dataesr/scientific-paragraphs-categorization huggingface dataset:
After 48 h the incubated eleuthero embryos were morphologically screened, and the mean scores calculated, as described in methods. Three independent experiments were performed, the data were pooled and the mean ± SD was calculated. Hence, a total of six eleuthero embryos were processed per concentration, except in the case of Med samples (n = 10) and RLM samples (n = 10). For the statistical analysis, the mean score of RLM was compared with the mean scores of the other samples by using one-way ANOVA with Dunnett's multiple comparison test. ** p ≤ 0. 01, *** p ≤ 0. 001.
Control conditions consisted out of eleuthero embryos exposed to the RLM extract (without compound spiking) in the medium (indicated as RLM), and eleuthero embryos exposed to the medium without the RLM extract and without spiking (indicated as Med). After 48 h the incubated eleuthero embryos were morphologically screened, and the mean scores calculated, as described in methods. Three independent experiments were performed, the data were pooled and the mean ± SD was calculated. Hence, a total of 30 eleuthero embryos were processed per condition. For the statistical analysis, the mean score of RLM was compared with the mean scores of the other samples by using one-way ANOVA with Dunnett's multiple comparison test. *** p ≤ 0. 001. As mentioned before, malathion could be recovered only in small amounts from the samples exposed to RLM (calculated conc < 6 µ M).
The bar charts show the results after incubation of three dpf zebrafish eleuthero embryos with 4-fold dilutions of reconstituted extracts of processed samples that were analyzed on their content (see Figure  3 ). Control conditions consisted out of eleuthero embryos exposed to the RLM extract (without compound spiking) in the medium (indicated as RLM), and eleuthero embryos exposed to the medium without the RLM extract and without spiking (indicated as Med). After 48 h the incubated eleuthero embryos were morphologically screened, and the mean scores calculated, as described in methods. Three independent experiments were performed, the data were pooled and the mean ± SD was calculated. Hence, a total of 30 eleuthero embryos were processed per condition. For the statistical analysis, the mean score of RLM was compared with the mean scores of the other samples by using one-way ANOVA with Dunnett's multiple comparison test.
All samples were analyzed in a positive ion mode. The scan rate was set to 120-1000 m/z. Data acquisition and peak processing were performed using the OpenLAB CDS Chemstation Edition 01. 04 software (Agilent, Waldbronn, Germany) and Compass 1. 3 EsquireControl Version 6. 2 (Bruker Daltonik, Billerica, MA, USA). All calculations concerning the evaluation of the recorded data were made in MS Excel (Microsoft Corporation, Seattle, USA). The compounds were separated on an Acquity BEH C18 column (100 mm-2. 1 mm, dp = 1. 7 µm) from Waters (Milford, MA, USA) at a flow rate of 0. 4 mL/min. Gradient elution was performed starting at 97:3 (v/v) 10 mM ammonium formate (pH 2. 8 modified with formic acid):ACN, and changed to 18:82 (v/v) 10 mM ammonium formate (pH 2. 8):ACN in 10. 5 min. After elution of the compounds, a cleaning step using 100% ACN was applied for 1.
Funding: This research was funded by  MarPipe , a fellowship from  H2020-Marie Skłodowska-Curie Innovative Training Networks  PhD, proposal number: 721421 (A. G. ), the  Vietnamese government 's project  911   KU Leuven  (X. -B. N. ),  ARIADME , a European FP7 ITN Community's  Seventh Framework Program  under Grant Agreement No. 607517  (S. K. ),  ChromaFish , an individual fellowship from  H2020-Marie Skłodowska-Curie Actions  (MSCA post-doc), project number  799806  (M. M. ), the  Development Project of Shanghai Peak Disciplines-Integrative Medicine , proposal number: 20150407 (X. W. ) and by  L'Oréal  (contract  C150353 ).
Acknowledgments Authors want to thank all breeders and all veterinary students who participated in improvement of knowledge about passive immune transfer in the dog, and particularly  Charlotte Aggouni ,  Amélie Albaret ,  Morgane Delebarre ,  Leslie Garrier ,  Milène Gonnier ,  Barbara Hanse ,  Morgane Mantelli ,  Maelys Martin ,  Cynthia Olivier ,  Laurène Plante ,  Chloé Robic ,  Lisa Rossig ,  Camille Viaud.
Statistical analyses We have used the MedCalc® statistical software (Ostend, Belgium) for all of the statistical analyses. Statistical associations between the clinicopathologic characteristics were evaluated using Chi-2 tests for categorical variables, one-way analysis of variance between a continuous and a categorical variable, and linear regression analysis among continuous variables. Univariate survival analyses were performed using the Kaplan-Meier method and log-rank tests, while multivariate survival analyses relied on Cox proportional hazards models. The results are expressed as the Hazard Ratio (HR), its 95% confidence interval (95% CI), and the p-value of each covariate. The significance threshold was set at < 0. 05.
