH, detection of pathogenic bacteria occurring in environmental samples and causing acute and often fatal diseases (Bacillus anthracis, Yersinia pestis, Francisella tularensis, and Brucella melitensis) was optimized in a multiplexed format to allow the maximum sensitivity and specificity (Wilson et al., 2005) .
T7135 39337-39662 Sentence denotes Also, using DDH, detection of pathogenic bacteria occurring in environmental samples and causing acute and often fatal diseases (Bacillus anthracis, Yersinia pestis, Francisella tularensis, and Brucella melitensis) was optimized in a multiplexed format to allow the maximum sensitivity and specificity (Wilson et al., 2005) .
TextSentencer_T216 39663-39771 Sentence denotes DNA was extracted robotically and in combination with DDH a rapid reliable screening approach was developed.
T1865 39663-39771 Sentence denotes DNA was extracted robotically and in combination with DDH a rapid reliable screening approach was developed.
TextSentencer_T217 39772-39995 Sentence denotes Detection limits were from 100 fg to 10 pg starting DNA concentration when primer sets were multiplexed; in some cases the limits of detection were higher when primer sets were tested separately (range from 10 fg to 10 pg).
T200 39772-39995 Sentence denotes Detection limits were from 100 fg to 10 pg starting DNA concentration when primer sets were multiplexed; in some cases the limits of detection were higher when primer sets were tested separately (range from 10 fg to 10 pg).
TextSentencer_T218 39996-40219 Sentence denotes Besides the in-house assays developed for multiplex detection of bacteria described above, there are also commercial solutions based on xMAP technology for detection of the most common gastrointestinal pathogens and toxins.
T87996 39996-40219 Sentence denotes Besides the in-house assays developed for multiplex detection of bacteria described above, there are also commercial solutions based on xMAP technology for detection of the most common gastrointestinal pathogens and toxins.
TextSentencer_T219 40220-40491 Sentence denotes The xTAG R Gastrointestinal Pathogen Panel is a multiplex nucleic acid test designed for detection of various bacterial, viral and parasitic nucleic acids in human stool samples (Beckmann et al., 2014; Perry et al., 2014; Wessels et al., 2014; Zboromyrska et al., 2014) .
T1132 40220-40491 Sentence denotes The xTAG R Gastrointestinal Pathogen Panel is a multiplex nucleic acid test designed for detection of various bacterial, viral and parasitic nucleic acids in human stool samples (Beckmann et al., 2014; Perry et al., 2014; Wessels et al., 2014; Zboromyrska et al., 2014) .
TextSentencer_T220 40492-40880 Sentence denotes The panel allows qualitative detection of Campylobacter sp., Clostridium difficile (toxin A/B), Escherichia coli O157, Enterotoxigenic E. coli (ETEC) LT/ST, Shiga-like toxin producing E. coli (STEC) stx1/stx2, Salmonella sp., Shigella sp., Vibrio cholerae, Yersinia enterocolitica, HAdV serotypes 40 and 41, NoV GI and GII, Rotavirus A, Giardia, Cryptosporidium and Entamoeba histolytica.
T82302 40492-40880 Sentence denotes The panel allows qualitative detection of Campylobacter sp., Clostridium difficile (toxin A/B), Escherichia coli O157, Enterotoxigenic E. coli (ETEC) LT/ST, Shiga-like toxin producing E. coli (STEC) stx1/stx2, Salmonella sp., Shigella sp., Vibrio cholerae, Yersinia enterocolitica, HAdV serotypes 40 and 41, NoV GI and GII, Rotavirus A, Giardia, Cryptosporidium and Entamoeba histolytica.
TextSentencer_T221 40881-41196 Sentence denotes The xTAG GPP was tested and compared with routine tests, which are used in clinical diagnostic laboratories for screening of 17 kinds of enteropathogens, e.g., qRT-PCR kit for detection of viruses, culture methods for detection of bacteria or microscopic examination for detection of parasites (Deng et al., 2015) .
T7191 40881-41196 Sentence denotes The xTAG GPP was tested and compared with routine tests, which are used in clinical diagnostic laboratories for screening of 17 kinds of enteropathogens, e.g., qRT-PCR kit for detection of viruses, culture methods for detection of bacteria or microscopic examination for detection of parasites (Deng et al., 2015) .
TextSentencer_T222 41197-41313 Sentence denotes Samples with discordant results between the routine tests and xTAG GPP were tested by singleplex PCR and sequencing.
T49009 41197-41313 Sentence denotes Samples with discordant results between the routine tests and xTAG GPP were tested by singleplex PCR and sequencing.
TextSentencer_T223 41314-41386 Sentence denotes The overall sensitivity of xTAG GPP was 96.3% and specificity was 99.8%.
T58394 41314-41386 Sentence denotes The overall sensitivity of xTAG GPP was 96.3% and specificity was 99.8%.
TextSentencer_T224 41387-41511 Sentence denotes The sensitivity of xTAG GPP was 100% for all enteropathogens except Salmonella sp. (84.9%) and C. difficile toxin B (88.6%).
T86476 41387-41511 Sentence denotes The sensitivity of xTAG GPP was 100% for all enteropathogens except Salmonella sp. (84.9%) and C. difficile toxin B (88.6%).
TextSentencer_T225 41512-41801 Sentence denotes The specificity was 100% for all targets except Salmonella sp. (99.2%), Shigella sp. (99.7%), C. difficile toxin B (99.2%), and norovirus GII (98.8%). xTAG GPP is also capable of detecting coinfections; 35 coinfections were detected using xTAG GPP, which is more than by the routine tests.
T39472 41512-41801 Sentence denotes The specificity was 100% for all targets except Salmonella sp. (99.2%), Shigella sp. (99.7%), C. difficile toxin B (99.2%), and norovirus GII (98.8%). xTAG GPP is also capable of detecting coinfections; 35 coinfections were detected using xTAG GPP, which is more than by the routine tests.
TextSentencer_T226 41802-42073 Sentence denotes However, the authors also reported some disadvantages as xTAG GPP failed to detect some important diarrheal pathogens (Aeromonas, Plesiomonas shigelloides) often detected by routine diagnostic tests; further, the detection of Salmonella exhibited low sensitivity (84.9%).
T33085 41802-42073 Sentence denotes However, the authors also reported some disadvantages as xTAG GPP failed to detect some important diarrheal pathogens (Aeromonas, Plesiomonas shigelloides) often detected by routine diagnostic tests; further, the detection of Salmonella exhibited low sensitivity (84.9%).
TextSentencer_T227 42074-42157 Sentence denotes Ligation assays are also often used for multiplex detection of pathogenic bacteria.
T68259 42074-42157 Sentence denotes Ligation assays are also often used for multiplex detection of pathogenic bacteria.
TextSentencer_T228 42158-42342 Sentence denotes The main advantage over direct hybridization methods is the ability to simultaneously detect diverse signatures such as unique sequences, SNPs, indels and repeats (Song et al., 2010) .
