Examining HPO by organ and system to facilitate practical use by clinicians.

The Human Phenotype Ontology (HPO) is widely used for annotating clinical text data, and sufficient annotation is crucial for the effective utilization of clinical texts. It was known that the use of LLMs can successfully extract symptoms and findings, but cannot annotate them with the HPO. We hypothesized that one of the potential issue for this is the lack of appropriate terms in the HPO.

TRIM32 inhibits Venezuelan equine encephalitis virus infection by targeting a late step in viral entry.

Alphaviruses are mosquito borne RNA viruses that are a reemerging public health threat. Alphaviruses have a broad host range, and can cause diverse disease outcomes like arthritis, and encephalitis. The host ubiquitin proteasome system (UPS) plays critical roles in regulating cellular processes to control the infections with various viruses, including alphaviruses.

jPOST environment accelerates the reuse and reanalysis of public proteome mass spectrometry data.

jPOST (https://jpostdb.org/) comprises jPOSTrepo (https://repository.jpostdb.

The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF.

Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that are used for further downstream analysis of new spectra. There are many different formats used for encoding spectral libraries, but none have undergone a standardization process to ensure broad applicability to many applications. As part of the Human Proteome Organization Proteomics Standards Initiative (PSI), we have developed a standardized format for encoding spectral libraries, called mzSpecLib (https://psidev.

Berberine promotes K-linked polyubiquitination of HNF4α, leading to the inhibition of HBV replication.

The current antiviral agents for the treatment of chronic infection with hepatitis B virus (HBV) do not completely remove covalently closed circular DNA (cccDNA) and integrated viral DNA fragments from patients. Berberine is an isoquinoline alkaloid extracted from various plants and has been reported to inhibit the replication of various types of DNA. In this study, we tested the effects of berberine and its derivatives on HBV infection.

Customizing GPT for natural language dialogue interface in database access.

The paper presents Anatomy3DExplorer, a customized ChatGPT designed as a natural language dialogue interface for exploring 3D models of anatomical structures. It illustrates the significant potential of large language models (LLMs) as user-friendly interfaces for database access. Furthermore, it showcases the seamless integration of LLMs and database APIs, within the GPTS framework, offering a promising and straightforward approach.

CAMSAP3 forms dimers via its α-helix domain that directly stabilize non-centrosomal microtubule minus ends.

Microtubules are vital components of the cytoskeleton. Their plus ends are dynamic and respond to changes in cell morphology, whereas the minus ends are stable and serve a crucial role in microtubule seeding and maintaining spatial organization. In mammalian cells, the calmodulin-regulated spectrin-associated proteins (CAMSAPs), play a key role in directly regulating the dynamics of non-centrosomal microtubules minus ends.

Mitogen-activated protein kinase 4 phosphorylates MYC2 transcription factors to regulate jasmonic acid signaling and herbivory responses in maize.

Regulation of responses induced by herbivory and jasmonic acid (JA) remains poorly understood in the important staple crop maize (Zea mays). MYC2 is the key transcription factor regulating many aspects of JA signaling, while mitogen-activated protein kinases (MAPKs or MPKs) play important roles in various plant physiological processes. Using a combination of reverse genetics, transcriptome analysis, and biochemical assays, we elucidated the important role of mitogen-activated protein kinase 4 (MPK4) in maize resistance to insects and in JA signaling.

Gentle Rhodamines for Live-Cell Fluorescence Microscopy.

Rhodamines have been continuously optimized in brightness, biocompatibility, and color to fulfill the demands of modern bioimaging. However, the problem of phototoxicity caused by the excited fluorophore under long-term illumination has been largely neglected, hampering their use in time-lapse imaging. Here we introduce cyclooctatetraene (COT) conjugated rhodamines that span the visible spectrum and exhibit significantly reduced phototoxicity.

Transcytosable and Ultrasound-Activated Liposome Enables Deep Penetration of Biofilm for Surgical Site Infection Management.

Biofilm-associated surgical site infection (BSSI) is a common and grievous postoperative complication lacking effective remedies, mainly due to the poor drug accumulation and penetration in the biofilms featured by dense extracellular polymeric substances (EPSs). Here, it is found that the vascular cell adhesion molecule-1 (VCAM1) is highly overexpressed in the vascular cells of BSSI. It is proposed that the combination of VCAM1-mediated transcytosis and ultrasonic cavitation can consecutively overcome the biological barriers of vascular endothelial cells and EPS for biofilm eradication.

