bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating the Influence of prolonged Stroop task on mental fatigue and the consequences on corticospinal and corticocortical excitability: A pilot study
Authors: Salihu Abubakar Tijjani , Hill Keith D. , Zoghi Maryam , Jaberzadeh Shapour 
Published: December 2023

AbstractChanges in the corticospinal (CSE) and cortico-cortical (CCE) excitability of the primary motor cortex (M1) may underlie the effect of mental fatigue on physical performance. To date, research on this subject has predominantly focused on the examination of CSE, with limited exploration of effects of mental fatigue on CCE. This study aims to investigate the influence of mental fatigue induced through prolonged cognitive activity on both CSE and CCE. Fifteen healthy adults (aged 29.13±7.15 years) participated in assessments of CSE (Motor evoked potential - MEP amplitude) and CCE (Intracortical facilitation - ICF, short-interval intracortical inhibition - SICI, and long-interval intracortical inhibition - LICI) before and after a 60-minute Stroop task (experimental condition) or watching a documentary (control condition). Subjective mental fatigue was measured using the mental fatigue visual analogue scale (M-VAS), and workload associated with the tasks was assessed using the National Aeronautics and Space Administration (NASA) task load index. Objective mental fatigue was defined by the time-related decline in Stroop task performance. The study results revealed no significant differences in M-VAS, CSE and CCE between the two conditions. Stroop task performance did not exhibit significant changes over time. However, participants perceived the Stroop task to be more mentally demanding and effortful than watching the documentary (p<0.05). Further analysis of Stroop task performance at individual participants level identified two sub-groups of participants: one exhibiting deteriorating performance with time (fatigued subgroup) and the other showing improved performance (non-fatigued subgroup). Descriptively, cortical inhibition increased (reduced SICI and ICF values) from pre to post Stroop task in the fatigued subgroup, while the non-fatigued group displayed an opposite pattern. The findings suggest that mental fatigue may lead to increased cortical inhibition, highlighting the need for further investigation with a larger sample size.
Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer
Authors: Qin Youwen , Tong Xin , Mei Wei-Jian , Cheng Yanshuang , Zou Yuanqiang , Han Kai , Yu Jiehai , Jie Zhuye , Zhang Tao , Zhu Shida , Jin Xin , Wang Jian , Yang Huanming , Xu Xun , Zhong Huanzi , Xiao Liang , Ding Pei-Rong 
Published: December 2023

AbstractThe incidence of young-onset colorectal cancer (yCRC) has been increasing in recent decades, but little is known about the gut microbiome of these patients. Most studies have focused on old-onset CRC (oCRC), and it remains unclear whether CRC signatures derived from old patients are valid in young patients. To address this, we assembled the largest yCRC gut metagenomes to date from two independent cohorts and found that the CRC microbiome had limited association with age across adulthood. Differential analysis revealed that well-known CRC-associated taxa, such asClostridium symbiosum,Peptostrptococcus stomatis,Parvimonas micraandHungatella hathewayi, were significantly enriched (false discovery rate <0.05) in both old- and young-onset patients. Almost all oCRC-associated metagenomic pathways had directionally concordant changes in young patients. Importantly, CRC-associated virulence factors (fadA,bft) were enriched in both oCRC and yCRC compared to their respective controls. Moreover, the microbiome-based classification model had similar predication accuracy for CRC status in old- and young-onset patients, underscoring the consistency of microbial signatures across different age groups.
The Natural History of Vision-Related Quality of Life after Unilateral Occipital Stroke
Authors: Dogra Neil , Redmond Bryan V. , Lilley Selena , Johnson Brent A. , Lam Byron L. , Tamhankar Madhura , Feldon Steven E. , Fahrenthold Berkeley , Yang Jingyi , Huxlin Krystel R. , Cavanaugh Matthew R. 
Published: December 2023

