Notes

Influence associated with COVID-19 Outbreak upon Management of Kid Oncology People: Report through Resource-limited Placing.
Within the scope and the available evidence, we opine that some of the PCD-like observations in bacteria seem to be the manifestation of genetic selfism by Restriction-Modification systems and Toxin-Antitoxin systems.Spartina spp. are widely distributed salt marsh plants that have a recent history of hybridization and polyploidization. These events have resulted in a heightened tolerance to hydrocarbon contaminants, but the effects of this phenomenon on the rhizosphere microbial communities are unknown. Here, we grew two parental Spartina species, their hybrid and the resulting allopolyploid in salt marsh sediments that were contaminated or not with phenanthrene. The DNA from the rhizosphere soil was extracted and the bacterial 16S rRNA gene was amplified and sequenced, whereas the abundances of the genes encoding for the PAH (polycyclic aromatic hydrocarbon) ring-hydroxylating dioxygenase (RHD) of Gram-negative and Gram-positive bacteria were quantified by real-time PCR. Both the contamination and the plant genotype significantly affected the bacterial communities. In particular, the allopolyploid S. anglica harbored a more diverse bacterial community in its rhizosphere. The interspecific hybrid and the allopolyploid also harbored significantly more copies of the PAH-RHD gene of Gram-negative bacteria in their rhizosphere than the parental species, irrespective of the contamination treatments. Overall, our results are showing that the recent polyploidization events in the Spartina affected its rhizosphere bacterial communities, both under normal and contaminated conditions, possibly increasing its phytoremediation potential.
Copy number variation (CNV) is an important category of unbalanced structural rearrangement. While methods for detecting CNV in high throughput targeted sequencing have become increasingly sophisticated, dedicated tools for interactive and dynamic visualization of CNV from these data are still lacking. We describe reconCNV, a tool that produces an interactive and annotated web-based dashboard for viewing and summarizing CNVs detected in next-generation sequencing (NGS) data. reconCNV is designed to work with delimited result files from most NGS CNV callers with minor adjustments to the configuration file. The reconCNV output is an HTML file that is viewable on any modern web browser, requires no backend server, and can be readily appended to existing analysis pipelines. In addition to a standard CNV track for visualizing relative fold change and absolute copy number, the tool includes an auxiliary variant allele fraction track for visualizing underlying allelic imbalance and loss of heterozygosity. A feature to mask assay-specific technical artifacts and a direct HTML link out to the UCSC Genome Browser are also included to augment the reviewer experience. By providing a light-weight plugin for interactive visualization to existing NGS CNV pipelines, reconCNV can facilitate efficient NGS CNV visualization and interpretation in both research and clinical settings.

The source code and documentation including a tutorial can be accessed at https//github.com/rghu/reconCNV as well as a Docker image at https//hub.docker.com/repository/docker/raghuc1990/reconcnv.

Supplementary data are available at Bioinformatics online.
Supplementary data are available at Bioinformatics online.
During the current COVID-19 health crisis virtual geriatric clinics have become increasingly utilised to complete outpatient consultations, although concerns exist about feasibility of such virtual consultations for older people. The aim of this rapid review is to describe the satisfaction, clinic productivity, clinical benefit, and costs associated with the virtual geriatric clinic model of care.

A rapid review of PubMed, MEDLINE and CINAHL databases was conducted up to April 2020. Two independent reviewers extracted the information. Four subdomains were focused on satisfaction with the virtual geriatric clinic, clinic productivity, clinical benefit to patients, costs and any challenges associated with the virtual clinic process.

Nine studies with 975 patients met our inclusion criteria. All were observational studies. Seven studies reported patients were satisfied with the virtual geriatric clinic model of care. Productivity outcomes included reports of cost-effectiveness, savings on transport, and imtricians to continue to provide an outpatient service, despite the encountered inherent challenges.
Accurate diagnostic strategies to identify SARS-CoV-2 positive individuals rapidly for management of patient care and protection of health care personnel are urgently needed. The predominant diagnostic test is viral RNA detection by RT-PCR from nasopharyngeal swabs specimens, however the results are not promptly obtainable in all patient care locations. Routine laboratory testing, in contrast, is readily available with a turn-around time (TAT) usually within 1-2 hours.

We developed a machine learning model incorporating patient demographic features (age, sex, race) with 27 routine laboratory tests to predict an individual's SARS-CoV-2 infection status. Laboratory testing results obtained within 2 days before the release of SARS-CoV-2 RT-PCR result were used to train a gradient boosting decision tree (GBDT) model from 3,356 SARS-CoV-2 RT-PCR tested patients (1,402 positive and 1,954 negative) evaluated at a metropolitan hospital.

The model achieved an area under the receiver operating characteristic curv in areas where RT-PCR testing is not accessible due to financial or supply constraints.
Voice assistants have become increasingly embedded in consumer electronics, as the quality of their interaction improves and the cost of hardware continues to drop. Despite their ubiquity, these assistants remain underutilized as a means of accessing biological research data. Gene Teller is a voice assistant service based on the Alexa Skills Kit and Amazon Lambda functions that enables scientists to query for gene-centric information in an intuitive manner. It includes several features, such as synonym disambiguation and short-term memory, that enable a natural conversational interaction, and is extensible to include new resources. The underlying architecture, based on S3 and AWS Lambda, is cost-efficient and scalable.

