bluuebunny/crossref_metadata_2025_split huggingface dataset:
Val8‐GLP‐1 remodels synaptic activity and intracellular calcium homeostasis impaired by amyloid β peptide in rats
Authors: Wang Xiao‐Hui , Yang Wei , Hölscher Christian , Wang Zhao‐Jun , Cai Hong‐Yan , Li Qing‐Shan , Qi Jin‐Shun 
Published: January 2013

AbstractType 2 diabetes mellitus (T2DM) is a risk factor for Alzheimer's disease (AD) in the elderly. Glucagon‐like peptide‐1 (GLP‐1), a modulator in T2DM therapy, has been shown to have neuroprotective properties. However, the native GLP‐1 can be rapidly degraded by the enzyme dipeptidyl peptidase IV (DPP IV); the neuroprotective mechanism of GLP‐1 in the central nervous system is still an open question, and whether GLP‐1 can prevent amyloid β (Aβ)‐induced synaptic dysfunction and calcium disorder is still unclear. The present study, by using patch clamp and calcium imaging techniques, investigated the effects of Val8‐GLP‐1(7–36), a GLP‐1 analogue with profound resistance to DPP IV, on the excitatory and inhibitory synaptic transmission and intracellular calcium concentration ([Ca2+]i) in the absence or presence of Aβ1–40. The results showed that 1) Aβ1–40 significantly reduced the frequency of miniature excitatory postsynaptic currents (mEPSCs) and miniature inhibitory postsynaptic currents (mIPSCs) in CA1 pyramidal neurons of rat brain slices; 2) Val8‐GLP‐1(7–36) did not affect the activity of miniature postsynaptic currents but effectively protected against the Aβ1–40‐induced decrease in mEPSC and mIPSC frequency; 3) Aβ1–40 significantly increased [Ca2+]i in primary neuronal cultures; and 4) Val8‐GLP‐1(7–36) alone did not change the intracellular calcium level but prevented Aβ1–40‐induced persistent elevation of [Ca2+]i. These findings demonstrate for the first time that central application of Val8‐GLP‐1(7–36) could protect against Aβ‐induced synaptic dysfunction and intracellular calcium overloading, suggesting that the neuroprotection of GLP‐1 may be involved in the remodeling of synaptic activity and intracellular calcium homeostasis in the brain. © 2013 Wiley Periodicals, Inc.
Rangeland Degradation in a Semi‐Arid Communal Savannah of Swaziland: Long–Term DIP‐Tank Use Effects on Woody Plant Structure, Cover and their Indigenous Use in Three Soil Types
Authors: Beyene Solomon T. 
Published: January 2013

AbstractThis study investigated dip‐tank use effects on the surrounding woody vegetation cover and encroachment level and on their indigenous utilisation. Eight dip tanks, three in deep‐pale‐brown old alluvium sandy, three in deep‐yellow‐red loamy, and two in rock outcrops and stony ground soils, were selected. Woody vegetation survey was conducted at 50, 100, 150, 300, 500, 700 and 900 m from each dip tank. Dichrostachys cinerea and Acacia tortilis were the dominant woody species in all areas. In deep‐pale‐brown old alluvium sandy soils, D. cinerea density was affected by distance from dip tank up to 150 m (p = 0∙03), where the density of A. tortilis was low (p = 0∙02). In deep‐yellow‐red loamy soils, the lowest and highest (p = 0∙05) D. cinerea densities were recorded at 150 and 700 m from the dip tank, respectively. Inconsistent results were found on the piosphere formation of total woody density and cover. Nevertheless, large areas surrounding the dip tank had a bush cover of >50 per cent. This study concluded that there was heavy bush encroachment around many dip tanks despite the harvest for woody species by the community. Therefore, there is a need to develop a sustainable and integrated bush control programme that provides conservation plans for species valuable for food and livelihood security. The programme should be based on communal participation and consider shifting of old dip‐tank sites and protecting the areas from disturbance. Indiscriminate (burning) or selective (manual) or a combination of the two bush control methods may be initially recommended after a rest period of at least two consecutive growing seasons. Copyright © 2013 John Wiley & Sons, Ltd.
Mimicking Native Extracellular Matrix with Phytic Acid‐Crosslinked Protein Nanofibers for Cardiac Tissue Engineering
Authors: Ravichandran Rajeswari , Seitz Vera , Reddy Venugopal Jayarama , Sridhar Radhakrishnan , Sundarrajan Subramanian , Mukherjee Shayanti , Wintermantel Erich , Ramakrishna Seeram 
Published: January 2013

