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arXiv 2017年

作者： Birzu, Gabriel Hallatschek, Oskar Korolev, Kirill S. Department of Physics Boston University BostonMA02215 United States Departments of Physics and Integrative Biology University of California BerkeleyCA94720 United States Department of Physics Graduate Program in Bioinformatics Boston University BostonMA02215 United States

Short Abstract: Traveling waves describe diverse natural phenomena from crystal growth in physics to range expansions in biology. Two classes of waves exist with very different properties: pulled and pushed. Pulled waves are driven by high growth rates at the expansion edge, where the number of organisms is small and fluctuations are large. In contrast, fluctuations are suppressed in pushed waves because the region of maximal growth is shifted towards the population bulk. Although it is commonly believed that expansions are either pulled or pushed, we found an intermediate class of waves with bulk-driven growth, but exceedingly large fluctuations. These waves are unusual because their properties are controlled by both the leading edge and the bulk of the front. Long Abstract: Epidemics, flame propagation, and cardiac rhythms are classic examples of reaction-diffusion waves that describe a switch from one alternative state to another. Only two types of waves are known: pulled, driven by the leading edge, and pushed, driven by the bulk of the wave. Here, we report a distinct class of semi-pushed waves for which both the bulk and the leading edge contribute to the dynamics. These hybrid waves have the kinetics of pushed waves, but exhibit giant fluctuations similar to pulled waves. The transitions between pulled, semi-pushed, and fully-pushed waves occur at universal ratios of the wave velocity to the Fisher velocity. We derive these results in the context of a species invading a new habitat by examining front diffusion, rate of diversity loss, and fluctuation-induced corrections to the expansion velocity. All three quantities decrease as a power law of the population density with the same exponent. We analytically calculate this exponent taking into account the fluctuations in the shape of the wave front. For fully-pushed waves, the exponent is -1 consistent with the central limit theorem. In semi-pushed waves, however, the fluctuations average out much more slowly, a

关键词： Population statistics

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Genetic drift in range expansions is very sensitive to density feedback in dispersal and growth

arXiv

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arXiv 2019年

作者： Birzu, Gabriel Matin, Sakib Hallatschek, Oskar Korolev, Kirill S. Department of Physics Boston University BostonMA02215 United States Departments of Physics and Integrative Biology University of California BerkeleyCA94720 United States Department of Physics and Graduate Program in Bioinformatics Boston University BostonMA02215 United States

Theory predicts rapid genetic drift in expanding populations due to the serial founder effect at the expansion front. Yet, many natural populations maintain high genetic diversity in the newly colonized regions. Here, we investigate whether density-dependent dispersal could provide a resolution of this paradox. We find that genetic drift is dramatically suppressed when dispersal rates increase with the population density because many more migrants from the diverse, high-density regions arrive at the expansion edge. When density-dependence is weak or negative, the effective population size of the front scales only logarithmically with the carrying capacity. The dependence, however, switches to a sublinear power law and then to a linear increase as the density-dependence becomes strongly positive. To understand these results, we introduce a unified framework that predicts how the strength of genetic drift depends on the density-dependence in both dispersal and growth. This theory reveals that the transitions between different regimes of diversity loss are controlled by a single, universal parameter: the ratio of the expansion velocity to the geometric mean of dispersal and growth rates at expansion edge. Importantly, our results suggest that positive density-dependence could dramatically alter evolution in expanding populations even when its contributions to the expansion velocity is small. Copyright © 2019, The Authors. All rights reserved.

关键词： Expansion

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Fast and Effective Clustering Method for Ancestry Estimation

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Procedia Computer Science 2019年 157卷 306-312页

作者： Arif Budiarto Bharuno Mahesworo James Baurley Teddy Suparyanto Bens Pardamean Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 BioRealm LLC USA Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta 11480 Indonesia

Ancestry estimation which provides family history information is one of the most popular services in direct-to-consumer genomic testing. It is also an important task which aimed to reduce the confounding by ancestry on the relationship of genotypes and disease risk in assocation studies. Several methods have been developed to generate the best ancestry estimated scores even though some of them are still facing inefficient computation time. In this paper, a combination method between KMeans clustering and PCA is proposed estimate ancestry estimation from SNP genotyping data. This method was compared with baseline model, called fastSTRUCTURE, in term of the quality of clustering and computation time. Public data from 1000 Genome project is used to train and evaluate the proposed model and the baseline model. The proposed model can successfully generate clusters with better accuracy than fastSTRUCTURE (91.02% over 90.39%). More importantly, it can boost the computation time until 100 times faster than fastSTRUCTURE (from 490 seconds to 4.86 seconds).

