bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neural basis of perceptual surface qualities: Evidence from EEG decoding
Authors: Orima Taiki , Wakita Suguru , Motoyoshi Isamu 
Published: February 2024

AbstractThe human visual system can easily recognize object material categories and estimate surface properties such as glossiness and smoothness. A number of psychophysical and computational studies suggest that the material perception depends on global feature statistics of the entire image at multiple processing levels. Neural representations of such global features, which is independent of precise retinotopy, may be captured even by EEG that have low spatial resolution. To test this possibility, here we measured visual evoked potentials (VEPs) for 191 natural images consisting of 20 categories of materials. We then sought to classify material categories and surface properties from the VEPs, and to reconstruct the rich phenomenological appearance of materials themselves via neural representations of global features as estimated from the VEPs. As a result, we found that material categories were correctly classified by the VEPs even at latencies of 150 ms or less. The apparent surface properties were also significantly classified within 175 ms (lightness, colorfulness, and smoothness) and after 200 ms (glossiness, hardness, and heaviness). In a subsequent reverse-correlation analysis, we further found that the VEPs at these latencies are highly correlated with low- and high-level global feature statistics of the surface images; Portilla-Simoncelli texture statistics and style information in deep convolutional neural network (dCNN), indicating that neural activities about such global features are reflected in the VEPs that enabled successful classification of materials. To demonstrate this idea more directly, we trained deep generative models (MVAE models) that reconstruct the surface image itself from the VEPs via style information (gram matrix of the dCNN output). The model successfully reconstructed realistic surface images, a part of which were nearly indistinguishable from the original images. These findings suggest that the neural representation of statistical image features, which were formed at short latencies in the visual cortex and reflected even in EEG signals, not simply enable human visual system to recognize material categories and evaluate surface properties but provides the essential basis for rich and complex phenomenological qualities of natural surfaces.
Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex
Authors: Carr Caleb R. , Crawford Katharine H. D. , Murphy Michael , Galloway Jared G. , Haddox Hugh K. , Matsen Frederick A. , Andersen Kristian G. , King Neil P. , Bloom Jesse D. 
Published: February 2024

AbstractLassa virus is estimated to cause thousands of human deaths per year, primarily due to spillovers from its natural host,Mastomysrodents. Efforts to create vaccines and antibody therapeutics must account for the evolutionary variability of Lassa virus’s glycoprotein complex (GPC), which mediates viral entry into cells and is the target of neutralizing antibodies. To map the evolutionary space accessible to GPC, we use pseudovirus deep mutational scanning to measure how nearly all GPC amino-acid mutations affect cell entry and antibody neutralization. Our experiments define functional constraints throughout GPC. We quantify how GPC mutations affect neutralization by a panel of monoclonal antibodies and show that all antibodies are escaped by mutations that exist among natural Lassa virus lineages. Overall, our work describes a biosafety-level-2 method to elucidate the mutational space accessible to GPC and shows how prospective characterization of antigenic variation could aid design of therapeutics and vaccines.
Process evaluation of a New psychosocial goal-setting and manualised support intervention for Independence in Dementia (NIDUS-Family)
Authors: Wyman Danielle , Butler LT , Morgan-Trimmer Sarah , Bright Peter , Barber Julie , Budgett Jessica , Walters Kate , Lang I , Rapaport P , Banks Sara , Palomo Marina , Orgeta Vasiliki , Livingston Gill , Rockwood K , Lord K , Manthorpe J , Dow B , Hoe J , Cooper Claudia 
Published: February 2024

