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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
52 4123-4133 Species denotes outpatient Tax:9606
1 53-72 Disease denotes 2019-nCoV infection MESH:C000657245
5 159-168 Species denotes 2019-nCoV Tax:2697049
6 346-355 Species denotes 2019-nCoV Tax:2697049
7 392-406 Disease denotes critically ill MESH:D016638
11 1010-1018 Species denotes patients Tax:9606
12 1313-1318 Species denotes human Tax:9606
13 1499-1517 Disease denotes infectious disease MESH:D003141
21 2412-2420 Species denotes patients Tax:9606
22 1756-1775 Disease denotes 2019-nCoV infection MESH:C000657245
23 1931-1936 Disease denotes fever MESH:D005334
24 1944-1949 Disease denotes cough MESH:D003371
25 1961-1969 Disease denotes diarrhea MESH:D003967
26 2101-2130 Disease denotes lymphocytopenia and hypoxemia MESH:D000860
27 2470-2489 Disease denotes 2019-nCoV infection MESH:C000657245
37 2600-2611 Species denotes coronavirus Tax:11118
38 2769-2777 Species denotes patients Tax:9606
39 3180-3189 Species denotes 2019-nCoV Tax:2697049
40 3203-3210 Species denotes patient Tax:9606
41 3469-3473 Species denotes nCoV Tax:2697049
42 3474-3482 Species denotes patients Tax:9606
43 2828-2847 Disease denotes infectious diseases MESH:D003141
44 2904-2909 Disease denotes fever MESH:D005334
45 3071-3089 Disease denotes Infectious Disease MESH:D003141
50 3696-3705 Species denotes 2019-nCoV Tax:2697049
51 3706-3714 Species denotes patients Tax:9606
53 4170-4178 Species denotes patients Tax:9606
65 4519-4528 Species denotes 2019-nCoV Tax:2697049
66 4529-4537 Species denotes patients Tax:9606
67 4860-4869 Species denotes 2019-nCoV Tax:2697049
68 5327-5335 Species denotes patients Tax:9606
69 5704-5713 Species denotes 2019-nCoV Tax:2697049
70 5318-5326 Disease denotes infected MESH:D007239
71 5422-5431 Disease denotes infection MESH:D007239
72 5526-5535 Disease denotes infection MESH:D007239
73 5646-5651 Disease denotes fever MESH:D005334
74 5761-5780 Disease denotes 2019-nCoV infection MESH:C000657245
75 5869-5878 Disease denotes pneumonia MESH:D011014
77 6051-6057 Disease denotes stress MESH:D000079225
84 6070-6079 Species denotes 2019-nCoV Tax:2697049
85 6111-6130 Disease denotes psychosocial stress MESH:D000079225
86 6162-6167 Disease denotes death MESH:D003643
87 6202-6221 Disease denotes 2019-nCoV infection MESH:C000657245
88 6356-6362 Disease denotes stress MESH:D000079225
89 6367-6377 Disease denotes depression MESH:D000275
99 6441-6450 Species denotes 2019-nCoV Tax:2697049
100 6829-6838 Species denotes 2019-nCoV Tax:2697049
101 6839-6847 Species denotes patients Tax:9606
102 6922-6931 Species denotes 2019-nCoV Tax:2697049
103 6932-6940 Species denotes patients Tax:9606
104 6691-6710 Chemical denotes lopinavir/ritonavir MESH:C558899
105 6533-6555 Disease denotes neuromuscular blockade MESH:D020879
106 6857-6866 Disease denotes mortality MESH:D003643
107 6909-6918 Disease denotes mortality MESH:D003643

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T37 6441-6450 SP_7 denotes 2019-nCoV
T36 6585-6596 GO:0015671 denotes oxygenation
T35 6674-6689 CHEBI:50858;CHEBI:50858 denotes corticosteroids
T18 5704-5713 SP_7 denotes 2019-nCoV
T17 5761-5770 SP_7 denotes 2019-nCoV
T16 5897-5920 UBERON:0001558 denotes lower respiratory tract
T1 53-62 SP_7 denotes 2019-nCoV
T34 6691-6700 CHEBI:31781;CHEBI:31781;DG_23 denotes lopinavir
T33 6701-6710 DG_30 denotes ritonavir
T32 6829-6838 SP_7 denotes 2019-nCoV
T31 6922-6931 SP_7 denotes 2019-nCoV
T30 6070-6079 SP_7 denotes 2019-nCoV
T29 6162-6167 GO:0016265 denotes death
T28 6202-6211 SP_7 denotes 2019-nCoV
T27 4519-4528 SP_7 denotes 2019-nCoV
T26 4747-4759 GO:0000003 denotes reproductive
T25 4860-4869 SP_7 denotes 2019-nCoV
T24 4901-4912 UBERON:0001004 denotes respiratory
T23 4942-4946 UBERON:0000165 denotes oral
T22 4978-4981 UBERON:0000970 denotes eye
T21 5013-5018 NCBITaxon:10239 denotes viral
T20 5157-5162 NCBITaxon:10239 denotes virus
T19 5551-5558 GO:0065007 denotes control
T15 3696-3705 SP_7 denotes 2019-nCoV
T14 3990-3998 CHEBI:75958;CHEBI:75958 denotes solution
T13 4100-4110 GO:0040011 denotes ambulatory
T12 2600-2611 NCBITaxon:11118 denotes coronavirus
T11 3180-3189 SP_7 denotes 2019-nCoV
