> top > docs > PMC:7033348 > annotations

PMC:7033348 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 2542-2546 Body_part denotes back http://purl.org/sig/ont/fma/fma25056
T2 22999-23007 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T3 23371-23379 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 19223-19228 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 27-35 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T2 135-144 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T3 170-178 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 2474-2482 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T5 2474-2478 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T6 2570-2579 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T7 3159-3192 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T8 3194-3198 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T9 3313-3317 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T10 7731-7741 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T11 7762-7766 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T12 7768-7773 Disease denotes Ebola http://purl.obolibrary.org/obo/MONDO_0005737
T13 7784-7793 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T14 7799-7805 Disease denotes dengue http://purl.obolibrary.org/obo/MONDO_0005502
T15 8393-8397 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 285-286 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 299-304 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T3 308-313 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T4 327-330 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T5 362-367 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T6 409-412 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T7 641-642 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 1425-1426 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 1493-1494 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 2186-2189 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T11 2386-2389 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T12 2550-2551 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 2631-2633 http://purl.obolibrary.org/obo/CLO_0001022 denotes Li
T14 2631-2633 http://purl.obolibrary.org/obo/CLO_0007314 denotes Li
T15 2661-2673 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T16 2729-2730 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 2736-2742 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T18 2780-2781 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 2824-2829 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T20 2833-2838 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T21 2852-2855 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T22 2885-2886 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 2930-2933 http://purl.obolibrary.org/obo/CLO_0001001 denotes 813
T24 3258-3261 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T25 3358-3370 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T26 3507-3512 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T27 3520-3521 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 3735-3736 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 3774-3776 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T30 4177-4178 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 4520-4521 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T32 4585-4586 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 4896-4897 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 5108-5111 http://purl.obolibrary.org/obo/CLO_0054061 denotes 132
T35 6361-6365 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T36 6930-6932 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T37 7159-7161 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T38 7697-7698 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T39 7851-7855 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T40 8019-8020 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T41 8122-8123 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 8143-8144 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T43 8271-8272 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 8574-8575 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T45 8910-8912 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T46 9000-9002 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T47 9171-9173 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T48 9448-9450 http://purl.obolibrary.org/obo/CLO_0009718 denotes yt
T49 9488-9489 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T50 9792-9794 http://purl.obolibrary.org/obo/CLO_0009718 denotes yt
T51 9864-9865 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T52 9959-9960 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53 9986-9987 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T54 10359-10360 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T55 12254-12255 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T56 12431-12432 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 12753-12754 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T58 13220-13221 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T59 13244-13245 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T60 14003-14006 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T61 14535-14538 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2 a
T62 15005-15006 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 15029-15030 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T64 15403-15405 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2a
T65 15604-15606 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2a
T66 15990-15991 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67 16588-16589 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T68 16987-16988 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69 17011-17012 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T70 17582-17583 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T71 17740-17741 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T72 20301-20308 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T73 20589-20590 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T74 20726-20728 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T75 20842-20844 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T76 20940-20941 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T77 21488-21489 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T78 21704-21710 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T79 21715-21716 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T80 21787-21788 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T81 22139-22142 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T82 22151-22152 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T83 23008-23009 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T84 23305-23309 http://purl.obolibrary.org/obo/CLO_0008416 denotes Peer