ABSTRACTIntroductionWe report a process evaluation embedded within a UK Randomised Controlled Trial (RCT), which demonstrated that New Interventions for independence in Dementia Study (NIDUS)-Family (a manualised, multimodal psychosocial intervention), was effective relative to usual care, on the primary outcome of Goal Attainment Scaling (GAS) over one year. We aimed to test and refine a hypothesised theory of change model delineating key causal assumptions for impact mechanisms.MethodsIn 2021-22, intervention-arm dyads completed an acceptability questionnaire developed to test causal assumptions. We interviewed dyads and their intervention facilitators, purposively selected for diverse follow-up GAS scores and sociodemographic diversity. Matching observational data were collected from intervention session recordings, using a checklist developed to test causal assumptions. We thematically analysed data, then integrated qualitative and quantitative data.Results174/204 (85.3%) dyads allocated to NIDUS-Family, fully completed the intervention, 18 partially completed it, while 12 received none. 47/192 (24.5%) of carers receiving any sessions completed the acceptability questionnaire. 27/58 (47%) dyads purposively selected, and 9/10 facilitators participated in qualitative interviews; and we observed 12 sessions. We identified four themes: A) ‘Someone to talk to helps dyads feel supported’; B) ‘NIDUS-Family helps carers change their perspective’; C) ‘Personalisation helps people living with dementia maintain their identity’; and D) ‘Small steps help dyads move forward’.ConclusionKey causal pathway mechanisms were: regular sessions with a consistent facilitator providing space to discuss priorities, supporting carers to consider new perspectives and approaches to personalising care; and planning small actionable steps towards goals. Findings will support NIDUS-Family implementation.
Evaluation of three control strategies to limit mpox outbreaks in an agent based model
Authors: Brainard Julii , Lake Iain , Hunter Paul R. 
Published: February 2024

AbstractMost of the 2022 mpox outbreaks in high income countries, which predominantly affected men who have sex with men, peaked less than two months after detection. To stop the outbreaks, people were encouraged to limit new sex partners, take up any offers for smallpox vaccination, and self-isolate. The relative contributions of each of these strategies to outbreak reduction are hard to know. To consider the potential relative efficacy of each of these measures individually, we constructed agent-based models using plausible partnership counts, reasonable behaviour choices and published information about smallpox vaccination uptake rates in the UK context during 2022. Compared to a baseline, no intervention scenario, partner reduction was more effective at preventing generation of secondary cases than the vaccine rollout at the speed that the smallpox vaccine rollout occurred in the UK in 2022. These findings suggest that partner reduction by the most affected community rather than pharmaceutical intervention was largely to credit for causing case numbers to peak as early as they did.
Single-nucleus RNA sequencing reveals cellular and molecular dynamics of white and brown adipose tissue in a mouse model of type-2 diabetes
Authors: Gaynor Taylah L. , Hsu Ian , Krstevski Crisdion , Farrugia Gabriella E. , Dona Malathi S. I. , Cohen Charles D. , Drew Brian G. , Pinto Alexander R. 
Published: February 2024

SummaryExcessive adipose tissue expansion is often linked with type-2 diabetes. Despite recent efforts mapping adipose tissue changes in obesity using single-cell omics, an understanding of cellular and gene expression changes in a model of type 2 diabetes, and the transcriptional circuitry controlling it, is still lacking. Here, we use single-nucleus RNA sequencing to analyze the remodeling of gonadal white and interscapular brown adipose tissue from female and male mice with or without diabetes. Analysis of 51,877 nuclei revealed altered phenotypes in every cell population in type 2 diabetes. This included an immunoregulatory response, and changes in extracellular matrix, energy generation, and hormone responses. Key transcription factors were inferred as cell-specific and non-specific nodes controlling diabetes-linked phenotypes. Finally, female-to-male population heterogeneity and gene expression differences were observed. Here we provide a resource detailing how adipose tissue remodeling, and the molecular mechanisms governing it, may contribute to cardiometabolic disease.
Protein interaction map of APOBEC3 enzyme family reveals deamination-independent role in cellular function
Authors: Jang Gwendolyn M. , Sudarsan Arun Kumar Annan , Shayeganmehr Arzhang , Munhoz Erika Prando , Lao Reanna , Gaba Amit , Rodríguez Milaid Granadillo , Love Robin P. , Polacco Benjamin J. , Zhou Yuan , Krogan Nevan J. , Kaake Robyn M. , Chelico Linda 
Published: February 2024

