bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding Nurse Perceptions of Caring for Patients With Alcohol Use Disorder
Authors: Hyde Ashley , Johnson Emily , Bray Christina , Meier Tiara , Carbonneau Michelle , Spiers Jude , Tandon Puneeta 
Published: June 2024

Abstract

Background
Alcohol use disorder (AUD), the problematic consumption of alcohol, affects 107 million people worldwide. Individuals with AUD experience high morbidity and increased mortality. Nurses practicing in acute care are ideally positioned to deliver quality interventions to patients with AUD, including screening and brief intervention; formal training and assessment of baseline knowledge, attitudes, and perceptions are necessary.

Aims and Objectives
The aim of this study was to explore the knowledge, attitudes, and perceptions of acute care nurses caring for patients with AUD.

Design
This study used a cross-sectional survey design.

Methods
The Survey of Attitudes and Perceptions was completed by 93 nurses working in six acute care centers (seven medicine units) across Alberta. Data were analyzed using descriptive and inferential statistics.

Results
Few participants reported receiving any prior structured training on AUD, with the majority reporting limited knowledge of alcohol and the effects of alcohol consumption. Although most participants said that caring for patients with AUD was a part of their professional role, few felt satisfied or motivated to work with this group of patients. Responses to individual questions or subdomains of the survey did not significantly differ by length of time in professional role, employment status, or sex.

Conclusion
Our results indicate that nurses need to learn more about caring for patients with AUD. Developing tailored educational interventions that are mindful of the importance of knowledge, support, satisfaction, and motivation is necessary to improve the quality of care for patients with AUD.
Effect of an Online Intervention on Nursing Students' Alcohol Consumption and Social Support
Authors: Gonçalves Jamila Souza , Oliveira Jaqueline Lemos de , Almeida Janaína Cristina Pasquini de , Morero Juceli Andrade Paiva , Pegoraro Natália Priolli Jora , Zanetti Maria Olívia Barboza , Souza Jacqueline de 
Published: June 2024

Abstract

Objective
This research aimed to evaluate the impact of custom-developed software on nursing students' alcohol consumption and perception of social support.

Method
A quasi-experimental study was conducted with 88 students in the early years of nursing courses at a Brazilian public university. The members of the intervention group (n = 40) participated in a lecture delivered by a nurse and used online software developed based on cognitive behavioral techniques and social skills training. The members of the control group (n = 48) participated only in the lecture. Data on alcohol consumption profiles and social support characteristics were collected. Descriptive statistics, an analysis of variance test, and the Dunnett's test were utilized for data analysis.

Results
Alcohol consumption decreased in both groups without significant differences between them. However, in terms of frequency of use, binge drinking, and the number of drinks consumed, a significant decrease occurred among participants in the intervention group. Regarding social support, both groups showed an increase in satisfaction with support and a decrease in the number of supporters. This reduction was less pronounced in the intervention group than in the control group.

Conclusion
This investigation presents relevant results that suggest the potential of using online technologies as supplemental materials for promoting students' mental health.
ArtSpective™ for Perinatal Substance Use
Authors: Shuman Clayton J. , Choberka David , Morgan Mikayla E. , Boyd Carol J. 
Published: June 2024

Abstract

Objective
The purpose of this proof-of-concept pilot study was to test the initial feasibility and limited efficacy of ArtSpective™ for perinatal substance use (PSU), a novel, arts-based intervention designed to decrease stigmatizing attitudes toward PSU.

Methods
Using a pre–post mixed methods quasi-experimental design, ArtSpective™ for PSU was pilot tested for proof of concept among a convenience sample of 11 undergraduate and graduate students with experience in maternal–infant nursing from a Midwestern U.S. nursing school. As a proof-of-concept pilot study, we evaluated feasibility (acceptability, demand, and implementation) and limited efficacy. Participants completed presurveys and postsurveys that included satisfaction items, demographic items, and an adapted version of the Attitudes About Drug Use in Pregnancy Scale and participated in a focus group. Focus group data were analyzed using constant comparative methods, and survey data were analyzed using descriptive statistics and Wilcoxon signed rank tests.

