dataesr/scientific-paragraphs-categorization huggingface dataset:
DNA manipulations DNA manipulations were carried out according to standard techniques. C. difficile genomic DNA for use in cloning and PCR analysis was prepared as described previously  [9]. Polymerase chain reactions (PCR) used Failsafe TM PCR system (Epicentre) and Taq polymerase (Promega) in accordance with the manufacturers' protocols using primers detailed in Table  1. Primer design for amplification of DNA from C. difficile 630 Derm and R20291 strains were based on the available C. difficile genomes from the EMBL/GenBank databases with accession numbers AM180356 and FN545816 respectively. The oligonucleotides and the plasmids/strains used in this study are listed in Table  1  and Table  2 , respectively. All DNA manipulations and cloning procedures were performed as per Sambrook  [43].
Vector Construction Plasmid pMTL-YN18 (accession number; JX465728), used to create a pyrE 2 mutant in R20291, is an equivalent vector to pMTL-JH18  [9]  in which the pCB102 replicon was replaced with that of pBP1 (isolated from pMTL82251), using the flanking AscI and FseI sites specifically created for this purpose  [17]. Plasmid pMTL-YN1 (accession number; JX465729) was made by cloning a 1,753 bp SbfI/AscI fragment between the corresponding restriction sites of plasmid pMTL-JH20  [9]. This fragment was generated from the 630Derm genome by PCR using the primers pyrE-int-SbfI-F and pyrEcomplement-Asc1-R, and carries a truncated copy of pyrE, lacking the first 50 nucleotides of the structural gene, together with 1200 bp from immediately 39 to the stop codon of pyrE, which includes the entire coding sequence of CD0188 of 630Derm.
To generate the equivalent pyrE correction vector (pMTL-YN2, accession number; JX465732) for R20291, the pCB102 replicon of pMTL-YN1 was replaced with that of pBP1 from pMTL82251 (using the AscI and FseI sites) and the 630Derm DNA between the SbfI and AscI sites replaced with the equivalent region from the R20291 genome. In this case, the DNA was synthesized by DNA2. 0 specific to the R20291 chromosome by PCR as two contiguous SbfI/NdeI and NdeI/AscI fragments. The PyrE complementation vector pMTL-ME2 was constructed by inserting the C. sporogenes ATCC 15579 pyrE gene into pMTL83151. The pyrE gene was amplified by PCR from genomic DNA prepared from Clostridium sporogenes ATCC 15579 using primers Csp-pyrE-HpaI-sF1 and Csp-pyrE-HpaI-sR1. The PCR product was digested with HpaI and gel purified followed by cloning in same orientation as catP in pMTL83151  [17]  linearized with the same enzyme.
To construct the ACE overexpression plasmids pMTL-YN1X (accession number; JX465731) and pMTL-YN2X (accession number; JX465734), a 214 bp NotI/NdeI fragment encompassing the C. sporogenes fdx promoter was isolated from plasmid pMTL82253 and inserted between the equivalent sites of pMTL-JH14  [9]. The plasmid obtained (pMTL-JH14::Pcspfdx) was cleaved with NheI, and ligated to two, annealed oligonucleotides (Cpa-TT-Oligo-1 and Cpa-TT-Oligo-2) which encompassed the transcriptional terminator of the Clostridium pasteurianum ferredoxin gene. A 517 bp NotI/NheI fragment (encompassing the fdx promoter, lacZ' and multiple cloning sites, and the transcriptional terminator of the C. pasteurianum ferredoxin gene) was then isolated from the resultant plasmid (pMTL-ME6X) and inserted between the equivalent sites in pMTL-YN1 and pMTLYN2, to yield pMTL-YN1X and pMTL-YN2X, respectively.
In parallel, pMTL-ME6X was digested with EcoRI and NheI and the released 293 bp fragment inserted between the equivalent sites of pMTL-JH14  [9]  to make pMTL-ME6C. This plasmid was then cleaved with NotI and NheI, and the released 323 bp fragment inserted between the equivalent sites of pMTL-YN1 and pMTLYN2, to yield the complementation vectors pMTL-YN1C (accession number; JX465730) and pMTL-YN2C (accession number; JX465733), respectively.
