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https://www.readbyqxmd.com/read/29785071/identification-of-cis-regulatory-elements-associated-with-salinity-and-drought-stress-tolerance-in-rice-from-co-expressed-gene-interaction-networks
#1
Pragya Mishra, Nisha Singh, Ajay Jain, Neha Jain, Vagish Mishra, Pushplatha G, Kiran P Sandhya, Nagendra Kumar Singh, Vandna Rai
Rice, a staple food crop, is often subjected to drought and salinity stresses thereby limiting its yield potential. Since there is a cross talk between these abiotic stresses, identification of common and/or overlapping regulatory elements is pivotal for generating rice cultivars that showed tolerance towards them. Analysis of the gene interaction network (GIN) facilitates identifying the role of individual genes and their interactions with others that constitute important molecular determinants in sensing and signaling cascade governing drought and/or salinity stresses...
2018: Bioinformation
https://www.readbyqxmd.com/read/29784817/topography-of-epithelial-mesenchymal-plasticity
#2
Francesc Font-Clos, Stefano Zapperi, Caterina A M La Porta
The transition between epithelial and mesenchymal states has fundamental importance for embryonic development, stem cell reprogramming, and cancer progression. Here, we construct a topographic map underlying epithelial-mesenchymal transitions using a combination of numerical simulations of a Boolean network model and the analysis of bulk and single-cell gene expression data. The map reveals a multitude of metastable hybrid phenotypic states, separating stable epithelial and mesenchymal states, and is reminiscent of the free energy measured in glassy materials and disordered solids...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29783647/type-and-location-of-wearable-sensors-for-monitoring-falls-during-static-and-dynamic-tasks-in-healthy-elderly-a-review
#3
REVIEW
Rosaria Rucco, Antonietta Sorriso, Marianna Liparoti, Giampaolo Ferraioli, Pierpaolo Sorrentino, Michele Ambrosanio, Fabio Baselice
In recent years, the meaning of successful living has moved from extending lifetime to improving the quality of aging, mainly in terms of high cognitive and physical functioning together with avoiding diseases. In healthy elderly, falls represent an alarming accident both in terms of number of events and the consequent decrease in the quality of life. Stability control is a key approach for studying the genesis of falls, for detecting the event and trying to develop methodologies to prevent it. Wearable sensors have proved to be very useful in monitoring and analyzing the stability of subjects...
May 18, 2018: Sensors
https://www.readbyqxmd.com/read/29776182/optimal-stabilization-of-boolean-networks-through-collective-influence
#4
Jiannan Wang, Sen Pei, Wei Wei, Xiangnan Feng, Zhiming Zheng
Boolean networks have attracted much attention due to their wide applications in describing dynamics of biological systems. During past decades, much effort has been invested in unveiling how network structure and update rules affect the stability of Boolean networks. In this paper, we aim to identify and control a minimal set of influential nodes that is capable of stabilizing an unstable Boolean network. For locally treelike Boolean networks with biased truth tables, we propose a greedy algorithm to identify influential nodes in Boolean networks by minimizing the largest eigenvalue of a modified nonbacktracking matrix...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29758683/markovian-robots-minimal-navigation-strategies-for-active-particles
#5
Luis Gómez Nava, Robert Großmann, Fernando Peruani
We explore minimal navigation strategies for active particles in complex, dynamical, external fields, introducing a class of autonomous, self-propelled particles which we call Markovian robots (MR). These machines are equipped with a navigation control system (NCS) that triggers random changes in the direction of self-propulsion of the robots. The internal state of the NCS is described by a Boolean variable that adopts two values. The temporal dynamics of this Boolean variable is dictated by a closed Markov chain-ensuring the absence of fixed points in the dynamics-with transition rates that may depend exclusively on the instantaneous, local value of the external field...
April 2018: Physical Review. E
https://www.readbyqxmd.com/read/29758614/general-method-to-find-the-attractors-of-discrete-dynamic-models-of-biological-systems
#6
Xiao Gan, Réka Albert
Analyzing the long-term behaviors (attractors) of dynamic models of biological networks can provide valuable insight. We propose a general method that can find the attractors of multilevel discrete dynamical systems by extending a method that finds the attractors of a Boolean network model. The previous method is based on finding stable motifs, subgraphs whose nodes' states can stabilize on their own. We extend the framework from binary states to any finite discrete levels by creating a virtual node for each level of a multilevel node, and describing each virtual node with a quasi-Boolean function...
April 2018: Physical Review. E
https://www.readbyqxmd.com/read/29755834/sample-complexity-of-the-boolean-multireference-alignment-problem
#7
Emmanuel Abbe, João M Pereira, Amit Singer
The Boolean multireference alignment problem consists in recovering a Boolean signal from multiple shifted and noisy observations. In this paper we obtain an expression for the error exponent of the maximum A posteriori decoder. This expression is used to characterize the number of measurements needed for signal recovery in the low SNR regime, in terms of higher order autocorrelations of the signal. The characterization is explicit for various signal dimensions, such as prime and even dimensions.
