bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors Related to the Utilization of Digital Adherence Technologies in Tuberculosis Care: A Qualitative Study Among Adults in DS-TB Treatment, Health Care Providers and Other Key Stakeholders in Tanzania
Authors: Gonçalves Tasca Bianca , Mganga Andrew , Leung Chung Lam , Shilugu Lucas , Pell Christopher , Onjare Baraka , Luvanda Nicholaus , de Groot Liza , van Kalmthout Kristian , Fielding Katherine , Jerene Degu 
Published: December 2023

AbstractNumerous challenges, such as lengthy treatmenst courses, side effects, and distance to healthcare facilities contribute to suboptimal Tuberculosis (TB) treatment completion. Digital adherence technologies (DATs), such as smart pillboxes and medication labels, could be an alternative to facilitate TB treatment continuation.In-depth interviews with people undergoing treatment for drug susceptible TB, health care providers (HCPs) and other key stakeholders were conducted to evaluate their experiences with DATs in ten health facilities across four different regions in Tanzania. This study is part of a multi country cluster randomized trials conducted under the ASCENT consortium.Interviews were conducted with a total of 41 individuals, 19 people with TB and 22 HCPs and key stakeholders. One of the main findings indicates that participants found that the daily reminders provided by the DATs, particularly the alarm from the smart pillboxes, helped in supporting treatment continuation and establishing a routine around medicine intake. DATs use was linked with reducing the financial burden of treatment, improving people with TB-HCPs relationship, and decreasing workload for HCPs. Although DATs were generally perceived as reliable, occasional technical malfunctions, such as battery depletion in smart pillboxes, were reported. The requirement of having access to a cellphone and a power source emerged as specific barriers for medication label users.This study highlights the initial willingness and sustained enthusiasm for using DATs among respondents. DATs were perceived as useful tools, aiding individuals with treatment continuation through daily reminders and fostering stronger connections with HCPs. Nevertheless, issues such as poor network connectivity and the need for access to a working cellphone posed difficulties in usage. Findings from this study suggest the potential for improvements in the technologies and indicate that a thorough assessment of people’s life conditions and needs prior to treatment initiations is important to determine the suitability of providing a DAT.
Visuo-motor updating in individuals with heightened autistic traits
Authors: Pomè Antonella , Zimmermann Eckart 
Published: December 2023

SUMMARYAutism Spectrum Disorder (ASD) presents a range of challenges, including heightened sensory sensitivities. Here, we examine the idea that sensory overload in ASD may be linked to issues with efference copy mechanisms, which predict the sensory outcomes of self-generated actions, such as eye movements. Efference copies play a vital role in maintaining visual and motor stability. Disrupted efference copies hinder precise predictions, leading to increased reliance on actual feedback and potential distortions in perceptions across eye movements. In our first experiment, we tested how well healthy individuals with varying levels of autistic traits updated their mental map after making eye movements. We found that those with more autistic traits had difficulty using information from their eye movements to update the spatial representation of their mental map, resulting in significant errors in object localization. In the second experiment, we looked at how participants perceived an object displacement after making eye movements. Using a trans-saccadic spatial updating task, we found that those with higher autism scores exhibited a greater bias, indicating under-compensation of eye movements and a failure to maintain spatial stability during saccades. Overall, our study underscores efference copy’s vital role in visuo-motor stability, aligning with Bayesian theories of autism, potentially informing interventions for improved action-perception integration in autism.
A near-complete dataset of plant growth form, life history, and woodiness for all Australian plants
Authors: Wenk Elizabeth , Coleman David , Gallagher Rachael , Falster Daniel 
Published: December 2023

