dataesr/scientific-paragraphs-categorization huggingface dataset:
Only studies comparing the effect of both animal and plant proteins were included. A second systematic search was performed in parallel with the use of the electronic search tool ProQuest Dialog, with which we searched in 4 different databases: BIOSIS Previews, CAB ABSTRACTS, Embase, and MEDLINE. The same inclusion and exclusion criteria were used. The keywords used to retrieve literature are presented in Supplemental Table  2. The selection of the articles was performed by a second reviewer, and results from the 2 systematic searches were combined. Quality assessment. Each study was assessed with the use of a quality score methodology as illustrated in Supplemental Table  3. The methodology was derived from a quality score recently used by Voortman et al. (14)  and adapted for acute intervention studies and measurements related to body composition.
A score ranging from 0 to 2 was allocated for each of the 5 following characteristics: study design, population size, exposure, adjustment for potential confounders, and subject characteristics. The score of these 5 characteristics was summed up, with a score of 10 representing the highest quality and a score of 0 representing the lowest quality. High quality was assigned to studies with a score of $6, whereas low quality was assigned to studies with a score <6. Data extraction. Data on study design, population size, exposure (description of the dietary intervention), adjustment for potential confounders or subject characteristics, and outcome measurements were extracted for the quality assessment. The results of each comparison between plant-and animal-sourced proteins were reported for each of the following outcomes: d Fasting total, LDL, and HDL cholesterol; LDL:HDL cholesterol ratio; fasting TGs; postprandial TGs after a protein-based meal d Systolic and diastolic blood pressure d Fasting glucose and insulin, postprandial glucose and insulin after a protein-based meal, homeostasis model assessment index d BMI, waist circumference, body weight, and lean body mass The percentage difference between groups was extracted when the comparison was statistically significant.
Additional data on study design, number of participants, population characteristics (including age, sex, and health status), protein form and supply, and isoflavone quantity were extracted and taken into account for subsequent data analysis. A qualitative synthesis of the evidence was performed. Specifically, we deemed evidence to be strong if at least one-half of the higher-quality studies or two-thirds of the lower-quality studies reported consistent results and moderate if at least one-third of the higher-quality studies or one-half of the lower-quality studies reported consistent results. Below these thresholds, findings were considered to be inconclusive. Results of high-quality studies (i. e. , with a score $6) and low-quality studies (i. e. , with a score <6) were also analyzed separately to evaluate whether or not different conclusions would be drawn depending on the quality of the study.
Acknowledgments TC-D, DA-M, JA, LE, and LGK designed the research; TC-D and LE conducted the research; TC-D, DA-M, LE, LGK, and DT analyzed the data; TC-D wrote the paper; and JA, CG, LGK, and DT had primary responsibility for the final content. All authors read and approved the final manuscript. by guest on May 29, 2017 jn. nutrition. orgDownloaded from.
5  However, prosthetic approaches do not yet allow sufficient resolution for face recognition or locomotion in an unknown environment. 6 ] [9] [10] [11] [12] [13] [14] [15]  Expression of channelrhodopsin in RGCs might allow greater spatial resolution and acuity than that achieved with current prosthetic devices. This has motivated a large body of proof-of-concept studies in rodents and other small animals, which have shown the feasibility of the approach,  [7] [8] [9] [10] [16] [17] [18]  and a first-in-human phase 1 clinical trial was initiated recently (ClinicalTrials. gov NCT025 736). However, the use of genetically encoded opsins for vision restoration has several setbacks in terms of clinical development. First, optogenetically equipped cells require very high-level opsin expression, as there is no amplification cascade behind microbial opsins.
Retinas were dark-adapted 1 hr prior to recordings. Full-field light stimuli were applied with a Polychrome V monochromator (Olympus) driven by a STG2008 stimulus generator (MCS). Output light intensities were calibrated to range from 1 Â 10 14 photons/cm 2 /s to 1 Â 10 17 photons/cm 2 /s. Stimuli were presented for 2 s, with 10-s intervals. The wavelength sensitivity of responses was determined by stimulating 10 times, from 400 nm to 650 nm, with 10-nm steps. The order of the tested wavelengths was randomized to prevent any adaptation of the retina. Raw extracellular RGC activity was amplified and sampled at 20 kHz. Resulting data was stored and filtered with a 200-Hz high-pass filter for subsequent offline analysis using Spike2 software (version 7; CED). Single-unit raster plots were obtained using a combination of template matching and cluster grouping based on principal component analysis of the waveforms.
