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https://www.readbyqxmd.com/read/28230998/influence-of-the-anomeric-conformation-in-the-intermolecular-interactions-of-glucose
#1
Imanol Usabiaga, Jorge González, Iker León, Pedro Felipe Arnaiz, Emilio J Cocinero, Jose A Fernandez
Carbohydrates are together with amino acids, DNA bases and lipids the building blocks of living beings. They play a central role in basic functions as immunity and signaling, which are governed by non-covalent interactions between sugar units and/or with other biomolecules. To get insights on such interactions between monosaccharide units, we used a combination of mass-resolved laser spectroscopy in supersonic expansions and molecular structure calculations. The results obtained clearly demonstrate that the small stability difference between the α/β anomers of glucopyranose derivatives is reversed and amplified during molecular aggregation, making the complexes of the β-anomers significantly more stable...
February 23, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28230815/conceptual-foundations-of-systems-biology-explaining-complex-cardiac-diseases
#2
REVIEW
George E Louridas, Katerina G Lourida
Systems biology is an important concept that connects molecular biology and genomics with computing science, mathematics and engineering. An endeavor is made in this paper to associate basic conceptual ideas of systems biology with clinical medicine. Complex cardiac diseases are clinical phenotypes generated by integration of genetic, molecular and environmental factors. Basic concepts of systems biology like network construction, modular thinking, biological constraints (downward biological direction) and emergence (upward biological direction) could be applied to clinical medicine...
February 21, 2017: Healthcare (Basel, Switzerland)
https://www.readbyqxmd.com/read/28230789/fungal-ribotoxins-a-review-of-potential-biotechnological-applications
#3
REVIEW
Miriam Olombrada, Rodrigo Lázaro-Gorines, Juan C López-Rodríguez, Álvaro Martínez-Del-Pozo, Mercedes Oñaderra, Moisés Maestro-López, Javier Lacadena, José G Gavilanes, Lucía García-Ortega
Fungi establish a complex network of biological interactions with other organisms in nature. In many cases, these involve the production of toxins for survival or colonization purposes. Among these toxins, ribotoxins stand out as promising candidates for their use in biotechnological applications. They constitute a group of highly specific extracellular ribonucleases that target a universally conserved sequence of RNA in the ribosome, the sarcin-ricin loop. The detailed molecular study of this family of toxic proteins over the past decades has highlighted their potential in applied research...
February 21, 2017: Toxins
https://www.readbyqxmd.com/read/28230528/biologically-plausible-learning-in-recurrent-neural-networks-reproduces-neural-dynamics-observed-during-cognitive-tasks
#4
Thomas Miconi
Neural activity during cognitive tasks exhibits complex dynamics that flexibly encode task-relevant variables. Chaotic recurrent networks, which spontaneously generate rich dynamics, have been proposed as a model of cortical computation during cognitive tasks. However, existing methods for training these networks are either biologically implausible, and/or require a continuous, real-time error signal to guide learning. Here we show that a biologically plausible learning rule can train such recurrent networks, guided solely by delayed, phasic rewards at the end of each trial...
February 23, 2017: ELife
https://www.readbyqxmd.com/read/28229245/drug-use-and-sexual-hiv-transmission-risk-among-men-who-have-sex-with-men-and-women-msmw-men-who-have-sex-with-men-only-msmo-and-men-who-have-sex-with-women-only-mswo-and-the-female-partners-of-msmw-and-mswo-a-network-perspective
#5
Typhanye V Dyer, Maria R Khan, Milagros Sandoval, Abenaa Acheampong, Rotrease Regan, Melissa Bolyard, Pedro Mateu-Gelabert, Samuel R Friedman
We described drug use, sex risk, and STI/HIV among men who have sex with men and women (MSMW) and their female partners. We used the Network, Norms and HIV/STI Risk among Youth (NNAHRAY) study to evaluate drug use, sex risk, and biologically-confirmed STI/HIV in (1) MSMW and men who had sex with men only (MSMO) versus men who had sex with women only (MSWO) and (2) female partners of MSMW versus female partners of MSWO (N = 182 men, 152 women). MSMW versus MSWO had 30 to 60% increased odds of substance use, over twice the odds of multiple partnerships, and almost five times the odds of sex trade and HIV infection...
