Risk of admission to hospital for self-harm after admission to hospital for COVID-19: French nationwide longitudinal study.

Background: Assessing the risk of subsequent self-harm after hospitalisation for COVID-19 is critical for mental health care planning during and after the pandemic.

Aims: This study aims to compare the risk of admission to hospital for self-harm within 12 months following a COVID-19 hospitalisation during the first half of 2020, with the risk following hospitalisations for other reasons.

Method: Using the French administrative healthcare database, logistic regression models were employed to analyse data from patients admitted to hospitals in metropolitan France between January and June 2020.

Mental health of pregnant women during the SARS-CoV-2 pandemic in France: Evolution of self-perceived psychological state during the first lockdown, and anxiety frequency two months after the lockdown ended.

Previous pandemics and related lockdowns have had a deleterious impact on pregnant women's mental health. We studied the impact of the SARS-CoV-2/Covid-19 pandemic and France's first lockdown on pregnant women's mental health. A cross-sectional study was conducted in July 2020 using a web-questionnaire completed by 500 adult women who were pregnant during the first lockdown in France (March-May 2020).

Hospitalization for COVID-19 is associated with a higher risk of subsequent hospitalization for psychiatric disorders: A French nationwide longitudinal study comparing hospitalizations for COVID-19 and for other reasons.

Introduction: Although COVID-19 has been associated with psychiatric symptoms in patients, no study to date has examined the risk of hospitalization for psychiatric disorders after hospitalization for this disease.

Objective: We aimed to compare the proportions of hospitalizations for psychiatric disorders in the 12 months following either hospitalization for COVID-19 or hospitalization for another reason in the adult general population in France during the first wave of the current pandemic.

Methods: We conducted a retrospective longitudinal nationwide study based on the national French administrative healthcare database.

Hospitalised traumatic brain injury victims in France: An analysis of the French hospital discharge database for 2011-2016.

Background: Traumatic brain injury (TBI) is a major public health problem because of its severity and frequency. No recent national epidemiological study on TBI victims is currently available in France.

Objective: This study aimed to quantify and characterise TBI victims and analyse temporal trends.

Clinical, pathological and loss of heterozygosity differences in Wilms tumors between Asian and non-Asian children.

Wilms tumor demonstrates significant interethnic epidemiological, histological and outcome differences, and is rare and poorly studied among Asians. We compared the clinicopathological, and loss of heterozygosity (LOH) profile and survival outcomes of Asian and non-Asian patients with Wilms tumor. Clinical charts and histological slides from patients with malignant renal tumors over a period of 20 years were retrospectively reviewed.

Biological significance and prognostic relevance of peripheral blood neutrophil-to-lymphocyte ratio in soft tissue sarcoma.

Peripheral blood indices of systemic inflammation such as the neutrophil-lymphocyte ratio (NLR) have been shown to be prognostic in various cancers. We aim to investigate the clinical significance of these indices in patients with soft tissue sarcoma (STS). Seven hundred and twelve patients with available blood counts at diagnosis and/or metastatic relapse were retrospectively examined.

Treatment and outcomes of melanoma in Asia: Results from the National Cancer Centre Singapore.

Background: Acral melanoma (AM) and mucosal melanoma (MM) make up more than half of melanomas in Asia but comprise only 5% of cases in Caucasians, where cutaneous melanoma (CM) predominates. AM and MM are thought to be genetically and biologically distinct from CM. We report the characteristics and outcomes of melanoma patients from the National Cancer Centre Singapore.

Germline Mutations in Cancer Predisposition Genes are Frequent in Sporadic Sarcomas.

Associations of sarcoma with inherited cancer syndromes implicate genetic predisposition in sarcoma development. However, due to the apparently sporadic nature of sarcomas, little attention has been paid to the role genetic susceptibility in sporadic sarcoma. To address this, we performed targeted-genomic sequencing to investigate the prevalence of germline mutations in known cancer-associated genes within an Asian cohort of sporadic sarcoma patients younger than 50 years old.

Cellular adhesiveness and cellulolytic capacity in Anaerolineae revealed by omics-based genome interpretation.

Background: The Anaerolineae lineage of Chloroflexi had been identified as one of the core microbial populations in anaerobic digesters; however, the ecological role of the Anaerolineae remains uncertain due to the scarcity of isolates and annotated genome sequences. Our previous metatranscriptional analysis revealed this prevalent population that showed minimum involvement in the main pathways of cellulose hydrolysis and subsequent methanogenesis in the thermophilic cellulose fermentative consortium (TCF).

Results: In further pursuit, five high-quality curated draft genomes (>98 % completeness) of this population, including two affiliated with the inaccessible lineage of SBR1031, were retrieved by sequence-based multi-dimensional coverage binning.

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads.

Background: Because of the short read length of high throughput sequencing data, assembly errors are introduced in genome assembly, which may have adverse impact to the downstream data analysis. Several tools have been developed to eliminate these errors by either 1) comparing the assembled sequences with some similar reference genome, or 2) analyzing paired-end reads aligned to the assembled sequences and determining inconsistent features alone mis-assembled sequences. However, the former approach cannot distinguish real structural variations between the target genome and the reference genome while the latter approach could have many false positive detections (correctly assembled sequence being considered as mis-assembled sequence).

