bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneous selection and counter‐selection for the directed evolution of proteases in E. coli using a cytoplasmic anchoring strategy
Authors: Carrico Zachary M. , Strobel Kathryn L. , Atreya Meera E. , Clark Douglas S. , Francis Matthew B. 
Published: December 2015

ABSTRACTWith the goal of generating new enzymes that can cleave custom sequences, this article describes a selection strategy for evolving proteases with desirable characteristics. Positive selection and counter‐selection are combined to select for and against specified cleavage sequences simultaneously. Cleavage of the positive selection sequence permits E. coli growth, and cleavage of the counter‐selection sequence slows growth. Growth occurs when cleavage of the positive selection sequence releases β‐lactamase into the periplasm where it can confer antibiotic resistance. The counter‐selection traps β‐lactamase in the cytoplasm, preventing antibiotic resistance and growth. Thus, proteases with a preference for the positive selection sequence relative to the counter‐selection sequence grow more rapidly. This system was used to select a tobacco etch virus (TEV) protease mutant with new substrate compatibility. Biotechnol. Bioeng. 2016;113: 1187–1193. © 2015 Wiley Periodicals, Inc.
High‐throughput investigation of endothelial‐to‐mesenchymal transformation (EndMT) with combinatorial cellular microarrays
Authors: Wang Zongjie , Calpe Blaise , Zerdani Jalil , Lee Youngsang , Oh Jonghyun , Bae Hojae , Khademhosseini Ali , Kim Keekyoung 
Published: December 2015

ABSTRACTIn the developing heart, a specific subset of endocardium undergoes an endothelial‐to‐mesenchymal transformation (EndMT) thus forming nascent valve leaflets. Extracellular matrix (ECM) proteins and growth factors (GFs) play important roles in regulating EndMT but the combinatorial effect of GFs with ECM proteins is less well understood. Here we use microscale engineering techniques to create single, binary, and tertiary component microenvironments to investigate the combinatorial effects of ECM proteins and GFs on the attachment and transformation of adult ovine mitral valve endothelial cells to a mesenchymal phenotype. With the combinatorial microenvironment microarrays, we utilized 60 different combinations of ECM proteins (Fibronectin, Collagen I, II, IV, Laminin) and GFs (TGF‐β1, bFGF, VEGF) and were able to identify new microenvironmental conditions capable of modulating EndMT in MVECs. Experimental results indicated that TGF‐β1 significantly upregulated the EndMT while either bFGF or VEGF downregulated EndMT process markedly. Also, ECM proteins could influence both the attachment of MVECs and the response of MVECs to GFs. In terms of attachment, fibronectin is significantly better for the adhesion of MVECs among the five tested proteins. Overall collagen IV and fibronectin appeared to play important roles in promoting EndMT process. Great consistency between macroscale and microarrayed experiments and present studies demonstrates that high‐throughput cellular microarrays are a promising approach to study the regulation of EndMT in valvular endothelium. Biotechnol. Bioeng. 2016;113: 1403–1412. © 2015 Wiley Periodicals, Inc.
Design and evaluation of a cognitive system to teach software change control
Authors: Chentouf Zohair 
Published: December 2015

ABSTRACTThis article presents a cognitive agent‐based software tool for teaching software change control decisions. The tool simulates the cognitive processes of software professionals involved in the software change decision. It allows students to assess their reasoning in comparison with the agent's one. The experimental results proved that the proposed tool was well accepted by students. © 2015 Wiley Periodicals, Inc. Comput Appl Eng Educ 24:347–355, 2016; View this article online at wileyonlinelibrary.com/journal/cae; DOI 10.1002/cae.21710
Molecular Assembly Line: Stepwise Hydrogenation of Multifunctional Substrates over Catalyst Mixtures
Authors: Tomkins Patrick , Gebauer‐Henke Ewa , Müller Thomas E. 
Published: December 2015

