dataesr/scientific-paragraphs-categorization huggingface dataset:
ACKNOWLEDGMENTS This work was partially supported by the  Swiss National Science Foundation  (grant  31003A_140945 ); a grant from the  Swiss Translational Medicine program ; and grants from the  Agence Nationale pour la Recherche , the  JPND program on ModelPolyQ, Neuratris  (Grant  Q5  " Investment for the future "  ANR-11-INBS-0011 ),  Repair-HD  ( FP7  grant  602245 ), the  Laboratoire d'Excellence Revive  ( Investissement d'Avenir ; grant  ANR-10-LABX-73 ), the  French National Health Institute (INSERM) , and the  AFM-Téléthon (Association Française contre les Myopathies ).
5 (PerCp-cy5. 5), PerCp-eFluor 710, allophycocyanine (APC), Alexa Fluor 700 (AF700) and Qdot-605: anti-CD4 (FITC), anti-CD4 (AF700), anti-CD11a (FITC), anti-CD8a (PE), anti-GL7 (PE), anti-CD49d (PerCp-eFluor 710), anti-CD62L (PeCy5), anti-CD95 (PeCy7), anti-IgM (PerCp-cy5. 5), anti-PD-1 (APC), anti-IgG (APC) and CD19 (Qdot-605) (all antibodies from BD Bioscience, Mountain View, CA). Before staining, a total of 5 × 10 5 living cells, were treated with Fc-Block (clone 2. 4 G2, BD Bioscience, Mountain View, CA). Dead cells were excluded during analysis according to their light-scattering characteristics. Data and analyses were performed with LSRFortessa (Becton Dickinson, Grenoble, France) or four-color FACSCalibur (Becton Dickinson, Grenoble, France) using FlowJo software (Tree Star, Ashland, OR, USA) or CellQuest Pro software (Becton Dickinson, Grenoble, France).
Acknowledgements We thank  Peter Smooker  and  Kim Taylor  ( Department of Biotechnology and Environmental Biology, RMIT University, Bundoora, Australia ) for providing P. berghei HRF plasmid, the  CEPIA (Centre d'élevage, de production et d'infection des anopheles, Institut Pasteur, Paris)  for providing Anopheles mosquitoes. We are indebted to  Jacques Bellalou  (Platform of the recombinant proteins,  Institut Pasteur, Paris)  who provided the recombinant PbHRF protein. We thank  Dr. Sylvie Garcia  and  Malika Serra-Hassoun  ( Institut Pasteur, Paris ) for their technical advices. We thank  Pierre-Henri Commere (Imagopole, Institut Pasteur, Paris)  for technical help in Facs analysis. This work was funded by an  Institut   Pasteur grant  to SM. C. D. G. is supported by a post-doctoral fellowship from the  Helmut Horten Foundation, Agno, Switzerland.
Results Analysis of Differentially Expressed Genes (DEG). Samples of the cerebellum, thalamus-pituitary and liver of tilapia that were treated with equimolar doses of T2 or T3 (25 nM) per 12 h (as well as tissues from non-TH treated controls) were sequenced using the Illumina GAIIx platform. We previously showed that this hormone concentration and exposure period does not induce an hyperthyroidal state  8. Following a quality control check, the resulting short reads were mapped to the tilapia coding sequences (CDS). The statistics for sequencing and mapping are shown in Supplemental Data S1. From the mapping results, we used the effective counts obtained with the eXpress program, to perform differential expression analysis. Gene expression data were obtained through the edgeR bioconductor by comparing the control condition vs T2-or T3-treated groups for each tissue (Supplemental Figure  S2 ).
Furthermore, a greater number of genes were regulated by T2 in the liver, while T3 regulated a higher number of genes in the cerebellum and thalamus-pituitary (Fig. 1 ). In each tissue, we also examined how many T2 or T3 responsive genes were specifically up-or down-regulated. We noted that both thyronines had a tendency to primarily up-regulate genes in the liver, while the hormones down-regulated many genes in the CNS. (Fig. 1 ). To confirm and validate some of the results obtained from the differential expression analysis, we validated two genes per tissue that were specifically up-regulated by either T2 or T3 and quantified expression using real-time PCR (RT-qPCR). This independent experiment in tilapia juveniles followed the methods as for RNA-seq (see Materials and Methods). Data were congruent with RNA-seq (Supplemental Figure  S4 ) for luc7-like 1 (LUC7L, p < 0.
