dataesr/scientific-paragraphs-categorization huggingface dataset:
The database used in this study In addition to the hardware architecture of the sensing system composed of sensors, microcontroller, RF module and battery, the sensing system has a test protocol for the induction of emotions. A simple and effective protocol to stimulate the person on whom the acquisition is made is required. This protocol stimulates the person on whom the data is acquired to feel and express the different emotions and thus, it is of considerable help for the construction of a physiological signal database. The signal acquisition method is essential as it strongly influences the efficiency of the detection. Indeed, the quality of the signals (thus the detection) is not the same when the acquired data is simulated or real, hence the problem of the definition of an adequate and effective protocol.
These protocols call upon methods of induction of emotions to acquire a database in which the influence of each emotional state has been faithfully reflected. Several protocols for induction of emotional states exist in the literature. As an example, we can cite the one proposed by  Clynes Manfred [29]  which consists of stimulating the subject with different musical melodies and/or images to produce eight emotional states. This method, called the Sentics Cycle, is defended by its initiator as a method for training to feel each of the emotional states considered. The international emotional picture system (IAPS) developed by Lang et al. [30] , is another protocol for induction of emotional states. The IAPS system was adopted by many studies. In particular, it was used by Faiza Abat in his thesis work  [31]  in view of the simplicity of his manipulation.
Finally, another protocol based on films is proposed in the literature for the induction of emotions  [film, 2017]. The emotional reactions provoked by the latter are often too weak when we talk about complex emotions  [31]. In our work, we used a physiological signal database established by Jennifer Healey during her PhD  [10]  held at MIT (Massachusetts Institute of Technology). This database serves as a reference for the vast majority of people working on emotion detection. It allows a comparison of different algorithms for emotion recognition on the same data. During 32 days, an actor on whom 4 physiological signal sensors (EMG, RESPiration, GSR, BVP ) sampled at a frequency of 20 Hz were connected, was stimulated to express and feel eight emotions: No-emotion, Anger, Hate, Grief, Love, Romantic Love, Joy and Reverence.
Due to problems such as the detachment of an electrode or the malfunction of a sensor, on the 32 days of acquisition, only 20 have been perfectly acquired and are therefore the only data we use. The Sentics cycle method developed by Manfred Clynes  [32]  was used, which involves stimulating the actor with music or images so that he feels and expresses a given emotional activity. Every day, the actor sitting on a chair with a backrest and connected to the 4 physiological signal sensors was stimulated to express each emotion for a period of 3 to 4 minutes. The interested reader by this acquisition protocol is invited to refer to these different works for more details  [10, 29, 32]. The Table  2  regroups the images used in the MIT protocol to encourage the actor to express the eight emotions taken into account as well as the description, intensity and valency of these different emotional states.
Results and Comparisons After regrouping all these physiological signals, we used the k cross validation method with k=3 to validate the hyper-parameters of our classifiers. We have chosen to validate our parameters using the pessimistic method which consists in subdividing the database into three bases: the learning base ɛ, the validation base υ and the test base τ. In this pessimistic method, one learns the prediction function on ɛ, validates its parameters on the υ data, and tests the performance on the data τ. This method eliminates the bias on the optimistic method because the data on which the performance of the prediction function was estimated was unknown for the function at the time of its implementation and the validation of its parameters. This method is therefore a generalization of the classification, because we can expect the same order of performances when we change the test data.
The PGQ is reliable and valid for both pregnant and postpartum women with pregnancy-related LPP. 24 inally, physical activity levels were objectively measured at each trimester of pregnancy using the Acti-Graph GT3X (ActiGraph, Pensacola, Florida, USA), a  Open access triaxial accelerometer measuring data in a 60 s epoch. The women were instructed to wear the monitor over the hip on an elastic belt for 7 consecutive days from wake-up time to bedtime. They were allowed to remove the accelerometer when sleeping, showering or engaging in water activities. Furthermore, the women received a daily diary to document wear and non-wear time periods and water activities. According to the method used in the Canadian Health Measures Survey, valid data were defined as 4 days or more of monitoring for 10 hours or more of wear time per day.