AbstractThe synthesis of many chemical products requires multiple steps. To simplify the overall synthesis by combining consecutive reaction steps, the concept of a “molecular assembly line” promises to yield high reaction rates and selectivities. In this study, mixtures of carbon nanotube (CNT)‐supported catalysts were used to demonstrate the potential of this concept on hand of the hydrogenation of nitrobenzene via aniline to cyclohexylamine. Mixtures of Pt/CNT, having a high activity in nitrobenzene hydrogenation, and of Ru/CNT, highly selective for the hydrogenation of aniline to cyclohexylamine, provided high activity at constant high selectivity. Varying the Pt:Ru ratio to 5:95 was found to be the best case scenario, for which the rates of the two consecutive reaction steps are balanced. The use of catalyst mixtures rather than bimetallic catalysts avoids complex phenomena such as phase separation or migration of one of the metals to the surface of the bimetallic particles.
Dual‐Emission Luminescence of Magnesium Coordination Polymers Based on Mixed Organic Ligands
Authors: Wu Zhao‐Feng , Tan Bin , Deng Zhong‐Hua , Xie Zai‐Lai , Fu Jing‐Jing , Shen Nan‐Nan , Huang Xiao‐Ying 
Published: December 2015

AbstractPresented herein are two luminescent magnesium coordination polymers (Mg‐CPs), namely [Mg2(H2O)2(2‐NDC)4(1,10‐phen)2] (1) and [Mg2(H2O)(1,4‐NDC)2(1,10‐phen)] (2), in which 2‐NDCH=2‐naphthalenecarboxylic acid, 1,4‐NDCH2=1,4‐naphthalene dicarboxylic acid, and 1,10‐phen=1,10‐phenanthroline. Based on the mixed ligands, the title compounds exhibit linker‐based photoluminescence (PL) properties thanks to the unique configuration of the Mg2+ ions. The two compounds show interesting dual emission on excitation of the different luminophores of the mixed linkers. In particular, the emissions of compound 2 could be tuned from green to yellow simply by varying the excitation energies. Furthermore, 2 could be excited by using a commercial λ=450 nm blue LED chip to generate white‐light emission, which allows the fabrication of a white‐light‐emitting diode (WLED) with 20 lm W−1 luminous efficacy. This work may provide a new method for designing tunable PL CPs by using the low‐cost and abundant magnesium ion.
Accurate low complexity modeling of twisted pairs suitable for G.fast frequencies
Authors: Lafata Pavel 
Published: December 2015

SummaryAs the higher and higher frequency bands of existing metallic cables in access networks are being continuously exploited by modern transmission technologies, such as the G.fast, the necessity of providing accurate and suitable modeling of their transmission characteristics is evident. Therefore, this paper is focused on modeling of a propagation constant of twisted pairs and metallic cables at high frequencies up to 250 MHz, and an innovative arsinh model is proposed and described. This new model is based on an idea of adopting inverse hyperbolic sine function for modeling of both secondary line coefficients, attenuation constant and phase constant, and its main motivation is to provide their accurate estimations for G.fast frequencies up to 250 MHz for various types of metallic cables while maintaining a low computational complexity. The proposed model was compared with numerous characteristics measured for various real metallic cables as well as with several existing models in order to illustrate its potential. The results, which are presented within this paper, clearly illustrate that the proposed arsinh model generally outperforms existing standard models based on the equal number of required parameters. Copyright © 2015 John Wiley & Sons, Ltd.
Fgf3‐Fgf4‐cis: A new mouse line for studying Fgf functions during mouse development
Authors: Anderson Matthew J. , Southon Eileen , Tessarollo Lino , Lewandoski Mark 
Published: December 2015

SummaryThe fibroblast growth factor (FGF) family consists of 22 ligands in mice and humans. FGF signaling is vital for embryogenesis and, when dysregulated, can cause disease. Loss‐of‐function genetic analysis in the mouse has been crucial for understanding FGF function. Such analysis has revealed that multiple Fgfs sometimes function redundantly. Exploring such redundancy between Fgf3 and Fgf4 is currently impossible because both genes are located on chromosome 7, about 18.5 kb apart, making the frequency of interallelic cross‐over between existing mutant alleles too infrequent to be practicable. Therefore, we retargeted Fgf3 and Fgf4 in cis, generating an Fgf3 null allele and a conditional Fgf4 allele, subject to Cre inactivation. To increase the frequency of cis targeting, we used an F1 embryonic stem cell line that contained 129/SvJae (129) and C57BL/6J (B6) chromosomes and targeting constructs isogenic to the 129 chromosome. We confirmed cis targeting by assaying for B6/129 allele‐specific single‐nucleotide polymorphisms. We demonstrated the utility of the Fgf3Δ‐Fgf4flox‐cis mouse line by showing that the caudal axis extension defects found in the Fgf3 mutants worsen when Fgf4 is also inactivated. This Fgf3Δ‐Fgf4flox‐cis line will be useful to study redundancy of these genes in a variety of tissues and stages in development. genesis 54:91–98, 2016. Published 2016. This article is a US Government work and is in the public domain in the USA.
Diversity without complementarity threatens vegetation patterns in arid lands
Authors: Ursino Nadia , Callegaro Chiara 
Published: December 2015

