Article
Materials Science, Multidisciplinary
L. Dal Negro, Y. Zhu, Y. Chen, M. Prado, F. A. Pinheiro
Summary: The study investigates wave localization in aperiodic structures showcasing the multiscale complexity of arithmetic functions. Through analysis of tight-binding Schrodinger equation models, the research reveals the multifractal properties of energy spectra and the widespread localization of spatial eigenmodes.
Article
Physics, Multidisciplinary
Ting-Li Chen, Elizabeth P. P. Chou, Hsieh Fushing
Summary: This research selects collections of major factors embedded within response-versus-covariate dynamics based on information theoretic measurements through Categorical Exploratory Data Analysis (CEDA) computing paradigm, exploring the relevance to Wiener-Granger causality. The selection task identifies a chief collection and several secondary collections, with reliability checks through algorithmic computations.
Article
Biochemistry & Molecular Biology
Nathaniel Charest, Yuning Shen, Yei-Chen Lai, Irene A. Chen, Joan-Emma Shea
Summary: The identification of catalytic RNAs through experimental means is limited by the available sequence space. In this study, the researchers propose a method to predict additional ribozyme sequences by extrapolating from a limited data set, using information theory and a simple model of the epistatic fitness landscape. The predictions were experimentally validated, confirming the accuracy of the approach and discovering novel evolutionary links between ribozyme families.
Article
Biotechnology & Applied Microbiology
Amin R. Mohamed, Marina Naval-Sanchez, Moira Menzies, Bradley Evans, Harry King, Antonio Reverter, James W. Kijas
Summary: This study successfully documented the transcriptome and epigenome changes in key genes and pathways involved in sexual maturation in Atlantic salmon. Using a Systems Biology approach, regulatory networks and important genes were identified, revealing the crucial factors in the onset of maturation. The results provide a comprehensive view of the spatiotemporal changes in a complex trait and offer new insights for manipulating puberty in economically important aquaculture species.
Article
Environmental Studies
D. Oudes, A. van den Brink, S. Stremke
Summary: This paper examines the different spatial configurations of multifunctional solar power plants to reflect a range of contemporary societal considerations. By proposing different types such as mixed-production, nature-inclusive, and landscape-inclusive, it supports and optimizes the transformation of energy systems.
ENERGY RESEARCH & SOCIAL SCIENCE
(2022)
Article
Environmental Studies
Sara Prybutok, Galen Newman, Kayode Atoba, Garett Sansom, Zhihan Tao
Summary: The study evaluates ecosystem services along the Texas Coast using models, showing that only around 13% of the area has high nature-based solutions, while nearly 1/4 has low NBS. Due to development increases, most areas are at risk of becoming low NBS areas in the future if no action is taken.
Article
Computer Science, Information Systems
Nguyen Ho, Huy Vo, Mai Vu, Torben Bach Pedersen
Summary: Recent advancements in computing and data technologies have made analyzing Big Data across multiple datasets essential for extracting valuable insights. Techniques need to be fast, scalable, and assist users in prioritizing correlations across different temporal scales to focus on important relationships. AMIC is a method that uses mutual information to identify correlations in large time series, with a focus on scalability and effectiveness.
IEEE TRANSACTIONS ON BIG DATA
(2021)
Article
Optics
E. Omugbe, O. E. Osafile, I. B. Okon, E. S. Eyube, E. P. Inyang, U. S. Okorie, A. Jahanshir, C. A. Onate
Summary: In this study, we investigated the bound states and quantum theoretic-information measurements of an alpha-deformed Kratzer-type potential. The results showed that the potential parameters strongly influence the localization and delocalization of the position of a nano particle.
EUROPEAN PHYSICAL JOURNAL D
(2022)
Article
Immunology
Yuchen Zhong, Chaojing Zheng, Weiyuan Zhang, Hongyu Wu, Meng Wang, Qian Zhang, Haiyang Feng, Guiyu Wang
Summary: By integrating multi-omics data and bioinformatics, this study thoroughly explores the function of ESPL1 in cancer and validates its impact on proliferation and drug sensitivity in various cancer cell lines.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Materials Science, Multidisciplinary
O. Dyck, M. Ziatdinov, S. Jesse, F. Bao, A. Yousefzadi Nobakht, A. Maksov, B. G. Sumpter, R. Archibald, K. J. H. Law, S. Kalinin
Summary: The structure, bonding, and chemical dynamics of reactions at surfaces and interfaces are closely tied to the energetic landscape where each atom resides. Moving atoms under electron beam excitation can be utilized to probe energy landscapes along confined step edges, offering insights into atomic-scale potentials and the possibility for predictive atom-by-atom fabrication.
