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https://www.readbyqxmd.com/read/28231289/rehr-an-r-package-for-manipulating-and-analysing-electronic-health-record-data
#1
David A Springate, Rosa Parisi, Ivan Olier, David Reeves, Evangelos Kontopantelis
Research with structured Electronic Health Records (EHRs) is expanding as data becomes more accessible; analytic methods advance; and the scientific validity of such studies is increasingly accepted. However, data science methodology to enable the rapid searching/extraction, cleaning and analysis of these large, often complex, datasets is less well developed. In addition, commonly used software is inadequate, resulting in bottlenecks in research workflows and in obstacles to increased transparency and reproducibility of the research...
2017: PloS One
https://www.readbyqxmd.com/read/28231128/effects-of-processing-temperature-on-color-properties-of-dry-cured-hams-made-without-nitrite
#2
Giovanni Parolari, Agnese Aguzzoni, Tania Toscani
Dry cured hams were investigated for their ability to develop red color even at low temperature (3-4 °C) and in the absence of added nitrites; results were compared with those obtained from nitrite-free hams made at conventional warm maturing temperatures. Colorimetric parameters (L*, a*, b*, and hue) and concentration of the main pigments Zn protoporphyrin IX (ZnPP) and heme were measured at three stages of preparation (six, nine, and 12 months), showing that red color was successfully formed at low temperatures, though at a slower rate and less intensively than under warm conditions...
April 29, 2016: Foods (Basel, Switzerland)
https://www.readbyqxmd.com/read/28230844/network-neuroscience
#3
REVIEW
Danielle S Bassett, Olaf Sporns
Despite substantial recent progress, our understanding of the principles and mechanisms underlying complex brain function and cognition remains incomplete. Network neuroscience proposes to tackle these enduring challenges. Approaching brain structure and function from an explicitly integrative perspective, network neuroscience pursues new ways to map, record, analyze and model the elements and interactions of neurobiological systems. Two parallel trends drive the approach: the availability of new empirical tools to create comprehensive maps and record dynamic patterns among molecules, neurons, brain areas and social systems; and the theoretical framework and computational tools of modern network science...
February 23, 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28228766/cell-wall-remodeling-in-abscission-zone-cells-during-ethylene-promoted-fruit-abscission-in-citrus
#4
Paz Merelo, Javier Agustí, Vicent Arbona, Mário L Costa, Leandro H Estornell, Aurelio Gómez-Cadenas, Silvia Coimbra, María D Gómez, Miguel A Pérez-Amador, Concha Domingo, Manuel Talón, Francisco R Tadeo
Abscission is a cell separation process by which plants can shed organs such as fruits, leaves, or flowers. The process takes place in specific locations termed abscission zones. In fruit crops like citrus, fruit abscission represents a high percentage of annual yield losses. Thus, understanding the molecular regulation of abscission is of capital relevance to control production. To identify genes preferentially expressed within the citrus fruit abscission zone (AZ-C), we performed a comparative transcriptomics assay at the cell type resolution level between the AZ-C and adjacent fruit rind cells (non-abscising tissue) during ethylene-promoted abscission...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28228091/exploring-the-transcriptome-of-non-model-oleaginous-microalga-dunaliella-tertiolecta-through-high-throughput-sequencing-and-high-performance-computing
#5
Lina Yao, Kenneth Wei Min Tan, Tin Wee Tan, Yuan Kun Lee
BACKGROUND: RNA-Seq technology has received a lot of attention in recent years for microalgal global transcriptomic profiling. It is widely used in transcriptome-wide analysis of gene expression., particularly for microalgal strains with potential as biofuel sources. However, insufficient genomic or transcriptomic information of non-model microalgae has limited the understanding of their regulatory mechanisms and hampered genetic manipulation to enhance biofuel production. As such, an optimal microalgal transcriptomic database construction is a subject of urgent investigation...
