bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity selection algorithms
Authors: Gillet Valerie J. 
Published: June 2011

AbstractMolecular diversity has been an important topic in chemoinformatics for the last two decades following the introduction of high‐throughput screening and combinatorial chemistry techniques. This article reviews the main algorithms that have been developed for assessing the diversity of a set of compounds and for selecting a diverse subset of compounds from a larger library. Particular focus is given to recent trends including the use of scaffolds as a way of assessing molecular diversity and the importance now given to optimizing multiple properties simultaneously in an attempt to reduce late stage attrition during the drug development stage of drug discovery. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 580‐589 DOI: 10.1002/wcms.33This article is categorized under:

Computer and Information Science > Chemoinformatics
The Cambridge Structural Database: experimental three‐dimensional information on small molecules is a vital resource for interdisciplinary research and learning
Authors: Groom Colin R. , Allen Frank H. 
Published: June 2011

AbstractCrystal structure determination is the method of choice for the analysis of novel chemical compounds from monatomic metals to proteins and viruses, with some 700,000 crystal structures published so far. Of these, over 500,000 (70%) are carbon‐containing organic and metal‐organic small molecules, for which experimental three‐dimensional (3D) numerical results are stored in the Cambridge Structural Database (CSD), together with two‐dimensional chemical structure information and text and numerical fields that record chemical and physical properties. The CSD is fully searchable using an Internet search engine or specialist‐distributed software that provides advanced facilities for structure display and data analysis, including many special features for understanding molecular recognition processes such as protein–ligand interactions. Two knowledge bases derived from the CSD provide immediate access to information on intramolecular geometry and intermolecular interactions. CSD information is heavily used in academic and industrial research that relies on knowledge of 3D molecular geometry and intermolecular interactions, for example, in structural chemistry and biology, drug discovery, materials design and development, and in crystallography itself. As a teaching tool, the CSD has a fundamental role to play in illustrating the 3D chemical concepts that are essential for those who study chemistry as a principal or subsidiary subject. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 368–376 DOI: 10.1002/wcms.35This article is categorized under:

Computer and Information Science > Chemoinformatics
First‐principles prediction of acidities in the gas and solution phase
Authors: Ho Junming , Coote Michelle L. 
Published: June 2011

AbstractThis paper provides an overview of contemporary computational protocols toward accurate prediction of acidities in the gas and aqueous phase. The performance of various density functional theory (DFT) methods and ab initio composite procedures, such as the G3MP2(+) method, for the prediction of gas‐phase acidities of a range of neutral and cationic acids is presented. Various methods for solution pKa predictions are also reviewed where the emphasis is on thermodynamic cycle‐based methods that combine ab initio or experimental gas‐phase energies with solvation free energies from continuum solvent models. The prediction of accurate solvation free energies, especially for ionic species, represents the bottleneck for accurate pKa prediction via the direct or absolute method. The success and limitations of alternative thermodynamic cycles are discussed and some of the difficulties and future challenges associated with the applications of these methods on more complicated molecules are also highlighted. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 649–660 DOI: 10.1002/wcms.43This article is categorized under:

Structure and Mechanism > Molecular Structures
Cooperative dynamics of proteins unraveled by network models
Authors: Eyal Eran , Dutta Anindita , Bahar Ivet 
Published: June 2011

AbstractRecent years have seen a significant increase in the number of computational studies that adopted network models for investigating biomolecular systems dynamics and interactions. In particular, elastic network models have proven useful in elucidating the dynamics and allosteric signaling mechanisms of proteins and their complexes. Here we present an overview of two most widely used elastic network models, the Gaussian Network Model (GNM) and Anisotropic Network Model (ANM). We illustrate their use in (i) explaining the anisotropic response of proteins observed in external pulling experiments, (ii) identifying residues that possess high allosteric potentials, and demonstrating in this context the propensity of catalytic sites and metal‐binding sites for enabling efficient signal transduction, and (iii) assisting in structure refinement, molecular replacement and comparative modeling of ligand‐bound forms via efficient sampling of energetically favored conformers. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 426–439 DOI: 10.1002/wcms.44This article is categorized under:

Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
GROMACS—the road ahead
Authors: van der Spoel David , Hess Berk 
Published: June 2011

AbstractMolecular dynamics (MD) simulations form a powerful tool that is complementary to experiments and theory. They allow detailed investigations of both biological and chemical systems at the atomic level at timescales ranging from femtoseconds to milliseconds. Mechanisms and processes not accessible to experimental techniques can be followed in ‘real time’, and hypotheses based on experiments or theoretical arguments can be tested. Limits on the accuracy of results are mainly due to the physical models, the ratio of the complexity of the problem and the amount of computer time. Here, we review the state of the art in MD simulations with a focus on imminent challenges for the GROMACS (GROningen MAchine for Chemical Simulation) software. New hardware puts new requirements on software, while the breadth of applications and the amount of physical models implemented are increasing rapidly, highlighting shortcomings in the architecture of the programs. We sketch a road map for a popular scientific software package and discuss some of the choices to be made. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 710–715 DOI: 10.1002/wcms.50This article is categorized under:

Software > Molecular Modeling
Selected features of the polarizable continuum model for the representation of solvation
Authors: Tomasi Jacopo 
Published: June 2011

AbstractThe characteristics of a computational method addressing the description of solvent effects are here presented in a concise way, by selecting for the presentation a topic of large interest, i.e., the electronic, electric, and magnetic properties of molecules. The selection of these properties imposes a choice on the computational methods. They must be of quantum ab initio nature, and possibly treated at a high level of the quantum theory. In such a framework, continuum models are more adequate than the alternative models based on a discrete description of the solvent, because of the high computational cost associated with discrete models coupled to high quantum mechanics levels. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 855–867 DOI: 10.1002/wcms.54This article is categorized under:

Molecular and Statistical Mechanics > Molecular Interactions
Reaction path Hamiltonian and the unified reaction valley approach
Authors: Kraka Elfi 
Published: June 2011

AbstractOne of the major goals of chemistry is to control chemical reactions with the purpose of generating new compounds with useful properties. Control of a chemical reaction implies a detailed understanding of its mechanism as it results from the breaking and forming of chemical bonds. In practice, it is rather difficult to get a detailed mechanistic and dynamical description of even the simplest chemical reactions. This has to do with the fact that apart from reactants, products, and possible stable intermediates, all other molecular forms encountered during a reaction have such a short lifetime that standard experimental means are not sufficient to detect and describe them. Progress in modern laser spectroscopy seems to provide an access to transient species with lifetimes in the pico‐ to femtosecond region; however, computational investigations utilizing state‐of‐the art methods of quantum chemistry, in particular ab initio methods, provide still the major source of knowledge on reaction mechanism and reaction dynamics. The reaction path Hamiltonian model has proven as a powerful tool to derive the dynamics of a chemical reaction by following the reacting species along the reaction path from reactants to products as traced out on the potential energy surface. In this article, the original reaction path Hamiltonian will be reviewed, extensions and applications over the past decades will be summarized, and a new perspective, namely to use it in form of the unified reaction valley approach to derive a deep and systematic insight into the mechanism of a chemical reaction will be introduced. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 531–556 DOI: 10.1002/wcms.65This article is categorized under:

Electronic Structure Theory > Ab Initio Electronic Structure Methods
Two personal perspectives on a key issue in contemporary 3D QSAR
Authors: Clark Robert D. , Norinder Ulf 
Published: June 2011

AbstractChemists working with small molecules are under enormous pressure to be able to reliably predict how biological systems in particular and the environment in general will respond to the deployment of the corresponding compounds as medicines, cosmetics, or in other manufactured goods. To be specific and robust, any such prediction must be based on an implicit or explicit mathematical model of how chemical structure relates to biological activity—i.e., on some postulated quantitative structure–activity relationship (QSAR). Such models are necessarily limited in how broadly they can be applied. Their applicability domain depends on the structural diversity of the data set used, but also on the descriptors used to characterize how that structural variation relates to the activity in question. In principle, descriptors based on the molecular interaction fields produced by atoms distributed in three‐dimensional (3D) space should be the most general of all, but finding suitable conformations and alignment is a challenge. One way to obtain these is by taking the structure of the macromolecular target into account as well, as is done in scoring ligand/receptor complexes for virtual screening. Unfortunately, the available docking tools are generally not up to the task. Here, we share some personal observations and opinions on two possible ways to address this shortcoming: implicitly, by iterative rescoring of docked poses obtained using derived 3D QSARs; and explicitly, by evaluating ligand interaction fields with respect to target atoms rather than against generalized probe atoms. © 2011 John Wiley & Sons, Ltd.This article is categorized under:

Computer and Information Science > Chemoinformatics
Fatty liver deposition and sparing: a pictorial review
Authors: Décarie Patrick-Olivier , Lepanto Luigi , Billiard Jean-Sébastien , Olivié Damien , Murphy-Lavallée Jessica , Kauffmann Claude , Tang An 
Published: June 2011

Abstract

Objective
Fatty liver deposition is a very common finding, but it has many atypical patterns of distribution that can represent diagnostic pitfalls. The purpose of this pictorial essay is to review different patterns of fatty liver deposition and sparing.

Methods
We searched our archive retrospectively, reviewed the literature, and identified six patterns of liver steatosis.

Results
Steatosis may be diffuse, geographic, focal, subcapsular, multifocal or perivascular.

Conclusions
Previous knowledge of atypical patterns of steatosis distribution may prevent misdiagnosis of infiltrative disease or focal liver lesions. When an unusual form of fatty liver deposition is suspected on ultrasound or computed tomography, magnetic resonance imaging may be used to confirm the diagnosis.
Gender role expectations of pain mediate sex differences in cold pain responses in healthy Libyans
Authors: Alabas O.A. , Tashani O.A. , Johnson M.I. 
Published: June 2011

AbstractPrevious studies found a relationship between response to experimentally‐induced pain and scores for the gender role expectations of pain (GREP) questionnaire. Findings were similar in individuals from America, Portugal and Israel suggesting that gender role expectations may be universal. The aim of this study was to translate and validate Arabic GREP using Factor Analysis and to investigate if sex differences to cold‐pressor pain in healthy Libyan men and women are mediated through stereotypical social constructs of gender role expectations and/or pain‐related anxiety. One hundred fourteen university students (58 women) underwent two cycles of cold pressor pain test to measure pain threshold, tolerance, intensity, and unpleasantness. Participants also completed the Arabic GREP questionnaire and the Pain Anxiety Symptom Scale‐Short form (PASS‐20). It was found that Libyan men had higher pain thresholds and tolerances than women (mean difference, 95% CI: threshold = 4.69 (s), −0.72 to 10.1, p = 0.005; tolerance = 13.46 (s), 0.5–26.4, p = 0.018). There were significant differences between sexes in 6 out of 12 GREP items (p < 0.004 after Bonferonni adjustment). The results of mediational analysis showed that GREP factors were the mediators of the effects of sex on pain threshold (z = −2.452, p = 0.014 for Self Sensitivity); (z = −2.563, p = 0.01, for Self Endurance) and on pain tolerance (z = −2.538, p = 0.01 for Self Endurance). In conclusion, sex differences in response to pain were mediated by gender role expectations of pain but not pain‐related anxiety.
The influence of maternal vulnerability and parenting stress on chronic pain in adolescents in a general population sample: The TRAILS study
Authors: Darlington A.‐S.E. , Verhulst F.C. , De Winter A.F. , Ormel J. , Passchier J. , Hunfeld J.A.M. 
Published: June 2011

AbstractInvestigating possible psychosocial predictors of unexplained chronic pain in adolescents is crucial in understanding its development and prevention. A general population sample of adolescents (n = 2230) from the TRAILS cohort study was investigated longitudinally to assess the influence of maternal vulnerability, in terms of anxiety, depression and stress, and parenting stress at age 10–12 years, on the presence of chronic pain at age 12–15 years. Of these adolescents, 269 (12.9%) reported experiencing chronic pain, of which 77% reported severe chronic pain and 22% reported multiple chronic pain. Maternal anxiety, maternal stress and higher levels of parenting stress were related to chronic pain at a later age. Subgroup analyses showed similar results for adolescents with severe chronic pain. Mediation analyses indicated that parenting stress mediates the effect between maternal anxiety, or stress, and chronic pain. The findings suggest that interventions to diminish maternal feelings of anxiety and stress, while in turn adjusting maternal behaviour, may prevent the development of chronic pain in adolescence.
Arbeit und Gesundheit – ein Interventionsfeld im Wandel
Authors: Schmucker Rolf 
Published: June 2011

