FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format.

A key output of the NIH-Common Fund 4D Nucleome (4DN) project is the open publication of datasets related to the structure of the human cell nucleus and the genome. Recent years have seen a rapid expansion of multiplexed Fluorescence In Situ Hybridization (FISH) or FISH-omics methods, which quantify the spatial organization of chromatin in single cells, sometimes together with RNA and protein measurements, and provide an expanded understanding of how 3D higher-order chromosome structure relates to transcriptional activity and cell development in both health and disease. Despite this progress, results from Chromatin Tracing FISH-omics experiments are difficult to share, reuse, and subject to third-party downstream analysis due to the lack of standard specifications for data exchange.

Association of gene polymorphisms and SNP loci with susceptibility to rosacea.

Objectives: The major histocompatibility complex class I chain-related gene A (), a component of the human leukocyte antigen () gene complex, is involved in the pathogenesis of various diseases including cancers and autoimmune disorders. Rosacea, a chronic inflammatory skin disease with a complex pathogenesis, potentially influenced by genetic and autoimmune factors. This study aims to investigate the relationship among gene polymorphisms, single nucleotide polymorphisms (SNPs), and susceptibility to rosacea, thereby offering new insights into the disease mechanism.

HIF-1α: A Key Factor Mediating Tumor Cells from Digestive System to Evade NK Cell Killing via Activating Metalloproteinases to Hydrolyze MICA/B.

Malignant tumors of the digestive system are widespread and pose a serious threat to humans. Immune escape is an important factor promoting the deterioration of malignant tumors in the digestive system. Natural killer cells (NK cells) are key members of the anti-tumor and immune surveillance system, mainly exerting cytotoxic effects by binding to the activating receptor natural killer cell group 2D (NKG2D) on their cell surface with the corresponding ligands (major histocompatibility complex class I chain-related protein A/B, MICA/B) on the surface of tumor cells.

A Multimodal Spatial and Epigenomic Atlas of Human Adult Lung Topography.

Developing high-resolution reference maps of disease-susceptible spatial niches is a critical step to mitigating the profound effects of lung disease. Here, we present an integrated multimodal single-nucleus human lung atlas (snHLA) profiling 746,047 nuclei from 49 mapped lung blocks spanning clinically relevant distal airways, alveoli, and interstitium across 11 healthy adults. Integrating snRNA-seq and SNARE-seq2, which co-assays chromatin accessibility and gene expression from the same nucleus, we resolved 70 molecularly distinct populations and captured 332,846 accessible chromatin regions, nominating new transcriptional regulators of human lung cell diversity.

Single-Cell Epigenomics Uncovers Heterochromatin Instability and Transcription Factor Dysfunction during Mouse Brain Aging.

The mechanisms regulating transcriptional changes in brain aging remain poorly understood. Here, we use single-cell epigenomics to profile chromatin accessibility and gene expression across eight brain regions in the mouse brain at 2, 9, and 18 months of age. In addition to a significant decline in progenitor cell populations involved in neurogenesis and myelination, we observed widespread and concordant changes of transcription and chromatin accessibility during aging in glial and neuronal cell types.

Two major human phenotypes of MICA molecules and their differential activation to NK cells via NKG2D receptor.

Introduction: The major histocompatibility complex class I-related gene A (), is a highly polymorphic gene, serve as a crucial role in immune regulator through its interaction with the NKG2D receptor on natural killer (NK) cells. These polymorphisms may influence immune responses, disease susceptibility, and transplant outcomes. However, the precise mechanisms by which polymorphisms modulate NKG2D receptor activation remain poorly understood.

Release mechanism of sustained-release persulfate materials based on stearic acid.

Polycyclic aromatic hydrocarbons (PAHs) in groundwater demonstrate poor degradability and wide contamination plumes. The widely utilized in-situ chemical oxidation technology can effectively oxidize and degrade PAHs in groundwater. However, conventional in-situ chemical oxidation for PAHs in groundwater faces challenges including rapid reaction of oxidants and potential rebound of pollutant concentrations.

Left upper division segmentectomy is not a simple procedure: experience from two high-volume centers.

Background: Whether left upper division segmentectomy (LUDS) is a simple procedure remains controversial. This study aimed to compare the outcomes of LUDS with those of simple segmentectomy (SS) (excluding LUDS) and complex segmentectomy (CS) at two high-volume centers.

Methods: We retrospectively reviewed 1565 patients who underwent thoracoscopic segmentectomy for early-stage lung cancer between February 2015 and February 2020.

Study of the Microstructure, Physical and Mechanical Properties of Zirconium Disilicide Ceramics: Synthesis, Experimental Characterization and Theoretical Calculations.

Zirconium disilicide (ZrSi) is often used in high-temperature applications due to its excellent mechanical properties and thermal stability. This study aims to investigate the microstructure and physical and mechanical properties of ZrSi ceramics prepared under high-pressure and high-temperature (HPHT) sintering conditions. The research results show that the density, Vickers hardness, and fracture toughness of the ZrSi ceramic sample reach 4.

Efficient Photocatalytic Synthesis of Hydrogen Peroxide Facilitated by Triptycene-Based 3D Covalent Organic Frameworks.

