dataesr/scientific-paragraphs-categorization huggingface dataset:
FRAP data are analysed in three ways: 1. Direct analysis of the FRAP curve for the bleached half of the tip. Lack of recovery is strong evidence of immobility on the timescale of the experiment. Rapid, but partial, recovery, are indicative signatures of a mobile pool and an immobile pool. 2. Comparative analysis of unnormalized intensities in the unbleached tip region and cytoplasm. Photobleaching due to imaging lowers the final intensity; this effect and a small immobile pool may be indistinguishable. To counter this problem, the identical photobleaching-due-to-imaging received by the unbleached tip region and cytoplasm is used to probe the dynamics. Unnormalized intensity plots (background-subtracted) allow direct comparison of the amount that is unintentionally bleached and then recovers in the tip and the cytoplasm.
The study was to focus on the relationship between wave motion (mass sperm motility, measured by a mass sperm motility score, manually assessed by artificial insemination (AI) center operators) and fertility in male sheep. A dataset of 711,562 artificial inseminations performed in seven breeds by five French AI centers during the 2001-2005 time period was used for the analysis. Factors influencing the outcome of the insemination, which is a binary response observed at lambing of either success (1) or failure (0), were studied using a joint model within each breed and AI center (eight separate analyses). The joint model is a multivariate model where all information related to the female, the male and the insemination process were included to improve the estimation of the factor effects. Results were consistent for all analyses.
Analysis of fertility data AI was defined as a success (y = 1) if lambing occurred during a breed specific appropriate interval of time after AI, otherwise it was considered as a failure (y = 0). The intervals of time after AI were 141-151 d for the VEN breed, 142-152 d for the LAC and TEX breeds, 143-153 d for the BMC breed, 144-156 d for the BaB breed, and 144-158 d for the MTR and MTN breeds. The AI result (y = 0 or 1) was the variable of interest because the mean for this variable corresponded to the lambing rate. For a given insemination, information was collected from the AI center that made the semen collection and recorded the insemination data and from the French national performance recordings through which data are assimilated for each individual ewe's production performance. Thus, a detailed description of each insemination (from semen collection and female estrous synchronization to lambing) was available.
Findings depended on the species as well as the way AI was performed  (David et al. , 2011). In the present study, data resulting from the French national performance recordings and AI centers were used. Information from both sexes was used for analysis of the large data set which allows for a strong statistical relevance of the results. Furthermore, fertility was assessed from in vivo results which are more reliable fertility indicators than in vitro findings  (Rodriguez-Martinez, 2003). In the context of animal AI, a single ejaculate is used to inseminate several females. Thus, being able to select the ejaculates that will be used to produce the straws of semen used for insemination is a key component in a breeding selection scheme  (Colenbrander et al. , 2003). This is why, in the present study, the relationship between male factors, especially mass sperm motility, and fertility were the focus while other factors of variation were used as correction variables but were not of interest as related to the primary goal of the study.
Acknowledgments The research was supported by  Agence Nationale pour la Recherche (ANR)  under grant  MOTIMO  ( ANR-11-MONU-009-01 ), by the  National Science Foundation (NSF)  under grant  RNMS11-07444  ( KI-Net ), by the  Engineering and Physical Sciences Research Council (EPSRC)  under grant ref:  EP/M006883/1  and by the innovating action "BELIA". The authors thank the AI centers who provided the data. Pierre Degond is on leave from  CNRS ,  Institut de Mathématiques de Toulouse, France. Pierre Degond  acknowledges support from the  Royal Society  and the  Wolfson foundation  through a  Royal Society Wolfson Research Merit Award.
Results of the central study laboratory using the FilmArray GI Panel A total of 745 runs were needed to analyse all 709 samples on the FilmArray GI Panel (data not shown). Failed attempts (n = 36; 4. 8%) were attributable to either software errors (ten runs/36 fails; 27. 8%) or loss of vacuum pressure in the pouches (26 runs/36 fails; 72. 2%). The median number of days between sampling and testing at the central study laboratory was 11 (IQR 7 days). The overall positivity rate was 384 positive samples among 709 specimens (54. 2%), with similar rates in each round (Table  1 ). Among the 709 samples that were screened, in 187 a single bacterium was detected (26. 4%), in 62 a single virus With the exception of Entamoeba histolytica and V. cholerae, all of the 22 targeted pathogens were detected at least once.
