dataesr/scientific-paragraphs-categorization huggingface dataset:
Bench studies have become the preferred way to evaluate the performance of airway equipment, since clinical trials are not specifically required before marketing these devices. However, it is difficult to assess the efficiency of ventilation without recording physiological data. This review analyses how efficiency of manual ventilation has been defined in recent studies, and how their results may be affected. We searched electronic databases from 2000 to April 2014. The main inclusion criterion was the analysis of performance of ventilation. Nine relevant articles were selected from 53 eligible publications. Most studies used the same parameters; tidal volume and ventilation rate. However, there were significant differences between the definitions of performance of ventilation, both in terms of criteria of judgement and methods of analysis.
Methods We searched electronic databases including Medline, Google, Clinical Trials and Cochrane from 2000 to April 2014. The key words were 'bag valve mask', 'manual ventilation' and 'ventilation performance', used individually and in combination. Our inclusion criteria were the analysis of performance of adult ventilation for the functional evaluation of manual ventilation devices. Articles were excluded if they were written in a language other than English or French, or if they were dealing with paediatric practice. We excluded articles that had inadequate information about judgment criteria and analysis methods for the assessment of performance of the devices studied. We also reviewed international guidelines for cardiopulmonary resuscitation (CPR) and emergency cardiovascular care (ECC) to see how efficiency of manual ventilation was defined in them.
Second, the low number of relevant articles limits the scope of this review. We also excluded articles written in languages other than English or French. In conclusion, this review has shown significant heterogeneity in the variables used for the evaluation of successful ventilation. Defining accepted judgment criteria and an adequate method of analysis is crucial for the interpretation of these studies, and for reaching unbiased conclusions. This is even more important for bench studies, where ventilatory data cannot be correlated with physiological measurements or patient outcomes. It would be interesting to apply these different definitions to a database to evaluate their impact on performance of ventilation. However, none of these various approaches are able to provide a clear understanding of efficiency of ventilation over a full time period.
Methods We conducted a retrospective, non-interventional study in a large (1250 beds) tertiary care centre in France. Using our electronic medical database (Nadis w software), we exhaustively identified all patients who received a DBLR, either as monotherapy or dual therapy. Patients with at least a plasma viral load (PVL) available ≥1 month after simplification, # The Author 2015. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http:// creativecommons. org/licenses/by-nc/4. 0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.
permissions@oup. com J Antimicrob Chemother 2016; 71: 1046 -1050 doi:10. 1093/jac/dkv430 Advance Access publication 27 December 2015 which allowed us to determine the regimen's efficacy, were included in the study. Of note, all decisions to switch to a DBLR were validated by the local HIV experts team, as recommended by French guidelines. 2 All participants provided written informed consent for the anonymous use of their clinical and biological data for biomedical research at the time their data were entered into the electronic database. Therefore, this study did not need to be approved by a research ethics committee. The primary endpoint was the proportion of patients who maintained virological suppression (HIV RNA ,50 copies/mL, US FDA Snapshot analysis with ITT analysis) at the last follow-up visit.
e. ,50 copies/mL) PVL, history of virological failure (and drug resistanceassociated mutations, if any) and reasons for switching to a DBLR. Follow-up data (i. e. after switching to a DBLR) included relevant clinical events, CD4+ count, PVL, CPK and serum creatinine levels, genotype at failure (if any) and ART changes (if any). Blood samples were taken at 1-4 month intervals, as recommended by national guidelines. Data are expressed as the median (IQR), mean+SD, n, % or n (%). Continuous variables were compared using a paired t-test or the Wilcoxon test.
The urine culture was positive, and the isolate was identified at the genus level using phenotypic methods including Gram staining, catalase test and growth on bile esculin azide agar and 6. 5% NaCl media. The primary bacteriologic diagnosis indicated that the isolated strain belonged to the genus Enterococcus. The biochemical identification using an API 20 Strep system (bio-Mérieux, Marcy l'Etoile, France) could not identify the species involved. Characterization of the clinical isolate to the species level was achieved by MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry) (Microflex; Bruker Daltonics, Bremen, Germany) using Flex Control and Biotyper 3. 0 software (Bruker Daltonics) as previously described  [3]. The identification of the strain by MALDI-TOF MS revealed the E.