AbstractTabular records of plant trait data are essential for diverse research purposes. Here we present scorings for a trio of core plant traits, plant growth form, woodiness, and life history, for nearly all accepted taxon concepts included in the Australian Plant Census (APC). This dataset is predominately derived from Australia’s state and national floras, supplemented by the taxonomic literature and diverse web resources. In total, 29,993 species and infraspecific taxa were scored for plant growth form, 30,279 for woodiness, and 30,056 for life history, with taxa scored as displaying a single or multiple trait values, as appropriate. This resource will enable rapid assessment of plant responses to disturbance events and new biogeographic analyses of trait distributions.
The Art of Brainwaves: A Survey on Event-Related Potential Visualization Practices
Authors: Mikheev Vladimir , Skukies René , Ehinger Benedikt V. 
Published: December 2023

AbstractElectroencephalography (EEG) and event-related potentials (ERPs) have been analyzed for more than 70 years. Yet, we know little about how practitioners visualize the results of their analyses. Here, we designed an online survey (n=213) targeting M/EEG practitioners from novice to expert level. Our primary goal is to better understand the visualization tools currently in use, the challenges researchers face, and their experiences and opinions on how best to display their brain data. Finally, we explored whether researchers are aware of more general visualization issues. In this paper we provide an overview of the most popular ERP visualization tools. Then, we found that the community does not have a unique nomenclature to refer to some plot types, and we propose a set of recommendations to name the most popular ERP plot types. Finally, we provide an analysis of practitioner feature preferences for software developers and conclude with further recommendations for ERP practitioners.
Addressing Heterogeneity in direct analysis of Extracellular Vesicles and analogues using Membrane-Sensing Peptides as Pan-Affinity Probes
Authors: Gori Alessandro , Frigerio Roberto , Gagni Paola , Burrello Jacopo , Panella Stefano , Raimondi Andrea , Bergamaschi Greta , Lodigiani Giulia , Romano Miriam , Zendrini Andrea , Radeghieri Annalisa , Barile Lucio , Cretich Marina 
Published: December 2023

AbstractExtracellular vesicles (EVs), crucial mediators of cell-to-cell communication, hold immense potential for diagnostic applications due to their ability to enrich protein biomarkers in body fluids. However, challenges in isolating EVs from complex biological specimens hinder their widespread use. In this frame, integrated isolation-and-analysis workflows are the go-to strategy, most of which see the prevalence of immunoaffinity methods. Yet, the high heterogeneity of EVs poses challenges, as proposed ubiquitous markers are less homogenously prevalent than believed, raising concerns about the reliability of downstream biomarker discovery programs. This issue extends to the burgeoning field of engineered EV-mimetics and bio-nanoparticles, where conventional immune-affinity methods may lack applicability. Addressing these challenges, we introduce the use Membrane Sensing Peptides (MSP) as “universal” affinity ligands for both EVs and EV-analogues. Employing a streamlined process integrating on-bead capture and vesicle phenotyping through Single Molecule Array (SiMoA) technology, we showcase the application of MSP ligands in the integrated analysis of circulating EVs in blood derivatives, eliminating the need for prior EV isolation. Demonstrating the possible clinical translation of MSP technology, we directly detect an EV-associated epitope signature in serum and plasma samples, demonstrating its potential for distinguishing patients with myocardial infarction versus stable angina. At last, notably, MSP exhibits a unique capability to enable the analysis of tetraspanin-lacking Red Blood Cell derived EVs (RBC-EVs). Overall, unlike traditional antibody-based methods, MSP probes work agnostically, overcoming limitations associated with surface protein abundance or scarcity. This highlights the potential of MSP in advancing EV analysis for clinical diagnostics and beyond. Of note, this represents also the first-ever peptide-based application in SiMoA technology.
Age-Related Differences in Human Cortical Microstructure Depend on the Distance to the Nearest Vein
Authors: Knoll Christoph , Doehler Juliane , Northall Alicia , Schreiber Stefanie , Rotta Johanna , Mattern Hendrik , Kuehn Esther 
Published: December 2023

