bluuebunny/crossref_metadata_2025_split huggingface dataset:
SPCR-05 ENVIRONMENTAL ENRICHMENT AMONG BRAINTUMOR SURVIVORS
Authors: Figuracion Karl Cristie , Hunt David , Donald Christine Mac , Thompson Hilaire 
Published: August 2023

Abstract
Individuals from underserved communities who received photon radiation are at a disproportionately increased risk of accelerated aging and symptom burden that significantly impacts independence and overall functioning. There is limited knowledge of environmental factors that mitigate these long-term sequelae. The aim of the study is to explore if higher levels of environmental enrichment (EE) are neuroprotective against accelerated brain aging experienced by brain tumor (BT) survivors who received radiation.
METHODS: The study employed a retrospective cohort design among persons with low-grade glioma treated with radiation approximately 5 years from the original diagnosis (N=39). EE consists of social network/engagement, physical activity, and employment status/financial stability measured by the Berkman-Syme Social Network Index, International Physical Activity Questionnaire, Vocational Index Scale, and Socioeconomic Questionnaires, respectively. EE at enrollment is classified into high, moderate, or low levels. Montreal Cognitive Assessment and Symbol Digit Modality Test at enrollment measure cognitive function. Karnofsky Performance Status Scale and the MD Anderson Symptom Inventory – BT module at enrollment are used to measure functional status. Cortical volume is measured using temporal brain MRI images from the time of diagnosis, 3 and 5 years after diagnosis. Images are processed using FreeSurfer segmentation software. Linear mixed models will estimate mean cerebral atrophy and explore the association to cognitive and functional data across time adjusted for covariates.
RESULTS: Research analysis in progress. Thirty-nine participants have been enrolled in the study. The median age is 44, 22 are male, and 27 are female. There are 18 Individuals diagnosed with Astrocytoma and 19 with Oligodendroglioma. Thirty-three percent of individuals have low EE, 43.5% have moderate EE, and 23% have high EE.
CONCLUSION: BT survivors are at an increased risk of accelerated aging and progressive neurological decline. EE may serve as a positive stimulation that improves neuroplasticity and reduces accelerated aging after brain radiation.
Neurocognitive Outcomes in Multiethnic Pediatric Brain Tumor Patients Treated With Proton Versus Photon Radiation
Authors: Unnikrishnan Soumya , Yip Anthony T. , Qian Alexander S. , Salans Mia A. , Yu Justin D. , Huynh-Le Minh-Phuong , Reyes Anny , Stasenko Alena , McDonald Carrie , Kaner Ryan , Crawford John R. , Hattangadi-Gluth Jona A. 
Published: August 2023

Background:
We analyzed post-radiation (RT) neurocognitive outcomes in an ethnically diverse pediatric brain tumor population undergoing photon radiotherapy (XRT) and proton radiotherapy (PRT).

Procedure:
Post-RT neurocognitive outcomes from 49 pediatric patients (37% Hispanic/Latino) with primary brain tumors were analyzed. Tests included cognitive outcomes, behavioral outcomes, and overall intelligence. For each outcome, proportion of patients with cognitive impairment (scores <1.5 SD) was calculated. The Fisher exact tests compared proportion of patients with impairment and t tests compared T-scores between XRT (n=32) and PRT (n=17) groups. Linear regression assessed associations between radiation modality and outcomes.

Results:
Median follow-up was 3.2 and 1.8 years in the XRT and PRT groups, respectively. The median RT dose was 54.0 Gy. We found impairment in 16% to 42% of patients across most neurocognitive domains except executive function. There was no difference in scores between XRT and PRT groups. Regression analyses revealed no association of neurocognitive outcomes with radiation modality. Non-Hispanic patients had better Verbal Comprehension Index and General Ability Index scores than Hispanic patients (P<0.05).

Conclusions:
Among pediatric patients with brain tumors receiving RT, all cognitive domains were affected except executive function. Radiation modality was not associated with neurocognitive outcomes. Hispanic patients may be more vulnerable to posttreatment cognitive effects that warrant further study.
Creating a Community of Nurse Educator Scholars
Authors: Schuler Monika S. , Vottero Beth , Altmiller Gerry 
Published: August 2023

Background:
Engaging in scholarship is a critical component of being an effective nurse educator and can have a significant impact on the nursing profession as a whole.

