dataesr/scientific-paragraphs-categorization huggingface dataset:
4 Our data suggest that this effect of in utero smoke exposure might potentially occur through mechanisms involving EPB41L3 (see the additional text in this article's Online Repository). For childhood tobacco smoke exposure, the discovery genomewide meta-analysis consisted of 3,048 cases and 3,509 control subjects derived from 9 studies (see Table  E1 ). Overall, childhood tobacco smoke exposure increased the risk of childhood-onset asthma (see Fig  E1 ). A total of 538,233 SNPs were included in the interaction meta-analysis. Fig E4 in this article's Online Repository at www. jacionline. org shows the Manhattan plot. We identified 35 SNPs in the discovery sample with a P value of less than 10 24 based on the fixed effect model. Four of these SNPs were excluded because they showed heterogeneity, and the P value of the random effect was greater than 10 24.
T. Keil  has received one or more grants from or has one or more grants pending with  EU-FP7. Y. Lee  has received one or more grants from or has one or more grants pending with the  European Union  and the  German Research Foundation. M. Kabesch  has been supported by one or more grants from the  European Union , the  German Ministry of Education and Research , and the  German Research Foundation  and has received one or more payments for lecturing from or is on the speakers' bureau for the  European Respiratory Society , the  European Academy of Allergy and Clinical Immunology , the  American Thoracic Society ,  Novartis , and  GlaxoSmithKline. M. Farrall  has been supported by one or more grants from and has received support for travel from  EU FP7. G. H. Koppelman  has been supported by one or more grants from the  European Union  and has received one or more grants from or has one or more grants pending with the  Netherlands Asthma Foundation , Stichting Asthma Bestrijding.
Study setting and design This was a prospective study cohort study that included young children (0-59 months of age) with severe malnutrition, respiratory symptoms and radiological pneumonia as previously described in detail  [14]. In brief, eligible children admitted to the Dhaka Hospital of icddr,b between April 2011 and June 2012 were enrolled following informed consent. Demographic, contact details (phone and address) and clinical data were collected prospectively on standardized data collection proforma. Radiographs were interpreted independently by a radiologist and a study pediatrician (MJC). Radiological pneumonia was defined as the presence of end-point consolidation or other (non-end-point) infiltrate in lungs according to the WHO radiological classification of pneumonia  [15]. Severe malnutrition was defined in children as severe wasting [z score for weight for height ,23 of the median of the WHO anthropometry] or severe underweight [z score for weight for age ,24 of the median of the WHO anthropometry], or the presence of nutritional edema.
It was planned that all children discharged receiving antituberculosis treatment were followed until completion of the course i. e. for 6 months. For this study, all care-givers were provided instructions verbally in local language regarding follow-up. They were requested to return to the hospital at 12 weeks following discharge but advised that if their children developed any symptoms or signs of illness at any time prior to this, then they should either return to the hospital or consult with a study physician by mobile phone at any time. The phone numbers of the study physicians were provided during discharge and all caregivers had access to mobile phones. No funding was provided for potential phone call costs. If any of the caregivers did not attend the 12-week post-discharge follow-up, the study staff attempted to contact them via mobile phone.
Data analysis All data were entered into SPSS for Windows (version 15. 0; SPSS Inc, Chicago) and Epi-Info (version 6. 0, USD, Stone Mountain, GA). Follow-up was planned prospectively and ethically approved. However, the primary objective of this study that determined sample size was to determine prevalence of sepsis and tuberculosis, as previously reported  [14]. We used this sample of patients to determine characteristics associated with postdischarge death. Differences in proportions were compared by the Chi-square test. Differences of means were compared by Student's t-test for normally distributed data and Mann-Whitney test was used for comparison of data that were not normally distributed. Strength of association was determined by calculating odds ratio (OR) and their 95% confidence intervals (CIs).