T10 1756-1765 SP_7 denotes 2019-nCoV
T9 1898-1909 UBERON:0001004 denotes respiratory
T8 2003-2009 UBERON:0007023 denotes adults
T7 2101-2116 CL:0000542 denotes lymphocytopenia
T6 2148-2153 UBERON:0001443 denotes chest
T5 2470-2479 SP_7 denotes 2019-nCoV
T4 1313-1318 SP_6;NCBITaxon:9606 denotes human
T3 159-168 SP_7 denotes 2019-nCoV
T2 346-355 SP_7 denotes 2019-nCoV

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 2148-2153 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T2 4978-4981 Body_part denotes eye http://purl.org/sig/ont/fma/fma54448
T3 5897-5920 Body_part denotes lower respiratory tract http://purl.org/sig/ont/fma/fma45662

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 2148-2153 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T2 4978-4981 Body_part denotes eye http://purl.obolibrary.org/obo/UBERON_0000970
T3 5897-5920 Body_part denotes lower respiratory tract http://purl.obolibrary.org/obo/UBERON_0001558
T4 5903-5920 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 53-72 Disease denotes 2019-nCoV infection http://purl.obolibrary.org/obo/MONDO_0100096
T2 63-72 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T3 1499-1517 Disease denotes infectious disease http://purl.obolibrary.org/obo/MONDO_0005550
T4 1560-1563 Disease denotes flu http://purl.obolibrary.org/obo/MONDO_0005812
T5 1756-1775 Disease denotes 2019-nCoV infection http://purl.obolibrary.org/obo/MONDO_0100096
T6 1766-1775 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T7 1961-1969 Disease denotes diarrhea http://purl.obolibrary.org/obo/MONDO_0001673
T8 2101-2116 Disease denotes lymphocytopenia http://purl.obolibrary.org/obo/MONDO_0003783
T9 2470-2489 Disease denotes 2019-nCoV infection http://purl.obolibrary.org/obo/MONDO_0100096
T10 2480-2489 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T11 2828-2838 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T12 2858-2861 Disease denotes IDH http://purl.obolibrary.org/obo/MONDO_0017326
T13 2977-2980 Disease denotes IDH http://purl.obolibrary.org/obo/MONDO_0017326
T14 3071-3081 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T15 3255-3258 Disease denotes IDH http://purl.obolibrary.org/obo/MONDO_0017326
T16 3325-3328 Disease denotes IDH http://purl.obolibrary.org/obo/MONDO_0017326
T17 3647-3650 Disease denotes IDH http://purl.obolibrary.org/obo/MONDO_0017326
T18 4467-4477 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T19 5422-5431 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T20 5526-5535 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T21 5761-5780 Disease denotes 2019-nCoV infection http://purl.obolibrary.org/obo/MONDO_0100096
T22 5771-5780 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T23 5869-5878 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T24 6202-6221 Disease denotes 2019-nCoV infection http://purl.obolibrary.org/obo/MONDO_0100096
T25 6212-6221 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T26 6367-6377 Disease denotes depression http://purl.obolibrary.org/obo/MONDO_0002050

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 26-27 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 151-152 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 302-314 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T4 504-505 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 655-656 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 1274-1277 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T7 1313-1318 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T8 1603-1604 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 1785-1786 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 2148-2153 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T11 2987-2988 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 3041-3044 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T13 3057-3058 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 3118-3121 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T15 3309-3310 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 3537-3538 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 3558-3561 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T18 4549-4550 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 4978-4981 http://www.ebi.ac.uk/efo/EFO_0000827 denotes eye
