dataesr/scientific-paragraphs-categorization huggingface dataset:
tant to identify other key functional traits associated with the family, to improve our understanding of community assembly. Overall in this study, clustering patterns suggest that environmental filtering could be a significant ecological process acting at the local community scales, among reef sites within atolls and among coral colonies, and evolutionary mechanisms (trait convergence, labile rates of trait diversification) driving compositional patterns in palaemonid local communities in the Chagos Archipelago and possibly across the archipelago metacommunity. ACK N OWLED G M ENTS A UK Natural Environment Research Council (NERC) CASE studentship (NERC grant reference: NE/1018298/1) and funding from The Bertarelli Foundation enabled this study, and Selfridges' Project Ocean funded a berth and expedition costs on the Chagos Science Expedition 2012.
Inclusion criteria and data assessment in the derivation series This study was conducted on a derivation series of 121 WM patients consecutively treated at the Service d'Hematologie Clinique of the Centre Hospitalier de Lens or the Centre Hospitalier Universitaire d'Amiens between 1993 and 2016. Inclusion criteria were (1) proven WM according to international workshop recommendations 22 ; (2) symptomatic WM requiring the initiation of at least first-line treatment according to the criteria of the second international workshop 2 (namely, in case of constitutional symptoms, cytopenia, symptomatic hepatomegaly, symptomatic splenomegaly, bulky and/or symptomatic lymphadenopathy, mIgM-related symptoms, or hyperviscosity syndrome); and (3) informed consent obtained according to the recommendations of the protocol approved by the institutional review board.
Inclusion criteria and data assessment in the independent validation series An independent series of 119 consecutive patients treated in the Hematology Unit of the University Hospital of Toulouse and in the hospitals of the region Midi Pyrenee, France, from 2005 to 2015 with a rituximab-fludarabine combination  23  or a cyclophosphamide, dexamethasone, and rituximab regimen  24  was used for the validation of main results. Inclusion criteria were similar. The date, the depth of optimal response and the date of progression were recorded, but systematic SMIC monitoring was not available. Informed consent was also obtained from all patients.
To take into account the violation of proportional hazards assumption for the sIPSSWM, a time by sIPSSWM covariate was introduced in multivariable Cox regression models. The Harrell C index associated with the latter models was calculated as previously reported. 28 We also assessed the prognostic values of these variables after second-and third-line treatment using the same approach. In order to take into account the influence of death unrelated to WM, we introduced the onset of response, progression, and second treatment initiation, each coded as a time-dependent covariate, in cause-specific proportional hazards regression models  27  with 2 competing events (death from WM [related] or an unrelated cause) as previously reported. 19 In cases without a definitive conclusion regarding the relationship between cause of death and WM, survival data were censored at the time of last follow-up.
Because of the limited number of deaths  18  in the 95 patients in the validation series with available information, we could not validate the time-dependent Cox proportional hazard model adjusted for sIPSSWM, according to guidelines on the number of events per variable required in multivariate models. 27 Analyses of the prognostic value of onset of response was not validated, because no systematic SMIC monitoring was available. Statistical tests were performed using the 2-tailed a level of 0. 05. Data were analyzed with the SAS software package, release 9. 4 (2011; SAS Institute, Cary, NC) and R package release 3. 4. 1 (R Foundation for Statistical Computing, Vienna, Austria).
Assessment of the long-term prognostic role of events observed during follow-up cannot be obtained from prospective multicenter clinical trials. For this purpose, we took advantage of continuously updated clinical databases with very prolonged follow-up and careful monitoring of information throughout the evolution of the disease. Furthermore, our results seem to be robust to treatment regimens. Contrary to derivation series, all patients of the validation series received immunochemotherapy according to only 2 regimens; the results observed in the validation series were concordant with those observed in the derivation series, supporting a broad reproducibility. Finally, once a sufficient number of events are recorded, similar analysis should probably be regularly repeated in the future, given the high number of new therapeutic approaches, especially the introduction of Bruton tyrosine kinase inhibitors, that may improve the depth of responses, modify the response paradigm, and/or improve the outcome.
