dataesr/scientific-paragraphs-categorization huggingface dataset:
Studies from Kilifi ,  Kenya received Wellcome Trust  core funding ( OXF-COR03 ). DJN and JAGS are supported by personal awards from the  Wellcome Trust  ( 102975 ,  098532 ). Data from  Cape Town ,  South Africa , are funded by the  Bill & Melinda Gates Foundation  ( OPP 1017641 ) and the  MRC South Africa. The study from Vietnam by  Nagasaki University  is supported by the  Japan Initiative for Global Research Network on Infectious Diseases  ( J-GRID ) from  Ministry of Education, Culture, Sport, Science, & Technology in Japan , and  Japan Agency for Medical Research and Development (AMED). The funding agency does not have any role in writing the report. PB is an employee of GSK Vaccines. We acknowledge  Leilei Huang  and  Huayu Zhang  for preparing the maps of location of studies.
Brain sequences were available from 10 subjects with HAND. 71 different physicochemical amino acids scales were analyzed for 10 functional domains of Nef. Evolved neural networks (ENNs) were applied to training and testing data sets to classify 1) brain from non-brain sequences and 2) cancer from non-cancer sequences. The best ENN was assayed for performance on the training, testing, and a third validation dataset of sequences with unknown etiology. Each sequence was scored and a binary threshold was used to discriminate samples into one of the two classes. Results: Nef sequences from subjects with either HAND or cancers at death were classified with 84. 5% and 90% true positive accuracy, respectively. Our approach elucidated structure-function properties of disease specific Nef that were not discernable from primary sequence information alone.
Methods: The DRONE study was a multicenter prospective study enrolling individuals starting a DBR and followed-up during 48 weeks (W48) (NCT02557997). Total HIV-DNA in peripheral blood mononuclear cells (PBMCs) and serum immune activation biomarkers (sCD14, sCD163, IL-6us and IP-10) were measured. CD32a+ CD4 T-cells were sorted in a subgroup of participants. Bayesian analysis was used to estimate the posterior probability distribution of HIV-DNA levels. Results: A total of 169 participants achieved or maintained virological control on DBR. According to the clinical stage of HIV infection, participants were assigned to different groups: acute infections (AI, n=20), ART-naïve chronic infections (CI, n=21), individuals in virological success on ART (VS, n=116) and virological failures at baseline (VF, n=12).
Twenty-four hours post transfection, 1. 10 5 pcDNA3 (vector control) or pcDNA3-GAr-transfected H1299 cells were trypsinized and selected in growth medium supplemented with geneticin. Surviving colonies were allowed to grow for 15 days and stained with 4% (v/v) Giemsa stain. Colonies were then quantified using Clono counter programme. Flow cytometry. Cells expressing indicated constructs were fixed by overnight incubation in cold 70% ethanol. After 30 min incubation with 100 U/ml RNase A (Sigma-Aldrich) at 37 °C, propidium iodide (10 µg/ml)-stained cells were analysed with an LSR flow cytometer and CellQuest software (Becton-Dickinson). ChIP assays. ChIP assays were performed using a kit according to the manufacturer's instructions (Upstate). The cleared samples were incubated overnight with the anti-E2F1 (H137) anti-E2F2 (sc-632) or anti-E2F3 (sc-56666) rabbit polyclonal antibodies.
Acknowledgements This work was supported by  Equipe Labellisée la Ligue Contre le Cancer , the  Inserm , the  RECAMO  projects  GACR P206/12/G151 ,  MEYS-NPS I-L01413 ,  Cancerforskningsfonden Norr  and  Cancerfonden   160598. S. V. G. was supported by la  Ligue Contre le Cancer  and S. P. by the  ARC  and PACRI. We thank  Dr O. Bischof  for providing us cmv-E2F1 and pRb constructs,  Dr K. Münger  for cmv-HPV16-E7 construct and  Prof. Dr L. Z. Penn  for pGL2-c-myc promoter-luciferase constructs.
Two crossed polarizers are placed outside the electromagnet and a 632. 8 nm He-Ne laser is used for sample analysis. The emergent laser beam is recorded by a ThorLab photovoltaic cell and the data are collected to get realtime plots. The Fréedericksz transition threshold was determined by slowly increasing the applied field. It was found to be 0. 047 T for the pure liquid crystal and 0. 062 T for the cell containing the ferroparticles. The transition occurs when a significant change of the light intensity is measured while the strength of the applied field is increased (Figure  4 ). In dynamic measurements a magnetic field higher than the critical Fréedericksz threshold was suddenly applied and the light intensity was recorded as a function of the time. The same measurement was carried out after the field was switched off.