25 Pregnant women were encouraged to maintain their usual activities. Data were processed using the Actilife software V. 6. 13. 2 (ActiGraph, Florida, USA). The accelerometer data obtained were averaged across valid wear days. To derive the activity frequency, intensity and duration of the measured activity in counts per minute per day, the Freedson equation was used: sedentary (<100 counts), light (100-1951 counts), moderate (1952-5724), vigorous (5725-9498), and very vigorous (>9498),  26  as previously used in pregnant women. 27 Non-wear time was defined as a period of zero counts for ≥60 consecutive minutes, admitting a maximum of two consecutive minutes between 1 and 100 counts/min. When a third observation was between 1 and 100 counts or one observation was more than 100 counts, the non-wear period was ended.
statistical analysis Means and SD, as well as percentages, were computerised for variables of interest. Student's t-test was used to compare socio-demographic and anthropometric characteristics between SP and FT women. For categorical variables, the χ 2 test was used. The MIXED procedure of SAS software was used to test the effect of time (trimesters), group (SP and FT women) and potential interaction effects on the outcome measures (ie, the severity of pregnancy-related LPP and anxiety levels (objective 1), and physical activity behaviours (objective 2)). The assumption of sphericity was tested using Mauchly's Test of Sphericity. Variables  Open access that did not meet the sphericity assumption were analysed following a Geisser Greenhouse correction. When a significant effect of time, group or interaction effect was found, post-hoc analyses were conducted using the Tukey test.
5-24. 9 kg/m 2 ) and had a university degree. Women's LPP history, related or not to a previous pregnancy, was also similar between the groups, with approximately 50% of the women reporting a history of LPP (table  1 ). Finally, the prevalence and severity of pregnancy-related LPP, anxiety and physical activity levels were not different between SP and FT pregnant women at study entry (table  1 ). Data showed that on average, women considered LPP as moderate  Open access (4/10) and were slightly anxious (35/80). Moreover, based on daily steps and physical activity recommendations,  28 29  our population was considered inactive. In our study, a total of 8 (13. 5%), 8 (13. 5%) and 9 (15%) women removed the accelerometer to do water activities (aqua gym, swimming or bathing) during TR1, TR2 and TR3, respectively.
5%). 41 This suggests a possible recruitment bias and limits the generalisability of our results. Third, although accelerometers provide a valid and objective measure of physical activity levels, non-waterproof accelerometers underestimate several types of physical activity, such as water activities. In our data set, several women removed the accelerometer to do water activities (aqua gym, swimming or bathing) during TR1, TR2 and TR3, suggesting that we possibly underestimated the level of physical activity of these women. We also had missing physical activity data because some women did not wear the accelerometer for at least 10 hours per day for at least 4 days. Finally, physical activity levels were assessed only for a 7 day period during each trimester of pregnancy. Given that each trimester lasts for more than a week, the data obtained and the results reported in relation to physical activity levels do not truly reflect the evolution of physical activity levels over each trimester and over the entire course of pregnancy.
Acknowledgements The authors would like to acknowledge and thank  Sophie Drouin , the coordinator of the fertility clinic, as well as the medical team who assisted with the recruitment, and all the women who participated to the project. Contributors S-MR, MD and VB contributed to the study concept and design; EL and AS-L acquired the data; S-MR, MD and EL performed the statistical analysis and interpreted the data; EL and SMR drafted the manuscript; MD, AS-L and VB critically reviewed the manuscript for important intellectual content. All authors read and approved the final manuscript.
9 million people are thought to be at risk of contracting a DENV infection  [12]. Although hospitalized dengue cases have been reported since 1979 and recorded in a national database since 2008  [13, 14] , very few have been laboratory-confirmed  [11]. Because only a limited number of studies have been conducted so far  [12, [14] [15] [16] [17] [18] [19] [20] [21] [22] , little is known about the epidemiology of dengue or the DENV serotypes circulating within the country. Here, we present DENV molecular epidemiological data from patients at 3 different hospitals in Laos: the provincial hospital of Luang Namtha in the north and the provincial hospital of Salavan in the south for 2008 to 2010, and Mahosot Hospital in the capital city of Vientiane (central Laos) for 2006 to 2010. written informed consent and if their responsible physician suspected dengue based on the 1997 WHO guidelines and requested laboratory tests.