Two-Photon Imaging and Electrophysiological Recordings A custom-made two-photon microscope equipped with a Â25 water immersion objective (XLPLN25xWMP/NA1. 05; Olympus) with a pulsed femtosecond laser (InSight DeepSee; Newport Corporation) was used for imaging CatCh-GFP-positive retinal ganglion cells. AAV-treated retinas from rd1 mice were isolated in oxygenized (95% O 2 , 5% CO 2 ) Ames' medium (Sigma-Aldrich). For live twophoton imaging, retinas were placed in the recording chamber of the microscope, and z stacks were acquired using the excitation laser at a wavelength of 930 nm. Images were processed offline using ImageJ software (NIH). During imaging, the retina was superfused with oxygenized Ames' medium. We used an Axon Multiclamp 700B amplifier for whole-cell patchclamp and cell-attached recordings.
Linear multisite silicon microprobes (16 electrodes at 50-mm intervals) were used for recordings. For each acquisition, after averaging over the 200 trials, the electrode showing the VEP with maximal peak amplitude was selected for quantification. The stimulation consisted of 200-ms pulses of blue light repeated 200 times at 1 Hz triggered by a Digidata digitizer (Axon). Signals were analyzed in MATLAB using custom scripts. For local field potentials, signals were low-pass filtered at 300 Hz and averaged over the 200 trials.
ACKNOWLEDGMENTS The authors thank the  Sanofi Optovision team, Xavier Palazzi ,  Claire-Maelle Fovet ,  Valérie Fradot , and  Florian Senlaub  for technical help and scientific advice. This work was supported by  Sanofi ,  INSERM ,  UPMC , the  CNRS, FRM (Fondation pour la Recherche Medicale) , the  Agence Nationale pour la Recherche Investissements d'Avenir Recherche Hospitalo-Univesritaire en santé (RHU)  ( Light4Deaf  and  ANR: OPTIMA) , the  E-Rare Project (OPTOREMODE) , the  Foundation Fighting Blindness (Wynn-Gund  translational research award  TA-GT-0911-0543-UPMC-WG ), the  Fédération des Aveugles de France , the  City of Paris , the  Regional Council of Ile-de-France , the  French State program  " Investissements d'Avenir " managed by the  Agence Nationale de la Recherche  ( LIFESENSES ; grant  ANR-10-LABX-65 ), the  European Research Council (ERC)  (OptogenRet; starting grant  309776 ), the  Deutsche Forschungsgemeinschaft (DFG).
Acknowledgements We thank  Tula Saison-Behmoaras  for her support. This work was supported by  Muséum National d'Histoire Naturelle (MNHN) ,  Centre National de la Recherche Scientifique (CNRS) ,  Institut National de la Santé et de la Recherche Médicale (INSERM), France ;  Plan Nacional de Investigación Científica  (grant  SAF2014-51825-R ), Spain. CC and VN's team in Barcelona holds the Quality Mention from the  Generalitat de Catalunya  ( 2014SGR96 ). AS was the recipient of a fellowship  Formació d'Investigadors  from the  Generalitat de Catalunya.
1  Experimental design: 6 of the 12 rats undergoing light stress (LS group) were culled 1 day after LS (LS_1 group) while the other 6 were culled 1 week after LS (LS_7 group). Six non-exposed rats were sacrificed at the same sampling time (control group). After culling, one eye was randomly chosen for immunohistochemistry (IHC) analysis whilst the retina of the fellow eye was used for the metabolomics analysis in samples (CV threshold of 30 %). The software Analyst (SCIEX) was used for MS data collection and the software MetIDQ (Biocrates) was used to monitor the entire assay workflow.
Acknowledgements This work was funded by  "Berthe Fouassier" fellowship  from the  Fondation de France  (grant allocated to JMCB). We also acknowledge the support from the  INSERM, CNRS , the  University-Hospital of Angers , the  Région Pays de la Loire  and  Angers Loire Métropole. This work was also supported by grants from the following patients' foundations: Fondation VISIO,  Ouvrir les Yeux ,  Union Nationale des Aveugles et Déficients Visuels , Association contre les  Maladies Mitochondriales ,  Retina France ,  Association Point de Mire and Association de Spécialisation et d'Orientation Scientifique. GT acknowledges the support of the  Australian Research Council  via a  Future Fellowship , under contract  FT140100645.