Each cassette was cloned between the SbfI and AscI restriction recognition sites in pMTL-YN3 (accession number; JX465735) to create pMTL-YN3::630spo0A*, pMTL-YN3::630cwp84* and pMTL-YN3::630mtlD*. Similarly, pMTL-YN3::R20291spo0A* and pMTL-YN3::R20291cwp84* were made by cloning the allelic exchange cassettes between the AscI and SbfI sites in pMTL-YN4 (accession number; JX465736). The spo0A knockout cassette was synthesized by DNA2. 0 which consists of a 672 bp LHA (bases 1412012 to 1412789 on the forward strand of C. difficile 630 Derm genome) fused to a 800 bp RHA (bases 1413275 to 1414074 on the forward strand of C. difficile 630 Derm genome) which were designed to make an in-frame deletion removing codons 65 to 226, inclusive, out of a total of 275 codons). For the equivalent in C. difficile R20291, a 778 bp LHA (bases 1319650 to 1320427 on the forward strand of the C.
Results Differential display experiments identify p53 as a potential mediator of the p38MAPK pathway. CGR8 mouse ESCs were induced to differentiate by forming embryoid bodies (EBs) and, at day 3, treated or not by the specific p38MAPK inhibitor PD169316, and mRNAs were extracted and analyzed by microarray experiments 48 h later. For each condition, three mRNA batches were hybridized on DNA chips spotted with 44 K mouse gene-specific sequences, and regulations of genes of interest were confirmed by reverse-transcriptase quantitative PCR (RT-qPCR) technique (data not shown). Among the identified targets, we focused our attention on one gene upregulated in our experiments, Bcl2, a well-known p53-inhibited gene. 19, 20 nterestingly, Bcl2 has already been described as a p38MAPK-inhibited gene and involved in ESC neurogenesis.
Membranes were incubated with antibodies against either mouse p53 (Cell Signaling), Lamin B1 (BioLegend, Ozyme) or ERK2 (Santa Cruz Biotechnology, Clinisciences, Nanterre, France). Immunofluorescence staining. Differentiated EBs were washed and fixed at day 7 in 3% paraformaldehyde for 15 min at room temperature (RT). Cell membranes were permeabilized in phosphate-buffered saline (PBS)-0. 1% Triton X-100 for 15min at RT and incubated with an anti-Troponin T (CT3) or an anti-MHC (MF2Ds) (DSHB, Iowa City, IA, USA) in PBS-10% fetal bovine serum for 1 h. After three washes in PBS, cells were incubated with anti-mouse ALEXA488 or ALEXA546 (Invitrogen) for 1 h at RT. Cell imaging was performed using a Nikon microscope Eclipse 90I. Z-stack pictures were obtained by using a Nikon Digital Sight DS-1QM camera controlled by NIS element AR software (Nikon, Champigny sur Marne, France).
1A ). LTD was induced by tetanic stimulation (HFS: 100 pulses at 100 Hz repeated twice at 20 s; 10 Hz and 1 Hz: 100 pulses at 10 Hz or 1 Hz repeated twice at 20 s; theta-burst protocol: 5 bursts of 5 pulses, 100 Hz within burst, 200 ms interburst interval, repeated four times) after at least 15 min of stable baseline recording. The magnitude of LTD was estimated by comparing averaged responses 30 -40 min after the induction protocol with baseline-averaged responses 0 -10 min before the induction protocol. All data were acquired with Axograph X software (AxoGraph Scientific) and analyzed with Origin Pro (OriginLab), and Igor Pro (Wavemetrix). Statistical comparisons were performed using Student's t test. Results are reported as mean Ϯ SEM. All drugs were bath-applied following dilution into the external solution from concentrated stock solutions.
ANALYSIS OF DATA For categorical variables (sex, consumption, or not of alcohol), we compared the level of aggressive behavior (OAS scale score) according to the presence or not of each parameter. For quantitative data (scores of impulsivity and sensation seeking, amount of alcohol, cigarettes, or cannabis), we made a correlation analysis between agitation scores and these variables. We applied a Bonferroni correction to control the increase in Type I error rate with multiple tests. We also performed a logistic regression to identify predictors of high OAS scores (superior to 3).
Indeed, the output measures are means calculated per simulation on all clones growing on the virtual grassland. Because the clone number increases with the tested density, the variability of the mean result due to external noise decreases, as well as the number of required simulations. The large simulation campaigns were run on the shared software platform BOINC  (Anderson 2004 ) using volunteer computing  (Smaoui-Feki et al 2009). Five output measures were calculated to characterise the clone performance (biomass and number of ramets) and architecture (number of rhizomes, mean lengths of the primary and secondary rhizomes). Primary rhizomes started from the initial ramet and branched in the secondary rhizomes.
