bluuebunny/crossref_metadata_2025_split huggingface dataset:
A highly conserved sRNA downregulates multiple genes, including a σ54transcriptional activator, in the virulence mode ofBordetella pertussis
Authors: Sim Minji , Nguyen Jeffers , Škopová Karolína , Yoo Kyungyoon , Tai Chin-Hsien , Knipling Leslie , Chen Qing , Kim David , Nolan Summer , Elaksher Rawan , Majdalani Nadim , Lorenzi Hernan , Stibitz Scott , Moon Kyung , Hinton Deborah M. 
Published: November 2024

ABSTRACTBacterial sRNAs together with the RNA chaperone Hfq post-transcriptionally regulate gene expression by affecting ribosome binding or mRNA stability. In the human pathogenBordetella pertussis, the causative agent of whooping cough, hundreds of sRNAs have been identified, but their roles inB. pertussisbiology are mostly unknown. Here we characterize a Hfq-dependent sRNA (S17), whose level is dramatically higher in the virulence (Bvg+) mode. We show that transcription from a σA-dependent promoter yields a long form of 190 nucleotides (nts) that is processed by RNase E to generate a shorter, more stable form (S17S) of 67 nts. Using RNA-seq and RT-qPCR, we identify 92 genes whose expression significantly increases in the absence of S17. Of these genes, 70 contain sequences at/near their ribosome binding sites (RBSs) that are complementary to single-stranded (ss) regions (Sites 1 or 2) of S17S. The identified genes include those encoding multiple transporters and 3 transcriptional regulators. Using alacZtranslational reporter system, we demonstrate that S17S directly represses one of these genes,BP2158, a σ54- dependent transcriptional regulator, suggesting the repression of a σ54regulon in the Bvg+mode. We find that the S17S region containing Sites 1 and 2 is 100% conserved throughout various Betaproteobacteria species, and the S17S target sites are often conserved in the homologs of theB. pertussistarget genes. We speculate that S17S regulation represents a highly conserved process that fine-tunes gene expression in the Bvg+mode ofB. pertussisand perhaps under other conditions in related bacteria.IMPORTANCERegulation of gene expression involves controlling transcription, translation, and transcript degradation. sRNAs with short sequences complementary to an mRNA sequence are involved in post-transcriptional regulation by aiding or interfering with either ribosome binding or nuclease attack. In the human pathogenBordetella pertussis, the causative agent of whooping cough, hundreds of sRNA have been identified, but their functions remain largely unknown. We have characterized a sRNA that is abundant in the virulence mode ofB. pertussisand serves to down-regulate multiple genes including transcriptional regulators and various transporters. We demonstrate that this sRNA directly represses a transcriptional factor, suggesting that it influences the regulation of specificB. pertussisregulons. The high conservation of this sRNA and its targets within Betaproteobacteria suggests a conserved pathway for gene regulation.
The “Ocular Response Function” for encoding and decoding oculomotor related neural activity
Authors: Gehmacher Quirin , Schubert Juliane , Kaltenmaier Aaron , Weisz Nathan , Press Clare 
Published: November 2024

