bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing amblyopic perception under naturalistic viewing conditions
Authors: Meier Kimberly , Tarczy-Hornoch Kristina , Boynton Geoffrey M. , Fine Ione 
Published: October 2022

AbstractCurrent assessments of interocular interactions in amblyopia use rivalrous stimuli, with conflicting stimuli in each eye, which does not reflect vision under typical circumstances. Here we measure interocular interactions in observers with amblyopia, strabismus with equal vision, and controls using a non-rivalrous stimulus. Observers used a joystick to continuously report perceived contrast of dichoptic grating stimuli, identical except that the stimulus was contrast-modulated independently in each eye over time. Consistent with previous studies, a model predicting the time-course of perceived contrast found increased amblyopic eye attenuation, and reduced contrast normalization of the fellow eye by the amblyopic eye, in amblyopic participants compared to controls. However, these suppressive interocular effects were weaker than those found in previous studies, suggesting that rivalrous stimuli may overestimate the effects of amblyopia on interocular interactions during naturalistic viewing conditions.
Single-nucleus expression characterization of non-enhancing region of recurrent high-grade glioma
Authors: Patel Kunal S. , Tessema Kaleab K. , Kawaguchi Riki , Alvarado Alvaro G. , Muthukrishnan Sree Deepthi , Hagiwara Akifumi , Swarup Vivek , Liau Linda M. , Wang Anthony , Yong William , Geschwind Daniel H. , Nakano Ichiro , Goldman Steven A. , Everson Richard , Ellingson Benjamin M. , Kornblum Harley I. 
Published: October 2022

AbstractBackgroundNon-enhancing (NE) infiltrating tumor cells beyond the contrast-enhancing (CE) bulk of tumor are potential propagators of recurrence after gross total resection of high-grade glioma.MethodsWe leveraged single-nucleus RNA-sequencing on 15 specimens from 5 high grade gliomas to compare prospectively identified biopsy specimens acquired from CE and NE regions. Additionally, 24 CE and 22 NE biopsies had immunohistochemical staining for Ki67 to identify proliferative cell burden.ResultsTumor cells in NE regions are enriched in neural progenitor cell-like cellular states, while CE regions are enriched for mesenchymal-like states. These NE glioma cells have similar proportions of proliferative and putative glioma stem cells relative to CE regions, without significant differences in % Ki67 staining. Tumor cells in NE regions exhibit upregulation of genes previously associated with lower grade gliomas. Cell-, gene-, and pathway-level analyses of the tumor microenvironment in the NE region reveal relative downregulation of tumor-mediated neovascularization and presence of cell-mediated immune response, but increased glioma-to-non-pathological cellular interactions.ConclusionsThis comprehensive analysis illustrates differing tumor and non-tumor landscapes of CE and NE regions in high-grade gliomas, highlighting the NE region as an area harboring likely initiators of recurrence in a pro-tumor microenvironment and identifying possible targets for future design of NE-specific adjuvant therapy.Key PointsSignificant proliferating tumor burden exist in non-enhancing regions of glioma; non-enhancing regions have unique tumor and non-tumor expression propertiesImportance of StudyStandard of care treatment for glioblastoma relies on visualization of tumor via contrast-enhanced magnetic resonance imaging. However, non-enhancing regions harbor tumor cells that should be targets for adjuvant therapy given these regions are not resected in surgery. To begin addressing these infiltrating non-enhancing tumor cells, we thoroughly characterize the tumor and non-tumor microenvironment of non-enhancing regions in high grade gliomas. Understanding the total tumor burden, proliferating tumor ratio, and presence of putative glioma stem cells may help design adjuvant therapies for these unique population of tumor cells. Understanding the non-tumor immune and vascular microenvironment may help target these areas in regards to drug delivery and immunotherapy. Overall, in a disease marked by significant intratumoral heterogeneity, we focus identifying therapeutic strategies for areas not addressed at surgery.
Pre-saccadic enhancement of target stimulus motion influences post-saccadic smooth eye movements
Authors: Coop Shanna H. , Crutcher Garrett W. , Abrham Yonatan T. , Bucklaew Amy , Mitchell Jude F. 
Published: October 2022