AbstractBackground/ObjectivesStroke damage to the primary visual cortex induces large, homonymous visual field defects that impair daily living. Here, we asked if vision-related quality of life (V-QoL) is impacted by time since stroke.Subjects/MethodsWe conducted a retrospective meta-analysis of 95 occipital stroke patients (F/M=26/69, 27-78 years old, 0.5 to 373.5 months post-stroke) in whom V-QoL was estimated using the National Eye Institute Visual Functioning Questionnaire (NEI-VFQ) and its 10-item neuro-ophthalmic supplement (Neuro10). Visual deficit severity was represented by the Perimetric Mean Deviation (PMD) calculated from 24-2 Humphrey visual fields. Data were compared with published cohorts of visually-intact controls. The relationship between V-QoL and time post-stroke was assessed across participants, adjusting for deficit severity and age with a multiple linear regression analysis.ResultsOccipital stroke patients had significantly lower NEI-VFQ and Neuro10 composite scores than controls. All subscale scores describing specific aspects of visual ability and functioning were impaired except for ocular pain and general health, which did not differ significantly from controls. Surprisingly, visual deficit severity was not correlated with either composite score, both of which increased with time post-stroke, even when adjusting for PMD and age.ConclusionsV-QoL appears to improve with time post-occipital stroke, irrespective of visual deficit size or patient age at insult. This may reflect the natural development of compensatory strategies and lifestyle adjustments. Thus, future studies examining the impact of rehabilitation on daily living in this patient population should consider the possibility that their V-QoL may change gradually over time, even without therapeutic intervention.
Emergence of preference coding in the macaque lateral prefrontal cortex by neurofeedback of unit activity related to working memory
Authors: Noritake Atsushi , Samejima Kazuyuki , Watanabe Masataka , Sakagami Masamichi 
Published: December 2023

AbstractTechniques utilizing neurofeedback, a form of biofeedback using neural signals from the brain, have been applied lately to higher association areas such as the lateral prefrontal cortex (LPFC); however, it remains unexplored how well neurofeedback using unit activity in the LPFC modulates its working memory-related activity and performance. To address this issue, we provided neurofeedback of LPFC unit activity during a delay period to two monkeys while they performed a delayed matching-to-paired-sample task. In the task, neurofeedback allowed the animals to shorten the delay length by increasing delay activity and make an earlier choice. Neurofeedback significantly increased delay activity in two-thirds of task-related neurons. Notably, in 16% of these neurons, a preference for delay activity and performance dependent on the stimulus emerged. Although neurofeedback decreased performance primarily due to choice errors, the disassociation of neurofeedback linkage rescued performance. Further, the neuronal activity of simultaneously recorded neurons without neurofeedback linkage suggests that neurofeedback reconfigured the net activity of the LPFC to adapt to new situations. These findings indicate that LPFC neurons can dynamically multiplex different types of information to adapt to environmental changes. Thus, we demonstrated the significant potential of neurofeedback using unit activity to investigate information processing in the brain.
AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification
Authors: Kim Jung , Naqvi Ammar S. , Corbett Ryan J. , Kaufman Rebecca S. , Vaksman Zalman , Brown Miguel A. , Miller Daniel P. , Phul Saksham , Geng Zhuangzhuang , Storm Phillip B. , Resnick Adam C. , Stewart Douglas R. , Rokita Jo Lynne , Diskin Sharon J. 
Published: December 2023

AbstractSummaryWith the increasing rates of exome and whole genome sequencing, the ability to classify large sets of germline sequencing variants using up-to-date American College of Medical Genetics – Association for Molecular Pathology (ACMG-AMP) criteria is crucial. Here, we present Automated Germline Variant Pathogenicity (AutoGVP), a tool that integrates germline variant pathogenicity annotations from ClinVar and sequence variant classifications from a modified version of InterVar (PVS1 strength adjustments, removal of PP5/BP6). This tool facilitates large-scale, clinically-focused classification of germline sequence variants in a research setting.Availability and ImplementationAutoGVP is an open-source dockerized workflow implemented in R and freely available on GitHub athttps://github.com/diskin-lab-chop/AutoGVP.
A novel “ceasefire” model to explain efficient seed transmission ofXanthomonas citripv.fuscansto common bean
Authors: Darrasse Armelle , Tarkowski Łukasz Paweł , Briand Martial , Lalanne David , Chen Nicolas W.G. , Barret Matthieu , Verdier Jerome 
Published: December 2023