Article
Multidisciplinary Sciences
J. Shepard Bryan, Prithviraj Basak, John Bechhoefer, Steve Presse
Summary: This study introduces a new Bayesian method for inferring potentials from trajectories corrupted by Markovian measurement noise without assuming prior functional form on the potentials. By introducing structured kernel interpolation priors, this method can be extended to the analysis of large datasets.
Article
Biochemistry & Molecular Biology
Li-Li Zhu, Zheng Wu, Rong-Kun Li, Xin Xing, Yong-Sheng Jiang, Jun Li, Ya-Hui Wang, Li-Peng Hu, Xu Wang, Wei-Ting Qin, Yong-Wei Sun, Zhi-Gang Zhang, Qin Yang, Shu-Heng Jiang
Summary: The study comprehensively analyzed multidimensional omic data of PDAC tumors, revealing molecular events associated with aerobic glycolysis and identifying long non-coding RNAs involved in PDAC aerobic glycolysis. Loss-of-function studies demonstrated that silencing of LINC01559 and UNC5B-AS1 significantly inhibited the glycolytic capacity of PDAC cells, and high expression of these two lncRNAs correlated with poor patient prognosis.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Medicine, Research & Experimental
Samadrita Bhattacharyya, Rahul K. Kollipara, Gabriela Orquera-Tornakian, Sean Goetsch, Minzhe Zhang, Cameron Perry, Boxun Li, John M. Shelton, Minoti Bhakta, Jialei Duan, Yang Xie, Guanghua Xiao, Bret M. Evers, Gary C. Hon, Ralf Kittler, Nikhil V. Munshi
Summary: A comprehensive CCS-enriched CRE database named CCS-ATAC was established for studying CCS-wide and component-specific regulatory functions. CCS component-specific gene regulatory networks (GRNs) were constructed using transcription factor (TF) motifs, and specific TF sub-networks were identified and confirmed. CCS-ATAC was leveraged to improve annotation of existing human variants related to cardiac rhythm, and a potential dysregulated enhancer-target pair by a specific SNP was nominated.
JOURNAL OF CLINICAL INVESTIGATION
(2023)
Article
Green & Sustainable Science & Technology
Thalita Monteiro Obal, Jovani Taveira de Souza, Romulo Henrique Gomes de Jesus, Antonio Carlos de Francisco
Summary: The lack of partnerships between biomass generating producers is a major obstacle to efficient biogas production. This paper proposes a new clustering algorithm, BiogasCluster, to determine the optimal number of clusters for generating a renewable energy community. The algorithm was implemented in R language and demonstrated its efficiency in generating stable clusters in various scenarios. This study provides important guidance for creating strategic partnerships in bioenergy generation and assessing the potential for establishing clusters of rural properties.
Article
Environmental Studies
Dora Isabel Rodrigues Ferreira, Jose-Manuel Sanchez-Martin
Summary: There is no consensual methodology to assess landscape preferences and identify tourism potential. This study focuses on using photographs with pairwise comparison and the analytic hierarchy process (AHP) methodology to measure preferences for landscape typologies in Tagus International Nature Reserve. The findings suggest that cultural tourism/rural mixed and agritourism are highly valued.
Article
Virology
Elisabet Pujadas, Nnaemeka Ibeh, Matthew M. Hernandez, Aneta Waluszko, Tatyana Sidorenko, Vanessa Flores, Biana Shiffrin, Numthip Chiu, Alicia Young-Francois, Michael D. Nowak, Alberto E. Paniz-Mondolfi, Emilia M. Sordillo, Carlos Cordon-Cordo, Jane Houldsworth, Melissa R. Gitman
JOURNAL OF MEDICAL VIROLOGY
(2020)
Letter
Critical Care Medicine
Elisabet Pujadas, Fayzan Chaudhry, Russell McBride, Felix Richter, Shan Zhao, Ania Wajnberg, Girish Nadkarni, Benjamin S. Glicksberg, Jane Houldsworth, Carlos Cordon-Cardo
LANCET RESPIRATORY MEDICINE
(2020)
Article
Multidisciplinary Sciences
J. Abante, Y. Fang, A. P. Feinberg, J. Goutsias
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Ishan Paranjpe, Kumardeep Chaudhary, Kipp W. Johnson, Suraj K. Jaladanki, Shan Zhao, Jessica K. De Freitas, Elisabet Pujdas, Fayzan Chaudhry, Erwin P. Bottinger, Matthew A. Levin, Zahi A. Fayad, Alexander W. Charney, Jane Houldsworth, Carlos Cordon-Cardo, Benjamin S. Glicksberg, Girish N. Nadkarni
Summary: This study explored the association between SARS-CoV-2 viral load and acute kidney injury (AKI) in hospitalized COVID-19 patients. The findings revealed a weak but significant association between viral load and in-hospital AKI, suggesting a potential role of viral load in COVID-19 associated AKI.