Results
Participants reported high demand and satisfaction with the intervention and provided recommendations to improve scalability. ArtSpective™ demonstrated significant improvement in stigma toward PSU (pre vs. post: p = .003; d = .633).

Conclusion
ArtSpective™ for PSU demonstrated initial feasibility and limited efficacy for improving nurse attitudes toward PSU. Efforts are needed to further test this novel intervention, adapt it to augment existing educational interventions, and improve its scalability.
Systemic autoimmune disease patients’ blood immunome reveals specificities and commonalities among different diagnostic entities
Authors: Rybakowska Paulina , Van Gassen Sofie , Barturen Guillermo , Sánchez Carlos Pérez , Ibáñez-Costa Alejandro , Varela Nieves , Castro Rafaela Ortega , Fernández-Roldán Concepción , Jiménez-Moleón Inmaculada , Ortego Norberto , Raya Enrique , Quesada Rocío Aguilar , López-Pedrera Chary , Collantes Eduardo , Saeys Yvan , Marañón Concepción , Alarcón-Riquelme Marta E. 
Published: June 2024

1AbstractBackgroundSystemic autoimmune diseases (SADs) are characterized by internal heterogeneity, overlapping clinical symptoms, and shared molecular pathways. Therefore, they are difficult to diagnose and new tools allowing precise diagnosis are needed. Molecular-based reclassification studies enable to find patterns in a diagnosis-independent way.ObjectiveTo evaluate the possibility of using high-content immunophenotyping for detecting patient subgroups in the context of precise treatment.MethodsWhole blood high-content immunophenotyping of 101 patients with 7 systemic autoimmune diseases and 22 controls was performed using 36-plex mass cytometry panel. Patients were compared across diagnostic entities and re-classified using Monte Carlo reference-based consensus clustering. Levels of 45-plex multiplexed cytokine were measured and used for cluster characterization.ResultsDifferential analysis by diagnosis did not reveal any disease-specific pattern in the cellular compositions and phenotypes but rather their relative similarities. Accordingly, patients were classified into phenotypically distinct groups composed of different diagnostic entities sharing common immunophenotypes and cytokine signatures. These features were mainly based on granulocyte activation and CD38 expression in discrete lymphocyte populations and were related to Th17 or IFN-dependent cytokines.ConclusionsOur data indicate that specific individuals could potentially benefit from the same line of treatment independently of their diagnosis and emphasize the possibility of using immunophenotyping as a stratification tool in precision rheumatology.2Graphical abstractKey messagesWhole blood immmunophenotyping could be used to stratify systemic autoimmune patients, thus it is a useful tool in precision medicine.Patients’ groups could benefit from the same line of treatment.
Ex vivoSIM-AFM measurements reveal the spatial correlation of stiffness and molecular distributions in 3D living tissue
Authors: Shioka Itsuki , Morita Ritsuko , Yagasaki Rei , Wuergezhen Duligengaowa , Yamashita Tadahiro , Fujiwara Hironobu , Okuda Satoru 
Published: June 2024

AbstractLiving tissues each exhibit a distinct stiffness, which provides cells with key environmental cues that regulate their behaviors. Despite this significance, our understanding of the spatiotemporal dynamics and the biological roles of stiffness in three-dimensional tissues is currently limited due to a lack of appropriate measurement techniques. To address this issue, we propose a new method combining upright structured illumination microscopy (USIM) and atomic force microscopy (AFM) to obtain precisely coordinated stiffness maps and biomolecular fluorescence images of thick living tissue slices. Using mouse embryonic skin as a representative tissue with mechanically heterogeneous structures inside, we validate the measurement principle of USIM-AFM. Live measurement of tissue stiffness distributions revealed the highly heterogeneous mechanical nature of embryonic skin as well as the role of collagens in maintaining its integrity. Furthermore, quantitative comparisons of stiffness distributions of preserved tissue samples unveiled the distinct impacts of conventional tissue preservation techniques on the tissue stiffness pattern. This series of experiments highlights the importance of live mechanical testing of tissue-scale samples. Our USIM-AFM technique provides a new methodology to reveal the dynamic nature of tissue stiffness and its correlation with biomolecular distributions in live tissues and thus could serve as a technical basis for exploring tissue-scale mechanobiology.Graphical Abstract
Brain representation in conscious and unconscious vision
Authors: Mei Ning , Soto David 
Published: June 2024