Phylogeny-structured carbohydrate metabolism across microbiomes collected from different units in wastewater treatment process.

Background: With respect to global priority for bioenergy production from plant biomass, understanding the fundamental genetic associations underlying carbohydrate metabolisms is crucial for the development of effective biorefinery process. Compared with gut microbiome of ruminal animals and wood-feed insects, knowledge on carbohydrate metabolisms of engineered biosystems is limited.

Results: In this study, comparative metagenomics coupled with metabolic network analysis was carried out to study the inter-species cooperation and competition among carbohydrate-active microbes in typical units of wastewater treatment process including activated sludge and anaerobic digestion.

A Simple Algorithm for Finding All k-Edge-Connected Components.

The problem of finding k-edge-connected components is a fundamental problem in computer science. Given a graph G = (V, E), the problem is to partition the vertex set V into {V1, V2,…, Vh}, where each Vi is maximized, such that for any two vertices x and y in Vi, there are k edge-disjoint paths connecting them. In this paper, we present an algorithm to solve this problem for all k.

Predicting drug-target interaction for new drugs using enhanced similarity measures and super-target clustering.

Predicting drug-target interaction using computational approaches is an important step in drug discovery and repositioning. To predict whether there will be an interaction between a drug and a target, most existing methods identify similar drugs and targets in the database. The prediction is then made based on the known interactions of these drugs and targets.

IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information.

Metatranscriptomic analysis provides information on how a microbial community reacts to environmental changes. Using next-generation sequencing (NGS) technology, biologists can study the microbe community by sampling short reads from a mixture of mRNAs (metatranscriptomic data). As most microbial genome sequences are unknown, it would seem that de novo assembly of the mRNAs is needed.

Time trends in pulmonary embolism mortality in France, 2000-2010.

Background: Pulmonary Embolism (PE) is a potentially fatal complication of venous thrombosis. Recent and comprehensive estimates of PE incidence and mortality are scarce. Moreover, while contemporary mortality trends of PE would enable the evaluation of prevention and quality of care, such data are lacking.

PERGA: a paired-end read guided de novo assembler for extending contigs using SVM and look ahead approach.

Since the read lengths of high throughput sequencing (HTS) technologies are short, de novo assembly which plays significant roles in many applications remains a great challenge. Most of the state-of-the-art approaches base on de Bruijn graph strategy and overlap-layout strategy. However, these approaches which depend on k-mers or read overlaps do not fully utilize information of paired-end and single-end reads when resolving branches.

Sequence assembly using next generation sequencing data--challenges and solutions.

Sequence assembling is an important step for bioinformatics study. With the help of next generation sequencing (NGS) technology, high throughput DNA fragment (reads) can be randomly sampled from DNA or RNA molecular sequence. However, as the positions of reads being sampled are unknown, assembling process is required for combining overlapped reads to reconstruct the original DNA or RNA sequence.

MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning.

Background: Taxonomic annotation of reads is an important problem in metagenomic analysis. Existing annotation tools, which rely on the approach of aligning each read to the taxonomic structure, are unable to annotate many reads efficiently and accurately as reads (~100 bp) are short and most of them come from unknown genomes. Previous work has suggested assembling the reads to make longer contigs before annotation.

Effective moment feature vectors for protein domain structures.

Imaging processing techniques have been shown to be useful in studying protein domain structures. The idea is to represent the pairwise distances of any two residues of the structure in a 2D distance matrix (DM). Features and/or submatrices are extracted from this DM to represent a domain.

DDGni: dynamic delay gene-network inference from high-temporal data using gapped local alignment.

Motivation: Inferring gene-regulatory networks is very crucial in decoding various complex mechanisms in biological systems. Synthesis of a fully functional transcriptional factor/protein from DNA involves series of reactions, leading to a delay in gene regulation. The complexity increases with the dynamic delay induced by other small molecules involved in gene regulation, and noisy cellular environment.

Cutaneous versus non-cutaneous angiosarcoma: clinicopathologic features and treatment outcomes in 60 patients at a single Asian cancer centre.

Background: Angiosarcoma (AS) is an uncommon soft tissue sarcoma with dismal prognosis that presents either cutaneously (C-AS) or non-cutaneously (NC-AS). We compared the clinical features and treatment outcomes between these 2 groups.

Methods: A single-centre study evaluating 60 AS patients between 2002 and 2012 was performed.

Brain metastasis in sarcoma: Does metastasectomy or aggressive multi-disciplinary treatment improve survival outcomes.

Aim: Brain metastasis is rare in sarcoma. Prognostic factors, optimal management strategies and therapeutic outcomes of such patients are not well studied. We aimed to evaluate the incidence, clinical characteristics and treatment outcomes of parenchymal brain metastasis in sarcoma patients.

IDBA-MT: de novo assembler for metatranscriptomic data generated from next-generation sequencing technology.

High-throughput next-generation sequencing technology provides a great opportunity for analyzing metatranscriptomic data. However, the reads produced by these technologies are short and an assembling step is required to combine the short reads into longer contigs. As there are many repeat patterns in mRNAs from different genomes and the abundance ratio of mRNAs in a sample varies a lot, existing assemblers for genomic data, transcriptomic data, and metagenomic data do not work on metatranscriptomic data and produce chimeric contigs, that is, incorrect contigs formed by merging multiple mRNA sequences.