dataesr/scientific-paragraphs-categorization huggingface dataset:
Improvement of distributed models over lumped models This analysis specifically addresses the question whether calibrated distributed models can provide improved event simulations compared to lumped models in mountainous regions. Using the same events from Section 3. 4, three specific measures of improve-ment were computed: % improvement in peak flow, % improvement in runoff event volume, and improvement in peak time error in hours (Eqs. (8a)-(8c) in Appendix D). The calibrated simulations from the LMP model were used as the benchmark. Fig. 13  presents the three measures of improvement for the calibrated models, along with the inter-model average of the values. It is desirable to achieve values greater than zero in each of the plots. Each data point is the average value of the measure for a specific model in a specific basin over many events.
Rain and snow partitioning DMIP 2 West intended to address the important issue of rainsnow partitioning. Primarily this was to be addressed via the use of radar-detected observations of freezing level from HMT-West  (Minder and Kingsmill, 2013; White et al. , 2010 White et al. , , 2002) )  after participants set-up and ran their models with the baseline DMIP 2 West gridded precipitation and temperature data. Participants would then make additional simulations using the radar-based estimates of the rain-snow line to note the improvement. Delays in DMIP 2 West caused by the need to generate a new QPE data set precluded the use of HMT-West data in formal experiments with participants. Nonetheless, using the DMIP 2 West modeling framework,  Mizukami et al. (2013)  tested the OHD and LMP models with and without the HMT-West radar-derived rain-snow data for the 2005-2006 winter period.
Estimation of models inputs and model sensitivity to existing data The distributed models used gridded forms of the precipitation and temperature data widely used by NWS RFCs in mountainous areas for hydrologic model parameter calibration. In the study basins, the density of precipitation and temperature gauges was sufficient to develop useful gridded estimates of these variables over a 20-year span. A sufficient number of hourly (recording) rain gauges were available to distribute daily precipitation observations. These data were able to support effective model calibration and good simulations through the validation period, evidenced by %Bias values within or near the ±5% criteria for NWS model calibration  (Smith et al. , 2003) , low cumulative runoff errors, and high values of r mod. For this study, careful quality control of the raw precipitation data was essential.
g. ,  Clark et al. , 2011; Butts et al. , 2004). The benefits of using the HMT-West data sets of additional surface temperature  (Lundquist et al. , 2008)  and precipitation, optical disdrometer, vertically pointing radar-based freezing level  (Mizukami et al. , 2013; Minder and Kingsmill, 2013; Lundquist et al. , 2008; White et al. , 2010 White et al. , , 2002)) , soil moisture, and gap-filling radar-derived QPE (e. g. ,  Gourley et al. , 2009)  should continue to be explored. These data sets should also aid in the diagnosis of modeling improvements. DMIP 2 West was always intended to be a multi-institutional and multi-model evaluation of the QPE, disdrometer, soil moisture, radar-freezing level, and other observations afforded by the rich instrumentation deployments in HMT-West. The intent was to first generate streamflow and SWE simulations using the 'basic' DMIP 2 West gage-only QPE and temperature fields.
After calibrating and running their models with the basic data, it was planned to have participants rerun their models using the HMT-West data (radar QPE, snow level, and soil moisture) to note the improvements gained by advanced observations. However, both DMIP 2 West and HMT-West experienced major delays, with the unfortunate result being that the HMT-West data sets could not be explored in formal DMIP 2 West experiments. Based on our experience with deriving precipitation, temperature, and evaporation forcing data sets for DMIP 2 West, continued work in deriving these forcings in complex terrain is of near-paramount importance for model testing, development, and calibration. Continued work is needed to address gage network density issues in mountainous areas. This is true for gage-only QPE and for the use of rain gages to bias-adjust radar estimates of precipitation.
In spite of the enormous effort involved, data sets covering a large number of basins would support additional experiments and lead to broader conclusions (e. g. ,  Andréassian et al. , 2009 Andréassian et al. , , 2006)). River Forecast Centers within the NWS should consider the use of the OHD model. Other operational forecasting agencies should consider the use of distributed models in complex terrain. For the foreseeable future, such models should be viewed as complements to existing lumped forecast models rather than outright replacements. Appendix A. Models used in DMIP 2 West (See Table  A1 ) Howard of NSSL assisted with processing the PRISM data. The careful reviews and comments from the journal reviewers and editors have contributed to the clarity of this paper. Appendix D. Statistical equations used in the analysis of DMIP 2 West results.