T85 23305-23309 http://purl.obolibrary.org/obo/CLO_0050081 denotes Peer
T86 23380-23381 http://purl.obolibrary.org/obo/CLO_0001020 denotes A

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 2631-2633 Chemical denotes Li http://purl.obolibrary.org/obo/CHEBI_30145
T2 3946-3948 Chemical denotes Ho http://purl.obolibrary.org/obo/CHEBI_49648
T3 3985-3999 Chemical denotes pharmaceutical http://purl.obolibrary.org/obo/CHEBI_52217
T4 5783-5798 Chemical denotes antiviral drugs http://purl.obolibrary.org/obo/CHEBI_36044
T5 5783-5792 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T6 5793-5798 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T7 9250-9258 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T8 9721-9729 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T9 9940-9948 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T10 22480-22482 Chemical denotes GC http://purl.obolibrary.org/obo/CHEBI_73890
T11 22704-22706 Chemical denotes KR http://purl.obolibrary.org/obo/CHEBI_74553
T12 22711-22713 Chemical denotes GC http://purl.obolibrary.org/obo/CHEBI_73890
T13 22753-22755 Chemical denotes YL http://purl.obolibrary.org/obo/CHEBI_75003
T14 23361-23363 Chemical denotes Co http://purl.obolibrary.org/obo/CHEBI_27638

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 135-144 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T2 2570-2579 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T3 4522-4527 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T4 4587-4592 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 710-716 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T2 1448-1454 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T3 1475-1481 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T4 2379-2385 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T5 7907-7913 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T6 7954-7960 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T7 7998-8004 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T8 8032-8038 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T9 11255-11261 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T10 11573-11579 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T11 11667-11673 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T12 12147-12153 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T13 12184-12190 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T14 12460-12474 http://purl.obolibrary.org/obo/GO_0040007 denotes growth pattern
T15 18007-18013 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T16 21027-21033 http://purl.obolibrary.org/obo/GO_0040007 denotes growth

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-94 Sentence denotes Real-time forecasts of the COVID-19 epidemic in China from February 5th to February 24th, 2020
T2 96-104 Sentence denotes Abstract
T3 105-236 Sentence denotes The initial cluster of severe pneumonia cases that triggered the COVID-19 epidemic was identified in Wuhan, China in December 2019.
T4 237-385 Sentence denotes While early cases of the disease were linked to a wet market, human-to-human transmission has driven the rapid spread of the virus throughout China.
T5 386-610 Sentence denotes The Chinese government has implemented containment strategies of city-wide lockdowns, screening at airports and train stations, and isolation of suspected patients; however, the cumulative case count keeps growing every day.
T6 611-825 Sentence denotes The ongoing outbreak presents a challenge for modelers, as limited data are available on the early growth trajectory, and the epidemiological characteristics of the novel coronavirus are yet to be fully elucidated.
T7 826-1128 Sentence denotes We use phenomenological models that have been validated during previous outbreaks to generate and assess short-term forecasts of the cumulative number of confirmed reported cases in Hubei province, the epicenter of the epidemic, and for the overall trajectory in China, excluding the province of Hubei.
T8 1129-1280 Sentence denotes We collect daily reported cumulative confirmed cases for the 2019-nCoV outbreak for each Chinese province from the National Health Commission of China.
T9 1281-1519 Sentence denotes Here, we provide 5, 10, and 15 day forecasts for five consecutive days, February 5th through February 9th, with quantified uncertainty based on a generalized logistic growth model, the Richards growth model, and a sub-epidemic wave model.
T10 1520-1804 Sentence denotes Our most recent forecasts reported here, based on data up until February 9, 2020, largely agree across the three models presented and suggest an average range of 7409–7496 additional confirmed cases in Hubei and 1128–1929 additional cases in other provinces within the next five days.
T11 1805-1957 Sentence denotes Models also predict an average total cumulative case count between 37,415 and 38,028 in Hubei and 11,588–13,499 in other provinces by February 24, 2020.
T12 1958-2118 Sentence denotes Mean estimates and uncertainty bounds for both Hubei and other provinces have remained relatively stable in the last three reporting dates (February 7th – 9th).
T13 2119-2243 Sentence denotes We also observe that each of the models predicts that the epidemic has reached saturation in both Hubei and other provinces.
T14 2244-2412 Sentence denotes Our findings suggest that the containment strategies implemented in China are successfully reducing transmission and that the epidemic growth has slowed in recent days.
T15 2414-2426 Sentence denotes Introduction
T16 2427-2681 Sentence denotes The ongoing epidemic of the novel coronavirus (SARS-CoV-2) is primarily affecting mainland China and can be traced back to a cluster of severe pneumonia cases identified in Wuhan, China in December 2019 (Li et al., 2020; World Health Organization, 2020).
T17 2682-2814 Sentence denotes Early cases of the disease have been linked to a live animal seafood market in Wuhan, pointing to a zoonotic origin of the epidemic.
T18 2815-3065 Sentence denotes However, human-to-human transmission has driven its rapid spread with a total of 37,289 confirmed cases, including 813 deaths, in China and 302 confirmed cases imported in multiple countries as of February 9, 2020 (Chinese National Health Committee).
