dataesr/scientific-paragraphs-categorization huggingface dataset:
Presence-absence data When considering presence-absence data for SDM, the most common biases arise from assumption of perfect detection and stationary hosts. Disease occurrence depends on the spatial distribution of the disease reservoir and intermediate hosts. We used zero-in ation binomial models  (18)  to recognize imperfect detection of occurrence. Autocorrelation and non-stationarity of the mammalian hosts were taken into account using intrinsic conditional autoregressive (iCAR) models to avoid overestimation of spatial inference and prediction in the models  (16). We extracted distributional data on the global occurrence of Filoviridae, Coronaviridae and Henipavirus human disease outbreak over time from WHO archives, Promed mail and published studies (Supplementary Table. 1). In cases where the origin of the outbreaks was unclear, we restricted down to the general region or district of origin.
Bioclimatic and population predictor datasets We extracted climatic and elevation covariates such as monthly maximum and minimum temperatures, rainfall and elevation from global Bioclim data  (19)  at spatial resolution of 2. 5 minutes or about 4. 5km at the equator. We used Moderate Resolution Imaging Spectroradiometer (MODIS) Land Cover Type (MCD12Q1) data  (20)  and human-included land use change from human activities from the Global Human Modi cation of Terrestrial Systems data set  (21). Finally, we used Gridded Population of the World, Version 4 (GPWv4) for the human population density raster  (22). The raster layers were resampled to a xed resolution of 4. 5km and stacked to a raster brick. We obtained the geographical distribution and spatial extent of the primary hosts and reservoir mammals from the IUCN red list  (23)  and the list of mammals is listed in supplementary table 2.
Model tting and Model prediction The models were tted using the r package "hsdm" which uses a hierarchical Bayesian approach incorporating spatial dependency into the analysis taking by accounting for geographical clumping which can be explained by biological (reservoirs and hosts movement) or bioclimatic variables. In our study, we analyzed the data using binomial and ZIB hierarchal SDM models with and without spatial autoregression. The ZIB models combines a Binomial process for observability and a Bernoulli process for habitat suitability  (24, 25). To model spatial autocorrelation, we used SDM with Gaussian intrinsic conditional autoregressive (iCAR)  (26). The model is tted using a Bayesian framework that allows the use of pre-validated predictors and the generation of parameter uncertainties.
Patients who had suprarenal clamping during their vascular surgery were also excluded as this clamping phase can seriously impact renal function. For each eligible patient, we recorded, from our hospital health records, the plasma creatinine concentration prior to surgery (the most recent result available in the 3 months before surgery), the highest creatinine concentration during the seven postoperative days, and the creatinine concentration at long-term follow up (between 6 months and 2 years; if multiple creatinine values were available, the measurement closest to 1 y following surgery was always selected). If no long-term creatinine measurement was available in the hospital database, attempts were made to contact the patients and/or their general practitioners to obtain any values that had been measured elsewhere.
For factors that were considered by the authors to be clinically equivalent measures of the same feature (for example weight and BMI, or Child-Pugh score and Child-Pugh class), only the factor with the strongest significance was included. The risk of developing longterm renal injury is presented as an odds ratio with 95% confidence intervals. Statistical analyses were done using Minitab 16 (Paris, France and Medcalc Software LTD, Ostend, Belgium) and R (www. r-project. org).
Discussion In a cohort of 815 patients who underwent intermediateto high-risk abdominal surgery, more than one fifth of patients (21%) who developed mild postoperative AKI had mild renal injury long term, and 2. 5% developed moderate to severe long-term renal injury. This observation demonstrates that even a slight increase in postoperative creatinine can be important and should not be neglected. Stated a different way, development of mild postoperative AKI more than tripled the odds of having renal injury 1 y after surgery compared to patients without postoperative AKI. Our results are in agreement with the only available study which examines the association of mild AKI with long-term renal injury  [20]. This study, recently published by Turan et al. , utilized a large database from the Cleveland Clinic that included more than 15,000 patients who underwent a variety of non-cardiac surgical procedures ranging from low to high-risk.