Sequences analysis Data sets. DENV sequences were extracted from a database of all Flavivirus genus complete coding DNA sequences (CDS) available on GenBank at the end of the year 2013. The DENV complete CDS data sets included 1,373 sequences for DENV-1, 998 sequences for DENV-2, 670 sequences for DENV-3 and 123 sequences for DENV-4. All envelope sequences available on the European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database in April 2014 were recovered in order to build envelope datasets for each serotype. Unsuitable sequences (length <1,000 bases, number of N>50) were removed. Final datasets for envelope sequences included 3,108 sequences for DENV-1, 3,067 sequences for DENV-2, 1,817 sequences for DENV-3, 859 sequences for DENV-4. Sequences obtained for this study were aligned with those datasets using ClustalX 2.
1  [28]. Recombination. Indication of molecular recombination was investigated for each alignment of complete CDS using the Recombination Detection Program (RDP) version 4 software  [29]. RDP, GENCONV and MAXCHI methods were used for primary screening and BOOT-SCAN and SISCAN methods were used to check for recombination signals  [29] [30] [31] [32] [33]. For optimal recombination detection, the automask procedure was selected. Recombination events with an average p-value with RDP lower than E-10 were selected for downstream phylogenetic analyses. Neighbor-Joining trees using Mega 6. 06 software with Kimura-2 model  [34] , bootstrap resampling with 500 replicates, were built from the alignment used for RDP analysis. Two trees were produced and compared for each recombination event: one using sequences located between the putative recombination breakpoint positions and a second one which excluded the putative recombinant region.
Phylogenetic analysis. The best maximum-likelihood (ML) method to be used for tree building was determined for each serotype alignment using the MEGA6 software. For each serotype, two trees were subsequently built with either the complete CDS or the envelope alignment using the best ML method previously determined (General Time Reversible Model with invariant sites and a gamma distribution of rates across sites for DENV-1 and DENV-4 alignments, General Time-Reversible Model with gamma distributed rates across sites for DENV-2 alignment and Tamura-Nei model with gamma distributed rates across sites for DENV-3 alignment) and bootstrap resampling with 500 replicates on RAXML8. 0. 0 software  [35].
The Chinese outbreak has been shown to originate from Laos  [38]. The strains published by Lao et al. [22]  were not included in our dataset since they were submitted to Genbank in November 2014. The 58 genotype II strains are however closely related to our sequences, with more than 99% identity in envelope sequence. Strains from Myanmar from 2005 to 2009 and one strain from Singapore from 2008 are also part of the cluster. likelihood (ML) method (General Time Reversible Model with invariant sites and a gamma distribution of rates across sites) and bootstrap resampling with 500 replicates. 81 Lao strains are dispersed in 10 clusters (bootstrap >70) shaded here in separate colors. The bootstrap values are displayed on the tree only for those clusters. The list of the strains grouped in the different clusters is provided in S6 Table.
0. 0 software. Bootstrap values are only displayed for the genotype nodes. Genotypes distribution is illustrated by color-shaded boxes. A subtree containing Lao strains was extracted from this tree and displayed in details in S11 Fig. A subtree containing the Lao strain was extracted from the tree built with the complete data set of DENV-4 envelope sequences displayed in S8 Fig. The  Lao strain from this study was from Salavan from 2009 and is shown by a blue triangle. Genbank accession numbers followed by country (ISO code) and year of isolation are provided for each strain. For the nodes that have been collapsed for simplification purposes (shown by triangles), descendant strains are only described by country and years. The province of origin is indicated for the strain from this study (SV: Salavan).
(TIFF) S8 Fig. Phylogenetic tree built with DENV-4 envelop sequences. 859 DENV-4 envelop sequences downloaded from the EMBL database in April 2014 were aligned with the DENV-4sequences from this study. The tree was built using a maximum-likelihood (ML) method (General Time Reversible Model with invariant sites and a gamma distribution of rates across sites) and bootstrap resampling with 500 replicates on the RAXML8. 0. 0 software. Bootstrap values are only displayed for the genotype nodes. Genotypes distribution is illustrated by color-shaded boxes. A subtree containing Lao strains was extracted from this tree and displayed in details in S12 Fig. (TIFF) S9 Fig. Subtrees from phylogenic tree built with DENV-1 envelope sequences. Six subtrees containing Lao strains were extracted from the tree built with the complete data set of DENV-1 envelop sequences displayed in S5 Fig.
