bluuebunny/crossref_metadata_2025_split huggingface dataset:
spARC recovers human glioma spatial signaling networks with graph filtering
Authors: Kuchroo Manik , Miyagishima Danielle F. , Steach Holly R. , Godavarthi Abhinav , Takeo Yutaka , Duy Phan Q. , Barak Tanyeri , Erson-Omay E. Zeynep , Youlten Scott , Mishra-Gorur Ketu , Moliterno Jennifer , McGuone Declan , Günel Murat , Krishnaswamy Smita 
Published: August 2022

AbstractBiological networks operate within architectural frameworks that influence the state and function of cells through niche-specific factors such as exposure to nutrients and metabolites, soluble signaling molecules, and direct cognate cell-cell communication. Spatial omics technologies incorporate environmental information into the study of biological systems, where the spatial coordinates of cells may directly or indirectly encode these micro-anatomical features. However, they suffer from technical artifacts, such as dropout, that impede biological discovery. Current methods that attempt to correct for this fail to adequately integrate highly informative spatial information when recovering gene expression and modelling cell-cell dynamicsin situ. To address this oversight, we developed spatial Affinity-graph Recovery of Counts (spARC), a data diffusion-based filtration method that shares information between neighboring cells in tissue and related cells in expression space, to recover gene dynamics and simulate signalling interactions in spatial transcriptomics data. Following validation, we applied spARC to 10 IDH-mutant surgically resected human gliomas across WHO grades II-IV in order to study signaling networks across disease progression. This analysis revealed co-expressed genes that border the interface between tumor and tumor-infiltrated brain, allowing us to characterize global and local structure of glioma. By simulating paracrine signalingin silico, we identified an Osteopontin-CD44 interaction enriched in grade IV relative to grade II and grade III astrocytomas, and validated the clinical relevance of this signaling axis using TCGA.
Atypical speech production of multisyllabic words and phrases by children with developmental dyslexia
Authors: Keshavarzi Mahmoud , Liberto Giovanni M. Di , Gabrielczyk Fiona , Wilson Angela , Macfarlane Annabel , Goswami Usha 
Published: August 2022

AbstractThe prevalent ‘core phonological deficit’ model of dyslexia proposes that the reading and spelling difficulties characterizing affected children stem from prior developmental difficulties in processing speech sound structure, for example perceiving and identifying syllable stress patterns, syllables, rhymes and phonemes. Yet spoken word production appears normal. This suggests an unexpected disconnect between speech input and speech output processes. Here we investigated the output side of this disconnect from a speech rhythm perspective by measuring the speech amplitude envelope (AE) of multisyllabic spoken phrases. The speech AE contains crucial information regarding stress patterns, speech rate, tonal contrasts and intonational information. We created a novel computerized speech copying task in which participants copied aloud familiar spoken targets like “Aladdin”. Seventy-five children with and without dyslexia were tested, some of whom were also receiving an oral intervention designed to enhance multi-syllabic processing. Similarity of the child’s productions to the target AE was computed using correlation and mutual information metrics. Similarity of pitch contour, another acoustic cue to speech rhythm, was used for control analyses. Children with dyslexia were significantly worse at producing the multi-syllabic targets as indexed by both similarity metrics for computing the AE. However, children with dyslexia were not different from control children in producing pitch contours. Accordingly, the spoken production of multisyllabic phrases by children with dyslexia is atypical regarding the AE. Children with dyslexia may not appear to listeners to exhibit speech production difficulties because their pitch contours are intact.Research HighlightsSpeech production of syllable stress patterns is atypical in children with dyslexia.Children with dyslexia are significantly worse at producing the amplitude envelope of multi-syllabic targets compared to both age-matched and reading-level-matched control children.No group differences were found for pitch contour production between children with dyslexia and age-matched control children.It may be difficult to detect speech output problems in dyslexia as pitch contours are relatively accurate.
Interpretable Chirality-Aware Graph Neural Network for Quantitative Structure Activity Relationship Modeling in Drug Discovery
Authors: Liu Yunchao “Lance” , Wang Yu , Vu Oanh , Moretti Rocco , Bodenheimer Bobby , Meiler Jens , Derr Tyler 
Published: August 2022