Covalent organic frameworks (COFs) are widely studied for hydrogen peroxide (H₂O₂) photosynthesis, with 3D COFs standing out for their porous structures and chemical stability. However, the difficult preparation of 3D COFs and the low efficiency in separating photo-generated electrons and holes (e and h) limits the efficient production of HO. In this study, two kinds of [6+3] 3D COFs (XJU-1, XJU-2) with significant charge separation, achieving record-breaking H₂O₂ photocatalysis rates of 34 777 and 11 922 µmol g⁻¹ h⁻¹, respectively.

Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery.

Loop-extrusion machinery, comprising the cohesin complex and CCCTC-binding factor CTCF, organizes the interphase chromosomes into topologically associating domains (TADs) and loops, but acute depletion of components of this machinery results in variable transcriptional changes in different cell types, highlighting the complex relationship between chromatin organization and gene regulation. Here, we systematically investigated the role of 3D genome architecture in gene regulation in mouse embryonic stem cells under various perturbation conditions. We found that acute depletion of cohesin or CTCF disrupts the formation of TADs, but affects gene regulation in a gene-specific and context-dependent manner.

Characterization of large transgene integrations in Chinese hamster ovary cells using a bioengineered mammalian transposase.

We present the first use of a bioengineered mammalian transposase system derived from Myotis lucifugus (bMLT) for integration of expression vectors into the CHO genome, focusing on GFP and trastuzumab production. Initially, CHO-K1 cells are transfected with a GFP reporter and varying amounts of bMLT DNA or mRNA. GFP expression is monitored over 17 weeks without selective pressure.

Oncologic outcomes of three-dimensional navigation-guided segmentectomy for early-stage non-small cell lung cancer >2-3 cm.

Background: The outcomes of segmentectomy for small (≤2 cm) non-small cell lung cancer (NSCLC) have been well demonstrated. This study aimed to investigate whether segmentectomy could achieve comparable oncologic outcomes with lobectomy for >2-3 cm lung cancer.

Methods: Patients who underwent segmentectomy or lobectomy for NSCLC >2-3 cm were retrospectively screened.

Theoretical kinetic studies on intramolecular H-migration reactions of peroxy radicals of diethoxymethane.

Diethoxymethane (DEM), a promising carbon-neutral fuel, has high reactivity at low temperatures. The intramolecular hydrogen migration reaction of the DEM peroxy radicals can be viewed as a critical step in the low temperature oxidation mechanism of DEM. In this work, multistructural transition state theory (MS-TST) was utilized to calculate the high-pressure limit rate constants of 1,5, 1,6 and 1,7 H-migration reactions for DEM peroxy radicals.

Incidence and risk factors of in-hospital venous thromboembolism in non-oncological urological inpatients: A single center experience.

Objective: To determine incidence and risk factors for venous thromboembolism (VTE) development of in-hospital VTE in urological inpatients who underwent non-oncological surgery in a tertiary hospital in China.

Methods: Consecutive 1453 inpatients who were admitted to a non-oncological urological ward in the tertiary hospital from January 1, 2018 to December 31, 2018 were enrolled in the study, and the VTE events were diagnosed by ultrasound or computed tomographic pulmonary angiography. Patients' occurrence of VTE and characteristics which may contribute to the development of VTE were collected and analyzed as incidence and risk factors.

The Protective Effect of Vitexin on Hypertensive Nephropathy Rats.

Introduction: Vitexin is a natural flavonoid compound extracted from Vitex leaves or seeds, exhibiting various pharmacological activities including anticancer, antihypertensive, anti-inflammatory, and spasmolytic effects. However, its protective effects on hypertensive nephropathy (HN) and the underlying mechanisms remain unclear.

Methods: Spontaneous hypertension rats were fed a high-sugar and high-fat diet for 8 weeks to induce the disease HN model.

[Clinical Multi-features Analysis of Cystic Lung Adenocarcinoma and Construction of Invasive Risk Prediction Model].

Background: Cystic lung cancer, a special type of lung cancer, has been paid more and more attention. The most common pathological type of cystic lung cancer is adenocarcinoma. The invasiveness of cystic lung adenocarcinoma is vital for the selection of clinical treatment and prognosis.

The safety and efficacy of the fissure-first approach in lung segmentectomy for patients with incomplete fissures.

Background: Lung segmentectomy has gained much more attention as an important surgical method for treating early-stage lung cancer. However, incomplete fissures increase the difficulty of lung segmentectomy. The aim of this study was to analyze the safety and efficacy of the fissure-first approach in precision resection of lung segments for patients with incomplete fissures.

Theoretical Study of the Temperature- and Pressure-Dependent Rate Constants for Nine Reactions between CO ( = 0-4), O ( = 1-3), CO, and CO during the Radiolysis of Carbon Dioxide.

We investigate the reaction pathways of nine important CO-related reactions using the revDSD-PBEP86-D3(BJ)/jun-cc-pV(T+d)Z level and simultaneously employ an accurate composite method (jun-Cheap) based on coupled-cluster (CC) theory. Subsequently, the Rice-Ramsperger-Kassel-Marcus/master equation (RRKM/ME) is solved to calculate the temperature- and pressure-dependent rate constants. This work investigates reactions involving transition states that have been overlooked in previous literature, including the dissociation of singlet-state CO, the triple channel formation of CO + CO to form CO, and the formation of O + CO.

An end-to-end multi-scale airway segmentation framework based on pulmonary CT image.

. Automatic and accurate airway segmentation is necessary for lung disease diagnosis. The complex tree-like structures leads to gaps in the different generations of the airway tree, and thus airway segmentation is also considered to be a multi-scale problem.