dataesr/scientific-paragraphs-categorization huggingface dataset:
Transcriptome analysis (RNAseq) Total RNA was isolated as detailed in Appendix Supplementary Methods, polyA RNA was enriched (NEBNext Poly(A) mRNA Magnetic Isolation Module #E7490), and libraries were prepared for sequencing (NEBNext Ultra II RNA library prep Set for Illumina #E7770L) and barcoded (NEBNext Multiplex Oligo for Illumina #E7335L, #E7500L, #E7710L, #E7730L), all according to the manufacturer's instructions. 75-bp single-end reads were obtained by sequencing on an Illumina NextSeq 500 instrument using a NextSeq 500/550 High Output Kit v2 (75 cycles, Illumina). Sequencing reads were aligned to the yeast transcriptome (ENSEMBL R64-1-1, annotation version 94) using STAR (v. 2. 6. 0a). Read counts per gene were provided by STAR, and TPM expression values were calculated with RSEM (v.
Acknowledgements We thank  S. Brill ,  A. Buchberger , and  M. Hochstrasser  for materials;  Sven Schkölziger ,  Alexander Strasser ,  Katrin Strasser ,  Jochen Rech ,  Florian Paasch , and  Ludwig Rieger  for technical assistance;  Kerstin Maier  and  Assa Yeroslaviz  for help with microarray analysis;  Marja Driessen  for help with RNA sequencing;  Julian Stingele  and  Florian Wilfling  for providing data;  Johannes Heipke  for plasmid construction;  Julian Stingele ,  Ivan Psakhye ,  Neysan Donnelly ,  Florian Paasch , and members of the  Jentsch and Pfander laboratories  for fruitful discussions and critical reading of the manuscript. Research in the B. P. laboratory is supported by  Max Planck Society , the collaborative research cluster ( SFB1064 ), and project grants from the  German Research Council (DFG).
Data availability Yeast strains and plasmids are available on request. ChIP-chip, RNAseq, and microarray data are available from Gene Expression Omnibus (GEO, https://www. ncbi. nlm. nih. gov/geo/) entry GSE118818. Expanded View for this article is available online. B, and 4A and B, and D, Appendix Figs S1,. TS performed analysis of ChIPchip and RNAseq data. RP and BHH performed analysis of de novo motif searches. MH and BP wrote the manuscript, and all authors commented on the manuscript.
We sequenced an equal number of colonies originating from each stock. We found 39 colonies to correspond to Lactobacillus plantarum, a major constituent of our wild-type strain microbiota, and one to S. xylosus, which was originating from the infested stock. These data also suggest that the intestinal barrier is impaired in infested flies. In keeping with the results obtained with "naturally" infested flies, we found that the overall bacterial content of T. ratisbonensis-injected flies increased (Supplementary Fig. 1g ). Death was however not caused by the unhampered bacterial proliferation of the host microbiota, as axenically-grown flies succumbed earlier to the injection of spores (Supplementary Fig. 1h ). The enhanced death rate after injection of T. ratisbonensis of sterile flies may be related to their increased lipid stores (see below)  26, 27.
Taken together, our data indicate that PA is a critical metabolite for the proliferation of T. ratisbonensis in Drosophila. They do not however exclude the possibility that other metabolites may also be important for the parasite. Indeed, it is not clear at this stage how the parasite is able to scavenge host phospholipids coming from the different membranes of the host cell, for instance those of mitochondria or basal/lateral cytoplasmic membranes. How the parasite imports host PA present in the endoplasmic reticulum (ER), LDs, or mitochondria remains to be established and may involve a process akin to that used for transferring PA from the ER to the inner mitochondrial membrane  31  , although we did not find any predicted protein encoding homologs to known PA transporters in the microsporidiaDB database that yields access to 27 microsporidian genomes  32.
Parasite culture The microsporidia Tubulinosema ratisbonensis was propagated and harvested as described  24, 41. The Human lung fibroblasts (MRC-5) cells used for this purpose (a kind gift of Pr. Caspar Franzen  41  ) were grown in Dulbecco's modified eagle medium (DMEM+ GlutaMAX: Gibco), supplemented with 10% (v/v) fetal calf serum (FCS) and 1% (v/v) PenStrep (Invitrogen) in a tissue culture incubator under 5% CO 2 at 37°C. The cell culture was intermittently tested for the presence of mycoplasma. The MRC-5 cell line was not authenticated and does not appear in the databases of commonly misidentified cell lines maintained by ICLAC and NCBI Biosample. Fly strains Fly lines were raised on two different media at 25°C with 65% humidity. For 25 L of nutrient "poor" medium (standard medium), 1.
