Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST

BACKGROUND: TBLASTN is a mode of operation for BLAST that aligns protein sequences to a nucleotide database translated in all six frames. We present the first description of the modern implementation of TBLASTN, focusing on new techniques that were used to implement composition-based statistics for translated nucleotide searches. Composition-based statistics use the composition of the sequences being aligned to generate more accurate E-values, which allows for a more accurate distinction between true and false matches. Until recently, composition-based statistics were available only for protein-protein searches. They are now available as a command line option for recent versions of TBLASTN and as an option for TBLASTN on the NCBI BLAST web server. RESULTS: We evaluate the statistical and retrieval accuracy of the E-values reported by a baseline version of TBLASTN and by two variants that use different types of composition-based statistics. To test the statistical accuracy of TBLASTN, we ran 1000 searches using scrambled proteins from the mouse genome and a database of human chromosomes. To test retrieval accuracy, we modernize and adapt to translated searches a test set previously used to evaluate the retrieval accuracy of protein-protein searches. We show that composition-based statistics greatly improve the statistical accuracy of TBLASTN, at a small cost to the retrieval accuracy. CONCLUSION: TBLASTN is widely used, as it is common to wish to compare proteins to chromosomes or to libraries of mRNAs. Composition-based statistics improve the statistical accuracy, and therefore the reliability, of TBLASTN results. The algorithms used by TBLASTN are not widely known, and some of the most important are reported here. The data used to test TBLASTN are available for download and may be useful in other studies of translated search algorithms

Evaluation of a COVID-19 fundamental nursing care guideline versus usual care: The COVID-NURSE cluster randomized controlled trial.

This is the final version. Available from Wiley via the DOI in this record. DATA AVAILABILITY STATEMENT: Deidentified individual participant data and a data dictionary will be made available following publication of these results in the University of Exeter's Open Research Exeter repository (https://ore.exeter.ac.uk/repository) to researchers undertaking secondary analyses, with a signed data access agreement after approval of a proposal.AIM: To evaluate the impact of usual care plus a fundamental nursing care guideline compared to usual care only for patients in hospital with COVID-19 on patient experience, care quality, functional ability, treatment outcomes, nurses' moral distress, patient health-related quality of life and cost-effectiveness. DESIGN: Parallel two-arm, cluster-level randomized controlled trial. METHODS: Between 18th January and 20th December 2021, we recruited (i) adults aged 18 years and over with COVID-19, excluding those invasively ventilated, admitted for at least three days or nights in UK Hospital Trusts; (ii) nurses caring for them. We randomly assigned hospitals to use a fundamental nursing care guideline and usual care or usual care only. Our patient-reported co-primary outcomes were the Relational Aspects of Care Questionnaire and four scales from the Quality from the Patient Perspective Questionnaire. We undertook intention-to-treat analyses. RESULTS: We randomized 15 clusters and recruited 581 patient and 418 nurse participants. Primary outcome data were available for 570-572 (98.1%-98.5%) patient participants in 14 clusters. We found no evidence of between-group differences on any patient, nurse or economic outcomes. We found between-group differences over time, in favour of the intervention, for three of our five co-primary outcomes, and a significant interaction on one primary patient outcome for ethnicity (white British vs. other) and allocated group in favour of the intervention for the 'other' ethnicity subgroup. CONCLUSION: We did not detect an overall difference in patient experience for a fundamental nursing care guideline compared to usual care. We have indications the guideline may have aided sustaining good practice over time and had a more positive impact on non-white British patients' experience of care. IMPLICATIONS FOR THE PROFESSION AND/OR PATIENT CARE: We cannot recommend the wholescale implementation of our guideline into routine nursing practice. Further intervention development, feasibility, pilot and evaluation studies are required. IMPACT: Fundamental nursing care drives patient experience but is severely impacted in pandemics. Our guideline was not superior to usual care, albeit it may sustain good practice and have a positive impact on non-white British patients' experience of care. REPORTING METHOD: CONSORT and CONSERVE. PATIENT OR PUBLIC CONTRIBUTION: Patients with experience of hospitalization with COVID-19 were involved in guideline development and writing, trial management and interpretation of findings.Medical Research Counci

Genome-Wide Association Study of Lp-PLA2 Activity and Mass in the Framingham Heart Study

