bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Hostile Environment
Authors: Worman Dawn , Nimkar Swateja 
Published: March 2023

Background:
The literature regarding the increased risk of violence toward registered nurses and health care workers is plentiful; yet, data on prelicensure nursing student exposure to violent patient behaviors are limited and did not exist for the university's nursing program.

Purpose:
The purpose of this exploratory study was to examine nursing student exposure to patient aggression or violent behavior in a prelicensure nursing program in the Midwestern United States.

Methods:
The research design was an exploratory study using surveys completed by nursing students in their junior and senior years.

Results:
Almost 74% of male students and 85% of female students experienced some form of verbal aggression from their patients, with a statistically significant difference between male and female nursing students on their exposure to sexual harassment. Students also experienced extreme emotions and feelings.

Conclusions:
The survey results reveal nursing students are exposed to patient aggression or violent behavior, do not feel prepared to manage these situations, and desire faculty mentoring.
Brief Report: How Do We Reach Men? Offering HIV Testing in Evenings and Weekends in the HPTN 071 (PopART) Community-Based Trial in South Africa
Authors: Yang Blia , Sloot Rosa , Floyd Sian , Awoniyi Dolapo , Griffith Sam , Ayles Helen , Fidler Sarah , Hayes Richard , Vermund Sten H. , Bock Peter ,   HPTN 071 (PopART) study team
Published: March 2023

Background:
Unknown HIV status and consequent low antiretroviral treatment coverage among men living with HIV combined with high-risk behavior is a key driver of the HIV epidemic in high-burden settings. We investigated whether conducting household visits during nontraditional shifts increased the number of men recruited for community-based HIV testing, compared with traditional weekday shifts in the HPTN 071 (PopART) trial in South Africa.

Methods:
We used data captured during household visits among individuals aged 15 years or older in 6 communities in South Africa from September 2016 to September 2017. Successful recruitment required community HIV care providers (CHiPs) accessing a household member and completing the study questionnaire. Linear regression analysis compared mean successful recruitments between the different shift types stratified by sex.

Results:
During 187 days, 62,455 successful household visits were completed. Recruitment of men and women was higher in weekends, for men highest on Sundays (Coef: 11.2, 95% CI: 8.7 to 13.7), for women highest on Saturdays (Coef: 11.3, 95% CI: 7.6 to 15.1), indicating a mean of 11.2 more men recruited on Sunday shifts, compared with traditional weekday shifts was similar when comparing traditional weekday shifts with nontraditional weekday shifts for both men and women.

Conclusion:
Conducting household visits during the weekends led to increased recruitment for participation in the PopART intervention among both men and women. This suggests that targeting households during the weekend can be an effective and easy-to-implement strategy to increase the number of men accessed for HIV testing that can be integrated into a wide range of community-based services.
The Unexpected Protective Role of Thrombosis in Sepsis-Induced Inflammatory Lung Injury Via Endothelial Alox15
Authors: Evans Colin E. , Zhang Xianming , Machireddy Narsa , Zhao You-Yang 
Published: March 2023