Problem:
Nurse educators are expected to teach and simultaneously engage in scholarship. Barriers include heavy workloads and lack of resources including faculty mentors. Evidence supports that organized work groups support success.

Approach:
Members of the Quality and Safety Education for Nurses (QSEN) Academic Task force were queried about scholarly activity as a result of engagement with fellow task force members.

Outcomes:
Scholarly outcomes included numerous peer-reviewed publications, teaching tips, presentations, and grants.

Conclusion:
Participating in national work groups can serve as a platform for fostering a community of scholars to make meaningful contributions to the profession.
A unique human cord blood CD8+CD45RA+CD27+CD161+T cell subset identified by flow cytometric data analysis using Seurat
Authors: Reyes Julen Gabirel Araneta , Ni Duan , Santner-Nanan Brigitte , Pinget Gabriela Veronica , Kraftova Lucie , Ashhurst Thomas Myles , Marsh-Wakefield Felix , Wishart Claire Leana , Tan Jian , Hsu Peter , King Nicholas Jonathan Cole , Macia Laurence , Nanan Ralph 
Published: August 2023

AbstractAdvances in single cell analysis, especially cytometric approaches, have profoundly innovated immunological research. This has resulted in an expansion of high dimensional data, posing great challenges for comprehensive and unbiased analysis. Conventional manual analysis thus becomes untenable, while most computational methods lack flexibility and interoperability, hampering usability. Here, for the first time, we adapted Seurat, a single cell RNA sequencing (scRNA-seq) analysis package, for end-to-end flow cytometric data analysis. We showcased its robust analytical capacity by analyzing the adult blood and cord blood T cell profiles, which was validated by Spectre, another cytometric data analysis package, and manual analysis. Importantly, a unique CD8+CD45RA+CD27+CD161+T cell subset, was identified in cord blood and characterized using flow cytometry and scRNA-seq analysis from a published dataset. Collectively, Seurat possesses great potential for cytometric data analysis. It facilitates thorough interpretations of high dimensional data using a single pipeline, implementing data-driven investigation in clinical immunology.
The importance of DNA sequence for nucleosome positioning in transcriptional regulation
Authors: Sahrhage Malte , Paul Niels Benjamin , Beißbarth Tim , Haubrock Martin 
Published: August 2023

ABSTRACTNucleosome positioning is a key factor for transcriptional regulation. Nucleosomes regulate the dynamic accessibility of chromatin and interact with the transcription machinery at every stage. Influences to steer nucleosome positioning are diverse, and the according importance of the DNA sequence in contrast to active chromatin remodeling has been subject of long discussion. In this study, we evaluate the functional role of DNA sequence for all major elements along the process of transcription. We developed a random forest classifier based on local DNA structure that assesses the sequence-intrinsic support for nucleosome positioning. On this basis, we created a simple data resource that we applied genome-wide to the human genome. In our comprehensive analysis, we found a special role of DNA in mediating the competition of nucleosomes with cis-regulatory elements, in enabling steady transcription, for positioning of stable nucleosomes in exons and for repelling nucleosomes during transcription termination. In contrast, we relate these findings to concurrent processes that generate strongly positioned nucleosomes in vivo that are not mediated by sequence, such as energy-dependent remodeling of chromatin.GRAPHICAL ABSTRACT
Pathogenic mutations of human phosphorylation sites affect protein-protein interactions
Authors: Rrustemi Trendelina , Meyer Katrina , Roske Yvette , Uyar Bora , Akalin Altuna , Imami Koshi , Ishihama Yasushi , Daumke Oliver , Selbach Matthias 
Published: August 2023