Previous analysis on mt mRNAs showed that their size is close to that of their coding sequence (CDS) indicating the existence of very short 5 -and 3 -UTRs (untranslated regions). This was confirmed for a few transcripts using S1 nuclease protection and primer extension experiments  (13, 14). In this work, the C. reinhardtii mt transcripts were analyzed using different methods (Supplementary Figure  S1A ): 5 and 3 RACE (Rapid Amplification of cDNA Ends), cRT-PCR (circular Reverse Transcription-Polymerase Chain Reaction) and three protocols based on Illumina single-end sequencing, namely sRNA-Seq (small RNA sequencing, TruSeq), directional WTSS (Whole Transcriptome Shotgun Sequencing, stranded TruSeq) and bi-directional WTSS (non-stranded TruSeq, public data retrieved from SRA). Our results shed light on two singular characteristics of the mRNA transcripts.
For RT-PCR analysis, 4 g total RNA treated with DNAse RQ1 (Promega) was reverse transcribed in a 40 l reaction, using 2,5 M oligo(dG) primer or a mix of 2. 5 M oligo(dT) and 12 ng/l random hexamer primer (Promega). Sequence alignments were generated with MacVector software as described in more details in Supplementary Figure S1B. In order to monitor possible artifacts, 1 ng of synthetic transcript was incubated with 3,5 g of total RNA and 3 RACE analysis was performed. Analysis of this synthetic transcript showed that 1-2 additional nucleotides are observed at the 3 extremity and in very few cases more than 3 nt (Supplementary Figure  S1C ). For 3 RACE and cRT-PCR analysis, sequences with more than 3 nt added were therefore considered as bona fide 3 -tails.
Illumina sequencing Single-end 50 nt directional WTSS and sRNA-Seq Illumina datasets (SRA accessions, resp. : SRX2725800 to SRX2725809 and SRX2725861 to SRX2725864) were used, along with ninety bi-directional WTSS datasets (single-end 100 nt) retrieved from SRA as described in  (20). WTSS reads were mapped to the mt genome (EU306622) using bwa (mem). sRNA-Seq reads were mapped with either bwa (aln) or Bowtie2 to allow soft-clipping  (21, 22). Analysis of the mappings used bamtools, bedtools and the IGV browser  (23) (24) (25).
Reannotation of the Chlamydomonas mt genome Combining various approaches, the mature 5 -and 3 -ends of all mt transcripts of C. reinhardtii were precisely determined. Our genome browser (http://chlamy-organelles. ibpc. fr) presents the data as well as a novel annotation that are proposed. Compared to the previous one (EU306622), one mis-sense error in the cob CDS is corrected, the start of nad2 is moved three codons upstream, we modify the ends of almost all rRNAs and reintroduce rrnL3a and rrnL2b present in the initial annotation (NC 001638). Therefore, the C. reinhardtii mt genome encodes 8 mRNAs, 3 tRNAs and 14 rRNA fragments (4 for the SSU, 10 for the LSU), (Figure  1 ).
Intercistronic maturation generates adjacent 3 -and 5termini for almost all RNAs Concerning transcript processing, the near-absence of WTSS reads connecting successive cistrons indicates that the two primary transcripts that originate in the cox1 nad5 intergenic region are very efficiently processed into monocistronic RNAs (Figure  2 ). Gray et al. (12)  previously showed that nad5, nad2 and cox1 mRNAs lack 5 -UTR. Here, 5 RACE experiments carried out on all mRNAs extend this analysis and indicate that almost all mRNA molecules start at the A of the AUG start codon, meaning that they do not have a 5 -UTR (Figure  2A ). In addition, the 5 -end of all mRNAs (except nad1 and cob) is marked by a cluster of sRNAs starting at the AUG initiation codon. A similar result was observed for most rRNAs, (Supplementary Figure  S2 ).
e. ending close to the start of the next transcript) were more likely to show C-rich tails than the truncated ones, where tails were fewer and shorter (Supplementary Figures  S3  and 4 ). The analysis of WTSS data confirmed the presence of C-rich tails on mt mRNAs (Figure  5B-D ). C prevailed at almost all positions of the tails (e. g. Figure  5C ), even more than with other methods (Supplementary Figure  S4 ), with a smaller proportion of A/U-rich and composite tails. WTSS provides deep coverage, but because it involves priming the reverse transcriptase with degenerate oligonucleotides, it rarely reaches the 3 -end and it is biased toward G/C rich sequences. The ligation-based methods (3 RACE, cRT-PCR) were therefore favored to describe the composition and length of the tails. Because 3 -A-rich tails within transcripts are associated with their degradation in bacteria and chloroplasts  (32) , polycytidylation sites were searched inside transcripts.
