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https://www.readbyqxmd.com/read/28653341/opensimroot-widening-the-scope-and-application-of-root-architectural-models
#1
Johannes A Postma, Christian Kuppe, Markus R Owen, Nathan Mellor, Marcus Griffiths, Malcolm J Bennett, Jonathan P Lynch, Michelle Watt
OpenSimRoot is an open-source, functional-structural plant model and mathematical description of root growth and function. We describe OpenSimRoot and its functionality to broaden the benefits of root modeling to the plant science community. OpenSimRoot is an extended version of SimRoot, established to simulate root system architecture, nutrient acquisition and plant growth. OpenSimRoot has a plugin, modular infrastructure, coupling single plant and crop stands to soil nutrient and water transport models. It estimates the value of root traits for water and nutrient acquisition in environments and plant species...
June 27, 2017: New Phytologist
https://www.readbyqxmd.com/read/28653013/estimation-of-signal-and-noise-for-a-whole-body-research-photon-counting-ct-system
#2
Zhoubo Li, Shuai Leng, Zhicong Yu, Steffen Kappler, Cynthia H McCollough
Photon-counting detector CT has a large number of acquisition parameters that require optimization, particularly the energy threshold configurations. Fast and accurate estimation of both signal and noise in photon-counting CT (PCCT) images can facilitate such optimization. Using the detector response function of a research PCCT system, we derived mathematical models for both signal and noise estimation, taking into account beam spectrum and filtration, object attenuation, water beam hardening, detector response, radiation dose, energy thresholds, and the propagation of noise...
April 2017: Journal of Medical Imaging
https://www.readbyqxmd.com/read/28652353/disentangling-the-effects-of-selection-and-loss-bias-on-gene-dynamics
#3
Jaime Iranzo, José A Cuesta, Susanna Manrubia, Mikhail I Katsnelson, Eugene V Koonin
We combine mathematical modeling of genome evolution with comparative analysis of prokaryotic genomes to estimate the relative contributions of selection and intrinsic loss bias to the evolution of different functional classes of genes and mobile genetic elements (MGE). An exact solution for the dynamics of gene family size was obtained under a linear duplication-transfer-loss model with selection. With the exception of genes involved in information processing, particularly translation, which are maintained by strong selection, the average selection coefficient for most nonparasitic genes is low albeit positive, compatible with observed positive correlation between genome size and effective population size...
June 26, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28652334/dissecting-and-modeling-zeaxanthin-and-lutein-dependent-nonphotochemical-quenching-in-arabidopsis-thaliana
#4
Michelle Leuenberger, Jonathan M Morris, Arnold M Chan, Lauriebeth Leonelli, Krishna K Niyogi, Graham R Fleming
Photosynthetic organisms use various photoprotective mechanisms to dissipate excess photoexcitation as heat in a process called nonphotochemical quenching (NPQ). Regulation of NPQ allows for a rapid response to changes in light intensity and in vascular plants, is primarily triggered by a pH gradient across the thylakoid membrane (∆pH). The response is mediated by the PsbS protein and various xanthophylls. Time-correlated single-photon counting (TCSPC) measurements were performed on Arabidopsis thaliana to quantify the dependence of the response of NPQ to changes in light intensity on the presence and accumulation of zeaxanthin and lutein...
June 26, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28652171/common-and-diverse-elements-of-ion-channels-and-receptors-underlying-electrical-activity-in-endocrine-pituitary-cells
#5
REVIEW
Patrick A Fletcher, Arthur Sherman, Stanko S Stojilkovic
The pituitary gland contains six types of endocrine cells defined by hormones they secrete: corticotrophs, melanotrophs, gonadotrophs, thyrotrophs, somatotrophs, and lactotrophs. All these cell types are electrically excitable, and voltage-gated calcium influx is the major trigger for their hormone secretion. Along with hormone intracellular content, G-protein-coupled receptor and ion channel expression can also be considered as defining cell type identity. While many aspects of the developmental and activity dependent regulation of hormone and G-protein-coupled receptor expression have been elucidated, much less is known about the regulation of the ion channels needed for excitation-secretion coupling in these cells...
June 23, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28652129/evolutionary-dynamics-and-significance-of-multiple-subclonal-mutations-in-cancer
#6
REVIEW
Robert A Beckman, Lawrence A Loeb
For the last 40 years the authors have collaborated on trying to understand the complexities of human cancer by formulating testable mathematical models that are based on mutation accumulation in human malignancies. We summarize the concepts encompassed by multiple mutations in human cancers in the context of source, accumulation during carcinogenesis and tumor progression, and therapeutic consequences. We conclude that the efficacious treatment of human cancer by targeted therapy will involve individualized, uniquely directed specific agents singly and in simultaneous combinations, and take into account the importance of targeting resistant subclonal mutations, particularly those subclones with alterations in DNA repair genes, DNA polymerase, and other genes required to maintain genetic stability...
