bluuebunny/crossref_metadata_2025 huggingface dataset:
The effects of a large‐scale wind farm on breeding season survival of female mallards and blue‐winged teal in the Prairie Pothole Region
Authors: Gue C. Tanner , Walker Johann A. , Mehl Katherine R. , Gleason Jeffrey S. , Stephens Scott E. , Loesch Charles R. , Reynolds Ronald E. , Goodwin Brett J.
Published: August 2013

The wetlands and grasslands of the Prairie Pothole Region (PPR) make it the most productive breeding habitat for North American ducks. The growth rate of mallard (Anas platyrhynchos) populations is sensitive to changes in survival of adult females during the breeding season. Much of the PPR is suitable for large‐scale wind‐energy development and collisions of breeding females with wind turbines may be a novel source of mortality in this area. We assessed the effects of wind energy on breeding female mallard and blue‐winged teal (A. discors) survival by monitoring 77 radio‐marked mallards and 88 blue‐winged teal during the 2009 and 2010 breeding seasons at the Tatanka Wind Farm (TWF) near Kulm, North Dakota. During the same period, we monitored 70 female mallards and 75 blue‐winged teal at an adjacent reference site without wind turbines (REF). We used an information‐theoretic approach to investigate relationships between female survival and site (TWF vs. REF), year (2009 vs. 2010), and date. Collision mortalities were rare. Only 1 radio‐marked female mallard and no blue‐winged teal collided with wind turbines. Most mortalities were caused by predators (78.3%; 36/46), irrespective of species and site. For mallards, the best‐approximating model indicated that breeding season survival was 1) lowest when a high proportion of radio‐marked females were incubating, and 2) dependent on year and site such that expected survival () in 2009 was higher at TWF ( = 0.90, 85% CI = 0.79–0.98) than at REF ( = 0.83, 85% CI = 0.68–0.95), but expected survival in 2010 was lower at TWF ( = 0.62, 85% CI = 0.46–0.79) than at REF ( = 0.84, 85% CI = 0.72–0.94). For blue‐winged teal, the constant model was the best‐approximating model and indicated that expected female survival was 0.75 (85% CI = 0.69–0.82). The most competitive model for blue‐winged teal that included the effect of wind turbines indicated that expected survival at TWF ( = 0.71, 85% CI = 0.62–0.79) was lower than survival at REF ( = 0.81, 85% CI = 0.73–0.89). The limited number of collisions observed for female mallards and blue‐winged teal nesting at TWF suggests that wind turbines had no direct effect on female survival. Thus, conservation strategies that include protection of wetland and grassland habitat in wind‐developed landscapes will most likely not cause a direct reduction in survival of breeding females due to collisions with wind turbines. © 2013 The Wildlife Society.
Use of capture–recapture models with mark‐resight data to estimate abundance of Aleutian cackling geese
Authors: Sanders Todd A. , Trost Robert E.
Published: August 2013

The Aleutian cackling goose (Branta hutchinsii leucopareia) was listed as endangered in 1967, downgraded to threatened in 1990, and removed from protection under the endangered species act in 2001. Accurate determination of population status continues to be a priority for management agencies because of the population's past listing as endangered, the species status as a game bird, and because population expansion has resulted in increased crop damage complaints. We compared estimates of marked Aleutian goose abundance from available mark‐resight data during 1996–2012 using capture–recapture Jolly–Seber (POPAN formulation) and robust design (closed capture) models. We derived an estimate of Aleutian goose abundance by expanding an estimate of marked‐bird abundance by the ratio of total to marked geese. Robust design models provided strong evidence of even‐flow and Markovian temporary emigration from observable to unobservable states between annual sampling periods, and POPAN estimates were biased as a result of this movement. The observable population increased in abundance from 790 in 1975 to 134,703 (SE = 10,866, 95% CI = 113,405–156,002) geese in 2012. However, total (observable and unobservable) population size was 216,564 geese based on an estimated probability (0.622) of being available for observation. Annual survival probability was 0.80 (SE = 0.05). Current data collection allows estimation of annual observable abundance with a coefficient of variation of ≤8%. Robust design offers a means of estimating abundance of partially marked wildlife populations in the presence or absence of temporary emigration, which can result from partial study area access and is likely a common situation for many populations. Mark‐resight is a cost‐effective approach (compared to capture–recapture studies and aerial surveys) that can be applied to successfully estimate demographic parameters of other populations. © 2013 The Wildlife Society.
Coupling climate risks, eco‐systems, and anthropogenic decisions using South American and Sub‐Saharan farming activities
Authors: Seo S. Niggol
Published: August 2013

This paper provides an analysis of the interplays between climate risks, eco‐systems and adaptation decisions using South American and Sub‐Saharan African farm surveys. Climate risk indicators such as seasonal Coefficient of Variation in Precipitation (CVP) and Diurnal Temperature Range (DTR) are matched with major eco‐systems. Adoption decisions of the six natural resource enterprises are modelled using a spatial Logit model. First, this paper finds that climate risks are higher in the grasslands and meadow eco‐systems in South America as they are high in the lowland arid zones in Africa. However, climate risks across the continent are, compared with Sub‐Saharan Africa, much lower in South America. Second, a higher temperature implies a higher climate risk in Africa, which is not the case in South America owing to the predominant influences of regional weather events such as the ENSO. Third, while the CVP is a dominant risk factor in Africa, the DTR is a dominant risk factor in South America due to the vast ranges of the Andes Mountain. Winter DTR is predicted to fall by 3 °C under both the UKMO and the GISS scenarios by the middle of this century. Altered climate risks will push a large number of farmers to switch away from a crops‐only enterprise due to a large decrease in daily temperature variability. Farmers adapt by increasing a crops‐livestock enterprise in the grasslands with wood cover and subtropical drought‐deciduous forests. This paper provides a coupled analysis of global (climate), local (eco‐systems) and individual (adaptation) processes.
Selenium alters miRNA profile in an intestinal cell line: Evidence that miR‐185 regulates expression of GPX2 and SEPSH2
Authors: Maciel‐Dominguez Anabel , Swan Daniel , Ford Dianne , Hesketh John
Published: August 2013