T91148 42158-42342 Sentence denotes The main advantage over direct hybridization methods is the ability to simultaneously detect diverse signatures such as unique sequences, SNPs, indels and repeats (Song et al., 2010) .
TextSentencer_T229 42343-42482 Sentence denotes MOL-PCR was initially optimized for the detection of the biothreat agents Bacillus anthracis, Yersinia pestis, and Francisella tularensis .
T85361 42343-42482 Sentence denotes MOL-PCR was initially optimized for the detection of the biothreat agents Bacillus anthracis, Yersinia pestis, and Francisella tularensis .
TextSentencer_T230 42483-42729 Sentence denotes The pathogen-specific sets of MOLigo pair probes were designed and their specificity and sensitivity were tested using similar species of Bacillus anthracis, Yersinia pestis, and Francisella tularensis and dilutions of isolated DNA, respectively.
T26052 42483-42729 Sentence denotes The pathogen-specific sets of MOLigo pair probes were designed and their specificity and sensitivity were tested using similar species of Bacillus anthracis, Yersinia pestis, and Francisella tularensis and dilutions of isolated DNA, respectively.
TextSentencer_T231 42730-42982 Sentence denotes MOLigo pairs, which showed the highest specificity and sensitivity, were selected for compilation of a final probe panel, which was validated on extracted DNA from infected rodent liver and spleen, human blood or pleural fluid spiked with pathogen DNA.
T73240 42730-42982 Sentence denotes MOLigo pairs, which showed the highest specificity and sensitivity, were selected for compilation of a final probe panel, which was validated on extracted DNA from infected rodent liver and spleen, human blood or pleural fluid spiked with pathogen DNA.
TextSentencer_T232 42983-43069 Sentence denotes Nine from 10 unknown samples were successfully identified using the final probe panel.
T40232 42983-43069 Sentence denotes Nine from 10 unknown samples were successfully identified using the final probe panel.
TextSentencer_T233 43070-43203 Sentence denotes The results also showed the ability of this method to simultaneously detect multiple different signatures (SNPs, indels and repeats).
T972 43070-43203 Sentence denotes The results also showed the ability of this method to simultaneously detect multiple different signatures (SNPs, indels and repeats).
TextSentencer_T234 43204-43494 Sentence denotes The versatility of MOL-PCR was utilized when simultaneous detection of Bacillus anthracis, Yersinia pestis, and Francisella tularensis was supplemented by characterization of antibiotic resistance (ciprofloxacin and doxycycline) of these bacteria based on SNP analysis (Song et al., 2010) .
T25408 43204-43494 Sentence denotes The versatility of MOL-PCR was utilized when simultaneous detection of Bacillus anthracis, Yersinia pestis, and Francisella tularensis was supplemented by characterization of antibiotic resistance (ciprofloxacin and doxycycline) of these bacteria based on SNP analysis (Song et al., 2010) .
TextSentencer_T235 43495-43693 Sentence denotes The allelespecific probes for detection and characterization of all the known resistance determinants performed well when tested individually, but multiplex use did not provide satisfactory results.
T63869 43495-43693 Sentence denotes The allelespecific probes for detection and characterization of all the known resistance determinants performed well when tested individually, but multiplex use did not provide satisfactory results.
TextSentencer_T236 43694-43872 Sentence denotes Due to the ability to simultaneously detect diverse signatures such as unique sequences, SNPs, indels, and repeats, MOL-PCR can be used as a genotyping method as described below.
T56856 43694-43872 Sentence denotes Due to the ability to simultaneously detect diverse signatures such as unique sequences, SNPs, indels, and repeats, MOL-PCR can be used as a genotyping method as described below.
TextSentencer_T237 43873-44127 Sentence denotes A MOL-PCR-based 8plex SNP typing method for Mycobacterium tuberculosis complex (MTBC) based on two phylogenetically equivalent sets of SNP markers that are specific for the six main human-associated lineages of MTBC was introduced (Stucki et al., 2012) .
T57496 43873-44127 Sentence denotes A MOL-PCR-based 8plex SNP typing method for Mycobacterium tuberculosis complex (MTBC) based on two phylogenetically equivalent sets of SNP markers that are specific for the six main human-associated lineages of MTBC was introduced (Stucki et al., 2012) .
TextSentencer_T238 44128-44371 Sentence denotes MOL-PCR was compared with TaqMan qPCR and the obtained results showed that the sensitivity and specificity of both methods were similar (specificity 100%, sensitivity 98.6% MOL-PCR, 98.8% TaqMan) and that both methods were of comparative cost.
T14522 44128-44371 Sentence denotes MOL-PCR was compared with TaqMan qPCR and the obtained results showed that the sensitivity and specificity of both methods were similar (specificity 100%, sensitivity 98.6% MOL-PCR, 98.8% TaqMan) and that both methods were of comparative cost.
TextSentencer_T239 44372-44496 Sentence denotes MOL-PCR was ideal for classification of unknown isolates, while TaqMan qPCR was faster for confirmation of unknown isolates.
T44780 44372-44496 Sentence denotes MOL-PCR was ideal for classification of unknown isolates, while TaqMan qPCR was faster for confirmation of unknown isolates.
TextSentencer_T240 44497-44712 Sentence denotes MOL-PCR was also successfully used for genotyping of Bacillus anthracis in a 13-plex assay to score 13 phylogenetically lineagespecific canonical SNPs within the genome of Bacillus anthracis (Thierry et al., 2013) .
T85860 44497-44712 Sentence denotes MOL-PCR was also successfully used for genotyping of Bacillus anthracis in a 13-plex assay to score 13 phylogenetically lineagespecific canonical SNPs within the genome of Bacillus anthracis (Thierry et al., 2013) .
TextSentencer_T241 44713-44864 Sentence denotes Allele-specific primer extension was applied for identification of bacteria (Lin et al., 2008) even though it is more commonly used for SNP genotyping.
T88923 44713-44864 Sentence denotes Allele-specific primer extension was applied for identification of bacteria (Lin et al., 2008) even though it is more commonly used for SNP genotyping.
TextSentencer_T242 44865-45046 Sentence denotes ASPE was used for the identification of Acinetobacter sp. and antimicrobial susceptibilities of the clinical Acinetobacter species isolates were also determined (Lin et al., 2008) .
T54524 44865-45046 Sentence denotes ASPE was used for the identification of Acinetobacter sp. and antimicrobial susceptibilities of the clinical Acinetobacter species isolates were also determined (Lin et al., 2008) .
TextSentencer_T243 45047-45191 Sentence denotes The 16S-23S rRNA gene intergenic spacer (ITS) regions of 13 distinct Acinetobacter species were amplified and then multiplex ASPE was performed.
T87103 45047-45191 Sentence denotes The 16S-23S rRNA gene intergenic spacer (ITS) regions of 13 distinct Acinetobacter species were amplified and then multiplex ASPE was performed.
