bluuebunny/crossref_metadata_2025_split huggingface dataset:
Volatiles from low R:FR-treated maize plants increase the emission of herbivore-induced plant volatiles in their neighbors
Authors: Escobar-Bravo Rocío , Schimmel Bernardus C.J. , Erb Matthias 
Published: October 2024

ABSTRACTLow Red (R) to Far Red (FR) light ratios, a light signal associated with vegetation shade, can prompt intact maize (Zea mays) plants to constitutively emit more volatiles when exposed to herbivory-induced plant volatiles (HIPVs). Here we investigated how simulated shading affects priming responses in the context of volatile-mediated plant-plant interactions. Receiver maize plants were exposed to either constitutive volatile organic compounds (cVOCs) or HIPVs from emitter maize plants, while we manipulated R:FR light conditions of receivers or emitters. Priming responses in the receivers were then assessed by measuring real-time volatile emissions following simulated herbivory. We show that low R:FR light enhances HIPVs emissions in plants previously exposed to HIPVs from neighbours independently of the light conditions of emitters. We also demonstrate that both cVOCs and HIPVs emitted by maize grown under low R:FR amplify HIPVs emissions in their neighbours. This amplified response could not be explained by FR-mediated changes in the release of green leaf volatiles or terpenoids by emitters, thus suggesting the involvement of other VOCs. We conclude that volatile-mediated plant-plant interactions can be expected to become more intense in denser canopies due to light-mediated amplification of volatile emission and responsiveness.
Predicting The Pathway Involvement For All Pathway and Associated Compound Entries Defined in the Kyoto Encyclopedia of Gene and Genomes
Authors: Huckvale Erik D. , Moseley Hunter N.B. 
Published: October 2024

AbstractBackground/ObjectivesPredicting the biochemical pathway involvement of a compound could facilitate the interpretation of biological and biomedical research. Prior prediction approaches have largely focused on metabolism, training machine learning models to solely predict on metabolic pathways. However, there are many other types of pathways in cells and organisms which are of interest to biologists;MethodsWhile several publications have made use of the metabolites and metabolic pathways available in the Kyoto Encyclopedia of Genes and Genomes (KEGG), we downloaded all the compound entries with pathway annotations available in KEGG. From this data, we constructed a dataset where each entry contained features representing compounds combined with features representing pathways followed by a binary label indicating whether the given compound is associated with the given pathway. We trained multi-layer perceptron binary classifiers on variations of this dataset;ResultsThe model trained on all KEGG compounds and pathways scored an overall mean performance of 0.847, median of 0.848, and standard deviation of 0.0098.ConclusionsThe mean performance of 0.847 with a standard deviation of 0.0098 for all KEGG pathways, compared to the performance of 0.800 and standard deviation of 0.021 of metabolic KEGG pathways only, demonstrates the capability to effectively predict biochemical pathways in general in addition to those specifically related to metabolism. Moreover, the improvement in the performance demonstrates additional transfer learning with the inclusion of non-metabolic pathways.
Genetic Adaptation to Amoxicillin inEscherichia coli: The Limited Role ofdinBandkatE
Authors: Teichmann Lisa , Wenne Marcus , Luitwieler Sam , Dugar Gaurav , Bengtsson-Palme Johan , Kuile Benno ter 
Published: October 2024

AbstractBacteria can quickly adapt to sub-lethal concentrations of antibiotics. Several stress and DNA repair genes contribute to this adaptation process. However, the pathways leading to adaptation by acquisition ofde novomutations remain poorly understood. This study explored the roles of DNA polymerase IV (dinB) and catalase HP2 (katE) inE. coli’s adaptation to amoxicillin. These genes are thought to play essential roles in beta-lactam resistance -dinBin increasing mutation rates andkatEin managing oxidative stress. By comparing the adaptation rates, transcriptomic profiles, and genetic changes of wild-type and knockout strains, we aimed to clarify the contributions of these genes to beta-lactam resistance. While all strains exhibited similar adaptation rates and mutations in thefrdDgene andampCoperon, several unique mutations were acquired in the ΔkatEand ΔdinBstrains. Overall, this study distinguishes the contributions of general stress-related genes on the one hand, anddinB,andkatEon the other hand, in development of beta-lactam resistance.
The impact of barcode-assisted medication administration on medication administration errors in non-unit-dose settings: a systematic review
Authors: Tan Weicong , Bingham Gordon , Tong Erica , Bonakdeh Erfan Shakibaei , Wang Weiqing 
Published: October 2024