SummaryAlthough seed represents an important means of plant pathogen dispersion, the seed-pathogen dialogue remains largely unexplored.A multi-omic approach (i.e.dual RNAseq, plant small RNAs and methylome) was performed at different seed developmental stages of common bean (Phaseolus vulgarisL.) during asymptomatic colonization byXanthomonas citripv.fuscans(Xcf).In this condition,Xcfdid not produce disease symptoms, neither affect seed development. Although, an intense molecular dialogue, via important transcriptional changes, was observed at the early seed developmental stages with down-regulation of plant defense signal transduction, via action of plant miR, and upregulation of the bacterial Type 3 Secretion System. At later seed maturation stages, molecular dialogue between host and pathogen was reduced to few transcriptome changes, but marked by changes in DNA methylation of plant defense and germination genes, in response toXcfcolonization, potentially acting as defense priming to prepare the host for the post-germination battle. This distinct response of infected seeds during maturation, with a more active role at early stages refutes the widely diffused assumption considering seeds as passive carriers of microbes.Finally, our data support a novel plant-pathogen interaction model, specific to the seed tissues, which differs from others by the existence of distinct phases during seed-pathogen interaction with seeds first actively interacting with colonizing pathogens, then both belligerents switch to more passive mode at later stages. We contextualized this observed scenario in a novel hypothetical model that we called “ceasefire”, where both the pathogen and the host benefit from temporarily laying down their weapons until the moment of germination.
Mu-opioid receptor knockout on Foxp2-expressing neurons reduces aversion-resistant alcohol drinking
Authors: Carvour Harrison M. , Roemer Charlotte A. E. G. , Underwood D’Erick P. , Padilla Edith S. , Sandoval Oscar , Robertson Megan , Miller Mallory , Parsadanyan Natella , Perry Thomas W. , Radke Anna K. 
Published: December 2023

AbstractMu-opioid receptors (MORs) in the amygdala and striatum are important in addictive and rewarding behaviors. The transcription factorFoxp2is a genetic marker of intercalated (ITC) cells in the amygdala and a subset of striatal medium spiny neurons (MSNs), both of which express MORs in wild-type mice and are neuronal subpopulations of potential relevance to alcohol-drinking behaviors. For the current series of studies, we characterized the behavior of mice with genetic deletion of the MOR geneOprm1inFoxp2-expressing neurons (Foxp2-Cre/Oprm1fl/fl). Male and female Foxp2-Cre/Oprm1fl/flmice were generated and heterozygous Cre+ (knockout) and homozygous Cre-(control) animals were tested for aversion-resistant alcohol consumption using an intermittent access (IA) task, operant responding for a sucrose reward, conditioned place aversion (CPA) to morphine withdrawal, and locomotor sensitization to morphine. The results demonstrate that deletion of MOR onFoxp2-expressing neurons renders mice more sensitive to quinine-adulterated ethanol (EtOH). Mice with the deletion (vs. Cre-controls) also consumed less alcohol during the final sessions of the IA task, responded less for sucrose under an FR3 schedule, and were less active at baseline and following morphine injection.Foxp2-MOR deletion did not impair the ability to learn to respond for reward or develop a conditioned aversion to morphine withdrawal. Together, these investigations demonstrate thatFoxp2-expressing neurons may be involved in escalation of alcohol consumption and the development of compulsive-like alcohol drinking.
Postural Stability During Illusory Self-Motion - Interactions of Vision and Touch
Authors: Yu Yingjia , Bakshi Avijit , Lackner James R. , Graybiel Ashton 
Published: December 2023

AbstractThe role of vision in stabilizing balance has been studied exhaustively. Other studies have shown that non-supportive light touch of the fingertip with a surface also can significantly stabilize postural balance. We have studied how vision and cutaneous information jointly affect balance. We used a head-mounted display to simulate a virtual room that rotated about a vertical axis centered with the standing subject’s z-axis. Subjects viewing the display’s rotational displacement soon experienced self-motion and displacement. We assessed how the moving visual input destabilized posture and how it interacted with touch cues that stabilized posture. A novel result is how balance is influenced by the onset of visual motion and the illusion of self-rotation. We discovered that motion perceptions are coupled with stochastic aspects of balance. Changes in the perception of types of motion – none, environment-, and self-rotation – distinctively influence metrics that encode for the stochasticity of balance and do not influence those that filter the stochasticity out. We reconfirmed the significant effects of touch in stabilizing balance and discovered how it interacts with the visual perception of motion. We also found lingering effects of past motion perception, which keep influencing the stochasticity of balance even when visual motion is long stopped. Our findings provide insights into multisensory interaction effects in postural balance and suggest novel future research directions.
Combined Partial-Nitrification and Phosphorus Removal with the co-Existence of Nitrite-resistant phosphorous accumulating organisms (PAOs) and nitrifiers in the treatment of high-strength manure digestate
Authors: Yan Yuan , Guo Peibo , Baldwin Mathew , Li Guangyu , Yoon Hyun , McGuire Philip , Sang Yi , Reid Matthew C. , Rudek Joseph , Gu April Z. 
Published: December 2023