AbstractIn computer-aided drug discovery, quantitative structure activity relation models are trained to predict biological activity from chemical structure. Despite the recent success of applying graph neural network to this task, important chemical information such as molecular chirality is ignored. To fill this crucial gap, we proposeMolecular-KernelGraphNeuralNetwork (MolKGNN) for molecular representation learning, which features SE(3)-/conformation invariance, chiralityawareness, and interpretability. For our MolKGNN, we first design a molecular graph convolution to capture the chemical pattern by comparing the atom’s similarity with the learnable molecular kernels. Furthermore, we propagate the similarity score to capture the higher-order chemical pattern. To assess the method, we conduct a comprehensive evaluation with nine well-curated datasets spanning numerous important drug targets that feature realistic high class imbalance and it demonstrates the superiority of MolKGNN over other GNNs in CADD. Meanwhile, the learned kernels identify patterns that agree with domain knowledge, confirming the pragmatic interpretability of this approach. Our codes are publicly available athttps://github.com/meilerlab/MolKGNN.
Stac1 Regulates Sensory Stimulus Induced Escape Locomotion
Authors: Linsley Jeremy W. , Perez Nadia , Hsu I-Uen , Yang Yuyang , Jasti Naveen , Waalkes Matthew , Horstick Eric J. , Kuwada John Y. 
Published: August 2022

ABSTRACTThe stac family of genes are expressed by several cell types including neurons and muscles in a wide variety of animals. In vertebrates, stac3 encodes an adaptor protein specifically expressed by skeletal muscle that regulates L-type calcium channels (CaChs) and excitation-contraction coupling. The function of Stac proteins expressed by neurons in the vertebrate CNS, however, is unclear. To better understand neuronal Stac proteins, we identified the stac1 gene in zebrafish. stac1 is expressed selectively in the embryonic CNS including in Kolmer-Agduhr (KA) neurons, the cerebral fluid-contacting neurons (CSF-cNs) in the spinal cord. Previously CSF-cNs in the spinal cord were implicated in locomotion by zebrafish larvae. Thus, expression of stac1 by CSF-cNs and the regulation of CaChs by Stac3 suggest the hypothesis that Stac1 may be important for normal locomotion by zebrafish embryos. We tested to see if optogenetic activation of CSF-cNs was sufficient to induced swimming in embryos as it is in larvae. Indeed, optogenetic activation of CSF-cNs in embryos induced swimming in embryos. Next, we generated stac1-/- null embryos and found that both mechanosensory and noxious stimulus-induced swimming were decreased. We further found that zebrafish embryos respond more vigorously to tactile stimulation in the light compared to the dark. Interestingly, light enhancement of touch-induced swimming was eliminated in stac1 mutants. Thus, Stac1 regulates escape locomotion in zebrafish embryos perhaps by regulating the activity of CSF-cNs.SIGNIFICANCE STATEMENTThe stac genes are a small family of genes found in neurons and muscle in both vertebrates and invertebrates. Stac3 is a muscle protein that controls excitation-contraction coupling via regulation of L-type calcium channels and in humans a STAC3 mutation is responsible for a congenital myopathy. The function of neural Stac proteins, however, is unknown in vertebrates. The findings of this report show that neural stac1 is expressed by cerebral fluid-contacting neurons (CSF-cNs) in the spinal cord of zebrafish embryos and that it is necessary for normal sensory stimulus induced escape swimming. To our knowledge this is the first demonstration of a function for stac genes in neurons in the vertebrate nervous system.
Fan cells in lateral entorhinal cortex directly influence medial entorhinal cortex through synaptic connections in layer 1
Authors: Vandrey Brianna , Armstrong Jack , Brown Christina M. , Garden Derek L. F. , Nolan Matthew F. 
Published: August 2022

