Current transcriptome database and biomarker discovery for immunotherapy by immune checkpoint blockade.

Immune checkpoint blockade (ICB) has revolutionized the current immuno-oncology and significantly improved clinical outcome for cancer treatment. Despite the advancement in clinics, only a small subset of patients derives immune response to the ICB therapy. Therefore, a robust predictive biomarker that identifies potential candidate becomes increasingly crucial in delivering this technology to the public.

Machine learning approach identifies inflammatory gene signature for predicting survival outcomes in hepatocellular carcinoma.

Background: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths worldwide, often linked to chronic inflammation. Our study aimed to probe inflammation pathways at the genetic level and pinpoint biomarkers linked to HCC patient survival.

Methods: We analyzed gene transcriptome data from 246 resectable stage I and II HCC patients from The Cancer Genome Atlas (TCGA).

The relationship between dexmedetomidine administration and prognosis in patients with sepsis-induced coagulopathy: a retrospective cohort study.

This study aimed to investigate whether dexmedetomidine provides survival benefit in critically ill patients with sepsis-induced coagulopathy (SIC). Patients with sepsis-induced coagulopathy admitted to the ICU were identified from the Medical Information Marketplace for Intensive Care (MIMIC)-IV database. They were divided into two groups: patients who started dexmedetomidine within 48 h of ICU admission and lasted for more than 4 h and patients who did not receive dexmedetomidine as a control group.

A 52-week follow-up, multi-center, randomized, double-blinded comparison of efficacy and safety of two hyaluronic acid fillers for the treatment of moderate-to-severe nasolabial folds in Chinese population.

Introduction: To investigate the efficacy and safety of Cutegel MAX (Cutegel) in the correction of moderate-to-severe nasolabial folds (NLFS) compared to Restylane (Restylane, control).

Methods: This study was a 52-week, multicenter, randomized, double-blinded, active-controlled clinical trial. Qualified participants with moderate-to-severe NLFs were randomly assigned in a 1:1 ratio to receive Cutegel or Restylane.

A Case of Complex Giant Rhinophyma Treated With Cosmetic Surgery.

Rhinophyma leads to severe facial deformities and significant social pressure for patients. Patients often seek medical intervention due to cosmetic defects and functional impairments, such as nasal congestion and airway collapse. Currently, there are numerous treatment modalities for rhinophyma, each with distinct advantages and disadvantages, leading to a lack of consensus in nasal vegetation management.

Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy.

Facioscapulohumeral muscular dystrophy (FSHD) is linked to abnormal derepression of the transcription activator DUX4. This effect is localized to a low percentage of cells, requiring single-cell analysis. However, single-cell/nucleus RNA-seq cannot fully capture the transcriptome of multinucleated large myotubes.

The effect of justice sensitivity on malevolent creativity: the mediating role of anger and the moderating role of emotion regulation strategies.

Background: the AMORAL model emphasizes the close connection of individuals' belief system and malevolent creativity. Belief in a just world theory (BJW) states that people have a basic need to believe that the world they live in is just, and everyone gets what they deserve. Therefore, justice matters to all people.

Damage sensing through TLR9 Regulates Inflammatory and Antiviral Responses During Influenza Infection.

Host response aimed at eliminating the infecting pathogen, as well as the pathogen itself, can cause tissue injury. Tissue injury leads to the release of a myriad of cellular components including mitochondrial DNA, which the host senses through pattern recognition receptors. How the sensing of tissue injury by the host shapes the anti-pathogen response remains poorly understood.

Measuring the composition of the tumor microenvironment with transcriptome analysis: past, present and future.

Interactions between tumor cells and immune cells in the tumor microenvironment (TME) play a vital role the mechanisms of immune evasion, by which cancer cells escape immune elimination. Thus, the characterization and quantification of different components in the TME is a hot topic in molecular biology and drug discovery. Since the development of transcriptome sequencing in bulk tissue, single cells and spatial dimensions, there are increasing methods emerging to deconvolute and subtype the TME.

New rabies viral resources for multi-scale neural circuit mapping.

Comparisons and linkage between multiple imaging scales are essential for neural circuit connectomics. Here, we report 20 new recombinant rabies virus (RV) vectors that we have developed for multi-scale and multi-modal neural circuit mapping tools. Our new RV tools for mesoscale imaging express a range of improved fluorescent proteins.

Comprehensive analysis of ALG3 in pan-cancer and validation of ALG3 as an onco-immunological biomarker in breast cancer.

ALG3 has significant modulatory function in the process of tumor development. Yet how ALG3 involves in the advancement of different malignancies isn't fully understood. We performed a pan-cancer assessment on ALG3 utilizing datasets from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) to examine its tumor-related roles across malignancies and its link to particular molecules and cells in the tumor microenvironment (TME).

Machine Learning Predicts Oxaliplatin Benefit in Early Colon Cancer.

Purpose: A combination of fluorouracil, leucovorin, and oxaliplatin (FOLFOX) is the standard for adjuvant therapy of resected early-stage colon cancer (CC). Oxaliplatin leads to lasting and disabling neurotoxicity. Reserving the regimen for patients who benefit from oxaliplatin would maximize efficacy and minimize unnecessary adverse side effects.

scGEM: Unveiling the Nested Tree-Structured Gene Co-Expressing Modules in Single Cell Transcriptome Data.

Background: Single-cell transcriptome analysis has fundamentally changed biological research by allowing higher-resolution computational analysis of individual cells and subsets of cell types. However, few methods have met the need to recognize and quantify the underlying cellular programs that determine the specialization and differentiation of the cell types.

