dataesr/scientific-paragraphs-categorization huggingface dataset:
Study interventions The SNAP40 device will be placed onto the participant's arm. The opposite arm will therefore be available for any standard observation recordings in the department at the discretion of the clinical team. The information from the SNAP40 device will be observed by the research team only and will not be used as an alternative to standard care or clinical observations of the participant whilst they are in the ED. The participant will continue to have their vital signs monitored by the clinical team as per standard practice. The SNAP40 wearable device will continuously monitor participants throughout their stay and transmit three key signals: photoplethysmograph (PPG) waveform using green, red and infrared light; skin temperature and movement. Anonymised SNAP40 monitoring data will be transmitted continuously by the SNAP40 device via a secure Wi-Fi connection to a SNAP40 server located in the ED.
The anonymised SNAP40 monitoring data will be transmitted along with the date and time of the observation and the unique device ID. This will allow the anonymised monitoring data to be associated with the participant study number. The anonymised SNAP40 monitoring data will be securely stored with access restricted to the study staff and authorised SNAP40 personnel. This anonymised SNAP40 monitoring data may be used by SNAP40 in future for product development. Signal processing algorithms developed by SNAP40 will calculate heart rate, respiratory rate, blood pressure and oxygen saturations from the PPG every 2 s. The SNAP40 device measures change in blood pressure. The SNAP40 device will alert the study researcher in real time via a smartphone or tablet application should the participant's vital sign physiology change from one NEWS category to a higher one in any of pulse/heart rate, respiratory rate, skin temperature or oxygen saturation reading.
Raw data from the Mindray monitors will not be extracted and stored. Total time spent recording all observations will be noted for at least 25 patients in the study. To do this, the research team will, where possible, time how long clinical staff spend recording each observation on the NEWS chart. If the researcher is unable to time an observation being completed by a staff member, this will be indicated on the CRF. The total number of observations recorded, along with the total number timed and not timed will also be recorded on the CRF. The NEWS chart recordings noted on the participant's ED shock chart (i. e. blood pressure, pulse/heart rate, respiratory rate, oxygen saturation reading, core temperature using a tympanic temperature probe and neurological status assessed by GCS) will also be reviewed, and any deterioration in NEWS score will be recorded in the CRF.
It is hoped that the researcher will observe, in real time, the response to any deterioration in NEWS and record this on the CRF. However if this is missed, the researcher will retrospectively ask the member of staff taking care of the patient what was done, if anything, about it. A photocopy of the participant's ED shock chart will be taken prior to them leaving the ED in order to allow this data to ensure all data is collected and allow it to be checked later on if necessary. This chart will be anonymised with the participant study number and kept with the participant's study paperwork. The participant's CHI number, episode number, participant study number and their allocated SNAP40 'identifier' number will be recorded on a separate database held on a secure password protected drive. This database will only be able to be accessed by NHS study staff and will not leave the NHS.
Confidentiality All evaluation forms, reports and other records will be identified in a manner designed to maintain participant confidentiality. All paper records including CRFs will be kept in a secure storage area, in this case in a locked filing cabinet in the EMERGE office which has limited access. The participant's CHI number, episode number, participant study number and their allocated SNAP40 'identifier' number will be recorded on a separate electronic database held on a secure password protected drive. This database will only be able to be accessed by NHS study staff and will not leave the NHS. This will also ensure that no participant identifiable information is contained with the CRF or electronic CRF. The anonymised SNAP40 monitoring data will be securely stored with access restricted to the study staff and authorised SNAP40 personnel.
This anonymised SNAP40 monitoring data may be used by SNAP40 in future for product development. Anonymised information collected on the CRF will be entered onto a secure database. Members of the study team including those from the University of Edinburgh's Clinical Trials Unit will view this. This anonymised information may be made available to other researchers in future. No patient identifiable information will leave NHS Lothian in any form whatsoever. The CI and study site staff involved with this study may not disclose or use for any purpose other than performance of the study, any data, record or other unpublished, confidential information disclosed to those individuals for the purpose of the study.