ABSTRACTHuman APOBEC3 enzymes are a family of single-stranded (ss)DNA and RNA cytidine deaminases that act as part of the intrinsic immunity against viruses and retroelements. These enzymes deaminate cytosine to form uracil which can functionally inactivate or cause degradation of viral or retroelement genomes. In addition, APOBEC3s have deamination independent antiviral activity through protein and nucleic acid interactions. If expression levels are misregulated, some APOBEC3 enzymes can access the human genome leading to deamination and mutagenesis, contributing to cancer initiation and evolution. While APOBEC3 enzymes are known to interact with large ribonucleoprotein complexes, the function and RNA dependence is not entirely understood. To further understand their cellular roles, we determined by affinity purification mass spectrometry (AP-MS) the protein interaction network for the human APOBEC3 enzymes and map a diverse set of protein-protein and protein-RNA mediated interactions. Our analysis identified novel RNA-mediated interactions between APOBEC3C, APOBEC3H Haplotype I and II, and APOBEC3G with spliceosome proteins, and APOBEC3G and APOBEC3H Haplotype I with proteins involved in tRNA methylation and ncRNA export from the nucleus. In addition, we identified RNA-independent protein-protein interactions with APOBEC3B, APOBEC3D, and APOBEC3F and the prefoldin family of protein folding chaperones. Interaction between prefoldin 5 (PFD5) and APOBEC3B disrupted the ability of PFD5 to induce degradation of the oncogene cMyc, implicating the APOBEC3B protein interaction network in cancer. Altogether, the results uncover novel functions and interactions of the APOBEC3 family and suggest they may have fundamental roles in cellular RNA biology, their protein-protein interactions are not redundant, and there are protein-protein interactions with tumor suppressors, suggesting a role in cancer biology.
A 20-year time-series of a freshwater lake reveals seasonal dynamics and environmental drivers of viral diversity, ecology, and evolution
Authors: Zhou Zhichao , Tran Patricia Q. , Martin Cody , Rohwer Robin R. , Baker Brett J. , McMahon Katherine D. , Anantharaman Karthik 
Published: February 2024

AbstractLong-term ecological studies are powerful tools to investigate microbiomes and ecosystem change but have mostly ignored viruses. Here, we leveraged a 20-year time-series of a freshwater lake to characterize 1.3 million viral genomes over time, seasonality, and environmental factors. We identified 578 auxiliary metabolic gene (AMG) clusters representing over 150,000 AMGs, the most abundant of which, includingpsbAfor photosynthesis,pmoCfor methane oxidation, andkatGfor hydrogen peroxide decomposition, were consistently represented in viruses across decades and seasons. We observed positive associations and niche differentiation between virus-host pairs during seasonal change including in keystone taxa, Cyanobacteria, methanotrophs, and Nanopelagicales. Environmental constraints, specifically inorganic carbon and ammonium influenced viral abundances over time, and highlighted roles of viruses in both “top-down” and “bottom-up” interactions. Key evolutionary processes shaping gene and genome-wide selection included favored fitness genes, reduced genomic heterogeneity, and dominant sub-populations carrying specific genes. Overall, our study advances understanding of diversity, ecological dynamics, and evolutionary trajectories of viruses in Earth’s microbiomes and ecosystems.
De novomutations mediate phenotypic switching in an opportunistic human lung pathogen
Authors: Poret Alexandra J. , Schaefers Matthew , Merakou Christina , Mansour Kathryn E. , Lagoudas Georgia K. , Cross Ashley R. , Goldberg Joanna B. , Kishony Roy , Uluer Ahmet Z. , McAdam Alexander J. , Blainey Paul C. , Vargas Sara O. , Lieberman Tami D. , Priebe Gregory P. 
Published: February 2024