Mapping of Sequencing Data Mapping of the Color Space sequencing reads to the reference genome (UCSC Homo sapiens hg19 from UCSC) was performed with the Lifetech Lifescope 2. 5. 1 bioinformatics software suite, after ''a priori'' error correction with the SAET procedure. The resulting alignment files (pairwise Input and Experiment) in standard. bam format were analyzed for peak calling directly with the MACS software version 1. 4. 1  [20]. In addition, the. bam alignments were converted to the. bed format with the bamToBed bedtools utility and used for peak calling with the SICER analysis software  [21]  in order to take into account the heterogeneous nature of these DNA -protein interactions which may include quite long areas of interaction. All intersections between MACS and SICER bed files and genome-wide features was performed with the bedTools v2.
Peak Identification Exploratory data analysis of the sequencing and mapping results, of the MACS peak quality, of the relative annotation and further peak calling were performed with the commercial Integromics SeqSolve bioinformatic software suite. Correlation of MACS and SICER peaks (Experiment versus Input) with known NCBI RefSeq gene structure and annotation was performed with in-house Genomnia perl scripts or with the ChIPpeakAnno Bioconductor library, version 2. 10  [22]. Differential peak analysis was performed with the SICER-df. sh routine of the SICER software or with the Bioconductor DiffBind library  [23] , complemented by in-house Genomnia perl scripts. Removal of open chromatin (false positives) regions was performed using ''A comprehensive collection of signal artifact blacklist regions in the Table  1.
Confocal Microscopy Confocal analysis was performed as previously described  [1]. Sample were analysed with a Zeiss LSM510 Meta Confocal Microscope with 63x magnification. For each samples 10 independent fields were analyzed and representative images are shown. Colocalization mask was obtained by LSM510 software to produce images containing exclusively colocalized regions. SEM of 4 experiments. *p,0,05 B) C27IM were transfected with the eNOS dominant negative mutant (S1177A) or empty vector for 48h in presence or absence of E2 added 1h prior to harvesting. Levels of pri-miR-34a were analysed by qRT-PCR. Data represent the mean 6 SEM of 3 experiments. *p,0,05 C) C27IM (left), LNCaP cells (middle) and HUVEC (right) were transfected with the eNOS dominant negative mutant (S1177A) or empty vector for 48 h in presence or absence of E2 added 1 h prior to harvesting.
0 at the Sanger Institute. The hybridization was performed according to the miRCURY TM LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria). After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2. 0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY TM LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc. , USA) and the image analysis was carried out using the ImaGene 9. 0 software (BioDiscovery, Inc. , USA). The quantified signals were background corrected (Normexp with offset value 10 [24] and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. Differential expression of miRNAs between groups was performed using a t-test onetail after which a p value ,0.
05 was considered statistically significant. A total of 52 miRs were used to generate a heatmap where red and green colors indicate high and low expression respectively. A two-way supervised clustering analysis was performed using Pearson's correlations and Ward's criteria as a linkage rule. C27IM cell line was hybridized twice with correlation = 0,92. Microarrays data have been deposited in the Curie database at http://microarrays. curie. fr/, login username and password are available upon request.
eNOS ChIP-seq was conducted and eNOS-associated DNA regions (peaks) were identified using two algorithms, MACS 1. 4. 1 (Linux version or as incorporated in the commercial software SeqSolve TM from Integromics) and SICER v1. 1, to minimize peak caller bias and to consider the 'extended' nature of the interaction of eNOS/ER complexes with chromatin  [20, 21]. Differential analysis of called peaks or extended regions (islands) was also performed with two methods, comparing and intersecting the results, for the same reasons (see Methods and  [22, 23, 29, 30] ). The number of sequencing reads and eNOS-binding events for each cell line, untreated or exposed to E2 , are shown in Table  S1. Under both conditions, the eNOS-containing DNA peaks were found widely distributed across the genome with conserved hyperdensity regions, as shown superimposed to the human chromosome ideograms for both cell lines (Figure  S2 ).
