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https://www.readbyqxmd.com/read/27922834/complexity-of-generic-biochemical-circuits-topology-versus-strength-of-interactions
#1
Mikhail Tikhonov, William Bialek
The historical focus on network topology as a determinant of biological function is still largely maintained today, illustrated by the rise of structure-only approaches to network analysis. However, biochemical circuits and genetic regulatory networks are defined both by their topology and by a multitude of continuously adjustable parameters, such as the strength of interactions between nodes, also recognized as important. Here we present a class of simple perceptron-based Boolean models within which comparing the relative importance of topology versus interaction strengths becomes a quantitatively well-posed problem...
December 6, 2016: Physical Biology
https://www.readbyqxmd.com/read/27917388/similar-environments-but-diverse-fates-responses-of-budding-yeast-to-nutrient-deprivation
#2
Saul M Honigberg
Diploid budding yeast (Saccharomyces cerevisiae) can adopt one of several alternative differentiation fates in response to nutrient limitation, and each of these fates provides distinct biological functions. When different strain backgrounds are taken into account, these various fates occur in response to similar environmental cues, are regulated by the same signal transduction pathways, and share many of the same master regulators. I propose that the relationships between fate choice, environmental cues and signaling pathways are not Boolean, but involve graded levels of signals, pathway activation and master-regulator activity...
August 2016: Microbial Cell
https://www.readbyqxmd.com/read/27909083/continual-maintenance-of-remission-defined-by-the-acr-eular-criteria-in-daily-practice-leads-to-better-functional-outcomes-in-patients-with-rheumatoid-arthritis
#3
Kumi Shidara, Ayako Nakajima, Eisuke Inoue, Daisuke Hoshi, Naoki Sugimoto, Yohei Seto, Eiichi Tanaka, Shigeki Momohara, Atsuo Taniguchi, Hisashi Yamanaka
OBJECTIVE: To evaluate longterm functional outcomes in rheumatoid arthritis (RA) based on the number of times that the American College of Rheumatology (ACR)/European League Against Rheumatism (EULAR) or the 28-joint Disease Activity Score (DAS28) remission criteria were fulfilled. METHODS: Patients with RA who participated in all 6 data collections in an observational cohort from 2008 to 2010 and who fulfilled the DAS28 remission criteria at baseline were studied...
December 1, 2016: Journal of Rheumatology
https://www.readbyqxmd.com/read/27907269/remission-rates-with-tofacitinib-treatment-in-rheumatoid-arthritis-a-comparison-of-various-remission-criteria
#4
Josef S Smolen, Daniel Aletaha, David Gruben, Samuel H Zwillich, Sriram Krishnaswami, Charles Mebus
OBJECTIVE: Tofacitinib is an oral Janus kinase inhibitor for the treatment of rheumatoid arthritis (RA). Throughout tofacitinib clinical studies, a 28-joint Disease Activity Score (DAS28)-based analysis was used to assess outcomes. In this study, remission rates by various remission criteria were evaluated across five Phase 3 randomized controlled studies. METHODS: Tofacitinib was dosed 5 or 10 mg twice daily (BID), either as monotherapy, or with background methotrexate or other conventional synthetic disease-modifying antirheumatic drugs (DMARDs)...
December 1, 2016: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/27900435/enzyme-based-logic-gates-and-circuits-analytical-applications-and-interfacing-with-electronics
#5
REVIEW
Evgeny Katz, Arshak Poghossian, Michael J Schöning
The paper is an overview of enzyme-based logic gates and their short circuits, with specific examples of Boolean AND and OR gates, and concatenated logic gates composed of multi-step enzyme-biocatalyzed reactions. Noise formation in the biocatalytic reactions and its decrease by adding a "filter" system, converting convex to sigmoid response function, are discussed. Despite the fact that the enzyme-based logic gates are primarily considered as components of future biomolecular computing systems, their biosensing applications are promising for immediate practical use...
