dataesr/scientific-paragraphs-categorization huggingface dataset:
IV. DATA ANALYSIS A. Thermal point The experimental data were fitted by a multi-level R-matrix code SAMMY  [25] , which also accounts for the resolution function of the neutron beam, Doppler broadening of capture resonances, multiple scattering and self-shielding effects. A reasonable fit for energies up to 10 keV was obtained by considering two resonances with negative energy, as adopted in the latest versions of the evaluated data libraries, as well as suggested by Mughabghab in his latest compilation  [26]. In combination with the transmission data, the negative reso-nances may be used for characterization of the bound states of a nucleus. The energy and neutron width of the two resonances were fixed at the value adopted from the ENDF/B-VII. 1 parameters database -accessed via JANIS interface [27] -while the capture width was left free.
[12] , and in agreement within 0. 4% with the recommended value of 4370 mb from Mughabghab [26]. The systematic uncertainty originates from the uncertainties on the neutron flux (2% at thermal energies), weighting function (2%) and the beam interception factor (1. 3%). The statistical error was determined from the uncertainty on the fit parameters. The significance of the thermal value is related to nickel being an important structural material of interest for current and future nuclear reactors. A comparison with previous measured and evaluated thermal values is listed in Table  III , where the n TOF results are compared against evaluations from ENDF/B-VII. 0 and ENDF/B-VII. 1. In addition, the available experimental data from the EX-FOR database  [5]  are listed, most of them reported as Maxwellian averages at 25.
For the neutron spin I n = 1/2 and the 58 Ni ground state spin I58 Ni = 0, the statistical spin factor g s : g s = 2J + 1 (2I n + 1)(2I58 Ni + 1) (4) depends only on the resonance spin J. The orbital angular momentum , resonance spin J and initial values for the resonance widths Γ n and Γ γ were adopted from the ENDF/B-VII. 1 parameters database  [10]. Out of 56 resonances listed therein up to 122 keV, 5 could not be resolved, i. e. distinguished from the fluctuations in the baseline of the n TOF yield due to the very small associated kernels. These are the resonances at 24. 77 keV, 35. 06 keV, 48. 47 keV, 83. 97 keV and 92. 73 keV. In addition, no new resonances were found. In the course of the fitting procedure the largest of the widths was kept fixed -with exception of cases when Γ n and Γ γ were comparable -while the smaller one was left free in order to accurately reproduce the resonance shapes.
Since all other major libraries essentially reproduce the evaluations in ENDF/B-VII. 0, the n TOF results call for a revision of the 58 Ni capture data in those data libraries. In Fig. 8  the available MACSs from KADoNIS v0. 3 compilation  [31]  are also shown. The plotted data are listed in Table  V  for all kT values found in KADoNIS v0. 3 database. Both the statistical and systematic uncertainty in the MACS have been obtained by error propagation, starting from the values reported for the resolved and unresolved resonance region. Systematic uncertainties are the same as those for the systematic uncertainty of kernels. The impact of our new results on the s-process was  studied with a full 25M stellar model with an initial metal content of Z =0. 02  [35]. The s-process nucleosynthesis is provided by the post-processing NuGrid code MPPNP  [36].
VI. CONCLUSIONS The radiative neutron capture cross section of 58 Ni has been measured in a wide energy range from 27 meV up to 400 keV, taking advantage of the high instantaneous neutron flux available at the n TOF facility at CERN, together with the low neutron sensitivity of two liquid C 6 D 6 scintillation detectors. Analyzing the highresolution capture data by means of the R-matrix code SAMMY, a total of 51 resonances have been identified up to 122 keV. Completing the analysis of the unresolved resonance region by the code SESH, the Maxwellian aver-aged cross sections have been calculated for the temperature range kT = 5-100 keV of astrophysical importance. Our data confirm the most recent findings by Guber et al. [6]  within kT = 10 -60 keV range. The decrease of the new MACS causes an increase of 60% of the final s-process abundance of 58 Ni.
