dataesr/scientific-paragraphs-categorization huggingface dataset:
ACKNOWLEDGMENTS We thank  CERN  for the very successful operation of the LHC, as well as the support staff from our institutions without whom ATLAS could not be operated efficiently. We acknowledge the support of  ANPCyT , Argentina; YerPhI, Armenia;  ARC, Australia ;  BMWFW  and  FWF , Austria; ANAS, Azerbaijan; SSTC, Belarus;  CNPq  and  FAPESP, Brazil ;  NSERC ,  NRC  and  CFI ,  Canada ; CERN; CONICYT, Chile; CAS,  MOST  and  NSFC , China; COLCIENCIAS, Colombia; MSMT CR, MPO CR and VSC CR, Czech Republic; DNRF,  DNSRC  and  Lundbeck Foundation , Denmark; EPLANET,  ERC  and  NSRF ,  European Union ;  IN2P3-CNRS ,  CEA-DSM/IRFU , France; GNSF, Georgia; BMBF,  DFG ,  HGF ,  MPG  and  AvH Foundation, Germany ;  GSRT  and  NSRF, Greece ;  RGC, Hong Kong SAR, China ;  ISF, MINERVA, GIF, I-CORE and Benoziyo Center, Israel ;  INFN, Italy ;  MEXT  and  JSPS, Japan ; CNRST, Morocco; FOM and  NWO, Netherlands ;  BRF  and  RCN, Norway ;  MNiSW  and  NCN , Poland; GRICES and FCT, Portugal; MNE/IFA, Romania;  MES of Russia  and  NRC KI , Russian Federation; JINR; MSTD, Serbia; MSSR, Slovakia; ARRS and MIZŠ, Slovenia; DST/NRF, South Africa; MINECO, Spain;  SRC and Wallenberg Foundation, Sweden ;  SER ,  SNSF  and  Cantons of Bern and Geneva, Switzerland ;  NSC, Taiwan ;  TAEK, Turkey ;  STFC , the  Royal Society and Leverhulme Trust ,  United Kingdom ;  DOE  and  NSF ,  United States of America.
Viral persistence Fifty microliters (10 µL for iterative drying) of the virus inocula were applied to the middle of each petri dish lid (35-mm diameter [Falcon]), and dried under the air flow of a class II biological safety cabinet at room temperature. The air flow speed was 0. 4 m s -1 and the relative humidity was measured using a relative humidity meter (Temperature and Humidity Data logger, IHM). Medium (1 mL) was added to recover dried virus inocula. The infectious titers of harvested fluids were then determined and the results expressed as described above.
Acknowledgements This work was supported by  University Lille 2  and  CHRU Lille  and has been partially funded by  Nord-Pas de Calais region (CPER)  and  European Union (FEDER). The authors thank  Jessica Gachet  and  Nathalie Debooser  ( Lille, France ) and  Dr. Maren Eggers  ( Stuttgart, Germany ) for their helpful discussions.
2006; Itano et al. 2008 ). An abnormal production of HA boosts anomalous biologic processes, as observed in several tumors, in which it stimulates invasion and metastasis, and facilitates angiogenesis, among other functions  (Toole 2004; Itano et al. 2008). 4-Methylumbelliferone (4MU) is a modified coumarin (7-hydroxy-4-methylcoumarin), widely used orally as choleretic or biliary antispasmodic in humans (Heparvit ™ )  (Takeda and Aburada 1981)  as well as in clinical trials in patients with chronic hepatitis B and C (ClinicalTrials. gov identifier: NCT 00225537)  (Takeda and Aburada 1981). 4MU inhibits HA-chain elongation by competition, since it is glucuronidated by endogenous UDP-glycosiltransferase. Then, uridine diphosphate glucuronic acid (UDP-GlcUA) molecules, which are substrate of HA synthases, are depleted to form 4MU-GlcUA  (Kultti et al.