AbstractThe development of robust frameworks to understand how the human brain represents conscious and unconscious perceptual contents is paramount to make progress in the neuroscience of consciousness. Recent functional MRI studies using multi-voxel pattern classification analyses showed that unconscious contents could be decoded from brain activity patterns. However, decoding does not imply a full understanding of neural representations. Here we re-analysed data from a high-precision fMRI study coupled with representational similarity analysis based on convolutional neural network models to provide a detailed information-based approach to neural representations of both unconscious and conscious perceptual content. The results showed that computer vision model representations strongly predicted brain responses in ventral visual cortex and in fronto-parietal regions to both conscious and unconscious contents. Moreover, this pattern of results generalised when the models were trained and tested with different participants. Remarkably, these observations results held even when the analysis was restricted to observers that showed null perceptual sensitivity. In light of the highly distributed brain representation of unconscious information, we suggest that the functional role of fronto-parietal cortex in conscious perception is unlikely to be related to the broadcasting of information, as proposed by the global neuronal workspace theory, and may instead relate to the generation of meta-representations as proposed by higher-order theories.
Oxygen Sensor-Guided Fine Needle Biopsy Studies of Human Cancer Xenografts in Mice
Authors: McDonald Robert C. , Fischer Andrew H. , Rusckowski Mary 
Published: June 2024

AbstractAn oxygen sensor-mounted fine-needle biopsy tool was used forin vivomeasurement of oxygen levels in tumor xenografts. The system provides a means of measuring the oxygen content in harvested tumor tissue from specific locations. Oxygen in human tumor xenografts in a murine model was observed for over 1 min. Tissues were mapped in relation to oxygen tension (pO2) readings and sampled for conventional cytological examination. Careful modeling of the pO2readings over 60 seconds yielded a diffusion coefficient for oxygen at the sensor tip, providing additional diagnostic information about the tissue before sampling. Oxygen level measurement may provide a useful adjunct to the use of biomarkers in tumor diagnosis.
Injury distance limits the transcriptional response to spinal injury
Authors: Wang Zimei , Kumaran Manojkumar , Batsel Elizabeth , Testor-Cabrera Sofia , Beine Zac , Ribelles Alicia Alvarez , Tsoulfas Pantelis , Venkatesh Ishwariya , Blackmore Murray G. 
Published: June 2024

AbstractThe ability of neurons to sense and respond to damage is fundamental to homeostasis and nervous system repair. For some cell types, notably dorsal root ganglia (DRG) and retinal ganglion cells (RGCs), extensive profiling has revealed a large transcriptional response to axon injury that determines survival and regenerative outcomes. In contrast, the injury response of most supraspinal cell types, whose limited regeneration constrains recovery from spinal injury, is mostly unknown. Here we employed single-nuclei sequencing in mice to profile the transcriptional responses of diverse supraspinal cell types to spinal injury. Surprisingly, thoracic spinal injury triggered only modest changes in gene expression across all populations, including corticospinal tract (CST) neurons. Moreover, CST neurons also responded minimally to cervical injury but much more strongly to intracortical axotomy, including upregulation of numerous regeneration and apoptosis-related transcripts shared with injured DRG and RGC neurons. Thus, the muted response of CST neuron to spinal injury is linked to the injury’s distal location, rather than intrinsic cellular characteristics. More broadly, these findings indicate that a central challenge for enhancing regeneration after a spinal injury is the limited sensing of distant injuries and the subsequent modest baseline neuronal response.
CD4+tumor-infiltrating lymphocytes secreting T cell-engagers induce regression of autologous patient-derived non-small cell lung cancer xenografts
Authors: Jiménez-Reinoso Anaïs , Molero-Abraham Magdalena , Cirauqui Cristina , Blanco Belén , Garrido-Martin Eva M. , Nehme-Álvarez Daniel , Domínguez-Alonso Carmen , Ramírez-Fernández Ángel , Díez-Alonso Laura , Nuñez-Buiza Ángel , González-Murillo África , Tobes Raquel , Pareja Eduardo , Ramírez-Orellana Manuel , Rodriguez-Peralto José L. , Ferrer Irene , Zugazagoitia Jon , Paz-Ares Luis , Álvarez-Vallina Luis 
Published: June 2024