AbstractStandard models for spatial and episodic memory suggest that the lateral entorhinal cortex (LEC) and medial entorhinal cortex (MEC) send parallel independent inputs to the hippocampus, each carrying different types of information. Here, we evaluate the possibility that information is integrated between divisions of the entorhinal cortex prior to reaching the hippocampus. We demonstrate that fan cells in layer 2 (L2) of LEC that receive neocortical inputs, and that project to the hippocampal dentate gyrus, also send axon collaterals to layer 1 (L1) of the MEC. Activation of fan cell inputs evokes monosynaptic glutamatergic excitation of stellate and pyramidal cells in L2 of the MEC, typically followed by inhibition that contains fast and slow components mediated by GABAA and GABAB receptors, respectively. Fan cell inputs also directly activate interneurons in L1 and L2 of MEC, with synaptic connections from L1 interneurons accounting for slow feedforward inhibition of L2 principal cell populations. The relative strength of excitation and inhibition following fan cell activation differs substantially between neurons and is largely independent of anatomical location. Our results demonstrate that the LEC, in addition to directly influencing the hippocampus, can activate or inhibit major hippocampal inputs arising from the MEC. Thus, local circuits in the superficial MEC may combine spatial information with sensory and higher order signals from the LEC, providing a substrate for integration of ‘what’ and ‘where’ components of episodic memories.
The Origin of Cysteine and its Catabolism in Mammalian Tissues and Tumors
Authors: Yoon Sang Jun , Combs Joseph A. , Falzone Aimee , Prieto-Farigua Nicolas , Caldwell Samantha , Ackerman Hayley D. , Flores Elsa R. , DeNicola Gina M. 
Published: August 2022

SUMMARYCysteine plays critical roles in cellular biosynthesis, enzyme catalysis, and is an essential contributor to redox metabolism. While cultured cells are highly dependent on exogenous cystine for proliferation and survival, how diverse tissues obtain and use cysteine in vivo has not been characterized. We comprehensively interrogated cysteine metabolism in normal murine tissues and the cancer that arise from them using stable isotope 13C-serine and 13C-cystine tracing. We found that de novo cysteine synthesis was highest in normal liver and pancreas and absent in lung tissue. In tumors, cysteine synthesis was either inactive or downregulated during tumorigenesis. By contrast, cystine uptake and metabolism to downstream metabolites was a universal feature of normal tissues and tumors. Differences in cysteine catabolism were evident across tumor types, including glutathione synthesis. Thus, cystine is a major contributor to the cysteine pool in tumors and cysteine catabolic pathways are differentially active across tumor types.
Subclinical Atherosclerosis is Associated with Discrepancies in BAFF and APRIL Levels and Altered Breg Potential of Precursor-like Marginal Zone B-Cells in HIV Treated Individuals
Authors: Aranguren Matheus , Doyon-Laliberté Kim , El-Far Mohamed , Chartrand-Lefebvre Carl , Routy Jean-Pierre , Barril Jean Guy , Trottier Benoît , Tremblay Cécile , Durand Madeleine , Poudrier Johanne , Roger Michel ,   Canadian HIV and Aging Cohort Study
Published: August 2022