Acknowledgments The authors thank  Dr. Mélanie Pohu ,  Dr. Floriane Morio , and  Dr. Clotilde de Brito , who helped in collecting the clinical and follow-up data, as well as the veterinary pathologists ( Dr. Jean-Loïc Le Net ,  Dr. Virginie Théau ,  Dr. Pierre Lagourette ,  Dr. Olivier Albaric  and  Dr. Sophie Labrut ) who performed the initial diagnoses of feline mammary carcinomas, and the technicians in histopathology ( Mr. Bernard Fernandez ,  Mrs. Florence Lezin , and  Mrs. Catherine Guéreaud ) who made the slides. We are very grateful to  Prof. Dominique Fanuel  (DVM) for critical review of this work. Finally, we thank the referring veterinarians and the owners of the cats included in this study, who gave us the clinical and follow-up data. AMaROC, Oniris ( Nantes Atlantic College of Veterinary Medicine, Food Science and Engineering) ,  Oniris site Chantrerie ,  CS40706 ,  44307 ,  Cedex 3, Nantes, France.
soft palate measurements Image analysis was performed using an open source software (Horos, open source code software, Lesser General Public License (LGPL) at horosproject. org). Studies were anonymised and randomised. Before initiating the measurement protocol, multiplanar reconstructions were created to align the three planar axes with the hard palate, centred on the suture between maxillary bones (figure  1 ). A mid-sagittal image of the soft palate was then created and used for the measurements. All measurements were evaluated independently on three separate occasions by three observers (one European College Veterinary Diagnostic Imaging (ECVDI) diplomate, one European College Veterinary Surgeons (ECVS) diplomate and one third-year ECVDI resident) who were blinded to the patient's medical history and clinical status.
statistical analysis All statistical analyses were performed using the SPSS statistical package V. 17 (SPSS). Intraobserver reliability for all measurements was assessed using intraclass correlation coefficient (ICC). For each observer and dog, the ICC (with 95% CI) was calculated based on the three sets of data using a two-way random effects. Interobserver  reliability between the three observers was calculated in a similar manner. The following categories for expressing levels of reliability were used: excellent reliability, 0. 90 to 0. 99; good reliability, 0. 80 to 0. 89; fair reliability, 0. 70 to 0. 79; moderate reliability, 0. 59 to 0. 69; and poor reliability, <0. 59. 7  8.
Adult patients who were consulting or admitted for a one-dayhospitalization fulfilled the questionnaire. Demographic data (age, sex, occupational category, education level), presence of neurological disease, patient already familiar with the department or first visit, reasons for the external consultation or for the one-dayhospitalization were collected. When the patient came for urodynamic study, learning of urinary intermittent self-catheterization, perineal electrophysiology, intradetrusor injection of botulinum toxin A, urinary sphincter injection of botulinum toxin A or limb injection of botulinum toxin A, the reason for the visit was considered as invasive. Non-invasive reasons of consulting were: medical consultation and learning of posterior tibial nerve stimulation. The questionnaire and the collected data were anonymous.
Study Setting and Design The study was performed in MSM enrolled in the ongoing CohMSM prospective cohort study, which was designed to assess the feasibility and interest of implementing a quarterly global HIV prevention care intervention in this key population (registered with ClinicalTrials. gov, number NCT02626286). MSM were recruited and followed up between June 2015 and June 2018 in 4 community-based clinics already providing MSM-specific prevention, care, and support in Bamako (Mali), Abidjan (Côte d'Ivoire), Ouagadougou (Burkina Faso), and Lomé (Togo). Eligibility criteria were as follows: aged 18 years or older, reporting at least 1 episode of anal intercourse with another man in the previous 3 months, and being HIV negative or having discovered HIV infection at enrollment. At enrollment and during the intervention's quarterly follow-up visits, participants benefited from clinical examination, HIV testing, screening and treatment for other STIs (using the syndromic approach), and individualized peer-based support.
HIV/HBV-coinfected participants were offered tenofovir disoproxil fumarate (TDF) plus lamivudine (3TC) or emtricitabine (FTC) as part of ART. Vaccination against hepatitis B was part of the comprehensive intervention and was offered free of charge to participants who tested negative for both HBsAg and anti-HBs. Like the other interventions' components, HBV vaccination was promoted by both physicians and peer educators. Hepatitis B vaccine was administered as a 3-dose regimen (day 0, month 1, and month 6) or, from November 2016, as a 4-dose regimen (day 0, day 7, day 21, and month 12). Specific appointments were given outside the usual quarterly follow-up visits if needed. Vaccination status was assessed at every visit using participant and/or study site medical records. Finally, sociodemographic and behavioral data were collected at enrollment using a standardized face-to-face questionnaire administered by trained research assistants.