AbstractPrimates move their eyes 2-3 times per second to bring objects of interest to central, high-resolution vision. For moving objects, they use a combination of rapid saccadic eye movements along with smooth following movements to track targets continuously. Each saccadic eye movement produces perceptual enhancements for the target. And for saccades that are made to moving targets, or stationary apertures that contain motion, there is a smooth post-saccadic following response (PFR) of the target motion (Kwon et al, 2019). This PFR occurs involuntarily even when the motion is task irrelevant and could provide an automatic behavioral read-out of the target’s motion. However, PFR movements are small, so it is unclear how reliable they would be as a trial-by-trial read-out. Here we examined PFR in marmoset monkeys performing a foraging task that requires almost no training and which has been shown to involve pre-saccadic neural enhancements of motion selective responses in visual area MT (Coop et al., 2024). We found that PFR in marmosets is highly consistent with humans and could be used to read-out the target motion. More so, we found that the motion in non-target apertures also influenced PFR but to a lesser extent than the target. The gain of PFR was distributed equally between target and non-target apertures before the saccade, and then was rapidly enhanced only for the target motion in driving the post-saccadic following. Thus, PFR provides a behavioral measure of target enhancement relative to distracters in addition to providing a read-out of the target’s motion.Significance StatementUsing a saccade foraging paradigm in marmoset monkeys we measured visual motion integration and pre-saccadic enhancement based on the smooth following eye movements made after a saccade to a motion aperture. We find that marmosets exhibit post-saccadic following behaviors akin to humans, underscoring the evolutionary continuity in visual processing across primates. This following response provided an estimate of target motion that was half as accurate as explicitly trained reports but required minimal training to achieve. It also provided an estimate of the pre-saccadic enhancement for the target relative to distracters in the visual field.
Isotopic niches do not follow the expectations of niche conservatism in the bird genusCinclodes
Authors: Rader Jonathan A. , Matute Daniel R. 
Published: October 2022

AbstractPhenotypic traits are expected to be more similar among closely related species than among species that diverged long ago (all else being equal). This pattern, known as phylogenetic niche conservatism, also applies to traits that are important to determine the niche of species. To test this hypothesis on ecological niches, we analyzed isotopic data from 254 museum study skins from 12 of the 16 species of the bird genusCinclodesand measured stable isotope ratios for four different elements: Carbon, Nitrogen, Hydrogen and Oxygen. We find that all traits, measured individually, or as a composite measurement, lack any phylogenetic signal, which in turn suggests a high level of lability in ecological niches. We compared these metrics to the measurements of morphological traits in the same genus and found that isotopic niches are uniquely evolutionarily labile compared to other traits. Our results suggest that, inCinclodes, the realized niche evolves much faster than expected by the constraints of phylogenetic history and poses the question of whether this is a general pattern across the tree of life.
Partitioning variance in a signaling trade-off under sexual selection reveals among-individual covariance in trait allocation
Authors: Reichert Michael S. , de la Hera Iván , Moiron Maria 
Published: October 2022

ABSTRACTUnderstanding the evolution of traits subject to trade-offs is challenging because phenotypes can (co)vary at both the among- and within-individual levels. Among-individual covariation indicates consistent, possibly genetic, differences in how individuals resolve the trade-off, while within-individual covariation indicates trait plasticity. There is also the potential for consistent among-individual differences in behavioral plasticity, although this has rarely been investigated. We studied the sources of (co)variance in two characteristics of an acoustic advertisement signal that trade off with one another and are under sexual selection in the gray treefrog,Hyla chrysoscelis: call duration and call rate. We recorded males on multiple nights calling spontaneously and in response to playbacks simulating different competition levels. Call duration, call rate, and their product, call effort, were all repeatable both within and across social contexts. Call duration and call rate covaried negatively, and the largest covariance was at the among-individual level. There was extensive plasticity in calling with changes in social competition, and we found some evidence for among-individual variance in call rate plasticity. The significant negative among-individual covariance in trait values is perpendicular to the primary direction of sexual selection in this species, indicating potential limits on the response to selection.
Seg2Link: an efficient and versatile solution for semi-automatic cell segmentation in 3D image stacks
Authors: Wen Chentao , Matsumoto Mami , Sawada Masato , Sawamoto Kazunobu , Kimura Koutarou D 
Published: October 2022

