Editorial Material
Biology
Timothy J. f Mitchison
Summary: NK cells play a role in cancer immunosurveillance and therapy, with live cell imaging revealing diverse programmed cell death pathways induced in targeted cancer cells. The state of the target cell actin cytoskeleton influences pathway choice, with a novel death pathway called granzyme-induced necroptosis potentially important in cancer immunotherapy.
Review
Immunology
Erandi Perez-Figueroa, Pablo Alvarez-Carrasco, Enrique Ortega, Carmen Maldonado-Bernal
Summary: Neutrophils play a crucial role in innate immune response by executing various effector functions. When activated, they undergo cell death processes to ensure the proper elimination of pathogens and damaged cells, contributing to timely resolution of inflammation. Neutrophils' cell death mechanisms include apoptosis, pyroptosis, necrosis, and others, ultimately maintaining homeostasis in the organism.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Claire Coderch, Javier Arranz-Herrero, Estanislao Nistal-Villan, Beatriz de Pascual-Teresa, Sergio Rius-Rocabert
Summary: STING is an adaptor protein involved in immune response activation in vertebrates. Its induction can trigger early immune response and be used in cancer immune treatments. Understanding the activation of STING is crucial in designing therapeutic drugs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Marina Barba-Aliaga, Paula Alepuz, Jose E. Perez-Ortin
Summary: In eukaryotic cells, three nuclear RNA polymerases may have evolved from a single enzyme in a common ancestor with archaea. This diversity allows each polymerase to specialize in synthesizing different types of transcripts, potentially influencing the evolution of regulatory mechanisms to adapt to environmental changes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Neurosciences
David Mazaud, Anna Capano, Nathalie Rouach
Summary: Astrocytes play a major role in the brain by contributing to functions such as energy supply, neurotransmission, and behavior. They achieve this through forming intercellular networks, releasing neuroactive factors, and using connexins to modulate neurotransmission at various levels. Astroglial connexins regulate neuronal activity and behavior through diverse functions, including gap junction channels, hemichannels, and nonchannel processes.
Article
Environmental Studies
Talbot M. Andrews, Reuben Kline, Yanna Krupnikov, John Barry Ryan
Summary: When individuals are presented with too many easy ways to engage in climate change mitigation, they may feel less efficacious and subsequently engage in fewer mitigation behaviors. This suggests that more is not always better when it comes to communicating ways individuals can help stop climate change.
JOURNAL OF ENVIRONMENTAL PSYCHOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Mariacristina Filice, Sandra Imbrogno, Alfonsina Gattuso, Maria Carmela Cerra
Summary: Teleost fish have remarkable ability to tolerate dramatic stresses, with the heart playing a crucial role in the stress response by modulating cardiac function and maintaining molecular equilibrium. The nitric oxide synthase (NOS)/nitric oxide (NO) system in fish is essential for adapting to stress, including variations in O-2 and thermal regimes.
Article
Materials Science, Multidisciplinary
Jinsoo Park, Yao Luo, Jin-Jian Zhou, Marco Bernardi
Summary: This work presents a rigorous framework for studying phonon-induced spin relaxation and decoherence by computing the spin-spin correlation function and its vertex corrections due to electron-phonon interactions. The method is applied to GaAs spin relaxation and is shown to unify different spin decoherence mechanisms. It enables quantitative studies of spin relaxation, decoherence, and transport in various materials and devices.
Review
Genetics & Heredity
E. Sila Ozdemir, Anna M. Koester, Xiaolin Nan
Summary: The formation of Ras multimers, such as dimers and nanoclusters, is a new and exciting research area in the field of Ras biomedicine. Significant progress has been made in understanding the structure of Ras multimers and the mechanisms that regulate their formation. This article synthesizes current knowledge on Ras multimers, particularly the presence of multiple G-domain interfaces, and explores how membrane nanodomain composition and structure influence their formation.
Review
Microbiology
Annika Jasmin Walter, Maarten A. A. van de Klundert, Stephanie Jung
Summary: Chronic infection with HBV can cause liver diseases, and the majority of the disease is related to chronic inflammation caused by disrupted antiviral responses and aberrant innate immune reactions. Cells infected with HBV communicate with other cells through direct interaction and secretion of factors into the environment. These factors can be small molecules, proteins, or complex structures like extracellular vesicles. This article reviews how HBV infection affects the communication between infected cells and their environment and discusses its impact on viral persistence and related pathology.
Article
Computer Science, Information Systems
Hossein Shoushtari, Thomas Willemsen, Harald Sternberg
Summary: This paper explores the challenges and solutions for indoor pedestrian navigation in GNSS shaded areas, evaluating autonomous and infrastructure-based positioning methods. The study finds that relying solely on autonomous solutions may not always provide robust positioning, leading to a discussion on the benefits of incorporating infrastructure-based position estimation.
