bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pharmacophore Identification, Molecular Docking, Virtual Screening, and In Silico ADME Studies of Non‐Nucleoside Reverse Transcriptase Inhibitors
Authors: Pirhadi Somayeh , Ghasemi Jahan B. 
Published: November 2012

AbstractNon‐nucleoside reverse transcriptase inhibitors (NNRTIs) have gained a definitive place due to their unique antiviral potency, high specificity and low toxicity in antiretroviral combination therapies used to treat HIV. In this study, chemical feature based pharmacophore models of different classes of NNRT inhibitors of HIV‐1 have been developed. The best HypoRefine pharmacophore model, Hypo 1, which has the best correlation coefficient (0.95) and the lowest RMS (0.97), contains two hydrogen bond acceptors, one hydrophobic and one ring aromatic feature, as well as four excluded volumes. Hypo 1 was further validated by test set and Fischer validation method. The best pharmacophore model was then utilized as a 3D search query to perform a virtual screening to retrieve potential inhibitors. The hit compounds were subsequently subjected to filtering by Lipinski’s rule of five and docking studies by Libdock and Gold methods to refine the retrieved hits. Finally, 7 top ranked compounds based on Gold score fitness function were subjected to in silico ADME studies to investigate for compliance with the standard ranges.
Prediction of hERG Potassium Channel Blocking Actions Using Combination of Classification and Regression Based Models: A Mixed Descriptors Approach
Authors: Kar Supratik , Roy Kunal 
Published: November 2012

AbstractA set of 242 compounds with diverse molecular structures and having different mechanisms of therapeutic actions was used to develop classification and regression based QSAR models for the identification of potential hERG channel blockers. The developed in silico models made it possible to obtain a quantitative interpretation of the structural information and physicochemical properties of the molecules for their hERG binding affinity along with exploration of the discriminant functions differentiating between lower and higher hERG blocking potency compounds by the classification approach. The developed models were rigorously validated internally as well as externally with the application of the principles of Organization for Economic Cooperation and Development (OECD) for the validation purpose. The test for domain of applicability was also carried out for checking reliability of the predictions. Pharmacological distribution diagrams (PDDs) were employed as a visualizing technique for the classification approach. Important fragments relevant to hERG binding affinity were identified through critical analysis and interpretation of the developed models. Finally, the developed models were implemented to screen hERG channel blocking properties for a huge number compounds of the DrugBank database. In silico prediction for hERG channel blocking potential for each of the DrugBank compounds is possible from the developed models.
Re‐analysis of an original CMTX3 family using exome sequencing identifies a known BSCL2 mutation
Authors: Chaudhry Rabia , Kidambi Aditi , Brewer Megan Hwa , Antonellis Anthony , Mathews Katherine , Nicholson Garth , Kennerson Marina 
Published: November 2012

ABSTRACTIntroductionCharcot–Marie–Tooth (CMT) disease is a group of peripheral neuropathies affecting both motor and sensory nerves. CMTX3 is an X‐linked CMT locus, which maps to chromosome Xq26.3–q27.3. Initially, CMTX3 was mapped to a 31.2‐Mb region in 2 American families. We have reexamined 1 of the original families (US‐PED2) by next generation sequencing.MethodsThree members of the family underwent exome sequencing. Candidate variants were validated by PCR and Sanger sequencing analysis.ConclusionNo pathogenic coding variants localizing to the CMTX3 region were identified. However, exome sequencing identified a known BSCL2 mutation (N88S). This study demonstrates the power of exome sequencing as a tool to identify gene mutations for a small family in the absence of statistically significant linkage data. Muscle Nerve 47: 922–924, 2013
Dynamics of electrospinning of poly(caprolactone) via a multi‐nozzle spinneret connected to a twin screw extruder and properties of electrospun fibers
Authors: Senturk‐Ozer Semra , Ward Daniel , Gevgilili Halil , Kalyon Dilhan M. 
Published: November 2012

