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https://www.readbyqxmd.com/read/29244957/hypercementosis-associated-with-enpp1-mutations-and-gaci
#1
V Thumbigere-Math, A Alqadi, N I Chalmers, M B Chavez, E Y Chu, M T Collins, C R Ferreira, K FitzGerald, R I Gafni, W A Gahl, K S Hsu, M S Ramnitz, M J Somerman, S G Ziegler, B L Foster
Mineralization of bones and teeth is tightly regulated by levels of extracellular inorganic phosphate (Pi) and pyrophosphate (PPi). Three regulators that control pericellular concentrations of Pi and PPi include tissue-nonspecific alkaline phosphatase (TNAP), progressive ankylosis protein (ANK), and ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1). Inactivation of these factors results in mineralization disorders affecting teeth and their supporting structures. This study for the first time analyzed the effect of decreased PPi on dental development in individuals with generalized arterial calcification of infancy (GACI) due to loss-of-function mutations in the ENPP1 gene...
December 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/29244826/magpie-simplifying-access-and-execution-of-computational-models-in-the-life-sciences
#2
Christoph Baldow, Sebastian Salentin, Michael Schroeder, Ingo Roeder, Ingmar Glauche
Over the past decades, quantitative methods linking theory and observation became increasingly important in many areas of life science. Subsequently, a large number of mathematical and computational models has been developed. The BioModels database alone lists more than 140,000 Systems Biology Markup Language (SBML) models. However, while the exchange within specific models classes has been supported by standardisation and database efforts, the generic application and especially the re-use of models is still limited by practical issues such as easy and straight forward model execution...
December 15, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29244758/protein-subcellular-localization-with-gaussian-kernel-discriminant-analysis-and-its-kernel-parameter-selection
#3
Shunfang Wang, Bing Nie, Kun Yue, Yu Fei, Wenjia Li, Dongshu Xu
Kernel discriminant analysis (KDA) is a dimension reduction and classification algorithm based on nonlinear kernel trick, which can be novelly used to treat high-dimensional and complex biological data before undergoing classification processes such as protein subcellular localization. Kernel parameters make a great impact on the performance of the KDA model. Specifically, for KDA with the popular Gaussian kernel, to select the scale parameter is still a challenging problem. Thus, this paper introduces the KDA method and proposes a new method for Gaussian kernel parameter selection depending on the fact that the differences between reconstruction errors of edge normal samples and those of interior normal samples should be maximized for certain suitable kernel parameters...
December 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29244501/origins-of-enzyme-catalysis-experimental-findings-for-c-h-activation-new-models-and-their-relevance-to-prevailing-theoretical-constructs
#4
Judith P Klinman, Adam R Offenbacher, Shenshen Hu
The physical basis for enzymatic rate accelerations is a subject of great fundamental interest and of direct relevance to areas that include the de novo design of green catalysts and the pursuit of new drug regimens. Extensive investigations of C-H activating systems have provided considerable insight into the relationship between an enzyme's overall structure and the catalytic chemistry at its active site. This Perspective highlights recent experimental data for two members of distinct, yet iconic C-H activation enzyme classes, lipoxygenases and prokaryotic alcohol dehydrogenases...
December 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29244177/online-bayesian-phylogenetic-inference-theoretical-foundations-via-sequential-monte-carlo
#5
Vu Dinh, Aaron E Darling, Frederick A Matsen Iv
Phylogenetics, the inference of evolutionary trees from molecular sequence data such as DNA, is an enterprise that yields valuable evolutionary understanding of many biological systems. Bayesian phylogenetic algorithms, which approximate a posterior distribution on trees, have become a popular if computationally expensive means of doing phylogenetics. Modern data collection technologies are quickly adding new sequences to already substantial databases. With all current techniques for Bayesian phylogenetics, computation must start anew each time a sequence becomes available, making it costly to maintain an up-to-date estimate of a phylogenetic posterior...
December 13, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29243252/predicting-calvarial-growth-in-normal-and-craniosynostotic-mice-using-a-computational-approach
#6
Arsalan Marghoub, Joseph Libby, Christian Babbs, Erwin Pauws, Michael J Fagan, Mehran Moazen
During postnatal calvarial growth the brain grows gradually and the overlying bones and sutures accommodate that growth until the later juvenile stages. The whole process is coordinated through a complex series of biological, chemical and perhaps mechanical signals between various elements of the craniofacial system. The aim of this study was to investigate to what extent a computational model can accurately predict the calvarial growth in wild-type (WT) and mutant type (MT) Fgfr2C342Y/+ mice displaying bicoronal suture fusion...
December 15, 2017: Journal of Anatomy
https://www.readbyqxmd.com/read/29243243/shikonin-inhibits-myeloid-differentiation-protein-2-to-prevent-lipopolysaccharide-induced-acute-lung-injury
#7
Yali Zhang, Tingting Xu, Zheer Pan, Xiangting Ge, Chuchu Sun, Chun Lu, Hongjin Chen, Zhongxiang Xiao, Bing Zhang, Yuanrong Dai, Guang Liang
BACKGROUND AND PURPOSE: Acute lung injury (ALI) is a challenging clinical syndrome which manifests as an acute inflammatory response. Myeloid differentiation protein 2 (MD2) has an important role in mediating lipopolysaccharide (LPS)-induced inflammation. Currently, there are no effective molecular-based therapies for ALI or viable biomarkers for predicting the severity of disease. Recent preclinical studies have shown that shikonin (SHI), a natural naphthoquinone, prevents LPS-inflammation...
