GGN-GO: geometric graph networks for predicting protein function by multi-scale structure features.

Recent advances in high-throughput sequencing have led to an explosion of genomic and transcriptomic data, offering a wealth of protein sequence information. However, the functions of most proteins remain unannotated. Traditional experimental methods for annotation of protein functions are costly and time-consuming.

Deletion variants calling in third-generation sequencing data based on a dual-attention mechanism.

Deletion is a crucial type of genomic structural variation and is associated with numerous genetic diseases. The advent of third-generation sequencing technology has facilitated the analysis of complex genomic structures and the elucidation of the mechanisms underlying phenotypic changes and disease onset due to genomic variants. Importantly, it has introduced innovative perspectives for deletion variants calling.

ViroISDC: a method for calling integration sites of hepatitis B virus based on feature encoding.

Background: Hepatitis B virus (HBV) integrates into human chromosomes and can lead to genomic instability and hepatocarcinogenesis. Current tools for HBV integration site detection lack accuracy and stability.

Results: This study proposes a deep learning-based method, named ViroISDC, for detecting integration sites.

scIALM: A method for sparse scRNA-seq expression matrix imputation using the Inexact Augmented Lagrange Multiplier with low error.

Single-cell RNA sequencing (scRNA-seq) is a high-throughput sequencing technology that quantifies gene expression profiles of specific cell populations at the single-cell level, providing a foundation for studying cellular heterogeneity and patient pathological characteristics. It is effective for developmental, fertility, and disease studies. However, the cell-gene expression matrix of single-cell sequencing data is often sparse and contains numerous zero values.

Preparation and Properties of Starch-Cellulose Composite Aerogel.

In this study, we conducted research on the preparation of aerogels using cellulose and starch as the primary materials, with the addition of N,N'-methylenebisacrylamide (MBA) as a cross-linking agent. The chemical, morphological and textural characteristics of the aerogels were found to be influenced by the proportions of cellulose, starch, and cross-linking agent that were utilized. An increase in the proportion of cellulose led to stronger adsorption forces within the aerogel structure.

Enhancing maize's nitrogen-fixing potential through ZmSBT3, a gene suppressing mucilage secretion.

Maize (Zea mays) requires substantial amounts of nitrogen, posing a challenge for its cultivation. Recent work discovered that some ancient Mexican maize landraces harbored diazotrophic bacteria in mucilage secreted by their aerial roots. To see if this trait is retained in modern maize, we conducted a field study of aerial root mucilage (ARM) in 258 inbred lines.

Harnessing ultrasound in photocatalysis: Synthesis and piezo-enhanced effect: A review.

The photocatalytic technique has drawn far-ranging interests in addressing the current issues; however, its property suffers from the limited visible light response and rapid recombination of carriers. To address these issues, two specific approaches have been proposed to enhance the photocatalytic activity: (1) ultrasound-assisted synthesis has been utilized to prepare photocatalysts, resulting in refined grain size, increased specific surface area, and reduced photogenerated carrier recombination; (2) sonophotocatalysis and piezoelectric enhanced photocatalysis have been developed to accelerate the reaction, which utilizes the synergism between ultrasound and light. On one side, sonophotocatalysis generates cavitation bubbles which induce more reactive radicals for redox reactions.

CTCs Detection and Whole-exome Sequencing Might Be Used to Differentiate Benign and Malignant Pulmonary Nodules.

Background: Low-density computed tomography (LDCT) improved early lung cancer diagnosis but introduces an excess of false-positive pulmonary nodules data. Hence, accurate diagnosis of early-stage lung cancer remains challenging. The purpose of the study was to assess the feasibility of using circulating tumour cells (CTCs) to differentiate malignant from benign pulmonary nodules.

Predictive Factors of Menstrual Recovery After Laparoscopic Sleeve Gastrectomy in Polycystic Ovary Syndrome Women with Obesity.

Objective: To explore the predictors of menstrual recovery in polycystic ovary syndrome (PCOS) women with obesity following laparoscopic sleeve gastrectomy (LSG).

Methods: A total of 88 PCOS patients with obesity and 76 control patients with obesity aged 18-45 years were enrolled between May 2013 and December 2020. PCOS was diagnosed using the Rotterdam diagnostic criteria (2003).

Myeloid FoxO1 depletion attenuates hepatic inflammation and prevents nonalcoholic steatohepatitis.

Hepatic inflammation is culpable for the evolution of asymptomatic steatosis to nonalcoholic steatohepatitis (NASH). Hepatic inflammation results from abnormal macrophage activation. We found that FoxO1 links overnutrition to hepatic inflammation by regulating macrophage polarization and activation.

Redevelopment of urban brownfield sites in China: Motivation, history, policies and improved management.

Rapid urbanisation in China has resulted in an increased demand for land in towns and cities. To upgrade and modernise, China has also moved many major industries from urban centres to less populated areas. With the high economic value of urban land, the transformation and utilisation of brownfield areas have become important economically and socially.