AbstractConcurrent biological phosphorus (P) recovery and nitrogen (N) removal in treating high-strength wastewater (such as anaerobic digestate) has been considered incompatible due to presumed conflicts in the conflicting optimum conditions required by phosphorous accumulating organisms (PAO) and nitrifiers. However, this study achieved a stable nitrite accumulation while still maintained PAO activities in one sequencing batch reactor for treating the manure digestate under two aeration schemes (continuous versus intermittent aeration). Nitrite accumulated up to 80.5 ± 21.1 mg-N/L under continuous aeration (6 h) mode. Switching to intermittent aeration (equivalent to 3 h) halved nitrite accumulation but increased total nitrogen removal efficiency from 53.5 ± 12.2% to 84.7 ± 9.4%. Mass balance analysis indicates that nearly all ammonia was removed as N2O. Both Enhanced Biological Phosphorus Removal (EBPR) activity assessment and phenotypic trait detection via single cell Raman spectrum (SCRS) confirmed the existence of yet to be identified PAOs that are resistant to high nitrite inhibition in our system. Visual Minteq calculation indicates that high concentrations of Ca in manure digestate may form precipitates and influence the bioavailability of P forms. Therefore, both biotic and abiotic pathways lead to a total P removal rate around 61.0 ± 6.8%. This study highlights new opportunities to combine short-cut nitrogen removal via partial nitrification, nitrous oxide (N2O) collection, and EBPR in commercial farm-collected digested manure wastewater. Higher N and P removal efficiency could potentially be achieved by tuning aeration schemes in combination with down-stream anammox process.SynopsisConcurrent partial nitrification, N2O accumulation, and EBPR activity were found, leading to the exploration of novel nitrite-resistant PAOs, simultaneously N/P recovery, and waste-energy conversion in treating high strength wastewater.
Offline RL for generative design of protein binders
Authors: Tarasov Denis , Mbou Sob Ulrich A. , Arbesú Miguel , Siboni Nima , Boyer Sebastien , Skwark Marcin , Smit Andries , Bent Oliver , Pretorius Arnu 
Published: December 2023

AbstractOffline Reinforcement Learning (RL) offers a compelling avenue for solving RL problems without the need for interactions with an environment, which may be expensive or unsafe. While online RL methods have found success in various domains, such asde novoStructure-Based Drug Discovery (SBDD), they struggle when it comes to optimizing essential properties derived from protein-ligand docking. The high computational cost associated with the docking process makes it impractical for online RL, which typically requires hundreds of thousands of interactions during learning. In this study, we propose the application of offline RL to address the bottleneck posed by the docking process, leveraging RL’s capability to optimize non-differentiable properties. Our preliminary investigation focuses on using offline RL to conditionally generate drugs with improved docking and chemical properties.
Neotelomeres and Telomere-Spanning Chromosomal Arm Fusions in Cancer Genomes Revealed by Long-Read Sequencing
Authors: Tan Kar-Tong , Slevin Michael K. , Leibowitz Mitchell L. , Garrity-Janger Max , Li Heng , Meyerson Matthew 
Published: December 2023