T19 3066-3344 Sentence denotes While the early transmission potential of this novel coronavirus appeared similar to that of severe acute respiratory syndrome (SARS) (Riou & Althaus, 2020), the current tally of the epidemic has already surpassed the total cases reported for the SARS outbreaks in 2002–2003 (W.
T20 3345-3424 Sentence denotes World Health Organization, 2003; Wu, Leung, & Leung, 2020; Zhang et al., 2020).
T21 3425-3547 Sentence denotes The timing and location of the outbreak facilitated the rapid transmission of the virus within a highly mobile population.
T22 3548-3716 Sentence denotes The initial reporting of observed cases occurred during the traditional Chinese New Year, when the largest population movement takes place every year (Ai et al., 2020).
T23 3717-3966 Sentence denotes Further, Wuhan is a highly populated city with more than 11 million residents and is connected to many cities in China through public transportation, such as buses, trains, and flights (Lai et al., 2020; Read, Bridgen, Cummings, Ho, & Jewell, 2020).
T24 3967-4120 Sentence denotes In the absence of pharmaceutical interventions, rapid action was required by the Chinese government to mitigate transmission within and outside of Wuhan.
T25 4121-4406 Sentence denotes On January 23, 2020, the Chinese government implemented a strict lockdown of Wuhan, followed by several nearby cities in subsequent days; the lockdowns include temporarily suspending all public transportation and advising residents to remain at home (Du et al., 2020; Wu et al., 2020).
T26 4407-4662 Sentence denotes Further, many high-speed rail stations and airports have implemented screening measures to detect travelers with a fever, specifically those traveling from Wuhan, and those with a fever are referred to public hospitals (Lai et al., 2020; Wu et al., 2020).
T27 4663-4785 Sentence denotes Within hospitals, patients who fulfill clinical and epidemiological characteristics of 2019-nCoV are immediately isolated.
T28 4786-4942 Sentence denotes The number of 2019-nCoV cases in Wuhan quickly outnumbered the available number of beds in hospitals, putting a substantial burden on the healthcare system.
T29 4943-5174 Sentence denotes Consequently, the government rapidly built and launched two new hospitals with capacity for 1,600 and 1,000 beds, respectively, in Wuhan in addition to the existing 132 quarantine sites with more than 12,500 beds (Steinbuch, 2020).
T30 5175-5350 Sentence denotes To anticipate additional resources to combat the epidemic, mathematical and statistical modeling tools can be useful to generate timely short-term forecasts of reported cases.
T31 5351-5543 Sentence denotes These predictions can include estimates of expected morbidity burden that can help guide public health officials preparing the medical care and other resources needed to confront the epidemic.
T32 5544-5752 Sentence denotes Short-term forecasts can also guide the intensity and type of interventions needed to mitigate an epidemic (Funk, Camacho, Kucharski, Eggo, & Edmunds, 2016; Shanafelt, Jones, Lima, Perrings, & Chowell, 2017).
T33 5753-5983 Sentence denotes In the absence of vaccines or antiviral drugs for 2019-nCoV, the effective implementation of nonpharmaceutical interventions, such as personal protection and social distancing, will be critical to bring the epidemic under control.
T34 5984-6174 Sentence denotes In this emerging epidemic, the epidemiological data is limited, and the epidemiological parameters needed to calibrate elaborate mechanistic transmission models are not yet fully elucidated.
T35 6175-6404 Sentence denotes Real-time short-term forecasts must be based on dynamic phenomenological models that have been validated during previous outbreaks (Chowell et al., 2016; Pell, Kuang, Viboud, & Chowell, 2018)(Bürger, Chowell, & Lara-Díıaz, 2019).
T36 6405-6673 Sentence denotes We employ several dynamic models to generate and assess 5, 10, and 15 day ahead forecasts of the cumulative number of confirmed cases in Hubei province, the epicenter of the epidemic, and the overall trajectory of the epidemic in China excluding the province of Hubei.
T37 6675-6682 Sentence denotes Methods
T38 6684-6688 Sentence denotes Data
T39 6689-6911 Sentence denotes We obtained daily updates of the cumulative number of reported confirmed cases for the 2019-nCoV epidemic across provinces in China from the National Health Commission of China website (Chinese National Health Commission).