Discussion The results of the EUCODI study impressively underline the wide spectrum of possible enteric pathogens in patients with community-acquired gastroenteritis: with the exception of Entamoeba histolytica and V. cholerae, all of the 22 targeted  potential pathogens were detected at least once. This underscores the importance of using a comprehensive test spectrum for the work-up of samples from patients with community-acquired gastroenteritis. In our European study, the FilmArray GI Panel detected at least one organism in 54% of the samples, whereas the local laboratory protocols detected at least one organism in 18. 1% of the samples. Data from the manufacturer's clinical trials in the USA had yielded a nearly identical positivity rate: possible pathogens were detected in 832 of 1556 patients (53.
In contrast, miR-15a-3p was similarly regulated in the isolated aneurysmal cells tested as well in the whole aorta. Mir-15a-3p has been described to be a regulator of angiogenesis through its interaction with Vascular Endothelial Growth Factor  [31]. Interestingly, ATLOs require endothelial venules to interact with the media and other inflammatory cells  [32] , and are triggered by chemokines, which could be regulated in response to the enhanced development of ATLOs  [16]. To underline the utility of analyzing microdissected ATLOs, we evaluated the expression of the three selected miRNAs in whole biopsies of aneurysmal and control aorta. The three miRNAs, miR-15a-3p, miR-30a-5p and miR-489-3p, were down-regulated 0. 6-, 0. 25-and 0. 2-fold, respectively (Figure  3 ). These latter data confirmed the interest to study individually the cells as shown by the inverse expression of miR-489-3p in the whole aneurysmal aorta.
Finally, slides were mounted with Glycergel (DAKO Corporation) and analyzed with an Axioplan 2 microscope (Carl Zeiss, Marly Le Roi, France), which includes an HRc camera (AxioVision-Deconvolution 3D, Carl Zeiss). The relative quantification of the thickness and area of ATLO was performed using ImageJ software (Version 1. 45, Bethesda, MD, USA).
RNA Extraction, miRNA Screening and qRT-PCR Analyses RNA was extracted from 10 mm 2 of LCM-isolated areas with 200 μL TRI Reagent ® (Ambion, Austin, TX, USA), according to the manufacturer's instructions, and from 200 μL plasma with the miRNeasy Mini Kit (Qiagen, Venlo, The Netherlands), also according to the manufacturer's instructions. Syn-cel-miR-39 miScript miRNA Mimic (Qiagen) (5 µL) was added to each plasma sample as a spike-in control and used for calibration. LCM-dissected areas abundant in ATLOs obtained from two different aortic tissue samples were screened for miRNA expression with the human miRNA 8 × 15 k microarray (850 known human miRNAs, according to the Sanger database version 12. 0, Agilent Technologies). Tissue samples were analyzed individually on the same microarray. After dephosphorylation and denaturation, the RNA samples were labeled with Cyanine 3-pCp, then purified with micro Bio-Spin 6 chromatography columns (Bio-Rad Laboratories, Hercules, CA, USA).
The purified labeled miRNAs were incubated with the array in hybridization chambers (Agilent) for 20 h at 55 °C. The slides were then washed as described in the protocol. The microarray was then run on a SureScan microarray scanner (Agilent Technologies, Santa Clara, CA, USA). Raw data were acquired with Feature Extraction Software (Version 10. 7. 3. 1, Agilent, Santa Clara, CA, USA). Data are available at the Gene Expression Omnibus (GEO) (www. ncbi. nlm. nih. gov/geo) under the accession number GSE63541. We used the R package script AgiMicroRna for normalization. The miRNAs detected in ATLOs were selected based on their normalized values calculated with positive and negative controls. We then considered a miRNA detected in ATLOs when associated with a positive normalized value obtained with the 16 probes corresponding to the miRNA for the two samples tested.
Acknowledgments We thank  Jo Ann Cahn  for improving our English. The study was supported by a grant: Fighting Aneurysmal Disease (Health- F2-2008-200647 ) from the  European Union. The sponsors had no role in the design of the study, in the collection, analyses and interpretation of data, in the writing of the manuscript, or in the decision to publish the results. We are grateful to the coordination team of multiretrieval organs of  Professor Pruvot 's transplant unit ( CHRU Lille, France ).