AbstractPatterns found in mixed communities including grass, shrubs and trees function as natural water‐harvesting systems in arid and semi‐arid regions throughout the world. Furthermore, self‐organizing vegetation patterns may be indicators of environmental shifts in climate and land use change scenarios. Therefore, net facilitation, leading to resource concentration within vegetation patches, should be imitated and preserved.This study analyses the ecological feedback between niche adaptation of similar band‐forming species, and the environment in which species thrive. A minimal model for two coexisting species and the soil moisture balance was formulated to improve our understanding of the effects of species differentiation on the dynamics of plants and resources on single pattern and landscape scales.The model outcomes suggest that pattern‐forming‐species communities arise as a result of niche differentiation (driven e.g. by evolutionary changes), whereas similar adaptation strategies to cope with harsh conditions may lead to impoverishment of environmental resources and loss of vegetation cover and diversity. Copyright © 2015 John Wiley & Sons, Ltd.
Increased mortality with elevated plasma endothelin‐1 in acute heart failure: an ASCEND‐HF biomarker substudy
Authors: Perez Antonio L. , Grodin Justin L. , Wu Yuping , Hernandez Adrian F. , Butler Javed , Metra Marco , Felker G. Michael , Voors Adriaan A. , McMurray John J. , Armstrong Paul W. , Starling Randall C. , O'Connor Christopher M. , Tang W. H. Wilson 
Published: December 2015

AimsEndothelin‐1 (ET‐1) is an endogenous vasoconstrictor implicated in pulmonary and systemic hypertension, as well as ventricular dysfunction, through effects on vascular smooth muscle, the kidneys, and cardiomyocytes. We aimed to determine the association between serial ET‐1 levels and acute heart failure patient outcomes.Methods and resultsWe measured plasma ET‐1 at baseline, 48–72 h, and 30 days in a cohort of 872 patients hospitalized with acute heart failure from the ASCEND‐HF trial (randomized to nesiritide vs. placebo), and its association with 30‐day mortality, 180‐day mortality, in‐hospital death or worsening heart failure, and 30‐day mortality or rehospitalization. Median ET‐1 was 7.6 [interquartile range (IQR) 5.9–10] pg/mL at baseline, 6.3 (IQR 4.9–8.1) pg/mL at 48–72 h, and 5.9 (IQR 4.7–7.9) pg/mL at 30 days (P < 0.001). Baseline and 48–72 h ET‐1 were found to be independently associated with 180‐day mortality in a multivariable analysis [hazard ratio (HR) 1.6, 95% confidence interval (CI) 1.3–2.0, P < 0.001 and HR 1.5, 95% CI 1.2–1.9, P = 0.001, respectively, log‐transformed]. ET‐1 that was measured at 48–72 h was also independently associated with death or worsening heart failure prior to discharge [odds ratio (OR) 1.6, 95% CI 1.03–2.4, P = 0.03]. These independent associations remained significant after including NT‐proBNP in the multivariable analysis.ConclusionsWe observed an independent association between elevated ET‐1 and short‐term in‐hospital clinical outcomes and 180‐day mortality in hospitalized patients with acute heart failure ET‐1 provided additional prognostic information which was incremental to that yielded by NT‐proBNP.
Structure and Bonding of an Intergrowth Phase Ca7Ag2+xGe7–x (x ≈ 2/3) Featuring a Zintl‐Type Polyanionic Chain
Authors: Ponou Siméon , Doverbratt Isa , Lidin Sven , Miller Gordon J. 
Published: December 2015

