dataesr/scientific-paragraphs-categorization huggingface dataset:
| Types of paternal interventions We found that 10 of the 14 interventions were paternal SCC. Of these, two  28, 33  related to 30-min sessions with three collected measures, before, during and after SSC. In one study the duration of the intervention was 45 min  24  and in two  27, 30  it was 60 min. In two studies the session lasted 60 min over 3 days. 31, 32 In one case continuous paternal SSC began in the delivery room and continued for almost 24 h a day. 25  two studies, tactile  13  and massage stimulation  23  were performed. The tactile stimulation consisted of 10-min periods each day, for 5 consecutive days, whereas the massage stimulation consisted of eight sessions of 60 min each and was preceded by a period of observation. One intervention aimed to improve parental participation, and consisted of individualised interactions between fathers and TA B L E 1 Search terms and strategy to identify the studies from electronic databases preterm infants that lasted 50-60 min each.
The population was preterm infants in NICUs, the intervention focused on fathers and the comparisons were no intervention, standard care or mothers' interventions. The outcomes of interest were any physiological measures, behavioural responses, biochemical, psychological and subjective feelings of the infants and, or, fathers. The study design included experimental studies. The CINAHL, Cochrane Central Register of Controlled Trials, Embase, PubMed and PsycINFO electronic databases were used. develop new, multimodal and interactive interventions that provide fathers with positive contact with their preterm infants. K E Y W O R D S early intervention, father, neonatal intensive care unit, preterm infants, systematic review Key Notes • Most early interventions in neonatal intensive care units have been aimed at, or driven by, mothers.
reference Place of study Study design Setting description NICU level Infant state at test Population Number GA -PNA (mean ± standard deviation; range) Intervention Control Type Details review process Screening Identification Records identified from: Databases (n=5530) PubMed (n=1187) Embase (n=1485) The Cochrane Central Registrer of Controlled trials (n=612) PsychINFO (n=874) Cinahl (n=1372) Records screened (n = 1604) Reports sought for retrieval (n = 36) Reports assessed for eligibility (n = 16) P-SSC P-SSC P-SSC Parent participation Improvement program 60 min Each period (before, during and after SSC) began 60 min after feeding 30 min Phases: pre-SSC, during-SSC and post-SSC. Study procedures and data collection occurred in the early afternoon on each study day. NR A 2-week program on three stages: an individualised interaction stage, a pre-M-SSC M-SSC M-SSC Standard care routine participation stage and an active participation visits stage (50-60 min each).
Participants Using the database of Cannes General Hospital, we extracted data from patients admitted to the Department of Internal Medicine for fever and active solid tumors from January 2015 to November 2019, with available PCT measurements at symptoms onset. Data were collected from electronic medical records and included: age, gender, underlying cancer and stage thereof, comorbid conditions, vital signs, imaging data, microbiological data and laboratory markers. Among laboratory markers, leucocyte count, CRP, PCT and CRP/PCT upon admission were collected.
Diagnostic Criteria Each file was reviewed in order to confirm the final diagnosis and the etiology of fever. In particular, microbiological, radiological and clinical data were reviewed and physicians who had been directly involved in the care of patients took part in this analysis. According to the final diagnosis, patients were divided into the following groups: -Fever with microbiologically documented infection (FMDI), when a causative pathogen was isolated from microbiological cultures. Bacteremia was considered when one positive culture was obtained, with the exception of coagulase-negative Staphylococci, which required at least two positive blood cultures to confirm bacteremia. -Fever with clinically documented infection (FCDI), when clinical and/or radiological signs were in favor of infection, but microbiological cultures were negative.
Zebrafish embryo malformation data Spawning groups were obtained from a colony of adult wild-type zebrafish (Danio rerio) of the 'Westaquarium strain' maintained at the fish facilities of the Aquatic Ecology and Toxicology Group at the University of Heidelberg (licensed under no. 35-9185. 64/BH). All experiments were based on OECD TG 236 and associated work  (Braunbeck et al. , 2015; Braunbeck and Lammer, 2006; Embry et al. , 2010; Lammer et al. , 2009; OECD, 2013) ; however, as an adjustment, for better observation of effects, exposure of the embryos was extended to 120 hours post-fertilization (hpf). According to  Strähle et al. (2012) , an extension of the exposure period to 120 hpf is possible without violation of the current EU animal welfare legislation (EU, 2010) and is recommended in cases of inconclusive observations after 96 hpf.