AbstractAge-related differences in cortical microstructure are used to understand the neuronal mechanisms that underlie human brain ageing. The cerebral vasculature contributes to cortical ageing, but its precise interaction with cortical microstructure is poorly understood. In a cross-sectional study, we combine venous imaging with vessel distance mapping (VDM) to investigate the interaction between venous distances and age-related differences in the microstructural architecture of the primary somatosensory cortex (S1), the primary motor cortex (M1), and additional areas in frontal cortex as non-sensorimotor control regions. We scanned 18 younger adults and 17 older adults using 7T-MRI to measure age-related changes in quantitative T1 (qT1) values, positive QSM (pQSM) values, and negative QSM (nQSM) values at 0.5 mm isotropic resolution. We modelled different cortical depths using an equi-volume approach and assessed the distance of each voxel to its nearest vein using VDM. Our data reveal a dependence of cortical qT1 and pQSM values on venous distance. In addition, there is an interaction between venous distance and age on qT1 values, driven by lower qT1 values in older compared to younger adults in voxels that are closer to a vein. Together, our data show that the local venous architecture explains a significant amount of variance in standard measures of cortical microstructure and should be considered in neurobiological models of human brain organisation and cortical ageing.
Endangered Przewalski’s horse,Equus przewalskii, cloned from historically cryopreserved cells
Authors: Novak Ben J. , Ryder Oliver A. , Houck Marlys L. , Putnam Andrea S. , Walker Kelcey , Russell Lexie , Russell Blake , Walker Shawn , Arenivas Sanaz Sadeghieh , Aston Lauren , Veneklasen Gregg , Ivy Jamie A. , Koepfli Klaus-Peter , Rusnak Anna , Simek Jaroslav , Zhuk Anna , Phelan Ryan 
Published: December 2023

AbstractTwo endangered Przewalski’s horse stallions were cloned from fibroblast cells cultured and cryopreserved in 1980. These stallions are clones of a male that lived from 1975-1998 that pedigree analyses identified as a genetically valuable male for present-day conservation breeding. This is the first time that multiple healthy clones have been produced for an endangered species.
Single cell proteomics characterization of bone marrow hematopoiesis with distinct Ras pathway lesions
Authors: Karra Laila , Finger Anna-Marie , Shechtman Lauren , Krush Milana , Huang Rita Meng-Yao , Prinz Morgan , Tennvooren Iliana , Bahl Kriti , Hysienaj Lisiena , Gonzalez Paulina G. , Combes Alexis J. , Gonzalez Hugo , Argüello Rafael J , Spitzer Matthew H. , Roose Jeroen P. 
Published: December 2023

ABSTRACTNormal hematopoiesis requires constant prolific production of different blood cell lineages by multipotent hematopoietic stem cells (HSC). Stem- and progenitor- cells need to balance dormancy with proliferation. How genetic alterations impact frequency, lineage potential, and metabolism of HSC is largely unknown. Here, we compared induced expression of KRASG12Dor RasGRP1 to normal hematopoiesis. At low-resolution, both Ras pathway lesions result in skewing towards myeloid lineages. Single-cell resolution CyTOF proteomics unmasked an expansion of HSC- and progenitor- compartments for RasGRP1, contrasted by a depletion for KRASG12D. SCENITH™ quantitates protein synthesis with single-cell precision and corroborated that immature cells display low metabolic SCENITH™ rates. Both RasGRP1 and KRASG12Delevated mean SCENITH™ signals in immature cells. However, RasGRP1-overexpressing stem cells retain a metabolically quiescent cell-fraction, whereas this fraction diminishes for KRASG12D. Our temporal single cell proteomics and metabolomics datasets provide a resource of mechanistic insights into altered hematopoiesis at single cell resolution.
Nanopore adaptive sampling to identify the NLR-gene family in melon (Cucumis meloL.)
Authors: Belinchon-Moreno Javier , Berard Aurelie , Canaguier Aurelie , Chovelon Véronique , Cruaud Corinne , Engelen Stéfan , Feriche-Linares Rafael , Le-Clainche Isabelle , Marande William , Rittener-Ruff Vincent , Lagnel Jacques , Hinsinger Damien , Boissot Nathalie , Faivre Rampant Patricia 
Published: December 2023

