A novel label-free method to determine equilibrium dissociation constants of antibodies binding to cell surface proteins.

Solution-based affinity assays are used for the selection and characterization of proteins that could be developed into therapeutic molecules. However, these assays have limitations for cell-surface proteins as in most cases their purification requires detergent solubilization and are unlikely to assume conformations in solution that resemble their native states in cell membranes. This report describes a novel electrochemiluminescence-based method, called MSD-CAT, for the affinity analysis of antibodies binding to cell-surface receptors.

The role of homogenization cycles and Poloxamer 188 on the quality of mitochondria isolated for use in mitochondrial transplantation therapy.

Mitochondrial transplantation (MTx) offers a promising therapeutic approach to mitigate mitochondrial dysfunction in conditions such as ischemia-reperfusion (IR) injury. The quality and viability of donor mitochondria are critical to MTx success, necessitating the optimization of isolation protocols. This study aimed to assess a rapid mitochondrial isolation method, examine the relationship between mitochondrial size and membrane potential, and evaluate the potential benefits of Poloxamer 188 (P-188) in improving mitochondrial quality during the isolation process.

NIRS-BIDS: Brain Imaging Data Structure Extended to Near-Infrared Spectroscopy.

Functional near-infrared spectroscopy (fNIRS) is an increasingly popular neuroimaging technique that measures cortical hemodynamic activity in a non-invasive and portable fashion. Although the fNIRS community has been successful in disseminating open-source processing tools and a standard file format (SNIRF), reproducible research and sharing of fNIRS data amongst researchers has been hindered by a lack of standards and clarity over how study data should be organized and stored. This problem is not new in neuroimaging, and it became evident years ago with the proliferation of publicly available neuroimaging datasets.

Waste marble sludge and calcined clay brick powders in conventional cement farina production for cleaner built environment.

In the manufacturing of some sectors, such as marble and brick, certain byproducts, such as sludge, powder, and pieces containing valuable chemical compounds, emerge. Some concrete plants utilize these byproducts as mineralogical additives in Turkey. The objective of the experimental study is to ascertain whether the incorporation of waste from the marble and brick industries, in powder form, into cement manufacturing as a mineralogical additive or substitute is a viable option.

Developing anti-TDE vaccine for sensitizing cancer cells to treatment and metastasis control.

Tumor-derived exosomes (TDEs) mediate oncogenic communication, which modifies target cells to reinforce a tumor-promoting microenvironment. TDEs support cancer progression by suppressing anti-tumor immune responses, promoting metastasis, and conferring drug resistance. Thus, targeting TDEs could improve the efficacy of anti-cancer treatments and control metastasis.

A compendium of Amplification-Related Gain Of Sensitivity genes in human cancer.

While the effect of amplification-induced oncogene expression in cancer is known, the impact of copy-number gains on "bystander" genes is less understood. We create a comprehensive map of dosage compensation in cancer by integrating expression and copy number profiles from over 8000 tumors in The Cancer Genome Atlas and cell lines from the Cancer Cell Line Encyclopedia. Additionally, we analyze 17 cancer open reading frame screens to identify genes toxic to cancer cells when overexpressed.

Simultaneous aerobic and anaerobic respiration in hot spring chemolithotrophic bacteria.

Aerobic and anaerobic organisms and their functions are spatially or temporally decoupled at scales ranging from individual cells to ecosystems and from minutes to hours. This is due to competition for energy substrates and/or biochemical incompatibility with oxygen (O). Here we report a chemolithotrophic Aquificales bacterium, Hydrogenobacter, isolated from a circumneutral hot spring in Yellowstone National Park (YNP) capable of simultaneous aerobic and anaerobic respiration when provided with hydrogen (H), elemental sulfur (S), and O.

Who is American? A comprehensive analysis of the American = White/Foreign = Asian stereotype (2007-2023).

Against the backdrop of increasing ethnic diversity in the U.S., we replicate, extend, and challenge previous examinations of the American = White/Foreign = Asian stereotype in the largest sample to date (N = 666,623 respondents) over 17 years (2007-2023).

Strengthening biopolymer adhesives through ureolysis-induced calcium carbonate precipitation.

Common adhesives for nonstructural applications are manufactured using petrochemicals and synthetic solvents. These adhesives are associated with environmental and health concerns because of their release of volatile organic compounds (VOCs). Biopolymer adhesives are an attractive alternative because of lower VOC emissions, but their strength is often insufficient.

A global dataset of freshwater fish trophic interactions.

Freshwater management and research frequently rely on trophic data to manage freshwater fishes, yet it is difficult to perform a simple search of dietary information for any one species. FishBase represents the largest effort to organize freshwater dietary data into a singular, navigable dataset. Nonetheless, FishBase excludes a large portion of the ecological literature because it was developed before the creation of most modern scientific search engines.

Optimal life-cycle adaptation of coastal infrastructure under climate change.

Climate change-related risk mitigation is typically addressed using cost-benefit analysis that evaluates mitigation strategies against a wide range of simulated scenarios and identifies a static policy to be implemented, without considering future observations. Due to the substantial uncertainties inherent in climate projections, this identified policy will likely be sub-optimal with respect to the actual climate trajectory that evolves in time. In this work, we thus formulate climate risk management as a dynamic decision-making problem based on Markov Decision Processes (MDPs) and Partially Observable MDPs (POMDPs), taking real-time data into account for evaluating the evolving conditions and related model uncertainties, in order to select the best possible life-cycle actions in time, with global optimality guarantees for the formulated optimization problem.