Methods: In this study, we present scGEM, a nested tree-structured nonparametric Bayesian model, to reveal the gene co-expression modules (GEMs) reflecting transcriptome processes in single cells.

Amphiregulin couples IL1RL1 regulatory T cells and cancer-associated fibroblasts to impede antitumor immunity.

Regulatory T (T) cells and cancer-associated fibroblasts (CAFs) jointly promote tumor immune tolerance and tumorigenesis. The molecular apparatus that drives T cell and CAF coordination in the tumor microenvironment (TME) remains elusive. Interleukin 33 (IL-33) has been shown to enhance fibrosis and IL1RL1 T cell accumulation during tumorigenesis and tissue repair.

Machine learning in the prediction of post-stroke cognitive impairment: a systematic review and meta-analysis.

Objective: Cognitive impairment is a detrimental complication of stroke that compromises the quality of life of the patients and poses a huge burden on society. Due to the lack of effective early prediction tools in clinical practice, many researchers have introduced machine learning (ML) into the prediction of post-stroke cognitive impairment (PSCI). However, the mathematical models for ML are diverse, and their accuracy remains highly contentious.

Revealing the Impact of Genomic Alterations on Cancer Cell Signaling with an Interpretable Deep Learning Model.

Cancer is a disease of aberrant cellular signaling resulting from somatic genomic alterations (SGAs). Heterogeneous SGA events in tumors lead to tumor-specific signaling system aberrations. We interpret the cancer signaling system as a causal graphical model, where SGAs affect signaling proteins, propagate their effects through signal transduction, and ultimately change gene expression.

An interpretable deep learning framework for genome-informed precision oncology.

Cancers result from aberrations in cellular signaling systems, typically resulting from driver somatic genome alterations (SGAs) in individual tumors. Precision oncology requires understanding the cellular state and selecting medications that induce vulnerability in cancer cells under such conditions. To this end, we developed a computational framework consisting of two components: 1) A representation-learning component, which learns a representation of the cellular signaling systems when perturbed by SGAs, using a biologically-motivated and interpretable deep learning model.

Anatomical organization of temporally correlated neural calcium activity in the hippocampal CA1 region.

Hippocampal CA1 neuronal ensembles generate sequential patterns of firing activity that contribute to episodic memory formation and spatial cognition. Here we used calcium imaging to record neural ensemble activities in mouse hippocampal CA1 and identified CA1 excitatory neuron sub-populations whose members are active across the same second-long period of time. We identified groups of hippocampal neurons sharing temporally correlated neural calcium activity during behavioral exploration and found that they also organized as clusters in anatomical space.

Sauchinone inhibits breast cancer cell proliferation through regulating microRNA-148a-3p/HER-2 axis.

Background: Sauchinone is extracted from the root of Saururus chinensis and exhibits potent antitumor effects in various human cancers. However, how sauchinone is involved in breast cancer has not been well studied.

Methods: Cells apoptosis, cell proliferation, and cycle distribution were evaluated.

Mask-related adverse skin reactions in orientals during COVID-19: Prevalence, social-psychological impacts and risk factors for acne exacerbation.

Background: COVID-19 pandemic has caused mask-related skin problems on health-care professions, yet very few studies have investigated the prevalence in oriental general population.

Objective: To investigate the prevalence of mask-related adverse skin reactions in Orientals, to explore psychological influence, to identify risk factors for mask-related acne exacerbation.

Methods: We performed a survey through social media.

An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.

Cells within a tumor microenvironment (TME) dynamically communicate and influence each other's cellular states through an intercellular communication network (ICN). In cancers, intercellular communications underlie immune evasion mechanisms of individual tumors. We developed an individualized causal analysis framework for discovering tumor specific ICNs.

Cognitively impaired aged Octodon degus recapitulate major neuropathological features of sporadic Alzheimer's disease.

The long-lived Chilean rodent (Octodon degus) has been reported to show spontaneous age-dependent neuropathology and cognitive impairments similar to those observed in human AD. However, the handful of published papers on degus of differing genetic backgrounds yield inconsistent findings about sporadic AD-like pathological features, with notably differing results between lab in-bred degus versus outbred degus. This motivates more extensive characterization of spontaneously occurring AD-like pathology and behavior in degus.

Degenerate mapping of environmental location presages deficits in object-location encoding and memory in the 5xFAD mouse model for Alzheimer's disease.

A key challenge in developing diagnosis and treatments for Alzheimer's disease (AD) is to detect abnormal network activity at as early a stage as possible. To date, behavioral and neurophysiological investigations in AD model mice have yet to conduct a longitudinal assessment of cellular pathology, memory deficits, and neurophysiological correlates of neuronal activity. We therefore examined the temporal relationships between pathology, neuronal activities and spatial representation of environments, as well as object location memory deficits across multiple stages of development in the 5xFAD mice model and compared these results to those observed in wild-type mice.

A genomic and transcriptomic study toward breast cancer.

Breast carcinoma is well recognized to be having the highest global occurrence rate among all cancers, being the leading cause of cancer mortality in females. The aim of this study was to elucidate breast cancer at the genomic and transcriptomic levels in different subtypes so that we can develop more personalized treatments and precision medicine to obtain better outcomes. In this study, an expression profiling dataset downloaded from the Gene Expression Omnibus database, GSE45827, was re-analyzed to compare the expression profiles of breast cancer samples in the different subtypes.