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https://www.readbyqxmd.com/read/29777005/predictors-of-survival-in-211-patients-with-stage-iv-pulmonary-and-gastroenteropancreatic-mibg-positive-neuroendocrine-tumors-treated-with-i-131-mibg
#1
Ari Kane, Matthew P Thorpe, Jorge D Oldan, Brandon A Howard, Jason Zhu, Michael A Morse, Terence Wong, Neil A Petry, Robert Reiman, Salvador Borges-Neto
Purpose: This retrospective analysis identifies predictors of survival in a cohort of patients with mIBG positive stage IV pulmonary and gastroenteropancreatic neuroendocrine tumor (P/GEP-NET) treated with I-131 mIBG therapy, in order to inform treatment selection and post-treatment monitoring. Methods: Survival, symptoms, imaging, and biochemical response were extracted via chart review from n = 211 P/GEP-NET patients treated with mIBG between 1991-2014. For patients with computed tomography (CT) follow up ( n = 125), imaging response was assessed by Response Evaluation Criteria on Solid Tumors (RECIST) 1...
May 18, 2018: Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine
https://www.readbyqxmd.com/read/29745904/structural-analysis-of-a-petri-net-model-of-oxidative-stress-in-atherosclerosis
#2
Adam Kozak, Dorota Formanowicz, Piotr Formanowicz
Atherosclerosis is a complex process of gathering sub-endothelial plaques decreasing lumen of the blood vessels. This disorder affects people of all ages, but its progression is asymptomatic for many years. It is regulated by many typical and atypical factors including the immune system response, a chronic kidney disease, a diet rich in lipids, a local inflammatory process and a local oxidative stress that is here one of the key factors. In this study, a Petri net model of atherosclerosis regulation is presented...
June 2018: IET Systems Biology
https://www.readbyqxmd.com/read/29745860/modeling-biological-systems-with-uncertain-kinetic-data-using-fuzzy-continuous-petri-nets
#3
Fei Liu, Siyuan Chen, Monika Heiner, Hengjie Song
BACKGROUND: Uncertainties exist in many biological systems, which can be classified as random uncertainties and fuzzy uncertainties. The former can usually be dealt with using stochastic methods, while the latter have to be handled with such approaches as fuzzy methods. RESULTS: In this paper, we focus on a special type of biological systems that can be described using ordinary differential equations or continuous Petri nets (CPNs), but some kinetic parameters are missing or inaccurate...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29724587/petri-net-controller-synthesis-based-on-decomposed-manufacturing-models
#4
Abbas Dideban, Hashem Zeraatkar
Utilizing of supervisory control theory on the real systems in many modeling tools such as Petri Net (PN) becomes challenging in recent years due to the significant states in the automata models or uncontrollable events. The uncontrollable events initiate the forbidden states which might be removed by employing some linear constraints. Although there are many methods which have been proposed to reduce these constraints, enforcing them to a large-scale system is very difficult and complicated. This paper proposes a new method for controller synthesis based on PN modeling...
April 30, 2018: ISA Transactions
https://www.readbyqxmd.com/read/29688425/effect-of-yearling-steer-sequence-grazing-of-perennial-and-annual-forages-in-an-integrated-crop-and-livestock-system-on-grazing-performance-delayed-feedlot-entry-finishing-performance-carcass-measurements-and-systems-economics
#5
S Sentürklü, D G Landblom, R Maddock, T Petry, C J Wachenheim, S I Paisley
In a 2-yr study, spring-born yearling steers (n = 144), previously grown to gain < 0.454 kg·steer-1·d-1, following weaning in the fall, were stratified by BW and randomly assigned to three retained ownership rearing systems (3-replications) in early May. Systems were: 1) feedlot (FLT), 2) steers that grazed perennial crested wheatgrass (CWG) and native range (NR) before feedlot entry (PST), and 3) steers that grazed perennial CWG and NR, and then field pea-barley mix (PBLY) and unharvested corn (UC) before feedlot entry (ANN)...