Acknowledgments The authors thank  Veronique Leblond  for support and very fruitful comments and the referees for their valuable comments, which led to improvements in the manuscript. The members of the  French Innovative Leukemia Organization CLL  group are:  C. Algrin  ( Grenoble, France ),  T. Aurran  ( Marseille, France ),  J. N. Bastie  ( Dijon, France ),  M. C. Bene  ( Nancy, France ),  A. Brion  ( Besançon, France ),  J. Broseus  ( Nancy, France ),  G. Cartron  ( Montpellier, France ),  A. Clavert  ( Angers, France ),  F. Cymbalista  ( Bobigny, France ),  C. Dartigeas  ( Tours, France ),  F. Davi  ( Paris, France ),  S. De Guibert  ( Rennes, France ),  M. H. Delfau  ( Créteil, France ),  A. Delmer  ( Reims, France ),  M. S. Dilhuydy  ( Bordeaux, France ),  B. Drenou  ( Mulhouse, France ),  B.
Most modern CPU architectures offer SIMD (single instruction multiple data) instructions, allowing to perform the same operation on multiple data points in one CPU cycle, leading to what is known as the vectorization of computation. Vectorization in used routinely in data-intensive applications like multimedia processing  [23]  or deep learning  [8, 27] , and is finding its way to data management, particularly in the sub-field of in-memory databases  [32, 22]. Relevant examples from a related field are the performant regular expression engine Hyperscan  [29]  and the competitive engine of the RUST language  [10] , both relying crucially on vectorization. In the context of streaming processing of tree-structured data, an early work on parabix by Cameron et al. studies the use of SIMD instructions to accelerate XML parsing  [4].
Proposition 13. It is decidable if the query realized by a given restricted depth-register automaton is an RPQ. Unlike in graph databases, where RPQs are viewed as binary queries selecting suitably connected pairs of nodes  [3] , in our setting RPQs are treated primarily as unary queries selecting nodes suitably connected to the root. But we can also treat them as boolean queries, defining sets of trees that contain a node-or a leaf-suitably connected to the root. The leaf variant will be instrumental in the characterization results of Section 3. We write EL for the set of trees that contain a branch labelled by a word from L, and AL for the set of trees with all branches labelled by words from L. Note that (AL) c = E(L c ). Languages of the form AL can express useful and nontrivial schema restrictions, as they are able to specify which labels are allowed in the children of a node, depending on regular properties of the path from the root.
Evaluation of genetic diversity in virus stocks and Aedes mosquitoes The genetic diversity was evaluated using complete viral genome sequences from virus stocks used to infect mosquitoes and from positive mosquito heads (presence of virus was assessed using a TCID 50 assay; see below). Data were generated by next generation sequencing and we considered in our analyses all the substitutions with a frequency !2%. We first evaluated the genetic diversity in virus stocks used to infect mosquitoes (the sequence of the infectious clone was used as a reference). Not surprisingly, transfection of the infectious clone led to production of clonal viral population and no mutation was detected in the IC_virus. In contrast, transfection of amplicons led to a higher genetic diversity and 13 mutations were detected in ISA_virus (Table  1 ).
This result is in accordance with our previous work  [11]. Of note, only minority mutations (substitution frequency <50%) were detected in ISA_virus and therefore both viruses had identical consensus sequence. We then evaluated the genetic diversity from grounded heads of Aedes mosquito. Based on our experiment, it is difficult to generate complete genome sequences from individual mosquito heads. Thereby, we initiated analyses with eight heads per condition. Finally, data from three to eight heads per condition were used. To evaluate the impact of the reverse genetics method used, we compared the number of minority and majority mutations (substitution frequency < and ! 50% respectively) found for each condition. No clear trend can be found with minority mutations (Fig  1A ): no impact of the reverse genetic method was observed in Ae.