T40 6912-7088 Sentence denotes The data contains 34 areas, including provinces, municipalities, autonomous regions, and special administrative regions; here we refer to the regions collectively as provinces.
T41 7089-7189 Sentence denotes Data updates were collected daily at 12 p.m. (GMT-5), between January 22, 2020 and February 9, 2020.
T42 7190-7355 Sentence denotes The short time-series is affected by irregularities and reporting lags, so the cumulative curves are more stable and likely yield more stable and reliable estimates.
T43 7356-7540 Sentence denotes Therefore, we analyze the cumulative trajectory of the epidemic in Hubei province, the epicenter of the outbreak, as well as the cumulative aggregate trajectory of all other provinces.
T44 7542-7548 Sentence denotes Models
T45 7549-7881 Sentence denotes We generate short-term forecasts in real-time using three phenomenological models that have been previously used to derive short-term forecasts for a number of epidemics for several infectious diseases, including SARS, Ebola, pandemic influenza, and dengue (Chowell, Tariq, & Hyman, 2019; Pell et al., 2018; Wang, Wu, & Yang, 2012).
T46 7882-8088 Sentence denotes The generalized logistic growth model (GLM) extends the simple logistic growth model to accommodate sub-exponential growth dynamics with a scaling of growth parameter, p (Viboud, Simonsen, & Chowell, 2016).
T47 8089-8254 Sentence denotes The Richards model also includes a scaling parameter, a, to allow for deviation from the symmetric logistic curve (Chowell, 2017; Richards, 1959; Wang et al., 2012).
T48 8255-8435 Sentence denotes We also include a recently developed sub-epidemic wave model that supports complex epidemic trajectories, including multiple peaks (i.e., SARS in Singapore (Chowell et al., 2019)).
T49 8436-8573 Sentence denotes In this approach, the observed reported curve is assumed to be the aggregate of multiple underlying sub-epidemics (Chowell et al., 2019).
T50 8574-8650 Sentence denotes A detailed description for each of the models is included in the Supplement.
T51 8652-8672 Sentence denotes Short-term forecasts
T52 8673-8791 Sentence denotes We calibrate each model to the daily cumulative reported case counts for Hubei and other provinces (all except Hubei).
T53 8792-8919 Sentence denotes While the outbreak began in December 2019, available data on cumulative case counts are available starting on January 22, 2020.
T54 8920-9029 Sentence denotes Therefore, the first calibration process includes 15 observations: from January 22, 2020 to February 5, 2020.
T55 9030-9218 Sentence denotes Each subsequent calibration period increases by one day with each new published daily data, with the last calibration period between January 22, 2020 and February 9, 2020 (19 data points).
T56 9219-9318 Sentence denotes We estimate the best-fit model solution to the reported data using nonlinear least squares fitting.
T57 9319-9701 Sentence denotes This process yields the set of model parameters Θ that minimizes the sum of squared errors between the model f(t,Θ) and the data yt; where ΘGLM = (r, p, K), ΘRich = (r, a, K), and ΘSub = (r, p, K 0 , q, C thr) correspond to the estimated parameter sets for the GLM, the Richards model, and the sub-epidemic model, respectively; parameter descriptions are provided in the Supplement.
T58 9702-9797 Sentence denotes Thus, the best-fit solution f(t,Θˆ) is defined by the parameter set Θˆ=argmin∑t=1n(f(t,Θ)−yt)2.
T59 9798-9851 Sentence denotes We fix the initial condition to the first data point.
T60 9852-9985 Sentence denotes We then use a parametric bootstrap approach to quantify uncertainty around the best-fit solution, assuming a Poisson error structure.
T61 9986-10092 Sentence denotes A detailed description of this method is provided in prior studies (Chowell, 2017; Roosa & Chowell, 2019).
T62 10093-10248 Sentence denotes The models are refitted to the M = 200 bootstrap datasets to obtain M parameter sets, which are used to define 95% confidence intervals for each parameter.
T63 10249-10391 Sentence denotes Each of the M model solutions to the bootstrap curves is used to generate m = 30 simulations extended through a forecasting period of 15 days.
T64 10392-10475 Sentence denotes These 6000 (M × m) curves construct the 95% prediction intervals for the forecasts.
