dataesr/scientific-paragraphs-categorization huggingface dataset:
1 Dna binding factor OBF/OcaB DNA binding factor DNA binding factor helix-loop-helix DNA binding factor inhibitor hlh DNA binding factor inhibitor hlh DNA binding factor DNA binding factor DNA binding factor V(D)J recombination V(D)J recombination ID Probe Set Accession Number Gene Genes known to be up-regulated in signaling-deficient pre-B cells 10463123 NM_009345 Dntt 10438064 NM_016982 Vpreb1 10438060 ENSMUST00000100136 Igll1 10427628 NM_008372 Il7r Genes known to be down-regulated in signaling-deficient pre-B cells 10500677 NM_013486 Cd2 10469278 NM_008367 Il2ra 10450154 NM_010378 H2-Aa 10562132 NM_001043317 Cd22 Transcription regulators and V(D)J recombination 10390640 NM_011771 Ikzf3 10384020 NM_017401 Polm 10502510 NM_010723 Lmo4 10404389 NM_013674 Irf4 10438415 ENSMUST00000103752 Igl-V2 10438405 M94350 Igl-V1 10562812 NM_019866 Spib 10364559 NM_007880 Arid3a 10594001 NM_019689 Arid3b 10554370 NM_175433 Zfp710 10374333 NM_001025597 Ikzf1 10560964 NM_011138 Pou2f2 10517090 NM_001080819 Arid1a 10371662 NM_011461 Sp1c 10585276 NM_011136 Pou2af1 10359770 NM_011137 Pou2f1 10370837 NM_011548 E2a 10399691 NM_010496 Id2 10509163 NM_008321 Id3 10576034 NM_008320 Irf8 10512669 NM_008782 Pax5 10485372 NM_009019 Rag1 10485370 NM_009020 Rag2 a p value in ANOVA analysis.
RNA isolation and cDNA synthesis The T. aestivum cDNA econding putative AP endonuclease (taape1) was identified by its homology to the human Ape1 (AAH02338) and Arabidopsis Ape1L genes (At3g48425). Using the cDNA sequence of putative taape1 from Genbank accession AK333560, the forward primer, taape1 Dir: d(CTGCACTCA-TATGAAGCGCTTCTTCCAGCC) and the reverse primer, taape1 Rev: d(CCAGGATCCTTAGCCGGAGCTCTTCGAT-TC) were designed and used for RT-PCR. The underlined bases in primers are the restriction sites of NdeI and BamHI endonucleases, respectively. Total RNA was isolated from young leaves of T. aestivum variety Kazakhstanskaya 10 by trizol method. The yield and purity of RNA was determined spectrophotometrically and the quality of RNA was tested on 1% formaldehyde agarose gel. The first strand of cDNA was synthesized by reverse transcription using 5 mg of total RNA as a template under the following conditions: 200 U RevertAid M-MuLV reverse transcriptase (Thermo Scientific, Lithuania) with 0.
TaApe1L model building The three-dimensional model of TaApe1L was built based on its homology to human APE1 using SWISS-MODEL homology modeling server  [24]. Three structures of human APE1 were taken as templates: a 1. 92-A ˚structure of APE1 bound to Mg 2+ (PDB ID 4LND, chain A  [25] ), a 2. 65-A ˚structure of APE1 bound to abasic DNA substrate in the absence of metal ions (1DEW, chain A  [26] ), and a 2. 39-A ˚structure of APE1 bound to cleaved DNA product and Mg 2+ (4IEM, chain A  [27] ). The target (TaApe1L) and the templates were aligned using Clustal Omega  [28] ), the target sequence was clipped to fully align with the template, and loops. 3 amino acids long in the target were eliminated. All such loops were on the outer surface of the protein far away from the metalbinding sites; there were no loops in the aligned template sequence.
Structural modelling and comparative analysis of human and wheat AP endonucleases In order to rationalize the unusual preference for Mn 2+ , which is often interchangeable with Mg 2+ in biological systems, we have modeled the three-dimensional structure of TaApe1L based on its homology to APE1, for which several crystal structures have been solved  [25, 26, 27, 34, 35, 36]  (Figure  3 ). Three structures of human APE1 representing different snapshots along the reaction pathway were taken as templates: APE1 bound to Mg 2+ (4LND)  [25] , APE1 bound to abasic DNA in the absence of metal ions (1DEW)  [26] , and APE1 bound to cleaved DNA product and Mg 2+ (4IEM)  [27]. Of these, the model based on the apo protein (4LND) was the best based both on the global QMEAN4 score (0. 62, Z-score 22. 295, which puts the model quality within the population of experimental structures in the Protein Data Bank) and on the concordance of local estimators (QMEAN local score, Anolea mean force potential, GROMOS empirical force field energy) that all gave favorable conformational energy around the metalbinding sites.