Randomised controlled trials of nutrition and cancer are rare compared with observational studies. For less frequent cancers, the evidence from observational studies comes mainly from casecontrol studies. In these studies, dietary intake is assessed using questionnaires after cancer diagnosis, and they are more prone to recall and selection biases than are prospective observational studies. For more frequent cancers, most of the existing data on the relationship between diet and cancer risk comes from prospective observational studies, in which dietary assessment takes place before cancer diagnosis. The identification of new cancer cases during follow-up includes record linkage with cancer and mortality registries, self-reporting by study participants with further confirmation through medical records, or a combination of methods to minimise losses to follow-up and increase data reliability.
neoformans-specific data only, which suggests that C. neoformans-specific data contributes significantly to the high genome coverage of CryptoNet. Importantly, C. neoformans belongs to the basidiomycota phylum. In contrast, many other popular laboratory fungi, including S. cerevisiae, belong to the ascomycota phylum. S. cerevisiae data are not expected, therefore, to be sufficient for the study of C. neoformans, which belongs to a distant phylogeny group. To the best of our knowledge, CryptoNet is the first genome-scale gene network for a fungal species in the basidiomycota phylum. CryptoNet may therefore provide insights into pathway evolution between two distinct phyla of the fungal kingdom. CryptoNet identifies novel genes for C. neoformans pathogenicity. The effective retrieval of known virulence genes by CryptoNet suggests that other highly ranked genes are also likely involved in the virulence of C.
Notably, 12 of the 29 identified genes (,41%) for the C. neoformans virulence phenotypes could not have been predicted by YeastNet-derived links alone, due to the lack of either conserved genes (five of the 12) or conserved links. This result clearly demonstrates the importance of species-specific data for the prediction of C. neoformans pathogenicity. CryptoNet identifies new antifungal drug resistance genes. One major reason that cryptococcosis treatment fails is antifungal drug resistance. The emerging complexity of the drug-mediated cell death process suggests that a group of drug resistance genes collaborate to overcome drug stress. The elucidation of the complete set of drug resistance genes may therefore facilitate the development of more efficacious antifungal treatments. Some C. neoformans genes that change their expression levels during the early adaptation to drug stress may provide clues about the mode of action of antifungal drugs and cellular strategies to overcome drug stress.
Discussion In this study, we have demonstrated the feasibility of networkassisted identification of novel genes for pathogenicity and antifungal drug resistance in C. neoformans. Network-assisted gene prioritization requires two technical components. First is the need to construct a highly accurate and comprehensive gene network for the target species. We have demonstrated that heterogeneous genomics data can be effectively integrated into a single gene network for C. neoformans. CryptoNet is distinct from the previously constructed fungal networks from several clinical and evolutionary perspectives. CryptoNet is the first genome-scale co-functional network for a fungal pathogen and covers ,81% of the coding genome. In our study, we demonstrated the power of CryptoNet in the study of pathogenicity and drug resistance, which are major challenges in the development of medicine for infectious diseases.
Second, CryptoNet cannot be utilized to determine the causality of functional relationships between genes. Third, network-based inferences require known pathway genes to apply the guilt-by-association method or expression data to use the contextassociated hub method. The limitation of network coverage will be overcome gradually as more genomics or proteomics data for C. neoformans becomes available. For example, large-scale proteinprotein interaction data for C. neoformans will significantly expand the current network view. From the systems genetics perspective, in which we imagine each phenotype as a system composed of genetic components, the geneto-phenotype association mapping is critical to the understanding of the genetic organization of complex phenotypes. A bottom-up reconstruction of phenotypic systems as gene networks will not only account for the emergent properties of genetic perturbations but also provide novel functional insights into the individual genetic components of the relevant pathways.
Acknowledgments We thank  Sunmo Yang  for computational support. This work was supported by grants from the  National Research Foundation of Korea  to I. L. ( 2008-0061897  and  2010-0017649 ) and Y. S. B. ( 2008-0061963  and  2010-0029117 ). This work was also supported in part by the  NIH/NIAID   R01-AI050438-10  to J. H.
