dataesr/scientific-paragraphs-categorization huggingface dataset:
Ethics statements The study was conducted in the Belinga mountains (northeast Gabon), where Ebola outbreaks occurred in  1994-1996 and 2001-2002. All the capture events, animal handling, euthanasia and transfer of samples across country borders were Gabon. There are no patents, products in development, or marketed products to declare. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials, as detailed in the online guide for authors. performed in accordance with the guidelines of the American Society of Mammalogists (http://www. mammalsociety. org/committees/animal-care-anduse) [15] : bats were captured following recommendations by Kunz and Parsons  [16]  and identified by trained field biologist. Captured bats were removed carefully from nets as soon as possible to minimize injury, drowning, strangulation, or stress.
Blast and phylogenetic analysis The viral sequences obtained were first compared to those available in the public database using the algorithm "Blastn" from BLAST program  [20]  and then aligned with homologous sequences of Paramyxoviridae reference strains from GenBank, using the MEGA program version 5  [21]. Bayesian inference of phylogeny was done using MrBayes V. 3. 2 software and the GTR+G+I nucleotide substitution model  [22]  for two million generations with a burn-in of 25%.
Identification and molecular characterization One of three hnRT-PCR, Respiro-, Morbilli-and Henipaviruses PCR (RMH-PCR) assays yielded an amplicon of 559 base pairs (bp) from diseased bat, in collaborative work with the Bonn Institute of Virology Bonn (Germany). The PCR product was sequenced with dye terminator chemistry (Applied Biosystems). No other virus was detected in the diseased bat. Blast and phylogenetic analysis confirmed that the sequence from diseased bat, designated BatPV GB09 478 (Genbank accession number HQ660155), belonged to the Paramyxoviridae family. It showed 65% and 66% nucleotide identity, respectively, with JPV and BeiPV, and had pairwise nucleotide identities of 36-42% with the Henipavirus group and 37-40% with the Morbillivirus group. Phylogenetic analysis indicated that this bat PV, that we named Belinga bat virus (BelPV), clustered with unclassified paramyxoviruses and was located between the genera Morbillivirus and Henipavirus (Fig.
Acknowledgments We thank all the persons involved in sample collections, and especially  Andre De  ´licat,  Peggy Motsch , DieudonneNkogue,  Tabea Binger ,  Peter Vallo , and  Nil Rahola. We acknowledge  Hei ¨di Lanc  ¸on for improving the English. CIRMF is supported by the  Government of Gabon, Total-Fina-Elf Gabon, and Ministere de la Cooperation Francaise.
METHODS FOR PRESENT REVIEW A review of the literature available until May 2014 was carried out by searching the PubMed database with reference combination of the following keywords: '(Toxoplasma gondii OR toxoplasmosis) AND Portugal'. Our initial search indicated 52 references, out of which 29 references on T. gondii infection or toxoplasmosis in humans and/or animals from Portugal were selected. Databases of universities, research institutes and scientific societies and the reference lists of all the retrieved articles were also searched for published reports deemed as relevant to this review. After this, three additional papers were retrieved from non-indexed but peer-reviewed Portuguese journals. A set of 32 papers is reviewed in the main document. Four abstracts from the proceedings of national conferences, another abstract from the proceedings of an international conference, four master's dissertations and two doctoral theses also accounted for the scientific literature used to prepare the present review.
The stray cats were captured from different areas of Lisbon by the municipal services. It is noteworthy that a very high percentage of cats from Portugal had high titres (Table  2 ). In the study by  Waap et al. ( 2012) , 68 (36•3%) out of 187 seropositive cats had MAT titres of 18 000 or higher reaching as much as 162 000. One of us has never encountered such high MAT titres from cats from other parts of the world (J. P. Dubey, personal observations). This result may be due to the T. gondii strains or very high environmental contamination leading to repeated infections in cats. Risk factors such as age, gender, diet and lifestyle were assessed in these four surveys. Gender did not affect the seropositivity. Age was one of the main risk factors; seroprevalence increased with age. Age-related data were: 14•6% seropositivity in 2-11 months old vs 51•7% in 3-to 6-year-old cats  (Lopes et al.
Food animals as sources of infection Poultry, pork, beef and mutton are the most important source of meat consumed by humans in Portugal. Little is known of the relative risk of T. gondii infection with respect to meat sold in grocery stores. Although T. gondii antibodies were found in 7•5% (Table  1 ) and 29•2% of cattle (Supplement 1, Table  S1  in Online version only), viable T. gondii has rarely been isolated from beef in other countries  (Dubey, 2010). Thus, the role of beef in the epidemiology of T. gondii is uncertain. In addition to data in Table  4 , viable T. gondii was isolated from a bovine foetus  (Canada et al. 2002). During the course of an investigation on Neospora caninum (a protozoan similar to T. gondii) bovine fetal tissues were bioassayed in mice. For this, homogenates of fetal brains were inoculated intraperitoneally into mice and protozoa harvested from the peritoneal cavity of infected mice were seeded on to cell cultures.