Acknowledgements This article results from individual contributions of all the co-authors. The highly complex world of HDL subclasses is presented by  Laura Calabresi. The multifaceted composition of the HDL proteome is discussed by  Anatol Kontush. Protein isoforms, including translational and posttranslational modifications, are reviewed by  Mats Lindahl. Rapidly  growing knowledge of the HDL lipidome is discussed by  Marie Lhomme. W. Sean Davidson  presents a brief history of structural studies of HDL, critically reviews existing models of HDL structure, and together with  M. John Chapman  draws conclusions and discusses future perspectives. Open Access This chapter is distributed under the terms of the Creative Commons Attribution Noncommercial License, which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.
Cell cycle B-cell lines were pulsed with 10 mmol/L BrdUrd, washed 3 times and cultured at 10 5 cells/mL. One million cells were harvested for each condition, fixed, and permeabilized (FITC-BrdU Flow Kit, BD Pharmingen). After 7-AAD staining, cell-cycle phases were analyzed on BrdUrd pos cells using ModFit software (Verity Software House).
Acknowledgments The authors thank the  Centre de Ressources Biologiques (CRB)-Sant e of Rennes hospital, Pr. Thierry Fest  and  Patrick Tas  for providing nonmalignant and follicular lymph nodes,  Christophe Ruaux  for providing tonsil samples, and the  BREHAT network  for follicular lymphoma bone marrow samples. The authors also thank  Severine Moullec  and  J-Philippe St  ephant for technical assistance.
As shown in Supplemental Figure  2A , at birth Alk expression was slightly increased in mutated ganglia compared to Wt ganglia, and this increase was somewhat higher in the case of the Alk F1178L mutation compared with the Alk R1279Q mutation. This was confirmed by RT-q-PCR and an increase was also documented at the adult stage in mutants (data not shown). Altogether, our results therefore demonstrate that expression of Alk mutants triggers prolonged neurogenesis in sympathetic ganglia. However, we did not observe any tumor in these KI mice, indicating that activated Alk is not by itself sufficient to induce neuroblastic tumors.
Analysis of sympathetic ganglia Animals were killed and immediately dissected to collect SCG and stellate ganglia. Ganglia were fixed and surface was evaluated (x2. 5, Leica DMR, Vega v2. 1 ClaraVision software). Ganglia were then included in agarose and paraffin-embedded. Alternatively, they were fixed for immunostaining or immediately frozen in liquid nitrogen for RNA extraction. Immunostaining and quantification of islet1-and ki67-positive cells E12. 5 and E14. 5 mouse embryos and P0 stages were fixed in 4% paraformaldehyde overnight, washed with PBS and immersed in 30% sucrose for 24 h. After embedding in Tissue Tek 12 µm cryosections were collected. After antigen retrieval in 10 mM sodium citrate buffer pH 6. 0 at 95°C for 20 min sections were incubated overnight at 4°C in PBS/10% FCS/1% BSA with anti-mouse ki67 (BioLegend) and mouse anti-islet1 (Developmental Studies Hybridoma Bank) diluted 1:200 and 1:40, respectively.
Genomic profiling Genomic DNA from mouse tumors was analyzed versus reference normal DNA. The samples were labeled and co-hybridized to the NimbleGen Mouse CGH 3x720K WG-T arrays according to the manufacturer's protocol. Arrays were washed and then scanned on a GenePix 4000B Scanner using GenePix 5. 0 software. Raw data were normalized using NimbleScan v2. 5 software (Roche NimbleGen). The normalized data were processed using NimbleScan softwares.
Treatment of human NB cell lines with TAE-684 and expression analysis Human NB cell lines were genotyped by DNA fingerprinting (PowerPlex, Promega) and have been previously described  [42]. They were grown in RPMI 1640 medium (Invitrogen) supplemented with 10% FCS and antibiotics. They were treated in triplicate with 0. 3 μM TAE-684 (Novartis) or DMSO (VWR) for 6 hours. Then expression profiling on the Affymetrix HG-U133PLUS2 platform was performed according to the manufacturer's protocol. The CLB-Ga cell line was treated with 0. 3 μM TAE-684 and harvested in duplicate at 6 different time points (10', 30', 60', 120', 240' and 360') for subsequent expression profiling on a custom Agilent 44k expression array using labeling and hybridization protocols of the manufacturer. Affymetrix array data were normalized using the RMA method, while Agilent expression profiling data were normalized using VSN (variance stabilization and normalization) in R packages affy and limma, respectively.