Scope

Intake of the essential micronutrient selenium (Se) has health implications. This work addressed whether some effects of Se on gene expression are exerted through microRNAs (miRNA).

Methods and results

Human colon adenocarcinoma cells (Caco‐2) were grown in Se‐deficient or Se‐adequate medium for 72 h. RNA was extracted and subjected to analysis of 737 miRNA using microarray technology. One hundred and forty‐five miRNA were found to be expressed in Caco‐2 cells. Twelve miRNA showed altered expression after Se depletion: miR‐625, miR‐492, miR‐373*, miR‐22, miR‐532–5p, miR‐106b, miR‐30b, miR‐185, miR‐203, miR1308, miR‐28–5p, miR‐10b. These changes were validated by quantitative real‐time PCR (RT‐qPCR). Transcriptomic analysis showed that Se depletion altered expression of 50 genes including selenoproteins GPX1, SELW, GPX3, SEPN1, SELK, SEPSH2 and GPX4. Pathway analysis identified arachidonic acid metabolism, glutathione metabolism, oxidative stress, positive acute phase response proteins and respiration of mitochondria as Se‐sensitive pathways. Bioinformatic analysis identified 13 transcripts as targets for the Se‐sensitive miRNA; three were predicted to be recognised by miR‐185. Silencing of miR‐185 increased GPX2 and SEPSH2 expression.

Conclusions

We propose that miR‐185 plays a role in up‐regulation of GPX2 and SEPHS2 expression. In the case of SEPHS2 this may contribute to maintaining selenoprotein synthesis. The data indicate that micronutrient supply can regulate the cell miRNA expression profile.
Polymorphisms in the SCD1 gene are associated with indices of stearoyl CoA desaturase activity and obesity: A prospective study
Authors: Martín‐Núñez Gracia María , Cabrera‐Mulero Rebeca , Rojo‐Martínez Gemma , Gómez‐Zumaquero Juan Miguel , Chaves Felipe Javier , de Marco Griselda , Soriguer Federico , Castaño Luis , Morcillo Sonsoles
Published: August 2013

Scope

The serum fatty acid (FA) composition is influenced by dietary fat and the endogenous production of FAs. Stearoyl CoA desaturase 1 (SCD1) is the rate‐limiting enzyme catalyzing the synthesis of MUFAs from saturated FAs. Variations in SCD1 activity have been associated with obesity, diabetes, or inflammation. We evaluated the associations between genetic variation of the SCD1 gene, SCD1 activity, intake of oil, and obesity in a population‐based prospective study in southern Spain.

Methods and results

We collected phenotypic, metabolic, nutritional, and genetic information. The type of dietary fat was assessed from samples of cooking oil taken from the participants’ kitchens and analyzed by GC. A total of nine single nucleotide polymorphisms (SNPs) of the SCD1 gene were analyzed by SNPlex technology. We found a significant association between SCD1 genetic variation and enzyme activity in four of nine polymorphisms studied. An interaction between rs10883463 and olive oil intake on the [18:1/18:0] desaturase index was found (p = 0.009). We also showed that genetic variations in the SCD1 gene were associated with obesity.

Conclusion

Our results show a relationship between genetic variation of the SCD1 gene, enzyme activity, and the risk of obesity, an association that is not independent of the type of oil consumed.
Active macro‐zone approach for incremental elastoplastic‐contact analysis
Authors: Cucco F. , Terravecchia S. , Zito L.
Published: August 2013

The symmetric boundary element method, based on the Galerkin hypotheses, has found an application in the nonlinear analysis of plasticity and in contact‐detachment problems, but both dealt with separately. In this paper, we want to treat these complex phenomena together as a linear complementarity problem.

A mixed variable multidomain approach is utilized in which the substructures are distinguished into macroelements, where elastic behavior is assumed, and bem‐elements, where it is possible that plastic strains may occur. Elasticity equations are written for all the substructures, and regularity conditions in weighted (weak) form on the boundary sides and in the nodes (strong) between contiguous substructures have to be introduced, in order to attain the solving equation system governing the elastoplastic‐contact/detachment problem. The elastoplasticity is solved by incremental analysis, called for active macro‐zones, and uses the well‐known concept of self‐equilibrium stress field here shown in a discrete form through the introduction of the influence matrix (self‐stress matrix). The solution of the frictionless contact/detachment problem was performed using a strategy based on the consistent formulation of the classical Signorini equations rewritten in discrete form by utilizing boundary nodal quantities as check elements in the zones of potential contact or detachment. Copyright © 2013 John Wiley & Sons, Ltd.
A finite element variational multiscale method for steady‐state natural convection problem based on two local gauss integrations
Authors: Zhang Yunzhang , Hou Yanren , Zheng Haibiao
Published: August 2013

