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https://www.readbyqxmd.com/read/28196071/how-green-are-the-streets-an-analysis-for-central-areas-of-chinese-cities-using-tencent-street-view
#1
Ying Long, Liu Liu
Extensive evidence has revealed that street greenery, as a quality-of-life component, is important for oxygen production, pollutant absorption, and urban heat island effect mitigation. Determining how green our streets are has always been difficult given the time and money consumed using conventional methods. This study proposes an automatic method using an emerging online street-view service to address this issue. This method was used to analyze street greenery in the central areas (28.3 km2 each) of 245 major Chinese cities; this differs from previous studies, which have investigated small areas in a given city...
2017: PloS One
https://www.readbyqxmd.com/read/28191571/a-computer-based-prediction-platform-for-the-reaction-of-ozone-with-organic-compounds-in-aqueous-solution-kinetics-and-mechanisms
#2
Minju Lee, Lorenz C Blum, Emanuel Schmid, Kathrin Fenner, Urs von Gunten
Ozonation of secondary wastewater effluents can reduce the discharge of micropollutants by transforming their chemical structures. Therefore, a better understanding of the formation of transformation products during ozonation is important. In this study, a computer-based prediction platform for the kinetics and mechanisms of the reactions of ozone with organic compounds was developed to enable in silico predictions of transformation products. With the developed prediction platform, reaction kinetics expressed as second-order rate constants for the reactions of ozone with selected organic compounds (kO3, M(-1) s(-1)) can be predicted based on an adapted kO3 prediction model from a previous study (Lee et al...
February 13, 2017: Environmental Science. Processes & Impacts
https://www.readbyqxmd.com/read/28187407/synthetic-biology-open-language-sbol-version-2-1-0
#3
Jacob Beal, Robert Sidney Cox, Raik Grünberg, James McLaughlin, Tramy Nguyen, Bryan Bartley, Michael Bissell, Kiri Choi, Kevin Clancy, Chris Macklin, Curtis Madsen, Goksel Misirli, Ernst Oberortner, Matthew Pocock, Nicholas Roehner, Meher Samineni, Michael Zhang, Zhen Zhang, Zach Zundel, John Gennari, Chris Myers, Herbert Sauro, Anil Wipat
Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards...
December 18, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28181878/using-inspiration-from-synaptic-plasticity-rules-to-optimize-traffic-flow-in-distributed-engineered-networks
#4
Jonathan Y Suen, Saket Navlakha
Controlling the flow and routing of data is a fundamental problem in many distributed networks, including transportation systems, integrated circuits, and the Internet. In the brain, synaptic plasticity rules have been discovered that regulate network activity in response to environmental inputs, which enable circuits to be stable yet flexible. Here, we develop a new neuro-inspired model for network flow control that depends only on modifying edge weights in an activity-dependent manner. We show how two fundamental plasticity rules, long-term potentiation and long-term depression, can be cast as a distributed gradient descent algorithm for regulating traffic flow in engineered networks...
February 9, 2017: Neural Computation
https://www.readbyqxmd.com/read/28177012/dynamics-of-capillary-transport-in-semi-solid-channels
#5
Johanna Andersson, Anna Ström, Tobias Gebäck, Anette Larsson
Capillary action has been described by Lucas and Washburn and extensively studied experimentally in hard materials, but few studies have examined capillary action in soft materials such as hydrogels. In tissue engineering, cells or dispersions must be often distributed within a hydrogel via microporous paths. Capillary action is one way to disperse such substances. Here, we examine the dynamics of capillary action in a model system of straight capillaries in two hydrogels. The channels had a circular cross-section in the micrometer size range (180-630 μm)...