AbstractRecent advances in microscopy techniques, especially in electron microscopy, are transforming biomedical studies by acquiring large quantities of high-precision 3D cell image stacks. However, to study cell morphology and connectivity in organs such as brains, scientists must first perform cell segmentation, which involves extracting individual cell regions of various shapes and sizes from a 3D image. This remains a great challenge because automatic cell segmentation can contain numerous errors, even with advanced deep learning methods. For biomedical research that requires cell segmentation in large 3D image stacks, an efficient semi-automated software solution is still needed. We created Seg2Link, which generates automatic segmentations based on deep learning predictions and allows users to quickly correct errors in the segmentation results. It can perform automatic instance segmentation of 2D cells in each slice, 3D cell linking across slices, and various manual corrections, in order to efficiently transform inaccurate deep learning predictions into accurate segmentation results. Seg2Link’s data structure and algorithms were also optimized to process 3D images with billions of voxels on a personal computer quickly. Thus, Seg2Link offers a simple and effective way for scientists to study cell morphology and connectivity in 3D image stacks.
Architecture and topologies of gene regulatory networks associated with breast cancer, adjacent normal, and normal tissues
Authors: Kumar Swapnil , Vindal Vaibhav 
Published: October 2022

AbstractMost cancer studies employ adjacent normal tissues to tumors (ANTs) as controls, which are not completely normal and represent a pre-cancerous state. However, the regulatory landscape of ANTs and how it differs from tumor and non-tumor-bearing normal tissues is largely unexplored. Among cancers, breast cancer is the most commonly diagnosed cancer and a leading cause of death in women worldwide, with a lack of sufficient treatment regimens due to various reasons. Hence, we aimed to gain deeper insights into normal, pre-cancerous, and cancerous regulatory systems of the breast tissues towards the identification of ANT and subtype-specific candidate genes. For this, we constructed and analyzed eight gene regulatory networks (GRNs), including five different subtypes (viz.Basal, Her2, LuminalA, LuminalB, and Normal-Like), one ANT, and two normal tissue networks. Whereas several topological properties of these GRNs enabled us to identify tumor-related features of ANT; escape velocity centrality (EVC+) identified 24 functionally significant common genes, including well-known genes such asE2F1, FOXA1, JUN, BRCA1, GATA3, ERBB2,andERBB3across different subtypes and ANT. Similarly, the EVC+ also helped us to identify tissue-specific key genes (Basal: 18, Her2: 6, LuminalA: 5, LuminalB: 5, Normal-Like: 2, and ANT: 7). Additionally, differential correlation along with functional, pathway, and disease annotations highlighted the cancer-associated role of these genes. In a nutshell, the present study revealed ANT and subtype-specific regulatory features and key candidate genes which can be explored further usingin vitroandin vivoexperiments for better and effective disease management at an early stage.
Feasibility of linking markers of dementia-related health in primary care medical records to cognitive function assessed in a specialist dementia service
Authors: Marshall Michelle , Campbell Paul , Bailey James , Chew-Graham Carolyn A , Croft Peter , Frisher Martin , Hayward Richard , Negi Rashi , Rathod-Mistry Trishna , Singh Swaran , Robinson Louise , Sumathipala Athula , Thein Nwe , Walters Kate , Weich Scott , Jordan Kelvin P 
Published: October 2022