Data analysis All analyses were performed using Stata 12. 0 (StataCorp, College Station, TX, USA). Gametocytaemia values were log-transformed to obtain a normal distribution and Student's t test was used to compare mean log-gametocytaemia between infectious and non-infectious gametocytaemic blood. Results are presented as geometric means of original values for each group. Sporozoite production was evaluated by the arithmetic mean number of sporozoites obtained per mosquito dissected from a given batch. Spearman's correlation coefficient was used to assess the relationships between gametocytaemia and sporozoite production, and between gametocytaemia and mosquito mortality in infected mosquito batches; Mann-Whitney test was used to analyse if transmitters and non-transmitters differed in their age distribution.
545). Mosquito mortality at day 14 post feeding was variable for the batches that became infected (Fig. 2 ), but it did not correlate with the mean number of sporozoites per mosquito (Spearman's ρ = 0. 179, p = 0. 282). The overall mortality for all the mosquito batches that became infected was 46 %. The dataset from on which these analyses were based is provided in Additional file 1.
Over the study period a total of about 91 million P. vivax sporozoites were obtained at the SMRU, with a total of more than a million sporozoites obtained from each of 21 patient samples out of the 38 that were considered as transmitters. It should be noted that for 29 of the patients, the number of mosquitoes available for salivary gland dissection was less than 100, yet for 14 of these more than a million sporozoites were obtained. Thus, the data obtained indicate that female A. cracens are highly susceptible to infection by P. vivax, with about 70 % of the subject samples leading to the production of salivary gland sporozoites. For the purposes of this study it was not deemed necessary or desirable to use molecular methods to detect or quantify gametocytes. It was important that the blood sample was conveyed to the laboratory for the feeding with the minimum of delay.
Immunohistochemistry (IHC) Ten micrometre thick tissue sections from the frontal lobe, approximate Brodmann area 9 (BA9), were immunohistochemically stained with two different anti-clusterin antibodies (dilution 1:200-2000, Ab#69644 and Ab104652, Abcam, Cambridge, UK). Ten images from the neocortex and underlying WM were captured using a Zeiss Axioplan 2 (Zeiss, Oberkochen, Germany) microscope and analysed using Image Pro Plus software (V. 4. 0, Media Cybernetics, Silver Spring, MD, USA). The per cent area of an image covered by the stain was assessed (per cent area; %A) as an indication of the extent of clusterin immunostaining. To assess the intensity of the immunostaining per area (%A) and between sections, we also determined the integrated optical density as a measure of the mean immunoreactivity (IR) for each sample.
The Image Pro analysis software assigns an individual IOD between 0 and 255 grey levels for each stained pixel in the delineated object, depending on the stained pixel intensity. All of the individual grey levels are summed for the entire stained object, and this total sum is divided by the number of pixels contained within the object, which gives the mean pixel IOD per object. From these mean IOD's per object, a total IOD was determined for all stained objects within an image or series of images. Clusterin immunostaining in axons was scored in each case as follows: 0, no axonal staining; 1, infrequent, short punctate staining; 2, infrequent staining of individual axons; 3, patches of punctate staining with swollen axonal lengths; 4, tracts of densely stained and swollen axons but unstained areas still apparent; 5, complete areas of densely stained and swollen axons (Figure  S1 ).
Statistical analysis Results were analysed using spss (IBM, V 19. 0, IBM Corporation, Armonk, NY, USA). Where relevant, following analysis of variance (anova), post hoc analysis was performed using Tukey's post hoc. Axonal damage scores used ordinal data and were analysed for between-group effects using Kruskal-Wallis H test followed by Mann-Whitney U test post hoc. For axonal staining, disease groups were compared the respective age-matched controls and the differences between the groups tested using Mann-Whitney U test. Histograms were presented as mean ± 2 SEM, and values of P < 0. 05 were considered significant.
Acknowledgements J. L. Taylor was funded by a  Newcastle University Faculty of Medical Sciences  summer studentship. We thank  Drs Glyn Nelson ,  Alison Spilsbury  and  Trevor Booth  for excellent assistance with confocal imaging and image co-localization analysis. Post-mortem brain tissue was obtained from the  Newcastle brain tissue resource (NBTR). We thank the patients and families for their contributions to this study. Our work was supported by grants from the  UK Medical Research Council  ( MRC ,  G0500247 ),  Newcastle Centre for Brain Ageing and Vitality (BBSRC, EPSRC ,  ESRC  and  MRC, LLHW) and Alzheimer's Research (ARUK). The NBTR is funded by a grant from the  UK MRC  ( G0400074 ) with further support from the  Newcastle NIHR Biomedical Research Centre in Ageing and Age Related Diseases award  to the  Newcastle upon Tyne Hospitals NHS Foundation Trust , and a grant from the  Alzheimer's Society and ART  as part of the Brains for Dementia Research Project.
statistical analysis Pair t-test was used for comparisons of GFR before and after RIRS. Independent-sample t-test and chi-square tests were used for comparisons of means and proportions, respectively. Univariate and multivariate regression models were used to assess the influence of different variables on renal function outcomes. Only factors that were significant in univariate analysis were considered for multivariate analysis. All tests were done using SPSS® version 10.