December 15, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/29243094/hierarchical-design-of-artificial-proteins-and-complexes-toward-synthetic-structural-biology
#8
REVIEW
Ryoichi Arai
In multiscale structural biology, synthetic approaches are important to demonstrate biophysical principles and mechanisms underlying the structure, function, and action of bio-nanomachines. A central goal of "synthetic structural biology" is the design and construction of artificial proteins and protein complexes as desired. In this paper, I review recent remarkable progress of an array of approaches for hierarchical design of artificial proteins and complexes that signpost the path forward toward synthetic structural biology as an emerging interdisciplinary field...
December 14, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29241666/identification-of-human-circadian-genes-based-on-time-course-gene-expression-profiles-by-using-a-deep-learning-method
#9
Peng Cui, Tingyan Zhong, Zhuo Wang, Tao Wang, Hongyu Zhao, Chenglin Liu, Hui Lu
Circadian genes express periodically in an approximate 24-h period and the identification and study of these genes can provide deep understanding of the circadian control which plays significant roles in human health. Although many circadian gene identification algorithms have been developed, large numbers of false positives and low coverage are still major problems in this field. In this study we constructed a novel computational framework for circadian gene identification using deep neural networks (DNN) a deep learning algorithm which can represent the raw form of data patterns without imposing assumptions on the expression distribution...
December 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29241664/distinguishing-three-subtypes-of-hematopoietic-cells-based-on-gene-expression-profiles-using-a-support-vector-machine
#10
Yu-Hang Zhang, Yu Hu, Yuchao Zhang, Lan-Dian Hu, Xiangyin Kong
Hematopoiesis is a complicated process involving a series of biological sub-processes that lead to the formation of various blood components. A widely accepted model of early hematopoiesis proceeds from long-term hematopoietic stem cells (LT-HSCs) to multipotent progenitors (MPPs) and then to lineage-committed progenitors. However, the molecular mechanisms of early hematopoiesis have not been fully characterized. In this study, we applied a computational strategy to identify the gene expression signatures distinguishing three types of closely related hematopoietic cells collected in recent studies: (1) hematopoietic stem cell/multipotent progenitor cells; (2) LT-HSCs; and (3) hematopoietic progenitor cells...
December 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29240844/correction-computational-and-biological-evidences-on-the-serotonergic-involvement-of-setacn-antidepressant-like-effect-in-mice
#11
Mariana G Fronza, Lucimar M Pinto Brod, Angela Maria Casaril, Manoela Sacramento, Diego Alves, Lucielli Savegnago
[This corrects the article DOI: 10.1371/journal.pone.0187445.].
2017: PloS One
https://www.readbyqxmd.com/read/29240763/costs-of-task-allocation-with-local-feedback-effects-of-colony-size-and-extra-workers-in-social-insects-and-other-multi-agent-systems
#12
Tsvetomira Radeva, Anna Dornhaus, Nancy Lynch, Radhika Nagpal, Hsin-Hao Su
Adaptive collective systems are common in biology and beyond. Typically, such systems require a task allocation algorithm: a mechanism or rule-set by which individuals select particular roles. Here we study the performance of such task allocation mechanisms measured in terms of the time for individuals to allocate to tasks. We ask: (1) Is task allocation fundamentally difficult, and thus costly? (2) Does the performance of task allocation mechanisms depend on the number of individuals? And (3) what other parameters may affect their efficiency? We use techniques from distributed computing theory to develop a model of a social insect colony, where workers have to be allocated to a set of tasks; however, our model is generalizable to other systems...
December 14, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29240760/novel-linear-motif-filtering-protocol-reveals-the-role-of-the-lc8-dynein-light-chain-in-the-hippo-pathway
#13
Gábor Erdős, Tamás Szaniszló, Mátyás Pajkos, Borbála Hajdu-Soltész, Bence Kiss, Gábor Pál, László Nyitray, Zsuzsanna Dosztányi
Protein-protein interactions (PPIs) formed between short linear motifs and globular domains play important roles in many regulatory and signaling processes but are highly underrepresented in current protein-protein interaction databases. These types of interactions are usually characterized by a specific binding motif that captures the key amino acids shared among the interaction partners. However, the computational proteome-level identification of interaction partners based on the known motif is hindered by the huge number of randomly occurring matches from which biologically relevant motif hits need to be extracted...
