bluuebunny/crossref_metadata_2025_split huggingface dataset:
A systematic and meta-analytic review of non-verbal auditory memory in the brain
Authors: Campo Fulvia Francesca , Carlomagno Francesco , Yılmaz Betül , Quaranta Luis , Carraturo Giulio , Rivolta Davide , Brattico Elvira 
Published: November 2024

AbstractWhile sounds are essential for human development, existing research primarily emphasizes visual and spatial memory and speech in relation to auditory processes, with a lack of a cohesive understanding of memory mechanisms for non-verbal sounds. This systematic review and coordinate-based meta-analysis of neuroimaging findings aims to comprehensively organize the literature for identifying the key brain mechanisms involved in short-term memory, working memory, and long-term memory for non-verbal auditory information. Additionally, we aimed to identify whether and how individual differences in neural memory processes related to auditory expertise (musicianship), aging or auditory impairments such as amusia are explored in the literature. Our review included ninety studies meeting the selection criteria, with only thirteen studies containing brain coordinates could be included in the meta-analysis. The coordinate-based meta-analysis identified a frontal hub for non-verbal auditory memory encompassing the medial frontal gyrus, cingulate gyrus and superior frontal gyrus.
UniOP: a universal operon prediction for high-throughput prokaryotic (meta-)genomic data using intergenic distance
Authors: Su Hong , Zhang Ruoshi , Söding Johannes 
Published: November 2024

AbstractThe study of the deluge of metagenomic and genomic sequences is challenging due to the severe lack of function information. Predicting operons, groups of functionally related genes in prokaryotic genomes, is critical for bridging this gap. However, existing methods for operon prediction heavily rely on experimental data, functional annotations, or extensive characterization of homologous genes, making it difficult to accurately predict operons in newly sequenced or poorly characterized genomes. Here, we introduce UniOP, an unsupervised approach that uses a statistical model to predict operons from intergenic distances directly derived from the target genomic sequence. UniOP not only outperforms alternative approaches on ten complete genomes but also shows superior results on 3269 metagenome-assembled genomes across 13 bacterial and 2 archaeal phyla. Furthermore, we explored enhancing UniOP by incorporating the conservation of gene neighborhood and strandedness in respective genomes and examined the influence of Pfam annotations and motif searching on its performance.
Single-cell spatial transcriptomics of fixed, paraffin-embedded biopsies reveals colitis-associated cell networks
Authors: Mennillo Elvira , Lotstein Madison L. , Lee Gyehyun , Johri Vrinda , Ekstrand Christina , Tsui Jessica , Hou Julian , Leet Donna E. , He Jun Yan , Mahadevan Uma , Eckalbar Walter , Oh David Y. , Fragiadakis Gabriela K. , Kattah Michael G. , Combes Alexis J. 
Published: November 2024

ABSTRACTBackground & AimsImaging-based, single-cell spatial transcriptomics (iSCST) using formalin-fixed, paraffin-embedded (FFPE) tissue could transform translational research by retaining all tissue cell subsets and spatial locations while enabling the analysis of archived specimens. We aimed to develop a robust framework for applying iSCST to archived clinical FFPE mucosal biopsies from patients with inflammatory bowel disease (IBD).MethodsWe performed a comprehensive benchmarking comparison of three iSCST platforms capable of analyzing FFPE specimens. We analyzed FFPE mucosal biopsies (n=57) up to 5 years old from non-IBD controls (HC; n=9) and patients with ulcerative colitis (UC;n=11). After platform-specific cell segmentation, we applied a uniform data processing pipeline to all datasets, including transcript detection, cell annotation, differential gene expression, and neighborhood enrichment. Transcriptomic signatures identified with iSCST were validated using external, publicly available bulk transcriptomic datasets.ResultsA custom 290-plex Xenium gene panel exhibited the highest sensitivity and specificity for transcript detection, enabling precise identification and quantification of diverse cell subsets and differentially expressed genes across cell types and disease states. We mapped transcriptionally distinct fibroblast subsets to discrete spatial locations and identified inflammation-associated fibroblasts (IAFs) and monocytes as a colitis-associated cellular neighborhood. We also identified signatures associated with Vedolizumab (VDZ) responsiveness. VDZ non-responders were characterized by an IAF-monocyte transcriptional signature, while responders exhibited enrichment of epithelial gene sets.ConclusionsOur optimized iSCST framework for archived FFPE biopsies provides unique advantages for assessing the role of colitis-associated cellular networks in routinely collected clinical samples. FFPE-based biomarkers could integrate with existing clinical workflows and potentially aid in risk-stratifying patients.
SIMPL: Scalable and hassle-free optimization of neural representations from behaviour
Authors: George Tom M , Glaser Pierre , Stachenfeld Kimberly , Barry Caswell , Clopath Claudia 
Published: November 2024