T65 10477-10484 Sentence denotes Results
T66 10485-10602 Sentence denotes We generated 5, 10, and 15 day ahead forecasts for Hubei and other provinces excluding Hubei for 5 consecutive dates:
T67 10603-10640 Sentence denotes February 5, 2020 to February 9, 2020.
T68 10641-10874 Sentence denotes Fig. 1, Fig. 2, Fig. 3 represent the range of 5, 10, and 15 day ahead forecasts, respectively, by the date generated, and we compare the daily short-term forecasts of cumulative case counts across dates as more data become available.
T69 10875-11026 Sentence denotes Current cumulative reported case counts as of February 9, 2020 are 27,100 for Hubei and 10,189 in other provinces (Chinese National Health Commission).
T70 11028-11045 Sentence denotes Model calibration
T71 11046-11235 Sentence denotes Our results for Hubei province indicate that the parameter estimates for the three models tend to stabilize and decrease in uncertainty as more data become available (Supplemental Table 1).
T72 11236-11367 Sentence denotes In particular, the growth rate r decreases and appears to be converging over time, particularly for the GLM and sub-epidemic model.
T73 11368-11503 Sentence denotes Parameter K also follows this general trend, with prediction intervals decreasing significantly in width as more data become available.
T74 11504-11631 Sentence denotes Importantly, the p estimates from the GLM indicate that the epidemic growth in Hubei is close to exponential (p = 0.99 (95% CI:
T75 11632-11657 Sentence denotes 0.98, 1) – February 9th).
T76 11658-11821 Sentence denotes Further, growth rate and scaling parameter estimates have remained relatively stable over the last three reporting dates, while estimates of K are still declining.
T77 11822-11915 Sentence denotes This may correlate with the effectiveness of control measures or the slowing of the epidemic.
T78 11916-12084 Sentence denotes For the trajectory that aggregates all other provinces (excluding Hubei), the parameter estimates follow trends that differ from those for Hubei (Supplemental Table 2).
T79 12085-12301 Sentence denotes While the three models estimated stable and nearly equivalent growth rates in Hubei, the estimated growth rates for other provinces vary across models and do not follow a distinct trend as more data become available.
T80 12302-12385 Sentence denotes However, the scaling and size parameters remain relatively stable across all dates.
T81 12386-12512 Sentence denotes Further, the p estimates from the GLM reveal a consistent sub-exponential growth pattern in other provinces (p = 0.67 (95% CI:
T82 12513-12541 Sentence denotes 0.64, 0.70) – February 9th).
T83 12543-12565 Sentence denotes 5-days ahead forecasts
T84 12566-12756 Sentence denotes The latest 5-day ahead forecasts, generated on February 9, 2020, estimate an average of 34,509–34,596 total cumulative cases in Hubei by February 14, 2020 across the three models (Fig. 1 a).
T85 12757-12873 Sentence denotes For other provinces, the models predict an average range of 11,317–12,118 cumulative cases by February 14 (Fig. 1b).
T86 12874-13084 Sentence denotes Based on cumulative reported cases as of February 9th, these estimates correspond with an average of 7409–7496 additional cases in Hubei and 1128–1929 additional cases in other provinces within the next 5 days.
T87 13085-13247 Sentence denotes Fig. 1 Forecasting results for 5-days ahead estimates, generated daily from February 5–9, 2020, of cumulative reported cases in Hubei (a) and other provinces (b).
T88 13248-13369 Sentence denotes The mean case estimate is represented by the dots, while the lines represent the 95% prediction intervals for each model.
T89 13370-13595 Sentence denotes Comparing the 5-day ahead forecasts generated daily on February 5–9, 2020, the GLM and Richards models yield comparable prediction intervals in Hubei, while the sub-epidemic model yields wider intervals than the other models.
T90 13596-13795 Sentence denotes Also, 5 day ahead forecasts from the sub-epidemic model on February 5th and 6th predict significantly higher case counts in Hubei compared to forecasts generated on February 7th and beyond (Fig. 1a).
T91 13796-13970 Sentence denotes For other provinces, the GLM and Richards model yield intervals of similar widths, but the GLM predicts higher case counts than the Richards model across all dates (Fig. 1b).
T92 13971-14115 Sentence denotes Further, the sub-epidemic model has significantly wider prediction intervals compared to the other models for all forecasts for other provinces.