In this article, supposing that the velocity, pressure, and temperature are approximated by the elements , and applying the orthogonal projection technique, we introduce two Gauss integrations as a stabilizing term in the common variational multiscale (VMS) method and derive a new VMS (Two Gauss VMS) method for steady‐state natural convection problem. Comparing with the common VMS method, the Two Gauss VMS method does not need to introduce any extra variable and reduces the degrees of freedom of the discrete system a lot, but gets the same stabilized result. The effectiveness and stability of the Two Gauss VMS method are further demonstrated through two numerical examples. © 2013 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 30: 361–375, 2014
Occupation‐Based Family‐Centered Therapy Approach for Young Children with Feeding Problems in South Korea; A Case Study
Authors: An Sun‐Joung L.
Published: August 2013

Documenting the effectiveness of an occupation‐based family‐centered therapy approach, when providing therapy for a young child with feeding problems, is needed in a culture such as Korea, which has a strong medical model of service. A case study was conducted involving a 16‐month‐old boy with feeding problems. An occupation‐based family‐centered therapy approach was carried out for 10 weeks. The results indicated that this approach addressed the physical components of the child's feeding problems and also the parent‐child bonding, which together improved the overall family dynamics. Although these results may stimulate clinicians to consider an alternative approach to a medical model, further research with a larger sample is needed to provide sufficient evidence for therapists to shift to a new service delivery model. Copyright © 2013 John Wiley & Sons, Ltd.
Deposition of gallium oxide nanodots prepared from metal‐assembling dendrimer molecules isolated by the spacing of the nonmetal‐assembling dendrimer molecules in the two‐dendrimers mixture monolayer
Authors: Hirano Isao , Imaoka Takane , Yamamoto Kimihisa
Published: August 2013

Phenylazomethine dendrimers (DPA) can precisely incorporate metal chlorides onto the imine sites in a stepwise fashion. Such precise dendrimer–metal complexes allow the preparation of size‐controlled subnanometer metal particles. We now propose a novel approach for the fabrication of size‐controlled subnanometer metal oxide dots isolated on a substrate using two different‐type dendrimers. One is a fourth‐generation phenylazomethine dendrimer (DPAG4) and the other is a benzylether dendrimer (BzEG3) with a zinc porphyrin core. Even though the diameter of BzEG3 corresponds to that of DPAG4, BzEG3 has no metal‐complexing site. Upon dip coating on a highly oriented pyrolytic graphite substrate by the mixed solution of the metal chloride‐assembling DPAG4 molecules and BzEG3 molecules, the dendrimer monolayer was immobilized on the substrate. The concentration of the dendrimer mixture was determined in order to separate each DPAG4–metal chloride complex molecule by BzEG3. Monodispersed metaloxide nanodot arrays could be obtained from the dendrimer monolayer in which DPAG4–metal chloride complex molecule is well isolated by the BzEG3 as a spacer after the hydrolysis of metal chlorides followed by the complete removal of dendrimers. Copyright © 2013 John Wiley & Sons, Ltd.
Overcoming resistance to sonic hedgehog inhibition by targeting p90 ribosomal S6 kinase in pediatric medulloblastoma
Authors: Pambid Mary Rose , Berns Rachel , Adomat Hans H. , Hu Kaiji , Triscott Joanna , Maurer Norbert , Zisman Natalia , Ramaswamy Vijay , Hawkins Cynthia E. , Taylor Michael D. , Dunham Christopher , Guns Emma , Dunn Sandra E.
Published: August 2013

Background

Molecular subtyping has allowed for the beginning of personalized treatment in children suffering from medulloblastoma (MB). However, resistance inevitably emerges against these therapies, particularly in the Sonic Hedgehog (SHH) subtype. We found that children with SHH subtype have the worst outcome underscoring the need to identify new therapeutic targets.

Procedure

High content screening of a 129 compound library identified agents that inhibited SHH MB growth. Lead molecular target levels, p90 ribosomal S6 kinase (RSK) were characterized by immunoblotting and qRT‐PCR. Comparisons were made to human neural stem cells (hNSC). Impact of inhibiting RSK with the small molecule BI‐D1870 or siRNA was assessed in growth assays (monolayer, neurosphere, and soft agar). NanoString was used to detect RSK in a cohort of 66 patients with MB. To determine BI‐D1870 pharmacokinetics/pharmacodynamics, 100 mg/kg was I.P. injected into mice and tissues were collected at various time points.

Results

Daoy, ONS76, UW228, and UW426 MB cells were exquisitely sensitive to BI‐D1870 but unresponsive to SHH inhibitors. Anti‐tumor growth corresponded with inactivation of RSK in MB cells. BI‐D1870 had no effect on hNSCs. Inhibiting RSK with siRNA or BI‐D1870 suppressed growth, induced apoptosis, and sensitized cells to SHH agents. Notably, RSK expression is correlated with SHH patients. In mice, BI‐D1870 was well‐tolerated and crossed the blood–brain barrier (BBB).

Conclusions

RSK inhibitors are promising because they target RSK which is correlated with SHH patients as well as cause high levels of apoptosis to only MB cells. Importantly, BI‐D1870 crosses the BBB, acting as a scaffold for development of more long‐lived RSK inhibitors. Pediatr Blood Cancer 2014;61:107–115. © 2013 Wiley Periodicals, Inc.
Ultrasound‐assisted Extraction with LC–TOF/MS Identification and LC–UV Determination of Imazamox and its Metabolites in Leaves of Wheat Plants
Authors: Rojano‐Delgado Antonia M. , Priego‐Capote Feliciano , Prado Rafael De , de Castro María Dolores Luque
Published: August 2013

Introduction

imazamox is a herbicide used in many legominous and cereal crops. There are few methods in the literature for determination of imazamox and its metabolites in plants because of the lack of commercial standards or owing to expensive and/or complex synthesis.