The signal was detected by 0. 1% diaminobenzidine (Sigma-Aldrich), 4% glucose, 0. 08% ClNH 4 , 5% nickel ammonium sulfate in 0. 2 M AcNa and 0. 05% H 2 O 2. Densitometric analysis was performed by taking 10 images/ slide at 400× (Nikon Eclipse E800, Nikon, Buenos Aires, Argentina) and percentage of positive area was calculated with ImageJ software (National Institutes of Health, Bethesda, MD).
MATERIALS AND METHODS All consecutive patients admitted in our stroke unit with a stroke of unknown time of onset and treated by reperfusion therapy between October 2010 and October 2013 were included in this study. The patient demographics, risk factors, and clinical and imaging data were prospectively registered in our stroke databank. The NIHSS score was systematically assessed by a stroke neurologist on admission. This study was approved by the local ethics committee. Consent for treatment was obtained from the patients or their family before the endovascular procedure. The inclusion criteria were as follows: 1) patients with acute stroke without a known time of symptom onset, presenting to our emergency department within 4 hours after the first found abnormal time (FAT); 2) acute ischemic lesions within the anterior circulation on DWI; 3) an ASPECTS of Ն5; 4) the presence of a DWI/FLAIR mismatch according to Thomalla et al 3 ; 5) the presence of a clinically relevant impairment in social, occupational, or other important areas of functioning following a physician evaluation; and 6) the presence of clinical-diffusion mismatch between stroke severity and volume of DWI lesions assessed by visual inspection.
Statistical Analysis Patients with a favorable or poor outcome were compared by using the Student t or Mann-Whitney test for continuous variables and the 2 or Fisher test for categoric variables. Bivariate logistic regressions were used to identify predictors of favorable outcome. Potential independent predictors (P Ͻ. 25 in bivariate logistic regressions) were included in a multivariate logistic regression, built by stepwise procedure. Adjusted odds ratios and their 95% confidence intervals were calculated. The statistical significance threshold was set at 5%. Statistical analyses were conducted by using SAS software 9. 2 (SAS Institute, Cary, North Carolina).
Population Data Overall, 41 patients with unclear-onset stroke in the anterior circulation (median age, 72 years; range, 17-89 years; female/ male ratio, 26:15) were included. Baseline clinical and radiologic features and main clinical outcomes at day 90 are presented in the Online Table. The median time interval between last-seen-normal time and hospital admission was 490 minutes (interquartile range, 255-641 minutes). The mean NIHSS score was 14. 5 Ϯ 5. 7. The median time interval from FAT to MR imaging was 135 minutes (interquartile range, 109 -158 minutes) and 517 minutes (interquartile range, 314 -678 minutes) from last-seen-normal time. The median DWI ASPECTS was 8 (range, 5-10). Thirty-six patients (88%) showed an arterial occlusion in the anterior circulation. Occlusion sites were the proximal MCA (M1) in 28 cases (68.
20  Indeed, a number of studies have provided support for penumbral-imaging selection, by using the perfusiondiffusion mismatch criteria for the treatment of acute ischemic stroke  [7] [8] [9] 12  because salvage of the ischemic penumbra has formed the theoretic basis of recanalization therapies. Thi  criterion may be particularly helpful in late time windows, when the proportion of patients with penumbral tissue steadily decreases. Last, the results of Diffusion and Perfusion Imaging Evaluation for Understanding Stroke Evolution Study 2 demonstrated that reperfusion was associated with increased good functional outcome at day 9 in a defined target mismatch profile. 21  Obvious limitations of our monocentric observational study were the small number of patients, a retrospective analysis of our prospective dataset performed, and no control group.
ML is a subfield of computer science and artificial intelligence that deals with the construction and study of systems that can learn from data, rather than follow explicitly programmed instructions. Commonly applied in complex data scenarios, such as financial and technological settings, it may be suitable for outcome prediction of HSCT. Study design involved two phases. The first, focused on development of several ML based prediction models of day 100 TRM. A cohort of 28,236 acute leukemia, adult allogeneic HSCT recipients were analyzed. Twenty four variables were included. In the second phase, by applying a repetitive computerized simulation, factors necessary for optimal prediction were explored: algorithm type, size of data set, number of included variables, and performance in specific subpopulations.