February 22, 2017: AIDS and Behavior
https://www.readbyqxmd.com/read/28228687/reproductive-biology-and-variation-of-nuclear-ribosomal-its-and-ets-sequences-in-the-calligonum-mongolicum-complex-polygonaceae
#6
Wei Shi, Jun Wen, Yanfeng Zhao, Gabriel Johnson, Borong Pan
To explore the biosystematics of the Calligonum mongolicum complex (Polygonaceae), the flowering phenological period, breeding and pollination characters and seed set of the complex (Calligonum Mongolicum Turze, Calligonum chinense A. Los., Calligonum gobicum A. Los., Calligonum pumilum A. Los. and Calligonum zaidamense A. Los.) were documented in the Turpan Eremophyte Botanical Garden, China. The sequences of the nuclear ribosomal ITS and ETS region were employed to differentiate the Calligonum mongolicum complex and other species in sect...
2017: PhytoKeys
https://www.readbyqxmd.com/read/28228539/three-dimensional-printing-spiders-back-and-forth-glue-application-yields-silk-anchorages-with-high-pull-off-resistance-under-varying-loading-situations
#7
Jonas O Wolff, Marie E Herberstein
The anchorage of structures is a crucial element of construction, both for humans and animals. Spiders use adhesive plaques to attach silk threads to substrates. Both biological and artificial adhesive structures usually have an optimal loading angle, and are prone to varying loading situations. Silk anchorages, however, must cope with loading in highly variable directions. Here we show that the detachment forces of thread anchorages of orb-web spiders are highly robust against pulling in different directions...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28228173/optimization-of-vascular-casting-for-three-dimensional-fluorescence-cryo-imaging-of-collateral-vessels-in-the-ischemic-rat-hindlimb
#8
Janina C V Schwarz, Monique G J T B van Lier, Erik N T P Bakker, Judith de Vos, Jos A E Spaan, Ed VanBavel, Maria Siebes
Development of collateral vessels, arteriogenesis, may protect against tissue ischemia, however, quantitative data on this process remain scarce. We have developed a technique for replicating the entire arterial network of ischemic rat hindlimbs in three dimensions (3D) based on vascular casting and automated sequential cryo-imaging. Various dilutions of Batson's No. 17 with methyl methacrylate were evaluated in healthy rats, with further protocol optimization in ischemic rats. Penetration of the resin into the vascular network greatly depended on dilution; the total length of casted vessels below 75 µm was 13-fold higher at 50% dilution compared with the 10% dilution...
February 2017: Microscopy and Microanalysis
https://www.readbyqxmd.com/read/28228108/expression-profiling-and-bioinformatic-analyses-suggest-new-target-genes-and-pathways-for-human-hair-follicle-related-micrornas
#9
Lara M Hochfeld, Thomas Anhalt, Céline S Reinbold, Marisol Herrera-Rivero, Nadine Fricker, Markus M Nöthen, Stefanie Heilmann-Heimbach
BACKGROUND: Human hair follicle (HF) cycling is characterised by the tight orchestration and regulation of signalling cascades. Research shows that micro(mi)RNAs are potent regulators of these pathways. However, knowledge of the expression of miRNAs and their target genes and pathways in the human HF is limited. The objective of this study was to improve understanding of the role of miRNAs and their regulatory interactions in the human HF. METHODS: Expression levels of ten candidate miRNAs with reported functions in hair biology were assessed in HFs from 25 healthy male donors...
