Integrating genetic and gene expression data in network-based stratification analysis of cancers.

Background: Cancers are complex diseases that have heterogeneous genetic drivers and varying clinical outcomes. A critical area of cancer research is organizing patient cohorts into subtypes and associating subtypes with clinical and biological outcomes for more effective prognosis and treatment. Large-scale studies have collected a plethora of omics data across multiple tumor types, providing an extensive dataset for stratifying patient cohorts.

DNAcycP2: improved estimation of intrinsic DNA cyclizability through data augmentation.

Loop-seq is a pioneering high-throughput assay that enables the simultaneous quantification of intrinsic cyclizability across a large set of DNA fragments. However, the assay's reliance on biotin-tethered elongated DNA fragments introduces a tethering effect, leading to biased cyclizability measurements. We demonstrate that the current de-biasing technique is inadequate for fully mitigating this bias.

NLSDeconv: an efficient cell-type deconvolution method for spatial transcriptomics data.

Summary: Spatial transcriptomics (ST) allows gene expression profiling within intact tissue samples but lacks single-cell resolution. This necessitates computational deconvolution methods to estimate the contributions of distinct cell types. This article introduces NLSDeconv, a novel cell-type deconvolution method based on non-negative least squares, along with an accompanying Python package.

[Spatio-temporal Evolution of Drought and Its Impact on Key Resources in the Important Ecological Functional Area: A Case Study in the Yellow River Basin].

This study explored the characteristics of spatial and temporal changes in drought in the Yellow River Basin from 2001 to 2020 based on TVPDI, surface runoff, vegetation net primary productivity, and grain yield data. Further, the effects of drought on water resources, grain resources, and vegetation resources were also analyzed using data spatialization methods, slope trend analysis, and Pearson correlation analysis. The results showed that:① The spatial distribution of drought in the Yellow River basin was stepped from southeast to northwest, and 60.

BoostMEC: predicting CRISPR-Cas9 cleavage efficiency through boosting models.

Background: In the CRISPR-Cas9 system, the efficiency of genetic modifications has been found to vary depending on the single guide RNA (sgRNA) used. A variety of sgRNA properties have been found to be predictive of CRISPR cleavage efficiency, including the position-specific sequence composition of sgRNAs, global sgRNA sequence properties, and thermodynamic features. While prevalent existing deep learning-based approaches provide competitive prediction accuracy, a more interpretable model is desirable to help understand how different features may contribute to CRISPR-Cas9 cleavage efficiency.

Association between sleep duration and chest pain in US adults: A cross-sectional study.

Objective: Herein, we purposed to explore the association of sleep duration with chest pain among adults in US.

Methods: This research work enrolled 13,274 subjects in the National Health and Nutrition Examination Survey (NHANES) from 2011 to 2018. The association of sleep duration with chest pain among adults in US was evaluated by Multivariable logistic regression.

[Seasonal dynamics of the physicochemical properties of biological crusts exopolysaccharides and the microbial community structure].

Exopolysaccharides (EPS), an important substance of cyanobacteria in resisting stresses, are the main form of carbon storage in biocrusts and play an important role in material cycling and stability of biocrusts. In this study, the biocrusts in different seasons (January, April, July, October) were collected from Gurbantunggut Desert, and the dynamics of EPS content, composition, morphological characteristics and microbial community structures were analyzed. The results showed that: 1) The excretion of EPS showed obvious seasonal dynamics.

DNAcycP: a deep learning tool for DNA cyclizability prediction.

DNA mechanical properties play a critical role in every aspect of DNA-dependent biological processes. Recently a high throughput assay named loop-seq has been developed to quantify the intrinsic bendability of a massive number of DNA fragments simultaneously. Using the loop-seq data, we develop a software tool, DNAcycP, based on a deep-learning approach for intrinsic DNA cyclizability prediction.

The Hypertension Related Gene G-Protein Coupled Receptor Kinase 4 Contributes to Breast Cancer Proliferation.

Purpose: Clinical studies have shown that breast cancer risk is increased in hypertensive women. The underlying molecular mechanism remains undetermined. The current study tests our hypothesis that G protein coupled receptor kinase 4 (GRK4) is a molecule that links hypertension and breast cancer.

Establishment and Clinical Application of the Concept of Invalid Extraction Rates in Follicular Unit Extraction.

Objective: This study aims to establish the concept of invalid extraction rates in follicular unit extraction and evaluate its clinical value.

Methods: The present study involved 30 patients with alopecia. Three young surgeons (nominated A, B, and C) each performed follicular unit extraction on a randomly selected portion of the donor site of each patient for ten minutes.

RiboDiPA: a novel tool for differential pattern analysis in Ribo-seq data.

Ribosome profiling, also known as Ribo-seq, has become a popular approach to investigate regulatory mechanisms of translation in a wide variety of biological contexts. Ribo-seq not only provides a measurement of translation efficiency based on the relative abundance of ribosomes bound to transcripts, but also has the capacity to reveal dynamic and local regulation at different stages of translation based on positional information of footprints across individual transcripts. While many computational tools exist for the analysis of Ribo-seq data, no method is currently available for rigorous testing of the pattern differences in ribosome footprints.

[Symbiotic bacteria facilitate algal growth and oil biosynthesis in Scenedesmus obliquus].

We isolated bacteria from the phycosphere of Scenedesmus obliques and sequenced 16S rDNAs to establish algae-bacterial co-culture systems. Further, we examined effects of the bacteria on algal growth, and parameters associated with physio-biochemical and oil-producing characteristics of S. obliquus.