Samples of cDNA were diluted to 1/20 into milliQ water. Quantification was performed by qPCR using SYBR Green (BioRad) as described previously  24  , using the primer couples shown in Table  S2. Only experiments with qPCR efficiency over 90% were validated. Each qPCR analysis was performed with Drosophila ubiquitous gene RpL32 normalization. Of note, results were essentially similar when the normalization was performed per number of infected flies. Fluorescence quantification Fluorescence quantification was achieved using the ImageJ program  48. Channels were separated and analyzed by measuring the fluorescent signal intensity for each channel.
Acknowledgments We are grateful to  Miriam Yamba  and  Marie-Céline Lacombe  for expert technical assistance. We would like to thank  Drs. Frédéric Delbac ,  Alex Gould ,  Bruno Lemaitre , and  Pierre Léopold  for informative discussions and suggestions, and  Dr. Samuel Liégeois  for critical reading of the manuscript. Transgenic fly stocks were obtained from the  Vienna Drosophila Resource Center (VDRC , www. vdrc. at). Stocks obtained from the  Bloomington Drosophila Stock Center  ( NIH P40OD018537 ) were used in this study. This work has been funded by  CNRS, University of Strasbourg ,  Fondation pour la Recherche Médicale (Equipe FRM  to D. F. and  FDT20140930952  to A. F. ),  Agence Nationale de la Recherche  ( BEELOSS ,  ANR-11-EQPX-0022 ), and the  Institut d'Etude Avancée de l'Université de Strasbourg.
Data availability The datasets, including the 16S rRNA DNA sequences of bacteria retrieved in the hemolymph of control or infected flies, generated during and/or analyzed during the current study are available in the "Phosphatidic acid as a limiting host metabolite for the proliferation of the microsporidium Tubulinosema ratisbonensis in Drosophila flies " repository: https://figshare. com/s/c6ef12b7c46e81e58bb1.
The dimensions and boundary conditions are listed in Table  1. Note that dL = 0 represents no-leak case. Three-dimensional governing equations for steady state, incompressible flow in Cartesian coordinate are expressed as: 0 u v w x y z          (1) 2 u u u P u v w u x y z x                   2 v v v P u v w v x y z y                   (2) 2 w w w P u v w w x y z z                   CFD software ANSYS FLUENT (2013) was utilized to solve steady three dimensional (3D) Navier-Stokes equations to capture the flow phenomena. In the present study, the Reynolds number (Re) ranges over 1. 2 × 10 7 ~ 3. 2 × 10 7 which is much larger than critical value for the turbulent pipe flow. Therefore, the flow is turbulent and the k-ε turbulence model was adopted due to its applicability for fully developed flow with fast convergence.
Results Conventional immunohistochemistry reveals no differences between ADAD and eoSAD cases in total or non-fibrillar Aβ. We included a group of 14 patients with eoSAD, 10 patients with ADAD carrying a PSEN1 mutation and 9 healthy controls. Demographic, clinical and genetic data are shown in Supplementary Table  S1. Detailed neuropathological data of the cases is shown in Supplementary Table  S2. As expected, eoSAD cases had a later age of onset and death and higher frequency of the APOEε4 allele compared to ADAD cases. We employed conventional immunohistochemistry of consecutive sections to examine the differences in total and non-fibrillar Aβ immunoreactivity (using the NAB61 antibody) between ADAD, eoSAD and control cases. We found higher amyloid load in ADAD and eoSAD cases (p < 0. 001) compared to controls but without differences between the AD groups (Fig.
Finally, these settings provided a set of images of 2048 × 2048 with effective pixel dwell time of 5. 9 µs. Image processing and analysis. For the analysis of AT images, MATLAB software (The Math Works, Inc. , Natick, MA, USA) was used. Image stacks of each channel comprising all 70 nm consecutive sections were first registered using a rigid registration followed by an affine registration of a reference channel. Aligned sections were segmented using an automated mean local thresholding. Additionally, objects that were not in at least two consecutive sections or that were less than 3px were considered background and removed. After identification of three-dimensional structures, the density and size of individual entities were quantified. In order to perform the 3D visualization of the human amyloid plaque, the 2D images were stacked in a whole 3D reconstruction.