AbstractOculomotor activity provides critical insights into cognition and health, with growing evidence demonstrating its involvement in various cognitive functions such as attention, memory, and sensory processing. Furthermore, eye movements are emerging as significant indicators of psychopathologies and neurological disorders, including schizophrenia, dementia, depression, and tinnitus. Despite its crucial importance across domains, the role of oculomotion has often been underexplored in neuroimaging studies - largely due to methodological challenges. Eye movements have traditionally been viewed as artefacts in the neural signal, leading to the exclusion of epochs containing them, or correction methods to remove their influence. However, this strategy does not allow us to determine their role in a range of neural effects or mapping between tasks and neural responses. To enable such nuanced investigations in typical function and disease, we introduce what we term “Ocular Response Functions”. We used simultaneous magnetoencephalographic and eye-tracking recordings during the resting-state combined with temporal response functions to precisely map the relationship between oculomotion and neural activity. Our approach allows for the temporally and spatially precise prediction of neural activity based on ocular action, and vice versa. We further validate this method in a passive listening task, highlighting its potential for uncovering cognitive insights in experimental settings. By providing a robust framework for examining the interplay between eye movements and neural processes, our method opens new avenues for both research and clinical applications, potentially advancing early detection and intervention strategies for neurological and psychiatric disorders.
A novel mouse model for developmental and epileptic encephalopathy by Purkinje cell-specific deletion ofScn1b
Authors: Isaac Guillén F. , Geist Mendee A. , Cheng Shao-Ying , Harris Arwen M. , Treviño Martha E. , Brumback Audrey C. , Nishiyama Hiroshi , Howard MacKenzie A. 
Published: November 2024

AbstractLoss of function variants ofSCN1Bare associated with a range of developmental and epileptic encephalopathies (DEEs), including Dravet syndrome. These DEEs feature a wide range of severe neurological disabilities, including changes to social, motor, mood, sleep, and cognitive function which are notoriously difficult to treat, and high rates of early mortality. While the symptomology ofSCN1B-associated DEEs indicates broad changes in neural function, most research has focused on epilepsy-related brain structures and function. Mechanistic studies ofSCN1B/Scn1bhave delineated diverse roles in development and adult maintenance of neural function, via cell adhesion, ion channel regulation, and other intra- and extra-cellular actions. However, use of mouse models is limited as knockout ofScn1b, globally and even in some cell-specific models (e.g., Parvalbumin+ interneuron-specific knockout) in adult mice, leads to severe and progressive epilepsy, health deterioration, and 100% mortality within weeks. Here, we report findings of a novel transgenic mouse line in whichScn1bwas specifically deleted in cerebellar Purkinje cells. Unlike most existing models, these mice did not show failure to thrive or early mortality. However, we quantified marked decrements to Purkinje cell physiology as well as motor, social, and cognitive dysfunction. Our data indicate that cerebellar Purkinje cells are an important node for dysfunction and neural disabilities inSCN1B-related DEEs, and combined with previous work identify this as a potentially vital site for understanding mechanisms of DEEs and developing therapies that can treat these disorders holistically.
Humans and marmosets share similar face recognition signatures in shape-based visual face discrimination behavior
Authors: Jeon You-Nah , Cho Hector Y. , Green Ashley C. , Issa Elias B. 
Published: November 2024

ABSTRACTOur ability to identify faces is thought to depend on high-level visual processing in the brain. Nonetheless, studies of face recognition have generally relied on 2D face photographs where low-level strategies relying on texture and appearance cues can be employed to adequately support high face identification performance. Here, we designed a fine face discrimination task under 3D pose and lighting variation that was purely based on shape, a task which challenged state-of-the-art artificial vision systems compared to object recognition tasks. In contrast, humans performed this shape based face task at comparable levels to their object recognition performance. We then tested one of the smallest simian primates on this human-level, machine-difficult visual task, the common marmoset – a small, New World monkey. Marmosets successfully discriminated between face identities across 3D viewing conditions based purely on face shape. Their face recognition performance was on par with their object recognition performance and exhibited face-specific behavioral signatures similar to humans, including lower performance for inverted faces, faces lit from below, and contrast reversed faces. These results demonstrate that a high-level visual behavior, invariant face recognition based purely on geometry and not additional texture and appearance cues, is shared across simian primates from among the smallest to the most advanced, consistent with the presence of common underlying high-level visual brain areas across simian primates.
Uncovering the shared genetic contributors to primary and secondary hypertension using whole genome sequencing in a national disease cohort
Authors: Manoj Megha , Sadeghi-Alavijeh Omid , Gale Daniel P. 
Published: November 2024