June 9, 2017: DNA Repair
https://www.readbyqxmd.com/read/28651999/a-physiologically-based-model-for-tramadol-pharmacokinetics-in-horses
#7
Roberto Andrea Abbiati, Petra Cagnardi, Giuliano Ravasio, Roberto Villa, Davide Manca
This work proposes an application of a minimal complexity physiologically based pharmacokinetic model to predict tramadol concentration vs time profiles in horses. Tramadol is an opioid analgesic also used for veterinary treatments. Researchers and medical doctors can profit from the application of mathematical models as supporting tools to optimize the pharmacological treatment of animal species. The proposed model is based on physiology but adopts the minimal compartmental architecture necessary to describe the experimental data...
June 23, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28651969/projectivity-is-the-mathematical-code-of-syntax-comment-on-dependency-distance-a-new-perspective-on-syntactic-patterns-in-natural-languages-by-haitao-liu-et-al
#8
https://www.readbyqxmd.com/read/28651870/advanced-nutrient-removal-from-surface-water-by-a-consortium-of-attached-microalgae-and-bacteria-a-review
#9
REVIEW
Junzhuo Liu, Yonghong Wu, Chenxi Wu, Koenraad Muylaert, Wim Vyverman, Han-Qing Yu, Raúl Muñoz, Bruce Rittmann
Innovative and cost-effective technologies for advanced nutrient removal from surface water are urgently needed for improving water quality. Conventional biotechnologies, such as ecological floating beds, or constructed wetlands, are not effective in removing nutrients present at low-concentration. However, microalgae-bacteria consortium is promising for advanced nutrient removal from wastewater. Suspended algal-bacterial systems can easily wash out unless the hydraulic retention time is long, attached microalgae-bacteria consortium is more realistic...
June 13, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28651375/chromatographic-and-computational-assessment-of-lipophilicity-of-new-anticancer-acetylenequinoline-derivatives
#10
Krzysztof Marciniec, Stanislaw Boryczka
The lipophilicity of a series of anticancer propargylquinoline derivatives is investigated using both chromatographic and computational methods. The parameters of the tested compounds' relative lipophilicity (logkw) are determined experimentally by the high-performance liquid chromatographic method (RP-HPLC, Accucore C18 column), using mixtures of acetonitrile and water as mobile phases. Mobile phase acetonitrile concentrations range between 50 and 80%. The logk values of the investigated compounds are linearly dependent upon the acetonitrile concentration...
June 23, 2017: Journal of Chromatographic Science
https://www.readbyqxmd.com/read/28651070/assessment-of-temporal-predictive-models-for-health-care-using-a-formal-method
#11
Ward van Breda, Mark Hoogendoorn, A E Eiben, Matthias Berking
Recent developments in the field of sensor devices provide new possibilities to measure a variety of health related aspects in a precise and fine-grained manner. Subsequently, more empirical data will be generated than ever before. While this greatly improves the opportunities for creating accurate predictive models, other types of models besides the more traditional machine learning approaches can provide insights into temporal relationships in the data. Models that express temporal relationships between states in a mathematical manner are examples of such models...
June 17, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28650823/bi-level-and-bi-objective-p-median-type-problems-for-integrative-clustering-application-to-analysis-of-cancer-gene-expression-and-drug-response-data
#12
Anton V Ushakov, Xenia Klimentova, Igor Vasilyev
Recent advances in high-throughput technologies have given rise to collecting large amounts of multidimensional heterogeneous data that provide diverse information on the same biological samples. Integrative analysis of such multisource datasets may reveal new biological insights into complex biological mechanisms and therefore remains an important research field in systems biology. Most of the modern integrative clustering approaches rely on independent analysis of each dataset and consensus clustering, probabilistic or statistical modeling, while flexible distance-based integrative clustering techniques are sparsely covered...
October 27, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28649713/mechanistic-modeling-of-the-loss-of-protein-sieving-due-to-internal-and-external-fouling-of-microfilters
#13
Glen R Bolton, Alex J Apostolidis
Fed-batch and perfusion cell culture processes used to produce therapeutic proteins can utilize microfilters for product harvest. In this study, new explicit mathematical models of sieving loss due to internal membrane fouling, external membrane fouling, or a combination of the two were generated. The models accounted for membrane and cake structures and hindered solute transport. Internal membrane fouling was assumed to occur due to the accumulation of foulant on either membrane pore walls (pore-retention model) or membrane fibers (fiber-retention model)...
