GraphCPP: The new state-of-the-art method for cell-penetrating peptide prediction via graph neural networks.

Background And Purpose: Cell-penetrating peptides (CPPs) are short amino acid sequences that can penetrate cell membranes and deliver molecules into cells. Several models have been developed for their discovery, yet these models often face challenges in accurately predicting membrane penetration due to the complex nature of peptide-cell interactions. Hence, there is a need for innovative approaches that can enhance predictive performance.

Disrupted sense of agency-related ownership and disownership increase in the Rubber Hand Illusion.

Empirical evidence suggests that body ownership and the sense of agency operate as an interactive system correlated with the level of consciousness during tasks involving modifications in body representation. This study sought to elucidate the nature of this association by documenting the verbal manifestations of this interaction. Specifically, the study aimed to reveal the role of a sense of agency in the individual sensitivity to the Rubber Hand Illusion (RHI).

Enhancing risk stratification models in localized prostate cancer by novel validated tissue biomarkers.

Background: Localized prostate cancer (PCa) is a largely heterogeneous disease regarding its clinical behavior. Current risk stratification relies on clinicopathological parameters and distinguishing between indolent and aggressive cases remains challenging. To improve risk stratification, we aimed to identify new prognostic markers for PCa.

Surface-enhanced infrared spectroscopic study of extracellular vesicles using plasmonic gold nanoparticles.

Extracellular vesicles (EVs), sub-micrometer lipid-bound particles released by most cells, are considered a novel area in both biology and medicine. Among characterization methods, infrared (IR) spectroscopy, especially attenuated total reflection (ATR), is a rapidly emerging label-free tool for molecular characterization of EVs. The relatively low number of vesicles in biological fluids (∼10 particle/mL), however, and the complex content of the EVs' milieu (protein aggregates, lipoproteins, buffer molecules) might result in poor signal-to-noise ratio in the IR analysis of EVs.

MFIB 2.0: a major update of the database of protein complexes formed by mutual folding of the constituting protein chains.

While the majority of proteins with available structures are able to fold independently and mediate interactions only after acquiring their folded state, a subset of the known protein complexes contains protein chains that are intrinsically disordered in isolation. The Mutual Folding Induced by Binding (MFIB) database collects and classifies protein complexes, wherein all constituent protein chains would be unstable/disordered in isolation but fold into a well-defined 3D complex structure upon binding. This phenomenon is often termed as cooperative folding and binding or mutual synergistic folding (MSF).

Electrophysiological indices of reward anticipation as ADHD risk and prognostic biomarkers.

The attention-deficit/hyperactivity disorder (ADHD) clinical phenotype has limitations for deciphering ADHD etiology and predicting prognosis. Although relative to the clinical phenotype, intermediate phenotypes may have better explanatory and prognostic power, the extent to which ADHD intermediate phenotypes are associated with ADHD risk and prognosis is unknown. The aim of this study was to evaluate evidence for event-related potential (ERP) measures of reward anticipation as ADHD risk and prognostic biomarkers.

The homodimerization domain of the Stl repressor is crucial for efficient inhibition of mycobacterial dUTPase.

The dUTPase is a key DNA repair enzyme in Mycobacterium tuberculosis, and it may serve as a novel promising anti-tuberculosis target. Stl repressor from Staphylococcus aureus was shown to bind to and inhibit dUTPases from various sources, and its expression in mycobacterial cells interfered with cell growth. To fine-tune and optimize Stl-induced inhibition of mycobacterial dUTPase, we aimed to decipher the molecular details of this interaction.

Recognition of BACH1 quaternary structure degrons by two F-box proteins under oxidative stress.

Ubiquitin-dependent proteolysis regulates diverse cellular functions with high substrate specificity, which hinges on the ability of ubiquitin E3 ligases to decode the targets' degradation signals, i.e., degrons.

An experimental and computational study of the unimolecular-decay reaction of diethyl-substituted Criegee intermediate (CH)COO.

We have performed direct kinetic measurements to determine the thermal unimolecular-decay rate coefficient of (CH)COO as a function of temperature (223-296 K) and pressure (4-100 torr) using time-resolved UV-absorption spectroscopy. The stabilised (CH)COO Criegee intermediate was produced by photolysing 3-bromo-3-iodopentane ((CH)CIBr) with 213 nm radiation in the presence of O. We performed quantum-chemistry calculations and master-equation simulations to complement the experimental work.

Intact ultrafast memory consolidation in adults with autism and neurotypicals with autism traits.

The processes of learning and memory consolidation are closely interlinked. Therefore, to uncover statistical learning in autism spectrum disorder (ASD), an in-depth examination of memory consolidation is essential. Studies of the last five years have revealed that learning can take place not only during practice but also during micro rest (<1 min) between practice blocks, termed micro offline gains.

Optimizing the composition of LaF:Yb,Tm upconverting nanoparticles synthesised by the co-precipitation method to improve the emission intensity.

LaF:1-6 mol%Yb,0.1 mol%Tm nanoparticles with upconversion properties were synthesised by the co-precipitation method. Particles were characterized by transmission electron microscopy coupled with energy-dispersive spectrometry, inductively coupled plasma optical emission spectrometry, X-ray diffraction, and simultaneous thermogravimetry and differential thermal analysis.