Genome Screening and Lectin Production Strategies The construction of sponge cDNA libraries is a complementary method to directly access to the lectin gene sequences. Therefore, cDNA libraries from the hexactinellid sponge Aphrocallistes vastus (Schulze, 1886)  [56]  and the demosponges Cinachyrella sp. [65] , Ephydatia fluviatilis (Linnaeus, 1759)  [42] , Geodia cydonium (Jameson, 1811)  [66] , Lubomirskia baicalensis (Pallas, 1773)  [52]  and Suberites domuncula (Olivi, 1792)  [51]  were screened using degenerate primers  [52, 56]  or EST-sequence libraries. A phylogenetic alignment was implemented using the software MEGA 6 in order to compare protein sequences of sponge lectins to other animal lectins from GenBank. A neighbor-joining phylogenetic tree from this alignment using 1000 bootstrap repeats is shown in Figure  1.
Search Searches were performed in Pubmed, Embase and Sport-Discus databases in June 2014 without time limit. The following search terms were used as free text or MeSH terms: muscle strength, muscle endurance, isokinetic, isometric, power, maximum voluntary contraction, muscle fatig*, aerobic capacity, aerobic fitness, maximum oxygen consumption, cardiovascular fitness, endurance, physical fitness, back pain, backache, spinal pain, children, adolescent, teen. The search strategy was designed in collaboration with a librarian from the University of Paris-Sud.
Screening The first author made the search in the databases and selected the potentially relevant full texts from titles and abstracts. This selection was repeated three months later to be sure that the first author could not remember the first selection (i. e. blind to his first choices), with the same results. The same investigator screened if other references could be found by tracking references from articles. The first and second author independently assessed if articles could be included in the review according to the inclusion and exclusion criteria based on the full texts. The selection process is summarised in Fig. 1 , according to the PRISMA 2009 flow diagram  [18]. The reasons for exclusion are specified in this diagram. The selected articles were then divided between the three topics.
Data analysis and synthesis The three reviews were performed separately but using the same procedure, as described above. The results of the methodological assessment were summarised in Tables 1, 2, 3; one table for each research question. A methodological quality score was obtained for each article. No cut-point for level of quality was established. The results were summarised in Tables 4, 5, 6. All the BP variables listed in the method section of the included articles were included in these tables, even if they were not reported in relation to the independent variables (BME, BMS, and AC). According to the type of results reported in the articles, the possibility of conducting a meta-analysis was assessed for each research question. Meta-analysis could be performed only if appropriate information was available in each included study.
Quality assessment of articles on BMS The quality scores in the four reviewed articles were 56 %, 56 %, 78 % and 78 % (Table  1 ). Studied factor: back muscle strength All the articles assessed BMS with a dynamometer. In one study  [25] , reference was made to a previous study having shown the measurement to be reliable whereas in two of the studies, reliability was tested and shown to be acceptable in one  [24] , but results were unreported in the other  [26]. In the fourth study  [27] , the dynamometer was calibrated and it was reported that the method had been previously shown to be reliable and valid. In general, these data can therefore probably be trusted. Outcome measure: back pain BP was clearly defined in all the articles as well as the description of the BP assessment. However, only one article reported a recall period of one month or less  [24] , which was considered suitable in young people.
The aim was "to establish reference data and pattern of back extensor strength in school-aged Nigerian adolescents". The BME was assessed with the Biering-Sorensen test. The history of LBP and present LBP was assessed by questionnaire. The difference in BME was tested for those with or without a history of LBP using a t-test. The same was done for present LBP. The fourth relevant article, Perry et al. [31] , also describes a cross-sectional study in which 1608 adolescents, all aged 14, were included (response rate: 69 %). The aim of this study was to determine if physical fitness is related to increased risk of BP. The BME was assessed with the Biering-Sorensen test. Information on BP was obtained by a questionnaire including lifetime prevalence of pain, pain in the last month, chronic pain and also pain diagnosis.