The RNA integrity numbers (RINs) were generated using the Agilent 2100 Expert Software (Version. B. 02. 08. SI648 Agilent Technologies). Only samples with RINs >7. 0 were used for mRNA analysis. Poly-A RNA enrichment was performed for each sample using 1. 5 mg of total RNA according to the New England Bio-Labs Ultra Directional RNA library prep for Illumina kit (New England Biolabs Inc, Ipswich, Massachusetts). The number of biological replicates was 6 per each of 6 dose group (including controls), per time point, that is N ¼ 6 animals/dose Â 6 doses Â 3 time points ¼ 108 samples in total. A dual barcode scheme was used to multiplex 36 samples together for each RNA-Seq experiment; for each individual time point, the control and treated rats (n ¼ 36) were run together on a flow cell using an Illumina NextSeq500 (San Diego, California).
Bioinformatics to Identify Differentially Expressed Genes and Gene Ontology Pathway Analysis A number of quality control metrics were employed to assess the quality of RNA-Seq data generated for each sample. This included per base quality, per base sequence content, and the presence of adaptors. The RNA-Seq reads were aligned with TopHat (https://ccb. jhu. edu/software/tophat/index. shtml) using the rat rn6 genome using (rat rn6: http://useast. ensembl. org/Rattus_norvegicus/Info/Index). RNA-Seq data were normalized using Cuffnorm to the expression levels from the different RNA-Seq libraries (http://cole-trapnell-lab. github. io/cufflinks/cuffnorm/index. html). Cufflinks was used to conduct to identify differentially expressed genes (DEG; http:// cole-trapnell-lab. github. io/cufflinks/). Principal component analysis was used to visualize patterns in the data, and hierarchical clustering was used to check for any groups in the data.
For each treatment day (days 5, 15, or 31), the RNA-Seq expression signal was compared from each exposure level (0. 5, 1. 5, 3. 0, 6. 0, and 12. 0) to the corresponding unexposed control from the same day. The DEG with P value. 005 and fold change !+1. 5 were uploaded into the "Functional Annotation Tool" of the Database for Annotation, Visualization and Integrated Discovery (DAVID), available at https://david. ncifcrf. gov/, to determine the most enriched gene ontology terms, using ENSEMBLE IDs of the identified DEGs, False discovery rate-adjusted Fisher exact P value <. 05, and DAVID's default settings.
Quantitative Real-Time Polymerase Chain Reaction The real-time polymerase chain reaction (qRT-PCR) reactions were amplified using 20 ng of cDNA template, TaqMan ® Fast Advanced Master Mix (ABI), and TaqMan ® Gene Expression Assays (ABI) as indicated in Table  1. The qRT-PCR was performed using a ViiA™ 7 qRT-PCR System (ABI) with manufacturer's recommended thermal cycling conditions for TaqMan ® Fast Advanced Master Mix (50 C for 2 minutes, 95 C for 20 seconds, 95 C for 1 second, and 60 C for 20 seconds for 40 cycles). The mRNA levels were quantified using the cycle threshold (C T ) values for the target genes of interest and the endogenous reference gene, Gapdh. Data were reported as the relative quantification (RQ; where RQ ¼ 2 -(DDCT) ) of treated animals normalized to the control group using DataAssist™ v3.
0 À1. 60 No Dnase1l3 Deoxyribonuclease 1-like 3 3. 0 1. 57 Yes Tnnt2 Troponin T Type 2 (cardiac) 12. 0 À1. 69 No, but related gene Tnnt3 -Yes Trpc1 Transient receptor potential cation channel, 12. 0 1. 51 No subfamily C, member 1 33 breviations: DEG, differentially expressed genes; DAVID, Database for Annotation, Visualization and Integrated Discovery; BMD, benchmark dose. a BMDExpress Data Viewer in conjunction with ingenuity pathway analysis was used to identify genes relevant to calcium signaling among the DEG identified in association with AA exposure on day 31 in the rat testes. b Chepelev et al. 33.
The other efficient structure based on the concatenation between BICM-ID and a STBC was called bit-interleaved space-time coded modulation with iterative decoding (BI-STCM-ID)  [35]. Since V-BLAST offers high spectral efficiencies by dividing the incoming data into multiple sub-streams and sending each sub-stream to a dedicated antenna, ST-BICM-ID can achieve a desired high transmission rate at the expense of loosing some degrees of diversity and increasing the decoding complexity. For BI-STCM-ID, STBC provides the highest diversity advantage for MIMO systems with a low complexity decoding algorithm. Although its association with a powerful channel code can improve both diversity gain and coding gains, this scheme suffers from the transmission rate. The transmitters of these two iteratively decoded MIMO systems are depicted in Fig.