AbstractBackgroundPatients with sepsis-induced acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) commonly suffer from severe pulmonary thrombosis, but clinical trials of anti-coagulant therapies in sepsis and ARDS patients have failed. ARDS patients with thrombocytopenia also exhibit increased mortality, and widespread pulmonary thrombosis is often seen in coronavirus disease 2019 (COVID-19) ARDS patients.MethodsEmploying different amounts of microbeads to induce various levels of pulmonary thrombosis. Acute lung injury was induced by either lipopolysaccharide i.p. or cecal ligation and puncture. Endothelial cell (EC)-targeted nanoparticle coupled with CDH5 promoter was employed to delivery plasmid DNA expressing the CRISPR/Cas9 system for EC-specific gene knockout or expressing Alox15 for EC-specific overexpression. Additionally, thrombocytopenia was induced by genetic depletion of platelets usingDTRPf4Cremice by breedingPf4Cre mice into the genetic background ofDTRmice.ResultsWe show that while severe pulmonary thrombosis or thrombocytopenia augments sepsis-induced ALI, the induction of mild pulmonary thrombosis conversely reduces endothelial cell (EC) apoptosis, ALI, and mortality via sustained expression of endothelial arachidonate 15-lipoxygenase (Alox15). EndothelialAlox15knockout via EC-targeted nanoparticle delivery of CRISPR/Cas9 plasmid DNA in adult mice abolished the protective impact of mild lung thrombosis. Conversely, overexpression of endothelialAlox15inhibited the increases in ALI caused by severe pulmonary thrombosis. The clinical relevance of the findings was validated by the observation of reduced ALOX15-expressing ECs in lung autopsy samples of ARDS patients. Additionally, restoration of pulmonary thrombosis in thrombocytopenic mice also normalized endotoxemia-induced ALI.ConclusionWe have demonstrated that moderate levels of thrombosis protect against sepsis-induced inflammatory lung injury via endothelial Alox15. Overexpression of Alox5 inhibits severe pulmonary thrombosis-induced increase of ALI. Thus, activation of ALOX15 signaling represents a promising therapeutic strategy for treatment of ARDS, especially in sub-populations of patients with thrombocytopenia and/or severe pulmonary thrombosis.
Atypical beta-band effects in children with dyslexia in response to rhythmic audio-visual speech
Authors: Keshavarzi Mahmoud , Mandke Kanad , Macfarlane Annabel , Parvez Lyla , Gabrielczyk Fiona , Wilson Angela , Goswami Usha 
Published: March 2023

AbstractChildren with dyslexia are known to show impairments in perceiving speech rhythm, which impact their phonological development. Neural rhythmic speech studies have reported atypical delta phase in children with dyslexia, but beta band effects have not yet been studied. It is known that delta phase modulates the amplitude of the beta band response during rhythmic tasks via delta-beta phase-amplitude coupling (PAC). Accordingly, the atypical delta band effects reported for children with dyslexia may imply related atypical beta band effects. Here we analyse EEG data collected during a rhythmic speech paradigm from 51 children (21 typically-developing; 30 with dyslexia) who attended to a talking head repeating “ba” at 2Hz. Phase entrainment in the beta band, angular velocity in the beta band, power responses in the beta band and delta-beta PAC were assessed for each child and each group. Phase entrainment in the beta band was only significant for children without dyslexia. Children with dyslexia did not exhibit any phase consistency, and beta-band angular velocity was significantly faster compared to control children. Power in the beta band was significantly greater in the children with dyslexia. Delta-beta PAC was significant in both groups. The data are interpreted with respect to temporal sampling theory.
Sequencing accuracy and systematic errors of nanopore direct RNA sequencing
Authors: Liu-Wei Wang , van der Toorn Wiep , Bohn Patrick , Hölzer Martin , Smyth Redmond , von Kleist Max 
Published: March 2023

AbstractDirect RNA sequencing (dRNA-seq) on the Oxford Nanopore Technologies (ONT) platforms can produce reads covering up to full-length gene transcripts while containing decipherable information about RNA base modifications and poly-A tail lengths. Although many published studies have been exploring and expanding the potential of dRNA-seq, the sequencing accuracy and error patterns remain understudied. We present the first comprehensive evaluation of accuracy and systematic errors in dRNA-seq data from diverse species, as well as synthetic RNA. Deletions significantly outnumbered mismatches/insertions, while the median read accuracy exhibited species-level variation. In addition to homopolymer errors, we observed systematic biases across nucleotides and heteropolymeric motifs in all species. In general, cytosine/uracil-rich regions were more likely to be erroneous than guanines/adenines. Moreover, the systematic errors were strongly dependent on local sequence contexts. By examining raw signal data, we identified underlying signal-level features potentially associated with the error patterns. While read quality scores approximated error rates at base and read levels, failure to detect DNA adapters may lead to data loss. By comparing distinct basecallers, we reason that some sequencing errors are attributable to signal insufficiency rather than algorithmic (base-calling) artefacts. Lastly, we discuss the implications of such error patterns for downstream applications of dRNA-seq data.
High-Throughput Bioprinting of the Nasal Epithelium using Patient-derived Nasal Epithelial Cells
Authors: Derman I. Deniz , Yeo Miji , Castaneda Diana Cadena , Callender Megan , Horvath Mian , Mo Zengshuo , Xiong Ruoyun , Fleming Elizabeth , Chen Phylip , Peeples Mark E. , Palucka Karolina , Oh Julia , Ozbolat Ibrahim T. 
Published: March 2023