February 8, 2017: Soft Matter
https://www.readbyqxmd.com/read/28173698/a-visual-language-for-protein-design
#6
Robert Sidney Cox Iii, James Alastair McLaughlin, Raik Gruenberg, Jake Beal, Anil Wipat, Herbert Sauro
As protein engineering becomes more sophisticated, practitioners increasingly need to share diagrams for communicating protein designs. To this end, we present a draft visual language, Protein Language, that describes the high-level architecture of an engineered protein with a few easy-to-draw glyphs, intended to be compatible with other biological diagram languages such as SBOL and SBGN. Protein Language con- sists of glyphs for representing important features (e.g., globular domains, recognition and localization sequences, sites of covalent modification, cleavage and catalysis), rules for composing these glyphs to represent complex architectures, and rules constraining the scaling and styling of diagrams...
February 7, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28158178/dynamic-maternal-gradients-control-timing-and-shift-rates-for-drosophila-gap-gene-expression
#7
Berta Verd, Anton Crombach, Johannes Jaeger
Pattern formation during development is a highly dynamic process. In spite of this, few experimental and modelling approaches take into account the explicit time-dependence of the rules governing regulatory systems. We address this problem by studying dynamic morphogen interpretation by the gap gene network in Drosophila melanogaster. Gap genes are involved in segment determination during early embryogenesis. They are activated by maternal morphogen gradients encoded by bicoid (bcd) and caudal (cad). These gradients decay at the same time-scale as the establishment of the antero-posterior gap gene pattern...
February 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28145461/tuning-the-allosteric-regulation-of-artificial-muscarinic-and-dopaminergic-ligand-gated-potassium-channels-by-protein-engineering-of-g-protein-coupled-receptors
#8
Christophe J Moreau, Jean Revilloud, Lydia N Caro, Julien P Dupuis, Amandine Trouchet, Argel Estrada-Mondragón, Katarzyna Nieścierowicz, Nicolas Sapay, Serge Crouzy, Michel Vivaudou
Ligand-gated ion channels enable intercellular transmission of action potential through synapses by transducing biochemical messengers into electrical signal. We designed artificial ligand-gated ion channels by coupling G protein-coupled receptors to the Kir6.2 potassium channel. These artificial channels called ion channel-coupled receptors offer complementary properties to natural channels by extending the repertoire of ligands to those recognized by the fused receptors, by generating more sustained signals and by conferring potassium selectivity...
February 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28129557/decoding-transcriptional-states-in-cancer
#9
REVIEW
Jasper Wouters, Zeynep Kalender Atak, Stein Aerts
Gene regulatory networks determine cellular identity. In cancer, aberrations of gene networks are caused by driver mutations that often affect transcription factors and chromatin modifiers. Nevertheless, gene transcription in cancer follows the same cis-regulatory rules as normal cells, and cancer cells have served as convenient model systems to study transcriptional regulation. Tumours often show regulatory heterogeneity, with subpopulations of cells in different transcriptional states, which has important therapeutic implications...
January 24, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28127303/reverse-engineering-gene-regulatory-networks-from-measurement-with-missing-values
#10
Oyetunji E Ogundijo, Abdulkadir Elmas, Xiaodong Wang
BACKGROUND: Gene expression time series data are usually in the form of high-dimensional arrays. Unfortunately, the data may sometimes contain missing values: for either the expression values of some genes at some time points or the entire expression values of a single time point or some sets of consecutive time points. This significantly affects the performance of many algorithms for gene expression analysis that take as an input, the complete matrix of gene expression measurement. For instance, previous works have shown that gene regulatory interactions can be estimated from the complete matrix of gene expression measurement...
December 2016: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/28125977/supporting-clinical-rules-engine-in-the-adjustment-of-medication-scream-protocol-of-a-multicentre-prospective-randomised-study
#11
Carlota Mestres Gonzalvo, Hugo A J M de Wit, Brigit P C van Oijen, Kim P G M Hurkens, Rob Janknegt, Jos M G A Schols, Wubbo J Mulder, Frans R Verhey, Bjorn Winkens, Paul-Hugo M van der Kuy
BACKGROUND: In the nursing home population, it is estimated that 1 in every 3 patients is polymedicated and given their considerable frailty, these patients are especially prone to adverse drug reactions. Clinical pharmacist-led medication reviews are considered successful interventions to improve medication safety in the inpatient setting. Due to the limited available evidence concerning the benefits of medication reviews performed in the nursing home setting, we propose a study aiming to demonstrate a positive effect that a clinical decision support system, as a health care intervention, may have on the target population...