T20 5137-5141 http://purl.obolibrary.org/obo/CLO_0050509 denotes 2, 7
T21 5157-5162 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T22 5835-5836 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 5897-5920 http://purl.obolibrary.org/obo/UBERON_0001558 denotes lower respiratory tract
T24 6171-6172 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 6200-6201 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 6222-6225 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T27 6576-6584 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T28 6962-6964 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T29 7151-7153 http://purl.obolibrary.org/obo/CLO_0001022 denotes Li
T30 7151-7153 http://purl.obolibrary.org/obo/CLO_0007314 denotes Li

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 3990-3998 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T2 6674-6689 Chemical denotes corticosteroids http://purl.obolibrary.org/obo/CHEBI_50858
T3 6691-6710 Chemical denotes lopinavir/ritonavir http://purl.obolibrary.org/obo/CHEBI_145924
T4 6691-6700 Chemical denotes lopinavir http://purl.obolibrary.org/obo/CHEBI_31781
T5 6701-6710 Chemical denotes ritonavir http://purl.obolibrary.org/obo/CHEBI_45409
T6 6742-6752 Chemical denotes interferon http://purl.obolibrary.org/obo/CHEBI_52999
T7 7151-7153 Chemical denotes Li http://purl.obolibrary.org/obo/CHEBI_30145

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-91 Sentence denotes Critical care response to a hospital outbreak of the 2019-nCoV infection in Shenzhen, China
T2 93-185 Sentence denotes Beginning at early December 2019, there is an outbreak of a novel 2019-nCoV in Wuhan, China.
T3 186-341 Sentence denotes Then, Public Health Emergency of International Concern (PHEIC) was declared on 30 January 2020, by the World Health Organization (WHO) Emergency Committee.
T4 342-468 Sentence denotes The 2019-nCoV pandemic could lead to an influx of critically ill into the already strained hospital systems in mainland China.
T5 469-636 Sentence denotes Dealing with the pandemic requires a robust hospital- and city-wide command and control structure that could make quick and informed decisions among Chinese hospitals.
T6 637-800 Sentence denotes We recommend that a proper plan can enable the local government, healthcare systems, hospitals, and healthcare workers to better cope with such public eventuality.
T7 801-897 Sentence denotes The response should be flexible and adjustable according to the size of the population impacted.
T8 899-917 Sentence denotes The main challenge
T9 918-1133 Sentence denotes The main challenge may include (1) early identification of outbreak, (2) rapid expansion of patients, (3) high risk of nosocomial transmission, (4) unpredictability of size impacted, and (5) lack of backup resource.
T10 1134-1245 Sentence denotes These challenges have caused severe shortage of healthcare workers, medical materials, and beds with isolation.
T11 1246-1461 Sentence denotes The Spring Festival holiday has greatly aggravated the shortage of human resources and heavy traffic flow due to the vacation of healthy workers and factory workers, which further magnified the risk of transmission.
T12 1462-1593 Sentence denotes The key point is to discriminate the infectious disease outbreak from regular clustering cases of flu-like diseases at early stage.
T13 1594-1712 Sentence denotes There is a trade-off between false alarm causing population panic and delayed identification leading to social crisis.
T14 1714-1731 Sentence denotes Clinical features
T15 1732-1832 Sentence denotes Early identification of 2019-nCoV infection presents a major challenge for the frontline clinicians.
T16 1833-2054 Sentence denotes Its clinical symptoms largely overlap with those of common acute respiratory illnesses, including fever (98%), cough (76%), and diarrhea (3%), often more severe in older adults with pre-existing chronic comorbidities [1].
T17 2055-2135 Sentence denotes Usually, the laboratory abnormalities include lymphocytopenia and hypoxemia [1].
