keyword
MENU ▼
Read by QxMD icon Read
search

Agent based model

keyword
https://www.readbyqxmd.com/read/27922601/the-effect-of-extrinsic-mortality-on-genome-size-evolution-in-prokaryotes
#1
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/27920532/the-effect-of-magnetic-nanoparticles-on-neuronal-differentiation-of-induced-pluripotent-stem-cell-derived-neural-precursors
#2
Klára Jiráková, Monika Šeneklová, Daniel Jirák, Karolína Turnovcová, Magda Vosmanská, Michal Babič, Daniel Horák, Pavel Veverka, Pavla Jendelová
INTRODUCTION: Magnetic resonance (MR) imaging is suitable for noninvasive long-term tracking. We labeled human induced pluripotent stem cell-derived neural precursors (iPSC-NPs) with two types of iron-based nanoparticles, silica-coated cobalt zinc ferrite nanoparticles (CZF) and poly-l-lysine-coated iron oxide superparamagnetic nanoparticles (PLL-coated γ-Fe2O3) and studied their effect on proliferation and neuronal differentiation. MATERIALS AND METHODS: We investigated the effect of these two contrast agents on neural precursor cell proliferation and differentiation capability...
2016: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/27920432/discovery-of-an-enzyme-and-substrate-selective-inhibitor-of-adam10-using-an-exosite-binding-glycosylated-substrate
#3
Franck Madoux, Daniela Dreymuller, Jean-Phillipe Pettiloud, Radleigh Santos, Christoph Becker-Pauly, Andreas Ludwig, Gregg B Fields, Thomas Bannister, Timothy P Spicer, Mare Cudic, Louis D Scampavia, Dmitriy Minond
ADAM10 and ADAM17 have been shown to contribute to the acquired drug resistance of HER2-positive breast cancer in response to trastuzumab. The majority of ADAM10 and ADAM17 inhibitor development has been focused on the discovery of compounds that bind the active site zinc, however, in recent years, there has been a shift from active site to secondary substrate binding site (exosite) inhibitor discovery in order to identify non-zinc-binding molecules. In the present work a glycosylated, exosite-binding substrate of ADAM10 and ADAM17 was utilized to screen 370,276 compounds from the MLPCN collection...
December 2016: Scientific Reports
https://www.readbyqxmd.com/read/27919958/dietary-flavonoids-luteolin-and-quercetin-suppressed-cancer-stem-cell-properties-and-metastatic-potential-of-isolated-prostate-cancer-cells
#4
Pei-Hsun Tsai, Chia-Hsiung Cheng, Chun-Yu Lin, Ying-Tang Huang, Lung-Ta Lee, Chithan C Kandaswami, Yo-Chuen Lin, Kevin Po-Hao Lee, Chin-Chun Hung, Jiuan-Jiuan Hwang, Ferng-Chun Ke, Geen-Dong Chang, Ming-Ting Lee
A highly invasive Du145-III subline was isolated by three successive passages of the parental Du145 prostate tumor cell line (Du145-P) through a Boyden chamber with matrigel-coated membrane support. Du145-III cells showed great invasion potential based on their increased ability to spread/migrate and enhanced expression/secretion of the matrix metalloproteinase 9 (MMP9). Du145-III cells exerted vasculogenic mimicry (VM) properties, reminiscent of endothelial cell characteristics and expressed elevated levels of cancer stem cell (CSC) markers, including Nanog, Sox2, CD44 and ABCG2 and ability to self-renew...
December 2016: Anticancer Research
https://www.readbyqxmd.com/read/27919007/challenges-in-assignment-of-allosteric-effects-in-cytochrome-p450-catalyzed-substrate-oxidations-to-structural-dynamics-in-the-hemoprotein-architecture
#5
Peter Hlavica
Cytochrome P450s (CYP) represent a superfamily of b-type hemoproteins catalyzing NAD(P)H-dependent oxidative biotransformation of a vast array of natural and xenobiotic compounds. Many eu- and prokaryotic members of this class of monooxygenases display complex non-Michaelis-Menten saturation kinetics, suggestive of homo-/heterotropic cooperativity arising from substrate-/effector-induced allosteric interactions. Here, the paradigm of multiple-ligand occupancy of the catalytic pocket in combination with enzyme oligomerization provides the most favored explanations for the atypical kinetic patterns...
