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https://www.readbyqxmd.com/read/28454100/a-mathematical-theory-of-the-transcription-repression-tr-therapy-of-cancer-whether-and-how-it-may-work
#1
Yuxin Chen, Haijun Wen, Chung-I Wu
Transcription repression (TR) therapy of cancer has been widely discussed. Here, TR refers to global repression of transcription rather than specific targeting of cancer-causing genes such as MYC. TR drugs inhibit transcription by binding to the transcribed DNA or to RNA polymerase; for example, actinomycin D has been extensively used in research and therapy to shut down transcription globally [1-7]. As proliferating cells demand a high rate of transcription, restricting transcript production could be effective in slowing down cell proliferation...
April 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28453546/improved-approximation-of-spatial-light-distribution
#2
David Kaljun, Tina Novak, Janez Žerovnik
The rapid worldwide evolution of LEDs as light sources has brought new challenges, which means that new methods are needed and new algorithms have to be developed. Since the majority of LED luminaries are of the multi-source type, established methods for the design of light engines cannot be used in the design of LED light engines. This is because in the latter case what is involved is not just the design of a good reflector or projector lens, but the design of several lenses which have to work together in order to achieve satisfactory results...
2017: PloS One
https://www.readbyqxmd.com/read/28453436/the-maths-of-memory
#3
Jose Borghans, Ruy M Ribeiro
Mathematical modeling reveals that long-term immunological memory is maintained in a manner that is even more dynamic than previously thought.
April 28, 2017: ELife
https://www.readbyqxmd.com/read/28453365/a-novel-method-for-designing-and-optimizing-the-layout-of-facilities-in-bathroom-for-the-elderly-in-home-based-rehabilitation
#4
Duojin Wang, Jing Wu, Qinglian Lin
PURPOSE: The home-based rehabilitation of elderly patients improves their autonomy, independence and reintegration into society. Hence, a suitable environment plays an important role in rehabilitation, as do different assistance technologies. The majority of accidents at home involving elderly people occur in the bathroom. Therefore, the planning of the layout of facilities is important in this potentially dangerous area. This paper proposes an approach towards designing and optimizing the layout of facilities in the bathroom, based on logistical and nonlogistical relationships...
April 28, 2017: Disability and Rehabilitation. Assistive Technology
https://www.readbyqxmd.com/read/28449533/can-mathematics-replace-anatomy-to-establish-recommendations-in-lung-cancer-surgery
#5
EDITORIAL
Marc Riquet, Ciprian Pricopi, Antoine Legras, Alex Arame, Alain Badia, Françoise Le Pimpec Barthes
The greater the number of lymph node (LN) sampled (NLNsS) during lung cancer surgery, the lower the risk of underestimating the pN-status and the better the outcome of the pN0-patients due to stage-migration. Thus, regarding LN sampling "to be or not to be", number is the question. Recent studies advocate removing 10 LNs. The most suitable NLNsS is unfortunately impossible to establish by mathematics. A too high NLNsS variability exists, based on anatomy, surgery and pathology. The methodology may vary according to Inter-institutional differences in the surgical approach regarding LN inspection and number sampling...
March 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28448796/reconciling-epigenetic-memory-and-transcriptional-responsiveness
#6
Amanda G Fisher, Michael P H Stumpf, Matthias Merkenschlager
The molecular basis of cellular memory is important but poorly understood. Using estimates of histone dynamics, Martin Howard and colleagues construct a mathematical model that helps to explain both the stability and flexibility of Polycomb-mediated gene regulation in cellular memory.
April 26, 2017: Cell Systems
https://www.readbyqxmd.com/read/28448493/variable-habitat-conditions-drive-species-covariation-in-the-human-microbiota
#7
Charles K Fisher, Thierry Mora, Aleksandra M Walczak
Two species with similar resource requirements respond in a characteristic way to variations in their habitat-their abundances rise and fall in concert. We use this idea to learn how bacterial populations in the microbiota respond to habitat conditions that vary from person-to-person across the human population. Our mathematical framework shows that habitat fluctuations are sufficient for explaining intra-bodysite correlations in relative species abundances from the Human Microbiome Project. We explicitly show that the relative abundances of closely related species are positively correlated and can be predicted from taxonomic relationships...
April 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28447817/a-unified-framework-for-bounded-and-unbounded-numerical-estimation
#8
Dan Kim, John E Opfer
Representations of numerical value have been assessed by using bounded (e.g., 0-1,000) and unbounded (e.g., 0-?) number-line tasks, with considerable debate regarding whether 1 or both tasks elicit unique cognitive strategies (e.g., addition or subtraction) and require unique cognitive models. To test this, we examined how well a mixed log-linear model accounted for 86 5- to 9-year-olds' estimates on bounded and unbounded number-line tasks and how well it predicted mathematical performance. Compared with mixtures of 4 alternative models, the mixed log-linear model better predicted 76% of individual children's estimates on bounded number lines and 100% of children's estimates on unbounded number lines...
