Article
Genetics & Heredity
Liliya Doronina, Graham M. Hughes, Diana Moreno-Santillan, Colleen Lawless, Tadhg Lonergan, Louise Ryan, David Jebb, Bogdan M. Kirilenko, Jennifer M. Korstian, Liliana M. Davalos, Sonja C. Vernes, Eugene W. Myers, Emma C. Teeling, Michael Hiller, Lars S. Jermiin, Juergen Schmitz, Mark S. Springer, David A. Ray
Summary: The relationships among laurasiatherian clades are highly disputed in mammalian phylogeny. This study attempted to unravel these relationships using two independent genome-level approaches, but the results showed contradictory phylogenetic signals. The positions of some clades received consistent support, while the relationships of others were contradictory. Further research incorporating unsampled laurasiatherian lineages and synergistic analyses of different methods could help resolve these conflicting patterns.
Article
Biochemistry & Molecular Biology
Frederick R. Jaya, Jessie C. Tanner, Michael R. Whitehead, Paul Doughty, J. Scott Keogh, Craig C. Moritz, Renee A. Catullo
Summary: When closely related species come into contact via range expansion, selection favors minimizing costly interspecies reproductive interactions. In a study on a toadlet species complex from northern Australia, population genomic data revealed the geographic origin and secondary contact, providing evidence for reproductive character displacement following range expansion.
Article
Agriculture, Dairy & Animal Science
Mitsuki Kondo, Yoshinori Ikenaka, Shouta M. M. Nakayama, Yusuke K. Kawai, Mayumi Ishizuka
Summary: In this study, the evolutional features of the UGT gene family in Carnivora were clarified. Specific gene expansions of UGT1As in Canidae, brown bear, and black bear, as well as genetic duplications of UGT2Bs in Canidae, some Mustelidae, and Ursidae were identified. Additionally, gene contractions or complete loss of UGT1A7-12 were observed in phocids, some otariids, felids, and some Mustelids. These findings suggest significant evolutionary differences of UGTs even among closely related species and emphasize the importance of appropriate approaches for assessing pharmacokinetics and toxicokinetics in wildlife carnivores.
Article
Behavioral Sciences
Ronald A. Fernandez-Gomez, Jorge E. Morales-Mavil, Laura T. Hernandez-Salazar, J. Roberto Sosa-Lopez
Summary: This study assessed the behavioural responses of olive sparrows to geographical variation in songs, revealing an asymmetrical response pattern and a correlation between response intensity and acoustic similarity. This suggests that males from different populations may use a similar mechanism to recognize signals and that song divergence could act as a premating barrier for some populations.
Article
Computer Science, Information Systems
Boyu Fan, Xiang Su, Jianwei Niu, Pan Hui
Summary: EmgAuth is a novel smartphone unlocking system based on electromyography (EMG) and Siamese network. It effectively authenticates users and is resilient to rotation, making it more secure than traditional unlocking systems.
IEEE TRANSACTIONS ON MOBILE COMPUTING
(2023)
Article
Ecology
Yonghua Wu
Summary: Using a molecular phyloecological approach, this study examined the adaptive evolution of digestive system-related genes in carnivorous and herbivorous mammals within Laurasiatheria. The results show intensified selection of fat and protein utilization in carnivorous lineages, consistent with their high-protein and high-fat diets. Interestingly, herbivorous lineages exhibited a similar selection pattern, suggesting that the selection of digestive system-related genes is not solely determined by nutrient components in their diets.
BMC ECOLOGY AND EVOLUTION
(2022)
Article
Behavioral Sciences
Gina M. Calabrese, Karin S. Pfennig
Summary: The study on spadefoot toads revealed that despite differences in female preferences and male signals across populations, there was no correlation between them, potentially due to the impact of gene flow from heterospecifics on male call rates. This suggests that the independent evolution of female preferences and male sexual signals may hinder reproductive isolation between populations.
BEHAVIORAL ECOLOGY
(2021)
Article
Ecology
Maidie Sinitambirivoutin, Patrik Nosil, Samuel Flaxman, Jeffrey Feder, Zachariah Gompert, Vasilis Dakos
Summary: Species formation is a fundamental topic in biology and theoretical studies have investigated the conditions and dynamics of speciation. Both gradual and abrupt speciation events have been observed, with the latter being driven by positive feedback loops. Early warning signals (EWS) have been developed to anticipate abrupt transitions, based on statistical patterns observed before such transitions. In this study, the authors investigate the presence of EWS in speciation dynamics using a theoretical model, finding evidence for EWS and identifying particular metrics as reliable indicators of upcoming abrupt speciation events. These findings contribute to our understanding of the mechanisms underlying EWS and their potential application in predicting speciation events.
