bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revisiting the folding kinetics of bacteriorhodopsin
Authors: Schlebach Jonathan P. , Cao Zheng , Bowie James U. , Park Chiwook 
Published: November 2011

AbstractThe elucidation of the physical principles that govern the folding and stability of membrane proteins is one of the greatest challenges in protein science. Several insights into the folding of α‐helical membrane proteins have come from the investigation of the conformational equilibrium of H. halobium bacteriorhodopsin (bR) in mixed micelles using SDS as a denaturant. In an effort to confirm that folded bR and SDS‐denatured bR reach the same conformational equilibrium, we found that bR folding is significantly slower than has been previously known. Interrogation of the effect of the experimental variables on folding kinetics reveals that the rate of folding is dependent not only on the mole fraction of SDS but also on the molar concentrations of mixed micelle components, a variable that was not controlled in the previous study of bR folding kinetics. Moreover, when the molar concentrations of mixed micelle components are fixed at the concentrations commonly employed for bR equilibrium studies, conformational relaxation in the transition zone is slower than hydrolysis of the retinal Schiff base. As a result, the conformational equilibrium between folded bR and SDS‐denatured bR cannot be achieved under the conventional condition. Our finding suggests that the molar concentrations of mixed micelle components are important experimental variables in the investigation of the kinetics and thermodynamics of bR folding and should be accounted for to ensure the accurate assessment of the conformational equilibrium of bR without the interference of retinal hydrolysis.
Highly controlled InAs nanowires on Si(111) wafers by MOVPE
Authors: Ghalamestani Sepideh Gorji , Johansson Sofia , Borg B. Mattias , Dick Kimberly A. , Wernersson Lars‐Erik 
Published: November 2011

AbstractWe have investigated epitaxial growth of InAs layers on 2″ Si (111) substrates by Metalorganic Vapor Phase Epitaxy. Structural and morphological characterization results confirm high quality of the obtained thin layers. Then, we have utilized the InAs layers as substrates for InAs nanowire growth and Au nanoparticles were lithographically defined at various positions on the surface. Statistical analysis performed on the InAs nanowires grown on 2″ substrates demonstrates our full control on the position, diameter and vertical alignment across the wafer. One possible device application of the aforementioned structure is wrap‐gated Metal‐Oxide‐Semiconductor Field‐Effect Transistors where the InAs layer is employed as the bottom contact and the InAs nanowires act as channel materials. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Numerical analysis of short‐gate GaN HEMTs with Fe‐doped buffer layers
Authors: Hirose Mayumi , Takada Yoshiharu , Tsuda Kunio 
Published: November 2011

AbstractThe influence of Fe‐doped GaN buffer layers on microwave GaN HEMT performance was analyzed using a two‐dimensional numerical model. The device structure model was based on a fabricated Ka‐band AlGaN/GaN HEMT with a 0.2‐µm gate. Deep acceptors brought about by Fe doping were introduced in the GaN buffer layer model, and the concentration profile was based on the Fe concentration profile measured by SIMS. The slow turn‐off of Fe doping was taken into account. The simulated drain current showed a sharp current‐off in the 0.2‐µm gate device, and it was found that this characteristic was influenced by the slow turn‐off Fe‐doping profile. To discuss the effect on drain current collapse in high‐frequency large‐signal operation, ionized deep acceptor concentrations were simulated and compared between the on‐state and off‐state. The results showed that the ionized concentration increases in the off‐state in the area of slow turn‐off Fe‐doping. It is expected that the ionization is one of the causes of drain current collapse in the 0.2‐µm gate device. The simulated results also indicated enhanced collapse in the 0.2‐µm gate device in comparison with the results for a 0.6‐µm gate device (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Self-Renewal of Leukemia Stem Cells in Friend Virus-Induced Erythroleukemia Requires Proviral Insertional Activation of Spi1 and Hedgehog Signaling but Not Mutation of p53
Authors: Hegde Shailaja , Hankey Pamela , Paulson Robert F. 
Published: November 2011