AbstractDespite their lack of a defined 3D structure, intrinsically disordered regions (IDRs) of proteins play important biological roles. Many IDRs contain short linear motifs (SLiMs) that mediate protein-protein interactions (PPIs), which can be regulated by post-translational modifications like phosphorylation. 20% of pathogenic missense mutations are found in IDRs, and understanding how such mutations affect PPIs is essential for unraveling disease mechanisms. Here, we employed peptide-based interaction proteomics to investigate 36 disease-causing mutations affecting phosphorylation sites. Our results unveiled significant differences in interactomes between phosphorylated and non-phosphorylated peptides, often due to disrupted phosphorylation-dependent SLiMs. We focused on a mutation of a serine phosphorylation site in the transcription factor GATAD1, which causes dilated cardiomyopathy. We found that this phosphorylation site mediates interaction with 14-3-3 family proteins. Follow-up experiments revealed the structural basis of this interaction and suggest that 14-3-3 binding affects GATAD1 nucleocytoplasmic transport by masking a nuclear localisation signal. Our results demonstrate that pathogenic mutations of human phosphorylation sites can significantly impact protein-protein interactions, offering fresh insights into potential molecular mechanisms underlying pathogenesis.
Island demographics and trait associations in white-tailed deer
Authors: Cars Brooklyn S. , Kessler Camille , Hoffman Eric A. , Côté Steeve D. , Koelsch Daniel , Shafer Aaron B.A 
Published: August 2023

AbstractWhen a population is isolated and composed of few individuals, genetic drift is the paramount evolutionary force that results in the loss of genetic diversity. Inbreeding might also occur, resulting in genomic regions that are identical by descent, manifesting as runs of homozygosity (ROHs) and the expression of recessive traits. Likewise, the genes underlying traits of interest can be revealed by comparing fixed SNPs and divergent haplotypes between affected and unaffected individuals. Populations of white-tailed deer (Odocoileus virginianus) on islands of Saint Pierre and Miquelon (SPM, France) have high incidences of leucism and malocclusions, both considered genetic defects; on the Florida Keys islands (USA) deer exhibit smaller body sizes, a polygenic trait. Here we aimed to reconstruct island demography and identify the genes associated with these traits in a pseudo case-control design. The two island populations showed reduced levels of genomic diversity and a build-up of deleterious mutations compared to mainland deer; there was also significant genome-wide divergence in Key deer. Key deer showed higher inbreeding levels, but not longer ROHs, consistent with long-term isolation. We identified multiple trait-related genes in ROHs includingLAMTOR2which has links to pigmentation changes, andNPVFwhich is linked to craniofacial abnormalities. Our mixed approach of linking ROHs, fixed SNPs and haplotypes matched a high number (∼50) of a-priori body size candidate genes in Key deer. This suite of biomarkers and candidate genes should prove useful for population monitoring, noting all three phenotypes show patterns consistent with a complex trait and non-Mendelian inheritance.
Effects of calibrated blue–yellow (–S+[L+M], +S–[L+M]) changes in light on the human circadian clock
Authors: Blume Christine , Cajochen Christian , Schöllhorn Isabel , Slawik Helen C. , Spitschan Manuel 
Published: August 2023

AbstractEvening exposure to short-wavelength light can acutely affect the circadian clock located in the suprachiasmatic nuclei, sleep, and alertness. The intrinsically photosensitive retinal ganglion cells (ipRGCs) expressing the photopigment melanopsin are thought to be the primary drivers of these effects. Much less is known about the contribution of the colour-sensitive cones. Using calibrated silent-substitution changes in light colour along the blue-yellow axis, we investigated whether mechanisms of colour vision affect the human circadian system and sleep. In a 32.5-h repeated within-subjects protocol, 16 healthy participants (8 women, 18-35 years old) were exposed to three different light scenarios for 1 h starting 30 min after habitual bedtime: a control condition (“background”, 93.5 photopic lux), intermittently flickering yellow-bright light (1 Hz, 30s on-off, 123.5 photopic lux), and intermittently flickering blue-dim light (1 Hz, 30s on-off; 67.0 photopic lux). Importantly, there was no difference in melanopsin excitation (163.2±2.1 lux melanopic EDI) between the three lighting conditions, allowing us to determine the unique contribution of the blue-yellow colour system. Our analyses did not yield conclusive evidence for differences between the three lighting conditions regarding circadian melatonin phase delays, melatonin suppression, subjective sleepiness, psychomotor vigilance, or sleep. Thus, in this study, we found no evidence that evening light changing along the blue-yellow dimension under moderate light levels typical for room illumination has a major impact on the human circadian clock or sleep. Our work underscores the previously demonstrated primary role of melanopsin-containing ipRGCs in mediating these effects.
Non-sequential alignment of binding sites for fast peptide screening
Authors: Guyon Frédéric , Moroy Gautier 
Published: August 2023