TextSentencer_T244 45192-45362 Sentence denotes It was shown that this multiplex identification of Acinetobacter sp. is applicable also for determination of antibiotic resistance of the clinical Acinetobacter isolates.
T1152 45192-45362 Sentence denotes It was shown that this multiplex identification of Acinetobacter sp. is applicable also for determination of antibiotic resistance of the clinical Acinetobacter isolates.
TextSentencer_T245 45363-45565 Sentence denotes ASPE was compared with SBCE for identification of bacterial samples (Ye et al., 2001) and both methods provided similar results as they managed to correctly classify 17 bacterial species into 17 groups.
T46301 45363-45565 Sentence denotes ASPE was compared with SBCE for identification of bacterial samples (Ye et al., 2001) and both methods provided similar results as they managed to correctly classify 17 bacterial species into 17 groups.
TextSentencer_T246 45566-45698 Sentence denotes In addition to MBMNA also MBMI can be used for the direct multiplex detection of bacteria and their products (Dunbar et al., 2003) .
T94033 45566-45698 Sentence denotes In addition to MBMNA also MBMI can be used for the direct multiplex detection of bacteria and their products (Dunbar et al., 2003) .
TextSentencer_T247 45699-45943 Sentence denotes In MBMI direct fluorescence (detection antibody that incorporates a fluorescent label) is used for detection of reaction or of emerging product in contrast to ELISA and, in addition, MBMI enables measurement of multiple analytes simultaneously.
T91644 45699-45943 Sentence denotes In MBMI direct fluorescence (detection antibody that incorporates a fluorescent label) is used for detection of reaction or of emerging product in contrast to ELISA and, in addition, MBMI enables measurement of multiple analytes simultaneously.
TextSentencer_T248 45944-46076 Sentence denotes For this reason, MBMI is preferred because time for detection is reduced and also test sensitivity is increased (Jun et al., 2012) .
T26062 45944-46076 Sentence denotes For this reason, MBMI is preferred because time for detection is reduced and also test sensitivity is increased (Jun et al., 2012) .
TextSentencer_T249 46077-46584 Sentence denotes Capture sandwich immunoassays (CS) were successfully applied for detection of organism-specific antibodies using microspheres coupled with antibodies for Salmonella, Campylobacter, Escherichia coli, and Listeria and it has been demonstrated that MBMI is a suitable method for multiplex detection of bacteria occurring in foodstuffs or for detection of Brucella sp. from milk using capturesensitive monoclonal antibodies for the lipopolysaccharide (LPS) O-antigen of Brucella sp. (Silbereisen et al., 2015) .
T74011 46077-46584 Sentence denotes Capture sandwich immunoassays (CS) were successfully applied for detection of organism-specific antibodies using microspheres coupled with antibodies for Salmonella, Campylobacter, Escherichia coli, and Listeria and it has been demonstrated that MBMI is a suitable method for multiplex detection of bacteria occurring in foodstuffs or for detection of Brucella sp. from milk using capturesensitive monoclonal antibodies for the lipopolysaccharide (LPS) O-antigen of Brucella sp. (Silbereisen et al., 2015) .
TextSentencer_T250 46585-46946 Sentence denotes MBMI was also applied to test bacterial contamination of foods through the detection of staphylococcal enterotoxin B (SEB) , staphylococcal toxin A (SEA), and toxic shock syndrome toxin (TSST) produced by various strains of Staphylococcus aureus (Simonova et al., 2014) using sandwich immunoassays in which microspheres were conjugated with specific antibodies.
T94923 46585-46946 Sentence denotes MBMI was also applied to test bacterial contamination of foods through the detection of staphylococcal enterotoxin B (SEB) , staphylococcal toxin A (SEA), and toxic shock syndrome toxin (TSST) produced by various strains of Staphylococcus aureus (Simonova et al., 2014) using sandwich immunoassays in which microspheres were conjugated with specific antibodies.
TextSentencer_T251 46947-47123 Sentence denotes A similar approach was used for the detection of pneumococcal serotype-specific polysaccharide and C-polysaccharide (C-Ps) antigens from urine samples (Sheppard et al., 2011) .
T7936 46947-47123 Sentence denotes A similar approach was used for the detection of pneumococcal serotype-specific polysaccharide and C-polysaccharide (C-Ps) antigens from urine samples (Sheppard et al., 2011) .
TextSentencer_T252 47124-47227 Sentence denotes For the detection, MBMI was combined with the Binax NOW Streptococcus pneumoniae antigen detection kit.
T92726 47124-47227 Sentence denotes For the detection, MBMI was combined with the Binax NOW Streptococcus pneumoniae antigen detection kit.
TextSentencer_T253 47228-47543 Sentence denotes The specificity of MBMI was determined by testing 85 serotypes of S. pneumoniae and other strains of streptococci; 18 of the 26 non-pneumococcal serotypes gave C-P positive results, which showed that MBMI could be used for diagnosis of infection caused by S. pneumoniae only in combination with the Binax NOW assay.
T59120 47228-47543 Sentence denotes The specificity of MBMI was determined by testing 85 serotypes of S. pneumoniae and other strains of streptococci; 18 of the 26 non-pneumococcal serotypes gave C-P positive results, which showed that MBMI could be used for diagnosis of infection caused by S. pneumoniae only in combination with the Binax NOW assay.
TextSentencer_T254 47544-47626 Sentence denotes Parasitic zoonoses are recorded worldwide and some of them have endemic character.
T73588 47544-47626 Sentence denotes Parasitic zoonoses are recorded worldwide and some of them have endemic character.
TextSentencer_T255 47627-47869 Sentence denotes Parasitic agents may pass from animals to humans in several ways, e.g., by direct contact, vector, consumption of raw or undercooked foodstuffs containing the infective stages or by infective stages released into environment (Hubalek, 2003) .
T5308 47627-47869 Sentence denotes Parasitic agents may pass from animals to humans in several ways, e.g., by direct contact, vector, consumption of raw or undercooked foodstuffs containing the infective stages or by infective stages released into environment (Hubalek, 2003) .
TextSentencer_T256 47870-48079 Sentence denotes In the context of animal health and human food consumption, a list of the top ten parasites has been defined by the UN's Food and Agriculture Organization (FAO) and World Health Organization (WHO) ( Table 3) .
T97479 47870-48079 Sentence denotes In the context of animal health and human food consumption, a list of the top ten parasites has been defined by the UN's Food and Agriculture Organization (FAO) and World Health Organization (WHO) ( Table 3) .
TextSentencer_T257 48080-48385 Sentence denotes Although in the last decades a number of novel diagnostic methodological approaches has been developed, the current diagnosis of some parasitic diseases is still based only on a combination of clinical signs, anamnesis, and direct visual identification of parasitological objects (Anderson et al., 2015) .