April 27, 2017: Developmental Psychology
https://www.readbyqxmd.com/read/28447812/a-computational-model-of-fraction-arithmetic
#9
David W Braithwaite, Aryn A Pyke, Robert S Siegler
Many children fail to master fraction arithmetic even after years of instruction, a failure that hinders their learning of more advanced mathematics as well as their occupational success. To test hypotheses about why children have so many difficulties in this area, we created a computational model of fraction arithmetic learning and presented it with the problems from a widely used textbook series. The simulation generated many phenomena of children's fraction arithmetic performance through a small number of common learning mechanisms operating on a biased input set...
April 27, 2017: Psychological Review
https://www.readbyqxmd.com/read/28447592/the-phantom-derivative-method-when-a-structure-model-is-available-about-its-theoretical-basis
#10
Maria Cristina Burla, Giovanni Luca Cascarano, Carmelo Giacovazzo, Giampiero Polidori
This study clarifies why, in the phantom derivative (PhD) approach, randomly created structures can help in refining phases obtained by other methods. For this purpose the joint probability distribution of target, model, ancil and phantom derivative structure factors and its conditional distributions have been studied. Since PhD may use n phantom derivatives, with n ≥ 1, a more general distribution taking into account all the ancil and derivative structure factors has been considered, from which the conditional distribution of the target phase has been derived...
May 1, 2017: Acta Crystallographica. Section A, Foundations and Advances
https://www.readbyqxmd.com/read/28446878/computational-model-predicts-the-effects-of-targeting-cellular-metabolism-in-pancreatic-cancer
#11
Mahua Roy, Stacey D Finley
Reprogramming of energy metabolism is a hallmark of cancer that enables the cancer cells to meet the increased energetic requirements due to uncontrolled proliferation. One prominent example is pancreatic ductal adenocarcinoma, an aggressive form of cancer with an overall 5-year survival rate of 5%. The reprogramming mechanism in pancreatic cancer involves deregulated uptake of glucose and glutamine and other opportunistic modes of satisfying energetic demands in a hypoxic and nutrient-poor environment. In the current study, we apply systems biology approaches to enable a better understanding of the dynamics of the distinct metabolic alterations in KRAS-mediated pancreatic cancer, with the goal of impeding early cell proliferation by identifying the optimal metabolic enzymes to target...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28446703/efficient-use-of-sentinel-sites-detection-of-invasive-honeybee-pests-and-diseases-in-the-uk
#12
Matt J Keeling, Samik Datta, Daniel N Franklin, Ivor Flatman, Andy Wattam, Mike Brown, Giles E Budge
Sentinel sites, where problems can be identified early or investigated in detail, form an important part of planning for exotic disease outbreaks in humans, livestock and plants. Key questions are: how many sentinels are required, where should they be positioned and how effective are they at rapidly identifying new invasions? The sentinel apiary system for invasive honeybee pests and diseases illustrates the costs and benefits of such approaches. Here, we address these issues with two mathematical modelling approaches...
April 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28445754/probing-the-dynamics-of-clot-bound-thrombin-at-venous-shear-rates
#13
Laura M Haynes, Thomas Orfeo, Kenneth G Mann, Stephen J Everse, Kathleen E Brummel-Ziedins
In closed system models of fibrin formation, exosite-mediated thrombin binding to fibrin contributes to clot stability and is resistant to inhibition by antithrombin/heparin while still susceptible to small, active-site inhibitors. Each molecule of fibrin can bind ∼1.6 thrombin molecules at low-affinity binding sites (Kd = 2.8 μM) and ∼0.3 molecules of thrombin at high-affinity binding sites (Kd = 0.15 μM). The goal of this study is to assess the stability of fibrin-bound thrombin under venous flow conditions and to determine both its accessibility and susceptibility to inhibition...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28445470/the-credibility-crisis-in-research-can-economics-tools-help
#14
Thomas Gall, John P A Ioannidis, Zacharias Maniadis
The issue of nonreplicable evidence has attracted considerable attention across biomedical and other sciences. This concern is accompanied by an increasing interest in reforming research incentives and practices. How to optimally perform these reforms is a scientific problem in itself, and economics has several scientific methods that can help evaluate research reforms. Here, we review these methods and show their potential. Prominent among them are mathematical modeling and laboratory experiments that constitute affordable ways to approximate the effects of policies with wide-ranging implications...
