dataesr/scientific-paragraphs-categorization huggingface dataset:
In 2017, we also recorded whether each individual reported participation in the 2015 campaign. All data collected on paper forms were entered into an electronic database using double-entry for quality control. An automated script was developed with Stata version 15. 1 to identify discrepancies between the two series of data entries from a given year, and all discrepancies were resolved by reference to the paper form. The 2015 data were matched to those from 2017 by use of participant name, age, village of residence and, when available, the individual barcode assigned to them in 2015. We assumed that names of individuals who participated in both campaigns might have been spelt differently, and we used a semi-automated algorithm to generate lists of likely matches. All matches with a high degree of certainty were validated manually.
Acknowledgments This research was funded by the  Bill & Melinda Gates Foundation  and, in part, by the  Division of Intramural Research of the National Institute of Allergy and Infectious Diseases (US National Institutes of Health ). We thank the residents of the Okola health district in Cameroon (especially the village chiefs and deputies) for their active participation in the study. We also thank the personnel from the  Cameroon Ministry of Public Health  for their assistance in the field.
At the end of the incubation period, the cells were treated with MTT (5 mg/mL in Phosphate Buffered Saline (PBS)) for 4 h at 37 • C. Subsequently, 10% Sodium Dodecyl Sulfate (SDS) in 10 mM hydrochlorid acid was added to dissolve the formazan, and then the cells were incubated overnight at 37 • C. The production of formazan which is directly proportional to the viable cell number was read as absorbance values at 540 nm using Infinite 200 (Tecan, Lyon, France) with Magellan data analysis software. Experiments were done in triplicate. Cell viability percentage curves and IC 50 were calculated using Microsoft Excel 2010 from Microsoft Corporation, Microsoft Casablanca (Casablanca, Morocco). The curves were fitted as logarithmic tendency curves then IC 50 were calculated using their log equations.
Apoptosis Annexin-V staining Cells were seeded to 6 wells plates (Ø35 mm) at 2 × 10 5 cells/well for the MDA-MB-468 and BT-20 cells, and at 3 × 10 5 cells/well for HCC70 cells, and allowed to attach to the well bottom overnight. Cells were treated with berberine at the doses of 0. 2, 0. 5 and 1 µM, and incubated for 120 h and 144 h in 37 • C with 5% CO 2. DMSO (0. 005%) was used as control. After incubation, both attached and detached cells were harvested and washed twice by PBS (1X). Next, the cells were then stained with 1% Annexin-V-FITC diluted in 4-(2-hydroxyethyl)-1-piperazine ethane sulfonic (HEPES) buffer for 15 min at RT in the dark. Cells were then washed and stained with 1% propodium iodide diluted in HEPES buffer. The analysis and populations quantification were achieved through LSRII flow cytometer (Becton Dickinson) using DIVA™ and FlowJo softwares.
Molecular Analysis by Western Blotting and Antibodies Briefly, 1 × 10 6 of MDA-MB-468 and BT-20 cells, and 1. 5 × 10 6 of HCC70 cells were seeded in (Ø90mm) Petri dishes and allowed to attach overnight, then treated with berberine at 0. 5 and 1 µM, and then incubated for 120 and 144 h in 37 • C with 5% CO 2. DMSO (0. 005%) was used as control. For whole cell protein lysates, the samples were prepared according to the established protocol  [32]. Briefly, the lysates were collected using the Laemmli 1X buffer. Proteins dosage was done by BCA Protein assay kit reducing Agent Compatible (Perbio, ref 23250). Proteins concentrations were read as absorbance values at 562 nm using Infinite 200 (Tecan, Lyon, France) with Magellan data analysis software. Equivalent amounts of protein lysates (20 µg), were separated by electrophoresis in acrylamide gel (Bio-Rad TGX 4-15%) starting with 15 mA then increasing to 25 mA, then blotted onto nitrocellulose membrane (Bio-Rad, Marnes la Coquette, France).
