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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id tao:has_standard_notation
21 155-162 Species denotes patient Tax:9606
22 358-365 Species denotes patient Tax:9606
23 448-459 Species denotes coronavirus Tax:11118
24 461-464 Species denotes CoV Tax:11118
25 473-483 Species denotes SARS-CoV-2 Tax:2697049
26 547-560 Species denotes coronaviruses Tax:11118
27 568-583 Species denotes Betacoronavirus Tax:694002
28 103-108 Disease denotes fever MESH:D005334
29 110-119 Disease denotes dizziness MESH:D004244
30 140-145 Disease denotes cough MESH:D003371
31 266-285 Disease denotes respiratory disease MESH:D012140
32 308-316 Disease denotes COVID-19 MESH:C000657245
33 434-442 Disease denotes COVID-19 MESH:C000657245
49 609-619 Species denotes SARS-CoV-2 Tax:2697049
50 649-662 Species denotes Coronaviridae Tax:11118
51 679-685 Species denotes humans Tax:9606
52 697-700 Species denotes CoV Tax:11118
53 740-748 Species denotes SARS-CoV Tax:694009
54 1007-1013 Species denotes people Tax:9606
55 1025-1033 Species denotes SARS-CoV Tax:694009
56 1061-1066 Species denotes human Tax:9606
57 1140-1150 Species denotes SARS-CoV-2 Tax:2697049
58 782-791 Disease denotes pneumonia MESH:D011014
59 812-845 Disease denotes severe acute respiratory syndrome MESH:D045169
60 1245-1253 Disease denotes COVID-19 MESH:C000657245
61 1389-1397 Disease denotes COVID-19 MESH:C000657245
62 1539-1547 Disease denotes COVID-19 MESH:C000657245
63 1626-1632 Disease denotes deaths MESH:D003643
66 1806-1816 Species denotes SARS-CoV-2 Tax:2697049
67 1955-1965 Species denotes SARS-CoV-2 Tax:2697049
72 3752-3767 Chemical denotes petroleum jelly MESH:D010577
73 3799-3812 Chemical denotes polypropylene MESH:D011126
74 3921-3926 Chemical denotes nylon MESH:D009757
75 3698-3702 Disease denotes fits MESH:D012640
82 4977-4981 Chemical denotes NaCl MESH:D012965
83 4985-4990 Chemical denotes water MESH:D014867
84 5626-5632 Disease denotes breath MESH:D004417
85 5722-5728 Disease denotes breath MESH:D004417
86 5815-5821 Disease denotes breath MESH:D004417
87 5018-5022 Mutation denotes C28P p.C28P
90 6935-6943 Chemical denotes elastane MESH:D011140
91 6993-7006 Chemical denotes polypropylene MESH:D011126
93 8149-8158 Disease denotes infection MESH:D007239
95 9797-9803 Disease denotes breath MESH:D004417
98 12761-12768 Species denotes ferrets Tax:9669
99 12872-12882 Species denotes SARS-CoV-2 Tax:2697049
101 13709-13714 Species denotes human Tax:9606
103 13994-14002 Disease denotes COVID-19 MESH:C000657245
106 15125-15128 Species denotes SAR Tax:2698737
107 15129-15134 Species denotes CoV-2 Tax:2697049
109 15286-15294 Disease denotes COVID-19 MESH:C000657245
111 15686-15694 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 103-108 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T2 110-119 Phenotype denotes dizziness http://purl.obolibrary.org/obo/HP_0002321
T3 140-145 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T4 782-791 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T17 0-150 Sentence denotes On 26 December 2019, a 41-year-old male was admitted to the Central Hospital of Wuhan, presenting with fever, dizziness and an unproductive cough [1].
T18 151-317 Sentence denotes The patient, a worker at a seafood market in Wuhan, was one of the first reported cases of a newly emerging severe respiratory disease, which we now know as COVID-19.
T19 318-608 Sentence denotes Metagenomic analysis of a sample of the patient’s bronchoalveolar lavage fluid revealed that the causative agent of COVID-19 is a coronavirus (CoV); named SARS-CoV-2, owing to its phylogenetic relatedness to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus).
T20 609-686 Sentence denotes SARS-CoV-2 is the seventh member of the Coronaviridae known to infect humans.
