bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metaproteogenomics resolution of a high-CO2aquifer community suggests an active symbiotic lifestyle of groundwater Gracilibacteria
Authors: Figueroa-Gonzalez Perla Abigail , Bornemann Till L. V. , Hinzke Tjorven , Maaß Sandra , Trautwein-Schult Anke , Starke Joern , Moore Carrie J. , Esser Sarah P. , Plewka Julia , Hesse Tobias , Schmidt Torsten C. , Schreiber Ulrich , Bor Batbileg , Becher Dörte , Probst Alexander J. 
Published: December 2023

AbstractBackgroundBacteria of the Candidate Phyla Radiation (CPR), constituting about 25% of the bacterial biodiversity, are characterized by small cell size and patchy genomes without complete key metabolic pathways, suggesting a symbiotic lifestyle. Gracilibacteria (BD1-5), which are part of the CPR branch, possess alternate coded genomes and have not yet been cultivated. However, besides genomic evidence, little is known about the lifestyle of Gracilibacteria, their temporal dynamics, and activity in natural ecosystems, particularly in groundwater, where they were initially been genomically resolved. Therefore, we here aimed to investigate Gracilibacteria activityin situand to discern expressed genes involved in their lifestyle, using the metaproteogenome of Gracilibacteria as a function of time in the cold-water geyser Wallender Born in the Volcanic Eifel region in Germany.ResultsWe coupled genome-resolved metagenomics and metaproteomics to investigate a cold-water geyser microbial community enriched in Gracilibacteria across a 12-day time-series. Groundwater was collected and sequentially filtered to fraction CPR and other bacteria. Based on 670 Gbps of metagenomic data, 1129 different ribosomal protein S3 marker genes and 751 high-quality genomes (123 population genomes after dereplication), we identified dominant bacteria belonging to Galionellales and Gracilibacteria along with keystone microbes, which were low in genomic abundance but substantially contributing to proteomic abundance. Seven high-quality Gracilibacteria genomes showed typical limitations, such as limited amino acid or nucleotide synthesis, in their central metabolism but no co-occurrence with potential hosts. The genomes of these Gracilibacteria encoded for a high number of proteins related to a symbiotic or even predatory lifestyle,e.g., type IV and type II secretion system subunits and features related to cell-cell interactions and cell motility, which were also detected on protein level.ConclusionsCoupling metagenomics to metaproteomics enabled us to identify microbial keystone taxa in a high-CO2aquifer, and to reveal microbial dynamics of Gracilibacteria. We posit that Gracilibacteria might be successful microbial predators in this ecosystem, potentially aiding in population control of this highly perturbed microbial geyser community from the deep biosphere.
Congress of multiple dimers is needed for cross-phosphorylation of IRE1α and its RNase activity
Authors: Orsi Andrea , Sitia Roberto , van Anken Eelco , Vitale Milena , Bakunts Anush 
Published: December 2023

AbstractThe unfolded protein response can switch from a pro-survival to a maladaptive, pro-apoptotic mode. During endoplasmic reticulum (ER) stress, IRE1α sensors dimerize, are phosphorylated and activate XBP1 splicing, increasing folding capacity in the ER protein factory. The steps that turn the IRE1α endonuclease activity against endogenous mRNAs during maladaptive ER stress are still unknown. Here we show that although necessary, IRE1α dimerization is not sufficient to trigger phosphorylation. Random and/or guided collisions amongst IRE1α dimers are needed to elicit cross-phosphorylation and endonuclease activities. Thus, reaching a critical concentration of IRE1α dimers in the ER membrane is a key event. Formation of stable IRE1α clusters is not necessary for RNase activity. However, clustering could modulate the potency of the response promoting interactions between dimers and decreasing the accessibility of phosphorylated IRE1α to phosphatases. The stepwise activation of IRE1α molecules and their low concentration at steady state prevent excessive responses, unleashing full-blown IRE1 activity only upon intense stress conditions.
Transcriptional signatures of fentanyl use in the mouse ventral tegmental area
Authors: Fox Megan E , Montemarano Annalisa , Ostman Alexandria E , Basu Mahashweta , Herb Brian , Ament Seth A. , Fox Logan D. 
Published: December 2023