We performed cDNA synthesis by using qScript cDNA SuperMix (Quantabio, Beverly, MA, USA) and PCR amplification by using AccuStart II PCR ToughMix (Quantabio). We processed PCR products by using Illustra ExoProStar 1-Step (GE Healthcare, Little Chalfont, UK) according to the manufacturer's instructions before Sanger sequencing. We analyzed sequence data by using DNASTAR Lasergene 12 SeqMan Pro (DNASTAR, Madison, WI, USA) and performed sequence alignment by using ClustalW in MEGA 5. 01 (http://www. megasoftware. net/). We constructed phylogenetic trees by using the maximum-likelihood method in MEGA 5. 01. Herd information for 2015 was available for 84 herds of origin of these nasal swab specimens. Data were obtained from the Animal Identification and Movement System database of the Department of Agriculture, Food, and Marine of Ireland (https://www.
Nine of the influenza D virus-positive samples had a C t <25 and were selected for sequencing. We obtained partial sequences for 5 samples and deposited the sequences in GenBank (accession nos. KY992090-KY992103). Phylogenetic analysis (online Technical Appendix Figure  1 , https://wwwnc. cdc. gov/EID/article/24/2/17-0759-Techapp1. pdf) showed that the 5 influenza D virus isolates from Ireland clustered with viruses from Europe in the D/swine/OK/1334/2011 clade. We also determined the distribution of positive and negative samples at county level in Ireland (online Technical Appendix Figure  2 ). Herd information was available for 10 of the influenza D virus-positive herds and for 74 comparison herds (for which the nasal swab specimens were negative for influenza D virus but which had clinical respiratory disease outbreaks).
Statistical Analyses The primary efficacy objective of the present study was to evaluate the clinical efficacy of the test formula in terms of the number of patients with combined CMA symptoms at day 14 and day 28. Secondary objectives included an evaluation of adherence to the nutritional therapy in each group in terms of the volume of AAF consumed daily, and further description of specific CMA symptoms on days 0, 14, and 28 and their evolution (appearance, no change, or disappearance of symptoms). For anthropometric data, z scores were calculated based on WHO growth data  (27). The change from baseline (day 0) was compared between groups by analysis of covariance using age at baseline as a covariate. AEs were also assessed as a secondary safety objective. The normality of quantitative data was assessed using the Shapiro-Wilk test and comparisons performed using the Student t test if the distribution for each group was normal and using the Wilcoxon Mann-Whitney test if at least one of the distributions was not normal.
Qualitative comparisons were performed using the Chi 2 or Fisher exact test. In addition, a generalized estimating equations model was used to compare the evolution of qualitative data taking into account covariates of formula, time, and formulaÃtime, and the nature of the parameter (binary or ordinal) and other factors including age, treatment duration, and nature of the CMA. All statistical comparisons used a 5% significance threshold (P ¼ 0. 05). The evaluation of CMA symptoms, adherence to treatment, nutritional intake, and anthropometric data was performed using the per protocol (PP) set (all included patients who were randomized and completed the study with no major protocol deviation). The assessment of AEs was performed using the safety set (SS) (all included patients who had at least one administration of the test or reference formula).
The intent-to-treat (ITT) set was used to evaluate patient characteristics and demography (all included patients who were randomized). Based on previous clinical studies  (11, 13, 17, 20, (28) (29) (30) , for an alpha level of 0. 05 for statistical significance and a power of 80%, a sample size of 48 patients (24 patients per group) was considered sufficient to detect a significant difference in the number of patients presenting CMA symptoms between groups. Assuming an attrition rate of 10%, an overall sample size of 54 patients was appropriate to meet the primary objective of the study. The statistical analyses were done using SAS Version 9. 3 (SAS Institute, Cary, NC).