Therefore, a causal relation cannot be proven. Second, we excluded patients using a maximum creatinine cut-off value of 1. 5 mg/dl and not using estimated glomerular filtration rate. Third, we were unable to determine if the long-term creatinine value that was obtained was collected in a stable patient or in someone experiencing a new onset acute illness. Fourth, we only included patients who underwent moderate to high-risk open abdominal surgery  [27]  so that the data cannot be extrapolated to other types of surgery (neurosurgical,  cardiac, etc). Moreover, we did not exclude the 9 patients (~1%) who underwent an open nephrectomy as this small number likely has a negligible impact on the study results. Fifth, as urine output was not used for the AKI classification ("modified" KDIGO classification), this may have led to an "underestimation" of the incidence of postoperative AKI in our study cohort.
Three-Dimensional Printing of the Dosage Forms A cube of 10 mm side was modeled using Openscad software version 2015. 03. The design was then imported to the 3D printer's software Repetier version 2. 1. 6. FFF 3D printing were performed using a Prusa i3 Mk3S printer equipped with a 0. 6 mm nozzle (Prusa Research, Prague, Czech Republic). Oral forms were printed on a steel tray with a smooth polyethyleneimine coating supplied with the printer. Oral forms were printed using the settings presented in Table  3. The nozzle temperature was optimized to obtain a constant flow as well as oral forms with suitable resolution. Once the slicing operation is performed, the length of filament to be used by the printer is indicated by the printer driver software. Three filaments lengths (50. 2, 301. 2 and 401.
Characterization of D-Sorbitol Polymorphism tendency is known to be an essential data for the development of an oral form. A modification of D-Sorbitol crystalline form can impact flowability of the entire formulation. [46]. Therefore, all the D-Sorbitols selected for this study were analyzed by X-ray powder diffraction in order to verify their crystalline form. The five D-Sorbitols present an identical XRD pattern that proves their existence in the same crystalline form as showed by Figure  2. In order to observe the impact of the size and shape of the particles on the entire formulation extrusion process, five D-Sorbitol with different particle properties were selected. PSD measurement of D-Sorbitol Figure  3      Powder moisture can impact formulation flowability and product quality  [47, 48].
Slides were washed in 1% BSA before incubation with anti-IgG specific secondary antibodies conjugated to Alexa Fluor 488 (1:4000) or Alexa Fluor 546 (1:2000) (Invitrogen) for 1 h. Slides were washed in PBS, and DNA was stained with DAPI and mounted with Slowfade (Molecular Probes). Images were acquired using MetaView (Universal Imaging) software, on a Zeiss Axioplan 2 microscope equipped with a Photometrics CoolSnap CCD camera (Roper Scientific). Flagellum length measurements and processing of images were completed in Ima-geJ (https://imagej. nih. gov/ij/).
Acknowledgments We thank  Eva Gluenz  ( University of Oxford ) for the kind gift of the L. mexicana Cas9-T7 cell line and pT and pPLOT plasmids. We acknowledge the  MEA platform, University of Montpellier , and the imaging facility MRI, member of the national infrastructure France-BioImaging infrastructure. Special thanks to  Elodie Jublanc  from the  MRI-DBS platform ,  Talip Aydogan  for help with TEM picture acquisition and  Marie-Pierre Blanchard  from the  MRI  for guiding super-resolution acquisition. We also thank  Melanie Bonhivers (Univ. of Bordeaux)  for fruitful discussions and  Diane McMahon-Pratt  ( Yale School of Public Health ) for the gift of anti-PFR2 antibodies. Finally, we thank the team of EuPathDB (https://eupathdb. org/eupathdb/),without which this study would not have been possible.
Funding: PB, YS and RMC were funded by the  French LabEx ParaFrap  ( ANR-11-LABX-0024 ), the  Centre National de la Recherche Scientifique (CNRS)  and the  University of Montpellier. JCM was funded by the  Wellcome Trust  ( 200807/Z/16/Z ). PV and SV were funded by the  European Union project, Research Infrastructures  for the Control of.
