bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reducing the dimensionality of the protein‐folding search problem
Authors: Chellapa George D. , Rose George D. 
Published: June 2012

AbstractHow does a folding protein negotiate a vast, featureless conformational landscape and adopt its native structure in biological real time? Motivated by this search problem, we developed a novel algorithm to compare protein structures. Procedures to identify structural analogs are typically conducted in three‐dimensional space: the tertiary structure of a target protein is matched against each candidate in a database of structures, and goodness of fit is evaluated by a distance‐based measure, such as the root‐mean‐square distance between target and candidate. This is an expensive approach because three‐dimensional space is complex. Here, we transform the problem into a simpler one‐dimensional procedure. Specifically, we identify and label the 11 most populated residue basins in a database of high‐resolution protein structures. Using this 11‐letter alphabet, any protein's three‐dimensional structure can be transformed into a one‐dimensional string by mapping each residue onto its corresponding basin. Similarity between the resultant basin strings can then be evaluated by conventional sequence‐based comparison. The disorder → order folding transition is abridged on both sides. At the onset, folding conditions necessitate formation of hydrogen‐bonded scaffold elements on which proteins are assembled, severely restricting the magnitude of accessible conformational space. Near the end, chain topology is established prior to emergence of the close‐packed native state. At this latter stage of folding, the chain remains molten, and residues populate natural basins that are approximated by the 11 basins derived here. In essence, our algorithm reduces the protein‐folding search problem to mapping the amino acid sequence onto a restricted basin string.
Metal organic frameworks for drug delivery and environmental remediation: A molecular docking approach
Authors: Rodrigues Marcelo O. , de Paula Marcos V. , Wanderley Kaline A. , Vasconcelos Iane B. , Alves Severino , Soares Thereza A. 
Published: June 2012

AbstractMetal organic frameworks (MOFs) are promising materials for the controlled release of drugs. Molecular docking methods have been successfully applied to the fast screening of lead compounds starting from the three‐dimensional structure of proteins. We apply molecular docking calculations to MOFs as a fast approach to distinguish between good and poor drug candidates for incorporation. The approach can predict the binding behavior of different guest molecules in agreement to experimental measurements using X‐ray powder diffraction, thermogravimetry–differential thermal analysis, and UV–vis spectroscopy techniques. It can also identify the overall binding mode of tested compounds and estimate binding affinity differences above the error of 2 kcal mol−1 or 8.4 kJ mol−1 associated with the empirical scoring function used in the calculations. This exploratory investigation indicates that the molecular docking technique may be useful in the fast screening of drug candidates for adsorption to coordination polymers for controlled drug delivery and/or environmental remediation. © 2012 Wiley Periodicals, Inc.
Density functional studies of the structural variety of the Cu2S2 core of the CuA site
Authors: Takano Yu , Okuyama Orio , Shigeta Yasuteru , Nakamura Haruki 
Published: June 2012

AbstractThe biological CuA site functions as the proximate electron‐transfer intermediate from an electron source in cytochrome c oxidase and nitrous oxide reductase. It provides a characteristic electronic structure for rapid electron transfer. In the CuA site, two copper ions bridged with two bridging cysteinyl thiolate groups form an almost planar Cu2S2 core. Each copper ion is coordinated equatorially with a histidine residue and axially with either a methionine residue or a carbonyl group of the polypeptide backbone. Three‐dimensional X‐ray crystallographic structures show that the structural variety of the Cu2S2 core of the CuA site with a short CuCu distance of 2.34–2.59 Å and a SS distance of 3.76–4.24 Å. In the present study, we address the origin of the structural variety of the Cu2S2 core of the CuA site, using the density functional theory. Our computation demonstrated that we found the structural dependence of the energy gap between the σ and πu oxidized states, the ionization potentials, and total energies, though the structural variety is insensitive to the shape and symmetry of the σ and πu redox active molecular orbitals and the πu ground state of the Cu2S2 core of the CuA site. In addition, the σ oxidized state is more robust to the structural changes in ionization potentials and total energies than the πu oxidized state. This robustness indicates the small reorganization energy in the redox reaction between σ oxidized and reduced states of the CuA site. The optimized Cu2S2 cores have almost same structures in all the states, indicating that surrounding proteins are responsible for the structural variety of the Cu2S2 core of the CuA site. © 2012 Wiley Periodicals, Inc.
A material design on new sodium ion conductor for sodium–sulfur battery. I. NaAlO(CN)2 and NaxAl1‐x/3(CN)3 perovskite
Authors: Onishi Taku 
Published: June 2012

