Article
Neurosciences
Zachary F. Gerring, Jackson G. Thorp, Eric R. Gamazon, Eske M. Derks
Summary: This study uses global genetic correlation analysis to reveal local bivariate genetic correlations between psychiatric and substance use disorders, and identifies shared credible causal genes through fine-mapping.
BIOLOGICAL PSYCHIATRY
(2022)
Article
Biology
Adriano Rutz, Maria Sorokina, Jakub Galgonek, Daniel Mietchen, Egon Willighagen, Arnaud Gaudry, James G. Graham, Ralf Stephan, Roderic Page, Jiri Vondrasek, Christoph Steinbeck, Guido F. Pauli, Jean-Luc Wolfender, Jonathan Bisson, Pierre-Marie Allard
Summary: Contemporary bioinformatic and chemoinformatic capabilities have the potential to reshape knowledge management, analysis, and interpretation in natural products research. However, the reliance on disparate and specialized databases poses challenges for data access and integration. The LOTUS initiative aims to address these challenges by consolidating and sharing referenced structure-organism pairs on an open platform, promoting collaboration and transformative research.
Article
Green & Sustainable Science & Technology
Gokhan Gliven, Elveda Ozdilek
Summary: Trade liberalization may lead to resource depletion and utility losses, indirectly affecting productivity levels through the cross-border impact of economic activities. This study aims to examine the impacts of trade liberalization on welfare, resource protection, and labor allocation in a two-country, two-good small open-economy model where two countries share a common renewable resource stock. The findings suggest that trade can bring welfare gains for both countries, even if the shared resource stocks are severely depleted, when they specialize in manufacturing goods of comparative advantage.
JOURNAL OF CLEANER PRODUCTION
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Petra J. van Houdt, Sudarshan Ragunathan, Michael Berks, Zaki Ahmed, Lucy E. Kershaw, Oliver J. Gurney-Champion, Sirisha Tadimalla, Jonathan Arvidsson, Yu Sun, Jesper Kallehauge, Ben Dickie, Simon Levy, Laura Bell, Steven Sourbron, Michael J. Thrippleton
Summary: This article introduces a community-led open-source code repository established by the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI) to promote sharing and testing of perfusion imaging processing software. The repository contains multiple implementations of perfusion processing steps and provides an automated unit-testing framework for evaluation. The results show that differences in output parameters mainly occur in the pharmacokinetic models, while other aspects of the implementations have similar output values.
MAGNETIC RESONANCE IN MEDICINE
(2023)
Article
Biology
Dominique G. Roche, Ilias Berberi, Fares Dhane, Felix Lauzon, Sandrine Soeharjono, Roslyn Dakin, Sandra A. Binning
Summary: Many leading journals in ecology and evolution require open data upon publication, but there is little oversight to ensure data completeness and reusability. This study found that data archiving quality was associated with the identity of the principal investigator (PI), but not with journal open data policy, PI gender, or PI corresponding author status. Improving research data management training and culture within PI groups may be crucial for enhancing data archiving quality.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Economics
Gabriela Kol'vekova, Manuela Raisova, Martin Zoricak, Vladimir Gazda
Summary: Population growth and human well-being lead to increased use of scarce resources, necessitating innovative proposals for fair redistribution policies. Utilising common-pool resources offers an economic solution, but coordinating participants' interests is challenging. Introducing voting can improve the efficiency of public goods provision.
COMPUTATIONAL ECONOMICS
(2021)
Article
Ecology
Matthias Buchecker, Marius Fankhauser, Raphael Gaus
Summary: The study demonstrates the effectiveness of promoting social learning among stakeholders through participatory processes, leading to a convergence of problem perspectives and diffusion of social learning effects to the wider public. This highlights the importance of participatory integrated planning on the regional level in successfully implementing landscape-management decisions.
Article
Radiology, Nuclear Medicine & Medical Imaging
Wieslaw L. Nowinski
Summary: Despite the development of various brain-related resources, there is currently no large, systematic, comprehensive, extendable, and beautiful 3D reconstructed image repository of a living human brain that extends to the head and neck. In this study, the author created such a repository and populated it with images derived from a 3D atlas constructed from MRI and CT scans. The repository features multiple standard views, modes of presentation, and spatially co-registered image sequences, and contains galleries constructed from different tissue classes.
JOURNAL OF DIGITAL IMAGING
(2022)
Article
Genetics & Heredity
Emily A. Smith, Kevin G. Libuit, Curtis J. Kapsak, Michelle R. Scribner, Sage M. Wright, John Bell, Christina Morales, Megan Crumpler, Sharon Messenger, Jill K. Hacker, Katya Ledin, Carol Glaser, Kathleen Jacobson, Joel R. Sevinsky, Debra A. Wadford
Summary: During the COVID-19 pandemic, the capacity for pathogen genomics in public health expanded rapidly. However, many public health laboratories lacked the infrastructure to handle the large amount of SARS-CoV-2 sequence data. The California Department of Public Health, in partnership with Theiagen Genomics, created a SARS-CoV-2 genomic surveillance system called California COVIDNet. This initiative combined the efforts of over 40 sequencing laboratories across government, academia, and industry to establish a successful bioinformatics infrastructure.