Abstract
Friend virus induces erythroleukemia through a characteristic two-stage progression. The prevailing model proposes that during the initial, polyclonal stage of disease most of the infected cells terminally differentiate, resulting in acute erythrocytosis. In the late stage of disease, a clonal leukemia develops through the acquisition of new mutations—proviral insertional activation of Spi1/Pu.1 and mutation of p53. Previous work from our laboratory demonstrated that Friend virus activates the bone morphogenic protein 4 (BMP4)-dependent stress erythropoiesis pathway, which leads to the rapid expansion of stress erythroid progenitors, which are the targets for Friend virus in the spleen. We recently showed that stress erythroid progenitors have intrinsic self-renewal ability and therefore could function as leukemia stem cells (LSCs) when infected with Friend virus. Here, we show that the two stages of Friend virus-induced disease are caused by infection of distinct stress progenitor populations in the spleen. The development of leukemia relies on the ability of the virus to hijack the intrinsic self-renewal capability of stress erythroid progenitors leading to the generation of LSCs. Two signals are required for the self-renewal of Friend virus LSCs proviral insertional activation of Spi1/Pu.1 and Hedgehog-dependent signaling. Surprisingly, mutation of p53 is not observed in LSCs. These data establish a new model for Friend virus-induced erythroleukemia and demonstrate the utility of Friend virus as a model system to study LSC self-renewal.
Disclosure of potential conflicts of interest is found at the end of this article.
Further delineation of pontocerebellar hypoplasia type 6 due to mutations in the gene encoding mitochondrial arginyl‐tRNA synthetase, RARS2
Authors: Glamuzina Emma , Brown Ruth , Hogarth Kieran , Saunders Dawn , Russell‐Eggitt Isabelle , Pitt Matthew , de Sousa Carlos , Rahman Shamima , Brown Garry , Grunewald Stephanie 
Published: November 2011

AbstractPontocerebellar hypoplasia type 6 (PCH6) (MIM #611523) is a recently described disorder caused by mutations in RARS2 (MIM *611524), the gene encoding mitochondrial arginyl‐transfer RNA (tRNA) synthetase, a protein essential for translation of all mitochondrially synthesised proteins. This case confirms that progressive cerebellar and cerebral atrophy with microcephaly and complex epilepsy are characteristic features of PCH6. Additional features of PCH subtypes 2 and 4, including severe dystonia, optic atrophy and thinning of the corpus callosum, are demonstrated. Congenital lactic acidosis can be present, but respiratory chain dysfunction may be mild or absent, suggesting that disordered mitochondrial messenger RNA (mRNA) translation may not be the only mechanism of impairment or that a secondary mechanism exists to allow some translation. We report two novel mutations and expand the phenotypic spectrum of this likely underdiagnosed PCH variant, where recognition of the characteristic neuroradiological phenotype could potentially expedite genetic diagnosis and limit invasive investigations.
Glycine Surfactants Derived from Dodecenyl Succinic Anhydride
Authors: Dix Leslie , Moon Andrew 
Published: November 2011

AbstractWe report the synthesis and properties of two surfactants with a novel head group based on glycine. A monocarboxylic surfactant N‐glycine methyl ester (2‐dodecen‐1‐yl succinamic acid) (I) was prepared by ring opening of an n‐alkyl succinic anhydride. Hydrolysis of the ester functionality yields a dicarboxylic acid II. The sodium salts of I and II were effective surfactants at neutral pH giving a low minimum surface tension (<30 mN m−1 at 20 °C). At high pH (~12) the surface activity of both surfactants is reduced compared to neutral pH, indicating that at neutral pH an ‘acid soap’ is formed. The pKa of the acid form of the surfactants was determined. Addition of calcium ions reduced the CMC of II but did not reduce the surface tension above the CMC. The resistance of II to calcium ion precipitation was measured at pH 7.
Solid–mush interface conditions for mushy layers
Authors: Gewecke Nicholas R. , Schulze Tim P. 
Published: November 2011