T21 687-1018 Sentence denotes The first CoV to achieve international notoriety was SARS-CoV; linked to clusters of ‘atypical pneumonia’ (later named SARS; severe acute respiratory syndrome) initially presenting in the Chinese Province of Guangdong, in 2003, before spreading first to Hong Kong and then to some 26 countries; infecting more than 8000 people [2].
T22 1019-1230 Sentence denotes While SARS-CoV originated from bats, with human transmission occurring via an intermediate host [3], the true origins of SARS-CoV-2 remain unknown (though bats, pangolins and snakes have all been suggested [4]).
T23 1231-1349 Sentence denotes As with SARS, COVID-19 spread rapidly from its Chinese epicenter, though with a considerably farther reach and impact.
T24 1350-1429 Sentence denotes On 11 March 2020, the WHO declared the COVID-19 outbreak a global pandemic [5].
T25 1430-1637 Sentence denotes At the time of writing, 216 countries & territories and two international conveyances have reported cases of COVID-19, with the total number approaching 64 million and over 1.4 million associated deaths [6].
T26 1638-1821 Sentence denotes Previously we suggested that, in the absence of an effective vaccine, ‘do-it-yourself’ (DIY) face masks were likely to play an important role in stemming the spread of SARS-CoV-2 [7].
T27 1822-1973 Sentence denotes The scientific evidence appears to support this, with several reports outlining the role of face coverings in stemming the spread of SARS-CoV-2 [8–13].
T28 1974-2120 Sentence denotes However, as the world now faces an inevitable ‘second wave’, it is essential that we redouble our efforts to halt the spread of the virus [14–16].
T29 2121-2203 Sentence denotes One approach is to refine and improve face masks, both in terms of fabric and fit.
T30 2204-2306 Sentence denotes Face masks worn in a pandemic function more effectively as source control rather than protection [17].
T31 2307-2429 Sentence denotes Particles can escape from the mask in two ways- either direct penetration of the fabric, or leakage around the sides [18].
T32 2430-2684 Sentence denotes While inward leakage testing is part of the requirements for personal protective equipment (PPE) masks in European Standard (EN) 149, the standard for medical masks, EN 14683, does not have any requirement for a leakage test – neither inward nor outward.
T33 2685-2812 Sentence denotes The European Committee for Standardisation Workshop Agreement (CWA) 17553 for face coverings also has no quantitative fit test.
T34 2813-2891 Sentence denotes In fact, to our knowledge, a standard test for outward leakage does not exist.
T35 2892-3021 Sentence denotes When both leakage and fabric penetration are considered for workplace usage of PPE, the result is the assigned protection factor.
T36 3022-3134 Sentence denotes These values typically show far lower protection than would be assumed from the performance of the fabric alone.
T37 3135-3238 Sentence denotes We propose a new metric to take into account outward leakage, which we call outward suppression factor.
T38 3239-3356 Sentence denotes One would expect outward leakage to be more challenging to fix as the exhaling pressure potentially reduces the seal.
T39 3357-3554 Sentence denotes While many recent studies have focused on the penetration of aerosols through various domestic fabrics [19], comparatively fewer studies have looked at outward leakage as opposed to inward leakage.
T40 3555-3825 Sentence denotes Better fitting medical or N95 masks have been found to significantly improve the source control of particles from a dummy head [17] and better fits have been achieved with an improved mask design, petroleum jelly [20], adhesive tape or fluffed polypropylene fibers [21].
T41 3826-4013 Sentence denotes For cloth masks, the only study explicitly addressing fit found a large benefit from wearing a nylon stocking worn over the top of a mask [22], although they measured inward leakage only.
T42 4014-4237 Sentence denotes Other studies that measured the overall outward mask performance by collecting air around the head did not attempt to separate leakage from fabric penetration as a parameter which contributes to the mask efficiency [23,24].
T43 4238-4351 Sentence denotes The extractive techniques used in many of these studies cannot alone distinguish between leakage and penetration.
T44 4352-4419 Sentence denotes Laser sheets, on the other hand, can visualize the leakage in situ.
T45 4420-4592 Sentence denotes A flat laser sheet is not optimal for this purpose, for example in the study of Fischer et al. [25], it is not clear whether leakages would be detected in their laser beam.
T46 4593-4743 Sentence denotes Herein we describe, for the first time, the use of a curved laser sheet for simultaneous yet separable detection of both mask leakage and penetration.
T47 4744-4881 Sentence denotes We envisage this to be used as a tool for mask designers to improve performance without diminishing the breathability of the mask fabric.
