dataesr/scientific-paragraphs-categorization huggingface dataset:
Materials and methods Microbial sampling and high-throughput sequencing Sampling was from the Canadian research icebreaker CCGS Amundsen in August 2009, as part of the International Polar Year, project MALINA. Detailed methods are given in Supplementary Information and all ancillary data for the MALINA project are available at http://malina. obs-vlfr. fr. Samples for microbial analysis were selected on the downward conductivity-temperature-salinity (CTD) cast, based on salinity, temperature, relative nitrate and chlorophyll fluorescence traces (Supplementary Table  S1 ). For this study, six stations, three east of the Mackenzie Canyon (stations 430, 460 and 540), one west of the canyon (station 760) and two within the canyon (620 and 670) were sampled (Figure  1 ). Four depths were sampled at each station: surface (Z SURF ), the SCM (Z SCM ) and waters from above and below the SCM (Z a-SCM and Z b-SCM , respectively).
Sequence processing and microbial community analyses Care was given to avoid generation of spurious operational taxonomic units (OTUs), leading to inflation in microbial biodiversity. To this end, we combined QIIME v. 1. 6 (Caporaso et al. , 2010b)  and USEARCH v. 6  (Edgar, 2010 (Edgar, , 2011) )  sequence preprocessing pipelines. Sequences shorter than 150 nucleotides were removed and remaining sequences were 'denoized' using the QIIME built-in 'denoizer' program (Supplementary Table  S2 ). The resulting reads were then aligned using pyNAST  (Caporaso et al. , 2010a)  with the Silva 18S alignment  (Pruesse et al. , 2007)  as a template; aligned sequences were manually inspected and 5 0 /3 0 -trimmed. Additional sequence quality controls were performed through the USEARCH quality-filtering pipeline  (Edgar, 2010) ; putative chimeras were detected with UCHIME  (Edgar et al.
, 2011)  using the Silva 18S database (release 108) as reference. Remaining sequences were clustered in OTUs using a 98% sequence identity cutoff with UCLUST  (Edgar, 2010)  and singleton OTUs (i. e. , cluster composed of a single sequence) were discarded from this study. OTU sequence representatives were selected as the most abundant sequence within the cluster. OTU representatives were taxonomically classified via the mothur Bayesian classifier  (Schloss et al. , 2009)  with a custom-curated 18S sequence database as the reference data set, which was an updated version of  Comeau et al. (2011)  as in  Monier et al. (2013). Sequences from OTUs classified as multicellular organisms (Opisthonkonta or Streptophyta) were discarded from the study as we chose to focus on microbial diversity.
Phylogenetic analyses All ecological analyses based on phylogenetic information (UniFrac, phylogenetic diversity (PD) and net relatedness index (NRI)) were based on a phylogenetic tree reconstructed with an approximate maximum-likelihood approach as in FastTree v. 2. 1  (Price et al. , 2010)  using the 'accurate' mode (i. e. , -slownni -mlacc 4; with pseudocounts). The phylogenetic reconstruction was based on an alignment of final OTUs, aligned with pyNAST and manually curated. UniFrac d W5000 (weighted) and d UW5000 (unweighted) distances  (Lozupone and Knight, 2005)  were computed on data sets subsampled at an even depth of 5000 sequences using generalized UniFrac procedure  (Chen et al. , 2012)  implemented in the R package 'GUniFrac' v. 1. Clusters based on d W5000 were generated using hierarchical clustering.
One thousand jackknife replicates (with 3750 sequences, i. e. , 75% of the subsampled data sets) were used to assess clustering robustness. PD rarefactions analyses were also conducted on samples rarefied to 5000 sequences; PD values were measured following Faith's definition (i. e. , total branch length of the OTU phylogenetic tree) and computed every 20 sequences using 100 subsampling iterations. PD values were computed using the R package 'picante' v. 1. 6 (Kembel et al. , 2010). Other a-diversity measures, Chao1 estimator and Shannon index, were computed with QIIME. NRI values were computed using 'picante', through the commands ses. mpd ( À 1 Â NRI) on abundance weighted data, and tips of the original phylogenic tree were shuffled to generate randomized phylogenetic relationships (null.