Transcriptome sequencing was conducted using Genome Analyzer GAIIx (Illumina) at the genome sequencing facility of our university located at "Instituto de Biotecnología-UNAM". A configuration for pair-end reads with a 72 bp read length was used. GEO accession number GSE96046. Bioinformatics analysis. Quality Control (QC) of raw reads was performed using FASTQC software  33  and contamination and adapter removal was carried out using in-house Perl scripts. QC' ed reads were mapped using the Bowtie 1. 1. 2  34 aligner to the annotated reference genome Oreochromis_niloticus (Orenil1. 0. cds. all, 21,437 coding genes) CDS downloaded using BioMart from Ensembl repository database. Quantification and repetitiveness normalisation were carried out using eXpress software 1. 5  35. Total effective counts for each sample were merged; a matrix was generated using the "abundance_estimates_to_matrix.
pl" Perl script included in the Trinity pipeline  36. DEG analysis was performed using R Bioconductor tool edgeR  37  through the "run_DE_analysis. pl" script from Trinity and the merged count matrix. Pairwise comparisons among each sample type (Control vs T2 or Control vs T3, each with its respective biological replicate) were performed. To determine DEG, a False Discovery Rate (FDR) of adjusted p < 0. 05 was used.
Pathway Studio V9 (Elsevier) operating with the ResNet 11. 0 database was used to obtain further insight into pathways affected by treatment to T2 or T3. This database is built primarily from mammalian data but also contains fish-specific transcripts. Official names for tilapia genes were mapped to the program using homologs for mammals. Although there are clear differences between fish and mammals and there are some genes that will have different/unique/novel roles in species, it is expected that the majority of gene function is conserved in vertebrates and it is much more powerful to leverage all of what we know in vertebrates in terms of gene function and relation, as opposed to a restricted subset (fish-specific data, for which there is vastly less than mammals). Literature evidence to construct relationships between genes and their functions were based largely on mammalian studies but also included evidence from other taxa.
Acknowledgements Aurora Olvera is a doctoral student from the  Programa de Doctorado en Ciencias Biomédicas ,  Universidad Nacional Autónoma de México (UNAM)  and has received  CONACyT fellowship 245201. This study was supported by grants from  PAPIIT IN 204517 and CONACyT 219833. We greatly acknowledge the technical support of  MS Patricia Villalobos Aguilera ,  MS Jerome Verleyen ,  Dr. Ricardo Alfredo Grande Cano, MS Adriana González Gallardo, MS Aberto Lara Rubalcava  and  MA Graham Angus. We thank  Dr. Carlos Valverde  for the ongoing support.
Physical and chemical data Organic pollutants were measured using analytical techniques based on gas chromatography-tandem mass spectrometry and liquid chromatography-tandem and hybrid mass spectrometry  (Masiá et al. , 2013; Osorio et al. , 2014). To assess the toxic risk at each sampling site, toxic units (TU) were calculated using the measured concentrations of the compound (MEC) and respective acute toxicity data (EC50) for Daphnia sp. The sums of toxic units for each of the compound families (TU pesticides and TU metals in Table  1 ) were calculated as the risk estimate posed by different groups of toxicants. The major contributors to the pesticide toxicity risk were insecticides (e. g. , chlorpyriphos or chlorfenvinphos) whereas copper was the main contributor to the metal toxicity risk.
Biological traits Traits were derived from a European database compiled by  Tachet et al. (2010)  and completed for Mediterranean taxa by Bonada et al. (Bonada and Dolédec, 2011; Bonada et al. , 2007). In this database, the affinity of each taxon for a given trait state or category is quantified by a score with a value of 0 if there is no affinity of the taxon for the trait state or category, 1 if low affinity, 2 if medium affinity and ≥3 if strong affinity (i. e. , fuzzy coding approach;  Chevenet et al. , 1994). Trait information at the genus or species level was used when data was available, otherwise subfamily or family level information was used (for Chironomidae, Oligochaetae and Enchytraeidae, respectively). However, if taxonomic levels higher than species are used, the trait structure of assemblages is generally conserved  (Dolédec et al.
"Deposit feeding" combined the frequency affinities of taxa for absorption through tegument and deposit feeding sensu stricto. For each taxon, dispersal ability was assessed using an index similar to that proposed by  Bonada et al. (2012) , which uses the four dispersal categories (aquatic passive, aquatic active, aerial passive and aerial active) of the  Tachet et al. (2010)  database. Aquatic passive was weighted by 1, aquatic active by 5, aerial passive by 10 and aerial active by 20. The dispersal ability of each taxon was thus computed as the weighted mean across the dispersal categories. Finally, we computed the food diversity ingested by each taxon as a Simpson index ( p 1-∑ , i 2 with p i as the proportion of a given food item).
