bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endothelial Cell-Specific Molecule-1 Inhibits Albuminuria in Diabetic Mice
Authors: Zheng Xiaoyi , Higdon Lauren , Gaudet Alexandre , Shah Manav , Balistieri Angela , Li Catherine , Nadai Patricia , Palaniappan Latha , Yang Xiaoping , Santo Briana , Ginley Brandon , Wang Xiaoxin X. , Myakala Komuraiah , Nallagatla Pratima , Levi Moshe , Sarder Pinaki , Rosenberg Avi , Maltzman Jonathan S. , de Freitas Caires Nathalie , Bhalla Vivek 
Published: October 2021

AbstractDiabetic kidney disease (DKD) is the most common cause of kidney failure in the world, and novel predictive biomarkers and molecular mechanisms of disease are needed. Endothelial cell-specific molecule-1 (Esm-1) is a secreted proteoglycan that attenuates inflammation. We previously identified that a glomerular deficiency of Esm-1 associates with more pronounced albuminuria and glomerular inflammation in DKD-susceptible relative to DKD-resistant mice, but its contribution to DKD remains unexplored. In this study, we show that lower circulating Esm-1 predicts progressive stages of albuminuria in patients with diabetes. In DKD-susceptible mice, Esm-1 inversely correlates with albuminuria and glomerular leukocyte infiltration. Using hydrodynamic tail-vein injection, we show that over-expression of either mouse or human Esm-1 reduces diabetes-induced albuminuria relative to saline-injected controls independent of leukocyte infiltration. Using a complementary approach, we find that constitutive deletion of Esm-1 in DKD-resistant mice increases the degree of diabetes-induced albuminuria versus wild-type controls. Mechanistically, over-expression of Esm-1 attenuates diabetes-induced podocyte injury. By glomerular RNAseq, we identify that Esm-1 attenuates diabetes-induced up-regulation of interferon-stimulated genes, and Esm-1 inhibits expression of kidney disease-promoting and interferon-related genes, includingAckr2andCxcl11. In conclusion, we demonstrate that Esm-1 protects against diabetes-induced albuminuria, and podocytopathy, possibly through select interferon signaling.
EEG-based clusters differentiate psychological distress, sleep quality and cognitive function in adolescents
Authors: Forbes Owen , Schwenn Paul E. , Wu Paul Pao-Yen , Santos-Fernandez Edgar , Xie Hong-Bo , Lagopoulos Jim , McLoughlin Larisa T. , Sacks Dashiell D. , Mengersen Kerrie , Hermens Daniel F. 
Published: October 2021

1AbstractIntroductionTo better understand the relationships between brain activity, cognitive function and mental health risk in adolescence there is value in identifying data-driven subgroups based on measurements of brain activity and function, and then comparing cognition and mental health symptoms between such subgroups.MethodsHere we implement a multi-stage analysis pipeline to identify data-driven clusters of 12-year-olds (M = 12.64, SD = 0.32) based on frequency characteristics calculated from resting state, eyes-closed electroencephalography (EEG) recordings. EEG data was collected from 59 individuals as part of their baseline assessment in the Longitudinal Adolescent Brain Study (LABS) being undertaken in Queensland, Australia. Applying multiple unsupervised clustering algorithms to these EEG features, we identified well-separated subgroups of individuals. To study patterns of difference in cognitive function and mental health symptoms between core clusters, we applied Bayesian regression models to probabilistically identify differences in these measures between clusters.ResultsWe identified 5 core clusters which were associated with distinct subtypes of resting state EEG frequency content. EEG features that were influential in differentiating clusters included Individual Alpha Frequency, relative power in 4 Hz bands up to 16 Hz, and 95% Spectral Edge Frequency. Bayesian models demonstrated substantial differences in psychological distress, sleep quality and cognitive function between these clusters. By examining associations between neurophysiology and health measures across clusters, we have identified preliminary risk and protective profiles linked to EEG characteristics.ConclusionIn this work we have developed a flexible and scaleable pipeline to identify subgroups of individuals in early adolescence on the basis of resting state EEG activity. These findings provide new clues about neurophysiological subgroups of adolescents in the general population, and associated patterns of health and cognition that are not observed at the whole group level. This approach offers potential utility in clinical risk prediction for mental and cognitive health outcomes throughout adolescent development.
An Optimal Policy Model for Concurrent Uncertainty Estimation During Decision Making
Authors: Li Xiaodong , Su Ruixin , Chen Yilin , Yang Tianming 
Published: October 2021