Author summary Vector-borne Diseases (Infravec2grant agreement No  731060 ) and by  ERD Funds , project  CePaViP  ( 16_019/0000759 ). DRR was supported by  ANR grants LabEx ParaFrap  ( ANR-11-LABX-0024 ),  ANR-FWF   PRCI  ( ANR-20-CE91-0003 ), and  ANR   Flagel-Ome  ( ANR-19-CE17-0014-03 ). The imaging facility MRI, member of the national infrastructure France-BioImaging infrastructure was funded by the  French National Research Agency  ( ANR-10-730 INBS-04 ,  «Investments  for the future»). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Thus, this situation may also explain the failure to complain about dyspareunia or NMCPP among women  [7, 8]. This observation may reflect an attitude in the general population that prevents women from seeking and doctors from providing the appropriate clinical care  [3, [9] [10] [11]. It may also reveal that chronic pelvic pain is an underestimated and neglected symptom that women have to deal with. Accordingly, using a health system database appears unreliable for estimating the prevalence of chronic pelvic pain symptoms because it represents only people that are using this health care system. Those who do not seek medical care for many reasons are not referenced in these databases although they may have symptoms that potentially require medical advice. Also, a cohort specially designed for chronic pelvic pain among women is exposed to the risk of selection bias: women who agreed to participate were more likely to have chronic pain because they could be believed to have a better follow-up.
However, the population in France is quite different from other European or northern American countries because of differences within health care systems or socio-economic inequalities, leading to the impossibility of having any reliable estimates on CPP in France on the basis of previous studies abroad  [12]. The CONSTANCES cohort study, designed for several epidemiological purposes, provides a new French database of information collected from the general population of France. This nationwide cohort fits our objective of estimating the prevalence of dysmenorrhea, dyspareunia, and NMCPP among women in the general population, according to their severity and overlapping relations  [13, 14]. We further hypothesize that these three types of chronic pelvic pain are highly prevalent symptoms and that their prevalence may be different according to age.
Women included within the CONSTANCES cohort were offered a free medical examination and asked to complete a variety of surveys (lifestyle, quality of life, reproductive and gynaecological health, and medical history) at enrollment. Recruitment began in late 2012 and was still ongoing at the time of the study. People recruited to be part of this project were randomly sent a postal invitation (based on the number of the General Health Insurance Fund). Algorithms and statistical methods to invite people being part of this project were used to avoid selection bias, as the participation rate after the first postal invitation to be part of the cohort was estimated at 7%  [13]. In order to minimize selection effects on estimates calculated from data cohort, "a control cohort", drawn from a random sample of non-participants, was designed with 400,000 non-participants who were previously invited to be part of the cohort but declined  [14].
Study Design Women included for this study were all those aged 18-49 years within the CON-STANCES cohort from the beginning of the recruitment (late 2012) until the end of 2017. We used only data at inclusion and no follow-up data as the recruitment was still ongoing when the analysis was performed. Each woman who agreed to participate was asked on enrollment in CONSTANCES to complete a self-administered questionnaire, comprising questions previously developed in France in order to evaluate endometriosis-related pain symptoms  [17, 18]. These items assess the intensity or frequency of dysmenorrhea, dyspareunia, and NMCPP  [4]. The topic of chronic pelvic pain was investigated only in women younger than 50 years given that the proportion of perimenopausal and post-menopausal women rises continuously from this age.
E ach year, the European Renal Association-European Dialysis and Transplant Association (ERA-EDTA) Registry reports on the frequency and outcomes of dialysis and kidney transplantation (KTx) in Europe. 1, 2 This report is based on data from national and regional renal registries in Europe and several countries bordering the Mediterranean Sea. However, not all European countries have a renal registry, and, hence, the ERA-EDTA Registry annual report cannot provide a complete overview of kidney replacement therapy (KRT) in Europe. Furthermore, comprehensive conservative management (CCM) has become an alternative to KRT for patients with end-stage kidney disease (ESKD), in particular for those who are older, those who have multiple comorbidities, and those who have an unfavorable prognosis. 3 Up to now, little is known about the frequency of CCM in patients with ESKD in individual European countries.
