Hordeum I genome unlocks adaptive evolution and genetic potential for crop improvement.

Crop wild relatives (CWRs) are invaluable for crop improvement. Among these, Hordeum I-genome species exhibit exceptional tolerance to alkali and salt stresses. Here we present a chromosome-scale genome assembly of Hordeum brevisubulatum (II, 2n = 2x =14) and genome resequencing of 38 diploid germplasms spanning 7 I-genome species.

A study on the impact of meteorological and emission factors on PM concentrations based on machine learning.

PM pollution, a major environmental and health concern, is influenced by a complex interplay of emission sources and meteorological conditions. Accurately identifying these factors and their contributions is essential for effective pollution management. This study applies Positive Matrix Factorization (PMF) to identify primary sources of PM and uses the Light Gradient Boosting Machine (LightGBM) model, SHapley Additive exPlanations (SHAP), and Partial Dependence Plots (PDP) to quantitatively assess the impact of meteorological and emission factors on PM concentrations.

Effect of perceived stress on psychological distress in hepatocellular carcinoma patients undergoing TACE: the mediating role of experiential avoidance and the moderating role of trait mindfulness.

Objective: The aim of this study was to explore the moderated mediation mechanism of the relationships among perceived stress, psychological distress, experiential avoidance and trait mindfulness of hepatocellular carcinoma (HCC) patients after transarterial chemoembolization (TACE) in China.

Methods: This study utilized a cross-sectional approach to gather data from 458 HCC patients undergoing TACE. Participants completed self-report measures assessing psychological distress, perceived stress, experiential avoidance and trait mindfulness.

A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity.

A pan-transcriptome describes the transcriptional and post-transcriptional consequences of genome diversity from multiple individuals within a species. We developed a barley pan-transcriptome using 20 inbred genotypes representing domesticated barley diversity by generating and analyzing short- and long-read RNA-sequencing datasets from multiple tissues. To overcome single reference bias in transcript quantification, we constructed genotype-specific reference transcript datasets (RTDs) and integrated these into a linear pan-genome framework to create a pan-RTD, allowing transcript categorization as core, shell or cloud.

The allelic mutation of NBS-LRR gene causes premature senescence in wheat.

Premature senescence has a significant impact on the yield and quality of wheat crops. The process is controlled by multiple and intricate genetic pathways and regulatory elements, whereby the discovery of additional mutants provides important insights into the molecular basis of this important trait. Here, we developed a premature senescence wheat mutant je0874, its leaves started to show yellow before heading stage; with plant growth and development, the degree of yellowing worsened rapidly, and chlorophyll content in flag leaf was reduced by 93.

Association between urinary phthalate metabolites and sarcopenia in US adults from NHANES 2011-2018.

Background: Phthalates, widely used as chemical additives, are often found as mixtures in the environment. However, the combined impact of phthalate exposure on sarcopenia remains unclear.

Objective: This study aimed to investigate the relationships between phthalates and sarcopenia in adults.

Corrigendum: Advances in understanding the regulation of pluripotency fate transition in embryonic stem cells.

[This corrects the article DOI: 10.3389/fcell.2024.

Biomechanical differences of Asian knee osteoarthritis patients during standing and walking using statistical parametric mapping: A cross-sectional study.

Background: Biomechanics of knee osteoarthritis (KOA) patients have been extensively studied using motion capture systems, but less have explored standing knee joint angles with the walking parameters, particularly in Asians. We aim to determine gait biomechanical differences between healthy and KOA participants in an Asian population using One-dimensional Statistical Parametric Mapping (SPM1D) and explore if they are associated with standing joint angles.

Methods: A total of 20 KOA and 24 healthy stood upright and walked 10 m at self-selected speeds.

Pangenome and pantranscriptome as the new reference for gene-family characterization: A case study of basic helix-loop-helix (bHLH) genes in barley.

Genome-wide identification and comparative gene-family analyses have commonly been performed to investigate species-specific evolution linked to various traits and molecular pathways. However, most previous studies have been limited to gene screening in a single reference genome, failing to account for the gene presence/absence variations (gPAVs) in a species. Here, we propose an innovative pangenome-based approach for gene-family analyses based on orthologous gene groups (OGGs).

