dataesr/scientific-paragraphs-categorization huggingface dataset:
Analysis of the MT Bundle Dynamics with Kymographs Time-lapse movies were treated with filters (equalize light, low pass and flatten background of Metamorph software) to improve signal/noise ratio. Kymographs of the MTs were generated using Metamorph and analyzed with ImageJ (Rasband, W. S. , ImageJ, U. S. National Institutes of Health, Bethesda, Maryland, USA, http:// rsb. info. nih. gov/ij/, 1997-2008). In the present study, we considered as bundle all arrays that contain at least 2 distinguishable MTs, as judged by the presence of several MT traces on the kymographs. Kymographs where several MT traces could not be unambiguously distinguished have not been considered as bundles. Elongation/ shortening rates correspond to the slope of elongating/shrinking MTs inside the bundles respectively.
This work was funded by grants from the  CNRS , the  CEA  and from the  French Research Ministry  (D. P and V. F). We also thank the  Agence Nationale de la Recherche  ( ANR-08-Syscom_013 , J-L. M. ) and the  Institute of Complex Systems IXXI-Rhone-Alpes  (J-L. M). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Locus Primer sequences (5 ′ -3 ′ ) http://www. bioone. org/loi/apps (population P around Montpellier, and population C around Dijon). GPS coordinates of the four populations are in Table  2. For each of the four populations a voucher has been deposited in the Botanical Institute of Montpellier herbarium collection (voucher accession numbers: population C, MPU000543; population E, MPU000544; population M, MPU000545; and population P, MPU000546). Nineteen to 40 individuals were sampled per population ( Table  2  ). Total DNA was extracted from dried plant tissue using the DNeasy96 Plant Kit (QIAGEN) following the manufacturer's protocol for dry plant tissue, with an additional lysis step of incubation at 65 ° C for 90 min. Multiplex PCR amplifi cation was performed with the same protocol as cited above.
The ICC's were 0 or nearly so for all outcomes (knowledge, decisional comfort, medication adherence), indicating no clustering, so analyses were not adjusted for clustering. Furthermore, in a secondary analysis, all results were the same after adjusting for clustering (data not shown). Secondary outcomes of satisfaction with knowledge transfer, change in laboratory values, and post-index visit cardiovascular risk knowledge (statin discussion only) were compared using a Fisher's exact test. The postindex visit, 3 and 6 months knowledge (diabetes medication discussion only) was compared using the Wilcoxon rank sum test. Study data were recorded and managed using the Research Electronic Data Capture (REDCap) system  [19]. All analysis and data management were conducted using SAS (version 9. 2) or Stata statistical software (version 11.
Acknowledgements Olmsted Medical Center,  Alice Medlyn , RN 1 ;  Linda Paradise , RN 1 ; Randy Hemann, MD 2 ;  Daniel Swartz , MD 2 ; Linda Williams, MD 2 ; Craig Thauwald, MD 2 ;  Daniel Pesch , MD 2 ;  Shaun Dekutoski , MD 2 ;  Dale Loeffler ,  DO 2  ;  Penny Louise Flavin ,  RN 2. Mayo Clinic , Sara Heim 1  ;  Vicki Clark  1 ; Kasey Boehmer 3 ;  Laura Pelaez , MD 2 ;  Jennifer Pecina 2 , MD ;  Gregory Bartel , MD 2 ;  Marc Matthews , MD 2. 1. Study coordinator. 2. Site champion. 3. Administrative support.
MLV and SIN-MLV vectors share the same integration profile in the genome of human HSPCs To generate a high-definition integration profile of SIN MLV integrations in human HSPCs, we transduced umbilical cord blood-derived CD34 + cells with a previously described SIN-MLV vector carrying a GFP expression cassette under the control of the human elongation factor 1a (EFS) promoter  [16, 21]. Cells were transduced at 40 to 60% efficiency, and were selected for GFP expression by cell sorting 10 days after infection, to dilute unintegrated vectors. Vector-genome junctions were amplified from genomic DNA by ligation-mediated (LM)-PCR and pyrosequenced as previously described  [4]. Raw sequences (available at the NCBI Sequence Read Archive with the accession number SRA061405) were processed by a previously described bioinformatic pipeline  [4]  and mapped on the University of California at Santa Cruz (UCSC) hg19 release of the human genome (http://genome.