7 using 1PAM matrix and -addfragments mode  (Katoh and Frith, 2012). These sequences were then placed on the Picozoa reference phylogenetic tree using RAxML evolutionary placement algorithm. Statistical analyses b-Diversity significance was assessed using UniFrac Monte Carlo significance test on d W5000 with 10 000 randomizations, as implemented in QIIME. All subsequent statistical analyses were computed in the R environment v. 3 (http://www. r-project. org). Mantel tests for assessing the correlation between d W5000 and depth or geographical distances were computed with the Pearson's correlation method and 10 000 permutations using the R package 'vegan' v. 2  (Oksanen et al. , 2007). To determine the contextual variables driving the microbial community compositions, we first followed a methodology similar to  Martiny et al.
(2011). We removed redundant environmental and biological variables (Supplementary Table  S1 ) by using varclus  (R package 'Hmisc' v. 3. 12; Harrell, 2008)  with Spearman's correlation (r 2 cutoff: 0. 8; PO 4 and salinity had r 2 40. 8 but were retained for subsequent analyses). Non-redundant variables best explaining community dissimilarity matrix (d W5000 ) were then identified using the BEST procedure (i. e. , best subset of environmental variables with maximum rank correlation with community dissimilarities;  Clarke and Ainsworth, 1993). The resulting nine variables best explaining the d W5000 matrix were fitted as vectors onto the nonmetric multidimensional scaling ordination (NMDS) ordination and used for permutational analyses of variance on distance matrix analysis, which were computed using 'vegan' (envfit and adonis functions, respectively, both using 10 000 permutations).
Overall significance of the model composed of the nine BEST-selected variables in explaining d W5000 was assessed using multiple regressions on matrices ('ecodist' R package v. 1. 2; Goslee and Urban, 2007; 10 000 permutations and Spearman's correlations). Differences in PD, NR and taxonomic composition mean among community clusters were tested using ANOVA and pairwise differences were evaluated with Tukey's HSD test. Statistical analyses of sample taxonomic enrichments were computed with Metastats  (White et al. , 2009)  using 1000 bootstrap permutations and a 0. 05 significance threshold.
Acknowledgements We thank the  Canadian Coast Guard crew of the Canadian research icebreaker CCGS Amundsen. We are grateful to  AM Comeau  and  E Medrinal  for laboratory work, and to MP Simmons and  SW Kembel  for comments. This study was conducted as part of the  MALINA Scientific Program  led by MB and funded by the  French National Research Agency (ANR) ,  INSU-CNRS  ( Institut National des Sciences de l'Univers -Centre National de la Recherche Scientifique ),  CNES  ( Centre National d'Etudes Spatiales)  and  ESA  ( European Space Agency). Computing support was provided by  CLUMEQ/Compute Canada. Additional funding was provided by the  Natural Science and Engineering Council (NSERC) of Canada  to CL, and  Fond Quebecois de Recherches Nature et Technologies (FQRNT) for Quebec Ocean , and is a contribution to ArcticNet.
Literature search Literature search was based on the Medline database covering the years 1990-2013. Articles that contained relevant information for the review, namely, use of parameters of sagittal balance (pelvic and spine parameters) for surgery in DSD were selected. The search strategy included the following keywords in all fields using different combinations, with the Boolean operators OR and AND: sagittal balance, sagittal imbalance, spinopelvic alignment, pelvic tilt, sacral slope, sacral tilt, pelvic incidence, spinopelvic parameters, degenerative spine, degenerative lumbar disc disease, degenerative spondylolisthesis, degenerative kyphosis, degenerative scoliosis, and lumbar spinal stenosis. Publications on isthmic spondylolisthesis or tumours were excluded. Surgical techniques included posterior lumbar interbody fusion (PLIF), transforaminal lumbar interbody fusion (TLIF) and Smith-Petersen osteotomy; transpedicular osteotomy, dynamic stabilisation and intervertebral disc arthroplasty were excluded from this literature search.
Modelling of UreA in the outward-facing cavity conformation Results obtained for strains bearing mutations Y106F and W82F show that there is a reduction in the initial transport rate which does not correlate with K m and K i changes (table  1 ). This may suggest that urea can bind to the protein but the mutation somehow impairs the conformational rearrangements of the protein along the translocation process. To acquire a different structural perspective on the role of these residues, we undertook the construction of a model of UreA based on the structure of the Nucleobase-Cation-Symport-1 benzylhydantoin transporter from M. liquefaciens (Mhp1; PDB code 2JLN  [29] ). Although Mhp1 shows less amino acid sequence identity with UreA than vSGLT (see Experimental procedures), this model was constructed to obtain an insight into the possible role of the amino acids identified in the outward closed conformation.