Maraviroc, the only licensed CCR5 antagonist, has been recently shown to be active in vitro against HIV-2 R5-tropic viruses  [10] [11] [12]  and a limited number of case reports also showed an early in vivo virological response to maraviroc-based treatment  [13] [14] [15]. Thus, CCR5 inhibitors may represent a new antiretroviral drug class in the HIV-2 limited arsenal as demonstrated in vitro with maraviroc. Cenicriviroc is a new dual CCR5 and CCR2 antagonist. This new compound has completed Phase 2b development for treatment of HIV-1 infection (NCT01338883)  [16] [17] [18]. Cenicriviroc is administered once daily and is suitable for single-tablet regimen combination products  [19]. This point is of a particular interest, because of the complex and twice-daily dosing of maraviroc, and also because of the lack of once-daily dosing therapeutic regimen in HIV-2 due to the natural resistance of HIV-2 to non-nucleoside reverse transcriptase inhibitors and the decrease susceptibility to some protease inhibitors.
Acknowledgments Address all correspondence and requests for reprints to: The Endocrine Society, 2055 L Street NW, Suite 600, Washington, DC 20036. E-mail: govt-prof@endocrine. org. Telephone:  202-971-3636. Address all commercial reprint requests for orders 101 and more to: https://www. endocrine. org/corporate-relations/commercial-reprints. Address all reprint requests for orders for 100 or fewer to Society Services, Telephone:  202-971-3636. E-mail: societyservices@endocrine. org, or Fax:  202-736-9705. Cosponsoring Association:  European Society of Endocrinology. The  Intramural Research Program  of the  Eunice Kennedy Shriver Institute of Child Health  and  Human Development  provided salary support to  Dr Nieman  for her work on this manuscript. Disclosure Summary: The authors have nothing to disclose.
Acknowledgments We gratefully acknowledge the contributions of  Marion Joni ,  Yun Jiao , and  Natalie Guley  to the studies described here. We thank  Dr. Kenji Morita  for his comments on our work and the manuscript. Supported by  NS-19620 ,  NS-28721 , The  Methodist Hospitals Endowed Professorship in Neuroscience (AR) , the  Ministerio de Educación y Ciencia  ( BFU2006-06744 ),  CIBERNED  ( CB06/05/0006 ), the  Fondo de Investigaciones Sanitarias  ( PI050137 ), the  Fundación de Investigación Médica Mutua Madrileña , the  UTE- project /FIMA , the  CNRS  ( Centre National de la Recherche Scientifique ) and  Aix-Marseille University.
Methods IKONE study design. The IKONE study (Clinical-Trials. gov Identifier: NCT02175797) is a pivotal, prospective, open-label, nonrandomized, multicenter study. Patients implanted with devices under investigation were invited by the investigators to enroll in the study. They performed a pre-MRI visit between 6 and 8 weeks after pacemaker implantation. The MRI examination was performed within 24 hours after the pre-MRI visit; devices were interrogated just after the MRI examination (post-MRI assessment). A followup visit was planned 1 month after (1-month post-MRI) visit. Devices were interrogated for lead measurements and recordings (pacing capture threshold [PCT], sensing amplitude, and impedance in each cardiac cavities, if applicable) pre-MRI, post-MRI, and at 1-month post-MRI. The study was terminated after completion of the 1-month follow-up visit.
35 ms). All other analyses were performed on the enrolled population. The primary endpoints were tested using a onesided t-test with an alpha risk of 0. 025; a Bonferroni adjustment was applied to correct multiplicity and the alpha risk set to 0. 0125. All other analyses are descriptive statistics. Missing data for primary and secondary criteria regarding electrical stability were not replaced. All analyses were conducted using the SAS ® software release 9. 2 (SAS Institute, Cary, NC, USA).
Separate analyses were conducted for each dependent variable. Finally, we examined the correlation between log dietary phylloquinone intake and each subscore of the FBRS. Lastly, we performed a sensitivity analysis after removing the participants who used VKA (n = 31). p-Values < 0. 05 were considered significant. All statistics were performed using SPSS (v19. 0, IBM corporation, Chicago, IL, USA) and RevMan (v5. 1, Nordic Cochrane Centre, Copenhagen, Denmark).
