bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis by flow cytometry of calcium influx kinetics in peripheral lymphocytes of patients with rheumatoid arthritis
Authors: Bajnok Anna , Kaposi Ambrus , Kovács László , Vásárhelyi Barna , Balog Attila , Toldi Gergely
Published: January 2013

The transient increase of the cytoplasmic free calcium level in T lymphocytes plays a key role in initiating and maintaining the autoimmune reaction in rheumatoid arthritis (RA). Kv1.3 and IKCa1 potassium channels are important regulators of the maintenance of calcium influx during lymphocyte activation and present a possible target for selective immunomodulation. We aimed to compare peripheral T lymphocyte calcium influx kinetics upon activation in patients with recently diagnosed and established RA, and to demonstrate the differences in analysis of kinetic flow cytometry data when using two different algorithms. We took peripheral blood samples from nine patients with recently diagnosed and six patients with established RA. We evaluated calcium influx kinetics following activation in CD4, Th1, Th2, and CD8 cells applying an approach based on smoothing of median fluorescence values (FlowJo) and an algorithm based on function fitting (FacsKin). We assessed the sensitivity of the above subsets to specific inhibition of the Kv1.3 and IKCa1 potassium channels. Th2 cells of patients with established RA react slower to activating stimuli, whereas CD8 cells show a faster reaction than in patients with recently diagnosed RA. While initially Th1 cells are less sensitive to the inhibition of Kv1.3 and IKCa1 channels in RA, their sensitivity increases along with the duration of the disease. With the algorithm of function fitting instead of smoothing, more statistically significant differences of potassium channel inhibition between the two RA groups could be demonstrated. The function fitting algorithm applied by FacsKin is suitable to provide a common basis for evaluating and comparing flow cytometry kinetic data. © 2013 International Society for Advancement of Cytometry
Folate, Homocysteine and the Cardiac Neural Crest
Authors: Rosenquist Thomas H.
Published: January 2013

Congenital heart defects (CHD) are the most common congenital defects worldwide, and perigestational folate supplementation (PFS) is the most effective large‐scale intervention to date for reducing CHD. This review is based upon the following premises: that the majority of CHD result from disruption of development of the cardiac neural crest (CNC); and that the CNC is highly responsive to folate and homocysteine. The following roles of folate are discussed in relation to CNC development: one‐carbon metabolism in support of mitosis and gene methylation; and gene regulation via direct activity of the folate receptor. The following roles of hyperhomocysteinemia are discussed in the same context: increased oxidative stress; disruption of gene methylation; homocysteinylation of key proteins; and NMDA receptor binding. It is proposed that well‐focused advances in folate‐CNC research could lead to development of strategies, in addition to PFS, to facilitate normal CNC and heart development, and thereby further reduce CHD. Developmental Dynamics 242:201–218, 2013. © 2013 Wiley Periodicals, Inc.
Tbx1 is required for second heart field proliferation in zebrafish
Authors: Nevis Kathleen , Obregon Pablo , Walsh Conor , Guner‐Ataman Burcu , Burns C. Geoffrey , Burns Caroline E.
Published: January 2013

Background: The mammalian outflow tract (OFT) and primitive right ventricle arise by accretion of newly differentiated cells to the arterial pole of the heart tube from multi‐potent progenitor cells of the second heart field (SHF). While mounting evidence suggests that the genetic pathways regulating SHF development are highly conserved in zebrafish, this topic remains an active area of investigation. Results: Here, we extend previous observations demonstrating that zebrafish tbx1 (van gogh, vgo) mutants show ventricular and OFT defects consistent with a conserved role in SHF‐mediated cardiogenesis. Surprisingly, we reveal through double in situ analyses that tbx1 transcripts are excluded from cardiac progenitor cells and differentiated cardiomyocytes, suggesting a non‐autonomous role in SHF development. Further, we find that the diminutive ventricle in vgo animals results from a 25% decrease in cardiomyocyte number that occurs subsequent to heart tube stages. Lastly, we report that although SHF progenitors are specified in the absence of Tbx1, they fail to be maintained due to compromised SHF progenitor cell proliferation. Conclusions: These studies highlight conservation of Tbx1 function in zebrafish SHF biology. Developmental Dynamics 242:540–549, 2013. © 2013 Wiley Periodicals, Inc.
Intraspecific variation buffers projected climate change impacts onPinus contorta
Authors: Oney Brian , Reineking Björn , O'Neill Gregory , Kreyling Juergen
Published: January 2013