Only bootstrap values over 70 are reported on the figure. The Lao strains are dispersed in ten clusters (bootstrat>70): clusters 1, 2 and 3 in subtree 1 (A); cluster 4 and 5 in subtrees 2 and 3 respectively (B); clusters 6 and 10 in subtrees 4 and 5 respectively (C); clusters 7, 8 and 9 in subtree 6 (D). Strains from Vientiane are indicated by diamonds, strains from LNT by squares and strains from SV by triangles. Strains isolated in 2007 are in yellow, 2008 in orange, 2009 in blue, 2010 in green, and 2011 in pink. Other Lao strains are indicated by brown circles. Lao strains from imported cases are indicated by black circles. Strains are indicated by Genbank accession number followed by country (ISO code) and year of isolation. For the nodes that have been collapsed for simplification purposes (shown by triangles), descendant strains are only described by country and years.
The province of origin is indicated for the strains from this study (VTE: Vientiane, SV: Salavan, LNT: Luang Namtha). (TIF) S10 Fig. Subtree from phylogenic tree built with DENV-2 envelope sequences. A subtree containing Lao strains was extracted from the tree built with the complete data set of DENV-2 envelop sequences displayed in S6 Fig. Only bootstrap values over 70 are reported on the figure. The Lao strains are dispersed in three clusters (bootstrat>70). Strains from Vientiane are indicated by diamonds, strains from LNT by squares and strains from SV by triangles. Strains isolated in 2008 are in orange, 2009 in blue, and 2010 in green. Lao strains from imported cases are shown by black circles. Genbank accession numbers followed by country (ISO code) and year of isolation are provided for each strain.
Genbank accession numbers, followed by country (ISO code) and year of isolation are provided for each strain. For the nodes that have been collapsed for simplification purposes (shown by triangles), descendant strains are only described by country and years. The province of origin is indicated for the strains from this study (VTE: Vientiane). (TIFF) S12 Fig. Subtree from phylogenic tree built with DENV-4 envelope sequences.
Acknowledgments We are very grateful to the patients and to Assoc. Prof. Bounthaphany Bounxouei  the director of  Mahosot Hospital , to the late  Dr Rattanaphone Phetsouvanh , director of the  Microbiology Laboratory , to the staff of the  Infectious Disease Center and Microbiology laboratory , to the director and staff of  Luang Namtha  and  Salavan Provincial Hospitals , especially  Phatsana Basy  and  Dr Sommay Keomany , to Assoc. Prof. Chanphomma Vongsamphan  the director of  Department of Health Care ,  Ministry of Health , and to Assoc. Prof. Bounkong Syhavong , minister of  Health, Lao PDR  for their very kind help and support. We are very grateful to the  staff of UMR "Unitedes Virus Emergents ",  Magali Gilles  and  Reine de Chesse.
This study investigated Vegfa expression in the pars tuberalis (PT) of the pituitary and medio-basal hypothalamus (MBH) of sheep, across seasons and reproductive states. It has recently been proposed that season impacts alternative splicing of Vegfa mRNA in the PT, which shifts the balance between angiogenic VEGFAxxx and anti-angiogenic VEGFAxxxb isoforms (with xxx the number of amino acids of the mature VEGFA proteins) to modulate seasonal breeding. Here, we used various RT-PCR methodologies and analysis of RNAseq datasets to investigate seasonal variation in expression and splicing of the ovine Vegfa gene. Collectively, we identify 5 different transcripts for Vegfa within the ewe PT/MBH, which correspond to splicing events previously described in mouse and human. All identified transcripts encode angiogenic VEGFAxxx isoforms, with no evidence for alternative splicing within exon 8.