November 29, 2016: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/27891762/judicial-reliance-on-parental-iq-in-appellate-level-child-welfare-cases-involving-parents-with-intellectual-and-developmental-disabilities
#6
Ella Callow, Munazza Tahir, Maurice Feldman
BACKGROUND: Parents with intellectual and developmental disabilities (IDDs) are over-represented in child welfare cases. Although IQ per se is an invalid indicator of parenting abilities, this study examined the prevalence of judicial consideration of parental IQ test evidence in US appellate cases. METHODS: The present authors conducted Boolean searches of Westlaw Corporation's case database since 1999. The present authors used a six-question checklist to survey the 42 most recent American appellate cases involving termination of parental rights (TPR) decisions that included evidence of parental intellectual and developmental disabilities based on IQ...
November 27, 2016: Journal of Applied Research in Intellectual Disabilities: JARID
https://www.readbyqxmd.com/read/27891072/estimating-propensity-parameters-using-google-pagerank-and-genetic-algorithms
#7
David Murrugarra, Jacob Miller, Alex N Mueller
Stochastic Boolean networks, or more generally, stochastic discrete networks, are an important class of computational models for molecular interaction networks. The stochasticity stems from the updating schedule. Standard updating schedules include the synchronous update, where all the nodes are updated at the same time, and the asynchronous update where a random node is updated at each time step. The former produces a deterministic dynamics while the latter a stochastic dynamics. A more general stochastic setting considers propensity parameters for updating each node...
2016: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/27869177/repressor-logic-modules-assembled-by-rolling-circle-amplification-platform-to-construct-a-set-of-logic-gates
#8
Hua Wei, Bo Hu, Suming Tang, Guojie Zhao, Yifu Guan
Small molecule metabolites and their allosterically regulated repressors play an important role in many gene expression and metabolic disorder processes. These natural sensors, though valuable as good logic switches, have rarely been employed without transcription machinery in cells. Here, two pairs of repressors, which function in opposite ways, were cloned, purified and used to control DNA replication in rolling circle amplification (RCA) in vitro. By using metabolites and repressors as inputs, RCA signals as outputs, four basic logic modules were constructed successfully...
November 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27866978/stability-and-structural-properties-of-gene-regulation-networks-with-coregulation-rules
#9
Jonathan Warrell, Musa Mhlanga
Coregulation of the expression of groups of genes has been extensively demonstrated empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use of shared regulatory motifs, which allow the coordinated expression of modules (and module groups) of functionally related genes across the genome. Coregulation can also arise through the physical association of multi-gene complexes through chromosomal looping, which are then transcribed together. We present a general formalism for modeling coregulation rules in the framework of Random Boolean Networks (RBN), and develop specific models for transcription factor networks with modular structure (including module groups, and multi-input modules (MIM) with autoregulation) and multi-gene complexes (including hierarchical differentiation between multi-gene complex members)...
November 17, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27866650/evidence-based-and-personalized-medicine-it-s-and-not-or
#10
REVIEW
Sahar Mokhles, Johanna Jm Takkenberg, Tom Treasure
Good clinical practice is an amalgamation of personalized medicine with evidence-based medicine in the best interests of patient. Hence, our title uses Boolean operators to indicate that it is [AND] not [OR]. This is the syntax of formal searching for systematic reviews, ensuring that all the evidence is found. Comprehensive evidence-based guidance can thus be formulated. Many residents and fellows around the world, and their chiefs, are now exposed to consensus documents, white papers, levels of appropriateness, and guidelines and are in many jurisdictions expected to comply with them...