For this, a cox1 specific primer positioned far-upstream cox1 3 end was used in 3 RACE experiments. This analysis identified 61 transcripts truncated within the CDS, but none carried a C-rich tail, (Supplementary Figure  S5A ). WTSS revealed the presence of 3 -tails within the CDS of cox1 and cob, but the density was 33 and 805 times lower than over The asterisk (*) indicates the main position(s) of the 3 -end, used to calculate the size of the 3 -UTR (numbers in brackets). The UTR sequence is shown under the x-axis, with the stop codon and the first nucleotides of the next gene highlighted in colors. For rrnL3a, two start positions (TC or GC) were observed in 5 RACE and sRNA data (Supplementary Figure  S2 ) respectively. The chart in black indicates the coverage, expressed as reads per million, of directional WTSS reads starting inside the gene of interest.
Comparison of mRNA and rRNA tails In order to determine whether C-rich tails are specific of mRNAs or not, the 3 -ends of the 14 rRNA fragments were analyzed by 3 RACE. Out of 304 sequences obtained, only 18 tails were found (6%), all short and A/U-rich, and in only 9 of the rRNA modules (Supplementary Figure  S3 ). Directional WTSS confirmed the enrichment of rRNA tails in A/U compared to mRNAs, but some C nucleotides were also found, especially toward tail ends (Figure  5D , E and Supplementary Figure  S4 ). These results were confirmed using a standard 20-cycle PCR protocol on oligo(dG)primed cDNA: amplification was observed for all mRNAs, but not rRNAs (Figure  5F ), in spite of the abundance of the templates. So far, polycytidylation has been reported neither for plastidial nor for cytosolic mRNAs.
parva and S. obliquus. This trait was not found in the other species examined, in particular in the green algae P. minor, O. tauri, Chlorella sorokiana and C. subellipsoidea. It therefore appears that the molecular process leading to C-rich tails is specific to the Chlorophyceae class. To further explore the Chlorophyceae, genome-wide WTSS datasets retrieved from the SRA or MMETSP databases were also analyzed (Supplementary Table  S3 ). In the colonial alga Volvox carteri, complete intercistronic cleavage were found, mRNAs starting at AUG and C-rich tails at the end of the mRNAs, with rRNA tails enriched in As. The major difference with C. reinhardtii was that most 3 -UTR ended far upstream of the next gene. In P. parva, most mRNAs appeared to lack a 5 -UTR and showed Crich tails, but the enrichment in A near the start was usually more pronounced than in C.
The genomic DNA (gDNA) of S. specialis strain GW41-1564 T was sequenced using a paired-end strategy and the MiSeq Illumina sequencer (Illumina Inc, San Diego, CA, USA). The paired-end Nextera library was constructed from 1 ng of fragmented gDNA and loaded on two flow cells. The library was barcoded in order to be mixed with 12 or 15 other projects and sequenced using a 2 ϫ 250-bp format. The sequencing produced a total of 4,096,640 paired-end reads. The obtained Illumina reads were assembled using the SPAdes software (http:// bioinf. spbau. ru/spades) (5). Open reading frames (ORFs) were predicted using Prodigal  (6). The predicted bacterial protein sequences were searched using BLASTp against the Clusters of Orthologous Groups (COG) and the GenBank databases. tRNA gene detection was performed using the tRNAScanSE tool (7), whereas ribosomal RNA genes were predicted using RNAmmer  (8).
The genome from S. specialis strain GW41-1564 T is 5,874,245 bp in length with a GϩC content of 72. 72%. After assembly, the genome is composed of 143 scaffolds (composed of 168 contigs). Of the 5,550 predicted genes, 64 were RNAs (three complete rRNA operons, two additional 5S rRNAs, and 53 tRNAs) and 5,486 were protein-coding genes. A total of 3,786 genes were assigned a putative function, and 306 genes were identified as ORFans. The remaining genes were annotated as hypothetical proteins  (1,268 genes). This strain has four antibiotic resistance genes, and 59 genes were predicted as nonribosomal peptide synthases or polyketide synthases. Twenty-one bacteriocin-encoding genes were also identified in this genome. Accession number(s). The genome sequence of Streptomyces specialis strain GW41-1564 T was deposited in GenBank under the accession number FAXE01000000.