Temperature ramped between set temperatures each hour, with the peak temperature of each day reached at 2:00 p. m. , and the minimum at 5:00 a. m. We programmed a photoperiod of 12:12 (L:D) h cycle, with alternations occurring at 8:00 a. m. and 8:00 p. m. Relative humidity was maintained between 70 and 80% across all experiments. We measured relative humidity, air and water temperature using HOBO data loggers (Onset, Cape Cod, MA). Air temperature and humidity were measured using the External Temperature/Relative Humidity data logger (U23 proV2) and water temperature was measured using the Pendant Temperature/Light data logger (8K-UA-002-08). Because of the small volume of water in larval rearing cups, water temperature followed air temperature closely. There was an average 1-to 2-h lag between air and water maximum and minimum temperatures (Fig.
1 ). Despite the lag, water temperature averaged within 0. 6ЊC of the programmed air temperature. As for the slight delay in air temperature under the small diurnal temperature regime, we suspect that the internal clocks for data loggers and incubators were not synchronized. We cannot reaccess the original data to conÞrm this because the loggers have since been reset. Nonetheless, recorded temperatures still indicate that mosquitoes were exposed to the intended temperature proÞle. Under each of these three temperature regimes, termed constant temperature (DTR ϭ 0ЊC), small DTR (DTR ϭ 7. 6ЊC), and large DTR (DTR ϭ 18. 6ЊC), we conducted two experiments. We measured immature survival and development time, fecundity, clutch size, and length of the gonotrophic cycle during 14 d of daily access to human blood.
We counted the total number of completed gonotrophic cycles only for females that survived to the end of the experiment (a maximum of 20 d) because including the estimates for females that died prematurely does not accurately measure their reproductive potential. We did, however, include all data on when blood meals were taken and the length of each gonotrophic cycle for all females. The University of California at Davis Institutional Review Board determined that this experiment (allowing mosquitoes to take bloodmeal from people) did not meet the criteria for human subjects research and thus, did not require human subjects approval. Statistical Analysis. Analyses were conducted using SPSS (version 15; SPSS Inc. , Chicago, IL) and SAS (version 9. 3, SAS, Inc. , Cary, NC). For immature stages, we used a multivariate analysis of variance (MANOVA) to test egg-pupa development time and larval survival estimates.
Acknowledgments We thank  W. K. Reisen  for continued practical and material support;  A. Ponlawat  for collecting and sending mosquito eggs;  S. Olkowski  for technical support during exper-iments,  M. V. Armijos ,  S. A. Juliano , and three anonymous reviewers for providing constructive comments on earlier versions of the manuscript. This research beneÞted from discussions with working group members in the  Research and Policy for Infectious Disease Dynamics (RAPIDD) program  of the  Science and Technology Directorate, Department of Homeland Security , and the  Fogarty International Center, National Institutes of Health  and was funded by grant  EF-0914384  from the  Ecology of Infectious Disease program  of the  National Science Foundation.
Data from the two crystal forms were collected on beamline ID14-1 at the ESRF, Grenoble, France. An initial model for the TrV structure was obtained by molecular replacement with the AMoRe program  (Navaza, 2001)  using data to 4 A ˚resolution collected from the rhombohedral crystal form. The search model was a full capsid of 60 protomers of a polyalanine version of CrPV VP1, VP2, VP3 and VP4 (PDB entry 1b35;  Tate et al. , 1999). The three best solutions had an R factor of 45% and a correlation coefficient of 30% and were related by the crystallographic threefold symmetry axis, indicating that the virus lies on this axis with one third of the capsid in the asymmetric unit. This confirms the analysis of the self-rotation function as described in  Rozas-Dennis et al. (2004). The next best solution had an R factor of 49% and a correlation coefficient of 21%.
Homology modelling A theoretical atomic model of VP4 from TrV was generated using the MODELLER software  (Sali & Blundell, 1993; Eswar et al. , 2006). In order to provide all of the neighbouring contacts as a context for modelling, we employed template atomic coordinates of five copies of VP4 from a CrPV penton (previously superimposed on its TrV counterpart) combined with the coordinates of a VP1-VP3 TrV penton. Symmetry mates for the atomic model of the CrPV protomer (PDB entry 1b35;  Tate et al. , 1999)  and its TrV equivalent (PDB entry 3nap) were generated with O  (Jones et al. , 1991)  using the first five VIPER matrices for each structure  (Carrillo-Tripp et al. , 2009) , which contain the required transformations to build a penton; after joining all of the resulting structures, they were superimposed using LSQMAN and their chain IDs were normalized using MOLEMAN2  (Kleywegt & Jones, 1994).