Study design and oversight The trial is a prospective, multi-site, single-arm, worldwide clinical study evaluating the safety and efficacy of the TPS. Briefly, the study will implant up to 720 patients at up to 70 centres worldwide. All participants must satisfy standard criteria for de novo pacemaker implantation with Class I or II indications and provide written informed consent. The trial design is described in detail elsewhere. 9 The trial is sponsored by the manufacturer, Medtronic. The protocol was approved by the Ethics Committee at each participating institution and associated national and local regulatory agencies. Data of this ongoing study are collected by trained centre personnel, and data integrity maintained via programmatic edit checks and source data verification by the sponsor.
Therapy initiation and follow-up Enrolled patients undergo system implant attempt and then are followed, including adverse event and device evaluation, at implant, hospital discharge, 1, 3, 6, and 12 months post-implant. Implanted patients are evaluated semi-annually until trial closure. Cardiovascular, procedure, and system-related adverse events are adjudicated by an independent clinical events committee. Initially, pacemaker-dependent patients were excluded. Twenty-five implanted patients underwent 24 h ambulatory ECG and device function (markers and EGMs) monitoring (Model ER220, Medtronic plc, Mounds View, MN, USA). After comprehensive review of the ambulatory ECG and safety data by the trial's independent data monitoring committee, allowance of pacemaker-dependent patients was determined.
5% confidence interval (CI). A one-sample t-test comparing the observed mean 3-month pacing capture threshold to the null value of 2. 0 V was used to test the efficacy objective. In addition, paired t-tests were used to compare electrical variables measured at implant and the 3-month visit. Statistical calculations were performed using SAS (SAS Institute, Cary, NC, USA) or R (www. r-project. org) and validated per the sponsor's operating procedures. The procedure duration was defined as the time from the insertion of the TPS introducer to removal. Time to hospital discharge was defined as the number of days from implant to hospital discharge.
Results Patient recruitment began 5 December 2013 and the 60th 3-month visit accrued on 11 August 2014, triggering evaluation of the early performance objectives. At the time of database closure for this analysis, 140 patients had an attempted implant and all were successfully implanted. The TPS was implanted in these 140 patients in 23 study centres by 37 physicians in 11 countries and were followed to an average of 1. 9 + 1. 8 months (range 0 -6. 5 months). Step 2, middle panel: the device is deployed and its tines penetrate the myocardium. Step 3, lower panel: the delivery catheter is pulled back from the device, which is still retained by a tether. After fixation and electrical checks, the tether will be cut and removed, as will the delivery system be. RV, right ventricle. Patients were mostly male (60.
7%), of mean age 77. 0 + 10. 2 years, height range 144 -190 cm, and weight range 41 -148 kg (Table  1 ). The most common primary indications for pacing were atrioventricular (AV) block (66%, or 93 of 140 patients) and symptomatic sinus node dysfunction (29%, or 40 of 140 patients). Nine (6%) patients were not felt to be appropriate for implantation of conventional transvenous lead pacing systems due to a variety of reasons such as compromised venous access, previous infection, and cancer with need for indwelling catheter. Confirmation of appropriate pacemaker operation from the 24 h ambulatory ECG analysis by the trial's data monitoring committee was achieved 3 weeks prior to database closure, enabling pacemaker-dependent patient enrolment. Two pacemaker-dependent patients were subsequently implanted and included in this analysis.
Conclusion Early performance assessment shows the TPS pacemaker can safely and effectively be applied. It is premature to draw definitive conclusions about the benefits of this system. Long-term safety and benefit associated with the absence of a subcutaneous pulse generator and transvenous lead will further be evaluated in the trial. However, these early results meet and exceed initial pre-specified expectations. The fact that such data were obtained in a multicentre study involving 37 investigators at 23 different centres around the world with a variety of patients is encouraging.