November 25, 2016: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/27917409/gadolinium-functionalized-peptide-amphiphile-micelles-for-multimodal-imaging-of-atherosclerotic-lesions
#6
Sang Pil Yoo, Federico Pineda, John C Barrett, Christopher Poon, Matthew Tirrell, Eun Ji Chung
The leading causes of morbidity and mortality globally are cardiovascular diseases, and nanomedicine can provide many improvements including disease-specific targeting, early detection, and local delivery of diagnostic agents. To this end, we designed fibrin-binding, peptide amphiphile micelles (PAMs), achieved by incorporating the targeting peptide cysteine-arginine-glutamic acid-lysine-alanine (CREKA), with two types of amphiphilic molecules containing the gadoliniuim (Gd) chelator diethylenetriaminepentaacetic acid (DTPA), DTPA-bis(stearylamide)(Gd), and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[(poly(ethylene glycol) (PEG))-2000]-DTPA(Gd) (DSPE-PEG2000-DTPA(Gd))...
November 30, 2016: ACS Omega
https://www.readbyqxmd.com/read/27917281/gene-therapy-based-on-interleukin-12-loaded-chitosan-nanoparticles-in-a-mouse-model-of-fibrosarcoma
#7
Saiedeh Razi Soofiyani, Somayeh Hallaj-Nezhadi, Farzaneh Lotfipour, Akbar Mohammad Hosseini, Behzad Baradaran
OBJECTIVES: Interleukin-12 (IL-12) as a cytokine has been proved to have a critical role in stimulating the immune system and has been used as immunotherapeutic agents in cancer gene therapy. Chitosan as a polymer, with high ability of binding to nucleic acids is a good candidate for gene delivery since it is biodegradable, biocompatible and non-allergenic polysaccharide. The objective of the present study was to investigate the effects of cells transfected with IL-12 loaded chitosan nanoparticles on the regression of fibrosarcoma tumor cells (WEHI-164) in vivo...
November 2016: Iranian Journal of Basic Medical Sciences
https://www.readbyqxmd.com/read/27916841/market-model-for-resource-allocation-in-emerging-sensor-networks-with-reinforcement-learning
#8
Yue Zhang, Bin Song, Ying Zhang, Xiaojiang Du, Mohsen Guizani
Emerging sensor networks (ESNs) are an inevitable trend with the development of the Internet of Things (IoT), and intend to connect almost every intelligent device. Therefore, it is critical to study resource allocation in such an environment, due to the concern of efficiency, especially when resources are limited. By viewing ESNs as multi-agent environments, we model them with an agent-based modelling (ABM) method and deal with resource allocation problems with market models, after describing users' patterns...
November 29, 2016: Sensors
https://www.readbyqxmd.com/read/27915183/search-for-new-potential-anticonvulsants-with-anxiolytic-and-antidepressant-properties-among-derivatives-of-4-4-diphenylpyrrolidin-2-one
#9
Katarzyna Malawska, Aleksandra Rak, Beata Gryzło, Kinga Sałat, Małgorzata Michałowska, Elżbieta Żmudzka, Krzysztof Lodarski, Barbara Malawska, Katarzyna Kulig
BACKGROUND: The aim of this study was to synthesize a series of new N-Mannich bases derived from 4,4-diphenylpyrrolidin-2-one having differently substituted 4-phenylpiperazines as potential anticonvulsant agents with additional (beneficial) pharmacological properties. METHODS: The target compounds 8-12 were prepared in one step from the 4-substituted phenylpiperazines, paraformaldehyde, and synthesized 4,4-diphenylpyrrolodin-2-one (7) by a Mannich-type reaction...
September 22, 2016: Pharmacological Reports: PR
https://www.readbyqxmd.com/read/27913508/risk-stratification-and-management-of-acute-pulmonary-embolism
#10
Cecilia Becattini, Giancarlo Agnelli
The clinical management of patients with acute pulmonary embolism is rapidly changing over the years. The widening spectrum of clinical management strategies for these patients requires effective tools for risk stratification. Patients at low risk for death could be candidates for home treatment or early discharge. Clinical models with high negative predictive value have been validated that could be used to select patients at low risk for death. In a major study and in several meta-analyses, thrombolysis in hemodynamically stable patients was associated with unacceptably high risk for major bleeding complications or intracranial hemorrhage...