ABSTRACTAdoptive transfer of tumor-infiltrating lymphocytes (TIL) has shown remarkable results in melanoma, but only modest clinical benefit in other cancers, even after TIL have been genetically modified to improve their tumor homing, cytotoxic potential or overcoming cell exhaustion. The requiredex vivoTIL expansion process may induce changes in the T cell clonal composition, which could likely compromise the tumor reactivity of TIL preparations and ultimately the success of TIL therapy. A promising approach based on the production of bispecific T cell engagers (TCE) by engineered T cells (STAb-T therapy) improves the efficacy of current T cell redirection strategies against tumor-associated antigens in hematological tumors. We studied the TCRβ repertoire in non-small cell lung cancer (NSCLC) tumors and inex vivoexpanded TIL from two unrelated patients. We generated TIL secreting anti-epidermal growth factor receptor (EGFR) x anti-CD3 TCE (TILSTAb) and tested their antitumor efficacyin vitroandin vivousing a NSCLC patient-derived xenograft (PDX) model in which tumor fragments and TIL from the same patient were transplanted intohIL-2NOG mice. We confirmed that the standard TIL expansion protocol promotes the loss of tumor-dominant T cell clones and the overgrowth of virus-reactive TCR clonotypes that were marginally detectable in primary tumors. We demonstrated the antitumor activity of TILSTAbbothin vitroandin vivowhen administered intratumorally and systemically in an autologous immune-humanized PDX EGFR+NSCLC mouse model, where tumor regression was mediated by TCE-redirected CD4+TIL bearing non-tumor dominant clonotypes.SIGNIFICANCEEpithelial tumor-derived TIL can be engineered to secrete TCE capable of redirecting T cells bearing non-tumor-dominant clonotypes regardless of their phenotype, which could have broad applications in immunotherapy for solid tumors.
CTCF regulates global chromatin accessibility and transcription during rod photoreceptor development
Authors: Chen Dahong , Keremane Saumya , Wang Silu , Lei Elissa P. 
Published: June 2024

ABSTRACTChromatin architecture facilitates accurate transcription at a number of loci, but it remains unclear how much chromatin architecture is involved in global transcriptional regulation. Previous work has shown that rapid depletion of the architectural protein CTCF in cell culture strongly alters chromatin organization but results in surprisingly limited gene expression changes. This discrepancy has also been observed when other architectural proteins are depleted, and one possible explanation is that full transcriptional changes are masked by cellular heterogeneity. We tested this idea by performing multi-omics analyses with sorted post-mitotic mouse rods, which undergo synchronized development, and identified CTCF-dependent regulation of global chromatin accessibility and gene expression. Depletion of CTCF leads to dysregulation of ∼20% of the entire transcriptome (>3,000 genes) and ∼41% of genome accessibility (>26,000 sites), and these regions are strongly enriched in euchromatin. Importantly, these changes are highly enriched for CTCF occupancy, suggesting direct CTCF binding and transcriptional regulation at these active loci. CTCF mainly promotes chromatin accessibility of these direct binding targets, and a large fraction of these sites correspond to promoters. At these sites, CTCF binding frequently promotes accessibility and inhibits expression, and motifs of transcription repressors are found to be significantly enriched. Our findings provide different and often opposite conclusions from previous studies, emphasizing the need to consider cell heterogeneity and cell type specificity when performing multi-omics analyses. We conclude that the architectural protein CTCF binds chromatin and regulates global chromatin accessibility and transcription during rod development.
Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES
Authors: Gupta Anshu , Mirarab Siavash , Turakhia Yatish 
Published: June 2024