February 22, 2017: BMC Dermatology
https://www.readbyqxmd.com/read/28227909/neuromorphic-circuit-modeling-directional-selectivity-in-the-visual-cortex
#10
Saeid Barzegarjalali, Alice C Parker, Saeid Barzegarjalali, Alice C Parker, Alice C Parker, Saeid Barzegarjalali
We have designed a neuromorphic circuit that models directional selectivity in the visual cortex, where selected neurons fire depending on the direction of object motion, along with the size and orientation of the object. The neuromorphic circuit is biomimetic. It consists of neurons and synapses, and models biological mechanisms. Neurons (including the Axon Hillock and the Dendritic Arbor) are designed with CMOS technology and synapses (both excitatory and inhibitory) are designed with Carbon Nanotube Transistors...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227870/identifying-disease-network-perturbations-through-regression-on-gene-expression-and-pathway-topology-analysis
#11
Georgios N Dimitrakopoulos, Panos Balomenos, Aristidis G Vrahatis, Kyriakos Sgarbas, Anastasios Bezerianos, Georgios N Dimitrakopoulos, Panos Balomenos, Aristidis G Vrahatis, Kyriakos Sgarbas, Anastasios Bezerianos, Kyriakos Sgarbas, Panos Balomenos, Georgios N Dimitrakopoulos, Anastasios Bezerianos, Aristidis G Vrahatis
In Systems Biology, network-based approaches have been extensively used to effectively study complex diseases. An important challenge is the detection of network perturbations which disrupt regular biological functions as a result of a disease. In this regard, we introduce a network based pathway analysis method which isolates casual interactions with significant regulatory roles within diseased-perturbed pathways. Specifically, we use gene expression data with Random Forest regression models to assess the interactivity strengths of genes within disease-perturbed networks, using KEGG pathway maps as a source of prior-knowledge pertaining to pathway topology...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227700/prediction-of-oral-cancer-recurrence-using-dynamic-bayesian-networks
#12
Konstantina Kourou, George Rigas, Konstantinos P Exarchos, Costas Papaloukas, Dimitrios I Fotiadis, Konstantina Kourou, George Rigas, Konstantinos P Exarchos, Costas Papaloukas, Dimitrios I Fotiadis, George Rigas, Konstantinos P Exarchos, Dimitrios I Fotiadis, Costas Papaloukas, Konstantina Kourou
We propose a methodology for predicting oral cancer recurrence using Dynamic Bayesian Networks. The methodology takes into consideration time series gene expression data collected at the follow-up study of patients that had or had not suffered a disease relapse. Based on that knowledge, our aim is to infer the corresponding dynamic Bayesian networks and subsequently conjecture about the causal relationships among genes within the same time-slice and between consecutive time-slices. Moreover, the proposed methodology aims to (i) assess the prognosis of patients regarding oral cancer recurrence and at the same time, (ii) provide important information about the underlying biological processes of the disease...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227230/a-biologically-inspired-image-classifier-adaptive-feature-detection
#13
Jeffrey C Ames, Konstantinos P Michmizos, Jeffrey C Ames, Konstantinos P Michmizos, Jeffrey C Ames, Konstantinos P Michmizos
Today's artificial neural networks use computational models and algorithms inspired by the knowledge of the brain in the '90s. Powerful as they are, artificial networks are impressive but their domain specificity and reliance on vast numbers of labeled examples are obvious limitations. About a decade ago, spiking neural networks (SNNs) emerged as a new formalism that takes advantage of the spike timing and are particularly versatile when depicting spatio-temporal representations. The challenge now is to design rules for SNNs that can help them interact with their environment just like humans do...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227099/a-large-scale-detailed-neuronal-model-of-electrical-stimulation-of-the-dentate-gyrus-and-perforant-path-as-a-platform-for-electrode-design-and-optimization
#14
Clayton S Bingham, Kyle Loizos, Gene Yu, Andrew Gilbert, Jean-Marie Bouteiller, Dong Song, Gianluca Lazzi, Theodore W Berger, Clayton S Bingham, Kyle Loizos, Gene Yu, Andrew Gilbert, Jean-Marie Bouteiller, Dong Song, Gianluca Lazzi, Theodore W Berger, Kyle Loizos, Gene Yu, Theodore W Berger, Gianluca Lazzi, Jean-Marie Bouteiller, Clayton S Bingham, Dong Song, Andrew Gilbert
Owing to the dramatic rise in treatment of neurological disorders with electrical micro-stimulation it has become apparent that the major technological limitation in deploying effective devices lies in the process of designing efficient, safe, and outcome specific electrode arrays. The time-consuming and low-fidelity nature of gathering test data using experimental means and the immense control and flexibility of computational models, has prompted us and others to build models of electrical stimulation of neural networks that can be simulated in a computer...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227036/using-i2b2-to-bootstrap-rural-health-analytics-and-learning-networks
#15