AbstractWe often postpone or even avoid making decisions when we feel uncertain. Uncertainty estimation is not an afterthought of decision making but a dynamic process that accompanies decision making in parallel and affects decision making. To study concurrent uncertainty estimation during decision making, we adapted the classic random-dots motion direction discrimination task to allow a reaction-time measure of uncertainty responses. Subjects were asked to judge whether a patch of random dots was moving left or right. In addition, they could seek assistance by choosing to look at a second stimulus that had the same direction but high coherence any time during the task. The task allows us to measure the reaction time of both the perceptual decisions and the uncertainty responses. The subjects were more likely to choose the uncertainty response when the motion coherence was low, while their reaction times of the uncertainty responses showed individual variations. To account for the subjects’ behavior, we created an optimal policy decision model in which decisions are based on the value functions computed from the accumulated evidence using a drift-diffusion process. Model simulations captured key features of the subjects’ choices, reaction times, and proportions of uncertainty responses. Varying model parameters explained individual variations in the subjects and the correlations between decision accuracy, proportions of uncertainty responses, and reaction times at the individual level. Our model links perceptual decisions and value-based decisions and indicates that concurrent uncertainty estimation may be based on comparisons between values of uncertainty responses and perceptual decisions, both of which may be derived from the same evidence accumulation process during decision making. It provides a theoretical framework for future investigations, including the ones that aim at the underlying neural mechanism.
Coral niche construction: coral recruitment increases along a coral-built structural complexity gradient
Authors: Brambilla Viviana , Baird Andrew H. , Barbosa Miguel , Dehnert Inga , Madin Joshua T. , Peddie Clare , Dornelas Maria A. 
Published: October 2021

AbstractNiche construction is the process through which organisms modify environmental states in ways favourable to their own fitness. Here, we test experimentally whether scleractinian corals can be considered niche constructors. In particular, we demonstrate a positive feedback involved in corals building structures which facilitate recruitment. Coral larval recruitment is a key process for coral reef persistence. Larvae require low flow conditions to settle from the plankton, and hence the presence of colony structures that can break the flow is expected to facilitate coral recruitment. Here, we show an increase in settler presence on artificial tiles deployed in the field along a gradient of coral-built structural complexity. Structural complexity had a positive effect on settlement, with an increase of 15,71% of settler presence probability along the range of structural complexity considered. This result provides evidence that coral built structural complexity creates conditions that facilitate coral settlement, while demonstrating that corals meet the criteria for ecological niche construction.
Short-term plasticity in the visual thalamus
Authors: Kurzawski Jan W. , Lunghi Claudia , Biagi Laura , Tosetti Michela , Morrone Maria Concetta , Binda Paola 
Published: October 2021

ABSTRACTWhile there is evidence that the visual cortex retains a potential for plasticity in adulthood, less is known about the subcortical stages of visual processing. Here we asked whether short-term ocular dominance plasticity affects the visual thalamus. We addressed this question in normally sighted adult humans, using ultra-high field (7T) magnetic resonance imaging combined with the paradigm of short-term monocular deprivation. With this approach, we previously demonstrated transient shifts of perceptual eye dominance and ocular dominance in visual cortex (Binda et al., 2018). Here we report evidence for short-term plasticity in the ventral division of the pulvinar (vPulv), where the deprived eye representation was enhanced over the non-deprived eye. This pulvinar plasticity effect was similar as previously seen in visual cortex and it was correlated with the ocular dominance shift measured behaviorally. In contrast, there was no short-term plasticity effect in Lateral Geniculate Nucleus (LGN), where results were reliably different from vPulv, despite their spatial proximity. We conclude that the visual thalamus retains potential for short-term plasticity in adulthood; the plasticity effect differs across thalamic subregions, possibly reflecting differences in their cortical connectivity.
A live yeast supplementation to gestating ewes improves bioactive molecules composition in colostrum with no impact on its bacterial composition and beneficially affects immune status of the offspring
Authors: Dunière Lysiane , Renaud Justin B , Steele Michael A , Achard Caroline S , Forano Evelyne , Chaucheyras-Durand Frédérique 
Published: October 2021

