dataesr/scientific-paragraphs-categorization huggingface dataset:
Jessell); and Phox2b (1:500; gift from J. -F. Brunet, Institut de Biologie de l'École Normale Supérieure). Alexa 488-(A11001, A11008), FITC-(715-095-150, 706-095-148), Cy3-(715-165-150, 711-165-152, 706-165-148) and Cy5-conjugated (715-175-150, 711-175-152) secondary antibodies were used (Invitrogen or Jackson Immunoresearch, 1:2,000). For quantification, 100 cells in random fields were scored for coexpression of transgene and motor neuron markers by at least two independent authors (n = 1). Data distribution was assumed to be normal, but this was not formally tested. No statistical methods were used to pre-determine sample sizes, but our sample sizes are similar to those generally employed in the field.
Expression analysis RNA was extracted with Qiagen RNAeasy at different time points following manufacturer's instructions. For quantitative PCR analysis, cDNA was synthesized using SuperScript III (Invitrogen) and amplified using SYBR green brilliant PCR amplification kit (Stratagene) and quantified using an Mx3000 thermocycler (Stratagene). Data distribution was assumed to be normal, but this was not formally tested. No statistical methods were used to predetermine sample sizes, but our sample sizes are similar to those generally employed in the field. One independent differentiation was considered to be a biological replicate (n = 1). We used primers to Actb (TGAGAGGGA AATCGTGCGTGACAT and ACCGCTCGTTGCCAATAGTGATGA), eIsl1 (GTTGGAGAAAGTGGGAAATGAC and TAGAACAGACTTCATGCGCTTC), eNgn2 (TCGGCTTTAACTGGAGTGCC and GTGTGTTGTCGTTCTCGTGC), eLhx (CGTAGCCTCTAAATGCGAGA and TGGCAAAGGTGTCTGTTCAC), ePhox2a (CTCCTCCAACTGTGCGCTT and CTTGTAGGGAACTGCCG AGT), Hb9 (GAACACCAGTTCAAGCTCAACA and CTCTTCCGTCTT CTCCTCACTG), Tbx20 (TGACATTGAGAGGGAGAGTGTG and GAAG ATGACGATACCCAGGAAC), Chat (CGGTTTATTCTCTCCACCAG and TAACAGGCTCCATACCCATT) and Vacht (AGACTATGCCACGCTCTTCG and AGGCTCCTCGGGATACTTGT).
For arrays, RNA was amplified using NuGen Applause bundle amplification and labeling kit according to manufacturer's instructions. Labeled cDNA hybridized to Affymetrix Mouse Gene 1. 0 ST microarrays. Arrays were scanned using the GeneChip Scanner 3000. Data analysis was carried out using the oneChannelGUI BioConductor package  46. RMA-sketch normalization was performed across all arrays. Differentially expressed genes were defined by ranking all probesets by the moderated tstatistic-derived P value (adjusted for multiple testing using Benjamini & Hochberg's method and setting a threshold of P < 0. 001). Expression clustering of normalized data transformed by fold-change with respect to the average of the control replicates was performed using the MeV software (version 4. 7). When clustering the expression data, MeV used average linkage clustering with Pearson correlation as the distance metric.
DNA motif analysis De novo motif-finding was performed in 200-bp windows centered on the 500 top-ranked peaks for each examined subset of ChIP-seq binding events. GimmeMotifs (van Heeringen and Veenstra) was used to discover motifs by running and combining results from the motiffinders MDmodule, MEME, GADEM, MotifSampler, trawler, Improbizer, MoAn and BioProspector. The settings "-w 200 -a large -g mm9 -f 0. 5 -l 500" were used with GimmeMotifs.
Comparison of peaks and expression To compare peak locations with gene expression, we focused only on the genes that were probed on the Affymetrix Mouse Gene 1. 0ST array that also had annotations in the Ensembl mouse annotation (release 62). We defined a peak as being located near a gene (or vice versa) if the peak was located within 10 kbp of the gene's TSS or was overlapping the gene body (up to a maximum of 500 kbp from the TSS). Data distribution was assumed to be normal, but this was not formally tested. No statistical methods were used to pre-determine sample sizes, but our sample sizes are similar to those generally employed in the field.
Electrophysiology For whole-cell patch-clamp recordings, NIP and NIL cells were co-cultured with mouse primary cortical astrocytes. Briefly, astrocytes were prepared as previously described  50  and plated on 25-mm diameter coverslips at a density of 50,000 cells per well in a six-well plate. 4 d following astrocyte plating, freshly dissociated NIP and NIL cells were added to the wells at a density of 100,000 cells per well. Cultures were maintained for 7 d before recording. Current-clamp recordings were performed using an Axopatch 2B amplifier. Data were digitized using a Digidata 1322A digital to analog converter and were recorded at a 10-kHz sample rate using pClamp 10 software (all equipment from Molecular Devices). Patch pipettes were fabricated using a P-97 pipette puller (Sutter Instruments).