Methods: This cross-sectional study (NCT01954264) was conducted between October and November, 2013, corresponding to the high malaria transmission season, in four sites with Health and Demographic Surveillance Systems (DSS) [two sites with moderate-to-high malaria endemicity in Burkina Faso (Nouna and Saponé) and two sites with low malaria endemicity in Senegal (Keur Socé and Niakhar)]. Children (N = 2421) were randomly selected from the DSS lists of the study sites and were stratified into two age groups (6 months-4 years and 5-9 years). A blood sample was collected from each child to evaluate parasite prevalence of Plasmodium falciparum and other Plasmodium species and gametocyte density by microscopy, and rapid diagnosis test in the event of fever within 24 h. Case report forms were used to evaluate malaria control measures and other factors.
Study design and area This epidemiological, cross-sectional study was carried out at four sites with Health and Demographic Surveillance Systems (HDSS) in Burkina Faso and Senegal (NCT01954264). The first site was located in the area of Nouna at about 300 km from Ouagadougou (northwestern Burkina Faso), where malaria is hyper-to holoendemic, the malaria transmission peak occurs at the end of the rainy season (June to October), and reduced transmission is observed during the dry season (December to May)  [15]. The second site in Burkina Faso was located in Saponé (30 km southwest of Ouagadougou), where malaria transmission is also seasonal, and the peak is observed at the end of the rainy season in September  [16]. The third site was located in the Keur Socé area (200 km southeast of Dakar, Senegal), which is characterized by the alternation of a long dry season and a short rainy season from July to November, and has a peak in malaria transmission between October and November  [17, 18].
Data collection This study was conducted during or just after the rainy season, at the peak of malaria transmission. Data were collected at one visit between 19 October and 25 November, 2013, and no follow-up was done (Fig. 1 ). Internet-based electronic case report forms were used to record demographic details, relevant medical history, malaria control measures used in the household, malaria risk factors, antimalaria medication and other medication received within 14 days, and history of fever in the last 24 h. Axillary body temperature at the time of the survey was measured by trained personnel according to the study protocol. The malaria control measures evaluated at the individual level were the use of mosquito bed nets the night before the visit, mosquito coils, insecticide sprays, and commercial and traditional repellents over 7 days, and IRS on interior walls in previous 12 months.
The other factors evaluated in this study were age, gender, study centre, number of persons living in the same house, localization (rural vs urban area; town vs countryside), main house construction material (walls, floor, roof, windows/eaves, nets), main source of drinking water, and availability of electricity. Each study site was requested to provide centre-specific information about control measures from the malaria control programme in the study area and, if available, meteorological data for the study site, such as rainfall and temperature. The information was collected in the form of a questionnaire recorded in a separate database.
Statistical methods The target sample size was 2400 children (600 at each participating site), according to the following stratification by age groups: 6 months-<1 year-olds (N = 60), 1 and 2 year-olds (N = 120 per group), 3 and 4 year-olds (N = 50 per group), and 5, 6, 7, 8, and 9 year-olds (N = 40 per group). To allow for 10% non-response, 660 children over all age categories were randomly selected from the demographic surveillance system databases of each site. This sample size ensured sufficiently narrow confidence intervals (CIs) around centre-wise PP estimates (with a maximum relative standard error of 0. 25) in children from the 6 months-4 years (JTEG definition) and 29 years (WHO definition) age groups for sites with low (<10%), moderate (10-50%), or high (>50%) endemicity. Continuous variables were described with mean, standard deviation (SD), median, and range.
Acknowledgements The authors thank the study participants. They also acknowledge the investigators and their clinical teams for their contribution to the study and their support and care of participants. The authors thank the global and regional clinical teams of  GlaxoSmithKline Vaccines  for their contribution to the study, the  R&D group  for analyses of laboratory work, the scientific writers for clinical protocol and clinical report writing and the statistician team for input on statistical analysis. The authors also thank  Myriam Wilbaux  ( XPE Pharma & Science, Belgium c/o GlaxoSmithKline Vaccines ) for publication management and  Claire Verbelen  and  Alexandra Arion (XPE Pharma & Science, Belgium)  for drafting the manuscript.
The unfortunate result has been that proper statistical analyses have not been carried out for most of the theories of greatest current interest. This is in spite of the fact that the LHC and other experiments have yet to discover any direct evidence for SUSY, heavily constraining the minimal variant  [89] [90] [91] [92] [93]. It is therefore essential that as many new ideas as possible are rigorously tested with global fits. Even working within the limited theoretical context for which they were designed, existing global fits do not offer a public framework that can be easily extended to integrate new observables, datasets and likelihood functions into the fit as they become available. Neither do they provide any standardised or streamlined way to deal with the complex interfaces to external codes for calculating specific observables or experimental likelihoods.