AbstractIntroductionExtreme early-onset hypertension (EEHTN) defines a cohort of patients with a persistent blood pressure above 160/100mmHg under 30 years of age. This cohort is at heightened risk of complications and often undergo a diagnostic odyssey. We used Whole Genome Sequencing (WGS) data provided by the 100,000 Genomes Project (100KGP), to quantify the genetic contributors to EEHTN and to ascertain the diagnostic utility of WGS.MethodsWe performed sequencing-based genome-wide association studies (GWAS) in 901 unrelated EEHTN cases and 20852 ancestry matched unaffected controls. The analysis was inclusive of individuals with diverse genetic ancestry. Enrichment of common, low-frequency minor allele frequency (MAF) > 0.1% and rare (MAF < 0.1%) single-nucleotide variant (SNV), insertion/deletion variants (indels) and rare structural variant (SV) alleles on a genome-wide and per-gene basis was sought using a generalised linear mixed model approach to account for population structure. A validated polygenic risk score (PRS) for hypertension (HTN) was applied to the EEHTN cohort and a primary HTN cohort.ResultsAnalysis of rare SNVs and indels revealedPKD1(P=2.70 x 10-13) as significantly associated with EEHTN. This signal was lost when we excluded those with known renal disease. 81.5% of the individuals harbouring qualifyingPKD1variants had known cystic kidney disease (CyKD), this is replicated in the UK Biobank (UKBB). There were no common SNVs or rare SV associations with EEHTN. PRS discriminated between cases and controls (P = 2.2x10-16) but not between patients with PHTN or secondary HTN.ConclusionsThese findings represent a thorough examination of the genetic architecture of a national EEHTN cohort using well-controlled statistical methodology. The low diagnostic yield of WGS in this group brings into question its utility as a population level clinical tool but provides insights into EEHTN biology. The PRS findings suggest shared genetic contributors to early-onset extreme hypertension and primary hypertension ascertained at any age.
Recurrent hyper-motif circuits in developmental programs
Authors: Adler Miri , Medzhitov Ruslan 
Published: November 2024

AbstractDuring embryogenesis, homogenous groups of cells self-organize into stereotypic spatial and temporal patterns that make up tissues and organs. These emergent patterns are controlled by transcription factors and secreted signals that regulate cellular fate and behaviors through intracellular regulatory circuits and cell-cell communication circuits. However, the principles of these circuits and how their properties are combined to provide the spatio-temporal properties of tissues remain unclear. Here we develop a framework to explore building-block circuits of developmental programs. We use single-cell gene expression data across developmental stages of the human intestine to infer the key intra- and inter-cellular circuits that control developmental programs. We study how these circuits are joined into higher-level hyper-motif circuits and explore their emergent dynamical properties. This framework uncovers design principles of developmental programs and reveals the rules that allow cells to develop robust and diverse patterns.
Targeted detection of endogenous LINE-1 proteins and ORF2p interactions
Authors: Nielsen Mathias I. , Wolters Justina C. , Rosas Bringas Omar G. , Jiang Hua , Di Stefano Luciano H. , Oghbaie Mehrnoosh , Hozeifi Samira , Nitert Mats J. , van Pijkeren Alienke , Smit Marieke , ter Morsche Lars , Mourtzinos Apostolos , Deshpande Vikram , Taylor Martin S. , LaCava John 
Published: November 2024