Objective

To develop a method based on liquid chromatography and ultraviolet absorption detection for simultaneous determination of imazamox and its metabolites in plants.

Methods

Sample preparation was based on ultrasound‐assisted extraction (70 W power and duty cycle of 0.7 s/s for 10 min) with subsequent filtration of the extracts and clean‐up and concentration prior to chromatographic separation and detection at 240 nm. The chromatographic analysis was completed in 30 min using a Luna® HILIC column. Identification and confirmatory analysis of the presence of imazamox and its metabolites in extracts from treated plants was performed by LC–TOF/MS in high resolution mode for precursor ions. The metabolites were quantified using a surrogate approach based on an imazamox standard. The method was validated by analysing wheat samples treated with 200 g per hectare of active ingredient imazamox.

Results

The linear dynamic range of the calibration curve was within 0.27–600 µg/mL, with a correlation coefficient of 0.998 and precision – studied at 0.1 and 2 µg/mL – of 2.9% and 5.0% for repeatability, and 4.7% and 6.9% for reproducibility, respectively.

Conclusion

The analytical characteristics of the method make it recommendable for evaluating the metabolism of imazamox in plants. Copyright © 2013 John Wiley & Sons, Ltd.
Vibrational Spectroscopy as a Rapid Quality Control Method for Melaleuca alternifolia Cheel (Tea Tree Oil)
Authors: Tankeu Sidonie , Vermaak Ilze , Kamatou Guy , Viljoen Alvaro
Published: August 2013

Introduction

Tea tree oil (TTO) is an important commercial oil which has found application in the flavour, fragrance and cosmetic industries. The quality is determined by the relative concentration of its major constituents: 1,8‐cineole, terpinen‐4‐ol, α‐terpineol, α‐terpinene, terpinolene, γ‐terpinene and limonene. Gas chromatography coupled to mass spectrometry (GC–MS) is traditionally used for qualitative and quantitative analyses but is expensive and time consuming.

Objective

To evaluate the use of vibrational spectroscopy in tandem with chemometric data analysis as a fast and low‐cost alternative method for the quality control of TTO.

Methods

Spectral data were acquired in both the mid‐infrared (MIR) and near infrared (NIR) wavelength regions and reference data obtained using GC–MS with flame ionisation detection (FID). Principal component analysis (PCA) was used to investigate the data by observing clustering and identifying outliers. Partial least squares (PLS) multivariate calibration models were constructed for the quantification of the seven major constituents.

Results

High correlation coefficients (R2) of ≥ 0.75 were obtained for the seven major compounds and 1,8‐cineole showed the best correlation coefficients for both MIR and NIR data (R2 = 0.97 and 0.95, respectively). Low values were obtained for the root mean square error of estimation (RMSEE) and root mean square error of prediction (RMSEP) values thereby confirming accuracy.

Conclusion

The accurate prediction of the external dataset after introduction into the models confirmed that both MIR and NIR spectroscopy are valuable methods for quantification of the major compounds of TTO when compared with the reference data obtained using GC–MS. Copyright © 2013 John Wiley & Sons, Ltd.
Mixed matrix membranes of H‐ZSM5‐loaded poly(vinyl alcohol) used in pervaporation dehydration of alcohols: Influence of silica/alumina ratio
Authors: Suhas Dharupaneedi P. , Aminabhavi Tejraj M. , Raghu Anjanapura V.
Published: August 2013

Mixed matrix membranes of poly(vinyl alcohol) loaded with zeolite particles having different silica alumina ratio were prepared and used in the pervaporation dehydration of ethanol and isopropanol (IPA) from their aqueous mixtures. The membranes were characterized by physicochemical techniques that revealed higher interaction between polymer and zeolite particles having higher alumina than those with lower alumina in the zeolite framework. Both, membrane selectivity to water and flux were increased as the alumina content in the zeolite increases. Separation factors of zeolite with lower alumina incorporated membranes were, respectively, 236 and 334 for the feed mixture compositions of 4 wt% water in ethanol and 10 wt% water in IPA at 30°C. On the other hand, membranes containing zeolites with higher alumina content showed slightly higher separation factors of 349 and 568, respectively, for the same feed mixtures at 30°C. Such an incremental improvement in membrane performance with increase in alumina content in the zeolite framework is attributed to favorable interaction between zeolite particles and the polymer matrix. POLYM. ENG. SCI., 54:1774–1782, 2014. © 2013 Society of Plastics Engineers
The quest for a better system for evaluating pi‐electron substituent constant: a comparison of benzoic, acrylic and tria‐, penta‐, heptafulvene‐based carboxylic acids. A computational study
Authors: Oziminski Wojciech P.
Published: August 2013