Data sources Nationally, data on malaria diagnosis, laboratory confirmation and treatment are collected at health facility level, compiled at district level and forwarded to the national level. These data are housed in the IDSR and the CBS systems. The CBS is a patient-level, malaria specific database implemented in 2012 as part of the goal to achieve malaria elimination, while the IDSR is an aggregated general surveillance system that contains malaria case reports. The 2008-2013 IDSR data and 2013-2014 CBS data were utilised in this study; data variables were extracted from both databases. During 2008-2014, 50 487 cases of malaria were reported in Botswana; the number of cases diagnosed using RDTs and/or blood microscopy improved from 6% in 2008 to 89% in 2013. This study showed that the use of malaria diagnostic tests improved malaria diagnosis and reduced the number of reported clinical cases (which previously included presumptive and confirmed cases).
We utilised routine programme data from two sources, the IDSR and CBS systems. Programme data were compiled and analysed to gain insights into the realities of malaria diagnosis and treatment. Furthermore, by selecting the most affected districts in Botswana, the risk of methodological bias was limited. Study limitations include the use of retrospective programme data, which has been reported to have inherent challenges. 2  Furthermore, data were sourced from two different malaria reporting systems, which have been noted to have incongruences. 18 Data prior to 2012 would have been useful to better understand trends in testing and treating by health workers across the three levels of health facilities. Finally, no data were available from the private health facilities, which make up a small, but important portion of the health sector.
Search strategy The review was performed according to Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines  [9]. The search was conducted in accordance with the principles outlined in the Cochrane Handbook for Systematic Reviews of Interventions  [10]. Studies were identified by searching electronic databases and relevant websites. Highly sensitive electronic searches were conducted to identify published and ongoing studies of adjuvant radiotherapy for pN1 penile cancer. Searches were limited to studies published from 1946 onwards to May 2017 but no language restrictions were imposed (Apendix 1). The search was complemented by additional sources, including relevant systematic reviews and the reference lists of included studies which were hand searched to identify additional potentially relevant studies.
Quantity and quality of evidence A total of 913 articles were identified by the literature search. Of these, 40 articles were selected for full-text screening and 7 studies (including 1605 patients) were eligible for inclusion (PRISMA Flowchart -Figure  1 )  [7] [8] [9] [10] [11] [12] [13]. However, there was overlap with respect to included patients between two of the studies  [12, 13]  and it was not possible to determine in all of the studies how many men underwent AIRT. All studies were retrospective series; six of which were published manuscripts and one of which was a conference abstract. In all of the included studies the reporting of outcomes was poor, particularly with respect to treatment toxicity and long term side effects. Overall the studies had a high RoB (Table  3 ). None of the included studies included an a priori protocol and the outcome data for the majority of the studies, with respect to both recurrence and survival, was limited in relation to AIRT.
[18]  reporting a retrospective multi-centre analysis of data from four international tertiary cancer centres. The study examined the role of ENE and AIRT in men with penile cancer. The study included 93 men with a median age of 65. 3 years and a median follow up of 9. 4 months. Of those men 72% and 49% had ENE in the inguinal and pelvic lymph nodes respectively. In men with ENE infield failure occurred in 17/50 (34%) in those who received AIRT and 10/38 (26. 3%) in those who did not (p=ns). In men without ENE (LN status not further defined in the abstract) infield recurrence occurred in 5/50 (10%) and 3/24 (12. 5%) of those who did and did not receive AIRT respectively (p=ns). The authors further comment that AIRT was not associated with improved overall survival (p=0. 073) or reduced recurrence rate (p=0.
The differences in reported regional recurrence rates (43% at 3 years vs. 16. 4% at 5 years, respectively) are not explained but might be due to referral bias and delay. The risk of referral bias in the series by Graafland et al is likely to be lower. Unfortunately, there is insufficient data presented by Johnstone et al. to give significant weight to any conclusions from the data, as the potential biases are all uncertain. However, it is highly likely that selection bias in that data set is high and problematic as the number of patients is very small for an international multicentre dataset. Despite this they do present the largest published data set in high risk patients, those with ENE. This is the very cohort that the current iteration of the EAU guidelines suggest consideration be given to AIRT and for which this data indicates AIRT has no significant impact upon either recurrence or survival.