We also identify transcripts in which both exons 6 and 7 are skipped (leading to VEGFA120) and transcripts in which cryptic splice sites within exon 6 are used. However, neither our extensive RT-PCR analysis nor our investigation of recent ovine RNAseq datasets  [9, 10]  provided experimental support for the existence of endogenous anti-angiogenic Vegfaxxxb transcripts in the ovine PT/MBH, regardless of season or reproductive status. This suggests that such Vegfaxxxb transcripts are either extremely rare or that they do not exist at all, which makes it very unlikely that such anti-angiogenic isoforms play a significant role in seasonal physiology. Furthermore, using a step-by-step empirical approach to PCR primer design we provide evidence that detection of these isoforms in prior studies, including studies in human cell lines and tissues  [14]  might be artefactual, as previously suggested by Harris et al.
5% agarose gel and migrated at 80-110V in Tris-EDTA-Acetic acid (TEA) buffer for ~30min. For qRT-PCR, the optimal cDNA dilution and calibration curves for Vegfa and VegfR2 primer pairs (Eurofins) were established using cDNA synthesized from an equimolar mix of individual RNA from each experiment. As a negative control, the same mix with water instead of RT was prepared. Quantitative PCR was performed using CFX-96 Real-Time PCR Detection System (Bio-Rad) and Sso Adv Universal SYBR Green Supermix (Bio-Rad). All samples (unknown, standard curves) were assessed in triplicate and Rplp0 (ribosomal subunit P0, a. k. a 36B4) was used as a housekeeping gene; Rlpl0 expression did not display any statistical differences between groups (data not shown). The quantification of mRNA level was obtained by the 2 -DCT method and data are presented as fold-increase compared to the condition with the lowest expression level.
Analysis of Illumina RNA-seq datasets We analyzed two independent RNA-seq datasets generated by Illumina sequencing. The first dataset was generated using the same MBH RNA samples which are used here to perform qRT-PCR as well as RT-PCR. All details regarding the procedures, thorough validation and outcomes of these RNA-seq experiments (comparisons between May/August/November = Expt 1 under M&M and comparisons between SP/LP/LP-THX = Expt 2 under M&M) have recently been published  [10]. The second dataset was independently generated using RNA extracted from the PT of castrated rams (see details in  [9] ). First, the data were re-mapped to Oar_V4. 0 (ftp://ftp. ncbi. nlm. nih. gov/genomes/genbank/vertebrate_mammalian/Ovis_aries/ latest_assembly_versions/GCA_000298735. 2_Oar_v4. 0) using STAR RNA-seq aligner and standard mapping options  [18].
STAR allows the identification of de novo and annotated splice junctions and the algorithm uses quality scores to increase its efficacy. Annotation from ftp:// ftp. ncbi. nih. gov/Ovis_aries/GFF/ref_Oar_v4. 0_top_level. gff3. gz were used to define known junctions. Novel junctions are identified by STAR based on uniquely mapping reads. Using a custom perl script the junctions were filtered for the Vegfa gene. The data represent all the junctions identified with >10 reads.
Analysis of RNA-seq datasets: Strong support for the existence of Vegfaxxx splice variants but not for Vegfaxxxb isoforms We next analyzed two independent RNA-seq datasets generated by Illumina sequencing. A summary of the results is presented in Table  2  and S2 Fig. Collectively, the two datasets yielded 11407 intron-spanning uniquely mapping reads (UMR), which cover all known exonic junctions of the Vegfa gene (see S2 Fig). The data provide strong support for the existence of all splice-variants identified previously, with the exception of the rare b1c transcript (see 5 th column of Table  2  and Fig 2). Importantly, 408 of these UMR cover the junction between exon 5 and exon 8 (highlighted in grey) while 2285 cover the junction between exon 7 and exon 8 (also highlighted in grey). Thus, a total of 2693 UMR support the existence of the canonical splice site for exon 8.
Discussion Our analysis of Vegfa expression in the PT/MBH of sheep, across seasons and reproductive states, using RT-PCR and analysis of RNAseq datasets, led to the identification of five Vegfa splice variants. These different splice variants have been previously identified in mouse and human tissues, which suggests phylogenetical conservation of Vegfa splicing events. All the sequences identified in this work correspond to Vegfaxxx transcripts, with no evidence for usage of an alternative splice site in exon8. This suggested that identification of anti-angiogenic Vegfaxxxb transcripts in prior studies may have been caused by methodological issues with PCR. We therefore devised an empirical approach, which led to the identification of the minimal sequence requirements of an error-prone "exon 8b-specific primer".