bluuebunny/crossref_metadata_2025 huggingface dataset:
Kinetic parameter estimation of solvent‐free reactions monitored by 13C NMR spectroscopy, a case study: Mono‐ and di‐(hydroxy)ethylation of aniline with ethylene carbonate
Authors: Lucchini Vittorio , Fabris Massimo , Noè Marco , Perosa Alvise , Selva Maurizio
Published: January 2011

The kinetics of solvent‐free reactions can be followed in situ by 13C nuclear magnetic resonance (NMR) spectroscopy, provided that the reaction mixture can be maintained liquid at the monitoring temperature. The pros and cons of the technique and the correct translation of the signal intensities into concentrations are discussed. A good model for this investigation is the reaction of ethylene carbonate (1) with aniline (2) at 140°C, two alkylation products of N‐mono‐ and N, N‐bis‐(2‐hydroxy)ethylation of aniline form (compounds 3 and 4, respectively). The overall reaction occurs with heavy volume shrinking, so that the physical as well as the chemical features evolve during the course of the process. The chemical evolution is described by the kinetic constants k1 and k2 of the two N‐alkylation steps, the physical evolution by the time‐dependent activity coefficients α(t). Two complementary procedures are utilized for the determination of these parameters. © 2011 Wiley Periodicals, Inc. Int J Chem Kinet 43: 154–160, 2011
Towards the Generation of Self‐Healing Materials by Means of a Reversible Photo‐induced Approach
Authors: Froimowicz Pablo , Frey Holger , Landfester Katharina
Published: January 2011

Photo‐induced reversibility as a tool for self‐healing: a reversible photo‐induced dendritic macromonomer was synthesized and proven to form networks with different features depending on the crosslinking conditions. While networks formed from aqueous systems exhibited a reversible change in their crosslinking degree, networks generated in bulk underwent fully reversibility. The latter was then exploited for generating self‐healing materials by means of a photo‐induced treatment.

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Clinical correlates of similar pathologies in parkinsonian syndromes
Authors: Song Yun Ju Christine , Huang Yue , Halliday Glenda Margaret
Published: January 2011

Background:

There have been no previous studies assessing the severity of regional atrophy, cell loss and lesion densities between the overlapping conditions of Parkinson's disease (PD), progressive supranuclear palsy (PSP) and multiple system atrophy (MSA) and relating these pathologies to different clinical features.

Methods:

Clinical indices and basal ganglia, brainstem, and cerebellar pathology from 43 longitudinally studied cases (PD = 8, PSP = 15, MSA = 12, controls = 8) were compared. A point‐counting method was used to evaluate subregional volumes, and α‐synuclein and phospho‐tau immunohistochemistry was used to assess pathological inclusions and stage disease severity. Logistic regression analyses were used to identify pathological associations with clinical features.

Results:

All PD, PSP, and MSA cases had severe degeneration of the substantia nigra. Clinical features correlated with tissue loss and the severity of inclusion pathologies. Levodopa responsiveness and a lack of resting tremor was associated with preservation of pallidal volume, the presence of gait ataxia was associated with atrophy of the putamen, and the parkinsonian‐plus phenotype with early falls and supranuclear vertical gaze abnormalities had more substantial midbrain atrophy and greater inclusion pathology in the caudate nucleus.

Discussion:

This is the first study to compare the severity of regional pathologies across parkinsonian conditions. The data show that tissue loss and inclusion densities in certain regions correlate with clinical indices, with regional volume changes likely to be the best indicator of clinical progression of disease. © 2011 Movement Disorder Society
Phenotype of the 202 adenine deletion in the parkin gene: 40 years of follow‐up
Authors: Hassin‐Baer Sharon , Hattori Nobutaka , Cohen Oren S. , Massarwa Magdalena , Israeli‐Korn Simon D. , Inzelberg Rivka
Published: January 2011

Background:

We describe the four decades follow‐up of 14 parkin patients belonging to two large eight‐generation‐long in‐bred Muslim‐Arab kindreds.

Results:

All patients had a single base‐pair of adenine deletion at nucleotide 202 of exon 2 (202A) of the parkin gene (all homozygous, one heterozygous). Parkinson's disease onset age was 17–68 years. Special features were intractable axial symptoms (low back pain, scoliosis, camptocormia, antecollis), postural tremor, and preserved cognition.

Conclusions:

The 202A deletion of the parkin gene causes early‐onset Parkinson's disease with marked levodopa/STN‐DBS–resistant axial features. Postural tremor and preserved cognition, even after 40 years of disease, were also evident. © 2010 Movement Disorder Society
Validation of screening instruments for neuroepidemiological surveys of tic disorders
Authors: Cubo Esther , Sáez Velasco Sara , Delgado Benito Vanesa , Ausín Villaverde Vanesa , Maria Trejo Gabriel y Galán Jose , Martín Santidrián Asuncion , Macarrón Vicente Jesús , Cordero Guevara José , Louis Elan D. , Benito‐León Julian
Published: January 2011

Background:

The main purpose was to validate a multistage protocol to screen tic disorders in mainstream and special education centers and to investigate whether telephone‐based interviews were accurate to diagnose tic disorders when compared with in‐person neurological interviews.