AbstractHigh-dimensional neural activity in the brain is known to encode low-dimensional, time-evolving, behaviour-related variables. A fundamental goal of neural data analysis consists of identifying such variables and their mapping to neural activity. The canonical approach is to assume the latent variablesarebehaviour and visualize the subsequent tuning curves. However, significant mismatches between behaviour and the encoded variables may still exist — the agent may be thinking of another location, or be uncertain of its own — distorting the tuning curves and decreasing their interpretability. To address this issue a variety of methods have been proposed to learn this latent variable in an unsupervised manner; these techniques are typically expensive to train, come with many hyperparameters or scale poorly to large datasets complicating their adoption in practice. To solve these issues we propose SIMPL (Scalable Iterative Maximization of Population-coded Latents), an EM-style algorithm which iteratively optimizes latent variables and tuning curves. SIMPL is fast, scalable and exploits behaviour as an initial condition to further improve convergence and identifiability. We show SIMPL accurately recovers latent variables in biologically-inspired spatial and non-spatial tasks. When applied to a large rodent hippocampal dataset SIMPL efficiently finds a modified latent space with smaller, more numerous, and more uniformly-sized place fields than those based on behaviour, suggesting the brain may encode space with greater resolution than previously thought.
Nimodipine reduces microglial activationin vitroas evidenced by morphological phenotype, phagocytic activity and next generation RNA sequencing
Authors: Pesti István , Varga Valentin , Qorri Erda , Frank Rita , Kata Diana , Vinga Krisztián , Szarvas Péter Archibald , Menyhárt Ákos , Gulya Károly , Bari Ferenc , Farkas Eszter 
Published: November 2024

AbstractBackgroundNimodipine, an L-type voltage-gated calcium channel blocker, achieves vasorelaxation by suppressing Ca2+-dependent activation of cerebrovascular smooth muscle cells and is used to prevent delayed ischemic deficit following subarachnoid hemorrhage. Our preclinical drug repurposing studies raised the possibility that nimodipine may attenuate the pro-inflammatory shift in microglial function in response to brain injury. We analyzed the effects of nimodipine on activated microglia at the level of morphological and functional phenotypes, as well as their transcriptomic profile.MethodsLive brain slice preparations from C57BL/6 mice and primary microglia cultures from the cortex of neonatal Sprague Dawley rats were used. Brain slices were subjected to ischemia, and microglial cultures were activated with lipopolysaccharide (LPS; 20 ng/ml). Both preparations were treated with nimodipine (5-10-20 μM). The degree of arborization was evaluated in Iba1-stained microglia and expressed as a transformation index (TI). Phagocytic activity of cultured microglia was visualized using fluorescent microbeads. TNFα levels in the cultures were measured with ELISA. Total RNA was isolated from microglia and processed for next generation RNA sequencing to determine differentially expressed genes.ResultsNimodipine suppressed the ameboid morphological transformation and increased phagocytosis triggered by ischemia in brain slices and LPS in microglia cultures. At the transcriptional level, LPS resulted in a pro-inflammatory microglial phenotype, affecting the expression of cytokines, the complement system and phagocytosis-related genes. Focusing on the role of calcium in microglial activation, LPS increased RNA transcription of ionotropic purinergic and some TRP channels but decreased the expression of voltage- and ligand-gated calcium channels. In the endoplasmic reticulum, LPS downregulated gene expression of Ryr and IP3 receptors and increased transcription of the SERCA calcium pump gene. Nimodipine co-administered with LPS altered the expression of 110 genes in the opposite direction to LPS activation, of which at least 20 were associated with microglial immune response, 7 with cell adhesion and 2 with autophagy regulation.ConclusionThe effect of nimodipine goes beyond cerebral vasorelaxation. Nimodipine attenuates microglial activation by modulating Ca2+-dependent gene expression involved in intracellular signaling cascades to drive microglial immune responses. Consideration should be given to expanding the medical field of indication of nimodipine.
A translocation-competent pore is required forShigella flexnerito escape from the double membrane vacuole during intercellular spread
Authors: Raab Julie E. , Harju Tucker B. , Toperzer Jody D. , Duncan-Lowey Jeffrey K. , Goldberg Marcia B. , Russo Brian C. 
Published: November 2024