Acknowledgments We would like to thank  I. Lieberam  ( King's College ) for assistance introducing the Hb9-GFP transgene, members of the  Wichterle laboratory  for helpful comments,  S. Brenner-Morton  and  T. Jessell  ( Columbia University ) for sharing clones of Isl monoclonal antibodies,  J. -F. Brunet  for Phox2a and Phox2b antibodies, and  I. Schieren  for technical assistance with flow cytometry. E. O. M. receives funding from the  Damon Runyon Cancer Research Foundation  ( DRG-1937-07 ). Personnel and work were supported by the  Project ALS foundation and US National Institutes of Health  grants  P01 NS055923  (D. K. G. and H. W. ) and  R01 NS078097  (H. W. ).
Acknowledgements The authors are grateful to the Director,  Botanical Survey of India (BSI) ,  Kolkata (India)  and the Dept. of  Forest, Environment and Wild Life Management, Gangtok (India)  for providing facilities during this study. The first author is indebted to  Annemieke Verbeken  ( Belgium ) for providing some invaluable literature. Special thanks are also given to  S. K. Rai , and  R. K. Ram  of  BSI, Gangtok  for assisting the first author in many ways. The help rendered by  S. C. Maikap  in obtaining the scanning electron micrographs of basidiospores is also duly acknowledged.
083%/min, a rate at least 7 times slower than the forensiX tube. In the forensiX tube, the nylon flocked swab (which was attached to a plastic stem) was completely dry within 4 hours, and the cotton swab (which was attached to a wood stem), dried to a level of 10% remaining water within 6 hours. Under the experimental conditions of 24 ± 2 ∘ C and a relative humidity of 50 ± 5%, the swab in the Sarstedt tube dried completely in approximately 29 hours (extrapolated from the Sarstedt data in Figure  3 ).
Immunoblotting-Immunoblotting, using protein lysates from neonatal brain, heart, liver, and quadriceps/hamstring muscles to detect SCOT (rabbit anti-SCOT; Proteintech Group), actin (rabbit anti-actin; Sigma), HMGCS2 (rabbit anti-mHMGCS; Santa Cruz Biotechnology), PDH-E1␣ (rabbit antipyruvate dehydrogenase E1-␣ subunit antibody; Abcam ab155096), phosphoserine 293 PDH-E1␣ (PhosphoDetect TM anti-PDH-E1␣ (Ser(P)-293 rabbit antibody; Millipore AP1062), and BDH1 (rabbit anti-BDH1; Proteintech Group) was performed as described previously  (34). Band intensities were quantified densitometrically using QuantityOne software (Bio-Rad). In Vitro Ketogenesis of Hepatic Explants-Neonatal mice were sacrificed by decapitation. Livers were collected and weighed, and each liver was placed in a single well of a 6-well tissue culture plate containing 2 ml of phosphate-buffered saline (PBS) on ice.
These cells express green fluorescence protein (GFP). Mesenchymal stem cells (MSCs) were purchased from Stem Cells, Inc (MSC-001 F, Vancouver, CA) maintained and expanded in culture using MesenCult W MSC Basal Medium completed with Mesenchymal Stem Cell Stimulatory Supplements (Stem Cell Inc, Vancouver, CA). Their ability to differentiate in adipocytes, osteoblasts and chnodrocytes was verified as instructed by the supplier (data not shown). All cultured cells were incubated at 37°C under a water-saturated 95% air-5% CO 2 atmosphere. Shaking cultures were performed similarly using a rocking plates at low speed.
Analysis of transfer by flow cytometry After co-culture, cells were trypsinized, resuspended and washed with PBS. Fluorescence (FL) was quantified on a SORP FACSAria2 (BD Biosciences). Data were processed with FACSDiva 6. 3 software (BD Biosciences). Doublets were excluded by FSC-W x FSC-H and SSC-W x SSC-H analysis; eGFP fluorescence was acquired with 488 nm blue laser and 510/50 nm emission, Mitotracker Deep Red was acquired with 640 nm red laser and 670/14 nm emission. Figures display the median of fluorescence intensity (mfi) relative to control. Single stained channels were used for compensation and fluorophore minus one (FMO) controls were used for gating. 20,000 events were acquired per sample.