December 14, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29239855/experimental-verification-of-stopping-power-prediction-from-single-and-dual-energy-computed-tomography-in-biological-tissues
#14
Christian Möhler, Tom Russ, Patrick Wohlfahrt, Alina Elter, Armin Runz, Christian Richter, Steffen Greilich
An experimental setup for consecutive measurement of ion and x-ray absorption in tissue or other materials is introduced. With this setup using a 3D-printed sample container, the reference stopping-power ratio (SPR) of materials can be measured with an uncertainty of below 0.1%. A total of 65 porcine and bovine tissue samples were prepared for measurement, comprising five samples each of 13 tissue types representing about 80% of the total body mass (three different muscle and fatty tissues, liver, kidney, brain, heart, blood, lung and bone)...
December 14, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/29238817/finite-element-framework-for-computational-fluid-dynamics-in-febio
#15
Dr Gerard A Ateshian, Jay J Shim, Steve A Maas, Jeffrey A Weiss
The mechanics of biological fluids is an important topic in biomechanics, often requiring the use computational tools to analyze problems with realistic geometries and material properties. This study describes the formulation and implementation of a finite element framework for computational fluid dynamics (CFD) in FEBio, a free software designed to meet the computational needs of the biomechanics and biophysics communities (febio.org). This formulation models nearly incompressible flow with a compressible isothermal formulation that uses a physically realistic value for the fluid bulk modulus...
December 13, 2017: Journal of Biomechanical Engineering
https://www.readbyqxmd.com/read/29238276/computer-aided-drug-discovery-in-plant-pathology
#16
REVIEW
Gnanendra Shanmugam, Junhyun Jeon
Control of plant diseases is largely dependent on use of agrochemicals. However, there are widening gaps between our knowledge on plant diseases gained from genetic/mechanistic studies and rapid translation of the knowledge into target-oriented development of effective agrochemicals. Here we propose that the time is ripe for computer-aided drug discovery/design (CADD) in molecular plant pathology. CADD has played a pivotal role in development of medically important molecules over the last three decades. Now, explosive increase in information on genome sequences and three dimensional structures of biological molecules, in combination with advances in computational and informational technologies, opens up exciting possibilities for application of CADD in discovery and development of agrochemicals...
December 2017: Plant Pathology Journal
https://www.readbyqxmd.com/read/29237571/identification-of-genes-related-to-proliferative-diabetic-retinopathy-through-rwr-algorithm-based-on-protein-protein-interaction-network
#17
Jian Zhang, Yan Suo, Min Liu, Xun Xu
Proliferative diabetic retinopathy (PDR) is one of the most common complications of diabetes and can lead to blindness. Proteomic studies have provided insight into the pathogenesis of PDR and a series of PDR-related genes has been identified but are far from fully characterized because the experimental methods are expensive and time consuming. In our previous study, we successfully identified 35 candidate PDR-related genes through the shortest-path algorithm. In the current study, we developed a computational method using the random walk with restart (RWR) algorithm and the protein-protein interaction (PPI) network to identify potential PDR-related genes...
December 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29237427/clinical-applications-and-effectiveness-of-guided-implant-surgery-a-critical-review-based-on-randomized-controlled-trials
#18
Marco Colombo, Carlo Mangano, Eitan Mijiritsky, Mischa Krebs, Uli Hauschild, Thomas Fortin
BACKGROUND: Nowadays implant placement protocols are widespread among clinicians all over the world. However, available literature, only partially analyses what can be potential benefits for the clinicians and patients, often focusing just on specific aspects, such as accuracy. The purpose of this review is to compare computer guided implant placement with conventional treatment protocols. METHODS: A search strategy according to the P-I-C-O format was developed and executed using an electronic MEDLINE plus manual search from 2000 up to December 2016...
December 13, 2017: BMC Oral Health
https://www.readbyqxmd.com/read/29237080/cardiopulmonary-coupling-spectrogram-as-an-ambulatory-clinical-biomarker-of-sleep-stability-and-quality-in-health-sleep-apnea-and-insomnia
#19
Robert Joseph Thomas, Christopher Wood, Matt Travis Bianchi
Study Objectives: Ambulatory tracking of sleep and sleep pathology is rapidly increasing with the introduction of wearable devices. The objective of this study was to evaluate a wearable device which used novel computational analysis of the electrocardiogram (ECG), collected over multiple nights, as a method to track the dynamics of sleep quality in health and disease. Methods: This study used the electrocardiogram as a primary signal, a wearable device, the M1, and an analysis of cardiopulmonary coupling to estimate sleep quality...
December 9, 2017: Sleep
https://www.readbyqxmd.com/read/29237040/conceptual-and-computational-framework-for-logical-modelling-of-biological-networks-deregulated-in-diseases
#20
Arnau Montagud, Pauline Traynard, Loredana Martignetti, Eric Bonnet, Emmanuel Barillot, Andrei Zinovyev, Laurence Calzone
Mathematical models can serve as a tool to formalize biological knowledge from diverse sources, to investigate biological questions in a formal way, to test experimental hypotheses, to predict the effect of perturbations and to identify underlying mechanisms. We present a pipeline of computational tools that performs a series of analyses to explore a logical model's properties. A logical model of initiation of the metastatic process in cancer is used as a transversal example. We start by analysing the structure of the interaction network constructed from the literature or existing databases...
December 8, 2017: Briefings in Bioinformatics
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