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Diagnosis involving individual papillomavirus (HPV) Genetic make-up in benign laryngeal lesions and also role associated with tobacco use being an causing aspect.
Under the Clinical Trials Act, investigators receive a scientific/ethical review by a certified review board (CRB). The identification of investigators in charge is mandated and they are required to submit the conflict of interest management plan to CRB. After the CRB review, the principal investigator must submit the trial plan to the government, and the content is uploaded to the newly established clinical trial registry site, the Japan Registry of Clinical Trials. CONCLUSIONS The enforcement of the new Clinical Trials Act was supposed to improve the reliability of academic clinical trials in Japan; however, the financial and administrative burden may reduce clinical trial activity in the years to come. © The Author(s) 2020. Published by Oxford University Press.OBJECTIVES To investigate prolonged carriage of MRSA in adults from the general population living in a livestock-dense area, using WGS. METHODS A cross-sectional study during 2014-15 among 2492 adults without professional livestock contact identified 14 (0.6%) nasal MRSA carriers, 10 of which carried livestock-associated (LA)-MRSA of multiple-locus variable-number tandem repeat analysis (MLVA) complex (MC) 398. Two years later, 12 MRSA-positive and 88 MRSA-negative participants provided a second nasal swab and filled in a short questionnaire. Isolates from persons who were MRSA positive at both timepoints were compared using MLVA and isolates with the same MLVA type were sequenced. The WGS data were used for core-genome MLST (cgMLST) and resistome analysis, including sequenced isolates from the national MRSA surveillance. selleck kinase inhibitor RESULTS All MRSA-negative persons tested negative again, while 6 of the 12 initially MRSA-positive persons tested positive again. MLVA revealed that isolate pairs from five individuals had the same MLVA type, of which three were LA-MRSA. cgMLST showed that the distance between these isolate pairs ranged between 3 and 13 genes, while the minimum distance to unrelated isolates from the national MRSA surveillance was 38 genes. Moreover, the resistome present in the five isolate pairs was identical within each pair. None of the prolonged carriers was hospitalized during the 3 months before the sampling moment and none of them with LA-MRSA had contact with livestock in this period. CONCLUSIONS Prolonged carriage of MRSA, including LA-MRSA, can be demonstrated after more than 30 months in persons without professional livestock contact. © The Author(s) 2020. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email [email protected] Current knowledge on HIV-1 resistance to integrase inhibitors (INIs) is based mostly on subtype B strains. This contrasts with the increasing use of INIs in low- and middle-income countries, where non-B subtypes predominate. MATERIALS AND METHODS HIV-1 drug resistance genotyping was performed in 30 HIV-1-infected individuals undergoing virological failure to raltegravir. Drug resistance mutations (DRMs) and HIV-1 subtype were characterized using Stanford HIVdb and phylogenetic analyses. RESULTS Of the 30 integrase (IN) sequences, 14 were characterized as subtype F (47%), 8 as subtype B (27%), 7 as BF recombinants (23%) and 1 as a putative CRF05_DF (3%). In 25 cases (83%), protease and reverse transcriptase (PR-RT) sequences from the same individuals confirmed the presence of different BF recombinants. Stanford HIVdb genotyping was concordant with phylogenetic inference in 70% of IN and 60% of PR-RT sequences. INI DRMs differed between B and F IN subtypes, with Q148K/R/H, G140S and E138K/A being more prevalent in subtype B (63% versus 0%, P = 0.0021; 50% versus 0%, P = 0.0096; and 50% versus 0%, P = 0.0096, respectively). These differences were independent of the time on raltegravir therapy or viral load at the time of genotyping. INI DRMs in subtype F IN genomes predicted a lower level of resistance to raltegravir and no cross-resistance to second-generation INIs. CONCLUSIONS Alternative resistance pathways to raltegravir develop in subtypes B and F IN genomes, with implications for clinical practice. Evaluating the role of HIV-1 subtype in development and persistence of mutations that confer resistance to INIs will be important to improve algorithms for resistance testing and optimize the use of INIs. © The Author(s) 2020. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email [email protected] Since 2012, the incidence of vancomycin-resistant Enterococcus faecium (VREfm) has increased dramatically in Copenhagen and vanA E. faecium has become endemic and polyclonal. OBJECTIVES To examine whether a patient with a positive VRE clinical sample had the same VREfm in a preceding screening sample (within 60 days). METHODS We performed a 30 month retrospective study. From our laboratory information system (LIS), we identified all patients with an invasive VREfm isolate and a VREfm rectal screening isolate within 60 days before infection. VREfm pairs (screening isolate and invasive isolate) were whole-genome sequenced. link2 All isolates were analysed using SeqSphere and core-genome MLST (cgMLST) types were determined. We examined all isolates for the presence of the three most dominant vanA plasmids in the Capital Region of Denmark. Two novel vanA plasmids were closed by Nanopore/Illumina sequencing. RESULTS We found a total of 19 VREfm pairs. Of these, 13 patients had pairs with matching cgMLST types and vanA plasmids and a median number of 6 days from identification of carriage to clinical infection. One patient had a pair with non-matching cgMLST types but matching vanA plasmids and 24 days between identification of carriage to clinical infection. Five patients had pairs with non-matching cgMLST types and non-matching vanA plasmids and a median number of 18 days from identification of carriage to clinical infection. CONCLUSIONS Of our 19 pairs, 13 were a match regarding cgMLST types (68%) and 1 more (5%) had matching vanA plasmids. Infection was thus preceded by colonization with the same isolates in 13 out of 19 patients. The five mismatches (26%) could be explained by the longer interval between colonization and infection. © The Author(s) 2020. