Article
Multidisciplinary Sciences
Bertrand Jern Han Wong, Weijia Kong, Limsoon Wong, Wilson Wen Bin Goh
Summary: Despite technological advances in proteomics, incomplete coverage and inconsistency issues persist. Network-based approaches, such as Functional Class Scoring (FCS), can help resolve these issues by using protein complex information to recover missing proteins.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Saad M. Darwish, Raad A. Ali, Adel A. Elzoghabi
Summary: Most educators agree that essays are the best way to evaluate students' understanding, guide their studies, and track their growth as learners. Manually grading student essays is a tedious but necessary part of the learning process. Automated Essay Scoring (AES) provides a feasible approach to completing this process.
APPLIED SCIENCES-BASEL
(2023)
Article
Biochemistry & Molecular Biology
Marcio L. Acencio, Miguel Vazquez, Konika Chawla, Astrid Laegreid, Martin Kuiper
Summary: Prior knowledge of transcription factors is crucial for understanding transcriptional regulation. TFCheckpoint 2.0 is an integrated resource that provides an easy and versatile cross-referencing system for viewing and downloading collections of transcription factors.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Evangelos Karatzas, Fotis A. Baltoumas, Eleni Aplakidou, Panagiota Kontou, Panos Stathopoulos, Leonidas Stefanis, Pantelis G. Bagos, Georgios A. Pavlopoulos
Summary: This article introduces Flame (v2.0), a web tool that combines and visualizes results from popular functional enrichment applications. Flame utilizes aGOtool, g: Profiler, WebGestalt, and Enrichr pipelines to present their outputs separately or in combination. It offers interactive plots for intuitive representations and easier interpretation.
Article
Microbiology
Benjamin S. Beresford-Jones, Samuel C. Forster, Mark D. Stares, George Notley, Elisa Viciani, Hilary P. Browne, Daniel J. Boehmler, Amelia T. Soderholm, Nitin Kumar, Kevin Vervier, Justin R. Cross, Alexandre Almeida, Trevor D. Lawley, Virginia A. Pedicord
Summary: This study constructed the Mouse Gastrointestinal Bacteria Catalogue (MGBC) to identify functionally equivalent taxa between the gut microbiotas of humans and mice. It also provided a publicly deposited collection of bacterial isolates to facilitate experimental investigation of individual commensal bacteria functions.
CELL HOST & MICROBE
(2022)
Article
Biochemistry & Molecular Biology
Catherine M. Farrell, Tamara Goldfarb, Sanjida H. Rangwala, Alexander Astashyn, Olga D. Ermolaeva, Vichet Hem, Kenneth S. Katz, Vamsi K. Kodali, Frank Ludwig, Craig L. Wallin, Kim D. Pruitt, Terence D. Murphy
Summary: RefSeq Functional Elements (RefSeqFEs) are experimentally validated human and mouse nongenic elements provided by NCBI, offering rich functional details and transparent experimental evidence, with multiple uses for basic functional discovery, bioinformatics studies, and genetic variant interpretation.
Article
Chemistry, Analytical
Xiaojun Sun, Huan Sun, Xian Han, Ping-Chung Chen, Yun Jiao, Zhiping Wu, Xue Zhang, Zhen Wang, Mingming Niu, Kaiwen Yu, Danting Liu, Kaushik Kumar Dey, Ariana Mancieri, Yingxue Fu, Ji-Hoon Cho, Yuxin Li, Suresh Poudel, Tess C. Branon, Alice Y. Ting, Junmin Peng
Summary: Proteome profiling is a powerful tool in biological and biomedical studies. In this study, a proximity labeling strategy using TurboID was presented for single-cell-type proteomics of mouse brain. This approach allows labeling of specific cell-type proteomes without the need for cell isolation and includes steps for protein purification and quantitative analysis.
ANALYTICAL CHEMISTRY
(2022)
Article
Computer Science, Interdisciplinary Applications
Wenwen Li, Sizhe Wang, Sheng Wu, Zhining Gu, Yuanyuan Tian
Summary: Knowledge graph is a cutting-edge technology for integrating diverse datasets to address scientific questions. This paper evaluates popular semantic data repositories and compares their performance in managing and supporting spatial queries. The results show that Virtuoso performs the best in both non-spatial and spatial-semantic queries, while Ontop is a good solution for spatial and complex queries.