The membranes were then saturated with 5% BSA+TBS/0. 1% Tween for 1 h at RT. The blotted membranes were incubated with different primary antibodies for 2 h at RT, and then washed four times with TBS/0. 1% Tween 5 min each, at RT. The membranes were then followed by incubations with secondary antibodies labeled with horseradish peroxidase (Jackson Immuno Research Laboratories, Interchim, Clichy, France) for 1 h at RT. The proteins were visualized using ECL kit (Amersham Pharmacia Biotech, Orsay, France). The quantification was performed using a LAS-3000 Luminescent Image analyser and Multi Gauge software (Fuji, FSVT, Courbevoie, France). Actin was detected for normalisation between samples using anti-beta-actin primary antibody at the dilution of 1:2000 (Sigma-Aldrich, Saint Quentin Fallavier, France).
The purified Vero cell rabies vaccine (PVRV; Verorab ® , Sanofi Pasteur) has been used in rabies prevention since 1985. Evolving rabies vaccination trends, including shorter intradermal (ID) regimens with reduced volume, along with WHO recommendation for ID administration has driven recent ID PVRV regimen assessments. Thus, a consolidated review comparing immunogenicity of PVRV ID regimens during pre-exposure prophylaxis (PrEP) and post-exposure prophylaxis (PEP) is timely and beneficial in identifying gaps in current research. A search of seven databases for studies published from 1985 to November 2019 identified 35 studies. PrEP was assessed in 10 studies (n = 926) with 1-3-site, 1-3-visit regimens of up to 3-months duration. Seroconversion (rabies virus neutralizing antibodies [RVNA] ≥ 0.
Materials and Methods A literature search was executed across seven databases, Embase, Medline, Chemical Abstracts, Biosis, TrialTrove, ClinicalTrials. gov, and EudraCT to identify relevant studies published from 1985 to 21 November 2019 for inclusion in this review. The following keyword combination was used as appropriate across the articles databases: rabies vaccine OR (rabies* AND (vaccin* OR immuniz* OR pre exposure prophylaxis OR post exposure prophylaxis)) AND Verorab OR other Verorab tradenames OR Vero cell line OR Vero* OR pvrv* AND intradermal drug administration OR intradermal* OR intracutaneous* OR ID (within 2 words of vaccin* OR injection* OR syringe*). For the clinical trials databases, the following keyword combination was used as appropriate: Verorab OR PVRV OR 'purified inactivated Vero rabies vaccine' OR 'purified Vero rabies vaccine' AND intradermal OR ID.
Initially, the titles and abstracts (where available) of citations identified were appraised for relevance by T. M. (first author). The full text of potentially suitable studies was obtained and reviewed to identify relevant data. In addition, bibliographies of relevant review articles identified were searched for additional studies not captured by the database searches. Articles were chosen for inclusion in line with the PICOS approach  [19]. There were no restrictions applied on the type of patient/participant. All prospective studies assessing ID PVRV during PrEP or PEP or following booster or simulated PEP that were available in English and reported primary immunogenicity data (i. e. , rabies virus neutralizing antibodies [RVNA] titers, geometric mean titers [GMTs], seroconversion rates) were included.
Results A total of 144 potentially relevant citations were identified from the databases searched and other sources, of which 35 met the inclusion criteria (Figure  1 ). There was considerable heterogeneity across studies in terms of study designs, regimens, number of vaccination sites, vaccine potency, population assessed, and time series reported, precluding a meaningful pooled/meta-analysis of the RVNA titers. The intention here is to display the available data to allow the reader to assess general trends within selected groupings. Seroconversion was defined as a titer ≥ 0. 5 IU/mL in all studies. intradermal* OR intracutaneous* OR ID (within 2 words of vaccin* OR injection* OR syringe*). For the clinical trials databases, the following keyword combination was used as appropriate: Verorab OR PVRV OR 'purified inactivated Vero rabies vaccine' OR 'purified Vero rabies vaccine' AND intradermal OR ID.
Results A total of 144 potentially relevant citations were identified from the databases searched and other sources, of which 35 met the inclusion criteria (Figure  1 ). There was considerable heterogeneity across studies in terms of study designs, regimens, number of vaccination sites, vaccine potency, population assessed, and time series reported, precluding a meaningful pooled/meta-analysis of the RVNA titers. The intention here is to display the available data to allow the reader to assess general trends within selected groupings. Seroconversion was defined as a titer ≥ 0. 5 IU/mL in all studies.