Methods:

A school‐based survey of children and adolescents (6–16 years). A proxy report questionnaire for tic disorders was completed by teachers, observers, and parents. The diagnosis was confirmed by the neurologist based on the Diagnostic and Statistical Manual of Mental disorders (DSM‐IV TR) criteria. The sensitivity, specificity, positive and negative predictive values, the likelihood ratio for a positive result (LR+), and the Kappa coefficients (k) for telephone‐based interviews reliability were calculated.

Results:

One hundred twenty subjects, 57 from special education center and 63 from a mainstream school were studied. The sensitivity of the proxy report questionnaire was 58% and 36% when completed by the observers (mainstream and special education center, respectively), 40 and 73% when completed by the teachers, and 58 and 36% when completed by the parents. Using any of these 3 screening sources, the sensitivity was 92%, the positive predictive value was 38%, and negative predictive value was 97% (mainstream schools), whereas the sensitivity was 82%, the positive predictive value was 20%, and negative predictive value was 82% (special education centers). Parents (mainstream schools) and teachers (special education center) produced the highest LR+ (7.25 and 1.26, respectively) and the intraobserver reliability of the telephone‐based interviews versus in‐person neurological interviews gave akcoefficient of 0.83.

Conclusions:

The efficiency of different screening instruments for tic disorders seems to vary in different settings. Telephone‐based interviews may be a valid and convenient backup to ascertain the diagnosis of tic disorders when face‐to‐face neurological examination is not possible. © 2011 Movement Disorder Society
Mitochondrial mimicry of multiple system atrophy of the cerebellar subtype
Authors: Mehta Arpan R. , Fox Susan H. , Tarnopolsky Mark , Yoon Grace
Published: January 2011

Background: We describe a patient with clinical and radiological findings suggestive of multiple system atrophy of the cerebellar subtype (MSA‐C). Methods/Results: Sequencing of the polymerase‐γ 1 (POLG1) gene revealed the patient had compound heterozygous mutations of the POLG1 gene. Muscle biopsy revealed the presence of multiple mitochondrial DNA deletions and depletion, confirming the pathogenic nature of the POLG1 mutations. Discussion: This case expands the spectrum of phenotypes associated with POLG1 mutations to include multiple system atrophy and prompts further consideration regarding whether routine screening for POLG1 mutations is indicated in this patient population. © 2011 Movement Disorder Society
Classification of Aurora‐A Kinase Inhibitors Using Self‐Organizing Map (SOM) and Support Vector Machine (SVM)
Authors: Wang Liyu , Wang Zhi , Yan Aixia , Yuan Qipeng
Published: January 2011

Two classification models of 148 Aurora‐A kinase inhibitors were developed to separate active and weakly potent active inhibitors of Aurora‐A kinase. Each molecule was represented by 12 selected molecular descriptors calculated by the ADRIANA.Code. Then the classification models were built using a Kohonen’s Self‐Organizing Map (SOM) and a Support Vector Machine (SVM) method, respectively, which could be used for virtual screening an existing database to find possible new lead compounds with higher activity. The prediction accuracy of the models for the training and test sets are 96.6 % and 90.0 % for SOM, 93.2 % and 93.3 % for SVM.
Childhood Obesity and Environmental Chemicals
Authors: La Merrill Michele , Birnbaum Linda S.
Published: January 2011

Childhood and adolescent rates of obesity and overweight are continuing to increase in much of the world. Risk factors such as diet composition, excess caloric intake, decreased exercise, genetics, and the built environment are active areas of etiologic research. The obesogen hypothesis, which postulates that prenatal and perinatal chemical exposure can contribute to risk of childhood and adolescent obesity, remains relatively underexamined. This review surveys numerous classes of chemicals for which this hypothesis has been explored. We focus on human data where they exist and also discuss the findings of rodent and cell culture studies. Organochlorine chemicals as well as several classes of chemicals that are peroxisome proliferator‐activated receptor agonists are identified as possible risk factors for obesity. Recommendations for future epidemiologic and experimental research on the chemical origins of obesity are also given. Mt Sinai J Med 78:22–48, 2011. © 2011 Mount Sinai School of Medicine
Community Engagement in Children's Environmental Health Research
Authors: Brenner Barbara L. , Manice Melissa P.
Published: January 2011

Community engagement strategies and skills can build trust and reduce historical mistrust between researchers, communities, and populations being studied, as well as contribute to the quality of study designs, methods, and dissemination of findings. This review paper discusses why community engagement is of increasing importance in children's environmental health research, describes models and the continuum of methods that are used, and discusses their challenges and benefits. Two case studies, representing different study designs and using different community engagement models and methods, and lessons learned from these cases, are described. Community engagement methods are best understood on a continuum based on the degree to which community members or representatives of community populations are involved in research planning, decision‐making, and dissemination. Methods along this continuum include community consultation, community‐based participatory research, and community consent to research. Community engagement knowledge and skills are especially important in the conduct of children's environmental health research, with its emphasis on reducing environmental risks at the community level, the increasing focus on genetics and gene‐environment interactions, and the importance placed on translation of scientific results into behaviors and policies that protect the community. Across study designs, whether qualitative survey research, an observational epidemiology study, or a randomized intervention trial, understanding community interests, norms, and values is necessary to describe attitudes and behaviors of specific population groups, build evidence of cause and effect between environmental exposures and health, and demonstrate the effectiveness of interventions to reduce risks. Mt Sinai J Med 78:85–97, 2011. © 2011 Mount Sinai School of Medicine
Climate Change, Aeroallergens, and Pediatric Allergic Disease
Authors: Sheffield Perry E. , Weinberger Kate R. , Kinney Patrick L.
Published: January 2011