AbstractA functional scaffold fabricated is developed from natural polymers, favoring regeneration of the ischemic myocardium. Hemoglobin/gelatin/fibrinogen (Hb/gel/fib) nanofibers are fabricated by electrospinning and are characterized for morphology, scaffold composition, functional groups and hydrophilicity. It is hypothesized that ex vivo pretreatment of mesenchymal stem cells (MSCs) using 5‐azacytidine and such a functional nanofibrous construct having a high oxygen‐carrying potential could lead to enhanced cardiomyogenic differentiation of MSCs and result in superior biological and functional effects. The combination of a functional nanofibrous scaffold composed of natural polymers and crosslinked with a natural crosslinking agent, phytic acid, and stem cell biology may prove to be a novel therapeutic device for treatment of myocardial infarction. magnified image
“Plasma‐Click” Based Strategy for Obtaining Antibacterial Surfaces on Implants
Authors: Braceras Iñigo , Oyarbide Joseba , Azpiroz Patxi , Briz Nerea , Ipiñazar Enrique , Álvarez Noelia , Atorrasagasti Garbiñe , Fratila Raluca M. , Aizpurua Jesus M. 
Published: January 2013

AbstractBiomaterials with surface antibacterial properties are promising components for medical implants that might provide an alternative to conventional systemic antibiotic treatments. Herein is reported a general method, based on plasma polymerization techniques, to promote the formation of “clickable surfaces” which can be conjugated with chemically modified antibiotics (e.g., azido‐vancomycin) under very mild conditions. The procedure is comprised of three operations: (i) surface alkylcarboxylation with acrylic acid/CO2 plasma, (ii) alkyne functionalization by condensation with propargylamine, and (iii) in situ Cu(I)‐catalyzed alkyne–azide conjugation with azidovancomycin. The antibacterial activity of the resulting functionalized surfaces has been assessed against Staphylococcus epidermidis. magnified image
Prediction of phenotypes of missense mutations in human proteins from biological assemblies
Authors: Wei Qiong , Xu Qifang , Dunbrack Roland L. 
Published: January 2013

AbstractSingle nucleotide polymorphisms (SNPs) are the most frequent variation in the human genome. Nonsynonymous SNPs that lead to missense mutations can be neutral or deleterious, and several computational methods have been presented that predict the phenotype of human missense mutations. These methods use sequence‐based and structure‐based features in various combinations, relying on different statistical distributions of these features for deleterious and neutral mutations. One structure‐based feature that has not been studied significantly is the accessible surface area within biologically relevant oligomeric assemblies. These assemblies are different from the crystallographic asymmetric unit for more than half of X‐ray crystal structures. We find that mutations in the core of proteins or in the interfaces in biological assemblies are significantly more likely to be disease‐associated than those on the surface of the biological assemblies. For structures with more than one protein in the biological assembly (whether the same sequence or different), we find the accessible surface area from biological assemblies provides a statistically significant improvement in prediction over the accessible surface area of monomers from protein crystal structures (P = 6e‐5). When adding this information to sequence‐based features such as the difference between wildtype and mutant position‐specific profile scores, the improvement from biological assemblies is statistically significant but much smaller (P = 0.018). Combining this information with sequence‐based features in a support vector machine leads to 82% accuracy on a balanced dataset of 50% disease‐associated mutations from SwissVar and 50% neutral mutations from human/primate sequence differences in orthologous proteins. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Loop prediction for a GPCR homology model: Algorithms and results
Authors: Goldfeld Dahlia A. , Zhu Kai , Beuming Thijs , Friesner Richard A. 
Published: January 2013