In addition, ID PVRV PEP rapidly induces RVNA titers that exceed the 0. 5 IU/mL threshold, irrespective of concomitant use of RIG across the numerous regimens assessed, which appears to persist above the threshold for at least five years in the majority of subjects. Although numerous PrEP and PEP regimens with ID PVRV have been assessed, data are generally lacking for current, recently updated, WHO-recommended ID regimens. In particular, the current recommended 2-site 1-week (2-0-2) PrEP regimen has not been assessed with ID PVRV; a study is currently being conducted to investigate this schedule (NCT03700242 [VAJ00001 study]). The diversity/heterogeneity/variability in regimen/potency/population demonstrated in this review underscores the continued need for studies to examine immunogenicity related to ID administration both across vaccine type and regimen in multiple populations.
Data Collected The following clinical data were collected from each patient's medical records: date PD was started, age, sex, height, weight, BMI, body surface area, history of pregnancy, urinary volume, comorbidities, Charlson Comorbidity Index, IPP value, date of assessment, and IPV. Centralized reading of all the abdominal tomodensitometries was done in the hospital in Reims by an operator blinded to the clinical data. TKV, liver volume, and the volume of the abdominal cavity were measured by contouring using OxiriX software. The kidneys, liver, and abdominal cavity were manually outlined. The area of each region of interest was calculated and then multiplied by the slice thickness. Finally, all slice volumes were added together to calculate the volume of each 3-dimensional structure (Figure  2 ).
Material and Methods Medical records were obtained from a Veterinary Pathology Laboratory in France (LAPVSO-Laboratoire D'Anatomie Pathologique Vétérinaire du Sud-Ouest, Toulouse, France). These were mined for all data corresponding to canine liver samples that tested positive to rhodanine staining, coming from a Veterinary Referral Hospital in Paris  (Centre Hospitalier Vétérinaire Fregis, Arcueil, France) , between May 2010 and March 2017. The corresponding medical records were obtained from the same referral center for a more complete database. The information gathered from the medical records included age, sex, breed, presenting complaint(s), clinical sign(s), clinicopathologic data, ultrasound (US) findings, biopsy collection method, histopathological results, treatment, and follow-up.
Biopsy collection method was detailed and correlated with the respective quality of the sample. Data concerning quality of sample was based on the histopatology report and the subjective assessment performed by the pathologist being defined as poor, acceptable or good. Hematoxyline-Eosine and Rhodanine staining were performed on all biopsy samples. The latter product stains intrahepatic copper granules, allowing for a qualitative assessment of hepatic copper accumulation  (Johnston et al. , 2013). CAH was classified as periportal (zone 1), centrilobular (zone 3) or multifocal according to rhodadine staining pattern within the hepatic acinus. In detail, hepatic acinus is divided into three zones according to the distance from oxygenated blood. Zone 1 corresponds to the periportal region, zone 3 refers to the acinus periphery, and zone 2 is interspersed inbetween them  (Mescher, 2016).
Conflict of interest The Authors declare that there is no conflict of interest Authors contribution A. Rodrigues were involved on the data collection and preparation of the manuscript; R. O. Leal, M. Girod, and J. Hernandez supervised the preparation of the manuscript, contributing for the scientific background and discussing its main time points; E. Guery and C. Dally were involved on data collection at LAPVSO contributing for the histopathology results, figures and pathology feedback; E. Gomes reviewed all the imaging database, contributing for the US results feedback.
Study limitations. The main limitations of our study were its retrospective nature. As many patients were referred from different neurosurgical centers their follow up was difficult to obtain. Therefore, some delays of obliteration may be overestimated. Larger population databases with strict follow up protocols or multicentric studies are needed to increase the weight of statistical analysis and confirm our favorable results. Other limitation is that part of the patients underwent brain MRI to conclude to obliteration. In this respect, MRI is not considered as being as such sensitive and specific as the DSA and could overestimate the rate of obliteration.
Acknowledgements This article has been greatly motivated by fruitful discussions with the researchers of the Systems Biology Group Lab -www. sbglab. org-settled at the  Department of Experimental Medicine, Sapienza University of Rome (Italy ) and, in particular, with  M. Bizzarri  and  S. Dinicola. The authors are also grateful to  A. Corli  for constructive conversations about the Zeldovich equation reported at the end of Section 3. 3.