Carboxylic acids based on exo‐substituted tria‐, penta‐, heptafulvenes and ethylene (acrylic acids) were examined in order to determine if they are more sensitive to the substituent effect than benzoic acid – the system originally employed by Hammett. In order to accomplish this task, all possible structural isomers of benzoic acid, tria‐, penta‐ and heptafulvene‐based carboxylic acids, acrylic and methacrylic acids substituted by 13 substiuents (BH2, CHO, CN, COCN, NO2, CF3, Me, Cl, F, OH, OMe, NH2 and NMe2) were optimized at the B3LYP/6‐311++G(d,p) level of theory, and Gibbs free energies of carboxylic group dissociation (ΔGdis) were calculated. These energies were subsequently intercorrelated, and from the slopes of linear regressions, it was estimated which system is associated with greatest changes of ΔGdis due to substitution and thus is most sensitive to the substituent effect. It was found that all fulvene‐based carboxylic acids have greater range of ΔGdis change than benzoic acid, but the largest range of change was observed in the case of acrylic and methacrylic acids. The acrylic acid as the most sensitive system to substitution could replace benzoic acid for an improved version of substituent constant used to measure pi‐electron substituent effect. Copyright © 2013 John Wiley & Sons, Ltd.
Observed octameric assembly of a Plasmodium yoelii peroxiredoxin can be explained by the replacement of native “ball‐and‐socket” interacting residues by an affinity tag
Authors: Gretes Michael C. , Karplus P. Andrew
Published: August 2013

Peroxiredoxins (Prxs) are ubiquitous and efficient antioxidant enzymes crucial for redox homeostasis in most organisms, and are of special importance for disease‐causing parasites that must protect themselves against the oxidative weapons of the human immune system. Here, we describe reanalyses of crystal structures of two Prxs from malaria parasites. In addition to producing improved structures, we provide normalizing explanations for features that had been noted as unusual in the original report of these structures (Qiu et al., BMC Struct Biol 2012;12:2). Most importantly, we provide evidence that the unusual octameric assembly seen for Plasmodium yoelii Prx1a is not physiologically relevant, but arises because the structure is not of authentic P. yoelii Prx1a, but a variant we designate PyPrx1aN* that has seven native N‐terminal residues replaced by an affinity tag. This N‐terminal modification disrupts a previously unrecognized, hydrophobic “ball‐and‐socket” interaction conserved at the B‐type dimer interface of Prx1 subfamily enzymes, and is accommodated by a fascinating two‐residue “β‐slip” type register shift in the β‐strand association at a dimer interface. The resulting change in the geometry of the dimer provides a simple explanation for octamer formation. This study illustrates how substantive impacts can occur in protein variants in which native residues have been altered.
Crystal structure of the Alpha subunit PAS domain from soluble guanylyl cyclase
Authors: Purohit Rahul , Weichsel Andrzej , Montfort William R.
Published: August 2013

Soluble guanylate cyclase (sGC) is a heterodimeric heme protein of ∼150 kDa and the primary nitric oxide receptor. Binding of NO stimulates cyclase activity, leading to regulation of cardiovascular physiology and providing attractive opportunities for drug discovery. How sGC is stimulated and where candidate drugs bind remains unknown. The α and β sGC chains are each composed of Heme‐Nitric Oxide Oxygen (H‐NOX), Per‐ARNT‐Sim (PAS), coiled‐coil and cyclase domains. Here, we present the crystal structure of the α1 PAS domain to 1.8 Å resolution. The structure reveals the binding surfaces of importance to heterodimer function, particularly with respect to regulating NO binding to heme in the β1 H‐NOX domain. It also reveals a small internal cavity that may serve to bind ligands or participate in signal transduction.
Substrate‐dependent dynamics of UDP‐galactopyranose mutase: Implications for drug design
Authors: Boechi Leonardo , de Oliveira Cesar Augusto F. , Da Fonseca Isabel , Kizjakina Karina , Sobrado Pablo , Tanner John J. , McCammon J. Andrew
Published: August 2013

Trypanosoma cruzi is the causative agent of Chagas disease, a neglected tropical disease that represents one of the major health challenges of the Latin American countries. Successful efforts were made during the last few decades to control the transmission of this disease, but there is still no treatment for the 10 million adults in the chronic phase of the disease. In T. cruzi, as well as in other pathogens, the flavoenzyme UDP‐galactopyranose mutase (UGM) catalyzes the conversion of UDP‐galactopyranose to UDP‐galactofuranose, a precursor of the cell surface β‐galactofuranose that is involved in the virulence of the pathogen. The fact that UGM is not present in humans makes inhibition of this enzyme a good approach in the design of new Chagas therapeutics. By performing a series of computer simulations of T. cruzi UGM in the presence or absence of an active site ligand, we address the molecular details of the mechanism that controls the uptake and retention of the substrate. The simulations suggest a modular mechanism in which each moiety of the substrate controls the flexibility of a different protein loop. Furthermore, the calculations indicate that interactions with the substrate diphosphate moiety are especially important for stabilizing the closed active site. This hypothesis is supported with kinetics measurements of site‐directed mutants of T. cruzi UGM. Our results extend our knowledge of UGM dynamics and offer new alternatives for the prospective design of drugs.
Expanding the frontiers of protein–protein modeling: From docking and scoring to binding affinity predictions and other challenges
Authors: Pallara Chiara , Jiménez‐García Brian , Pérez‐Cano Laura , Romero‐Durana Miguel , Solernou Albert , Grosdidier Solène , Pons Carles , Moal Iain H. , Fernandez‐Recio Juan
Published: August 2013

