Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction.

Summary: Neoplastic tumors originate from a single cell, and their evolution can be traced through lineages characterized by mutations, copy number alterations, and structural variants. These lineages are reconstructed and mapped onto evolutionary trees with algorithmic approaches. However, without ground truth benchmark sets, the validity of an algorithm remains uncertain, limiting potential clinical applicability. With a growing number of algorithms available, there is urgent need for standardized benchmark sets to evaluate their merits. Benchmark sets rely on in silico simulations of tumor sequence, but there are no accepted standards for simulation tools, presenting a major obstacle to progress in this field. Availability and implementation: All analysis done in the paper was based on publicly available data from the publication of each accessed tool.

Obesity-associated microbiomes instigate visceral adipose tissue inflammation by recruitment of distinct neutrophils.

Neutrophils are increasingly implicated in chronic inflammation and metabolic disorders. Here, we show that visceral adipose tissue (VAT) from individuals with obesity contains more neutrophils than in those without obesity and is associated with a distinct bacterial community. Exploring the mechanism, we gavaged microbiome-depleted mice with stool from patients with and without obesity during high-fat or normal diet administration. Only mice receiving high-fat diet and stool from subjects with obesity show enrichment of VAT neutrophils, suggesting donor microbiome and recipient diet determine VAT neutrophilia. A rise in pro-inflammatory CD4+ Th1 cells and a drop in immunoregulatory T cells in VAT only follows if there is a transient spike in neutrophils. Human VAT neutrophils exhibit a distinct gene expression pattern that is found in different human tissues, including tumors. VAT neutrophils and bacteria may be a novel therapeutic target for treating inflammatory-driven complications of obesity, including insulin resistance and colon cancer.

Enhancing GaN/AlxGa1-xN-Based Heterojunction Phototransistors: The Role of Graded Base Structures in Performance Improvement.

This research explores the architecture and efficacy of GaN/AlxGa1-xN-based heterojunction phototransistors (HPTs) engineered with both a compositionally graded and a doping-graded base. Employing theoretical analysis along with empirical fabrication techniques, HPTs configured with an aluminum compositionally graded base were observed to exhibit a substantial enhancement in current gain. Specifically, theoretical models predicted a 12-fold increase, while experimental evaluations revealed an even more pronounced improvement of approximately 27.9 times compared to conventional GaN base structures. Similarly, HPTs incorporating a doping-graded base demonstrated significant gains, with theoretical predictions indicating a doubling of current gain and experimental assessments showing a 6.1-fold increase. The doping-graded base implements a strategic modulation of hole concentration, ranging from 3.8 × 1016 cm-3 at the base-emitter interface to 3.8 × 1017 cm-3 at the base-collector junction. This controlled gradation markedly contributes to the observed enhancements in current gain. The principal mechanism driving these improvements is identified as the increased electron drift within the base, propelled by the intrinsic electric field inherent to both the compositionally and doping-graded structures. These results highlight the potential of such graded base designs in enhancing the performance of GaN/AlxGa1-xN HPTs and provide crucial insights for the advancement of future phototransistor technologies.

3D genomic mapping reveals multifocality of human pancreatic precancers.

Pancreatic intraepithelial neoplasias (PanINs) are the most common precursors of pancreatic cancer, but their small size and inaccessibility in humans make them challenging to study1. Critically, the number, dimensions and connectivity of human PanINs remain largely unknown, precluding important insights into early cancer development. Here, we provide a microanatomical survey of human PanINs by analysing 46 large samples of grossly normal human pancreas with a machine-learning pipeline for quantitative 3D histological reconstruction at single-cell resolution. To elucidate genetic relationships between and within PanINs, we developed a workflow in which 3D modelling guides multi-region microdissection and targeted and whole-exome sequencing. From these samples, we calculated a mean burden of 13 PanINs per cm3 and extrapolated that the normal intact adult pancreas harbours hundreds of PanINs, almost all with oncogenic KRAS hotspot mutations. We found that most PanINs originate as independent clones with distinct somatic mutation profiles. Some spatially continuous PanINs were found to contain multiple KRAS mutations; computational and in situ analyses demonstrated that different KRAS mutations localize to distinct cell subpopulations within these neoplasms, indicating their polyclonal origins. The extensive multifocality and genetic heterogeneity of PanINs raises important questions about mechanisms that drive precancer initiation and confer differential progression risk in the human pancreas. This detailed 3D genomic mapping of molecular alterations in human PanINs provides an empirical foundation for early detection and rational interception of pancreatic cancer.

The effect of quiet eye training on golf putting performance in pressure situation.