AbstractWe theoretically designed the new sodium ion‐conductors such as NaAlO(CN)2 and NaxAl1‐x/3(CN)3 perovskite. From the viewpoint of the energetics and bonding, the sodium ion‐conductive mechanism was investigated for LaAlO3, NaAlO(CN)2, and NaxAl1‐x/3(CN)3 perovskite. It was concluded that NaAlO(CN)2 perovskite can be utilized as a sodium ion‐conductor for sodium–sulfur battery. © 2012 Wiley Periodicals, Inc.
Influence of intermolecular interactions on spectral‐luminescent properties of a polyatomic molecule
Authors: Komarov Platon Valerievich , Plotnikov Viktor Georgievich 
Published: June 2012

AbstractA dependence of spectral‐luminescent properties of heteroaromatic molecules on interactions with medium is reviewed and discussed. The nonspecific interactions modify, in some cases, an order of electronic states of a different orbital nature. It is shown that, in case of a protic solvent, the energy shift due to the nonspecific interactions is comparable with the energy shift due to the H‐bonding. The possible applications of considered concepts are suggested in the field of design of optical chemical sensors. © 2012 Wiley Periodicals, Inc.
Principles and practices of the Circle of Trust® approach
Authors: Chadsey Terry , Jackson Marcy 
Published: June 2012

AbstractThis chapter describes the history, rationale, and core content of the principles and practices that define the Circle of Trust® approach as developed by Parker J. Palmer and the Center for Courage & Renewal. Courage to Teach®, Courage to Lead®, and other Courage & Renewal programs are built upon this distinctive approach.
The Circle of Trust® approach and a counselor training program: A hand in glove fit
Authors: Goodell Judith A. 
Published: June 2012

AbstractThis chapter describes how the principles and practices of a Circle of Trust® approach are infused into the Master's in Counseling Psychology program, marriage and family therapy emphasis, at the University of San Francisco. The interface between the Circle of Trust® approach and other on‐campus activities is described; the model is proposed as of value to all in higher education independent of role or discipline.
Innovative energy policy in a developing country context: experiences from UNEP's PROSOL initiative
Authors: Ölz Samantha , Agbemabiese Lawrence 
Published: June 2012

AbstractAs is the case in several other countries of the Middle East and North Africa region, fossil energy resources have long dominated Tunisiaŉs energy sector. However, concerns about depleting fossil fuels, rising prices, and growing demand have driven interest in the countryŉs substantial but largely untapped solar energy resources. In 2005, the Tunisian government, with the support of the United Nations Environment Programme, launched PROSOL, an innovative financing scheme to revitalize an anemic solar water heater (SWH) market. PROSOL has been a resounding success, which has spurred similar policy initiatives in neighboring countries. On the basis of in‐depth reviews of project progress reports, external evaluations, and stakeholder interviews, we analyze Tunisiaŉs experience with the PROSOL initiative with a view to extracting practical lessons that might inform replication in other developing countries. Drawing on the concept of a technological innovation system (TIS), we isolate and address key questions including: why and how public and private agents may either support or hamper a given technological innovation; and how, in the Tunisian case, new SWH interest groups and networks emerge around new technology initiatives such as PROSOL. Our findings highlight the central role of public policy in removing barriers to the market diffusion of proven renewable energy technologies. In the Tunisian case, the establishment by law of a substantial capital cost subsidy while exempting SWHs from value added tax and decreasing custom duties enabled SWH systems to compete effectively against conventional energy sources such as natural gas or liquid petroleum gas. The study also confirms the importance of capacity building, buttressed by an effective communication and outreach strategy, targeting key actors including government policy makers, the national utility, financial institutions, and SWH vendors.This article is categorized under:

Energy Policy and Planning > Economics and Policy
Energy and Development > Economics and Policy
Energy and Development > Systems and Infrastructure
A Comparison of the Interactive Systems Framework (ISF) for Dissemination and Implementation and the CDC Division of HIV/AIDS Prevention's Research‐to‐Practice Model for Behavioral Interventions
Authors: Collins Charles B. , Edwards Arlene E. , Jones Patricia L. , Kay Linda , Cox Pamela J. , Puddy Richard W. 
Published: June 2012

AbstractTranslating evidence‐based HIV/STD prevention interventions and research findings into applicable HIV prevention practice has become an important challenge for the fields of community psychology and public health due to evidence‐based interventions and evidence‐based practice being given higher priority and endorsement by federal, state, and local health department funders. The Interactive Systems Framework (ISF) for Dissemination and Implementation and the Division of HIV/AIDS Prevention (DHAP) Research‐to‐Practice model both address this challenge. The DHAP model and the ISF are each presented with a brief history and an introduction of their features from synthesis of research findings through translation into intervention materials to implementation by prevention providers. This paper describes why the ISF and the DHAP model were developed and the similarities and differences between them. Specific examples of the use of the models to translate research to practice and the subsequent implications for support of each model are provided. The paper concludes that the ISF and the DHAP model are truly complementary with some unique differences, while both contribute substantially to addressing the gap between identifying effective programs and ensuring their widespread adoption in the field.Special Issue: Advances in Bridging Research and Practice Using the Interactive System Framework for Dissemination and Implementation; Guest Editors: Abraham Wandersman, Paul Flaspohler, Catherine A. Lesesne, Richard Puddy; Action Editor: Emilie Phillips Smith
Trans Fatty Acids: Induction of a Pro‐inflammatory Phenotype in Endothelial Cells
Authors: Harvey Kevin A. , Walker Candace L. , Xu Zhidong , Whitley Phillip , Siddiqui Rafat A. 
Published: June 2012

AbstractEpidemiological data have shown an association of the intake of industrial produced trans fatty acids (TFA) and sudden cardiac death. The present study examines the impact of elaidic acid (t18:1n‐9) and linoelaidic acid (t18:2n‐6) on the human aortic endothelial cell functional response. Trans fatty acids predominately incorporated into the phospholipid component while only a minute fraction of the total fatty acids (FA) incorporated into triacylglycerol. Trans fatty acids incorporated into the plasma membranes at the expense of the saturated‐FA, stearic, palmitic, and to a lesser extent, myristic acid. Both t18:1n‐9 and t18:2n‐6 induced a pro‐inflammatory response by elevating surface expression of intercellular adhesion molecule‐1 (ICAM‐1). Neither oleic nor linoleic evoked a pro‐inflammatory phenotype under the maximal 50 µM treatments. Both TFA and stearic acid increased phosphorylation of the ICAM‐1 transcriptional regulator, nuclear factor‐κβ (NF‐κβ), while oleic and linoleic acids did not appear to alter the phosphorylation status. Elaidic acid minimally affected endothelial cell growth, whereas linoelaidic acid completely inhibited growth at 100 µM and imparted limited cytotoxicity up to 300 µM. Stearic acid induced cytotoxicity at concentrations above 75 µM, while oleic and linoleic acids evoked gradual dose‐dependent growth inhibition with cytotoxicity occurring only at linoleic acid concentrations greater than 200 µM. In conclusion, t18:1n‐9 and t18:2n‐6 fatty acids effectively incorporated into the phospholipid component of endothelial cells and subsequently induce a pro‐inflammatory phenotype.
Gastrointestinal symptoms and weight loss in cancer patients receiving chemotherapy
Authors: Sánchez-Lara Karla , Ugalde-Morales Emilio , Motola-Kuba Daniel , Green Dan 
Published: June 2012