Target genes included genes coding for enzymes of the prostaglandins (PGs; PTGS2, PGES, and PGFS) and progesterone (P 4 ; 3HSD) synthesis pathways, genes associated with apoptosis (BAX and BCL2), and quality markers (IGFR2 and OCT4), using GAPDH transcription as an internal control. This housekeeping gene was chosen using the NormFinder software, comparing three candidate genes: GAPDH, -actin, and H2A. 1  [19]. Primers were chosen using an online software package (http://bioinfo. ut. ee/primer3/) (Table  1 ) and were validated following the use of different concentrations and the observation that each pair generated a single amplicon with the predicted molecular size. The qRT-PCR was performed with an ABI Prism 7900 (Applied Biosystems, Life 12 Technologies, USA) sequence detection system using Maxima SYBR Green/ROX qPCR 13 Master Mix (number K0222, Fermentas, Thermo Scientific, USA).
The PCR reactions were performed in 96-well plates. Each PCR reaction well (20 L) contained 2 L of RT product, 5 pmol/L of forward and reverse primers, and 10 L SYBR Green PCR master mix. The qRT-PCR was performed under the following conditions: 95 ∘ C for 10 min, followed by 40 cycles at 94 ∘ C for 15 sec and 60 ∘ C for 60 sec. Melting curves were acquired (15 s at 95 ∘ C, 30 s at 60 ∘ C, and 15 s at 95 ∘ C) to ensure that a single product was amplified in the reaction. In order to exclude the possibility of genomic DNA contamination in RNA samples, the reactions were also run either on blank-only buffer samples or in absence of the reverse transcriptase enzyme. The specificity of the PCR products for all examined genes was confirmed by gel electrophoresis and by sequencing. Data regarding relative mRNA quantification was analyzed with the Real-Time PCR Miner algorithm  [20].
Acknowledgments This research was funded by Grant  PTDC/CVT/65690/2006  from  Foundation for Science and Technology (FCT). This research was supported by  Grants-in-Aid for Scientific Research  from the  Polish National Science Centre  ( 2012/05/E/NZ9/03480 ). Dorota Boruszewska  and  Ilona Kowalczyk-Zieba  were supported by the  European Union  within the  European Social Fund  ( DrINNO3 ).
A total of 188 chronic lymphocytic leukemia patients with poor prognostic features (unmutated IGHV, n=137; IGHV3-21 subset #2, n=51) were sequenced on the HiSeq 2000 and data were analyzed using well-established bioinformatics tools. Using a conservative cutoff of 10% for the mutant allele, we found that 114/180 (63%) patients carried at least one mutation, with mutations in ATM, BIRC3, NOTCH1, SF3B1 and TP53 accounting for 149/177 (84%) of all mutations. We selected 155 mutations for Sanger validation (variant allele frequency, 10-99%) and 93% (144/155) of mutations were confirmed; notably, all 11 discordant variants had a variant allele frequency between 11-27%, hence at the detection limit of conventional Sanger sequencing. Technical precision was assessed by repeating the entire HaloPlex procedure for 63 patients; concordance was found for 77/82 (94%) mutations.
Data analysis and variant calling Illumina sequencing adapters were removed using Cutadapt (v. 0. 9. 5) and trimmed reads were aligned to the hg19 human reference genome (February 2009 assembly) using MosaikAligner version 2. 1. 33 (http://arxiv. org/abs/1309. 1149)  27 with the following parameter settings: -hs 15, -ms 7, -mhp 100, -act 35, -minp 0. 95 and -mmp 0. 05, allowing for a maximum of 5% mismatches per read. Tumor variants were identified using VarScan 2 in mpileup2cns mode with detection thresholds of 20x coverage, variant allele frequency 0. 1, a minimum of 10 reads supporting the variant, and an average base quality of 15 at the variant position. 28 n addition to the 188 CLL cases, 18 samples from normal tissue (buccal swabs or sorted T cells) were also included in the sequencing run and bioinformatically processed.