Prevalence of KRT On 31 December 2016, 690,173 patients in 45 countries received KRT for ESKD. Figure  3  shows the prevalence of KRT by treatment modality. Portugal had the highest prevalence of KRT (1906 pmp), followed by Cyprus (1575 pmp) and Belgium (1286 pmp). The prevalence of center hemodialysis was highest in Portugal (1143 pmp), Greece (979 pmp), and Romania (887 pmp), and that of home hemodialysis (HHD) was highest in Denmark (28 pmp), Finland (25 pmp), and the United The aims of this study were to determine the frequency of dialysis and kidney transplantation and to estimate the regularity of comprehensive conservative management (CCM) for patients with kidney failure in Europe. This study uses data from the ERA-EDTA Registry. Additionally, our study included supplemental data from Armenia, Germany, Hungary, Ireland, Kosovo, Luxembourg, Malta, Moldova, Montenegro, Slovenia and additional data from Israel, Italy, Slovakia using other information sources.
DISCUSSION The current study presents the most extensive data on the frequency of KRT for ESKD in Europe so far. In addition to ERA-EDTA Registry data, data on 10 more countries (Armenia, Germany, Hungary, Ireland, Kosovo, Luxembourg, Malta, Moldova, Montenegro, and Slovenia) were included. This implies that, with the exception of some small countries (Andorra, Liechtenstein, Monaco, San Marino, and Vatican City), all nations in Europe were represented. Moreover, this study estimated the frequency of CCM for ESKD in 33 European countries.
According to our results, the vast majority of European patients started on hemodialysis, whereas only about 4% underwent preemptive KTx, which is slightly higher than in the United States (2. 8%). 6 Trend analysis of data from 14 countries from the ERA-EDTA Registry database suggests a slight increase in the crude incidence of KRT in Europe over the period 2012 to 2016. 7 veral factors may contribute to the international differences in KRT incidence. First, they may be due to variation in the prevalence of chronic kidney disease (CKD) stages 3 to 5 in the general population,  8  which, in turn, may be explained by differences in the prevalence of risk factors for CKD, such as diabetes mellitus. 9 Second, international differences may exist in the progression of CKD and in mortality of patients with CKD (e.
Strengths and limitations The main strengths of this study are the virtually full coverage of Europe and the provision of detailed information on the frequency of KRT, including center hemodialysis, HHD, PD, and KTx from living and deceased donors separately, as well as on CCM. This study also has several limitations. First, some data (e. g. , on the type of kidney donor) were unavailable for some countries. Second, for certain countries, the frequency of KRT modalities was estimated or derived from personal communication or scientific papers. Furthermore, we estimated the prevalence of patients living with a functioning kidney transplant for 5 countries with unknown prevalence. The frequency of CCM was estimated by several nephrologists per country based on a survey, and the sample may not be representative to all nephrologists in the country.
g. , through educating patients and health care professionals and better aligned reimbursement for dialysis and CCM). Countries can learn from each other how to increase these treatment options. It is desirable to set up structural data collections on the frequency of CCM as these are currently missing, and on the frequency of KRT in countries where such data collections do not exist. The existing national and regional renal registries are valuable in assessing the frequency of KRT and may therefore play an important role in reducing European inequalities in kidney care. METHODS Table  2  provides an overview of all sources used to determine the frequency of dialysis, KTx, and CCM as treatment for patients with ESKD by country. Countries considered to be geographically in both Europe and Asia (Armenia, Georgia, Russia, and Turkey) were also included, as well as Israel and Tunisia, because they also provided 2016 data to the ERA-EDTA Registry.