ACKNOWLEDGMENTS M. Pignatari  acknowledges significant support from  NSF  grants  PHY 02-16783  and  PHY 09-22648  ( Joint Institute for Nuclear Astrophysics, JINA ) and  EU MIRG-CT-2006-046520. The continued work on codes and in disseminating data is made possible through funding from the  Ambizione  grant of the SNSF (MP, Switzerland). M. Pignatari also thanks for support from  Euro-GENESIS. NuGrid data is served by  Canfar/CADC. T. Rauscher  acknowledges the support from the  EU-ROCORES Programme EuroGENESIS , as well as the  Swiss NSF. In addition, the support from the  EN-SAR /THEXO European  FP7 Programme  and the  Hungarian Academy of Sciences  are gratefully recognized.
Standard matter and a cosmological constant are not required in order to get a sensible value of H. Indeed, SST appears to give rise to a new cosmology. Another specific property of the spinorial space-time is the existence of a privileged space direction for each point of the cosmic space-time  [9, 15]. This is a direct consequence of the use of two complex coordinates, instead of the usual four real ones, to describe the cosmic space-time position. Cosmic SU(2) transformations correspond to space translations, and the privileged space direction is associated to the SU(2) generator that leaves unchanged the space-time position spinor  [15, 29]. Space translations following this generator leave the cosmic space-time position spinor invariant up to a complex phase. Thus, the possible existence of a privileged space direction in WMAP and Planck data on Cosmic Microwave Background (CMB) should not be considered as a strange phenomenon even if further data and analyses are required to confirm and interpret such a result.
Such a strong result is close to Planck data that suggest H 67. 3 km/s/Mpc and t 13. 82 Gyr leading to H t 0. 95. The H t = 1 relation can thus be a suitable limit for the evolution of the Universe, as the standard matter density is expected to decrease with the Universe expansion faster than the SST curvature term  [10, 18]. Since no critical speed has yet been introduced, the Universe corresponding to the cosmic SST can be naturally assumed to be much larger than our visible Universe. As discussed above, another important cosmological implication of the SST geometry is the existence of a privileged space direction for each commoving observer. Standard cosmology using only real space-time coordinates cannot exhibit such a geometric property, as the possible memory of an underlying spinorial space-time structure is lost from the beginning by such an approach.
g. Plasmodium species, P. vivax + W. bancrofti and P. falciparum + P. knowlesi. Amplification consisted of one cycle of denaturation at 95°C for 15 min followed by 45 cycles at 95°C for 20 s, 60°C for 1 min and 40°C for 30 s. Analysis of the singleplex and multiplex data was performed with the LightCycler 480 software (Roche Applied Science, Penzberg, Germany). PCR grade water was used as notemplate control. DNA from W. bancrofti, P. falciparum and P. vivax served as positive controls, and DNA extracted from human blood and An. dirus free of Plasmodium and W. bancrofti served as negative controls. All real-time PCR assays were carried out in duplicate, and samples that did not produce fluorescence before the threshold of 40 cycles (Ct) were considered negative. Questionable samples with a single positive well were retested.
Anopheles scanloni and An. rampae were only collected in Binh Phuoc Province. This is the first discovery of An. scanloni in Vietnam and the first time An. rampae has been found so far south in the country. Comparative analysis of DNA sequences from these two species showed a high degree of similarity with sequences of these species recorded in GenBank (http://www. ncbi. nlm. nih. gov/). The sequences for the Vietnamese species are deposited in GenBank under accession numbers KJ746968-KJ746995.
Acknowledgements We express our gratitude to the staff of the  Department of Parasitology and Entomology of the Military Preventive Medicine Centre ,  Ho Chi Minh City, Vietnam , for organizing and participating in the fieldwork. CTN gratefully acknowledges  Philippe Clair  ( qPCR platform, Faculty of Sciences, Montpellier ) for his expert advice and help in conducting real-time PCR during the laboratory work in France. Fieldwork was funded by the  Direction de la Coopération de Sécurité et de Défense, Ministry of Foreign Affairs, France. We are grateful to the personnel of the Military Mission, especially the  Defence Attaché of the French Embassy in Vietnam , for logistical and administrative assistance. This study was made possible through support provided to CTN by  IRD-DPF, Marseille, France.
If at least one live triatomine was found in a domestic unit (DU), this house was classified as being infested and was sprayed by trained field workers from the Ministry of Health with deltamethrin at a rate of 25 mg a. i per m 2 as previously described  [11]. Spraying included all structures found in the domicile and peridomicile and were supervised by staff from PUCE. Houses found to be not-infested were not sprayed. Sylvatic populations of triatomines (defined as populations sampled in both cultivated and natural vegetation) were sampled following the randomized sampling design developed by Suarez-Davalos et al. [8]. During each visit the coordinates of 70 points were randomly generated within the quadrat using the Spatstat package of R Software (R Development Core Team 2012). In the case that the distance between two points was ,3 m, the whole randomization was rerun (see  [8]  for more details).