T48 4883-4902 Sentence denotes Materials & methods
T49 4903-4947 Sentence denotes The experimental setup is shown in Figure 1.
T50 4948-5190 Sentence denotes The aerosol consisted of 10% NaCl in water from a nebulizer (Omron NE-C28P, mass median aerodynamic diameter of 3 μm) fed through one of the lung ports of a dummy head (Laerdal airway management trainer) lying face upward on an optical bench.
T51 5191-5387 Sentence denotes Prior to measurement, the airway was primed with aerosol by turning on the nebulizer briefly while squeezing the attached lung ten-times, then waiting for 30 s for the exhaled aerosol to disperse.
T52 5388-5541 Sentence denotes A fume extractor was running continuously above the head (ULT Jumbo Filter Trolley 2.0 running at 0.3 m/s in a position 15 cm above the tip of the nose).
T53 5542-5633 Sentence denotes After initiating the camera acquisition, the lung was squeezed by hand to deliver a breath.
T54 5634-5713 Sentence denotes These were measured to deliver 300 ml quite reproducibly (wright respirometer).
T55 5714-5835 Sentence denotes For the breath duration of 1 s, the average flow of 0.3 l/s is similar to the peak flow for a normal breath 0.5 m/s [26].
T56 5836-5987 Sentence denotes The aerosol was visualized with a conical laser sheet generated with a 488 nm DPSS laser (Coherent Sapphire 75 mW) and axicon lens (Thorlabs AX1220-A).
T57 5988-6149 Sentence denotes The conical cyan sheet surrounds the face at a distance of approximately 2.5 cm from the nose and at a closer distance at the cheek to allow space for the masks.
T58 6150-6250 Sentence denotes A beam block was used at the axicon’s aperture to prevent direct illumination of parts of the dummy.
T59 6251-6260 Sentence denotes Figure 1.
T60 6262-6332 Sentence denotes Photographs of the setup, showing the laser cone on an unmasked dummy.
T61 6333-6479 Sentence denotes The extractor is turned off to enhance laser appearance (A) view from the left (B) view from top parallel to laser (C) view from the right bottom.
T62 6480-6578 Sentence denotes The camera was a 2048*2048 pixel sCMOS array (Andor Sona 4BV11) with Nikkor 50 mm F1.8 AI MF lens.
T63 6579-6651 Sentence denotes It recorded a sequence of 30 frames at 7 Hz (acquisition time of 10 ms).
T64 6652-6787 Sentence denotes Raw 16-bit images were processed in SAOimage DS9 by applying the ‘bb’ colormap on a value range of 100–20,000 counts using log scaling.
T65 6788-6835 Sentence denotes The masks and dummy used are shown in Figure 2.
T66 6836-7007 Sentence denotes The three-layer mask in Figure 2B has two outer layers each 0.4-mm thick made of 80% polyester 20% elastane with the internal filter layer being 1.0 mm 100% polypropylene.
T67 7008-7131 Sentence denotes The filter covers the area of the mouth and nose but around chin, cheeks and nose bridge the fabric is just a single layer.
T68 7132-7254 Sentence denotes Compliance with the testing methods of the CWA 17553 was claimed by the supplier but packaging was not marked accordingly.
T69 7255-7264 Sentence denotes Figure 2.
T70 7266-7300 Sentence denotes Photographs of the test materials.
T71 7301-7410 Sentence denotes (A) the unmasked dummy, (B) three-layer mask with middle filter layer removed, (C) single-layer textile mask.
T72 7411-7525 Sentence denotes Bottom row: (D) CE marked FFP1 personal protective equipment mask, (E) CE marked Type 2 medical mask, (F) bandana.
T73 7526-7649 Sentence denotes The single layer mask in Figure 2C is of unknown 1.0-mm thick material, of a design which was cheaply and widely available.
T74 7650-7692 Sentence denotes Compliance with CWA 17553 was not claimed.
T75 7693-7807 Sentence denotes The CE-marked FFP1 respirator mask in Figure 2D has no exhalation valve and it is marked as complying with EN 149.
T76 7808-7920 Sentence denotes The CE-marked type 2 medical mask in Figure 2E had a metal nose clip which was cinched down firmly on the dummy.
T77 7921-7973 Sentence denotes The packaging was marked as complying with EN 14683.
T78 7974-8103 Sentence denotes The bandana or neck gaiter in Figure 2(f) was 0.33 mm thick 100% polyester and was folded into three layers in these experiments.