Variants detected within the normal tissues facilitated the detection of recurrent variants which likely arose during library preparation or as a sequencing error and were subsequently removed from the tumor call files. Variants had to meet the following conditions to be included in downstream analysis: (i) be located within an exonic or splicing region; (ii) be non-synonymous; (iii) not be listed in the European 1,000 genomes variant database; (iv) not be listed in dbSNP137 unless also listed in the Catalogue of Somatic Mutations in Cancer (COSMIC)65 database; and (v) have a variant allele frequency >0. 1 (Figure  1A ).
Assessing the reproducibility of targeted next-generation sequencing To estimate technical precision and reproducibility, we repeated the procedure with 63 CLL cases that had been included in the initial sequencing run and were found to carry at least one mutation. A new gene panel including six of the prognostic genes, i. e. BIRC3, NOTCH1, POT1, SF3B1, TP53 and XPO1, was designed and the entire experimental setup was independently replicated, i. e. new libraries were prepared (using the same genomic DNA) and resequenced on the HiSeq2000. Data analysis and variant calling were performed as detailed above and runs were compared.
6%) (Figure  2A ). A total of 177 mutations were detected, comprising 97 unique mutations and 11 recurrent mutations or recurrently mutated codons. Recurrent mutations were observed in five of the nine genes analyzed, i. e. SF3B1, NOTCH1, TP53, POT1 and XPO1, and accounted for 80/177 (45%) of all mutations (Online Supplementary Table  S3 ). We detected single nucleotide variants and deletions or insertions, with missense single nucleotide variants being the most prevalent (113/177; 64%) (Figure  2B ). haematologica | 2015; 100(3) Figure  1. Filtering procedure for data analysis and variant annotation. Following library preparation and sequencing, the next steps include quality assessment, read alignment against a reference genome and variant calling. Filtering criteria were imposed to minimize false-positive rates and included the removal of variants that were supported by less than ten reads, removing variants located in intergenic, intronic or untranslated regions and recurrent library preparation/sequencing errors, as well as removing synonymous variants and those that are present in dbSNP137 and do not have a COSMIC ID.
In contrast, we retained 'single nucleotide polymorphisms' (SNPs) with a COSMIC ID on the grounds that they may in fact represent true somatic mutations of pathogenic relevance. This strategy of retaining single nucleotide polymorphisms that have been assigned a COSMIC ID led to the identification of 14 cases with potentially pathogenic variants within TP53 (n=11), ATM (n=2) and XPO1 (n=1) (Online Supplementary Table  S3 ). Ten of these cases were subsequently sequenced by the Sanger method and all were validated. These results demonstrate that for certain, well-characterized genes such as TP53, somatic mutations may be inadvertently removed by filtering out all mutations found in single nucleotide polymorphism databases. Figure  1A  outlines the filtering procedure implemented in this study.
A B repeating the experiment using a new panel design, which included six of the aforementioned prognostic genes i. e. BIRC3, NOTCH1, POT1, SF3B1, TP53 and XPO1. KLHL6 and MYD88 were excluded from the second panel since, given the nature of our cohort, very few cases were found to harbor mutations in these genes using the initial HaloPlex gene panel (one and two cases, respectively). Hence, for validation purposes the addition of these genes would not have added much value. Regarding ATM, the very size of the gene limited its appeal for the validation procedure. The new panel was then tested on 63 CLL patients who were found to carry at least one mutation in the initial sequencing run. By comparing data acquired from each sequencing run sample-by-sample, we found that 77/82 (94%) variants demonstrated concordance and could, thus, be considered as true positives (Online Supplementary Table  S4 ).
g. PolyPhen and SIFT, however, caveats exist regarding the use of predictive software and while such software may be valuable as a screening tool for identifying alleles of high pathogenic potential, none has been clinically validated. 37 However, this is not specifically a new challenge and as larger cohorts are studied and combined with functional analyses, the ability to discriminate pathogenic variants from incidental mutations i. e. those unrelated to the disease, should improve. Of equal importance is the issue of how to handle big biodata in a diagnostically/clinically meaningful manner; our study also provides evidence that it is possible to devise a data analysis pipeline based on published algorithms that achieves haematologica | 2015; 100(3) Figure  3. Localization and frequencies of mutations within ATM, NOTCH1, SF3B1 and TP53.
Union, the  Swedish Cancer Society , the  Swedish Research Council , the  Lion's Cancer Research Foundation ,  Uppsala , and the  European Community 's  7th Framework Program  ( FP7/2007-2013)  under grant agreement n. 259796 (DiaTools),  Associazione Italiana per la Ricerca sul Cancro (AIRC)  ( Special Program Molecular Clinical Oncology 5 per mille # 9965 ), Milano, Italy;  Ricerca Finalizzata 2010  ( RF-2010-2318823 ),  Ministero della Salute, Roma, Italy ; KRIPIS action, funded by the  General Secretariat for Research and Technology of Greece  and the  European Regional Development Fund  of the  EU  under the O. P. Competitiveness and Entrepreneurship, NSRF 2007-2013, by project  MSMT-CR VaVPI CZ. 1. 05/1. 1. 00/02. 0068 ( CEITEC ), research grants  IGA-MZ-CR   NT13493-4/2012  and  FNB Sup 14/13  and 7 th FP  Health  project  NGS-PTL/2012-2015/n.
