Pan-cancer multi-omic model of LINE-1 activity reveals locus heterogeneity of retrotransposition efficiency.

Somatic mobilization of LINE-1 (L1) has been implicated in cancer etiology. We analyzed a recent TCGA data release comprised of nearly 5000 pan-cancer paired tumor-normal whole-genome sequencing (WGS) samples and ~9000 tumor RNA samples. We developed TotalReCall an improved algorithm and pipeline for detection of L1 retrotransposition (RT), finding high correlation between L1 expression and "RT burden" per sample.

TM7SF2 as a Potential Biomarker in Colorectal Cancer: Implications for Metastasis.

Colorectal cancer (CRC) is a commonly fatal cancer and ranks as the fourth most prevalent in men and third in women worldwide. While early-stage survival rates are high, they significantly decrease with recurrence and metastasis. Thus, the early detection and treatment of metastasis-related factors can significantly improve survival rates.

Contribution of retroelements to birth defects and childhood cancers.

Insertion of active retroelements-L1s, s, and SVAs-can disrupt proper genome function and lead to various disorders including cancer. However, the role of retroelements (DNRTs) in birth defects and childhood cancers has not been well characterized due to the lack of adequate data and efficient computational tools. Here, we examine whole-genome sequencing data of 3,244 trios from 12 birth defect and childhood cancer cohorts in the Gabriella Miller Kids First Pediatric Research Program.

Near-gapless and haplotype-resolved apple genomes provide insights into the genetic basis of rootstock-induced dwarfing.

Dwarfing rootstocks have transformed the production of cultivated apples; however, the genetic basis of rootstock-induced dwarfing remains largely unclear. We have assembled chromosome-level, near-gapless and haplotype-resolved genomes for the popular dwarfing rootstock 'M9', the semi-vigorous rootstock 'MM106' and 'Fuji', one of the most commonly grown apple cultivars. The apple orthologue of auxin response factor 3 (MdARF3) is in the Dw1 region of 'M9', the major locus for rootstock-induced dwarfing.

Biogas production prediction model of food waste anaerobic digestion for energy optimization using mixup data augmentation-based global attention mechanism.

Achieving rapid, efficient, and cost-effective anaerobic digestion (AD) of food waste is a key means to improve the efficiency of food waste treatment. However, in view of the shortage of historical anaerobic digestion data, the limitation of general neural networks in predicting biogas production, and its sensitivity to abnormal variation points, achieving accurate prediction of biogas production is not easy. This paper proposes a novel biogas production prediction model of food waste AD for energy optimization based on the mixup data augmentation integrating an improved global attention mechanism long short-term memory (LSTM).

ERα-associated translocations underlie oncogene amplifications in breast cancer.

Focal copy-number amplification is an oncogenic event. Although recent studies have revealed the complex structure and the evolutionary trajectories of oncogene amplicons, their origin remains poorly understood. Here we show that focal amplifications in breast cancer frequently derive from a mechanism-which we term translocation-bridge amplification-involving inter-chromosomal translocations that lead to dicentric chromosome bridge formation and breakage.

Novel risk assessment model of food quality and safety considering physical-chemical and pollutant indexes based on coefficient of variance integrating entropy weight.

Food safety is important for sustainable social and economic development and people's health. The traditional single risk assessment model is one-sided to the weight distribution of food safety factors including physical-chemical and pollutant indexes, which cannot comprehensively assess food safety risks. Therefore, a novel food safety risk assessment model combining the coefficient of variation (CV) integrating the entropy weight (EWM) (CV-EWM) is proposed in this paper.

A Multicenter, Randomized, Open-Label Study to Compare the Efficacy and Safety of Tacrolimus and Corticosteroids in Combination With or Without Mycophenolate Mofetil in Liver Transplantation Recipients Infected With Hepatitis B Virus.

Background: Mycophenolate mofetil exhibits pharmacologic mechanisms different from calcineurin inhibitors. Therefore, the dose of calcineurin inhibitors can be reduced along with side effects for effective immunosuppression. We aimed to evaluate the efficacy and safety of tacrolimus and corticosteroid in combination with or without mycophenolate mofetil in living donor liver transplantation (LDLT) recipients infected with hepatitis B virus (HBV).

Deciphering transcriptome alterations in bone marrow hematopoiesis at single-cell resolution in immune thrombocytopenia.

Immune thrombocytopenia (ITP) is an autoimmune disorder, in which megakaryocyte dysfunction caused by an autoimmune reaction can lead to thrombocytopenia, although the underlying mechanisms remain unclear. Here, we performed single-cell transcriptome profiling of bone marrow CD34 hematopoietic stem and progenitor cells (HSPCs) to determine defects in megakaryopoiesis in ITP. Gene expression, cell-cell interactions, and transcriptional regulatory networks varied in HSPCs of ITP, particularly in immune cell progenitors.

The global burden of disease attributable to ambient fine particulate matter in 204 countries and territories, 1990-2019: A systematic analysis of the Global Burden of Disease Study 2019.

Understanding the spatio-temporal patterns of the disease burden attributable to ambient PM2.5 across the world is essential for the prevention of related diseases, as well as ambient PM2.5 control.

Whole-genome analysis reveals the contribution of non-coding de novo transposon insertions to autism spectrum disorder.

Background: Retrotransposons have been implicated as causes of Mendelian disease, but their role in autism spectrum disorder (ASD) has not been systematically defined, because they are only called with adequate sensitivity from whole genome sequencing (WGS) data and a large enough cohort for this analysis has only recently become available.

Results: We analyzed WGS data from a cohort of 2288 ASD families from the Simons Simplex Collection by establishing a scalable computational pipeline for retrotransposon insertion detection. We report 86,154 polymorphic retrotransposon insertions-including > 60% not previously reported-and 158 de novo retrotransposition events.