Software The dynamic model simulations and MCMC calibrations were performed with GNU MCSIM version 6. 1. 0 (https://www. gnu. org/software/mcsim) (Bois, 2009). We used the R software version 3. 5. 2 for plotting and miscellaneous statistical analyses (R Development Core Team, 2013). The model code and the MCMC specification file are shown in Supplemental Material, Section 6.
Model fit to the data Each MCMC chain of 30,000 iterations took 9 hours to complete on a Dell Precision 5530 laptop computer (with Intel Core i7-8850H CPU clocked at 2. 6GHz) using the Linux subsystem. Figure  4  shows all observed transition counts plotted against the corresponding maximum posterior (best) model predictions. Note that the predictions are expected values, rather than integer counts, so there is a layer of randomness in the data that is not taken into account in this plot. Note also that the graph uses logarithmic scales for readability. Since null values (mostly for observations) cannot be shown on such a plot, we assigned them an arbitrary value of 0. 1, only for plotting purposes; some of them fall far away from the identity line because of that artifact. Furthermore, the data are integers and the model predictions reals, so there will always be a mismatch.
While there is no obvious effect of VPA on hatching time or extent, the model estimates separately hatching in normal and malformed embryos, and we found the latter to have a reduced hatching rate. Please note that one type of malformations is "lack of hatch" and could be modeled as a censored piece of data on hatching time. The shape of the individual sub-models linking internal concentration to transition intensities was determined with a standard two-step approach: First, estimate transition intensities for each exposure group, independently; second, determine empirically the relationship of the estimates with concentration. Another route for determining those relationships would be to link them to mechanistic quantitative AOP models  (Battistoni et al. , 2019) , but that would require much more data.
Conclusion The multistate malformation model we propose is very general and versatile. It could be applied to analyze data on many chemicals in the zebrafish and in other species, in particular rodents. There is nothing specific to the zebrafish about the general framework; the definition of the states, the possible transitions between them would need to be adapted, and a specific PBPK model should be used, but the method would stay the same. For different chemicals, the sub-models linking malformation rates and exposure concentration would simply need to be fine-tuned with chemical-specific data. We showed how to do that using Bayesian inference with GNU MCSim, but a maximum likelihood approach and other software like R packages could also be used, at the eventual cost of some loss of flexibility in setting up hierarchical models for variability for example.
Human studies All studies were approved by the Institutional Review Board at Washington University in St. Louis, MO, USA and the Ethics Committee of the Montpellier University Hospital (CSF-NeuroBANK #DC-2008-417 at the certified NFS 96-900 CHU resource center BB-0033-00031 [http:// www. biobanques. eu]). All participants or their delegates consented to the collection and sharing of biofluid samples. Exclusion criteria included contradiction to lumbar punctures (LPs) or lumbar catheters including a bleeding disorder, active anticoagulation, and active infection. Authorization to handle personal data was granted by the French Data Protection Authority (CNIL) under the number 1709743 v0. AMC and individuals with mild AD were recruited at the Knight Alzheimer Disease Research Center (ADRC) at Washington University School of Medicine as part of Stable Isotope Labeling Kinetics (SILK) studies.
AMC are volunteers who were enrolled for research purposes and are cognitively normal. This included two distinct cohorts of symptomatic participants (WashU-A, and WashU-B). Individuals from the WashU-A cohort participated in 36hr lumbar catheter studies. 21 Individuals from the WashU-B cohort participated in the SILK study that involved five LPs over 4 months. 22 Individuals were diagnosed by clinical assessment and classified according to the Clinical Dementia Rating (CDR â ). 23 In addition to interviews of patient and collateral source, brain PET imaging data and diagnostic CSF results were reviewed if available. This cohort includes clinical AD patients who did not have biomarkers consistent with AD, who were classified as non-AD dementia. WashU-A cohort was further classified with Amyloid PET positivity based on PiB imaging.
Post-HJ5. 1 immunoprecipitated CSF samples containing tau internal standards were sequentially immunoprecipitated with Tau1 mid-domain and HJ8. 5 N-terminus tau antibodies. After washing, samples were digested with trypsin, desalted, and analyzed on Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA). MS method measuring pT217 and pT181 was described previously. 3 yloid and Tau PET imaging Amyloid PiB-PET, AV45-PET, and Tau AV1451-PET imaging measurements were performed in a subset of AD and AMC participants from the Knight ADRC at Washington University School of Medicine. Data were collected and processed as previously described. 22.