Overall in group 1 (PP set) patients consumed 60. 05 AE 38. 45 g of the test product per day. Baseline demographic and anthropometric characteristics were similar in each group-for the ITT set in group 1 and group 2, respectively, the median (range) age at inclusion was 13. 0 (6-25) months and 13. 0 (5-35) months, gestation was 39. 0 (35-41) weeks and 38. 0 (35-40) weeks, weight was 3. 50 (1. 7-4. 2) kg and 3. 10 (1. 8-3. 6) kg, height was 0. 495 (0. 43-0. 52) m and 0. 490 (0. 43-0. 53) m, and head circumference was 35. 0 (30-36) cm and 34. 0 (29-36) cm. In each group there were more boys than girls (76. 5% and 58. 8% boys in group 1 and group 2) and most were born by vaginal delivery (76. 5% in each group). The demographic data were similar for the PP and ITT sets.
Acknowledgments: The authors acknowledge the study site personnel for the conduct of the study and also all enrolled infants and parents/legal guardian(s) for their participation. In particular, the authors acknowledge  Florence Villard-Truc, MD, Marie-Helene Thierry, MD, Celine Lagrange, MD, Anne-Sophie Brunet, MD, and Benedicte Douvillez, MD  for study conduct. This manuscript was prepared with the assistance of a professional medical writer,  Dr Andrew Lane  (Lane Medical Writing), in accordance with the European Medical Writers Association guidelines and Good Publication Practice.
Primers used for amplification and sequencing reactions are listed in Table  1. The fragments amplified correspond to partial sequences, not comprising the totality of each gene (see Table  1  for details). Distance to the nearest breakpoint (Mb) was estimated by counting the number of cytological bands in the map of Kunze-Mühl and Müller  [50]  assuming that all bands contain the same DNA content (82 Kb) as in  [51]. Distances were around 0. 082 Mb for PhKGamma and around 0. 574 Mb for the other 3 genes (Fig. 2 ). DNA amplification and sequencing was carried out as in  [45]  with an annealing temperature of 5 s at 54 °C during the amplification reaction. For each individual two sequences were obtained, from forward and reverse primers (see primer sequences in Table  1 ). Both sequences were assembled using SeqMan II from the Lasergene program (DNASTAR) to get one final sequence per individual.
Analyses were performed excluding gaps. For a visual representation of the genetic differences between arrangements and populations in the PhKgamma and Ubc-E2H gene regions, pairwise F ST values were used to compute a Principal Coordinate Analysis (pcoa in R package ape version 3. 5 (http://ape-package. ird. fr/). A locus-by-locus analysis of Molecular variance (AMOVA) was performed on Arlequin v3. 5. 2  [59]  to test for genetic differentiation (F CT ) between arrangements at each specific polymorphic site. A hierarchical structure was considered with two groups corresponding to the two arrangements (A 2 vs A ST ), with the different localities and individuals sampled within these groups. Gene conversion tracts (GCTs) were detected using the algorithm defined by  [60]. Linkage disequilibrium (LD) between pairs of informative sites was assessed and the statistical significance analysed with a chi-square test after Bonferroni correction.
These analyses were performed for each arrangement and gene region, as well as for the concatenated dataset. The overall linkage disequilibrium statistic ZnS was estimated for informative sites. LD was also estimated between polymorphic informative sites through r 2 estimates. Deviations from neutrality were tested using Tajima's D  [61]  for each chromosomal arrangement and locality. Population size changes were also determined using R 2  [62]. Statistical significance was obtained by coalescent simulations (5000 replicates) considering free recombination, as it seems most suitable when analysing D. subobscura genes whether located inside or outside chromosomal arrangements (see  [33] ). All neutrality tests were performed after removing recombinant individuals (with indication of GCTs). The DnaSP v5 program  [53]  was used to perform the GCTs and linkage disequilibrium analyses as well as neutrality tests.
06, P = 0. 002 for π and π sil ; Z = 2. 93, P = 0. 003 for S; Z = 2. 98, P = 0. 003 for Ɵ sil ). No differences in the divergence per silent site values (K sil ) relative to D. pseudoobscura were found between the two arrangements (Wilcoxon matched pairs test; Z = 0. 24, P = 0. 814). Higher nucleotide diversity was found for Hfw and Nipsnap (Table  2  and Additional file 3), which might possibly indicate a higher substitution rate in these two more distally located regions. High significant genetic differentiation between the A ST and A 2 arrangements was detected within each locality and also between localities for Ubc-E2H and PhKgamma (see Figs. 3  and 4  and Additional file 2) and also the concatenated dataset of all genes (see Additional file 4). On the other hand, Hfw and Nipsnap did not show significant differentiation between arrangements whether from the same or different localities (see Additional file 4).
