iGTP: Learning interpretable cellular embedding for inferring biological mechanisms underlying single-cell transcriptomics.

Deep-learning models like Variational AutoEncoder have enabled low dimensional cellular embedding representation for large-scale single-cell transcriptomes and shown great flexibility in downstream tasks. However, biologically meaningful latent space is usually missing if no specific structure is designed. Here, we engineered a novel interpretable generative transcriptional program (iGTP) framework that could model the importance of transcriptional program (TP) space and protein-protein interactions (PPI) between different biological states.

Clinical Characteristics, Species Distribution, and Drug Resistance of Non-Tuberculous Mycobacteria Lung Disease in Qingdao, China.

Objective: To analyze the clinical characteristics, species distribution and drug resistance of patients with non-tuberculous mycobacteria (NTM) lung disease in Qingdao, China.

Methods: Clinical data of patients with NTM lung disease and pulmonary tuberculosis (TB) treated at Qingdao Chest Hospital from July 2021 to July 2023 were retrospectively analyzed.

Results: The prevalence of NTM lung disease was 8.

scEMB: Learning context representation of genes based on large-scale single-cell transcriptomics.

Background: The rapid advancement of single-cell transcriptomic technologies has led to the curation of millions of cellular profiles, providing unprecedented insights into cellular heterogeneity across various tissues and developmental stages. This growing wealth of data presents an opportunity to uncover complex gene-gene relationships, yet also poses significant computational challenges.

Results: We present scEMB, a transformer-based deep learning model developed to capture context-aware gene embeddings from large-scale single-cell transcriptomics data.

Radiation-Induced Lymphopenia is a Causal Mediator of Survival After Chemoradiation Therapy for Esophagus Cancer.

Purpose: Radiation-induced lymphopenia (RIL) is common during chemoradiation therapy. Severe lymphopenia is associated with reduced survival. Proton beam therapy (PBT), with its substantially more compact dose distributions, spares circulating lymphocytes and immune organs at risk to a greater extent than photon therapy.

Clinical Translation of a Deep Learning Model of Radiation-Induced Lymphopenia for Esophageal Cancer.

Purpose: Radiation-induced lymphopenia is a common immune toxicity that adversely impacts treatment outcomes. We report here our approach to translate a deep-learning (DL) model developed to predict severe lymphopenia risk among esophageal cancer into a strategy for incorporating the immune system as an organ-at-risk (iOAR) to mitigate the risk.

Materials And Methods: We conducted "virtual clinical trials" utilizing retrospective data for 10 intensity-modulated radiation therapy (IMRT) and 10 passively-scattered proton therapy (PSPT) esophageal cancer patients.

High throughput profiling identified PA-L106R amino acid substitution in A(H1N1)pdm09 influenza virus that confers reduced susceptibility to baloxavir in vitro.

Baloxavir acid (BXA) is a pan-influenza antiviral that targets the cap-dependent endonuclease of the polymerase acidic (PA) protein required for viral mRNA synthesis. To gain a comprehensive understanding on the molecular changes associated with reduced susceptibility to BXA and their fitness profile, we performed a deep mutational scanning at the PA endonuclease domain of an A (H1N1)pdm09 virus. The recombinant virus libraries were serially passaged in vitro under increasing concentrations of BXA followed by next-generation sequencing to monitor PA amino acid substitutions with increased detection frequencies.

Personalized Composite Dosimetric Score-Based Machine Learning Model of Severe Radiation-Induced Lymphopenia Among Patients With Esophageal Cancer.

Purpose: Radiation-induced lymphopenia (RIL) is common among patients undergoing radiation therapy (RT)' Severe RIL has been linked to adverse outcomes. The severity and risk of RIL can be predicted from baseline clinical characteristics and dosimetric parameters. However, dosimetric parameters, e.

DeepFace: Deep-learning-based framework to contextualize orofacial-cleft-related variants during human embryonic craniofacial development.

Orofacial clefts (OFCs) are among the most common human congenital birth defects. Previous multiethnic studies have identified dozens of associated loci for both cleft lip with or without cleft palate (CL/P) and cleft palate alone (CP). Although several nearby genes have been highlighted, the "casual" variants are largely unknown.

LPAR6 Participates in Neuropathic Pain by Mediating Astrocyte Cells via ROCK2/NF-κB Signal Pathway.

Neuropathic pain (NPP) is a common type of chronic pain. Glial cells, including astrocytes (AS), are believed to play an important role in the progression of NPP. AS cells can be divided into various types based on their expression profiles, among which A1 and A2 types have clear functions.

Pan-Cancer Analysis of the LOX Family Reveals that LOX Affects Tumor Prognosis by Affecting Immune Infiltration.

The lysyl oxidase (LOX) gene family encodes for a group of copper-dependent enzymes that play a crucial role in the cross-linking of collagen and elastin fibers in the extracellular matrix (ECM). Dysregulation of LOX gene expression has been implicated in various pathological conditions, including cancer. Several studies have shown that the LOX gene family is involved in cancer progression and metastasis.

Severe Lymphopenia During Chemoradiation Therapy for Esophageal Cancer: Comprehensive Analysis of Randomized Phase 2B Trial of Proton Beam Therapy Versus Intensity Modulated Radiation Therapy.