Acknowledgements The authors would like to thank all brain donors and their relatives for generous brain donation for research and the  Neurological Tissue Bank  of the  IDIBAPS-Hospital Clinic-Biobank  for data and sample procurement. This work was supported by  FISPI14/1561 ,  FISPI17/1896   Fondo Europeo de Desarrollo Regional (FEDER) ,  Unión Europea , " Una manera de hacer Europa ",  PERIS SLT002/16/00408-01  and  Marató TV3  to  Alberto Lleó  and  CIBERNED. Tara Spires-Jones  is supported by an  ERC  consolidator award and the  UK Dementia Research Institute  and gratefully acknowledges affiliations with  Edinburhg Neuroscience  and the  FENS-Kavli Network of Excellence. Pablo Loza-Alvarez  and  Jordi Andilla  acknowledge financial support from the  Spanish Ministry of Economy and Competitiveness  through the  "Severo Ochoa" program for Centres of Excellence in R&D  ( SEV-2015-0522 ), from  Fundació Privada Cellex, Fundación Mig-Puig , from  Generalitat de Catalunya  through the  CERCA program and form Laser lab europe  (Grant agreement No.
Metagenomic Sequence Analysis The fosmid DNA of the clone hits was extracted using the NucleoBond Xtra Midi kit from Macherey-Nagel (France). Fosmids were then sequenced using the Ion Torrent S5 System at the GeT-Biopuces Platform (Toulouse, France). Read assembly was performed using Masurca 2. The assembled contigs were cleaned from the pCC1FOS vector sequence using Crossmatch 3. ORF detection and functional annotation was performed using the RAST annotation server 4   (Aziz et al. , 2008). CAZyme encoding genes were identified by BLAST analysis of the predicted ORFs against the full-length sequences of glycoside hydrolases (GH), polysaccharide lyases (PL), carbohydrate esterases (CE), carbohydrate-binding modules (CBM), and glycosyltransferases (GT) included in the CAZy database 5  , using a cut-off E-value of 7•10-6.
Sequences that aligned over their entire length with a sequence in the database with >50% identity were directly assigned to the same family as the subject sequence. The remaining ones were subjected in parallel to (i) a BLAST search against a library built with partial sequences corresponding to individual GH, PL, CE, CBM, and GT modules and (ii) a HMMER2 search using Hidden Markov models (HMM2) built for each CAZy module family, allowing a view of CAZyme modularity  (Lombard et al. , 2014). The contigs' entire nucleotidic sequences were blasted against the non-redundant database of the NCBI and against each other to examine their divergence from the reference strain genomes, and the redundancy between clone hits. Taxonomic assignation of the metagenomic sequences was determined using the PhyloPythias program 6  (model type: Generic 2013-800 Genera).
Prevalence Analyses The homolog sequences of the translated ORFs were searched for in the translated catalog of 9. 9 million reference genes using BLASTP (E-value = 0, identity ≥ 90%). This catalog consisted of the gut metagenomic sequences of 1,267 subjects from three continents (United States, China and Europe): 139 US HMP samples, 760 European fecal samples from the MetaHIT project and 368 Chinese fecal samples  (Li et al. , 2014). The microbial gene richness in the human gut was assessed by recovering the occurrence frequency data of homologous sequences of the catalog from the 9. 9 million gene frequency table in the 1,267 subjects 8. The frequency values have no unit. They are normalized to account for sampling and sequencing biases generated by the diverse origins of the cohorts constituting the catalog.
Locus D Assigned to Bacteroides uniformis The last Bacteroides contig, namely contig 13P9, which includes sequence 33D18 (Figure  2D ), shared 99% identity with a genomic locus from B. uniformis An67, a strain which is not included in the PUL database. This metagenomic PUL contains a GH2-, a GH3-, and a CE7-encoding gene. The GH2 family contains β-Dmannosidases, explaining activity on X-β-D-Man (Table  2  and Figure 1 ). Due to its position at the end of the contig, the GH3encoding gene is truncated and probably not functional here, but some of the characterized proteins of the family are known to act on β-N-acetylhexosamines, of which the acetyl groups could be hydrolysed by the CE7 enzyme. This metagenomic locus is probably involved in the catabolism of human N-glycans by uncultured bacteria, and/or B.
, 2012). This is consistent with the CAZy gene content of the F. prausnitzii genomes. We indeed found several F. prausnitzii sequences in the CAZy database that had been assigned to families as GH2-and GH3-containing members active on β-D-N-acetylglucosamine, β-D-N-acetylhexosamine and β-Dglucosamine linkages, although none of these F. prausnitzii enzymes has been biochemically characterized to date. In any case, F. prausnitzii is far from being as well equipped with glycan-degrading enzymes as the Bacteroides species described above. Nevertheless, our results demonstrate that this species has the potential to interact with mucus. This could explain the above mentioned modulation of the effect of B. thetaiotaomicron on the intestinal mucus barrier, resulting in a modification in goblet cell differentiation and mucin glycosylation  (Wrzosek et al.