AbstractBackgroundNanopore Adaptive Sampling (NAS) offers a promising approach for assessing genetic diversity in targeted genomic regions. Herein, we design and validate an experiment to enrich a set of resistance genes in several melon cultivars as a proof of concept.ResultsWe showed that each of the 15 regions we identified in two newly assembled melon genomes (subspeciesmelo) were successfully and accurately reconstructed as well as in a third cultivar from theagrestissubspecies. We obtained a fourfold enrichment, independently from the samples, but with some variations according to the enriched regions. In theagrestiscultivar, we further confirmed our assembly by PCR. We discussed parameters that can influence enrichment and accuracy of assemblies generated through NAS.ConclusionsAltogether, we demonstrated NAS as a simple and efficient approach to explore complex genomic regions. This approach finally unlocks the characterization of resistance genes for a large number of individuals, as required for breeding new cultivars responding to the agroecological transition.
Proinflammatory Cytokines Suppress Nonsense-Mediated RNA Decay to Impair Regulated Transcript Isoform Processing in Pancreatic β-Cells
Authors: Ghiasi Seyed. M. , Marchetti Piero , Piemonti Lorenzo , Nielsen Jens H. , Porse Bo T. , Mandrup-Poulsen Thomas , Rutter Guy A. 
Published: December 2023

AbstractProinflammatory cytokines are implicated in pancreatic β-cell failure in type 1 and type 2 diabetes and are known to stimulate alternative RNA splicing and the expression of Nonsense-Mediated RNA Decay (NMD) components. Here, we investigate whether cytokines regulate NMD activity and identify transcript isoforms targeted in β-cells. A luciferase-based NMD reporter transiently expressed in rat INS1(832/13), human-derived EndoC-βH3 or dispersed human islet cells is used to examine the effect of proinflammatory cytokines (Cyt) on NMD activity. Gain- or loss-of function of two key NMD components UPF3B and UPF2 is used to reveal the effect of cytokines on cell viability and function. RNA-sequencing and siRNA-mediated silencing are deployed using standard techniques. Cyt attenuate NMD activity in insulin-producing cell lines and primary human β-cells. These effects are found to involve ER stress and are associated with downregulation of UPF3B. Increases or decreases in NMD activity achieved by UPF3B overexpression (OE) or UPF2 silencing, raises or lowers Cyt-induced cell death, respectively, in EndoC-βH3 cells, and are associated with decreased or increased insulin content, respectively. No effects of these manipulations are observed on glucose-stimulated insulin secretion. Transcriptomic analysis reveals that Cyt increase alternative splicing (AS)-induced exon skipping in the transcript isoforms, and this is potentiated by UPF2 silencing. Gene enrichment analysis identifies transcripts regulated by UPF2 silencing whose proteins are localized and/or functional in extracellular matrix (ECM) including the serine protease inhibitor SERPINA1/α-1-antitrypsin, whose silencing sensitises β-cells to Cyt cytotoxicity. Cytokines suppress NMD activity via UPR signalling, potentially serving as a protective response against Cyt-induced NMD component expression. Our findings highlight the central importance of RNA turnover in β-cell responses to inflammatory stress.
Comparative Hox genes expression within the dimorphic annelidStreblospio benedictireveals patterning variation during development
Authors: Aguilar-Camacho Jose Maria , Harry Nathan D. , Zakas Christina 
Published: December 2023

