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https://www.readbyqxmd.com/read/29449795/foundations-for-streaming-model-transformations-by-complex-event-processing
#1
István Dávid, István Ráth, Dániel Varró
Streaming model transformations represent a novel class of transformations to manipulate models whose elements are continuously produced or modified in high volume and with rapid rate of change. Executing streaming transformations requires efficient techniques to recognize activated transformation rules over a live model and a potentially infinite stream of events. In this paper, we propose foundations of streaming model transformations by innovatively integrating incremental model query, complex event processing (CEP) and reactive (event-driven) transformation techniques...
2018: Software and Systems Modeling
https://www.readbyqxmd.com/read/29420292/the-pirna-targeting-rules-and-the-resistance-to-pirna-silencing-in-endogenous-genes
#2
Donglei Zhang, Shikui Tu, Michael Stubna, Wei-Sheng Wu, Wei-Che Huang, Zhiping Weng, Heng-Chi Lee
Piwi-interacting RNAs (piRNAs) silence transposons to safeguard genome integrity in animals. However, the functions of the many piRNAs that do not map to transposons remain unknown. Here, we show that piRNA targeting in Caenorhabditis elegans can tolerate a few mismatches but prefer perfect pairing at the seed region. The broad targeting capacity of piRNAs underlies the germline silencing of transgenes in C. elegans Transgenes engineered to avoid piRNA recognition are stably expressed. Many endogenous germline-expressed genes also contain predicted piRNA targeting sites, and periodic An/Tn clusters (PATCs) are an intrinsic signal that provides resistance to piRNA silencing...
February 2, 2018: Science
https://www.readbyqxmd.com/read/29410997/substrate-modified-thermal-stability-of-mono-and-few-layer-mos2
#3
Xuewen Wang, Wen Fan, Ziwei Fan, Wanyu Dai, Kunlei Zhu, Shengzhe Hong, Yufei Sun, Junqiao Wu, Kai Liu
Two-dimensional semiconducting transition metal dichalcogenides have been employed as key components in various electronic devices. The thermal stability of these ultrathin materials must be carefully considered in device applications because the heating caused by current flow, light absorption, or other harsh environmental conditions is usually unavoidable. In this work, we found that the substrate plays a role in modifying the thermal stability of mono- and few-layer MoS2. Triangular etching holes, which are considered to initiate from defect sites, form on MoS2 when the temperature exceeds a threshold...
February 7, 2018: Nanoscale
https://www.readbyqxmd.com/read/29383567/risk-factors-analysis-and-death-prediction-in-some-life-threatening-ailments-using-chi-square-case-based-reasoning-%C3%AF-2-cbr-model
#4
D A Adeniyi, Z Wei, Y Yang
A wealth of data are available within the health care system, however, effective analysis tools for exploring the hidden patterns in these datasets are lacking. To alleviate this limitation, this paper proposes a simple but promising hybrid predictive model by suitably combining the Chi-square distance measurement with case-based reasoning technique. The study presents the realization of an automated risk calculator and death prediction in some life-threatening ailments using Chi-square case-based reasoning (χ2 CBR) model...
January 30, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29382868/error-gated-hebbian-rule-a-local-learning-rule-for-principal-and-independent-component-analysis
#5
Takuya Isomura, Taro Toyoizumi
We developed a biologically plausible unsupervised learning algorithm, error-gated Hebbian rule (EGHR)-β, that performs principal component analysis (PCA) and independent component analysis (ICA) in a single-layer feedforward neural network. If parameter β = 1, it can extract the subspace that major principal components span similarly to Oja's subspace rule for PCA. If β = 0, it can separate independent sources similarly to Bell-Sejnowski's ICA rule but without requiring the same number of input and output neurons...
