dataesr/scientific-paragraphs-categorization huggingface dataset:
However, almost no inter-annual cycle has been observed  (Deville et al. , 2012)  for the Durzon karst system from surface absolute gravity measurements, and therefore, the transfer time should be less than 1 year. The range of transfer time is also in accordance with the model re-sult obtained for the Durzon karst system. An intermediate transfer time of the epikarst reservoir to the infiltration zone of about 6-12 months can be proposed for altered dolomite karst with a lack of high transmissive fractures. This characteristic transfer time is in accordance with the models fitted using continuous superconducting gravity data  (Fores et al. , 2017). However, only a small part of the NWI is stored in the limestone epikarst (BESS, SEOU) after the recharge period. A short transfer time (< 6 months) in the limestone karst is therefore necessary and can be due to open fractures as observed in surface.
Sequencing of PCR products and multiple sequence alignment In order to validate the different species identified by PCR in gel electrophoresis, the 18S rRNA gene of P. vivax and the DARC-coding gene of the P. vivax infected individuals were sequenced commercially by Inqaba Biotec, West Africa Ltd, Pretoria (Quote No. NG2018/13544). Request was also made for purification of PCR products prior sequencing. For each fragment, sequencing was carried out from both the 5′ and 3′ directions (2× coverage). Consensus sequences from both the forward and reverse sequences were generated using the BioEdit computer software. Multiple sequence alignment of the 18S rRNA of the vivax isolates and the human Duffy gene was done with BioEdit. Sequences generated from the current study were aligned with their respective reference sequences; P.
Statistical analysis All other data aside the sequences were analysed using Statistical Package for Social Sciences (SPSS) version 21. 0 (SPSS, Inc. Chicago IL, USA). Furthermore, the performance of each diagnostic test method was calculated by means of sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) using nested PCR as a gold standard. Kappa's statistics was used to test the level of agreement between the diagnostic tools. P < 0. 05 was considered statistically significant. For ease of cartographic representation of the diversity of mixed species originating from the different study areas, Eti-Osa and Ibeju were grouped as Lagos Islandowing to their location on the part of Lagos state surrounded by the Lagos lagoon and extending into the Atlantic ocean while Oredo and Ikpoba-Okha were grouped as Edo due to their supposed boundary sharing on the western part of Ikpoba-Okha.
malariae, P. falciparum/P. ovale and P. falciparum/P. vivax infection. This is followed by Kosofe and Lagos Island with P. falciparum, P. malariae mono infections as well as P. falciparum/P. malariae mixed infections. The least diversed site by species composition is seen in Ikorodu (Fig. 3 ). In order to authenticate the PCR results with regards to vivax infections, sequencing of the 18S rRNA was carried out on all P. vivax isolates (4 mixed and 1 mono infection). The sequences of the 18S rRNA genes, accompanied by multiple sequence alignment with its reference sequences (U03079. 1) showed perfect homology (100% similarity) (Fig. 4 ). The newly generated sequences of the 18S rRNA genes of all four species will be deposited in the GenBank (MK131265-MK131269). The sequences of the Duffy gene were trimmed to 620 bp which is more than sufficient to cover the -33rd nucleotide position.
Acknowledgements The authors appreciate the willingness of the study participants for their consent in donating blood samples. MAO is grateful to the  Economic Community of West African States (ECOWAS)  for the partial fund towards her Ph. D. programme. Appreciations are also due to the Rector of the  Universite Cheikh Anta Diop de Dakar, Senegal. The authors thank  Mrs. Ayanlere  and  Mr. Agbayewa  for their support in sample collection,  Mr. Samuel Oladele  for the microscopic analysis of smears.
g. , needleleaf/tundra dominance); (H2) climate-controlled patterns of Holocene BB were mitigated at a regional scale by trees' flammability; (H3) land use had a limited explanatory power during most of the Holocene, except for the southernmost European boreal regions concerned by farming practices. An alternative hypothesis would be that each region displays its own temporal trend under the complex effect of plant migrations, trajectories of precipitation pattern or interaction between temperature and precipitation, which control the evapotranspiration and thus fuel moisture, and biomass productivity and accumulation. The use of a west-east northern boreal sector based on four site clusters from Alaska to northern Fennoscandia enabled testing our hypotheses with a different climatic pattern, a rather homogeneous vegetation dominated by tundra shrubs/trees and boreal needleleaf evergreen trees and an evenly low importance of land use, while a north-south European boreal sector of three site clusters from northern to southern Fennoscandia provided the opportunity to explore our hypotheses with a dataset characterized by a gradual variation in climate, a change in vegetation composition from boreal needleleaf evergreen trees in the north to boreal and cool-temperate broadleaf trees in the south, and a progressive increase towards the south of land use importance (Figure  1 ).
