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https://www.readbyqxmd.com/read/27923060/the-limitations-of-model-based-experimental-design-and-parameter-estimation-in-sloppy-systems
#1
Andrew White, Malachi Tolman, Howard D Thames, Hubert Rodney Withers, Kathy A Mason, Mark K Transtrum
We explore the relationship among experimental design, parameter estimation, and systematic error in sloppy models. We show that the approximate nature of mathematical models poses challenges for experimental design in sloppy models. In many models of complex biological processes it is unknown what are the relevant physical mechanisms that must be included to explain system behaviors. As a consequence, models are often overly complex, with many practically unidentifiable parameters. Furthermore, which mechanisms are relevant/irrelevant vary among experiments...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27922944/oocyte-vitrification-for-elective-fertility-preservation-the-past-present-and-future
#2
Vinay Gunnala, Glenn Schattman
PURPOSE OF REVIEW: Oocyte cryopreservation is no longer experimental and one of its rapidly growing indications is elective fertility preservation. Currently there is no sufficient evidence to support its practice and therefore its place in IVF remains uncertain. RECENT FINDINGS: Vitrification has superior post-thaw survival and fertilization outcomes compared with oocytes that were frozen with the slow-freeze technique. Oocyte vitrification produces similar IVF outcomes compared with fresh oocytes and is not associated with further obstetrical or perinatal morbidity...
December 5, 2016: Current Opinion in Obstetrics & Gynecology
https://www.readbyqxmd.com/read/27922826/phenotypic-spandrel-absolute-discrimination-and-ligand-antagonism
#3
Paul François, Mathieu Hemery, Kyle A Johnson, Laura N Saunders
We consider the general problem of sensitive and specific discrimination between biochemical species. An important instance is immune discrimination between self and not-self, where it is also observed experimentally that ligands just below the discrimination threshold negatively impact response, a phenomenon called antagonism. We characterize mathematically the generic properties of such discrimination, first relating it to biochemical adaptation. Then, based on basic biochemical rules, we establish that, surprisingly, antagonism is a generic consequence of any strictly specific discrimination made independently from ligand concentration...
December 6, 2016: Physical Biology
https://www.readbyqxmd.com/read/27922601/the-effect-of-extrinsic-mortality-on-genome-size-evolution-in-prokaryotes
#4
Piotr Bentkowski, Cock van Oosterhout, Ben Ashby, Thomas Mock
Mortality has a significant role in prokaryotic ecology and evolution, yet the impact of variations in extrinsic mortality on prokaryotic genome evolution has received little attention. We used both mathematical and agent-based models to reveal how variations in extrinsic mortality affect prokaryotic genome evolution. Our results suggest that the genome size of bacteria increases with increased mortality. A high extrinsic mortality increases the pool of free resources and shortens life expectancy, which selects for faster reproduction, a phenotype we called 'scramblers'...
December 6, 2016: ISME Journal
https://www.readbyqxmd.com/read/27922181/evaluation-of-gas-and-carbon-transport-in-a-methanogenic-bioelectrochemical-system-bes
#5
Christy M Dykstra, Spyros G Pavlostathis
Bioelectrochemical systems (BESs) may be used to upgrade anaerobic digester biogas by directly converting CO2 to CH4 .The objective of this study was to evaluate gas (N2 , CO2 , CH4 , and H2 ) and carbon transport within a methanogenic BES. Four BES configurations were evaluated: abiotic anode with abiotic cathode (AAn-ACa), bioanode with abiotic cathode (BAn-ACa), abiotic anode with biocathode (AAn-BCa), and bioanode with biocathode (BAn-BCa). Transport of N2 , a gas commonly used for flushing anoxic systems, out of the anode headspace ranged from 3...
December 6, 2016: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/27921356/time-processing-impairments-in-preschoolers-at-risk-of-developing-difficulties-in-mathematics
#6
Valentina Tobia, Luca Rinaldi, Gian Marco Marzocchi
The occurrence of time processing problems in individuals with Development Dyscalculia (DD) has favored the view of a general magnitude system devoted to both numerical and temporal information. Yet, this scenario has been partially challenged by studies indicating that time difficulties can be attributed to poor calculation or counting skills, which can support reasoning on time in school-aged children and adults. Here, we tackle this debate by exploring the performance of young children before they fully develop the symbolic number system...
December 5, 2016: Developmental Science
https://www.readbyqxmd.com/read/27921334/synacton-and-individual-activity-of-synthetic-and-natural-corticotropins
#7
T V Vyunova, L A Andreeva, K V Shevchenko, N F Myasoedov
Short endogenous peptides represent one of the most important constituents of the mammalian body's general regulatory system. Some synthesized analogs and modified natural peptides (eg, corticotropins) also show high biological activity. Nevertheless, the mechanism of action of regulatory peptides remains unclear. To explain the effects of peptides of intermolecular processes, the hypothesis that a synactonal mechanism underlies the action of regulatory peptides, exemplified by the heptapeptide Semax, has been proposed...