AbstractWe present loop structure prediction results of the intracellular and extracellular loops of four G‐protein‐coupled receptors (GPCRs): bovine rhodopsin (bRh), the turkey β1‐adrenergic (β1Ar), the human β2‐adrenergic (β2Ar) and the human A2a adenosine receptor (A2Ar) in perturbed environments. We used the protein local optimization program, which builds thousands of loop candidates by sampling rotamer states of the loops' constituent amino acids. The candidate loops are discriminated between with our physics‐based, all‐atom energy function, which is based on the OPLS force field with implicit solvent and several correction terms. For relevant cases, explicit membrane molecules are included to simulate the effect of the membrane on loop structure. We also discuss a new sampling algorithm that divides phase space into different regions, allowing more thorough sampling of long loops that greatly improves results. In the first half of the paper, loop prediction is done with the GPCRs' transmembrane domains fixed in their crystallographic positions, while the loops are built one‐by‐one. Side chains near the loops are also in non‐native conformations. The second half describes a full homology model of β2Ar using β1Ar as a template. No information about the crystal structure of β2Ar was used to build this homology model. We are able to capture the architecture of short loops and the very long second extracellular loop, which is key for ligand binding. We believe this the first successful example of an RMSD validated, physics‐based loop prediction in the context of a GPCR homology model. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Lethal mutations in the major homology region and their suppressors act by modulating the dimerization of the rous sarcoma virus capsid protein C‐terminal domain
Authors: Dalessio Paula M. , Craven Rebecca C. , Lokhandwala Parvez M. , Ropson Ira J. 
Published: January 2013

AbstractAn infective retrovirus requires a mature capsid shell around the viral replication complex. This shell is formed by about 1500 capsid protein monomers, organized into hexamer and pentamer rings that are linked to each other by the dimerization of the C‐terminal domain (CTD). The major homology region (MHR), the most highly conserved protein sequence across retroviral genomes, is part of the CTD. Several mutations in the MHR appear to block infectivity by preventing capsid formation. Suppressor mutations have been identified that are distant in sequence and structure from the MHR and restore capsid formation. The effects of two lethal and two suppressor mutations on the stability and function of the CTD were examined. No correlation with infectivity was found for the stability of the lethal mutations (D155Y‐CTD, F167Y‐CTD) and suppressor mutations (R185W‐CTD, I190V‐CTD). The stabilities of three double mutant proteins (D155Y/R185W‐CTD, F167Y/R185W‐CTD, and F167Y/I190V‐CTD) were additive. However, the dimerization affinity of the mutant proteins correlated strongly with biological function. The CTD proteins with lethal mutations did not dimerize, while those with suppressor mutations had greater dimerization affinity than WT‐CTD. The suppressor mutations were able to partially correct the dimerization defect caused by the lethal MHR mutations in double mutant proteins. Despite their dramatic effects on dimerization, none of these residues participate directly in the proposed dimerization interface in a mature capsid. These findings suggest that the conserved sequence of the MHR has critical roles in the conformation(s) of the CTD that are required for dimerization and correct capsid maturation. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Spin‐helical transport in normal and superconducting topological insulators
Authors: Tkachov G. , Hankiewicz E. M. 
Published: January 2013

AbstractIn a topological insulator (TI) the character of electron transport varies from insulating in the interior of the material to metallic near its surface. Unlike, however, ordinary metals, conducting surface states in TIs are topologically protected and characterized by spin helicity whereby the direction of the electron spin is locked to the momentum direction. In this paper we review selected topics regarding recent theoretical and experimental work on electron transport and related phenomena in two‐dimensional (2D) and three‐dimensional (3D) TIs.The review provides a focused introductory discussion of the quantum spin Hall effect in HgTe quantum wells as well as transport properties of 3DTIs such as surface weak antilocalization, the half‐integer quantum Hall effect, s + p‐wave induced superconductivity, superconducting Klein tunneling, topological Andreev bound states and related Majorana midgap states. These properties of TIs are of practical interest, guiding the search for the routes towards topological spin electronics.
Demonstrating the In Situ Biodegradation Potential of Phenol Using Bio‐Sep® Bio‐Traps® and Stable Isotope Probing
Authors: Williams Neil , Hyland Amy , Mitchener Richard , Sublette Kerry , Key Katherine C. , Davis Greg , Ogles Dora , Baldwin Brett , Biernacki Anita 
Published: January 2013