The degree to which aeroallergens are contributing to the global increase in pediatric allergic disease is incompletely understood. We review the evidence that links climate change to changes in aeroallergens such as pollen and outdoor mold concentrations and, subsequently, aeroallergen association with pediatric allergic disease. We specifically explore the evidence on both the exacerbation and the development of allergic disease in children related to outdoor pollen and mold concentrations. Pediatric allergic diseases include atopic dermatitis or eczema, allergic rhinitis or hay fever, and some types of asthma in children, typically defined as < 18 years of age. We discuss how the timing of aeroallergen exposure both in utero and in childhood could be associated with allergies. We conclude that the magnitude and type of health impacts due to climate change will depend on improved understanding of the relationship between climatic variables, multiple allergen factors, and allergic disease. Improved public‐health strategies such as adequate humidity control, optimum air filtration and ventilation, and improved anticipatory public‐health messaging will be critical to adaptation. Mt Sinai J Med 78:78–84, 2011. © 2011 Mount Sinai School of Medicine
Environmental Neurotoxicants and Developing Brain
Authors: Miodovnik Amir
Published: January 2011

The brain of infants and children is uniquely sensitive to environmental neurotoxicants at levels far below those that are known to harm adults. There are multiple windows of vulnerability during which environmental exposures can interfere with normal development. The timing and duration of neurotoxicant exposures during development can give rise to a broad spectrum of structural and functional deficits. Only about 200 chemicals out of more than 80,000 registered with the United States Environmental Protection Agency have undergone extensive neurotoxicity testing, and many chemicals found in consumer goods are not required to undergo any neurodevelopmental testing. The cumulative effects of co‐contaminants and the difficulties in analyzing biomarkers of exposure in human tissues have complicated comprehensive risk assessment. Furthermore, population‐based studies that measure subtle effects on neurobehavioral outcomes are challenging to interpret and costly to conduct. Despite the fact that developmental neurotoxicity may be more severe and irreversible compared with adult toxicity, there is a relative paucity of toxicological data on developing systems for many high‐production chemicals. This article provides an overview of the adverse neurological, cognitive, and behavioral outcomes associated with environmental exposures, with an emphasis on human studies.Mt Sinai J Med 78:58–77, 2011.©2011 Mount Sinai School of Medicine
Protein adsorption materials based on conducting polymers: polypyrrole modified with ω‐(N‐pyrrolyl)‐octylthiol
Authors: Zhang Zhihong , Liang Yan , Liang Ping , Li Chao , Fang Shaoming
Published: January 2011

In order to fabricate a new polymer matrix for application in biochips and to understand the mechanism of adsorption of proteins on conducting polymers, we prepared polypyrrole (PPy) functionalized with ω‐(N‐pyrrolyl)‐octylthiol moieties. The chemical structure of the polymer could be controlled by varying the concentration of pyrrole added as the monomer. Initially, ω‐(N‐pyrrolyl)‐octylthiol was self‐assembled into a monolayer on a gold surface. Thereafter, a layer of uniform and smooth PPy was obtained by the chemical copolymerization of pyrrole and the ω‐(N‐pyrrolyl)‐octylthiol. Bovine serum albumin (BSA) adsorption on the polymer was investigated using surface plasmon resonance spectroscopy and cyclic voltammograms. The chemical structure and monomer components of the as‐prepared films were characterized using Fourier transform infrared spectroscopy and X‐ray photoelectron spectroscopy. Water contact angle measurements were used to assess the surface wettability of the films throughout the preparative procedure. The kinetics of BSA adsorption onto the polymer could be controlled by varying the copolymer thickness and the pH value of the buffer solutions used. Moreover, the electroactivity was changed upon BSA binding. The results suggest that the new conducting polymer may potentially be applied as a more sensitive and reliable matrix in protein sensors. Copyright © 2011 Society of Chemical Industry
Synthesis and characterization of 3,4‐diaryl‐substituted polythiophene derivatives
Authors: Saini Geeta , Jacob Josemon
Published: January 2011

A series of polythiophene derivatives bearing 3,4‐diaryl substituents were synthesized starting from commercially available 3,4‐dibromothiophene. The effects of two different aryl substituents, either a 5‐octyl‐2‐thienyl or a 4‐octylphenyl, were investigated in this study. To minimize steric effects on polymerization and conjugation, polymers were synthesized with a bithiophene or a triple‐bond spacer. The resulting polymers show varying solubility in common organic solvents and their UV‐visible absorption spectra in solution exhibit maxima in the range 434–484 nm, which are significantly red‐shifted as compared to those of 3,4‐dialkyl‐substituted polythiophenes. Gel permeation chromatography analysis using polystyrene standards shows a weight‐average molecular weight range of 1.50 × 104–4.40 × 104 g mol−1 for the various polymers. Copyright © 2011 Society of Chemical Industry
Cold unfolding of β‐hairpins: A molecular‐level rationalization
Authors: Riccio Angelo , Graziano Giuseppe
Published: January 2011