T2258 48080-48385 Sentence denotes Although in the last decades a number of novel diagnostic methodological approaches has been developed, the current diagnosis of some parasitic diseases is still based only on a combination of clinical signs, anamnesis, and direct visual identification of parasitological objects (Anderson et al., 2015) .
TextSentencer_T258 48386-48606 Sentence denotes The most common conventional diagnostic methods, such as microscopic examination, biochemical assays or ELISA, are available, but they are laborious, time-consuming and in many cases not reliable (Navidad et al., 2013) .
T22146 48386-48606 Sentence denotes The most common conventional diagnostic methods, such as microscopic examination, biochemical assays or ELISA, are available, but they are laborious, time-consuming and in many cases not reliable (Navidad et al., 2013) .
TextSentencer_T259 48607-48909 Sentence denotes Improvements in this field are represented by molecular methods, including also routine PCR diagnostics, increasingly used for detection mainly of intestinal parasites, which are easy to recover from fecal specimens (Taniuchi et al., 2011) or potentially useful for other parasites found in secretions.
T8488 48607-48909 Sentence denotes Improvements in this field are represented by molecular methods, including also routine PCR diagnostics, increasingly used for detection mainly of intestinal parasites, which are easy to recover from fecal specimens (Taniuchi et al., 2011) or potentially useful for other parasites found in secretions.
TextSentencer_T260 48910-49146 Sentence denotes With regard to the fact that parasites might exhibit very strictly confined localization within the host's bodyintracellular/extracellular or tissue/organ, sampling can be very problematic and it often leads to a false negative results.
T65725 48910-49146 Sentence denotes With regard to the fact that parasites might exhibit very strictly confined localization within the host's bodyintracellular/extracellular or tissue/organ, sampling can be very problematic and it often leads to a false negative results.
TextSentencer_T261 49147-49240 Sentence denotes Outbreaks of diarrheal diseases are caused by a wide range of pathogens, including parasites.
T84218 49147-49240 Sentence denotes Outbreaks of diarrheal diseases are caused by a wide range of pathogens, including parasites.
TextSentencer_T262 49241-49364 Sentence denotes Stool microscopy (detection of eggs, parts of bodies etc.) is the gold standard in the diagnostics of intestinal parasites.
T67913 49241-49364 Sentence denotes Stool microscopy (detection of eggs, parts of bodies etc.) is the gold standard in the diagnostics of intestinal parasites.
TextSentencer_T263 49365-49474 Sentence denotes However, the presence of parasites in stool may vary and could be naturally low, requiring multiple sampling.
T57825 49365-49474 Sentence denotes However, the presence of parasites in stool may vary and could be naturally low, requiring multiple sampling.
TextSentencer_T264 49475-49580 Sentence denotes In fact, up to 80% of all cases of diarrhea remain without confirmed etiology (Vernacchio et al., 2006) .
T38886 49475-49580 Sentence denotes In fact, up to 80% of all cases of diarrhea remain without confirmed etiology (Vernacchio et al., 2006) .
TextSentencer_T265 49581-49737 Sentence denotes Therefore, there is space for the development of more sensitive diagnostic assays (Taniuchi et al., 2011) , which should provide more precise determination.
T6842 49581-49737 Sentence denotes Therefore, there is space for the development of more sensitive diagnostic assays (Taniuchi et al., 2011) , which should provide more precise determination.
TextSentencer_T266 49738-49863 Sentence denotes Among the modern molecular diagnostic methods qPCR assays are most frequently used for determination of intestinal parasites.
T79352 49738-49863 Sentence denotes Among the modern molecular diagnostic methods qPCR assays are most frequently used for determination of intestinal parasites.
TextSentencer_T267 49864-50064 Sentence denotes In areas where co-infections are common (up to 22% of cases are caused by two or more pathogens) (Jansen et al., 2008; Friesema et al., 2012) , the application of multiplex assays is of great benefit.
T49174 49864-50064 Sentence denotes In areas where co-infections are common (up to 22% of cases are caused by two or more pathogens) (Jansen et al., 2008; Friesema et al., 2012) , the application of multiplex assays is of great benefit.
TextSentencer_T268 50065-50136 Sentence denotes Several pioneering works have been published in relation to this topic.
T26025 50065-50136 Sentence denotes Several pioneering works have been published in relation to this topic.
TextSentencer_T269 50137-50551 Sentence denotes To date, in parasitology, improved multiplex qPCR assays were adapted to DDH, which enables parallel diagnosis of seven intestinal parasites (Taniuchi et al., 2011) ; separate reactions were optimized -3plex for protozoa (Cryptosporidium sp., Giardia intestinalis, and Entamoeba histolytica) and 4-plex for helminths (Ancylostoma duodenale, Ascaris lumbricoides, Necator americanus, and Strongyloides stercoralis).
T23369 50137-50551 Sentence denotes To date, in parasitology, improved multiplex qPCR assays were adapted to DDH, which enables parallel diagnosis of seven intestinal parasites (Taniuchi et al., 2011) ; separate reactions were optimized -3plex for protozoa (Cryptosporidium sp., Giardia intestinalis, and Entamoeba histolytica) and 4-plex for helminths (Ancylostoma duodenale, Ascaris lumbricoides, Necator americanus, and Strongyloides stercoralis).
TextSentencer_T270 50552-50618 Sentence denotes The final calculated sensitivity was 83% and specificity was 100%.
T11690 50552-50618 Sentence denotes The final calculated sensitivity was 83% and specificity was 100%.
TextSentencer_T271 50619-50719 Sentence denotes The results of both DDH assays were equivalent or better in comparison to the parent multiplex qPCR.
T2240 50619-50719 Sentence denotes The results of both DDH assays were equivalent or better in comparison to the parent multiplex qPCR.
TextSentencer_T272 50720-50927 Sentence denotes Moreover, this approach has been developed as a commercial diagnostic xTAG GPP tool-a 19-plex assay, which enables inter alia detection of the protozoa G. intestinalis, E. histolytica and Cryptosporidium sp.
T42887 50720-50927 Sentence denotes Moreover, this approach has been developed as a commercial diagnostic xTAG GPP tool-a 19-plex assay, which enables inter alia detection of the protozoa G. intestinalis, E. histolytica and Cryptosporidium sp.
TextSentencer_T273 50928-51241 Sentence denotes The overall performance of xTAG GPP compared with conventional methods (standard culture, microscopic examination, immunochromatographic tests, qPCR) showed a sensitivity of 94.5% (range 90 to 97%) and a specificity of 99% (range 98,5% to 99,9%) (Claas et al., 2013; Mengelle et al., 2013; Navidad et al., 2013) .
T19087 50928-51241 Sentence denotes The overall performance of xTAG GPP compared with conventional methods (standard culture, microscopic examination, immunochromatographic tests, qPCR) showed a sensitivity of 94.5% (range 90 to 97%) and a specificity of 99% (range 98,5% to 99,9%) (Claas et al., 2013; Mengelle et al., 2013; Navidad et al., 2013) .