Impact of Thermal History on the Kinetic Response of Thermoresponsive Poly(diethylene glycol monomethyl ether methacrylate)--poly(poly(ethylene glycol)methyl ether methacrylate) Thin Films Investigated by In Situ Neutron Reflectivity.

The impact of thermal history on the kinetic response of thin thermoresponsive diblock copolymer poly(diethylene glycol monomethyl ether methacrylate)--poly(poly(ethylene glycol) methyl ether methacrylate), abbreviated as PMEOMA--POEGMA, films is investigated by in situ neutron reflectivity. The PMEOMA and POEGMA blocks are both thermoresponsive polymers with a lower critical solution temperature. Their transition temperatures (TTs) are around 25 °C (TT, PMEOMA) and 60 °C (TT, POEGMA).

Mobilizable antibiotic resistance genes are present in dust microbial communities.

The decades-long global trend of urbanization has led to a population that spends increasing amounts of time indoors. Exposure to microbes in buildings, and specifically in dust, is thus also increasing, and has been linked to various health outcomes and to antibiotic resistance genes (ARGs). These are most efficiently screened using DNA sequencing, but this method does not determine which microbes are viable, nor does it reveal whether their ARGs can actually disseminate to other microbes.

Thermoresponsive Diblock Copolymer Films with a Linear Shrinkage Behavior and Its Potential Application in Temperature Sensors.

The linear shrinkage behavior in thermoresponsive diblock copolymer films and its potential application in temperature sensors are investigated. The copolymer is composed of two thermoresponsive blocks with different transition temperatures (TTs): di(ethylene glycol) methyl ether methacrylate (MEOMA; TT = 25 °C) and poly(ethylene glycol) methyl ether methacrylate (OEGMA; TT = 60 °C) with a molar ratio of 1:1. Aqueous solutions of PMEOMA--POEGMA show a three-stage transition upon heating as seen with optical transmittance and small-angle X-ray scattering: dissolution (T < TT), self-assembled micelles with core-shell structure (TT < T < TT), and aggregation of collapsed micelles (T > TT).

MicroRNA-498 promotes proliferation, migration, and invasion of prostate cancer cells and decreases radiation sensitivity by targeting PTEN.

Prostate cancer (PCa) remains the secondary highest cause of cancer-related death in the United States in men. It has been reported that microRNAs can serve as key regulators in tumor development and progression in various cancers including PCa. In this study, we examined the effect of miR-498 on proliferation, radiosensitivity, invasion, and migration of PCa cells.

Pro-Apoptotic Effects of Estetrol on Long-Term Estrogen-Deprived Breast Cancer Cells and at Low Doses on Hormone-Sensitive Cells.

Purpose: Postmenopausal women with estrogen receptor-positive breast cancers often respond initially to tamoxifen or aromatase inhibitor therapy. Resistance to these treatments usually develops within 12 to 18 months. Clinical studies have demonstrated that high-dose estrogen can induce regression of these endocrine-resistant tumors.

Functional Phosphine Derivatives Having Stationary and Flexible Chiralities: Their Preparation and Chirality Controlling.

Various functional secondary and tertiary phosphines, or their derivatives, containing stationary chiral phosphorus and flexible chiral axis were prepared, which could be further modified to afford diversely chelating ligands. The flexible axial chirality was fixed by stereogenic phosphorus via a cyclic linkage of chemical bonds or coordination with a metallic ion.

DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis.

RNA degradation affects RNA-seq quality when profiling transcriptional activities in cells. Here, we show that transcript degradation is both gene- and sample-specific and is a common and significant factor that may bias the results in RNA-seq analysis. Most existing global normalization approaches are ineffective to correct for degradation bias.

Enhanced Stain Removal and Comfort Control Achieved by Cross-Linking Light and Thermo Dual-Responsive Copolymer onto Cotton Fabrics.

Enhanced capabilities of stain removal and comfort control are simultaneously achieved by the light and thermo dual-responsive copolymer poly(triethylene glycol methyl ether methacrylate- co-ethylene glycol methacrylate- co-acrylamide azobenzene) (P(MEOMA- co-EGMA- co-AAAB)) cross-linked on cotton fabrics. P(MEOMA- co-EGMA- co-AAAB) is synthesized by sequential atom transfer radical polymerization with a molar ratio of 8 (MEOMA):1 (EGMA):1 (AAAB). The MEOMA units induce a thermoresponsive behavior to the copolymer.

Chinese herbal medicine Shenzhuo Formula treatment in patients with macroalbuminuria secondary to diabetic kidney disease: study protocol for a randomized controlled trial.

Background: Diabetic kidney disease (DKD) is a serious complication associated with diabetes mellitus and can cause end-stage renal disease (ESRD). Traditional Chinese medicine (TCM) is widely used in China to treat DKD, and in particular microalbuminuria and macroalbuminuria. This study will address the efficacy and safety of Shenzhuo Formula (SZF), a frequently prescribed TCM, in DKD patients with macroalbuminuria.

Nucleophilic Substitution of P-Stereogenic Chlorophosphines: Mechanism, Stereochemistry, and Stereoselective Conversions of Diastereomeric Secondary Phosphine Oxides to Tertiary Phosphines.

A diastereomeric mixture of secondary phosphine oxide is stereospecifically converted to chlorophosphine salt by treatment with oxalyl chloride, which stereoselectively affords P-inverted or retained tertiary phosphines, depending on the substitution with aliphatic or aromatic Grignard reagents, respectively, in high to 99% yield and 99:1 dr. The repulsion of π-electron on aryl to lone electron pair on phosphorus is proposed for the P-retained substitution.