Isolated β‐hairpins in water have a temperature dependence of their conformational stability qualitatively resembling that of globular proteins, showing both cold and hot unfolding transitions. It is shown that a molecular‐level rationalization of this cold unfolding can be provided extending the approach devised for globular proteins (Graziano G. Phys Chem Chem Phys 2010; 12:14245‐14252). The decrease in the solvent‐excluded volume upon folding, measured by the decrease in the solvent accessible surface area, produces a gain in configurational/translational entropy of water molecules that is the main stabilizing contribution of the folded conformation. This always stabilizing Gibbs energy contribution has a parabolic‐like temperature dependence in water and is exactly counterbalanced at two temperatures (i.e., the cold and hot unfolding temperatures) by the always destabilizing Gibbs energy contribution due to the loss in conformational degrees of freedom of the peptide chain. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Synthesis of new compounds related to the commercial fungicide tricyclazole
Authors: Balcer Jesse L , DeAmicis Carl V , Johnson Peter L , Klosin Jerzy , Whiteker Gregory T , Srinivas Rao C , Dai Donghua
Published: January 2011

BACKGROUND: Tricyclazole is a commercial fungicide used to control rice blast. As part of re‐registration activities, samples of metabolites and process impurities are required. In addition, isotopically labeled tricyclazole samples are also required.

RESULTS: Four new compounds related to tricyclazole are reported. An isotopically labeled sample of tricyclazole was prepared that contained two 15N atoms and one 13C atom. Radiolabeled tricyclazole with 14C at the triazole C3 position was also synthesized. A new process impurity in technical tricyclazole was identified and synthesized. A new metabolite of tricyclazole was identified, independently synthesized and characterized by X‐ray crystallography.

CONCLUSION: A previously unreported metabolite of tricyclazole has been identified and structurally characterized. In addition, a new process impurity has been identified by independent synthesis. Identification of these new compounds has facilitated the continued registration of this important fungicide. Copyright © 2011 Society of Chemical Industry
Electrical penetration graph evidence that pymetrozine toxicity to the rice brown planthopper is by inhibition of phloem feeding
Authors: He Yueping , Chen Li , Chen Jianming , Zhang Juefeng , Chen Liezhong , Shen Jinliang , Zhu Yu Cheng
Published: January 2011

BACKGROUND: Pymetrozine is a valuable novel insecticide for control of sucking insects, including the brown planthopper Nilaparvata lugens (Stål), one of the most serious pests on rice. This study was conducted to elucidate the action mechanisms of pymetrozine on the feeding behaviour of the planthopper.

RESULTS: The activity test showed that pymetrozine primarily functioned as an antifeedant that caused starvation and death in N. lugens, rather than having neurotoxicity. Pymetrozine‐treated insects died at a significantly slower speed than insects treated with starvation. Electrical penetration graph (EPG) data indicated that pymetrozine significantly increased the duration of non‐probing periods and had a strong inhibition to phloem ingestion. The inhibition was strongly dose dependent, resulting in a complete suppression of the activity in the phloem region when the pymetrozine concentration was increased to 400 mg L−1. Starvation caused by inhibition of phloem ingestion might be a major toxicity mechanism of pymetrozine. EPG data also showed that pymetrozine had no significant effect on stylet movement and duration of xylem sap ingestion.

CONCLUSION: The study revealed that pymetrozine disturbed the feeding behaviour of N. lugens mainly by increasing the non‐probe period and inhibiting phloem ingestion. The inhibition resulted in a slow death similar to starvation. Copyright © 2011 Society of Chemical Industry
Using ensemble techniques to advance adaptive one‐factor‐at‐a‐time experimentation
Authors: Sudarsanam Nandan , Frey Daniel D.
Published: January 2011

Ensemble Methods are proposed as a means to extendbiAdaptive One‐Factor‐at‐a‐Time (aOFAT) experimentation. The proposed method executes multipleaOFAT experiments on the same system with minor differences in experimental setup, such as ‘starting points’. Experimental conclusions are arrived at by aggregating the multiple, individualaOFATs. A comparison is made to test the performance of the new method with that of a traditional form of experimentation, namely a single fractional factorial design which is equally resource intensive. The comparisons between the two experimental algorithms are conducted using a hierarchical probability meta‐model and an illustrative case study. The case is a wet clutch system with the goal of minimizing drag torque. In this study, the proposed procedure was superior in performance to using fractional factorial arrays consistently across various experimental settings. At the best, the proposed algorithm provides an expected value of improvement that is 15% higher than the traditional approach; at the worst, the two methods are equally effective, and on average the improvement is about 10% higher with the new method. These findings suggest that running multiple adaptive experiments in parallel can be an effective way to make improvements in quality and performance of engineering systems and also provides a reasonable aggregation procedure by which to bring together the results of the many separate experiments. Copyright © 2011 John Wiley & Sons, Ltd.
Tunable synthesis of starch‐poly(vinyl acetate) bioconjugate
Authors: Xiao Congming , Lu Derong , Xu Shanjun , Huang Li
Published: January 2011