Acknowledgments We thank the participants and families for their contribution to this study. We thank  Megan Arb ,  Theresa Arb ,  Melissa Sullivan ,  Wendy Sigurdson ,  Tamara Donahue  for IRB protocol development and recruitment at Washington University, and  Dr. Sylvain Lehmann ,  Karim Bennys ,  Cecilia Marelli ,  Christophe Hirtz at Montpellier. We thank  Kathryn Draege  for the brain tumor CSF collection. We thank  Drs. Robert Swarm ,  Lesley Rao ,  Jacob Aubuchon  for performing lumbar punctures. We thank members of the  Bateman lab for discussion , especially  Dr. Kanta Horie  for initial feedback and  Andrew Espeland  for the initial analyses and exploration of the data. We thank the  Clinical, Biomarker , and  Imaging Cores  at the  Washington University School of Medicine  for participant evaluation, samples, and data collection.
Y. ), an infectious diseases specialist (E. C. ), a microbiologist (O. J. -L. ), a psychologist (K. C. ), a general practitioner (S. S. ) and a patient representative from an HS patient association. Members had no conflicts of interest and a strict methodology was followed. 2 Firstly, a systematic review of the literature was performed to compile references from study inception to September 2018. Assistance was provided by the French National Health Authority medical health librarian (supporting information available on request from the author). Eight physicians specializing in methodology then extracted data from each report (supporting information available on request from the author) and analysed the methodology and risk of bias using the Appraisal of Guidelines for Research & Evaluation instrument for guidelines, the Assessing Methodological quality for Systematic Reviews tool for systematic reviews and the risk-of-bias tool for randomized controlled trials (Cochrane Collaboration).
Acknowledgments: a full list of acknowledgments is available in File S1 (see Supporting Information). A. Bertolotti iD  ,  E. Sbidian iD  ,  O. Join-Lambert ,  I. Bourgault-Villada ,  M. Moyal-Barracco ,  P. Perrot ,  N. Jouan ,  Y. Yordanov ,  S. Sidorkiewicz ,  K. Chazelas , M. -F. Bru-Dapres,  E. Caumes ,  J. -F. Sei , for the HS working group,  O. Chosidow iD  and  M. Beylot-Barry  iD and on behalf of the  Centre of Evidence  of the  French Society of Dermatology  INSERM  CIC1410 ,  CHU R eunion, Saint Pierre, La R eunion, France The complete list of author affiliations is available in File S1 (see Supporting Information). Email: antoine_bertolotti@yahoo. fr.
Data Collection Three investigators (PAL, SS, LG) reviewed patients' medical records, collecting the following data for each patient: date of birth, date of UC diagnosis, age at diagnosis according to the Montreal classification,  20  family history of IBD, smoking status (nonsmoker, former smoker, or active smoker), history of stricture, history of appendectomy and colectomy, disease extent with the cumulative Montreal classification,  20  previous IBD medical treatments before the stricture diagnosis or the end of follow-up for patients without stricture (including start and end date of therapy), and date of the last follow-up. Moreover, the following characteristics were recorded when strictures were identified: date of diagnosis, location, length, surmountable by endoscopy, need for colectomy, and association with dysplasia or colorectal cancer.
Statistical Analysis Categorical variables were described by numbers and percentages and continuous variables by median and interquartile range (Q1; Q3). Patients' characteristics were compared between the 2 involved centers by using c 2 and Fisher tests as appropriate. Survival curves were built by using the Kaplan-Meier method. Bivariable and multivariable Cox proportional hazards models were performed to identify predictive factors for colorectal strictures in UC. Variables with P value <. 2 in the bivariable Cox model were eligible for the multivariable model. A stepwise selection procedure was applied to retain significant factors. The significant threshold was fixed at 5%. All analyses were performed by using SAS software version 9. 4 (SAS Institute, Cary, NC).