Purpose: Lymphocytes play an important role in antitumor immunity; however, they are also especially vulnerable to depletion during chemoradiation therapy (CRT). The purpose of this study was to compare the incidence of grade 4 lymphopenia (G4L) between proton beam therapy (PBT) and intensity modulated photon radiation therapy (IMRT) in patients with esophageal cancer treated with CRT in a completed randomized trial and to ascertain patient heterogeneity to G4L risk based on treatment and established prognostic factors.

Methods And Materials: Between April 2012 and March 2019, a single-institution, open-label, nonblinded, phase 2 randomized trial (NCT01512589) was conducted at the University of Texas MD Anderson Cancer Center.

Incorporating Heterogeneous Features into the Random Subspace Method for Bearing Fault Diagnosis.

In bearing fault diagnosis, machine learning methods have been proven effective on the basis of the heterogeneous features extracted from multiple domains, including deep representation features. However, comparatively little research has been performed on fusing these multi-domain heterogeneous features while dealing with the interrelation and redundant problems to precisely discover the bearing faults. Thus, in the current study, a novel diagnostic method, namely the method of incorporating heterogeneous representative features into the random subspace, or IHF-RS, is proposed for accurate bearing fault diagnosis.

Non-invasive arterial blood pressure measurement and SpO estimation using PPG signal: a deep learning framework.

Background: Monitoring blood pressure and peripheral capillary oxygen saturation plays a crucial role in healthcare management for patients with chronic diseases, especially hypertension and vascular disease. However, current blood pressure measurement methods have intrinsic limitations; for instance, arterial blood pressure is measured by inserting a catheter in the artery causing discomfort and infection.

Method: Photoplethysmogram (PPG) signals can be collected via non-invasive devices, and therefore have stimulated researchers' interest in exploring blood pressure estimation using machine learning and PPG signals as a non-invasive alternative.

vacA affects the expression of COX-2 in the duodenal mucosa of patients with duodenitis.

Duodenitis refers to inflammation that occurs in the duodenum. (Hp) is a known risk factor for duodenitis. This paper attempted to analyze the correlation between Hp virulence genotypes and the initiation and development of duodenal bulbar inflammation (DBI) to lay the foundation for the management of duodenitis induced by Hp infection.

Thermally stable threshold selector based on CuAg alloy for energy-efficient memory and neuromorphic computing applications.

As a promising candidate for high-density data storage and neuromorphic computing, cross-point memory arrays provide a platform to overcome the von Neumann bottleneck and accelerate neural network computation. In order to suppress the sneak-path current problem that limits their scalability and read accuracy, a two-terminal selector can be integrated at each cross-point to form the one-selector-one-memristor (1S1R) stack. In this work, we demonstrate a CuAg alloy-based, thermally stable and electroforming-free selector device with tunable threshold voltage and over 7 orders of magnitude ON/OFF ratio.

Suppresses the Proliferation of CRC Bone Metastatic Cells via the Ras/Raf/MEK/ERK Signaling Pathway.

Background: The improvements in the treatment of colorectal cancer (CRC) and prolongation of survival time have improved the incidence of bone metastasis. Forkhead box D3 (FOXD3) is involved in the development of CRC. However, the role and mechanism of FOXD3 in CRC bone metastases development are unknown.

Technology challenges among deaf and hard of hearing elders in China during COVID-19 pandemic emergency isolation: A qualitative study.

Digital technology can be an effective tool to facilitate emergency assistance in a pandemic, but many deaf and hard-of-hearing elders may experience challenges in using and adopting these technologies. In the context of the second wave of the COVID-19 outbreak, this study employs a qualitative research method based on in-depth interviews to explore technology challenges among deaf and hard-of-hearing elders in China. The results showed that this group's technology challenges arose mainly from barriers to the mastery of digital technology tools, among which barriers to the use of smartphones, to the accessibility of online medical consultations, and to the presentation of health codes, were most noteworthy.

[Clinical features and genetic analysis of two Chinese pedigrees affected with Joubert syndrome].

Objective: To explore the clinical characteristics and genetic basis of two Chinese pedigrees affected with Joubert syndrome.

Methods: Clinical data of the two pedigrees was collected. Genomic DNA was extracted from peripheral blood samples and subjected to high-throughput sequencing.

Bilateral Orbital Plasmacytomas With Orbital Compartment Syndrome.

Orbital plasmacytomas are uncommon soft-tissue plasma cell neoplasms that are associated with a monoclonal or myeloma protein. There are four types of plasma cell neoplasms: multiple myeloma (MM), monoclonal gammopathy of undetermined significance (MGUS), amyloidosis, and plasmacytoma. Plasmacytomas may be classified as medullary, occurring only within the bone, or extramedullary, occurring in soft tissues.

Combined Strategy of Wound Healing Using Thermo-Sensitive PNIPAAm Hydrogel and CS/PVA Membranes: Development and In-Vivo Evaluation.

Past studies have shown that the hot spring effect can promote wound healing. Mild thermal stimulation and metal ions can promote angiogenesis. In this study, the hot spring effect was simulated by thermosensitive PNIPAAm hydrogel loaded with copper sulfide nanoparticles.