Article
Education & Educational Research
Deanna Kuhn
Summary: Metacognition, as a construct, plays various roles in different fields but is connected by key features and a shared framework. Inhibitory cognitive control is proposed as a necessary condition for metacognitive competence, with metacognition also being recognized as a disposition, not just a competence. This disposition, rooted in epistemology, supports effective management of individuals' minds, allowing for maximum control over thoughts and knowledge revision both individually and in social interactions.
EDUCATIONAL PSYCHOLOGIST
(2022)
Article
Microbiology
Kevin Ehemann, Maria Juliana Mantilla, Felipe Mora-Restrepo, Andrea Rios-Navarro, Maritza Torres, Adriana Marcela Celis Ramirez
Summary: This article reviews the advances in the experimental field for Malassezia, highlighting the need for further research on the interactions between Malassezia and the host.
Article
Agronomy
Hendrik Poorter, Xinyou Yin, Nouf Alyami, Yves Gibon, Thijs L. Pons
Summary: This paper summarizes how plants respond to various environmental factors through meta-analysis and introduces the concept of 'MetaPhenomics'. By creating generalized dose-response curves using relative trait responses from independent experiments, the study reveals the diverse ways plants are affected by and adapt to their environment.
Review
Biology
Jiri Vachtenheim, Lubica Ondrusova
Summary: Advanced melanoma is difficult to cure, with resistant cells developing universally and requiring further drug therapy. Multiple mechanisms lead to the development of resistance, emphasizing the need for personalized treatment. Combined therapy may be an effective approach to reducing drug resistance.
Article
Statistics & Probability
Michael A. Newton, Nicholas G. Polson, Jianeng Xu
Summary: The Weighted Bayesian Bootstrap (WBB) method is introduced and developed for machine learning and statistics, providing uncertainty quantification by sampling from a high dimensional posterior distribution. The WBB is computationally fast and scalable using off-the-shelf optimization software, and has theoretical justification under suitable regularity conditions on the statistical model. Applications in regularized regression, trend filtering, and deep learning are demonstrated, with suggestions for future research directions.
CANADIAN JOURNAL OF STATISTICS-REVUE CANADIENNE DE STATISTIQUE
(2021)
Article
Biochemical Research Methods
Zihao Zheng, Aisha M. Mergaert, Irene M. Ong, Miriam A. Shelef, Michael A. Newton
Summary: Peptide microarrays are a powerful tool in immunoproteomics, but face challenges with high dimensionality and small sample sizes in experiments. The MixTwice tool addresses limitations in reproducibility and power of current methods by computing local FDR statistics and local false sign rate statistics, effectively estimating generative parameters and identifying non-null peptides. Numerical experiments demonstrate its accuracy and reproducibility in identifying meaningful peptide markers in different signal strengths.
Article
Mathematical & Computational Biology
Tien Vo, Akshay Mishra, Vamsi Ithapu, Vikas Singh, Michael A. Newton
Summary: The Graph-based Mixture Model (GraphMM) is proposed for large-scale testing with graph-associated data to control local false-discovery rates. Compared to procedures that ignore the graph, GraphMM performs better when non-null cases form connected subgraphs. In a study of brain changes associated with Alzheimer's disease onset, GraphMM produces greater yield than conventional large-scale testing procedures.
Article
Biology
Peng Yu, Spencer Ericksen, Anthony Gitter, Michael A. Newton
Summary: This study addresses an important experimental design problem in early-stage drug discovery, focusing on prioritizing compounds for testing when little is known about the target protein. The Informer-based ranking (IBR) method is introduced as a solution, which selects a set of informer compounds and prioritizes the remaining compounds based on new bioactivity experiments. The Bayes Optimal Informer SEt (BOISE) method is proposed to efficiently solve this two-stage decision problem and outperforms other available methods in predicting protein-kinase inhibition and anticancer drug sensitivity.
Article
Oncology
Hemanth K. Potluri, Tun L. Ng, Michael A. Newton, Douglas G. McNeel
Summary: Antibody responses to off-target cancer-associated proteins may not necessarily indicate antigen spread, especially in vaccine strategies that use GM-CSF as an adjuvant. Evaluating T cell responses to non-target antigens is a preferred approach for detecting immune-mediated antigen spread following immunotherapies.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2022)
Article
Pathology
Santina M. Snow, Kristina A. Matkowskyj, Morgan Maresh, Linda Clipson, Tien N. Vo, Katherine A. Johnson, Dustin A. Deming, Michael A. Newton, William M. Grady, Perry J. Pickhardt, Richard B. Halberg
Summary: Colorectal cancer is a leading cause of cancer death in the United States, with standard treatments including chemotherapy and more recent targeted therapies based on molecular profiling. Low levels of DDAH1 and GAL3ST2 proteins in human CRC correlate with poor patient outcomes, which could impact prognosis and therapy selection methods.