January 30, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29382397/exploiting-graph-kernels-for-high-performance-biomedical-relation-extraction
#6
Nagesh C Panyam, Karin Verspoor, Trevor Cohn, Kotagiri Ramamohanarao
BACKGROUND: Relation extraction from biomedical publications is an important task in the area of semantic mining of text. Kernel methods for supervised relation extraction are often preferred over manual feature engineering methods, when classifying highly ordered structures such as trees and graphs obtained from syntactic parsing of a sentence. Tree kernels such as the Subset Tree Kernel and Partial Tree Kernel have been shown to be effective for classifying constituency parse trees and basic dependency parse graphs of a sentence...
January 30, 2018: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29375928/computational-redesign-of-acyl-acp-thioesterase-with-improved-selectivity-toward-medium-chain-length-fatty-acids
#7
Matthew J Grisewood, Néstor J Hernandez Lozada, James B Thoden, Nathanael P Gifford, Daniel Mendez-Perez, Haley A Schoenberger, Matthew F Allan, Martha E Floy, Rung-Yi Lai, Hazel M Holden, Brian F Pfleger, Costas D Maranas
Enzyme and metabolic engineering offer the potential to develop biocatalysts for converting natural resources into a wide range of chemicals. To broaden the scope of potential products beyond natural metabolites, methods of engineering enzymes to accept alternative substrates and/or perform novel chemistries must be developed. DNA synthesis can create large libraries of enzyme-coding sequences, but most biochemistries lack a simple assay to screen for promising enzyme variants. Our solution to this challenge is structure-guided mutagenesis in which optimization algorithms select the best sequences from libraries based on specified criteria (i...
June 2, 2017: ACS Catalysis
https://www.readbyqxmd.com/read/29364123/cep4hfp-complex-event-processing-for-heart-failure-prediction
#8
Afef Mdhaffar, Ismael Bouassida Rodriguez, Khalil Charfi, Leila Abid, Bernd Freisleben
This paper presents a novel health analysis approach for heart failure prediction. It is based on the use of complex event processing (CEP) technology, combined with statistical approaches. A CEP engine processes incoming health data by executing threshold-based analysis rules. Instead of having to manually set up thresholds, our novel statistical algorithm automatically computes and updates thresholds according to recorded historical data. Experimental results demonstrate the merits of our approach in terms of speed, precision, and recall...
December 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/29347233/dynamics-and-energy-spectra-of-aperiodic-discrete-time-quantum-walks
#9
N Lo Gullo, C V Ambarish, Th Busch, L Dell'Anna, C M Chandrashekar
We investigate the role of different aperiodic sequences in the dynamics of single quantum particles in discrete space and time. For this we consider three aperiodic sequences, namely, the Fibonacci, Thue-Morse, and Rudin-Shapiro sequences, as examples of tilings the diffraction spectra of which have pure point, singular continuous, and absolutely continuous support, respectively. Our interest is to understand how the order, intrinsically introduced by the deterministic rule used to generate the aperiodic sequences, is reflected in the dynamical properties of the quantum system...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29321267/extreme-call-amplitude-from-near-field-acoustic-wave-coupling-in-the-stridulating-water-insect-micronecta-scholtzi-micronectinae
#10
Andrew Reid, David J W Hardie, David Mackie, Joseph C Jackson, James F C Windmill
Underwater acoustic transducers, particularly at low frequencies, are beset by problems of scale and inefficiency due to the large wavelengths of sound in water. In insect mating calls, a high call volume is usually desirable, increasing the range of signal transmission and providing a form of advertisement of the signaller's quality to a potential mate; however, the strength of the call is constrained by body size and by the need to avoid predators who may be listening in. Male crickets and water boatmen avoid some of the limitations of body size by exploiting resonant structures, which produce sharply tuned species-specific songs, but call frequency and volume remain linked to body size...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29303191/strain-engineering-of-van-der-waals-heterostructures
#11
Paul A Vermeulen, Jefta Mulder, Jamo Momand, Bart J Kooi
Modifying the strain state of solids allows control over a plethora of functional properties. The weak interlayer bonding in van der Waals (vdWaals) materials such as graphene, hBN, MoS2, and Bi2Te3 might seem to exclude strain engineering, since strain would immediately relax at the vdWaals interfaces. Here we present direct observations of the contrary by showing growth of vdWaals heterostructures with persistent in-plane strains up to 5% and we show that strain relaxation follows a not yet reported process distinctly different from strain relaxation in three-dimensionally bonded (3D) materials...