5 , see also Additional file 5). Curiously, in the intronic region of PhKgamma significant genetic differentiation between A ST individuals from different localities was observed (see Additional file 5). A locus-by-locus analysis of Molecular variance (AMOVA) was performed to test the genetic differentiation (F CT ) between arrangements at each specific polymorphic site using a hierarchical structure (see Methods). Again, differentiation between arrangements was observed exclusively in non-coding regions (see Additional file 6). On average F ST values between arrangements found in the same locality or in different localities showed similar values in both PhKgamma and Ubc-E2H and the concatenated dataset (see Additional file 2 and Additional file 4; see also Figs. 3  and 4 ). In these regions, differentiation between arrangements was similar across localities with the exception of Rasquera for PhKgamma (see Additional file 7).
However, this exception was due to the recombinant individuals from Rasquera (four individuals presenting gene conversion tracks, see below). Pairwise genetic distances, based on the concatenated dataset of PhKgamma and Ubc-E2H, were correlated with their geographic distance with Mantel tests. No significant association between genetic and geographic distances was found for individuals carrying A 2 (r 2 = 0. 004, P = 0. 462), or A ST (r 2 = 0. 017, P = 0. 284). Similar results are also obtained for the two genes separately (see Figs. 3  and 4 ). In agreement with this, no particular haplotype in any arrangement showed consistent indications of directional changes in frequency with latitude. Gene conversion tracts (GCT) were detected only in PhKgamma and in four individuals, all of them from Rasquera.
Linkage disequilibrium In general, levels of linkage disequilibrium (LD) were low in all gene regions and arrangements analysed (see Additional file 8). Using the concatenated dataset of all four genes and considering both arrangements, LD between pairs of polymorphic sites (R 2 ) showed only 35 significant comparisons out of a total of 2415 (P < 0. 001, chi-square with Bonferroni correction). Importantly, the majority of the significant LD comparisons were observed between sites from the same gene region, indicating short-range LD (see also Additional file 9). In fact, only 12 of the 35 significant comparisons corresponded to LD between distinct gene regions -6 of them between PhKgamma and Ubc-E2H (namely between positions 358-360 bp from PhKgamma and position 60 bp from Ubc-E2H, see below).
Acknowledgments The authors thank  Margarida Matos ,  Inês Fragata  and  Josiane Santos  for helpful discussions and suggestions. We also thank  Gemma Calabria ,  João Picão-Osório  and  Olga Dolgova  for help in inversion polymorphism scoring,  Neus Perez  for help in the genetic analyses and  Montse Peiró  for help in the in situ hybridizations.
Availability of data and materials Data supporting the conclusions of this article are included within the article and in its additional files. All gene sequences are deposited in GenBank with accession numbers: MG877856 -MG877894 (Nipsnap), MG877895 -MG877930 (Hfw), MG877931 -MG878006 (PhKgamma) and MG878007 -MG878083 (Ubc-E2H).
Research Male partners and maternity care in Burkina Faso Marina AS Daniele et al. We collected baseline data through interviews at enrolment using a questionnaire on the women's demographic and socioeconomic characteristics, including age, parity, ethnicity, religion, occupation and educational level, on their reproductive health history and on their male partner's characteristics. During follow-up interviews with the women at home, we collected data on health and behavioural outcomes 3 and 8 months postpartum. Their male partners were not interviewed. All questionnaires were in French, which was translated into local languages (i. e. Dioula and Moore) verbally. We conducted field trials of the questionnaires with nonparticipating women attending the study centres. To assess compliance with the study arm assignment and adher-ence to the intervention, participants' names and identification numbers were recorded at each study session.