AbstractSynthetic opioids such as fentanyl contribute to the vast majority of opioid-related overdose deaths, but fentanyl use remains broadly understudied. Like other substances with misuse potential, opioids cause lasting molecular adaptations to brain reward circuits, including neurons in the ventral tegmental area (VTA). The VTA contains numerous cell types that play diverse roles in opioid use and relapse, however it is unknown how fentanyl experience alters the transcriptional landscape in specific subtypes. Here, we performed single nuclei RNA sequencing to study transcriptional programs in fentanyl experienced mice. Male and female C57/BL6 mice self-administered intravenous fentanyl (1.5 µg/kg/infusion) or saline for 10 days. After 24 hr abstinence, VTA nuclei were isolated and prepared for sequencing on the 10X platform. We identified different patterns of gene expression across cell types. In dopamine neurons, we found enrichment of genes involved in growth hormone signaling. In dopamine-glutamate-GABA combinatorial neurons, and some GABA neurons, we found enrichment of genes involved in Pi3k-Akt signaling. In glutamate neurons, we found enrichment of genes involved in cholinergic signaling. We identified transcriptional regulators for the differentially expressed genes in each neuron cluster, including downregulation of transcriptional repressor Bcl6, and upregulation of Wnt signaling partner Tcf4. We also compared the fentanyl-induced gene expression changes identified in mouse VTA with a published rat dataset in bulk VTA, and found overlap in genes related to GABAergic signaling and extracellular matrix interaction. Together, we provide a comprehensive picture of how fentanyl self-administration alters the transcriptional landscape of the mouse VTA, that serves for the foundation for future mechanistic studies.
Learning Image Memorability with Feedback-Based Training
Authors: Revsine Cambria , Bainbridge Wilma A. 
Published: December 2023

AbstractMemorability, or the likelihood that an image is later remembered, is an intrinsic stimulus property that is remarkably consistent across viewers. Despite this consistency in what people remember and forget, previous findings suggest a lack of consistency in what individuals subjectively believe to be memorable and forgettable. We aimed to improve the ability of participants to judge memorability using a feedback-based training paradigm containing face images (Experiment 1) or scene images (Experiment 2 and its replication and control experiments). Overall, participants were fairly accurate at categorizing the memorability of images. In response to the training, participants were able to improve their memorability judgments of scenes, but not faces. Those who used certain strategies to perform the task, namely relying on characteristic features of the scenes, showed greater learning. Although participants improved slightly over time, they never reached the level of ResMem, the leading DNN for estimating image memorability. These results suggest that with training, human participants can better their understanding of image memorability, but may be unable to access its full variance.
Mechanics limit ecological diversity and promote heterogeneity in confined bacterial communities
Authors: Ma Tianyi , Rothschild Jeremy , Halabeya Faisal , Zilman Anton , Milstein Joshua N. 
Published: December 2023

AbstractMulti-species bacterial populations often inhabit confined and densely packed environments where spatial competition determines the ecological diversity of the community. However, the role of mechanical interactions in shaping the ecology is still poorly understood. Here we study a model system consisting of two populations of non-motileE. colibacteria competing within open, monolayer micro-channels. The competitive dynamics is observed to be bi-phasic: after seeding, either one strain rapidly fixates or both strains orient into spatially stratified, stable communities. We find that mechanical interactions with other cells and local spatial constraints influence the resulting community ecology in unexpected ways, severely limiting the overall diversity of the communities while simultaneously allowing for the establishment of stable, heterogeneous populations of bacteria displaying disparate growth rates.Surprisingly, the populations have a high probability of coexisting even when one strain has a significant growth advantage. A more coccus morphology is shown to provide a selective advantage, but agent based simulations indicate this is due to hydrodynamic and adhesion effects within the microchannel and not from breaking of the nematic ordering. Our observations are qualitatively reproduced by a simple Pólya urn model, which suggests the generality of our findings for confined population dynamics and highlights the importance of early colonization conditions on the resulting diversity and ecology of bacterial communities. These results provide fundamental insights into the determinants of community diversity in dense confined ecosystems where spatial exclusion is central to competition as in organized biofilms or intestinal crypts.
Cell type-specific enrichment of somatic aneuploidy in the mammalian brain
Authors: Mukamel Eran A. , Liu Hanqing , Behrens M. Margarita , Ecker Joseph R. 
Published: December 2023

