Small-RNA sequencing reveals potential serum biomarkers for gallbladder cancer: Results from a three-stage collaborative study of large European prospective cohorts.

Gallbladder cancer (GBC) is an aggressive disease with limited treatment options but high prevention potential. GBC tumours take 10-20 years to develop, a timeframe that holds potential for early detection. MicroRNAs (miRNAs) play a central role in abnormal cell processes, and circulating miRNAs may constitute valuable biomarkers of early disease.

Gut Microbial Utilization of the Alternative Sweetener, D-Allulose, via AlsE.

D-allulose, a rare sugar with emerging potential as a low-calorie sweetener, has garnered attention as an alternative to other commercially available alternative sweeteners, such as sugar alcohols, which often cause severe gastrointestinal discomfort. D-allulose-6-phosphate 3-epimerase (AlsE) is a prokaryotic enzyme that converts D-allulose-6-phosphate into D-fructose-6-phopshate, enabling its use as a carbon source. However, the taxonomic breadth of AlsE across gut bacteria remains poorly understood, hindering insights into the utilization of D-allulose by microbial communities.

RummaGEO: Automatic mining of human and mouse gene sets from GEO.

The Gene Expression Omnibus (GEO) has millions of samples from thousands of studies. While users of GEO can search the metadata describing studies, there is a need for methods to search GEO at the data level. RummaGEO is a gene expression signature search engine for human and mouse RNA sequencing perturbation studies extracted from GEO.

Protocol for using Multiomics2Targets to identify targets and driver kinases for cancer cohorts profiled with multi-omics assays.

The availability of multi-omics data applied to profile cancer cohorts is rapidly increasing. Here, we present a protocol for Multiomics2Targets, a computational pipeline that can identify driver cell signaling pathways, protein kinases, and cell-surface targets for immunotherapy. We describe steps for preparing the data, uploading files, and tuning parameters.

Harmonizome 3.0: integrated knowledge about genes and proteins from diverse multi-omics resources.

By processing and abstracting diverse omics datasets into associations between genes and their attributes, the Harmonizome database enables researchers to explore and integrate knowledge about human genes from many central omics resources. Here, we introduce Harmonizome 3.0, a significant upgrade to the original Harmonizome database.

Accounting for the impact of genotype and environment on variation in leaf respiration of wheat in Mexico and Australia.

An approach to improving radiation use efficiency (RUE) in wheat is to screen for variability in rates of leaf respiration in darkness (Rdark). We used a high-throughput system to quantify variation in Rdark among a diverse range of spring wheat genotypes (301 lines) grown in two countries (Mexico and Australia) and two seasons (2017 and 2018), and in doing so quantify the relative importance of genotype (G) and environment (E) in influencing variations in leaf Rdark. Through careful design, residual (unexplained) variation represented less than 10% of the total observed.

Gut microbiota diversity is prognostic and associated with benefit from chemo-immunotherapy in metastatic triple-negative breast cancer.

The gut microbiota influences multiple aspects of human health and disease. Several studies have indicated an association between the gut microbiota and response to immune checkpoint inhibitors in various cancers, but there is scarce data from breast cancer. The randomized ALICE trial demonstrated improved progression-free survival (PFS) from adding the programmed cell death 1 ligand 1 (PD-L1) inhibitor atezolizumab (atezo) to immunomodulating chemotherapy (chemo) in metastatic triple-negative breast cancer (mTNBC), even for PD-L1 disease.

Plasmodium vivax antigen candidate prediction improves with the addition of Plasmodium falciparum data.

Intensive malaria control and elimination efforts have led to substantial reductions in malaria incidence over the past two decades. However, the reduction in Plasmodium falciparum malaria cases has led to a species shift in some geographic areas, with P. vivax predominating in many areas outside of Africa.

Computational-driven discovery of AI-2 quorum sensing inhibitor targeting the 5'- methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) to combat drug-resistant Helicobacter pylori.