Article
Computer Science, Information Systems
Huichun Li, Xin Li, Xue Zhang, Chengli Zhao, Zhengming Wang
Summary: This study aims to solve the problem of social system modeling and emergency prediction by using the hierarchical inference model and critical transition theory. Experiments on two social system datasets confirm the effectiveness of the TNS method in capturing early warning signals and identifying sensitive groups.
INFORMATION SCIENCES
(2023)
Article
Computer Science, Artificial Intelligence
Domenico Buongiorno, Giacomo Donato Cascarano, Irio De Feudis, Antonio Brunetti, Leonarda Carnimeo, Giovanni Dimauro, Vitoantonio Bevilacqua
Summary: Deep Learning has shown remarkable performance in various tasks such as image recognition, machine translation, and self-driving cars, boosting advancements in physiological signal processing. There has been an exponential increase in studies using DL methods for EMG signal processing, with a focus on hand gesture classification, speech and emotion classification, sleep stage classification, and other applications. The prevalence of convolutional neural networks (CNN) as the most used topology in DL architectures highlights the progress and potential of this field.
Article
Biology
Jawad Ahmad Dar, Kamal Kr Srivastava, Alok Mishra
Summary: Chest or upper body auscultation became prevalent after the invention of the stethoscope, which made the practice suitable and hygienic. Lung diseases are a major cause of death globally, and respiratory sounds provide crucial information about lung conditions.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Review
Computer Science, Artificial Intelligence
Luis Guarda, Juan E. Tapia, Enrique Lopez Droguett, Marcelo Ramos
Summary: This paper presents a Deep Learning-based method for drowsiness detection using CapsNet and spectrogram images of EEG signals. The proposed CapsNet model outperforms the traditional Convolutional Neural Network in terms of accuracy and sensitivity. This method is effective for handling small amounts of data and biomedical signals.
EXPERT SYSTEMS WITH APPLICATIONS
(2022)
Article
Chemistry, Analytical
Yang An, Hak Keung Lam, Sai Ho Ling
Summary: This paper proposes an automatic denoising method based on generative adversarial network (GAN) for denoising EEG signals. By defining a new loss function and using a new normalization method, this method can effectively remove noise and retain the original information and energy. Experimental results show that the proposed method achieves comparable performance to traditional manual denoising methods and enables automation of the denoising process, saving time.
Article
Cell Biology
Francesca Alu, Alessandro Orticoni, Elda Judica, Maria Cotelli, Paolo Maria Rossini, Francesca Miraglia, Fabrizio Vecchio
Summary: The study found that elderly participants showed higher levels of disorder in the central, parietal, and occipital brain regions compared to younger participants, indicating a decrease in neural network synchronization associated with the aging process. This reduced synchronization may be due to the decline in cerebral connections typically observed in aging, highlighting the importance of understanding brain dynamics using entropy parameters for developing personalized rehabilitation programs and future research on neurodegenerative diseases.
MECHANISMS OF AGEING AND DEVELOPMENT
(2021)
Article
Engineering, Biomedical
Rong Yao, Jiayue Xue, Haifang Li, Qianshan Wang, Hongxia Deng, Shuping Tan
Summary: This study used pinning control theory to adjust brain regions interaction in first-episode schizophrenia, revealing abnormal right frontal lobe activity and higher brain network synchronization in schizophrenia patients during a short-term memory task. The synchronization was positively correlated with response time and negatively correlated with response accuracy, with differences in active brain regions between schizophrenia patients and healthy participants.