Discussion Strictures are challenging complications occurring in UC patients with long-standing disease. 2, 4, 14 We investigated data from 439 patients with UC followed at the Nancy University Hospital and at the Centre Hospitalier de Luxembourg to identify any risk factors for colorectal strictures. Strictures were found in 16 patients, accounting for an incidence rate of 3. 6% during a follow-up period of about 10 years. Importantly, 2 singlecenter cohort studies published in 1960s found an incidence of 6. 3%  18  and 11. 2%. 16 On the other hand, single-center cohort studies, published in the 1990s and 2011, showed incidence rates of 1. 5%,  14  3. 2%,  17  and 5%, respectively. 15 Our findings are in line with the most recent data, suggesting a decrease in the stricture incidence over time.
Finally, all included patients underwent medical treatment or surgery, meaning that patients referred to their center for colectomy were included, which is a major bias likely explaining this high percentage of stricture. The different results between studies could be explained by the operator-dependent heterogeneity of the stricture definition. In fact, stricture is generally defined as a localized and persistent narrowing of the gut lumen,  1, 12, 13, 18  but this narrowing is a subjective criterion and is based on physician's opinion. Moreover, no validated approach is available to identify strictures. Regarding dysplasia and colorectal cancer, we found rates of 42. 9% and 33. 3%, respectively, in patients with strictures. These data were significantly higher  compared with previous literature data.
STAR+METHODS Detailed methods are provided in the online version of this paper and include the following: audiobook extract was taken from the first chapter and half of the second chapter. The text is relatively suspenseful as it describes reports of an unknown monster that destroys ships. We divided the story into essays of approximately 1 minute each so that participants could take breaks between segments if they wished. d KEY RESOURCES The instructions given to the subject were 'to listen to the story and look at a fixation cross'. The stimuli were delivered by headphones -ER$1 Insert Earphones (Etymotic Research), using Psychopy v3. 1. 2. The EKG was recorded with two electrodes on the chest using SenseBox of ANT Neuro, sampled at 500Hz. EKG data was cut into the 16 epochs of approximately 1-minute corresponding to each audio-segment.
Computation of intersubject correlation of heart rate (ISC-HR) Previous studies have relied on the quantification of synchrony of neuroimaging based time series (i. e. , BOLD in fMRI  (Hasson et al. , 2015)  or signals from EEG electrodes  (Cohen et al. , 2018) ). We follow a similar logic for the electrocardiographic (EKG) signal. We focus on the modulation of heart rate, by doing so we can determine if subjects increase or decrease their heart rate simultaneously, independently of their absolute level of heart rate. Step 1: We measure the EKG signal and detrend it using a high-pass filter (0. 5 Hz cutoff) and subsequently notch filtered at either 50Hz (Experiment 1, 3 and 4) or 60 Hz (Experiment 2). We compute the instantaneous HR by detecting RR intervals from the EKG (Figure  1A ). Peaks of the R-wave were found using findpeaks (built-in MATLAB function).
Rouder et al. (2012)  formalizes this approach for the t test. The conventional Null hypothesis for the t test states that there is no difference between mean values of two groups and that mean values are normally distributed. For the alternative hypothesis Rouder assumes the Jeffreys-Zellner-Siow prior, which states that the effect size follows a Cauchy distribution, where effect size is the difference of means over the standard deviation. A similar default prior can be used for ANOVA  (Rouder et al. , 2012)  and regression problems  (Liang et al. , 2008). These default prior methods have the advantage that one can compute the BF directly from sample sizes and the t-statistics, F-statistics, or Rsquare, respectively. To compute a BF we use the MATLAB code of Bart Krekelberg, which implements these default priors (https://github.
ACKNOWLEDGMENTS This work was supported by the  Paris Brain Institute (France)  and the  program ''Investissements d'avenir''  ( ANR-10-IAIHU-06 );  Sorbonne PhD  grant (''recherches interdisciplinaires emergentes'' France to P. P. ); CARNOT maturation grant (Con&Heart to J. D. S. );  Sorbonne Universite  ´s  EMERGENCE (Brain-body interactions , a new window for conscious evaluation in brain-injured patients to J. D. S. );  EU-PerMed  ( Project PerBrain  to J. D. S. );  French Embassy UK  (Seeding Grant  2018  to J. D. S. and D. C. );  Medical Research Council New Investigator Research Grant (UK)  (to D. C. ); and the  National Science Foundation  ( DRL-1660548  to J. M. and L. P. ).