AbstractObjectiveThis study aims to investigate how barcode-assisted medication administration systems (BCMAs) can affect medication administration errors (MAEs) in non-unit-dose dispensing settings, since unit dose dispensing system can be a confounding variable affecting MAE rates.Materials and MethodsWe conducted a systematic review of articles on MEDLINE, EMBASE, EMCARE, CINAHL and Scopus. Studies are meticulously examined to exclude those with unit-dose dispensing setting.ResultsWe included 4 papers in the review. The categories of MAEs reported among these studies are heterogeneous. 2 studies give weak evidence and 1 study give moderate evidence that BCMA can lower some categories of MAEs. 1 studies gives weak evidence that BCMA increase the wrong administration time error.DiscussionStudies provide weak to moderate evidence that barcode-assisted medication administration can lower certain categories of medication administration errors. However, some reported findings are minimal.ConclusionMore multi-ward multi-hospital studies need to be conducted to provide stronger evidence on BCMA’s impact on MAEs, especially on dosage-related MAEs, in settings without unit dose dispensing systems.
Membrane Expression Enhances Folding, Multimeric Structure Formation, and Immunogenicity of Viral Capsid Proteins
Authors: Cui Junru , Yuan Fangfeng , Qin Jane , Jeon Ju Hyeong , Yun Dong Soo , Wang Tianlei , Xu Renhuan , Cao Helen , Chen Jianzhu 
Published: October 2024

AbstractViral capsid proteins are widely explored for subunit vaccine development but are often hampered by their complexity of production and low immunogenicity. Here, we report a simple approach to overcome these challenges by combining mRNA vaccine technology with protein engineering. Using African swine fever virus (ASFV) capsid proteins P72 and penton as models, we engineered them into membrane-bound and secreted forms, and compared their immunogenicity to the native intracellular form in mice and pigs through mRNA vaccination. The membrane-bound and secreted P72 and penton folded into their native multimeric structure independent of viral chaperone, therefore preserving their conformational epitopes. The membrane-bound P72 and penton also elicited significantly stronger antibody and T cell responses than their secreted or intracellular counterparts. Our study provides a simple approach to enhance folding, multimeric structure formation, and immunogenicity of viral capsid proteins for ASFV subunit vaccine development and immunogenicity of intracellular proteins in general.
Mapping the PTEN Mutation Landscape: Structural and Functional Drivers of Lung Cancer
Authors: Hossain Mohammad Uzzal , Sakib Mohammad Nazmus , Rahman A.B.Z. Naimur , Hasan SM Sajid , Nisha Nazia Hassan , Bhattacharjee Arittra , Chowdhury Zeshan Mahmud , Ahammad Ishtiaque , Das Keshob Chandra , Rahman Mohammad Shahedur , Salimullah Md. 
Published: October 2024

AbstractLung cancer is the predominant form of cancer globally, arising from the dysfunction of genetic mutations. Although PTEN mutation is crucial in the aetiology of lung cancer, the mapping of these major drivers has to be determined. We leverage computational algorithms on 43,855 SNPs of PTEN to discover the mutational impact contributing to lung cancer. Fifteen variations were identified as detrimental, and no pertinent studies have previously addressed their structural and functional aspects. Notably, seven variations were identified as the most significant contributors to lethal effects in functional aberration, as demonstrated by the computational assessment. Subsequently, molecular simulation elucidated the structural instability associated with these alterations. Furthermore, drug binding experiments at the mutational site corroborated the destabilization experiments by demonstrating the conformational alteration of the structure, resulting in varied amino acid interactions. In summary, the present study elucidates the influence of mutations in PTEN structure on its functional architecture.
How to select the best zero-shot model for the viral proteins?
Authors: Yu Yuanxi , Jiang Fan , Zhong Bozitao , Hong Liang , Li Mingchen 
Published: October 2024