METHODS A single-center retrospective study was performed in the Cancer Center of Caen (France), with approval from the CNIL data protection commission (n°2090357). All patients receiving postoperative chemoradiotherapy for HNSCC at high risk of recurrence between 2007 and 2016 were included. Surgery was required to have been curative. Patients with history of neck irradiation were excluded. Treatment was considered complete for 3 chemotherapy courses and full radiation dose without ≥3 days' interruption. Malnutrition was defined by body-mass index (BMI) <18 kg/m² or >5% body-weight loss. Toxicity was assessed according to the Common Terminology Criteria for Adverse Events (CTCAE, version 4. 0)  (12). Comorbidity was considered severe for scores ≥3 on any item of the Cumulative Illness Rating Scale (CIRS).
However, the studies available to date provide limited orientation for the management of CAT patients beyond 6 months after the index VTE mainly due to the relatively small patient sample size. Two large prospective cohort studies have documented the treatment of CAT patients with tinzaparin for 6 months. The PREDICARE study included 409 patients of whom 28 patients had a recurrent VTE, yielding a cumulative incidence of 7. 3% (95% CI: 4. 9-11. 1) while 15 patients had a major bleeding yielding a cumulative incidence of 3. 7% (95% CI: 2. 3%; 6. 0%) during the 6-month treatment period  [15]. A total of 310 CAT patients with objectively diagnosed VTE were enrolled to receive 6-month anticoagulant therapy with tinzaparin in the aXa study (NCT02898051; https://clinicaltrials. gov/ct2/show/NCT02898051).
Inclusion Criteria Adult patients with cancer and objectively diagnosed acute VTE previously included in both prospective observational cohort studies, aXa and PREDICARE, and who were still alive at the end of the initial 6-month treatment period with tinzaparin, and having given their consent for the use of their data were eligible to participate in Usual Care of Cancer Associated Thrombosis (USCAT), a retrospective non-interventional multicenter cohort study. The clinical protocol was submitted and approved by the Institutional Review Board of the University Hospital of Saint-Etienne, France (Institutional Review Board: IORG0007394, Number RBN342018/CHUSTE).
Data Management and Statistics The same independent investigator had access to the primary data and reviewed medical records of all included patients and recorded data in a standardized case report form. Relevant data, including patient demographics, cancer status and treatment, anticoagulant therapy, index VTE events, VTE recurrences, bleeding events and deaths were collected up to 12 months after the index VTE event. Information on changes in cancer status, cancer treatment and anticoagulant therapy was collected. A sample size of 250 to 300 patients was considered appropriate to allow analyses of 6-to-12-month data following the index VTE based on descriptive statistics. The cumulative incidence of VTE recurrences and bleeding events was estimated by the Kalbfleisch and Prentice method to take in account the competing risk of death and the cumulative incidence of deaths was estimated by the Kaplan Meier method.
This observation is consistent with the recently reported increased risk of bleeding in patients with gastrointestinal cancers  [20, 21]  and confirms the need of careful precautions when using an anticoagulant treatment in these patients. The influence of the cancer site on the clinical course of VTE during the initial 6-month treatment had also been analyzed in 3,947 cancer patients enrolled in the Registro Informatizado de la Enfermedad TromboEmbólica (RIETE registry)  [22]. During course of the anticoagulant therapy, rates of VTE recurrence as rates of major bleeding were higher in patients with lung and colorectal cancer. This strongly suggests the need to develop cancer-specific anticoagulant strategies in the management of patients with CAT. The ongoing prospective double blind API-CAT study (APIxaban Cancer Associated Thrombosis, NCT03692065; https://clinicaltrials.
gov/ct2/show/NCT03692065) is the first randomized controlled trial (RCT) to document critical outcomes in CAT patients during the period following 6-month treatment with any anticoagulant. Patients are randomized to receive either apixaban 5mg bid or apixaban 2. 5 mg bid with the objective of assessing the optimal long-term dosing regimen. The stratification according to the cancer site may contribute to the tailoring of patient management according to the nature of the underlying malignancy. Considering the profile of patients having experienced a VTE recurrence, our study suggests a close relationship between both the stage and progression of cancer, and the risk of VTE recurrence. These data recommend the extension of the anticoagulant therapy for as long as the cancer is active and/or the patient receives an antineoplastic treatment.