8-and 14-fold in C27IM and LNCaP cells, respectively) indicating a specific hormone-dependent eNOS relocalization along the genome. A quantitative sequence comparison of eNOS-associated peaks before and after E2 treatment revealed the existence of overlapping peaks between the two conditions, (6,805 common peaks in C27IM and 1,368 in LNCaP cells (Figure  1A ). A corresponding overlap of 5,190 and 1,630 genes in C27IM and LNCaP cells, respectively, was also found for eNOS-peaks associated with the nearest gene as annotated in the NCBI RefSeq database incorporated in the UCSC Genome Browser (http://www. ncbi. nlm. nih. gov/RefSeq/), (data not shown). The overlapping peaks (and associated genes) thus represent a sub-set of eNOS-bound regions that are not responsive to estradiol treatment, suggesting eNOS interactions with proteins others than ER.
Confocal microscopy revealed that E2 treatment increased the co-localization of HDAC4/eNOS and HDAC5/eNOS (Figure  5D, E ). Moreover, since HDAC4 and 5 do not bind directly DNA but acquire this property through their interaction with HDAC3  [43, 44] , ChIP assays were performed with antibodies to HDAC 3 and 4 as well as SIRT1 (Figure  5F ). Occupancy of the miR-34a promoter was observed essentially only after hormonal stimulation, HDAC4 and SIRT1 exhibiting the highest enrichment (with a maximum of 8. 4-and 10. 6-fold over control, respectively). These data substantiate the presence of hetero-complexes suggesting that the interplay among members of class I, IIa and III contributes to the estrogen-dependent repression of miR-34a in aggressive prostate cancer cells.
The effects obtained with the HDAC inhibitors favors the view of eNOS as a critical factor participating in chromatin remodeling complexes in association with different classes of histone deacetylases (Figure  5F ). Of interest, the small polyphenolic compound, Resveratrol, a classical SIRT1 activator, did not rescue miR-34a expression (Figure  5A ). This may be explained by an additive effect of Resveratrol on the eNOS/NO pathway given its known role on SIRT1 activation and NO production. On the other end, Resveratrol has structural similarity to the synthetic estrogen diethylstilbestrol and acts as an estrogen receptor partial agonist  [53, 54]. These features may provide an alternative interpretation of our data showing that in the presence of this ER ligand, the repression of miR-34a transcription induced by eNOS/ERb complex cannot be reversed.
This work was supported by the  Associazione Italiana Ricerca sul Cancro  to AFa;  Italian Ministry of Education, University , and Research Grants:  PRIN 2008NY72SJ  and  FIRB RBFR087JMZ  to  AFa  and  FIRB RBFR10URHP  to S. N. V. B. is recipient of a FIRC ( Federazione Italiana Ricerca sul Cancro) Fellowship. A. A. is supported by funding from  Susan G. Komen for the Cure Foundation. C. G. research is supported by the  LOEWE Center for Cell and Gene Therapy, Goethe University, Frankfurt (DE). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Background: A program, supported by the GEMHEP (Groupe d'étude Moléculaire des Hépatites), was established in 2007 in the sanitary district of Tokombéré, to prevent perinatal transmission of hepatitis B virus (HBV). It comprises screening for HBV surface antigen (HBsAg) in all pregnant women and vaccinating the newborn if tests are positive. Methods/Principal Findings: 1276 women were enrolled in the study after providing informed consent. Demographic data and blood samples were available for 1267 of the enrolled patients. HBsAg was determined locally using a rapid test (Vikia HBsAg, Biomerieux). Tests for HBV and HDV virological markers (HBeAg, anti-HDV antibodies (Ab), HBV-DNA, HDV-RNA, HBV and HDV genotypes) were performed on the confirmed HBsAg-positive samples in the virology unit of the Angers University Hospital (France).
Patient samples Since 2005, the GlaxoSmithKline foundation has been supporting a program initially dedicated to the prevention of mother-to-child transmission (PMTCT) of HIV. The reach of the program was broadened in 2007 with a new focus on strengthening healthcare both for mothers and for children less than five years of age. Within this setting and with the support of the GEMHEP, a new PMTCT program for HBV was established. We screened all pregnant women for HIV and HBsAg simultaneously. Our project was approved by the Ethics Committee at the University Hospital of Angers, France (Agreement #2013-49). Our data protection has been registered with the CNIL as statement number 1684412. The patients were informed that the samples could be used for research purposes. Only the pregnant women who provided informed consent were included.