RNA was isolated from PBMC using previously described methods  (Xie LN et al, Clinical Transplant. 2014; 28:314). For discovery of relevant miRs, we used NanoString nCounter miR assay as previously described  (Knouf EC et al, 2013. PLoS ONE 8: e69630)  comprising 654 endogenous miRs. Analysis of miR raw data was done using nSolver TM 2. 0 Software (NanoString Technologies, Inc. ) applying standard quality control tests. All samples contributed to the discovery analysis. MiRs.
Intriguingly, at least one miRNA, miRNA-128-2, can be expressed from two different promoters and by two different polymerases (Pol II and Pol III)  [18, 19]. Among the other small ncRNAs, transfert RNAs (tRNAs) can also be hosted in other genes. In the human genome, out of the 497 tRNA genes and 324 tRNA-derived pseudogenes supposed to be no longer functional, 47 (about 10%) were located in intron of coding genes and 32 (about 10%) in intron of non-coding genes (hg19). For example, the tRNA-Leu (anticodon TAA; chr6:69,204,486-69,204,568) is located in the intron 17 of the human brain-specific angiogenesis inhibitor 3 (BAI3; chr6:69,232,406-69,389,511) gene. -AS1 ) pseudogene; keratin associated protein 5-1 (KRTAP5-1) and 5 other paralog genes (KRTAP5-2 to -6); family with sequence similarity 99, member A (FAM99A) and member B (FAM99B) which are non-coding genes; interferon induced transmembrane protein 10 (IFITM10) and cathepsin D (CTSD) coding genes; one unannotated gene corresponding to EST GenBank AF085962.
Introns Can Be Retained within Coding Segments-When Alternative Splicing of Introns Participates in Proteome Diversification Alternative splicing (AS) is a mechanism that allows the inclusion of non-coding sequences (introns) or excision of coding segments (exons) within mature mRNAs. While AS of introns represents a major event in plants, it accounts for only 2 to 5% of all alternative events in humans  [61, 62]. However, given the 252,243 introns in the human genome (Table  2 ), this could still contribute to the generation of additional 5044 to 12,612 potential protein isoforms. Actually, 6157 introns from the UCSC Table Brower (Alt Events-Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes) have been described to be conserved between human and mouse, and further confirmed to exist in EST or cDNA databases, indicating that they may well be included in mRNAs under certain physiological conditions  [63].
The 3 nested genes are the oligodendrocyte myelin glycoprotein gene (OMG; chr17:29,621, 668-29,624,380), ecotropic viral integration site 2A (EVI2A; chr17:29,643,428-29,648,767) and 2B (EVI2B; chr17:29,630,788-29,641,130); (C) MOB kinase activator 2 gene (MOB2; chr11:1,490,685-1,785,501) contains 13 nested genes: dual specificity phosphatase 8 (DUSP8) coding gene; KRTAP5-1/KRTAP5-2 antisense RNA 1 (KRTAP5-AS1) pseudogene; keratin associated protein 5-1 (KRTAP5-1) and 5 other paralog genes (KRTAP5-2 to -6); family with sequence similarity 99, member A (FAM99A) and member B (FAM99B) which are non-coding genes; interferon induced transmembrane protein 10 (IFITM10) and cathepsin D (CTSD) coding genes; one unannotated gene corresponding to EST GenBank AF085962. Amazingly, KRTAP5-1 gene was embedded within and oriented in the opposite direction of KRTAP5-AS1 pseudogene intron, itself oriented in the opposite direction to MOB2 intron.