AbstractChronic inflammation persists in people living with HIV (PLHIV) despite antiretrovial therapy (ART), and is involved in their premature development of cardiovascular diseases (CVD) such as atherosclerosis. We have previously reported that an excess of “B-cell activating factor” (BAFF), an important molecule for the selection and activation of first line Marginal Zone (MZ) B-cell populations, is associated with deregulations of precursor-like MZ (MZp), whose potent B-cell regulatory (Breg) capacities are altered in PLHIV, early on and despite 1-2 years of ART. Based on these observations, and growing evidence that MZ populations are involved in atherosclerosis control, we designed a cross sectional study to explore the associations between BAFF and its analogue “A proliferation-inducing ligand” (APRIL) with subclinical CVD in long time treated individuals of the Canadian HIV and Aging Cohort Study (CHACS) imaging sub-study group. We also characterized the Breg profile of MZp from the blood of these individuals. Results were correlated with the total volume of atherosclerotic plaques (TPV) and with CVD risk factors and biomarkers. TPV was measured using cardiac computerised tomography angiography, and presence of CVD was defined as TPV > 0. We report that blood levels of BAFF are elevated and correlate positively with CVD and its risk factors in PLHIV from the CHACS, in contrast to APRIL levels, which correlate negatively with these factors. Expression levels of Breg markers such as NR4A3, CD39, CD73 and CD83 are significantly lower in PLHIV when compared to those of HIV-uninfected controls. In vitro experiments show that APRIL upregulates the expression of Breg markers by blood MZp from HIV-uninfected individuals, while this modulation is dampened by the addition of recombinant BAFF. Altogether, our observations suggest that strategies viewed to modulate levels of BAFF and/or APRIL could eventually represent a potential treatment target for CVD in PLHIV.
Band gap information extraction from materials science literature – a pilot study
Authors: Ghosh Satanu , Lu Kun 
Published: August 2022

PurposeThe purpose of this paper is to present a preliminary work on extracting band gap information of materials from academic papers. With increasing demand for renewable energy, band gap information will help material scientists design and implement novel photovoltaic (PV) cells.Design/methodology/approachThe authors collected 1.44 million titles and abstracts of scholarly articles related to materials science, and then filtered the collection to 11,939 articles that potentially contain relevant information about materials and their band gap values. ChemDataExtractor was extended to extract information about PV materials and their band gap information. Evaluation was performed on randomly sampled information records of 415 papers.FindingsThe findings of this study show that the current system is able to correctly extract information for 51.32% articles, with partially correct extraction for 36.62% articles and incorrect for 12.04%. The authors have also identified the errors belonging to three main categories pertaining to chemical entity identification, band gap information and interdependency resolution. Future work will focus on addressing these errors to improve the performance of the system.Originality/valueThe authors did not find any literature to date on band gap information extraction from academic text using automated methods. This work is unique and original. Band gap information is of importance to materials scientists in applications such as solar cells, light emitting diodes and laser diodes.
Construction and application of urban digital infrastructure—practice of “Urban Brain” in facing COVID-19 in Hangzhou, China
Authors: Yan Xiaoli , Li Tao 
Published: August 2022

PurposeThis paper aims to analyze Hangzhou Urban Brain in responding to COVID-19, including systematically sorting out the development mode, capabilities, composition and application of Urban Brain and exploring its role and effect. This paper tries to provide a reference for other cities' digital infrastructure construction through case analysis.Design/methodology/approachThe authors took Hangzhou Urban Brain as a typical case in urban digital infrastructure construction, and they conducted thorough research on its practice in facing COVID-19. The authors analyzed the key elements of Urban Brain, the application and the evaluation of Urban Brain through literature review, field investigation, questionnaire and interviews.FindingsHangzhou Urban Brain has been deeply applied in urban management and has a good foundation. Therefore, when the COVID-19 occurred, the Urban Brain played an important role. The detailed practices facing COVID-19 are mainly in five aspects: information collection and analysis, ensuring material supply by government–enterprise collaboration, using AI and Big Data to “Visualize” COVID-19, etc. Moreover, Urban Brain has won high evaluation. However, Hangzhou Urban Brain still has problems like data privacy and security, technical issues, etc.Originality/valueThis case study shows that Hangzhou's experience in Urban Brain construction is worthy of reference and promotion. Firstly, it can strengthen the understanding of digital infrastructure in responding to public health emergencies. Furthermore, it provides a reference for other urban governance worldwide by excavating the role and effect of digital infrastructure in preventing and controlling COVID-19. Thirdly, it explores how to improve the digital infrastructure construction to support public health challenges, which will help the cities grasp the actual value of data and make progress in this field. By this, it can provide references for cities in the world, especially in Asia to achieve sustainable city development.
Open innovation starts from home: the potentials of enterprise social media (ESM) in nurturing employee innovation
Authors: Abhari Kaveh , Zarei Mahsa , Parsons Mikay , Estell Pamela 
Published: August 2022