April 2017: PLoS Biology
https://www.readbyqxmd.com/read/28445057/experimental-and-numerical-study-of-the-evaporation-of-water-at-low-pressures
#15
Mohammad Amin Kazemi, David S Nobes, Janet A W Elliott
Although evaporation is considered to be a surface phenomenon, the rate of molecular transport across a liquid-vapor boundary is strongly dependent on the coupled fluid dynamics and heat transfer in the bulk fluids. Recent experimental thermocouple measurements of the temperature field near the interface of evaporating water into its vapor have begun to show the role of heat transfer in evaporation. However, the role of fluid dynamics has not been explored sufficiently. Here, we have developed a mathematical model to describe the coupling of the heat, mass, and momentum transfer in the fluids with the transport phenomena at the interface...
April 26, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28444398/plasma-transfusion-demystified-a-review-of-the-key-factors-influencing-the-response-to-plasma-transfusion
#16
Allen W Bryan, Elizabeth M Staley, Timothy Kennell, Alexander Z Feldman, Lance A Williams, Huy P Pham
Many studies have suggested that inappropriate plasma usage is common. An important factor contributing to futile plasma administration in most patients is the nonlinear relationship between coagulation-factor levels and the volume of plasma transfused. In this review, a validated mathematical model and data from the literature will be used to illuminate 3 key properties of plasma transfusion. Those properties are as follows: the effect of plasma transfusion on international normalized ratio (INR) is transient; for the same volume of transfused plasma, a greater reduction in INR is observed at higher initial INRs; and the effect of plasma transfusion on INR correction (ie, the difference between initial and final INRs) diminishes as more plasma is transfused...
April 24, 2017: Laboratory Medicine
https://www.readbyqxmd.com/read/28444384/e-science-technologies-in-a-workflow-for-personalized-medicine-using-cancer-screening-as-a-case-study
#17
Ola Spjuth, Andreas Karlsson, Mark Clements, Keith Humphreys, Emma Ivansson, Jim Dowling, Martin Eklund, Alexandra Jauhiainen, Kamila Czene, Henrik Grönberg, Pär Sparén, Fredrik Wiklund, Abbas Cheddad, Þorgerður Pálsdóttir, Mattias Rantalainen, Linda Abrahamsson, Erwin Laure, Jan-Eric Litton, Juni Palmgren
Objective: We provide an e-Science perspective on the workflow from risk factor discovery and classification of disease to evaluation of personalized intervention programs. As case studies, we use personalized prostate and breast cancer screenings. Materials and Methods: We describe an e-Science initiative in Sweden, e-Science for Cancer Prevention and Control (eCPC), which supports biomarker discovery and offers decision support for personalized intervention strategies...
April 21, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28444357/coordinated-regulations-of-mrna-synthesis-and-decay-during-cold-acclimation-in-arabidopsis-cells
#18
Toshihiro Arae, Shiori Isai, Akira Sakai, Katsuhiko Mineta, Masami Yokota Hirai, Yuya Suzuki, Shigehiko Kanaya, Junji Yamaguchi, Satoshi Naito, Yukako Chiba
Plants possess a cold acclimation system to acquire freezing tolerance through pre-exposure to non-freezing low temperatures. The transcriptional cascade of C-repeat binding factors (CBFs)/dehydration response element-binding factors (DREBs) is considered a major transcriptional regulatory pathway during cold acclimation. However, little is known regarding the functional significance of mRNA stability regulation in the response of gene expression to cold stress. The actual level of individual mRNAs is determined by a balance between mRNA synthesis and degradation...
April 21, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28444126/cimbinator-a-web-based-tool-for-drug-synergy-analysis-in-small-and-large-scale-datasets
#19
Åsmund Flobak, Miguel Vazquez, Astrid Lægreid, Alfonso Valencia
Motivation: Drug synergies are sought to identify combinations of drugs particularly beneficial. User-friendly software solutions that can assist analysis of large-scale datasets are required. Results: CImbinator is a web-service that can aid in batch-wise and in-depth analyzes of data from small-scale and large-scale drug combination screens. CImbinator offers to quantify drug combination effects, using both the commonly employed median effect equation, as well as advanced experimental mathematical models describing dose response relationships...
April 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28444104/psychomotor-ability-and-short-term-memory-and-reading-and-mathematics-achievement-in-children
#20
Cherée Murrihy, Maria Bailey, John Roodenburg
Objective: The aim of our study was to examine whether the findings from previous research, indicating the role of short-term memory as a mediator of the relationship between motor coordination and academic achievement in adolescents, is also evident in a younger child population. Method: The study utilized a quantative cross-sectional design involving 133 children aged 8-12. The McCarron Assessment of Neuromuscular Development (MAND) provided four indicators of psychomotor ability (Finger Nose, Walking, Balancing, and Jumping)...
April 24, 2017: Archives of Clinical Neuropsychology: the Official Journal of the National Academy of Neuropsychologists
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