Genetic diversity within a tree and alternative indexes for different evolutionary effects.

Trees, living for centuries, accumulate somatic mutations in their growing trunks and branches, causing genetic divergence within a single tree. Stem cell lineages in a shoot apical meristem accumulate mutations independently and diverge from each other. In plants, somatic mutations can alter the genetic composition of reproductive organs and gametes, impacting future generations.

Best holdout assessment is sufficient for cancer transcriptomic model selection.

Guidelines in statistical modeling for genomics hold that simpler models have advantages over more complex ones. Potential advantages include cost, interpretability, and improved generalization across datasets or biological contexts. We directly tested the assumption that small gene signatures generalize better by examining the generalization of mutation status prediction models across datasets (from cell lines to human tumors and vice versa) and biological contexts (holding out entire cancer types from pan-cancer data).

A specific and adaptable approach to track CD206 macrophages by molecular MRI and fluorescence imaging.

The mannose receptor (CD206, expressed by the gene ) is a surface marker overexpressed by anti-inflammatory and pro-tumoral macrophages. As such, CD206 macrophages play key roles in the immune response to different pathophysiological conditions and represent a promising diagnostic and therapeutic target. However, methods to specifically target these cells remain challenging.

Loss of does not affect bone and lean tissue in zebrafish.

Human genetic studies have nominated cadherin-like and PC-esterase domain-containing 1 () as a candidate target gene mediating bone mineral density (BMD) and fracture risk heritability. Recent efforts to define the role of in bone in mouse and human models have revealed complex alternative splicing and inconsistent results arising from gene targeting, making its function in bone difficult to interpret. To better understand the role of in adult bone mass and morphology, we conducted a comprehensive genetic and phenotypic analysis of in zebrafish, an emerging model for bone and mineral research.

Seeding and feeding milestones: the role of human milk microbes and oligosaccharides in the temporal development of infant gut microbiota.

Breastfeeding represents a strong selective factor for shaping the infant gut microbiota. Besides providing nutritional requirements for the infant, human milk is a key source of oligosaccharides, human milk oligosaccharides (HMOs), and diverse microbes in early life. This study aimed to evaluate the influence of human milk microbiota and oligosaccharides on the composition of infant faecal microbiota at one, three, and nine months postpartum.

Establishment and perturbation of human gut microbiome: common trends and variations between Indian and global populations.

Human gut microbial species are crucial for dietary metabolism and biosynthesis of micronutrients. Digested products are utilised by the host as well as several gut bacterial species. These species are influenced by various factors such as diet, age, geographical location, and ethnicity.

Diagnostic Accuracy of S100B in Predicting Intracranial Abnormalities on CT Imaging Following Mild Traumatic Brain Injury: A Systematic Review and Meta-analysis.

Traumatic brain injury (TBI) is a major cause of health loss and disabilities globally, burdening health care systems. Mild TBI is a common cause of emergency department visits. Computed tomography (CT) scans are the mainstay for acute TBI imaging.

Evaluation and refinement of thresholds for early migration of total knee replacements as an estimator of late aseptic loosening: an updated systematic review of RSA and survival studies.

Background And Purpose:  This study updates 2 parallel systematic reviews and meta-analyses from 2012, which established the 1-year radiostereometric (RSA) migration thresholds for tibial components of total knee replacements (TKR) based on the risk of late revision for aseptic loosening from survival studies. The primary aim of this study was to determine the (mis)categorization rate of the 2012 thresholds using the updated review as a validation dataset. Secondary aims were evaluation of 6-month migration, mean continuous (1- to 2-year) migration, and fixation-specific thresholds for tibial component migration.

Recent advances in centrifugal microfluidics for point-of-care testing.

Point-of-care testing (POCT) holds significant importance in the field of infectious disease prevention and control, as well as personalized precision medicine. The emerging microfluidics, capable of minimal reagent consumption, integration, and a high degree of automation, play a pivotal role in POCT. Centrifugal microfluidics, also termed lab-on-a-disc (LOAD), is a significant subfield of microfluidics that integrates crucial analytical steps onto a single chip, thereby optimizing the process and enabling high-throughput, automated analysis.

PCA-based spatial domain identification with state-of-the-art performance.

Motivation: The identification of biologically meaningful domains is a central step in the analysis of spatial transcriptomic data.

Results: Following Occam's razor, we show that a simple PCA-based algorithm for unsupervised spatial domain identification rivals the performance of ten competing state-of-the-art methods across six single-cell spatial transcriptomic datasets. Our reductionist approach, NichePCA, provides researchers with intuitive domain interpretation and excels in execution speed, robustness, and scalability.

Rickettsia parkeri forms extensive, stable contacts with the rough endoplasmic reticulum.

Upon invasion into the host cell, a subset of bacterial pathogens resides exclusively in the cytosol. While previous research revealed how they reshape the plasma membrane during invasion, subvert the immune response, and hijack cytoskeletal dynamics to promote their motility, it was unclear if these pathogens also interacted with the organelles in this crowded intracellular space. Here, we examined if the obligate intracellular pathogen Rickettsia parkeri interacts with the endoplasmic reticulum (ER), a large and dynamic organelle spread throughout the cell.

Evidence for gene essentiality in Leishmania using CRISPR.