GPX modulation promotes regenerative axonal fusion and functional recovery after injury through PSR-1 condensation.

Axonal fusion represents an efficient way to recover function after nerve injury. However, how axonal fusion is induced and regulated remains largely unknown. We discover that ferroptosis signaling can promote axonal fusion and functional recovery in C.

Phosphorylation-dependent WRN-RPA interaction promotes recovery of stalled forks at secondary DNA structure.

The WRN protein is vital for managing perturbed replication forks. Replication Protein A strongly enhances WRN helicase activity in specific in vitro assays. However, the in vivo significance of RPA binding to WRN has largely remained unexplored.

Short-term evolutionary implications of an introgressed size-determining supergene in a vulnerable population.

The Thorny Skate (Amblyraja radiata) is a vulnerable species displaying a discrete size-polymorphism in the northwest Atlantic Ocean (NWA). We conducted whole genome sequencing of samples collected across its range. Genetic diversity was similar at all sampled sites, but we discovered a ~ 31 megabase bi-allelic supergene associated with the size polymorphism, with the larger size allele having introgressed in the last ~160,000 years B.

Utilizing TP53 hotspot mutations as effective predictors of gemcitabine treatment outcome in non-small-cell lung cancer.

TP53 mutations are recognized to correlate with a worse prognosis in individuals with non-small cell lung cancer (NSCLC). There exists an immediate necessity to pinpoint selective treatment for patients carrying TP53 mutations. Potential drugs were identified by comparing drug sensitivity differences, represented by the half-maximal inhibitory concentration (IC50), between TP53 mutant and wild-type NSCLC cell lines using database analysis.

Automatic speech recognition predicts contemporaneous earthquake fault displacement.

Significant progress has been made in probing the state of an earthquake fault by applying machine learning to continuous seismic waveforms. The breakthroughs were originally obtained from laboratory shear experiments and numerical simulations of fault shear, then successfully extended to slow-slipping faults. Here we apply the Wav2Vec-2.

msiFlow: automated workflows for reproducible and scalable multimodal mass spectrometry imaging and microscopy data analysis.

Multimodal imaging by matrix-assisted laser desorption ionisation mass spectrometry imaging (MALDI MSI) and microscopy holds potential for understanding pathological mechanisms by mapping molecular signatures from the tissue microenvironment to specific cell populations. However, existing software solutions for MALDI MSI data analysis are incomplete, require programming skills and contain laborious manual steps, hindering broadly applicable, reproducible, and high-throughput analysis to generate impactful biological discoveries. Here, we present msiFlow, an accessible open-source, platform-independent and vendor-neutral software for end-to-end, high-throughput, transparent and reproducible analysis of multimodal imaging data.

Helioseismic inference of the solar radiative opacity.

The Sun is the most studied of all stars, and thus constitutes a benchmark for stellar models. However, our vision of the Sun is still incomplete, as illustrated by the current debate on its chemical composition. The problem reaches far beyond chemical abundances and is intimately linked to microscopic and macroscopic physical ingredients of solar models such as radiative opacity, for which experimental results have been recently measured that still await theoretical explanations.

The transcriptional response of cortical neurons to concussion reveals divergent fates after injury.

Traumatic brain injury (TBI) is a risk factor for neurodegeneration, however little is known about how this kind of injury alters neuron subtypes. In this study, we follow neuronal populations over time after a single mild TBI (mTBI) to assess long ranging consequences of injury at the level of single, transcriptionally defined neuronal classes. We find that the stress-responsive Activating Transcription Factor 3 (ATF3) defines a population of cortical neurons after mTBI.

Splicing accuracy varies across human introns, tissues, age and disease.

Alternative splicing impacts most multi-exonic human genes. Inaccuracies during this process may have an important role in ageing and disease. Here, we investigate splicing accuracy using RNA-sequencing data from >14k control samples and 40 human body sites, focusing on split reads partially mapping to known transcripts in annotation.

Finding gaps in the national electric vehicle charging station coverage of the United States.

The United States federal government has invested $7.5 billion into charging infrastructure, including the National Electric Vehicle Infrastructure Program, to build fast charging stations along designated highways for long-distance car travel. We develop a consecutive coverage metric to compute the percent of United States roads (traffic-weighted) that are consecutively accessible within 500 miles of each county.

Sanctuary for vulnerable Arctic species at the Borealis Mud Volcano.

Borealis is a recently discovered submerged mud volcano in the Polar North Atlantic, differing from the numerous methane seepages previously identified in the region. Here we show in situ observations from a remotely operated vehicle (ROV), capturing the release of warm (11.5 °C) Neogene sediments and methane-rich fluids from a gryphon at Borealis.

Integrating representation learning, permutation, and optimization to detect lineage-related gene expression patterns.

Recent barcoding technologies allow reconstructing lineage trees while capturing paired single-cell RNA-sequencing (scRNA-seq) data. Such datasets provide opportunities to compare gene expression memory maintenance through lineage branching and pinpoint critical genes in these processes. Here we develop Permutation, Optimization, and Representation learning based single Cell gene Expression and Lineage ANalysis (PORCELAN) to identify lineage-informative genes or subtrees where lineage and expression are tightly coupled.

Current Practices and Evidence of Aspirin Usage in Microvascular Surgery: A Systematic Review and Meta-Analysis.

Background: Acetylsalicylic acid (ASA) has been used in reconstructive microsurgery since the inception of the field. However, when compared to placebo groups, its efficacy is not confirmed. In our study, we hypothesize that the utility of ASA postoperatively in microvascular surgery is not associated with improved outcomes.