April 24, 2018: Journal of Animal Science
https://www.readbyqxmd.com/read/29650794/comprehensive-analysis-of-the-mutation-spectrum-in-301-german-als-families
#6
Kathrin Müller, David Brenner, Patrick Weydt, Thomas Meyer, Torsten Grehl, Susanne Petri, Julian Grosskreutz, Joachim Schuster, Alexander E Volk, Guntram Borck, Christian Kubisch, Thomas Klopstock, Daniel Zeller, Sibylle Jablonka, Michael Sendtner, Stephan Klebe, Antje Knehr, Kornelia Günther, Joachim Weis, Kristl G Claeys, Berthold Schrank, Anne-Dorte Sperfeld, Annemarie Hübers, Markus Otto, Johannes Dorst, Thomas Meitinger, Tim M Strom, Peter M Andersen, Albert C Ludolph, Jochen H Weishaupt
OBJECTIVES: Recent advances in amyotrophic lateral sclerosis (ALS) genetics have revealed that mutations in any of more than 25 genes can cause ALS, mostly as an autosomal-dominant Mendelian trait. Detailed knowledge about the genetic architecture of ALS in a specific population will be important for genetic counselling but also for genotype-specific therapeutic interventions. METHODS: Here we combined fragment length analysis, repeat-primed PCR, Southern blotting, Sanger sequencing and whole exome sequencing to obtain a comprehensive profile of genetic variants in ALS disease genes in 301 German pedigrees with familial ALS...
April 12, 2018: Journal of Neurology, Neurosurgery, and Psychiatry
https://www.readbyqxmd.com/read/29649267/anonymity-preserving-reputation-management-system-for-health-sector
#7
Farhana Jabeen, Zara Hamid, Wadood Abdul, Sanaa Ghouzali, Abid Khan, Saif Ur Rehman Malik, Mansoor Shaukat Khan, Sarfraz Nawaz
In health sector, trust is considered important because it indirectly influences the quality of health care through patient satisfaction, adherence and the continuity of its relationship with health care professionals and the promotion of accurate and timely diagnoses. One of the important requirements of TRSs in the health sector is rating secrecy, which mandates that the identification information about the service consumer should be kept secret to prevent any privacy violation. Anonymity and trust are two imperative objectives, and no significant explicit efforts have been made to achieve both of them at the same time...
2018: PloS One
https://www.readbyqxmd.com/read/29576759/petri-net-based-2d-design-of-dna-walker-circuits
#8
David Gilbert, Monika Heiner, Christian Rohr
We consider localised DNA computation, where a DNA strand walks along a binary decision graph to compute a binary function. One of the challenges for the design of reliable walker circuits consists in leakage transitions, which occur when a walker jumps into another branch of the decision graph. We automatically identify leakage transitions, which allows for a detailed qualitative and quantitative assessment of circuit designs, design comparison, and design optimisation. The ability to identify leakage transitions is an important step in the process of optimising DNA circuit layouts where the aim is to minimise the computational error inherent in a circuit while minimising the area of the circuit...
2018: Natural Computing
https://www.readbyqxmd.com/read/29543794/a-graphical-and-computational-modeling-platform-for-biological-pathways
#9
Alessandra Livigni, Laura O'Hara, Marta E Polak, Tim Angus, Derek W Wright, Lee B Smith, Tom C Freeman
A major endeavor of systems biology is the construction of graphical and computational models of biological pathways as a means to better understand their structure and function. Here, we present a protocol for a biologist-friendly graphical modeling scheme that facilitates the construction of detailed network diagrams, summarizing the components of a biological pathway (such as proteins and biochemicals) and illustrating how they interact. These diagrams can then be used to simulate activity flow through a pathway, thereby modeling its dynamic behavior...
April 2018: Nature Protocols
https://www.readbyqxmd.com/read/29506508/petri-net-based-prediction-of-therapeutic-targets-that-recover-abnormally-phosphorylated-proteins-in-muscle-atrophy
#10
Jinmyung Jung, Mijin Kwon, Sunghwa Bae, Soorin Yim, Doheon Lee
BACKGROUND: Muscle atrophy, an involuntary loss of muscle mass, is involved in various diseases and sometimes leads to mortality. However, therapeutics for muscle atrophy thus far have had limited effects. Here, we present a new approach for therapeutic target prediction using Petri net simulation of the status of phosphorylation, with a reasonable assumption that the recovery of abnormally phosphorylated proteins can be a treatment for muscle atrophy. RESULTS: The Petri net model was employed to simulate phosphorylation status in three states, i...