A well-established hemA mutant of Escherichia coli was used for the study and, for comparison, parallel experiments were performed on the corresponding wild-type strain. Global transcriptomic changes induced by CORM-3 and iCORM-3 were evaluated using a Two-Color Microarray-Based Prokaryote Analysis (FairPlay III Labeling) by Agilent Technologies (Inc. 2009). Data acquisition was carried out using Agilent Feature Extraction software (v6. 5) and data normalisation, as well as information about gene products and their function was obtained from GeneSpring GX v7. 3 (Agilent Technologies). Functional category lists were created using KEGG (Kyoto Encyclopedia of Genes and Genomes). Relevant regulatory proteins for each gene were identified, where available, using regulonDB and EcoCyc (World Wide Web).
Organisms Escherichia coli K12 MG1655 (wild-type strain) Escherichia coli K12 W3310 hemA::Km R (hemA mutant strain; Keio collection (1,2)). Sex N/A Data acquisition Transcriptomic data were acquired using a 'Two-Color Microarray-Based Prokaryote Analysis (FairPlay III Labeling)' by Agilent Technologies (Inc. 2009) and an Agilent DNA microarray scanner (G2505) controlled by Agilent Scan Control software (v8. 5).
Analysis of microarray data Data acquisition was carried out using Agilent Feature Extraction software (v6. 5), which allows measurement of the Cy3 and Cy5 fluorescence of each feature in the scanned microarray image. Data were normalised using GeneSpring GX v7. 3 (Agilent Technologies) by dividing the experimental channel by the control channel and applying a global LOWESS normalisation, which removes dye intensity-dependent artefacts caused by non-linearity of Cy5 and Cy3 fluorescence at low levels. Identification of statistically significant gene expression changes was achieved by applying a t-test with a 2-fold cut-off and p b 0. 05. Four replicates were obtained for each condition tested: two biological repeats of CORM-3-or iCORM-3-treated samples hybridised against an untreated control, each with two technical (dye-swap) repeats.
Statistical modelling of transcriptional responses Statistical data modelling was used to infer transcription factor (TF) activities based on the gene expression time-series generated from the microarray analyses. We used a probabilistic model  [6] , which integrates gene expression data with TF-target information (obtained from data bases such as EcoCyc) to determine the optimal TF activity profiles that can explain the expression data and compatibly with the constraints imposed by the network structure. The model adopts a log-linear approximation, expressing gene expression (log) changes as a weighted linear combination of changes in the activity of the TFs that regulate the genes in the network. A schematic representation of the model is given in Fig. 2 ; the approach is freely available as opensource software in the TFInfer tool  [7].
Acknowledgements The authors would like to thank all of the contributors to the original research article [3]. This work was supported in part by the  Biotechnology and Biological Sciences Research Council (UK, BBSRC)  ( BB/H016805/1 ), a  Postgraduate Studentship  to JLW and the  Leverhulme Trust  ( RPG-2013-041 ). G. S. acknowledges support from the  European Research Council  through grant  MLCS 306999.
, 2009; Harper et al. , 2011; Martin et al. , 2013) , with 100 nM BoNT/A-Hc-Atto647N added to the nerve terminal chambers only. For the single-particle tracking experiments, 1 nM BoNT/A-Hc-Atto647N was used. Devices were then returned to the original medium for 2 h before imaging. Images were acquired with a Zeiss LSM710 inverted microscope maintained at 37°C and 5% CO 2 and videos were analyzed for carrier kinetics using the spot function of Imaris software (Imaris version 7. 7; Bitplane). Kymographs were generated using ImageJ software using the plugin Multi-Kymograph. For immunofluorescence microscopy of fixed cells, microfluidic devices were removed and neurons were fixed at various time points with PBS containing 4% paraformaldehyde and 4% sucrose and then processed for immunocytochemistry as described previously  (Wen et al.