TextSentencer_T274 51242-51408 Sentence denotes If multiplexing more than 20 targets, the limit of detection might be reduced for individual targets when compared to single-target detection (Navidad et al., 2013) .
T221 51242-51408 Sentence denotes If multiplexing more than 20 targets, the limit of detection might be reduced for individual targets when compared to single-target detection (Navidad et al., 2013) .
TextSentencer_T275 51409-51595 Sentence denotes However, the identification of multiple pathogens revealed that very often (in up to 65% of samples), the physicians do not request testing for the proper pathogen (Claas et al., 2013) .
T41968 51409-51595 Sentence denotes However, the identification of multiple pathogens revealed that very often (in up to 65% of samples), the physicians do not request testing for the proper pathogen (Claas et al., 2013) .
TextSentencer_T276 51596-51699 Sentence denotes Therefore, multiplexing refines the diagnosis and contributes to the selection of a suitable treatment.
T32883 51596-51699 Sentence denotes Therefore, multiplexing refines the diagnosis and contributes to the selection of a suitable treatment.
TextSentencer_T277 51700-52068 Sentence denotes It was mentioned above that microsphere-based assays can be arranged also as multiplex indirect immunoassays, although the conventional singleplex ELISA still represents the gold standard in serodiagnostics for screening of individual human/animal or higher numbers of samples at a population level (Ruitenberg et al., 1983; Nockler et al., 2000; Dubey et al., 2005) .
T87143 51700-52068 Sentence denotes It was mentioned above that microsphere-based assays can be arranged also as multiplex indirect immunoassays, although the conventional singleplex ELISA still represents the gold standard in serodiagnostics for screening of individual human/animal or higher numbers of samples at a population level (Ruitenberg et al., 1983; Nockler et al., 2000; Dubey et al., 2005) .
TextSentencer_T278 52069-52209 Sentence denotes Recently, some studies have been done in order to improve the potential of this serological method and to upgrade it to the multiplex level.
T11972 52069-52209 Sentence denotes Recently, some studies have been done in order to improve the potential of this serological method and to upgrade it to the multiplex level.
TextSentencer_T279 52210-52372 Sentence denotes These studies are mostly focused on parasites with the ability to migrate through the tissues of the host's body -where PCR based detection would not be reliable.
T4642 52210-52372 Sentence denotes These studies are mostly focused on parasites with the ability to migrate through the tissues of the host's body -where PCR based detection would not be reliable.
TextSentencer_T280 52373-52537 Sentence denotes In this context, the most studied group of parasites are representatives from the phylum Nematoda, including also the important human pathogens, the Trichinella sp.
T22426 52373-52537 Sentence denotes In this context, the most studied group of parasites are representatives from the phylum Nematoda, including also the important human pathogens, the Trichinella sp.
TextSentencer_T281 52538-52757 Sentence denotes The larvae may infect humans during the ingestion of raw or undercooked meat, mainly pork (domestic pig, wild boar) and can induce disease, whose consequences can be fatal (Dupouy-Camet, 2000; Pozio and Murrell, 2006) .
T6859 52538-52757 Sentence denotes The larvae may infect humans during the ingestion of raw or undercooked meat, mainly pork (domestic pig, wild boar) and can induce disease, whose consequences can be fatal (Dupouy-Camet, 2000; Pozio and Murrell, 2006) .
TextSentencer_T282 52758-53071 Sentence denotes Inspection of meat for the most important species, Trichinella spiralis, is mandatory at slaughter (Anonymous, 2015) , but currently used methods like artificial digestion and microscopic examination of pooled meat samples (Nockler et al., 2000) are archaic and usually do not properly reflect the real infection.
T56270 52758-53071 Sentence denotes Inspection of meat for the most important species, Trichinella spiralis, is mandatory at slaughter (Anonymous, 2015) , but currently used methods like artificial digestion and microscopic examination of pooled meat samples (Nockler et al., 2000) are archaic and usually do not properly reflect the real infection.
TextSentencer_T283 53072-53259 Sentence denotes Therefore, serodiagnostic methods are considered as a possible alternative and xMAP technology in the form of ISA, using excretory/secretory (E/S) products, was also developed and tested.
T60031 53072-53259 Sentence denotes Therefore, serodiagnostic methods are considered as a possible alternative and xMAP technology in the form of ISA, using excretory/secretory (E/S) products, was also developed and tested.
TextSentencer_T284 53260-53337 Sentence denotes The effectivity of ISA was tested with T. spiralis-positive pig meat samples.
T31788 53260-53337 Sentence denotes The effectivity of ISA was tested with T. spiralis-positive pig meat samples.
TextSentencer_T285 53338-53478 Sentence denotes The system was developed as a duplex assay (with Toxoplasma gondii), using goat anti-swine secondary antibodies against specific antibodies.
T89402 53338-53478 Sentence denotes The system was developed as a duplex assay (with Toxoplasma gondii), using goat anti-swine secondary antibodies against specific antibodies.
TextSentencer_T286 53479-53637 Sentence denotes The results of this study corresponded to the infection status of the animals with an assay sensitivity of 68% and specificity of 100% (Bokken et al., 2012) .
T33321 53479-53637 Sentence denotes The results of this study corresponded to the infection status of the animals with an assay sensitivity of 68% and specificity of 100% (Bokken et al., 2012) .
TextSentencer_T287 53638-53954 Sentence denotes When the immunoglobulin binding protein A/G (generic Ig-binding protein), which can be used in multiple species in contrast with goat anti-swine secondary antibody, was included, the results showed a similar specificity of 95%, but an increase in sensitivity from 88% for anti-swine antibody to 94% with protein A/G.
T10921 53638-53954 Sentence denotes When the immunoglobulin binding protein A/G (generic Ig-binding protein), which can be used in multiple species in contrast with goat anti-swine secondary antibody, was included, the results showed a similar specificity of 95%, but an increase in sensitivity from 88% for anti-swine antibody to 94% with protein A/G.
TextSentencer_T288 53955-54182 Sentence denotes The xMAP technology-ISA exhibited 87% sensitivity and 95% specificity in comparison with the commercial Pourquier ELISA, and 98% sensitivity and 95% specificity in comparison with the Safepath ELISA (van der Wal et al., 2013) .
T94500 53955-54182 Sentence denotes The xMAP technology-ISA exhibited 87% sensitivity and 95% specificity in comparison with the commercial Pourquier ELISA, and 98% sensitivity and 95% specificity in comparison with the Safepath ELISA (van der Wal et al., 2013) .
TextSentencer_T289 54183-54348 Sentence denotes With the rising popularity of MBMIs, ISA was also developed for other members of Nematodes, such as representatives from the genus Toxocara (Anderson et al., 2015) .
T10887 54183-54348 Sentence denotes With the rising popularity of MBMIs, ISA was also developed for other members of Nematodes, such as representatives from the genus Toxocara (Anderson et al., 2015) .