Data Analyses Triatomine infestation. Four entomological indices were calculated to describe triatomine infestation levels in both synanthropic and sylvatic environments over the 7 sampling dates: (1) infestation index (number of positive houses or sylvatic collection point/number of houses or sylvatic collection points examined6100), (  2 ) density (number of triatomines collected/ number of houses or nests examined), (  3 ) crowding (number of triatomines collected/number of positive houses or nests), and (4) colonization index (number of houses or nests with nymphs/ number of positive houses or nests6100)  [11, 29]. Triatomine density interpolation mapping. To visualize the spatio-temporal dynamics of triatomine abundance in the studied community we built density interpolation maps using information on the number of triatomines collected at the coordinates of the 70-quadrat points at each visit.
The data were adjusted at a surface z(x,y) form, by means of the Gridfit function of the Software MATLAB 7. 0  [30]. Interpolations relating information between nearest neighbors were obtained to develop a Gridfit-modeled surface compiled with the plot of the sampled points (see Dangles et al. [31]  for more details). These plots were overlapped with maps of synanthropic infestation generated in  ArcMap 9. 3 (ESRI Inc. 1999 -2008). Multivariate and path analyses. We used ordination techniques coupled with path analyses to examine the direct and indirect effects of season (reflected by precipitation levels) on T. cruzi-infected abundance. First, in order to test whether landscape changes over the year (i. e. 7 sampling dates) affected the distribution of triatomines, multivariate analysis of variance (MANOVA) and canonical variate analyses (CVA) were performed on habitat type variables (crop, shrub, forest) and rodent host variables (squirrel, rat and mouse) associated with the locations where triatomines were found.
More complex models were not used because sample size would not support them. All variables were transformed to have a normal distribution using z scores and log transformation prior to analysis. Path analyses were run in the sem package  [35]  for R, version 2. 15. 1 (R Development Core Team 2013). Generalized linear model. Generalized linear model analyses (GLM) were further used to test the effect of specific   height and host) were not included in the same model. We also included a ''collection point'' variable to allow within-collection point comparisons while controlling for variation resulting from unmeasured collection point-specific parameters. Site was treated as fixed effects, but we obtained similar results by means of the generalized linear mixed model function (glmmPQL; MASS library for R), with sites as random effects.
Acknowledgments The authors are grateful to people of visited communities and entomologists from the  Ecuadorian National Chagas Control Program  for their helpful collaboration. They also thank  Anita G. Villacı  ´s, Sofia Ocan ˜a-Mayorga, Sofı ´a Mun ˜oz, Cesar  A. Yumiseva , and  Esteban G. Baus  for their technical assistance, and Frederique Breniere,  Claudio Lazzari ,  Ana Lucia Moncayo ,  Sofia Ocan ˜a-Mayorga ,  Anita Villacı  ´s and three anonymous reviewers for the critical review of the manuscript.
Methylation differences between PT and their matched metastasis or recurrence A collection of 17 PT/LR pairs, 11 PT/CL pairs, and 20 PT/ AM pairs was analyzed. The methylation data are available in the GEO database record number: GSE44870. Tables 1, 2 and 3 detail the summarized clinico-histopathological properties of each sample. Some of the PT/LR samples match in part the cohort studied by Bollet et al. [16] , and the corresponding sample numbers from both studies are provided in Table  2. Tables  S1, S2  and S3 provide more detailed characteristics. Within each of the three cohorts, pairs of tumors including a PT and a metastatic or relapse sample can be used to investigate whether particular patterns in methylation profiles can serve as marker for cancer progression. Within each cohort, investigations were made to detect differences at the methylome level between PT and the Table  2.