MICROBIAL GENOMICS
(2023)
Article
Medicine, General & Internal
Maria Jose Hernandez-Leal, Nuria Codern-Bove, Maria Jose Perez-Lacasta, Angels Cardona, Carmen Vidal-Lancis, Misericordia Carles-Lavila
Summary: The objective of this study was to reach a consensus among experts on the content and design of a handbook and guide for shared decision-making in breast cancer screening, using the Delphi method. The results showed that the handbook and guide were considered useful and innovative support materials for health professionals, but training and piloting plans are needed to facilitate their implementation.
Article
Plant Sciences
Benzhong Fu, Olakunle Olawole, Gwyn A. Beattie
Summary: Glutamicibacter sp. FBE-19 was isolated for its strong antagonism to the cucurbit bacterial blight pathogen Erwinia tracheiphila. The genome sequence revealed genes potentially contributing to its antagonistic activity, which may make it an effective biocontrol agent against E. tracheiphila.
Article
Management
Stephen E. Christophe, Hun Lee
Summary: The research found that IPO firms generally have lower overall CSR ratings compared to industry peers. However, this is because they selectively focus their efforts on CSR topics that are important to their industry. IPO firms with significant material CSR activities not only exhibit better financial performance, but also experience fewer instances of stock delistings.
ACADEMY OF MANAGEMENT DISCOVERIES
(2021)
Article
Psychology, Clinical
Gavin Foster, John Robertson, Sophia Pallis, Jose Segal
Summary: The Eastern Health Mental Health Service implemented an integrated treatment model known as the dual diagnosis clinician shared care model to improve outcomes for people with co-occurring mental health and substance use disorders. This study aims to provide evidence for a relatively unexplored model in clinical mental health services within the state of Victoria, Australia.
ADVANCES IN DUAL DIAGNOSIS
(2022)
Proceedings Paper
Computer Science, Artificial Intelligence
Hiroto Yonenoh, Reiji Suzuki, Takaya Arita
Summary: Computer simulations show that decreasing the finiteness of resources can promote language evolution while also decreasing linguistic diversity in terms of characteristic variation.
ADVANCES IN ARTIFICIAL INTELLIGENCE
(2021)
Article
Environmental Studies
Anamika SEN, Curtis Atkisson, Charlie Schweik
Summary: Open source software plays a significant role in our daily lives, and nonprofit organizations like the Apache Software Foundation support its development by providing collective services. Policies and norms implemented by ASF have an impact on projects. Analyzing the distribution of costs and benefits can determine the contribution and sustainability of the second-order actor. The study reveals that ASF policies have a fairly symmetric distribution of costs and benefits, which can aid projects by providing necessary services.
INTERNATIONAL JOURNAL OF THE COMMONS
(2022)
Article
Genetics & Heredity
Chiao-Lin Chen, Jonathan Rodiger, Verena Chung, Raghuvir Viswanatha, Stephanie E. Mohr, Yanhui Hu, Norbert Perrimon
G3-GENES GENOMES GENETICS
(2020)
Review
Cell Biology
Andrey A. Parkhitko, Elizabeth Filine, Stephanie E. Mohr, Alexey Moskalev, Norbert Perrimon
AGEING RESEARCH REVIEWS
(2020)
Article
Biochemical Research Methods
Baolong Xia, Gabriel Amador, Raghuvir Viswanatha, Jonathan Zirin, Stephanie E. Mohr, Norbert Perrimon
Article
Biochemistry & Molecular Biology
Yanhui Hu, Aram Comjean, Jonathan Rodiger, Yifang Liu, Yue Gao, Verena Chung, Jonathan Zirin, Norbert Perrimon, Stephanie E. Mohr
Summary: The FlyRNAi database at DRSC/TRiP provides online resources for functional genomics studies, focusing on Drosophila melanogaster. It includes gene-centric, reagent-centric, and data-centric resources to aid in ortholog mapping, identifying RNAi and CRISPR sgRNA reagents, and visualizing transcriptomics data and protein interactions. These features help biological and biomedical researchers efficiently integrate and analyze information for Drosophila and other species in functional genomics workflows.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Yanhui Hu, Verena Chung, Aram Comjean, Jonathan Rodiger, Fnu Nipun, Norbert Perrimon, Stephanie E. Mohr
G3-GENES GENOMES GENETICS
(2020)
Article
Genetics & Heredity
Stephanie E. Mohr, Sudhir Gopal Tattikota, Jun Xu, Jonathan Zirin, Yanhui Hu, Norbert Perrimon
Summary: Single-cell RNA sequencing experiments are powerful in identifying cell clusters with common gene expression patterns, but mapping these clusters to specific anatomical regions and tissues presents a major challenge. In Drosophila, various approaches are available for high-resolution spatial mapping of scRNAseq clusters, utilizing existing datasets and emerging technologies.