T93 14116-14329 Sentence denotes While the uncertainty of the predictions decreases as more data became available in Hubei, the uncertainty of the predictions for other provinces remain relatively stable, compared to forecasts from earlier dates.
T94 14331-14354 Sentence denotes 10-days ahead forecasts
T95 14355-14540 Sentence denotes The 10 day ahead forecasts generated on February 9, 2020 from the three models estimate between 36,854 and 37,230 cumulative cases, on average, in Hubei by February 19, 2020 (Fig. 2 a).
T96 14541-14701 Sentence denotes For other provinces, the latest 10 day ahead forecasts predict average cumulative case counts between 11,549 and 13,069 cases across the three models (Fig. 2b).
T97 14702-14868 Sentence denotes These estimates correspond with an additional 9754–10,130 cases in Hubei and an additional 1360–2880 cases reported in other provinces on average in the next 10 days.
T98 14869-15032 Sentence denotes Fig. 2 Forecasting results for 10-days ahead estimates, generated daily from February 5–9, 2020, of cumulative reported cases in Hubei (a) and other provinces (b).
T99 15033-15154 Sentence denotes The mean case estimate is represented by the dots, while the lines represent the 95% prediction intervals for each model.
T100 15155-15407 Sentence denotes 10 day ahead forecasts of case counts in Hubei generated on February 5th show significantly different results between the GLM and Richards versus the sub-epidemic model, with the sub-epidemic model predicting significantly higher case counts (Fig. 2a).
T101 15408-15608 Sentence denotes For forecasts generated after February 5th, the prediction intervals of the three models are comparable, with the GLM intervals having the lowest uncertainty, followed by the Richards model (Fig. 2a).
T102 15609-15727 Sentence denotes For other provinces, the sub-epidemic model yields significantly wider prediction intervals than the other two models.
T103 15728-15922 Sentence denotes Like the 5 day ahead forecasts, the 10 day ahead prediction intervals become increasingly narrow for Hubei when including more data, but uncertainty remains relatively stable in other provinces.
T104 15924-15947 Sentence denotes 15-days ahead forecasts
T105 15948-16098 Sentence denotes The latest 15 day ahead forecasts predict a cumulative reported case count between 37,415 and 38,028 cases, on average, in Hubei by February 24, 2020.
T106 16099-16235 Sentence denotes Further, the latest 15 day ahead forecasts suggest an average cumulative case count between 11,588 and 13,499 cases for other provinces.
T107 16236-16388 Sentence denotes These forecasts correspond with an additional 10,315–10,928 cases in Hubei and an additional 1399–3310 cases in other provinces within the next 15 days.
T108 16389-16591 Sentence denotes Again, the sub-epidemic model yields significantly higher forecasts for Hubei on February 5th, compared to the other models and compared to subsequent prediction intervals on following dates (Fig. 3 a).
T109 16592-16719 Sentence denotes The width of prediction intervals decreases as more data are included for each of the models in both Hubei and other provinces.
T110 16720-16850 Sentence denotes This is consistent with shorter-term forecasts in Hubei but differs from the pattern of shorter-term forecasts in other provinces.
T111 16851-17014 Sentence denotes Fig. 3 Forecasting results for 15-days ahead estimates, generated daily from February 5–9, 2020, of cumulative reported cases in Hubei (a) and other provinces (b).
T112 17015-17136 Sentence denotes The mean case estimate is represented by the dots, while the lines represent the 95% prediction intervals for each model.
T113 17138-17148 Sentence denotes Discussion
T114 17149-17343 Sentence denotes In this report, we provide timely short-term forecasts of the cumulative number of reported cases of the 2019-nCoV epidemic in Hubei province and other provinces in China as of February 9, 2020.
T115 17344-17497 Sentence denotes As the epidemic continues, we are also publishing online daily 10day ahead forecasts including each of the models presented here (Roosa & Chowell, 2020).
T116 17498-17722 Sentence denotes Based on the three models calibrated to data up until February 9, 2020, we forecast a cumulative number of reported cases between 37,415 and 38,028 in Hubei Province and 11,588–13,499 in other provinces by February 24, 2020.