In these two latter approaches, the false-discovery-rate adjustment method was used to correct P-values according to bias due to multiple-test comparisons. Statistical analyses and graphical outputs were computed with the ade4, vegan and corrplot packages implemented in the R software  (Core Team, 2015; Chessel et al. , 2004; Dray and Dufour, 2007; Dray et al. , 2007; Oksanen et al. , 2016).
Acknowledgments This study has been supported by the  EU   FP7  project  GLOBAQUA  [Grant Agreement No. 603629 ], the  NET-Scarce  project [Redes de Excelencia CTM2015-69780-REDC] and by the  Generalitat de Catalunya  [Consolidated Research Groups: 2014  SGR 418-Water and Soil Quality Unit  and  2014 SGR 291-ICRA]. MK  acknowledges  AGAUR  fellowship of the  Generalitat de Catalunya. Special thanks to  Laura Armendáriz  for the identification of the Oligochaeta.
In vivo rat model of I/R injury Rats were anesthetized with 20% urethane (120 mg/ kg, i. p. ) and artificially ventilated with a KTR-5 animal respirator (Hugo Sacks Electronik) with a volume of 2-3 ml at a rate of 70-75 breaths/min. Further preparation of animals was performed as described earlier  [37]. Arterial blood pressure was recorded with a pressure transducer (Statham p23Db, Oxnard, USA) using a polygraph Biograph-4 (St. Petersburg, Russia). The mean arterial pressure, heart rate and standard lead II ECG were recorded on a computer using a LabVIEW 7. 1 data acquisition system (National Instruments, USA). After 30-min stabilization of hemodynamic parameters (steady state), LAD coronary artery was occluded for 40 min to simulate regional ischemia; the duration of subsequent reperfusion was 1 h.
In the experimental series, G1 was administrated by i. v. bolus injection at the onset of reperfusion at doses of 0. 4; 0. 7; 1. 3; 2. 0 or 2. 7 μmol/kg (groups G1-0. 4; G1-0. 7; G1-1. 3; G1-2. 0 or G1-2. 7, respectively). An equal volume of saline (0. 5 ml) was injected in the control series of experiments. The influence of a vehicle, 0. 5% DMSO, on myocardial infarct size was studied in a separate series of experiments. Additionally, effects of i. v. G1 administration on hemodynamic data were evaluated. At the end of experiments, LAD coronary artery was occluded and 2 ml of 2% Evans Blue (Sigma, USA) solution was injected through the jugular vein to distinguish the myocardial nonischemic area from the AAR.
Determination of myocardial infarct size After staining with Evans Blue, the heart was excised and the LV was frozen. A frozen LV was transversely cut into 1. 5 mm thick slices which were incubated in 0. 1 M sodium phosphate buffer pH 7. 4, containing 1% 2,3,5-triphenyl-tetrazolium chloride (TTC, Sigma, USA) 10 min at 37°C. The slices were fixed in 10% formalin for 5 min. Then they were placed between two transparent glasses and captured using a scanner at 600 d. p. i. resolution; the saved images were analyzed by computerized planimetry using Imagecal software. The slices were then weighed for determination of LV weight. The AAR was expressed as a percentage of LV weight; MI was expressed as a percentage of the AAR in each group.
Statistical analysis Data are presented as means ± SEM. Results were analyzed by one-way ANOVA followed by Bonferroni multiple range test post-hoc analysis for calculation differences between more than two groups. Comparisons between two groups involved use of the Student's unpaired t-test. All statistical analyses were performed using SigmaPlot version 12 (Systat Software Inc, San Jose, CA). A p < 0. 05 was defined as significant.
In the experiments with proteins lacking phospholipolytic activity, the CaCl 2 -containing extracellular solution was used. Acetylcholine (ACh), cytisine (Cyt) or choline were applied on the whole cell surface using 4 s pulses with intervals not less than 6 min. Agonist-induced currents were monitored and digitized with a patch-clamp amplifier A-M Systems (USA), the data acquisition was performed using Digidata1200 B interface and pClamp6 software (Axon Instruments Inc. , USA). Aliquots of solutions of PLA 2 s in water were kept in the refrigerator and diluted using extracellular solution to the desired concentration immediately before use. The effects of PLA 2 s were determined by measuring the changes in peak current amplitude induced by the agonist after 5-min incubation with PLA 2 compared to the control responses before treatment and after prolonged washing.