AbstractMotivationPeptides are molecules involved in many essential biological activities by interacting with proteins in the body. They can also be used as therapeutic molecules, particularly to disrupt protein-protein interactions involved in disease. However, it is difficult to identify potential therapeutic peptides if the structure of the protein-protein complex to be inhibited has not been solved.ResultsThe PepIT program was developed to propose peptides that can interact with a given protein. PepIT is based on a non-sequential alignment algorithm to identify peptide binding sites that share geometrical and physicochemical properties with a surface region of the target protein. PepIT compares the entire surface of the target protein with the peptide binding sites of the Propedia dataset, which contains more than 19,000 high-resolution protein-peptide structures. Once a peptide binding site similar to a portion of the protein surface is found, the peptide bound to the binding site is repositioned on the corresponding portion of the protein surface.Availability and implementationThe PepIT source code is freely available athttps://github.com/DSIMB/pepitSupplementary informationSupplementary data are available online.
Meta-analysis of herbicide non-target effects on pest natural enemies
Authors: Zilnik Gabriel , Bergeron Paul , Chuang Angela , Diepenbrock Lauren , Hanel Aldo , Middleton Eric , Moretti Erica , Schmidt-Jeffris Rebecca 
Published: August 2023

AbstractA critical component of integrated pest management is minimizing disruption of biological control by reducing use of pesticides with significant non-target effects on natural enemies. Insecticide non-target effects testing for natural enemies has become increasingly common, but research examining the non-target effects of herbicides on natural enemies is scarce and recommendations regarding herbicide selectivity are non-existent. We used meta-analysis to summarize laboratory bioassays testing non-target effects of herbicides on arthropod natural enemies and identify patterns in taxon susceptibility and active ingredient toxicity. Data was extracted from 103 papers representing 801 total observations. Herbicides increased natural enemy mortality and decreased longevity, reproduction, and predation. Mesostigmatan mites and hemipterans were the most sensitive to herbicides and spiders, neuropterans, and hymenopterans were the least sensitive. Mortality was higher in juvenile predators versus parasitoids, but did not differ between adults; parasitoid juveniles are likely better protected within the host. In terms of acute mortality, metribuzin, glufosinate, and oxyfluorfen were the most harmful herbicides. Only nicosulfuron, rimsulfuron, pendimethalin, phenmedipham, atrazine, and urea did not increase natural enemy mortality. The large effect size of glufosinate is particularly concerning, as it is the most likely replacement herbicide for glyphosate in many crops. Many active ingredients remain under-studied. Our analysis indicates that herbicides have a strong potential to disrupt biological control in cropping systems.Simple SummaryReducing the use of pesticides that harm natural enemies of crop pests is important to pest management. Currently, there is limited information on how herbicides might affect natural enemies. The researchers found that herbicides increased natural enemy mortality and reduced their longevity and efficacy as predators. Some potential glyphosate replacement herbicides were more harmful than glyphosate. There was little or no data available for many herbicides and beneficial insects, indicating that much more research is needed on this topic.
Physiological roles of endocytosis and presynaptic scaffold in vesicle replenishment at fast and slow central synapses
Authors: Mahapatra Satyajit , Takahashi Tomoyuki 
Published: August 2023