June 2017: Proceedings
https://www.readbyqxmd.com/read/29754242/dna-based-analog-computing
#8
Daniel Fu, Shalin Shah, Tianqi Song, John Reif
The field of DNA computation makes use of DNA reactions to do molecular-scale computation. Most works in DNA computation execute digital computations such as evaluation of Boolean circuits. This chapter surveys novel DNA computation methods that execute analog computations, where the inputs and outputs are real values specified by the concentrations of particular DNA strands.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29754229/designed-transcriptional-regulation-in-mammalian-cells-based-on-tale-and-crispr-dcas9
#9
Tina Lebar, Roman Jerala
Transcriptional regulation lies at the center of many cellular processes and is the result of cellular response to different external and internal signals. Control of transcription of selected genes enables an unprecedented access to shape the cellular response. While orthogonal transcription factors from bacteria, yeast, plants, or other cells have been used to introduce new cellular logic into mammalian cells, the discovery of designable modular DNA binding domains, such as Transcription Activator-Like Effectors (TALEs) and the CRISPR system, enable targeting of almost any selected DNA sequence...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29745472/advanced-practice-radiation-therapists-an-australian-context
#10
REVIEW
Bronwyn Hilder, Pieter VanDam, Kathleen Doherty
The purpose of this scoping review is to examine the literature regarding the development, implementation, scope and extent of Advanced Practice Radiation Therapist (APRT) roles in Australia in peer reviewed journals, government reports, conference proceedings and reports. A search was undertaken of PubMed, Web of Science and CINAHL, the ASMIRT website and, and Google Scholar to identify relevant documents. Combinations of keywords with Boolean operators ((advanced practice) OR (advanced practitioner) OR (specialist)) AND ((radiation therapist) OR (radiation therapy)) were used...
May 10, 2018: Journal of Medical Radiation Sciences
https://www.readbyqxmd.com/read/29740342/automatic-screening-for-perturbations-in-boolean-networks
#11
Julian D Schwab, Hans A Kestler
A common approach to address biological questions in systems biology is to simulate regulatory mechanisms using dynamic models. Among others, Boolean networks can be used to model the dynamics of regulatory processes in biology. Boolean network models allow simulating the qualitative behavior of the modeled processes. A central objective in the simulation of Boolean networks is the computation of their long-term behavior-so-called attractors. These attractors are of special interest as they can often be linked to biologically relevant behaviors...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/29734222/progressive-lentivirus-infection-induces-natural-killer-cell-receptor-expressing-b-cells-in-the-gastrointestinal-tract
#12
Cordelia Manickam, Chiadika Nwanze, Daniel R Ram, Spandan V Shah, Scott Smith, Rhianna Jones, Brady Hueber, Kyle Kroll, Valerie Varner, Paul Goepfert, Stephanie Jost, R Keith Reeves
OBJECTIVE: Recently, a seemingly novel innate immune cell subset bearing features of natural killer and B cells was identified in mice. So-called NKB cells appear as first responders to infections, but whether this cell population is truly novel or is in fact a subpopulation of B cells and exists in higher primates remains unclear. The objective of this study was to identify NKB cells in primates and study the impact of HIV/SIV infections. DESIGN AND METHODS: NKB cells were quantified in both naïve and lentivirus infected rhesus macaques and humans by excluding lineage markers (CD3, CD127), and positive Boolean gating for CD20, NKG2A/C and/or NKp46...
May 3, 2018: AIDS
https://www.readbyqxmd.com/read/29720596/analog-approach-to-constraint-satisfaction-enabled-by-spin-orbit-torque-magnetic-tunnel-junctions
#13
Parami Wijesinghe, Chamika Liyanagedera, Kaushik Roy
Boolean satisfiability (k-SAT) is an NP-complete (k ≥ 3) problem that constitute one of the hardest classes of constraint satisfaction problems. In this work, we provide a proof of concept hardware based analog k-SAT solver, that is built using Magnetic Tunnel Junctions (MTJs). The inherent physics of MTJs, enhanced by device level modifications, is harnessed here to emulate the intricate dynamics of an analog satisfiability (SAT) solver. In the presence of thermal noise, the MTJ based system can successfully solve Boolean satisfiability problems...
May 2, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29706131/schistosomiasis-in-zambia-a-systematic-review-of-past-and-present-experiences
#14
Chester Kalinda, Moses J Chimbari, Samson Mukaratirwa
BACKGROUND: The speedy rate of change in the environmental and socio-economics factors may increase the incidence, prevalence and risk of schistosomiasis infections in Zambia. However, available information does not provide a comprehensive understanding of the biogeography and distribution of the disease, ecology and population dynamics of intermediate host snails. The current study used an information-theoretical approach to understand the biogeography and prevalence schistosomiasis and identified knowledge gaps that would be useful to improve policy towards surveillance and eradication of intermediate hosts snails in Zambia...
