Genetic diversity of two tropical tree species of the Dipterocarpaceae following logging and restoration in Borneo: high genetic diversity in plots with high species diversity

Background: The impact of logging and restoration on species diversity has been well studied in tropical forests. However, little is known about their effects on genetic diversity within species. Aims: We assess the degree of genetic diversity among dipterocarp seedlings used for enrichment planting of selectively logged forests in Sabah, Malaysia, and compare it with diversity in naturally regenerating seedlings. Methods: We sampled young leaf tissues from seedlings of Shorea leprosula and Parashorea malaanonan for DNA genotyping, using microsatellite markers. Results: The levels of genetic diversity (expected heterozygosity and rarefied allelic richness) of naturally regenerating seedlings were statistically indistinguishable among unlogged, once logged and repeatedly logged forest areas. Enrichment-planted seedlings of P. malaanonan exhibited similar levels of genetic diversity to naturally regenerating seedlings whereas those of S. leprosula had significantly lower genetic diversity than natural seedlings. Interestingly, reduction of genetic variation was consistently observed in single-species plots relative to mixed-species plots among enrichment-planted seedlings. Conclusions: There was no reduction of genetic variation in naturally regenerating dipterocarp seedlings in areas of selective logging. However, genetic variation of enrichment-planted seedlings was lower in single-species plots relative to mixed-species plots. This suggests that enrichment-planting strategies should adopt diverse mixtures that should promote levels of both species richness and genetic diversity within species

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Tocilizumab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

Background: In this study, we aimed to evaluate the effects of tocilizumab in adult patients admitted to hospital with COVID-19 with both hypoxia and systemic inflammation. Methods: This randomised, controlled, open-label, platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing several possible treatments in patients hospitalised with COVID-19 in the UK. Those trial participants with hypoxia (oxygen saturation <92% on air or requiring oxygen therapy) and evidence of systemic inflammation (C-reactive protein ≥75 mg/L) were eligible for random assignment in a 1:1 ratio to usual standard of care alone versus usual standard of care plus tocilizumab at a dose of 400 mg–800 mg (depending on weight) given intravenously. A second dose could be given 12–24 h later if the patient's condition had not improved. The primary outcome was 28-day mortality, assessed in the intention-to-treat population. The trial is registered with ISRCTN (50189673) and ClinicalTrials.gov (NCT04381936). Findings: Between April 23, 2020, and Jan 24, 2021, 4116 adults of 21 550 patients enrolled into the RECOVERY trial were included in the assessment of tocilizumab, including 3385 (82%) patients receiving systemic corticosteroids. Overall, 621 (31%) of the 2022 patients allocated tocilizumab and 729 (35%) of the 2094 patients allocated to usual care died within 28 days (rate ratio 0·85; 95% CI 0·76–0·94; p=0·0028). Consistent results were seen in all prespecified subgroups of patients, including those receiving systemic corticosteroids. Patients allocated to tocilizumab were more likely to be discharged from hospital within 28 days (57% vs 50%; rate ratio 1·22; 1·12–1·33; p<0·0001). Among those not receiving invasive mechanical ventilation at baseline, patients allocated tocilizumab were less likely to reach the composite endpoint of invasive mechanical ventilation or death (35% vs 42%; risk ratio 0·84; 95% CI 0·77–0·92; p<0·0001). Interpretation: In hospitalised COVID-19 patients with hypoxia and systemic inflammation, tocilizumab improved survival and other clinical outcomes. These benefits were seen regardless of the amount of respiratory support and were additional to the benefits of systemic corticosteroids. Funding: UK Research and Innovation (Medical Research Council) and National Institute of Health Research

Convalescent plasma in patients admitted to hospital with COVID-19 (RECOVERY): a randomised controlled, open-label, platform trial