In addition to protein–protein docking, this CAPRI edition included new challenges, like protein–water and protein–sugar interactions, or the prediction of binding affinities and ΔΔG changes upon mutation. Regarding the standard protein–protein docking cases, our approach, mostly based on the pyDock scheme, submitted correct models as predictors and as scorers for 67% and 57% of the evaluated targets, respectively. In this edition, available information on known interface residues hardly made any difference for our predictions. In one of the targets, the inclusion of available experimental small‐angle X‐ray scattering (SAXS) data using our pyDockSAXS approach slightly improved the predictions. In addition to the standard protein–protein docking assessment, new challenges were proposed. One of the new problems was predicting the position of the interface water molecules, for which we submitted models with 20% and 43% of the water‐mediated native contacts predicted as predictors and scorers, respectively. Another new problem was the prediction of protein–carbohydrate binding, where our submitted model was very close to being acceptable. A set of targets were related to the prediction of binding affinities, in which our pyDock scheme was able to discriminate between natural and designed complexes with area under the curve = 83%. It was also proposed to estimate the effect of point mutations on binding affinity. Our approach, based on machine learning methods, showed high rates of correctly classified mutations for all cases. The overall results were highly rewarding, and show that the field is ready to move forward and face new interesting challenges in interactomics. Proteins 2013; 81:2192–2200. © 2013 Wiley Periodicals, Inc.
Band tail filling effect in MBE‐grown ternary MgZnO epitaxial layers with high Mg content
Authors: Karaliūnas Mindaugas , Šukauskas Vilmantas , Kuokštis Edmundas , Ting Shao‐Ying , Huang Jeng‐Jie , Yang C.‐C.
Published: August 2013

In this work, the carrier localization effect is studied in molecular beam epitaxy grown MgZnO epitaxial layers. The photoluminescence (PL) investigation revealed the S ‐shaped PL peak position dependence on temperature. It is usually related to the carrier localization in randomly distributed potential field fluctuations. We have measured double blue‐shift of the PL peak position with increase of temperature for samples with higher (17–30%) Mg content in the alloys.

The two blue‐shifts are attributed to double‐scale potential field fluctuations with different average localization energy. The scanning near optical field microscopy experiment proved the presence of less than 100 nm width Mg rich areas with enhanced PL intensity. The atomic force microscopy and energy dispersive X‐ray diffraction experiments revealed a close relation of structural and optical quality with the evaluated average carriers localization energy. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Defect‐related mechanism of ferromagnetic behaviors for ZnCoO:H films formed by PLD with bias voltage application
Authors: Sasaki Kazuma , Komiyama Takao , Chonan Yasunori , Yamaguchi Hiroyuki , Aoyama Takashi
Published: August 2013

Ferromagnetic behaviors of Co‐doped ZnO films were investigated by using pulsed laser deposition (PLD) with the bias voltage application technique and by changing the partial pressure of oxygen ambient. The 50 V change in the PLD bias voltage caused the oxygen to zinc (O/Zn) ratio in the film to change by about 7%. Ferromagnetic behaviors were observed after the hydrogenation process. As the the O/Zn ratio in the ZnCoO:H films deviated more from the stoichiometric condition, the saturation magnetization (Ms) significantly decreased but sometimes increased. On the other hand, the deviation from the stoichiometric condition (that is the increase in the native defect concentration) significantly changed the carrier concentration. As the carrier concentration (Fermi level) increased, Ms increased first, then decreased, and finally increased again. Thus, the native defects certainly affected the Ms, but only through the shift of the Fermi level.
Study on growth rate of TiO2 nanostructured thin films: simulation by molecular dynamics approach and modeling by artificial neural network
Authors: Bahramian Alireza
Published: August 2013

Effects of the deposition process parameters on the thickness of TiO2 nanostructured film were simulated using the molecular dynamics (MD) approach and modeled by the artificial neural network (ANN) and regression method. Accordingly, TiO2 nanostructured film was prepared experimentally with the sol–gel dip‐coating method. Structural instabilities can be expected, due to short‐ and/or long‐range intermolecular forces, leading to the surface inhomogeneities. In the MD simulation, the Morse potential function was used for the inter‐atomic interactions, and equations of motion for atoms were solved by Verlet algorithm. The effect of the withdrawal velocity, drying temperature and number of deposited layers were studied in order to characterize the film thickness. The results of MD simulations are reasonably consistent with atomic force microscopy, scanning electron microscopy and Dektak surface profiler. Finally, the outputs from experimental data were analyzed by using the ANN in order to investigate the effects of deposition process parameters on the film thickness. In this case, various architectures have been checked using 75% of experimental data for training of the ANN. Among the various architectures, feed‐forward back‐propagation network with trainer training algorithm was found as the best architecture. Based on the R‐squared value, the ANN is better than the regression model in predicting the film thickness. The statistical analysis for those results was then used to verify the fitness of the complex process model. Based on the results, this modeling methodology can explain the characteristics of the TiO2 nanostructured thin film and growth mechanism varying with process conditions. © 2013 The Authors. Surface and Interface Analysis published by John Wiley & Sons Ltd.
Gaussian process modeling for engineered surfaces with applications to Si wafer production
Authors: Plumlee Matthew , Jin Ran , Roshan Joseph V. , Shi Jianjun
Published: August 2013

When producing engineered surfaces, the stochastic portion of the processing greatly affects the overall output quality. We propose a Gaussian process model that accounts for the impact of control variables on the stochastic elements of the produced surfaces. An optimization algorithm is outlined to find the maximum likelihood estimates of the model parameters. A case study involving the thickness surfaces of semiconductor wafers is examined that demonstrates the need for the proposed approach. Copyright © 2013 John Wiley & Sons Ltd
The Subventricular Zone Is Able to Respond to a Demyelinating Lesion After Localized Radiation
Authors: Capilla-Gonzalez Vivian , Guerrero-Cazares Hugo , Bonsu Janice M. , Gonzalez-Perez Oscar , Achanta Pragathi , Wong John , Garcia-Verdugo Jose Manuel , Quiñones-Hinojosa Alfredo
Published: August 2013