Daniel R Harris, Adam D Baus, Tamela J Harper, Traci D Jarrett, Cecil R Pollard, Jeffery C Talbert, Daniel R Harris, Adam D Baus, Tamela J Harper, Traci D Jarrett, Cecil R Pollard, Jeffery C Talbert, Jeffery C Talbert, Daniel R Harris, Traci D Jarrett, Tamela J Harper, Adam D Baus, Cecil R Pollard
We demonstrate that the open-source i2b2 (Informatics for Integrating Biology and the Bedside) data model can be used to bootstrap rural health analytics and learning networks. These networks promote communication and research initiatives by providing the infrastructure necessary for sharing data and insights across a group of healthcare and research partners. Data integration remains a crucial challenge in connecting rural healthcare sites with a common data sharing and learning network due to the lack of interoperability and standards within electronic health records...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226817/effective-connectivity-matrix-for-neural-ensembles
#16
Qi She, Winnie K Y So, Rosa H M Chan, Qi She, Winnie K Y So, Rosa H M Chan, Rosa H M Chan, Qi She, Winnie K Y So
In this paper, we present an efficient framework to study the directional interactions within the multiple-input multiple-output (MIMO) biological neural network from spiketrain data. We used an efficient generalized linear model (GLM) with Laguerre basis functions to model a MIMO neural system, and developed an Effective Connectivity Matrix (ECM) to visualize excitatory and inhibitory connections within the neural network. A new causality representation was developed based on system dynamics. Statistical test was applied to identify the significance of the measured causality...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226785/mechanisms-of-stochastic-focusing-and-defocusing-in-biological-reaction-networks-insight-from-accurate-chemical-master-equation-acme-solutions
#17
Gamze Giirsoy, Anna Terebus, Youfang Cao, Jie Liang, Gamze Gursoy, Anna Terebus, Youfang Cao, Jie Liang, Gamze Gursoy, Youfang Cao, Anna Terebus, Jie Liang
Stochasticity plays important roles in regulation of biochemical reaction networks when the copy numbers of molecular species are small. Studies based on Stochastic Simulation Algorithm (SSA) has shown that a basic reaction system can display stochastic focusing (SF) by increasing the sensitivity of the network as a result of the signal noise. Although SSA has been widely used to study stochastic networks, it is ineffective in examining rare events and this becomes a significant issue when the tails of probability distributions are relevant as is the case of SF...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226784/parameter-estimation-for-gene-regulatory-networks-a-two-stage-mcmc-bayesian-approach
#18
Niannan Xue, Wei Pan, Yike Guo, Niannan Xue, Wei Pan, Yike Guo, Wei Pan, Yike Guo, Niannan Xue
Genetic regulatory networks have emerged as a useful way to elucidate the biochemical pathways for biological functions. Yet, determination of the exact parametric forms for these models remain a major challenge. In this paper, we present a novel computational approach implemented in C++ to solve this inverse problem. This takes the form of an optimization stage first after which Bayesian filtering takes place. The key advantage of such a flexible, general and robust approach is that it provides us with a joint probability distribution of the model parameters instead of single estimates, which we can propagate to final predictions...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226783/learning-a-probabilistic-boolean-network-model-from-biological-pathways-and-time-series-expression-data
#19
Vardaan Pahuja, Ritwik Kumar Layek, Pabitra Mitra, Vardaan Pahuja, Ritwik Kumar Layek, Pabitra Mitra, Vardaan Pahuja, Ritwik Kumar Layek, Pabitra Mitra
The problem of inferring a stochastic model for gene regulatory networks is addressed here. The prior biological data includes biological pathways and time-series expression data. We propose a novel algorithm to use both of these data to construct a Probabilistic Boolean Network (PBN) which models the observed dynamics of genes with a high degree of precision. Our algorithm constructs a pathway tree and uses the time-series expression data to select an optimal level of tree, whose nodes are used to infer the PBN...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226779/biologically-inspired-design-of-feedback-control-systems-implemented-using-dna-strand-displacement-reactions
#20
Mathias Foo, Rucha Sawlekar, Vishwesh V Kulkarni, Declan G Bates, Mathias Foo, Rucha Sawlekar, Vishwesh V Kulkarni, Declan G Bates, Vishwesh V Kulkarni, Rucha Sawlekar, Declan G Bates, Mathias Foo
The use of abstract chemical reaction networks (CRNs) as a modelling and design framework for the implementation of computing and control circuits using enzyme-free, entropy driven DNA strand displacement (DSD) reactions is starting to garner widespread attention in the area of synthetic biology. Previous work in this area has demonstrated the theoretical plausibility of using this approach to design biomolecular feedback control systems based on classical proportional-integral (PI) controllers, which may be constructed from CRNs implementing gain, summation and integrator operators...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
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