METHOD DETAILS Experiment 1: auditory narratives All participants listened to a 16-minute extract of an audiobook read by a male British English voice (20,000 leagues under the sea. Author: Jules Verne. Read by: David Linski. Public Domain (P) 2017 Blackstone Audio, Inc. ) while their EKG was recorded. The Computation of Fractional Anisotropy index (FA index) Diffusion Tensor Images (DTI) were acquired on a 3T Siemens Skyra scanner (64 diffusion gradient directions, b value = 1000 s/mm 2 , TR/TE = 3000/80 ms, voxel size = 2x2x2 mm 3 ). DTI data were pre-processed using the FDT package from the Functional MRI of the Brain (FMRIB) software library (FSL) package 5. 01  (Jenkinson et al. , 2012). This consisted of: 1) correcting for motion and distortions caused by eddy currents; 2) brain segmentation using the brain extraction tool algorithm; 3) computing the fractional anisotropy (FA) maps using the diffusion-tensor model; 4) registration of the FA and MD maps on the FA template in the standard Montreal Neurological Institute (MNI) space using linear as well as nonlinear spatial transformations.
spa typing and multilocus sequence typing (MLST) Typing of the S. aureus protein A locus ( spa typing) was performed according to the methodology of Friedrich et al. [15]. Primers were used according to Stegger et al. [16]. Specific spa sequences were analysed using the Ridom StaphType software v. 2. 2. 1 (Ridom, Münster, Germany). MLST was performed based on seven housekeeping genes according to Enright et al. [17]. Sequence types (STs) were assigned according to the MLST website ( http://saureus. mlst. net ). Sequencing for spa and MLST determination was performed by Eurofins MWG Operon (Ebersberg, Germany).
MATERIALS AND METHODS Dataset description and selection The original dataset consisted of anonymised electronic data files collected from 696 French opticians' stores located in all French metropolitan departments between 2013 and 2019. Information came from the optical prescriptions provided by ophthalmologists. Relevant variables were year of birth, sex, prescription date, purchase date, type of prescription (glasses, contact lenses), type of vision correction (near vision, distance vision, progressive glasses, others), sphere and cylinder characteristics for both eyes. The spherical equivalent (SE) of the right eye only was used to quantify myopia. Myopia was defined by an SE ≤ -0. 50 D. 16  Individuals with at least two prescriptions for myopia correction separated by at least 6 months were eligible, the first prescription for myopia correction in opticians' stores participating in the study being considered as the baseline.
Dataset description The dataset included 136 333 myopic children and teenagers (mean age: 11. 3±3. 8; 55. 0% were female, 130 678 had SE > -6D). Median follow-up was 2. 7 years. Follow-up duration was ≥2 years, ≥3 years, ≥4 years and ≥5 years for 90 706 (66. 5%), 61 062 (44. 8%), 36 989 (27. 1%) and 17 995 (13. 2%) participants, respectively. Progressor status could be determined for 88 604 of them (second prescription 11 to 24 months after baseline) and 50 516 of the latter had a visit following the second prescription to estimate later progression. Demographic characteristics and refractive data are detailed in table  1.
| Characteristics of patient groups The age range of patients treated at the different tertiary epilepsy centers of the EpiCARE network varied considerably. Patients with Dravet syndrome (85%; 22 out of 26) and TSC (70%; 16 out of 23) were predominantly children and adolescents, whereas patients with autoimmune encephalitis were predominantly adults (57%; 12 out of 21) in most responding centers, followed by centers which treat both age groups equally (24%; 5 out of 21). In Unverricht-like diseases both age groups were equally represented in most responding institutions and in Unverricht-Lundborg the same proportion of the centers reported to have mostly adult (42%; 5 out of 12) or to have mostly pediatric patients (42%; 5 out of 12) in charge. These data naturally do not allow conclusions on the epidemiology of a given disease, but rather reflect the emphasis of the responding centers of the EpiCARE Network with respect to the age range (adults or pediatric populations) and particular scientific or clinical expertise.
The D-Rd group also received intravenous daratumumab (16 mg/kg, once weekly during cycles 1-2, once every 2 weeks in cycles 3-6, and once every 4 weeks thereafter). The primary endpoint was progression-free survival, and a secondary endpoint was overall survival (both assessed in the intention-to-treat population). Results presented here are from a prespecified interim analysis for overall survival. ClinicalTrials. gov number, NCT02252172.