Introduction The burden of lower respiratory tract infections (LRTIs) is a substantial public health concern. However, the epidemiology of LRTI and its bacterial aetiologies are poorly characterised, particularly in the African continent. Providing accurate data can help design cost-effective interventions to curb the burden of respiratory infections in Africa. Therefore, the aim of this systematic review and meta-analysis will be to determine the prevalence of respiratory Bacterial Aetiologies in people with low Respiratory tract Infections in Africa (BARIAFRICA) and associated factors. Methods and analysis We will search PubMed, EMBASE, Web of Science, African Journals Online, Cumulative Index to Nursing and Allied Health Literature, and Global Index Medicus to identify studies that reported the prevalence (of enough data to compute this estimate) of respiratory bacterial infections in people with LRTIs in Africa from 1 January 2000 to 31 March 2018, without any linguistic restrictions.
MEthOds And AnAlysIs design and registration This systematic review and meta-analysis protocol will be conducted following the Centre for Reviews and Dissemination guidelines. 10 The present BARIAFRICA systematic review and meta-analysis protocol was reported according to the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols. 11 The study protocol was registered with PROSPERO registration number CRD42018092359. Criteria to consider studies for this review Inclusion criteria 1. Types of studies: We will consider cross-sectional studies, case-control studies, baseline data of cohort studies, surveillance data, as well as control group (without any intervention) of clinical trials.
search strategy for identifying relevant studies The search strategy including the name of all African countries and their synonyms will be applied in electronic databases. The name of the country in the language relevant to that region will also be applied. Relevant articles will be searched by combining keywords in the field of lower respiratory infections and the names of African subregions. The following databases will be used: Medline through PubMed, EMBASE, Web of Science, Cumulative Index to Nursing and Allied Health Literature, African Journals Online, and Global Index Medicus. The search strategy used in PubMed is presented in online supplementary table 1. The search strategy will be adapted for other databases. The reference list of the eligible articles and relevant reviews will be manually searched to identify additional studies.
selection of studies for inclusion in the review Using the Rayyan application,  12  two review authors will independently select records based on titles and abstracts. Any disagreement will be solved by discussion and consensus, or will involve a third review author as an arbitrator. Studies in language different from English or French will be translated using Google Translate and considered for eligibility. Two review authors will independently evaluate the full text of the selected records. Discrepancies will be resolved by consensus or by an arbitration of a third review author. The agreement between the two first review authors will be estimated by Cohen's kappa coefficient. 13 sk of bias assessment The evaluation of included studies for risk bias will be done using an adapted version of the risk of bias tool for prevalence studies developed by Hoy et al.
data extraction and management Study characteristics such as name of the first author, year of publication, study population, number of bacteria searched, age range, study design, setting, diagnostic criteria and outcomes measured, location, country in which the study was conducted, criteria for sample selection and sample size, city, latitude, longitude, altitude, clinical presentation, number of clinical isolates, comorbid conditions/underlying conditions, number of patients tested, number of patients infected with bacteria, diagnostic technique used, and male proportion will be recorded. Prevalence by country will be calculated for multinational studies. Where cases and samples for estimating prevalence will not be available, we will contact the corresponding author of the study to request the missing information.
The countries will be grouped into regions according to the United Nations Statistics Division (UNSD). Lower respiratory infections will be classified as bronchitis, bronchiolitis and pneumonia. Data extraction will be done independently by two review authors. Disagreements between the two review authors will be solved by discussion, or if necessary will involve a third review author for arbitration. data synthesis Data will be analysed using the 'meta' and 'metafor' packages of the R statistical software (V. 3. 4. 4, R Foundation for Statistical Computing, Vienna, Austria). Unadjusted prevalence will be recalculated based on the information on crude numerators and denominators provided by individual studies. Prevalence will be reported with their 95% confidence and prediction intervals. To keep the effect of studies with extremely small or extremely large prevalence estimates on the overall estimate to a minimum, the variance of the study-specific prevalence will be stabilised with the Freeman-Tukey double arcsine transformation before pooling the data with the random-effects meta-analysis model.