| Records of past biomass burning activity Charcoal data from 88 sedimentary series located within the boreal biome (a transcontinental circumpolar band situated approximately between 50°N and 70°N latitude; Figure  2  and Supporting information Appendix S1) and covering part or all of the Holocene were selected from the latest version of the Global Charcoal Database (GCD v3,  Marlon et al. , 2016)  compiled by the Global Palaeofire Working Group (GPWG, www. paleofire. org) and from regional syntheses  (Clear, Molinari, & Bradshaw, 2014; Molinari et al. , 2013). Where multiple records (i. e. , macro-and micro-charcoal data) were available from the same site, all were included in the dataset. After selection, all charcoal records were first converted to a common time scale in calibrated years before present (hereafter cal yr BP), following the protocol described in  Power et al.
(2008)  by using either the original authors' published chronology or new agedepth models created using the median calibrated radiocarbon age. All charcoal data were then transformed to influx values (CHAR, i. e. , the number, area or weight of particles cm -2 year -1 ). In order to allow comparisons within and between charcoal records obtained from heterogeneous depositional environments and quantified with different laboratory techniques, a standardization procedure was required including a min-max rescaling of CHAR values followed by a Box-Cox transformation to homogenize the within-records variance  (Power et al. , 2008). Finally, a Z-score transformation was carried out using a base period most representative of the entire dataset (i. e. , the interval between 4,000 and 200 cal yr BP), excluding the industrial period due to the very different trends in charcoal records  (Marlon et al.
Composite curves for this study were produced with the method implemented in the R (R Core Team, 2016) package paleofire  (Blarquez et al. , 2014). A pairwise correlation between tCHAR Z-scores was performed to test if proximal sites had a high correlation coefficient compared with distant sites, for an estimation of the spatial dependence between Holocene trends in BB. Because each record had a different time-span and resolution, we trimmed the temporal extent for each pair of sites to the overlapping period and interpolated tCHAR Z-scores at 100 years temporal resolution.
, 2006 and Mauri et al. , 2015  in Supporting information). For North America, modern pollen data were derived from the Brown University dataset  (Avizinis & Webb, 1985)  and fossil pollen data were compiled from the North American Pollen database (NAPD). For the European sites, surface samples were obtained from the European Modern Pollen Database (EMPD) and fossil pollen data were compiled from the European Pollen Database (EPD). Chronological control was based on individually fitted age-depth models created for each pollen time series based on a calibrated radiocarbon time-scale. Radiocarbon dates were calibrated using the INTCAL98  (Stuiver et al. , 1998)  for North American series and the OX-CAL3. 5 program  (Bronk Ramsey, 2001)  for the European pollen time series. For this study, palaeoclimate data were expressed as standardized deviation (Z-scores) from the mean values for the period between 4,000 and 200 cal yr BP.
| Reconstruction of vegetation composition For an estimation of major changes in vegetation composition through time, fossil pollen data available from the same site or from a site located not more than 100 km away from a charcoal record (Figure  2 ) were extracted from the Neotoma database (www. neoto madb. org) or from the literature by digitizing the published diagrams using the program DATA MUGGER 1. 1  (Jones, 2011 ; see Supporting information Appendix S3 for more information). Mean pollen percentages at 1,000 years intervals were calculated for each selected site. In our analyses, chronological uncertainties were within the range of radiocarbon dates' uncertainties used to establish the agedepth models for each individual record. Pollen percentages threshold values proposed by  Davis and Jacobson (1985) ,  Davis, Schwartz, and Woods (1991) , Lisitsyna, Giesecke, and Hicks (2011) and  Pardoe (2001)  were used to establish the presence of a particular species within approximately 50 km from the study site on the basis of its pollen proportion in the sediment (Supporting information Appendix S4: Table  S1 ).
| Statistical analyses of proxy time series The R package relaimpo provides several metrics for assessing the relative importance of predictors in linear models  (Grömping, 2006). For our analyses, we firstly used the relaimpo package to calculate the importance of climate variability (mean July [for North America] or summer [for Fennoscandia] temperature anomalies and mean annual precipitation anomalies) and LU on BB over the Holocene (expressed as tCHAR Z-scores). The choice of using a linear model instead of a more elaborate technique was mainly due to its high interpretability (most users are acquainted with this technique). Furthermore, the (relatively low) amount of data did not allow using a more advanced method (i. e. , GAM, which would have required an explicit estimation of distributions).