Species distribution modeling (SDM) is an important tool to assess the impact of global environmental change. Many species exhibit ecologically relevant intraspecific variation, and few studies have analyzed its relevance forSDM. Here, we compared threeSDMtechniques for the highly variable speciesPinus contorta. First, applying a conventionalSDMapproach, we used MaxEnt to model the subject as a single species (species model), based on presence–absence observations. Second, we used MaxEnt to model each of the three most prevalent subspecies independently and combined their projected distributions (subspecies model). Finally, we used a universal growth transfer function (UTF), an approach to incorporate intraspecific variation utilizing provenance trial tree growth data. Different model approaches performed similarly when predicting current distributions. MaxEnt model discrimination was greater (AUC– species model: 0.94, subspecies model: 0.95,UTF: 0.89), but theUTFwas better calibrated (slope and bias – species model: 1.31 and −0.58, subspecies model: 1.44 and −0.43,UTF: 1.01 and 0.04, respectively). Contrastingly, for future climatic conditions, projections of lodgepole pine habitat suitability diverged. In particular, when the species' intraspecific variability was acknowledged, the species was projected to better tolerate climatic change as related to suitable habitat without migration (subspecies model: 26% habitat loss orUTF: 24% habitat loss vs. species model: 60% habitat loss), and given unlimited migration may increase amount of suitable habitat (subspecies model: 8% habitat gain orUTF: 12% habitat gain vs. species model: 51% habitat loss) in the climatic period 2070–2100 (SRESA2 scenario,HADCM3). We conclude that models derived from within‐species data produce different and better projections, and coincide with ecological theory. Furthermore, we conclude that intraspecific variation may buffer against adverse effects of climate change. A key future research challenge lies in assessing the extent to which species can utilize intraspecific variation under rapid environmental change.
A quantitative trait locus analysis of personality in wild bighorn sheep
Authors: Poissant J. , Réale D. , Martin J.G.A. , Festa‐Bianchet M. , Coltman D.W.
Published: January 2013

Personality, the presence of persistent behav105
ioral differences among individuals over time or contexts, potentially has important ecological and evolutionary consequences. However, a lack of knowledge about its genetic architecture limits our ability to understand its origin, evolution, and maintenance. Here, we report on a genome‐wide quantitative trait locus (QTL) analysis for two personality traits, docility and boldness, in free‐living female bighorn sheep from Ram Mountain, Alberta, Canada. Our variance component linkage analysis based on 238 microsatellite loci genotyped in 310 pedigreed individuals identified suggestive docility and boldness QTL on sheep chromosome 2 and 6, respectively. A lack of QTL overlap indicated that genetic covariance between traits was not modulated by pleiotropic effects at a major locus and may instead result from linkage disequilibrium or pleiotropic effects at QTL of small effects. To our knowledge, this study represents the first attempt to dissect the genetic architecture of personality in a free‐living wildlife population, an important step toward understanding the link between molecular genetic variation in personality and fitness and the evolutionary processes maintaining this variation.
Foraging by forest ants under experimental climatic warming: a test at two sites
Authors: Stuble Katharine L. , Pelini Shannon L. , Diamond Sarah E. , Fowler David A. , Dunn Robert R. , Sanders Nathan J.
Published: January 2013

Climatic warming is altering the behavior of individuals and the composition of communities. However, recent studies have shown that the impact of warming on ectotherms varies geographically: species at warmer sites where environmental temperatures are closer to their upper critical thermal limits are more likely to be negatively impacted by warming than are species inhabiting relatively cooler sites. We used a large‐scale experimental temperature manipulation to warm intact forest ant assemblages in the field and examine the impacts of chronic warming on foraging at a southern (North Carolina) and northern (Massachusetts) site in eastern North America. We examined the influence of temperature on the abundance and recruitment of foragers as well as the number of different species observed foraging. Finally, we examined the relationship between the mean temperature at which a species was found foraging and the critical thermal maximum temperature of that species, relating functional traits to behavior. We found that forager abundance and richness were related to the experimental increase in temperature at the southern site, but not the northern site. Additionally, individual species responded differently to temperature: some species foraged more under warmer conditions, whereas others foraged less. Importantly, these species‐specific responses were related to functional traits of species (at least at the Duke Forest site). Species with higher critical thermal maxima had greater forager densities at higher temperatures than did species with lower critical thermal maxima. Our results indicate that while climatic warming may alter patterns of foraging activity in predictable ways, these shifts vary among species and between sites. More southerly sites and species with lower critical thermal maxima are likely to be at greater risk to ongoing climatic warming.
Connectivity in a pond system influences migration and genetic structure in threespine stickleback
Authors: Seymour Mathew , Räsänen Katja , Holderegger Rolf , Kristjánsson Bjarni K.
Published: January 2013