AbstractColostrum quality is of paramount importance in the management of optimal ruminant growth and infectious disease prevention in early life. Live yeast supplementation effect during the last month of gestation was evaluated on ewes’ colostrum composition. Two groups of ewes (n=14) carrying twin lambs were constituted and twins were separated into groups (mothered or artificially-fed) 12h after birth. Nutrient, oligosaccharides (OS), IgG and lactoferrin concentrations were measured over 72h after lambing, and bacterial community was described in colostrum collected at parturition (T0). Immune passive transfer was evaluated through IgG measurement in lamb serum. In both groups, colostral nutrient, OS concentrations and IgG concentrations in colostrum and lamb serum decreased over time, (p < 0.01) except for lactose, which slightly increased (p < 0.001) and lactoferrin which remained stable. Bacterial population was stable over time with high relative abundances of Aerococcaceae, Corynebacteriaceae, Moraxellaceae and Staphylococcaceae in T0-colostrum. No effect of supplementation was observed in nutrient and lactoferrin concentrations. In supplemented ewes, colostral IgG level was higher at T0 and a higher level of serum IgG was observed in lambs born from supplemented mothers and artificially-fed, while no effect of supplementation was observed in the mothered lambs groups. Using a metabolomic approach, we showed that supplementation affected OS composition with significantly higher levels of colostral Neu-5Gc compounds up to 5h after birth. No effect of supplementation was observed on bacterial composition. Our data suggest that live yeast supplementation offsets the negative impact of early separation and incomplete colostrum feeding in neonate lambs.Graphical abstract
In vivomRNA delivery to virus-specific T cells by light-induced ligand exchange of MHC class I antigen-presenting nanoparticles
Authors: Su Fang-Yi , Zhao Qingyang , Dahotre Shreyas N. , Gamboa Lena , Bawage Swapnil Subhash , Silva Trenkle Aaron D. , Zamat Ali , Phuengkham Hathaichanok , Ahmed Rafi , Santangelo Philip J. , Kwong Gabriel A. 
Published: October 2021

AbstractSimultaneous delivery of mRNA to multiple populations of antigen (Ag)-specific CD8+T cells is challenging given the diversity of peptide epitopes and polymorphism of class I major histocompatibility complexes (MHCI). We developed Ag-presenting nanoparticles (APNs) for mRNA delivery using pMHCI molecules that were refolded with photocleavable peptides to allow rapid ligand exchange by UV light and site-specifically conjugated with a lipid tail for post-insertion into preformed mRNA lipid nanoparticles. Across different TCR transgenic mouse models (P14, OT-1, Pmel), UV-exchanged APNs bound and transfected their cognate Ag-specific CD8+T cells equivalent to APNs produced using conventionally refolded pMHCI molecules. In mice infected with PR8 influenza, multiplexed delivery of UV-exchanged APNs against three immunodominant epitopes led to ~50% transfection of a VHH mRNA reporter in cognate Ag-specific CD8+ T cells. Our data shows that UV-mediated peptide exchange can be used to rapidly produce APNs for mRNA delivery to multiple populations of Ag-specific T cellsin vivo.TeaserLight-induced rapid production of antigen-presenting nanoparticles for mRNA delivery to multiple virus-specific T cell populations.
Identification of antineoplastic agents for oral squamous cell carcinoma: an integrated bioinformatics approach using differential gene expression and network biology
Authors: Usman Abdussalam , Khan Faisal F. 
Published: October 2021

AbstractOral squamous cell carcinoma (OSCC) is the most common malignant epithelial neoplasm and anatomical subtype of head and neck squamous cell carcinoma (HNSCC) with an average 5-year survival rate of less than 50%. To improve the survival rate of OSCC, the discovery of novel anti-cancer drugs is urgently needed. In the present study, we performed metanalysis of 5 gene expression datasets (GSE23558, GSE25099, GSE30784, GSE37991 and TCGA-OSCC) that resulted in 1851 statistically significant DEGs in OSCC. The DEGs were involved in key biological pathways that drive the progression of OSCC. A comprehensive protein-protein interaction (PPI) network was constructed from the DEGs and the top protein clusters (modules) were extracted in Cytoscape. The DEGs from the top modules were searched for antineoplastic agents using L1000CDS2 server. The search resulted in a total of 37 perturbing agents from which 12 well-characterized antineoplastic agents were selected. The selected 12 antineoplastic agents namely Teniposide, Palbociclib, Etoposide, Fedratinib, Tivozanib, Afatinib, Vemurafenib, Mitoxantrone, Idamycin, Canertinib, Dovitinib and Selumetinib. These drugs showed interactions with the over expressed hub genes that regulate cellular proliferation and growth in OSCC progression. These identified antineoplastic agents are candidates for their potential role in treating OSCC.
Theβ-amylase7gene inZea maysencodes a protein with structural and catalytic properties similar to Arabidopsis BAM2
Authors: Ravenburg Claire M. , Riney McKayla B. , Monroe Jonathan D. , Berndsen Christopher E. 
Published: October 2021