AbstractConventional electrospinning is a simple process, suitable for the processing of solvated polymers at relatively low rates. It lacks the capabilities of conveying of solids, mixing of polymeric resins and devolatilization and has limited capabilities in melting and incorporation of fillers, including nanoparticles. The use of a twin screw extruder as the front end of the electrospinning process provides these capabilities but only becomes feasible at relatively high throughput rates. Such high rates of electrospinning can only be achieved by using multi‐nozzle spinnerets. However, the dynamics of electrospinning processes using multi‐nozzle spinnerets has not been well studied. Here a multi‐nozzle spinneret attached to a hybrid twin screw extrusion and electrospinning apparatus was employed for the characterization of the dynamics in terms of the electrospun mesh thickness distributions of poly(caprolactone), PCL, as a function of the principal parameters of the electrospinning process, i.e., applied voltage, distance of separation between the spinneret die, and the collector, i.e., a conductive mandrel, and its rotational speed. PCL fiber diameter and orientation distributions, as well as the thickness, crystallinity, and mechanical properties of the non‐woven meshes, were characterized to gain a basic understanding of how the electrospun mesh properties develop as a function of process parameters in the multi‐nozzle configuration. ENG. SCI., 2013. © 2012 Society of Plastics Engineers
Stress‐assisted formation of surface gratings on polymer films
Authors: Lin Chiao‐Chi , Yang Fuqian , Chin Joannie W. , Sung Lipiin , Lee Sanboh 
Published: November 2012

AbstractThe effect of biaxial‐residual–compressive surface stress on the surface modulation of solid films is analyzed. The results show that the biaxial compressive stress can create surface modulation with the orientation being 45° (135°) to the principal directions of the stresses. Using uniaxial tension, a complementary set of nonsymmetrical polymer ripple gratings is formed on the fracture surface of a polymer film that is sandwiched between two relatively glass slides. The effect of geometrical shape and boundary confinement is examined on the surface modulation. The orientation of the polymer ripple gratings is found to be 45° to the longitudinal direction of the films for long‐rectangular polymer thin films in accord with the analysis. POLYM. ENG. SCI., 2013. © 2012 Society of Plastics Engineers
Nocturnal phenotypical features of obstructive sleep apnea (OSA) in asthmatic children
Authors: Gutierrez Maria J. , Zhu Junjia , Rodriguez‐Martinez Carlos E. , Nino Cesar L. , Nino Gustavo 
Published: November 2012

AbstractBackgroundAsthma and obstructive sleep apnea (OSA) often coexists during childhood. To delineate this clinical association, we investigated the phenotypical features of OSA in asthmatic children. Specifically, we hypothesized that asthmatic children have a distinct OSA phenotype that involves a higher prevalence of Rapid‐Eye‐Movement (REM)‐related breathing abnormalities relative to children with OSA alone.MethodsWe conducted a retrospective cross‐sectional analysis of 141 children aged 2–12 years with OSA diagnosed by polysomnography (PSG) in our sleep center. Outcomes included PSG parameters, maximal %SaO2 REM desaturations and prevalence of REM‐related OSA. Multivariate linear regression model or logistic regression model was built to study the joint effect of asthma and OSA parameters with control for potential confounders (significance level P < 0.05).ResultsBaseline respiratory parameters, obstructive apnea–hypopnea index (OAHI) severity, and oxygenation during NREM sleep were unaffected by the presence of asthma in children with OSA. In contrast, maximal %SaO2 REM desaturation, REM–OAHI and prevalence of REM‐related OSA in children with moderate–severe OSA were significantly increased in asthmatic children with OSA compared to subjects with OSA alone. Multivariate analysis revealed that the association between asthma and REM‐related OSA parameters is independent of asthma control, BMI, age, and gender. The presence of REM‐related OSA in asthmatics was unaffected by rhinitis or atopic status.ConclusionThese results demonstrate that asthma is associated with REM‐related breathing abnormalities in children with moderate–severe OSA. The link between asthma and REM‐related OSA is independent of asthma control and obesity. Further research is needed to delineate the REM‐sleep biological mechanisms that modulate the phenotypical expression of OSA in asthmatic children. Pediatr Pulmonol. 2013; 48:592–600. © 2012 Wiley Periodicals, Inc.
The role of extended defects on the performance of optoelectronic devices in nitride semiconductors
Authors: Moustakas Theodore D. 
Published: November 2012