In this case, all the data were expressed as standardized deviations (Z-scores) from the mean values over the period between 4,000 and 200 cal yr BP. For each sector and cluster, the analyses were performed by comparing the previously constructed composite time series (Figures  3  and 4 ) with the charcoal composite curves (Figure  6 ), with a temporal resolution of 100 years. In a second step, we used the relaimpo package to estimate the relative importance of changes in major vegetation cover expressed as PFTs groups on Holocene BB. In this case, due to the lower temporal resolution (i. e. , 1,000 years) and the consequent lower data availability, the analyses were not performed on composite time series. Here we compared mean tCHAR Z-scores and mean percentage cover of different PFTs at 1,000 years intervals, by grouping together the sites included in the same sector or cluster.
To select the "optimal" model given all possible sets of predictors, we used the Akaike's information criterion (AIC) values  (Akaike, 1973). AIC incorporates both model fit and model complexity, with more complex models being penalised relative to simpler ones; better models have lower AIC values relative to others in the same candidate set  (Anderson, 2008; Zuur, Ieno, Walker, Saveliev, & Smith, 2009). Given the small number of predictors, we generated all possible models and the one with the lowest AIC value was selected. In case of two correlated predictors, this method chose the one which resulted in a better model. As we performed multiple tests based on the same dataset, we increased the rate of type I error. To control this error rate, we thus adjusted the p-values by using the Holm-Bonferroni correction  (Holm, 1979) , a standard procedure which incrementally decreases the α levels to reach significance.
Since our datasets were a set of composite curves or a set of PFTs percentages with the related tCHAR Z-scores per site, some of the covariates were unavoidably correlated to some extent with each other and this questioned the levels of the p-values. This has been further considered in Supporting information Appendix S5. Despite methodological difficulties, the use of the AIC allowed the selection of the model with the highest information content and the removal of variables that were correlated to another covariate but that did not increase the model's performance. However, during the evaluation of our results it has to be kept in mind that-to some degree-it was impossible to avoid violating the assumption of independence between covariates.
present study of Holocene boreal forests biomass burning has taken into consideration a broad spatial and temporal scale, and has explored the linkages between fire and climate components, fuel type and anthropogenic land cover change by means of a statistical approach. By considering six different site clusters and two different sectors, our results have underlined the spatial and temporal variability in BB existing within the boreal biome and have allowed a better understanding of the most important processes responsible for main changes in fire activity in these regions. However, additional highresolution analyses of charcoal series from regions inadequately represented by the present dataset (i. e. , most of all, Asia) are needed. It is in fact obvious that, despite the small amounts of data presently included in the GCD v3 from these areas (Hawthorne et al.
ACKNOWLEDGEMENTS This article is a contribution to the  PAGES Global Paleofire Working Group 2  ( GPWG2 ). We thank those people who have made this analysis possible through their contribution to the Global Charcoal Database and to the Neotoma Database. We are grateful to  André Viau  for sharing North American climate data with us. Financial support for CM was provided by the  Lund University Centre for Carbon Cycle and Climate Interaction (LUCCI , VR Linnaeus Grant  2007-2018 ,  2007-8228-54790-23 ). Furthermore, JOK and BASD were supported by the  European Research Council  (COEVOLVE,  313797 ). Finally, CC and OB were supported by the  European Commission  through the  IRSES Program NewForests  ( PIRSES-GA-2013-612645 ).
Children in group B received for 10 days the alternative treatment (OAM10) of omeprazole 2×20 mg/d with amoxicillin 50 mg/kg/d b. i. d. with a maximum of 2g/d and metronidazole 40 mg/kg/d b. i. d. with a maximum of 1. 5 g/d in children above 30 kg and 1g/d in children below 30 kg bodyweight. The dose of omeprazole was reduced to 2×10 mg/d in the same way as in the OAC7. Side effects could be reported at any time to the prescribing physician and withdrawal from the study was granted. Patients were seen at the end of the treatment period to collect data on side effects and evaluate their compliance by recounting the tablets. The H. pylori status was assessed 8-12 weeks after the termination of the treatment by a second upper GI endoscopy with biopsies processed for RUT, histology and culture, a 13 C UBT and an HpStAR.