AbstractBackgroundBoth the expression and activities of LINE-1 (L1) retrotransposons are known to occur in numerous cell-types and are implicated in pathobiological contexts such as aging-related inflammation, autoimmunity, and in cancers. L1s encode two proteins that are translated from bicistronic transcripts. The translation product ofORF1(ORF1p) has been robustly detected by immunoassays and shotgun mass spectrometry (MS). Yet, more sensitive detection methods would enhance the use of ORF1p as a clinical biomarker. In contrast, until now, no direct evidence of endogenous L1ORF2translation to protein (ORF2p) has been shown. Instead, assays for ORF2p have been limited to ectopic L1 ORF over-expression contexts and to indirect detection of endogenous ORF2p enzymatic activity, such as by the sequencing ofde novogenomic insertions. Immunoassays for endogenous ORF2p have been problematic, producing apparent false positives due to cross-reactivities, and shotgun MS has not yielded reliable evidence of ORF2p peptides in biological samples.ResultsHere we present targeted mass spectrometry assays, selected and parallel reaction monitoring (SRM and PRM, respectively) to detect and quantify L1 ORF1p and ORF2p at their endogenous abundances. We were able to quantify ORF1p and ORF2p present in our samples down to a range in the low attomoles. Confident in our ability to affinity enrich ORF2p, we describe an interactome associated with endogenous ORF2-containing macromolecular assemblies.ConclusionThis is the first assay to demonstrate sensitive and robust quantitation of endogenous ORF2p. The ability to assay ORF2p directly and quantitatively will improve our understanding of the developmental and diseased cell states where L1 expression and its activity naturally occur. The ability to simultaneously assay endogenous L1 ORF1p and ORF2p is an important step forward for L1 analytical biochemistry. Endogenous ORF2p interactomes can now be presented with confidence that ORF2p is among the enriched proteins.
Rigorous hydrodynamics from linear Boltzmann equations and viscosity-capillarity balance
Authors: Kogelbauer Florian , Karlin Ilya 
Published: November 2024

Exact closure for hydrodynamic variables is rigorously derived from the linear Boltzmann kinetic equation. Our approach, based on spectral theory, structural properties of eigenvectors, and the theory of slow manifolds, allows us to define a unique, optimal reduction in phase space close to equilibrium. The hydrodynamically constrained system induces a modification of entropy that ensures pure dissipation on the hydrodynamic manifold, which is interpreted as a nonlocal variant of Korteweg's theory of viscosity-capillarity balance. The rigorous hydrodynamic equations are exemplified on the Knudsen minimum paradox in a channel flow.

Published by the American Physical Society
2024
Differentiable master equation solver for quantum device characterization
Authors: Craig D. L. , Ares N. , Gauger E. M. 
Published: November 2024

Differentiable models of physical systems provide a powerful platform for gradient-based algorithms, with particular impact on parameter estimation and optimal control. Quantum systems present a particular challenge for such characterization and control, owing to their inherently stochastic nature and sensitivity to environmental parameters. To address this challenge, we present a versatile differentiable quantum master equation solver facilitating direct computation of steady-state solutions, and incorporate this solver into a framework for device characterization capable of dealing with additional nondifferentiable parameters. Our approach utilizes gradient-based optimization and Bayesian inference to provide estimates and uncertainties in quantum device parameters. To showcase our approach, we consider steady-state charge transport through electrostatically defined quantum dots. Using simulated data, we demonstrate efficient estimation of parameters for a single quantum dot, and model selection as well as the capability of our solver to compute time evolution for a double quantum dot system. Our differentiable solver stands to widen the impact of physics-aware machine learning algorithms on quantum devices for characterization and control.

Published by the American Physical Society
2024
What drives green banking operations in Bangladesh? Findings from PLS-SEM and BSEM
Authors: Rahman Md. Shahinur , Moral Iqbal Hossain , Akther Samia , Hossain Gazi Md. Shakhawat , Islam Waheda 
Published: November 2024