T79 8104-8239 Sentence denotes Dating from 2019 this was never intended for infection control, although the same material has been seen to be used as a face covering.
T80 8241-8248 Sentence denotes Results
T81 8249-8335 Sentence denotes Figure 3A–F shows images of the unmasked dummy and with five different face coverings.
T82 8336-8450 Sentence denotes The frames shown here are the brightest of the sequence of 30 frames, corresponding to the peak particle emission.
T83 8451-8537 Sentence denotes All other frames, together with raw data, are available in the supplemental materials.
T84 8538-8625 Sentence denotes Distinct differences in the effectiveness of the various materials can be clearly seen.
T85 8626-8748 Sentence denotes The unmasked dummy should have the highest particle emission, but the scattering plume appears relatively dim (Figure 3A).
T86 8749-8880 Sentence denotes This is because the narrow jet crosses the laser sheet quickly, so that at any one-time there are few particles in the laser sheet.
T87 8881-9070 Sentence denotes The three-layer mask shows some fabric penetration directly in front of the mouth and some turbulent leakage from under the eyes which crosses the laser cone above the forehead (Figure 3B).
T88 9071-9150 Sentence denotes The single-layer mask shows very high penetration and some leakage (Figure 3C).
T89 9151-9336 Sentence denotes The brightness of the penetrating aerosol is around five-times greater than even the unmasked dummy, but this is due to the slower, broader flow which fills the laser beam with aerosol.
T90 9337-9346 Sentence denotes Figure 3.
T91 9348-9376 Sentence denotes Testing mask fabric and fit.
T92 9377-9459 Sentence denotes Top row: (A) no mask, (B) three-layer textile mask, (C) single-layer textile mask.
T93 9460-9548 Sentence denotes Bottom row: (D) CE marked FFP1 PPE mask, (E) CE marked Type 2 medical mask, (F) bandana.
T94 9549-9607 Sentence denotes Intensity scaled to 100–20,000 counts with ‘bb’ colourmap.
T95 9608-9666 Sentence denotes Similarly, the bandana shows high penetration (Figure 3F).
T96 9667-9839 Sentence denotes In this case, the leakage appears less intense, likely as there is less resistance from the fabric that would otherwise force the breath to find a path of lower resistance.
T97 9840-9991 Sentence denotes The medical mask (Figure 3E) and FFP1 (Figure 3D) mask display no detectable penetration but instead show a few turbulent jets from the cheek and eyes.
T98 9992-10108 Sentence denotes The leakage at the cheek is easier to discern from inspection of the whole time series (see supplemental materials).
T99 10109-10241 Sentence denotes In the image of the FFP1 mask, the wisp in front of the mask can be seen to originate at the cheek and did not penetrate the fabric.
T100 10242-10397 Sentence denotes These leakage jets tend to be directed over the forehead, or across the cheek, and are only partly moved into the laser cone by the extraction air current.
T101 10399-10409 Sentence denotes Discussion
T102 10410-10559 Sentence denotes The FFP1 mask is the only one which must pass a fit test to be awarded a CE mark, and indeed it showed the lowest leakage and undetected penetration.
T103 10560-10717 Sentence denotes For the other mask types, the fabrics with lower penetration showed higher leakage, indicating that these masks displayed a trade-off between fabric and fit.
T104 10718-10818 Sentence denotes The scattering of light by small particles is described by Mie theory [27], and is quite non linear.
T105 10819-11019 Sentence denotes However, using the experimental setup described herein, these nonlinearities will smooth over to a large extent due to the breadth and angle of the laser cone, and wide distribution of particle sizes.
T106 11020-11116 Sentence denotes The brightness can, therefore, be taken as approximately proportional to the volume of material.
T107 11117-11293 Sentence denotes Although it is possible to extract pseudo-quantitative results from these images by merely summing up the brightness of each pixel, we caution against doing so for two reasons.
T108 11294-11454 Sentence denotes As seen in the no-mask image (Figure 3A), a narrow, fast-moving jet appears dim due to the small area of laser sheet it covers, despite carrying a large volume.
T109 11455-11519 Sentence denotes This weakness could be addressed by more complex image analysis.
T110 11520-11610 Sentence denotes Another caveat is that the results are dependent on the exact position of the laser sheet.
T111 11611-11726 Sentence denotes In the configuration used in the current study, for example, any leakage from under the chin would not be detected.
