bluuebunny/crossref_metadata_2025_split huggingface dataset:
Theoretical studies of electrostatic effect of protein environment on electronic structures and chemical indices of the active site of oxygenated and deoxygenated hemerythrin
Authors: Takano Yu , Yamaguchi Kizashi , Nakamura Haruki 
Published: April 2012

AbstractWe have studied the electrostatic effect of protein environment on electronic structures and chemical indices of the active site of oxygenated and deoxygenated hemerythrin (oxyHr and deoxyHr) using hybrid density functional calculations. We found that the UBHandHLYP method can be regarded as a reliable method for the nature of chemical bonds of Hr even in the protein. The electrostatic effects of the protein environment on oxyHr and deoxyHr greatly improve the magnetic couplings and provide the polarized electronic structures. The electrostatic effects on the active site of oxyHr hardly affect the shape and symmetry of singly occupied natural orbitals but contribute to the enhanced orbital interaction between the active core of Hr and oxygen molecule. This strong orbital interaction leads to easy binding of oxygen molecule to Hr for oxygen transport. Thus, our computation suggests that protein environment regulates the electronic structures of the active site to intensify the intrinsic ability of the active site and to express biological functions such as oxygen transport, energy conversion, and electron transfer. © 2012 Wiley Periodicals, Inc.
Temperature dependence of self‐assembled molecular capsules consisting of gear‐shaped amphiphile molecules with molecular dynamics simulations
Authors: Koseki Jun , Kita Yukiumi , Hiraoka Shuichi , Nagashima Umpei , Tachikawa Masanori 
Published: April 2012

AbstractMolecular dynamics simulations of hexameric molecular capsules constructed from gear‐shaped amphiphile molecules with the aid of solvophobic effect and van der Waals force were performed with general AMBER force field to elucidate the thermodynamical properties of the capsules. The optimized structure of the capsule 16 consisting of methylated gear‐shaped molecules (1) is a nearly cubic structure, whereas the distorted structure is found for the capsule 26 consisting of ones lacking three methyl groups, (2) so as to maximize the contact surface. Disassembly temperature for the demethylated capsule 26, ∼210 K, is much lower than that for the methylated one 16, ∼340 K, which is consistent with the corresponding experimental result that 16 is stable, whereas 2 exists as a monomer in aqueous methanol. © 2012 Wiley Periodicals, Inc.
Molecular Dynamics simulations of azanaphthoquinone annelated pyrrole derivatives as anticancer agent in DNA duplex
Authors: Punkvang Auradee , Pungpo Pornpan , Kamsri Pharit , Kasamsri Dararat , Srisupan Apinya , Saparpakorn Patchreenart , Hannongbua Supa , Wolschann Peter , Prueksaaroon Supakit , Pongprom Nipawan 
Published: April 2012

AbstractThe azanaphthoquinone annelated pyrrole derivatives were synthesized and characterized with an effort to develop novel DNA intercalating agents as anticancer compounds. To model the binding of these compounds in the intercalation site of the DNA duplex, molecular dynamics (MD) simulations using AMBER program were performed. Moreover, molecular mechanics/Poisson–Boltzmann surface area method was used to calculate the binding free energy of azanaphthoquinone annelated pyrrole derivatives in the intercalation site of the DNA duplex. On the basis of MD simulations, the π–π stacking interaction of azanaphthoquinone annelated pyrrole derivatives with base pairs of C and G is the crucial interaction for binding of these DNA intercalating agents. Moreover, the hydrogen bond interaction of side chain could enhance the binding affinity of azanaphthoquinone annelated pyrrole derivatives in the intercalation site. Therefore, the obtained results should be helpful for better understanding the binding of azanaphthoquinone annelated pyrrole derivatives in the intercalation site. © 2012 Wiley Periodicals, Inc.
Bonding Quality of Chemically‐Modified Soybean Protein Concentrate‐Based Adhesives in Particleboards from Rice Husks
Authors: Ciannamea E. M. , Martucci J. F. , Stefani P. M. , Ruseckaite R. A. 
Published: April 2012