Statistical analysis All quantitative data are expressed as mean ± standard error of the mean (SEM). Statistical analysis was performed using SigmaPlot 11 (Systat Software Inc. , Chicago, IL). A Shapiro-Wilk normality test, with a p = 0. 05 rejection value, was used to test normal distribution of data prior to further analysis. All pairwise multiple comparisons were performed by one way ANOVA followed by Holm-Sidak posthoc tests for data with normal distribution or by Kruskal-Wallis analysis of variance on ranks followed by Tukey posthoc tests, in case of failed normality test. Paired comparisons were performed by Student's t-tests or by Mann-Whitney rank sum tests in case of unequal variance or failed normality test. Statistical significance was accepted for p < 0. 05 (*), p < 0. 01 (**) or p < 0.
TnTs seemed similarly distributed among cell types. However, at a ratio of 1 MCF7 /1 stromal cell, only endothelial cells were able to transfer mitochondria to MCF7s (Figure  5A-B ). MSCs mitochondria transfer to cancer cells could only be visualized using an increased ratio (1/10) of MCF7/ MSCs (Additional file 1: Figure  S4 ). We then established a tri-culture system (MCF7, MSCs and E4 + ECs). TnTs were observed between all different cell types, however, in this setting, MCF7 only acquired E4 + ECs mitochondria (Figure  5C ). We could also detect uptake of E4 + ECs mitochondria by M-Orange-MSCs. Our data provided evidence for a preferential transfer of mitochondria from endothelial cells under our culture conditions. One of the most common criticisms of such experiment is the ability of the dyes to diffuse.
Acknowledgements This publication was made possible by grants from the  Qatar National Research Fund  under its  National Priorities Research Program  award number  NPRP 09-1174-3-291  and  NPRP 4-640-1-096. Its contents are solely the responsibility of the authors and do not necessarily represent the views of the  Qatar National Research Fund. We thank  Johannes Graumann  for critical reading of this paper and suggestions. We would like to acknowledge  Andrew Bliszczyk  for editorial assistance. We would like to thank  Huda Ali Ahmadi  for her help in video organization.
Statistical analysis A descriptive statistical analysis of the involved variables was performed in order to characterize the sample. Comparative analysis between eutrophic and obese groups was performed. The χ 2 test was used for qualitative variables. Given the non-normal distribution of the quantitative variables, the Mann-Whitney nonparametric test was applied. Statistical tests and plots were used to test normality. A significance level of 5% was adopted for all statistical analyses. Data were analyzed using the SPSS for Windows, version 16. 0, statistical software package.
To assess the burden, data are collected using questionnaires and there is a well defined methodology to built and validate QoL questionnaires. However, the burden questionnaires are still poorly developed. Two previous published questionnaires for evaluating the burden were established according to this rigorous methodology of QoL questionnaires: the "Burden of fibromyalgia" and the "Burden of chronic venous disorders"  [14, 16]. The aim of this study was to create and validate a French questionnaire to evaluate the burden on families of patients affected by ichthyosis.
, 2011). For camel milk, counting procedures that are specific for DNA should be used to measure SCC. Recently, bulk milk samples from our farm were analyzed with a DNA-specific, automatic cell counter  (Wernery et al. , 2008). We also reported preliminary data on SCC values in bulk milk using direct microscopic counting after pyronin Y-methyl green (PMG) staining  (Nagy et al. , 2013). It is important to analyze a large number of bulk milk samples and to compare different methods to provide guidelines and reference values for SCC in camel milk. The interaction between milk quality parameters and various factors influencing milk quality has been studied extensively in conventional dairy species. In cow and sheep milk, low bulk tank bacterial count is associated with low SCC and the increase in one parameter coincides with the increase of the other  (Jayarao et al.
Milking of Dromedaries: Milking Parlor and Milking Routine Dromedaries were milked twice a day with an automatic system in a 2 × 12 herringbone milking parlor. Milk yield (kg) of individual dromedaries was measured during each milking with an International Committee for Animal Recording (ICAR)-approved milk meter. Data were collected by herd management software  (Nagy et al. , 2013). Before milking, the udder and teats were manually stimulated by gentle massage and were cleaned with a disposable, nonwoven tissue containing surfactant and quaternary ammonium compound (Profilac Dermapre, WestfaliaSurge, Bönen, Germany; MPS udder wipes, Anichem, Dubai, United Arab Emirates). The udder was also evaluated by the milker for the presence of clinical mastitis and injury. Camels with clinical mastitis or after prophylactic treatment were milked by hand and the milk was discarded.