Advances in understanding the regulation of pluripotency fate transition in embryonic stem cells.

Embryonic stem cells (ESCs) sourced from the inner cell mass of blastocysts, are akin to this tissue in function but lack the capacity to form all extraembryonic structures. mESCs are transient cell populations that express high levels of transcripts characteristic of 2-cell (2C) embryos and are identified as "2-cell-like cells" (2CLCs). Previous studies have shown that 2CLCs can contribute to both embryonic and extraembryonic tissues upon reintroduction into early embryos.

Cathepsin C Promotes Tumorigenesis in Bladder Cancer by Activating the Wnt/β-catenin Signalling Pathway.

Background: Cathepsin C (CTSC) participates in the development of numerous cancers; however, its function in bladder cancer (BCa) remains largely unknown.

Methods: Bioinformatics prediction, quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay, and Western blot assay were used to determine CTSC expression in BCa tissues, paracancer tissues, BCa cells, and normal uroepithelial cells (SV-HUC-1). Colony formation, cell counting kit-8 (CCK-8), and Transwell assays were utilised to ascertain the involvement of CTSC in BCa.

The effectiveness of an exergame intervention for college students with subthreshold depression: protocol for a mixed methods study.

Background: Subthreshold depression (StD) is a condition that significantly influences the mental health and quality of life of college students and increases the risk of developing major depressive disorder (MDD). Exercise therapy has been found to be effective, but may not be enjoyable for everyone. exergames, as a form of exercise therapy, address the limitations of traditional exercise by incorporating gaming elements to make physical activity more entertaining and interactive.

SPI1-mediated transcriptional activation of CEP55 promotes the malignant growth of triple-negative breast cancer and M2 macrophage polarization.

Background: Triple-negative breast cancer (TNBC) is a subtype of breast cancer that lacks the expression of three receptors commonly targeted in breast cancer treatment. In this study, the research focused on investigating the role of centrosomal protein 55 (CEP55) in TNBC progression and its interaction with the transcription factor Spi-1 proto-oncogene (SPI1).

Methods: Various techniques including qRT-PCR, western blotting, and immunohistochemistry assays were utilized to examine gene expression patterns.

Increased expression of SLC25A18 is associated with Alzheimer's disease and is involved in Aβ42-induced mitochondrial dysfunction and apoptosis in neuronal cells.

Alzheimer's disease (AD) is currently one of the most serious public health concerns in the world. However, the best approach to treat AD has yet to be discovered, implying that we must continue to work hard to find new AD target genes. In this study, we further analysed Gene Expression Omnibus (GEO) data and discovered that the expression of the Mitochondria glutamate carrier SLC25A18 is associated with AD by screening the differentially expressed genes in different regions of the brains of Alzheimer's disease patients.

Malignant Gastrointestinal Neuroectodermal Tumor (GNET) Mimicking Small Bowel Lymphoma: A Case Report.

A malignant gastrointestinal neuroectodermal tumor (GNET) is a rare entity, characterized as a malignant mesenchymal neoplasm occurring exclusively near the gastrointestinal tract, prone to frequent local recurrence and metastasis. Here, we report a case of a 49-year-old male presented with abdominal pain and weight loss. The patient had a remote history of thymic B-cell lymphoma.

Drug target prediction through deep learning functional representation of gene signatures.

Many machine learning applications in bioinformatics currently rely on matching gene identities when analyzing input gene signatures and fail to take advantage of preexisting knowledge about gene functions. To further enable comparative analysis of OMICS datasets, including target deconvolution and mechanism of action studies, we develop an approach that represents gene signatures projected onto their biological functions, instead of their identities, similar to how the word2vec technique works in natural language processing. We develop the Functional Representation of Gene Signatures (FRoGS) approach by training a deep learning model and demonstrate that its application to the Broad Institute's L1000 datasets results in more effective compound-target predictions than models based on gene identities alone.