ABSTRACTType 3 secretion systems (T3SSs) enable bacterial virulence by translocating virulence proteins (effectors) into host cells.Shigella flexnerirequire T3SS to invade and to spread between cells in the colon. In order to spread,S. flexneriforms membrane protrusions that push into the adjacent host cell. These protrusions are resolved into double membrane vacuoles (DMVs) that the bacteria quickly escape. The mechanisms required for escape from the DMV are poorly understood, but the T3SS translocon pore protein IpaC is essential. Here, we show IpaC forms a pore that is competent for translocation of T3SS effectors as bacteria spread between cells. To do so, we used a genetic approach to test mutations of IpaC that disrupt its ability to translocate and to form pores. We show that during spread, IpaC is efficiently inserted into the plasma membrane, the membrane-embedded IpaC forms pore complexes, and the IpaC-dependent pores translocate effectors that are necessary forS. flexnerito escape the DMV. We further show that T3SS activation is regulated through a distinct mechanism at spread compared to at invasion; activation of T3SS secretion does not require pore formation during spread. Thus, we show that a distinct regulation of the T3SS duringS. flexneriintercellular spread enables the placement of effectors both aroundS. flexneriand across membranes of the DMV. Altogether, this study provides new insights into howS. flexneriescapes the DMV.IMPORTANCEThe type 3 secretion system (T3SS) is required for virulence in many bacterial pathogens that infect humans. The T3SS forms a pore through which virulence proteins are delivered into host cells to enable bacterial infection. Our work investigates theShigellatranslocon pore protein IpaC, which is essential not only for bacteria to invade cells, but also for bacteria to spread between cells. An ability to spread between cells is essential for pathogenesis, thus understanding the mechanisms that enable spread is important for understanding howS. flexneriinfection causes illness. We show that IpaC delivers virulence factors across the host membrane forS. flexnerito efficiently spread. This study furthers our understanding of the mechanisms involved in T3SS secretion and of translocon pore function duringS. flexneriintercellular spread.
A toolkit for testing membrane localisation tags across species
Authors: Karapidaki Irene , Momose Tsuyoshi , Zilliox Marie , Averof Michalis 
Published: November 2024