AbstractObjectivesTo assess the feasibility of linking and comparing markers of dementia-related health recorded in primary care electronic health records (EHR) to assessments of cognitive function undertaken in a specialist dementia service.MethodsOne thousand patients in a UK secondary care specialist dementia service were invited to take part. Primary care EHR were requested from 72 general practices of consenting patients. Sixty-three previously established individual markers within 13 broader domains of dementia-related health were then extracted from primary care EHR and compared to cognitive assessments scores recorded in the dementia service EHR.Results258 (26%) patients consented to take part. At least one cognitive assessment score was recorded for 242 (94%) patients, but primary and secondary care EHR records could only be linked in 93 patients. 56 of these 93 patients had two cognitive assessments scores at least 12 months apart. In the patients with data available for analysis individuals with a higher number of markers and domains recorded in their primary care records had lower mean cognitive assessment scores (range 1.6-2.1 points), and after adjustment for earlier cognitive scores (range 2.0-2.5 points), indicating poorer cognitive function, although differences were not statistically significant.ConclusionThis feasibility study highlights the challenges in obtaining consent and linking primary and secondary care EHR in dementia, and in extracting cognitive function scores from dementia service EHR.
Vegetarianism and mental health: longitudinal evidence in the 1970 British Cohort Study
Authors: Gagné Thierry , Kurdi Vanessa 
Published: October 2022

ABSTRACTBackgroundReducing animal product consumption has benefits for population health and the environment. The relationship between vegetarianism and mental health, however, remains poorly understood. This study explores this relationship in a nationally representative birth cohort in Great Britain.MethodsWe use data from the 1970 British Cohort Study, which collected information on diet at age 30 (n= 11,204) and psychological distress (PD) using the nine-item Malaise Inventory at ages 26, 30, 34, 42, and 46-48. We first developed a statistical adjustment strategy by regressing PD at age 30 on vegetarianism and 14 potential confounders measured at ages 10 and 26 (including PD at age 26). We then ran multilevel growth curve models, testing whether within-person changes in PD between ages 30 and 46-48 differed by vegetarianism, before and after statistical adjustment. Models were reproduced using red meat consumption at age 30 as a sensitivity analysis.ResultsAt age 30, 4.5% of participants reported being vegetarian. In the cross-sectional models at age 30, vegetarians reported more distress compared with non-vegetarians in bivariate analysis (b = 0.30, 95%CI 0.09, 0.52), but this difference disappeared in the fully-adjusted model (b = 0.02, 95%CI -0.17, 0.21). In the longitudinal models between ages 30 and 46/48, there were no differences in within-person changes in psychological distress between vegetarians and non-vegetarians (p= .723). Sensitivity analyses yielded similar findings.ConclusionIn this British cohort, vegetarianism at age 30 was not associated with changes in psychological distress during mid-adulthood. Since psychological distress in early adulthood predicted vegetarianism at age 30, more studies are needed to disentangle the progression of this relationship over the life-course.
Understanding maternity care providers’ use of data: A qualitative study in Southern Tanzania
Authors: Unkels Regine , Al-beity Fadhlun Alwy , Julius Zamoyoni , Mkumbo Elibariki , Pembe Andrea B , Hanson Claudia , Mölsted-Alvesson Helle 
Published: October 2022

ABSTRACTIntroductionHealth information management system data is collected for national planning and evaluation but rarely used for health care improvements at the sub-national or facility-level in low-and-middle-income countries. Research suggests that perceived data quality and lack of feedback are contributing factors. We aimed to understand maternity care providers’ perceptions of data and how they use them, with a view to co-design interventions to improve data quality and use.MethodsWe based our research on constructivist grounded theory. We conducted 14 in-depth interviews, two focus group discussions with maternity care providers and 48 hours of observations in maternity wards of two rural hospitals in Southern Tanzania. Constant comparative data analysis was applied to develop initial and focused codes, sub-categories and categories continuously validated through peer and member checks.ResultsMaternity care providers appropriated numeric data on service provision to reconcile their professional values and demands from managers and the community with effects of a challenging working environment. They felt controlled by their managers’ data requirements and alienated from service provision data. Providers added informal documentation ways for their own narrative data needs to reflect on and improve service quality. These also assisted them to recreate social relationships with managers, clients and the community. The resulting documentation system led to duplication and increased systemic complexity.ConclusionsData from health information systems does not represent an independent and neutral entity but is embedded into the social realities of different users. Appropriation and use of data reflect these realities and users’ working environment. Interventions to improve data quality and use may need to incorporate the multitude of clinical and administrative documentation and data needs to avoid duplication and inefficiencies.
Geospatial assessment of racial/ethnic composition, social vulnerability, and lead service lines in New York City
Authors: Nigra Anne E. , Lieberman-Cribbin Wil , Bostick Benjamín C. , Chillrud Steven N. , Carrión Daniel 
Published: October 2022