TextSentencer_T290 54349-54495 Sentence denotes The infection by these parasites is typically peroral at areas contaminated by embryonated roundworm eggs, e.g., sand from childrens' playgrounds.
T48473 54349-54495 Sentence denotes The infection by these parasites is typically peroral at areas contaminated by embryonated roundworm eggs, e.g., sand from childrens' playgrounds.
TextSentencer_T291 54496-54713 Sentence denotes The recombinant T.canis and T. cati E/S antigens Tc-CTL-1 and Tc-TES-26 were used to detect toxocara-specific antibodies in sera from humans pre-diagnosed as positive for visceral and ocular larval migrans (VLM, OLM).
T30009 54496-54713 Sentence denotes The recombinant T.canis and T. cati E/S antigens Tc-CTL-1 and Tc-TES-26 were used to detect toxocara-specific antibodies in sera from humans pre-diagnosed as positive for visceral and ocular larval migrans (VLM, OLM).
TextSentencer_T292 54714-54864 Sentence denotes The specificity of ISA was 94% for both sets of samples, but there were differences in the sensitivity, which was 99% for VLM and 64% for OLM samples.
T305 54714-54864 Sentence denotes The specificity of ISA was 94% for both sets of samples, but there were differences in the sensitivity, which was 99% for VLM and 64% for OLM samples.
TextSentencer_T293 54865-55239 Sentence denotes It was recorded that a combination of recombinant antigens improves sensitivity in comparison with conventional immunoassays (e.g., Western Blot, ELISA), which employ native E/S antigens isolated from larvae (limited availability) that also exhibit cross-reactivity with antibodies from other helminthic infections so reducing its usefulness in regions with poly-parasitism.
T64053 54865-55239 Sentence denotes It was recorded that a combination of recombinant antigens improves sensitivity in comparison with conventional immunoassays (e.g., Western Blot, ELISA), which employ native E/S antigens isolated from larvae (limited availability) that also exhibit cross-reactivity with antibodies from other helminthic infections so reducing its usefulness in regions with poly-parasitism.
TextSentencer_T294 55240-55342 Sentence denotes Within the unicellular parasitic protozoa ISA was tested in representatives from the genus Toxoplasma.
T84157 55240-55342 Sentence denotes Within the unicellular parasitic protozoa ISA was tested in representatives from the genus Toxoplasma.
TextSentencer_T295 55343-55502 Sentence denotes Unlike T. spiralis, no such regulations for meat control exist for T. gondii, even though its prevalence is higher and health complications can be very severe.
T44995 55343-55502 Sentence denotes Unlike T. spiralis, no such regulations for meat control exist for T. gondii, even though its prevalence is higher and health complications can be very severe.
TextSentencer_T296 55503-55651 Sentence denotes Recombinant tachyzoite surface protein (SAG-1) was used for simultaneous serological detection in a set with T. spiralis E/S (Bokken et al., 2012) .
T13730 55503-55651 Sentence denotes Recombinant tachyzoite surface protein (SAG-1) was used for simultaneous serological detection in a set with T. spiralis E/S (Bokken et al., 2012) .
TextSentencer_T297 55652-55789 Sentence denotes Similarly to T. spiralis, the results exactly reflected the load of infection; sensitivity was 86% and specificity was 96% for T. gondii.
T84227 55652-55789 Sentence denotes Similarly to T. spiralis, the results exactly reflected the load of infection; sensitivity was 86% and specificity was 96% for T. gondii.
TextSentencer_T298 55790-55950 Sentence denotes The obtained results repeatedly underline the potential of these assays for further implementation in routine diagnostic screening of a wide range of parasites.
T3778 55790-55950 Sentence denotes The obtained results repeatedly underline the potential of these assays for further implementation in routine diagnostic screening of a wide range of parasites.
TextSentencer_T299 55951-56140 Sentence denotes As we have descibed, the ISA represents an improved methodological alternative to current serological diagnostics, enabling multiplex detection of pathogenic agents with higher sensitivity.
T47605 55951-56140 Sentence denotes As we have descibed, the ISA represents an improved methodological alternative to current serological diagnostics, enabling multiplex detection of pathogenic agents with higher sensitivity.
TextSentencer_T300 56141-56470 Sentence denotes Traditional diagnostic methods for the identifications of fungal pathogens are mostly based on phenotype analysis of fungal cultures or detection of antigens (polysaccharides), but these approaches are time-consuming and not very accurate (Diaz and Fell, 2004; Bovers et al., 2007; Landlinger et al., 2009; Babady et al., 2011) .
T42626 56141-56470 Sentence denotes Traditional diagnostic methods for the identifications of fungal pathogens are mostly based on phenotype analysis of fungal cultures or detection of antigens (polysaccharides), but these approaches are time-consuming and not very accurate (Diaz and Fell, 2004; Bovers et al., 2007; Landlinger et al., 2009; Babady et al., 2011) .
TextSentencer_T301 56471-56778 Sentence denotes Rapid and correct identification methods are important for efficient therapy (Diaz and Fell, 2004) , however, available qPCR assays have various levels of sensitivity and specificity and often have a limited range, targeting only a few yeasts or mold species (Landlinger et al., 2009; Babady et al., 2011) .
T73669 56471-56778 Sentence denotes Rapid and correct identification methods are important for efficient therapy (Diaz and Fell, 2004) , however, available qPCR assays have various levels of sensitivity and specificity and often have a limited range, targeting only a few yeasts or mold species (Landlinger et al., 2009; Babady et al., 2011) .
TextSentencer_T302 56779-57101 Sentence denotes The need for rapid and correct identifications of fungal pathogens was addressed by development of xMAP technology based detection methods (Diaz and Fell, 2004; Page and Kurtzman, 2005; Das et al., 2006; Bovers et al., 2007; Babady et al., 2011; Balada-Llasat et al., 2012; Farooqi et al., 2012; Landlinger et al., 2009) .
T59717 56779-57101 Sentence denotes The need for rapid and correct identifications of fungal pathogens was addressed by development of xMAP technology based detection methods (Diaz and Fell, 2004; Page and Kurtzman, 2005; Das et al., 2006; Bovers et al., 2007; Babady et al., 2011; Balada-Llasat et al., 2012; Farooqi et al., 2012; Landlinger et al., 2009) .
TextSentencer_T303 57102-57261 Sentence denotes Majority of xMAP applications for the multiplex detection and identification of fungal pathogens are based on the capture of fungal nucleic acid by DDH assays.
T73163 57102-57261 Sentence denotes Majority of xMAP applications for the multiplex detection and identification of fungal pathogens are based on the capture of fungal nucleic acid by DDH assays.