Lipoprotein-associated phospholipase A2 (Lp-PLA2) is an emerging risk factor and therapeutic target for cardiovascular disease. The activity and mass of this enzyme are heritable traits, but major genetic determinants have not been explored in a systematic, genome-wide fashion. We carried out a genome-wide association study of Lp-PLA2 activity and mass in 6,668 Caucasian subjects from the population-based Framingham Heart Study. Clinical data and genotypes from the Affymetrix 550K SNP array were obtained from the open-access Framingham SHARe project. Each polymorphism that passed quality control was tested for associations with Lp-PLA2 activity and mass using linear mixed models implemented in the R statistical package, accounting for familial correlations, and controlling for age, sex, smoking, lipid-lowering-medication use, and cohort. For Lp-PLA2 activity, polymorphisms at four independent loci reached genome-wide significance, including the APOE/APOC1 region on chromosome 19 (p = 6×10−24); CELSR2/PSRC1 on chromosome 1 (p = 3×10−15); SCARB1 on chromosome 12 (p = 1×10−8) and ZNF259/BUD13 in the APOA5/APOA1 gene region on chromosome 11 (p = 4×10−8). All of these remained significant after accounting for associations with LDL cholesterol, HDL cholesterol, or triglycerides. For Lp-PLA2 mass, 12 SNPs achieved genome-wide significance, all clustering in a region on chromosome 6p12.3 near the PLA2G7 gene. Our analyses demonstrate that genetic polymorphisms may contribute to inter-individual variation in Lp-PLA2 activity and mass

Design of a plasmonic metasurface laser accelerator with a tapered phase velocity for subrelativistic particles

A metallic metasurface-based laser-driven particle accelerator for subrelativistic particles is proposed and studied theoretically. The metasurface consists of a nonperiodic array of nanoslits which focuses the field of the driving laser, utilizing the phenomenon of extraordinary plasmonic transmission, to maximize the acceleration gradient. In order to account for the actual change in the particles’ velocity during their propagation through the structure, the separation between successive slits is not constant but rather optimized according to the expected trajectory of the particles. The metasurface laser accelerator (MLA) is designed for an ultrafast driving laser source operating at 2  μm wavelength. An approximate analytical model verified by particle tracking simulations predicts a net average acceleration with a normalized acceleration gradient of 1.34 times the incident laser field. Compared to other laser-driven accelerator designs, the MLA provides substantially higher efficiency, due to the field enhancement associated with nanoantennas, and relaxed fabrication challenges (especially for subrelativistic particles). It is found that the output particle beam is microbunched, suggesting the possibility of using a short MLA structure as a prebuncher to improve the initial capture efficiency in a subsequent longer MLA device. The impact of space-charge effects is also studied, and the loaded gradient and optimal bunch charge are estimated

Thigh-length compression stockings and DVT after stroke

Controversy exists as to whether neoadjuvant chemotherapy improves survival in patients with invasive bladder cancer, despite randomised controlled trials of more than 3000 patients. We undertook a systematic review and meta-analysis to assess the effect of such treatment on survival in patients with this disease

RAPSearch: a fast protein similarity search tool for short reads

<p>Abstract</p> <p>Background</p> <p>Next Generation Sequencing (NGS) is producing enormous corpuses of short DNA reads, affecting emerging fields like metagenomics. Protein similarity search--a key step to achieve annotation of protein-coding genes in these short reads, and identification of their biological functions--faces daunting challenges because of the very sizes of the short read datasets.</p> <p>Results</p> <p>We developed a fast protein similarity search tool RAPSearch that utilizes a reduced amino acid alphabet and suffix array to detect seeds of flexible length. For short reads (translated in 6 frames) we tested, RAPSearch achieved ~20-90 times speedup as compared to BLASTX. RAPSearch missed only a small fraction (~1.3-3.2%) of BLASTX similarity hits, but it also discovered additional homologous proteins (~0.3-2.1%) that BLASTX missed. By contrast, BLAT, a tool that is even slightly faster than RAPSearch, had significant loss of sensitivity as compared to RAPSearch and BLAST.</p> <p>Conclusions</p> <p>RAPSearch is implemented as open-source software and is accessible at <url>http://omics.informatics.indiana.edu/mg/RAPSearch</url>. It enables faster protein similarity search. The application of RAPSearch in metageomics has also been demonstrated.</p