Financial support. This study was supported by the  ANRS  ( France Recherche Nord & Sud Sida-hiv Hépatites ;  ANRS 12324 ) and  Expertise France  (Initiative  5% ). T. T. E. D. is the recipient of a doctoral fellowship from  ANRS  ( 12324-B99 ). Potential conflicts of interest. All authors: no reported conflicts of interest. All authors have submitted the  ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed. CohMSM Study Group. Clotilde Couderc ,  Bruno Granouillac ,  Suzanne Izard ,  Christian Laurent ,  Laura March ,  Martine Peeters ,  Laetitia Serrano  ( IRD, INSERM, Université de Montpellier, Unité TransVIHMI, Montpellier, France );  Cyril Berenger ,  Michel Bourrelly ,  Pierre-Julien Coulaud ,  Gwenaelle Maradan ,  Marion Mora ,  Luis Sagaon-Teyssier ,  Bruno Spire  ( INSERM, IRD, Université Aix-Marseille, Unité SESSTIM, Marseille, France );  Adeline Bernier ,  Paméla Palvadeau ,  Daniela Rojas Castro  ( Coalition Internationale Sida, Pantin, France );  Drissa Camara ,  Oumar Cisse ,  Alou Coulibaly ,  Bintou Dembélé Keita ,  Fodié Diallo ,  Mahamadou Diarra ,  Abdoul Aziz Keita ,  Kader Maiga ,  Aly Ouologuem ,  Fodé Traore  ( ARCAD-SIDA, Bamako, Mali );  Niamkey Thomas Aka ,  Camille Anoma ,  Stéphane-Alain Babo Yoro ,  Noufo Hamed Coulibaly ,  Rachelle Kotchi ,  Patrick Kouabenan ,  Malan Jean-Baptiste kouamé ,  Kpassou Julien Lokrou ,  Frédéric Dibi N'Guessan (Espace Confiance, Abidjan, Côte d'Ivoire) ;  Christian Coulibaly ,  Ter Tiero Elias Dah ,  Ousseni Ilboudo ,  Joseph Ouedraogo ,  Mamadou Ouedraogo ,  Elisabeth Thio ,  Juste Rodrigue Toure ,  Abdoulazziz Traore ,  Issa Traoré  ( Association African Solidarité, Ouagadougou, Burkina Faso );  Fiffou Yougbare  ( Centre National de Transfusion Sanguine, Ouagadougou, Burkina Faso );  Kouakou Kokouvi Selom Agbomadji ,  Mawuényégan Kouamivi Agboyibor ,  Messan Attiogbe ,  Aléda Mawuli Badjassim ,  Agbégnigan Lorette Ekon ,  Anouwarsadat Kokouba ,  Ephrem Mensah ,  Diimiln Joseph Strauss Tablissi ,  Kossi Jeff Yaka  ( Espoir Vie Togo, Lomé, Togo );  Claver Anoumou Yaotsé Dagnra  ( Laboratoire BIOLIM ,  Université de Lomé, Lomé, Togo ).
Imaging A single mosaic from adjacent 1 μm-step Z-stack images, (Figure  2A  and B ) taken using a 10x objective (NA 0. 5) on an AxioImager M2 (Carl Zeiss, Toronto, ON, Canada), was compiled using 3D Virtual Slice software (Stereo Investigator, MBF Bioscience, Williston, VT, USA). An apochromatically corrected 20x objective (NA 0. 75) (Figure  2C-F ) and 60x objective (NA 1. 4) (Figure  2G  and H and Figure  3A-P ) on a Nikon A1 laser scanning confocal microscope (Nikon Instruments, Melville, NY, USA) were also used to acquire images. Images are presented as maximum intensity projections from 23, 0. 85 μm-step Z-stacks (Figure  2C-F ), maximum intensity projections from 88, 0. 18 μm-step Z-stacks (Figure  3A -P), or as orthogonal views from 0. 1 μm-step Z-stacks (Figure  2G, H ).