Epifluorescence microscopy Samples for fluorescence microscopy were prepared as described previously  [58]. In brief, samples were incubated directly on sterile coverslips protected from light in liquid MM with proline (5 mM) as nitrogen source and appropriate supplements, at 258C for 14-16 h. For epifluorescence microscopy, samples were observed in an Olympus inverted microscope CKX31 with a U-MNIBA3 (for GFP) or U-MWIG3 (for RFP) filter, photographed with a Hamamatsu Orca Er rsob. royalsocietypublishing. org Open Biol. 4: 140070 camera and processed using IMAGE PRO v. 6. 0 software. For confocal microscopy, samples were observed in a Leica inverted microscope DMI6000CS with an I3 (for GFP) or N2. 1 (for RFP) filter. Images were acquired and processed using LASAF v. 2. 20 software. The resulting images were processed by Adobe PHOTOSHOP software.
Bioinformatics and modelling of UreA Sequences were obtained from the Aspergillus Comparative Database, Broad Institute (http://www. broad. mit. edu/ annotation/fungi/aspergillus), the Saccharomyces genome database (http://www. yeastgenome. org), the Candida Genome Database (http://www. candidagenome. org), The Arabidopsis Information Resource (http://www. arabidop sis. org), the Oryza sativa genome database (http://www. plantgdb. org/OsGDB) and from the National Center for Biotechnology Information (http://www. ncbi. nlm. nih. gov). PiDUR3 sequence was kindly provided by Morel et al. [10]. Multiple sequence alignments were carried out in MEGA v. 5. 0 software  [59]  with Muscle  [60]. Homologues of UreA with known structure were identified by performing a remote homology search on the Protein Data Bank (http:// www.
Funding statement. The work in Uruguay was partly supported by the Programa Especial de Desarrollo de las Ciencias Basicas (PEDECIBA) and by FOCEM (MERCOSUR Structural Convergence Fund, COF 03/11). M. S. received support from the Agencia Nacional de Investigacion e Innovacion (ANII) and Comision Sectorial de Investigacion Cientı ´fica (CSIC), UdelaR. S. P. was partially funded by FOCEM (MERCOSUR Structural Convergence Fund), COF 03/11. We thank G. Diallinas for providing the [ 14 C] experimental facilities.
MUC1 mRNA is a physiological target of miR455-3P. To identify potential miR455 target mRNAs, we employed the miRNA target prediction software miRecords. 39  Compiling lists of potential targets for miR455-3P and -5P, we noted at least eight genes that have been linked to hypoxia signaling (Figure  3a ). This raised our interest because miR210 expression is stimulated by hypoxia-inducible factors (HIF),  [40] [41] [42]  suggesting a potential hypoxia-related relationship between the three miRNAs we found to be differentially expressed in PE samples. To validate the predicted miR455-3P and -5P target mRNAs, we first performed dual luciferase miRNA reporter assays in BeWo cells. We fused the complete 3 0 UTRs of the predicted mRNAs to the RL reporter and tested miR455mediated repression in FSK versus control conditions (Figure  3a ).
Patient data are summarized in Table  1. 3 0 UTR cloning and dual luciferase assay. To construct the UTR vectors, a psicheck-2 vector (Promega, Madison, WI, USA) containing an Asc1 site was created. Briefly, the psicheck-2 vector was first digested with Not1/ Xho1, purified on a 1% agarose gel and extracted using QIAquick Gel Extraction Kit (Qiagen, Venlo, The Netherlands). The linearized vector was ligated to annealed oligonucleotides containing an Asc1 restriction site (Asc1 fwd and Asc1 rev, Supplementary Table  S2 ). The vector was digested using Asc1/Not1 enzymes and ciped (except for vectors containing perfect complementary sequences for miR455-3P and -5P). 3 0 UTRs were amplified from total RNA extracted from BeWo cells. Briefly, total RNA was reverse transcribed following a first-strand cDNA synthesis protocol from an AffinityScript Multiple Temperature cDNA synthesis kit (Agilent, Santa Clara, CA, USA) and amplified using an iProof High-Fidelity PCR kit (Biorad, Hercules, CA, USA).
RL activities were normalized to FL activity. Measurements were carried out in technical triplicates and are the results of three independent biological experiments. Data are presented either as RL/FL ratios or as percentage repression (ratio RL/FL in FSK conditions normalized to the ratio in DMSO conditions). Transient transfection siRNA and mimics. siRNA (MUC1, HIF2A, All Stars Negative Control) and synthetic miRNA/mimics (hsa-miR455-3 P and -5P) were purchased from Qiagen. Transient siRNA and miRNA mimic transfections in BeWo cells were performed with RNAimax (LifeTechnologies) following the manufacturer's protocol. RNA isolation and expression analysis. Total RNA with or without miRNAs was extracted from BeWo cells and placenta pieces using an mirVana miRNA Isolation Kit (LifeTechnologies).