January 5, 2018: Nanoscale
https://www.readbyqxmd.com/read/29301968/engineering-posttranslational-proofreading-to-discriminate-nonstandard-amino-acids
#12
Aditya M Kunjapur, Devon A Stork, Erkin Kuru, Oscar Vargas-Rodriguez, Matthieu Landon, Dieter Söll, George M Church
Incorporation of nonstandard amino acids (nsAAs) leads to chemical diversification of proteins, which is an important tool for the investigation and engineering of biological processes. However, the aminoacyl-tRNA synthetases crucial for this process are polyspecific in regard to nsAAs and standard amino acids. Here, we develop a quality control system called "posttranslational proofreading" to more accurately and rapidly evaluate nsAA incorporation. We achieve this proofreading by hijacking a natural pathway of protein degradation known as the N-end rule, which regulates the lifespan of a protein based on its amino-terminal residue...
January 4, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29299686/identification-of-optimal-feedback-control-rules-from-micro-quadrotor-and-insect-flight-trajectories
#13
Imraan A Faruque, Florian T Muijres, Kenneth M Macfarlane, Andrew Kehlenbeck, J Sean Humbert
This paper presents "optimal identification," a framework for using experimental data to identify the optimality conditions associated with the feedback control law implemented in the measurements. The technique compares closed loop trajectory measurements against a reduced order model of the open loop dynamics, and uses linear matrix inequalities to solve an inverse optimal control problem as a convex optimization that estimates the controller optimality conditions. In this study, the optimal identification technique is applied to two examples, that of a millimeter-scale micro-quadrotor with an engineered controller on board, and the example of a population of freely flying Drosophila hydei maneuvering about forward flight...
January 3, 2018: Biological Cybernetics
https://www.readbyqxmd.com/read/29288438/synthetic-biology-genome-mining-and-combinatorial-biosynthesis-of-nrps-derived-antibiotics-a-perspective
#14
Richard H Baltz
Combinatorial biosynthesis of novel secondary metabolites derived from nonribosomal peptide synthetases (NRPSs) has been in slow development for about a quarter of a century. Progress has been hampered by the complexity of the giant multimodular multienzymes. More recently, advances have been made on understanding the chemical and structural biology of these complex megaenzymes, and on learning the design rules for engineering functional hybrid enzymes. In this perspective, I address what has been learned about successful engineering of complex lipopeptides related to daptomycin, and discuss how synthetic biology and microbial genome mining can converge to broaden the scope and enhance the speed and robustness of combinatorial biosynthesis of NRPS-derived natural products for drug discovery...
December 29, 2017: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/29286314/integration-of-distributed-services-and-hybrid-models-based-on-process-choreography-to-predict-and-detect-type-2-diabetes
#15
Antonio Martinez-Millana, Jose-Luis Bayo-Monton, María Argente-Pla, Carlos Fernandez-Llatas, Juan Francisco Merino-Torres, Vicente Traver-Salcedo
Life expectancy is increasing and, so, the years that patients have to live with chronic diseases and co-morbidities. Type 2 diabetes is one of the most prevalent chronic diseases, specifically linked to being overweight and ages over sixty. Recent studies have demonstrated the effectiveness of new strategies to delay and even prevent the onset of type 2 diabetes by a combination of active and healthy lifestyle on cohorts of mid to high risk subjects. Prospective research has been driven on large groups of the population to build risk scores that aim to obtain a rule for the classification of patients according to the odds for developing the disease...