Sequence analysis of HBV and HDV strains HBV PCR products (covering the P and BCP/PC regions) and HDV PCR products were purified using Nucleospin Extract II columns (Machery Nagel) and then sequenced bidirectionally using the BigDye Terminator v3. 1 kit (Life Technologies). After purification, sequences of amplified nucleic acids were determined using an ABI 3130 xl sequencer (Life Technologies) and the nucleotide sequences analyzed with SeqScape® v2. 6 software (Life Technologies). Nucleotide sequences of the P region were compared with reference strains representing each of the genotypes A-H, obtained from GenBank. Genotyping of HBV was then determined by blast analysis, and full genome sequences representing the eight HBV genotypes were used as references. Phylogenic analyses in both the polymerase gene and the BCP and PC gene were performed to assess the genomic diversity of the strains.
Statistical analysis Quantitative variables were compared using Student t test. Qualitative variables were compared by the chi square test or the bilateral Fisher's exact test when the expected value of at least one cell in a contingency table was below 5. A p value of 0. 05 or less was considered significant. To assess risk factors, as our study was cross-sectional, we computed risk ratios (i. e. , ratio of prevalence in exposed and non-exposed women) and their 95% confidence intervals rather than odds ratios. HBV viral load was expressed as mean ± standard deviation (± SD). All statistical calculations were performed using SPSS software (IBM Corporation, Armonk, NY, USA).
HBV and HDV serological screening None of the 1276 pregnant women had been vaccinated against HBV or had received antiviral treatment. Demographic data and blood samples were available for 1267 of the enrolled patients. HBsAg was detected in 259 of 1267 sera (20. 4%) by the VIKIA HBsAg test. Negative and positive results for HBsAg were confirmed by EIA and neutralization  [25, 26]. HBeAg was found in 59 of the 259 HBsAg-positive pregnant women (22. 7%). Eight pregnant women were anti-HIVAb-positive. Nineteen of the 259 (7. 3 %) HBsAg-positive pregnant women were anti-HDV antibody (Ac) positive with anti-HDV IgM in 10/19 (53%) cases. No difference in age was observed for HBsAg carriers versus non carriers (24. 5 years versus 24. 3 years; p=0. 73) or HDV Ab carriers versus non carriers (26 years versus 24.
7% in Yaoundé blood donors in 2003  [31]. Our high HBsAg prevalence remains coherent with published data at the scale of central sub-Saharan Africa. Variable endemicity data are reported in other countries: 6. 5% in Zambia, 9. 5% in Gabon, 10. 9 % in Mauritania, 12. 6% in Ghana, 13. 8% in Senegal, 15. 5% in Mali and 25% in Zimbabwe  [32] [33] [34] [35] [36] [37]. Furthermore, HBV rate also differs intranationally in some countries with areas of high endemicity. In Nigeria, for example, studies reported varying seroprevalence rates of HBsAg seropositivity, i. e. , 26. 0%, 15. 1%, 13. 2% and 12. 6% according to location Figure  1. Results of the polymerase gene HBV amplification. The HBV DNA was amplified using a qualitative PCR with a threshold at 3 log UI/mL and the results were correlated with the HBeAg profile in HBsAg-positive pregnant women.
Acknowledgements We thank  Christian Aurenche , Director of  Tokombéré Hospital , for providing us the opportunity to work in the  Health Promotion Center of Tokombéré , which has been recognized by the  WHO Sasakawa health prize. We also thank all the pregnant women who participated in this study as well as the sanitary formations of the Tokombéré district for their collaboration. We also express our thanks to all those who helped us carry out our study particularly in Tokombéré:  Jean-Pierre ADOUKARA ,  François BEAUFILS ,  Amour BOUNE ,  Adèle CORTET ,  Rosette DAMZA ,  Christiane HURAUX ,  Sastique KARSIKAM ,  Amos LITINI ,  Joseph MANGAVE , RATOUA,  Jean-Paul TADA ,  Raymond TAOWE ,  Thierry YAOUBA , and in France,  Emmanuel GORDIEN ,  Ségolène BRICHLER  and  K. L. Erwin  for proofreading the English manuscript.