Starch‐poly(vinyl acetate) bioconjugate of controllable composition and structure was generated via a combination of RAFT polymerization and copper‐catalyzed alkene‐azide cycloaddition. Firstly, well‐defined alkyne‐terminated poly(vinyl acetate) (AT‐PVAc) was prepared by RAFT polymerization of vinyl acetate in the presence of an alkyne‐containing chain transfer agent. Secondly, azide‐functionalized starch (SN) was synthesized by the nucleophilic substitution reaction of starch tosylate and sodium azide. Then, the bioconjugate was obtained through the click reaction of AT‐PVAc and SN. FTIR, elemental analysis, and NMR were used to verify the structure of the intermediates and the bioconjugate. GPC measurements showed that the MW of AT‐PVAc linearly depended on the monomer conversion and the polydispersity indexes ranged from 1.09 to 1.28. TEM analysis exhibited the final product was able to self‐assemble into micelles in aqueous medium, which suggested the product was amphiphilic and confirmed the successful conjugation of starch and PVAc once more. The content of starch in the bioconjugate could be 47.8–89.2%, which was able to be tailored by the feeding ratio of SN/AT‐PVAc and the MW of AT‐PVAc.
The empirical valence bond model: theory and applications
Authors: Kamerlin Shina C. L. , Warshel Arieh
Published: January 2011

Recent years have seen an explosion in computer power, allowing for the examination of ever more challenging problems. For instance, a recent simulation study, which was the first of its kind, was able to actually explore the dynamical nature of enzyme catalysis on a millisecond timescale (Pisliakov AV, Cao J, Kamerlin SCL, Warshel A. Proc Natl Acad Sci U S A 2009, 106:17359.), something that as recently as a year or two ago would have been considered impossible. However, the questions that need addressing are nevertheless very complex, and experimental approaches can unfortunately often be inconclusive (Åqvist J, Kolmodin K, Florián J, Warshel A, Chem Biol 1999, 6:R71.) in answering them. Therefore, it is essential to have an approach that is both reliable and able to capture complex systems in order to resolve long‐standing controversies [particularly with regards to questions such as the origin of enzyme catalysis, where the relevant energy contributions cannot be separated without some computational models (Warshel A, Sharma PK, Kato M, Xiang Y, Liu H, Olsson MHM, Chem Rev 2006, 106:3210.)]. Herein, we will present the empirical valence bond (EVB) approach, which, at present, is arguably the most powerful tool for examining chemical reactivity in the condensed phase. We will illustrate the effectiveness of the EVB method when evaluating, for instance, catalytic effects and demonstrate that it is currently the optimal tool for elucidating challenging problems such as understanding the catalytic power of enzymes. Finally, the increasing appreciation of this approach can maybe best illustrated not only by its proliferation but also by attempts to capture its basic chemistry under a different name, as will be discussed in this work. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 30–45 DOI: 10.1002/wcms.10

This article is categorized under:

Electronic Structure Theory > Combined QM/MM Methods
A primer on qualitative valence bond theory – a theory coming of age
Authors: Shaik Sason , Hiberty Philippe C.
Published: January 2011

The use of valence bond (VB) theory as a general and wide‐ranging qualitative matrix of ideas and predictions is highlighted. Applications are demonstrated for chemical reactivity, properties of polyradicals, excited states, and chemical bonding. Highlighted subtopics include estimations of reaction barriers from simple properties of reactants and products; predictions of stable intermediates in organic, inorganic, and organometallic reactions; and predictions of reaction stereoselectivity. Additional coverage includes a pictorial model for ground and excited states of polyenes and polyradicals, predictions of Hund's rule violations, spin density polarizations and shifts, and a bonding rule in excited states of conjugated molecules. Discussion of new bonding ideas shows the far‐reaching prospects of qualitative VB theory. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 18‐29 DOI: 10.1002/wcms.7

This article is categorized under:

Structure and Mechanism > Molecular Structures
Noncovalent interactions in biochemistry
Authors: Riley Kevin E. , Hobza Pavel
Published: January 2011

Noncovalent interactions are known to play a key role in biochemistry. The knowledge of stabilization (relative) energies and their components is very important for understanding the nature of these interactions. Accurate and benchmark data on interaction (relative) energies and structures can be obtained from coupled‐cluster with single and double and perturbative triple excitations [CCSD(T)] calculations with extended basis of atomic orbitals or even at the complete basis set limit. These methods cannot be, however, used for systems larger than about 50 atoms. In this contribution, the applicability and performance of various recently introduced wavefunction and density functional methods are examined in detail. It is shown that a very good performance by some of these methods is obtained only by introducing empirical parameters fitted mostly to CCSD(T) benchmark data. Among the methods described, special attention is paid to two techniques. First, the symmetry‐adapted perturbation technique that allows obtaining not only accurate values of total interaction energies but also their components. Results of these calculations reveal a key role of dispersion energy in stabilizing the structures of biomolecular systems. Second, the semiempirical quantum chemical parameterized model 6 method (PM6) augmented by empirical terms describing the dispersion and H‐bonding energies. The method is suitable for much extended systems having several thousands of atoms and can be thus used, e.g., in the drug design. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 3‐17 DOI: 10.1002/wcms.8

This article is categorized under:

Structure and Mechanism > Computational Biochemistry and Biophysics
Untersuchungen an quaternären Fluoriden LiMIIMIIIF6, Über die Kationenverteilung in Fluortrirutilen
Authors: Viebahn W. , Epple P.
Published: January 2011

Inhaltsübersicht. Fluortrirutile LiMIIMIIIF6kristallisieren tetragonal in dor Raumgruppe P42/mnm mit Li in Position (2a) und MIIund MIIIstatistisch vorteilt in (4e). An Einkristallen und durch Pulvermessungen wurde die Verteilung der Kationen untersucht, wozu die neu dargestellte Rhodiumverbindung LiZnRhF6auf Grund des unterschiedlichen Streuvermögens der Kationen besonders geeignet war. Verbindungen LiCuMIIIF6zeigen die einfache Rutilstruktur.