The top 50 probes ranked by p-value then by absolute methylation variation between the primary tumor and its recurrence is also provided in Tables S4 (PTLR) and S5 (PTCL). No overlap existed between the three lists except for one gene (PI3K5R between the PT/AM and PT/LR datasets). All the corresponding quantilequantile plots are available in Figure  S1. On the PT/AM cohort, the SVM model correctly identified the PT and AM in 18 out of 20 held-out pairs (90% success rate, Pvalue = 2:0 Ã 10 {4 ) when considering the whole methylation profile probes. The SVM model obtained after dimensionality reduction by filtering the 22 most significant probes selected according to a Wilcoxon test gave a 100% accuracy. As illustrated in Figure  1 , good accuracy was still achieved when considering an increasing number of probes (Accuracy * 90% ).
Discussion We studied alterations of methylation profiles from primary breast carcinomas and different types of recurrences, namely, axillary metastases, local recurrences and contralateral breast carcinomas. For this particular dataset, we observed significant methylation differences for 49 CpG probes, which characterizes the progression between a PT and its AM. Consistent with this result, a multivariate analysis with a linear SVM classifier using a small subset of probes perfectly distinguished PTs from AMs with a 100% accuracy. Several significantly differentially methylated probes correspond to genes involved in cancer-related mechanisms such as cell death (MCF2L, RASSF5, RASSF6, CASZ1, SLC22A18, IFI27), tumorogenesis (CTSZ, TP73, CTSK, PIK3R1), KLK11, cell cycle (PPM1G, RANBP5, VAMP8) and cell differentiation (SMAF1, PAX6, PAX8).
Methylation profiles did not significantly differ depending on either ER, PR, HER2 and grade characteristics (min adjusted P-value = 0:09). To ensure that the data would be informative, genomic analyzes were restricted to tumors (primary and recurrences) in which at least 50% of cancer cells had been assessed by hematoxylin, eosin, and saffron staining of sections from snap-frozen samples. All the therapies were performed posterior to the biopsies of the primary tumors. Therefore, the studied methylation profiles are not modified by any potential effect of the treatments. The 22 healthy breast tissues are taken from healthy women who underwent cosmetic plastic surgery at the Institut Curie. Part of the PT/AM cohort is identical to the cohort studied by Bollet et al. [16]. All experiments were performed retrospectively and in accordance with the French Bioethics Law 2004-800, the French National Institute of Cancer (INCa) Ethics Charter and after approval by the Institut Curie review board and ethics committee (Comit de Pilotage of the Groupe Sein).
Data analysis A spatial normalization process was applied to all profiles  [42]. Among the 27,578 probes measured on each sample, 5 probes were removed due to missing values for some individuals, and all subsequent analysis was performed on the 27,573 remaining probes. Differentially methylated probes between PT and their matched AM, LR and CL are obtained using two-sided paired and unpaired Wilcoxon tests, correcting the p-values for multiple testing with the methods of Benjamini and Hochberg  [43]. Multivariate analysis was performed using a linear support vector machine (SVM) multidimensional classifier on either the complete methylation profile or after dimensional reduction by considering only the most significant probes based on the Wilcoxon test. A pvalue was calculated to assess the significance of the predictor accuracy compared to a predictor that would predict classes randomly.
Unsupervised classifications were performed with complete linkage agglomerative clustering using the MATLAB bioinformatics toolbox, while the support vector machine implemented in LIBSVM  [44]  was computed with a linear kernel and nested leave-one-out cross validation for parameter selection for supervised classification. The similarity between two copy number profiles is assessed with the partial identity score (PIS) as defined by Bollet et al. [16] , which is based on the quantity of shared breakpoints between the two profiles and their frequencies. Following  [16] , a recurrence from a matched PT/LR pair was considered TR based on copy numbers when the PIS between the PT and LR profiles was above the 95% quantile of the empirical PIS distribution between unrelated sample pairs. Similarly, a Methylation-Similarity score (MS) is defined based on the methylation profiles of a PT and its matched LR as the inverse of the Manhattan distance between their methylation profiles considered as 27,573-dimensional vectors.
LR are then classified as TR of its matched PT when the MS score is above the 95% quantile of the empirical MS distribution between unrelated pairs. As a baseline, these results were compared to the Manhattan distance between unrelated normal breast tissues. Metastasis-free survival was estimated by the Kaplan-Meier Method  [45]  and compared between the group of patients who were diagnosed as TR and the group diagnosed as NP using the log-rank test. The confidence interval of the hazard ratio was obtained using a semi-parametric Cox model  [46]. Computation was done using MATLAB packages Logrank  [47]  and KMPlot  [48].