1  Network of predicted interactions between mitochondriarelated proteins deregulated in Jurkat-Tat101. Medium confidence score level was 0. 400. Data supporting protein-protein interactions derived from experimental studies (dark purple lines), homology (light purple lines), databases (light blue lines), text mining (light green lines), concurrence (dark blue lines) and co-expression (black lines). Node colour is arbitrary. Differences in protein levels are specified in Table  1  proton transporter resulting in OXPHOS uncoupling also known as SLC25a9  [34] , and translocase of inner mitochondrial membrane 9 (TIMM9), a chaperone involved in the import of transmembrane proteins  [35] , which were respectively 3. 68-, 2. 69-and 2. 23-fold enhanced. The functional interconnection of these proteins was predicted in STRING database and is shown in Fig.
Intracellular Tat101 deregulated the expression of cytoskeleton proteins and activated small GTPases The interactions between mitochondria and the cytoskeleton influence mitochondrial functions including respiratory activity, fusion/fission processes and ROS biogenesis  [36, 37]. Therefore, the expression of cytoskeleton-related proteins was analyzed by LC-MS/MS and predicted protein interactions were analyzed by STRING database (Fig. 7a ). Jurkat-Tat101 cells, and to a lesser extent Jurkat-Tat72 cells, showed the deregulation of 20 cytoskeletonrelated proteins (Table  3 ). Only five deregulated proteins were tubulin-related. Fifteen actin-related proteins were altered in Jurkat-Tat101 cells. Three of these proteins were involved in small-GTPase signal transduction, including Rho GDP-dissociation inhibitor 2 (ARHGDIB) and GDP dissociation inhibitor beta protein (GDI2), which were -10.
PBLs expressing Tat-101 showed decreased synthesis of ATP and enhanced levels of lactate PBLs are a more physiological cellular system than T CD4+ Jurkat lymphocytes. Representative data were  confirmed using peripheral blood lymphocytes (PBLs) from healthy donors that were transfected with a vector expressing Tat101 protein or with pcDNA3 as negative control. pEGFP vector was co-transfected to measure the transfection efficiency, which was 15 % in all cases (Fig. 9a ). Nuclear localization of intracellular Tat was confirmed by immunofluorescence. The intracellular levels of ATP were significantly 2. 12-fold reduced in PBLs transiently expressing intracellular full-length Tat (p < 0. 05) (Fig. 9b ). Relative data showing lactate concentrations in PBLs expressing Tat after normalization with lactate concentrations in control PBLs from the same donor are shown.
Proteome analysis and criteria for protein identification Proteome analysis was performed as previously described  [15]. Briefly, 200 μg of trypsin-digested proteins were loaded into the LC-MS/MS system and analyzed using a C-18 reversed phase nano-column (Thermo-Fisher, San Jose, CA, USA). Real-time ionization and peptide fragmentation was performed on an orbital ion trap mass spectrometer (LTQ Orbitrap XL, Thermo Fisher Scientific, San Jose, CA, USA)  [85]. For peptide database searching, tandem mass spectra were analysed using Sequest (Thermo Fisher Scientific; version 1. 3. 0. 339) and X! Tandem (http://www. thegpm. org; version CYCLONE). Sequest and X! Tandem were searched with a fragment ion mass tolerance of 30 PPM and a parent ion tolerance of 15 PPM. Scaffold 3. 0 (Proteome Software Inc.
, Portland, OR, USA) was used to validate peptide identifications. Only peptide established at a probability greater than 95 % and with XCorr-score values above 1. 75 were accepted. Proteins related to mitochondria and cytoskeleton that changed at least ±2. 0-fold in Jurkat-Tat101 were selected and subjected to analysis with STRING 9. 0 database (http://string-db. org/) [86].
PCR and RT-PCR assays DNA and total RNA was isolated with QiAmp DNA blood mini kit and RNeasy Mini kit (Qiagen, Barcelona, Spain), respectively. cDNA was synthesized using GoScript Reverse Transcription System (Promega, WI, USA). Specific primers are described in Additional file 2: Table  S1. The expressions Ribosomal protein S18 (S18) was used as housekeeping gene. The PCR amplification was performed in a StepOnePlus ™ Real-Time PCR Systems (Applied Biosystems, CA) using SYBR Green. Data analysis was performed with 7500 software v2. 0. 6 and Ct values were normalized according to S18 amplification and analyzed with the formula 2 -∆∆Ct.