Investigations of the Quaternary Fluorides LiMIIMIIIF6. On the Distribution of Cations in Fluorotrirutiles

Abstract. Trirutiles LiMIIMIIIF6crystallize tetragonally in the space group P42/mnm with Li in position (2a) und MIIand MIIIstatistically distributed in (4e). By single‐crystal X‐Ray diffraction and by powder work cation ordering was examined for which the new compound LiZnRhF, was especially adapted. Compounds LiCuMIIIF6are disordered rutile phases.
The Effects of Children’s Migration on Elderly Kin’s Health: A Counterfactual Approach
Authors: Kuhn Randall , Everett Bethany , Silvey Rachel
Published: January 2011

Recent studies of migration and the left-behind have found that elders with migrant children actually experience better health outcomes than those with no migrant children, yet these studies raise many concerns about self-selection. Using three rounds of panel survey data from the Indonesian Family Life Survey, we employ the counterfactual framework developed by Rosenbaum and Rubin to examine the relationship between having a migrant child and the health of elders aged 50 and older, as measured by activities of daily living (ADL), self-rated health (SRH), and mortality. As in earlier studies, we find a positive association between old-age health and children’s migration, an effect that is partly explained by an individual’s propensity to have migrant children. Positive impacts of migration are much greater among elders with a high propensity to have migrant children than among those with low propensity. We note that migration is one of the single greatest sources of health disparity among the elders in our study population, and point to the need for research and policy aimed at broadening the benefits of migration to better improve health systems rather than individual health.
Folate supplementation differently affects uracil content in DNA in the mouse colon and liver
Authors: Kim Kyong-Chol , Jang Hyeran , Sauer Julia , Zimmerly Ella M. , Liu Zhenhua , Chanson Aurelie , Smith Donald E. , Friso Simonetta , Choi Sang-Woon
Published: January 2011

High folate intake may increase the risk of cancer, especially in the elderly. The present study examined the effects of ageing and dietary folate on uracil misincorporation into DNA, which has a mutagenic effect, in the mouse colon and liver. Old (18 months; n 42) and young (4 months; n 42) male C57BL/6 mice were pair-fed with four different amino acid-defined diets for 20 weeks: folate deplete (0 mg/kg diet); folate replete (2 mg/kg diet); folate supplemented (8 mg/kg diet); folate deplete (0 mg/kg diet) with thymidine supplementation (1·8 g/kg diet). Thymidylate synthesis from uracil requires folate, but synthesis from thymidine is folate independent. Liver folate concentrations were determined by the Lactobacillus casei assay. Uracil misincorporation into DNA was measured by a GC/MS method. Liver folate concentrations demonstrated a stepwise increase across the spectrum of dietary folate levels in both old (P = 0·003) and young (P < 0·001) mice. Uracil content in colonic DNA was paradoxically increased in parallel with increasing dietary folate among the young mice (P trend = 0·033), but differences were not observed in the old mice. The mean values of uracil in liver DNA, in contrast, decreased with increasing dietary folate among the old mice, but it did not reach a statistically significant level (P < 0·1). Compared with the folate-deplete group, thymidine supplementation reduced uracil misincorporation into the liver DNA of aged mice (P = 0·026). The present study suggests that the effects of folate and thymidine supplementation on uracil misincorporation into DNA differ depending on age and tissue. Further studies are needed to clarify the significance of increased uracil misincorporation into colonic DNA of folate-supplemented young mice.
Young women partition fatty acids towards ketone body production rather than VLDL-TAG synthesis, compared with young men
Authors: Marinou Kyriakoula , Adiels Martin , Hodson Leanne , Frayn Keith N. , Karpe Fredrik , Fielding Barbara A.
Published: January 2011

Before the menopause, women are relatively protected against CVD compared with men. The reasons for this sex difference are not completely understood, but hepatic fatty acid metabolism may play a role. The present study aimed to investigate the utilisation of plasma NEFA by the liver and to determine whether they are partitioned differently into ketone bodies and VLDL-TAG in healthy, lean young men and women. Volunteers were studied during a prolonged overnight fast (12–19 h) using an intravenous infusion of [U-13C]palmitate. After 12 h fasting, the women had a more advantageous metabolic profile with lower plasma glucose (P < 0·05) and TAG (P < 0·05) but higher plasma NEFA (P < 0·05) concentrations. Plasma 3-hydroxybutyrate (3-OHB) concentrations rose more in women than in men, and the transfer of13C from [U-13C]palmitate to plasma [13C]3-OHB reached a plateau 6–7 h after the start of the infusion in women but was still increasing at 6 h in men. This implies a slower 3-OHB production rate and/or dilution by other precursor pools in men. In women, the high isotopic enrichment of plasma 3-OHB suggested that systemic plasma fatty acids were the major source of 3-OHB production. However, in men, this was not observed during the course of the study (P < 0·01). There were no sex differences for the incorporation of13C into VLDL1- or VLDL2-TAG. The ability of young women to partition fatty acids towards ketone body production rather than VLDL-TAG may contribute to their more advantageous metabolic profile compared with young men.
Longevity of Zygocotyle lunata in Balb/c mice and long-term survival of digeneans in vertebrate hosts
Authors: Fried B. , LeSage K.E.
Published: January 2011