January 26, 2017: BMC Geriatrics
https://www.readbyqxmd.com/read/28125791/lessons-from-enzyme-kinetics-reveal-specificity-principles-for-rna-guided-nucleases-in-rna-interference-and-crispr-based-genome-editing
#12
REVIEW
Namita Bisaria, Inga Jarmoskaite, Daniel Herschlag
RNA-guided nucleases (RGNs) provide sequence-specific gene regulation through base-pairing interactions between a small RNA guide and target RNA or DNA. RGN systems, which include CRISPR-Cas9 and RNA interference (RNAi), hold tremendous promise as programmable tools for engineering and therapeutic purposes. However, pervasive targeting of sequences that closely resemble the intended target has remained a major challenge, limiting the reliability and interpretation of RGN activity and the range of possible applications...
January 25, 2017: Cell Systems
https://www.readbyqxmd.com/read/28122942/comparative-analysis-of-mitochondrial-n-termini-from-mouse-human-and-yeast
#13
Sarah E Calvo, Olivier Julien, Karl R Clauser, Hongying Shen, Kimberli J Kamer, James A Wells, Vamsi K Mootha
The majority of mitochondrial proteins are encoded in the nuclear genome, translated in the cytoplasm, and directed to the mitochondria by a N-terminal presequence that is cleaved upon import. Recently, N-proteome catalogs have been generated for mitochondria from yeast and from human U937 cells. Here we applied the subtiligase method to determine N-termini for 327 proteins in mitochondria isolated from mouse liver and kidney. Comparative analysis between mitochondrial N-termini from mouse, human, and yeast proteins shows that while presequences are poorly conserved at the sequence level, other presequence properties are extremely conserved including a length of ~20-60aa, a net charge between +3 to +6, and the presence of stabilizing amino acids at the N-termini of mature proteins that follows the N-end rule from bacteria...
January 25, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28107990/combined-use-of-peptide-ion-and-normalized-delta-scores-to-evaluate-milk-authenticity-by-ion-trap-based-proteomics-coupled-with-error-tolerant-searching
#14
Donatella Nardiello, Anna Natale, Carmen Palermo, Maurizio Quinto, Diego Centonze
A fundamental issue in proteomics is the peptide identification by database searching and the assessment of the goodness of fit between experimental and theoretical data. Despite the different number of ways to measure the quality of search results, the definition of a scoring criterion is still highly desirable in ion-trap based proteomics. Indeed, in order to fully take advantage of a low resolution MS/MS dataset, it is essential to strike a balance between greater information capture and reduced number of incorrect peptide assignments...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28094807/antimicrobial-probiotics-reduce-salmonella-enterica-in-turkey-gastrointestinal-tracts
#15
Brittany Forkus, Seth Ritter, Michail Vlysidis, Kathryn Geldart, Yiannis N Kaznessis
Despite the arsenal of technologies employed to control foodborne nontyphoidal Salmonella (NTS), infections have not declined in decades. Poultry is the primary source of NTS outbreaks, as well as the fastest growing meat sector worldwide. With recent FDA rules for phasing-out antibiotics in animal production, pressure is mounting to develop new pathogen reduction strategies. We report on a technology to reduce Salmonella enteritidis in poultry. We engineered probiotic E. coli Nissle 1917, to express and secrete the antimicrobial peptide, Microcin J25...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28094515/nanoporous-materials-for-the-onboard-storage-of-natural-gas
#16
K Vasanth Kumar, Kathrin Preuss, Maria-Magdalena Titirici, Francisco Rodríguez-Reinoso
Climate change, global warming, urban air pollution, energy supply uncertainty and depletion, and rising costs of conventional energy sources are, among others, potential socioeconomic threats that our community faces today. Transportation is one of the primary sectors contributing to oil consumption and global warming, and natural gas (NG) is considered to be a relatively clean transportation fuel that can significantly improve local air quality, reduce greenhouse-gas emissions, and decrease the energy dependency on oil sources...