The between-group mean difference of MMSE score was ´2. 14 (95% confidence interval (CI): ´3. 95; ´0. 33), and that of FBRS score was 0. 39 (95% CI: 0. 01; 0. 77) (Figure  1 ). Nutrients 2015, 7 5 dependent variable. Finally, we examined the correlation between log dietary phylloquinone intake and each subscore of the FBRS. Lastly, we performed a sensitivity analysis after removing the participants who used VKA (n = 31). p-Values < 0. 05 were considered significant. All statistics were performed using SPSS (v19. 0, IBM corporation, Chicago, IL, USA) and RevMan (v5. 1, Nordic Cochrane Centre, Copenhagen, Denmark).
Flow cytometry The expression of cell-surface antigens on isolated PBMCs was determined via single-parameter fluorescence-activated cell sorting (FACS) analysis using the following monoclonal antibodies (mAbs): (i) PE-conjugated anti-CD45R/B220 and PE-conjugated isotype-matched control mAbs (all purchased from R&D Systems, France) and (ii) carboxyfluorescein succinimidyl ester (CFSE, Invitrogen). A FACSCalibur flow cytometer (BD-Pharmingen) was used for data acquisition and analysis. After the gates were set to include only viable cells, 10 4 events per sample were collected and analyzed. For each marker, the threshold for positivity was defined relative to the nonspecific binding observed in the presence of the appropriate isotype control mAb.
Statistical analysis The data were tested for normality (using an Anderson-Darling test) and variance homogeneity prior to further statistical analyses. The data were normally distributed and were expressed as the means ± standard error of the mean (SEM). Significant differences between groups were analyzed using one-way analysis of variance (for more than two groups) followed by Tukey's post-test using SPSS software version 17. Differences were considered to be significant at * P < 0. 05 for diabetic vs. control, + P < 0. 05 for diabetic + propolis vs. control, or # P < 0. 05 for diabetic + propolis vs. diabetic.
05). We also monitored the plasma cytokine levels in the 3 experimental groups because these levels affect the normal function of immune cells. The accumulated data from 10 individual mice from each group are shown in Table  2. The diabetic mice exhibited aberrant and significantly elevated levels of pro-inflammatory cytokines (IL-1β, IL-6 and TNF-α) and markedly reduced levels of IL-2, IL-4 and IL-7 compared with the control nondiabetic mice (*P < 0. 05). Interestingly, treatment of diabetic mice with the ethanol-soluble derivative of propolis significantly ( # P < 0. 05) restored the levels of these plasma mediators to nearly normal levels compared with diabetes induction alone. In contrast, neither the induction of diabetes nor supplementation with propolis affected the plasma levels of IL-8 or IL-10.
Treatment of diabetic mice with propolis decreased the levels of free radicals in different organs The ROS levels were detected in the plasma and in tissue lysates of the bone marrow (the primary lymphoid organ and the origin of all immune cells), the spleen (a secondary lymphoid organ that is a site of antigen recognition), and the liver. The accumulated data from 10 individual mice from each group are shown in Fig. 1. The ROS levels of the diabetic mice were significantly higher than those of the control mice (*P < 0. 05). Oral supplementation of the diabetic mice with the ethanol-soluble derivative of propolis significantly restored the levels of ROS close to the level of control mice when compared to diabetes induction alone ( # P < 0. 05).
Diabetic mice exhibit markedly changed lipid profiles, displaying a tendency toward abnormal obesity The induction of diabetes is commonly associated with dyslipidemia, a phenomenon characterized by altered plasma lipid profiles and an increased risk of cardiovascular disease. Therefore, we monitored the lipid profiles in the 3 groups of animals. The accumulated data from 10 individual mice from each group are shown in Fig. 2. The LDL-C and total cholesterol levels were significantly higher in plasma of the diabetic mice than in that of the control non-diabetic mice (*P < 0. 05). Similarly, the levels of MDA (a marker of oxidative lipid damage and a major oxidative product of peroxidized polyunsaturated fatty acids) were significantly higher in plasma of the diabetic mice than in that of the control non-diabetic mice (*P < 0.