, 2008). Permeabilization was performed using 0. 1% saponin, 0. 2% gelatin, and 1% BSA in PBS. Imaging was performed on a Zeiss LSM 710 confocal microscope and analyzed with Zen (Zeiss) and ImageJ software. All images were processed using Adobe Photoshop CS 5. 1 and figures were compiled using Adobe Illustrator CS 5. 1. Electron microscopy. Rat hippocampal neurons cultured in microfluidic devices were stimulated as described above and then incubated for a further 3-4 h, after which the cells were washed in PBS, the microfluidic device removed, and the cells fixed in 2. 5% glutaraldehyde in PBS. To measure BoNT/A-Hc-HRP trafficking, rat hippocampal neurons cultured in microfluidic devices were treated as described for confocal microscopy except that 100 nM BoNT/A-Hc-HRP was added to the nerve terminal chambers for the period of stimulation.
Cells were returned to growth medium for 3 h before fixation. After fixation, cells were processed for 3,39-diaminobenzidine (DAB) cytochemistry using standard protocols. Fixed cells were contrasted with 1% osmium tetroxide and 4% uranyl acetate before dehydration and embedding in LX-112 resin  (Harper et al. , 2011). Ultrathin sections (ϳ60 nm) were cut using an ultramicrotome (UC64; Leica). Sections were visualized on a transmission electron microscope (model 1011; JEOL) equipped with a cooled charge-coupled device camera (Morada; Olympus). Autophagosomes within the cell soma proximal region of the microfluidic channel were counted and scored for the presence or absence of the DAB reaction product using ImageJ software. p75 NTR and LysoTracker labeling and colocalization analysis. DIV 14 hippocampal neurons cultured in microfluidic devices were incubated at 37°C with 50 nM LysoTracker for 30 min or with an antibody against the extracellular domain of p75 NTR (1/500 diluted) for 1 h  (Matusica et al.
, 2013). After incubation, neurons were pulse-chase labeled with fluorescently labeled BoNT/A-Hc under high K ϩ or low K ϩ conditions as described above and then washed with culture medium before being imaged with an iLas 2 microscope (Roper Scientific) fitted with a 100ϫ oil-immersion objective (numerical aperture 1. 49; Nikon) and a highperformance EMCCD camera (Photometrics, Evolve 512 Delta) with MetaMorph software. Axons were visualized in microgrooves using liveimaging buffer containing the following (in mM): 25 HEPES, 145 NaCl, 5. 6 KCl, 0. 5 MgCl 2, 2. 2 CaCl 2 , and 5. 6 D-glucose, pH 7. 4. Time-lapse images of two fluorophores were captured at 0. 1-0. 3 s intervals for 95 s. Carriers were tracked automatically with the "surface" function of Imaris software (Imaris version 7. 7; Bitplane) and the same parameter settings were used in both the low K ϩ -and high K ϩ -treated groups.
The colocalization ratio between different channels was calculated with the "colocalization" function of Imaris software, with the ratio of all time points accumulated to generate the total ratio within a movie. Statistical analyses and bar graphs were generated using Prism 6 (GraphPad Software). In vivo injection of mCherry-BoNT/A-Hc. BoNT/A-Hc fused to mCherry was generated in pGEX-KG by introducing the mCherry sequence into the vector, followed by the BoNT/A-Hc sequence (aa 873-1296, NCBI sequence P10845;  Binz et al. , 1990). The mCherry-BoNT/ A-Hc protein was expressed in the BL21 strain of E. coli as a GST C-terminal fusion protein before being purified on glutathione Sepharose beads (GE Healthcare) and eluted using thrombin. Further purification was performed by gel filtration using a Superdex 200 10/200 GL column (GE Healthcare).
For in vivo experiments, male C57BL/6 mice were anesthetized with isoflurane, followed by intraplantar injections of mCherry-BoNT/A-Hc (1 g) into the right foot. After 24 h, the mice were killed and slices were prepared from the L4 -S2 region of the spinal cord. Slices containing a red fluorescent signal in the lateral column were selected under a dissecting fluorescent microscope (Nikon, SMZ1500) and labeled for immunofluorescence microscopy using LC3 or LAMP1 antibodies. Images were acquired on an A1R laser confocal microscope (Nikon) and analyzed with NIS elements software. Single-particle detection of internalized BoNT/A-Hc in hippocampal axons. Transfected neurons cultured in microfluidic devices on glassbottomed culture dishes (In Vitro Scientific, catalog #D29-20-1. 5-N) were stimulated with high K ϩ buffer for 5 min with 1 nM BoNT/A-Hc-Atto647N added to the nerve terminal chamber only, and then washed 3 times with culture medium and chased for 2-4 h in a 37°C incubator.