January 17, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28088572/bcs-class-iv-drugs-highly-notorious-candidates-for-formulation-development
#17
REVIEW
Rohan Ghadi, Neha Dand
BCS class IV drugs (e.g., amphotericin B, furosemide, acetazolamide, ritonavir, paclitaxel) exhibit many characteristics that are problematic for effective oral and per oral delivery. Some of the problems associated include low aqueous solubility, poor permeability, erratic and poor absorption, inter and intra subject variability and significant positive food effect which leads to low and variable bioavailability. Also, most of the class IV drugs are substrate for P-glycoprotein (low permeability) and substrate for CYP3A4 (extensive pre systemic metabolism) which further potentiates the problem of poor therapeutic potential of these drugs...
January 11, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28072422/the-fitness-costs-and-trade-off-shapes-associated-with-the-exclusion-of-nine-antibiotics-by-ompf-porin-channels
#18
Katherine Phan, Thomas Ferenci
The trade-off relationship between antibiotic exclusion and nutrient access across the Gram-negative outer membrane is determined by structural constraints in porin channels. The precise nutritional cost of exclusion is unknown for different antibiotics, as are the shapes of the nutrition-susceptibility trade-off. Using a library of 10 engineered isogenic Escherichia coli strains with structural modifications of OmpF porin expressed at a constant level, susceptibilities were measured for nine antibiotics and the nutritional fitness costs estimated by competitions in chemostats...
January 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28063980/plant-viral-nanoparticles-based-her2-vaccine-immune-response-influenced-by-differential-transport-localization-and-cellular-interactions-of-particulate-carriers
#19
Sourabh Shukla, Jay T Myers, Sarah E Woods, Xingjian Gong, Anna E Czapar, Ulrich Commandeur, Alex Y Huang, Alan D Levine, Nicole F Steinmetz
Cancer vaccines are designed to elicit an endogenous adaptive immune response that can successfully recognize and eliminate residual or recurring tumors. Such approaches can potentially overcome shortcomings of passive immunotherapies by generating long-lived therapeutic effects and immune memory while limiting systemic toxicities. A critical determinant of vaccine efficacy is efficient transport and delivery of tumor-associated antigens to professional antigen presenting cells (APCs). Plant viral nanoparticles (VNPs) with natural tropism for APCs and a high payload carrying capacity may be particularly effective vaccine carriers...
March 2017: Biomaterials
https://www.readbyqxmd.com/read/28058285/large-hyperpolarizabilities-at-telecommunication-relevant-wavelengths-in-donor-acceptor-donor-nonlinear-optical-chromophores
#20
Animesh Nayak, Jaehong Park, Kurt De Mey, Xiangqian Hu, Timothy V Duncan, David N Beratan, Koen Clays, Michael J Therien
Octopolar D2-symmetric chromophores, based on the MPZnM supermolecular motif in which (porphinato)zinc(II) (PZn) and ruthenium(II) polypyridyl (M) structural units are connected via ethyne linkages, were synthesized. These structures take advantage of electron-rich meso-arylporphyrin or electron-poor meso-(perfluoroalkyl)porphyrin macrocycles, unsubstituted terpyridyl and 4'-pyrrolidinyl-2,2';6',2″-terpyridyl ligands, and modulation of metal(II) polypyridyl-to-(porphinato)zinc connectivity, to probe how electronic and geometric factors impact the measured hyperpolarizability...
December 28, 2016: ACS Central Science
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