TextSentencer_T304 57262-57684 Sentence denotes To perform rapid and accurate identifications of fungal pathogens in immunocompromised individuals, the DDH was designed detect a wide range of the most commonly occurring clinically relevant fungal pathogens including species of the genera Aspergillus and Candida and other important pathogens such as Cryptococcus, Fusarium, Trichosporon, Mucor, Rhizopus, Penicillium, Absidia, and Acremonium (Landlinger et al., 2009 ).
T45019 57262-57684 Sentence denotes To perform rapid and accurate identifications of fungal pathogens in immunocompromised individuals, the DDH was designed detect a wide range of the most commonly occurring clinically relevant fungal pathogens including species of the genera Aspergillus and Candida and other important pathogens such as Cryptococcus, Fusarium, Trichosporon, Mucor, Rhizopus, Penicillium, Absidia, and Acremonium (Landlinger et al., 2009 ).
TextSentencer_T305 57685-57892 Sentence denotes The DDH was used mainly for identifications of fungi due to its ability to detect coinfections with multiple fungal species in patients and may contribute to improved diagnosis of invasive fungal infections.
T15128 57685-57892 Sentence denotes The DDH was used mainly for identifications of fungi due to its ability to detect coinfections with multiple fungal species in patients and may contribute to improved diagnosis of invasive fungal infections.
TextSentencer_T306 57893-58114 Sentence denotes Studies employing xMAP technology were developed and successfully used to identify individual fungal species within Candida sp. (Page and Kurtzman, 2005; Farooqi et al., 2012) , or Trichosporon sp. (Diaz and Fell, 2004) .
T1137 57893-58114 Sentence denotes Studies employing xMAP technology were developed and successfully used to identify individual fungal species within Candida sp. (Page and Kurtzman, 2005; Farooqi et al., 2012) , or Trichosporon sp. (Diaz and Fell, 2004) .
TextSentencer_T307 58115-58240 Sentence denotes In these studies, DDH assays for fast and accurate detection and identification of important fungal pathogens were developed.
T21314 58115-58240 Sentence denotes In these studies, DDH assays for fast and accurate detection and identification of important fungal pathogens were developed.
TextSentencer_T308 58241-58362 Sentence denotes In another study, the xMAP technology was used for genotyping of human pathogenic Fusarium sp. (O'Donnell et al., 2007) .
T12623 58241-58362 Sentence denotes In another study, the xMAP technology was used for genotyping of human pathogenic Fusarium sp. (O'Donnell et al., 2007) .
TextSentencer_T309 58363-58412 Sentence denotes Fusaria were genotyped also by sequence analysis.
T60248 58363-58412 Sentence denotes Fusaria were genotyped also by sequence analysis.
TextSentencer_T310 58413-58586 Sentence denotes The independent comparison of the results obtained via xMAP technology with results obtained via sequencing showed the xMAP incorrectly identified some of Fusarium isolates.
T99306 58413-58586 Sentence denotes The independent comparison of the results obtained via xMAP technology with results obtained via sequencing showed the xMAP incorrectly identified some of Fusarium isolates.
TextSentencer_T311 58587-58938 Sentence denotes Besides the in-house assays described above, commercial kits have also been developed for the detection of fungal pathogens by xMAP, e.g., xTAG R Fungal Analyte-Specific Reagents (ASR) assay and the sensitivity and specificity of the assay were tested within identification of fungal isolates and positive blood culture bottles (Babady et al., 2011) .
T68833 58587-58938 Sentence denotes Besides the in-house assays described above, commercial kits have also been developed for the detection of fungal pathogens by xMAP, e.g., xTAG R Fungal Analyte-Specific Reagents (ASR) assay and the sensitivity and specificity of the assay were tested within identification of fungal isolates and positive blood culture bottles (Babady et al., 2011) .
TextSentencer_T312 58939-59086 Sentence denotes The Candida 7-plex assay was tested within 43 of Candida strains and 16 bacterial strains with no-cross-reaction with any of the bacterial strains.
T38411 58939-59086 Sentence denotes The Candida 7-plex assay was tested within 43 of Candida strains and 16 bacterial strains with no-cross-reaction with any of the bacterial strains.
TextSentencer_T313 59087-59129 Sentence denotes The sensitivity and specificity were 100%.
T90850 59087-59129 Sentence denotes The sensitivity and specificity were 100%.
TextSentencer_T314 59130-59310 Sentence denotes Using 11-plex assay were tested 51 mold species and the assay correctly identified all species of Aspergillus, with 100% specificity and sensitivity except A. niger (0/8 isolates).
T18811 59130-59310 Sentence denotes Using 11-plex assay were tested 51 mold species and the assay correctly identified all species of Aspergillus, with 100% specificity and sensitivity except A. niger (0/8 isolates).
TextSentencer_T315 59311-59436 Sentence denotes Other molds were identify also with 100% specificity and sensitivity except Mucor (0/6 isolates) and Rhizopus (1/6 isolates).
T65162 59311-59436 Sentence denotes Other molds were identify also with 100% specificity and sensitivity except Mucor (0/6 isolates) and Rhizopus (1/6 isolates).
TextSentencer_T316 59437-59587 Sentence denotes Besides the testing of fungal isolates also positive blood culture bottles were tested for the presence of Candida species using Candida 7-plex assay.
T34551 59437-59587 Sentence denotes Besides the testing of fungal isolates also positive blood culture bottles were tested for the presence of Candida species using Candida 7-plex assay.
TextSentencer_T317 59588-59659 Sentence denotes The sensitivity and specificity of the assay was 100% for each species.
T71474 59588-59659 Sentence denotes The sensitivity and specificity of the assay was 100% for each species.
TextSentencer_T318 59660-59857 Sentence denotes The mold 11plex assay did not detect one Rhizopus species and the A. niger strains, so the results were similar as the previous mentioned results in the course of identification of fungal isolates.
T10941 59660-59857 Sentence denotes The mold 11plex assay did not detect one Rhizopus species and the A. niger strains, so the results were similar as the previous mentioned results in the course of identification of fungal isolates.
TextSentencer_T319 59858-60123 Sentence denotes In addition, ASR for identification of Candida species do not distinguish between members of Candida complexes, e.g., phenotypically indistinguishable groups II and III of C. parapsilosis (group I), which have been renamed Candida orthopsilosis and C. metapsilosis.
T96364 59858-60123 Sentence denotes In addition, ASR for identification of Candida species do not distinguish between members of Candida complexes, e.g., phenotypically indistinguishable groups II and III of C. parapsilosis (group I), which have been renamed Candida orthopsilosis and C. metapsilosis.
TextSentencer_T320 60124-60245 Sentence denotes Similarly, ASR for identification of A. fumigatus were unable to distinguish between members of the A. fumigatus complex.
T5754 60124-60245 Sentence denotes Similarly, ASR for identification of A. fumigatus were unable to distinguish between members of the A. fumigatus complex.
TextSentencer_T321 60246-60333 Sentence denotes The results showed that xTAG R Fungal ASR assay could be used as an adjunct to culture.
T82857 60246-60333 Sentence denotes The results showed that xTAG R Fungal ASR assay could be used as an adjunct to culture.