November 17, 2016: Annals of Thoracic Surgery
https://www.readbyqxmd.com/read/27862413/reconfigurable-magnetic-logic-combined-with-nonvolatile-memory-writing
#11
Zhaochu Luo, Ziyao Lu, Chengyue Xiong, Tao Zhu, Wei Wu, Qiang Zhang, Huaqiang Wu, Xixiang Zhang, Xiaozhong Zhang
In the magnetic logic, four basic Boolean logic operations can be programmed by a magnetic bit at room temperature with a high output ratio (>10(3) %). In the same clock cycle, benefiting from the built-in spin Hall effect, logic results can be directly written into magnetic bits using an all-electric method.
November 15, 2016: Advanced Materials
https://www.readbyqxmd.com/read/27861624/an-algorithm-for-finding-the-singleton-attractors-and-pre-images-in-strong-inhibition-boolean-networks
#12
Zhiwei He, Meng Zhan, Shuai Liu, Zebo Fang, Chenggui Yao
The detection of the singleton attractors is of great significance for the systematic study of genetic regulatory network. In this paper, we design an algorithm to compute the singleton attractors and pre-images of the strong-inhibition Boolean networks which is a biophysically plausible gene model. Our algorithm can not only identify accurately the singleton attractors, but also find easily the pre-images of the network. Based on extensive computational experiments, we show that the computational time of the algorithm is proportional to the number of the singleton attractors, which indicates the algorithm has much advantage in finding the singleton attractors for the networks with high average degree and less inhibitory interactions...
2016: PloS One
https://www.readbyqxmd.com/read/27853326/prevalence-of-low-back-pain-in-health-care-workers-and-comparison-with-other-occupational-categories-in-iran-a-systematic-review
#13
REVIEW
Ramin Mehrdad, Narges Sadat Shams-Hosseini, Sara Aghdaei, Mina Yousefian
BACKGROUND: There are few research studies evaluating the significance of low back pain (LBP) in Iran, even though the majority of locally published surveys are written in the Persian language. In the present review study, we aimed at appraising published articles related to the burden of LBP and its divergence among different jobs. METHODS: A comprehensive search was conducted in all accessible national and international electronic databases from 1948 to mid-2012...
November 2016: Iranian Journal of Medical Sciences
https://www.readbyqxmd.com/read/27834352/multistate-memristive-tantalum-oxide-devices-for-ternary-arithmetic
#14
Wonjoo Kim, Anupam Chattopadhyay, Anne Siemon, Eike Linn, Rainer Waser, Vikas Rana
Redox-based resistive switching random access memory (ReRAM) offers excellent properties to implement future non-volatile memory arrays. Recently, the capability of two-state ReRAMs to implement Boolean logic functionality gained wide interest. Here, we report on seven-states Tantalum Oxide Devices, which enable the realization of an intrinsic modular arithmetic using a ternary number system. Modular arithmetic, a fundamental system for operating on numbers within the limit of a modulus, is known to mathematicians since the days of Euclid and finds applications in diverse areas ranging from e-commerce to musical notations...
November 11, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27822928/factors-contributing-to-discordance-between-the-2011-acr-eular-criteria-and-physician-clinical-judgment-for-the-identification-of-remission-in-patients-with-rheumatoid-arthritis
#15
Yoon Kyoung Sung, Soo Kyung Cho, Dam Kim, Bo Young Yoon, Chan Bum Choi, Hoon Suk Cha, Jung Yoon Choe, Won Tae Chung, Seung Jae Hong, Jae Bum Jun, Young Mo Kang, Jinseok Kim, Tae Hwan Kim, Tae Jong Kim, Eunmi Koh, Choong Ki Lee, Jisoo Lee, Shin Seok Lee, Sung Won Lee, Hye Soon Lee, Yeon Ah Lee, Sung Hoon Park, Dae Hyun Yoo, Wan Hee Yoo, Sang Cheol Bae
Remission is a primary end point of in clinical practice and trials of treatments for rheumatoid arthritis (RA). The 2011 American College of Rheumatology/European League Against Rheumatism (ACR/EULAR) remission criteria were developed to provide a consensus definition of remission. This study aimed to assess the concordance between the new remission criteria and the physician's clinical judgment of remission and also to identify factors that affect the discordance between these two approaches. A total of 3,209 patients with RA were included from the KORean Observational Study Network for Arthritis (KORONA) database...