Sequence alignment A comparative study was performed by aligning the aminoacid sequences of the three major coat proteins from the following dicistroviruses: TrV, HiPV, PSIV, BQCV, CrPV and DCV. The criterion employed for the selection of the viruses was based on the availability of experimental data delimiting the N-termini of the coat proteins, although the members of the proposed Aparavirus genus were excluded for being excessively divergent in terms of sequence similarity. The alignment was performed using the Expresso mode of the T-Coffee package (Di Tommaso et al. , 2011;  Armougom et al. , 2006; O'Sullivan et al. , 2004; Poirot et al. , 2004; Notredame et al. , 2000) , which incorporates structural information into multiple sequence alignments. The sequence order was kept as input. Secondary-structure assignment was performed with DSSP  (Kabsch & Sander, 1983 ) using chains A, B and C (VP1, VP2 and VP3, respectively) from the atomic model of TrV as input and it was overlaid on top of the alignment using the ESPript software  (Gouet et al.
Close-range salt-bridge analysis For this study, the reference protomer and all of its symmetry-related equivalents within a distance of 50 A ˚were analyzed. Symmetry mates were generated with O  (Jones et al. , 1991)  and edited with MOLEMAN2  (Kleywegt & Jones, 1994). Salt bridges were then calculated using the WHAT IF software  (Vriend, 1990). All interactions with a distance greater than 4 A ˚were discarded  (Kumar & Nussinov, 2002).
In enteroviruses and in CrPV, the residues are numbered from 1001, 2001, 3001 and 4001 for VP1, VP2, VP3 and VP4, respectively, and we also follow this convention in this manuscript. The electron density was interpreted according to the published amino-acid sequence translated from the deposited genomic nucleotide sequence (GenBank accession No. AF178440;  Czibener et al. , 2000) , with a minor discrepancy in VP3 residue 3054, which corresponds to valine in the sequence but displays an electron density that is more compatible with methionine. Taking into account that this residue is conserved as methionine in all of the other dicistroviruses that we have analyzed, this difference probably arises from an error in the original sequencing  (Czibener et al. , 2000). Overall, the TrV capsid displays icosahedral symmetry with pseudo-triangulation number P = 3 (Fig.
, 2002). However, it is intriguing that the motif is conserved between VP1 and VP3, which share only about 12% sequence identity. In this respect, it is noteworthy that when comparing TrV VP1 with the protein database with the DALI server  (Holm & Rosenstro ¨m, 2010) , the highest score is for CrPV VP1 as expected, but picornavirus VP3 is close behind, suggesting a relatively close relation between the two proteins. In contrast, when looking at VP2, the closest match after CrPV is the jelly roll from the capsid protein of Norwalk virus, which is not a picornavirus and exhibits T = 3 symmetry. It is of course impossible to define an evolutionary path from these data, but it serves to highlight how intriguing the conservation of the DDF triad in VP3 and VP1 within the same structural motif is.
If this virus is to be used as a biological control against Chagas disease, the more knowledge that we can gather about it the better prepared we will be to overcome the inherent difficulties that are related to this type of approach. The atomic coordinates and structure factors for TrV have been deposited in the Protein Data Bank (http://www. pdb. org) as entry 3nap. The theoretical model for VP4 has been deposited in the Protein Model DataBase (http://mi. caspur. it/ PMDB) with code PM0077751. Phylogenetic classification of the available Dicistroviridae genome sequences constructed using the MEGA5 software  (Tamura et al. , 2011). The type species of each genus is boxed. Two genera have been accepted so far: Cripavirus and Aparavirus (continuous ellipse). The proposed Triatovirus genus  (Agirre et al.
DSC analysis DSC measurements were carried out with a DSC Q100 from TA Instruments. Data were integrated from the recorded output computational software. The instrument was calibrated and tested with a high purity indium metal. Due to their high ability to absorb moisture when exposed to air, the samples were loaded and sealed quickly. About 1 to 5 mg of salts were introduced into an aluminium sealed-type DSC pan. A hole of c. a. 0. 5 mm in diameter was made in the top of the sealed pan to evacuate the water evolved during the dehydration. The flow of dry nitrogen was maintained constant at 50 cm 3 /min to get a stationary vaporization  [10]. Samples were heated from 274 K to either 473 K or 573 K (depending on their melting temperature) with a heating rate of 5 K/min. This temperature was maintained one minute and then samples were cooled to 274 K at 15 K/min.