15 Only studies conducted in populations with close clinical presentation/underlying conditions and with same laboratory diagnostic technique will be pooled together. If it is not possible to conduct meta-analysis, data will be synthesised using a narrative approach. Egger's test will be used to detect the presence of publication bias. 16 A p value <0. 10 on Egger's test will be considered indicative of statistically significant publication bias. Heterogeneity will be evaluated by the χ² test on Cochran's Q statistic,  17  which will be quantified by H and I² values. The I² statistic estimates the percentage of total variation across studies due to true between-study differences rather than chance. In general, I² values greater than 60%-70% indicate the presence of substantial heterogeneity.
25 in univariable analysis will be required. For categorical variables, the global p value will be considered for inclusion in multivariable models. We will apply a manual forward selection procedure to identify factors independently associated with the variation of the overall prevalence. We will successively add in the model the more significantly associated variables. The final model that will be considered is the one with the lowest Bayesian Information Criterion. A p value <0. 05 will be considered statistically significant. Following crude overall prevalence, we will conduct two sensitivity analyses to assess the robustness of our findings. The first one will include only studies with low risk of bias and the second only studies reporting data of a full year(s) period (complete season(s)).
Statistical Analysis In the present study, the PASW statistics software version 18 (IBM, New York, USA) was used. The test of normality was determined by a package of Kolmogorov-Smirnov test (lilliefors correction) completed with histogram and normal Q-Q plot graph. For each analysis, RIL and block were considered as fixed factors, while trait was considered as dependent factor. Tests were performed two-sided with a significance level of 5 %. Tukey-test was used to know the differences among genotypes. Phenotypic (r p ) as well as Genetic (r g ) relationships between two traits were calculated using components of variance as follows: r p = Cov p (xy) / (var p (x) var p (y)) 0. 5 and r g = Cov g (xy) / (var g (x) var g (y)) 0. 5 where Cov p is the covariance of phenotype between traits x and y and var p is the variance of phenotype.
RESULTS The HBV preS1 NTCP-interacting domain showed a high degree of conservation among the examined viral genomes especially between aa 9 and 21 (in the genotype D consensus sequence). As compared with the virion morphogenesis domain, the NTCPinteracting domain had a smaller proportion of HBV genotype-unrelated changes comprising > 1% of the quasispecies (25. 5% vs 31. 8%), but a larger proportion of genotype-associated viral polymorphisms (34% vs 27. 3%), according to consensus sequences from GenBank patterns of HBV genotypes A to H. Variation/conservation in both domains depended on viral genotype, with genotype C being the most highly conserved and genotype E the most variable (limited finding, only 2 genotype E included). Of note, proline residues were highly conserved in both domains, and serine residues showed changes only to threonine or tyrosine in the virion morphogenesis domain.
Furthermore, several single nucleotide polymorphisms (SNPs) that may change the physiological function of NTCP as the key transporter for bile salt homeostasis and affect HBV entry have been identified in SLC10A1  [21]  , and most of them show an ethnicitydependent profile  [22, 23]. The rs2296651 SNP in SLC10A1 (g. 69778476G>A, GenBank accession number NC_000014. 9), which causes the S267F variant, has been identified in Asian populations at a prevalence of 3. 1% to 9. 2% [22]. Previous studies focusing on rs2296651 and HBV infection have yielded conflicting results  [24, 25]  , and the role of this SNP in cirrhosis and hepatocellular carcinoma remains uncertain  [26]. However, as synthetic myristoylated lipopeptides share the same aa sequence with the NTCP-interacting domain, it is reasonable to think that the presence of this SNP might influence the effectiveness of these therapies.