AbstractIn this paper I am addressing the fundamental question as to why the performance of optoelectronic devices based on nitride semiconductors is insensitive to high concentration of extended defects, which is not the case for traditional III–V compounds. There are three important differences between these two families of semiconductors, which contribute to this finding: (a) the chemical bonds in nitrides are strongly ionic while are mostly covalent in III–V compounds. This leads to the bunching of the surface states as well as the states associated with dangling bonds in edge dislocations near the band edges, which prevents them from being non‐radiative recombination centers. Furthermore, the surface states have less effect on the surface Fermi level position; (b) the nitrides can exist in the wurtzite structure (equilibrium) and the cubic structure (metastable) and the enthalpy of formation of the two allotropic forms differs only by a few meV. Thus, conversions between the two phases occur easily by creation of stacking faults along the closed packed (0001) and (111) planes. As a result basal plane stacking faults are abundant in both compounds and alloys. This leads to strong band structure potential fluctuations; (c) additional band structure potential fluctuations exist in InGaN and AlGaN alloys, due to phase separation and alloy ordering. Both types of potential fluctuations contribute to exciton localization and thus efficient radiative recombination even at room temperature.
Topological insulators from the perspective of first‐principles calculations
Authors: Zhang Haijun , Zhang Shou‐Cheng 
Published: November 2012

Abstractmagnified imageTopological insulators are new quantum states with helical gapless edge or surface states inside the bulk band gap. These topological surface states are robust against weak time‐reversal invariant perturbations without closing the bulk band gap, such as lattice distortions and non‐magnetic impurities. Recently a variety of topological insulators have been predicted by theories, and observed by experiments. First‐principles calculations have been widely used to predict topological insulators with great success. In this review, we summarize the current progress in this field from the perspective of first‐principles calculations. First of all, the basic concepts of topological insulators and the frequently‐used techniques within first‐principles calculations are briefly introduced. Secondly, we summarize general methodologies to search for new topological insulators. In the last part, based on the band inversion picture first introduced in the context of HgTe, we classify topological insulators into three types with s–p, p–p and d–f, and discuss some representative examples for each type.magnified imageSurface states of topological insulator Bi2Se3 consist of a single Dirac cone, as obtained from first‐principles calculations.(© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Predicting simulation parameters of biological systems using a Gaussian process model
Authors: Zhu Xiangxin , Welling Max , Jin Fang , Lowengrub John 
Published: November 2012

AbstractFinding optimal parameters for simulating biological systems is usually a very difficult and expensive task in systems biology. Brute force searching is infeasible in practice because of the huge (often infinite) search space. In this article, we propose predicting the parameters efficiently by learning the relationship between system outputs and parameters using regression. However, the conventional parametric regression models suffer from two issues, thus are not applicable to this problem. First, restricting the regression function as a certain fixed type (e.g. linear, polynomial, etc.) introduces too strong assumptions that reduce the model flexibility. Second, conventional regression models fail to take into account the fact that a fixed parameter value may correspond to multiple different outputs due to the stochastic nature of most biological simulations, and the existence of a potentially large number of other factors that affect the simulation outputs. We propose a novel approach based on a Gaussian process model that addresses the two issues jointly. We apply our approach to a tumor vessel growth model and the feedback Wright–Fisher model. The experimental results show that our method can predict the parameter values of both of the two models with high accuracy. © 2012 Wiley Periodicals, Inc. Statistical Analysis and Data Mining, 2012
Flexible, Planar‐Integrated, All‐Solid‐State Fiber Supercapacitors with an Enhanced Distributed‐Capacitance Effect
Authors: Liu Bin , Tan Dongsheng , Wang Xianfu , Chen Di , Shen Guozhen 
Published: November 2012

AbstractFlexible and highly efficient energy storage units act as one of the key components in portable electronics. In this work, by planar‐integrated assembly of hierarchical ZnCo2O4 nanowire arrays/carbon fibers electrodes, a new class of flexible all‐solid‐state planar‐integrated fiber supercapacitors are designed and produced via a low‐cost and facile method. The as‐fabricated flexible devices exhibit high‐efficiency, enhanced capacity, long cycle life, and excellent electrical stability. An enhanced distributed‐capacitance effect is experimentally observed for the device. This strategy enables highly flexible new structured supercapacitors with maximum functionality and minimized size, thus making it possible to be readily applied in flexible/portable photoelectronic devices.
Synthesis and Structural Diversity of Four Coordination Polymers with the Ligand 1‐(3‐Aminopropyl)‐imidazole
Authors: Qi Zhao‐Peng , Li Pei‐Yu , Chen Long , Li Chang‐Jiang , Liu Wei‐Bing , Cheng Xing , Kang Zong‐Hui 
Published: November 2012