AbstractHuman nasal epithelial cells (hNECs) are an essential cell source for the reconstruction of the respiratory pseudostratified columnar epithelium composed of multiple cell types in the context of infection studies and disease modeling. Hitherto, manual seeding has been the dominant method for creating nasal epithelial tissue models. However, the manual approach is slow, low-throughput and has limitations in terms of achieving the intricate 3D structure of the natural nasal epithelium in a uniform manner. 3D Bioprinting has been utilized to reconstruct various epithelial tissue models, such as cutaneous, intestinal, alveolar, and bronchial epithelium, but there has been no attempt to use of 3D bioprinting technologies for reconstruction of the nasal epithelium. In this study, for the first time, we demonstrate the reconstruction of the nasal epithelium with the use of primary hNECs deposited on Transwell inserts via droplet-based bioprinting (DBB), which enabled high-throughput fabrication of the nasal epithelium in Transwell inserts of 24-well plates. DBB of nasal progenitor cells ranging from one-tenth to one-half of the cell seeding density employed during the conventional cell seeding approach enabled a high degree of differentiation with the presence of cilia and tight-junctions over a 4-week air-liquid interface culture. Single cell RNA sequencing of these cultures identified five major epithelial cells populations, including basal, suprabasal, goblet, club, and ciliated cells. These cultures recapitulated the pseudostratified columnar epithelial architecture present in the native nasal epithelium and were permissive to respiratory virus infection. These results denote the potential of 3D bioprinting for high-throughput fabrication of nasal epithelial tissue models not only for infection studies but also for other purposes such as disease modeling, immunological studies, and drug screening.
Towards a Neurobiologically-driven Ontology of Mental Functions: A Data-driven Summary of the Twenty Years of Neuroimaging Meta-Analyses
Authors: Dugré Jules R. , Potvin Stéphane 
Published: March 2023

ABSTRACTA persistent effort in neuroscience has been to pinpoint the neurobiological substrates that support mental processes. The Research Domain Criteria (RDoC) aims to develop a new framework based on fundamental neurobiological dimensions. However, results from several meta-analysis of task-based fMRI showed substantial spatial overlap between several mental processes including emotion and anticipatory processes, irrespectively of the valence. Consequently, there is a crucial need to better characterize the core neurobiological processes using a data-driven techniques, given that these analytic approaches can capture the core neurobiological processes across neuroimaging literature that may not be identifiable through expert-driven categories. Therefore, we sought to examine the main data-driven co-activation networks across the past 20 years of published meta-analyses on task-based fMRI studies. We manually extracted 19,822 coordinates from 1,347 identified meta-analytic experiments. A Correlation-Matrix-Based Hierarchical Clustering was conducted on spatial similarity between these meta-analytic experiments, to identify the main co-activation networks. Activation likelihood estimation was then used to identify spatially convergent brain regions across experiments in each network. Across 1,347 meta-analyses, we found 13 co-activation networks which were further characterized by various psychological terms and distinct association with receptor density maps and intrinsic functional connectivity networks. At a fMRI activation resolution, neurobiological processes seem more similar than different across various mental functions. We discussed the potential limitation of linking brain activation to psychological labels and investigated potential avenues to tackle this long-lasting research question.
A transthalamic pathway crucial for perception
Authors: Mo C. , McKinnon C. , Sherman S. M. 
Published: March 2023