Global burden of lung cancer attributable to ambient fine particulate matter pollution in 204 countries and territories, 1990-2019.

Introduction: Understanding the latest global spatio-temporal pattern of lung cancer burden attributable to ambient fine particulate matter pollution (PM) is crucial to prioritize global lung cancer prevention, as well as environment improvement.

Methods: Data on lung cancer attributable to ambient PM were downloaded from the Global Burden of Disease Study (GBD) 2019. The numbers and age-standardized rates on lung cancer mortality (ASMR) and disability-adjusted life years (ASDR) were estimated by age, sex, region, and country.

BamSnap: a lightweight viewer for sequencing reads in BAM files.

Summary: Despite the improvement in variant detection algorithms, visual inspection of the read-level data remains an essential step for accurate identification of variants in genome analysis. We developed BamSnap, an efficient BAM file viewer utilizing a graphics library and BAM indexing. In contrast to existing viewers, BamSnap can generate high-quality snapshots rapidly, with customized tracks and layout.

HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data.

Unlabelled: Hi-C is a common technique for assessing 3D chromatin conformation. Recent studies have shown that long-range interaction information in Hi-C data can be used to generate chromosome-length genome assemblies and identify large-scale structural variations. Here, we demonstrate the use of Hi-C data in detecting mobile transposable element (TE) insertions genome-wide.

The design and construction of reference pangenome graphs with minigraph.

The recent advances in sequencing technologies enable the assembly of individual genomes to the quality of the reference genome. How to integrate multiple genomes from the same species and make the integrated representation accessible to biologists remains an open challenge. Here, we propose a graph-based data model and associated formats to represent multiple genomes while preserving the coordinate of the linear reference genome.

Effect of on the Once-Daily Tacrolimus Conversion in Stable Liver Transplant Patients.

Cytochrome P450 () polymorphism influences tacrolimus metabolism, but its effect on the drug pharmacokinetics in liver transplant recipients switched to once-daily extended-release formulation remains unknown. The aim of this study is to analyze the effect of polymorphism on liver function after once-daily tacrolimus conversion in liver transplant patients. A prospective open-label study included 60 stable liver transplant recipients who underwent 1:1 conversion from twice-daily tacrolimus to once-daily tacrolimus.

Role of Interleukin 17A in Aortic Valve Inflammation in Apolipoprotein E-deficient Mice.

Interleukin 17A (IL17A) is reported to be involved in many inflammatory processes, but its role in aortic valve diseases remains unknown. We examined the role of IL17A based on an ApoE mouse model with strategies as fed with high-fat diet or treated with IL17A monoclonal antibody (mAb). 12 weeks of high-fat diet feeding can elevate cytokines secretion, inflammatory cells infiltration and myofibroblastic transition of valvular interstitial cells (VICs) in aortic valve.

Identification and Genotyping of Transposable Element Insertions From Genome Sequencing Data.

Transposable element (TE) mobilization is a significant source of genomic variation and has been associated with various human diseases. The exponential growth of population-scale whole-genome sequencing and rapid innovations in long-read sequencing technologies provide unprecedented opportunities to study TE insertions and their functional impact in human health and disease. Identifying TE insertions, however, is challenging due to the repetitive nature of the TE sequences.

Deposition of Durable Micro Copper Patterns into Glass by Combining Laser-Induced Backside Wet Etching and Laser-Induced Chemical Liquid Phase Deposition Methods.

Glass is a well-known non-conductive material that has many useful properties, and considerable research has been conducted into making circuits on glass. Many deposition techniques have been studied, and laser-induced chemical liquid phase deposition (LCLD) is a well-known and cost-effective method for rapid prototyping of copper deposition on glass. However, the deposition results from the LCLD method on the surface of glass, which shows an issue in its detachment from the substrates because of the relatively low adhesion between deposited copper and the nontreated glass surface.

A Randomized Phase II Study of Perioperative Chemotherapy Plus Bevacizumab Versus Postoperative Chemotherapy Plus Bevacizumab in Patients With Upfront Resectable Hepatic Colorectal Metastases.

Introduction: Whether patients with resectable colorectal liver metastases (CRLM) gain a survival benefit from perioperative chemotherapy remains controversial. The benefit of including bevacizumab in chemotherapy also remains unclear.

Material And Methods: Seventy-six patients with CRLM were randomly assigned to either 6 cycles of FOLFOX (folinic acid, 5-fluorouracil, and oxaliplatin)/FOLFIRI (folinic acid, 5-fluorouracil, and irinotecan) with bevacizumab before and after surgery or 12 cycles after surgery.

HiNT: a computational method for detecting copy number variations and translocations from Hi-C data.

The three-dimensional conformation of a genome can be profiled using Hi-C, a technique that combines chromatin conformation capture with high-throughput sequencing. However, structural variations often yield features that can be mistaken for chromosomal interactions. Here, we describe a computational method HiNT (Hi-C for copy Number variation and Translocation detection), which detects copy number variations and interchromosomal translocations within Hi-C data with breakpoints at single base-pair resolution.

Clinical outcomes of transcatheter versus surgical pulmonary valve replacement: a meta-analysis.

Background: Transcatheter pulmonary valve replacement (TPVR) has currently been a well-established alternative operation method to surgical pulmonary valve replacement (SPVR) in patients with pulmonary valve dysfunction in the form of stenosis and/or regurgitation. We conducted a meta-analysis to evaluate the main clinical outcomes after TPVR and SPVR.

Methods: We systematically searched the references of relevant literatures from PubMed and the Cochrane Library published between January 2000 and December 2018 and followed The Preferred Reporting Items for Systematic reviews and Meta-analysis (PRISMA) for this study.