AbstractSingle crystals of a new ternary phase, Ca7Ag2+xGe7–x [x = 0.48(3)], were obtained from as side‐product of high‐temperature solid‐state reactions, and its crystal structure determined by X‐ray diffraction methods. Following the Zintl concept, the anionic substructure consists of a novel pentameric Zintl anion [Ge5]12– with C2v local symmetry, as well as [AgxGe2–x](6–3x)– units accounting for [Ge2]6– dimers and isolated Ge4– (and Ag+) species sharing the same atomic sites. DFT‐level band structure calculations were carried out on a hypothetical, fully ordered model (x = 0). We found that the electronic structure associated with the planar W‐shaped [Ge5]12– polyanions is more suited to optimize the structure's stability than the helical configuration of the isoelectronic [Se5]2–, in the context of incomplete charge transfer from the electropositive metal Ca. Thus, the antibonding states at the Fermi level that are centered on the two [Gen](2n+2)– oligomers can be depopulated by means of Ge‐to‐Ca electron back donation, strengthening at the same time the Ge–Ge bonds. These antibonding states also endow the system with substantial electronic flexibility, which may result in some phase width. Finally, plausible local ordering models of Ag/Ge mixing in [AgxGe2–x](6–3x)– units for x = 2/3, as expected from the Zintl concept, are briefly discussed within the “coloring problem” approach.
Membrane Electrode Assemblies for Water Electrolysis using WO3‐Supported IrxRu1‐xO2 Catalysts
Authors: Baumann Nils , Cremers Carsten , Pinkwart Karsten , Tübke Jens 
Published: December 2015

AbstractA hydrogen economy is one of the most promising concepts for the future energy infrastructure. The conversion of sunlight into hydrogen (H2) using directly coupled photovoltaics (PV) and a proton exchange membrane (PEM) water electrolysis cell could compliment the required hydrogen production by using excess renewable electricity. It has many advantages such as producing pure hydrogen at high photon‐to‐chemical energy efficiency and simple technical operation, but it suffers from the high cost of the catalyst. Here we show single‐cell tests using commercial membranes and an in‐house synthesized WO3‐supported IrxRu1‐xO2 anode catalyst. The catalyst was synthesized by Adam’s Fusion protocol and loaded onto the support using an annealing procedure. Membrane electrode assemblies (MEAs) were prepared using an airbrush spraying technique. The electrolysis activity was greatly increased by adding tungsten carbide (WC) to the support, leading to a higher current density than commercial MEAs; however it also showed very fast degradation, losing most of the activity in minutes. The biggest issue in terms of stability seems to be on the cathode side of the cell.
Production and Storage of Gasifiable Slurries Based on Flash‐Pyrolyzed Straw
Authors: Nicoleit Thomas , Dahmen Nicolaus , Sauer Jörg 
Published: December 2015

AbstractBy means of the bioliq® process at Karlsruhe Institute of Technology, flash‐pyrolyzed straw is converted into slurries made of pyrolysis condensates and char. These slurries can be gasified to produce syngas and, subsequently, synthetic fuels and chemicals. Investigations show that a stable slurry of the pyrolysis products is not miscible, as the condensates tend to split into organic and an aqueous phases. Thus, application of two different slurries is suggested: The organic condensates can be gasified directly, and the aqueous condensates can be mixed with 40 wt % ground straw char. This latter slurry is the focus of this work, which describes the mixing, settling, and stirring behavior. Grinding the porous and elongated char particles decelerates sedimentation and also decreases the viscosity. Thus, higher‐concentrated slurries can be mixed, which leads to higher stability.
A Primer on the Genetics of Comorbid Eating Disorders and Substance Use Disorders
Authors: Munn‐Chernoff Melissa A. , Baker Jessica H. 
Published: December 2015

AbstractEating disorders (EDs) and substance use disorders (SUDs) frequently co‐occur; however, the reasons for this are unclear. We review the current literature on genetic risk for EDs and SUDs, as well as preliminary findings exploring whether these classes of disorders have overlapping genetic risk. Overall, genetic factors contribute to individual differences in liability to multiple EDs and SUDs. Although initial family studies concluded that no shared familial (which includes genetic) risk between EDs and SUDs exists, twin studies suggest a moderate proportion of shared variance is attributable to overlapping genetic factors, particularly for those EDs characterized by binge eating and/or inappropriate compensatory behaviours. No adoption or molecular genetic studies have examined shared genetic risk between these classes of disorders. Research investigating binge eating and inappropriate compensatory behaviours using emerging statistical genetic methods, as well as examining gene–environment interplay, will provide important clues into the aetiology of comorbid EDs and SUDs. Copyright © 2015 John Wiley & Sons, Ltd and Eating Disorders Association.
Pharmaceuticals in the environment—Global occurrences and perspectives
Authors: aus der Beek Tim , Weber Frank-Andreas , Bergmann Axel , Hickmann Silke , Ebert Ina , Hein Arne , Küster Anette 
Published: December 2015