T18 2136-2277 Sentence denotes The initial chest radiographs may vary from minimal abnormality to bilateral ground-glass opacity or subsegmental areas of consolidation [1].
T19 2278-2490 Sentence denotes In addition, asymptomatic cases and lack of diagnosis kits result in delayed or even missed diagnosis inevitable and makes many other patients, visitors, and healthcare workers exposed to the 2019-nCoV infection.
T20 2492-2545 Sentence denotes Critical care response at the hospital and city level
T21 2547-2557 Sentence denotes City level
T22 2558-2732 Sentence denotes Critical care response to the outbreak of coronavirus should happen not only at the level of hospital, but also at the level of the city which is dominated by the government.
T23 2733-2863 Sentence denotes At the early stage, the size of the patients’ population is not beyond the capability of local infectious diseases hospital (IDH).
T24 2864-2981 Sentence denotes The general hospital is responsible for fever triage, identifying suspected cases, and transferring to the local IDH.
T25 2982-3026 Sentence denotes Such a plan is mandatory for every hospital.
T26 3027-3190 Sentence denotes Shenzhen city has established a preexisting Infectious Disease Epidemic Plan (IDEP), which has facilitated managing and containing local outbreak of the 2019-nCoV.
T27 3191-3368 Sentence denotes In case the patient load exceeds the hospital capability of the IDH, new IDHs should be considered either by building a temporary new IDH or reconstructing an existing hospital.
T28 3369-3679 Sentence denotes Wuhan, the epicenter of the outbreak, is racing against time to build two specialized hospitals for nCoV patients, namely Huoshenshan and Leishenshan hospital, whereas a different strategy has been undertaken in Shenzhen city by reconstructing an existing hospital to become an IDH with capability of 800 beds.
T29 3681-3695 Sentence denotes Hospital level
T30 3696-3833 Sentence denotes 2019-nCoV patients should be admitted to single-bedded, negative pressure rooms in isolated units with intensive care and monitoring [2].
T31 3834-3907 Sentence denotes Clinical engineering should have plans to reconstruct standard rooms [2].
T32 3908-3999 Sentence denotes Retrofitting the rooms with externally exhausted HEPA filters may be an expedient solution.
T33 4000-4240 Sentence denotes Also, the general hospital may consider procedures such as suspending elective surgeries, canceling ambulatory clinics and outpatient diagnostic procedures, transferring patients to other institutions, and restricting hospital visitors [2].
T34 4241-4423 Sentence denotes More importantly, because the hospitals’ ability to respond to the outbreak largely depends on their available ICU beds, the plan to increase ICU bed capacity needs to be determined.
T35 4425-4507 Sentence denotes Key points for preventing transmission of infectious agents in healthcare settings
T36 4508-4736 Sentence denotes Caring for 2019-nCoV patients represents a substantial exposure risk for ICU staff because of the following reasons: highly contagious with multiple transmission route, high exposure dose, long daily contact hours, and ICU stay.
T37 4737-4855 Sentence denotes The basic reproductive number was estimated to be 2.2 (95% CI, 1.4 to 3.9) [3], or as high as between 3.6 and 4.0 [4].
T38 4856-5001 Sentence denotes The 2019-nCoV is proved to be transmitted by respiratory droplets, contact, and fecal-oral, even transmission through the eye is possible [5, 6].
T39 5002-5146 Sentence denotes The higher viral load and aerosol-generating procedures, such as non-invasive ventilation, magnify the exposure and transmission risk [2, 7, 8].
T40 5147-5270 Sentence denotes Moreover, virus shedding can be prolonged and last for > 3 weeks according to some literature and our unpublished data [2].
T41 5271-5414 Sentence denotes Healthcare providers and those in contact with infected patients should utilize contact, droplet, and airborne precautions with N95 respirator.
T42 5415-5618 Sentence denotes Strict infection prevention and control practices have been implemented and audited in our units following the infection prevention and control plan published by China’s National Health Committee (CNHC).
T43 5619-5746 Sentence denotes In addition, well-equipped fever clinic as triage station with trained staff knowing 2019-nCoV case definitions is established.
T44 5747-6036 Sentence denotes For suspected 2019-nCoV infection, several key points are crucial procedures: recording a detailed history, standardizing pneumonia workup, obtaining lower respiratory tract specimens [2, 8], and implementing droplet isolation to break the transmission chain in the healthcare setting [2].