AbstractAfter exocytosis, release sites are cleared of vesicular residues to replenish with transmitter-filled vesicles. Endocytic and scaffold proteins are thought to underlie this site-clearance mechanism. However, the physiological significance of this mechanism at diverse mammalian central synapses remains unknown. Here, we tested this in a physiologically optimized condition using action potential evoked EPSCs at fast calyx synapse and relatively slow hippocampal CA1 synapse, in post-hearing mice brain slices at 37°C and in 1.3 mM [Ca2+]. Pharmacological block of endocytosis enhanced synaptic depression at the calyx synapse, whereas it attenuated synaptic facilitation at the hippocampal synapse. Block of scaffold protein activity likewise enhanced synaptic depression at the calyx but had no effect at the hippocampal synapse. At the fast calyx synapse, block of endocytosis or scaffold protein activity significantly enhanced synaptic depression as early as 10 ms after the stimulation onset. Unlike previous reports, neither endocytic blockers nor scaffold protein inhibitors prolonged the recovery from short-term depression. We conclude that the release-site clearance by endocytosis can be a universal phenomenon supporting vesicle replenishment at both fast and slow synapses, whereas the presynaptic scaffold mechanism likely plays a specialized role in vesicle replenishment predominantly at fast synapses.
Cross-family small GTPase ubiquitination by the intracellular pathogenLegionella pneumophila
Authors: Steinbach Adriana M. , Bhadkamkar Varun L. , Jimenez-Morales David , Stevenson Erica , Jang Gwendolyn M. , Krogan Nevan J. , Swaney Danielle L. , Mukherjee Shaeri 
Published: August 2023

AbstractThe intracellular bacterial pathogenLegionella pneumophila(L.p.) manipulates eukaryotic host ubiquitination machinery to form its replicative vacuole. While nearly 10% ofL.p.’s arsenal of ∼330 secreted effector proteins have been biochemically characterized as ubiquitin ligases or deubiquitinases, a comprehensive measure of temporally resolved changes in the endogenous host ubiquitinome during infection has not been undertaken. To elucidate howL.phijacks ubiquitin signaling within the host cell, we undertook a proteome-wide analysis of changes in protein ubiquitination during infection. We discover thatL.p.infection results in increased ubiquitination of host proteins regulating subcellular trafficking and membrane dynamics, most notably 63 of ∼160 mammalian Ras superfamily small GTPases. We determine that these small GTPases predominantly undergo non-degradative monoubiquitination, and link ubiquitination to recruitment to theLegionella-containing vacuole membrane. Finally, we find that the bacterial effectors SidC/SdcA play a central, but likely indirect, role in cross-family small GTPase ubiquitination. This work highlights the extensive reconfiguration of host ubiquitin signaling by bacterial effectors during infection and establishes simultaneous ubiquitination of small GTPases across the Ras superfamily as a novel consequence ofL.p.infection. This work positionsL.p.as a tool to better understand how small GTPases can be regulated by ubiquitination in uninfected contexts.
Human bone tissue-derived ECM hydrogels: Controlling physicochemical, biochemical, and biological properties through processing parameters
Authors: Kim Yang-Hee , Cidonio Gianluca , Kanczler Janos M. , Oreffo Richard OC , Dawson Jonathan I 
Published: August 2023

AbstractDecellularized tissues offer significant potential as biological materials for tissue regeneration due to their ability to preserve the complex compositions and architecture of the native extracellular matrix (ECM). While the use of decellularized ECM hydrogels from bovine and porcine bone tissues has been extensively studied, the evaluation and derivation of decellularized matrices from human bone tissue remain largely unexplored.The objective of this study was to investigate how the physiochemical and biological properties of ECM hydrogels derived from human bone ECM could be controlled by manipulating bone powder size (45-250 μm, 250-1000 μm, and 1000-2000 μm) and ECM composition through modulation of digestion time (3, 5, and 7 days).The current studies demonstrate that a reduction in material bone powder size and an increase in ECM digestion time resulted in enhanced protein concentrations in the ECM hydrogels, accompanied by the presence of a diverse array of proteins. Furthermore, these adjustments in the physicochemical properties generated improved gelation strength of the hydrogels. The evaluation of human bone marrow-derived stromal cells (HBMSCs) cultured on ECM hydrogels derived from 45-250 μm bone powder, treated for 7 days, demonstrated enhanced osteogenic differentiation compared to hydrogels derived from both larger bone powders and collagen gels.In conclusion, this study highlights the significant promise of human bone ECM hydrogels as biologically active materials for bone regeneration. The ability to manipulate digestion time and bone powder size enables the generation of hydrogels with enhanced release of ECM proteins and appropriate gelation and rheological properties, offering new opportunities for application in bone tissue engineering.