This study used Balb/c mice to examine the longevity of Zygocotyle lunata in a murine host. Of 11 mice, each exposed to 20 Z. lunata cysts, six were infected with a total of 12 worms from 11 to 24 weeks postinfection (PI). Live worms recovered at 24 weeks PI had a mean body area of about 25 mm2. These worms produced viable eggs with well-developed miracidia following embryonation in artificial spring water for 2 weeks at 28°C. The Balb/c mouse is a useful model to study longevity of this paramphistomid trematode for at least 6 months PI. An additional aspect of this article is a review of the pertinent literature published from 1937 to 2007 on ageing and longevity of digeneans.
Endoparasite fauna of five Gadiformes fish species from the coast of Chile: host ecology versus phylogeny
Authors: Chávez R.A. , González M.T. , Oliva M.E. , Valdivia I.M.
Published: January 2011

The aims of the present study were to compare, using multivariate analyses, the degree of similarity of the endoparasite fauna of five fish species belonging to the order Gadiformes:Merluccius gayi,Merluccius australis,Macruronus magellanicus(Gadoidei) andMicromesistius australisandNezumia pulchella(Macrouroidei), from the southern and central Chilean coast, and to evaluate whether the composition of the endoparasite fauna was determined by phylogenetic or ecological relationships. We employed our database ofMerluccius australis,M. magellanicusandMicromesistius australis, which was complemented with published information forM. magellanicus,Merluccius australis,Micromesistius australis,M. gayiandN. pulchella. A higher number of endoparasite species was recorded forMerluccius australis,Micromesistius australisandM. magellanicus, namelyAnisakissp. andHepatoxylon trichiuri, which is the most prevalent parasite among these hosts.Aporocotyle wilhelmiandHysterothylaciumsp. were detected only inM. gayi, whereasLepidapedonsp. was found exclusively inN. pulchella. These results suggest that fish ecology rather than host phylogeny was the most important factor for the determination of similarity in parasite composition. This result could be explained by the similar trophic patterns of hosts and by the predominance of generalist larval species among these fish parasite communities.
Amplification of neutrino oscillations by a density ripple in dense plasmas
Authors: SHUKLA P. K.
Published: January 2011

It is shown that a pre-existing electron density ripple in a dense plasma can excite electron neutrino oscillations. For our purposes, we use the dispersion relation for neutrino oscillations and derive the Mathieu equation for the propagation of neutrino oscillations in the presence of a spatially oscillating electron density ripple. The Mathieu equation predicts instability of neutrino oscillations. The criterion under which instability occurs is presented. Analytical expressions for the neutrino oscillation frequency and the growth rate are obtained. The possible relevance of our investigation to non-thermal neutrino oscillations in dense plasma environments (e.g. the supernovae, the core of white dwarf stars etc.) is briefly mentioned.
Come Buy Hot Corn! Music, Sentiment, and Morality in 1850s New York
Authors: GRIMES ROBERT R.
Published: January 2011

In the 1850s, the residents of, and visitors to, New York City experienced a world of rapid and sometimes chaotic change. Various reform movements—including Temperance, Abolition, and Women's Rights—became stronger and more widely known through various media. In 1853 a simple story published in the pages of theNew York Tribunetook the city by storm. “Hot Corn,” the story of Little Katy, a child peddler, is ostensibly a temperance tale, but something made the story resonate among the public. Soon minstrel songs, sheet music, lectures, novels, and melodramas followed, purporting to herald a new moral crusade against drunkenness, poverty, and child abuse, parallelingUncle Tom's Cabinand the Abolition movement. Within eighteen months, however, the “Hot Corn” phenomenon had faded almost as quickly as it had begun.
The low frequency dynamics of supercooled LiBr, 6H2O
Authors: Bove L. , Dreyfus C. , Polian A. , Bonello B. , Malfanti I. , Taschin A. , Torre R. , Pick R. M.
Published: January 2011

We present results of a series of experiments performed on LiBr, 6H20 from room temperature down to 172 K ≈ 1.2Tg. These ultrasound, Brillouin and depolarized light scattering, and transient grating experiments show that, above 215 K, this solution behaves like supercooled water: its zero frequency sound velocity C0 continuously decreases with decreasing temperature, and the reorientational dynamics of the water molecules can be directly detected at some temperatures of this domain. Conversely, below 215 K, a new regime sets in, where the apparent C0 is practically temperature independent and where a β, Arrenhius like, relaxation process coexists with the usual, Vogel–Fulcher like, α relaxation process of the supercooled liquid. These results are similar to those recently obtained in LiCl, 6H2O. The onset of the new regime is possibly due to an increase of the interaction of the water molecules with a neighboring Li+ ion when lowering the temperature. We also compare our results with published dielectric data on water solutions of glass forming polyalcohols. Some of them present a low temperature splitting of their relaxation time similar to what is found in LiBr, 6H2O.
Microwave N2–Ar plasma torch. I. Modeling
Authors: Henriques J. , Tatarova E. , Ferreira C. M.
Published: January 2011