Data collection on KRT ERA-EDTA Registry data. National and regional renal registries that submitted individual patient data or aggregated data on the year 2016 to the ERA-EDTA Registry were included. The details of methods of data collection and data processing have been described elsewhere. 1 l renal registries contributing individual patient data to the ERA-EDTA Registry followed national legislation with regard to ethics committee approval and patient informed consent. Other sources. For countries not providing data to the ERA-EDTA Registry, other sources were used to determine the frequency of KRT. These sources included insurance data (Germany),  37  the chapter on international comparisons in the US Renal Data System report (Hungary and Israel),  6  personal communication (Cyprus and Ireland), Newsletter Transplant (Armenia, Malta, and Moldova),  38  the Eurotransplant annual report (Germany, Luxembourg, and Slovenia),  39  a scientific article on the results of a survey among nephrologists (Kosovo, Montenegro, and Slovenia),  40  and a scientific article on the results of a survey among representatives of eastern European countries of the International Society of Nephrology Regional Board (Montenegro) (Table  2 ).
36 For some countries, we used estimates on the incidence of dialysis (Germany), the incidence of KRT (Hungary), and the prevalence of dialysis (Armenia, Malta, and Moldova). The Global Observatory on Donation and Transplantation data 27 were used to obtain the number of KTx procedures performed in Armenia, Germany, Hungary, Ireland, Italy (entire country), Malta, Montenegro, Moldova, and Slovenia. Data from Luxembourg were obtained from the Eurotransplant annual report. 39 finitions of the frequency of KRT. The modality-specific incidence on day 1 was defined as the number of patients starting on each modality in 2016 and expressed as pmp. The modalityspecific incidence, pmp, was also examined on day 91 after KRT initiation, because some patients receive hemodialysis for a short period while preparations are made for PD.
The modality-specific prevalence was defined as the number of patients on each modality on 31 December 2016. Both the prevalence and the number of transplants performed in 2016 were also expressed as pmp. Some exceptions to these rules are described in the footnotes of the tables and figures. As general population data, we used the midyear population of 2016, as provided by Eurostat,  41  for countries sending individual patient data to the ERA-EDTA Registry. Exceptions to this approach were Austria, Bosnia and Herzegovina, the Spanish regions, and the United Kingdom, which provided their own population data. For countries providing aggregated data to the ERA-EDTA Registry, we used population data as provided by the national registry. For countries not providing data to the ERA-EDTA Registry in 2016, we used the midyear population of 2016, as provided by Eurostat.
78). For the analyses on the frequency of CCM in each country, we calculated the median and interquartile range (presented in main article as distributions were skewed) as well as the mean and SD of the percentages of CCM. In the figures, we present the results of countries with at least 5 survey respondents. The supplement includes the results of all countries. The frequencies of KRT and CCM are presented as unadjusted results. The analyses were performed using SAS software version 9. 4. 43.
ACKNOWLEDGEMENTS The authors would like to thank the patients and staff of all the dialysis and transplant units who have contributed data via their national and regional renal registries to the  European Renal Association-European Dialysis and Transplant Association (ERA-EDTA) Registry. In addition, we would like to thank the persons and organizations listed in the paragraph " AFFILIATED REGISTRIES " for their contribution to the work of the  ERA-EDTA Registry. The authors are grateful to all nephrologists and kidney transplant surgeons who completed "The  Effect of Differing Kidney Disease Treatment Modalities and Organ Donation and Transplantation Practices on Health Expenditure and Patient Outcomes" Nephrologist survey. In addition, we would like to thank all colleagues who pretested the survey, provided advice about the ethical approval in their country, or helped to distribute the survey in their country or personal network.
Parasitological data The prevalence of Schistosoma japonicum infection from 1991 to 2014 were collected by cross-sectional surveys each year, which were through the organization of Health professionals in Anhui Institute of Parasitic Diseases (AIPD). The data were obtained by annual village-based area surveys including residents aged 5 to 65 years based on a two-pronged diagnostic approach: First, all participants were screened by the Indirect Hemagglutination Assay (IHA)  [28]  test for anti-schistosomiasis antibodies and then the Kato-Katz technique  [29]  was applied using three thick smears from stool samples of all seropositive individuals. The prevalence is calculated as the number of positive fecal tests divided by the number of blood tests. The number of sample villages ranging from 60 to 132 in our study, and we included those with more than 100 participants.