Axon channels were visualized in live-imaging buffer at 37°C. Cells were acquired on a motorized inverted microscope (Nikon, TiE) equipped with a perfect focus system under slightly oblique illumination (ILas 2 ; Roper Scientific) using a 100 ϫ 1. 49 numerical aperture CFI Apo objective (Nikon). Time-lapse movies were captured at 20 frames/s through an EM-CCD (Evolve512 delta; Photometrics) using MetaMorph software (Molecular Devices) for the indicated period and analyzed using custommade single-molecule analysis software  (Kechkar et al. , 2013; Nair et al. , 2013). To isolate trajectories of carriers that underwent directed motion from nonspecific noise and immobile objects, we selected the trajectories based on their duration (Ͼ25 consecutive frames) and with a mean square displacement (MSD)  (Steyer and Almers, 1999; Papadopulos et al.
, 2013)  to label the surface p75 NTR of neurons cultured in microfluidic devices. The labeled neurons were subjected to 5 min of BoNT/A-Hc-Atto647 pulse labeling at their nerve terminals under high K ϩ or low K ϩ conditions, and then washed and chased at 37°C for 2-4 h. The dual fluorophores were subsequently imaged sequentially at 0. 3 s intervals with a high-sensitivity EMCCD for 95 s and videos were analyzed for colocalization. In unstimulated neurons, 20. 5 Ϯ 2. 7% of BoNT/A-Hc carriers labeled for p75 NTR (Fig. 5A-C ). This colocalization ratio was not significantly altered by high K ϩ stimulation, with 17. 9 Ϯ 3. 0% of BoNT/A-Hc carriers also labeling for p75 NTR (Fig. 5A-C ). These data indicate that some BoNT/A-Hc carriers are indeed transported to the soma via the same endosomal pathway as p75 NTR.
We thank the  Bordeaux Imaging Center , part of the FranceBioImaging national infrastructure supported by the  French National Research Agency  ( ANR-10-INSB-04 );  Rowan Tweedale  for critical reading of the manuscript; and  Rachel Gormal ,  Vanesa Tomatis ,  Luke Hammond ,  Victor Anggono , and  Dusan Matusica  for expert technical assistance.
Comparative Genomic Hybridization (CGH) The CGH was performed using genomic DNA from the tumor samples co-hybridized with an equimolar mix of 10 ethnically-matched (finnish) DNA samples on NimbleGen 12x135K CGH arrays, which 60-mer probes spaced every 13 kb on average. Sample processing, hybridization and data acquisition were performed at Nimblegen according to an in-house standard protocol. CGH microarray data are available in the ArrayExpress database (www. ebi. ac. uk/arrayexpress) under accession number E-MTAB-2873. CGH data were analyzed as log2 values of the ratio between the fluorescences of tumor and reference genomic DNA samples, using MeV software (TM4 suite, http://www. tm4. org).
CGH and transcriptome correlations For large-scale alterations, the CGH data were averaged for sliding windows of 130 kb over the relevant chromosomes. For the transcriptomic data, we used our previously published data from the 10 tumors, as described in  [9]  (NimbleGen Human Expression 12 × 135 K array set, accession E-MTAB-483 in the ArrayExpress database). The two independent transcriptomic hybridizations were averaged for each transcript, and then we computed the average expression levels for each gene. To better measure the impact of large-scale genomic alterations on gene expression we divided the expression values for genes located within aneuploid regions by their mean expression in the tumors without the analyzed alteration. Expression ratios above/ below 1 in the natural scale (or above/below 0 in log2 scale) in aneuploid regions are suggestive of a "correlation" between genomic duplications/deletions and gene expression.