ACKNOWLEDGMENTS The  U830 Inserm laboratory  is supported by grants from the  Institut National du Cancer , the  Ligue Nationale contre le Cancer (Equipe labellisée) , the  Association Hubert Gouin ,  Les Bagouz à Manon ,  les amis de Claire, la Fédération Enfants et Santé et la Société Française de Lutte contre les Cancers et les Leucémies de l'Enfant et l'Adolescent. A. C. is the recipient of a fellowship of the Fondation ARC pour la recherche sur le cancer. L. L. -D. is the recipient of a fellowship of the Ecole Polytechnique. K. De P. is a post-doctoral researcher with the  FWO-Flanders (Fund for Scientific Research -Flanders ). G. S. is supported by the Annenberg foundation. The laboratory of H. R. is supported by the  Wilhelm-Sander-Stiftung. We thank  D. Gentien  and  C. Hego  from  the translational department of Institut Curie  for Affymetrix profiling experiments and  S.
During the third week, they were invited to come to the laboratory and they were randomly assigned to either a cycling session or a finger tapping session that lasted 30 minutes each. At the start of the session, all individuals sat silently for 5 minutes in silence before performing a 2-minute trial of cycling or of tapping at their "preferred and most comfortable pace". This pace was used to set the metronome frequency that was used during the remaining of the experimental session. Both groups performed a sensori-motor synchronization and continuation task with the explicit instruction to perform movements in synchrony with a regular tone sequence and to continue even when the metronome stopped. The metronome was generated by a program written in Matlab and was played through speakers. All tones had the same pitch (640Hz) and the same duration (100 ms).
Interestingly, the cysteine connectivity is very different from what was reported before by Krey et al. [62] , with only one common disulfide bond. Moreover, the masking of neutralizing epitopes by glycans and the definition of the CD81 binding site in this new structure confirms previous experimental results  [79] [80] [81]. Altogether, these new data bring E1 on the spotlight as the new HCV fusion protein candidate. Now that this long-awaited structural insight into E2 protein is available, efforts will probably be concentrated on the determination of E1 structure and of the virion-exposed E1E2 complex, and ultimately to break the code of HCV fusion. A representative for each major genus of the Flaviviridae family is shown: TBEV E protein for the flaviviruses (PDB ID 1SVB  [82] ), BVDV E2 protein for the pestiviruses (PDB ID 2YQ2  [76] ) and finally HCV E2 protein for the hepaciviruses (PDB ID 4MWF  [78] ).
Acknowledgments We are grateful to  C. M. Rice  and  M. T. Catanese  for the permission to reproduce their published electron microscopy picture. TP is supported by grants from the  Deutsche Forschungsgemeinschaft  ( SFB 900 , project  A6 , and  PI 734/2-1 ), from the  Helmholtz Association  ( SO-024 ,  HAI-IDR SO-073 ) and from the  European Research Council  ( ERC-2011-StG_281473-VIRAFRONT ).
We note that the actual lack of studies is very similar to the earlier development of hos-pital centric operations management models where research issues were initially found to be not structured, multi-dimensional and complex  (Roth and Menor 2003). The classification upon which we built the existing literature review is based on the hierarchical operations management decision framework presented in Section 3. Based on this framework, this section aims at presenting how the highlighted areas in Figure  2  have been approached in the studies published so far. The databases used were Web of Science, Sciencedirect, Scholar Google, Elsevier and the keywords were home (health) care, operations management, decision making, human resources planning and materials planning. As such, in contrast with other services such as retail, we did not find papers that deal with the above-mentioned long-term decisions.
Ethics statement The study was approved by the regional Ethics Committee (CPP Ile de France VII, SC12-006, January 2012). As we did not conduct a therapeutic study, Ethics Committee approved the use of an oral informed consent. It was preoperatively given by patients after written and oral information. After oral consent, every patient was recorded in the database of medical research department of our institute. A data book of the protocol with a description and the list of the demographic, clinic and biologic data necessary to be manually collected during the study were placed in every anesthetic file. The trial was registered on ClinicalTrials. gov with registry number 02063009. We conducted prospective study between March and June 2012 at Gustave Roussy Institute. All consecutive patients fitted with a port, undergoing major gynecologic surgery requiring measurement of CI by TPTD by the PICCO2 device (Pulsion Medical Systems, Munich, Germany) in accordance with our local hemodynamic protocol were enrolled.
