Deep learning reveals determinants of transcriptional infidelity at nucleotide resolution in the allopolyploid line by goldfish and common carp hybrids.

During DNA transcription, the central dogma states that DNA generates corresponding RNA sequences based on the principle of complementary base pairing. However, in the allopolyploid line by goldfish and common carp hybrids, there is a significant level of transcriptional infidelity. To explore deeper into the causes of transcriptional infidelity in this line, we developed a deep learning model to explore its underlying determinants.

Identification of hub genes and potential molecular mechanisms related to radiotherapy in thyroid cancer.

Radiotherapy is a common approach during the treatment of thyroid cancer (THCA). It is urgent to identify the radiotherapy-related gene and explore the underlying mechanisms. An message RNA expression clinical data was gained from the Cancer Genome Atlas.

Case Report: Reversible alien hand syndrome caused by cerebral infarction.

Introduction: Alien hand syndrome (AHS) is a rare apraxia syndrome that may arise from several neurological disorders including stroke. Given the uncommon symptoms, stroke with AHS as its main manifestation often results in diagnostic challenges and treatment delays.

Case Presentation: We herein presented a case of post-stroke AHS caused by corpus callosum infarction.

Upregulated FSP1 by GPD1/1L mediated lipid droplet accumulation enhances ferroptosis resistance and peritoneal metastasis in gastric cancer.

To successfully metastasize, cancer cells must evade detachment induced cell death, known as anoikis. Unraveling the mechanisms that gastric cancer (GC) circumvent anoikis and achieve peritoneal metastasis especially during unanchored growth, could significantly improve patient outcomes. Our study reveals that GC cells exhibit increased lipid peroxidation, MDA production, and cell death during suspension culture, which can be mitigated by the intervention with liproxstatin-1 and ferrostatin-1.

High specific surface area MMT/NO intercalated modified MgAl-LDH core-shell composites: effective inhibition for steel in Cl contaminated saturated Ca(OH) solution.

This study developed nitrate-intercalated layered double hydroxides (NO-LDHs) and their core-shell composites (NO-LDHs@MMT) through an co-precipitation method with montmorillonite (MMT). The corrosion inhibition performance for Q235 steel in simulated concrete pore solutions (saturated Ca(OH) + 3.5 wt% NaCl) was systematically investigated.

Novel Visualization of Building Earthquake Response Recorded by a Dense Network of Sensors.

The strong motion records collected in full-scale structures provide the ultimate evidence of how real structures, in situ, respond to earthquakes. This paper presents a novel method for visualization, in three dimensions (3D), of the collective motion by a dense array of sensors in a building. The method is based on one- and two-dimensional biharmonic spline interpolation of the motion recorded by multiple sensors on the same or multiple floors.

Identification of polyamine metabolism-related prognostic biomarkers for predicting breast cancer prognosis, immune microenvironment, and candidate drugs.

In this study, polyamine metabolism related genes (PMRGs) were used to establish a breast cancer (BC) prognostic model. Using PMRGs, TCGA BC samples were divided into cluster1 and cluster2. A 13-gene BC prognostic model was constructed by screening differential genes.

Establishment of a Mass Concrete Strength-Monitoring Method Using Barium Titanate-Bismuth Ferrite/Polyvinylidene Fluoride Nanocomposite Piezoelectric Sensors with Temperature Stability.

Mass concrete is widely used in large-scale projects, including metro upper cover structures, water conservancy dams, and heavy equipment foundations, among others, necessitating the process of health monitoring in mass concrete construction. The development of reliable and simple strength-monitoring methods for mass concrete is challenging because the inner temperature of mass concrete is high and changes a lot. This study proposes a strength-monitoring approach for mass concrete using barium titanate-bismuth ferrite/polyvinylidene fluoride (BT-BFO/PVDF) nanocomposite piezoelectric sensors, wherein the new sensors are embedded as actuators and sensors in mass concrete.

Puzzle Hi-C: An accurate scaffolding software.

High-quality, chromosome-scale genomes are essential for genomic analyses. Analyses, including 3D genomics, epigenetics, and comparative genomics rely on a high-quality genome assembly, which is often accomplished with the assistance of Hi-C data. Curation of genomes reveal that current Hi-C-assisted scaffolding algorithms either generate ordering and orientation errors or fail to assemble high-quality chromosome-level scaffolds.

Acceleration of Photoinduced Electron Transfer by Modulating Electronegativity of Substituents in Stable Zr-Metal-Organic Frameworks to Boost Photocatalytic CO Reduction.

Photoreduction of CO with water into chemical feedstocks of fuels provides a green way to help solve both the energy crisis and carbon emission issues. Metal-organic frameworks (MOFs) show great potential for CO photoreduction. However, poor water stability and sluggish charge transfer could limit their application.

Pt-S Bond-Enabled Temperature-Dependent Phosphorescence in S-Heteroaryl Tetradentate Pt(S^C^N^O) Complexes.

This study presents the rare examples of S-heteroaryl tetradentate Pt(S^C^N^O) luminescent complexes ( and ) containing a Pt-S bond. The presence of the Pt-S bond allows the novel Pt(S^C^N^O) complexes to exhibit temperature-dependent phosphorescent emission behavior. The exhibits dual-emission phenomena and biexponential transient decay spectra above 250 K, indicating the presence of two minimal excited states in the potential energy surface (PES) of the T state.

Construction of a prognostic model for breast cancer based on moonlighting genes.

Breast cancer (BRCA) is a highly heterogeneous disease, with significant differences in prognosis among patients. Existing biomarkers and prognostic models have limited ability to predict BRCA prognosis. Moonlighting genes regulate tumor progression and are associated with cancer prognosis.