AbstractPredicting the fitness of viral proteins holds notable implications for understanding viral evolution, advancing fundamental biological research, and informing drug discovery. However, the considerable variability and evolution of viral proteins make predicting mutant fitness a major challenge. This study introduces the ProPEC, a Perplexity-based Ensemble Model, aimed at improving the performance of zero-shot predictions for protein fitness across diverse viral datasets. We selected five representative pretrained language models (PLMs) as base models. ProPEC, which integrates perplexity-weighted scores from these PLMs with GEMME, demonstrates superior performance compared to individual models. Through parameter sensitivity analysis, we highlight the robustness of perplexity-based model selection in ProPEC. Additionally, a case study on T7 RNA polymerase activity dataset underscores ProPEC’s predictive capabilities. These findings suggest that ProPEC offers an effective approach for advancing viral protein fitness prediction, providing valuable insights for virology research and therapeutic development.TOC Graphic
Investigating Mechanically Activated Currents from Trigeminal Neurons of Non-Human Primates
Authors: Lindquist Karen A , Mecklenburg Jennifer , Hovhannisyan Anahit H. , Ruparel Shivani , Akopian Armen N. 
Published: October 2024

AbstractIntroductionPain sensation has predominantly mechanical modalities in many pain conditions. Mechanically activated (MA) ion channels on sensory neurons underly responsiveness to mechanical stimuli. The study aimed to address gaps in knowledge regarding MA current properties in higher order species such as non-human primates (NHP; common marmosets), and characterization of MA currents in trigeminal (TG) neuronal subtypes.MethodsWe employed patch clamp electrophysiology and immunohistochemistry (IHC) to associate MA current types to different marmoset TG neuronal groups. TG neurons were grouped according to presumed marker expression, action potential (AP) width, characteristic AP features, after-hyperpolarization parameters, presence/absence of AP trains and transient outward currents, and responses to mechanical stimuli.ResultsMarmoset TG were clustered into 5 C-fiber and 5 A-fiber neuronal groups. The C1 group likely represent non-peptidergic C-nociceptors, the C2-C4 groups resembles peptidergic C-nociceptors, while the C5 group could be either cold-nociceptors or C-low-threshold-mechanoreceptors (C-LTMR). Among C-fiber neurons only C4 were mechanically responsive. The A1 and A2 groups are likely A-nociceptors, while the A3-A5 groups probably denote different subtypes of A-low-threshold-mechanoreceptors (A-LTMRs). Among A-fiber neurons only A1 was mechanically unresponsive. IHC data was correlated with electrophysiology results and estimates that NHP TG has ∼25% peptidergic C-nociceptors, ∼20% non-peptidergic C-nociceptors, ∼30% A-nociceptors, ∼5% C-LTMR, and ∼20% A-LTMR.ConclusionOverall, marmoset TG neuronal subtypes and their associated MA currents have common and unique properties compared to previously reported data. Findings from this study could be the basis for investigation on MA current sensitizations and mechanical hypersensitivity during head and neck pain conditions.
A Method for Electrical Stimulus Artifact Removal Exploiting Neural Refractoriness: Validation by Contrasting Cathodic and Anodic Stimulation
Authors: Nakhmani A. , Block J. , Awad M. , Olson J. , Smith R. , Bentley J.N. , Holland M. , Brinkerhoff S.A. , Gonzalez C. , Moffitt M. , Walker H. 
Published: October 2024