AbstractThe aim of the present study was to upgrade the bonding quality and water resistance of medium‐density particleboards based on rice husks (RH) as a wood substitute and soybean protein concentrate (SPC) as the binder via chemical modification of SPC. Alkali (A), citric acid (CA) and boric acid (BA) were used to modify proteins and the carbohydrate complex in SPC. The effect of chemical treatment performed on SPC was followed by Fourier transform infrared, differential scanning calorimetry, thermo‐gravimetric analysis and initial apparent viscosity measurements. Board properties were evaluated in terms of internal bond (IB) and physical properties. Results revealed that boards bonded with SPC treated with boric acid, exhibited the highest IB and the lowest water absorption and thickness swelling at 2 and 24 h, due to cross‐linking reactions with exposed OH‐groups in the amorphous region of cellulose of RH. Results demonstrate that boric acid‐modified–SPC‐bonded boards met the requirements of IB recommended by the US Standard ANSI A208.1‐2009 for M1, MS, M2 and M3‐grade medium‐density particleboards but failed to pass the thickness swelling required. This issue of BSPC‐RH boards is compensated for by the benefit of being formaldehyde‐free which makes them suitable for indoor applications.
Superconductive sodalite-like clathrate calcium hydride at high pressures
Authors: Wang Hui , Tse John S. , Tanaka Kaori , Iitaka Toshiaki , Ma Yanming 
Published: April 2012

Hydrogen-rich compounds hold promise as high-temperature superconductors under high pressures. Recent theoretical hydride structures on achieving high-pressure superconductivity are composed mainly of H
2
fragments. Through a systematic investigation of Ca hydrides with different hydrogen contents using particle-swam optimization structural search, we show that in the stoichiometry CaH
6
a body-centered cubic structure with hydrogen that forms unusual “sodalite” cages containing enclathrated Ca stabilizes above pressure 150 GPa. The stability of this structure is derived from the acceptance by two H
2
of electrons donated by Ca forming an “H
4
” unit as the building block in the construction of the three-dimensional sodalite cage. This unique structure has a partial occupation of the degenerated orbitals at the zone center. The resultant dynamic Jahn–Teller effect helps to enhance electron–phonon coupling and leads to superconductivity of CaH
6
. A superconducting critical temperature (T

c

) of 220–235 K at 150 GPa obtained from the solution of the Eliashberg equations is the highest among all hydrides studied thus far.
Atom-by-atom nucleation and growth of graphene nanopores
Authors: Russo Christopher J. , Golovchenko J. A. 
Published: April 2012

Graphene is an ideal thin membrane substrate for creating molecule-scale devices. Here we demonstrate a scalable method for creating extremely small structures in graphene with atomic precision. It consists of inducing defect nucleation centers with energetic ions, followed by edge-selective electron recoil sputtering. As a first application, we create graphene nanopores with radii as small as 3 Å, which corresponds to 10 atoms removed. We observe carbon atom removal from the nanopore edge in situ using an aberration-corrected electron microscope, measure the cross-section for the process, and obtain a mean edge atom displacement energy of 14.1 ± 0.1 eV. This approach does not require focused beams and allows scalable production of single nanopores and arrays of monodisperse nanopores for atomic-scale selectively permeable membranes.
LOESS correction for length variation in gene set-based genomic sequence analysis
Authors: Aboukhalil Anton , Bulyk Martha L. 
Published: April 2012

