Development and validation of an explainable model of brain injury in premature infants: A prospective cohort study.

Background: Preterm brain injury (PBI) is a prevalent complication in preterm infants, leading to the destruction of critical structural and functional brain connections and placing a significant burden on families. The timely detection of PBI is of paramount importance for the prevention and treatment of the condition. However, the absence of specific clinical manifestations in the early stages of PBI renders it susceptible to misdiagnosis and missed diagnoses.

Discovery of Small Molecule Inhibitors Targeting CTNNB1 (β-catenin) for Endometrial cancer: Employing 3D QSAR, Drug-Likeness Assessment, ADMET Predictions, Molecular Docking and Simulation.

Background: Endometrial carcinoma (EC) is a type of cancer that originates in the lining of the uterus, known as the endometrium. It is associated with various treatment options such as surgery, radiation therapy, chemotherapy, and hormone therapy, each presenting unique challenges and limitations. Beta-catenin, a protein involved in the development and progression of several cancers, including EC, plays a crucial role.

MvMRL: a multi-view molecular representation learning method for molecular property prediction.

Effective molecular representation learning is very important for Artificial Intelligence-driven Drug Design because it affects the accuracy and efficiency of molecular property prediction and other molecular modeling relevant tasks. However, previous molecular representation learning studies often suffer from limitations, such as over-reliance on a single molecular representation, failure to fully capture both local and global information in molecular structure, and ineffective integration of multiscale features from different molecular representations. These limitations restrict the complete and accurate representation of molecular structure and properties, ultimately impacting the accuracy of predicting molecular properties.

Role of small molecules as drug candidates for reprogramming somatic cells into induced pluripotent stem cells: A comprehensive review.

With the use of specific genetic factors and recent developments in cellular reprogramming, it is now possible to generate lineage-committed cells or induced pluripotent stem cells (iPSCs) from readily available and common somatic cell types. However, there are still significant doubts regarding the safety and effectiveness of the current genetic methods for reprogramming cells, as well as the conventional culture methods for maintaining stem cells. Small molecules that target specific epigenetic processes, signaling pathways, and other cellular processes can be used as a complementary approach to manipulate cell fate to achieve a desired objective.

Identification of different myofiber types in pigs muscles and construction of regulatory networks.

Background: Skeletal muscle is composed of muscle fibers with different physiological characteristics, which plays an important role in regulating skeletal muscle metabolism, movement and body homeostasis. The type of skeletal muscle fiber directly affects meat quality. However, the transcriptome and gene interactions between different types of muscle fibers are not well understood.

PLZF protein forms a complex with protein TET1 to target TCF7L2 in undifferentiated spermatogonia.

The transcription factor promyelocytic leukemia zinc finger (PLZF, also known as ZBTB16) is critical for the self-renewal of spermatogonial stem cells (SSCs). However, the function of PLZF in SSCs is not clear. Here, we found that PLZF acted as an epigenetic regulator of stem cell maintenance and self-renewal of germ cells.

Rapid conversion of porcine pluripotent stem cells into macrophages with chemically defined conditions.

A renewable source of porcine macrophages derived from pluripotent stem cells (PSCs) would be a valuable alternative to primary porcine alveolar macrophages (PAMs) in the research of host-pathogen interaction mechanisms. We developed an efficient and rapid protocol, within 11 days, to derive macrophages from porcine PSCs (pPSCs). The pPSC-derived macrophages (pPSCdMs) exhibited molecular and functional characteristics of primary macrophages.

Unveiling the multi-target compounds of Rhazya stricta: Discovery and inhibition of novel target genes for the treatment of clear cell renal cell carcinoma.

Clear cell renal cell carcinoma (ccRCC) is a prevalent kidney malignancy with a pressing need for innovative therapeutic strategies. In this context, emerging research has focused on exploring the medicinal potential of plants such as Rhazya stricta. Nevertheless, the complex molecular mechanisms underlying its potential therapeutic efficacy remain largely elusive.

Integrated analysis of the ubiquitination mechanism reveals the specific signatures of tissue and cancer.

Background: Ubiquitination controls almost all cellular processes. The dysregulation of ubiquitination signals is closely associated with the initiation and progression of multiple diseases. However, there is little comprehensive research on the interaction and potential function of ubiquitination regulators (UBRs) in spermatogenesis and cancer.

SCM is potential resource for non-invasive preimplantation genetic testing based on human embryos single-cell sequencing.

The ongoing development of assisted reproductive technologies has provided hope to individuals struggling with infertility, promising the potential for a healthy pregnancy. One significant innovation in field of pre-implantation genetic screening (PGS) requires the biopsy of embryos or oocytes, which has potential implications for the health and development of the resultant offspring. Therefore, a non-invasive approach to preimplantation genetic screening is highly sought after.

Identification of molecular mechanisms underlying the therapeutic effects of Celosia Cristata on immunoglobulin nephropathy.