A publicly accessible version of Gene Teller is available as an Alexa Skill from the Amazon Marketplace at https//www.amazon.com/dp/B08BRD8SS8. The source code is freely available on GitHub at https//github.com/solinvicta/geneTeller.
A publicly accessible version of Gene Teller is available as an Alexa Skill from the Amazon Marketplace at https//www.amazon.com/dp/B08BRD8SS8. The source code is freely available on GitHub at https//github.com/solinvicta/geneTeller.
We hypothesize that poor QOL is highly prevalent in frail older adults and is associated with worse prognosis.

Predismissal standardized tests for frailty and QOL were prospectively administered to patients included in 2 cohorts. In cohort 1, 629 patients ≥ 65 years who underwent percutaneous coronary intervention (PCI) from 2005-2008, frailty (Fried criteria) and QOL [SF-36 and Seattle Angina Questionnaires (SAQ)] were ascertained. Cohort 2 included 921 patients ≥55 years who underwent cardiac catheterization (535 had PCI) from 2014-18 and frailty was determined by Rockwood criteria and QOL by single-item, self-reported health questionnaire. In cohort 1, 19% were frail and 20% patients in cohort 2 were frail with a frailty index>0.30. The median SAQ for physical limitation (58.9 vs. 82.2, p < 0.001); physical (29.5 vs. 43.9, p < 0.001) and mental (49.2 vs. 57.4, p < 0.001) component scores of SF-36 in cohort 1 were lower and self-rating of fair/poor health (56% vs 18%, p < 0.001) in cohort elderly patients undergoing cardiac catheterization or PCI, poor QOL is seen more frequently in frail patients. Both frailty and poor QOL had significant and independent association with long-term survival.Phytochromes are a class of photoreceptors found in plants and in some fungi, cyanobacteria, and photoautotrophic and heterotrophic bacteria. Although phytochromes have been structurally characterized in some bacteria, their biological and ecological roles in magnetotactic bacteria remain unexplored. Here, we describe the biochemical characterization of recombinant bacteriophytochrome (BphP) from magnetotactic bacteria Magnetospirillum magneticum AMB-1 (MmBphP). The recombinant MmBphP displays all the characteristic features, including the property of binding to biliverdin (BV), of a genuine phytochrome. Site-directed mutagenesis identified that cysteine-14 is important for chromophore covalent binding and photoreversibility. Arginine-240 and histidine-246 play key roles in binding to BV. learn more The N-terminal photosensory core domain of MmBphP lacking the C-terminus found in other phytochromes is sufficient to exhibit the characteristic red/far-red-light-induced fast photoreversibility of phytochromes. Moreover, our results showed MmBphP is involved in the phototactic response, suggesting its conservative role as a stress protectant. This finding provided us a better understanding of the physiological function of this group of photoreceptors and photoresponse of magnetotactic bacteria.
RNA-seq technology provides unprecedented power in the assessment of the transcription abundance and can be used to perform a variety of downstream tasks such as inference of gene-correlation network and eQTL discovery. However, raw gene expression values have to be normalized for nuisance biological variation and technical covariates, and different normalization strategies can lead to dramatically different results in the downstream study.

We describe a generalization of SVD-based reconstruction for which the common techniques of whitening, rank-k approximation, and removing the top k principal components are special cases. Our simple three-parameter transformation, DataRemix, can be tuned to reweigh the contribution of hidden factors and reveal otherwise hidden biological signals. In particular, we demonstrate that the method can effectively prioritize biological signals over noise without leveraging external dataset-specific knowledge, and can outperform normalization methods that make explicit use of known technical factors. We also show that DataRemix can be efficiently optimized via Thompson sampling approach, which makes it feasible for computationally expensive objectives such as eQTL analysis. Finally, we apply our method to the ROSMAP dataset and we report what to our knowledge is the first replicable trans-eQTL effect in human brain.

DataRemix is an R package which is freely available at GitHub (https//github.com/wgmao/DataRemix).
DataRemix is an R package which is freely available at GitHub (https//github.com/wgmao/DataRemix).
Respiratory failure appears to be the ultimate mechanism of death in most patients with severe COVID-19 infection. Studies of postmortem COVID-19 lungs largely report diffuse alveolar damage (DAD) and capillary fibrin thrombi, but we have also observed other patterns.

To report demographic and radiographic features along with macroscopic, microscopic, and microbiologic postmortem lung findings in patients with COVID-19 infections.

Patients with confirmed COVID-19 infection and postmortem examination (3/2020-5/2020) were included. Clinical findings were abstracted from medical records. Lungs were microscopically reviewed independently by 4 thoracic pathologists. Imaging studies were reviewed by a thoracic radiologist.

Eight patients (7 men, 87.5%; median age of 79 years, range, 69-96) died within a median of 17 days (range, 6-100) from onset of symptoms. The median lung weight was 1,220 g (range, 960-1,760); consolidations were found in 5 of 8 (62.5%) patients; gross thromboemboli were noted in one of 8 (12.
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