AR expression in the Leydig cells inhibits development/ differentiation of cells with adrenal characteristics in the testis Data above show that preventing differentiation of cells with adrenal characteristics in the testis depends on AR expression. To determine the cell types in which AR expression is essential for this effect we examined testicular adrenal transcript levels in different cell-specific models of AR deletion. Data in Fig. 5a  shows that the Sertoli cell AR are unlikely to be the major factor responsible for the effects seen as there was no change in Mc2r in the SCARKO mouse, although there was an increase in Cyp11b1 transcript levels in the same animals. In contrast, there were more marked changes in both Mc2r and Cyp11b1 in mouse models lacking AR in the PTM cells (Fig. 5a ).
Nevertheless, data from AR knockdown in MLTC-1 cells suggests that there may be a requirement for continued AR-mediated suppression of plasticity, since a reduction of AR in MLTC-1 cells is able to switch 'mature' Leydig cells towards an adrenal cell fate. Recent work has suggested that Hsd3b1 in the mouse testis is only expressed in fetal Leydig cells  [56]  which would suggest that the adult hpg mouse testis contains a (See figure on previous page. ) Fig. 5  Control of adrenal cell development/differentiation in the testis depends largely on AR expressed in the Leydig cells and peritubular myoid cells. a Testicular expression of Mc2r and Cyp11b1 in mice lacking ARs in different cell types. Transcript levels are measured relative to the external standard (Luc). Data were analysed by single-factor ANOVA or t-test, apart from Cyp11b1 levels in SCARKO, PTM.
Stereology For stereological analysis, testes were embedded in Technovit 7100 resin, cut into sections (20 μm), and stained with Harris' hematoxylin. The total testis volume was estimated using the Cavalieri principle  [63]. The optical disector technique  [64]  was used to count the number of Leydig cells in each testis. Leydig cells were recognised by their position, round nucleus and relatively abundant cytoplasm  [39, 65]. The numerical density of each cell type was estimated using an Olympus BX50 microscope fitted with a motorized stage (Prior Scientific Instruments, Cambridge, UK) and Stereologer software (Systems Planning Analysis, Alexandria, VA, USA). Stereological data for untreated hpg, hpg. SCARKO and hpg. ARKO animals in this study includes data from a previous study  [62]  plus additional animals.
Measurement of mRNA levels For data shown in Figs. 1, 2, 3 and 4, testis RNA was extracted using TRIzol (Life Technologies, Paisley, UK) and the RNA was reverse transcribed using random hexamers and Moloney murine leukemia virus reverse transcriptase (Superscript III, Life Technologies, Paisley, UK) as described previously  [66]. To allow specific mRNA levels to be expressed per testis and to control for the efficiency of RNA extraction, RNA degradation, and the reverse transcription step, an external mRNA standard was used  [67, 68]. The external standard was luciferase mRNA (Promega UK, Southampton, UK), and 1 ng was added to each testis at the start of the RNA extraction procedure. To measure transcript levels, real-time PCR was used with the SYBR green method in a 96-well plate format using an MX3000 cycler (Agilent Technologies, Berkshire, UK).
Reactions contained 5 μl 2 x SYBR mastermix (Agilent Technologies, Berkshire, UK), primer (100 nM) and template in a total volume of 10 μl. At the end of the amplification phase a melting curve analysis was carried out on the products formed. All primers were designed by Primer Express 2. 0 (Applied Biosystems, Warrington, UK) using parameters previously described  [69]. The primers used are described in Additional file 2. Results have been normalised to expression per Leydig cell as the transcripts measured here would be expected to be expressed specifically in steroidogenic/Leydig cells and Leydig numbers in all groups were increased by treatment with hCG. For data presented in Fig. 5 , RNA was extracted from either whole testes or cultured cells using RNeasy Mini kits (Qiagen Ltd. , Manchester, UK).
Available data on sex, breed, living conditions, age and presence or absence of clinical signs compatible with parasitoses were registered for each animal. Both faecal and blood samples were collected from dogs, that were also examined for fleas, ticks, ear mites and, in the presence of compatible skin lesions, body manges. Ethics approval is not applicable as all activities carried out on dogs in the present study have been performed by routine diagnostics procedures performed by veterinarians working on each study site. Consent to examine and sample the animals have been obtained, case by case, from local authorities, animal owners and animal right organisations. Therefore, no official ethics permission or further authorization was required.