Immunoglobulin A (IgA) nephropathy also known as Berger's disease, is a silent monster and perhaps the most prevalent glomerulonephritis that often accounts for end-stage kidney failure, thereby signifying a growing public health problem worldwide. The limited amount of available data and a broad spectrum of dysregulated physiological processes of IgAN make it a challenging task and a disproportionate economic load on the community health sector. Celosia cristata is an Amaranthaceous plant with attractive colorful inflorescences that are used in various regions of earth for the treatment of numerous ailments.

Super-enhancers conserved within placental mammals maintain stem cell pluripotency.

Despite pluripotent stem cells sharing key transcription factors, their maintenance involves distinct genetic inputs. Emerging evidence suggests that super-enhancers (SEs) can function as master regulatory hubs to control cell identity and pluripotency in humans and mice. However, whether pluripotency-associated SEs share an evolutionary origin in mammals remains elusive.

EPI-Mind: Identifying Enhancer-Promoter Interactions Based on Transformer Mechanism.

Motivation: Enhancer-Promoter Interactions (EPIs) is an essential step in the gene regulation process. However, the detection of EPIs by traditional wet experimental techniques is time-consuming and expensive. Thus, computational methods would be very useful for understanding the mechanism of EPIs.

Comprehensive comparison of two types of algorithm for circRNA detection from short-read RNA-Seq.

Motivation: Circular RNA is generally formed by the 'back-splicing' process between the upstream splice acceptor and the downstream donor in/not in the regulation of the corresponding RNA-binding proteins or cis-elements. Therefore, more and more software packages have been developed and they are mostly based on the identification of the back-spliced junction reads. However, recent studies developed two software tools that can detect circRNA candidates by constructing k-mer table or/and de Bruijn graph rather than reads mapping.

Single-cell transcriptome analysis of Bisphenol A exposure reveals the key roles of the testicular microenvironment in male reproduction.

Testicular development during juvenile is crucial for subsequent male reproductive function. However, it remains poorly understood about the contribution of the testis microenvironment to human germ cell maturation. Therefore, we systematically analyzed scRNA-seq transcriptome and found the dramatic changes in cell-type composition in human testis during puberty.

Ten Years of EWAS.

Epigenome-wide association study (EWAS) has been applied to analyze DNA methylation variation in complex diseases for a decade, and epigenome as a research target has gradually become a hot topic of current studies. The DNA methylation microarrays, next-generation, and third-generation sequencing technologies have prepared a high-quality platform for EWAS. Here, the progress of EWAS research is reviewed, its contributions to clinical applications, and mainly describe the achievements of four typical diseases.

Persulfidation-induced structural change in SnRK2.6 establishes intramolecular interaction between phosphorylation and persulfidation.

Post-translational modifications (PTMs), including phosphorylation and persulfidation, regulate the activity of SNF1-RELATED PROTEIN KINASE2.6 (SnRK2.6).

Single-cell RNA sequencing reveals atlas of dairy goat testis cells.

Single-cell RNA sequencing (scRNA-seq) is useful for exploring cell heterogeneity. For large animals, however, little is known regarding spermatogonial stem cell (SSC) self-renewal regulation, especially in dairy goats. In this study, we described a high-resolution scRNA-seq atlas derived from a dairy goat.

Histone demethylase complexes KDM3A and KDM3B cooperate with OCT4/SOX2 to define a pluripotency gene regulatory network.

The pluripotency gene regulatory network of porcine induced pluripotent stem cells(piPSCs), especially in epigenetics, remains elusive. To determine the biological function of epigenetics, we cultured piPSCs in different culture conditions. We found that activation of pluripotent gene- and pluripotency-related pathways requires the erasure of H3K9 methylation modification which was further influenced by mouse embryonic fibroblast (MEF) served feeder.

inhibits family phosphatases and activates MAPK signaling pathway to maintain pluripotency in porcine induced pluripotent stem cells.

LIN28A, an RNA-binding protein, plays an important role in porcine induced pluripotent stem cells (piPSCs). However, the molecular mechanism underlying the function of in the maintenance of pluripotency in piPSCs remains unclear. Here, we explored the function of in piPSCs based on its overexpression and knockdown.

FifBase: a comprehensive fertility-associated indicators factor database for domestic animals.

Fertility refers to the ability of animals to maintain reproductive function and give birth to offspring, which is an important indicator to measure the productivity of animals. Fertility is affected by many factors, among which environmental factors may also play key roles. During the past years, substantial research studies have been conducted to detect the factors related to fecundity, including genetic factors and environmental factors.

Dmrt1 regulates the immune response by repressing the TLR4 signaling pathway in goat male germline stem cells.

Double sex and mab-3-related transcription factor 1 (Dmrt1), which is expressed in goat male germline stem cells (mGSCs) and Sertoli cells, is one of the most conserved transcription factors involved in sex determination. In this study, we highlighted the role of Dmrt1 in balancing the innate immune response in goat mGSCs. Dmrt1 recruited promyelocytic leukemia zinc finger (Plzf), also known as zinc finger and BTB domain-containing protein 16 (Zbtb16), to repress the Toll-like receptor 4 (TLR4)-dependent inflammatory signaling pathway and nuclear factor (NF)-κB.