Background: Many patients with COVID-19 have been treated with plasma containing anti-SARS-CoV-2 antibodies. We aimed to evaluate the safety and efficacy of convalescent plasma therapy in patients admitted to hospital with COVID-19. Methods: This randomised, controlled, open-label, platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]) is assessing several possible treatments in patients hospitalised with COVID-19 in the UK. The trial is underway at 177 NHS hospitals from across the UK. Eligible and consenting patients were randomly assigned (1:1) to receive either usual care alone (usual care group) or usual care plus high-titre convalescent plasma (convalescent plasma group). The primary outcome was 28-day mortality, analysed on an intention-to-treat basis. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936. Findings: Between May 28, 2020, and Jan 15, 2021, 11558 (71%) of 16287 patients enrolled in RECOVERY were eligible to receive convalescent plasma and were assigned to either the convalescent plasma group or the usual care group. There was no significant difference in 28-day mortality between the two groups: 1399 (24%) of 5795 patients in the convalescent plasma group and 1408 (24%) of 5763 patients in the usual care group died within 28 days (rate ratio 1·00, 95% CI 0·93–1·07; p=0·95). The 28-day mortality rate ratio was similar in all prespecified subgroups of patients, including in those patients without detectable SARS-CoV-2 antibodies at randomisation. Allocation to convalescent plasma had no significant effect on the proportion of patients discharged from hospital within 28 days (3832 [66%] patients in the convalescent plasma group vs 3822 [66%] patients in the usual care group; rate ratio 0·99, 95% CI 0·94–1·03; p=0·57). Among those not on invasive mechanical ventilation at randomisation, there was no significant difference in the proportion of patients meeting the composite endpoint of progression to invasive mechanical ventilation or death (1568 [29%] of 5493 patients in the convalescent plasma group vs 1568 [29%] of 5448 patients in the usual care group; rate ratio 0·99, 95% CI 0·93–1·05; p=0·79). Interpretation: In patients hospitalised with COVID-19, high-titre convalescent plasma did not improve survival or other prespecified clinical outcomes. Funding: UK Research and Innovation (Medical Research Council) and National Institute of Health Research

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

An evaluation of life insurance markets of selected Asian countries

152 p.The economic performance of Asia in the 1990s has been remarkable. Although the 5 countries (Malaysia, The Philippines, Thailand, Indonesia and India) under studied are not totally representative of the Asian region, it indicates the vast potential abound in it. In support of this growing Asian economy, the financial sector, which includes the life insurance industry, would also undoubtedly expands.BUSINES

Developing a Training System for Web Fires [video]

TechCon2017 (CRUSER)Presented by LCDR Dan DeCicco, USN and NPS SEA 25 TDSI Cohort: Ryan Beall, Preston Tilus, Clayton Petty, Dor Kronzilber, Ang Chin Beng, Ang Pak Siang, Kan Wei Sheng, Ang Wee Kiong, Hoon Dingyao, Gay Wee Choon, Soh Yuan Wei, Yee Jian Hong, Ang Cheng Hai, Han Keng Siew, Foo Yueng Hao, Chin Hon Keong, See Hongze, Toh Ying Jie, Lai Wee, Tan Choon SengIncludes slidesSEA 25 TASKING: Design a fleet system of systems and concept of operations for employment of a cost effective training system capable of preparing naval warfighters to employ and leverage the web fires concepts and technologies in the 2025-2030 timeframe. Consider training across warfare specialties and missions; Conduct research to provide a solid foundation of knowledge requirements for a web fires fleet concept; Complete a gap analysis by comparing current fleet training with the required training to leverage cross domain and cross-platform capabilities in a warfighting environment; Scan for current examples of cross-domain training and current training simulation from DoD and industry; Develop a system architecture addressing responsible command, training requirements, training and exercise venues, and training participants to fill discovered gaps in meeting the knowledge requirements; Assess the proposed system against the principles of high velocity learning found in the CNO's "A Design for Maintaining Maritime SuperiorityNPS CRUSE

Genetic diversity of two tropical tree species of the Dipterocarpaceae following logging and restoration in Borneo: high genetic diversity in plots with high species diversity

Background The impact of logging and restoration on species diversity has been well studied in tropical forests. However, little is known about their effects on genetic diversity within species. Aims We assess the degree of genetic diversity among dipterocarp seedlings used for enrichment planting of selectively logged forests in Sabah, Malaysia, and compare it with diversity in naturally regenerating seedlings. Methods We sampled young leaf tissues from seedlings of Shorea leprosula and Parashorea malaanonan for DNA genotyping, using microsatellite markers. Results The levels of genetic diversity (expected heterozygosity and rarefied allelic richness) of naturally regenerating seedlings were statistically indistinguishable among unlogged, once logged and repeatedly logged forest areas. Enrichment planted seedlings of P. malaanonan exhibited similar levels of genetic diversity to naturally regenerating seedlings whereas those of S. leprosul ahad significantly lower genetic diversity than natural seedlings. Interestingly, reduction of genetic variation was consistently observed in single-species plots relative to mixed-species plots among enrichment-planted seedlings. Conclusions There was no reduction of genetic variation in naturally regenerating dipterocarp seedlings in areas of selective logging. However, genetic variation of enrichment-planted seedlings was lower in single-species plots relative to mixed-species plots. This suggests that enrichment-planting strategies should adopt diverse mixtures that should promote levels of both species richness and genetic diversity within specie