Article
Rheumatology
Aisha M. Mergaert, Zihao Zheng, Michael F. Denny, Maya F. Amjadi, S. Janna Bashar, Michael A. Newton, Vivianne Malmstrom, Caroline Gronwall, Sara S. McCoy, Miriam A. Shelef
ARTHRITIS & RHEUMATOLOGY
(2022)
Article
Multidisciplinary Sciences
Zijian Ni, Aman Prasad, Shuyang Chen, Richard B. Halberg, Lisa M. Arkin, Beth A. Drolet, Michael A. Newton, Christina Kendziorski
Summary: Spatial transcriptomics is a widely used approach for analyzing gene expression in tissues, with applications in molecular medicine and tumor diagnostics. The authors propose a model called SpotClean to adjust for spot swapping, improving the accuracy and effectiveness of downstream analysis.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Mithalesh K. Singh, Sarah Altameemi, Marcos Lares, Michael A. Newton, Vijayasaradhi Setaluri
Summary: Phenotypic plasticity of melanoma cells plays a crucial role in drug resistance, and DUSP proteins are involved in regulating this plasticity, making them potential targets for treating MAPKi-resistant melanoma.
SCIENTIFIC REPORTS
(2022)
Article
Oncology
Dareen Mikheil, Kirthana Prabhakar, Tun Lee Ng, Sireesh Teertam, B. Jack Longley, Michael A. Newton, Vijayasaradhi Setaluri
Summary: Both oncogenic and tumor suppressor roles have been assigned to Notch signaling in melanoma. In clinical trials, Notch inhibitors proved to be ineffective for melanoma treatment. Notch signaling has also been implicated in melanoma transdifferentiation, a prognostic feature in primary melanoma. Our study investigated the role of Notch signaling in melanoma tumor development and growth using a genetic mouse model and found that the loss of Notch1 or Notch2 can substitute the tumor suppressor function of Pten in melanomagenesis. However, the loss of Notch1 or Notch2 may accelerate tumor development in the absence of Pten, suggesting a tumor suppressor role for Notch1 and Notch2 in melanomagenesis. Additionally, our data show that NOTCH protein levels in human melanoma do not reliably predict melanoma aggressiveness.
Article
Microbiology
Susheel Bhanu Busi, Zhentian Lei, Lloyd W. Sumner, James M. Amos-Landgraf
Summary: The onset of colon cancer is strongly associated with differences in microbial taxa in the gastrointestinal tract. Utilizing a multi-omics approach, this study reveals the impact of the gut microbiome on the susceptibility to adenoma development and identifies metabolic and transcriptomic pathways involved. The findings enhance our understanding of the role of the gut microbiome in colon cancer and provide insights for potential biomarkers and therapeutic targets.
Article
Biochemical Research Methods
Matthew N. Bernstein, Zijian Ni, Aman Prasad, Jared Brown, Chitrasen Mohanty, Ron Stewart, Michael A. Newton, Christina Kendziorski
Summary: Recent advances in spatially resolved transcriptomics technologies have enabled the measurement of genome-wide gene expression profiles and their spatial mapping within tissues. This paper introduces SpatialCorr, a method for identifying sets of genes with spatially varying correlation structure. By testing the correlation of each gene set within tissue regions, as well as between and among regions, this method reveals differences in correlation induced by spatial factors.
CELL REPORTS METHODS
(2022)
Article
Statistics & Probability
Tun Lee Ng, Michael A. Newton
Summary: This article establishes the statistical properties of random-weighting methods in LASSO regression under different regularization parameters and suitable regularity conditions. By assigning random weights to terms in the objective function and optimizing them, we obtain a set of random-weighting estimators. The study shows that existing methods have conditional model selection consistency and conditional asymptotic normality at different growth rates. Moreover, an extension to these methods is proposed, demonstrating conditional sparse normality and consistency in a growing-dimension setting. The effectiveness of the proposed methodology is illustrated using synthetic and benchmark datasets, and its relationship to approximate nonparametric Bayesian analysis and perturbation bootstrap methods is discussed.
ELECTRONIC JOURNAL OF STATISTICS
(2022)
Review
Biotechnology & Applied Microbiology
Noah A. Kaitz, Cindy L. Zuleger, Peng Yu, Michael A. Newton, Richard J. Albertini, Mark R. Albertini
Summary: Somatic cell gene mutations arise from replication errors or DNA template damage. Changes in mutant cell frequencies reflect changes in DNA damaging exposures. Somatic mutations have a wide range of interpretations and can be used to study diseases and immune processes.
MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH
(2022)
Article
Oncology
Alyssa A. Leystra, Brock J. Gilsdorf, Amanda M. Wisinger, Elise R. Warda, Shanna Wiegand, Christopher D. Zahm, Kristina A. Matkowskyj, Dustin A. Deming, Naghma Khan, Quincy Rosemarie, Chelsie K. Sievers, Alexander R. Schwartz, Dawn M. Albrecht, Linda Clipson, Hasan Mukhtar, Michael A. Newton, Richard B. Halberg
Summary: The study found that intestinal tumors with a multi-ancestral architecture involving at least two distinct clones exhibited increased growth and invasiveness, along with an impact on the response to low-dose aspirin. Genetically distinct tumor-founding cells can contribute to early intratumoral heterogeneity, enhancing colon tumor progression and affecting the response to aspirin.