March 5, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29342275/hot-spot-kif5a-mutations-cause-familial-als
#11
David Brenner, Rüstem Yilmaz, Kathrin Müller, Torsten Grehl, Susanne Petri, Thomas Meyer, Julian Grosskreutz, Patrick Weydt, Wolfgang Ruf, Christoph Neuwirth, Markus Weber, Susana Pinto, Kristl G Claeys, Berthold Schrank, Berit Jordan, Antje Knehr, Kornelia Günther, Annemarie Hübers, Daniel Zeller, Christian Kubisch, Sibylle Jablonka, Michael Sendtner, Thomas Klopstock, Mamede de Carvalho, Anne Sperfeld, Guntram Borck, Alexander E Volk, Johannes Dorst, Joachim Weis, Markus Otto, Joachim Schuster, Kelly Del Tredici, Heiko Braak, Karin M Danzer, Axel Freischmidt, Thomas Meitinger, Tim M Strom, Albert C Ludolph, Peter M Andersen, Jochen H Weishaupt
Heterozygous missense mutations in the N-terminal motor or coiled-coil domains of the kinesin family member 5A (KIF5A) gene cause monogenic spastic paraplegia (HSP10) and Charcot-Marie-Tooth disease type 2 (CMT2). Moreover, heterozygous de novo frame-shift mutations in the C-terminal domain of KIF5A are associated with neonatal intractable myoclonus, a neurodevelopmental syndrome. These findings, together with the observation that many of the disease genes associated with amyotrophic lateral sclerosis disrupt cytoskeletal function and intracellular transport, led us to hypothesize that mutations in KIF5A are also a cause of amyotrophic lateral sclerosis...
January 12, 2018: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/29317313/the-role-of-fenton-reaction-in-ros-induced-toxicity-underlying-atherosclerosis-modeled-and-analyzed-using-a-petri-net-based-approach
#12
Dorota Formanowicz, Marcin Radom, Agnieszka Rybarczyk, Piotr Formanowicz
The superoxide-driven Fenton reaction plays an important role in the transformation of poorly reactive radicals into highly reactive ones. These highly reactive species (ROS), especially hydroxyl radicals can lead to many disturbances contributing to the endothelial dysfunction being a starting point for atherosclerosis. Although, iron has been identified as a possible culprit influencing formation of ROS, its significance in this process is still debatable. To better understand this phenomenon, the influence of blockade of Fenton reaction in a proposed Petri net-based model of the selected aspects of the iron ROS-induced toxicity in atherosclerosis has been evaluated...
March 2018: Bio Systems
https://www.readbyqxmd.com/read/29147538/scaling-behaviour-and-rate-determining-steps-in-filamentous-self-assembly
#13
Georg Meisl, Luke Rajah, Samuel A I Cohen, Manuela Pfammatter, Anđela Šarić, Erik Hellstrand, Alexander K Buell, Adriano Aguzzi, Sara Linse, Michele Vendruscolo, Christopher M Dobson, Tuomas P J Knowles
The formation of filaments from naturally occurring protein molecules is a process at the core of a range of functional and aberrant biological phenomena, such as the assembly of the cytoskeleton or the appearance of aggregates in Alzheimer's disease. The macroscopic behaviour associated with such processes is remarkably diverse, ranging from simple nucleated growth to highly cooperative processes with a well-defined lagtime. Thus, conventionally, different molecular mechanisms have been used to explain the self-assembly of different proteins...
October 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29112705/coloured-petri-nets-for-multilevel-multiscale-and-multidimensional-modelling-of-biological-systems
#14
Fei Liu, Monika Heiner, David Gilbert
Owing to the availability of data of one biological phenomenon at different levels/scales, modelling of biological systems is moving from single level/scale to multiple levels/scales, which introduces a number of challenges. Coloured Petri nets (ColPNs) have been successfully applied to multilevel, multiscale and multidimensional modelling of some biological systems, addressing many of these challenges. In this article, we first review the basics of ColPNs and some popular extensions, and then their applications for multilevel, multiscale and multidimensional modelling of biological systems...
November 3, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29090324/cumulative-effects-of-negative-life-events-and-family-stress-on-children-s-mental-health-the-bergen-child-study
#15
Tormod Bøe, Anna Sofia Serlachius, Børge Sivertsen, Keith J Petrie, Mari Hysing
PURPOSE: Numerous studies have documented that lower socioeconomic status (SES) is associated with increased mental health problems in children. One proposed pathway for this association has been differential exposure to accumulated risk factors in children of lower SES. The aim of the current study was to investigate the socioeconomic distribution of exposure to negative life events and family stress and to examine the direct and interactive association between lower SES and exposure to life events and family stress in relation with mental health problems...