IC 50 values were calculated using Sigma plot 11. 0 software using the Hill plot analysis. Xenopus oocytes. Plasmid pT7TS constructs of human nAChR α9 and α10 subunits were linearized with XbaI restriction enzymes (NEB, USA). Linearized plasmid constructs were subjected to in vitro cRNA transcription using T7 mMessagemMachine1 transcription kit (AMBION, USA). Mature Xenopus laevis female frogs used in this study were obtained commercially (NASCO, Fort Atkinson, WI, USA) and housed in a facility with 12:12 hours light:dark cycles, 18-20˚C ambient temperature. Animals were fed twice a week and maintained according to supplier recommendations (https://www. enasco. com/page/xen_care). All the appropriate actions were taken to minimize discomfort to frogs. The World Health Organization's International Guiding Principles for Biomedical Research Involving Animals were followed during experiments on animals.
Oocytes were prepared from mature female frogs by following the standard procedure described elsewhere  [29]. Stage V-VI oocytes were defolliculated with 2 mg/mL collagenase Type I (Life Technologies, USA) at room temperature (21-24˚C) for 2 h in ND96 solution composed of (in mM) 96 NaCl, 2 KCl, 1 CaCl 2 , 1 MgCl 2 and 5 HEPES at pH 7. 4. Oocytes were injected with 9. 2 ng of human nAChR α9 and α10 cRNA (in a ratio 1:1) and incubated at 18˚C in Barth's solution composed of (in mM) 88 NaCl, 1. 1 KCl, 2. 4 NaHCO 3 , 0. 3 Ca(NO 3 ) 2 , 0. 4 CaCl 2 , 0. 8 MgSO 4 and 15 HEPES-NaOH at pH 7. 6, supplemented with 40 μg/mL gentamicin and 100 μg/mL ampicillin for 4 days before electrophysiological recordings. Two-electrode voltage clamp recordings at a holding potential of -60 mV were made using turbo TEC-03X amplifier (Npi electronic, Germany) and WinWCP recording software (University of Strathclyde, UK).
0, containing 1 mg/ml of the bovine serum albumin (binding buffer). Then [ 125 I]α-Bgt was added to the reaction mixtures to a final concentration of 0. 2 nM. Simultaneously 15 μL Ni-NTA-agarose (QIAGEN) pre-washed in reaction buffer was added. After 6 min, the reaction was stopped by a rapid filtration on GF/C filters (Whatman) pre-soaked in 0. 25% polyethylenimine and the unbound radioactivity was removed from the filters by washes (3×4 ml) with the 20 mM Tris-HCl buffer. Nonspecific binding was determined by preliminary incubation of the ECD with 10 μM α-cobratoxin. The bound radioactivity was determined using Wizard 1470 Automatic Gamma Counter (Perkin Elmer). The data were analyzed using ORIGIN 7. 5 as a one-site dose-response curve. Surface plasmon resonance (SPR) experiments. SPR experiments were performed at 20˚C, using a Biacore 1 2000 system (GE Healthcare, Biacore AB).
The predictable quantum efficient detector (PQED) consists of two custom-made induced junction photodiodes that are mounted in a wedged trap configuration for the reduction of reflectance losses. Until now, all manufactured PQED photodiodes have been based on a structure where a SiO 2 layer is thermally grown on top of p-type silicon substrate. In this paper, we present the design, manufacturing, modelling and characterization of a new type of PQED, where the photodiodes have an Al 2 O 3 layer on top of n-type silicon substrate. Atomic layer deposition is used to deposit the layer to the desired thickness. Two sets of photodiodes with varying oxide thicknesses and substrate doping concentrations were fabricated. In order to predict recombination losses of charge carriers, a 3D model of the photodiode was built into Cogenda Genius semiconductor simulation software.
The obtained values were used to calculate absorption and reflectance losses using the transfer-matrix method (TMM). Reflectance losses were also measured from the backreflected beam of the PQED. In addition, detectors were characterized for temperature dependence of dark current, spatial uniformity of responsivity and photocurrent ratio, linearity, and absolute responsivity. In order to estimate recombination losses, a 3D simulation model of the photodiode structure was built into the semiconductor simulation software Cogenda Genius TCAD v. 1. 8. 0 [53]. With the exception of surface recombination velocity for electrons and holes, S 0 , and fixed charge of the Al 2 O 3 layer, the modelling parameters that cannot be arbitrarily selected in the manufacturing process were obtained from the wafer manufacturer or directly measured.