ABSTRACTPerception arises from activity between cortical areas, first primary cortex and then higher order cortices. This communication is served in part by transthalamic (cortico-thalamo-cortical) pathways, which ubiquitously parallel direct corticocortical pathways, but their role in sensory processing has largely remained unexplored. Here, we show that the transthalamic pathway linking somatosensory cortices propagates task-relevant information required for correct sensory decisions. Using optogenetics, we specifically inhibited the pathway at its synapse in higher order somatosensory thalamus of mice performing a texture-based discrimination task. We concurrently monitored the cellular effects of inhibition in primary or secondary cortex using two-photon calcium imaging. Inhibition severely impaired performance despite intact direct corticocortical projections, thus challenging the purely corticocentric map of perception. Interestingly, the inhibition did not reduce overall cell responsiveness to texture stimulation in somatosensory cortex, but rather disrupted the texture selectivity of cells, a discriminability that develops over task learning. This discriminability was more disrupted in the secondary than primary somatosensory cortex, emphasizing the feedforward influence of the transthalamic route. Transthalamic pathways thus appear critical in delivering performance-relevant information to higher order cortex and are critical hierarchical pathways in perceptual decision-making.
Micropolarity governs the structural organization of biomolecular condensates
Authors: Ye Songtao , Latham Andrew P. , Tang Yuqi , Hsiung Chia-Heng , Chen Junlin , Luo Feng , Liu Yu , Zhang Bin , Zhang Xin 
Published: March 2023

AbstractMicroenvironment is critical to the function of cells and organisms. One example is provided by biomolecular condensates, whose microenvironment can be vastly different from the surrounding cellular environments to engage unique biological functions. How microenvironments of biomolecular condensates affect their structure and function remains unknown. Here, we show that the arrangements and partitioning of biomolecules are dictated by the differences between the micropolarity of each subcompartment. Sufficient difference in micropolarity results in layered structures with the exterior shell presenting a more polar microenvironment than the interior core. Accordingly, micropolarity inversion is accompanied by conversions of the layered structures. These findings demonstrated the central role of the previously overlooked microenvironment in regulating the structural organization and function of membraneless organelles.
Spatial Transcriptomics Analysis of Gene Expression Prediction using Exemplar Guided Graph Neural Network
Authors: Yang Yan , Hossain Md Zakir , Stone Eric , Rahman Shafin 
Published: March 2023

AbstractSpatial transcriptomics (ST) is essential for understanding diseases and developing novel treatments. It measures the gene expression of each fine-grained area (i.e., different windows) in the tissue slide with low throughput. This paper proposes an exemplar guided graph network dubbed EGGN to accurately and efficiently predict gene expression from each window of a tissue slide image. We apply exemplar learning to dynamically boost gene expression prediction from nearest/similar exemplars of a given tissue slide image window. Our framework has three main components connected in a sequence: i) an extractor to structure a feature space for exemplar retrievals; ii) a graph construction strategy to connect windows and exemplars as a graph; iii) a graph convolutional network backbone to process window and exemplar features, and a graph exemplar bridging block to adaptively revise the window features using its exemplars. Finally, we complete the gene expression prediction task with a simple attention-based prediction block. Experiments on standard benchmark datasets indicate the superiority of our approach when compared with past state-of-the-art methods.Graphical AbstractIn this paper, we aim to predict gene expression of each window in a tissue slide image. Given a tissue slide image, we encode the windows to feature space, retrieve its exemplars from the reference dataset, construct a graph, and then dynamically predict gene expression of each window with our exemplar guided graph network.HighlightsWe propose an exemplar guided graph network to accurately predict gene expression from a slide image window.We design a graph construction strategy to connect windows and exemplars for performing exemplar learning of gene expression prediction.We propose a graph exemplar bridging block to revise the window feature by using its nearest exemplars.Experiments on two standard benchmark datasets demonstrate our superiority when compared with state-of-the-art approaches.
Difluoromethylornithine rebalances aberrant polyamine ratios in Snyder-Robinson syndrome: mechanism of action and therapeutic potential
Authors: Stewart Tracy Murray , Foley Jackson R. , Holbert Cassandra E. , Khomutov Maxim , Rastkari Noushin , Tao Xianzun , Khomutov Alex R. , Zhai R. Grace , Casero Robert A. 
Published: March 2023