June 26, 2017: Biotechnology Progress
https://www.readbyqxmd.com/read/28649444/reverse-engineering-highlights-potential-principles-of-large-gene-regulatory-network-design-and-learning
#14
Clément Carré, André Mas, Gabriel Krouk
Inferring transcriptional gene regulatory networks from transcriptomic datasets is a key challenge of systems biology, with potential impacts ranging from medicine to agronomy. There are several techniques used presently to experimentally assay transcription factors to target relationships, defining important information about real gene regulatory networks connections. These techniques include classical ChIP-seq, yeast one-hybrid, or more recently, DAP-seq or target technologies. These techniques are usually used to validate algorithm predictions...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28649439/mechanisms-of-action-of-sacubitril-valsartan-on-cardiac-remodeling-a-systems-biology-approach
#15
Oriol Iborra-Egea, Carolina Gálvez-Montón, Santiago Roura, Isaac Perea-Gil, Cristina Prat-Vidal, Carolina Soler-Botija, Antoni Bayes-Genis
Sacubitril/Valsartan, proved superiority over other conventional heart failure management treatments, but its mechanisms of action remains obscure. In this study, we sought to explore the mechanistic details for Sacubitril/Valsartan in heart failure and post-myocardial infarction remodeling, using an in silico, systems biology approach. Myocardial transcriptome obtained in response to myocardial infarction in swine was analyzed to address post-infarction ventricular remodeling. Swine transcriptome hits were mapped to their human equivalents using Reciprocal Best (blast) Hits, Gene Name Correspondence, and InParanoid database...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28649432/an-individual-based-model-for-collective-cancer-cell-migration-explains-speed-dynamics-and-phenotype-variability-in-response-to-growth-factors
#16
Damian Stichel, Alistair M Middleton, Benedikt F Müller, Sofia Depner, Ursula Klingmüller, Kai Breuhahn, Franziska Matthäus
Collective cell migration is a common phenotype in epithelial cancers, which is associated with tumor cell metastasis and poor patient survival. However, the interplay between physiologically relevant pro-migratory stimuli and the underlying mechanical cell-cell interactions are poorly understood. We investigated the migratory behavior of different collectively migrating non-small cell lung cancer cell lines in response to motogenic growth factors (e.g. epidermal growth factor) or clinically relevant small compound inhibitors...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28649210/the-relationship-between-handedness-and-mathematics-is-non-linear-and-is-moderated-by-gender-age-and-type-of-task
#17
Giovanni Sala, Michela Signorelli, Giulia Barsuola, Martina Bolognese, Fernand Gobet
The relationship between handedness and mathematical ability is still highly controversial. While some researchers have claimed that left-handers are gifted in mathematics and strong right-handers perform the worst in mathematical tasks, others have more recently proposed that mixed-handers are the most disadvantaged group. However, the studies in the field differ with regard to the ages and the gender of the participants, and the type of mathematical ability assessed. To disentangle these discrepancies, we conducted five studies in several Italian schools (total participants: N = 2,314), involving students of different ages (six to seventeen) and a range of mathematical tasks (e...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28649197/a-minimal-model-describing-hexapedal-interlimb-coordination-the-tegotae-based-approach
#18
Dai Owaki, Masashi Goda, Sakiko Miyazawa, Akio Ishiguro
Insects exhibit adaptive and versatile locomotion despite their minimal neural computing. Such locomotor patterns are generated via coordination between leg movements, i.e., an interlimb coordination, which is largely controlled in a distributed manner by neural circuits located in thoracic ganglia. However, the mechanism responsible for the interlimb coordination still remains elusive. Understanding this mechanism will help us to elucidate the fundamental control principle of animals' agile locomotion and to realize robots with legs that are truly adaptive and could not be developed solely by conventional control theories...
2017: Frontiers in Neurorobotics
https://www.readbyqxmd.com/read/28649196/estimation-of-time-varying-intrinsic-and-reflex-dynamic-joint-stiffness-during-movement-application-to-the-ankle-joint
#19
Diego L Guarín, Robert E Kearney
Dynamic joint stiffness determines the relation between joint position and torque, and plays a vital role in the control of posture and movement. Dynamic joint stiffness can be quantified during quasi-stationary conditions using disturbance experiments, where small position perturbations are applied to the joint and the torque response is recorded. Dynamic joint stiffness is composed of intrinsic and reflex mechanisms that act and change together, so that nonlinear, mathematical models and specialized system identification techniques are necessary to estimate their relative contributions to overall joint stiffness...
2017: Frontiers in Computational Neuroscience
https://www.readbyqxmd.com/read/28649118/numbers-for-the-innumerate-everyday-arithmetic-and-atlantic-capitalism
#20
Caitlin Rosenthal
In nineteenth-century America and the Atlantic world, the "rule of three" was usually regarded as the endpoint of a basic mathematics education. This essay considers the importance of the rule as a technology that enabled broader access to the calculations necessary to participate in the increasingly global market economy. Used by workmen, women, and even the enslaved, the rule and related tools translated basic literacy into practical numeracy. By doing so, it offered a diverse range of people the ability to negotiate more effectively...
2017: Technology and Culture
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