AbstractObjectiveTo present a novel method for removing stimulus transient that exploits the absolute refractory period of electrically excitable neural tissues.BackgroundElectrical stimulation often generates significant signal artifacts that can obscure important physiological signals. Removal of the artifact and understanding latent information from these signals could provide objective measures of circuit engagement, potentially driving advancements in neuromodulation research and therapies.MethodsWe conducted intracranial physiology studies on five consecutive patients with Parkinson’s disease who underwent deep brain stimulation (DBS) surgery as part of their routine care. Monopolar stimuli (either cathodic or anodic) were delivered in pairs through the DBS electrode across a range of inter-stimulus intervals. Recordings from adjacent unused electrode contacts used broadband sampling and precise synchronization to generate a robust template for the stimulus transient during the absolute refractory period. These templates of stimulus transient were then subtracted from recordings at different intervals to extract and analyze the residual neural potentials.ResultsAfter artifact removal, the residual signals exhibited absolute and relative refractory periods with timing indicative of neural activity. Cathodic and anodic DBS pulses generated distinct patterns of local tissue activation, showing phase independence from the prior stimulus. The earliest detectable neural responses occurred at short peak latencies (ranging from 0.19 to 0.38 ms post-stimulus) and were completely or partially obscured by the stimulus artifact prior to removal. Cathodic stimuli produced stronger local tissue responses than anodic stimuli, aligning with clinical observations of lower activation thresholds for cathodic stimulation. However, cathodic and anodic pulses induced artifact patterns that were equivalent but opposite.InterpretationThe proposed artifact removal technique enhances prior approaches by allowing direct measurement of local tissue responses without requirements for stimulus polarity reversal, template scaling, or specialized filters. This approach could be integrated into future neuromodulation systems to visualize stimulus-evoked neural potentials that would otherwise be obscured by stimulus artifacts.
Weakened airway epithelial junctions and enhanced neutrophil elastase release contribute to age-dependent bacteremia risk following pneumococcal pneumonia
Authors: Xu Shuying , Zhu Tianmou , Mou Hongmei , Tan Shumin , Leong John M. 
Published: October 2024

ABSTRACTStreptococcus pneumoniae(Sp; pneumococcus), the most common agent of community-acquired pneumonia, can spread systemically, particularly in the elderly, highlighting the need for adjunctive therapies. The airway epithelial barrier defends against bacteremia and is dependent upon apical junctional complex (AJC) proteins such as E-cadherin. After mouse lung challenge, pneumolysin (PLY), a keySpvirulence factor, stimulates epithelial secretion of an inflammatory eicosanoid, triggering the infiltration of polymorphonuclear leukocytes (PMNs) that secrete high levels of neutrophil elastase (NE), thus promoting epithelial damage and systemic infection. Here, pulmonary E-cadherin staining of intratracheally inoculated mice revealed PLY-mediated disruption of AJC independently of PMNs. Apical infection of air-liquid interface (ALI) respiratory epithelial monolayers similarly showed that PLY disrupts AJCs. This epithelial damage promoted PMN transmigration and bacterial apical-to-basolateral translocation, and pharmacologically fortifying epithelial barrier function diminished both barrier breachin vitroand bacteremiain vivo. E-cadherin staining afterSpintratracheal inoculation of >20-month-old mice, or apical infection of ALI monolayers derived from these mice, revealed an age-associated vulnerability to PLY-mediated AJC disruption, which in turn enhanced PMN migration and bacteremia. In addition, we found that PMNs from aged mice secrete increased levels of tissue-damaging NE. Simultaneous pharmacological inhibition of tissue-destructive NE and fortification of pulmonary epithelial barrier function was required to reduce the level ofSpbacteremia in aged mice to that of young mice. This work underscores the importance of fully characterizing the multifactorial sources of age-associated susceptibility in devising adjunctive therapies to mitigate invasive pneumococcal disease in the elderly.
Measuring DNA contents of animal and plant genomes with Gnodes, the long and short of it
Authors: Gilbert Donald G. 
Published: October 2024