Results Seven of the 112 recruited subjects were lost to follow up (5 in the OAM10 group and 2 in the OAC7 group) so that eventually data from 105 children were analyzed. The most common endoscopic finding (Table  1 ) in H. pylori-infected children was antral nodularity (76, 68%), whereas duodenal ulcer or erosions were observed in 5 children (4. 5%). Treatment compliance was evaluated according to the quantity of medication taken and considered as "good" in 98/105 (93%) patients, who took 100% of the medication, and as "average" in the 2/105 patients who took only 75%. None of them was considered as "poor" (taking less than 75% of the medication). Successful eradication of the infection was attained in 83 children, with an overall eradication rate of 74% by ITT and 79% by PP. Higher eradication rates were obtained with OAM10 than with OAC7, since treatment was successful in 44/55 (80%) by ITT and 44/50 (88%) by PP in the OAM10 group, and in 39/57 (68%) by ITT and 39/55 (71%) by PP in the OAC7 group.
Varying initial cell density Culture was prepared as in the "Bacterial strains, growth media, and culturing conditions" section except that the culture dilution ranged from 100-to 100,000-fold. Cultures were exposed to cefotaxime (0 or 100 mg/ml), time courses were measured by a plate reader, and the final cell density after 30 hours was recorded. Plate reader data analysis MATLAB (version 9. 2. 0. 556344, R2017a) was used to plot and characterize the time courses obtained from the plate reader (i. e. , recovery time, growth rate, and change in GFP over time).
Acknowledgments Funding: L. Y. acknowledges support from the  NIH  ( R01GM098642 ,  R01GM110494 , and  R24DK110492 ), the  Army Research Office  ( W911NF-14-1-0490 ), and the  David and Lucile Packard Foundation. G. B. acknowledges support from the  Agence Nationale de la Recherche  ( ANR-16-CE33-0018  and  ANR-16-CE12-0025 ). H. R. Me. acknowledges the  NSF   Graduate Research Fellowship Program. Author contributions: H. R. Me. conceived the research, designed and performed both modeling and experimental analyses, interpreted the results, and wrote the manuscript. V. A. assisted in model development, simulations, data interpretation, and manuscript revision. H. R. Ma. conducted and analyzed exogenous Bla experiments. A. J. Lo. and  A. J. Le. assisted in data interpretation and manuscript revisions.
In classical DXT analysis, the motions of the spots diffracted from the gold nanocrystals on the substrate's surface were tracked by TrackPy (v0. 3. 2 https://doi. org/10. 5281/zenodo. 60550), and the trajectories of the diffraction spots were analysed using a custom software written within IGOR Pro (Wavemetrics, Lake Oswego, OR). Lab-DXB measurements were conducted using laboratory X-ray sources (Rigaku FR-D: Cu anode, 50 kV, 60 mA), and time-resolved diffraction images were recorded using a 2D photon-counting detector (Pilatus 100 K, Dectris, Switzerland). The sample-to-detector distance was 30 mm, and the exposure time per frame and interval time were 1. 0 sec and 1. 003 sec, respectively. Fabrication of Gold Nanocrystals. Gold nanocrystals were fabricated via epitaxial growth on cleaved KCl (100) (area: 7 × 7 mm 2 ) under a 10 -4 -Pa vacuum.
Acknowledgements The authors are grateful to  Prof. Yasuteru Shigeta  ( University of Tsukuba ) for suggesting the importance of long-timescale protein motion analysis. This research was supported by the  Hyogo Science and Technology Association, JASRI President Fund, Sumitomo Foundation for Basic Science Research  (  170398 ),  JSPS   Grantin-Aid for Scientific Research on Innovative Areas '3D Active-Site Science'  (No. 26105005 ), and  AMED-CREST  funded by the  Japan Agency of Medical Research (AMED). DXT and DXB experiments were performed with the approval of the  Japan Synchrotron Radiation Research Institute  (Proposal Nos 2012B1379,  2013A1494 ,  2014B1205 ,  2014B1470 ,  2014B1954 ,  2015B1200 ,  2015A1229 ,  2016B1901 ,  2016B1130 , and  2017A1286 ).