T117 17723-17928 Sentence denotes Our models yield a good visual fit to the epidemic curves, based on residuals, with the sub-epidemic model outperforming the other models in terms of mean squared error (MSE) (Supplemental Tables 1 and 2).
T118 17929-18082 Sentence denotes Parameter estimation results from the GLM consistently show that the epidemic growth is near exponential in Hubei and sub-exponential in other provinces.
T119 18083-18294 Sentence denotes Overall, models predict similar ranges of short-term forecasts, except for those generated on February 5th, where the sub-epidemic model predicts significantly higher case counts than the other two models (Figs.
T120 18295-18300 Sentence denotes 1–3).
T121 18301-18519 Sentence denotes The sub-epidemic model predicts similar ranges to the other models for subsequent dates, so the higher ranges on February 5th may indicate that more data are required to inform the parameters of the sub-epidemic model.
T122 18520-18724 Sentence denotes We observe that the width of the prediction intervals decreases on average as more data are included for forecasts in Hubei; however, this pattern is not obvious for our analysis based on other provinces.
T123 18725-18855 Sentence denotes This can, in part, be attributed to the smaller case counts and smaller initial prediction interval range seen in other provinces.
T124 18856-19050 Sentence denotes Mean predictions and associated uncertainty remain relatively stable in other provinces though, while the mean estimates of 10 and 15 days ahead decrease significantly in Hubei (Fig. 2, Fig. 3).
T125 19051-19261 Sentence denotes This suggests that the epidemic lasts longer in Hubei compared to other provinces (Fig. 4, Fig. 5, Fig. 6 ), which may be attributed to intensive control efforts and large-scale social distancing interventions.
T126 19262-19417 Sentence denotes Therefore, it is not necessarily surprising that estimates from earlier dates, specifically prior to saturation, yield predictions with higher uncertainty.
T127 19418-19560 Sentence denotes Fig. 4 15-day ahead GLM forecasts of cumulative reported 2019-nCoV cases in China – Hubei and other provinces – generated on February 9, 2020.
T128 19561-19708 Sentence denotes Fig. 5 15-day ahead Richards forecasts of cumulative reported 2019-nCoV cases in China – Hubei and other provinces – generated on February 9, 2020.
T129 19709-19866 Sentence denotes Fig. 6 15-day ahead sub-epidemic model forecasts of cumulative reported 2019-nCoV cases in China – Hubei and other provinces – generated on February 9, 2020.
T130 19867-20161 Sentence denotes We retrieve the data from the Chinese media conglomerate Tencent (Chinese National Health Commission); however, the data show small differences in case counts compared to data of the epidemic reported by other sources (Johns Hopkins University Center for Systems Science and Engineering, 2020).
T131 20162-20344 Sentence denotes Importantly, the curves of confirmed cases that we employ in our study are reported according to reporting date and could be influenced by testing capacity and other related factors.
T132 20345-20518 Sentence denotes Further, there may be significant delays in identifying, isolating, and reporting cases in Hubei due to the magnitude of the epidemic, which could influence our predictions.
T133 20519-20655 Sentence denotes Incidence curves according to the date of symptom onset could provide a clearer picture of the transmission dynamics during an epidemic.
T134 20656-20778 Sentence denotes We also note that we analyzed the epidemic curves starting on January 22, 2020, but the epidemic started in December 2019.
T135 20779-20898 Sentence denotes Hence, the first data point accumulates cases up until January 22, 2020, as data were not available prior to this date.
T136 20899-21138 Sentence denotes The 2019-nCoV outbreak in China presents a significant challenge for modelers, as there are limited data available on the early growth trajectory, and epidemiological characteristics of the novel coronavirus have not been fully elucidated.
T137 21139-21438 Sentence denotes Our timely short-term forecasts based on phenomenological models can be useful for real-time preparedness, such as anticipating the required number of hospital beds and other medical resources, as they provide an estimate of the number of cases hospitals will need to prepare for in the coming days.
T138 21439-21591 Sentence denotes In future work, we plan to report the results of a retrospective analysis of forecasting performance across models based on various performance metrics.
T139 21592-21711 Sentence denotes Of note, the case definition changed on February 12, 2020 to count clinical cases that have not been laboratory tested.