To explores the effect and mechanism of quiet eye training on the accuracy of golfers´ putts in pressure situations and provides methods and basis for targeted attention training and control. 22 young golfers in China golf team aged from 13 to 18 were randomly assigned to the experimental group (quiet eye training group) and the control group (technical guidance group) according to gender. Both groups of participants underwent two consecutive weeks of push training (3 sets per day, 20 golf putts per set, rest for 3 min between sets) separately in accordance with the guidance of a professional psychological research group and an expert coach. Eye tracking technology, biofeedback technology, and subjective evaluation methods were used to test and analyze the push process of the two groups of participants before and after training under pressure situations (Eye movement behaviors and the heart rate were recorded by ASL Mobile Eye-XG and NeXus-2 biofeedback, pressure and state anxiety were evaluated by self-rating pressure scale and S-AI. Golf putting performance was recorded by a research graduate assistant). A higher hit ratio as well as lower pressure and SAI level was founded in quiet eye training group in the pressure situation, the quiet eye movement time and total fixation time was longer than technical group. The quiet eye training group has a better putting performance. Quiet eye training can improve the golf putting performance in pressure situations. After quiet eye training, the state anxiety decreased, the quiet eye movement time and the total fixation time increased in pressure situations.

Evaluation of simulation methods for tumor subclonal reconstruction.

Most neoplastic tumors originate from a single cell, and their evolution can be genetically traced through lineages characterized by common alterations such as small somatic mutations (SSMs), copy number alterations (CNAs), structural variants (SVs), and aneuploidies. Due to the complexity of these alterations in most tumors and the errors introduced by sequencing protocols and calling algorithms, tumor subclonal reconstruction algorithms are necessary to recapitulate the DNA sequence composition and tumor evolution in silico. With a growing number of these algorithms available, there is a pressing need for consistent and comprehensive benchmarking, which relies on realistic tumor sequencing generated by simulation tools. Here, we examine the current simulation methods, identifying their strengths and weaknesses, and provide recommendations for their improvement. Our review also explores potential new directions for research in this area. This work aims to serve as a resource for understanding and enhancing tumor genomic simulations, contributing to the advancement of the field.

Exogenous Sequences in Tumors and Immune Cells (Exotic): A Tool for Estimating the Microbe Abundances in Tumor RNA-seq Data.

The microbiome affects cancer, from carcinogenesis to response to treatments. New evidence suggests that microbes are also present in many tumors, though the scope of how they affect tumor biology and clinical outcomes is in its early stages. A broad survey of tumor microbiome samples across several independent datasets is needed to identify robust correlations for follow-up testing. We created a tool called {exotic} for "exogenous sequences in tumors and immune cells" to carefully identify the tumor microbiome within RNA sequencing (RNA-seq) datasets. We applied it to samples collected through the Oncology Research Information Exchange Network (ORIEN) and The Cancer Genome Atlas. We showed how the processing removes contaminants and batch effects to yield microbe abundances consistent with non-high-throughput sequencing-based approaches and DNA-amplicon-based measurements of a subset of the same tumors. We sought to establish clinical relevance by correlating the microbe abundances with various clinical and tumor measurements, such as age and tumor hypoxia. This process leveraged the two datasets and raised up only the concordant (significant and in the same direction) associations. We observed associations with survival and clinical variables that are cancer specific and relatively few associations with immune composition. Finally, we explored potential mechanisms by which microbes and tumors may interact using a network-based approach. Alistipes, a common gut commensal, showed the highest network degree centrality and was associated with genes related to metabolism and inflammation. The {exotic} tool can support the discovery of microbes in tumors in a way that leverages the many existing and growing RNA-seq datasets. SIGNIFICANCE: The intrinsic tumor microbiome holds great potential for its ability to predict various aspects of cancer biology and as a target for rational manipulation. Here, we describe a tool to quantify microbes from within tumor RNA-seq and apply it to two independent datasets. We show new associations with clinical variables that justify biomarker uses and more experimentation into the mechanisms by which tumor microbiomes affect cancer outcomes.

MicroRNA-32 promotes cell proliferation, migration and suppresses apoptosis in breast cancer cells by targeting FBXW7.

BACKGROUND: MicroRNAs are a class of small non-coding RNAs that are involved in many important physiological and pathological processes by regulating gene expression negatively. The purpose of this study was to investigate the effect of miR-32 on cell proliferation, migration and apoptosis and to determine the functional connection between miR-32 and FBXW7 in breast cancer. METHODS: In this study, quantitative RT-PCR was used to evaluate the expression levels of miR-32 in 27 breast cancer tissues, adjacent normal breast tissues and human breast cancer cell lines. The biological functions of miR-32 in MCF-7 breast cancer cells were determined by cell proliferation, apoptosis assays and wound-healing assays. In addition, the regulation of FBXW7 by miR-32 was assessed by qRT-PCR, Western blot and luciferase reporter assays. RESULTS: MiR-32 was frequently overexpressed in breast cancer tissue samples and cell lines as was demonstrated by qRT-PCR. Moreover, the up-regulation of miR-32 suppressed apoptosis and promoted proliferation and migration, whereas down-regulation of miR-32 showed an opposite effect. Dual-luciferase reporter assays showed that miR-32 binds to the 3'-untranslated region of FBXW7, suggesting that FBXW7 is a direct target of miR-32. Western blot analysis showed that over-expression of miR-32 reduced FBXW7 protein level. Furthermore, an inverse correlation was found between the expressions of miR-32 and FBXW7 mRNA levels in breast cancer tissues. Knockdown of FBXW7 promoted proliferation and motility and suppressed apoptosis in MCF-7 cells. CONCLUSIONS: Taken together, the present study suggests that miR-32 promotes proliferation and motility and suppresses apoptosis of breast cancer cells through targeting FBXW7.