Cell Counting The numbers of Aβ plaques, GFP-positive and GFAP-positive cells, and GFP-positive and GFAP-negative cells within the FUS-targeted areas of the brain were quantified using Stereo Investigator software on a Zeiss AxioImager M2 microscope. GFP expression associated with Aβ plaque was defined as the occurrence of plaque and GFP expression from the GFAP-positive cell body or projections overlapping in space. For coronal brain sections, six 40 μm-thick sections from the FUS-targeted regions were used at an interval of one in six for quantification. For axial brain sections, five 40 µm-thick sections were used at an interval of one in three. Quantification was done using an optical fractionator probe and 63x oil objective (NA= 1. 4) on an exhaustive grid covering all regions of the hippocampus and cortex with visible GFP expression.
The final number of plaque and cell counts was extrapolated from the section interval. The Cavalieri estimator probe within the Stereo Investigator software was used to estimate area of GFP expression. The mean number of GFP-positive cells, area of GFP expression and number of Aβ plaques were evaluated between the rAAV1/2-GFAP-GFP and rAAV1/2-HBA-GFP experimental groups using a two-tailed, unpaired t-test. The difference in number of GFAP-positive and GFAP-negative cells within the rAAV1/2-GFAP-GFP and rAAV1/2-HBA-GFP groups was evaluated using a two-way ANOVA and Bonferroni post-hoc comparison. A p value of less than 0. 05 was considered statistically significant for all analyses. All statistical analyses were performed using GraphPad Prism 5 (GraphPad Software, La Jolla, CA, USA).
Fluorescence Quantification The GFP and GFAP fluorescence intensity per unit volume, as well as GFP expression volume and surface area of a GFP and GFAP-positive cell, either associated or unassociated with Aβ plaque, was compared using the 3D Measurement module of Nikon Elements software (Nikon Instruments). This analysis was done using 0. 1 µm Z-stack images comprising the entire volume of the GFP-positive cell, taken with a 60x objective (NA 1. 4). A sample of 12 Z-stack images of GFP and GFAP-positive cells associated with Aβ plaque was used per rAAV1/2-GFAP-GFP or rAAV1/2-HBA-GFP group. A sample of 20 Z-stack images of GFP and GFAP-positive cells that were unassociated with Aβ plaque were used per rAAV group. The mean fluorescence per unit area, as well as volume and surface area of GFP expression were compared between GFP and GFAP-positive cells either associated or unassociated with Aβ plaque from the rAAV1/2-GFAP-GFP or rAAV1/2-HBA-GFP delivery group using a Kruskal-Wallis one-way analysis of covariance (Gaussian distribution not assumed) and Dunn's multiple comparison test post hoc (GraphPad Prism 5, GraphPad Software).
Acknowledgements The authors would like to thank  Drs. Paul Fraser ,  David Westaway , and  Peter St George Hyslop  for providing TgCRND8 mice for breeding. We also thank  Shawna Rideout  for her veterinary expertise and assistance, as well as  Dr. Alison Burgess  and  Kairavi Shah  for their technical assistance in running the MRIgFUS setup. The authors acknowledge  Kelly Markham-Coultes  and  Melissa Theodore  for animal care and preparation for FUS experiments. Funding was provided by the  Canadian Institutes of Health Research (CIHR)  # FRN93603  (IA), the  Natural Sciences and Engineering Research Council of Canada  # RGPIN-2014-04659  (IA), the  Weston Brain Institute  # TR130117  (IA), the  Ontario Graduate Scholarship (DWA) , and the  CIHR   Doctoral Research Award  (DWA). In addition, we acknowledge funding by The  National Institute of Biomedical Imaging and Bioengineering of the National Institutes of Health  ( R01 EB003268 ) (KH), the  Canadian Institutes for Health Research  ( FRN 119312 ) (KH), the  Canada Research Chair Program (KH) , and  Alzheimer Society Research Program  (post-doctoral fellowship  19-20 ).
The varying level of symptoms experienced by infected individuals lead to significant under or mis-reporting. This is further complicated by the surveillance structures and remoteness of some of the communities at risk from yellow fever. Furthermore, there is little data concerning the non-human primates https://landscan. ornl. gov/landscan-dataavailability. Environmental data: This was obtained from LP DAAC: https://lpdaac. usgs. gov/ and worldclim http://www. worldclim. org/ Yellow fever outbreaks: These were compiled from the WHO weekly epidemiologic record and disease outbreak news https://www. who. int/wer/en/ and https://www. who. int/csr/don/en/. Data elsewhere: The data from the WHO YF surveillance database and from recent serological surveys from WHO member states in Africa underlying the results presented in the study are available from World Health Organization (contact: William Perea, pereaw@who.
int or Laurence Cibrelus, cibrelusl@who. int or Jennifer Horton, jhorton@who. int). Code is available on github: https://github. com/mrc-ide/YFestimation. who act as the environmental reservoir of the disease. The relationship between different primate species, mosquito types and the human hosts can vary the severity of transmission. Tackling the uncertainty in model structures as well as parameters gives a start point from which to begin quantifying the importance of transmission routes for this virus. The uncertainty in yellow fever understanding leads to a number of challenges. In Africa, little is known about YF in non-human primates (NHP); because of this, it is difficult to assess how dynamics in NHP may affect epizootic events. Furthermore, the relative contribution of different transmission cycles to the burden of YF in humans is unclear from the limited data available.