To evaluate miRNA and pri-miRNA expression, RT-PCR was performed using a TaqMan MicroRNA reverse transcription kit and a High Capacity RNA to cDNA kit, respectively, followed by a TaqMan Universal Master Mix, no UNG (Life Technologies). The primers used for qPCR experiments were purchased from Life Technologies and are available upon request. All experiments were performed in triplicate using the StepOne plus real-time PCR system for 96-well plates or the 7900HT Fast realtime PCR system for 384-well plates (Life Technologies). All mRNA and miRNA data were normalized to RPLP0 and U6snRNA, respectively, except when stated otherwise. Preparation of small RNA libraries for high-throughput sequencing and bioinformatic analysis. The protocol from Emmerth et al. 56  was adapted for human small RNA libraries.
Low-complexity reads (o1%) were filtered out based on their dinucleotide entropy. All reads shorter than 14 nt were removed. Alignments to the Homo sapiens miRNA database (Human Genome Assembly hg19, mirBase v15) were performed with the software Bowtie (version 0. 12. 7, http://bowtie-bio. sourceforge. net). 59  The numbers of miRNA reads were normalized to the total number of reads of the library. For the purpose of logarithmic scale representation, a number of 2 reads was added to each normalized miRNA number. All statistical and bioinformatic analyses were carried out in R using Bioconductor. Protein isolation and western blotting. Total cellular protein was extracted using RIPA buffer (50 mM Tris-HCl pH 7. 5, 150 mM NaCl, 1% NP-40, 0. 5% sodium deoxycholate, 0. 1% SDS, 1 mM EDTA) supplemented with the Protease and Phosphatase Inhibitor Cocktail (Roche Applied Science).
1% PBS-Triton X-100 for 5 min. The slides were transferred to a humid chamber and, after 30 min blocking in PBS-BSA (10%) were incubated with primary antibody against CDH1 (ab1416, dilution 1/50, Abcam) in PBS-BSA (1%) overnight at 4 1C. Cells were washed and incubated with secondary antibody (A-11029, dilution 1/1000, Life Technologies) in PBS-BSA (1%) for 1 h at RT. After washing, DAPI was applied at a dilution of 1/10000. After extensive washing, the coverslips were mounted on slides with MOWIOL mounting medium. Fluorescent images were acquired using a Zeiss Axioplan 2 Imaging inverted fluorescence microscope in conjunction with a Zeiss Axiocam MRm monochromatic CCD camera or Zeiss Axiocam MRc color CCD camera and analyzed with Axiovision 4. 8. 2 software (Carl Zeiss AG, Oberkochen, Germany).
Acknowledgements. We are grateful to  Stephan Emmerth  and  Sophie Dessus-Babus  for help with small RNA library preparation,  Dimos Gaidatzis  and  Thierry Gostan  for bioinformatics support, and  Julien Bethune  for assistance with the Dual Luciferase Assay. We thank  Nicole Chiodetti  for excellent technical support in placenta processing. We would like to thank all the patients who participated in this study as well as  Professor Sinuhe Hahn ,  PD Dr. Irene Hoesli  and the study nurses of the  University Hospital of Basel  for recruitment of the patients. This work was supported by the  Swiss National Science Foundation. The  Friedrich Miescher Institute for Biomedical Research  is supported by the  Novartis Research Foundation.
Histology Tissues were fixed in 10% neutral buffered formalin, feet were decalcified (15% EDTA in 0. 1% phosphate buffer over 10 days), tissue was embedded in paraffin wax, and 6 mm-thick sections were cut and stained with hematoxylin-eosin. Sections were digitally scanned using Scan Scope XT digital slide scanner (Aperio, Vista, CA). Image analyses were undertaken using Aperio ImageScope Software (v10) and the Positive Pixel Count v9 algorithm (default settings).
cDNA was amplified and PCR products were detected using Rotorgene 6000 (Corbett Research, Mortlake, Australia) under the following cycling conditions: one cycle of 50uC for 2 min, one cycle of 95uC for 2 min, 45 cycles of 94uC for 5 sec, 60uC for 10 sec and 72uC for 30 sec. Data were analyzed using Rotor-Gene Real Time Analysis software (Corbett Research, Australia). Each sample was analyzed in duplicate and normalized to RPL13A mRNA as described  [48]. Negative-strand specific qRT PCR was undertaken essentially as described  [50]. cDNA was synthesized as described  [48]  with the exception that random hexamer oligonucleotides were substituted with 10 pg of a primer, that comprised a tag sequence linked to a CHIKV nsP1 sequence (59-GGCAGTATCGTGAAT-TCGATGCGACACGGAGACGCCAACATT-39; tag sequence in italics).