H 2 O 2 causes oxidation of DNA bases as well as single-strand breaks containing 39-blocking sugar-phosphate groups  [41]. The E. coli BH110 strain lacking Xth and Nfo AP endonucleases is extremely sensitive to both agents  [42]. As expected, the plasmid that directs the synthesis of Nfo conferred resistance to MMS and H 2 O 2 on BH110 cells. In contrast, neither the control empty vector nor a plasmid encoding TaApe1L restored resistance to MMS or H 2 O 2 (data not shown). These results suggest that both the very low AP endonuclease activity and the requirement for specific reaction conditions may contribute to the inefficient rescue of E. coli xth nfo grown on the media containing these genotoxic agents. Next, to examine whether TaApe1L is present during seedling growth, wheat seeds were germinated for four days, the seedlings were dissected, and the presence of TaApe1L was determined by Western blot analysis using rabbit polyclonal antibodies generated against the recombinant TaApe1L protein.
Discussion The tBLASTn search for homologues of human APE1 in Triticum aestivum cDNA databases revealed the presence of a DNA clone encoding for a putative AP endonuclease with a close homology to the Arabidopsis thaliana AtApe1L protein. We have isolated cDNA encoding the putative wheat AP endonuclease,  Each type of DNA substrates were used to measure a specific AP endonuclease activity under the appropriate optimal reaction conditions: THFNT for AP endonuclease activity, Exo20 THF NG for 39-repair phosphodiesterase activity, Exo20 P NG for 39-phosphatase activity and Exo20NG for 39R59 exonuclease activity (see Materials and Methods). b APE1-catalyzed AP site cleavage and 39R59 exonuclease activities were measured under BER and EXO conditions, respectively. All data taken from  [45]. referred here as TaApe1L, and characterized its protein product.
These results suggest that in germinating wheat, TaApe1L may function in the BER pathway to protect genome integrity in dividing and differentiated cells. The genome of A. thaliana, encodes three AP endonucleases homologous to human APE1: Arp, Ape1L and Ape2. Although the search of T. aestivum DNA sequence data bank identified only one AP endonuclease TaApe1L, it is very likely that the wheat genome also contains two other AP endonucleases homologous to Arabidopsis Arp and Ape2. To examine this possibility we performed a BLAST search for homologues of human APE1 in the fully sequenced genome of rice (Oryza sativa), a cereal related to wheat more closely than the eudicot Arabidopsis. As expected, we have identified rice homologues of Arp (GenBank: BAD68138. 1), Ape1L (Gene ID: 4351982) and Ape2 (Gene ID: 4347697).
This work was supported by grants from  Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan  [grants No  0145/ GF  and No  0738GF ] to A. K. B. and from  Agence Nationale pour la Recherche [ANR   Blanc 2010  Projet  ANR-09-GENO-000  to M. S. ] (http://www. agence-nationalerecherche. fr),Electricitede France (http://www. edf. fr)Contract Radioprotection [RB 2013-23 to M. S. ];  Centre National de la Recherche Scientifique  (http://www. cnrs. fr)[PICS  N5479-Russie , and  CNRS-INCA-MSHE Franco-Pologne  # 3037987  to M. S. ] and by  Fondation de France  (http://www. fondationdefrance. org)[# 2012 00029161  to A. A. I. ] and by  Polish-French  collaborative grants  Nu346/N-INCA/2008/0  and  Nu303 819540  [to B. T. ] and by  Russian Academy of Sciences  [ MKB 6.
12  to D. O. Z. ];  Russian Foundation for Basic Research  [ 12-04-33231 -mol_a_ved to I. R. G. ]; P. P. was supported by the fellowship from  International  PhD Projects Programme of Foundation for Polish Science: ''Studies of nucleic acids  and proteins -from basic to applied research''. The project is co-financed by  European Union -Regional Development Fund. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors have the following interests. This study was partially funded by a commercial source '' Electricite de France, EDF (Scientific Commission -Council of Radiation Protection) ''. There are no patents, products in development or marketed products to declare.