Blood examination (Table 5) Rickettsia conorii: Overall, 93 dogs (46. 5%) seroreacted to R. conorii. Twenty-two (11%) were also PCR positive and, at the blood smear examination, the samples of seven (3. 5%) of them were positive for corpuscles suggestive of Rickettsia spp. in the monocytes. Sequences from the 22 PCR products showed 99% identity with R. conorii GenBank Accession number U59730. 1. All dogs negative by serological analyses were also negative for Rickettsia spp. upon PCRs. Of the 93 R. conorii-seropositive dogs, 19 had a tick infestation and 6 scored also PCR-positive for R. conorii. The prevalence of R. conorii in the animals studied was found statistically related to the presence of lymphadenopathy (Fisher's exact test, p = 0. 0177) whilst no any relation was detected with signs like weight loss, pale mucous membrane, gastrointestinal disorders, conjunctivitis or dermatological manifestations (Fisher's exact test, p�0.
05). Anaplasmataceae: Nineteen dogs (9. 5%) were seropositive for E. canis, three of them being also positive at the PCR (100% homology with Genbank Accession number LC018188. 1), while the others were PCR-negative. Two dogs (1%) seroreacted for A. phagocytophilum/A. platys. One of them showed corpuscles suggestive of Anaplasma spp. in the neutrophils at the Giemsa staining and scored PCR-positive for A. phagocytophilum (homology of 100% with Genbank Accession number KY114936. 1), while the other was microscopically and PCR-negative. � dogs with mixed infections included. https://doi. org/10. 1371/journal. pntd. 0007003. t003 Ticks were present in 15/19 dogs seropositive for E. canis at the SNAP 4Dx Plus and 3 of them were among those that scored positive at the PCR. Babesia spp. : One dog (0.
5%) was serologically and PCR positive for B. canis showing homology of 99% with GenBank Accession number: KJ696714. 1, while all other dogs were negative. Leishmania infantum: A total of 13 (6. 5%) samples seroreacted for L. infantum and all of them were also PCR-sequencing positive, with 99-100% identity with L. infantum GenBank Accession number HM807524. 1. All seronegative dogs were also negative upon PCR. Dirofilaria spp. : One (0. 5%) of the examined dogs was positive for D. immitis, at both Knott's test and serology. Moreover, in three dogs (1. 5%) microfilariae of Dirofilaria repens were found in the Knott's test. Borrelia burgdorferi: None of the 200 sera examined for B. burgdorferi was found positive. Risk factor for exposure to parasites and VBDs. The percentage of dogs positive for at least one intestinal parasites and/or VBDs was similar between travelling (i.
Acknowledgments The authors thank  Carmine Merola  and  Raffaella Iorio  for the participation in this study. Special acknowledgments are due to the veterinarians in the Islands of the study:  Maria Danezi ,  Kalliopi Tsagari  and  Manina Vlastaridou  as well as to the  Greek Action of Volunteer Veterinarians (GAVV)  for their valuable help and excellent collaboration.
METHODS STUDY DESIGN. The ASSIST-ICD is a retrospective, multicenter observational study (NCT02873169) of durable mechanical circulatory support devices implanted in 19 French tertiary centers. The methods of this study have been previously published  (5). Briefly, patients aged ≥18 years implanted with axial HeartMate 2 (Abbott, Chicago, Illinois), Jarvik2000 (Jarvik Heart, Inc. , New York, New York), or centrifugal HeartWare pumps (Medtronic, Columbia Heights, Minnesota) between February 2006 and December 2016 were included in the final analysis. The type of pump implanted depended on the local heart team's decision in each center. Exclusion criteria were: patients who underwent total artificial heart placement or pulsatile flow LVAD; history of heart transplant; and VentrAssist (Ventracor, Chatswood, NSW, Australia) recipients.
Patients deceased during LVAD surgery were excluded from the final analysis. This study was approved by the regional ethic committees, the French Advisory Committee on the Treatment of Research Information in the Field of Health (CCTIRS), and the French National Commission of Informatics and Civil Liberties (CNIL). A nonopposition letter was sent to the patients, as requested by French authorities for retrospective studies. BASELINE ASSESSMENT AND FOLLOW-UP. Baseline data -including demographic characteristics, cardiac disease and heart failure history, VAs and radiofrequency ablation procedures prior to or after LVAD implantation history, echocardiography, and blood chemistry values -were collected from hospital files for all patients. Peri-operative data (such as the necessity of a combined surgery or a right extracorporeal life support) was collected.