Article
Pathology
Siraj M. El Jamal, Elisabet Pujadas, Irene Ramos, Clare Bryce, Zachary M. Grimes, Fatima Amanat, Nadejda M. Tsankova, Zarmeen Mussa, Sara Olson, Fadi Salem, Lisa Miorin, Teresa Aydillo, Michael Schotsaert, Randy A. Albrecht, Wen-Chun Liu, Nada Marjanovic, Nancy Francoeur, Robert Sebra, Stuart C. Sealfon, Adolfo Garcia-Sastre, Mary Fowkes, Carlos Cordon-Cardo, William H. Westra
Summary: In most cases where patients die from COVID-19-related organ failure, SARS-CoV-2 is not detectable in tissues. Even in severely damaged lungs, viral RNA or proteins were only detected in a minority of cases. This suggests that viral infection mainly triggers proinflammatory responses in multiple organs, rather than directly causing sustained tissue damage.
Review
Genetics & Heredity
Andrew E. Teschendorff, Andrew P. Feinberg
Summary: Single-cell omics is revolutionizing our understanding of cell biology and disease, but the analysis and interpretation of single-cell data face challenges. Concepts from statistical mechanics, including entropy, stochastic processes, and critical phenomena, are impacting single-cell data analysis. Embracing bottom-up modeling and a statistical mechanics analysis paradigm can enhance our understanding of single-cell systems biology. Teschendorff and Feinberg highlight how statistical mechanics-based single-cell analysis methods offer insights into developmental phenomena and cancer processes.
NATURE REVIEWS GENETICS
(2021)
Article
Engineering, Biomedical
Michael A. Koldobskiy, Garrett Jenkinson, Jordi Abante, Varenka A. Rodriguez DiBlasi, Weiqiang Zhou, Elisabet Pujadas, Adrian Idrizi, Rakel Tryggvadottir, Colin Callahan, Challice L. Bonifant, Karen R. Rabin, Patrick A. Brown, Hongkai Ji, John Goutsias, Andrew P. Feinberg
Summary: An information-theoretic analysis reveals methylation stochasticity differences in samples from pediatric acute lymphoblastic leukemia patients, indicating stochastic epigenomes marked by increased methylation entropy in specific regions and genes. Epigenetic changes in ALL converge on a shared set of genes overlapping with genetic drivers involved in chromosomal translocations across the disease spectrum.
NATURE BIOMEDICAL ENGINEERING
(2021)
Article
Pathology
Elisabet Pujadas, Michael Beaumont, Hardik Shah, Nadine Schrode, Nancy Francoeur, Sanjana Shroff, Clare Bryce, Zachary Grimes, Jill Gregory, Ryan Donnelly, Mary E. Fowkes, Kristin G. Beaumont, Robert Sebra, Carlos Cordon-Cardo
Summary: The study utilized advanced molecular techniques to identify different regulatory pathways and effectors in COVID-19 rapid autopsy tissues, revealing diverse expression patterns of virus receptors. Digital spatial profiling could distinguish different disease phenotypes. These findings contribute to a better understanding of the pathophysiology of COVID-19.
AMERICAN JOURNAL OF PATHOLOGY
(2021)
Article
Multidisciplinary Sciences
Jordi Abante, Sandeep Kambhampati, Andrew P. Feinberg, John Goutsias
Summary: CpelNano is a statistical method developed for quantification and analysis of 5mC methylation landscapes using nanopore data. It takes into account nanopore noise through a hidden Markov model (HMM) and estimates the associated methylation potential energy function using the expectation-maximization (EM) algorithm. Differential methylation analysis is performed via permutation-based hypothesis testing.