Neutral genetic structure of natural populations is primarily influenced by migration (the movement of individuals and, subsequently, their genes) and drift (the statistical chance of losing genetic diversity over time). Migration between populations is influenced by several factors, including individual behavior, physical barriers, and environmental heterogeneity among populations. However, drift is expected to be stronger in populations with low immigration rate and small effective population size. With the technological advancement in geological information systems and spatial analysis tools, landscape genetics now allows the development of realistic migration models and increased insight to important processes influencing diversity of natural populations. In this study, we investigated the relationship between landscape connectivity and genetic distance of threespine stickleback (Gasterosteus aculeatus) inhabiting a pond complex in Belgjarskógur, Northeast Iceland. We used two landscape genetic approaches (i.e., least‐cost‐path and isolation‐by‐resistance) and asked whether gene flow, as measured by genetic distance, was more strongly associated with Euclidean distance (isolation‐by‐distance) or with landscape connectivity provided by areas prone to flooding (as indicated byCarexsp. cover)? We found substantial genetic structure across the study area, with pairwise genetic distances among populations (DPS) ranging from 0.118 to 0.488. Genetic distances among populations were more strongly correlated with least‐cost‐path and isolation‐by‐resistance than with Euclidean distance, whereas the relative contribution of isolation‐by‐resistance and Euclidian distance could not be disentangled. These results indicate that migration among stickleback populations occurs via periodically flooded areas. Overall, this study highlights the importance of transient landscape elements influencing migration and genetic structure of populations at small spatial scales.
Mapping the Spin State in Spin‐Crossover Complex Assemblies: Current‐Imaging Tunnelling Spectroscopy (CITS)
Authors: Grohmann Andreas , Haryono Marco , Student Katja , Müller Paul , Stocker Michael
Published: January 2013

This microreview highlights recent techniques used to determine the spin state at or around room temperature in nanoscale objects composed of iron(II) spin‐crossover complexes. Complexes have been studied in the form of thin films, nanoparticles, single molecules or oligomolecular aggregates. Three approaches are presented: Surface plasmon polariton resonance in films on Ti/Au substrates, the determination of single‐particle current–voltage characteristics between gold electrodes, and current‐imaging tunnelling spectroscopy performed on highly oriented pyrolytic graphite‐adsorbed strings of oligonuclear, bead‐like complex aggregates.
Inherently Chiral Resorcin[4]arenes with Urea and Amide Side Arms: Synthesis, Structure and Chiral Recognition
Authors: Wiegmann Sebastian , Fukuhara Gaku , Neumann Beate , Stammler Hans‐Georg , Inoue Yoshihisa , Mattay Jochen
Published: January 2013

Starting from an inherently chiral aminomethyl‐substituted resorcin[4]arene, a series of urea and amide derivatives were synthesized; these new functionalities extend the macrocycle cavity and introduce new opportunities for chiral recognition. A pair of diastereomeric macrocycles was obtained by introducing (S)‐(–)‐1‐phenylethyl‐urea functionalities. Chiral recognition capabilities of the diastereomeric hosts were investigated by circular dichroism spectral titration to reveal modest R/S selectivities of up to 1.4 for mandelic acid and other related carboxylic guests.
Outlook—natural gas prices: Wall street marginally more optimistic about natural gas prices
Authors: Willett Robert E.
Published: January 2013

The last time I did one of these surveys,1 the sky was falling and some were even predicting brief periods for natural gas prices equal to zero, as oil producers would not even find places to store their associated natural gas. That zero did not happen, nor did gas prices “break the buck,” but they did find their way below the two‐dollar mark.
Association between depression and anxiety on blood pressure dysregulation and pulse in the Health and Retirement Study
Authors: Gould Christine E. , Beaudreau Sherry A.
Published: January 2013

Objective

Extreme blood pressure (BP) values are associated with symptoms of anxiety and depression, but findings from studies are conflicting. The present study tested linear and curvilinear models of the association between anxiety and depression symptoms and BP in the Health and Retirement Study. The relationship between anxiety and depressive symptoms and pulse was also tested.