AbstractThe effect of phenol concentration on phenol biodegradation at an industrial site in the south of Wales, United Kingdom, was investigated using standard Bio‐Sep® Bio‐Traps® and Bio‐Traps® coupled with stable isotope probing (SIP). Unlike many 13C‐amendments used in SIP studies (such as hydrocarbons) that physically and reversibly adsorb to the activated carbon component of the Bio‐Sep® beads, phenol is known to irreversibly chemisorb to activated carbon. Bio‐Traps® were deployed for 32 days in nine site groundwater monitoring wells representing a wide range of phenol concentrations. Bio‐Traps® amended with 13C‐phenol were deployed together with non‐amended Bio‐Traps® in three wells.Quantitative polymerase chain reaction (qPCR) analysis of Bio‐Traps® post‐deployment indicated an inhibitory effect of increasing phenol concentration on both total eubacteria and aerobic phenol‐utilizing bacteria as represented by the concentration of phenol hydroxylase gene. Despite the chemisorption of phenol to the Bio‐Sep® beads, activated carbon stable isotope analysis showed incorporation of 13C into biomass and dissolved inorganic carbon (DIC) in each SIP Bio‐Trap® indicating that chemisorbed amendments are bioavailable. However, there was a clear effect of phenol concentration on 13C incorporation in both biomass and DIC confirming phenol inhibition. These results suggest that physical reductions of the phenol concentrations in some areas of the plume will be required before biodegradation of phenol can proceed at a reasonable rate. © 2013 Wiley Periodicals, Inc.
Enhancing Reductive Dechlorination With Nutrient Addition
Authors: Fowler Troy , Reinauer Kimberly 
Published: January 2013

AbstractEnhanced reductive bioremediation (ERB) of halogenated organics has become widely accepted and implemented to reduce risks to human health and the environment posed by these compounds. The family of chlorinated ethenes (e.g., trichloroethene) is among the most common contaminants treated using ERB techniques. The number of microbial species able to fully dechlorinate ethenes is small, and many times their population numbers are low. As a result, many ERB practitioners have turned to the injection of designer bacteria within treatment zones as a means to accelerate the process. Otherwise, many remediation projects encounter “cis‐stall,'' or the accumulation of the cis‐1,2‐dichloroethene and vinyl chloride intermediates. This article discusses three unique case studies where the addition of a balanced macro‐ and micro‐nutrient source substantially accelerated the chlorinated ethene ERB process, independent of the electron‐donor substrate applied. © 2013 Wiley Periodicals, Inc.
Incorporating Bioavailability Considerations Into the Evaluation of Contaminated Sediment Sites
Authors: Sorell Tamara , McEvoy Kim 
Published: January 2013

AbstractIn March 2011, the Interstate Technology & Regulatory Council (ITRC) Contaminated Sediments Team published a web‐based Technical and Regulatory Guidance on the concepts, processes, and uses of bioavailability in a risk decision‐making framework at a contaminated sediment site. Bioavailability processes, as defined by the National Research Council (NRC; 2003), are the “individual physical, chemical, and biological interactions that determine the exposure of plants and animals to chemicals associated with soils and sediments.” Bioavailability assessment tools aid in the assessment of human and ecological exposure and development of site‐specific remedial objectives. The guidance provides information on the processes that may affect contaminant bioavailability within sediments to understand exposure within ecological and human receptors; supports the development of conceptual site models (CSMs); and describes available tools (biological, chemical, and physical) and models that are used to measure and characterize the fate and transport and potential bioavailability of contaminants. Case studies, referenced throughout the document, demonstrate the practical application of bioavailability measures. The guidance will describe the proper application of traditional and emerging sediment remediation technologies to support the selection of a remedy that is protective of human health and the environment. © 2013 Wiley Periodicals, Inc.
Improvements to TCE Microcosm Protocols for Biostimulation in Bedrock Aquifers
Authors: Druschel Stephen J. , Kinner Nancy E. 
Published: January 2013