Data The models were estimated at the resolution of the first administrative unit, often called a province. All data detailed below is resolved or aggregated at that level unless stated otherwise. This resolution was optimal for the YF occurrence data, other inputs such as environmental covariates were originally gridded. Yellow fever occurrence. A database of the provinces where outbreaks of yellow fever have been reported was compiled from 1984 to 2017. This was informed by data from the Weekly epidemiological record (WER), the WHO disease outbreak news (DON), the published literature and internal WHO outbreak records. Case-based surveillance for YF was established in 21 West and Central African countries and is recorded in the yellow fever surveillance database (YFSD) held by the African regional office of the World Health Organisation (AFRO).
This database is designed to use a very broad case definition (jaundice or haemorrhage with fever) to ensure high sensitivity (at the cost of low specificity of suspected cases). That means that most reported cases are not due to YF and only 1-2% will be lab-confirmed as YF. In addition to using the confirmed cases to inform the occurrence of YF, we use the above data as a proxy for surveillance effort in each country. Assuming an approximately constant incidence of the syndrome 'fever with jaundice and/or haemorrhage', the per-capita incidence of reported suspected cases yields information on the surveillance effort. We therefore aggregate this measure at country level and divide by the national population to be used as a covariate in the generalised linear model. Vaccination coverage. We use the methodology of Garske et al.
e. , R 0 and λ. We choose the pseudopriors to be approximations of the individual model posterior predicted values from previous MCMC runs, see the appendix for all distributions. These are calculated using the package fidistr in R assuming the posteriors of individual model runs are normally distributed, see supplementary material for fits. We adjust the variance of these fitted distributions in order to ease mixing between the two models as the pseudopriors do not affect the marginal posterior distributions of the models. This was performed by adjusting a scaling factor for the standard deviation for the R 0 pseudoprior to ensure that the values of the pseudopriors applied to the median values of the posterior outputs of both models have a difference close to zero. Each model has a prior which may affect the mixing between models and the final posterior model probability.
Study Design and Sample Collection The basis of our study involved data obtained from the POlish-Norwegian Study (PONS) project  [20, 21]. It was a cross-sectional study on the health status of the adult Polish population from the region of Swietokrzyskie, conducted in the years 2010-2012. The study included analyses of collected fasting blood samples, blood pressure, and anthropometric measurements. Extensive interviews were carried out in order to collect information about the participants' lifestyles during the last year. 13,172 participants, aged 37-66, volunteered to take part in the study. In further analyses, the data of 12,328 individuals were used (8234 women), and 844 participants were rejected due to incomplete data.
Socio-Demographic and Lifestyle Data Socio-demographic data and information on the participants' lifestyles were collected in face-to-face interviews using structured questionnaires. The socio-demographic variables included sex, age, and education (number of education years in total). As an indicator of socioeconomic position, we chose education, which, in our opinion, reflects health awareness and health behavior patterns better than income. Moreover, education is comparatively easy to measure in self-administered questionnaires, garners a high response rate, and is relevant to people regardless of age or working circumstances, unlike many other indicators of socioeconomic position. For each participant, the daily intake of pure ethanol was calculated, with the consideration of the mean alcohol content in specific alcoholic beverages and the frequency of intake (g/week).
Data and model characterization Based on data from 2013, 2 one observes, at the end of 2012, 361 biogas plants in the Lombardy region (40% of national total), mainly concentrated in two provinces (from now on called "regions"): Brescia (68 installations) and Cremona (137 installations). Five classes (size) of biogas plants (130, 250, 530, 999 and 2000 kWe), with different energy crop and manure requirements (Table  4 ), have been then assigned to the industrial-demand model (ReSI-M model described in 2. 1. 2). To ensure the model tractability, only maize silage is considered as energy crop used to feed the biogas plants of these regions. 3  The agricultural-supply model (described in 2. 1. 1) is fed with data input from a sample of ca. 60 farms. These data, i. e. on farm' structure, cost and yield were obtained from the RICA (Rete Italiana di Contabilità Agraria) dataset, the Italian office of FADN (Farm Accountancy Data Network).