December 2, 2016: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/27912754/bovine-mastitis-prevalence-risk-factors-and-isolation-of-staphylococcus-aureus-in-dairy-herds-at-hawassa-milk-shed-south-ethiopia
#11
Rahmeto Abebe, Hagere Hatiya, Mesele Abera, Bekele Megersa, Kassahun Asmare
BACKGROUND: Mastitis is a disease of major economic importance in dairy industry worldwide. It is of particular concern in developing countries like Ethiopia, where milk and milk products are scarce. The objectives of the study were to estimate the prevalence of mastitis, identify the cow-and herd-level potential risk factors and isolate Staphylococcus aureus, one of etiological agents for contagious mastitis, from cows positive for mastitis. A total of 529 lactating cows selected randomly from 95 herds were screened by California mastitis test (CMT) for sub-clinical mastitis...
December 3, 2016: BMC Veterinary Research
https://www.readbyqxmd.com/read/27911980/cell-based-dna-demethylation-detection-system-for-screening-of-epigenetic-drugs-in-2d-3d-and-xenograft-models
#12
Khushboo Agrawal, Viswanath Das, Miroslav Otmar, Marcela Krečmerová, Petr Džubák, Marián Hajdúch
Aberrant DNA methylation that results in silencing of genes has remained a significant interest in cancer research. Despite major advances, the success of epigenetic therapy is elusive due to narrow therapeutic window. A wide variety of naturally occurring epigenetic agents and synthetic molecules that can alter methylation patterns exist, however, their usefulness in epigenetic therapy remains unknown. This underlines the need for effective tumor models for large-scale screening of drug candidates with potent hypomethylation activity...
December 2, 2016: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/27911951/body-surface-area-and-baseline-blood-pressure-predict-subclinical-anthracycline-cardiotoxicity-in-women-treated-for-early-breast-cancer
#13
Paul Kotwinski, Gillian Smith, Jackie Cooper, Julie Sanders, Louise Ma, Albert Teis, David Kotwinski, Michael Mythen, Dudley J Pennell, Alison Jones, Hugh Montgomery
BACKGROUND AND AIMS: Anthracyclines are highly effective chemotherapeutic agents which may cause long-term cardiac damage (chronic anthracycline cardiotoxicity) and heart failure. The pathogenesis of anthracycline cardiotoxicity remains incompletely understood and individual susceptibility difficult to predict. We sought clinical features which might contribute to improved risk assessment. METHODS: Subjects were women with early breast cancer, free of pre-existing cardiac disease...
2016: PloS One
https://www.readbyqxmd.com/read/27911291/a-metal-free-method-for-producing-mri-contrast-at-amyloid-%C3%AE
#14
Silvia Hilt, Tang Tang, Jeffrey H Walton, Madhu Budamagunta, Izumi Maezawa, Tamás Kálai, Kálmán Hideg, Vikrant Singh, Heike Wulff, Qizhi Gong, Lee-Way Jin, Angelique Louie, John C Voss
Alzheimer's disease (AD) is characterized by depositions of the amyloid-β (Aβ) peptide in the brain. The disease process develops over decades, with substantial neurological loss occurring before a clinical diagnosis of dementia can be rendered. It is therefore imperative to develop methods that permit early detection and monitoring of disease progression. In addition, the multifactorial pathogenesis of AD has identified several potential avenues for AD intervention. Thus, evaluation of therapeutic candidates over lengthy trial periods also demands a practical, noninvasive method for measuring Aβ in the brain...
November 26, 2016: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/27910877/a-comprehensive-map-of-molecular-drug-targets
#15
Rita Santos, Oleg Ursu, Anna Gaulton, A Patrícia Bento, Ramesh S Donadi, Cristian G Bologa, Anneli Karlsson, Bissan Al-Lazikani, Anne Hersey, Tudor I Oprea, John P Overington
The success of mechanism-based drug discovery depends on the definition of the drug target. This definition becomes even more important as we try to link drug response to genetic variation, understand stratified clinical efficacy and safety, rationalize the differences between drugs in the same therapeutic class and predict drug utility in patient subgroups. However, drug targets are often poorly defined in the literature, both for launched drugs and for potential therapeutic agents in discovery and development...