December 2016: Journal of Korean Medical Science
https://www.readbyqxmd.com/read/27822054/impact-of-sodium-glucose-cotransporter-2-inhibitors-on-blood-pressure
#16
REVIEW
James W Reed
SGLT2 inhibitors are glucose-lowering agents used to treat type 2 diabetes mellitus (T2DM). These agents target the kidney to promote urinary glucose excretion, resulting in improved blood glucose control. SGLT2-inhibitor therapy is also associated with weight loss and blood pressure (BP) lowering. Hypertension is a common comorbidity in patients with T2DM, and is associated with excess morbidity and mortality. This review summarizes data on the effect of SGLT2 inhibitors marketed in the US (namely canagliflozin, dapagliflozin, or empagliflozin) on BP in patients with T2DM...
2016: Vascular Health and Risk Management
https://www.readbyqxmd.com/read/27818883/an-algorithm-for-judging-and-generating-multivariate-quadratic-quasigroups-over-galois-fields
#17
Ying Zhang, Huisheng Zhang
As the basic cryptographic structure for multivariate quadratic quasigroup (MQQ) scheme, MQQ has been one of the latest tools in designing MQ cryptosystem. There have been several construction methods for MQQs in the literature, however, the algorithm for judging whether quasigroups of any order are MQQs over Galois fields is still lacking. To this end, the objective of this paper is to establish a necessary and sufficient condition for a given quasigroup of order p(kd) to be an MQQ over [Formula: see text]...
2016: SpringerPlus
https://www.readbyqxmd.com/read/27805730/association-between-depression-and-resilience-in-older-adults-a-systematic-review-and-meta-analysis
#18
REVIEW
Maria Priscila Wermelinger Ávila, Alessandra Lamas Granero Lucchetti, Giancarlo Lucchetti
OBJECTIVE: The objective of this study is to determine whether resilience is associated with depressive symptoms in geriatric populations. METHOD: A systematic review and meta-analysis were performed (up to March 2015) following the Preferred Reporting Items for Systematic Reviews and Meta-analysis recommendations on three databases (PubMed/Medline, Scopus, and Web of Science) with no language restrictions, using a Boolean expression. For inclusion in the study, articles had to assess the older population (60 years or older), assess both depressive and resilience symptoms, and investigate the association between these two variables...
November 2, 2016: International Journal of Geriatric Psychiatry
https://www.readbyqxmd.com/read/27797783/pyboolnet-a-python-package-for-the-generation-analysis-and-visualisation-of-boolean-networks
#19
Hannes Klarner, Adam Streck, Heike Siebert
MOTIVATION: The goal of this project is to provide a simple interface to working with Boolean networks. Emphasis is put on easy access to a large number of common tasks including the generation and manipulation of networks, attractor and basin computation, model checking and trap space computation, execution of established graph algorithms as well as graph drawing and layouts. RESULTS: PyBoolNet is a Python package for working with Boolean networks that supports simple access to model checking via NuSMV, standard graph algorithms via NetworkX and visualisation via dot...
October 26, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27797768/visibool-visualization-and-simulation-of-boolean-networks-with-temporal-constraints
#20
Julian Schwab, Andre Burkovski, Lea Siegle, Christoph Müssel, Hans A Kestler
: Mathematical models and their simulation are increasingly used to gain insights into cellular pathways and regulatory networks. Dynamics of regulatory factors can be modeled using Boolean networks (BN), among others. Text-based representations of models are precise descriptions, but hard to understand and interpret. ViSiBooL aims at providing a graphical way of modeling and simulating networks. By providing visualizations of static and dynamic network properties simultaneously, it is possible to directly observe the effects of changes in the network structure on the behavior...
October 22, 2016: Bioinformatics
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