ABSTRACTBackgroundThe state of New York expects to receive $115 million in 2022 alone from the US Infrastructure Investment and Jobs Act to support the replacement of lead water service lines.ObjectivesTo determine the number and proportion ofPotential Leadwater service lines across New York City (NYC), and the association between racial/ethnic composition, housing vulnerability, and child lead exposure vulnerability with service line type (Potential Lead, Unknown) at the census tract level for N= 2,083 NYC tracts.MethodsWe used conditional autoregressive Bayesian Poisson models to assess the relative risk (median posterior estimates, and 95% credible interval, CrI) of service line type per 20% higher proportion of residents in a given racial/ethnic group, and per higher housing vulnerability and child lead exposure vulnerability index scores corresponding to the interquartile range. We also evaluated the associations in flexible natural cubic spline models.ResultsOut of 854,672 residential service line records, 136,891 (16.0%) werePotential Leadand 227,443 (26.6%) wereUnknown. In fully adjusted models, higher proportions of Hispanic/Latino residents and higher child lead exposure vulnerability were associated withPotential Leadservice lines in flexible spline models and linear models (RR 1.15, 95% CrI 1.11, 1.21, and RR 1.11, 95% CrI 1.02, 1.20, respectively). Associations were modified by borough;Potential Leadservice lines were associated with higher proportions of non-Hispanic White and non-Hispanic Asian residents in the Bronx and Manhattan, and with higher proportions of non-Hispanic Black residents in Queens.DiscussionNYC has a high number ofPotential LeadandUnknownservice lines. Communities with a high proportion of Hispanic/Latino residents and those with children who are already highly vulnerable to lead exposures from numerous sources are disproportionately impacted byPotential Leadservice lines. These findings can inform equitable service line replacement across NY state and NYC.
Hepatitis C care cascade among patients with and without tuberculosis: findings from nationwide programs in the country of Georgia, 2015-2020
Authors: Baliashvili Davit , Blumberg Henry M. , Gandhi Neel R. , Averhoff Francisco , Benkeser David , Shadaker Shaun , Gvinjilia Lia , Turdziladze Aleksandre , Tukvadze Nestani , Chincharauli Mamuka , Butsashvili Maia , Sharvadze Lali , Tsertsvadze Tengiz , Zarkua Jaba , Kempker Russell R. 
Published: October 2022

ABSTRACTBackgroundThe Eastern European country of Georgia initiated a nationwide hepatitis C virus (HCV) elimination program in 2015 to address a high burden of infection. Screening for HCV infection through antibody testing was integrated into multiple existing programs, including the National Tuberculosis Program (NTP). We sought to evaluate loss to follow-up (LTFU) from the hepatitis C care cascade among persons diagnosed with active tuberculosis (TB) disease.MethodsUsing national ID numbers, we merged databases of the HCV elimination program, NTP, and national death registry from January 1, 2015, to September 30, 2020. We estimated the proportion of patients with and without TB who were LTFU at each step of the HCV care cascade and explored temporal changes.ResultsAmong 11,985 patients with active TB, 9,065 (76%) were tested for HCV antibodies, and 1,665 (18%) had a positive result; LTFU from hepatitis C care was common, with 20% of patients with a positive antibody test not undergoing viremia testing, and 43% of patients with viremia not starting treatment for hepatitis C. Overall, among persons with confirmed viremic HCV infection, only 28% of patients with TB had a documented cure from HCV infection, compared to 55% among patients without TB. LTFU after positive antibody testing substantially decreased in the last three years, from 32% among patients diagnosed with TB in 2017 to 12% among those diagnosed in 2019.ConclusionsLTFU from hepatitis C care after a positive antibody or viremia test was high and more common among patients with TB than in those without TB. Better integration of TB and hepatitis C care systems can potentially reduce LTFU and improve patient outcomes. Existing large-scale programs for both TB and hepatitis C in Georgia create a unique opportunity for such integration to contribute to hepatitis C elimination efforts.