The (2 Tx, 1 Rx) Alamouti code and a (37, 21) CRSC code of 1/2 coding rate are considered as the inner and outer code, respectively. Moreover, we use an anti-Gray mapping scheme for the QPSK constellation. n it,1 = 10, n it,2 = 8 for GIIP decoding, and 8 iterations for real decoding are considered in this system. As Fig. 7  shows, there is almost no difference between the GIIP and real decoding. This is mainly explained by the property of the detector which delivers symbols that are not much correlated. Actually the Alamouti code links the data in independent pairs and the correlation effects are limited within these couples of symbols. Therefore, the classical iterative processing without GIIP is already close to ML processing. However this experiment was useful to demonstrate that the GIIP technique provides a tight lower bound to ML performance.
Nevertheless, the spreading code, acting as a repetition code, can be used to offer frequency diversity. Now, if all spreading codes are allocated to one single user, no loss in data rate is experienced and the system retains its capacity to exploit frequency diversity. Obviously, MAI is converted into Self Interference (SI). Depending on the designed detector at the receiver part, the diversity gain is not able to compensate for the BER degradation due to SI. This diversity technique has also been explored independently from another point of view by  [38]. It was then generalised by  [39]  under the name of Linear Precoding (LP). The baseband equivalent model of an LP-OFDM system is depicted in Fig. 8. Data are encoded using a BICM scheme with a rate R convolutional encoder. Coded bits are mapped onto complex symbols (s i ) chosen in the constellation χ (BPSK, QPSK, 2 q -QAM…) using Gray mapping.
Study Population The source cohort consisted of patients affected by diarrhea, admitted to the San Martino Hospital in Genoa, Italy, grouped by ward, and subjects in the community from the same regional area, whose stools were sent to the microbiology laboratory for CDTB detection. In the hospital, the spatial unit was the ward, which is a unit provided with rooms where a unique staff of health-care and co-workers are active. The study period was from April 2010 to March 2015. We evaluated the San Martino Hospital data set (TD-Synergy MultiLab, SIEMENS) including all CDTB analyses performed. The person-days of hospitalization were obtained for groups of wards through the Hospital Admission Service, Business Intelligence Discoverer Desktop (Oracle). The Institutional Ethics Committee of San Martino University Hospital approved the study (n.
Definition of Outcome CDI cases were defined as subject with at least one positive stool for CDTB. Toxin B was detected in fecal specimens through the Rapid Membrane Enzyme Immunoassay (Techlab Inc. ) according to the manufacturer's instructions. We considered the total number of patients and analyses, including the analyses repeated for single subjects and changes of result concerning single patients during time. We also reviewed the hospital database and the movements of patients analyzed for CDTB throughout the hospital, from the hospital to the community and vice-versa.
Validation of selected RNAseq data by quantitative RT-PCR. To validate the RNA-seq data, expression of hcpR1, hcp, hcpR2, nap and nrf in the presence of nitrate, sulphate and nitric oxide were analysed by qRT-PCR (Supplementary Fig. S2a  and b ). No significant effects of nitrate or NO on hcpR2 expression were detected by qRT-PCR. The expression profiles of the other targets mirrored those obtained by the RNA-seq analysis, although larger relative changes in expression of napC and hcp were observed in the qRT-PCR analysis. The RNA-seq data were also consistent with our earlier studies  14, 30  that demonstrated up-regulation of nap, hcpR1, and hcp and no change in expression of hcpR2, in response to nitrate or nitric oxide. Bioinformatic prediction of the extent of the HcpR1 regulon. The name HcpR was introduced to designate the transcription factor that regulates synthesis of the hybrid cluster protein and an associated electron transfer protein, FrdX  18, 19.
While this manuscript was in review, a paper describing the proteomic response of D. desulfuricans 27774 to nitrate was published on line. Only proteins soluble in a low ionic strength buffer were analysed, so inevitably there are major differences between the proteomic and our RNAseq data. However, increased accumulation of Nap proteins in response to nitrate was confirmed  64. Unexplained is why genes for aromatic amino acid biosynthesis are strongly induced during growth in the presence of nitrate, but genes for catalase and putative iron uptake are repressed. A possible explanation for the induction of fumarate reductase genes during growth with nitrate might be an increased need for succinyl CoA for heme synthesis, but this is mere speculation. These are just a few of the many research challenges revealed from the genome-wide RNA-seq data available from this study.