关键词： Ancestry Estimation Population Stratification Clustering bioinformatics Genomics

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Systems biology applications to study mechanisms of human immunodeficiency virus latency and reactivation

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World Journal of Clinical Infectious Diseases 2016年第2期6卷 6-21页

作者： Cory H White Bastiaan Moesker Angela Ciuffi Nadejda Beliakova-Bethell Graduate Program in Bioinformatics and Systems Biology University of California San Diego San Diego VA Medical Center and Veterans Medical Research Foundation Clinical and Experimental Sciences Faculty of Medicine University of Southampton Institute of Microbiology University Hospital of Lausanne (CHUV) and University of Lausanne Department of Medicine Univer-sity of California San Diego

Eradication of human immunodeficiency virus(HIV) in infected individuals is currently not possible because of the presence of the persistent cellular reservoir of latent infection. The identification of HIV latency biomarkers and a better understanding of the molecular mechanisms contributing to regulation of HIV expression might provide essential tools to eliminate these latently infected cells. This review aims at summarizing gene expression profiling and systems biology applications to studies of HIV latency and eradication. Studies comparing gene expression in latently infected and uninfected cells identify candidate latency biomarkers and novel mechanisms of latency control. Studies that profiled gene expression changes induced by existing latency reversing agents(LRAs) highlight uniting themes driving HIV reactivation and novel mechanisms that contribute to regulation of HIV expression by different LRAs. Among the reviewed gene expression studies, the common approaches included identification of differentially expressed genes and gene functional category assessment. Integration of transcriptomic data with other biological data types is presently scarce, and the field would benefit from increased adoption of these methods in future studies. In addition, designing prospective studies that use the same methods of data acquisition and statistical analyses will facilitate a more reliableidentification of latency biomarkers using different model systems and the comparison of the effects of different LRAs on host factors with a role in HIV reactivation. The results from such studies would have the potential to significantly impact the process by which candidate drugs are selected and combined for future evaluations and advancement to clinical trials.

关键词： Gene expression Microarrays RNA-Seq Systems biology Human immunodeficiency virus Viral latency Disease eradication Biomarkers Molecular mechanisms Latency reversing agents

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Automatic Generation of Balletic Motions

Automatic Generation of Balletic Motions

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IEEE/ACM International Conference on Cyber-Physical Systems (ICCPS)

作者： Amy LaViers Magnus Egerstedt Yushan Chen Calin Belta School of Electrical and Computer Engineering Georgia Institute of Technology Atlanta GA USA Department of Electrical and Computer Engineering Boston University Boston MA USA Department of Mechanical Engineering Division of Systems Engineering and the Bioinformatics Graduate Program Boston University MA USA

As cyber-physical systems become more prevalent, specifications for these systems must be formulated in a more nuanced manner. This paper presents a particular instantiation of such specification by proposing a framework that endows robotic motions with a sense of aesthetic style. Drawing inspiration from classical ballet, poses are cast as discrete states and movements as the transitions between these states. Thus, a given movement style is encoded in the availability of transitions at each state, and the dynamics of a complex physical trajectory are abstracted as a system which moves between these states. Using Linear Temporal Logic (LTL), we are able to further constrain the set of possible sequences through the transition system and thus prevent it from evolving through a sequence of states that is physically impossible or aesthetically undesirable. Our overarching objective is to facilitate subtle degrees of control over systems as such subtleties are required, more and more, to interact in a social and aesthetically driven world.