The ability to determine the essentiality of a gene in the protozoan parasite Leishmania is important to identify potential targets for intervention and understanding the parasite biology. CRISPR gene editing technology has significantly improved gene targeting efficiency in Leishmania. There are two commonly used CRISPR gene targeting methods in Leishmania; the stable expression of the gRNA and Cas9 using a plasmid containing a Leishmania ribosomal RNA gene promoter (rRNA-P stable protocol) and the T7 RNA polymerase based transient gRNA expression system in promastigotes stably expressing Cas9 (T7 transient protocol).

Genome-based development and clinical evaluation of a customized LAMP panel to rapidly detect, quantify, and determine antibiotic sensitivity of Escherichia coli in native urine samples from urological patients.

Purpose: We designed and tested a point of care test panel to detect E.coli and antibiotic susceptibility in urine samples from patients at the point of care in the urological department. The aim of this approach is to facilitate choosing an appropriate antibiotic for urinary tract infections (UTI) at first presentation in the context of increasing antibiotic resistance in uropathogens worldwide.

New Record of Rhipicephalus fulvus (Neumann, 1913) from Goats and Sheep in Northeastern Algeria After more than a Century.

Purpose: Tick diversity in Algeria has garnered increasing interest due to its implications for animal health and zoonotic diseases. Recent reports of abnormal ulcerative lesions in goats and sheep in the Cheria region of northeastern Algeria have raised concerns about a potential association with tick infestations. The aim of this study is to hypothesize the potential involvement of ticks in these unusual lesions.

Low-dimensional controllability of brain networks.

Identifying the driver nodes of a network has crucial implications in biological systems from unveiling causal interactions to informing effective intervention strategies. Despite recent advances in network control theory, results remain inaccurate as the number of drivers becomes too small compared to the network size, thus limiting the concrete usability in many real-life applications. To overcome this issue, we introduced a framework that integrates principles from spectral graph theory and output controllability to project the network state into a smaller topological space formed by the Laplacian network structure.

Orchard: Building large cancer phylogenies using stochastic combinatorial search.

Phylogenies depicting the evolutionary history of genetically heterogeneous subpopulations of cells from the same cancer, i.e., cancer phylogenies, offer valuable insights about cancer development and guide treatment strategies.

Autoregulation of the glial gene reversed polarity in Drosophila.

During development, cells of the nervous system begin as unspecified precursors and proceed along one of two developmental paths to become either neurons or glia. Work in the fruit fly Drosophila melanogaster has established the role of the transcription factor Glial cells missing (Gcm) in directing neuronal precursor cells to assume a glial cell fate. Gcm acts on many target genes, one of which is reversed polarity (repo).

Inferring effects of mutations on SARS-CoV-2 transmission from genomic surveillance data.

New and more transmissible variants of SARS-CoV-2 have arisen multiple times over the course of the pandemic. Rapidly identifying mutations that affect transmission could improve our understanding of viral biology and highlight new variants that warrant further study. Here we develop a generic, analytical epidemiological model to infer the transmission effects of mutations from genomic surveillance data.

Nanoscale self-assembly and water retention properties of silk fibroin-riboflavin hydrogel.

Silk-fibroin hydrogels have gained considerable attention in recent years for their versatile biomedical applications. The physical properties of a complex hydrogel, comprising silk fibroin and riboflavin, surpass those of the silk fibroin-hydrogel without additives. This study investigates silk fibroin-riboflavin (silk-RIB) hydrogel at the atomistic level to uncover molecular structures and chemical characteristics specific to silk fibroin and riboflavin molecules in an aqueous medium.

Droplets in open microfluidics: generation, manipulation, and application in cell analysis.

Open droplet microfluidics is an emerging technology that generates, manipulates, and analyzes droplets in open configuration systems. Droplets function as miniaturized reactors for high-throughput analysis due to their compartmentalization and parallelization, while openness enables addressing and accessing the targeted contents. The convergence of two technologies facilitates the localization and intricate manipulation of droplets using external tools, showing great potential in large-scale chemical and biological applications, particularly in cell analysis.

Multivariable Predictive Model of Postoperative Delirium in Cardiac Surgery Patients: Proteomic and Demographic Contributions.

Background: Delirium after cardiac surgery is common, morbid, and costly, but may be prevented with risk stratification and targeted intervention. In this study, we aimed to identify protein biomarkers and develop a predictive model for postoperative delirium in older patients undergoing cardiac surgery.

Methods: SomaScan analysis of 1305 proteins in the plasma from 57 older adults undergoing cardiac surgery requiring cardiopulmonary bypass was conducted to define delirium-specific protein signatures at baseline (preoperative baseline timepoint [PREOP]) and postoperative day 2 (POD2).

Albumin-based nanocarriers loaded with novel Zn(II)-thiosemicarbazone compounds chart a new path for precision breast cancer therapy.

This study explores the therapeutic potential of albumin-bound Zn(II)-thiosemicarbazone compounds (Alb-ZnTcA, Alb-ZnTcB) against breast cancer cells. Previous research indicates that these compounds hinder cancer cell proliferation by blocking DNA synthesis, promoting oxidative stress to induce apoptosis, and disrupting the cell cycle to inhibit cellular division. This study focuses on the loading and characterization of these potentially chemically unstable compounds on bovine serum albumin-based nanocarriers.

A genome-scale metabolic model for the denitrifying bacterium Thauera sp. MZ1T accurately predicts degradation of pollutants and production of polymers.

The denitrifying bacterium Thauera sp. MZ1T, a common member of microbial communities in wastewater treatment facilities, can produce different compounds from a range of carbon (C) and nitrogen (N) sources under aerobic and anaerobic conditions. In these different conditions, Thauera modifies its metabolism to produce different compounds that influence the microbial community.