ABSTRACTSomatic mutations alter the genomes of a subset of an individual’s brain cells1–3, impacting gene regulation and contributing to disease processes4,5. Mosaic single nucleotide variants have been characterized with single-cell resolution in the brain2,3, but we have limited information about large-scale structural variation, including whole-chromosome duplication or loss1,6,7. We used a dataset of over 415,000 single-cell DNA methylation and chromatin conformation profiles across the adult mouse brain to identify aneuploid cells comprehensively. Whole-chromosome loss or duplication occurred in <1% of cells, with rates up to 1.8% in non-neuronal cell types, including oligodendrocyte precursors and pericytes. Among all aneuploidies, we observed a strong enrichment of trisomy on chromosome 16, which is syntenic with human chromosome 21 and constitutively trisomic in Down syndrome. Chromosome 16 trisomy occurred in multiple cell types and across brain regions, suggesting that nondisjunction is a recurrent feature of somatic variation in the brain.
Anti-cancer drug Tamoxifen interferes withMycobacterium tuberculosisPhoPR mediated signaling and inhibits mycobacterial growth
Authors: Garg Abhishek , Pandit Mansi , Malhotra Vandana , Saini Deepak Kumar 
Published: December 2023

AbstractTwo-component signaling (TCS) systems empower all bacteria, including intracellular pathogens likeMycobacterium tuberculosis (M. tb)to regulate key pathways governing growth, physiology and virulence. Amongst allM. tbTCS systems, PhoPR and DevRS have been studied extensively for their roles in regulating persistence and virulence. Here, we report that besides its cognate response regulator PhoP, the PhoR sensor kinase displays several non-cognate interactions that augment its role in pathogenesis. We demonstrate that PhoR phosphorylates the DevR response regulator and furthermore, is itself subjected toO-phosphorylation by PknK, a Ser/Thr protein kinase (STPK), connecting TCS pathways with “eukaryotic-like” STPK driven phosphosignaling. This intersection of non-canonical regulatory pathways and the coregulation of PhoP and DevR regulons makeM. tbPhoR a potentially attractive drug target. We rationalized that disruption of PhoPR signaling cascade and the resulting dysregulation may result in decreased virulence ofM. tb. We tested this hypothesis by performing a high-throughput screen for compounds that inhibit autophosphorylation of PhoR sensor kinase. Screening of pharmacologically active, small molecule libraries yielded 11 potential inhibitors, of which one compound, Tamoxifen was able to attenuate PhoR autophosphorylation at micromolar concentrationsin vitroandin vivo. Tamoxifen not only inhibited growth ofMycobacterium bovisBCG in culture but also interrupted PhoPR-mediated downstream signaling. Quantitative expression analysis revealed suppression of target gene,aprAunder acidic conditions. Our findings highlight TCS sensor kinases as promising drug targets and underscore the applicability of clinically relevant anti-cancer drug tamoxifen as a repurposed anti-TB drug.
GSK3β phosphorylation catalyzes the aggregation of Tau into Alzheimer’s disease-like amyloid strain
Authors: Chakraborty Pijush , Ibáñez de Opakua Alain , Purslow Jeffrey A. , Fromm Simon A. , Chatterjee Debdeep , Zachrdla Milan , Puri Sambhavi , Wolozin Benjamin , Zweckstetter Markus 
Published: December 2023