Review
Genetics & Heredity
Jonathan Zirin, Justin Bosch, Raghuvir Viswanatha, Stephanie E. Mohr, Norbert Perrimon
Summary: The fruit fly, Drosophila melanogaster, has been an excellent model organism for biological and biomedical research due to its genetic and physiological similarities to humans and the availability of advanced genome manipulation technologies. The research community quickly adopted CRISPR technologies and has made significant advancements in mutagenesis, precise genome engineering, and other areas. The short lifespan and ease of genetics make fruit flies an ideal platform for in vivo applications and refinements of CRISPR-associated tools.
TRENDS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Raghuvir Viswanatha, Enzo Mameli, Jonathan Rodiger, Pierre Merckaert, Fabiana Feitosa-Suntheimer, Tonya M. Colpitts, Stephanie E. Mohr, Yanhui Hu, Norbert Perrimon
Summary: The authors have developed a new method for genetic screening in mosquito cell lines using a bioinformatics portal and optimized genetic exchange systems. This approach aids in identifying essential genes and those influencing host-pathogen interactions.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Jun Xu, Ah-Ram Kim, Ross W. Cheloha, Fabian A. Fischer, Joshua Shing Shun Li, Yuan Feng, Emily Stoneburner, Richard Binari, Stephanie E. Mohr, Jonathan Zirin, Hidde L. Ploegh, Norbert Perrimon
Summary: Expanding the repertoire of reagents for protein visualization and manipulation is important for understanding protein function. In this study, two short NanoTag epitopes and their corresponding nanobodies were characterized and their applications in Drosophila were demonstrated. The study also showed that CRISPR-mediated gene targeting can be used to tag endogenous proteins with the NanoTags.
Correction
Multidisciplinary Sciences
Raghuvir Viswanatha, Enzo Mameli, Jonathan Rodiger, Pierre Merckaert, Fabiana Feitosa-Suntheimer, Tonya M. Colpitts, Stephanie E. Mohr, Yanhui Hu, Norbert Perrimon
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Hong-Wen Tang, Kerstin Spirohn, Yanhui Hu, Tong Hao, Istvan A. Kovacs, Yue Gao, Richard Binari, Donghui Yang-Zhou, Kenneth H. Wan, Joel S. Bader, Dawit Balcha, Wenting Bian, Benjamin W. Booth, Atina G. Cote, Steffi de Rouck, Alice Desbuleux, Kah Yong Goh, Dae-Kyum Kim, Jennifer J. Knapp, Wen Xing Lee, Irma Lemmens, Cathleen Li, Mian Li, Roujia Li, Hyobin Julianne Lim, Yifang Liu, Katja Luck, Dylan Markey, Carl Pollis, Sudharshan Rangarajan, Jonathan Rodiger, Sadie Schlabach, Yun Shen, Dayag Sheykhkarimli, Bridget TeeKing, Frederick P. Roth, Jan Tavernier, Michael A. Calderwood, David E. Hill, Susan E. Celniker, Marc Vidal, Norbert Perrimon, Stephanie E. Mohr
Summary: This study uses advanced methods to identify protein-protein interactions in Drosophila, generating widely useful physical and data resources for the identification of new components in pathways, complexes, and processes. The generation of reference maps of interactome networks provides a protein-centric approach to discover new components in existing pathways, complexes, and processes, which is helpful for genetic studies. The results include the FlyBi dataset and the DroRI reference interaction network, which provide a foundation for building new hypotheses about protein networks and function.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Baolong Xia, Raghuvir Viswanatha, Yanhui Hu, Stephanie E. Mohr, Norbert Perrimon
Summary: This study establishes a CRISPR activation screening platform in Drosophila cells and identifies three novel rapamycin resistance genes. Mechanistic studies reveal that one of the genes enhances resistance by activating the RTK-Akt-mTOR signaling pathway, which requires cholesterol and clathrin-coated pits at the cell membrane. This research provides a novel platform for functional genetic studies in Drosophila cells.
Article
Biology
Nikki Coleman-Gosser, Yanhui Hu, Shiva Raghuvanshi, Shane Stitzinger, Weihang Chen, Arthur Luhur, Daniel Mariyappa, Molly Josifov, Andrew Zelhof, Stephanie E. Mohr, Norbert Perrimon, Amanda Simcox
Summary: Expression of activated Ras can generate continuous cell lines with characteristics of muscle, glia, and epithelium. Hormone treatment further induces differentiation into active muscle tissue and enhanced features of neuronal-like cells. Transcriptome analysis confirms the expression of cell-type-specific genes.
Review
Genetics & Heredity
Stephanie E. Mohr, Ah-Ram Kim, Yanhui Hu, Norbert Perrimon
Summary: This article discusses the importance of mining available information to understand the function of uncharacterized genes. It provides a guide on how to access information about these genes and suggests that mining available information can help prioritize genes for further study and provide starting points for experimental assays and other analyses.
Article
Biochemistry & Molecular Biology
Johana Vasquez-Procopio, Beatriz Osorio, Leticia Cortes-Martinez, Fidel Hernandez-Hernandez, Oscar Medina-Contreras, Emmanuel Rios-Castro, Aram Comjean, Fangge Li, Yanhui Hu, Stephanie Mohr, Norbert Perrimon, Fanis Missirlis