Einleitung
Der Belastungswandel in der Arbeitswelt hat zu neuen Herausforderungen für die gesundheitspolitische Steuerung geführt. Eine Reduzierung arbeitsbedingter Erkrankungen und eine Stärkung des salutogenen Potenzials von Arbeit erfordern Maßnahmen auf verschiedenen Interventionsebenen: In der Wirtschafts-, Arbeitsmarkt-, Sozial- und Tarifpolitik ebenso wie bei der Gestaltung des Arbeitsschutzes und der Betrieblichen Gesundheitsförderung.
Lupin seed γ-conglutin lowers blood glucose in hyperglycaemic rats and increases glucose consumption of HepG2 cells
Authors: Rosa Lovati Maria , Manzoni Cristina , Castiglioni Silvia , Parolari Anna , Magni Chiara , Duranti Marcello 
Published: June 2011

The aim of the present study was to evaluate the effect of a chronic oral γ-conglutin treatment in male Sprague–Dawley rats in which hyperglycaemia had been induced by supplying 10 %d-glucose in drinking-water. A γ-conglutin dosage of 28 mg/kg body weight was daily administered to animals for 21 d. Plasma glucose, insulin and glucose overloading were monitored. Chronic administration of glucose resulted in a statistically significant (P < 0·05) increase in fasting blood glucose (2·5-fold) and insulin (2·7-fold)v.the values recorded in control rats. Simultaneous treatment with γ-conglutin attenuated the rise in plasma glucose (1·9-fold) and insulin (1·8-fold) levels in the glucose-fed rats (P < 0·05). Fasting insulin and homeostasis model of insulin resistance were decreased by 34 and 48 % (P < 0·05), respectively, in the γ-conglutin-treated ratsv.the values found in pair-fed animals. To confirm these results with a different approach, HepG2 cells, grown for 24 and 48 h in Dulbecco's minimum essential medium containing different glucose concentrations (5·5, 11·1 and 16·5 mmol/l), were exposed to 10 μmol/l γ-conglutin with or without 10 mmol/l metformin or 100 nmol/l insulin. γ-Conglutin increased glucose consumption (from 1·5- to 2·5-fold) in HepG2 cells, under all experimental conditions; this effect was more evident after 48 h incubation. Moreover, in thisin vitromodel, the addition of γ-conglutin potentiated the activity of insulin and metformin in cell glucose consumption. These findings extend the previous ones and suggest the potential use of lupin γ-conglutin in the control of glycaemia.
Measured energy value of pistachios in the human diet
Authors: Baer David J. , Gebauer Sarah K. , Novotny Janet A. 
Published: June 2011

Previous studies have suggested that lipid from nuts is more poorly absorbed than that from other food sources. If lipid from nuts is poorly absorbed, then the metabolisable energy contained in the nuts is less than that predicted by the Atwater general factors. A crossover feeding study was conducted in which sixteen volunteers consumed pistachios for 3 weeks as part of a controlled diet. Pistachio doses were 0, 42 and 84 g/d. Urine and faecal samples were collected, and urine, faeces and diet were analysed for N, fat, total dietary fibre, ash and combustible energy. Blood was also collected after each treatment period and analysed for plasma lipids. Energy value of pistachio nuts was calculated from differences in energy excretion during the different dietary treatments. The measured energy density of pistachios was found to be 22·6 kJ/g, which is 5 % less than the currently accepted energy value of 23·7 kJ/g, as calculated using the Atwater general factors. The pistachio nut intervention lowered LDL-cholesterol by 6 %, but did not significantly change plasma total cholesterol, HDL-cholesterol or TAG. In conclusion, pistachio nuts contain less metabolisable energy than that calculated from the Atwater general factors. Accurate information about metabolisable energy content of foods is important for reliable food labelling.
Hepatoprotective and antioxidant activities of grapeseeds against ethanol-induced oxidative stress in rats
Authors: Dogan Abdulahad , Celik Ismail 
Published: June 2011