15% and variation of CI. 10%). Perioperative and anesthetic management were not modified by the study. Measurement of CI by TPTD was based on the average of 3 injections of cooled (,6uC) boluses of saline (15 ml)  [6]. We obtained a couple of measurements of the CI by successively injecting 3 boluses into the CVC (CI CVC ) and 3 boluses into the port (CI PORT ). The six saline boluses were administered within a maximum of 10 minutes and were randomly performed, as soon as the blood temperature had returned to its baseline value, as indicated by the device. After the 3 injections of cooled saline into each venous access, the following data were collected: Cardiac Index (CI PORT and CI CVC ), global end-diastolic volume index (GEDVi CVC and GEDVi PORT ), extravascular lung water index (EVLWi CVC and EVLWi PORT ) and central temperature variation (DT CVC and DT PORT ).
Search Searches were made in PubMed, PsycINFO, CINAHL and Embase databases for articles published until March 2014 without limits in relation to language or time. The search was uncomplicated; we used the following search terms as free text and MeSH terms: "puberty", pubert*" and "back pain". To select appropriate search terms, the first author consulted a documentalist at the University of Paris-Sud.
The latter method is often used in studies but does not provide transparent information on the real proportion of participants of the study sample. 2. Data collection. In order to limit expectation bias, two different persons, blind to each other's findings, should have collected information on back pain and puberty, unless at least one of these items was collected in a questionnaire. 3. The studied factor: puberty. The concept of puberty should be clearly defined, i. e. explaining how the puberty score was obtained and using a measure, stated to be valid and reliable. 4. The outcome measure: back pain. The outcome measure should be clearly defined. It should be explained how back pain was assessed and the recall period should be specified. In order to limit memory decay, the recall period should be minimized  [3].
It was decided to limit this period to one month because it has been shown previously in adults that there is a good correlation between data obtained in adults through real-time data capture by textmessages and a retrospective telephone interview with a one-month recall period  [19]. We considered that children would have fairly short recall ability but hoped that one-month would be acceptable also for them. Since there is no gold standard for "back pain", validity could not be established. At baseline, it should also be specified if study subjects were pain free and preferably, if they had never previously had back pain, in order to establish temporality. 5. Potential modifiers/confounders. We also investigated if associations between puberty and back pain were controlled for possible confounders or modifiers, particularly age and sex.
4. Temporality. In longitudinal studies, it would be necessary to include children who had never previously had back pain at baseline in order to see if the onset of puberty would be associated with the development of back pain. As back pain is relatively rare in childhood and lifetime data on back pain would be difficult to collect at this age, we considered it acceptable also to have defined children as having or not having back pain at the time around baseline, as probably the majority without back pain at that time would have been truly back pain free also prior to the study. We did not perform a meta-analysis because the definitions and reporting of back pain in the articles were found to be heterogeneous. Instead, findings were summarized in a narrative fashion. The final conclusion on causality was obtained in a subjective manner on the basis of the weight of all evidence in relation to strength of association, consistency, dose-response, and temporality.
Microarray assay and analysis A reference RNA was obtained pooling an equal amount of RNA of each sample (UT8, UT16 and T16) to normalize the data arising from the microarray experiment  [19]. Microarrays were performed using the Agilent protocol version 6. 5 (Low Input Quick Amp Labeling). Cyanine-3 CTP (Cy-3) fluorescent dye was used to label the samples and Cy-5 fluorescent dye to label the reference (RNA pool). The labelled cRNA were hybridized on the P. falciparum 4x44k Agilent custom microarrays developed in the parasitology laboratory of Army Biomedical Research Institute (Marseille). On these microarrays, 9,722 probes were spotted, corresponding to 5,144 genes. Microarrays were scanned using an Agilent Scanner (G2505B). Data were extracted and normalized from the scanned images using the Agilent Feature Extraction software (ver 9.