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email [email protected] The concurrent sampling design was developed for case-control studies of recurrent events. It involves matching for time. Standard conditional logistic-regression (CLR) analysis ignores the dependence among recurrent events. Existing methods for clustered observations for CLR do not fit the complex data structure arising from the concurrent sampling design. METHODS We propose to break the matches, apply unconditional logistic regression with adjustment for time in quintiles and residual time within each quintile, and use a robust standard error for observations clustered within persons. We conducted extensive simulation to evaluate this approach and compared it with methods based on CLR. We analysed data from a study of childhood pneumonia to illustrate the methods. RESULTS The proposed method and CLR methods gave very similar point estimates of association and showed little bias. The proposed method produced confidence intervals that achieved the target level of coverage probability, whereas the CLR methods did not, except when disease incidence was low. CONCLUSIONS The proposed method is suitable for the analysis of case-control studies with recurrent events. link3 © The Author(s) 2020. Published by Oxford University Press on behalf of the International Epidemiological Association.Cost-effectiveness thresholds are important decision rules that determine whether health interventions represent good value for money. In low- and middle-income countries, the World Health Organization (WHO) one to three times per capita gross domestic product (GDP) per disability-adjusted life years (DALYs) averted has been the most widely used threshold for informing resource allocation decisions. However, in 2016, the WHO withdrew recommendations for using this threshold, creating a significant vacuum in South Africa and many countries that rely on results of cost-effectiveness analyses for making resource allocation decisions. This study estimates a cost-effectiveness threshold that reflects the health opportunity cost of health spending in South Africa using a three-step approach. First, marginal returns to health spending was estimated as health spending elasticity for crude death rates using a fixed effect estimation approach. Second, the opportunity cost of health spending was estimated as DALYs avertor(s) 2020. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine.There is growing evidence supporting the effectiveness of a comprehensive school health program. However, implementation in developing countries is a challenge. Furthermore, the available information on the association between a comprehensive school health program and students' academic attainment is limited. In Kenya, a project to verify the effects of a comprehensive school health program was carried out in Mbita sub-county, Homa Bay County from September 2012 to August 2017. This study aimed to clarify the improvement of school health during the project years and the association between school health and students' academic attainment. Primary schools in Mbita sub-county were selected as study sites. We assessed 44 schools' scores on a school health checklist developed from the Kenyan Comprehensive School Health Program, the students' mean score on the Kenya Certificate of Primary Education (KCPE), and absenteeism during the project years (2013-16). The mean school health checklist score (n = 44 schools) was 135.6 in 2013, 169.9 in 2014, 158.2 in 2015 and 181.3 in 2016. The difference of the mean score between 2013 and 2016 was significant. In addition, correlation analysis showed a significant association between mean KCPE score in the project years and school health checklist score (Pearson's coefficient was 0.43, p = 0.004). The results of this study suggest improvements of school health by the implementation of the Kenyan Comprehensive School Health Program and students' academic attainment. © The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please email [email protected] Oryza officinalis complex is the largest species group in Oryza, with more than nine species from four continents, and is a tertiary gene pool that can be exploited in breeding programs for the improvement of cultivated rice. Most diploid and tetraploid members of this group have a C genome. Using a new reference C genome for the diploid species Oryza officinalis, and draft genomes for two other C genome diploid species O. eichingeri and O. rhizomatis, we examine the influence of transposable elements on genome structure and provide a detailed phylogeny and evolutionary history of the Oryza C genomes. The O. officinalis genome is 1.6 times larger than the A genome of cultivated O. sativa, mostly due to proliferation of Gypsy type long-terminal repeat (LTR) transposable elements, but overall syntenic relationships are maintained with other Oryza genomes (A, B and F). Draft genome assemblies of the two other C genome diploid species, O. eichingeri and O. rhizomatis, and short-read resequencing of a series of other C genome species and accessions reveal that after the divergence of the C genome progenitor, there was still a substantial degree of variation within the C genome species through proliferation and loss of both DNA and LTR transposable elements.
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