TextSentencer_T322 60334-60515 Sentence denotes The mold 11-plex assay has been developed specifically for the detection of specific species of mold, which may be reason why Rhizopus, Mucor, and A. niger have not been identified.
T38707 60334-60515 Sentence denotes The mold 11-plex assay has been developed specifically for the detection of specific species of mold, which may be reason why Rhizopus, Mucor, and A. niger have not been identified.
TextSentencer_T323 60516-60730 Sentence denotes Due to the equal treatment of infections caused by genera Mucor and Rhizopus, it would be better to design a panel to detect the most common genera of fungi, and not to focus on the detection of particular species.
T37025 60516-60730 Sentence denotes Due to the equal treatment of infections caused by genera Mucor and Rhizopus, it would be better to design a panel to detect the most common genera of fungi, and not to focus on the detection of particular species.
TextSentencer_T324 60731-60944 Sentence denotes The results showed that the xTAG R Fungal ASR assay is an attractive alternative to reference methods, due to its speed and ability to simultaneously identify multiple fungal species (Balada-Llasat et al., 2012) .
T30065 60731-60944 Sentence denotes The results showed that the xTAG R Fungal ASR assay is an attractive alternative to reference methods, due to its speed and ability to simultaneously identify multiple fungal species (Balada-Llasat et al., 2012) .
TextSentencer_T325 60945-61062 Sentence denotes DDH assay is able to not only identify the fungal pathogens, but it can be used for a genotyping of fungal pathogens.
T53068 60945-61062 Sentence denotes DDH assay is able to not only identify the fungal pathogens, but it can be used for a genotyping of fungal pathogens.
TextSentencer_T326 61063-61273 Sentence denotes It was applied for identification of closely related pathogenic yeasts Cryptococcus neoformans and Cryptococcus gattii that may cause meningoencephalitis in immunocompromised individuals (Bovers et al., 2007) .
T46011 61063-61273 Sentence denotes It was applied for identification of closely related pathogenic yeasts Cryptococcus neoformans and Cryptococcus gattii that may cause meningoencephalitis in immunocompromised individuals (Bovers et al., 2007) .
TextSentencer_T327 61274-61432 Sentence denotes Six haploid genotypic groups within these pathogens can be distinguished by several molecular methods e.g. PCR fingerprinting or intergenic spacer genotyping.
T7587 61274-61432 Sentence denotes Six haploid genotypic groups within these pathogens can be distinguished by several molecular methods e.g. PCR fingerprinting or intergenic spacer genotyping.
TextSentencer_T328 61433-61499 Sentence denotes Besides these haploid groups, hybrids have been described as well.
T82819 61433-61499 Sentence denotes Besides these haploid groups, hybrids have been described as well.
TextSentencer_T329 61500-61655 Sentence denotes AD hybrids are hybrids between the two varieties of C. neoformans and also hybrids between C. neoformans var. neoformans and C. gattii have been described.
T94353 61500-61655 Sentence denotes AD hybrids are hybrids between the two varieties of C. neoformans and also hybrids between C. neoformans var. neoformans and C. gattii have been described.
TextSentencer_T330 61656-61771 Sentence denotes The DDH has been adapted for the detection of the genotypes within Cryptococcus neoformans and Cryptococcus gattii.
T71132 61656-61771 Sentence denotes The DDH has been adapted for the detection of the genotypes within Cryptococcus neoformans and Cryptococcus gattii.
TextSentencer_T331 61772-61916 Sentence denotes The detection limit was calculated from 4 × 10 1 to 2 × 10 3 cells for the various specific probes for each of the six haploid genotypic groups.
T95738 61772-61916 Sentence denotes The detection limit was calculated from 4 × 10 1 to 2 × 10 3 cells for the various specific probes for each of the six haploid genotypic groups.
TextSentencer_T332 61917-62228 Sentence denotes The results showed that DDH is highly specific method and it is possible not only identify cryptococcal isolates at the species and genotype levels but also allows identification of hybrid isolates that have two alleles of the specific probes region and also able to identify cryptococci in cerebrospinal fluid.
T93810 61917-62228 Sentence denotes The results showed that DDH is highly specific method and it is possible not only identify cryptococcal isolates at the species and genotype levels but also allows identification of hybrid isolates that have two alleles of the specific probes region and also able to identify cryptococci in cerebrospinal fluid.
TextSentencer_T333 62229-62335 Sentence denotes However, the optimization of DNA extraction methods is needed before routine use in clinical laboratories.
T94031 62229-62335 Sentence denotes However, the optimization of DNA extraction methods is needed before routine use in clinical laboratories.
TextSentencer_T334 62336-62678 Sentence denotes Detection and identification of pathogens, as well as an understanding of pathogen variation, the pathogenesis of the diseases they cause, and timelines of infection and antimicrobial resistance, are all required in order to obtain the full picture of disease progression and to select effective cures for infected individuals or populations.
T78502 62336-62678 Sentence denotes Detection and identification of pathogens, as well as an understanding of pathogen variation, the pathogenesis of the diseases they cause, and timelines of infection and antimicrobial resistance, are all required in order to obtain the full picture of disease progression and to select effective cures for infected individuals or populations.
TextSentencer_T335 62679-62827 Sentence denotes As the amount of input data required for such decisions increases, so too does the number of tests that are required during laboratory examinations.
T7548 62679-62827 Sentence denotes As the amount of input data required for such decisions increases, so too does the number of tests that are required during laboratory examinations.
TextSentencer_T336 62828-63067 Sentence denotes The multiplex assays for the detection and typing of pathogens using xMAP technology are tools of choice as they are capable of providing all of the important information within a reasonable timeframe, and without excessive labor or costs.
T49657 62828-63067 Sentence denotes The multiplex assays for the detection and typing of pathogens using xMAP technology are tools of choice as they are capable of providing all of the important information within a reasonable timeframe, and without excessive labor or costs.
TextSentencer_T337 63068-63407 Sentence denotes The major improvement of xMAP assays is that they add another dimension to the simple detection, which is represented by the simultaneous analysis of many targets within a single sample, and they therefore represent complementary tools to procedures for the detection and quantification of pathogens such as qPCR, culture, or ELISA assays.
T39157 63068-63407 Sentence denotes The major improvement of xMAP assays is that they add another dimension to the simple detection, which is represented by the simultaneous analysis of many targets within a single sample, and they therefore represent complementary tools to procedures for the detection and quantification of pathogens such as qPCR, culture, or ELISA assays.
TextSentencer_T338 63408-63628 Sentence denotes The significance of such a complex approach for the multiplex detection has grown in recent years, which is documented by the increase in published data and of application of the commercial assays in routine diagnostics.
T7347 63408-63628 Sentence denotes The significance of such a complex approach for the multiplex detection has grown in recent years, which is documented by the increase in published data and of application of the commercial assays in routine diagnostics.