January 2018: Social Psychiatry and Psychiatric Epidemiology
https://www.readbyqxmd.com/read/28961696/holmes-a-graphical-tool-for-development-simulation-and-analysis-of-petri-net-based-models-of-complex-biological-systems
#16
Marcin Radom, Agnieszka Rybarczyk, Bartlomiej Szawulak, Hubert Andrzejewski, Piotr Chabelski, Adam Kozak, Piotr Formanowicz
Summary: Model development and its analysis is a fundamental step in systems biology. The theory of Petri nets offers a tool for such a task. Since the rapid development of computer science, a variety of tools for Petri nets emerged, offering various analytical algorithms. From this follows a problem of using different programs to analyse a single model. Many file formats and different representations of results make the analysis much harder. Especially for larger nets the ability to visualize the results in a proper form provides a huge help in the understanding of their significance...
December 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28932213/petri-net-based-model-of-helicobacter-pylori-mediated-disruption-of-tight-junction-proteins-in-stomach-lining-during-gastric-carcinoma
#17
Anam Naz, Ayesha Obaid, Faryal M Awan, Aqsa Ikram, Jamil Ahmad, Amjad Ali
Tight junctions help prevent the passage of digestive enzymes and microorganisms through the space between adjacent epithelial cells lining. However, Helicobacter pylori encoded virulence factors negatively regulate these tight junctions and contribute to dysfunction of gastric mucosa. Here, we have predicted the regulation of important tight junction proteins, such as Zonula occludens-1, Claudin-2 and Connexin32 in the presence of pathogenic proteins. Molecular events such as post translational modifications and crosstalk between phosphorylation, O-glycosylation, palmitoylation and methylation are explored which may compromise the integrity of these tight junction proteins...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28904393/microrna-pharmacogenomics-based-integrated-model-of-mir-17-92-cluster-in-sorafenib-resistant-hcc-cells-reveals-a-strategy-to-forestall-drug-resistance
#18
Faryal Mehwish Awan, Anam Naz, Ayesha Obaid, Aqsa Ikram, Amjad Ali, Jamil Ahmad, Abdul Khaliq Naveed, Hussnain Ahmed Janjua
Among solid tumors, hepatocellular carcinoma (HCC) emerges as a prototypical therapy-resistant tumor. Considering the emerging sorafenib resistance crisis in HCC, future studies are urgently required to overcome resistance. Recently noncoding RNAs (ncRNAs) have emerged as significant regulators in signalling pathways involved in cancer drug resistance and pharmacologically targeting these ncRNAs might be a novel stratagem to reverse drug resistance. In the current study, using a hybrid Petri net based computational model, we have investigated the harmonious effect of miR-17-92 cluster inhibitors/mimics and circular RNAs on sorafenib resistant HCC cells in order to explore potential resistance mechanisms and to identify putative targets for sorafenib-resistant HCC cells...
September 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28767374/continuous-petri-nets-and-microrna-analysis-in-melanoma
#19
Giulia Russo, Marzio Pennisi, Roberta Boscarino, Francesco Pappalardo
Personalized target therapies represent one of the possible treatment strategies to fight the ongoing battle against cancer. New treatment interventions are still needed for an effective and successful cancer therapy. In this scenario, we simulated and analyzed the dynamics of BRAF V600E melanoma patients treated with BRAF inhibitors in order to find potentially interesting targets that may make standard treatments more effective in particularly aggressive tumors that may not respond to selective inhibitor drugs...
July 31, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28754122/snoopy-s-hybrid-simulator-a-tool-to-construct-and-simulate-hybrid-biological-models
#20
Mostafa Herajy, Fei Liu, Christian Rohr, Monika Heiner
BACKGROUND: Hybrid simulation of (computational) biochemical reaction networks, which combines stochastic and deterministic dynamics, is an important direction to tackle future challenges due to complex and multi-scale models. Inherently hybrid computational models of biochemical networks entail two time scales: fast and slow. Therefore, it is intricate to efficiently and accurately analyse them using only either deterministic or stochastic simulation. However, there are only a few software tools that support such an approach...
July 28, 2017: BMC Systems Biology
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