February 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28226955/an-investigation-of-animal-and-human-bones-for-predicting-probable-location-of-fractures
#6
Irfan Manarvi, Irfan Manarvi, Irfan Manarvi
Predicting location of fracture in animal and human bones has been a keen area of research for the past few decades. It has been established that it is various types of stress that results into bone failure. Past studies were mostly based on experimental testing of variety of bones with limited accuracy equipment leading to experimental errors. An effort has been made in present research to use latest experimental testing equipment in parallel with some modern techniques and tools such as 3D scanners for creating computer models and Finite Element Analysis (FEA) to conduct structural analysis that could allow unlimited changes in boundary conditions expected to be faced by a bone...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226769/a-bi-directional-communication-paradigm-between-parallel-neuron-and-an-external-non-neuron-process
#7
Phillip J Hendrickson, Clayton Bingham, Dong Song, Theodore W Berger, Phillip J Hendrickson, Clayton Bingham, Dong Song, Theodore W Berger, Phillip J Hendrickson, Clayton Bingham, Dong Song, Theodore W Berger
In order to accurately model the pattern of activation due to electrical stimulation of the hippocampus, a multi-scale computational approach is necessary. At the system level, the Admittance Method (ADM) is used to calculate the extracellular voltages created by a stimulating electrode. At the network and cellular levels, a large-scale multi-compartmental neuron network is used to calculate cellular activation. This paper presents a bi-directional communication paradigm between the NEURON model and an external surrogate for the ADM solver, where at each time step, neurons share their membrane currents with the external process, and the external process shares calculated extracellular voltages with the neuronal network...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226577/semi-advised-learning-model-for-skin-cancer-diagnosis-based-on-histopathalogical-images
#8
Ammara Masood, Adel Al-Jumaily, Ammara Masood, Adel Al-Jumaily, Ammara Masood, Adel Al-Jumaily
Computer aided classification of skin cancer images is an active area of research and different classification methods has been proposed so far. However, the supervised classification models based on insufficient labeled training data can badly influence the diagnosis process. To deal with the problem of limited labeled data availability this paper presents a semi advised learning model for automated recognition of skin cancer using histopathalogical images. Deep belief architecture is constructed using unlabeled data by making efficient use of limited labeled data for fine tuning done the classification model...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226278/quantitative-methylene-blue-decolourisation-assays-as-rapid-screening-tools-for-assessing-the-efficiency-of-catalytic-reactions
#9
Jan Kruid, Ronen Fogel, Janice Leigh Limson
Identifying the most efficient oxidation process to achieve maximum removal of a target pollutant compound forms the subject of much research. There exists a need to develop rapid screening tools to support research in this area. In this work we report on the development of a quantitative assay as a means for identifying catalysts capable of decolourising methylene blue through the generation of oxidising species from hydrogen peroxide. Here, a previously described methylene blue test strip method was repurposed as a quantitative, aqueous-based spectrophotometric assay...
February 12, 2017: Chemosphere
https://www.readbyqxmd.com/read/28225208/weak-supramolecular-interactions-governing-parallel-and-antiparallel-dna-quadruplexes-insights-from-large-scale-qm-analysis-of-experimentally-derived-models
#10
Yevgen P Yurenko, Jan Novotný, Radek Marek
The topology and energetics of guanine (G) quadruplexes is governed by supramolecular interactions within their strands. In this work, we performed an extensive QM study of supramolecular interactions shaping the stems of (4+0) parallel (P) and (2+2) antiparallel (AP) systems. The large-scale (~ 400 atoms) models of P and AP were constructed from high-quality experimental structures. The results evidence that each of the P and AP structures is shaped by a distinct network of supramolecular interactions. The analysis of electron topological characteristics of H-bonds in P and AP systems indicates that the P model benefits from the stronger intra-tetrad H-bonding...