ABSTRACTTransgenic markers and tools have revolutionised how we study cells and developing organisms. Some of the elements needed to construct those tools are universally applicable (e.g. fluorescent proteins), while others are species-specific (e.g.cis-regulatory elements driving transcription). Membrane localisation signals targeting proteins to the plasma membrane have been identified in several model organisms. Unfortunately, these do not work equally well in different species, developmental stages and cell types. To generate a toolkit of membrane localisation tags that can be screened rapidly in diverse species, we collected 11 membrane localisation tags –known to localise proteins to the plasma membrane through different mechanisms– and fused them to the red fluorescent protein mScarlet3. Each tagged construct was placed downstream of a T7 promoter, allowing thein vitroproduction of tagged reporter mRNAs, which can be readily delivered to embryos or cell types of interest. The tags in this kit include signals for trafficking to the plasma membrane through the exocytic pathway with a transmembrane domain (SP-CD8tm) or a GPI anchor (SP-GPI), lipid-binding domains (PH, LactC2), signals for prenylation, palmitoylation and myristoylation (H-Ras, K-Ras, K-Ras-6R, GAP43, Lyn, Src64B), and a domain that targets proteins to the plasma membrane independently of exocytosis or lipid modification (RitC). We demonstrate the use of this toolkit in early embryos of the crustaceanParhyale hawaiensisand primary polyps of the hydrozoanClytia hemisphaerica.
resbos2 and the CDF
W
mass measurement
Authors: Isaacson Joshua , Fu Yao , Yuan C.-P. 
Published: November 2024

The recent collider detector at fermilab (CDF) W mass measurement of 80,433±9  MeV is the most precise direct measurement. However, this result deviates from the Standard Model predicted mass of 80,359.1±5.2  MeV by 7σ. The CDF experiment used an older version of the esos code that was only accurate at NNLL+NLO, while the esos2 code is able to make predictions at N3LL+NNLO accuracy. We determine that the data-driven techniques used by CDF capture most of the higher order corrections, and using higher order corrections would have an impact on the CDF result in total at the 10 MeV level. Additionally, we investigate the effects from handling the width of the W boson on the mass, PDF correlations, and scale uncertainties. We find that these contributions are consistent with those obtained by CDF.

Published by the American Physical Society
2024
Dark matter as the trigger of flavor changing neutral current decays of the top quark
Authors: Jueid Adil , Kanemura Shinya 
Published: November 2024

We suggest a simplified model that simultaneously addresses the dark matter problem and gives rise to top-quark flavor changing neutral current (FCNC) interactions at the one-loop order. The model consists of two extra SU(2)L gauge singlets: a colored mediator of spin zero (S) and a right-handed fermion (χ); both are odd under an Z2 symmetry. The right-handed fermion plays the role of the dark matter candidate. In this model, the presence of the two dark sector particles generates one-loop induced FCNC decays of the top quark into light quarks and bosons such as the gluon, the photon, the Z boson, or the Higgs boson. As a case study, we analyze the top-quark FCNC decays into light quarks (u or c) and Z or Higgs bosons. We then study the reliable solutions to the dark matter problem by estimating the regions in the parameter space that are consistent with the measurement of the dark matter relic density. We also revisit the bounds from the searches of dark matter in events with at least one high-pT jet and large missing transverse energy at the Large Hadron Collider (LHC). We then define four benchmark points that are consistent with the existing constraints from collider experiments and cosmology. We finally estimate, for these benchmark scenarios, the rates of a broad range of channels that can be used to probe the connection between the top FCNC transitions and dark matter, both at the HL-LHC and at a future 100 TeV collider.

Published by the American Physical Society
2024
Muonic force and nonstandard neutrino interactions at muon colliders
Authors: Jana Sudip , Klett Sophie 
Published: November 2024

The discovery of neutrino oscillations implies that neutrinos are massive and mixed, necessitating an extension of the Standard Model, which may require the introduction of nonstandard neutrino interactions (NSIs). We investigate the potential of a high-energy muon collider to probe such NSIs with muons, specifically focusing on muonic forces. By analyzing the monophoton signal from the process μ+μ−→νν¯γ, we explore four-fermion contact interactions involving two muons and two neutrinos. Moreover, we examine minimal models that generate scalar and vector-mediated NSIs and study their phenomenology. Projected sensitivities for the strength of NSIs, εαβμμ, are presented at a 95% confidence level for a center-of-mass energy of 3 TeV and integrated luminosities of L=1 and 10  ab−1, showcasing the complementarity between a muon collider and other experimental probes.