COMPUTERS ENVIRONMENT AND URBAN SYSTEMS
(2022)
Article
Biochemistry & Molecular Biology
Xiaoli Yu, Jiayin Zhou, Wen Song, Mengzhao Xu, Qiang He, Yisheng Peng, Yun Tian, Cheng Wang, Longfei Shu, Shanquan Wang, Qingyun Yan, Jihua Liu, Qichao Tu, Zhili He
Summary: Shotgun metagenome sequencing has opened up a new way to deepen our understanding of sulfur cycling microbial communities, but accurate analysis of these microbial communities remains technically challenging due to low coverage and inaccurate definition of sulfur cycling gene families in public databases.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Multidisciplinary Sciences
Jerome Ribot, Rachel Breton, Charles-Felix Calvo, Julien Moulard, Pascal Ezan, Jonathan Zapata, Kevin Samama, Matthieu Moreau, Alexis-Pierre Bemelmans, Valentin Sabatet, Florent Dingli, Damarys Loew, Chantal Milleret, Pierre Billuart, Glenn Dallerac, Nathalie Rouach
Summary: This study found that astrocytes control critical-period closure in the mouse visual cortex, involving regulation of the extracellular matrix to promote interneuron maturation. Unconventional astrocyte connexin signaling inhibits the expression of extracellular matrix-degrading enzyme MMP9 through a pathway involving RhoA-GTPase activation. Astrocytes are not only involved in influencing the activity of single synapses, but are also key elements in the experience-dependent wiring of brain circuits.
Article
Computer Science, Artificial Intelligence
Liang Hong, Haoshuai Xu, Xiaoyue Shi
Summary: This study proposes a reasoning-reuse method to construct a Brain Areas-Autism (BAA) ontology, facilitating the intelligent and efficient knowledge discovery and exploration in the domain research. The method involves ontology design by domain experts, knowledge extraction from scientific literature using NLP techniques, rule-based reasoning for ontology expansion, and qualitative and quantitative analysis for evaluation. The constructed BAA ontology with 929 entities and 1129 relationships enables the inference of 130 potential relationships between brain areas and autism.
INTERNATIONAL JOURNAL OF COMPUTATIONAL INTELLIGENCE SYSTEMS
(2021)
Article
Neurosciences
Milton H. Hamblin, Rabi Murad, Jun Yin, Gustavo Vallim, Jean-Pyo Lee
Summary: The study demonstrated the therapeutic potential of hNSC transplantation in aged mice post-stroke, showing significant reduction in infarct size and attenuation of proinflammatory factors and matrix metalloproteases induction. RNA sequencing analysis revealed differentially expressed genes and molecular pathways induced by hNSCs, providing insights for developing new therapies for early-stage stroke injury.
EXPERIMENTAL NEUROLOGY
(2022)
Article
Biology
Hind Baba Aissa, Romain W. Sala, Elena Laura Georgescu Margarint, Jimena Laura Frontera, Andres Pablo Varani, Fabien Menardy, Assunta Pelosi, Denis Herve, Clement Lena, Daniela Popa
Summary: The study found that in the DYT25 dystonia model, the excitability of the cerebello-thalamic pathways increased in the presymptomatic state, and asymptomatic mice after the first dystonic episode exhibited higher excitability, which persisted after cerebellar theta-burst stimulation. Stimulation administered during symptomatic states reduced cerebello-thalamic excitability and alleviated dystonic symptoms.
Review
Health Care Sciences & Services
Catherine Paquet, Jocelyne Whitehead, Rishabh Shah, Alayne Mary Adams, Damion Dooley, R. Nathan Spreng, Anna-Liisa Aunio, Laurette Dube
Summary: Social prescription programs aim to link primary care patients with community resources to improve their well-being. This study integrates scientific evidence with on-the-ground knowledge to develop an extensive list of intervention terms and keywords related to reducing social isolation and loneliness in older adults. The findings highlight effective intervention types and the need for efficient identification and structuring of resources to facilitate referrals for older adults.
JOURNAL OF MEDICAL INTERNET RESEARCH
(2023)
Article
Biology
Angela R. Wild, Peter W. Hogg, Stephane Flibotte, Glory G. Nasseri, Rocio B. Hollman, Danya Abazari, Kurt Haas, Shernaz X. Bamji
Summary: Protein S-palmitoylation is a reversible post-translational lipid modification that plays a critical role in neuronal development and plasticity. This study analyzed the expression data of proteins involved in regulating S-palmitoylation in the mouse nervous system and developed a web-tool to visualize their expression patterns. The researchers found region and cell-type specific expression patterns that provide insights into the function of palmitoylating and de-palmitoylating enzymes in the brain and neurological disorders. ZDHHC expression patterns were also utilized to predict and validate palmitoylating enzyme-substrate interactions.