AbstractBacteria evolving within human hosts encounter selective tradeoffs that render mutations adaptive in one context and deleterious in another. Here, we report that the cystic fibrosis-associated pathogenBurkholderia dolosaovercomes in-human selective tradeoffs by acquiring successive point mutations that alternate phenotypes. We sequenced the whole genomes of 931 respiratory isolates from two recently infected patients and an epidemiologically-linked, chronically-infected patient. These isolates are contextualized using 112 historical genomes from the same outbreak strain. Within both newly infected patients, diverse parallel mutations that disrupt O-antigen expression quickly arose, comprising 29% and 63% of theirB. dolosacommunities by 3 years. The selection for loss of O-antigen starkly contrasts with our previous observation of parallel O-antigen-restoring mutations after many years of chronic infection in the historical outbreak. Experimental characterization revealed that O-antigen loss increases uptake in immune cells while decreasing competitiveness in the mouse lung. We propose that the balance of these pressures, and thus whether O-antigen expression is advantageous, depends on tissue localization and infection duration. These results suggest that mutation-driven alternation during infection may be more frequent than appreciated and is underestimated without dense temporal sampling.
Meta-analysis of technology acceptance for mobile and digital libraries in academic settings using technology acceptance model (TAM)
Authors: Ali Irfan , Warraich Nosheen Fatima 
Published: February 2024

Purpose
The purpose of this paper is to measure the relationship of technology acceptance model (TAM) variables (PEOU and PU) with behavioral intention (BI) and attitude in mobile and digital libraries context. This study also examines the relationship of external variables (information quality and system quality) with TAM variables (PEOU and PU) in mobile and digital libraries context.

Design/methodology/approach
This meta-analysis was performed through PRISMA-P guidelines. Four databases (Google Scholar, Web of Science, Scopus and LISTA) were used for searching, and the search was conducted according to defined criteria.

Findings
Findings of this study revealed a large effect size of PU and PEOU with BI. There was also a large effect size of PU and PEOU with attitude. A medium effect size was found between SysQ → PU, InfoQ → PU and SysQ → PEOU. However, there was a small effect size between InfoQ and PEOU.

Originality/value
To the best of the authors’ knowledge, there was no study published till the time of conducting this meta-analysis. Hence, this study fills the literature gap. This study also confirms that TAM is a valid model in the acceptance and use of technology in mobile and digital libraries context. Thus, the findings of the present study are helpful for developers and designers in designing and developing mobile library apps. It will also be beneficial for library authorities and system librarians in designing and developing digital libraries in academic settings.
The role of B cells in systemic sclerosis
Authors: Fukasawa Takemichi , Yoshizaki‐Ogawa Asako , Sato Shinichi , Yoshizaki Ayumi 
Published: February 2024

AbstractSystemic sclerosis (SSc) is a rare and refractory systemic disease characterized by fibrosis and vasculopathy in the presence of autoimmune abnormalities. While the exact cause of SSc is incompletely understood, the specific autoantibodies identified in SSc are closely linked to disease severity and prognosis, indicating a significant role of autoimmune abnormalities in the pathogenesis of SSc. Although the direct pathogenic mechanisms of autoantibodies in SSc are not fully elucidated, numerous prior investigations have demonstrated the involvement of B cells in the pathogenesis of SSc through various mechanisms. Additionally, several clinical trials have explored the efficacy of B‐cell depletion therapy for SSc, with many reporting positive outcomes. However, the role of B cells in SSc pathogenesis is multifaceted, as they can both promote inflammation and exert inhibitory functions. This article provides an overview of the involvement of B cells in SSc development, incorporating the latest research findings.
Long‐term efficacy and safety of dutasteride 0.5 mg in Korean men with androgenetic alopecia: 5‐year data demonstrating clinical improvement with sustained efficacy
Authors: Choi Sangmin , Kwon Soon‐Hyo , Sim Woo‐Young , Lew Bark‐Lynn 
Published: February 2024