December 29, 2017: Sensors
https://www.readbyqxmd.com/read/29276582/nonlinear-oscillatory-dynamics-of-the-hardening-of-calcium-phosphate-bone-cements
#16
Vuk Uskoković, Julietta V Rau
Here we report on the nonlinear, oscillatory dynamics detected in the evolution of phase composition during the setting of different calcium phosphate cements, two of which evolved toward brushite and one toward hydroxyapatite as the final product. Whereas both brushite-forming cements contained ion-doped β-tricalcium phosphate as the initial phase, the zinc-containing one yielded scholzite as an additional phase during setting and the oscillations between these two products were pronounced throughout the entire 80 h setting period, long after the hardening processes was over from the mechanical standpoint...
2017: RSC Advances
https://www.readbyqxmd.com/read/29261643/a-mildly-relativistic-wide-angle-outflow-in-the-neutron-star-merger-event-gw170817
#17
K P Mooley, E Nakar, K Hotokezaka, G Hallinan, A Corsi, D A Frail, A Horesh, T Murphy, E Lenc, D L Kaplan, K De, D Dobie, P Chandra, A Deller, O Gottlieb, M M Kasliwal, S R Kulkarni, S T Myers, S Nissanke, T Piran, C Lynch, V Bhalerao, S Bourke, K W Bannister, L P Singer
GW170817 was the first gravitational wave detection of a binary neutron-star merger1. It was accompanied by radiation across the electromagnetic spectrum and localized2 to the galaxy NGC 4993 at a distance of 40 megaparsecs. It has been proposed that the observed γ-ray, X-ray and radio emission is due to an ultra-relativistic jet launched during the merger, directed away from our line of sight3-6. The presence of such a jet is predicted from models that posit neutron-star mergers as the central engines that drive short hard γ-ray bursts7,8...
December 20, 2017: Nature
https://www.readbyqxmd.com/read/29260340/molecular-structures-enumeration-and-virtual-screening-in-the-chemical-space-with-retropath2-0
#18
Mathilde Koch, Thomas Duigou, Pablo Carbonell, Jean-Loup Faulon
BACKGROUND: Network generation tools coupled with chemical reaction rules have been mainly developed for synthesis planning and more recently for metabolic engineering. Using the same core algorithm, these tools apply a set of rules to a source set of compounds, stopping when a sink set of compounds has been produced. When using the appropriate sink, source and rules, this core algorithm can be used for a variety of applications beyond those it has been developed for. RESULTS: Here, we showcase the use of the open source workflow RetroPath2...
December 19, 2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29235352/systems-approaches-to-understanding-and-designing-allosteric-proteins
#19
Srivatsan Raman
The study of allostery has a central place in biology due to the myriad roles of allosteric proteins in cellular function. As technologies to probe spatiotemporal resolution of biomolecules have become increasingly sophisticated, so has our understanding of the diverse structural and molecular mechanisms of allosteric proteins. Studies have shown that allosteric signal is transmitted a through a network of residue-residue interactions connecting distal sites on a protein. Linking structural and dynamical changes to the functional role of individual residues will give a more complete molecular view of allostery...
December 13, 2017: Biochemistry
https://www.readbyqxmd.com/read/29233745/retropath2-0-a-retrosynthesis-workflow-for-metabolic-engineers
#20
Baudoin Delépine, Thomas Duigou, Pablo Carbonell, Jean-Loup Faulon
Synthetic biology applied to industrial biotechnology is transforming the way we produce chemicals. However, despite advances in the scale and scope of metabolic engineering, the research and development process still remains costly. In order to expand the chemical repertoire for the production of next generation compounds, a major engineering biology effort is required in the development of novel design tools that target chemical diversity through rapid and predictable protocols. Addressing that goal involves retrosynthesis approaches that explore the chemical biosynthetic space...
December 9, 2017: Metabolic Engineering
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