Article
Neurosciences
Nanyan Zhang, Peng Zhong, Seung Min Shin, Jacob Metallo, Eric Danielson, Christopher M. Olsen, Qing-song Liu, Sang H. Lee
JOURNAL OF NEUROSCIENCE
(2015)
Article
Neurosciences
Ling Zhong, Joshua Brown, Audra Kramer, Kanwardeep Kaleka, Amber Petersen, Jamie N. Krueger, Matthew Florence, Matthew J. Muelbl, Michelle Battle, Geoffrey G. Murphy, Christopher M. Olsen, Nashaat Z. Gerges
JOURNAL OF NEUROSCIENCE
(2015)
Article
Engineering, Biomedical
Brian D. Stemper, Alok S. Shah, Rachel Chiariello, Christopher M. Olsen, Matthew D. Budde, Aleksandra Glavaski-Joksimovic, Michael McCrea, Shekar N. Kurpad, Frank A. Pintar
ANNALS OF BIOMEDICAL ENGINEERING
(2016)
Article
Neurosciences
Matthew J. Muelbl, Natalie N. Nawarawong, Patrick T. Clancy, Catherine E. Nettesheim, Yi Wei Lim, Christopher M. Olsen
PSYCHOPHARMACOLOGY
(2016)
Article
Clinical Neurology
Brian D. Stemper, Alok S. Shah, Matthew D. Budde, Christopher M. Olsen, Aleksandra Glavaski-Joksimovic, Shekar N. Kurpad, Michael McCrea, Frank A. Pintar
FRONTIERS IN NEUROLOGY
(2016)
Article
Biochemistry & Molecular Biology
Alexander I. Helfand, Christopher M. Olsen, Cecilia J. Hillard
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2017)
Article
Multidisciplinary Sciences
Matthew J. Muelbl, Megan L. Slaker, Alok S. Shah, Natalie N. Nawarawong, Clayton H. Gerndt, Matthew D. Budde, Brian D. Stemper, Christopher M. Olsen
SCIENTIFIC REPORTS
(2018)
Article
Engineering, Biomedical
Brian D. Stemper, Alok S. Shah, Frank A. Pintar, Michael McCrea, Shekar N. Kurpad, Aleksandra Glavaski-Joksimovic, Christopher Olsen, Matthew D. Budde
ANNALS OF BIOMEDICAL ENGINEERING
(2015)
Article
Neurosciences
Xiaojie Liu, Yong Liu, Peng Zhong, Brianna Wilkinson, Jinshun Qi, Christopher M. Olsen, K. Ulrich Bayer, Qing-song Liu
NEUROPSYCHOPHARMACOLOGY
(2014)
Article
Multidisciplinary Sciences
Yi Wei Lim, Nathan P. Meyer, Alok S. Shah, Matthew D. Budde, Brian D. Stemper, Christopher M. Olsen
Article
Neurosciences
Natalie N. Nawarawong, Megan Slaker, Matt Muelbl, Alok S. Shah, Rachel Chiariello, Lindsay D. Nelson, Matthew D. Budde, Brian D. Stemper, Christopher M. Olsen
EUROPEAN JOURNAL OF NEUROSCIENCE
(2019)
Review
Neurosciences
Christopher M. Olsen, John D. Corrigan
Summary: There is a high co-occurrence of risky substance use among adults with traumatic brain injury (TBI), although it is unknown if the neurologic sequelae of TBI can promote this behavior. This review provides an overview of key studies and proposes plausible mechanisms by which TBI could increase risky substance use. Factors that may limit detection of this relationship are also discussed.
BIOLOGICAL PSYCHIATRY
(2022)
Article
Biochemistry & Molecular Biology
Matthew J. Muelbl, Breanna Glaeser, Alok S. Shah, Rachel Chiariello, Natalie N. Nawarawong, Brian D. Stemper, Matthew D. Budde, Christopher M. Olsen
Summary: This study found interactive effects of traumatic brain injury (TBI) and oxycodone exposure on structural and functional neuroimaging measures, as well as correlational effects with drug seeking behavior. These findings suggest that TBI and opioid exposure may contribute to neuroadaptation associated with addiction liability.
Article
Behavioral Sciences
Hershel Raff, Breanna L. Glaeser, Aniko Szabo, Christopher M. Olsen, Carol A. Everson
Summary: Chronic sleep restriction alters the HPA axis diurnal rhythm and sexually dimorphic response to acute stress during opioid abstinence. Male rats show an increase in plasma ACTH and corticosterone in the morning during abstinence, and sleep restriction attenuates the stress response in male rats. Sleep restriction leads to an increase in hypothalamic PVN AVP mRNA and plasma copeptin in male rats during opioid abstinence.
STRESS-THE INTERNATIONAL JOURNAL ON THE BIOLOGY OF STRESS
(2023)
Article
Psychology, Biological
Christopher M. Olsen, Breanna L. Glaeser, Aniko Szabo, Hershel Raff, Carol A. Everson
Summary: Sleep restriction during abstinence did not significantly affect opioid seeking, while specific phenotypes and sex were associated with drug seeking behavior.
PHYSIOLOGY & BEHAVIOR
(2023)