AbstractDutasteride 0.5 mg is a dual inhibitor of 5α‐reductase type I and II and was approved in Korea in 2009 for treating androgenetic alopecia (AGA) in men. We investigated the 5‐year efficacy and safety of dutasteride 0.5 mg in Korean men with AGA using the basic and specific (BASP) classification. This retrospective analysis included 99 male AGA patients aged ≥18 years who were treated with dutasteride 0.5 mg for at least 5 years from October 2009 to December 2016 at Kyung Hee University Hospital in Gangdong. Patient photographs were scored using the BASP classification, and the Investigator Global Assessment (IGA) was performed using a seven‐point scale. Patient improvement (IGA score ≥1) and prevention of disease progression (IGA score ≥0) were 89.9% (89/99) and 93.9% (93/99), respectively. According to the BASP classification, 52.5% (52/99) of the basic type, 75% (15/20) of the specific F type, and 82.2% (60/73) of the specific V type showed clinical improvement after 5 years of treatment. Dutasteride demonstrated long‐term safety and efficacy in Korean male patients with AGA over a period of at least 5 years, with results comparable to those of other long‐term efficacy studies of finasteride 1 mg in male patients with AGA.
Ant handling changes myrmecochore seed coat microbiomes and alters diversity of seed‐borne plant pathogenic fungi
Authors: Lash Chloe L. , Cregger Melissa A. , Kinkopf Anne M. , Buerger Nicole , Klingeman Dawn M. , Kwit Charles 
Published: February 2024

Abstract

The putative benefits to seeds in myrmecochory (ant‐mediated seed dispersal) are often cast in a reward context. However, microbes have been mostly overlooked as seed mortality agents in myrmecochory, as have potential treatments provided by ant‐handling.

We investigated the effects of ant handling on the diversity of seed coat fungal communities of three myrmecochorous plant species.

Ant‐handling altered measures of both alpha and beta diversity of fungal communities. Ant‐handled seeds harboured different overall fungal communities and plant pathogen communities than non‐ant‐handled seeds. The myrmecochore pathogenic fungal community showed high dissimilarity (high pairwise community turnover) between ant‐handled and control seeds, while beta diversity measures for ant‐handled seeds and seeds with manually removed elaiosomes were less dissimilar.

Ant handling may offer an additional benefit to myrmecochorous seeds via the reduction in the seed coat pathogenic community, which may be driven by elaiosome removal or as a by‐product of ant cleaning behaviours and chemical secretions.

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Effects of leaf litter traits on terrestrial isopod and millipede consumption, assimilation and growth
Authors: Lam Weng Ngai , Slade Eleanor M. , Wardle David A. 
Published: February 2024

Abstract

Nutrient cycling through leaf litter consumption is an essential ecological function performed by macrodetritivorous invertebrates such as isopods and millipedes. Leaf litter consumption rates can vary greatly depending on the environment, consumer identity and litter traits, but generalizations about the effects of plant traits on macrodetritivore leaf litter consumption, assimilation and growth are not well established and are mostly indirectly inferred.

We conducted a systematic search of the global literature and obtained 456 standardized measures from laboratory experiments of relative consumption (RCR), assimilation (RAR) and growth (RGR) rates of terrestrial isopods and millipedes, extracted from 56 different articles. We investigated if commonly measured leaf traits, plant functional groups, prior microbial conditioning of leaves and climatic conditions affected these rates. We obtained data on commonly measured leaf traits from the TRY global plant trait database, inferred plant functional groups from taxonomic groupings and obtained climatic data from information reported within articles.

RCR, RAR and RGR varied greatly among macrodetritivore and plant species, but overall, there were no differences between isopods and millipedes. Microbial conditioning of litter greatly increased RCR. Plant functional group was an important predictor of RCR, with eudicot trees and forbs being consumed in greater quantities than magnoliid trees and grasses. Fresh leaf N:P ratio had a positive effect on RAR, and leaf N and C:N ratio had positive and negative effects on RGR, respectively, while climatic variables had weak effects on the three rates.

Our work shows that plant traits (both those associated with plant functional groups and commonly measured leaf traits) exert strong effects on resource processing rates by terrestrial macrodetritivores. Further, prior microbial conditioning of leaf litter has a large and globally consistent positive effect on macrodetritivore litter consumption, suggesting that they may consume little, if any, freshly senesced leaf material when microbially conditioned litter is available. Our results suggest that, where extremes of temperature or precipitation do not occur, variables reflective of food quality (leaf traits and microbe conditioning) are more important drivers of macrodetritivore leaf litter consumption than are extrinsic climatic variables.

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