Method

Participants were aged 50 to 104 (N = 4179) and completed the Health and Retirement Study Psychosocial Questionnaire and Physical Measurements in 2006. BP and pulse were measured using an automated cuff. The means of three BP and pulse measurements taken 45 to 60 s apart were used. Depressive and anxiety symptoms were measured with brief forms of the Center for Epidemiological Studies Depression Scale and Beck Anxiety Inventory.

Results

Ordinal regression analyses examined the relationship between BP and anxiety and depressive symptoms. In models adjusted for medical illness and medications, anxiety was associated with systolic hypotension, and depression was associated with diastolic hypotension. Higher pulse was associated with depression but not anxiety.

Conclusions

Findings suggest that BP dysregulation, specifically hypotension, may be a useful indicator of anxiety and depression. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.
Impact of climate change on diffuse pollutant fluxes at the watershed scale
Authors: Ahmadi Mehdi , Records Rosemary , Arabi Mazdak
Published: January 2013

This study aims to assess watershed‐scale impacts of changing climate on sediment, phosphorus, nitrogen and pesticide (atrazine) fluxes over the 21st century at the watershed scale. In particular, changes in dissolved and particulate forms of water quality constituents in response to climate change are investigated. The hydrologic model Soil and Water Assessment Tool was calibrated and evaluated in a primarily agricultural watershed in the Midwestern United States to simulate hydrologic and water quality processes on a daily basis over the 2015–2099 time horizon. The model was then driven with 112 distinct statistically downscaled climate projections representing Intergovernmental Panel on Climate Change Special Report on Emissions Scenarios (IPCC SRES) low, moderate and high greenhouse gas emission scenarios. Projected hydrologic and water quality responses were categorized according to the three IPCC SRES emission scenarios for summarizing and synthesizing results over early‐century (2015–2034), mid‐century (2045–2064) and late‐century (2080–2099) assessment. Results revealed clear warming trends in the study area, whereas small increases in precipitation were predicted. Streamflow, sediment and total nutrient loads did not differ noticeably between assessment periods. However, the proportion of dissolved to total nutrients increased significantly from early‐century to late‐century periods. With the exception of total atrazine in the mid‐century period, predicted pollutant loads for a given assessment period did not differ between emission pathways for a given assessment period. Changes in pollutant fluxes showed pronounced monthly variability. The projected increase in readily available forms of nutrients has important implications for the ecological health of water systems and management of drinking water supplies. Copyright © 2013 John Wiley & Sons, Ltd.
Catchment properties, function, and conceptual model representation: is there a correspondence?
Authors: Fenicia Fabrizio , Kavetski Dmitri , Savenije Hubert H. G. , Clark Martyn P. , Schoups Gerrit , Pfister Laurent , Freer Jim
Published: January 2013

This study investigates the possible correspondence between catchment structure, as represented by perceptual hydrological models developed from fieldwork investigations, and mathematical model structures, selected on the basis of reproducing observed catchment hydrographs. Three Luxembourgish headwater catchments are considered, where previous fieldwork suggested distinct flow‐generating mechanisms and hydrological dynamics. A set of lumped conceptual model structures are hypothesized and implemented using the SUPERFLEX framework. Following parameter calibration, the model performance is examined in terms of predictive accuracy, quantification of uncertainty, and the ability to reproduce the flow–duration curve signature. Our key research question is whether differences in the performance of the conceptual model structures can be interpreted based on the dominant catchment processes suggested from fieldwork investigations. For example, we propose that the permeable bedrock and the presence of multiple aquifers in the Huewelerbach catchment may explain the superior performance of model structures with storage elements connected in parallel. Conversely, model structures with serial connections perform better in the Weierbach and Wollefsbach catchments, which are characterized by impermeable bedrock and dominated by lateral flow. The presence of threshold dynamics in the Weierbach and Wollefsbach catchments may favour nonlinear models, while the smoother dynamics of the larger Huewelerbach catchment were suitably reproduced by linear models. It is also shown how hydrologically distinct processes can be effectively described by the same mathematical model components. Major research questions are reviewed, including the correspondence between hydrological processes at different levels of scale and how best to synthesize the experimentalist's and modeller's perspectives. Copyright © 2013 John Wiley & Sons, Ltd.
Full supervised learning for osteoporosis diagnosis using micro‐CT images
Authors: Xu Yan , Li Dianshi , Chen Qinlang , Fan Yubo
Published: January 2013