5. 3. 1). The annotation of the microarray was updated using the PlasmoDB 9. 0 annotations  [20]  and the Malaria Parasite Metabolic Pathways  [21]. The version 9. 0 of PlasmoDB introduced a new name code for each P. falciparum gene and updated the Gene Ontology (GO) annotation. Two-way ANOVA analyses (time-treatment) were performed with a FDR correction and a p-value of 0. 05 on normalized data using the Genespring GX software (ver 12. 0). The significant, differentially expressed probes were filtered using a fold change (FC) above two between UT8, UT16 and T16. Genespring allowed the computation of a hierarchical clustering (Euclidian metric, centroid method) and GO analyses. The significantly over-represented GOs were input in QuickGO  [22]  in order to produce an Ancestral Chart, representing these GOs with their relationships.
Study population The project will be carried out in eight districts representing five of the eight geographical zones of Tanzania and covering variations in malaria epidemiology and ecology. Fifteen districts, i. e. seven districts in addition to the eight previously mentioned, will be included in the mosquito insecticide resistance part of the project (Figure  2 ). The 15 districts were selected from the 23 districts enrolled in the population arm of the Sentinel Panel of Districts (SPD), SAmple Vital registration with Verbal autopsY (SAVVY)  [26]. The 23 SAVVY districts were selected using two-stage sampling with probability proportional to size (PPS) of districts and villages/Enumeration Areas (EAs) from the 2002 Population and Housing Census dataset  [27]. In each of the eight districts (Figure  2 ), all households within 6-20 villages/EAs were enrolled by the SAVVY programme for national representativeness in 2012/2013.
We will select ten SAVVY villages per district based on the proximity to district headquarters, except for Kinondoni (Dar es Salaam) where SAVVY only covered six EAs. Using the SAVVY baseline household information, 45 households per village will be randomly selected using the 'sample' function in the statistical software R 3. 1. 1 [28] , giving a total of 3,420 households nationwide. Fifty percent more households will be randomly selected as substitution households to accommodate for non-consent or household head absence. The 3,420 study households will be geo-referenced using Global Positioning System (GPS) points to create a GIS database including data on village and house characteristics, socioeconomic variables, net characteristics, and geographical variables, such as environment, land use and potential mosquito breeding sites.
Thus, randomisation is conducted by the field workers at the household level, resulting in 15 households per village receiving sufficient nets of one product to cover each sleeping space (Table  3 ). A questionnaire will be conducted in Kiswahili, the local language spoken throughout Tanzania, with household heads, or another adult, by the field team (Additional file 2). Respondents will be asked whether they received nets during two NMCP campaigns in 2009-2011. Nets from the campaigns are identifiable by their light-blue colour and size (single), allowing us to differentiate those nets from the campaign and those that might have come from the private sector or Non-Governmental Organisations Figure  1  Flow chart of retrospective and prospective data collection. After study district and village selection, 45 households will be randomly selected from each village for study inclusion.
By counting the holes by location, we will be able to take into account these factors when analysing the hole index data and give different weights to holes in different locations. To our knowledge, this formula has not yet been developed. One of our aims is therefore to incorporate hole location into the equation, and to compare its relative importance to a simpler model in terms of protection against mosquitoes in semi-field experiments. Holes will be counted both in the laboratory and in the field using a collapsible metal frame made out of locally available economical materials (Figure  3 ). In the field, holes in a maximum of three prospective nets will be counted per household due to logistical and time constraints.
Data analysis We will collect a set of response variables (Table  1 ) and explanatory variables. The explanatory variables will be collected from household questionnaires and observations and will include time after net distribution, net product, geographical location, patterns of net use (e. g. type of bed, frequency of net use), net status, washing and handling, perceptions of nets and socioeconomic status of the household. All response variables will be analysed using the statistical programs STATA ® 13 (http://www. stata. com/) and R (http://www. R-project. org/). Regression modelling including multivariate generalised linear models and generalised linear mixed models will be used to determine covariates affecting net durability components such as LLIN age, geographical location and data collected from household surveys.