AbstractStarch accumulates in the plastids of green plant tissue during the day to provide carbon for metabolism at night. Starch hydrolysis is catalyzed by members of the β-amylase (BAM) family, which inArabidopsis thaliana(At), includes nine structurally and functionally diverse members. One of these enzymes, AtBAM2, is a plastid-localized enzyme that is unique among characterized β-amylases since it is tetrameric and exhibits sigmoidal kinetics. Sequence alignments show that the BAM domains of AtBAM7, a catalytically inactive, nuclear-localized transcription factor with an N-terminal DNA binding domain, and AtBAM2 are more closely related to each other than they are to any other AtBAM. SinceBAM2is found in more ancient lineages, it was hypothesized thatBAM7evolved fromBAM2. However, analysis of the genomes of 48 flowering plants revealed 12 species that appear to have aBAM7gene but lack aBAM2gene. Upon closer inspection, these BAM7 proteins have a greater percent identity to AtBAM2 than to AtBAM7, and they share all of the AtBAM2 functional residues thatBAM7proteins normally lack. We hypothesize that these genes may encode a BAM2-like protein although they are currently annotated as BAM7-like genes. To test this hypothesis, we designed a cDNA of the short form of corn BAM7 (ZmBAM7-S) for expression inE. coli. Small Angle X-Ray Scattering data indicate that ZmBAM7-S has a tetrameric solution structure more similar to that of AtBAM2 than AtBAM1. In addition, partially purified ZmBAM7-S is catalytically active and exhibits sigmoidal kinetics. Together these data suggest that someBAM7genes may encode a functional BAM2. Exploring and understanding β-amylase gene structure could have impacts on the current annotation of genes.
On the brain networks organization of individuals with high versus average fluid intelligence: a combined DTI and MEG study
Authors: Bruzzone S.E.P. , Lumaca M. , Brattico E. , Vuust P. , Kringelbach M.L , Bonetti L. 
Published: October 2021

ABSTRACTThe neural underpinning of human fluid intelligence (Gf) has gathered a large interest in the scientific community. Nonetheless, previous research did not provide a full understanding of such intriguing topic. Here, we studied the structural (from diffusion tensor imaging, DTI) and functional (from magnetoencephalography (MEG) resting state) connectivity in individuals with high versus average Gf scores. Our findings showed greater values in the brain areas degree distribution and higher proportion of long-range anatomical connections for high versus average Gfs. Further, the two groups presented different community structures, highlighting the structural and functional integration of the cingulate within frontal subnetworks of the brain in high Gfs. These results were consistently observed for structural connectivity and functional connectivity of delta, theta and alpha. Notably, gamma presented an opposite pattern, showing more segregation and lower degree distribution and connectivity in high versus average Gfs. Our study confirmed and expanded previous perspectives and knowledge on the “small-worldness” of the brain. Further, it complemented the widely investigated structural brain network of highly intelligent individuals with analyses on fast-scale functional networks in five frequency bands, highlighting key differences in the integration and segregation of information flow between slow and fast oscillations in groups with different Gf.
Brain Functional Connectome Defines a Transdiagnostic Dimension Shared by Cognitive Dysfunction and Psychopathology in Preadolescents
Authors: Xiao Xiang , Hammond Christopher , Salmeron Betty Jo , Gu Hong , Zhai Tianye , Nguyen Hieu , Lu Hanbing , Ross Thomas J , Yang Yihong 
Published: October 2021