Radiation is a common tool in the treatment of brain tumors that induces neurological deficits as a side effect. Some of these deficits appear to be related to the impact of radiation on the neurogenic niches, producing a drastic decrease in the proliferative capacity of these regions. In the adult mammalian brain, the subventricular zone (SVZ) of the lateral ventricles is the main neurogenic niche. Neural stem/precursor cells (NSCs) within the SVZ play an important role in brain repair following injuries. However, the irradiated NSCs' ability to respond to damage has not been previously elucidated. In this study, we evaluated the effects of localized radiation on the SVZ ability to respond to a lysolecithin-induced demyelination of the striatum. We demonstrated that the proliferation rate of the irradiated SVZ was increased after brain damage and that residual NSCs were reactivated. The irradiated SVZ had an expansion of doublecortin positive cells that appeared to migrate from the lateral ventricles toward the demyelinated striatum, where newly generated oligodendrocytes were found. In addition, in the absence of demyelinating damage, remaining cells in the irradiated SVZ appeared to repopulate the neurogenic niche a year post-radiation. These findings support the hypothesis that NSCs are radioresistant and can respond to a brain injury, recovering the neurogenic niche. A more complete understanding of the effects that localized radiation has on the SVZ may lead to improvement of the current protocols used in the radiotherapy of cancer. Stem Cells  2014;32:59–69
Low‐temperature thermochronometry along the Kunlun and Haiyuan Faults, NE Tibetan Plateau: Evidence for kinematic change during late‐stage orogenesis
Authors: Duvall Alison R. , Clark Marin K. , Kirby Eric , Farley Kenneth A. , Craddock William H. , Li Chuanyou , Yuan Dao‐Yang
Published: August 2013

The Tibetan Plateau is a prime example of a collisional orogen with widespread strike‐slip faults whose age and tectonic significance remain controversial. We present new low‐temperature thermochronometry to date periods of exhumation associated with Kunlun and Haiyuan faulting, two major strike‐slip faults within the northeastern margin of Tibet. Apatite and zircon (U‐Th)/He and apatite fission‐track ages, which record exhumation from ~2 to 6 km crustal depths, provide minimum bounds on fault timing. Results from Kunlun samples show increased exhumation rates along the western fault segment at circa 12–8 Ma with a possible earlier phase of motion from ~30–20 Ma, along the central fault segment at circa 20–15 Ma, and along the eastern fault segment at circa 8–5 Ma. Combined with previous studies, our results suggest that motion along the Haiyuan fault may have occurred as early as ~15 Ma along the western/central fault segment before initiating at least by 10–8 Ma along the eastern fault tip. We relate an ~250 km wide zone of transpressional shear to synchronous Kunlun and Haiyuan fault motion and suggest that the present‐day configuration of active faults along the northeastern margin of Tibet was likely established since middle Miocene time. We interpret the onset of transpression to relate to the progressive confinement of Tibet against rigid crustal blocks to the north and expansion of crustal thickening to the east during the later stages of orogen development.
Testing Iberian kinematics at Jurassic‐Cretaceous times
Authors: Neres M. , Miranda J. M. , Font E.
Published: August 2013

Paleogeographic reconstructions of Iberia at the Mesozoic are still a matter of debate. The incompatibility between kinematic models and paleomagnetic data older than 120 Ma is a major problem for which no cause has yet been determined. Here we use a new method to investigate the origin of this misfit. We solve the inverse problem of finding the Euler poles that fit paleomagnetic poles with the Global Apparent Polar Wander Path (GAPWP) and then test their implications on Iberian reconstructions. We show that Iberian poles from the Early Cretaceous (mean poles for 123 and 130 Ma) are incompatible with the GAPWP, bringing into question their validity. Contrarily, Late Jurassic data (mean pole at 151 Ma) are compatible with the GAPWP and, thus, can be considered reliable. Based on these results, we propose a new magnetic reconstruction of Iberia and surrounding plates at ~150 Ma (M22 anomaly). This work provides new constraints for the kinematic evolution of Iberia during Jurassic‐Cretaceous. However, the development of a detailed and consensual model for the kinematic evolution of Iberia is dependent on the acquisition of new, high‐quality paleomagnetic data and a reevaluation of seafloor magnetic anomalies.
Optimizing FEG‐SEM combined with an SDD EDX system for automated GSR analysis
Authors: Izraeli Elad S. , Tsach Tsadok , Levin Nadav
Published: August 2013