ucsc. edu), to obtain 13,011 unique insertion sites. Two previously generated datasets of full-LTR MLV vector integrations  (32, 574)  and random sites (40,000) normalized for a number of parameters  [4]  were re-annotated on the hg19 release of the human genome and used for comparison. To identify differences in the integration preferences of MLV and SIN-MLV in HSPCs, we first analyzed the relationship between integration sites and Known Genes (UCSC definition) in the human genome: integration were annotated as TSS-proximal when occurring in an interval of 62. 5 kb from the TSS of any Known Gene, intragenic when occurring inside a Known Gene. 2. 5 kb from the TSS, and intergenic in all other cases. Intergenic and intragenic integrations were ,40% for both MLV and SIN-MLV, while TSS-proximal integrations were 22.
0 and 7. 7% respectively, P. 0. 1), and showed a virtually identical distribution at 62. 5 kb around the feature midpoint (Figure  S1B ). In all cases, there were significant differences between the distributions of the two MLV vectors and that of the random controls (P,10 215 ). We previously reported that MLV integrations are strongly associated with histone modifications marking transcriptionally active promoters and enhancers, with the specialized H2A. Z histone variant, and with binding sites for RNA Pol II and transcription factors in both HSCs and T cells  [4, 20, 23]. Taking advantage of published ChIP-Seq datasets on epigenetic features in the chromatin of human CD34 + HSPCs  [24] , we analyzed the association of MLV and SIN-MLV integrations with histone modifications marking active enhancers and promoters (H3K4me1, H3K4me3) and heterochromatin (H3K27me3), H2A.
Z and binding of Pol II. In all cases, there was no obvious difference between the two vectors: we observed a strong association with H3K4me1, H3K4me3, Pol II and H2A. Z, and no correlation with H3K27me3 (Figure  1C  and Figure  S1C ). All together, these data indicate that the absence of the U3 region of the LTR of the SIN-MLV vector causes no significant change in the integration preferences of MLV in the genome of human HSPCs.
The nonoverlapping clusters contained only 3 integrations and mapped less than 200-bp apart in the MLV and SIN-MLV datasets. We then looked at the integration clusters of both vectors in a number of individual loci characteristically hit at high frequency by MLV integration. Most of the loci highly targeted by MLV were targeted also by SIN-MLV. Whenever the numerosity was sufficient, we observed a striking overlap between the integration hot spots of the two vectors within the same loci. As examples, SIN-MLV integrations faithfully reproduced the MLV integration patterns in the LMO2, EVI2A/B, RUNX1, RUNX2, ZNF217-BCAS1, CD34, ELF1 and NFE2 loci, which were targeted at the same overall frequency and at the same hot spots within each locus (Figure  2  and Figure  S2 ). We also found SIN-MLV integrations mapping very closely to the MLV integrations in two hot spots (MECOM and PRDM16) observed in the CGD and WAS clinical trials  [13, 14, 15]  (Figure  S2 ).
Written informed consent was received from participants prior to inclusion in the study. Distribution of the distance of SIN-MLV (green bars) and MLV (red bars) integration sites from the TSS of targeted genes at 2,500 bp (a) or 50 bp (b) resolution. The percentage of genes targeted at each position is plotted on the y axis. The number of plotted sites is higher than the actual number of mapped integrations sites, since each site may relate to more than one gene. The black line indicates the distribution of random control sites. (c) The distribution of H3K4me1 (top panels) and H3K4me3 (lower panels) epigenetic marks in a 10-kb window around vector integration sites (IS) is shown for MLV integrations (left panels) or SIN-MLV integrations (right panels). The mean density of tags (tag/50 bp) of the reference dataset (i.
Genomic features were annotated when their genomic coordinates overlapped for $1 nucleotide with a 650-kb interval around each integration site. We used UCSC tracks for both cytosine-phosphate-guanosine (CpG) islands and conserved TFBSs. The genomic coordinates of 82,335 mammalian conserved non-coding sequences (CNCs) were previously described  [22]. For the association of the integrations with epigenetic marks, we re-annotated published ChIP-Seq data  [24]  in the UCSC hg19 release of the human genome, and analyzed the distribution of histone modifications (H3K4me1, H3K4me3, H3K27me3) H2A. Z and Pol II binding sites around the integrations, using the seqMINER platform  [41]. Previously generated MLV integrations and random control sequences datasets  [4]  were also re-annotated on the UCSC hg19 genome.