Two Investigations The ambition to describe interconnected STE curriculum determines the choice of methodology for collecting data. Two inquiries about the practices were selected:  The first one is a qualitative approach  (Coquidé, Le Tiec & Garel, 2007)  based on analysis of empirical data consisting in logbooks kept by 12 teachers during one year long. These data reveal the contents, activities and issues of STE. Indeed, the volunteers teachers had to relate their practice in these logs, between narrative and description of the perceived reality. These logbooks are highly personal and have the characteristics of a reflexive and professionnalizing writing  (Cros, 2003). These logs allowed me to conduct 3 interviews per teacher (one interview every 8 weeks). Interviews were used to explore the missing parts of STE curriculum and its interconnections with other teaching areas of activities.
Because the characteristics of future REDD+ projects are not yet clear, we used the methods defined by the Verified Carbon Standard (VCS) for improved forest management projects  [24, 25]  to calculate the breakeven carbon price and associated risk assessment for lengthened cutting cycles and increased minimum cutting diameters. Whenever relevant, we also complied with the technical standards defined by the forest legislation in Gabon. In particular, management parameters (including tree species growth rates, logging damage, etc. ) were taken from the management plan of the forest concession. Computations were based on real tree population data from the forest concession in Gabon, with a virtual implementation of the REDD+ project in this concession following the VCS methodology. All future forest dynamics (including during the virtual REDD+ project) were predicted using a classical model of forest dynamics based on transition matrices  [26].
Acknowledgements This study was supported by training grants given to the first author by the  French Ministry of Foreign Affairs  and by the  International Tropical Timber Organization. This study was also supported by the  AIRES-Sud  contract  n°7148  of the  Agence Inter-Établissements de Recherche pour le Développement (AIRD). Data from the Haut-Abanga concession were kindly provided by the private forest company  Rougier-Gabon. The ideas in this manuscript benefited from discussion with T. West and  F. E. Putz. The authors address special thanks to  A. Karsenty  who contributed to this study by providing comments and ideas.
EUROSTAT yield data We obtained the annual EUROSTAT regional crop yield statistics (according to administrative boundaries at the NUTS 2 level) for the period 1975-2009 from the European Commission (http://epp. eurostat. ec. europa. eu). This data set documents all primary crop types, such as barley, wheat, grain maize, etc. However, data for most of these crops are scarce. In this study we thus focus on four major crops with rather continuous spatiotemporal coverage: barley, wheat, grain maize and potatoes. In the EUROSTAT database, yield is reported as the amount of dry matter suitable for consumption  (Moors et al. , 2010). We first examined the length of the available yield records for each crop and region, thereby discarding time series below 10 yr in length. We subsequently filled gaps in the crop yield time series for the remaining regions using a simple linear interpolation method.
NDVI, up-scaled GPP, and FAPAR Bimonthly normalized difference vegetation index (NDVI) and fraction of absorbed photosynthetically active radiation (FAPAR) data derived from the Advanced Very High Resolution Radiometer (AVHRR) of the National Oceanic and Atmospheric Administration (NOAA) at a spatial resolution of 8 km during the period 1982-2008 were obtained from the NASA GIMMS (Global Inventory Modeling and Mapping Studies) group. The GIMMS NDVI and FAPAR data sets have been thoroughly corrected for orbit drift, clouds and atmospheric aerosols  (Tucker et al. , 2005) , and have already proved useful to identify long-term changes in vegetation greenness/activities  (Myneni et al. , 1997; Nemani et al. , 2003; Zhou et al. , 2001). In this study, we resampled the GIMMS NDVI and FAPAR data into monthly data with a spatial resolution of 0.
Climate data Monthly temperature (TMP) data from 1975 to 2009 at 0. 5 • × 0. 5 • spatial resolution were derived from the CRU (Climatic Research Unit) TS (time series) 3. 1 gridded global data set (http://www. cru. uea. ac. uk/). The 0. 5 • × 0. 5 • gridded water availability index (WAI) data from 1975 to 2009 were estimated based on a simple formula modified from  Kleidon and Heimann (1998). Monthly reanalysis data of the number of consecutive frost days (CFD) and the maximum of daily maximum temperature within a month (MMT) for more than 8000 stations over the globe were acquired from the European Climate Assessment (ECA) project (http: //www. ecad. eu). We then constructed monthly gridded data for CFD and MMT at a spatial resolution of 0. 5 • × 0. 5 • for the period 1975-2009 by performing a cubic spline spatial interpolation  (Tabor and Williams, 2010).