Abstract
Motivation: Sequence analysis algorithms are often applied to sets of DNA, RNA or protein sequences to identify common or distinguishing features. Controlling for sequence length variation is critical to properly score sequence features and identify true biological signals rather than length-dependent artifacts.
Results: Several cis-regulatory module discovery algorithms exhibit a substantial dependence between DNA sequence score and sequence length. Our newly developed LOESS method is flexible in capturing diverse score-length relationships and is more effective in correcting DNA sequence scores for length-dependent artifacts, compared with four other approaches. Application of this method to genes co-expressed during Drosophila melanogaster embryonic mesoderm development or neural development scored by the Lever motif analysis algorithm resulted in successful recovery of their biologically validated cis-regulatory codes. The LOESS length-correction method is broadly applicable, and may be useful not only for more accurate inference of cis-regulatory codes, but also for detection of other types of patterns in biological sequences.
Availability: Source code and compiled code are available from http://thebrain.bwh.harvard.edu/LM_LOESS/
Contact: mlbulyk@receptor.med.harvard.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Metab2MeSH: annotating compounds with medical subject headings
Authors: Sartor Maureen A. , Ade Alex , Wright Zach , States David , Omenn Gilbert S. , Athey Brian , Karnovsky Alla 
Published: April 2012

AbstractSummary: Progress in high-throughput genomic technologies has led to the development of a variety of resources that link genes to functional information contained in the biomedical literature. However, tools attempting to link small molecules to normal and diseased physiology and published data relevant to biologists and clinical investigators, are still lacking. With metabolomics rapidly emerging as a new omics field, the task of annotating small molecule metabolites becomes highly relevant. Our tool Metab2MeSH uses a statistical approach to reliably and automatically annotate compounds with concepts defined in Medical Subject Headings, and the National Library of Medicine's controlled vocabulary for biomedical concepts. These annotations provide links from compounds to biomedical literature and complement existing resources such as PubChem and the Human Metabolome Database.Availability: http://metab2mesh.ncibi.orgContact: akarnovs@umich.eduSupplementary information: Supplementary data are available at Bioinformatics online.
On the calculation of signal transduction ability of signaling transduction pathways in intracellular communication: systematic approach
Authors: Chen Bor-Sen , Wu Chia-Chou 
Published: April 2012

Abstract
Motivation: The major function of signal transduction pathways in cells is to sense signals from the environment and process the information through signaling molecules in order to regulate the activity of transcription factors. On the molecular level, the information transmitted by a small number of signal molecules is amplified in the internal signaling pathway through enzyme catalysis, molecular modification and via the activation or inhibition of interactions. However, the dynamic system behavior of a signaling pathway can be complex and, despite knowledge of the pathway components and interactions, it is still a challenge to interpret the pathways behavior. Therefore, a systematic method is proposed in this study to quantify the signal transduction ability.
Results: Based on the non-linear signal transduction system, signal transduction ability can be investigated by solving a Hamilton–Jacobi inequality (HJI)-constrained optimization problem. To avoid difficulties associated with solving a complex HJI-constrained optimization problem for signal transduction ability, the Takagi–Sugeno fuzzy model is introduced to approximate the non-linear signal transduction system by interpolating several local linear systems so that the HJI-constrained optimization problem can be replaced by a linear matrix inequality (LMI)-constrained optimization problem. The LMI problem can then be efficiently solved for measuring signal transduction ability. Finally, the signal transduction ability of two important signal transduction pathways was measured by the proposed method and confirmed using experimental data, which is useful for biotechnological and therapeutic application and drug design.
Contact: bschen@ee.nthu.edu.tw
Supplementary information: Supplementary data are available at Bioinformatics online.
Rknots: topological analysis of knotted biopolymers with R
Authors: Comoglio Federico , Rinaldi Maurizio 
Published: April 2012

Abstract
Motivation: Rknots is a flexible R package providing tools for the detection and characterization of topological knots in biological polymers. The package is well documented and provides a simple syntax for data import and preprocessing, structure reduction, topological analyses and 2D and 3D visualization. Remarkably, Rknots is not limited to protein knots and allows researchers from interdisciplinary fields to analyze different topological structures and to develop simple yet fully custom pipelines.
Availability: Rknots is distributed under the GPL-2 license and is available from the CRAN (the Comprehensive R Archive network) at http://cran.r-project.org/web/packages/Rknots
Contact: federico.comoglio@bsse.ethz.ch
Supplementary Information: Supplementary data are available at Bioinformatics online.
Gabapentin Inhibits γ-Amino Butyric Acid Release in the Locus Coeruleus but Not in the Spinal Dorsal Horn after Peripheral Nerve Injury in Rats
Authors: Yoshizumi Masaru , Parker Renee A. , Eisenach James C. , Hayashida Ken-ichiro 
Published: April 2012