Figure1. Genomic distribution and association with histone modifications of MLV and SIN-MLV integrations in human HSPCs. Distribution of the distance of SIN-MLV (green bars) and MLV (red bars) integration sites from the TSS of targeted genes at 2,500 bp (a) or 50 bp (b) resolution. The percentage of genes targeted at each position is plotted on the y axis. The number of plotted sites is higher than the actual number of mapped integrations sites, since each site may relate to more than one gene. The black line indicates the distribution of random control sites. (c) The distribution of H3K4me1 (top panels) and H3K4me3 (lower panels) epigenetic marks in a 10-kb window around vector integration sites (IS) is shown for MLV integrations (left panels) or SIN-MLV integrations (right panels). The mean density of tags (tag/50 bp) of the reference dataset (i.
Song analysis For song analyses, we used Avisoft SASLab pro v. 5. 1. 14 software and Praat v. 5. 3. 12. Song files were first high-pass filtered (FFT filtering, cut-off frequency: 1600 Hz) to remove the lowfrequency background noise. Then, we selected two songs per individual with the highest signal to noise ratio (N = 40, mean duration: 18667. 1 s). We analysed the first 20 s of song produced during the ascending phase and 20 s of song produced exactly in the middle of the level phase (Fig. 1 ). Songs were visualized on a sound spectrogram (FFT-length: 1024; Frame: 100%; Hamming window). A syllable was defined as a continuous trace on the sound spectrogram or a group of continuous traces spaced out by less than 25 ms (Fig. 2 ). Following methods described elsewhere  [4]  syllables were classified in syllable types according to their overall frequency modulation shapes and labelled on the sound spectrogram with a number.
Likewise the same syllable type found in the song of different individuals was labelled with the same number. Then, we examined the sequential organization of syllables using a custom made Matlab program (The MathWorks, Natick, MA, USA; see  [4] ). To this end, numbers corresponding to the syllable labels were entered into the program in the sequential order of their appearance in the song. By classifying sequences of syllables according to their length and the number of times they were Table  1. Measures of response recorded during playback experiments.
3 ). The duration of each stimulus was 80 s in total. We rescaled each song part to root mean square equalized amplitudes using a script implemented in Praat (www. gbeckers. nl/ pages/praat_scripts/rms_equalize. praat_script). When played back from the side of NR, stimuli consisting of 40 s of the ascending phase of the NR (the first 20 s of song produced during the ascending phase, broadcasted twice) followed by 40 s of the level phase of the NL (20 second of song produced exactly in the middle of the level phase, broadcasted twice) were named stimuli S1. Likewise, stimuli consisting of the ascending phase of the NL and the level phase of the NR were named stimuli S2. The same design was followed for the playback from the side of NL with S1 corresponding to the ascending phase of NL and the level phase of NR and S2 corresponding to the ascending phase of NR and the level phase of NL (Fig.
Acknowledgments We thank the farmers around the  University Paris Sud  for allowing us to work on their land. Roger Mundry  kindly provided the pDFA scripts and  Katia Lehongre  and  ChloeHuetz  for the Matlab scripts. We thank  Mihai Valcu  and  Christina Sommer  for statistical advice. We also thank  Hene Courvoisier  and  Elodie Briefer  for discussions. We are very grateful to three anonymous referees for comments and suggestions.
ELECTROPHYSIOLOGICAL RECORDINGS AND ANALYSIS When plated on primary cortical neurons or on primary glial cells, hNP-derived neurons were selected by their fluorescence. Recordings were done at room temperature (22-25 • C) using a Multiclamp 700A patch-clamp amplifier and pClamp 10. 2 software (Molecular Devices) as in  Cestèle et al. (2008). For the recordings of total ionic currents, signals were filtered at 10 kHz and sampled at 100 kHz. We recorded sodium currents using the whole-cell configuration of the patch-clamp technique. Recordings were usually started 5 min after the rupture of the membrane patch, to allow intracellular dialysis with the pipette solution. The external bath solution contained the following (in mM): 129 NaCl, 1. 25 NaH 2 PO 4 , 35 glucose, 1. 8 MgSO 2 , 1. 6 CaCl 2 , 3 KCl and 10 HEPES, pH 7.