December 6, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27921305/early-math-trajectories-low-income-children-s-mathematics-knowledge-from-ages-4-to-11
#8
Bethany Rittle-Johnson, Emily R Fyfe, Kerry G Hofer, Dale C Farran
Early mathematics knowledge is a strong predictor of later academic achievement, but children from low-income families enter school with weak mathematics knowledge. An early math trajectories model is proposed and evaluated within a longitudinal study of 517 low-income American children from ages 4 to 11. This model includes a broad range of math topics, as well as potential pathways from preschool to middle grades mathematics achievement. In preschool, nonsymbolic quantity, counting, and patterning knowledge predicted fifth-grade mathematics achievement...
December 6, 2016: Child Development
https://www.readbyqxmd.com/read/27921285/spatiotemporal-distribution-modeling-of-pet-tracer-uptake-in-solid-tumors
#9
Madjid Soltani, Mostafa Sefidgar, Hossein Bazmara, Michael E Casey, Rathan M Subramaniam, Richard L Wahl, Arman Rahmim
OBJECTIVE: Distribution of PET tracer uptake is elaborately modeled via a general equation used for solute transport modeling. This model can be used to incorporate various transport parameters of a solid tumor such as hydraulic conductivity of the microvessel wall, transvascular permeability as well as interstitial space parameters. This is especially significant because tracer delivery and drug delivery to solid tumors are determined by similar underlying tumor transport phenomena, and quantifying the former can enable enhanced prediction of the latter...
December 5, 2016: Annals of Nuclear Medicine
https://www.readbyqxmd.com/read/27920740/spaces-in-the-brain-from-neurons-to-meanings
#10
REVIEW
Christian Balkenius, Peter Gärdenfors
Spaces in the brain can refer either to psychological spaces, which are derived from similarity judgments, or to neurocognitive spaces, which are based on the activities of neural structures. We want to show how psychological spaces naturally emerge from the underlying neural spaces by dimension reductions that preserve similarity structures and the relevant categorizations. Some neuronal representational formats that may generate the psychological spaces are presented, compared, and discussed in relation to the mathematical principles of monotonicity, continuity, and convexity...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27920436/a-statistical-algorithm-showing-coenzyme-q10-and-citrate-synthase-as-biomarkers-for-mitochondrial-respiratory-chain-enzyme-activities
#11
D Yubero, A Adin, R Montero, C Jou, C Jiménez-Mallebrera, A García-Cazorla, A Nascimento, M M O'Callaghan, J Montoya, L Gort, P Navas, A Ribes, M D Ugarte, R Artuch
Laboratory data interpretation for the assessment of complex biological systems remains a great challenge, as occurs in mitochondrial function research studies. The classical biochemical data interpretation of patients versus reference values may be insufficient, and in fact the current classifications of mitochondrial patients are still done on basis of probability criteria. We have developed and applied a mathematic agglomerative algorithm to search for correlations among the different biochemical variables of the mitochondrial respiratory chain in order to identify populations displaying correlation coefficients >0...
December 2016: Scientific Reports
https://www.readbyqxmd.com/read/27920389/resistance-in-persisting-bat-populations-after-white-nose-syndrome-invasion
#12
Kate E Langwig, Joseph R Hoyt, Katy L Parise, Winifred F Frick, Jeffrey T Foster, A Marm Kilpatrick
Increases in anthropogenic movement have led to a rise in pathogen introductions and the emergence of infectious diseases in naive host communities worldwide. We combined empirical data and mathematical models to examine changes in disease dynamics in little brown bat (Myotis lucifugus) populations following the introduction of the emerging fungal pathogen Pseudogymnoascus destructans, which causes the disease white-nose syndrome. We found that infection intensity was much lower in persisting populations than in declining populations where the fungus has recently invaded...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27920175/bridging-the-gap-between-experimental-data-and-model-parameterization-for-chikungunya-virus-transmission-predictions
#13
Rebecca C Christofferson, Christopher N Mores, Helen J Wearing
Chikungunya virus (CHIKV) has experienced 2 major expansion events in the last decade. The most recently emerged sublineage (ECSA-V) was shown to have increased efficiency in a historically secondary vector, Aedes albopictus, leading to speculation that this was a major factor in expansion. Subsequently, a number of experimental studies focused on the vector competence of CHIKV, as well as transmission modeling efforts. Mathematical models have used these data to inform their own investigations, but some have incorrectly parameterized the extrinsic incubation period (EIP) of the mosquitoes, using vector competence data...
December 15, 2016: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/27919850/detection-and-differentiation-of-early-hepatocellular-carcinoma-from-cirrhosis-using-ct-perfusion-in-a-rat-liver-model
#14
Jin-Ping Li, Guang-Long Feng, Da-Qing Li, Hai-Bo Wang, De-Li Zhao, Yong Wan, Hui-Jie Jiang
BACKGROUND: Functional imaging such as CT perfusion can detect morphological and hemodynamic changes in hepatocellular carcinoma (HCC). Pre-carcinoma and early HCC nodules are difficult to differentiate by observing only their hemodynamics changes. The present study aimed to investigate hemodynamic parameters and evaluate their differential diagnostic cut-off between pre-carcinoma and early HCC nodules using CT perfusion and receiver operating characteristic (ROC) curves. METHODS: Male Wistar rats were randomly divided into control (n=20) and experimental (n=70) groups...