AbstractInference of species trees plays a crucial role in advancing our understanding of evolutionary relationships and has immense significance for diverse biological and medical applications. Extensive genome sequencing efforts are currently in progress across a broad spectrum of life forms, holding the potential to unravel the intricate branching patterns within the tree of life. However, estimating species trees starting from raw genome sequences is quite challenging, and the current cutting-edge methodologies require a series of error-prone steps that are neither entirely automated nor standardized. In this paper, we present ROADIES, a novel pipeline for species tree inference from raw genome assemblies that is fully automated, easy to use, scalable, free from reference bias, and provides flexibility to adjust the tradeoff between accuracy and runtime. The ROADIES pipeline eliminates the need to align whole genomes, choose a single reference species, or pre-select loci such as functional genes found using cumbersome annotation steps. Moreover, it leverages recent advances in phylogenetic inference to allow multi-copy genes, eliminating the need to detect orthology. Using the genomic datasets released from large-scale sequencing consortia across three diverse life forms (placental mammals, pomace flies, and birds), we show that ROADIES infers species trees that are comparable in quality with the state-of-the-art approaches but in a fraction of the time. By incorporating optimal approaches and automating all steps from assembled genomes to species and gene trees, ROADIES is poised to improve the accuracy, scalability, and reproducibility of phylogenomic analyses.Code and Data availabilityThe source code of ROADIES is freely available under the MIT License on GitHub (https://github.com/TurakhiaLab/ROADIES), and the documentation for ROADIES is available athttps://turakhia.ucsd.edu/ROADIES/. The details of the input datasets used in the manuscript are listed in Supplementary Tables 1-3. All inferred gene trees and species trees are to be deposited to Dryad with links to be made available on the aforementioned GitHub repository.Contactyturakhia@ucsd.edu
Interference underlies attenuation upon relearning in sensorimotor adaptation
Authors: Avraham Guy , Ivry Richard B 
Published: June 2024

AbstractSavings refers to the gain in performance upon relearning a task. In sensorimotor adaptation, savings is tested by having participants adapt to perturbed feedback and, following a washout block during which the system resets to baseline, presenting the same perturbation again. While savings has been observed with these tasks, we have shown that the contribution from implicit sensorimotor adaptation, a process that uses sensory prediction errors to recalibrate the sensorimotor map, is actually attenuated upon relearning (Avraham et al., 2021). In the present study, we test the hypothesis that this attenuation is due to interference arising from the washout block, and more generally, from experience with a different relationship between the movement and the feedback. In standard adaptation studies, removing the perturbation at the start of the washout block results in a salient error signal in the opposite direction to that observed during learning. As a starting point, we replicated the finding that implicit adaptation is attenuated following a washout period in which the feedback now signals a salient opposite error. When we eliminated visual feedback during washout, implicit adaptation was no longer attenuated upon relearning, consistent with the interference hypothesis. Next, we eliminated the salient error during washout by gradually decreasing the perturbation, creating a scenario in which the perceived errors fell within the range associated with motor noise. Nonetheless, attenuation was still prominent. Inspired by this observation, we tested participants with an extended experience with veridical feedback during an initial baseline phase and found that this was sufficient to cause robust attenuation of implicit adaptation during the first exposure to the perturbation. This effect was context-specific: It did not generalize to movements that were not associated with the interfering feedback. Taken together, these results show that the implicit sensorimotor adaptation system is highly sensitive to memory interference from a recent experience with a discrepant action-outcome contingency.