SCIENTIFIC REPORTS
(2021)
Article
Oncology
Emily K. W. Lo, Brian M. Mears, H. Carlo Maurer, Adrian Idrizi, Kasper D. Hansen, Elizabeth D. Thompson, Ralph H. Hruban, Kenneth P. Olive, Andrew P. Feinberg
Summary: Pancreatic ductal adenocarcinoma (PDAC) arises from the accumulation of somatic mutations and is frequently associated with pancreatic intraepithelial neoplasia (PanIN) lesions. The debate on whether PanINs and PDACs in humans originate from acinar or ductal cells still exists. DNA methylation changes during pancreatic neoplasia can provide insights into the cell type-of-origin of PanINs and PDACs.
Article
Biochemistry & Molecular Biology
Jason I. I. Feinberg, Rose Schrott, Christine Ladd-Acosta, Craig J. J. Newschaffer, Irva Hertz-Picciotto, Lisa A. A. Croen, M. Daniele Fallin, Andrew P. P. Feinberg, Heather E. E. Volk
Summary: There is a need to consider the paternal contributions to autism spectrum disorder (ASD) and explore the association between paternal autistic traits, sperm epigenome, and autistic traits in children. This study analyzed the genetic and epigenetic data of fathers and children from the Early Autism Risk Longitudinal Investigation (EARLI) cohort. The results showed significant associations between differentially methylated regions (DMRs) in the sperm epigenome and autistic traits in 3-year-old offspring. These findings highlight the potential importance of sperm epigenetic mechanisms in the development of autism.
MOLECULAR PSYCHIATRY
(2023)
Article
Biochemistry & Molecular Biology
Yuqi Fang, Zhicheng Ji, Weiqiang Zhou, Jordi Abante, Michael A. Koldobskiy, Hongkai Ji, Andrew P. Feinberg
Summary: Epigenetic information, inherited through DNA methylation, plays a crucial role in defining tissue identity. This study reveals that methylation entropy, which represents stochastic changes in DNA methylation, is associated with specific DNA binding motifs, regulatory DNA, and CpG density. Additionally, the contribution of methylation entropy to developmental patterns is comparable to that of methylation mean, and it is associated with conserved sequence and chromatin features. Furthermore, methylation entropy is directly related to gene expression variability in development, suggesting its involvement in developmental plasticity.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Multidisciplinary Sciences
Andrew P. Feinberg, Andre Levchenko
Summary: This review discusses modern approaches to epigenetic and gene regulation landscapes and their relevance to cancer etiology and the plasticity of cancerous states. The interplay between different types of regulatory landscapes and their changes in cancer progression are addressed. Cellular aging and intrinsic and extrinsic stimuli play important roles in modulating cellular states. Quantitatively mapping landscape alterations onto phenotypic outcomes can be used in therapy development.
Article
Medicine, Research & Experimental
Irina Petrache, Elisabet Pujadas, Aditya Ganju, Karina A. Serban, Alexander Borowiec, Beatrice Babbs, Irina A. Bronova, Nicholas Egersdorf, Patrick S. Hume, Khushboo Goel, William J. Janssen, Evgeny Berdyshev, Carlos Cordon-Cardo, Richard Kolesnick
Summary: The concentration of C16:0-ceramide in the plasma of COVID-19 patients was significantly increased compared to healthy individuals. Autopsied lungs of individuals with COVID-ARDS showed a massive elevation of C16:0-ceramide and exhibited a previously unrecognized microvascular ceramide-staining pattern and increased apoptosis. C16:0-ceramide may be implicated in the vascular injury associated with COVID-19.
Article
Endocrinology & Metabolism
Laura Ochoa-Callejero, Josune Garcia-Sanmartin, Pablo Villoslada-Blanco, Maria Iniguez, Patricia Perez-Matute, Elisabet Pujadas, Mary E. Fowkes, Rachel Brody, Jose A. Oteo, Alfredo Martinez
Summary: The study revealed significantly decreased levels of CGRP in COVID-19 patients, with even lower levels in patients treated with proton pump inhibitors. Immunofluorescence showed RAMP1 activity in smooth muscle cells of blood vessels, airway epithelium, and proliferating type II pneumocytes in COVID-19 samples.
JOURNAL OF THE ENDOCRINE SOCIETY
(2021)