PurposeEnvironmental threats are becoming severe in developing and undeveloped countries. It urges to know how green banking operations can foster sustainable development in these regions. This study aims to provide empirical evidence of the determinants of green banking operations in Bangladesh.Design/methodology/approachBased on the socially responsible investing (SRI) theory, this study examined the hypothesized relationships using a partial least square structural equation modeling (PLS-SEM) approach. The Bayesian SEM (BSEM) through a Markov Chain Monte Carlo (MCMC) approach was also used to validate the study's first-order model.FindingsThe findings show that sustainable innovativeness, green investment and green banking policy substantially and positively change green banking operations. Notably, green investment is the most influential predictor of green banking operations, driving banks to establish sustainable economic systems within the country.Practical implicationsThe findings offer valuable guidance for scholars, financial institutions, policymakers and bank managers to develop and implement effective strategies for green banking operations. These strategies may significantly contribute to achieving the sustainable development goals (SDGs) in Bangladesh.Originality/valueThis study is ground-breaking in associating sustainable innovativeness and green banking operations from a developing country. It enriches our understanding of green banking, aligning with existing literature. Additionally, PLS-SEM and BSEM provide strong validation of the proposed theoretical model.
From killer bunnies to talking cupcakes: theorizing the diverse universe of virtual influencers
Authors: Gambetti Rossella C. , Kozinets Robert V. 
Published: November 2024

Purpose
This study aims to expand understanding of the diversity of virtual influencer forms by investigating their nonhuman-like, animal and graphic or cartoon variations.

Design/methodology/approach
A three-year multisite longitudinal netnography studied 174 virtual influencers and spanned ten social media platforms. Typological categories were constructed from the data set, focusing on 14 influencers located across quadrants. In-depth findings were then developed for eight illustrative cases.

Findings
Findings deepen the knowledge of the virtual influencer sphere by highlighting diversity in human-like, nonhuman-like, imaginative and realistic forms. The authors postulate four types of virtual influencers: hyper-human, antihuman, pan-human and alter-human. These forms are linked to specific personalities and communication styles, addressing various consumer needs. Imaginatively represented virtual influencers may prompt audiences to reevaluate beliefs, values and behaviors. These findings challenge prior work’s focus on attractive, hyperreal and human-like virtual influencers, encouraging consideration of divergent types engaged in novel meaning-shaping activities and targeting different segments.

Research limitations/implications
This research paves the way for consumer and marketing researchers and practitioners to broaden their representations of virtual influencers beyond the human-like, beyond the commercial and into new worlds of fantasy, imagination and posthuman possibility.

Practical implications
Different types of virtual influencers speak to diverse audiences and convey marketing messages in subtly different ways. Some forms of virtual influencers fit into roles like defiant voices, oppositional characters, activists, educators, entertainers and change leaders. As the universe of virtual influencers diversifies, this research opens new avenues of marketing for brands.

Originality/value
This study pioneers comprehensive qualitative research across the universe of virtual influencers and their communities, exploring links to popular culture. It offers connections between virtual influencer forms and communication strategies for marketers.
Can cuteness soften my anxiety? The impact of conversational styles of service robots on consumer service acceptance
Authors: Yan Juanjuan , Luo Biao , Zhang Tanruiling 
Published: November 2024

Purpose
As artificial intelligence technology empowers service robots, they increasingly communicate with consumers in a human-like manner. This study aims to investigate the effect of service robots’ different conversational styles (competent conversational style vs. cute conversational style) on consumer service acceptance and demonstrate the moderating role of consumers’ technology anxiety.

Design/methodology/approach
Based on anthropomorphism theory and social presence theory, the authors conducted two scenario-based experiments (restaurant scenario and hotel scenario) to investigate this issue.

Findings
The results indicate that service robots’ conversational styles impact consumers’ willingness to accept the use of service robots through perceived social presence and positive emotion. Moreover, consumers perceived social presence and positive emotion play a serial mechanism. In addition, the effect of competent conversational style on consumers perceived social presence is less effective than that of cute conversational style. Finally, the authors demonstrate the moderating role of consumer technology anxiety in the relationship between conversational styles and perceived social presence.

Practical implications
To provide consumers with a positive human–robot interaction experience at the service front line, managers need to make better use of the conversational styles of service robots by comprehensively considering the characteristics of consumer technology anxiety.

Originality/value
This research extends the literature on service robots by integrating consumer characteristics and robots’ conversational styles. These findings highlight the effectiveness of cute conversational style in alleviating consumer technology anxiety.