Gunshot residue (GSR) analysis by scanning electron microscopy/energy dispersive x‐ray spectrometry (SEM/EDX) is routinely performed in forensic science laboratories. At the end of 2011, a field emission gun (FEG)‐SEM was installed at the authors' laboratory for this type of examination. Following the installation of the FEG‐SEM, an extensive process was conducted, in order to determine the optimal operating parameters of this instrument for GSR analysis. Because the nature of synthetic GSR samples (such as the European Network of Forensic Science Institutes GSR2011 proficiency test sample) is significantly different from casework samples, it was decided not to use them for this purpose. Instead, a GSR casework sample, previously analyzed by tungsten‐filament SEM as part of the laboratory's routine examinations, was selected. This sample was repeatedly analyzed (more than 200 times), under different operating conditions. The main parameters that were examined for the FEG‐SEM were the electron source accelerating voltage, the backscattered electrons image acquisition time, the magnification, the backscattered electrons image resolution, and the energy‐dispersive X‐ray spectrometry acquisition time. The smallest detected feature was calculated by the software, based on the set image resolution and magnification. For each set of parameters, the detected GSR particles were recorded, in addition to the total number of detected particles and the time taken for the run. It was found that for a given smallest detected feature, the effective search conditions were higher magnification and lower number of pixels per line. The present work includes a detailed description of the optimization process and its results. The process utilized in this work is applicable for other laboratories conducting similar type of GSR analysis as well. Copyright © 2013 John Wiley & Sons, Ltd.
Mutation of the CgPDR16 gene attenuates azole tolerance and biofilm production in pathogenic Candida glabrata
Authors: Culakova Hana , Dzugasova Vladimira , Perzelova Jana , Gbelska Yvetta , Subik Julius
Published: August 2013

The PDR16 gene encodes the homologue of Sec14p, participating in protein secretion, regulation of lipid synthesis and turnover in vivo and acting as a phosphatidylinositol transfer protein in vitro. This gene is also involved in the regulation of multidrug resistance in Saccharomyces cerevisiae and pathogenic yeasts. Here we report the results of functional analysis of the CgPDR16 gene, whose mutation has been previously shown to enhance fluconazole sensitivity in Candida glabrata mutant cells. We have cloned the CgPDR16 gene, which was able to complement the pdr16Δ mutation in both C. glabrata and S. cerevisiae. Along with fluconazole, the pdr16Δ mutation resulted in increased susceptibility of mutant cells to several azole antifungals without changes in sensitivity to polyene antibiotics, cycloheximide, NQO, 5‐fluorocytosine and oxidants inducing the intracellular formation of reactive oxygen species. The susceptibility of the pdr16Δ mutant strain to itraconazole and 5‐fluorocytosine was enhanced by CTBT [7‐chlorotetrazolo(5,1‐c)benzo(1,2,4)triazine] inducing oxidative stress. The pdr16Δ mutation increased the accumulation of rhodamine 6G in mutant cells, decreased the level of itraconazole resistance caused by gain‐of‐function mutations in the CgPDR1 gene, and reduced cell surface hydrophobicity and biofilm production. These results point to the pleiotropic phenotype of the pdr16Δ mutant and support the role of the CgPDR16 gene in the control of drug susceptibility and virulence in the pathogenic C. glabrata. Copyright © 2013 John Wiley & Sons, Ltd.
Alpha‐1 Couples: Interpersonal and Intrapersonal Predictors of Spousal Communication and Stress
Authors: Smith Rachel A. , Wienke Sara , Coffman Donna L.
Published: August 2013

Couples often discuss genetic test results, and then manage their implications together. This interdependence can lead to common, shared experiences, similar intrapersonal processes to manage shared stressors, or interpersonal influences between spouses, leading to different outcomes. This study sought to reveal the intracouple, intrapersonal, and interpersonal influences of genetic stigma and negative feelings on spousal communication and perceived stress with 50 couples in which one spouse is a member of a genetic disease registry. The results were analyzed with dyadic analysis, including multilevel modeling. The findings showed that registered members and their spouses were not statistically different in their mean levels of perceived genetic stigma, negative feelings about alpha‐1 antitrypsin deficiency (AATD), conversations with each other about the AATD test results, and their perceived stress. The findings also showed that their intracouple consistencies were not high, and their intrapersonal and interpersonal influences on communication and stress differed. The social implications of genetic research at the interpersonal level are discussed.
Kinetics of Isothermal Crystallization of Hydrogenated Castor Oil‐in‐Water Emulsions
Authors: Yang Dingzheng , Hrymak Andrew N. , Kedzior Stephanie
Published: August 2013

Kinetics of isothermal crystallization of hydrogenated castor oil in water emulsions exhibiting multiple crystal morphologies have been studied experimentally by DSC and polarized light microscopy. The induction time of nucleation increases with the increase of the isothermal temperature under which crystallization occurred. Crystal growth has been observed by microscopy showing that both crystal morphologies, fibers and rosettes, grow linearly at the initial stage of crystallization and then slow down to reach a plateau value. The Avrami model, which has been widely used in kinetics studies of triacylglycerol systems, was employed to fit experimental results at different isothermal temperatures. It was found that experimental trends could be captured by introducing the volume fraction of each type of morphology into three‐dimensional and one‐dimensional full Avrami models.
Das Lebensende alter Menschen aus multidisziplinärer Sicht
Authors: Kruse Andreas
Published: August 2013

Einleitung

Die Analyse der Lebenssituation des alten Menschen am Ende seines Lebens erfordert eine Integration von Theorien und Befunden aus unterschiedlichen Disziplinen. Für die Genetik steht vor allem die Häufung molekularer Schädigungen aufgrund von Zellschädigungen und abnehmender genetischer Kontrolle im Zentrum, für die Medizin chronische Erkrankungen (nicht selten assoziiert mit Demenz) und Gebrechlichkeit, für die Psychologie die Verbindung von Verletzlichkeit mit seelisch-geistigen Entwicklungspotenzialen, für die Soziologie die Weitergabe von Erfahrungen in einer Generationenfolge. Diese Perspektiven werden in dem Beitrag erörtert.