T140 21712-21839 Sentence denotes As a result in this change in reporting, the province of Hubei experienced a jump in the nuber of cases on February 13th, 2020.
T141 21840-21963 Sentence denotes This change in reporting will need to be taken into account in order to assess the accuracy of the forecasts reported here.
T142 21964-22099 Sentence denotes In conclusion, our most recent forecasts, based on data for the last three days (February 7th – 9th, 2020), remained relatively stable.
T143 22100-22205 Sentence denotes These models predict that the epidemic has reached a saturation point for both Hubei and other provinces.
T144 22206-22371 Sentence denotes This likely reflects the impact of the wide spectrum of social distancing measures implemented by the Chinese government, which likely helped stabilize the epidemic.
T145 22372-22470 Sentence denotes The forecasts presented are based on the assumption that current mitigation efforts will continue.
T146 22472-22479 Sentence denotes Funding
T147 22480-22548 Sentence denotes GC is supported by 10.13039/100000001NSF grants 1610429 and 1633381.
T148 22550-22556 Sentence denotes Ethics
T149 22557-22572 Sentence denotes Not applicable.
T150 22574-22598 Sentence denotes Data, code and materials
T151 22599-22681 Sentence denotes Data will be made available in an online repository upon acceptance of manuscript.
T152 22683-22703 Sentence denotes Author contributions
T153 22704-22870 Sentence denotes KR and GC conducted forecasts and data analysis; YL retrieved and managed data; All authors contributed to writing and revising subsequent versions of the manuscript.
T154 22871-22922 Sentence denotes All authors read and approved the final manuscript.
T155 22924-22957 Sentence denotes Declaration of competing interest
T156 22958-22997 Sentence denotes Authors declare no competing interests.
T157 22999-23029 Sentence denotes Appendix A Supplementary data
T158 23030-23108 Sentence denotes The following is the Supplementary data to this article:Multimedia component 1
T159 23110-23126 Sentence denotes Acknowledgements
T160 23127-23304 Sentence denotes We thank Homma Rafi (Director of Communications, School of Public Health, Georgia State University) for creating and maintaining the online record of daily short-term forecasts.
T161 23305-23370 Sentence denotes Peer review under responsibility of KeAi Communications Co., Ltd.
T162 23371-23483 Sentence denotes Appendix A Supplementary data to this article can be found online at https://doi.org/10.1016/j.idm.2020.02.002.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 27-35 Disease denotes COVID-19 MESH:C000657245
4 135-144 Disease denotes pneumonia MESH:D011014
5 170-178 Disease denotes COVID-19 MESH:C000657245
13 2474-2478 Disease denotes SARS MESH:D045169
14 2570-2579 Disease denotes pneumonia MESH:D011014
15 2782-2790 Disease denotes zoonotic MESH:D015047
16 2934-2940 Disease denotes deaths MESH:D003643
17 3159-3192 Disease denotes severe acute respiratory syndrome MESH:D045169
18 3194-3198 Disease denotes SARS MESH:D045169
19 3313-3317 Disease denotes SARS MESH:D045169
22 4522-4527 Disease denotes fever MESH:D005334
23 4587-4592 Disease denotes fever MESH:D005334
27 7731-7750 Disease denotes infectious diseases MESH:D003141
28 7762-7766 Disease denotes SARS MESH:D045169
29 8393-8397 Disease denotes SARS MESH:D045169

2_test

Id Subject Object Predicate Lexical cue
32110742-28038870-47437626 5695-5699 28038870 denotes 2016
32110742-27913131-47437627 6361-6365 27913131 denotes 2018
32110742-31499661-47437628 6398-6402 31499661 denotes 2019
32110742-27913131-47437629 7851-7855 27913131 denotes 2018
32110742-22889641-47437630 7875-7879 22889641 denotes 2012
32110742-27266847-47437631 8082-8086 27266847 denotes 2016
32110742-22889641-47437632 8248-8252 22889641 denotes 2012
T44406 5695-5699 28038870 denotes 2016
T52035 6361-6365 27913131 denotes 2018
T75543 6398-6402 31499661 denotes 2019
T48089 7851-7855 27913131 denotes 2018
T63529 7875-7879 22889641 denotes 2012
T61091 8082-8086 27266847 denotes 2016
T25904 8248-8252 22889641 denotes 2012