TG analysis The TG analyses were performed with a HI RES Modulated TGA2950 TG Analyzer from TA Instruments. The temperature calibration was made with a high purity indium sample by correspondence with its Curie temperature. Around 5 mg of sample were quickly placed into an opened platinum pan and immediately analysed. The flow rate of dry nitrogen was 90cm 3 /min. In order to compare these data with DSC analyses, the samples were heated to 473 K or 573 K with a rate of 5 K/min. The data allowed to determine the loss of water corresponding to each transition observed in DSC.
We address this source of bias by turning to behavioral indicators of gender discrimination in Senegal using Afrobarometer data from Senegal. We merge data from all three rounds  (2002, 2005, and 2008) , and focus on a subsample of Christian and Muslim respondents from the Joola and Serer language communities. These data allow us to measure behavior by focusing on the three questions that were common to all three rounds and which measured respondent behavior during the interview, rather than attitudes toward survey questions: the interviewer's assessment of whether the respondent's 20 We check the robustness of our results by adding, sequentially, controls for: whether the dictator personally knew someone who played in a previous session; the age of the dictator; the religiosity of the dictator; and the education and family income of the dictator, whether the dictator was born in France, and whether the dictator is a French national.
ACKNOWLEDGMENTS This research was funded by the  National Science Foundation , " Muslim Integration into EU Societies: Comparative Perspectives ," Grant  SES-0819635. The authors would like to thank participants at the 2011 Princeton University Luce Conference (Princeton, NJ), 2011 Annual Meeting of the  Midwest Political Science Association (Chicago, IL ), 2011 Spring meeting of the Working Group on African Political Economy ( La Jolla , CA), and 2011 Annual Meeting of the  American Political Science Association (Seattle, WA)  for helpful feedback. CLAIRE L. ADIDA  University of California San Diego DAVID D. LAITIN Stanford University MARIE-ANNE VALFORT Paris School of Economics -Paris I Panth eon Sorbonne University.
The previously defined cut-off score of 20 was used to identify participants as having well controlled (ACT score 20) or uncontrolled asthma (ACT score 520). Asthma control was also evaluated in relation to the Global Initiative for Asthma (GINA) guidelines  [1]. The GINA guidelines recommend evaluation of asthma control in relation to five characteristics: daytime symptoms, limitation of activities, nocturnal symptoms/awakenings, need for reliever/rescue medication and lung function. Participants were asked to report on the occurrence of day-and night-time asthma symptoms and the frequency with which these affected their planned activities as well as the frequency of rescue medication use in the previous week. Lung function data was not available so the remaining four characteristics were used as a proxy to define the level of asthma control as follows: (1) controlled: daytime symptoms no more than twice a week, no night-time symptoms, no limitation to activities in the previous four weeks and rescue medication use no more than once a week; (2) poorly controlled: daytime symptoms more than twice a week or night-time symptoms or limitation to activities in the previous four weeks or rescue medication use more than once a week; and (3) uncontrolled: three or more features of poorly controlled asthma.
The most common categories of triggers were climate, physical and air pollution (experienced by 450% of patients), followed by infection, house dust, animal allergy, pollen allergy and psychology (420 to550% of patients), then respiration, food, sleep, alcohol, mould and medication (all 520% of patients)  [15]. With the exception of mould, which was a much more common trigger in the present survey than in the Asthma Trigger Inventory (51% versus 2%), the frequency of triggers common to both datasets were broadly similar. Some of the triggers perceived by participants in this survey are not considered to be classic asthma triggers, for example coughing, strong odours and lying flat. Although coughing was the third most common trigger (reported by 68% of participants), it is a well-established symptom of asthma and is not listed as an asthma trigger by the GINA guidelines  [1].
Patients in CR at the time of RIC/NMA appear to have significantly lower TRM and risk of relapse as well as superior overall survival (OS). In limited earlier series, similar OS has been reported with RIC or myeloablative conditioning in this clinical setting  (20, 24). Using the large multicenter observational database from the Center for International Blood and Marrow Transplant Research (CIBMTR) we examined the outcome of secondary unrelated donor (URD) Allo-HCT for AML patients after failure of Autologous HCT to identify patients and HCT techniques most likely to be successful.