4 ). All inactive compounds and compounds active above 15 μM received docking scores below 29, except compound 2. Active compounds, usually hydroxamates, received favorable docking scores above 32, except HHA and compound 6 in case of hHDAC8. All hydroxamates show coordination to Zn 2+ with the hydroxamic acid group and fit nicely into the pocket of both smHDAC8 and hHDAC8. However, we also observed that the scoring functions (including ASP score) have problems for correctly ranking the non-hydroxamates. Beside the problem of correctly scoring different zinc-binding groups, we suppose that the known protein flexibility of HDACs might be responsible for the incorrect ranking of some compounds (2, 6 and HHA). For example, in case of compound 6, the conformational change of hHDAC8 upon binding of this ligand is observed in its X-ray structure (PDB ID: 3SFH)  [30].
Experimental Procedures Chemistry and inhibitors The inhibitors PCI-34051 and SAHA were purchased from Selleck Chemicals; SAA, at Biozol; and HHA, at Chemical Book. Synthetic procedures and spectral characterization data are presented in detail in the supplemental material. All chemicals were purchased from Sigma, Aldrich or Fluka and used without further purification. Starting materials, reagents and analytical-grade solvents were obtained from commercial sources. T 3 P 50% weight in THF and 50% weight in DMF were kindly donated by Archimica (Frankfurt, Germany). Chromatographic separations were performed on silica gel (15-40 mesh; Merck) using flash methodology. Reaction progress was monitored by analytical thin-layer chromatography on pre-coated silica gel (Kieselgel 60 F254) plates, and spots were detected by UV light (λ = 254 nm).
In all cases, spectroscopic data are in agreement with known compounds and assigned structures. HPLC purity determinations were performed on a JASCO HPLC system under isocratic conditions, using a PhenomenexSynergi Hydro RP-C18 column (250 mm × 4. 6 mm, 4 μm particle size). Elution was performed using 0. 05% of TFA in H 2 O/ACN 60/40 (v/v), at room temperature. The purity of all tested compounds was ≥ 98%, as measured by HPLC. Injection volumes were 2 μL, flow rate was 0. 5 mL/min and detection was performed with UV (λ = 254 nm).
Crystallization and X-ray data collection Co-crystallization of smHDAC8 together with 1a was performed using hanging-drop vapor diffusion technique. The smHDAC8/1a complex was formed by incubating the smHDAC8 protein (2 mg/mL) with 1a (5 mM resuspended in dimethylformamide) at 4 °C for 1 h. Diffraction-quality crystals were obtained at 17 °C after 3-4 days by mixing equal volumes of the smHDAC8/1a complexes with reservoir solution composed of 21% polyethylene glycol 3350 (Fluka) and 0. 2 M Na + /K + L-tartrate. Crystals used for X-ray data collection were briefly transferred in reservoir solution supplemented with 22% glycerol and flash-frozen in liquid nitrogen. Crystallographic data were collected at 100 K on in-house Rigaku MicroMax-007HF generator fitted with Osmic VariMax HF confocal optics and Saturn 944 CCD detector.
Computational methods The recently solved crystal structures of S. mansoni HDAC8 with SAHA (PDB ID: 4BZ6  [17] ) was used for the docking studies. For hHDAC8, several X-ray structures have been reported in complex with various inhibitors  [46]. We took the crystal structure 2V5X. pdb [47]  for the docking studies since it gave the best results in cross-docking of a large library of published and in-house HDAC8 inhibitors (data not shown). Structures were prepared with Schrödinger's Protein Preparation Wizard  [48]. Hydrogen atoms were added and the hydrogen bond network was optimized subsequently. The protonation states were predicted using the PROPKA tool within the Schrödinger program at pH 7. 0. Two conserved water molecules located near Zn 2+ were considered during the protein preparation process.