David Lee, University of Birmingham. EMSA mixtures were incubated at 25 °C for 30 minutes and then loaded onto 6% (w/v) acrylamide gels prepared with 0. 25 x TBE and 0. 2% (v/v) glycerol. Electrophoresis was in 0. 25 x TBE at 160 V for 90-180 minutes. Following electrophoresis, gels were fixed in 10% (v/v) acetic acid and 10% (v/v) methanol for 10 minutes. Fixed gels were transferred to 3 mm Whatman filter paper and dried under vacuum. Dried gels were stored in cassettes with a Fuji Imaging Phosphor screen overnight which were then visualised with the Bio-Rad Molecular FX Imager System and QuantityOne software (BioRad).
Each RNA sample was treated twice to remove any traces of DNA. Samples were checked by qPCR for DNA contamination without reverse transcription. The 5 samples with highest concentration and A 260 / A 230 ratio were transferred on dry ice to Oxford Gene Technologies (UK) for further quality control testing before RNA-seq analysis. Three samples from each growth condition were depleted for ribosomal RNA before reverse transcription. Analysis of the RNA-seq data. The automated workflow for the RNA-seq analysis was implemented in the snakemake programming language, and is available on the supporting website. The workflow includes the following sequential steps: i > read quality control with fastQC (www. bioinformatics. babraham. ac. uk/projects/fastqc/); ii > read mapping with bowtie2 in non-oriented paired-ends mode, with at most 1 mismatch per read, and all other options left to their default values  68, 69.
The genome sequence (fasta-formatted) and features (GTF-formatted) were downloaded from EnsemblGenomes Bacteria release 32 (http://bacteria. ensembl. org/ index. html) (strain identifier Desulfovibrio_desulfuricans_subsp_desulfuricans_str_atcc_27774. ASM2212v1); iii > assignment of reads per genes in each sample by using feature Counts (from the subread suite)  70. Finally the detection of "differentially expressed genes" (DEG) relied on the R library edgeR  71. We applied a threshold of 0. 05 on the adjusted p-value, and of 1. 5 on the fold change to select for DEG. Table  1  gives the number of differentially expressed genes for each comparison between growth conditions (Sulfate + NO vs Sulfate; Nitrate + NO vs Nitrate; Nitrate vs Sulfate; Nitrate + NO vs Sulfate + NO). A detailed technical report of all the statistical treatments (data exploration, differential analysis, cross-species functional enrichment) is available on the supporting website.
Analysis of regulatory sequences. The software suite Regulatory Sequence Analysis Tools (RSAT, http:// rsat. eu/) was used to analyse regions upstream of genes in the reference genome Desulfovibrio_desulfuricans_ ATCC_27774_uid59213, which was downloaded from NCBI. The tool retrieve-seq was used to retrieve promoter sequences up to 400 bp upstream from position -1 relative to the translation start codon up to the nearest neighbouring gene. The HcpR1 (Ddes_0528) binding sequence TGTGA-N6-TCACA, where N6 denotes a succession of 6 undefined nucleotides, was used to construct a seed matrix by setting an arbitrary weight of 8 on each residue of the binding site, and 0 on other nucleotides (Supplementary Fig. S2 ). The upstream sequences of all genes were scanned with matrix-scan to collect sequences matching this seed matrix with a p-value < 10 -4.
A GAMM was used because a non-linear relationship between the response variables (UPCR or proteinuria occurrence) and both "daof" and "age" explanatory variables was expected. A mixed model was used with patient ID as a random effect explanatory variable to take into account the non-independence of samples collected from the same patients and potential random individual variations between patients. The analysis was performed using the "gamm4" package (version 0. 2-3) under the R statistical environment (R Foundation, Vienna, Austria). Significance was assigned at p < 0. 050.
e. , σ π θ θ θ =     -    . θθ r K K 1 2 cos 2 cos 2 3 2 sin I I I 2 Where K I and K II are the mode I and II stress intensity factors, respectively. By using the MTS criterion, we could calculate the angle of the newly generated crack tip segment. We used commercially available extended finite element methods (XFEM) software for the 3D modelling of our void crack sample and calculated the stress information at the crack tip. By repeating infinitesimal growth and recalculation of the angle, we could successfully simulate the crack path, which has a periodic wavy shape just as that of our experimental result (Fig. 5 ). For a more detailed procedure of the simulation, see the Methods section. The wavelength was approximately four times the width, in excellent agreement with the experimental results.