AbstractMeasurement of DNA contents of genomes is valuable for understanding genome biology, including assessments of genome assemblies, but it is not a trivial problem. Measuring contents of DNA shotgun reads is complicated by several factors: biological contents of genomes at species, individual and tissue or cell levels, laboratory methods, sequencing technology and computational processing for measurement and assembly. This compares, and shares, complications with cytometric (Cym) and related molecular measurements of genome size and contents.There is an obvious discrepancy between cytometric measurements and current long-read genome assemblies (Asm): genome assemblies average 12% below Cym measured sizes, differing in amounts of duplicated content. This report examines five DNA read types to see if they can be used for more precise and reliable discrimination of major genome contents and sizes. The read types are short, accurate Illumina, long Pacific Biosciences, of low and high accuracy, and long Oxford Nanopore Technology of low and high accuracy. Gnodes is the measurement tool used, which maps DNA to assembly, and measures DNA copy numbers for major genome contents of genes, transposons, repeats, and others, using as a measurement unit the single copies of unique conserved genes. Public data of five well studied genomes, human, corn, zebrafish, sorghum and rice, are used for the primary evidence of this work.Results of this are mixed and open to interpretations: In broad terms, all DNA types measure about the same genome contents, at or below 90% agreement, which is a level that the other complications can contribute. For precision above a 90% level, long read types differ in supporting larger cytometric sizes (low accuracy reads), or smaller assembly sizes (high accuracy reads), with accurate short-reads roughly between. The weight of evidence suggests that low accuracy long reads are less biased for genome measurement, that high accuracy long reads have a bias of reduced duplications introduced by computational averaging or filtering. The several complicating factors noted can produce discrepancies larger than this average Cym - Asm difference, and are a problem to control.
Fibroblast growth factor-inducible 14 regulates satellite cell self-renewal and expansion during skeletal muscle repair
Authors: Tomaz da Silva Meiricris , Joshi Aniket S. , Kumar Ashok 
Published: October 2024

ABSTRACTSkeletal muscle regeneration in adults is predominantly driven by satellite cells. Loss of satellite cell pool and function leads to skeletal muscle wasting in many conditions and disease states.Here, we demonstrate that the levels of fibroblast growth factor-inducible 14 (Fn14) are increased in satellite cells after muscle injury. Conditional ablation of Fn14 in Pax7-expressing satellite cells drastically reduces their expansion and skeletal muscle regeneration following injury. Fn14 is required for satellite cell self-renewal and proliferation as well as to prevent precocious differentiation. Targeted deletion of Fn14 inhibits Notch signaling but leads to the spurious activation of STAT3 signaling in regenerating skeletal muscle and in cultured muscle progenitor cells. Silencing of STAT3 improves proliferation and inhibits premature differentiation of Fn14-deficient satellite cells. Furthermore, conditional ablation of Fn14 in satellite cells exacerbates myopathy in the mdx mouse model of Duchenne muscular dystrophy (DMD) whereas its overexpression improves the engraftment of exogenous muscle progenitor cells into the dystrophic muscle of mdx mice. Altogether, our study highlights the crucial role of Fn14 in the regulation of satellite cell fate and function and suggests that Fn14 can be a potential molecular target to improve muscle regeneration in muscular disorders.
Post-COVID-Syndrome patients might overestimate own cognitive impairment
Authors: Wöhrstein Sofia , Matuz Tamara , Rötzer Lilli , Karnath Hans-Otto 
Published: October 2024

AbstractAfter a COVID-19 infection, some patients experience long-term consequences known as Post-Covid Syndrome, which often includes cognitive impairment. We investigated the congruence between subjectively experienced and objectively measured cognitive deficits after a COVID-19 infection in an unselected, successively admitted cohort of 38 patients reporting subjective cognitive complaints (SCC). We employed a comprehensive neuropsychological test battery to assess objective cognitive impairment across various cognitive domains. Three different cut-off criteria were applied commonly used in the literature to define objective neurocognitive disorder (NCD). We observed a notably low congruence between SCC and NCD in Post-Covid Syndrome, regardless of the cut-off criterion. Depending on the cognitive domain, only 5% to maximally 36% of the SCC could be objectified. One possible explanation for this discrepancy could be the high rate of depressive symptoms observed in the group of patients studied, which may negatively influence the perception of own cognitive abilities. These findings emphasize the need for careful evaluation of SCC in Post-Covid Syndrome and suggest that treating depressive symptoms may also alleviate some of the perceived cognitive deficits.