April 30, 2018: Infectious Diseases of Poverty
https://www.readbyqxmd.com/read/29686737/chikungunya-and-diabetes-what-do-we-know
#15
REVIEW
Francisca Kalline de Almeida Barreto, Renan Magalhães Montenegro, Virginia Oliveira Fernandes, Rhaquel Oliveira, Lívia Aline de Araújo Batista, Akhtar Hussain, Luciano Pamplona de Góes Cavalcanti
Background: Chikungunya (CHIK) is a viral disease transmitted by mosquitoes. The first cases in Brazil were confirmed in 2014. Between 2016 and 2017, over 300,000 cases were identified during this period, with nearly 300 deaths. The clinical manifestations, pathogenesis and risk factors for occurrence of severe cases are not yet well understood, although it is known that the severity of the cases is associated with the presence of comorbidities, especially diabetes mellitus (DM). Objective: To review the medical literature for the associations between DM and CHIK and to understand the potential impact on metabolic state and its complications...
2018: Diabetology & Metabolic Syndrome
https://www.readbyqxmd.com/read/29684020/black-boxing-and-cause-effect-power
#16
William Marshall, Larissa Albantakis, Giulio Tononi
Reductionism assumes that causation in the physical world occurs at the micro level, excluding the emergence of macro-level causation. We challenge this reductionist assumption by employing a principled, well-defined measure of intrinsic cause-effect power-integrated information (Φ), and showing that, according to this measure, it is possible for a macro level to "beat" the micro level. Simple systems were evaluated for Φ across different spatial and temporal scales by systematically considering all possible black boxes...
April 23, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29678454/top-100-cited-articles-on-radiation-exposure-in-medical-imaging-a-bibliometric-analysis
#17
Jason Kinnin, Tarek N Hanna, Marc Jutras, Babar Hasan, Rick Bhatia, Faisal Khosa
BACKGROUND: Bibliometric analyses by highest number of citations can help researchers and funding agencies in determining the most influential articles in a field. The main objective of this analysis was to identify the top 100 cited articles addressing radiation exposure from medical imaging and assess their characteristics. METHODS: Relevant articles were extracted from the Scopus database after a systematic search by researchers using an iteratively defined Boolean search string...
March 20, 2018: Current Problems in Diagnostic Radiology
https://www.readbyqxmd.com/read/29671404/regulation-of-dual-specificity-phosphatases-in-breast-cancer-during-initial-treatment-with-herceptin-a-boolean-model-analysis
#18
Petronela Buiga, Ari Elson, Lydia Tabernero, Jean-Marc Schwartz
BACKGROUND: 25% of breast cancer patients suffer from aggressive HER2-positive tumours that are characterised by overexpression of the HER2 protein or by its increased tyrosine kinase activity. Herceptin is a major drug used to treat HER2 positive breast cancer. Understanding the molecular events that occur when breast cancer cells are exposed to Herceptin is therefore of significant importance. Dual specificity phosphatases (DUSPs) are central regulators of cell signalling that function downstream of HER2, but their role in the cellular response to Herceptin is mostly unknown...
April 11, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29671395/discovery-of-boolean-metabolic-networks-integer-linear-programming-based-approach
#19
Yushan Qiu, Hao Jiang, Wai-Ki Ching, Xiaoqing Cheng
BACKGROUND: Traditional drug discovery methods focused on the efficacy of drugs rather than their toxicity. However, toxicity and/or lack of efficacy are produced when unintended targets are affected in metabolic networks. Thus, identification of biological targets which can be manipulated to produce the desired effect with minimum side-effects has become an important and challenging topic. Efficient computational methods are required to identify the drug targets while incurring minimal side-effects...
April 11, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29665764/unicompartmental-knee-arthroplasty-for-spontaneous-osteonecrosis-of-the-knee-a-meta-analysis
#20
Julio J Jauregui, Christopher L Blum, Neil Sardesai, Craig Bennett, R Frank Henn, Farshad Adib
BACKGROUND: Spontaneous osteonecrosis of the knee (SONK) is a poorly understood but debilitating disease entity. Total knee arthroplasty (TKA) is the standard of care for those patients who fail conservative management, but considering SONK's predilection for affecting a single knee compartment, unicompartmental knee arthroplasty (UKA) appears to be a more tailored option. Unfortunately, conflicting data exist on the utility of UKA in SONK. Thus, the purpose of this study was to evaluate functional outcomes and revision rates of UKA in the setting of SONK...
May 2018: Journal of Orthopaedic Surgery
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