PurposeEnterprise social media (ESM) applications offer new opportunities for organizations to mobilize employees for open innovation, by promoting innovation beyond traditional R&D functions. Despite the popularity and success of these applications, current research has yet to fully explore the potential of ESM applications as a driver of employee-driven innovation, specifically through advancements in innovation culture. To fill this gap, this study proposes a theoretical framework that explains the role of ESM applications in facilitating employee innovation.Design/methodology/approach The authors administered a cross-sectional survey to collect data from professionals who use ESM applications regularly at work. Following a pilot study and instrument refinement, the authors conducted a field study to test measurement and the structural model by using the partial least square-structural equation modeling (PLS-SEM) method.FindingsThe findings of this study support the validity of the proposed theoretical model. First, the results confirmed the three antecedents of ESM use for innovation: perceived innovation possibilities enabled by ESM technology, the expected value of ESM use for innovation and organizational support for using ESM applications for innovation. Next, the results confirmed the importance of ESM use in encouraging individual innovation productivity in terms of product/service innovation, process innovation and social innovation. Finally, the results corroborated the mediating role of risk-taking and knowledge-sharing culture in the use of ESM to increase innovation productivity.Originality/valueThe findings presented here have implications for theory and practices that would concern fostering a supportive environment and building an organizational culture that promotes employees' innovation behavior (internal open innovation) by using social technologies.
Facilitating or inhibiting? The role of enterprise social media use in job performance
Authors: Shang Yufan , Pan Yan , Richards Malika 
Published: August 2022

PurposeOrganizations use enterprise social media (ESM) platforms to operate, function, and develop. However, the effectiveness of the use of ESM is inconclusive. This study aims to explore the mechanism and boundary conditions of the relationship between employee ESM use and job performance.Design/methodology/approachThis study uses a 2-wave survey design, with a final sample of 481 employees from a large automobile company.FindingsThe results indicate that ESM use is beneficial and detrimental to job performance. On the one hand, ESM use is positively related to work overload, decreasing job performance. On the other hand, ESM use is positively associated with informational support, increasing job performance. A mediation test revealed that both work overload and informational support mediate the relationship between ESM use and job performance. Furthermore, job autonomy weakens the positive relationship between ESM use and work overload, but strengthens the positive relationship between ESM use and informational support.Originality/valueThis study provides a more balanced view of how ESM use influences job performance by demonstrating the opposing mediating roles of work overload and informational support. Further, this study fills a research gap by considering job characteristics when examining the boundary conditions of ESM use. Third, this study validates the generalization of the job demands-resources model in social media research.
Leaders' advice networks over time: the role of beliefs and organizational learning during change implementation
Authors: Liou Yi-Hwa , Lee Yong-Shiuan , Chiang-Lin Tsung-Jui , Daly Alan J. 
Published: August 2022

PurposeEducational reform is a complex undertaking and the interactions between leaders as they go about a change are consequential for realizing desired outcomes. Advice relationships are one such interaction and can play a key role in driving knowledge transfer and development and as such are an important social capital asset supporting organizational change. Building on the growing scholarship around a social network approach to understanding educational leadership and systems change, the study draws from network concepts to examine advice relationships within a district-wide leadership team as the leaders engages a reform initiative, and what accounts for the development of these important relational ties.Design/methodology/approachQuantitative data were collected through an annual survey at six points over six years from the leadership team in one public school district in the Western United States, including perceptions of organizational learning, beliefs about reform, and reform-related advice relationships.FindingsUsing multilevel mixed modeling, findings reveal downward trends in leaders' advice-seeking and -receiving ties over time and that seeking and receiving advice is positively related to organizational learning, beliefs about reform impact, or beliefs about their efficacy in implementing the reform. However, views about reform-related resources are negatively associated with seeking and receiving advice ties over time.Originality/valueThis study contributes to the literature on the social side of change specifically related to leadership, reform, organizational learning, and leader beliefs about reform implementation. Further, the work offers practical implications for potential social infrastructure design for joint work.