Novel Vibrational Proteins.

Genetically encoded green fluorescent protein (GFP) and its brighter and redder variants have tremendously revolutionized modern molecular biology and life science by enabling direct visualization of gene regulated protein functions on microscopic and nanoscopic scales. However, the current fluorescent proteins (FPs) only emit a few colors with an emission width of about 30-50 nm. Here, we engineer novel vibrational proteins (VPs) that undergo much finer vibrational transitions and emit rather narrow vibrational spectra (0.

Insights into the distinct membrane targeting mechanisms of WDR91 family proteins.

WDR91 and SORF1, members of the WD repeat-containing protein 91 family, control phosphoinositide conversion by inhibiting phosphatidylinositol 3-kinase activity on endosomes, which promotes endosome maturation. Here, we report the crystal structure of the human WDR91 WD40 domain complexed with Rab7 that has an unusual interface at the C-terminus of the Rab7 switch II region. WDR91 is highly selective for Rab7 among the tested GTPases.

Endogenous Magnetic Lipid Droplet-Mediated Cascade-Targeted Sonodynamic Therapy as an Approach to Reversing Breast Cancer Multidrug Resistance.

Multidrug resistance (MDR) has emerged as a major barrier to effective breast cancer treatment, contributing to high rates of chemotherapy failure and disease recurrence. There is thus a pressing need to overcome MDR and to facilitate the efficient and precise treatment of breast cancer in a targeted manner. In this study, endogenous functional lipid droplets (IR780@LDs-FeO/OA) were developed and used to effectively overcome the limited diffusion distance of reactive oxygen species owing to their amenability to cascade-targeted delivery, thereby facilitating precise and effective sonodynamic therapy (SDT) for MDR breast cancer.

Systematic optimization of UCNPs-LFA for Helicobacter pylori nucleic acid detection at point-of-care.

Helicobacter pylori (Hp) prevail globally as the primary cause of gastritis, gastric ulcer, and potential gastric cancer, highlighting the need for rapid and precise point-of-care (POC) detection of Hp nucleic acid. Upconversion nanoparticle-based lateral flow assay (UCNPs-LFA) exhibit great potential in POC detection, due to their high optical stability and absence of background fluorescence. However, insufficient sensitivity for nucleic acid detection remains a key challenge.

Recent trends in edible algae functional proteins: Production, bio-functional properties, and sustainable food packaging applications.

In recent years, there has been a notable surge in the development and adoption of edible algae protein-based sustainable food packaging, which presents a promising alternative to traditional materials due to its biodegradability, renewability, and minimal environmental impact. Hence, this review aims to emphasize the sources, cultivation, and downstream potential of algal protein and protein complexes. Moreover, it comprehensively examines the advancements in utilizing protein complexes for smart and active packaging applications, while also addressing the challenges that must be overcome for the widespread commercial adoption of algal proteins to meet industry 4.

Long-Term Survival and Immune Reconstitution of Donor-Derived Chimeric Antigen Receptor T-Cell Therapy for Childhood Molecular Relapse of B-Cell Acute Lymphoblastic Leukemia After Allogeneic Hematopoietic Stem Cell Transplantation.

Measurable residual disease (MRD) after allogeneic hematopoietic stem cell transplantation (allo-HSCT) is an independent risk factor for relapse in patients with acute lymphoblastic leukemia (ALL). This study aimed to assess the efficacy, safety, and immune reconstitution of chimeric antigen receptor T-cell (CAR-T) therapy in patients with molecular relapse after allo-HSCT. Eleven patients with molecular relapse of B-cell-ALL who underwent CAR-T therapy after allo-HSCT were enrolled.

Biodegradation of DDT using multi-species mixtures: From genome-mining prediction to practical assessment.

DDT (dichlorodiphenyltrichloroethane) is a commonly used insecticide that is recalcitrant and highly stable in the environment. Currently, DDT residue contamination, especially in agricultural soil, is still a concern in many countries, threatening human health and the environment. Among the approaches to resolve such an issue, novel biodegradation-based methods are now preferred to physicochemical methods, due to the sustainability and the effectiveness of the former.