February 22, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28225009/transcriptomic-responses-of-the-olive-fruit-fly-bactrocera-oleae-and-its-symbiont-candidatus-erwinia-dacicola-to-olive-feeding
#11
Nena Pavlidi, Anastasia Gioti, Nicky Wybouw, Wannes Dermauw, Michael Ben-Yosef, Boaz Yuval, Edouard Jurkevich, Anastasia Kampouraki, Thomas Van Leeuwen, John Vontas
The olive fruit fly, Bactrocera oleae, is the most destructive pest of olive orchards worldwide. The monophagous larva has the unique capability of feeding on olive mesocarp, coping with high levels of phenolic compounds and utilizing non-hydrolyzed proteins present, particularly in the unripe, green olives. On the molecular level, the interaction between B. oleae and olives has not been investigated as yet. Nevertheless, it has been associated with the gut obligate symbiotic bacterium Candidatus Erwinia dacicola...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28223930/event-and-time-driven-techniques-using-parallel-cpu-gpu-co-processing-for-spiking-neural-networks
#12
Francisco Naveros, Jesus A Garrido, Richard R Carrillo, Eduardo Ros, Niceto R Luque
Modeling and simulating the neural structures which make up our central neural system is instrumental for deciphering the computational neural cues beneath. Higher levels of biological plausibility usually impose higher levels of complexity in mathematical modeling, from neural to behavioral levels. This paper focuses on overcoming the simulation problems (accuracy and performance) derived from using higher levels of mathematical complexity at a neural level. This study proposes different techniques for simulating neural models that hold incremental levels of mathematical complexity: leaky integrate-and-fire (LIF), adaptive exponential integrate-and-fire (AdEx), and Hodgkin-Huxley (HH) neural models (ranged from low to high neural complexity)...
2017: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/28223922/gut-microbiota-a-potential-regulator-of-neurodevelopment
#13
REVIEW
Paola Tognini
During childhood, our brain is exposed to a variety of environmental inputs that can sculpt synaptic connections and neuronal circuits, with subsequent influence on behavior and learning processes. Critical periods of neurodevelopment are windows of opportunity in which the neuronal circuits are extremely plastic and can be easily subjected to remodeling in response to experience. However, the brain is also more susceptible to aberrant stimuli that might lead to altered developmental trajectories. Intriguingly, postnatal brain development is paralleled by the maturation of the gut microbiota: the ecosystem of symbionts populating our gastro-intestinal tract...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28222698/atgc-transcriptomics-a-web-based-application-to-integrate-explore-and-analyze-de-novo-transcriptomic-data
#14
Sergio Gonzalez, Bernardo Clavijo, Máximo Rivarola, Patricio Moreno, Paula Fernandez, Joaquín Dopazo, Norma Paniego
BACKGROUND: In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a useful tool for detecting novel transcripts and genetic variations and for evaluating differential gene expression by digital measurements. The large and complex datasets resulting from functional genomic experiments represent a challenge in data processing, management, and analysis...
February 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28222598/drastic-compensation-of-the-electronic-and-solvation-effects-on-the-atp-hydrolysis-revealed-through-a-large-scale-qm-mm-simulations-combined-with-a-theory-of-solutions
#15
Hideaki Takahashi, Satoru Umino, Yuji Miki, Ryosuke Ishizuka, Shu Maeda, Akihiro Morita, Makoto Suzuki, Nobuyuki Matubayasi
Hydrolysis of adenosine triphosphate (ATP) is the "energy source" for a variety of biochemical processes. In the present work, we address key features of ATP hydrolysis: the relatively moderate value (about -10 kcal/mol) of the standard free energy ΔGhyd of reaction and the insensitivity of ΔGhyd to the number of excess electrons on ATP. We conducted quantum mechanical/molecular mechanical (QM/MM) simulation combined with the energy-representation theory of solutions to analyze the electronic-state and solvation contributions to ΔGhyd...