Published by the American Physical Society
2024
Dark matter limits from the tip of the red giant branch of globular clusters
Authors: Hong Haozhi , Vincent Aaron C. 
Published: November 2024

Capture and annihilation of weakly interacting massive particle (WIMP)-like dark matter in red giant stars can lead to faster-than-expected ignition of the helium core, and thus a lower tip of the red giant branch (TRGB) luminosity. We use data to place constraints on the dark matter-nucleon cross section using 22 globular clusters with measured TRGB luminosities, and place projections on the sensitivity resulting from 161 clusters with full phase space distributions observed by . Although limits remain weaker than those from Earth-based direct detection experiments, they represent a constraint that is fully independent of dark matter properties in the solar neighborhood, probing its properties across the entire Milky Way galaxy. Based on our findings, it is likely that the use of the TRGB as a standard candle in H0 measurements is very robust against the effects of dark matter.

Published by the American Physical Society
2024
Who cares about environmental, social and governance performance? Family versus non-family firms
Authors: Zhao Jiyang , Wang Xiaohong 
Published: November 2024

Purpose
This paper aims to explore the nexus between family involvement and environmental, social and governance (ESG) performance based on socioemotional wealth theory, and it also analyzes the potential influence mechanism.

Design/methodology/approach
Based on the categorization of China Stock Market & Accounting Research database, this study divides the Chinese listed firms into family and nonfamily firms and applies multiple regression methods to test the theoretical hypotheses.

Findings
Family involvement can incentivize corporations to enhance corporate transparency, which can in turn enhance their ESG performance. The role of family involvement in bolstering corporate ESG performance is negatively contingent on external financing constraints.

Originality/value
There are insufficient studies on the nexus between family ownership and ESG performance. The findings provide insights into helping policymakers formulate targeted measures to encourage corporations to be more active in promoting ESG initiatives.
Does language concreteness influence consumers’ perceived deception in online reviews?
Authors: Shi Xiaoxiao , Shan Wei , Du Zhaohua , Evans Richard David , Zhang Qingpu 
Published: November 2024

Purpose
Although online reviews have become a key source of information for consumer purchasing decisions, little is known about how the concreteness of language used in these reviews influences perceptions of deception. This study aims to address this important gap by drawing on psycholinguistic research and Language Expectancy Theory to examine how and when the concreteness of online reviews (abstract vs concrete) impacts consumers’ perceived deception.

Design/methodology/approach
Two scenario-based experiments were conducted to examine how the concreteness of online reviews (abstract vs concrete) influences consumers’ perceptions of deception, considering the mediating role of psychological distance to online reviews and the moderating effects of Machiavellianism (Mach) and reviewer identity disclosure.

Findings
Online reviews that include concrete language lead to lower perceived deception by reducing consumers’ psychological distance from the review. For consumers with higher levels of Mach, online reviews written in abstract (vs concrete) language result in higher perceived deception via psychological distance, while for consumers with lower Mach, online reviews written in concrete (vs abstract) language result in higher perceived deception via psychological distance.

Research limitations/implications
To the best of the authors’ knowledge, this study is one of the first to highlight the relevance of linguistic style (i.e. concrete review vs abstract review) on consumers’ perceived deception toward online reviews in the context of e-commerce.

Practical implications
The framework enables managers of online retailing platforms to identify the most effective strategies to decrease consumers’ perceived deception via the appropriate utilize of linguistic styles of online reviews.

Originality/value
This study contributes to both theory and practice by deepening knowledge of how and when the concreteness of online reviews (abstract vs concrete) affects consumers’ perceived deception and by helping managers of online retailing platforms make the most effective\ strategies for reducing consumers’ perceived deception toward online reviews during online shopping.