AbstractBackgroundCognitive dysfunction and high-order psychopathologic dimensions are two main classes of transdiagnostic factors related to psychiatric disorders. They may link to common or distinct core brain networks underlying developmental risk of psychiatric disorders.MethodThe current study is a longitudinal investigation with 11,875 youths aged 9-to 10-years-old at study onset, from the Adolescent Brain Cognitive Development study. A machine-learning approach based on canonical correlation analysis was used to identify latent dimensional associations of the resting-state functional connectome with multi-domain behavioral assessments of cognitive functions and psychopathological problems. For the latent rsFC factor showing a robust behavioral association, its ability to predict psychiatric disorders was assessed using two-year follow-up data and its genetic association was evaluated using twin data from the same cohort.ResultA latent functional connectome pattern was identified that showed a strong and generalizable association with the multi-domain behavioral assessments (5-fold cross validation: ρ = 0.68~0.73, for the training set (N = 5096); ρ = 0.56 ~ 0.58, for the test set (N = 1476)). This functional connectome pattern was highly heritable (h2= 74.42%, 95% CI: 56.76%-85.42%), exhibited a dose-response relationship with cumulative number of psychiatric disorders assessed concurrently and 2-years post-MRI-scan, and predicted the transition of diagnosis across disorders over the 2-year follow-up period.ConclusionThese findings provide preliminary evidence for a transdiagnostic connectome-based measure that underlies individual differences in developing psychiatric disorders in early adolescence.
The Respiratory Resistance Sensitivity Task: An Automated Method for Quantifying Respiratory Interoception and Metacognition
Authors: Nikolova Niia , Harrison Olivia , Toohey Sophie , Brændholt Malthe , Legrand Nicolas , Correa Camile , Vejlø Melina , Jensen Martin Snejbjerg , Fardo Francesca , Allen Micah 
Published: October 2021

AbstractThe ability to sense, monitor, and control respiration - e.g., respiratory interoception (henceforth, respiroception) is a core homeostatic ability. Beyond the regulation of gas exchange, enhanced awareness of respiratory sensations is directly related to psychiatric symptoms such as panic and anxiety. Indeed, chronic breathlessness (dyspnea) is associated with a fourfold increase in the risk of developing depression and anxiety, and the regulation of the breath is a key aspect of many mindfulness-based approaches to the treatment of mental illness. Physiologically speaking, the ability to accurately monitor respiratory sensations is important for optimizing cardiorespiratory function during athletic exertion, and can be a key indicator of illness. Given the important role of respiroception in mental and physical health, it is unsurprising that there is increased interest in the quantification of respiratory psychophysiology across different perceptual and metacognitive levels of the psychological hierarchy. Compared to other more popular modalities of interoception, such as in the cardiac domain, there are relatively few methods available for measuring aspects of respiroception. Existing inspiratory loading tasks are difficult to administer and frequently require expensive medical equipment, or offer poor granularity in their quantification of respiratory-related perceptual ability. To facilitate the study of respiroception, we here present a new, fully automated and computer-controlled apparatus and psychophysiological method, which can flexibly and easily measure respiratory-related interoceptive sensitivity, bias and metacognition, in as little as 30 minutes of testing, using easy to make 3D printable parts.
Diet and Domestication Drive Evolution of the Gut Holobiome
Authors: Ramanan Vivek , Mechery Shanti , Sarkar Indra Neil 
Published: October 2021

SummaryThe host microbiome encompasses all microorganisms of a host. Host and microbiome coevolution in the gut result in differing microbial compositions, functionality, and host diet [1]. Host diet modulates what macromolecules are used for gut microbial metabolism, which can determine digestion, health, and behavior [2, 3]. Microbial composition across animals provides data on how microbiomes segregate between species and diets [4]. Here we show that microbiome data from GenBank can model host evolution, providing a “holobiome” insight to the important roles of diet and domestication. The main findings of this study in respect to microbial composition among species were: (1) herbivores are more similar than hosts with other diets; (2) domesticated species are more similar than wild relatives; and (3) humans are distinct from primates. Microbial composition between diets indicates a difference in functionality, where protein and fiber degradation are seen more in carnivores and herbivores respectively. Additionally, herbivores show the most microbial diversity among the diets. Finally, this analysis informs us of gaps in current microbiome data collection, which is biased toward pathogens. Thus, the host-microbiome relationship depicts a complex web of microbial functionality, composition, and diet that impact coevolution.