Spatiotemporal patterns of the IAV for crop yield, NDVI, GPP and FAPAR We evaluated the IAV of detrended crop yield, and growingseason NDVI, GPP and FAPAR (called NDVI gs , GPP gs , and FAPAR gs hereafter) for each grid by calculating the coefficient of variation (CV), which has been demonstrated as an effective measure of year-to-year variability  (Cao et al. , 2003; Galloway, 1985). Regions with extensive irrigation (with irrigated area fraction ≥ 15 %) were masked out in our analysis to minimize the effects of human management on the IAV of productivity proxies. All data sets are compared on an annual basis. We subsequently quantified spatial patterns of the IAV for different productivity proxies. Spearman's rank correlation coefficients were used to assess the relationships between the IAV of crop yield, NDVI gs , GPP gs and FAPAR gs for each grid.
Acknowledgements. This work was funded by the  CARBO-Extreme project  ( FP7- ENV-2008-1-226701 ). The pan-European tree ring network used in this study is a collaborative effort of dozens of researchers. We thank all the participants of the workshop held in Frankfurt, Germany, in 2012 for the  CARBO-Extreme  project. We also thank  Martin Jung  at the  Max Planck Institute for Biogeochemistry and Nicolas Vuichard and Nathalie de Noblet-Ducoudré at Laboratoire des Sciences du Climat et de l'Environnement (LSCE)  for their valuable comments. C. Zang acknowledges funding by the  European Research Council  under the European Union's  Seventh Framework Programme  ( FP7/2007-2013) / ERC  grant agreement no. 282250. F. Babst acknowledges funding from the  Swiss National Science Foundation  (grant  PBSKP2_144034 ).
16 French guidelines recommend using singleton risk estimate tables without clearly addressing the pregnancy fetus issue. 17 he prevalence of DS has increased in association with an increase in average maternal age over the past two decades. 18, 19 1] [22]  The risk of Down syndrome specifically in monozygotic and in dizygotic pregnancies, as opposed to multiple pregnancies in general, has not been reported. Using data from EUROCAT, a network of European population-based registries of congenital anomaly, we previously demonstrated a lower than expected risk of chromosomal anomalies in babies from multiple births compared with singletons in 1990-2009, with the difference increasing over time. 20 The purpose of this paper is to determine the maternal age-specific prevalence of DS in monozygotic and in dizygotic pregnancies, and to explore the risk for each relative to singleton pregnancies.
Methods European Surveillance of Congenital Anomalies (EURO-CAT) is a network of population-based registries of congenital anomaly in 21 countries of Europe. EUROCAT collects standardised data that can be used to assess changes in the epidemiology of congenital anomalies and associated risk factors. 23, 24 Only DS cases were used in this analysis. The methods of registry case ascertainment are fully described elsewhere. 19, 25 The database includes live born congenital anomaly cases (LB), stillborn cases and fetal deaths after 20 weeks' gestation (FD), and prenatally diagnosed cases resulting in termination of pregnancy for fetal anomaly (TOPFA). Affiliated to EUROCAT is The National Down Syndrome Cytogenetic Register (NDSCR), a registry which does not routinely contribute case data to the EUROCAT central database but supplied such data specifically for this study.
The NDSCR ascertains all cases of DS from cytogenetic reports sent directly from all laboratories in England and Wales. 18 For this study we used all reports in this database of LB and FD from 20 weeks' gestational age and TOPFA. The NDSCR data replaced the data of five British regional EUROCAT registries. Criteria for inclusion of other EUROCAT registries in the study were that they should ascertain ≥80% of DS cases according to the EUROCAT DS data quality indicator (DQI) 2005-2009,  26  they should have complete data on multiple birth status for DS cases, and >80% completeness for maternal age for DS cases, and they should be able to provide data on population births by multiple birth status and maternal age. Ten registries (including the NDSCR, which represented 87% of the study population) in eight countries participated in this study (Table  1 ).
The Office of National Statistics (ONS) for England and Wales (for NDSCR) and four registries outside the UK were able to provide denominator data by maternal age and like and unlike sex (see Table  1 ), covering 94. 4% of our data. In total, 66. 4% of twin pairs were like sex in the UK, and 66. 0% outside the UK. Zygosity proportions were calculated using the Weinberg rule: DZ pairs = 2 (unlike sex pairs) and MZ pairs = all pairs -(DZ pairs). 27, 28 This meant that denominator data could be estimated for singleton, dizygotic and monozygotic twin deliveries. This was done for data from England and Wales, and for the combined data of the four non-UK countries for the years available, extrapolated to all seven non-UK countries for each 10-year period. When these denominators were used to estimate risk from monozygotic and dizygotic pregnancies relative to singletons, only DS cases from singleton and twin pregnancies were included, excluding cases from higher order multiple births (one case from each of 12 triplet pregnancies, all from England and Wales).