In accordance with this, the stage of lactation of the milking herd also showed a clear seasonal pattern, but its peak and nadir were different from those of the production parameters. We calculated the PPD for each production day, including all dromedaries that contributed to the bulk milk, and this PPD was used as summary data to characterize the stage of lactation of the entire milking herd. Mean PPD was the lowest during the spring (292 d) and highest during the autumn period (376 d). This finding corresponds to the reproductive physiology of the species and to present management practices. The seasonal pattern of PPD indicates that the proportions of early-lactating and late-lactating camels increased during the spring and autumn, respectively. As expected, production parameters were highly correlated.
The two spectrometers were set symmetrically on the two sides of the beam line in two kinematical settings corresponding to central momenta of 1:421 GeV=c at a scattering angle of 63. 16 and 1:389 GeV=c at a scattering angle of 65. 82. For each spectrometer, the scattering angles, momenta, and interaction positions at the target were reconstructed from trajectories measured with vertical drift chambers located in the focal plane. Two planes of plastic scintillators provided triggering and time-of-flight information for particle identification. Figure  1  shows the speed of the two particles detected in coincidence. One clearly sees protons and deuterons in coincidence, with no visible backgrounds, such as pp and dd coincidences, or pions. In analyzing the data from E03-101, the incident photon energy of the untagged beam was reconstructed event by event from the momentum and angles of the scattered particles under the assumption of two-body pd final-state kinematics.
The detected proton-deuteron pairs can result from either a photon or an electron disintegrating the 3 He nucleus. We took data with the radiator in and out of the beam, to extract the number of events resulting from photons produced in the bremsstrahlung radiator  [13, 17]. Event selection cuts on the target vertex and coincidence between the two spectrometers were applied using the same techniques as  [17]. The finite acceptance correction was determined using the standard Hall-A Monte Carlo simulation software MCEEP  [31]. The sources for the systematic uncertainties for E03-101 are described in  [17] ; for this analysis they are dominated by the finite acceptance correction, which is at the 4%-11% level. Experiment E93-044 used the CEBAF large acceptance spectrometer (CLAS) to measure various photoproduction reactions on 3 He and 4 He targets.
While the peak contains predominantly the pd events of interest, the broader structure contains background produced in the reaction 3 He ! pdX, where X could be one or more missing particles. The low-mass tail of the background events extends under the pd peak. Our kinematic cuts select the good pd events from the initial sample and reject background events. For simplicity, in Fig. 2  we show the events rejected by our kinematic cuts overlaid with the initial distribution. These background events exhibit smooth behavior under the deuteron peak and reproduce the background shape outside of the peak. The uncertainty of the yield extraction due to the remaining background events is ð2:30 AE 0:63Þ%. The CLAS acceptance for the reaction 3 He ! pd was evaluated by generating 2 Â 10 7 phase-space events and processing them through GSIM  [35] , a GEANT-3 program that simulates CLAS.
We thank  S. J. Brodsky ,  L. L. Frankfurt ,  M. M. Sargsian , and  M. Strikman  for helpful discussions. We thank the  JLab physics  and accelerator divisions for their support. This work was supported in part by the  U. S. National Science Foundation  under Grant No. PHY-0856010 , the  U. S. Department of Energy , the  Israel Science Foundation , the  U. S. -Israeli Bi-National Scientific Foundation , the  Chilean Comision Nacional de Investigacion Cientı ´fica y Tecnologica (CONICYT) , the  Istituto Nazionale di Fisica Nucleare , the  French Centre National de la Recherche Scientifique , the  French Commissariat al'Energie Atomique , the  UK Science and Technology Facilities Council (STFC) , the  Scottish Universities Physics Alliance (SUPA) , and the  National Research Foundation of Korea.
Nearby galaxy data Since the dust evolution models have often been 'calibrated' with nearby galaxy data (e. g. Lisenfeld & Ferrara 1998; Dwek 1998; Hirashita 1999 ), it would be interesting to examine if there is a difference in the D -Z relation between the GRB sample and nearby galaxies. For the uniformity of data, we select the samples compiled by Hirashita & Kuo (2011) (see the references therein for original data), who construct the sample based on an AKARI sample: eight blue compact dwarf galaxies (BCDs) and three spiral galaxies. Note that the dust content is measured by far-infrared emission, not by extinction. We also include two spiral galaxies whose dust content is measured by extinction to confirm that there is no systematic difference in the estimate of dust content. More data are seen in e.