Relationship of Vitamin A and Thyroid Function in Individuals With Obesity and After Laparoscopic Sleeve Gastrectomy.

Unlabelled: Vitamin A deficiency (VAD) occurs in obesity and may be associated with thyroid dysfunction. We aimed to investigate the association of VA with thyroid function in obesity and after laparoscopic sleeve gastrectomy (LSG). Nine hundred and seventy-six obese subjects were enrolled for this study and were divided into VAD, marginal vitamin A deficiency (MVAD), and vitamin A normal (NVA) groups.

An efficient scRNA-seq dropout imputation method using graph attention network.

Background: Single-cell sequencing technology can address the amount of single-cell library data at the same time and display the heterogeneity of different cells. However, analyzing single-cell data is a computationally challenging problem. Because there are low counts in the gene expression region, it has a high chance of recognizing the non-zero entity as zero, which are called dropout events.

The Changes in Body Composition in Obese Patients with Polycystic Ovary Syndrome after Laparoscopic Sleeve Gastrectomy:a 12-Month Follow-up.

Objectives: To investigate the changes in body fat distribution and predicting factors of these changes in polycystic ovary syndrome (PCOS) patients with obesity, after laparoscopic sleeve gastrectomy (LSG).

Methods: This study consecutively enrolled 153 patients with obesity aged 18-45 years (83 with PCOS and 70 control patients) who underwent LSG from May 2013 to September 2020 at the Department of Endocrinology, Shanghai Tenth People's Hospital, with a 12-month follow-up. Dual-energy X-ray absorptiometry (DEXA) was used to assess body fat distribution.

Incidence and Risk Factors of Hypogonadism in Male Patients With Latent Autoimmune Diabetes and Classic Type 2 Diabetes.

Objectives: This study aimed to compare the prevalence of hypogonadism between male patients with latent autoimmune diabetes (LADA) and type 2 diabetes (T2DM) and investigate the risk factors for hypogonadism in these patients.

Methods: This cross-sectional study evaluated 367 male patients with LADA (n=73) and T2DM (n=294) who visited the endocrinology department of Shanghai Tenth People's Hospital between January 2016 and October 2019 for diabetes management. Sex hormones, lipid profiles, sex hormone-binding globulin (SHBG), glycosylated hemoglobin A1c, beta-cell function, uric acid, and osteocalcin were determined in serum samples.

Cnngeno: A high-precision deep learning based strategy for the calling of structural variation genotype.

Genotype plays a significant role in determining characteristics in an organism and genotype calling has been greatly accelerated by sequencing technologies. Furthermore, most parametric statistical models are unable to effectively call genotype, which is influenced by the size of structural variations and the coverage fluctuations of sequencing data. In this study, we propose a new method for calling deletions' genotypes from the next-generation data, called Cnngeno.

Obesity-associated up-regulation of lipocalin 2 protects gastric mucosa cells from apoptotic cell death by reducing endoplasmic reticulum stress.

Gastric mucosal injury is a less well known complication of obesity. Its mechanism remains to be further elucidated. Here, we explored the protective role of lipocalin 2 (LCN2) against endoplasmic reticulum stress and cell apoptosis in gastric mucosa in patients and mice with obesity.

Glucose-Lipid Metabolism in Obesity with Elevated Prolactin Levels and Alteration of Prolactin Levels After Laparoscopic Sleeve Gastrectomy.

Purpose: We investigated the differences in metabolism between obesity with or without increased prolactin (PRL) and the change in PRL after laparoscopic sleeve gastrectomy (LSG).

Methods: Patients were divided into two groups: obesity with normal PRL (NP, n = 123) and high PRL (HP, n = 108). Glucose-lipid metabolism and inflammation were measured.

A review of the application of deep learning in medical image classification and segmentation.

Big medical data mainly include electronic health record data, medical image data, gene information data, etc. Among them, medical image data account for the vast majority of medical data at this stage. How to apply big medical data to clinical practice? This is an issue of great concern to medical and computer researchers, and intelligent imaging and deep learning provide a good answer.

Insulin-Like Growth Factor 1 Related to Chronic Low-Grade Inflammation in Patients with Obesity and Early Change of its Levels After Laparoscopic Sleeve Gastrectomy.

Background: Insulin-like growth factor 1 (IGF1) and insulin-like growth factor binding protein (IGFBP) have an influence on metabolism. However, changes in metabolism after sleeve gastrectomy (SG) are not clearly known. This study investigated the change in IGFBP3 levels in obesity after bariatric surgery.

Depletion of hepatic forkhead box O1 does not affect cholelithiasis in male and female mice.

Cholelithiasis is one of the most prevalent gastroenterological diseases and is characterized by the formation of gallstones in the gallbladder. Both clinical and preclinical data indicate that obesity, along with comorbidity insulin resistance, is a predisposing factor for cholelithiasis. Forkhead box O1 (FoxO1) is a key transcription factor that integrates insulin signaling with hepatic metabolism and becomes deregulated in the insulin-resistant liver, contributing to dyslipidemia in obesity.