T45 6038-6057 Sentence denotes Psychosocial stress
T46 6058-6157 Sentence denotes The risk of 2019-nCoV exposure may cause significant psychosocial stress on healthcare workers [2].
T47 6158-6257 Sentence denotes The death of a retired ENT physician from a 2019-nCoV infection has added to fears in January 2020.
T48 6258-6419 Sentence denotes Psychotherapists have also been invited to join medical teams to evaluate and deal with potential stress and depression for the safety of the healthcare workers.
T49 6421-6440 Sentence denotes Critical management
T50 6441-6653 Sentence denotes 2019-nCoV management was largely supportive, including intubation, early prone positioning, neuromuscular blockade, and extracorporeal membrane oxygenation (ECMO) according to the recommendations updated by CNHC.
T51 6654-6769 Sentence denotes Low-dose systematic corticosteroids, lopinavir/ritonavir, and atomization inhalation of interferon were encouraged.
T52 6770-6867 Sentence denotes These critical managements have worked well so far, as our 2019-nCoV patients had zero mortality.
T53 6868-6979 Sentence denotes On the contrary, the previously reported mortality of 2019-nCoV patients in Wuhan ranged from 11 to 15% [1, 9].
T54 6981-6997 Sentence denotes Publisher’s Note
T55 6998-7116 Sentence denotes Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
T56 7117-7130 Sentence denotes First Author:
T57 7131-7189 Sentence denotes Yong Liu and Jinxiu Li contributed equally to this article
T58 7191-7207 Sentence denotes Acknowledgements
T59 7208-7223 Sentence denotes Not applicable.
T60 7225-7247 Sentence denotes Authors’ contributions
T61 7248-7344 Sentence denotes All authors were major contributors in writing the manuscript and approved the final manuscript.
T62 7346-7353 Sentence denotes Funding
T63 7354-7382 Sentence denotes No funding sources declared.
T64 7384-7418 Sentence denotes Availability of data and materials
T65 7419-7434 Sentence denotes Not applicable.
T66 7436-7478 Sentence denotes Ethics approval and consent to participate
T67 7479-7557 Sentence denotes This article belongs to the final editorial and is exempt from ethical review.
T68 7559-7582 Sentence denotes Consent for publication
T69 7583-7598 Sentence denotes Not applicable.
T70 7599-7637 Sentence denotes Our study contains no individual data.
T71 7639-7658 Sentence denotes Competing interests
T72 7659-7717 Sentence denotes The authors declare that they have no competing interests.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 1898-1919 Phenotype denotes respiratory illnesses http://purl.obolibrary.org/obo/HP_0002086
T2 1931-1936 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T3 1944-1949 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T4 1961-1969 Phenotype denotes diarrhea http://purl.obolibrary.org/obo/HP_0002014
T5 2068-2092 Phenotype denotes laboratory abnormalities http://purl.obolibrary.org/obo/HP_0001939
T6 2101-2116 Phenotype denotes lymphocytopenia http://purl.obolibrary.org/obo/HP_0001888
T7 2121-2130 Phenotype denotes hypoxemia http://purl.obolibrary.org/obo/HP_0012418
T8 2904-2909 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T9 5646-5651 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T10 5869-5878 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T11 6367-6377 Phenotype denotes depression http://purl.obolibrary.org/obo/HP_0000716

2_test

Id Subject Object Predicate Lexical cue
32070391-27778310-23593171 3830-3831 27778310 denotes 2
32070391-27778310-23593172 3904-3905 27778310 denotes 2
32070391-27778310-23593173 4237-4238 27778310 denotes 2
32070391-27778310-23593174 5137-5138 27778310 denotes 2
32070391-22563403-23593175 5140-5141 22563403 denotes 7
32070391-26488195-23593176 5143-5144 26488195 denotes 8
32070391-27778310-23593177 5267-5268 27778310 denotes 2
32070391-27778310-23593178 5932-5933 27778310 denotes 2
32070391-26488195-23593179 5935-5936 26488195 denotes 8
32070391-27778310-23593180 6033-6034 27778310 denotes 2
32070391-27778310-23593181 6154-6155 27778310 denotes 2