, 2008; Joki-Korpela & Hyypia ¨, 2001). Sixteen different types of HPeV and several different genotypes have been identified  (Knowles et al. , 2012)  (http://www. picornaviridae. com/). The genome organization of HPeV is typical of the family, except that the VP0 protein appears The GenBank/EMBL/DDBJ accession number for the genome sequence of Sebokele virus 1 is HF677705. One supplementary figure and one supplementary table are available with the online version of this paper. not to be cleaved and its N terminus not myristoylated  (Knowles et al. , 2012; Stanway & Hyypia ¨, 1999). LV was first isolated from bank voles (Myodes glareolus) trapped in Sweden  (Niklasson et al. , 1998; Niklasson et al. , 1999). Few isolates of the LV species have been described and only five whole genome sequences are available.
The contigs were used independently for BLASTN and BLASTX identity searches against EMBL and UniProt databases, respectively. The blast2taxoclass program (http:// mobyle. pasteur. fr/cgi-bin/portal. py#forms::blast2taxoclass) was used for taxonomic classification, and demonstrated that most of the viral contigs were related to the family Picornaviridae, strongly suggesting that SEBV1 belonged to this family. The blast2genoclass program (http://mobyle. pasteur. fr/cgi-bin/portal. py#forms::blast2genoclass) was used for genomic annotation of contigs and high-scoring segment pairs (hsps) matching with picornaviruses were extracted. Extracted hsps were assembled using Sequencher 5. 0 software (Gene Codes Corporation) with default parameters, resulting in the generation of three main contigs covering nearly 99 % of the predicted genomic sequences (Fig.
1a ). Following BLASTX analysis, contigs presented a maximum amino acid (aa) identity of 61-65 % with parechoviruses. Attempts to culture the virus in several cell lines were all unsuccessful, so a second vial of SEBV1 was used to finalize the full-length genome sequence determination. Total RNA was extracted, amplified by RT-PCR with primers corresponding to contig sequences and subjected to Sanger sequencing (Fig. 1a  and Table  S1 , available in JGV Online). The final full-length sequence served as a reference for mapping reads generated by deep sequencing (CLC Assembly Cell). The mean coverage of each nucleotide position was 104 times (lower at the extremities), without any discrepancies being detected (Fig. 1b ). SEBV1 genomic sequence was compared to reference nucleotide and protein sequences from the different viral genera downloaded from GenBank.
BioEdit software  (Hall, 1999)  was used to translate DNA, and CLUSTAL X version 2. 0  (Larkin et al. , 2007; Thompson et al. , 1997)  was used for sequence alignments. Pairwise alignments were performed using CLC Main Workbench 5. 7. 2 software (CLC bio). Phylogenetic analyses of aa sequences were conducted by the neighbor-joining algorithm using MEGA 4. 0. 2 (Tamura et al. , 2007)  with a Poisson correction model and 1000 bootstrap replicates. Trees were visualized using the FigTree program, version 1. 3. 1 (available from http://tree. bio. ed. ac. uk/software/figtree). The GenBank accession numbers of the viral sequences used in the phylogenetic analyses are indicated in the trees. The genome of SEBV1 is 7537 nt long [excluding the poly(A) tail] and is organized as follows: a 59-UTR sequence of at least 754 nt, followed by an open reading frame of 6702 nt predicted to encode a polyprotein of 2233 aa, terminated by a 39-UTR of 81 nt and a polyadenylated tract.
Acknowledgements We are grateful to  Laurence Ma  ( Plate-forme Genomique ) for excellent technical expertise and  Nick J. Knowles  for information about new parechovirus species. We are grateful for the financial support of the  Agence Nationale pour la Recherche  ( ANR 09 MIEN 019 ) and the  Fondation pour la Recherche Medicale  ( FRM DMI20091117313 ).
Recently, this group suggested another modified version -MutMap + where they used the bulked DNA of mutant and wild-type progeny of M3 generation derived from selfing of an M2 heterozygous individual. That is, no cross between mutant and wild-type parental line is required  (Fekih et al. , 2013). Table  1  lists the 20 mutant collections available worldwide, associated information, and whether the phenomics database is available. We list several resources not listed in other recent reviews, including the ones at Cornell University, the Taiwan Agriculture Research Institute, the Chinese Academy of Agricultural Science, and the Brazil Plant Genomics and Breeding Center. Most of the 20 collections are japonica varieties, including Nipponbare (used in 11 resources), Tainung 67 (2), Dongjin (2), Zhonghua 11 (2), and Kitaano, Zhonghua 15, Hwayoung, Kitaake, Taichung 65, Yukihikari, Kinmaze, and BRS Querencia (1 each).