Cancer patients receiving chemotherapy have a high risk of malnutrition secondary to the disease and treatment, and 40–80 % of cancer patients suffer from different degrees of malnutrition, depending on tumour subtype, location, staging and treatment strategy. Malnutrition in cancer patients affects the patient's overall condition, and it increases the number of complications, the adverse effects of chemotherapy and reduces the quality of life. The aim of the present study was to evaluate weight-loss prevalence depending on the tumour site and the gastrointestinal (GI) symptoms of oncology patients receiving chemotherapy. We included 191 cancer patients receiving chemotherapy. Files of all patients were reviewed to identify symptoms that might potentially influence weight loss. The nutritional status of all patients was also determined. The cancer sites in the patients were as follows: breast (31·9 %); non-colorectal GI (18·3 %); colorectal (10·4 %); lung (5·8 %); haematological (13·1 %); others (20·5 %). Of these patients, 58 % experienced some degree of weight loss, and its prevalence was higher among the non-colorectal GI and lung cancer patients. Common symptoms included nausea (59·6 %), anorexia (46 %) and constipation (31·9 %). A higher proportion of patients with ≥ 5 % weight loss experienced anorexia, nausea and vomiting (OR 9·5, 2·15 and 6·1, respectively). In conclusion, these results indicate that GI symptoms can influence weight loss in cancer patients, and they should be included in early nutritional evaluations.
Plectocarpon stereocaulicola(Roccellaceae, Ascomycota), a new lichenicolous fungus from Bolivia
Authors: KUKWA Martin , ETAYO Javier , FLAKUS Adam 
Published: June 2012

AbstractA new gall-inducing lichenicolous fungus,Plectocarpon stereocaulicolaKukwa, Etayo and Flakus, is described from Bolivia from the thalli ofStereocaulonsp. The new species is characterized by black, epruinose rounded ascomata with a carbonized surface and a thalline pseudo-margin, as well as a non-carbonized, light brown sterile stromatic tissue in the lower part and 3-septate ascospores becoming brown and ornamented when mature.
Soil seed banks in a mature coniferous forest landscape: dominance of native perennials and low spatial variability
Authors: Abella Scott R. , Springer Judith D. 
Published: June 2012

AbstractSoil seed banks are important to vegetation recruitment, ecosystem functioning and land management. We evaluated composition of 0–5 cm soil seed banks and relationships of seed banks with forest community types (ranging from low-elevation pinyon–juniper to high-elevation bristlecone pine), vegetation cover and environmental variables within a 40,000-ha relatively undisturbed coniferous forest landscape in Nevada, USA. We collected samples from 36 sites and used the emergence method to assay seed banks. Seed density averaged 479 seeds m− 2across sites and a total of 39 taxa were detected. Most (79%) of these taxa were perennials and 35 of 39 (90%) were native. Moreover, 62% of seed-bank taxa were in the vegetation of mature forests, an uncommon finding in studies of forest soil seed banks. Seed-bank density, species richness and composition did not display strong relationships with forest community types, vegetation cover or environmental variables. Weak relationships likely arose from the relatively uniform seed-bank density among sites, where 50% of sites had seed densities in the range of 106–282 m− 2. Results suggest that while seed banks on this landscape are not large, they provide recruitment potential for some native perennial species of mature, relatively undisturbed communities.
Dose–response of germinating Rudbeckia mollis (Asteraceae) seeds exposed to various thermal scenarios
Authors: Kettner Keith , Pérez Hector Eduardo 
Published: June 2012

AbstractTemperature is a key environmental signal regulating germination. A thorough understanding of how seed populations respond to various temperatures can inform end-users regarding effective establishment strategies and forms the basis for questions related to a taxon's thermo-biology. Although abundant information exists regarding germination responses of economically important crops to several temperature scenarios, much less is known concerning the seed biology of wild germplasm. To address this, we examined the germination response of non-dormant Rudbeckia mollis seeds to various doses of constant or simulated seasonal diel temperatures. Germination response was sigmoidal. Seeds of R. mollis were capable of germinating within a few days to high percentages (>95%) at relatively cool constant (15–25°C) or 12-hour alternating (22/11–33/24°C) temperatures, with optimum temperatures for germination occurring at 25°C or 29/19°C. Germination was inhibited as temperatures increased to 30°C or 33/24°C with early and late germinating phenotypes displaying differential responses at these temperatures. No germination occurred at 35°C. Results are discussed in terms of seedling establishment of R. mollis outside its natural range and implications of climate change on germination.
Monitoring of acetyl salicylic acid-induced platelet inhibition with impedance aggregometry in children with systemic-to-pulmonary shunts
Authors: Romlin Birgitta S. , Wåhlander Håkan , Strömvall-Larsson Eva , Synnergren Mats , Baghaei Fariba , Jeppsson Anders 
Published: June 2012

