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Computational biology

Arnas Bakavičius, Marija Barisienė, Marius Snicorius, Dileta Valančienė, Darius Dasevičius, Algirdas Žalimas, Robertas Kvaščevičius, Henrikas Ramonas, Vitalijus Sokolovas, Feliksas Jankevičius
Introduction: Mixed epithelial and stromal tumour of the kidney (MEST) is a rare and distinctive neoplasm accounting for 0.2% of all renal cancers. Most of these tumours behave in a benign fashion but 13 cases with malignant transformation have already been reported. We present the first case of an extremely aggressive MEST with rapid recurrence after radical treatment, demonstrating objective response to chemotherapy. Case presentation: A 31-year-old female presented to the hospital complaining of gross hematuria...
2018: Acta Medica Lituanica
Lisa Lehnen, Wigbert Schorcht, Inken Karst, Martin Biedermann, Gerald Kerth, Sebastien J Puechmaille
Population sex ratios are of high ecological relevance, but are challenging to determine in species lacking conspicuous external cues indicating their sex. Acoustic sexing is an option if vocalizations differ between sexes, but is precluded by overlapping distributions of the values of male and female vocalizations in many species. A method allowing the inference of sex ratios despite such an overlap will therefore greatly increase the information extractable from acoustic data. To meet this demand, we developed a novel approach using Approximate Bayesian Computation (ABC) to infer the sex ratio of populations from acoustic data...
2018: PloS One
Alexandre Maes, Xavier Martinez, Karen Druart, Benoist Laurent, Sean Guégan, Christophe H Marchand, Stéphane D Lemaire, Marc Baaden
Proteomic and transcriptomic technologies resulted in massive biological datasets, their interpretation requiring sophisticated computational strategies. Efficient and intuitive real-time analysis remains challenging. We use proteomic data on 1417 proteins of the green microalga Chlamydomonas reinhardtii to investigate physicochemical parameters governing selectivity of three cysteine-based redox post translational modifications (PTM): glutathionylation (SSG), nitrosylation (SNO) and disulphide bonds (SS) reduced by thioredoxins...
June 21, 2018: Journal of Integrative Bioinformatics
Joonyeon Park, Myeongji Cho, Hyeon S Son
We designed and implemented simulation models of bacterial growth and antibiotic resistance to determine the appropriate antibiotics to use against antibiotic-resistant bacteria. Simulation models were designed using individual-based modeling, and a simulation tool, ARSim, was developed to conduct experiments using the models. Simulations of bacterial growth were conducted by virtually growing Klebsiella pneumoniae bacteria in a virtual environment with predefined parameters. Other experiments included predicting the effects of antibiotics when added to two different groups, one group of nonresistant bacteria and another group of both resistant and nonresistant bacteria...
June 21, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
M Natalia C Zarycz, Célia Fonseca Guerra
NMR spectroscopy is one of the most useful methods for detection and characterization of hydrogen bond (H-bond) interactions in biological systems. For H-bonds X-H⋯Y, where X and Y are O or N, it is generally believed that a decrease of 1H-shielding constants relates to a shortening of H-bonds donor-acceptor distance. Here, we investigated computationally the trend of 1H-shielding constants for hydrogen-bonded protons in a series of Guanine C8-substituted GC pair model compounds as a function of the molecular structure...
June 21, 2018: Journal of Physical Chemistry Letters
E Hammond, K S Chan, J C Ames, N Stoyles, C M Sloan, J Guo, J D Newell, E A Hoffman, J C Sieren
PURPOSE: Quantitative computed tomography (QCT) derived measures of lung density are valued methods for objectively characterizing lung parenchymal and peripheral airways disease and are being used in a growing number of lung disease focused trials. Detector and reconstruction improvements in CT technology have allowed for significant radiation dose-reduction in image acquisition with comparable qualitative image quality. We report the impact of detector type and reconstruction type on QCT lung density measures in relation to decreasing dose indices...
June 21, 2018: Medical Physics
John A Hawkins, Stephen K Jones, Ilya J Finkelstein, William H Press
Many large-scale, high-throughput experiments use DNA barcodes, short DNA sequences prepended to DNA libraries, for identification of individuals in pooled biomolecule populations. However, DNA synthesis and sequencing errors confound the correct interpretation of observed barcodes and can lead to significant data loss or spurious results. Widely used error-correcting codes borrowed from computer science (e.g., Hamming, Levenshtein codes) do not properly account for insertions and deletions (indels) in DNA barcodes, even though deletions are the most common type of synthesis error...