); PE-mIgG2b isotype control (clone 133303) from R&D Systems (Abingdon, England); FITC-CD146 (mIgG1; clone P1H12) from Millipore Ltd. , Bedford, MA, USA; FITC-CD105 (mIgG1; clone 166707), PE-CD144 (clone 16B1; mlgG1, E-Bioscience, Hatfield, England) APC-CD34 (clone BIRMA-K3, mlgG1, DakoCytomation, Glostrup, Denmark). Cells were analysed on a BD LSR II flow cytometer using FACSDiva software (BD Biosciences) as previously described  [34, 42, 43]. Cell viability was determined as negative staining for the Topro-3 dye (Invitrogen Ltd. ). Results for the phenotypic analyses of the UCB ECFC derived cells are presented in Figure  S1. Umbilical cord ECFC derived cells were CD31 + CD73 + CD105 + CD146 + CD144 + CD45 2 CD14 2 CD133 2 and displayed variable CD34 levels in culture, confirming their endothelial lineage phenotype.
Photographs of the stained nuclei were taken from a minimum of 10 fields of view (20X) for each membrane using an inverted TE300 microscope (Nikon Ltd. , London, England) fitted with a cooled CCD camera and Simple PCI software (Digital Pixel, Brighton, England) and experiments were performed repeated twice. Statistical analysis was performed using Student's t-test. For the in vitro blocking experiments, IL-8 and PDGF-AB/ BB were blocked in SS-AF-MSC-CM with the respective neutralizing Abs described above at a concentration of 5 mg/ml for 10-30 min at 4uC. CM was also incubated under the same conditions with irrelevant control Abs. For MMP-9 blocking experiments, the MMP-9 inhibitor-I (15 mM) was added in SS-AF-MSC-CM. Fresh EGM-2 medium and CM derived from HEK-293 T cells were used as control media.
eGFP labeled UCB ECFC (p4-6) were detached with trypsin-EDTA, counted, resuspended in complete EGM-2 medium and added to the wells with the preplated SS-AF-MSCs, BMSCs or hDF. The plates were gently swirled, incubated at 37uC and 5% CO 2 , the medium was changed every 2-3 days and the cells were cultured for up to 14 days at which point the cells were fixed, and eGFPexpressing tubules were photographed at 46 magnification on an inverted TE300 microscope (Nikon Ltd. ) fitted with a cooled CCD camera and Simple PCI software (Digital Pixel). Images were processed in Adobe Photoshop 7 and tubule numbers, lengths and number of junctions were quantified using Angiosys software (TCS Cellworks, Buckingham, England). To test the sensitivity of vascular tubule development to anti-angiogenic factors, SS-AF-MSCs, BMSCs or hDFs were co-cultured with UCB ECFC derived cells and SU6668 inhibitor (at 5 and 10 mM in DMSO; Calbiochem)  [42]  was added to co-cultured cells in triplicate wells in complete EGM-2 medium at the initiation of the culture.
Tubule Analysis Using Angiosys Software Quantitation of the vascular tubules was performed by photographing eGFP-expressing tubules at 46 magnification on an inverted TE300 microscope (Nikon Ltd) fitted with a cooled CCD camera and Simple PCI software (Digital Pixel). Images were processed in Adobe Photoshop 7 and image analysis of tubule numbers, lengths and number of junctions were quantified using Angiosys software (TCS Cellworks) as described  [41, 42]. For quantification, cells were cultured in triplicate, then 4 central fields/well were analyzed from each assay well. Results for the different groups assayed are expressed as means 6S. E. M.
Proteome Profiler Arrays of Conditioned Media (CM) For the preparation of the CM, 1610 6 SS-AF-MSCs, BMSCs, UCB ECFC or hDFs were cultured until 80% confluent in their respective media, and then the media were replaced with EBM-2 medium containing 0. 5% (v/v) FCS to prevent protein aggregation. The cells were cultured for a further 24 hours and the CM was collected and concentrated approximately 25-fold using ultra filtration units with a 3-kD cut-off (Millipore Ltd. Ltd. ), and analyzed for specific proteins using proteome profiler arrays for angiogenesis growth factors (Catalog # ARY007, R&D Systems Inc. , Minneapolis, USA) according to the manufacturer's instructions. Quantitation of the detected spots was performed using the Quantity One Software 4. 4. 1 (BioRad Laboratories Inc. , Amersham, England).
Images were taken with a Leica CTR MIC microscope and then the number of vessels per mm 2 and the diameter of each vessel (in microns) were estimated using the Image J 1. 386 software (http://rsb. info. nih. gov/ij/). Statistical analysis was performed using Student's t test, (*p,0. 05). A minimum of 15 fields of view (at 406 magnification) was analyzed from each photograph. Error bars indicate S. D. of the mean for 10 photographs from each group.