This suggests that the spatial variation of photocurrent ratio or reflectance could possibly be used to estimate the uniformity in the thickness of the oxide layer. Future work could include further investigation of these possibilities similarly as was done in  [3, 38]  for the p-type PQED. In order to predict recombination losses, a 3D simulation model of the photodiode structure was built into Cogenda Genius semiconductor simulation software. The input parameters in the simulation are either obtained from wafer manufacturer, selected in the manufacturing processing, or they can be directly measured. A novel method to extract the values for the fixed charge density and the surface recombination velocity of electrons and holes was developed, where the relative change of photocurrent as a function of bias voltage is measured, and the simulated bias voltage dependence of photocurrent is then fitted to the experimental data.
Acknowledgments The authors are grateful to  WMM Kessels  for discussions. The research leading to these results has received funding from the  European Metrology Research Programme (EMRP)  project  SIB57  ' New Primary Standards and Traceability for Radiometry '. The EMRP is jointly funded by the EMRP participating countries within EURAMET and the  European Union. Financial support from the  Academy of Finland  through the  Finnish Centre of Excellence in Atomic Layer Deposition  is also acknowledged.
In total, nine sites were surveyed during 1-6 nights each. Bats were mistnetted at their hunting and drinking places. In most cases, mistnetting was conducted until midnight (until 24. 00-01. 00), after which bat activity significantly decreased. Acoustic surveys were done using Pettersson D240 ultrasound time expansion detector and real time system Batlogger M. Sonogram analysis was conducted with BatSound and BatExplorer software. Criteria for computer-assisted identification of bat species were taken from M. Barataud's handbook  (Barataud, 2015). Mistnetted bats were weighted, and the following parameters were recorded: forearm length, length of the 3 rd and 5 th figure, sex, age, reproductive status of females. Measured bats were released near the catching sites. Mistnetted N. lasiopterus were fitted with LB-2X Transmitters for Bats (Holohil Systems Ltd.
Results and discussion During June and July of 2015-2016, we caught 297 bats at Stary Zhaden belonging to 12 species (tab. 1, 2). As it is shown in Table  2 , females predominated among all adult bats in the sample. No adult males of seven species were caught. The highest percentage of adult males was recorded for N. noctula (34 %), M. nattereri (33 %), and V. murinus (22 %). The sex ratio among subadult bats was nearly 1:1, which is common for European bats  (Strelkov, 1999). Myotis nattereri. Three bats (two lactating females and one male) were mistnetted at two sites. Acoustic survey confirmed the presence of the species at one more site. M. nattereri is not an abundant species in the zakaznik. It is recorded in forests and at small forest waterbodies. Our data for the first time confirm the breeding of Natterer's bat in the Pripyat Polesia region.
One adult male of Brandt's bat was caught in July 2010 in Pietrykaŭ district, Homiel region  (Shpak, 2010). These records suggest that the species regularly occurs in the Pripyat Polesia region. Our records of lactating females is the first proof of breeding of Brant's bat not only in the region, but also in the entire Belarus. Myotis daubentonii. One subadult bat was mistnetted at a seasonal paddle in a forest near Scviha floodplain. Our data show that Daubenton's bat clearly avoids mire landscapes, probably due to absence of large stable water bodies. Plecotus auritus. Twenty bats were mistnetted at four localities, including 19 lactating females. Acoustic signals were recorded at two more localities. The species is widespread in the zakaznik. Barbastella barbastellus. Thirteen bats were mistnetted at four localities, their presence also confirmed at 3 more localities by acoustic signals.
It is a common species in Stary Zhaden occurring at small forest islands in fen mires. Barbastelle bats were mistnetted only under the forest canopy. At one locality (forest compartment line in mixed pine-broadleaved forest 2 km away from the nearest waterbody), the barbastelle was the only mistnetted species. All barbastelles were adult lactating females. Our data for the first time confirm the breeding of the species in the Pripyat Polesia region. The nearest records of the barbastelle bat are known from Pripyatsky National Park  (Kusnezh et al. , 2012) , Rivne Nature Reserve, Ukraine  (Kusnezh, Dombrovski, 2013) , and from the Ukrainian part of the Chernobyl Exclusion Zone  (Gashchak et al. , 2013). In all above-mentioned cases, single specimens were recorded and their status was not identified.
Acknowledgments The work was implemented in frames of two projects:  Rufford Small Grant Project  " Study and Conservation of rare and endangered forest-dwelling species in natural forest-mire complexes of Southern Belarus " (2015) and  EUROBATS  project "Nyctalus lasiopterus in the far north?Population size and habitat use of a maternity colony in the Pripyat floodplains in the south of Belarus" (2016). Logistic support and additional tracking equipment was provided by  Frankfurt Zoological Society (Germany).