Acknowledgements This work was supported by the  National Research Foundation of Korea (NRF)  via grants funded by the  Korean government (MSIP)  ( 2015-055714 ,  2006-0093853 ). S. U. C. acknowledges support from the  Basic Science Research Program  through the  NRF , funded by the  MSIP  ( NRF-2015R1C1A1A02037070 ). Y. D. K. and J. H. were supported by grants from the  ONR  ( N00014-13-1-0602  and  N00014-13-1-0464 ) and  DE-SC0012592. J. H. J. , J. I. acknowledge support from the  Pohang University of Science and Technology  and the  Korea Institute of Science and Technology Information. M. R. C. acknowledges support from the  Dong-Joon Sohn Foundation Scholarship.
First validation by pressure distribution Once the simulation data are recorded, elementary contact reactions are easy to distinguish and to extract. However, the highly dynamic nature of the process causes a lot of noise. The mean reaction on all or part of the target plane area, as F for example, are averaged in a stabilized time range. The reactions are split into several concentric rings to catch the radial dependencies of the tool-fluid pressure, cf. Fig. 4  & 5. Let us recall that the three main models of AWJ erosion, Finnie  [24] , Bitter  [25]  and Hashish  [26, 27] , all consider that wear power of an AWJ, normal to the target plane, is directly linked to the square of impact velocity which is proportional to the pressure. The shape of this pressure is often seen as a double Gaussian fit with respect to radius r, relative to the granulometry, the velocity field distribution and the abrasive distribution respectively  [16].
These viruses were isolated and amplified by serial passages in brains of newborn mice. Brains were homogenized in Hanks' solution and centrifuged. Supernatants were lyophilized and stored in sealed glass vials at room temperature until 2011. Viral genomic material was extracted from lyophilizates that were resuspended in phosphate-buffered saline, retrotranscribed into cDNA using Super-Script III enzyme and random hexamers (Life Technologies, Inc. ), and amplified using the phi29 enzyme  (6). Sequencing was performed using a HiSeq 2000 sequencer (Illumina)  (7). Only regions of the reads matching the reference viral sequences were selected and used for the whole-genome sequence assembly using SPAdes version 3. 0. 0 (8, 9). Overall lengths were 11,805 and 11,786 nucleotides, with average coverages of 2,743ϫ and 404ϫ for ArB6445 and HB84P07, respectively.
The coding sequence lengths were 7,425 and 3,747 nucleotides for the first and second ORFs, respectively. The two viruses share Ͼ99% nucleic acid identity. Phylogenetic analyses showed close relatedness with other CHIKV isolated in the CAR and confirmed classification into the ECSA lineage, as previously described with partial sequences  (5). Unlike the S27-African prototype strain (GenBank accession no. NC_004162), a leaky stop codon near the nsP3 gene 3= end is present in both sequences. The 3=-UTR (which plays essential roles in arbovirus replication, evolution, and host adaptation) of both viruses exhibits the typical duplication pattern of other ECSA lineage strains  (10). Further investigations might help better understand the recent evolutionary history of CHIKV. Accession number(s).
Acknowledgements We thank  Yin Yang  for synthesizing the pristine materials. We also thank  Prof. D. D. Sarma  for the fruitful discussions concerning HAXPES. Experiments were performed on the GALAXIES beamline at SOLEIL Synchrotron, France under Proposal No. 20160097. We are grateful to  Denis Céolin  and  Jean-Pascal Rueff  for their assistance and to the  SOLEIL  staff for their smooth operation of the facility. We also thank  José Avila  and  Maria-Carmen Asensio  from the  ANTARES  beamline for recording the Co-XAS spectra. J. M. T. and G. A. acknowledge the funding from the  European Research Council (ERC)  ( FP/2014) / ERC  Grant-Project  670116-ARPEMA.
Background SAR97276A, is a choline analogue inhibiting the phospholipid biosynthesis of Plasmodium falciparum. Treatment options for severe malaria are limited and SAR97276A represents a drug candidate for this indication. Methods This is a report on two consecutive trials evaluating safety and efficacy of parenterally administered SAR97276A for the treatment of malaria. The first study was a phase 2, multicenter, open-label study at six African hospitals (NCT00739206). At first adults with uncomplicated malaria were included receiving a single dose SAR97296A (IM: 0. 18 mg/kg or IV: 0. 14 mg/kg) followed by repeated dosing with daily administration of the IM dose for three days in case of lack of efficacy of the single-dose regimen before age de-escalation. The second study was a phase 2, multicenter, randomized, controlled open label study at five African hospitals assessing safety and efficacy of a higher dose of SAR97276A IM once (0.