However, of the 487 eligible patients, only 55 patients could not be included in the USCAT study. Furthermore, clinical protocols and event adjudication in PREDICARE  [15]  and aXa (NCT02898051; https://clinicaltrials. gov/ct2/show/NCT02898051) studies were homogeneous, allowing the inclusion of a large study population in USCAT. Our study is the largest sample size of CAT patients enrolled after 6-month treatment with LMWH (n = 432) in an observational study with a relatively large number of patients having completed the 12-month follow-up (n = 332). Moreover, patients' characteristics were documented 6 months after the index VTE i. e. , at the time when the treatment strategy for the subsequent 6 months was to be discussed. A strength of this study is the use of a competitive risk method to estimate outcomes cumulative incidences whereas this method was inappropriately ignored in the other studies.
Objectives: Veno-arterial extracorporeal membrane oxygenation (VA-ECMO) is increasingly being used to treat patients with refractory severe heart failure. Large animal models are developed to help understand physiology and build translational research projects. In order to better understand those experimental models, we conducted a systematic literature review of animal models combining heart failure and VA-ECMO. Studies selection: A systematic review was performed using Medline via PubMed, EMBASE, and Web of Science, from January 1996 to January 2019. Animal models combining experimental acute heart failure and ECMO were included. Clinical studies, abstracts, and studies not employing VA-ECMO were excluded. Data extraction: Following variables were extracted, relating to four key features: (1) study design, (2) animals and their peri-experimental care, (3) heart failure models and characteristics, and (4) ECMO characteristics and management.
Results: Nineteen models of heart failure and VA-ECMO were included in this review. All were performed in large animals, the majority (n = 13) in pigs. Acute myocardial infarction (n = 11) with left anterior descending coronary ligation (n = 9) was the commonest mean of inducing heart failure. Most models employed peripheral VA-ECMO (n = 14) with limited reporting. Conclusion: Among models that combined severe heart failure and VA-ECMO, there is a large heterogeneity in both design and reporting, as well as methods employed for heart failure. There is a need for standardization of reporting and minimum dataset to ensure translational research achieve high-quality standards.
Inclusion and exclusion criteria Our review covered animal models of heart failure supported by VA-ECMO with no restriction to the publication language. This comprised studies of all types which matched the following PICO approach: (1) population defined as animals with heart failure; (2) intervention defined as animals treated with VA-ECMO; (3) controls defined as animals not treated with VA-ECMO (when the study involved more than one group); and (4) outcomes comprised data reporting quality, characteristics of heart failure, and ECMO support. Studies using VA-ECMO in the context of cardiac arrest were excluded, as extracorporeal cardiopulmonary resuscitation (ECPR) represents a different clinical scenario and carries its own definition  [9].
Search strategy and data extraction We used PubMed, Web of Science, and EMBASE to search for animal models of heart failure on VA-ECMO from January 1st, 1996 to January 1st, 2019. The search contained keywords relevant to cardiac failure and VA extracorporeal membrane oxygenation, applying pre-published animal filters when relevant  [10, 11]. References from identified studies and relevant review articles were also searched for additional eligible citations. The full search strategy is provided in the Supplementary materials. Two independent reviewers (SH and IR) initially screened articles based on their titles and abstracts. Full-text articles were subsequently independently reviewed (SH and SR) and data were extracted according to a data extraction form available in the Supplementary materials eTable 1.
Numerical methods The details of the numerical methods are described in  (14). Briefly, the above model is an oversimplified representation of COVID-19 outbreaks. The purpose of its use is to generate first approximations of how mitigation efforts modeled by the proxy parameter ℛC could quantitively translate into the attenuation of outbreaks. Linking specific measures to their influence on key epidemiological parameters will be important in the future management of COVID-19. The influences of reductions in ℛ0 on key epidemiological parameters were investigated using the Epidemic Calculator package (16) (Supplementary Material). This platform enables the user to set the parameters under focus here, namely, the total population size (N), the initial sub-population of infections individuals (I), the basic reproduction number (ℛ0), the day on which the mitigation measures begin and the resulting (lowered) reproduction number (ℛC).