This study was designed to evaluate the relationship between Programmed cell death protein 6 (PDCD6) polymorphisms and cancer susceptibility. The online databases were searched for relevant case-control studies published up to November 2017. Review Manage (RevMan) 5. 3 was used to conduct the statistical analysis. The pooled odds ratio (OR) with its 95% confidence interval (CI) was employed to calculate the strength of association. Overall, our results indicate that PDCD6 rs3756712 T>G polymorphism was significantly associated with decreased risk of cancer under codominant (OR = 0. 82, 95%CI = 0. 70-0. 96, p = 0. 01, TG vs TT; OR = 0. 53, 95%CI = 0. 39-0. 72, p < 0. 0001, GG vs TT), dominant (OR = 0. 76, 95%CI = 0. 66-0. 89, p = 0. 0004, TG+GG vs TT), recessive (OR = 0. 57, 95%CI = 0. 43-0.
METHODOLOGY A comprehensive search in PubMed, Web of Science, Scopus, and Google Scholar databases was performed for all articles describing an association between PDCD6 polymorphism and cancer risk published up to November 2017 without language restriction. The search strategy was "cancer, carcinoma, tumor, neoplasm", "PDCD6, programmed cell death 6", and "polymorphism, mutation, variant". Figure  2  summarized the process of identifying eligible studies. Relevant studies, eligible for the meta-analysis must meet the following criteria: 1) Original case-control studies of the correlation between the PDCD6 polymorphism and cancer; 2) studies provided sufficient information of the genotype frequencies of PDCD6 polymorphism in both cases and controls; 3) the studies have not repeated reports in the same population.
Statistical analysis Meta-analysis was carried out using Revman 5. 3 software, which was provided by the Cochrane Collaboration (Version 5. 3. Copenhagen: The Nordic Cochrane Centre, the Cochrane Collaboration, 2014) and STATA 14. 1 software (Stata Corporation, College Station, TX, USA). All of the data in the studies are dichotomous data, which has been expressed as odds ratios (ORs) with 95% confidence intervals (CIs) to assess the association between the polymorphisms and cancer. Hardy-Weinberg equilibrium (HWE) for each study was determined by the chi-square tests of control group data. Odds ratios (ORs) and 95% confidence intervals (CIs) were pooled to evaluate the association between the polymorphisms and risk of cancer. For each polymorphism the ORs were calculated for dominant, codominant, recessive, over-dominant, and allele genetic models.
Heterogeneity also assessed using the I 2 statistic, interpreted as the proportion of the total variation contributed by interstudy variation, and the Cochran chi-square Q-test, with a significance level of P < 0. 10 and I 2 > 50%. When significant heterogeneity values were returned, the random-effects model (the DerSimonian and Laird method) was used to estimate pooled ORs. Otherwise, the fixed-effects model (the Mantel-Haenszel method) was employed. The significance of the pooled OR was assessed by the Z-test, and P < 0. 05 was considered to be statistically significant. Publication bias was evaluated by funnel plot. The degree of asymmetry was measured using Egger's linear regression test; p < 0. 05 was considered significant publication bias  [2]. The characteristics and relevant data of the included studies are shown in Table  1.
FUNDING SG was supported by  CHRIM  operating grant,  Health Science Foundation  general operating grant and  Research Manitoba New Investigator operating grant. MJŁ kindly acknowledges the support from  NCN  grant #:  2016/21/B/NZ1/02812 , and by  LE STUDIUM Institute for Advanced Studies (region Centre-Val de Loire, France)  through its  Smart Loire Valley General Program , cofunded by the  Marie Sklodowska-Curie Actions , grant #  665790.
Introduction: Disclosure of HIV status to HIV-infected children and adolescents is a major care challenge. We describe current site characteristics related to disclosure of HIV status in resource-limited paediatric HIV care settings within the International Epidemiology Databases to Evaluate AIDS (IeDEA) consortium. Methods: An online site assessment survey was conducted across the paediatric HIV care sites within six global regions of IeDEA. A standardized questionnaire was administered to the sites through the REDCap platform. Results: From June 2014 to March 2015, all 180 sites of the IeDEA consortium in 31 countries completed the online survey: 57% were urban, 43% were health centres and 86% were integrated clinics (serving both adults and children). Almost all the sites (98%) reported offering disclosure counselling services.