Wellcome Open Research最新文献

We present a genome assembly from a male specimen of Sympetrum sanguineum (Ruddy Darter; Arthropoda; Insecta; Odonata; Libellulidae). The haplotype-resolved assembly contains two haplotypes with total lengths of 1,500.53 megabases and 1,304.05 megabases. Most of haplotype 1 is scaffolded into 13 chromosomal pseudomolecules, including the X sex chromosome, while haplotype 2 is scaffolded into 12 autosomes.

We present a genome assembly from a specimen of Ectobius pallidus (tawny cockroach; Arthropoda; Insecta; Blattodea; Ectobiidae). The assembly contains two haplotypes with total lengths of 2,087.55 megabases and 2,124.67 megabases, respectively. Most of haplotype 1 (98.55%) is scaffolded into 11 chromosomal pseudomolecules, while haplotype 2 is assembled to scaffold level. The mitochondrial genome has also been assembled and is 15.75 kilobases in length.

We present a genome assembly from an individual female Vulpes vulpes (red fox; Chordata, Mammalia, Carnivora, Canidae). The assembly comprises two haplotypes, with total lengths of 2,411.71 megabases and 2,398.53 megabases, respectively. For both haplotypes, 97.8% of haplotype 1 and 97.97% of haplotype 2 are scaffolded into 17 chromosomal pseudomolecules. Additionally, the mitochondrial genome has been assembled, with a total length of 16.68 kilobases.

We present a genome assembly from an individual female specimen of Brachypterus glaber (beetle; Arthropoda; Insecta; Coleoptera; Kateretidae). The genome sequence has a total length of 648.30 megabases. Most of the assembly (95.55%) is scaffolded into 11 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 21.86 kilobases in length. Gene annotation of this assembly on Ensembl identified 23,733 protein-coding genes.

We present a genome assembly from an individual male specimen of Allygus modestus (leafhopper; Arthropoda; Insecta; Hemiptera; Cicadellidae). The genome sequence has a total length of 1,819.90 megabases. Most of the assembly (99.86%) is scaffolded into 7 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.69 kilobases in length.

We present a genome assembly from an individual female specimen of Ostrinia nubilalis (European Corn Borer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a total length of 495.50 megabases. Most of the assembly (99.87%) is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.24 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,780 protein-coding genes.

Background: This study aimed to assess the current status of critical care services in 13 districts of Bagmati Province in Nepal, with a focus on access, infrastructure, human resources, and intensive care unit (ICU) services.

Methods: A cross-sectional survey was conducted among healthcare workers employed in 87 hospitals having medical/surgical ICUs across Bagmati Province. Data were collected through structured questionnaires administered via face-to-face and telephone survey. Descriptive analysis was used for data analysis, involving frequencies and percentages.

Results: From 87 hospitals, a total of 123 ICUs were identified in the province, providing 1167 beds and 615 functioning ventilators. The average ICU bed availability per 100,000 population was 19, ranging from 3.6 in Makwanpur to 33.9 in Kathmandu. Out of 13 districts, 95% of beds were concentrated in just four districts, while six had no ICU facilities. Of the available facilities, 69.9% were owned by private entities. One-to-one nurse-to-ventilated bed ratio was maintained by 63.4% of ICUs during daytime, and 62.6% at nighttime. Furthermore, 74.8% of ICUs had consultants trained in critical care medicine. While essential equipment availability was higher in Bagmati province, gaps existed in the availability of oxygen plants and isolation rooms. Similarly, many ICUs offered continuous medical education and cardiopulmonary resuscitation (CPR) training, but improvements were necessary in clinical audits, antibiotic stewardship programs, and research engagement.

Conclusions: Disparities in critical care resources were evident across districts in Bagmati Province, highlighting the need for a balanced and decentralized approach to ensure equitable access to care. Although there were disparities, numerous ICUs were effectively carrying out multiple critical care procedures. This study suggests conducting a nationwide mapping of ICU resources, prioritizing infrastructure development, optimizing resource allocation, and establishing national protocols.

The increasing threat from infection with drug-resistant pathogens is among the most serious public health challenges of our time. Formed by Wellcome in 2018, the Surveillance and Epidemiology of Drug-Resistant Infections Consortium (SEDRIC) is an international think tank whose aim is to inform policy and change the way countries track, share, and analyse data relating to drug-resistant infections, by defining knowledge gaps and identifying barriers to the delivery of global surveillance. SEDRIC delivers its aims through discussions and analyses by world-leading scientists that result in recommendations and advocacy to Wellcome and others. As a result, SEDRIC has made key contributions in furthering global and national actions. Here, we look back at the work of the consortium between 2018-2024, highlighting notable successes. We provide specific examples where technical analyses and recommendations have helped to inform policy and funding priorities that will have real-world impact on the surveillance and epidemiology of infections with drug-resistant pathogens.

Despite significant investment in High-Performance Computing (HPC) clusters by funding councils, there are still many researchers whose workflows could not benefit from the computation speed that is provided by these clusters. Reducing barriers to entry for these researchers would accelerate their scientific throughput, since they will be able to respond to results in a timely fashion, improving either their protocols or correcting any problems that might have arisen. This improves the quality of science, and therefore the return on investment, in computationally-intensive areas such as Cryogenic Electron Microscopy (cryo-EM). This paper outlines a technique, FlowCron, for users to analyse their data on a HPC facility with minimal training, increasing accessibility. FlowCron transfers the responsibilities of installation and upkeep of data processing pipelines from users to HPC systems administrators, simplifies the set up of HPC pipelines, and makes pipelines as reliable as possible once set up. The work described here has software dependencies that are common to the majority of HPC clusters. We achieve this by linking Globus and cron to produce an open-source system that requires little administrative support but provides a very easy way of running an analysis on a HPC system. The user starts the analysis through the Globus website and, when started, the data will be encrypted, uploaded to the HPC, analysed, and returned to the originating machine, along with a record of the analysis.

Background: There is limited knowledge regarding African genetic drivers of disease due to prohibitive costs of large-scale genomic research in Africa.

Methods: We piloted a scalable virtual genotyped cohort in South Africa that was affordable in this resource-limited context, cost-effective, scalable virtual genotyped cohort in South Africa, with participant recruitment using a tiered informed consent model and DNA collection by buccal swab. Genotype data was generated using the H3Africa Illumina micro-array, and phenotype data was derived from routine health data of participants. We demonstrated feasibility of nested case control genome wide association studies using these data for phenotypes type 2 diabetes mellitus (T2DM) and severe COVID-19.

Results: 2267346 variants were analysed in 459 participant samples, of which 229 (66.8%) are female. 78.6% of SNPs and 74% of samples passed quality control (QC). Principal component analysis showed extensive ancestry admixture in study participants. Of the 343 samples that passed QC, 93 participants had T2DM and 63 had severe COVID-19. For 1780 previously published COVID-19-associated variants, 3 SNPs in the pre-imputation data and 23 SNPS in the imputed data were significantly associated with severe COVID-19 cases compared to controls (p<0.05). For 2755 published T2DM associated variants, 69 SNPs in the pre-imputation data and 419 SNPs in the imputed data were significantly associated with T2DM cases when compared to controls (p<0.05).

Conclusions: The results shown here are illustrative of what will be possible as the cohort expands in the future. Here we demonstrate the feasibility of this approach, recognising that the findings presented here are preliminary and require further validation once we have a sufficient sample size to improve statistical significance of findings.We implemented a genotyped population cohort with virtual follow up data in a resource-constrained African environment, demonstrating feasibility for scale up and novel health discoveries through nested case-control studies.