Statistical analysis We tabulated baseline data using descriptive statistics and any major differences between study arms were identified by visual inspection. For primary and secondary outcomes, we tested the null hypothesis that the intervention had no effect in intention-to-treat analyses. These outcomes were treated as binary variables and we assessed the intervention's effect using generalized linear models with the Bernoulli/binomial family of distributions and the identity link. We report the magnitude of the effect as the risk difference (RD) between intervention and control arms, with 95% confidence intervals (CIs). To account for the possible effect of the study site, we included the recruitment primary health centre as a fixed effect in the generalized linear model and all effect estimates reported were adjusted for this variable.
27 Finally, more frequent postnatal contact with health workers probably reinforced the messages on exclusive breastfeeding and family planning. This study has several limitations. Methodologically, our inability to guarantee that outcome data collectors were fully blinded to the study allocation may have increased the risk of courtesy or social desirability bias in participants' responses. Second, all outcomes were self-reported and unvalidated instruments were used to assess relationship adjustment and satisfaction with care. Third, the exclusion of women advised to give birth in a referral hospital means that our findings may not be generalizable to this group. Fourth, women supplied baseline data on their male partners, whom we were unable to interview. Fifth, although very few men or couples in the control arm attended intervention sessions, their interactions in the community with participants from the intervention arm may have influenced the study's results.
Acknowledgements We thank: all study participants and health workers, particularly  Pauline Doly ,  Bachirou Doussa ,  Roukietou Konkobo ,  Haoua Maiga ,  Issouf Maiga ,  Angele Ouedraogo  and  Fadima Sanou ;  Nana Abga ,  Denise-Emma Bationo ,  Edgar Diboulo ,  Fatoumata Drabo ,  Ruffine Kando ,  Chantal Millogo ,  Diane Ouedraogo ,  Natacha Poda ,  Antoinette Sanou ,  Mamadou Siribie ,  Henri Some ,  Adjaratou Soulama ,  Fatoumata Traore  and  Maurice Yaogo  at  AfricSanté ;  Issiaka Bamba ,  Blahima Konate  and  Achille Soulama  at  Centre Muraz ;  Ian Askew ,  Harriet Birungi ,  Gisele Kabore ,  Placide Tapsoba  and  Nancy Termini  at the Population Council; and  Jenny Cresswell ,  Rebecca French ,  Christopher Grollman ,  Isabelle Lange  and  Sylvia Ma -rinova at the  London School of Hygiene & Tropical Medicine.
This article presents a new numerical method for facial reconstruction. The problem is the following: given a dry skull, reconstruct a virtual face that would help in the identification of the subject. The approach combines classical features as the use of a skulls/faces database and more original aspects: (1) an original shape matching method is used to link the unknown skull to the database templates; (2) the final face is seen as an elastic 3D mask that is deformed and adapted onto the unknown skull. In this method, the skull is considered as a whole surface and not restricted to some anatomical landmarks, allowing a dense description of the skull/face relationship. Also, the approach is fully automated. Various results are presented to show its efficiency.
These animation software packages use the same methodology as manual methods, allowing the expert to tune some modelling parameters and combine the human expertise with the flexibility of the software  [3]. However, this approach does not eliminate the subjectivity in the reconstruction. During the last 30 years, a large amount of work has been devoted to the conception of objective fully automated methods. The common pipeline of modern facial reconstruction software is described  [4]. First, an expert examines the unknown skull in order to determine anthropological parameters like age, gender and ethnicity. Then, a virtual replica of the dry skull is produced and represented according to the modelling parameters. A craniofacial template encoding face, skull and soft tissue information are derived from a head database.
Then, an admissible geometric transformation drives the adaptation of the craniofacial template onto the unknown skull, according to the "proximity" between the skulls. As a result, the template face is deformed onto the predicted face associated with the unknown skull, linking together information coming from both the database and the examination of the unknown skull. Finally, a skin texture and hairiness are added to the reconstructed face. The approach proposed in this article combines classical featuresas the anthropological expertise for classifying the unknown skull and the use of a head databasewith mathematical and computational skills as 3D geometric modelling. The contribution of this work is threefold. First, a method for generating a closed surface mesh model of the skull template is introduced.