AbstractBackgroundShunt thrombosis after implantation of systemic-to-pulmonary shunts in paediatric patients is common. Acetyl salicylic acid is used for anti-thrombotic treatment; however, the effect is rarely monitored, although it is known that the response varies. The aim was to determine the effects of acetyl salicylic acid medication on platelet aggregation in children with systemic-to-pulmonary shunts.MethodsA total of 14 children – median age 12 days; ranging from 3 to 100 days – were included in a prospective observational longitudinal study. All children were treated with oral acetyl salicylic acid (3–5 milligrams per kilogram once daily) after shunt implantation. Acetyl salicylic acid-dependent platelet aggregation in whole blood was analysed with impedance aggregometry (Multiplate®) after addition of arachidonic acid. Analyses were carried out before the primary operation, before and 5 and 24 hours after the first acetyl salicylic acid dose, and after 3–6 months of treatment. The therapeutic range for acetyl salicylic acid was defined as a test result less than 60 units.ResultsAcetyl salicylic acid reduced the arachidonic acid-induced platelet aggregation in all but one patient. Of the patients, 93% were in the therapeutic range 5 hours after acetyl salicylic acid intake, 86% were in the range after 24 hours, and 64% after 3–6 months.ConclusionsAcetyl salicylic acid reduces platelet aggregation after shunt implantation in paediatric patients, but a considerable percentage of the children are outside the therapeutic range. Monitoring of platelet aggregation has the potential to improve anti-platelet treatment after shunt implantation by identifying children with impaired acetyl salicylic acid response.
Association between Cognitive Activity and Cognitive Function in Older Hispanics
Authors: Marquine María J. , Segawa Eisuke , Wilson Robert S. , Bennett David A. , Barnes Lisa L. 
Published: June 2012

AbstractThere is limited research on the association between participation in cognitively stimulating activity and cognitive function in older Hispanics. The main purpose of the present study was to explore whether frequency of cognitive activity and its association with cognitive function in Hispanics is comparable to that of non-Hispanics. In a multiethnic cohort of 1571 non-demented older adults, we assessed past and current cognitive activity, availability of cognitive resources in the home in childhood and middle age, and five domains of cognitive function. The measures of cognitive activity and cognitive resources had adequate reliability and validity in our subset of Hispanic participants (n = 81). Hispanics reported lower levels of education, lower frequency of cognitive activity and less cognitive resources than non-Hispanic White (n = 1102) and non-Hispanic Black (n = 388) participants. Despite these differences the strength of the association between cognitive activity and cognitive function was comparable across ethnic groups. Because Hispanics have lower frequency of cognitive activity, the benefit of cognitive activity to late life cognitive function may be potentially larger in this segment of the population. Thus, interventions aimed at increasing frequency of participation in cognitively stimulating activity may offer a potential target to reduce cognitive impairment in Hispanics. (JINS, 2012, 18, 1–11)
Family support and weight-loss strategies among adolescents reporting sustained weight loss
Authors: Utter Jennifer , Denny Simon , Dixon Robyn , Ameratunga Shanthi , Teevale Tasileta 
Published: June 2012

AbstractObjectiveThe current research aims to describe the weight-control strategies and family support for young people reporting sustained weight loss in a large, population-based sample.DesignData were collected as part of Youth'07, a nationally representative survey of the health and well-being of New Zealand youth.SettingNew Zealand secondary schools, 2007.SubjectsSecondary-school students (n 9107).ResultsAmong young people who attempted weight loss in the previous year, 51 % reported long-term weight loss (lost weight and maintained weight loss for 6 months). Students reporting long-term weight loss were more likely to be male, but did not differ by age, ethnicity, socio-economic deprivation or measured weight status from students who reported temporary/recent weight loss or no weight loss. Students with long-term weight loss also reported healthier weight-control strategies (e.g. exercising, eating fewer fatty foods, eating fewer sweets), high parental support for healthy eating/activity and were less likely to report being teased about their weight by their family and having junk food available at home than students with temporary/recent weight loss or no weight loss.ConclusionsApproximately 50 % of young people attempting weight loss reported sustained weight loss. Young people who reported sustained weight loss appeared to have more family support than those who did not achieve this, suggesting the importance for weight-control services and interventions in adolescents of actively engaging the family.