AbstractFour new metal complexes {[Cu(api)2(H2O)]·(ClO4)2·CH3CN}n (1), [Cu(api)2(ClO4)2]n (2), [Cd(api)2(SCN)2]n (3) and [Ni(api)2(SCN)2]n (4) (api = 1‐(3‐Aminopropyl)‐imidazole) were synthesized by reactions of api and different metal salts under different conditions. Interestingly, complexes 1–3 exhibit various one dimensional (1D) double chain structures, while complex 4 shows a 2D layer structure. The results indicate that metal ions, anions, solvents, and the synthesis methods, have great influence on the formation and structure of the complexes.
On the trigonometric moment problem
Authors: ÁLVAREZ AMELIA , BRAVO JOSÉ LUIS , CHRISTOPHER COLIN 
Published: November 2012

AbstractThe trigonometric moment problem arises from the study of one-parameter families of centers in polynomial vector fields. It seeks to classify the trigonometric polynomials $Q$ which are orthogonal to all powers of a trigonometric polynomial $P$. We show that this problem has a simple and natural solution under certain conditions on the monodromy group of the Laurent polynomial associated to $P$. In the case of real trigonometric polynomials, which is the primary motivation of the problem, our conditions are shown to hold for all trigonometric polynomials of degree 15 or less. In the complex case, we show that there are a small number of exceptional monodromy groups up to degree 30 where the conditions fail to hold and show how counterexamples can be constructed in several of these cases.
On conjugations of circle homeomorphisms with two break points
Authors: AKHADKULOV HABIBULLA , DZHALILOV AKHTAM , MAYER DIETER 
Published: November 2012

AbstractLetfi∈C2+α(S1∖{ai,bi}),α>0,i=1,2, be circle homeomorphisms with two break pointsai,bi, that is, discontinuities in the derivativeDfi, with identical irrational rotation numberρandμ1([a1,b1])=μ2([a2,b2]), whereμiare the invariant measures offi,i=1,2. Suppose that the products of the jump ratios ofDf1andDf2do not coincide, that is,Df1(a1−0)/Df1(a1+0)⋅Df1(b1−0)/Df1(b1+0)≠Df2(a2−0)/Df2(a2+0)⋅Df2(b2−0)/Df2(b2+0) . Then the mapψconjugatingf1andf2is a singular function, that is, it is continuous onS1, butDψ(x)=0 almost everywhere with respect to Lebesgue measure.
Influence of fatty acid patterns on the intestinal absorption pathway of quercetin in thoracic lymph duct-cannulated rats
Authors: Murota Kaeko , Cermak Rainer , Terao Junji , Wolffram Siegfried 
Published: November 2012

Since it is known that dietary fats improve the bioavailability of the flavonol quercetin, we purposed to investigate whether this effect is due to increased lymphatic transport of quercetin. In rats with implanted catheters in the thoracic lymph duct, we administered quercetin into the duodenum with TAG emulsions containing either long-chain fatty acids (LCT) or medium-chain fatty acids (MCT). Controls received quercetin together with a glucose solution. LCT administration increased the lymphatic output of quercetin (19·1 (sem1·2) nmol/8 h) as well as the lymph-independent bioavailability of the flavonol, determined as area under the plasma concentration curve (1091 (sem142) μm× min). Compared with glucose administration, MCT neither increased the lymphatic output (12·3 (sem1·5) nmol/8 h) nor the bioavailability of quercetin (772 (sem99) μm× min) significantly (glucose group: 9·8 (sem1·5) nmol/8 h and 513 (sem55) μm× min, respectively). Because LCT are released within chylomicrons into the intestinal lymph while MCT are mainly released into the portal blood, we conclude from the present results that dietary fats that are mainly composed of LCT improve quercetin bioavailability by increasing its transport via the lymph, thereby circumventing hepatic first-pass metabolism of the flavonol. In addition, LCT could enhance quercetin absorption by improving its solubility in the intestinal tract.
SEX COMPOSITION OF THE WORKPLACE AND MORTALITY RISK
Authors: BARCLAY KIERON J. 
Published: November 2012