OLIGONUCLEOTIDE MICROARRAY DESIGN A genome-wide Wigglesworthia transcriptome analysis from G. p. gambiensis was performed using the Agilent Technologies oligonucleotide microarray format (www. agilent. com). The custom-made density array (8 × 15 K format; AMADID 050087, Agilent Technologies) was designed with 60-mer oligos specific to the 673 genes of the W. glossinidia chromosome from G. morsitans morsitans (NCBI Reference Sequence: NC_016893. 1) (Akman et al. , 2002). For each gene, 10 different unique probes designed by Hybrigenics (Clermont-Ferrand, France) were used. The Agilent design uses the uniqueness of probe sequences as one of the criteria for probe selection, to avoid cross-hybridization with non-target genes. The details of the array design and sample description are available at the Gene Expression Omnibus (GEO) under the accession number GPL18427.
MICROARRAY DATA ANALYSIS, GENE ONTOLOGY ANALYSIS AND DOWNSTREAM ANNOTATION The microarray approach has been used to analyse W. glossinidia gene expression, as its reliability had been validated by qPCR in our previous investigation on Sodalis differential gene expression  (Hamidou Soumana et al. , 2014). All microarray data are MIAME-compliant, and the raw and normalized data have been deposited in the MIAME-compliant GEO database  (Edgar et al. , 2002)  (GEO accession number GSE55931). Individual microarray quality was evaluated based on the QC report, pair-wise MA plots, and box plots. The results were extracted using the Feature Extraction software 11. 0. 1 (Agilent Technologies). The raw data files were imported to GeneSpring GX (version 12. 0, Agilent Technologies), which was used for background adjustment, quantile normalization of data  (Bolstad et al.
, 2003; Smyth et al. , 2005) , log-transformation, and gene clustering for the 24 microarrays. Gene ontology was performed only on genes with significant differential expression, using the GeneSpring database. An unpaired t-test was used for statistical analysis  (Qin et al. , 2012). A p-value below 0. 05 was considered as statistically significant and indicates significant differences between groups (e. g. , between NS 3-day samples/S 3-day samples, between I 10-day samples/NI 10-day samples, and between I 20-day samples/NI 20-day samples). The representation of each differentially expressed gene within each ontology category (including categories for molecular function, cellular component, and biological processes) was measured. A corrected p-value (Benjamini-Yekutelli correction) lower than 0.
5 indicates over-representation of the differentially expressed genes within that particular category. Wigglesworthia gene expression data were further analyzed via two-dimensional hierarchical clustering, while three-dimensional clustering of samples was analyzed by principle component analysis (PCA). Hierarchical clustering of differentially expressed genes was performed using average linkage and the Pearsoncentered distance metrics  (Claverie, 1999). Gene trees were created to group similar genes and to improve visualization of the data  (Butte, 2002). The relationship between genes is represented by a tree in this type of clustering, where branch length reflects the degree of similarity between genes. PCA was performed within GeneSpring on infected (or stimulated) vs. non-infected (or non-stimulated) conditions at the different experimental infection times using the list of genes.
GO ANNOTATION OF THE LIST OF DIFFERENTIALLY EXPRESSED GENES We hypothesized that some of the differentially expressed genes would be involved in downstream molecular pathways that are important for maintaining susceptibility or refractoriness to trypanosome infection. To identify which types of global cellular processes or specific molecular functions are responsive, the list of differentially expressed genes obtained comparing the different conditions (stimulated/non-stimulated, infected/noninfected) from the three time points (3, 10, and 20 days) was annotated using the GO database  (Blake and Harris, 2008). Each of the genes was assigned to molecular function, cellular component, and biological processes categories as designated by the GO database. Those GO categories significantly over-represented in the list of differentially expressed genes match a greater number of differentially expressed genes than would be expected by chance.
ACKNOWLEDGMENTS The authors thank the " Région Languedoc-Roussillon-Appel d'Offre Chercheur d'Avenir 2011 ," the  "Service de Coopération et d'Action Culturelle de l'Ambassade de France au Niger,"  and the  "Institut de Recherche pour le Développement"  for their financial support. I. Hamidou Soumana  is a PhD student supported by the  Niger French Embassy ,  Service de Coopération et d'Action Culturelle (SCAC).