ABSTRACTHox genes are transcriptional regulators that elicit cell positional identity along the anterior-posterior region of the body plan across different lineages of Metazoan. Comparison of Hox gene expression across distinct species reveals their evolutionary conservation, however their gains and losses in different lineages can correlate with body plan modifications and morphological novelty. We compare the expression of eleven Hox genes found withinStreblospio benedicti,a marine annelid that produces two types of offspring with distinct developmental and morphological features. For these two distinct larval types, we compare Hox gene expression through ontogeny using HCR (hybridization chain reaction) probes forin-situhybridization and RNA-seq data. We find that Hox gene expression patterning for both types is typically similar at equivalent developmental stages. However, some Hox genes have spatial or temporal differences between the larval types that are associated with morphological and life-history differences. This is the first comparison of developmental divergence in Hox genes expression within a single species and these changes reveal how body plan differences may arise in larval evolution.
A subcortical switchboard for exploratory, exploitatory, and disengaged states
Authors: Ahmadlou Mehran , Shirazi Maryam Yasamin , Zhang Pan , Rogers Isaac L. M. , Dziubek Julia , Hofer Sonja B. 
Published: December 2023

AbstractTo survive in evolving environments with uncertain resources, animals need to dynamically adapt their behavior and exhibit flexibility in choosing appropriate behavioral strategies, for example, to exploit familiar choices, to explore and acquire novel information, or to disengage altogether. Previous studies have mainly investigated how forebrain regions represent choice costs and values as well as optimal decision strategies during explore/exploit trade-offs. However, the neural mechanisms by which the brain implements alternative behavioral strategies such as exploiting, exploring or disengaging from the environment, remains poorly understood. Here we identify a neural hub critical for flexible switching between behavioral strategies, the median raphe nucleus (MRN). Using cell-type specific optogenetic manipulations, calcium fiber photometry and circuit tracing in mice performing diverse instinctive and learnt behavioral tasks, we found that the MRN’s main cell types, GABAergic, glutamatergic (VGluT2-positive), and serotonergic neurons, have complementary functions and drive exploitation, exploration and disengagement, respectively. Suppression of MRN GABAergic neurons, for instance through inhibitory input from lateral hypothalamus which conveys strong positive valence to the MRN, leads to perseverance in current actions and goals, and thus promotes exploitatory behavior. In contrast, activation of MRN VGluT2+ neurons drives exploratory behavior. Activity of serotonergic MRN neurons is necessary for general task engagement. Input from the lateral habenula conveying negative valence suppresses serotonergic MRN neurons, leading to disengagement. These findings establish the MRN as a central behavioral switchboard, uniquely positioned to flexibly control behavioral strategies. These circuits thus may also play an important role in the etiology and possible treatment of major mental pathologies such as depressive or obsessive-compulsive disorders.
Identification of new ciliary signaling pathways in the brain and insights into neurological disorders
Authors: Loukil Abdelhalim , Ebright Emma , Uezu Akiyoshi , Gao Yudong , Soderling Scott H , Goetz Sarah C. 
Published: December 2023

AbstractPrimary cilia are conserved sensory hubs essential for signaling transduction and embryonic development. Ciliary dysfunction causes a variety of developmental syndromes with neurological features and cognitive impairment, whose basis mostly remains unknown. Despite connections to neural function, the primary cilium remains an overlooked organelle in the brain. Most neurons have a primary cilium; however, it is still unclear how this organelle modulates brain architecture and function, given the lack of any systemic dissection of neuronal ciliary signaling. Here, we present the first in vivo glance at the molecular composition of cilia in the mouse brain. We have adaptedin vivoBioID (iBioID), targeting the biotin ligase BioID2 to primary cilia in neurons. We identified tissue-specific signaling networks enriched in neuronal cilia, including Eph/Ephrin and GABA receptor signaling pathways. Our iBioID ciliary network presents a wealth of neural ciliary hits that provides new insights into neurological disorders. Our findings are a promising first step in defining the fundamentals of ciliary signaling and their roles in shaping neural circuits and behavior. This work can be extended to pathological conditions of the brain, aiming to identify the molecular pathways disrupted in the brain cilium. Hence, finding novel therapeutic strategies will help uncover and leverage the therapeutic potential of the neuronal cilium.