T112 11727-11869 Sentence denotes However, when using additional laser sheets, it is apparent that almost all leakage occurs around the eyes and cheeks for the masks we tested.
T113 11870-11982 Sentence denotes These additional laser sheets complicate the interpretation of the images, even if using different laser colors.
T114 11983-12121 Sentence denotes Directing the cone straight onto the face to form a laser ring around the masks results in a large background scatter from the dummy skin.
T115 12122-12279 Sentence denotes Although this background can be reduced by black paint and image processing, this configuration would then require another laser sheet to detect penetration.
T116 12280-12497 Sentence denotes It is also important to note that the aerosol used in the current experimental setup has a mass median aerodynamic diameter of 3 μm but is also a broad distribution with 10% of the mass in particles larger than 10 μm.
T117 12498-12648 Sentence denotes This covers the range of particle sizes emitted from speech [28], but whether this also correlates to the infectious particles is not currently known.
T118 12649-12727 Sentence denotes Most of the fabric testing to date has focused on submicron particles [29,30].
T119 12728-12867 Sentence denotes However, a study of influenza in ferrets found the disease was transmitted in particles larger than 1.5 μm, but not smaller particles [31].
T120 12868-12979 Sentence denotes For SARS-CoV-2, we do not yet know which size of the aerosol is likely to carry the most infectious viral load.
T121 12980-13049 Sentence denotes Larger particles are more likely to be captured by the mask material.
T122 13050-13184 Sentence denotes To an extent this is also true for leaks, as larger particles are more likely to deposit due to impaction when passing around corners.
T123 13185-13260 Sentence denotes It is also unknown how different leakage patterns could affect infectivity.
T124 13261-13424 Sentence denotes Even the worst performing single-layer mask served to slow down the flow from the mouth, which would reduce the spread of particles even if they were not captured.
T125 13425-13517 Sentence denotes The fate of leakage jets directed to the side, or upward, would depend on the local airflow.
T126 13518-13720 Sentence denotes Furthermore, the dummy head used in this study is larger than 95% of adult male heads (tip of the nose to the back of head 237 mm), meaning that the masks were a tighter fit than the average human head.
T127 13721-13817 Sentence denotes The exact shape of the nose would also have a potentially considerable influence on the leakage.
T128 13818-13945 Sentence denotes Nonetheless, despite these limitations, our preliminary findings are clear – mask efficacy is dependent on both fabric and fit.
T129 13947-13957 Sentence denotes Conclusion
T130 13958-14217 Sentence denotes Given that the reproduction rate of COVID-19 is super-linearly related to both the efficacy of face coverings and the percentage of a population wearing face coverings, a small change in either will result in a large change in disease transmission rates [32].
T131 14218-14472 Sentence denotes It is therefore critical that universal public masking will involve optimally suppressive materials that are comfortable to wear for extended periods, can be produced in large quantities from common household materials, and are re-usable and inexpensive.
T132 14473-14551 Sentence denotes Importantly, such face coverings will not negatively impact PPE supplies [33].
T133 14552-14624 Sentence denotes Testing of pandemic masks has been largely focused on the material only.
T134 14625-14764 Sentence denotes We have demonstrated a technique based on a curved laser sheet that suggests fit is an important parameter in determining mask performance.
T135 14765-14968 Sentence denotes Measurements like this could help mask designers make improvements simply by altering the design rather than using a different fabric that may potentially be more expensive or have a lower breathability.
T136 14969-15193 Sentence denotes Quantitative analysis of the most efficient and effective face masks (in terms of both fit and fabric) will undoubtedly help to stem the spread of not just SAR-CoV-2 but also any illness spread through respiratory particles.
T137 15194-15208 Sentence denotes Summary points
T138 15209-15295 Sentence denotes The use of face masks has had a significant impact on limiting the spread of COVID-19.
T139 15296-15517 Sentence denotes We provide qualitative evidence based on a novel curved laser sheet which suggests that there is considerable variation in the efficacy of face masks depending not only on fabric type, but also on the fit around the face.
T140 15518-15695 Sentence denotes These results highlight the pressing need for more quantitative analyses based on real life usage to define the most effective face masks for controlling the spread of COVID-19.
T141 15696-15877 Sentence denotes Improved face masks will not only help to suppress the spread of the disease but will also assist in preserving vital personal protective equipment for essential frontline services.