Background
Gabapentin reduces acute postoperative and chronic neuropathic pain, but its sites and mechanisms of action are unclear. Based on previous electrophysiologic studies, the authors tested whether gabapentin reduced γ-amino butyric acid (GABA) release in the locus coeruleus (LC), a major site of descending inhibition, rather than in the spinal cord.

Methods
Male Sprague-Dawley rats with or without L5-L6 spinal nerve ligation (SNL) were used. Immunostaining for glutamic acid decarboxylase and GABA release in synaptosomes and microdialysates were examined in the LC and spinal dorsal horn.

Results
Basal GABA release and expression of glutamic acid decarboxylase increased in the LC but decreased in the spinal dorsal horn after SNL. In microdialysates from the LC, intravenously administered gabapentin decreased extracellular GABA concentration in normal and SNL rats. In synaptosomes prepared from the LC, gabapentin and other α2δ ligands inhibited KCl-evoked GABA release in normal and SNL rats. In microdialysates from the spinal dorsal horn, intravenous gabapentin did not alter GABA concentrations in normal rats but slightly increased them in SNL rats. In synaptosomes from the spinal dorsal horn, neither gabapentin nor other α2δ ligands affected KCl-evoked GABA release in normal and SNL rats.

Discussion
These results suggest that peripheral nerve injury induces plasticity of GABAergic neurons differently in the LC and spinal dorsal horn and that gabapentin reduces presynaptic GABA release in the LC but not in the spinal dorsal horn. The current study supports the idea that gabapentin activates descending noradrenergic inhibition via disinhibition of LC neurons.
Influence of Shielding TPN From Photooxidation on the Number of Early Blood Transfusions in ELBW Premature Neonates
Authors: Stritzke Amélie , Turcot Valérie , Rouleau Thérèse , Lavoie Jean‐Claude , Chessex Philippe 
Published: April 2012

ABSTRACTObjectives:The smallest premature neonates often receive blood transfusions early in life. Nonrestrictive transfusion policies are linked to deleterious outcomes. Exposure of total parenteral nutrition (TPN) to ambient light generates oxidation products associated with haemolysis in vitro. Shielding TPN from light limits oxidation. Our hypothesis was protecting TPN from light decreases haemolysis and therefore the need for early blood transfusions.Methods:Comparison of haemolysis between animals fed enterally and those receiving TPN, and exploratory case‐control retrospective analysis of transfusion counts in premature infants receiving light‐exposed or light‐protected TPN. The statistical analysis was analysis of variance and longitudinal binomial regression model adjusting for potential covariables of transfusion counts.Results:In animals, TPN is associated with higher (P < 0.05) haemolysis compared with enteral feeds; photoprotection induces lower peroxide load with no effect on the level of haemolysis. In premature infants, light‐exposed (n = 76) or light‐protected (n = 57) populations exhibited similar clinical characteristics. Initial haematocrit, gestational age, and index of disease severity had a significant effect on the number of transfusions. When adjusting for these covariables, photoprotection was no longer significant.Conclusions:Even though peroxides are associated in vitro with haemolysis, shielding TPN from light to reduce infused peroxides does not significantly decrease the need for early transfusions in premature infants.
Food safety knowledge, attitude and food handling practices of students
Authors: Sanlier Nevin , Konaklioglu Ece 
Published: April 2012