AbstractThe pathological deposition of proteins is a hallmark of several devastating neurodegenerative diseases. These pathological deposits comprise aggregates of proteins that adopt distinct structures named strains. However, the molecular factors responsible for the formation of distinct aggregate strains are unknown. Here we show that the serine/threonine kinase GSK3β catalyzes the aggregation of the protein tau into an Alzheimer’s disease-like amyloid strain. We demonstrate that phosphorylation by GSK3β, but not by several other kinases, promotes the aggregation of full-length tau through enhanced phase separation into gel-like condensate structures. Cryo-electron microscopy further reveals that the amyloid fibrils formed by GSK3β-phosphorylated tau adopt a fold comparable to that of paired helical filaments isolated from the brains of AD patients. Our results elucidate the intricate relationship between post-translational modification and the formation of tau strains in neurodegenerative diseases.
Rats rely on airflow cues for self-motion perception
Authors: Polat Lior , Harpaz Tamar , Zaidel Adam 
Published: December 2023

ABSTRACTSelf-motion perception is a vital skill for all species. It is an inherently multisensory process, that combines inertial (body-based) and relative (with respect to the environment) motion cues. While extensively studied in human and non-human primates, there is currently no paradigm to test self-motion perception in rodents using both inertial and relative self-motion cues. We developed a novel rodent motion simulator using two synchronized robotic arms to generate inertial, relative or combined (inertial and relative) cues of self-motion. Eight rats were trained to perform a task of heading-discrimination, similar to the popular primate paradigm. Strikingly, the rats relied heavily on airflow for relative self-motion perception, with little contribution from optic flow (performance in the dark was almost as good). Relative self-motion (airflow) was perceived with greater reliability vs. inertial. Disrupting airflow (using a fan or windshield) damaged relative, but not inertial, self-motion perception. However, whiskers were not needed for this function. Lastly, the rats integrated relative and inertial self-motion cues in a reliability-based (Bayesian-like) manner. These results implicate airflow as a dominant cue for self-motion perception in rats, and provide a new domain to investigate the neural bases of self-motion perception and multisensory processing in awake behaving rodents.
Sparse Representation for High-dimensional Multiclass Microarray Data Classification
Authors: Miri Maliheh , Sadeghi Mohammad Taghi , Abootalebi Vahid 
Published: December 2023

AbstractSparse representation of signals has achieved satisfactory results in classification applications compared to the conventional methods. Microarray data, which are obtained from monitoring the expression levels of thousands of genes simultaneously, have very high dimensions in relation to the small number of samples. This has led to the weaknesses of state-of-the-art classifiers to cope with the microarray data classification problem. The ability of the sparse representation to represent the signals as a linear combination of a small number of training data and to provide a brief description of signals led to reducing computational complexity as well as increasing classification accuracy in many applications. Using all training samples in the dictionary imposes a high computational burden on the sparse coding stage of high dimensional data. Proposed solutions to solve this problem can be roughly divided into two categories: selection of a subset of training data using different criteria, or learning a concise dictionary. Another important factor in increasing the speed and accuracy of a sparse representation-based classifier is the algorithm which is used to solve the related ℓ1–norm minimization problem. In this paper, different sparse representation-based classification methods are investigated in order to tackle the problem of 14-Tumors microarray data classification. Our experimental results show that good performances are obtained by selecting a subset of the original atoms and learning the associated dictionary. Also, using SL0 sparse coding algorithm increases speed, and in most cases, accuracy of the classifiers.
Big data analytics capability for competitive advantage and firm performance in Malaysian manufacturing firms
Authors: Chong Chu-Le , Abdul Rasid Siti Zaleha , Khalid Haliyana , Ramayah T. 
Published: December 2023