These cases who were triplets were also excluded when concordance was estimated. The ONS also supplied denominators for England and Wales by single year of maternal age for singleton and multiple births which were used for an additional analysis of the NDSCR data. All data were used for all the analyses unless otherwise stated. Outcome of pregnancy was available for all EUROCAT cases. For NDSCR, 3. 36% of cases for which outcomes were missing were excluded from the outcomes analysis only. Analysis of outcome of pregnancy was confined to 2000-2009, as this represents the most recent data. Data on early neonatal survival were not available for all NDSCR cases, so perinatal death rates could not be calculated. Multiple birth is defined for cases in EUROCAT guidelines according to the 'number of babies/fetuses delivered'  24  and this definition was also used for 'multiple pregnancy' in this study.
Results The proportion of older mothers (35 years and over) giving birth to singletons and to multiples increased in the 2000s from the preceding decade in nearly all countries (Figure  1 ). From 1990 to 1999, the total corrected prevalence of DS cases from multiple pregnancies per 10 000 births was 0. 2 ). This finding was consistent across the two datasets used (Figure  2 ). The relative risk of DS for  When the NDSCR data were analysed using single year of maternal age for mothers 35 years and over, the reduced risk in DS cases from multiple births was more apparent and further reduced in the 2000s compared with the 1990s (Figure  3 ; also see Table  S1 ). There was also a slight decrease in DS prevalence among singleton births over the two time periods. In 8. 7% (n = 54) of affected pairs the co-twins were concordant for DS, 51 same sex twin pairs (assumed to be monozygotic) and three unlike sex twin pairs.
I. INTRODUCTION Actual graph datasets are massive. The World Wide Web consists of trillions of unique links  [1] , Facebook contains over one billion active users  [2] , Twitter consists of millions of users, biological networks are also of similar sizes, e. g protein interaction networks, to name but a few. However, the growing size of graph datasets makes it challenging for performing usual computations over graphs, e. g community detection, counting triangles, identifying protein associations as well as many other computation tasks. A popular solution to this problem is to divide the graph over several clusters and then run parallel algorithms to perform computations. Graph partitioning is a NP-hard problem aiming to divide a graph dataset into distinct sets under the constraints of equilibrating the clusters' size and minimizing the number of edges crossing the clusters, this partitioning strategy is well known as the balanced graph partitioning problem.
C. Our contribution: In this paper, we are presenting a new heuristic for balanced graph partitioning called Fractional Greedy. We show that it yields high quality partitions with exact balanced parts' size and lower edges cut. At the same time, we introduce the partial restreaming partitioning which is a hybrid model of data streaming. In this model a portion of graph dataset is restreamed several times, and the rest of the graph dataset is streamed once, as in the streaming model used in  [6] ,  [7]. The main strength of this proposed method is avoiding restreaming the whole graph to minimize the runtime and the memory cost. In the proposed partial restreaming model, at most half of the graph is restreamed, this leads to faster processing and require only half of graph nodes to be kept in memory for subsequent iterations of the restream.
We show that by restreaming only a part of the graph dataset we obtain a good partition as in the setting of fully restreaming the graph dataset  [10]. We use LDG  [6]  and Fennel  [7]  and our proposed heuristic FG for partitioning. The three heuristics were adapted for our streaming model. We also introduce the partial selective restreaming partitioning, which follows the same idea behind the partial restreaming partitioning but in this case, we select the portions that we wish to restream depending on their average degree and density. This selective method perform well independently of the order in which the vertices arrive. The rest of the paper is organized as follows. In Section 2, we discuss the related work. In Section 3 we present our proposed heuristic and our partial restreaming approach.
C. Online methods Unlike offline methods, the online methods for partitioning do not require full information about the graph. In fact, this property makes the online methods the most suitable for processing massive graphs. To the best of our knowledge, online partitioning methods in streaming context were introduced by Stanton and Kliot  [6]. Tsourakakis et al. [7]  presented FENNEL as an online streaming partitioning method. These methods consist in single shot stream of dataset. Afterward, Nishimura et al. [10]  introduced the restreaming partitioning problem, consisting in several passes of stream dataset. 1) The streaming model: Recent work in streaming partitioning  [6] ,  [7] ,  [10]  adopts almost the same streaming graph model in which vertices arrive, each with its adjacency list.