Four models with different hydration of the binding pocket were generated for each protein. They were subjected to restrained energy minimization using the force field OPLS2005 (RMSD of the atom displacement for terminating the minimization 0. 3 Å). Ligands were prepared in MOE [49] (version 2012. 10; Chemical Computing Group, Montreal, Canada). Conformational search was performed using the Low Mode MD sampling with a minimum RMSD between the conformations of 0. 5 Å to obtain realistic starting conformations for the flexible ligands. Molecular docking was carried out on a Linux cluster using Glide (Schrödinger Inc, New York, USA)  [48]  in the standard precision mode. In addition, the docking program Gold 5. 2  [50]  was used. Finally, the docking complexes were rescored using several scoring functions (GlideSP, GoldScore, ChemScore, ASP, Chem-PLP).
Acknowledgments This work and the authors of this manuscript received funding from the  European Union 's  Seventh Framework Programme  for research, technological development and demonstration under grant agreements nos. 241865 (SEtTReND) and 602080 (A-ParaDDisE). Research on dual HDAC/Sirt inhibitors in the Jung laboratory is funded by the  Deutsche Forschungsgemeinschaft  ( Ju 295/10-2  within  CRU201 ). The work of C. R. , M. M. , J. C. , J. M. W. , E. L. , R. J. P. and J. L. was supported by institutional funds from the  Centre National de la Recherche Scientifique , the  Institut National de la Santé et de la Recherche Médicale , the  Université de Strasbourg  and the  Université de Lille 2 , the  French Infrastructure for Integrated Structural Biology  ( ANR-10-INSB-05-01 ) and by  Instruct (European Strategy Forum on Research Infrastructures ).
,Foster City,CA) interfaced to a personal computer using the Digidata 1200 interface and the pClamp software (ver 7. 0; Axon Inst. ). Prior to recording, oocytes were incubated in phorbol myristate acetate (PMA) at 100 nM in the pH 8 solution for 20-30 min. Currents were filtered at 100 Hz and digitized at 0. 5 kHz before storage and further analysis. During recording, oocytes were continuously superfused with the pH 8 solution. On TMEM176B-expressing oocytes, induction of an inward current was obtained by switching to a pH 5 solution (in mM NaCl, 100; KCl, 3; MgCl 2 , 2; MES, 15; pH 5).
To understand the mechanism by which ATDC + anti-CD3 therapy prolongs allograft survival we carried out experiments aiming at tracking injected ATDCs in vivo. We analyzed the graft, the draining-lymph node and the spleen 7 and 15 days after transplantation. ATDCs were found in skin graft both at days 7 and 15 posttransplantation whereas they could be detected in the draining lymph node only at day 15 (Figure  S1 ). ATDCs were not found in the spleen (data not shown). These observations strongly suggest that injected ATDCs uptake donor antigens in the graft and subsequently migrate to the draining lymph node.
We expressed TMEM176B in Xenopus oocytes and recorded the electric activity under whole-cell patch clamp. Because TMEM176B is localized in intracellular compartments, surface expression was achieved by a 20-30 min pretreatment with PMA (data not shown) as described for other ion channels  (32). This treatment resulted in the development of an inward current at a holding potential of -40 mV that was activated by acidification of the extracellular solution to pH 5 (Figure  4B ). Further analysis revealed that TMEM176B forms a nonselective monovalent cation channel because the current was abolished by substitution of extracellular Na + with NMDG (N-methyl-D-glucamine) but not K + and was not affected by substitution of intracellular Cl - with gluconate. This conductance was not blocked by Cd 2+ (0.
Acknowledgments This work was funded by  Fondation Progreffe ,  Vaincre la Mucoviscidose  and IMBIO. MH was supported by a  Junior Basic Science grant  from  ESOT. We are grateful to  Philippe Hulin  from the  IFR26 MicroPIcell imagery core facility Nantes, France , for excellent assistance with confocal microscopy, and to  Claire Usal  and  Emmanuel Merieau  for their great help in mouse experimentation. Tmem176b -/-(KO) mice were generated by " La Clinique de la souris," Strasbourg, France. Jeffrey Bluestone  and  Giovanna Lombardi  critically read the manuscript.
Methods Forty-five subjects from the general population of Schenefeld/ Hamburg and neighbouring communities were recruited into this study, with the allocation of 15 subjects per study group as follows: subjects with erythematotelangiectatic rosacea, with flushing and persistent central facial erythema and optional telangiectasia (mean age 54. 89 AE 10. 49 years; n = 15) and subjects with papulopustular rosacea defined as moderate to severe with persistent central facial erythema and transient papules and/or pustules (mean age 50. 86 AE 11. 2 years; n = 15), from the Galderma rosacea database; and 15 healthy subjects with no active skin disease (mean age 52. 38 AE 13. 68 years). Subjects with rosacea received no treatment and were asked to stop any treatment with benzoyl benzoate, lindane, pyrethrin, malathion, allethrin, crotamiton, and metronidazole at least 7 days before sampling.