December 2, 2016: Nature Reviews. Drug Discovery
https://www.readbyqxmd.com/read/27910875/an-integrated-modelling-framework-from-cells-to-organism-based-on-a-cohort-of-digital-embryos
#16
Paul Villoutreix, Julien Delile, Barbara Rizzi, Louise Duloquin, Thierry Savy, Paul Bourgine, René Doursat, Nadine Peyriéras
We conducted a quantitative comparison of developing sea urchin embryos based on the analysis of five digital specimens obtained by automatic processing of in toto 3D+ time image data. These measurements served the reconstruction of a prototypical cell lineage tree able to predict the spatiotemporal cellular organisation of a normal sea urchin blastula. The reconstruction was achieved by designing and tuning a multi-level probabilistic model that reproduced embryo-level dynamics from a small number of statistical parameters characterising cell proliferation, cell surface area and cell volume evolution along the cell lineage...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27909053/endoplasmic-reticulum-stress-and-ca2-depletion-differentially-modulate-the-sterol-regulatory-protein-pcsk9-to-control-lipid-metabolism
#17
Paul Lebeau, Ali Al-Hashimi, Sudesh Sood, Sarka Lhotak, Pei Yu, Gabriel Gyulay, Guillaume Pare, S R Wayne Chen, Bernardo Trigatti, Annik Prat, Nabil Seidah, Richard C Austin
Accumulating evidence implicates endoplasmic reticulum (ER) stress as a mediator of impaired lipid metabolism, thereby contributing to fatty liver disease and atherosclerosis. Previous studies demonstrated that ER stress can activate the sterol regulatory element-binding protein-2 (SREBP2), an ER localized transcription factor that directly upregulates sterol-regulatory genes, including PCSK9. Given that PCSK9 contributes to atherosclerosis by targeting low-density lipoprotein (LDL) receptor (LDLR) degradation, our present study investigates a novel mechanism by which ER stress plays a role in lipid metabolism by examining its ability to modulate PCSK9 expression...
December 1, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27908660/targeting-of-multiple-senescence-promoting-genes-and-signaling-pathways-by-triptonide-induces-complete-senescence-of-acute-myeloid-leukemia-cells
#18
Yanyan Pan, Mei Meng, Nana Zheng, Zhifei Cao, Ping Yang, Xiaodong Xi, Quansheng Zhou
Leukemia cells aberrantly overexpress senescence-suppression telomerase reverse transcriptase (TERT) and down-regulate key senescence-promoting genes to escape complete senescence, resulting in immortalization and malignant progression. Accordingly, induction of complete senescence is a sensible strategy for anti-leukemia therapy. However, effective senescence-based anti-leukemia drugs with low toxicity are currently lacking. In this study, we found that triptonide (chemical name diterpene triepoxide), a small molecule derived from the herb Tripterygium wilfordii Hook, strongly induced complete senescence in cultured acute myeloid leukemia (AML) cell lines, and potently inhibited growth and colony formation of U937 and HL-60 AML cell line with IC50 values of 7...
November 28, 2016: Biochemical Pharmacology
https://www.readbyqxmd.com/read/27908025/geometry-of-behavioral-spaces-a-computational-approach-to-analysis-and-understanding-of-agent-based-models-and-agent-behaviors
#19
Martin Cenek, Spencer K Dahl
Systems with non-linear dynamics frequently exhibit emergent system behavior, which is important to find and specify rigorously to understand the nature of the modeled phenomena. Through this analysis, it is possible to characterize phenomena such as how systems assemble or dissipate and what behaviors lead to specific final system configurations. Agent Based Modeling (ABM) is one of the modeling techniques used to study the interaction dynamics between a system's agents and its environment. Although the methodology of ABM construction is well understood and practiced, there are no computational, statistically rigorous, comprehensive tools to evaluate an ABM's execution...
November 2016: Chaos
https://www.readbyqxmd.com/read/27903912/the-complex-evolutionary-history-of-aminoacyl-trna-synthetases
#20
Anargyros Chaliotis, Panayotis Vlastaridis, Dimitris Mossialos, Michael Ibba, Hubert D Becker, Constantinos Stathopoulos, Grigorios D Amoutzias
Aminoacyl-tRNA synthetases (AARSs) are a superfamily of enzymes responsible for the faithful translation of the genetic code and have lately become a prominent target for synthetic biologists. Our large-scale analysis of >2500 prokaryotic genomes reveals the complex evolutionary history of these enzymes and their paralogs, in which horizontal gene transfer played an important role. These results show that a widespread belief in the evolutionary stability of this superfamily is misconceived. Although AlaRS, GlyRS, LeuRS, IleRS, ValRS are the most stable members of the family, GluRS, LysRS and CysRS often have paralogs, whereas AsnRS, GlnRS, PylRS and SepRS are often absent from many genomes...
November 29, 2016: Nucleic Acids Research
keyword
keyword
96463
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"