All green cells also expressed the human nuclei protein (hNa), demonstrating that the neuronal cells we obtained derived from human cells (Figure  3A ). As the infection efficiency of the EGFP-expressing lentivirus was lower than 100%, some non-green cells were also positive for hNa. We analyzed neuronal differentiation by immunofluorescence using MAP2 for labeling dendrites and VGLUT and Synaptophysin (Syn) for labeling synapses. hNP-derived neurons had elaborate dendritic arbors and many Synaptophysin-positive puncta, and VGLUT positive puncta were detected starting around day 60 of differentiation (Figure  3A  bottom). We observed that the majority of the neurons generated from hNP cell cultures were MAP2 and VGLUT positive neurons, and we basically did not detect MAP2 and GABA double-positive cells (data not shown), indicating that we mainly obtained excitatory neurons.
, 2012). The differentiation potential of these cells into glial cells has been also determined (data not shown). In summary, we describe a simple culture procedure to reproducibly and efficiently generate hNP cell lines from human iPSCs. These cells self-renew rapidly and can be stimulated to mature into different subtypes of neurons. We show that the rate of differentiation is strictly dependent on the strategy used to differentiate hNP cells and that the co-culture with rat cortical neurons is the most efficient way to obtain completely functional and morphologically developed neurons. The ability to obtain mature and functional neurons from self-renewing hNPs has major implications for regenerative medicine. Moreover, these lines will provide innovative experimental platforms to investigate mechanisms of neuronal differentiation and can serve as a model system for unveiling disease pathogenesis, for drug screening and toxicity tests.
ACKNOWLEDGMENTS This work was financially supported by  Comitato Telethon Fondazione Onlus , grant no. GGP09196  and  GGP11095  (to  Carlo Sala ) and  GGP10066  (to Domenico Delia),  Fondazione   CARIPLO  project number  2012-0593 ,  Italian Institute of Technology, Seed Grant, Ministry of Health  in the frame of  ERA-NET NEURON ,  PNR-CNR Aging Program 2012-2014  (to  Carlo Sala ),  LabEx ICST  (to  Massimo Mantegazza ) and  CNRS-PICS  (to  Massimo Mantegazza  and  Silvana Franceschetti ).
Tetranychus urticae females overwinter in a state of diapause. This facultative diapause is induced by short-day conditions during the period of juvenile development of females  [36]. In the present work, we examined the physiological similarities and specificities of cold hardiness and diapause by comparing the metabolic fingerprints of diapausing and nondiapausing females of T. urticae in the presence and absence of cold acclimation. In addition to the species' pest status, we believe that this chill tolerant mite  [19] , for which the complete genome has been recently published  [37] , may soon become a biological model for ecophysiological studies. We report the first metabolomics dataset for this species by conducting GC-MS analyses with an uncommon full automated online derivatization process that ensured a complete quality control.
Detection was achieved using MS detection in electronic impact (EI). In the present work, we used the selective ion monitoring mode (SIM) (electron energy: 270 eV), ensuring a precise annotation of the detected peaks. Then, we searched for the metabolites that were included in our spectral database (58 pure reference compounds, including the internal standard; Table  S1 ). The peaks were accurately annotated using both their mass spectra (two specific ions) and their retention time. Calibration curves were set using samples consisting of 58 pure reference compounds at levels of 1, 2, 5, 10, 20, 50, 100, 200, 500, 750, 1000, 1500 and 2000 mM. Chromatograms were deconvoluted using XCalibur v2. 0. 7 software (Thermo Fischer Scientific Inc, Waltham, MA, USA). Metabolite levels were quantified according to their calibration curves.
Statistical Analyses Two-way ANOVA with an acceptable significance level of P,0. 05 was performed for cold tolerance data analysis with SPSS version 16. 0 for windows. The correlation between survival and experimental temperature was determined using a binary logistic regression model  [38]. Among non-structural carbohydrates, amino acids and organic acids, 47 compounds (out of 58 from our library) were identified in female T. urticae, of which 7 were below the quantification limit of the GC-MS (see Table  S1 ). These seven compounds (dopamine, erythritol, galacturonic acid, gentiobiose, saccharose, succinate, and trehalose) were discarded from the multivariate analyses. First, metabolite concentrations, which were expressed as nmoles/mg fresh mass, were logtransformed. Variations in the quantities of total metabolites, total amino acids, and individual metabolites were then examined among the four experimental conditions (D, ND, DA5, NDA5) using an ANOVA with a Tukey post-hoc procedure.