PurposeThis study investigated the relationships among big data analytics capability (BDAC), low-cost advantage, differentiation advantage, market and operational performance underpinning the resource-based view (RBV) and the entanglement view of sociomaterialism (EVS) theories.Design/methodology/approachA total of 191 responses from members of the Federation of Malaysian Manufacturers were analysed using a structural equation modelling approach.FindingsThis study has conclusively demonstrated that BDAC is indeed a resource bundle comprising human skills, tangible and intangible resources. This study found that BDAC positively influences competitive advantage and firm performance. The differentiation advantage was found to be a key factor in explaining market performance. Theoretically, both RBV and EVS could be used to link BDAC, differentiation advantage and market performance to explain superior firm performance.Research limitations/implicationsFirst, the sample is restricted to the manufacturers in Malaysia. Second, a single independent variable, BDAC, is used as a higher-order capability to influence competitive advantage, and thus, superior firm performance. Third, this study uses a self-reported survey, which means that only one respondent from each firm answered the questions. Fourth, this study excludes the focused strategy as it aims to investigate the competitive strategy used in the broader industry environment, rather than in a specific segment pursuing a focused strategy.Practical implicationsFirst, BDAC is a valuable, rare, inimitable and non-substitutable tool for manufacturers to enhance their firm performance. Second, BDAC is crucial for manufacturing firms to reduce costs and differentiate themselves. Third, a low-cost advantage may not help manufacturers achieve greater market and operational performance.Originality/valueThe relationship among BDAC, low-cost advantage, differentiation advantage, market and operational performance within manufacturing industry is empirically tested.
Effectiveness of sponsorship type, sport team identification, team support and congruence
Authors: Mohammadi Sardar , Ghasemi Siani Mojtaba , Alonso Dos Santos Manuel 
Published: December 2023

PurposeThe aim of this paper is to investigate the interaction effect that sponsor-team congruence and team fan (home/rival team) have on the influence of different types of sports sponsorship (joint, corporate social responsibility [CSR]-linked and conventional sponsorship) on fans' attitudes and purchase intentions toward the sponsor.Design/methodology/approachTwo experimental studies were conducted on 391 and 297 participants. The data gathered underwent analysis through five multivariate general linear model analyses.FindingsThe study found that CSR-linked sponsorship had the strongest positive impact and the weakest negative impact on the attitude and purchase intention of home team supporters and the attitude of rival team supporters. Nonetheless, the sponsor-team congruence did not significantly moderate the relationship. Additionally, the research demonstrated that the fan identity of both home and rival teams moderates the impact of sports sponsorships on attitude and purchase intention.Originality/valuePrevious research has studied the effectiveness of sponsorship format types independently. This is the first research comparing sponsorship formats regarding fan type and congruence.
Does emotional intelligence impact service innovation capabilities? Exploring the role of diversity climate and innovation culture
Authors: Jegerson Devid , Jabeen Fauzia , Abdulla Hanan H. , Putrevu Jayaprada , Streimikiene Dalia 
Published: December 2023

PurposeThe study examines the impact of emotional intelligence on service innovation capabilities. Furthermore, it explored the mediating role of diversity climate and the moderating role of innovation culture.Design/methodology/approachAn online questionnaire helped to collect data from 257 public sector employees in the United Arab Emirates (UAE). The proposed hypotheses were analysed using structural equation modelling.FindingsBuilding on the ability model, the study found that employees' emotional intelligence has a positive impact on diversity climate; that diversity climate does not mediate the relationship between emotional intelligence and service innovation capabilities and that innovation culture has a moderating effect between diversity climate and service innovation capabilities.Originality/valueThe paper clarifies the emotional intelligence of the workforce and its ability to influence innovation culture and diversity climate in public organisations, ultimately benefiting service innovation capability research. As such, the study contributes to the literature by proposing and analysing some antecedents of service innovation capabilities in the context of public organisations. The study also offers policymakers information on what prevents innovation, which they can use to raise the bar on service quality requirements in the public sector.