SummaryThis study uses Swedish occupational register data to examine whether the proportion of men in administrative workplaces in the Swedish public service affects all-cause mortality risks amongst both males and females of working age. Using piecewise constant survival models to analyse occupational data from the Swedish administrative registers from 1995 to 2007, it was found that for males, a 1% increase in the proportion of males was associated with a 1.3% increase in mortality risk (hazard ratio, HR 1.013, 95% CI 1.007–1.020, p<0.001), but no association was found for females (HR 1.004, 95% CI 0.996–1.012, p=0.297). Adjustments were made for age, family status, education, occupational status, occupational segregation by sex, the total number of individuals in the workplace, level of government, region, period and variables reflecting the workplace structure by age, age by sex, occupation and education. A higher proportion of males may be related to (i) an increased exposure to risky health behaviours such as alcohol consumption and unhealthy dietary patterns, (ii) a tendency towards sickness presenteeism, and (iii) an increase in the levels of several well-established emotional stressors in the workplace, leading to an increased level of psychosocial stress. The findings and potential extensions of this research are discussed.
The effects of quarter-individual milking in conventional milking parlours on the somatic cell count and udder health of dairy cows
Authors: Müller Anika B , Rose-Meierhöfer Sandra , Ammon Christian , Brunsch Reiner 
Published: November 2012

The objective of this study was to examine the quarter health status of quarter-individually and conventionally milked cows. The MultiLactor®, a quarter-individual milking system (MULTI), has single guided tubes which provide milking on the quarter level with a low system vacuum level (37 kPa), sequential pulsation and periodic air inlet. The conventional milking system (CON) was equipped with a milking cluster where the system vacuum level was adjusted to 40 kPa. A total of 84 German Holstein cows, randomly divided into two groups, were included in the study. Over a period of 32 trial weeks, quarter foremilk samples were taken every week to determine somatic cell count (SCC). Bacteriological examinations and udder palpation were conducted at three different times. During the trial period, median SCC of quarter foremilk samples in both groups did not exceed the threshold value of 100 000 cells/ml. The results of theFtest showed that the milking system (P = 0·0587) and days in milk (DIM) (P = 0·8066) had no significant effects on the quarter health status. On the other hand, lactation (P = 0·0396), quarter health status in the previous week (P < 0·0001) and trial week (P = 0·0061) affected quarter health status significantly. The estimated probabilities of the occurrence of a suspicious quarter (SCC > 100 000 cells/ml) were 19·97% (CON) and 31·72% (MULTI). However, the test of differences in the Least Square Means (LSM) showed no significant differences (P = 0·0585) between CON and MULTI. The estimated probability of quarters becoming suspicious during the first lactation was 12·51% for both groups. With an increasing number of lactation, the probability of a quarter becoming suspicious clearly increased (2nd lactation: 32·73% and 3rd lactation: 36·19%). The results also showed that the percentage of quarters with bacteriological findings revealed a stronger increase over time for MULTI than for CON.
Artiguista, White, Cosmopolitan and Educated: Constructions of Nationhood in Uruguayan Textbooks and Related Narratives, 1868–1915
Authors: HENTSCHKE JENS R. 
Published: November 2012

AbstractUruguay's late nineteenth- and early twentieth-century economic modernisation and political institutionalisation were accompanied by the education reform led by José Pedro and Jacobo Varela, which was extended to the whole country during the administrations of José Batlle y Ordóñez. Schools were to insert future generations into the capitalist world market and a more liberal polity. This article explores how official manuals and related texts constructed the nation. They invented a foundation narrative that made José Artigas a protagonist of independence; converted Amerindians into extinct ancestors; represented European immigrants as dynamic elements who, rightly mixed, would form a new ethnic group and help the cosmopolitan lettered city to civilise the gaucho; and taught children that hard work and education held the key to prosperity.