Abstract

Pharmaceuticals are known to occur widely in the environment of industrialized countries. In developing countries, more monitoring results have recently become available, but a concise picture of measured environmental concentrations (MECs) is still elusive. Through a comprehensive literature review of 1016 original publications and 150 review articles, the authors collected MECs for human and veterinary pharmaceutical substances reported worldwide in surface water, groundwater, tap/drinking water, manure, soil, and other environmental matrices in a comprehensive database. Due to the heterogeneity of the data sources, a simplified data quality assessment was conducted. The database reveals that pharmaceuticals or their transformation products have been detected in the environment of 71 countries covering all continents. These countries were then grouped into the 5 regions recognized by the United Nations (UN). In total, 631 different pharmaceutical substances were found at MECs above the detection limit of the respective analytical methods employed, revealing distinct regional patterns. Sixteen substances were detected in each of the 5 UN regions. For example, the anti-inflammatory drug diclofenac has been detected in environmental matrices in 50 countries, and concentrations found in several locations exceeded predicted no-effect concentrations. Urban wastewater seems to be the dominant emission pathway for pharmaceuticals globally, although emissions from industrial production, hospitals, agriculture, and aquaculture are important locally. The authors conclude that pharmaceuticals are a global challenge calling for multistakeholder approaches to prevent, reduce, and manage their entry into and presence in the environment, such as those being discussed under the Strategic Approach to International Chemicals Management, a UN Environment Program. Environ Toxicol Chem 2016;35:823–835. © 2015 SETAC
Influence of mesh deformation on the quality of large eddy simulations
Authors: Keskinen Jukka‐Pekka , Vuorinen Ville , Kaario Ossi , Larmi Martti 
Published: December 2015

SummaryThe influence of mesh motion on the quality of large eddy simulation (LES) was studied in the present article. A three‐dimensional, turbulent pipe flow (Reτ=360) was considered as a test case. Simulations with both stretching and static meshes were carried out in order to understand how mesh motion affects the turbulence statistics. The spatial filtering of static and moving mesh direct numerical simulation (DNS) data showed how an ideal LES would perform, while the comparison of DNS cases with static and moving meshes revealed that no significant numerical errors arise from the mesh motion when the simulation is fully resolved. The comparison of the filtered fields of the DNS with a moving mesh with the corresponding LES fields revealed different responses to mesh motion from different numerical approaches. A straightforward test was applied in order to verify that the moving mesh works consistently in LES: when the mesh is stretched in the streamwise direction, the moving mesh results should be in between the two extremal resolutions between which the mesh is stretched. Numerical investigations using four different LES approaches were carried out. In addition to the Smagorinsky model, three implicit LES approaches were used: linear interpolation (non‐dissipative), the Gamma limiter (dissipative), and the scale‐selective discretisation (slightly dissipative). The results indicate that while the Smagorinsky and the scale‐selective discretisation approaches produce results consistent with the resolution of the non‐static mesh, the implicit LES with linear interpolation or the Gamma scheme do not. Copyright © 2016 John Wiley & Sons, Ltd.
Time‐lapse application of pressure transient analysis for monitoring compressible fluid leakage
Authors: Hosseini Seyyed A. , Alfi Masoud 
Published: December 2015

AbstractDetecting early leakage of gaseous fluids from deep formations into shallower formations has financial and environmental implications and could potentially save commercial projects from expensive remediation. Detection of CO2leakage in the context of CO2geological storage and methane leakage at hydraulic‐fracturing sites is a possible scenario in which the approach described herein could be used. Any vertical leakage from a deep formation will most likely start with brine leakage, followed by arrival of the gaseous phase at the leakage pathway (faults, plugged and abandoned wells, fractures, etc.). We apply well‐known pressure transient analysis (PTA) techniques to solving challenges related to leakage monitoring, including distinguishing between brine and gaseous‐phase leakage and detecting leaks that may occur over a long period of time. The latter development is important because small leaks may not be detected by simple monitoring of absolute change in pressure. The proposed analysis is based on time‐lapse measurement of monitoring‐zone storativity (or total compressibility), and without loss of generality, we apply our analysis to CO2leakage scenarios. Our numerical results suggest that if well‐known PTA techniques are used, CO2leaks can be detected, allowing the volume of leaked CO2into the monitoring zone to be estimated. © 2015 Society of Chemical Industry and John Wiley & Sons, Ltd