G-protein-coupled estrogen receptor 1 promotes peritoneal metastasis of gastric cancer through nicotinamide adenine dinucleotide kinase 1-mediated redox modulation.

Adipose tissue is the second most important site of estrogen production, where androgens are converted into estrogen by aromatase. While gastric cancer patients often develop adipocyte-rich peritoneal metastasis, the underlying mechanism remains unclear. In this study, we identified the G-protein-coupled estrogen receptor (GPER1) as a promoter of gastric cancer peritoneal metastasis.

Construction and validation of a metabolism-related prognostic model for thyroid cancer.

Metabolic reprogramming is a common pathological process of cancer. Expression of metabolism-related genes differs in thyroid cancer (TC) patients with different prognoses. This work committed to constructing a prognostic model for TC through identifying metabolism-related signatures.

Association filtering and generative adversarial networks for predicting lncRNA-associated disease.

Background: Long non-coding RNA (lncRNA) closely associates with numerous biological processes, and with many diseases. Therefore, lncRNA-disease association prediction helps obtain relevant biological information and understand pathogenesis, and thus better diagnose preventable diseases.

Results: Herein, we offer the LDAF_GAN method for predicting lncRNA-associated disease based on association filtering and generative adversarial networks.

Identification and validation of a five-gene prognostic signature based on bioinformatics analyses in breast cancer.

Background: This study aimed to identify prognostic signatures to predict the prognosis of breast cancer (BRCA) patients based on a series of comprehensive analyses of gene expression data.

Methods: The RNA-sequencing expression data and corresponding BRCA patient clinical data were collected from the Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) datasets. Firstly, the differently expressed genes (DEGs) related to prognosis between tumor tissues and normal tissues were ascertained by performing R package "limma".

ReHiC: Enhancing Hi-C data resolution via residual convolutional network.

High-throughput chromosome conformation capture (Hi-C) is one of the most popular methods for studying the three-dimensional organization of genomes. However, Hi-C protocols can be expensive since they require large amounts of sample material and may be time-consuming. Most commonly used Hi-C data are low-resolution.

From asymmetrical to balanced genomic diversification during rediploidization: Subgenomic evolution in allotetraploid fish.

A persistent enigma is the rarity of polyploidy in animals, compared to its prevalence in plants. Although animal polyploids are thought to experience deleterious genomic chaos during initial polyploidization and subsequent rediploidization processes, this hypothesis has not been tested. We provide an improved reference-quality de novo genome for allotetraploid goldfish whose origin dates to ~15 million years ago.

Rheology, Non-Isothermal Crystallization Behavior, Mechanical and Thermal Properties of PMMA-Modified Carbon Fiber-Reinforced Poly(Ethylene Terephthalate) Composites.

Poly(ethylene terephthalate) (PET) composites containing carbon fiber (CF) or polymethyl methacrylate (PMMA)-grafted carbon fiber (PMMA-g-CF) were prepared by melt compounding. The rheology, non-isothermal crystallization behavior, and mechanical and thermal properties of pure PET, PET/CF and PET/PMMA-g-CF composites were investigated. The results show that the addition of CF or PMMA-g-CF significantly increases the storage modulus (G'), loss modulus (G″), and complex viscosity (η*) of the composites at low frequency.

3,5-Disubstituted-indole-7-carboxamides as IKKβ Inhibitors: Optimization of Oral Activity via the C3 Substituent.

IκB kinase β (IKKβ or IKK2) is a key regulator of nuclear factor kappa B (NF-κB) and has received attention as a therapeutic target. Herein we report on the optimization of a series of 3,5-disubstituted-indole-7-carboxamides for oral activity. In doing so, we focused attention on potency, ligand efficiency (LE), and physicochemical properties and have identified compounds and ()- as having robust in vivo activity.

Paramedian Thalamic Ischemic Infarction: A Retrospective Clinical Observation.

Background: The study aimed to evaluate the clinical features in patients with bilateral and unilateral paramedian thalamic infarcts.

Methods: Twenty-one patients with paramedian thalamic infarcts were included, and their case records were reviewed. We focused on the patients' neuroimaging and neurological symptoms including the duration of coma, vertical gaze palsy, and memory impairment.

Homoeologue expression insights into the basis of growth heterosis at the intersection of ploidy and hybridity in Cyprinidae.

Hybridization and polyploidization are considered important driving forces that form new epigenetic regulations. To study the changing patterns of expression accompanying hybridization and polyploidization, we used RNA-seq and qRT-PCR to investigate global expression and homoeologue expression in diploid and tetraploid hybrids of Carassius auratus red var. (♀) (R) and Cyprinus carpio (♂) (C).

VennPainter: A Tool for the Comparison and Identification of Candidate Genes Based on Venn Diagrams.

VennPainter is a program for depicting unique and shared sets of genes lists and generating Venn diagrams, by using the Qt C++ framework. The software produces Classic Venn, Edwards' Venn and Nested Venn diagrams and allows for eight sets in a graph mode and 31 sets in data processing mode only. In comparison, previous programs produce Classic Venn and Edwards' Venn diagrams and allow for a maximum of six sets.

Genomic incompatibilities in the diploid and tetraploid offspring of the goldfish × common carp cross.

Polyploidy is much rarer in animals than in plants but it is not known why. The outcome of combining two genomes in vertebrates remains unpredictable, especially because polyploidization seldom shows positive effects and more often results in lethal consequences because viable gametes fail to form during meiosis. Fortunately, the goldfish (maternal) × common carp (paternal) hybrids have reproduced successfully up to generation 22, and this hybrid lineage permits an investigation into the genomics of hybridization and tetraploidization.