December 2016: Hepatobiliary & Pancreatic Diseases International: HBPD INT
https://www.readbyqxmd.com/read/27919524/demystifying-the-cytokine-network-mathematical-models-point-the-way
#15
REVIEW
Penelope A Morel, Robin E C Lee, James R Faeder
Cytokines provide the means by which immune cells communicate with each other and with parenchymal cells. There are over one hundred cytokines and many exist in families that share receptor components and signal transduction pathways, creating complex networks. Reductionist approaches to understanding the role of specific cytokines, through the use of gene-targeted mice, have revealed further complexity in the form of redundancy and pleiotropy in cytokine function. Creating an understanding of the complex interactions between cytokines and their target cells is challenging experimentally...
December 2, 2016: Cytokine
https://www.readbyqxmd.com/read/27918797/going-nuclear-evidence-implicating-the-cell-nucleus-in-mechanotransduction
#16
Spencer E Szczesny, Robert L Mauck
Biophysical stimuli presented to cells via micro-environmental properties (e.g., alignment, stiffness) or external forces have a significant impact on their function and behavior. Recently, the cell nucleus has been identified as a mechano-responsive organelle that contributes to the perception and response to mechanical stimuli. However, the specific mechanotransduction mechanisms that mediate these effects have not been clearly defined. Here, we review the evidence supporting (and refuting) three hypothetical nuclear mechanotransduction mechanisms: physical reorganization of chromatin, signaling at the nuclear envelope, and altered cytoskeletal structure/tension due to nuclear remodeling...
December 3, 2016: Journal of Biomechanical Engineering
https://www.readbyqxmd.com/read/27918656/aerobic-evaluation-in-elite-slalom-kayakers-using-tethered-canoe-system-a-new-proposal
#17
Homero Gustavo Ferrari, Leonardo H D Messias, Ivan G M Reis, Claudio A Gobatto, Filipe A B Sousa, Camila C S Serra, Fúlvia B Manchado-Gobatto
BACKGROUND: Among other aspects, aerobic fitness is indispensable for performance in slalom canoe. PURPOSE: The aims of the study were to propose the maximal lactate steady state (MLSS) and critical force (CF) tests using a tethered canoe system as new strategies for aerobic evaluation in elite slalom kayakers. Also, we studied the relationship between the aerobic parameters from these tests and the kayakers' performances. METHODS: Twelve male elite slalom kayakers from the Brazilian National Team participated in this study...
December 5, 2016: International Journal of Sports Physiology and Performance
https://www.readbyqxmd.com/read/27918588/optimization-of-a-multi-product-intra-supply-chain-system-with-failure-in-rework
#18
Singa Wang Chiu, Shin-Wei Chen, Chih-Kai Chang, Yuan-Shyi Peter Chiu
Globalization has created tremendous opportunities, but also made business environment highly competitive and turbulent. To gain competitive advantage, management of present-day transnational firms always seeks options to trim down various transaction and coordination costs, especially in the area of controllable intra-supply chain system. This study investigates a multi-product intra-supply chain system with failure in rework. To achieve maximum machine utilization, multiple products are fabricated in succession on a single machine...
2016: PloS One
https://www.readbyqxmd.com/read/27918587/an-alignment-free-algorithm-in-comparing-the-similarity-of-protein-sequences-based-on-pseudo-markov-transition-probabilities-among-amino-acids
#19
Yushuang Li, Tian Song, Jiasheng Yang, Yi Zhang, Jialiang Yang
In this paper, we have proposed a novel alignment-free method for comparing the similarity of protein sequences. We first encode a protein sequence into a 440 dimensional feature vector consisting of a 400 dimensional Pseudo-Markov transition probability vector among the 20 amino acids, a 20 dimensional content ratio vector, and a 20 dimensional position ratio vector of the amino acids in the sequence. By evaluating the Euclidean distances among the representing vectors, we compare the similarity of protein sequences...
2016: PloS One
https://www.readbyqxmd.com/read/27918434/mass-transport-through-nanostructured-membranes-towards-a-predictive-tool
#20
Siavash Darvishmanesh, Bart Van der Bruggen
This study proposes a new mechanism to understand the transport of solvents through nanostructured membranes from a fundamental point of view. The findings are used to develop readily applicable mathematical models to predict solvent fluxes and solute rejections through solvent resistant membranes used for nanofiltration. The new model was developed based on a pore-flow type of transport. New parameters found to be of fundamental importance were introduced to the equation, i.e., the affinity of the solute and the solvent for the membrane expressed as the hydrogen-bonding contribution of the solubility parameter for the solute, solvent and membrane...
December 2, 2016: Membranes
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