The spatial structure of a microwave plasma torch driven by an azimuthally symmetric surface wave operating in a N2–Ar mixture at atmospheric pressure is investigated. A two-dimensional (2D) self-consistent theoretical model is developed to investigate the entire spatial structure of the source, including the discharge zone, sustained by the field of the surface TM00 mode, and the postdischarge plasma. Maxwell’s equations, the rate balance equations for the most important excited species—vibrationally and electronically excited states, ions and nitrogen atoms N(S4)—and the Boltzmann equation for electrons are consistently solved. Model calculations of the 2D spatial distributions of species of interest such as charged particles (electrons and positive ions), N2(Χ Σ1g+,v) vibrationally excited molecules, N2(A Σ3u+) metastable molecules, and N(S4) ground state atoms are presented and discussed.
Evaluating force field accuracy with long-time simulations of a β-hairpin tryptophan zipper peptide
Authors: Hayre N. R. , Singh R. R. P. , Cox D. L.
Published: January 2011

We have combined graphics processing unit-accelerated all-atom molecular dynamics with parallel tempering to explore the folding properties of small peptides in implicit solvent on the time scale of microseconds. We applied this methodology to the synthetic β-hairpin, trpzip2, and one of its sequence variants, W2W9. Each simulation consisted of over 8 μs of aggregated virtual time. Several measures of folding behavior showed good convergence, allowing comparison with experimental equilibrium properties. Our simulations suggest that the intramolecular interactions of tryptophan side chains are responsible for much of the stability of the native fold. We conclude that the ff99 force field combined with ff96 ϕ and ψ dihedral energies and an implicit solvent can reproduce plausible folding behavior in both trpzip2 and W2W9.
Ballistic transport in GaN/AlGaN resonant tunneling diodes
Authors: Sakr S. , Warde E. , Tchernycheva M. , Julien F. H.
Published: January 2011

In this work we theoretically study the vertical transport in GaN/AlGaN resonant tunneling diodes in the ballistic regime. Heterostructures based on III-nitride compounds are characterized by a large conduction band discontinuity and a presence of an internal electric field, both of which have important effects on the electronic transport. Using the transfer matrix formalism, we investigate the effect of the energetic barrier height on the resonant current. Our calculations show an increase in the peak to valley ratio (PVR) with increasing Al content of the barriers which arises from the large decrease in the valley current. Furthermore, we show that the current resonances are different for positive and negative applied voltages. We also demonstrate that, due to the asymmetry of the conduction band profile, only one current direction leads to a significant PVR. Finally, we present an approach to achieve large PVR in both current directions by reducing the asymmetry induced by the internal field.
Transposable elements and small RNAs contribute to gene expression divergence between
Arabidopsis thaliana
and
Arabidopsis lyrata
Authors: Hollister Jesse D. , Smith Lisa M. , Guo Ya-Long , Ott Felix , Weigel Detlef , Gaut Brandon S.
Published: January 2011

Transposable elements (TEs) are often the primary determinant of genome size differences among eukaryotes. In plants, the proliferation of TEs is countered through epigenetic silencing mechanisms that prevent mobility. Recent studies using the model plant
Arabidopsis thaliana
have revealed that methylated TE insertions are often associated with reduced expression of nearby genes, and these insertions may be subject to purifying selection due to this effect. Less is known about the genome-wide patterns of epigenetic silencing of TEs in other plant species. Here, we compare the 24-nt siRNA complement from
A. thaliana
and a closely related congener with a two- to threefold higher TE copy number,
Arabidopsis lyrata
. We show that TEs—particularly siRNA-targeted TEs—are associated with reduced gene expression within both species and also with gene expression differences between orthologs. In addition,
A. lyrata
TEs are targeted by a lower fraction of uniquely matching siRNAs, which are associated with more effective silencing of TE expression. Our results suggest that the efficacy of RNA-directed DNA methylation silencing is lower in
A. lyrata
, a finding that may shed light on the causes of differential TE proliferation among species.
Length bias correction for RNA-seq data in gene set analyses
Authors: Gao Liyan , Fang Zhide , Zhang Kui , Zhi Degui , Cui Xiangqin
Published: January 2011

Motivation: Next-generation sequencing technologies are being rapidly applied to quantifying transcripts (RNA-seq). However, due to the unique properties of the RNA-seq data, the differential expression of longer transcripts is more likely to be identified than that of shorter transcripts with the same effect size. This bias complicates the downstream gene set analysis (GSA) because the methods for GSA previously developed for microarray data are based on the assumption that genes with same effect size have equal probability (power) to be identified as significantly differentially expressed. Since transcript length is not related to gene expression, adjusting for such length dependency in GSA becomes necessary.

Results: In this article, we proposed two approaches for transcript-length adjustment for analyses based on Poisson models: (i) At individual gene level, we adjusted each gene's test statistic using the square root of transcript length followed by testing for gene set using the Wilcoxon rank-sum test. (ii) At gene set level, we adjusted the null distribution for the Fisher's exact test by weighting the identification probability of each gene using the square root of its transcript length. We evaluated these two approaches using simulations and a real dataset, and showed that these methods can effectively reduce the transcript-length biases. The top-ranked GO terms obtained from the proposed adjustments show more overlaps with the microarray results.

Availability: R scripts are at http://www.soph.uab.edu/Statgenetics/People/XCui/r-codes/.

Contact:  xcui@uab.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.