AbstractIn this study, a factorial‐designed experiment of biostimulated trichloroethene (TCE) dechlorination in fractured bedrock aquifers using microcosms evaluated several potential biostimulants (i.e., nutrients, vitamins, and sterile groundwater). Substantial cost savings and resource efficiency can be provided by this approach because: factorial designs require relatively few microcosms per factor; the interpretation of the observations can proceed largely by common sense, simple arithmetic, and computer graphics; the observations can indicate promising directions for further experimentation and causative relationships; and designs can be suitably augmented when a more in‐depth exploration is needed.TCE degradation was evaluated using three methods of data analysis: (1) analysis of covariance (ANCOVA) between biotic and abiotic treatment trend‐line slopes; (2) calculation of biodegradation half‐life; and (3) effects screening by model fitting. Microcosm preparation with crushed rock in groundwater was found to more closely match the previously observed field rates than the preparation with only groundwater. Injection of nutrient and vitamin mixtures was made into microcosms that were previously aged to obtain consistent conditions, and the TCE concentration measured after incubating for 45 days. Comparison of results indicated that the nutrient mixture slows or inhibits the degradation of TCE compared to the sterile groundwater; however, the vitamin mixture offsets and nearly compensates for the inhibitory effect of the nutrient mixture. It is recommended that this factorial experiment be augmented with additional studies of individual or groups of compounds from the vitamin mixture using this methodology to isolate and identify the specific factor or interaction responsible for the inhibitory compensation. © 2013 Wiley Periodicals, Inc.
Lessons Learned About the Nature of Groundwater Contamination by PAHs: A Case History–Based Discussion
Authors: Brassington Rick 
Published: January 2013

AbstractObservations taken during the investigation and remediation of a water supply borehole contaminated by polycyclic aromatic hydrocarbons (PAHs) are used to discuss how existing methods can define such contamination. In this example, the PAH originated from carbon black used in a manufacturing process. The extent of the contamination was investigated and the flow path for the pollutants to enter the borehole identified. Two attempts were made to destroy the contaminants using hydrogen peroxide following different procedures. The observations made during the investigations, treatment, and sampling results are reviewed to determine possible explanations for the observed behavior and to assess the effectiveness of the treatment methods with the benefits of hindsight. © 2013 Wiley Periodicals, Inc.
Migration of VOC Plume in the Subsurface Domain at the Y‐12 National Security Site
Authors: Malek‐Mohammadi Siamak , Tachiev Georgio 
Published: January 2013

AbstractDuring the production of thermonuclear fusion weapons at the Y‐12 National Security Complex (Y‐12 NSC) in Oak Ridge, Tennessee, between 1950 and 1963, the regional environment was extensively contaminated by volatile organic compounds (VOCs). Old Salvage Yard (OSY) on the western side of the site has been characterized as the major source of VOCs. In order to analyze the long‐term fate and transport of chlorinated VOC sources, an integrated surface and subsurface flow and transport model was developed for the Y‐12 NSC using the hydrodynamic and transport numerical package MIKE‐SHE. The model was developed considering the recent hydrogeological investigations on preferential flow and transport pathways at the site. The model was calibrated using the recorded groundwater flow and water‐quality data. The modeling simulated migration of the VOC plume for the next 100 years. Considering a range of hydrogeological and transport parameters, uncertainty of the results is discussed. The modeling predicted that tetrachloroethene, trichloroethene, and 1,2‐dichloroethene may exceed human health–related risk levels for the next 10 to 20 years. However, the contamination is unlikely to migrate to surface water under the current hydrogeological conditions and will decay below acceptable risk levels within approximately 20 years. © 2013 Wiley Periodicals, Inc.
An embedding approach for the design of state‐feedback tracking controllers for references with jumps
Authors: Sanfelice Ricardo G. , Biemond J.J. Benjamin , van de Wouw Nathan , Heemels W.P.Maurice H. 
Published: January 2013

SUMMARYWe study the problem of designing state‐feedback controllers to track time‐varying state trajectories that may exhibit jumps. Both plants and controllers considered are modeled as hybrid dynamical systems, which are systems with both continuous and discrete dynamics, given in terms of a flow set, a flow map, a jump set, and a jump map. Using recently developed tools for the study of stability in hybrid systems, we recast the tracking problem as the task of asymptotically stabilizing a set, the tracking set, and derive conditions for the design of state‐feedback tracking controllers with the property that the jump times of the plant coincide with those of the given reference trajectories. The resulting tracking controllers guarantee that solutions of the plant starting close to the reference trajectory stay close to it and that the difference between each solution of the controlled plant and the reference trajectory converges to zero asymptotically. Constructive conditions for tracking control design in terms of LMIs are proposed for a class of hybrid systems with linear maps and input‐triggered jumps. The results are illustrated by various examples. Copyright © 2013 John Wiley & Sons, Ltd.