Early osteoporosis diagnosis is of important significance for reducing fracture risk. Image analysis provides a new perspective for noninvasive diagnosis in recent years. In this article, we propose a novel method based on machine‐learning method performed on micro‐CT images todiagnose osteoporosis. The aim of this work is to find a way to more effectively and accurately diagnose osteoporosis on which many methods have been proposed and practiced. In this method, in contrast to the previously proposed methods in which features are analyzed individually, several features are combined to build a classifier for distinguishing osteoporosis group and normal group. Twelve features consisting of two groups are involved in our research, including bone volume/total volume (BV/TV), bone surface/bone volume (BS/BV), trabecular number (Tb.N), obtained from the software of micro‐CT, and other four features from volumetric topological analysis (VTA). Support vector machine (SVM) method and k‐nearest neighbor (kNN) method are introduced to create classifiers with these features due to their excellent performances on classification. In the experiment, 200 micro‐CT images are used in which half are from osteoporosis patients and the rest are from normal people. The performance of the obtained classifiers is evaluated by precision, recall, and F‐measure. The best performance with precision of 100%, recall of 100%, and F‐measure of 100% is acquired when all the features are included. The satisfying result demonstrates that SVM and kNN are effective for diagnosing osteoporosis with micro‐CT images. Microsc. Res. Tech. 76:333–341, 2013. © 2013 Wiley Periodicals, Inc.
Serious safety events: Getting to Zero™
Authors: Hoppes Michelle , Mitchell Jacque L. , Venditti Ellen Grady , Bunting, Jr. Robert F.
Published: January 2013

To advance the goal of Getting to Zero and eliminating preventable harm, ASHRM is providing guidance for defining, investigating, and measuring serious safety events. The first step in this process is the recommendation for a common and standardized definition. A common definition for a serious safety event facilitates timely detection, rapid action, and future prevention. This paper outlines that definition, provides a skill‐based model for investigation, and explains a clear plan for how to conduct the investigation. A measurement system is described to determine the frequency of SSEs and comparison methods to determine events prevented, potential lives saved, and methods to demonstrate financial loss control. These methods and approach are consistent with ASHRM's core values and mission, which is safe and trusted healthcare.
TeamSTEPPS and patient safety in healthcare
Authors: Sheppard Faye , Williams Marcie , Klein Victor R.
Published: January 2013

Communication problems in healthcare are considered to be a leading cause of medical errors and often the root cause of sentinel events. This article will review the implementation of TeamSTEPPS in the two large health systems. The challenges in the implementation process, the successes, failures, and the obstacles will be discussed. Comparisons between the systems as well as lessons learned after implementation will be reviewed to enable hospitals and health systems to implement and sustain a successful TeamSTEPPS program.
Hypothermia and xenon: Novel noble guardians in hypoxic–ischemic encephalopathy?
Authors: Lobo N. , Yang B. , Rizvi M. , Ma Daqing
Published: January 2013

The financial and emotional cost of caring for children affected by hypoxic–ischemic encephalopathy (HIE) is enormous, and developing therapeutic strategies to prevent or ameliorate the severity of HI‐related brain injury remains a major priority. In the past, supportive management was the mainstay of treatment, but considerable progress has been made in identifying and developing neuroprotective strategies for neonates with HIE. The neuroprotective effects of several therapeutic modalities, including anticonvulsants, hyperbaric oxygen, and erythropoietin, have been investigated. This Mini‐Review discusses the potential of two neuroprotective agents that show the most promise thus far: xenon and therapeutic hypothermia. The pathogenesis of HIE involves more than one pathway, and intervening in multiple pathways may yield better results than interventions targeted at a single cellular level. The therapeutic benefits of xenon and hypothermia have been confirmed in several in vitro and in vivo studies, both individually and in combination. With promising results being reported, it is, perhaps, only a matter of time before xenon and hypothermia become established as a standard care for neonates with HIE. © 2013 Wiley Periodicals, Inc.
Effects of blast‐induced neurotrauma on the nucleus accumbens
Authors: Sajja Venkata Siva Sai Sujith , Galloway Matthew , Ghoddoussi Farhad , Kepsel Andrea , VandeVord Pamela
Published: January 2013

