Virseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation.

Despite the recent surge of viral metagenomic studies, it remains a significant challenge to recover complete virus genomes from metagenomic data. The majority of viral contigs generated from de novo assembly programs are highly fragmented, presenting significant challenges to downstream analysis and inference. To address this issue, we have developed Virseqimprover, a computational pipeline that can extend assembled contigs to complete or nearly complete genomes while maintaining extension quality.

Growth performance and enzymatic activities in monosex tilapia (Oreochromis niloticus) supplemented with Najas indica along with the compound identification of the extracts.

Recent research has looked at various macroalgae species as dietary components or feed additives for a variety of fish species due to their nutritional value. The objective of this study was to examine the impact of Najas indica, a macroalgae extract, on the growth performance, proximate composition, and metabolic activities of monosex tilapia (Oreochromis niloticus), while also isolating the compounds present. Three distinct solvents (n-hexane, ethyl acetate, and ethanol) were used to extract bioactive compounds from a coarse powder of macroalgae after drying and grinding, and gas chromatography-mass spectrometry (GC-MS) analysis was used to detect bioactive compounds.

Life cycle assessment of hydrothermal carbonization of municipal solid waste for waste-to-energy generation.

Municipal solid waste (MSW) management is a major concern for Bangladesh, given its high population density and increasing waste production rate. Conventional waste management methods, such as landfilling, result in high carbon emissions for the environment. With over 70% of MSW being organic, hydrothermal carbonization (HTC) has emerged as a promising technology for recovering energy and nutrients from such heterogeneous waste streams.

Pulmonary Cystic Echinococcosis: A Ruptured and Infected Cyst Presenting As Pyopneumothorax.

In this report, a case of 62-year-old female is described who came to the hospital with chief complaints of breathlessness and productive cough with salty whitish expectoration, which she had for two months, along with fever and right-sided chest pain, for three days. The case was identified as a ruptured pulmonary hydatid cyst with pyopneumothorax using contrast-enhanced computed tomography and chest X-ray. This was further supported by the antibody IgG test.

Association of Maternal Serum Homocysteine level with Maternal Birth Weight.

A baby's weight at birth is an important predictor of infant growth and survival. Low birth weight leads to an impaired growth of the infant and its attendant risks of a higher mortality and morbidity. Various studies found higher maternal plasma homocysteine level was associated with lower offspring birth weight.

Cancer germline predisposing variants and late mortality from subsequent malignant neoplasms among long-term childhood cancer survivors: a report from the St Jude Lifetime Cohort and the Childhood Cancer Survivor Study.

Background: Carriers of cancer predisposing variants are at an increased risk of developing subsequent malignant neoplasms among those who have survived childhood cancer. We aimed to investigate whether cancer predisposing variants contribute to the risk of subsequent malignant neoplasm-related late mortality (5 years or more after diagnosis).

Methods: In this analysis, data were included from two retrospective cohort studies, St Jude Lifetime Cohort (SJLIFE) and the Childhood Cancer Survivor Study (CCSS), with prospective follow-up of patients who were alive for at least 5 years after diagnosis with childhood cancer (ie, long-term childhood cancer survivors) with corresponding germline whole genome or whole exome sequencing data.

FastViromeExplorer-Novel: Recovering Draft Genomes of Novel Viruses and Phages in Metagenomic Data.

Despite the recent surge of viral metagenomic studies, recovering complete virus/phage genomes from metagenomic data is still extremely difficult and most viral contigs generated from de novo assembly programs are highly fragmented, posing serious challenges to downstream analysis and inference. In this study, we develop FastViromeExplorer (FVE)-novel, a computational pipeline for reconstructing complete or near-complete viral draft genomes from metagenomic data. The FVE-novel deploys FVE to efficiently map metagenomic reads to viral reference genomes, performs de novo assembly of the mapped reads to generate contigs, and extends the contigs through iterative assembly to produce final viral scaffolds.

Discovery of novel predisposing coding and noncoding variants in familial Hodgkin lymphoma.

Familial aggregation of Hodgkin lymphoma (HL) has been demonstrated in large population studies, pointing to genetic predisposition to this hematological malignancy. To understand the genetic variants associated with the development of HL, we performed whole genome sequencing on 234 individuals with and without HL from 36 pedigrees that had 2 or more first-degree relatives with HL. Our pedigree selection criteria also required at least 1 affected individual aged <21 years, with the median age at diagnosis of 21.

A rare variant analysis framework using public genotype summary counts to prioritize disease-predisposition genes.

Sequencing cases without matched healthy controls hinders prioritization of germline disease-predisposition genes. To circumvent this problem, genotype summary counts from public data sets can serve as controls. However, systematic inflation and false positives can arise if confounding factors are not controlled.

Parallel Evolution of Genome Streamlining and Cellular Bioenergetics across the Marine Radiation of a Bacterial Phylum.

Diverse bacterial and archaeal lineages drive biogeochemical cycles in the global ocean, but the evolutionary processes that have shaped their genomic properties and physiological capabilities remain obscure. Here we track the genome evolution of the globally abundant marine bacterial phylum across its diversification into modern marine environments and demonstrate that extant lineages are partitioned between epipelagic and mesopelagic habitats. Moreover, we show that these habitat preferences are associated with fundamental differences in genomic organization, cellular bioenergetics, and metabolic modalities.

FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data.

With the increase in the availability of metagenomic data generated by next generation sequencing, there is an urgent need for fast and accurate tools for identifying viruses in host-associated and environmental samples. In this paper, we developed a stand-alone pipeline called FastViromeExplorer for the detection and abundance quantification of viruses and phages in large metagenomic datasets by performing rapid searches of virus and phage sequence databases. Both simulated and real data from human microbiome and ocean environmental samples are used to validate FastViromeExplorer as a reliable tool to quickly and accurately identify viruses and their abundances in large datasets.

A Bayesian Assignment Method for Ambiguous Bisulfite Short Reads.

DNA methylation is an epigenetic modification critical for normal development and diseases. The determination of genome-wide DNA methylation at single-nucleotide resolution is made possible by sequencing bisulfite treated DNA with next generation high-throughput sequencing. However, aligning bisulfite short reads to a reference genome remains challenging as only a limited proportion of them (around 50-70%) can be aligned uniquely; a significant proportion, known as multireads, are mapped to multiple locations and thus discarded from downstream analyses, causing financial waste and biased methylation inference.