June 20, 2018: Proceedings of the National Academy of Sciences of the United States of America
Ricard Argelaguet, Britta Velten, Damien Arnol, Sascha Dietrich, Thorsten Zenz, John C Marioni, Florian Buettner, Wolfgang Huber, Oliver Stegle
Multi-omics studies promise the improved characterization of biological processes across molecular layers. However, methods for the unsupervised integration of the resulting heterogeneous data sets are lacking. We present Multi-Omics Factor Analysis (MOFA), a computational method for discovering the principal sources of variation in multi-omics data sets. MOFA infers a set of (hidden) factors that capture biological and technical sources of variability. It disentangles axes of heterogeneity that are shared across multiple modalities and those specific to individual data modalities...
June 20, 2018: Molecular Systems Biology
David L Brautigan, Shirish Shenolikar
Protein serine/threonine phosphatases (PPPs) are ancient enzymes, with distinct types conserved across eukaryotic evolution. PPPs are segregated into types primarily on the basis of the unique interactions of PPP catalytic subunits with regulatory proteins. The resulting holoenzymes dock substrates distal to the active site to enhance specificity. This review focuses on the subunit and substrate interactions for PPP that depend on short linear motifs. Insights about these motifs from structures of holoenzymes open new opportunities for computational biology approaches to elucidate PPP networks...
June 20, 2018: Annual Review of Biochemistry
Yang Qi, Jeffrey W Martin, Adam W Barb, François Thélot, Anthony Yan, Bruce R Donald, Terrence G Oas
The flexibility of biological macromolecules is an important structural determinant of function. Unfortunately, the correlations between different motional modes are poorly captured by discrete ensemble representations. Here, we present new ways to both represent and visualize correlated interdomain motions. Interdomain motions are determined directly from residual dipolar couplings (RDCs), represented as a continuous conformational distribution, and visualized using the disk-on-sphere (DoS) representation...
June 17, 2018: Journal of Molecular Biology
Venkatesh Inguva, Sagar V Kathuria, Osman Bilsel, Blair James Perot
Kinetic studies of biological macromolecules increasingly use microfluidic mixers to initiate and monitor reaction progress. A motivation for using microfluidic mixers is to reduce sample consumption and decrease mixing time to microseconds. Some applications, such as small-angle x-ray scattering, also require large (>10 micron) sampling areas to ensure high signal-to-noise ratios and to minimize parasitic scattering. Chaotic to marginally turbulent mixers are well suited for these applications because this class of mixers provides a good middle ground between existing laminar and turbulent mixers...
2018: PloS One
Andrej Duh, Marjan Slak Rupnik, Dean Korošak
Computational propaganda deploys social or political bots to try to shape, steer, and manipulate online public discussions and influence decisions. Collective behavior of populations of social bots has not been yet widely studied, although understanding of collective patterns arising from interactions between bots would aid social bot detection. In this study, we show that there are significant differences in collective behavior between population of bots and population of humans as detected from their Twitter activity...
June 2018: Big Data
Mackenna Hill, Estefania Rios, Shyam Kumar Sudhakar, Douglas Roossien, Ciara Maria Caldwell, Dawen Cai, Omar Ahmed, Scott Lempka, Cynthia A Chestek
OBJECTIVE: Neural recording is important for a wide variety of clinical applications. Until recently, recording from the surface of the brain, even when using micro-electrocorticography (µECoG) arrays, was not thought to enable recording from individual neurons. Recent results suggest that when the surface electrode contact size is sufficiently small, it may be possible to record single neurons from the brain's surface. In this study, we use computational techniques to investigate the ability of surface electrodes to record the activity of single neurons...
June 20, 2018: Journal of Neural Engineering
Dario Kringel, Catharina Lippmann, Michael J Parnham, Eija Kalso, Alfred Ultsch, Jörn Lötsch
BACKGROUND: Human genetic research has implicated functional variants of more than one hundred genes in the modulation of persisting pain. Artificial intelligence and machine learning techniques may combine this knowledge with results of genetic research gathered in any context, which permits the identification of the key biological processes involved in chronic sensitization to pain. METHODS: Based on published evidence, a set of 110 genes carrying variants reported to be associated with modulation of the clinical phenotype of persisting pain in eight different clinical settings was submitted to unsupervised machine-learning aimed at functional clustering...