Blast‐induced neurotrauma (BINT) leads to deterioration at the cellular level, with adverse cognitive and behavioral outcomes. The nucleus accumbens (NAC) plays an important role in reward, addiction, aggression, and fear pathways. To identify the molecular changes and pathways affected at an acute stage in the NAC, this study focused on a time course analysis to determine the effects of blast on neurochemical and apoptotic pathways. By using a rodent model of BINT, acute damage to the NAC was assessed by proton magnetic resonance spectroscopy (1H‐MRS), high‐performance liquid chromatography, immunohistochemistry, and Western blotting. The results demonstrated ongoing neuroprotective effects from elevated levels of Bcl‐2, an antiapoptotic marker, at 24 hr and N‐acetyl aspartate glutamate at 48 hr following blast exposure. Selective loss of serotonin levels at 24 hr, increased levels of inflammation (elevated glycerophosphocholine at 48 and 72 hr), and increased levels of glial fibrillary acidic protein were also observed at 24 and 48 hr, leading to disruptive energy status. Furthermore, active cell death was indicated by the increased levels of the apoptotic marker Bax, decreased actin levels, and signs excitotoxicity (glutamate/creatine). In addition, increased evels of caspase‐3, an apoptotic marker, confirm active cell death in NAC. It is hypothesized that blast overpressure causes inflammation and neurochemical changes that trigger apoptosis in NAC. This cascade of events may lead to stress‐related behavioral outcomes and psychiatric sequelae. © 2013 Wiley Periodicals, Inc.
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

Type 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

This 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

A 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.

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Perturbation of a nonautonomous problem in
Authors: Capelato E. , Schiabel‐Silva K. , Silva R.P.
Published: January 2013

In this paper, we prove a stability result about the asymptotic dynamics of a perturbed nonautonomous evolution equation in governed by a maximal monotone operator. Copyright © 2013 John Wiley & Sons, Ltd.
Phosphoproteome analysis of an early onset mouse model (TgCRND8) of Alzheimer's disease reveals temporal changes in neuronal and glia signaling pathways
Authors: Wang Fangjun , Blanchard Alexandre P. , Elisma Fred , Granger Matthew , Xu Hongbin , Bennett Steffany A. L. , Figeys Daniel , Zou Hanfa
Published: January 2013

Sustained exposure to soluble amyloid β (Aβ42) oligomers is predicted to impair synaptic function in the hippocampal‐entorhinal circuit, signaling synaptic loss and precipitating cognitive impairment in Alzheimer's disease. Regional changes in overall patterns of protein phosphorylation are likely crucial to promote transition from a presymptomatic to a symptomatic state in response to accumulating Aβ42. Here, we used unbiased proteomic approaches to compare the phosphoproteome of presymptomatic and symptomatic TgCRND8 mice and identify network disruptions in signaling pathways implicated in the manifestation of behavioral indices of learning and memory impairment. Phosphopeptide enrichment with triple isotopic dimethylation labeling combined with online multidimensional separation and MS was used to profile phosphoproteome changes in 2‐ and 6‐month‐old TgCRND8 mice and congenic littermate controls. We identified 1026 phosphopeptides representing 1168 phosphorylation sites from 476 unique proteins. Of these, 595 phosphopeptides from 293 unique proteins were reliably quantified and 139 phosphopeptides were found to change significantly in the hippocampus of TgCRND8 mice following conversion from a presymptomatic to a symptomatic state.
A Relational Typology of Project Management Offices
Authors: Müller Ralf , Glückler Johannes , Aubry Monique
Published: January 2013

This explorative article develops a relational typology of PMOs based on their roles with stakeholders. A multi-case study was used to identify the roles of PMOs in multiple-PMO settings. A three-dimensional role space allows locating the complex relational profiles that PMOs take on with respect to their stakeholders in practice. Superordinate, subordinate, and coequal roles were identified in a framework of servicing, controlling, and partnering in organizations. While servicing (subordinate role profile) and controlling (superordinate role profile) support organizational effectiveness and exploitation of knowledge, partnering (coequal role profile) creates the slack necessary for potential exploration of new knowledge.
“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

Biomaterials 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.

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Prediction of phenotypes of missense mutations in human proteins from biological assemblies
Authors: Wei Qiong , Xu Qifang , Dunbrack Roland L.
Published: January 2013

Single 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

We 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

An 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

In 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

The 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

Enhanced 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

In 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.