MTAN is an attainable therapeutic target for H. pylori because it may minimize virulence production, limit resistance, and impair quorum sensing without affecting gut flora. Here, 457 compounds with anti-H.

A diverse hidradenitis suppurativa cohort: A retrospective cross-sectional study of 13,130 patients from a large US health care system database from 1995 to 2022.

Background: Most epidemiological studies of hidradenitis suppurativa (HS) have described homogeneous patient populations.

Objective: To characterize demographics, modifiable health behaviors, and comorbidities of HS patients within a diverse cohort.

Methods: A retrospective cross-sectional study of 13,130 HS patients within a health care system was conducted.

Predictive and prognostic value of excision repair cross-complementing group 1 in patients with advanced gastric cancer.

Background: To define the optimal chemotherapy regimen for each patient we therefore used tissue from patients to identify molecular prognostic or predictive biomarkers.

Methods: Endoscopic biopsy specimens from primary lesions and surgical specimens on a phase III trial in patients with unresectable advanced or recurrent gastric cancer treated with docetaxel with cisplatin plus S-1 (DCS) or cisplatin plus S-1 (CS), were collected. We measured the mRNA expression of ERCC1 and analyzed SNPs in GSTP1 and ERCC1.

Alteration of methylation pattern and gene expression of FTO, PPARγ and Slc2a4 on pre-diabetes-induced BALB/c mice.

T2DM is a serious global health problem and usually caused by unhealthy diet, such diet with high carbohydrate or monosodium glutamate (MSG). In this study, we used the T2DM mice (BALB/c) model by exposing the mice with foods high in carbohydrate (HCD) or MSG (HMD) to determine the changes in molecular expression and methylation pattern of genes correlated to the development of T2DM. The data including clinical data, i.

The backpropagation algorithm implemented on spiking neuromorphic hardware.

The capabilities of natural neural systems have inspired both new generations of machine learning algorithms as well as neuromorphic, very large-scale integrated circuits capable of fast, low-power information processing. However, it has been argued that most modern machine learning algorithms are not neurophysiologically plausible. In particular, the workhorse of modern deep learning, the backpropagation algorithm, has proven difficult to translate to neuromorphic hardware.

Genomic insights into key mechanisms for carbon, nitrogen, and phosphate assimilation by the acidophilic, halotolerant genus Acidihalobacter members.

In-depth comparative genomic analysis was conducted to predict carbon, nitrogen, and phosphate assimilation pathways in the halotolerant, acidophilic genus Acidihalobacter. The study primarily aimed to understand how the metabolic capabilities of each species can determine their roles and effects on the microbial ecology of their unique saline and acidic environments, as well as in their potential application to saline water bioleaching systems. All four genomes encoded the genes for the complete tricarboxylic acid cycle, including 2-oxoglutarate dehydrogenase, a key enzyme absent in obligate chemolithotrophic acidophiles.

The role of astrocytes in depression, its prevention, and treatment by targeting astroglial gliotransmitter release.

The role of ventral hippocampus (vHipp) astroglial gliotransmission in depression was studied using chronic restraint stress (CRS) and chronic unpredictable mild stress (CUMS) rodent models. CRS increased Cx43 hemichannel activity and extracellular glutamate levels in the vHipp and blocking astroglial Cx43 hemichannel-dependent gliotransmission during CRS prevented the development of depression and glutamate buildup. Moreover, the acute blockade of Cx43 hemichannels induced antidepressant effects in rats previously subjected to CRS or CUMS.

BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes.

Secondary metabolites are compounds not essential for an organism's development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis.

Improving the suppressive power of homing gene drive by co-targeting a distant-site female fertility gene.

Gene drive technology has the potential to address major biological challenges. Well-studied homing suppression drives have been shown to be highly efficient in Anopheles mosquitoes, but for other organisms, lower rates of drive conversion prevent elimination of the target population. To tackle this issue, we propose a gene drive design that has two targets: a drive homing site where drive conversion takes place, and a distant site where cleavage induces population suppression.