Unravelling the Complexity of Amyloid Peptide Core Interfaces.

Amyloids, large intermolecular sandwiched β-sheet structures, underlie several protein misfolding diseases but have also been shown to have functional roles and can be a basis for designing smart and responsive nanomaterials. Short segments of proteins, called aggregation-prone regions (APRs), have been identified that nucleate amyloid formation. Here we present the database of 173 APR crystal structures currently available in the PDB, and a tool, ACW, for analyzing their topologies and the 267 inter-β-sheet interfaces of zipper regions assigned in these structures.

Quantitative Biodistribution of OMVs Using SPECT/CT Imaging with HYNIC-Duramycin Radiolabeling.

Bacterial outer membrane vesicles (OMVs) are emerging as important players in the host-microbiome interaction, while also proving to be a promising platform for vaccine development and targeted drug delivery. The available methods for measuring their biodistribution, however, are limited. We aimed to establish a high-efficiency radiolabeling method for the treatment of OMVs.

Association of modifiable risk factors with progression to dementia in relation to amyloid and tau pathology.

Background: Dementia preventive interventions targeting multiple modifiable risk factors are a promising approach. However, the impact of modifiable risk factors in the presence of beta-amyloid or phosphorylated-tau (p-tau) pathology is unclear.

Methods: The objective of the study was to examine the role of modifiable risk factors (vascular factors, depression, and smoking) in the progression to mild cognitive impairment (MCI) or dementia among 434 cognitively unimpaired (CU) and 611 individuals with MCI from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database.

Utilization of desilication products as efficient adsorbents for the removal of basic fuchsine.

Desilication products (DSPs) are one of the main components of bauxite residue, which is currently discharged without further usage. The present study reports on the use of DSPs as adsorbents for basic fuchsine dye. Using artificial spent liquor, we synthesized not only neat DSP but also solids in the presence of various organics, to account for their likely occurrence during the Bayer process.

Interaction Between Heavy Metals Posed Chemical Stress and Essential Oil Production of Medicinal Plants.

Plants exposed to abiotic stressors show diverse physiological, biochemical, and molecular responses. Biosynthesis of plant secondary metabolites-including essential oils-is a vital plant defense mechanism. As these bioactive compounds are widely used in the pharmaceutical, cosmetic and food industries, it is essential to understand how their production is affected in various environments.

Basal State Calibration of a Chemical Reaction Network Model for Autophagy.

The modulation of autophagy plays a dual role in tumor cells, with the potential to both promote and suppress tumor proliferation. In order to gain a deeper understanding of the nature of autophagy, we have developed a chemical reaction kinetic model of autophagy and apoptosis based on the mass action kinetic models that have been previously described in the literature. It is regrettable that the authors did not provide all of the information necessary to reconstruct their model, which made their simulation results irreproducible.

Deep learning-based spike sorting: a survey.

Deep learning is increasingly permeating neuroscience, leading to a rise in signal-processing applications for extracellular recordings. These signals capture the activity of small neuronal populations, necessitating 'spike sorting' to assign action potentials (spikes) to their underlying neurons. With the rise in publications delving into new methodologies and techniques for deep learning-based spike sorting, it is crucial to synthesise these findings critically.

Novel, Fluorine-Free Membranes Based on Sulfonated Polyvinyl Alcohol and Poly(ether-block-amide) with Sulfonated Montmorillonite Nanofiller for PEMFC Applications.

Novel blend membranes containing S-PVA and PEBAX 1657 with a blend ratio of 8:2 (referred to as SPP) were prepared using a solution-casting technique. In the manufacturing process, sulfonated montmorillonite (S-MMT) in ratios of 0%, 3%, 5%, and 7% was used as a filler. The crystallinity of composite membranes has been investigated by X-ray diffraction (XRD), while the interaction between the components was evaluated using Fourier-transform infrared spectroscopy (FT-IR).

A (sub)field guide to quality control in hippocampal subfield segmentation on high-resolution T-weighted MRI.

Inquiries into properties of brain structure and function have progressed due to developments in magnetic resonance imaging (MRI). To sustain progress in investigating and quantifying neuroanatomical details in vivo, the reliability and validity of brain measurements are paramount. Quality control (QC) is a set of procedures for mitigating errors and ensuring the validity and reliability of brain measurements.

Development and validation of a gene expression-based Breast Cancer Purity Score.

The prevalence of malignant cells in clinical specimens, or tumour purity, is affected by both intrinsic biological factors and extrinsic sampling bias. Molecular characterization of large clinical cohorts is typically performed on bulk samples; data analysis and interpretation can be biased by tumour purity variability. Transcription-based strategies to estimate tumour purity have been proposed, but no breast cancer specific method is available yet.

Comparative Study of Allosteric GPCR Binding Sites and Their Ligandability Potential.

The steadily growing number of experimental G-protein-coupled receptor (GPCR) structures has revealed diverse locations of allosteric modulation, and yet few drugs target them. This gap highlights the need for a deeper understanding of allosteric modulation in GPCR drug discovery. The current work introduces a systematic annotation scheme to structurally classify GPCR binding sites based on receptor class, transmembrane helix contacts, and, for membrane-facing sites, membrane sublocation.