PurposeThe number of reported food‐borne illnesses has increased recently in the world. In this respect, this study is carried out with the aim of investigating the food safety knowledge, attitude and food handling practices of university students in Turkey.Design/methodology/approachQuestionnaires were applied to 1,340 people volunteered in the study, regarding their knowledge, attitude and practices. The research data was collected through a face‐to‐face questionnaire. An overall number of 1,340 university students from three different institutions were included in this study. Gender distribution was 54.6 per cent for male while that of female was 45.4 per cent, and age range was between 18‐24 years.FindingsDepending on the respondents' gender, a statistically significant difference was found between male and female participants on total food safety knowledge, attitude and practice scores (p<0.001). In addition, there was a statistically significant difference between students' institutes (p<0.001). Also, a correlation was found between food safety knowledge attitude and practice (p<0.001).Research limitations/implicationsBecause the population of this study consisted of university students from different faculties in the city of Ankara, the results cannot be generalized to all students or to all ages. Comment on the results is limited due to responses being self reported, which are prone to bias by the subjects.Originality/valueTo the best of the authors' knowledge, limited studies focused on university students have been found in the Turkish literature and there is a lack of study concerning food safety knowledge, attitude and practice of university students in Ankara, Turkey. The originality of this study is to assess the level of food safety attitude, knowledge and food handling practice to investigate the association between the students' institutions and gender among university students in Turkey. There is a need to assess the food safety knowledge, attitude and practice of this target group as they are more likely to engage in risky eating behaviors, thus are more susceptible to food‐borne illnesses and they are more likely to engage in risky food handling practices because of their future roles as parents and food preparers for his/her family.
Generation Y preferences for wine
Authors: Chrysochou Polymeros , Krystallis Athanasios , Mocanu Ana , Leigh Lewis Rachel 
Published: April 2012

PurposeThe purpose of this paper is to explore differences in wine preferences between Generation Y and older cohorts in the USA.Design/methodology/approachA total of 260 US consumers participated in a web‐based survey that took place in April 2010. The best‐worst scaling method was applied measuring the level of importance given by participants to a list of most common attributes used in choice of wine. Independent sample t‐tests were applied to compare the best‐worst scores between Generation Y and older cohorts.FindingsDifferences were found in the level of importance that Generation Y gives to wine attributes in comparison to older cohorts. Generation Y was found to attach more importance to attributes such as “Someone recommended it”, “Attractive front label” and “Promotional display in‐store”, whereas older cohorts gave more importance to attributes such as “I read about it” and “Grape variety”. This suggests that Generation Y preferences for wine are driven by marketing added‐value activities such as promotions and labelling, whereas limited importance is given to information about wine, reflecting lack of subjective knowledge, experience and involvement about wine.Research limitations/implicationsThis research adds to generation‐based research in wine marketing and contributes towards a better understanding of the differences between generation cohorts in relation to their preferences towards wines.Originality/valueThis study is among the first to compare wine preferences of Generation Y with older cohorts using the best‐worst scaling method.
Nutritional and therapeutic potential of sunflower seeds: a review
Authors: Muhammad Anjum Faqir , Nadeem Muhammad , Issa Khan Muhammad , Hussain Shahzad 
Published: April 2012

PurposeThe purpose of this paper is to provide a comprehensive overview of multiple functions of sunflower seeds including their nutritional and nutraceutical benefits.Design/methodology/approachThe literature review is of the chemical composition of sunflower seeds, their health benefits and their utilization in different products.Findings“We are what we eat.” All living creatures need to take in nutrients to live. Nutrients provide energy for processes in the body and can promote growth, maintenance and repair. The classes of nutrients are carbohydrates, proteins, fats, vitamins, and minerals. Sunflower seeds are a good source of all these nutrients. Plant foods such as fruits, vegetables, oil crops and whole grains contain many components that are beneficial to human health. Research supports that some of these foods, as part of an overall healthful diet, have the potential to delay the onset of many age‐related diseases.Research limitations/implicationsCurrently available information on sunflower seeds is insufficient. These observations have led to continuing research aimed at identifying specific bioactive components in foods, such as antioxidants, which may be responsible for improving and maintaining health. Antioxidants are present in foods as vitamins, minerals, carotenoids, and polyphenols.Originality/valueThis review is unique in its comprehensive nature. This article will reflect the role of sunflower seeds as nutritional and nutraceutical package.