The present study was carried out to evaluate the hepatoprotective effect and antioxidant role of grape (Vitis viniferaL.) seeds (GS) against ethanol-induced oxidative stress. The hepatoprotective and antioxidant roles of the GS supplementation feed against ethanol-induced oxidative stress were evaluated by measuring liver damage serum marker enzymes, aspartate aminotransferase, alanine aminotransferase, γ-glutamyl transpeptidase and lactate dehydrogenase, antioxidant defence system such as GSH, glutathione reductase, superoxide dismutase, glutathioneS-transferase and glutathione peroxidase and malondialdehyde (MDA) content in various tissues of rats. Rats were divided into four experimental groups: I (control), II (20 % ethanol), III (15 % GS) and IV (20 % ethanol+15 % GS). According to the results, the level of serum marker enzymes was significantly increased in group II as compared to that of group I, but decreased in group IV as compared to that of group II. Also, administration of GS-supplemented food restored the ethanol-induced MDA, which was increased near the control level. The results indicated that GS could be as important as diet-derived antioxidants in preventing oxidative damage in the tissues by reducing the lipid oxidation or inhibiting the production of ethanol-induced free radicals in rats.
Medium-chain fatty acid nanoliposomes suppress body fat accumulation in mice
Authors: Liu Wei-Lin , Liu Wei , Liu Cheng-Mei , Yang Shui-Bing , Liu Jian-Hua , Zheng Hui-Juan , Su Kun-Ming 
Published: June 2011

Medium-chain fatty acids (MCFA) are widely used in diets for patients with obesity. To develop a delivery system for suppressing dietary fat accumulation into adipose tissue, MCFA were encapsulated in nanoliposomes (NL), which can overcome the drawbacks of MCFA and keep their properties unchanged. In the present study, crude liposomes were first produced by the thin-layer dispersion method, and then dynamic high-pressure microfluidisation (DHPM) and DHPM combined with freeze–thawing methods were used to prepare MCFA NL (NL-1 and NL-2, respectively). NL-1 exhibited smaller average size (77·6 (sd 4·3) nm), higher zeta potential ( − 40·8 (sd 1·7) mV) and entrapment efficiency (73·3 (sd 16·1) %) and better stability, while NL-2 showed narrower distribution (polydispersion index 0·193 (sd 0·016)). The body fat reduction property of NL-1 and NL-2 were evaluated by short-term (2 weeks) and long-term (6 weeks) experiments of mice. In contrast to the MCFA group, the NL groups had overcome the poor palatability of MCFA because the normal diet of mice was maintained. The body fat and total cholesterol (TCH) of NL-1 (1·54 (sd 0·30) g, P = 0·039 and 2·33 (sd 0·44) mmol/l, P = 0·021, respectively) and NL-2 (1·58 (sd 0·69) g, P = 0·041 and 2·29 (sd 0·38) mmol/l, P = 0·015, respectively) significantly decreased when compared with the control group (2·11 (sd 0·82) g and 2·99 (sd 0·48) mmol/l, respectively). The TAG concentration of the NL-1 group (0·55 (sd 0·14) mmol/l) was remarkably lower (P = 0·045) than the control group (0·94 (sd 0·37) mmol/l). No significant difference in weight and fat gain, TCH and TAG was detected between the MCFA NL and MCFA groups. Therefore, MCFA NL could be potential nutritional candidates for obesity to suppress body fat accumulation.
Increased Realism at Lower Cost: The Case for the Hybrid
Experiment
Authors: Dumitrescu Delia , Blais André 
Published: June 2011

AbstractWe propose an experimental design particularly adapted to the study
of individual behavior in collective action situations. The
experimental protocol improves on the artificiality that is commonly
present in lab and survey experiments to achieve a closer
replication of the real-life conditions of such decisions while
avoiding the high costs associated with field experiments. We
exemplify this design by means of a study on strategic voting in
elections.