February 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28222424/1%C3%AE-25-oh-2d3-sensitive-cytosolic-ph-regulation-and-glycolytic-flux-in-human-endometrial-ishikawa-cells
#16
Ni Zeng, Yuetao Zhou, Shaqiu Zhang, Yogesh Singh, Bing Shi, Madhuri S Salker, Florian Lang
BACKGROUND/AIMS: Tumor cell proliferation is modified by 1,25-Dihydroxy-Vitamin D3 (1,25(OH)2D3), a steroid hormone predominantly known for its role in calcium and phosphorus metabolism. Key properties of tumor cells include enhanced glycolytic flux with excessive consumption of glucose and formation of lactate. As glycolysis is highly sensitive to cytosolic pH, maintenance of glycolysis requires export of H+ ions and lactate, which is in part accomplished by Na+/H+ exchangers, such as NHE1 and monocarboxylate transporters, such as MCT4...
February 8, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28221767/construction-of-a-chassis-for-a-tripartite-protein-based-molecular-motor
#17
Lara Sioban Small, Marc Bruning, Andrew Thomson, Aimee L Boyle, Roberta Davies, Paul M G Curmi, Nancy R Forde, Heiner Linke, Derek N Woolfson, Elizabeth Bromley
Improving our understanding of biological motors, both to fully comprehend their activities in vital processes, and to exploit their impressive abilities for use in bionanotechnology, is highly desirable. One means of understanding these systems is through the production of synthetic molecular motors. We demonstrate the use of orthogonal coiled-coil dimers (including both parallel and anti-parallel coiled-coils) as a hub for linking other components of a previously described synthetic molecular motor, the Tumbleweed...
February 21, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28221756/pattern-recognition-using-carbon-nanotube-synaptic-transistors-with-an-adjustable-weight-update-protocol
#18
Sungho Kim, Bongsik Choi, Meehyun Lim, Jinsu Yoon, Juhee Lee, Hee-Dong Kim, Sung-Jin Choi
Recent electronic applications require an efficient computing system that can perform data processing with limited energy consumption. Inspired by the massive parallelism of the human brain, a neuromorphic system (hardware neural network) may provide an efficient computing unit to perform such tasks as classification and recognition. However, the implementation of synaptic devices (i.e., the essential building blocks for emulating the functions of biological synapses) remains challenging due to their uncontrollable weight update protocol and corresponding uncertain effects on the operation of the system, which can lead to a bottleneck in the continuous design and optimization...
February 21, 2017: ACS Nano
https://www.readbyqxmd.com/read/28221284/pain-interference-and-physical-function-demonstrate-poor-longitudinal-association-in-people-living-with-pain-a-promis-investigation
#19
Nicholas V Karayannis, John A Sturgeon, Ming Chih-Kao, Corinne Cooley, Sean C Mackey
A primary goal in managing pain is to reduce pain and increase physical function (PF). This goal is also tied to continuing payment for treatment services in many practice guidelines. Pain interference (PI) is often used as a proxy for measurement and reporting of PF in these guidelines. A common assumption is that reductions in PI will translate into improvement in PF over time. This assumption needs to be tested in a clinical environment. Consequently, we used the patient reported outcomes measurement information system (PROMIS) to describe the topology of the longitudinal relationship between PI in relation to PF...
February 16, 2017: Pain
https://www.readbyqxmd.com/read/28221037/computational-investigation-of-ligand-binding-to-the-peripheral-site-in-cyp3a4-conformational-dynamics-and-inhibitor-discovery
#20
Hanwen Du, Junhao Li, Yingchun Cai, Hongxiao Zhang, Guixia Liu, Yun Tang, Weihua Li
Human cytochrome P450 3A4 (CYP3A4) is a major drug-metabolizing enzyme responsible for the metabolism of ~50% of clinically used drugs and is often involved in drug-drug interactions. It exhibits atypical binding and kinetic behavior towards many ligands. Binding of ligands to CYP3A4 is a complex process. Recent studies from both crystallography and biochemistry suggested the existence of a peripheral ligand-binding site at the enzyme surface. However, the stability of ligand bound at this peripheral site and the possibility of discovering new CYP3A4 ligands based on this site remain unclear...
February 21, 2017: Journal of Chemical Information and Modeling
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