Evaluation of the benefits Sampling strategy and socio-economic survey. During the feasibility phase of the elimination project, field staff of the Ministry of Livestock conducted preliminary surveys in the target area and geo-referenced ,50% of the livestock farmers in their respective districts, and classed the cattle herds in three size categories (,20, 20-100,. 100). The 513 geo-referenced farms were used to develop a stratified sampling strategy based on cattle herd size and 192 farms were selected as a representative sample for each group (see Results section). These farms were surveyed from July to November 2010 using a carefully developed questionnaire. The final datasets of 186 farmers were considered accurate and these were used for the statistical analyses. The questionnaire was designed to capture instantaneous or recent data (between the two last rainy seasons) and contained mainly closed questions that allowed the collection of quantitative data sets.
The first section of the questionnaire dealt with the composition of households (sociological structure, main occupations of the head of the family), the second with equipment and farming resources, and the third with the composition of the livestock and their productivity. Detailed data were collected on cattle including herd structure (numbers per sex and age) and their productivity. Sales data were collected by cattle species for meat and milk production systems. The health constrains were prioritized by the farmers and the treatments were listed by species. Types of livestock production systems. Different farming systems were identified based on herd composition and cattle breeds. Tsetse presence/absence was assessed using habitat suitability as predicted by a Maxent model  [20]  that was developed using tsetse presence data obtained during the feasibility study of the tsetse elimination project  [14]  and environmental data derived from Landsat and MODIS data.
Materials Twelve samples from eleven skin garments (ten capes and a tunic) from seven peat bog localities in Denmark were selected for this study (Fig. 1 , Table  1 , Fig. S1  in File S1). All samples derive from the collection of skin objects at the National Museum of Denmark. The dataset for each garment (except for the Huldremose I find, for which two samples were collected from two different skin elements) consisted of three samples extracted from the same skin element, as these sewn together skin elements may derive from different species. A skin sample, measuring approximately 262 mm, was cut off for MS-based peptide sequencing, together with a few hairs for microscopy analyses (Fig. S1  in File S1). To validate the MS approach, three modern reference samples were also analysed (Table  1 ), representing the three common domesticated species that the archaeological samples most likely derived from (cow, goat, sheep).
In cases where ''LM+ SEM'' and ''MS'' identified cattle, ''MO+LM'' identified goatskin (sample 2 and 10). In two cases ''LM+SEM'' and ''MS'' disagree between horse and goat identifications (sample 1 and 8). The sample preparation procedure used for MS-based ancient peptide sequencing yielded protein recoveries estimated in the range between 1. 32 and 20. 13 mg of protein/g of extracted skin (Table  S2  in File S1). While yields for proteins extracted from ancient skins have not been reported earlier, these values appear to be similar or superior to the approximately 5 mg protein/g bone obtained from ancient bone  [52]. Skin samples from the same localities present similar values, suggesting that the protein yield could be related to archaeological site-specific preservation conditions. Statistics, reporting numbers of identified proteins and peptides for each sample, as well as the relative supporting tandem MS spectra, indicate that sample preparations based on procedure ''A'' enabled the recovery of richer datasets (Table  S2  in File S1).
Most of the proteins identified are collagens and keratins, in agreement with the nature of the samples analysed. However, the adopted approach also allowed the identification of proteins and peptides not previously reported in ancient skin samples  [43] , such as, leucine-rich-containing protein, serum albumin, selenium-binding protein and haemoglobin foetal subunit beta (Tables  S3  in File S1). The search strategy adopted enabled the determination of a set of species-specific peptides (Tables  S3 , S4 and S5 in File S1), within publicly available protein databases. Based on spectra matched against the complete bovine reference protein list and extended lists of sheep and goat proteins available in NCBI RefSeq (http://www. ncbi. nlm. nih. gov/refseq), it was possible to identify at least one species-diagnostic peptide for all samples except two: 9 and 11.