关键词： Automata Leg Legged locomotion Humans Trajectory Hip

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Connecting polymer collapse and the onset of jamming

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Physical Review E 2024年第3期109卷 034406-034406页

作者： Alex T. Grigas Aliza Fisher Mark D. Shattuck Corey S. O'Hern Graduate Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut 06520 USA Department of Mechanical Engineering and Materials Science Yale University New Haven Connecticut 06520 USA Benjamin Levich Institute and Physics Department The City College of New York New York New York 10031 USA Department of Physics Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA

Previous studies have shown that the interiors of proteins are densely packed, reaching packing fractions that are as large as those found for static packings of individual amino-acid-shaped particles. How can the interiors of proteins take on such high packing fractions given that amino acids are connected by peptide bonds and many amino acids are hydrophobic with attractive interactions? We investigate this question by comparing the structural and mechanical properties of collapsed attractive disk-shaped bead-spring polymers to those of three reference systems: static packings of repulsive disks, of attractive disks, and of repulsive disk-shaped bead-spring polymers. We show that the attractive systems quenched to temperatures below the glass transition T≪Tg and static packings of both repulsive disks and bead-spring polymers possess similar interior packing fractions. Previous studies have shown that static packings of repulsive disks are isostatic at jamming onset, i.e., the number of interparticle contacts Nc matches the number of degrees of freedom, which strongly influences their mechanical properties. We find that repulsive polymer packings are hypostatic at jamming onset (i.e., with fewer contacts than degrees of freedom) but are effectively isostatic when including stabilizing quartic modes, which give rise to quartic scaling of the potential energy with displacements along these modes. While attractive disk and polymer packings are often considered hyperstatic with excess contacts over the isostatic number, we identify a definition for interparticle contacts for which they can also be considered as effectively isostatic. As a result, we show that the mechanical properties (e.g., scaling of the potential energy with excess contact number and low-frequency contribution to the density of vibrational modes) of weakly attractive disk and polymer packings are similar to those of isostatic repulsive disk and polymer packings. Our results demonstrate that static

关键词： Jamming Polymer folding Protein folding Single polymer chains

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Comparing the Accuracy of Multiple Commercial Wearable Devices: A Method

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Procedia Computer Science 2019年 157卷 567-572页

作者： Bens Pardamean Haryono Soeparno Bharuno Mahesworo Arif Budiarto James Baurley Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 BioRealm LLC USA

To maintain a good fitness level, performing a minimum daily physical activity is important. Many people think that they have already met the suggested guidelines. However, most of them were wrong when they quantify their activity level using a personal activity tracker device. This problem indicates the need for personal physical activity tracker or wearable device to maintain the fitness level. However, as wide-range wearable devices available today, it is difficult to find the most suitable one regarding the price and quality. This paper proposes a study to explore the association between the quality and the price of the devices. The quality is evaluated by comparing the accuracy of the heart rate sensor and step counter of several wearable devices with the ground truth measurements. The test result is then analyzed using a series of statistical methods including, a paired t-test, Pearson’s correlation test, and Bland-Altman plot. Both t-test and correlation coefficient is used to plot the association between quality and price.

关键词： Wearable Device Fitness Tracker Correlation Heart Rate Step Counting Bland-Altman

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Multiomics Reveals Induction of Neuroblastoma SK-N-BE(2)C Cell Death by Mitochondrial Division Inhibitor 1 through Multiple Effects

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Journal of Proteome Research 2024年第1期23卷 301-315页

作者： Wang, Wei-Hsuan Kao, Yi-Chun Hsieh, Chiao-Hui Tsai, Shin-Yu Cheung, Chantal Hoi Yin Huang, Hsuan-Cheng Juan, Hsueh-Fen Genome and Systems Biology Degree Program Academia Sinica and National Taiwan University Taipei 106 Taiwan Department of Life Science National Taiwan University Taipei 106 Taiwan Center for Computational and Systems Biology National Taiwan University Taipei 106 Taiwan Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taipei 112 Taiwan Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei 106 Taiwan Center for Advanced Computing and Imaging in Biomedicine National Taiwan University Taipei 106 Taiwan