AbstractAlterations in the structure and location of telomeres are key events in cancer genome evolution. However, previous genomic approaches, unable to span long telomeric repeat arrays, could not characterize the nature of these alterations. Here, we applied both long-read and short-read genome sequencing to assess telomere repeat-containing structures in cancers and cancer cell lines. Using long-read genome sequences that span telomeric repeat arrays, we defined four types of telomere repeat variations in cancer cells: neotelomeres where telomere addition heals chromosome breaks, chromosomal arm fusions spanning telomere repeats, fusions of neotelomeres, and peri-centromeric fusions with adjoined telomere and centromere repeats. Analysis of lung adenocarcinoma genome sequences identified somatic neotelomere and telomere-spanning fusion alterations. These results provide a framework for systematic study of telomeric repeat arrays in cancer genomes, that could serve as a model for understanding the somatic evolution of other repetitive genomic elements.
3D structure of fibroblasts and macrophages in the healthy and cryo-ablated heart
Authors: Fernández Marbely C , Wülfers Eike M , Madl Josef , Feliz Stefanie Perez , Kohl Peter , Zgierski-Johnston Callum M , Schneider-Warme Franziska 
Published: December 2023

ABSTRACTIntroductionCardiac non-myocytes (NM) play important roles in heart development, homeostasis, and lesion repair. To assess the relevance of different NM populations for cardiac (patho)physiology, a quantitative assessment of their abundance and structure in the different heart chambers is an essential prerequisite. We here present an experimental approach to determine the distribution, dimensions, and 3D morphology of fibroblasts (FB) and macrophages (MΦ) in healthy and pathologically remodelled hearts.Methods and resultsWe used Cre-loxPrecombination to selectively target channelrhopsin-2 (ChR2)-eYFP to either FB or MΦ in healthy and cryo-ablated mouse hearts. Hearts were optically cleared using X-CLARITY and membrane-bound eYFP fluorescence was recorded by confocal microscopy. The resulting image stacks were segmented to generate 3D reconstructions of labelled cell populations innear native tissue. In doing so, we show that FB and MΦ have similar surface areas, volumes and morphologies, but that FB occupy larger fractional volumes than MΦ in all chambers of healthy murine hearts. Furthermore, MΦ appear primarily as single cells, whereas FB form extended networks of interconnected cells. In left-ventricular tissue following cryo-ablation, we observed large disordered networks of FB in the scar area with an increased volume occupied by FB both in the scar and remotely. In cryo-ablated ventricles, MΦ form comparatively small, but dense networks in the scar without changing their abundance in remote myocardium.ConclusionsOur study assesses the 3D distribution and structure of fluorescently labelled FB and MΦ in healthy and lesioned murine hearts. Based on 3D reconstructions of FB and MΦ networks, we quantified the surface areas and volumes of individual non-myocytes in the different chambers of the heart and in ventricular scar tissue, thus providing important quantitative data serving as basis for computational modelling of non-myocyte contributions to cardiac structure and physiology.
SARS-CoV-2 NSP13 interacts with TEAD to suppress Hippo-YAP signaling
Authors: Meng Fansen , Kim Jong Hwan , Tsai Chang-Ru , Steimle Jeffrey D. , Wang Jun , Shi Yufeng , Li Rich G. , Xie Bing , Deshmukh Vaibhav , Liu Shijie , Li Xiao , Martin James F. 
Published: December 2023

AbstractThe Hippo pathway is critical to organ development, homeostasis, and regeneration, facilitated by YAP/TEAD-mediated gene expression. Although emerging studies report Hippo-YAP dysfunction after viral infection, it is largely unknown in the context of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we analyzed RNA sequencing data from SARS-CoV-2 infected human lung samples and induced pluripotent stem cell–derived cardiomyocytes (iPSC-CMs), and observed a decrease in YAP target gene expression. In screening SARS-CoV-2 nonstructural proteins, we found that nonstructural protein 13 (NSP13), a conserved coronavirus helicase, inhibited YAP transcriptional activity independent of the upstream Hippo kinases LATS1/2. Consistently, introducing NSP13 into cardiomyocytes suppressed active YAP (YAP5SA)in vivo. Subsequent investigations on NSP13 mutants indicated that NSP13 helicase activity is crucial for suppressing YAP transactivation. Mechanistically, TEAD4 serves as a platform for recruiting NSP13 and YAP. NSP13 inactivates the YAP/TEAD4 transcription complex through its interacting proteins, such as transcription termination factor 2 (TTF2). These discoveries reveal a novel YAP/TEAD regulatory mechanism orchestrated by TEAD4, which provides molecular insights of Hippo-YAP regulation after SARS-CoV-2 infection.