Acknowledgments The authors thank the  Tarbiat Modares University (Tehran, Iran ) that funded the experiments and the travel of S. Khodayari to France. University of Rennes 1  ( Action Incitative de Recherche 2012-Collaborations Internationales ) assisted the stay of S. Khodayari in France. We thank one anonymous referee,  David Denlinger  ( Ohio State University, Columbus, USA ) and Vladimir Kos ˇtal ( Institute of Entomology, Biology Centre AS CR, Ceske Budejovice, Czech Republic ) for helpful comments on an earlier version of the paper. We are grateful to  Marie Chauris  for technical assistance.
Methods/design Overall study design This is a multicentre, randomized controlled trial using a 2×(2×2) factorial design across nine European countries. Pregnant women attending a participating antenatal clinic or hospital in one of these countries will be approached and asked to take part in the study. Baseline assessment will occur before 20 weeks gestation, immediately followed by randomization into one of the eight, pre-stratified intervention groups. Follow up measurements will occur at 24-28 weeks, 35-37 weeks and birth. This trial is funded by the European Union 7th framework (FP7/ 2007-2013) under Grant Agreement no. 242187, further local funding is received in some of the individual centres. All study procedures have been pilot tested and modified as necessary for the main study. The study was approved by the relevant ethical committees before the start of DALI (NRES Committee East of England -Norfolk:.
1. 1) [25]. In the end all lifestyle coaches should be able to 'roll with resistance', express empathy, develop discrepancy, support self-efficacy, elicit change talk, make complex reflections and ask open questions. The coaching sessions will be supervised and evaluated by a local MI trainer to optimise coaching quality and to minimize variation between coaches. Each counselling session will be recorded to understand the interaction between the coach and participant, with the participant's permission. The content, together with general characteristics, will be summarized in a report that is then filed in the database for future thematic analysis. In the pilot study lifestyle coaches have become acquainted with the protocol and the target group. Each coach has to confirm they have read the DALI study materials, provide written descriptions of some aspects of DALI, and attend an observed 'standardisation session' where their interaction with a mock participant is videoed.
Data collection Data will be collected from participants at four time points (see Table  1 ): baseline/screening measurement (<20 weeks), at 24-28 weeks, at 35-37 weeks and after delivery. These visits are scheduled mostly together with usual care visits, to minimize time consuming study visits. At these time points (except at delivery) an OGTT is performed. In between blood collections, participants will be asked to complete a questionnaire and anthropometric measurements will be performed as well. The women will be asked to wear an accelerometer for 3 days including a weekend/holiday day and write down their nutritional intake in a food diary for that period. These data can be sent back with a reply-paid envelope which is provided to them. At first trimester, 24-28 weeks and 35-37 weeks, data of obstetrical ultrasound examinations will be collected, depending on the study site whether these check-ups are usual care visits or additional to the study.
Participants will wear this device at least for three days, including two days during the week (Monday-Friday) and one day in the weekend (Saturday or Sunday) or a holiday day. Data from waking up until going to bed will be used for analysis. The participants will be asked to remove the accelerometer while swimming, showering or bathing, because it is not waterproof. At such non-wearing intervals participants will be asked to write down what they did in an activity log. For the purpose of the intervention the dietary behaviour questions will be closely linked to sub-behaviours targeted in the intervention. Therefore a list of 12 items has been formulated on which women can indicate the frequency (days per week) and amount (as large as the size of the palm of a hand or equal to 200 ml for fluids) of the specified food consumed.
Database All trial subject data is entered into a web-based electronic database using the Microsoft. Net development environment that is accessible from any web-enabled computer, tablet or cell phone. The database is housed on an SQL server that employs a certificate and is housed in a physically-secure location. Pages are in English and employ drop-down menus, pick-lists and text boxes, and are encrypted with Standard SSL level encryption. Operator entry is password protected. No personal identifiers for study subjects are housed within the database; rather they are cross-referenced to a unique study number, the first two digits of which indicate the geographic clinical site. The security and confidentiality standards of the database are compliant with those required under HIPAA privacy rules established by the National Institutes of Health, U.
Process evaluation Process evaluation  [76]  will be used to gain insight into the response rate of the target population (reach), behaviour changes, implementation, fidelity (the extent to which the intervention was delivered as planned), delivered dose (the amount of the intervention actually delivered) and participants perceptions (satisfaction). For this the recruitment database, counselling logs on the PDA, evaluation questionnaire and the MITI 3. 1. 1 code  [25]  will be used.