ABSTRACTSnyder-Robinson Syndrome (SRS) is caused by mutations in the spermine synthase (SMS) gene, the enzyme product of which converts the polyamine spermidine into spermine. Affecting primarily males, common manifestations of SRS include intellectual disability, osteoporosis, hypotonic musculature, and seizures, along with other, more variable symptoms. Currently, medical management focuses on treating symptoms without addressing the underlying molecular cause of the disease.Reduced SMS catalytic activity in cells of SRS patients causes the accumulation of spermidine, while spermine levels are reduced. The resulting exaggeration in spermidine-to-spermine ratio is a biochemical hallmark of SRS that tends to correlate with symptom severity in the patient. Our studies aim to pharmacologically manipulate polyamine metabolism to correct this polyamine imbalance and investigate the potential of this approach as a therapeutic strategy for affected individuals.Here we report the use of 2-difluoromethylornithine (DFMO; eflornithine), an FDA-approved inhibitor of polyamine biosynthesis, in re-establishing normal spermidine-to-spermine ratios in SRS patient cells. Through mechanistic studies, we demonstrate that, while reducing spermidine biosynthesis, DFMO also stimulates the conversion of existing spermidine into spermine in cell lines with hypomorphic variants ofSMS. Further, DFMO treatment induces a compensatory uptake of exogenous polyamines, including spermine and spermine mimetics, cooperatively reducing spermidine and increasing spermine levels. In aDrosophilaSRS model characterized by reduced lifespan, adding DFMO to the feed extends lifespan. As nearly all known SRS patient mutations are hypomorphic, these studies form a foundation for future translational studies with significant therapeutic potential.
Prenatal urban environment and blood pressure trajectories from childhood to early adulthood
Authors: Soares Ana Gonçalves , Santos Susana , Seyve Emie , Nedelec Rozenn , Puhakka Soile , Eloranta Aino-Maija , Mikkonen Santtu , Yuan Wen Lun , Lawlor Deborah A , Heron Jon , Vrijheid Martine , Lepeule Johanna , Nieuwenhuijsen Mark , Fossati Serena , Jaddoe Vincent W V , Lakka Timo , Sebert Sylvain , Heude Barbara , Felix Janine F , Elhakeem Ahmed , Timpson Nicholas J 
Published: March 2023

AbstractBackgroundPrenatal urban environmental exposures have been associated with blood pressure in children. The dynamic of these associations across childhood and later ages is unknown.ObjectivesTo assess associations of prenatal urban environmental exposures with blood pressure trajectories from childhood to early adulthood.MethodsRepeated measures of systolic (SBP) and diastolic blood pressure (DBP) were collected in up to 7,454 participants from a UK birth cohort. Prenatal urban exposures (n=42) covered measures of noise, air pollution, built environment, natural spaces, traffic, meteorology, and food environment. An exposome-wide association study approach was used. Linear spline mixed-effects models were used to model associations of each exposure with trajectories of blood pressure. Replication was sought in four independent European cohorts (N up to 9,261).ResultsIn discovery analyses, higher humidity was associated with a faster increase (mean yearly change in SBP for an interquartile range [IQR] increase in humidity: 0.29 mmHg/year, 95%CI 0.20; 0.39) and higher temperature with a slower increase (mean yearly change in SBP per IQR increase in temperature: -0.17 mmHg/year, 95%CI -0.28; -0.07) in SBP in childhood. Higher levels of humidity and air pollution were associated with faster increase in DBP in childhood and slower increase in adolescence. There was little evidence of an association of other exposures with change in SBP or DBP. Results for humidity and temperature, but not for air pollution, were replicated in other cohorts.ConclusionReplicated findings suggest that higher prenatal humidity and temperature could modulate blood pressure changes across childhood.