Mitochondrial division inhibitor 1 (Mdivi-1) is a well-known synthetic compound aimed at inhibiting dynamin-related protein 1 (Drp1) to suppress mitochondrial fission, making it a valuable tool for studying mitochondrial dynamics. However, its specific effects beyond Drp1 inhibition remain to be confirmed. In this study, we employed integrative proteomics and phosphoproteomics to delve into the molecular responses induced by Mdivi-1 in SK-N-BE(2)C cells. A total of 3070 proteins and 1945 phosphorylation sites were identified, with 880 of them represented as phosphoproteins. Among these, 266 proteins and 97 phosphorylation sites were found to be sensitive to the Mdivi-1 treatment. Functional enrichment analysis unveiled their involvement in serine biosynthesis and extrinsic apoptotic signaling pathways. Through targeted metabolomics, we observed that Mdivi-1 enhanced intracellular serine biosynthesis while reducing the production of C24:1-ceramide. Within these regulated phosphoproteins, dynamic dephosphorylation of proteasome subunit alpha type 3 serine 250 (PSMA3-S250) occurred after Mdivi-1 treatment. Further site-directed mutagenesis experiments revealed that the dephosphorylation-deficient mutant PSMA3-S250A exhibited a decreased cell survival. This research confirms that Mdivi-1’s inhibition of mitochondrial division leads to various side effects, ultimately influencing cell survival, rather than solely targeting Drp1 inhibition. © 2023 American Chemical Society.

关键词： Mdivi-1 multiomics neuroblastoma phosphoproteome proteome targeted metabolome

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Evidence of term-structure differences among folksonomies and controlled indexing languages

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Proceedings of the Association for Information Science and Technology 2009年第1期45卷 1-7页

作者： Benjamin M. Good Joseph T. Tennis The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Bioinformatics Graduate Program University of British Columbia Providence Heart + Lung Institute St. Paul's Hospital Vancouver BC Canada The Information School University of Washington Box 352840 Mary Gates Hall Suite 370 Seattle WA 98195-2840

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Regulatory Mechanisms Controlling Mosquito Reproduction

Regulatory Mechanisms Controlling Mosquito Reproduction

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The 5th International Symposium on Insect Physiology, Biochemistry and Molecular Biology

作者： Alexander S.Raikhel Tusar Saha Sourav Roy Lisa Johnson Keira Lucas Shiping Liu Bo Zhao Vlastimil Smykal Xiufeng Zhang Sang Woon Shin Jisu Ha Wei Dou Vladimir Kokoza Zhen Zou Department of Entomology and Institute for Integrative Genome Biology University of California Riverside Graduate Program in Cell Molecular and Developmental BiologyUniversity of California Riverside Graduate Program in Genomics Genetics and BioinformaticsUniversity of California Riverside The State Key Laboratory of Silkworm Genome Biology Southwest University College of Plant Protection Southwest University State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of ZoologyChinese Academy of Sciences

Mosquitoes transmit numerous devastating diseases to humans and animals due to obligatory blood feeding that is required for egg development. Elucidating molecular mechanisms underlying mosquito reproduction is of paramount importance for devising novel control approaches. In addition, mosquitoes represent outstanding models for investigating these events in insects in general. Two major insect hormones-juvenile hormone(JH) and20-hydroxyecdysone(20E)-regulate a plethora of physiological processes. In female mosquitoes,these hormones are responsible for controlling sequential reproductive phases. Transcriptomic analyses combined with RNA interference depletions of JH receptor Methoprene-tolerant(Met)and Ecdysone receptor(EcR) have revealed functions of these hormone receptors in activation and repression of gene cohorts during previtellogenic and vitellogenic phases, respectively. We identified how JH receptor mediates JH action on gene expression in mosquitoes and devised an approach of studying the subunit composition of this receptor. Using this technique we screened numerous natural compounds and isolated several molecules that serve as strong disruptors of JH receptor and JH action, providing a basis for developing a novel class of insecticides. We extensively investigated the role of Ecdysone Receptor in regulation of gene expression,uncovering the complexity of the 20 E genetic hierarchy that controls vitellogenic phase of female mosquito reproduction. Understanding of the molecular mechanisms of Ecdysone receptor-dependent gene repression is of great importance for devising future control methodologies. Small non-coding RNAs belonging to the class of micro RNAs(miR NA) have been implicated in regulation of numerous cellular and physiological processes in animals and plants. However, relatively little is known about mi RNA roles in non-Drosophilid insects. We have developed systemic and transgenic approaches for analyzing functions of miR NAs in mosquito repro

关键词： juvenile hormone methoprene-tolerant 20-hydroxyecdysone ecdysone receptor vitellogenesis microRNA

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