June 19, 2018: European Journal of Pain: EJP
Jonghoon Kim, Seong-Yoon Ryu, Seung-Hak Lee, Ho Yun Lee, Hyunjin Park
OBJECTIVES: Malignant tumours consist of biologically heterogeneous components; identifying and stratifying those various subregions is an important research topic. We aimed to show the effectiveness of an intratumour partitioning method using clustering to identify highly aggressive tumour subregions, determining prognosis based on pre-treatment PET and DWI in stage IV lung adenocarcinoma. METHODS: Eighteen patients who underwent both baseline PET and DWI were recruited...
June 19, 2018: European Radiology
Ziyi Chen, Lijun Quan, Anfei Huang, Qiang Zhao, Yao Yuan, Xuye Yuan, Qin Shen, Jingzhe Shang, Yinyin Ben, F Xiao-Feng Qin, Aiping Wu
The RNA sequencing approach has been broadly used to provide gene-, pathway-, and network-centric analyses for various cell and tissue samples. However, thus far, rich cellular information carried in tissue samples has not been thoroughly characterized from RNA-Seq data. Therefore, it would expand our horizons to better understand the biological processes of the body by incorporating a cell-centric view of tissue transcriptome. Here, a computational model named seq-ImmuCC was developed to infer the relative proportions of 10 major immune cells in mouse tissues from RNA-Seq data...
2018: Frontiers in Immunology
Keying Xu, Junwei Shi, Ali Pourmand, Thirupandiyur S Udayakumar, Nesrin Dogan, Weizhao Zhao, Alan Pollack, Yidong Yang
Gold nanoparticles (GNP) have been intensively investigated for applications in cancer imaging and therapy. Most imaging studies focused on microscopic imaging. Their potential as optical imaging probes for whole body small animal imaging has rarely been explored. Taking advantage of their surface plasmon resonance (SPR) properties, we aim to develop a noninvasive diffuse optical imaging method to map the distribution of a special type of GNP, gold nanorods (GNR), in small animals. We developed an integrated dual-modality imaging system capable of both x-ray computed tomography (XCT) and diffuse optical tomography (DOT)...
June 19, 2018: Scientific Reports
Nick Diederich, Thorsten Bartsch, Hermann Kohlstedt, Martin Ziegler
Memristive systems have gained considerable attention in the field of neuromorphic engineering, because they allow the emulation of synaptic functionality in solid state nano-physical systems. In this study, we show that memristive behavior provides a broad working framework for the phenomenological modelling of cellular synaptic mechanisms. In particular, we seek to understand how close a memristive system can account for the biological realism. The basic characteristics of memristive systems, i.e. voltage and memory behavior, are used to derive a voltage-based plasticity rule...
June 19, 2018: Scientific Reports
Alison E Casey, Ankit Sinha, Rajat Singhania, Julie Livingstone, Paul Waterhouse, Pirashaanthy Tharmapalan, Jennifer Cruickshank, Mona Shehata, Erik Drysdale, Hui Fang, Hyeyeon Kim, Ruth Isserlin, Swneke Bailey, Tiago Medina, Genevieve Deblois, Yu-Jia Shiah, Dalia Barsyte-Lovejoy, Stefan Hofer, Gary Bader, Mathieu Lupien, Cheryl Arrowsmith, Stefan Knapp, Daniel De Carvalho, Hal Berman, Paul C Boutros, Thomas Kislinger, Rama Khokha
The mammary epithelium depends on specific lineages and their stem and progenitor function to accommodate hormone-triggered physiological demands in the adult female. Perturbations of these lineages underpin breast cancer risk, yet our understanding of normal mammary cell composition is incomplete. Here, we build a multimodal resource for the adult gland through comprehensive profiling of primary cell epigenomes, transcriptomes, and proteomes. We define systems-level relationships between chromatin-DNA-RNA-protein states, identify lineage-specific DNA methylation of transcription factor binding sites, and pinpoint proteins underlying progesterone responsiveness...
June 19, 2018: Journal of Cell Biology
Giorgio Trenta
OBJECTIVES: The Probability of Causation (PC) was introduced to compensate objectively and more possible legally the U.S. diseased subjects involved in the nuclear armament activities. METHODS: The methodology is related to the attributable risk concept, but it is widely different from it, since it doesn't evaluate the "attributablity" from a collective point of view, but from a "personalistic" point, that is from the particular exposure condition, from the specific physical parameters and from the biological individual features of the single exposed subject...
November 2017: Giornale Italiano di Medicina del Lavoro Ed Ergonomia
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