BIOMEDICAL SIGNAL PROCESSING AND CONTROL
(2022)
Article
Biochemistry & Molecular Biology
Cath Tyner, Galt P. Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Christopher Eisenhart, Clayton M. Fischer, David Gibson, Jairo Navarro Gonzalez, Luvina Guruvadoo, Maximilian Haeussler, Steve Heitner, Angie S. Hinrichs, Donna Karolchik, Brian T. Lee, Christopher M. Lee, Parisa Nejad, Brian J. Raney, Kate R. Rosenbloom, Matthew L. Speir, Chris Villarreal, John Vivian, Ann S. Zweig, David Haussler, Robert M. Kuhn, W. James Kent
NUCLEIC ACIDS RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Jonathan Casper, Ann S. Zweig, Chris Villarreal, Cath Tyner, Matthew L. Speir, Kate R. Rosenbloom, Brian J. Raney, Christopher M. Lee, Brian T. Lee, Donna Karolchik, Angie S. Hinrichs, Maximilian Haeussler, Luvina Guruvadoo, Jairo Navarro Gonzalez, David Gibson, Ian T. Fiddes, Christopher Eisenhart, Mark Diekhans, Hiram Clawson, Galt P. Barber, Joel Armstrong, David Haussler, Robert M. Kuhn, W. James Kent
NUCLEIC ACIDS RESEARCH
(2018)
Article
Evolutionary Biology
Maximiliane Sparwel, Liliya Doronina, Gennady Churakov, Anja Stegemann, Juergen Brosius, Terence J. Robinson, Juergen Schmitz
GENOME BIOLOGY AND EVOLUTION
(2019)
Article
Biochemistry & Molecular Biology
Maximilian Haeussler, Ann S. Zweig, Cath Tyner, Matthew L. Speir, Kate R. Rosenbloom, Brian J. Raney, Christopher M. Lee, Brian T. Lee, Angie S. Hinrichs, Jairo Navarro Gonzalez, David Gibson, Mark Diekhans, Hiram Clawson, Jonathan Casper, Galt P. Barber, David Haussler, Robert M. Kuhn, W. James Kent
NUCLEIC ACIDS RESEARCH
(2019)
Article
Evolutionary Biology
Liliya Doronina, Olga Reising, Hiram Clawson, David A. Ray, Juergen Schmitz
SYSTEMATIC BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Christopher M. Lee, Galt P. Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Jairo Navarro Gonzalez, Angie S. Hinrichs, Brian T. Lee, Luis R. Nassar, Conner C. Powell, Brian J. Raney, Kate R. Rosenbloom, Daniel Schmelter, Matthew L. Speir, Ann S. Zweig, David Haussler, Maximilian Haeussler, Robert M. Kuhn, W. James Kent
NUCLEIC ACIDS RESEARCH
(2020)
Article
Genetics & Heredity
Jason D. Fernandes, Armando Zamudio-Hurtado, Hiram Clawson, W. James Kent, David Haussler, Sofie R. Salama, Maximilian Haeussler
Article
Biochemistry & Molecular Biology
Gennady Churakov, Fengjun Zhang, Norbert Grundmann, Wojciech Makalowski, Angela Noll, Liliya Doronina, Juergen Schmitz
Article
Genetics & Heredity
Jason D. Fernandes, Angie S. Hinrichs, Hiram Clawson, Jairo Navarro Gonzalez, Brian T. Lee, Luis R. Nassar, Brian J. Raney, Kate R. Rosenbloom, Santrupti Nerli, Arjun A. Rao, Daniel Schmelter, Alastair Fyfe, Nathan Maulding, Ann S. Zweig, Todd M. Lowe, Manuel Jr Jr Ares, Russ Corbet-Detig, W. James Kent, David Haussler, Maximilian Haeussler
Article
Biochemistry & Molecular Biology
Jairo Navarro Gonzalez, Ann S. Zweig, Matthew L. Speir, Daniel Schmelter, Kate R. Rosenbloom, Brian J. Raney, Conner C. Powell, Luis R. Nassar, Nathan D. Maulding, Christopher M. Lee, Brian T. Lee, Angie S. Hinrichs, Alastair C. Fyfe, Jason D. Fernandes, Mark Diekhans, Hiram Clawson, Jonathan Casper, Anna Benet-Pages, Galt P. Barber, David Haussler, Robert M. Kuhn, Maximilian Haeussler, W. James Kent
Summary: The UCSC Genome Browser database has been providing high-quality genomics data visualization and genome annotations for over two decades. New features and data tracks have been continuously added to accommodate advances in genomics and to keep data up-to-date, including new display modes, gene annotations, and tracks for human and mouse genomes. Recently, a genome browser with detailed annotation tracks for the SARS-CoV-2 RNA reference assembly was released.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Liliya Doronina, Olga Reising, Hiram Clawson, Gennady Churakov, Juergen Schmitz
Summary: This study investigates the phylogenetics of Euarchontoglires using whole-genome analysis and a marker system with minimal homoplasy. By analyzing presence/absence patterns of transposed elements, diagnostic insertions were identified and provided support for current resolutions of Primatomorpha and Euarchonta, as well as alternative phylogenetic scenarios.
Article
Evolutionary Biology
Gennady Churakov, Andrej Kuritzin, Konstantin Chukharev, Fengjun Zhang, Florian Wuennemann, Vladimir Ulyantsev, Juergen Schmitz
Summary: Retrophylogenomics utilizes genome-wide retrotransposon presence/absence insertion patterns to address questions in phylogeny and population genetics. We have developed an improved statistical tool that can simultaneously compare four lineages, allowing for the evaluation of multiple ancestral hybridizations/introgressions, ancestral incomplete lineage sorting, bifurcation, and polytomy. This tool is available for use by the scientific community through a user-friendly web R application.
SYSTEMATIC BIOLOGY
(2023)