AbstractA subtle issue in the study of mushy zones which form during the solidification of binary alloys is that there are two distinct types of solid–mush interfaces which may occur. One of these is a eutectic front and the other is a front which separates the mushy layer and, assuming complete solute rejection, a layer of pure solid. For semi-infinite-domain configurations that admit similarity solutions, such as those at a uniform initial temperature and concentration with an imposed cold temperature at the lower boundary, only one of the two types appears, and the type of front is determined by the various parameters of the system. In a finite domain, it is possible for each type of front to appear at different times. Specifically, the advance of the eutectic front is restricted by the isotherm associated with the eutectic temperature, and the other front type will appear over a longer time scale. Leading up to the time when the front changes type, the concentration being frozen into the solid decreases. This process writes a history of the system into the solid.
Resource partitioning in relation to cohabitation of Lactobacillus species in the mouse forestomach
Authors: Tannock Gerald W , Wilson Charlotte M , Loach Diane , Cook Gregory M , Eason Jocelyn , O'Toole Paul W , Holtrop Grietje , Lawley Blair 
Published: November 2011

Abstract
Phylogenetic analysis of gut communities of vertebrates is advanced, but the relationships, especially at the trophic level, between commensals that share gut habitats of monogastric animals have not been investigated to any extent. Lactobacillus reuteri strain 100–23 and Lactobacillus johnsonii strain 100–33 cohabit in the forestomach of mice. According to the niche exclusion principle, this should not be possible because both strains can utilise the two main fermentable carbohydrates present in the stomach digesta: glucose and maltose. We show, based on gene transcription analysis, in vitro physiological assays, and in vivo experiments that the two strains can co-exist in the forestomach habitat because 100–23 grows more rapidly using maltose, whereas 100–33 preferentially utilises glucose. Mutation of the maltose phosphorylase gene (malA) of strain 100–23 prevented its growth on maltose-containing culture medium, and resulted in the numerical dominance of 100–33 in the forestomach. The fundamental niche of L. reuteri 100–23 in the mouse forestomach can be defined in terms of ‘glucose and maltose trophism’. However, its realised niche when L. johnsonii 100–33 is present is ‘maltose trophism’. Hence, nutritional adaptations provide niche differentiation that assists cohabitation by the two strains through resource partitioning in the mouse forestomach. This real life, trophic phenomenon conforms to a mathematical model based on in vitro bacterial doubling times, in vitro transport rates, and concentrations of maltose and glucose in mouse stomach digesta.
Exploring binding site of human RBP4 towards discovery of novel inhibitor for treatment of cardiovascular diseases
Authors: Lakshmi Narayana Rao C , Raziya Beevi LA , Umamaheswari Amineni 
Published: November 2011

AbstractRetinol binding proteins (RBPs) are transport proteins that act by solubilizing and protecting their labile ligands in aqueous spaces. In addition, RBPs have diverse and specific functions in regulating the disposition, metabolism and activities of retinoids. Elevated levels of retinol-binding protein 4 (RBP4) are observed in cardiovascular disease conditions, which prompts it as a potential drug target. Therefore, computational approach methods were implemented herein to design a novel inhibitor for RBP4. Crystal structure (2wq9) of RBP4 was retrieved and investigated to locate retinol binding site residues (Lys29, Pro32, Leu35, Phe36, Leu37, Phe45, Ala55, Ala57, Met73, Val74, Gly75, Met88, Try90, His104, Gln117, Arg121, Try133, Phe135, Phe137). Five existing inhibitors of RBP4 were explored against more than one million entries of the Ligand.Info metadatabase to create an in-house library of 2000 compounds. A ligand dataset was prepared using LigPrep and filtered based on Lipinski’s rule of five and reactive group constraints. The crystal structure was optimized and energy minimized applying OPLS force field in Maestro v9.2. Thirteen leads were found to have good binding affinity towards RBP4 through virtual screening workflow of Maestro. Lead 1, namely equilenin (-12.87 kcal/mol) which showed better XPG score was proposed as a potential RBP4 inhibitor. Analysis of docking complexes for the proposed lead revealed a stable hydrogen bond network with good van der Waal interactions and binding orientations. Thus, equilenin would be useful for developing potential drug molecules for cardiovascular diseases.
Kinetics of the reaction of the heaviest hydrogen atom with H2, the 4Heμ + H2 → 4HeμH + H reaction: Experiments, accurate quantal calculations, and variational transition state theory, including kinetic isotope effects for a factor of 36.1 in isotopic mass
Authors: Fleming Donald G. , Arseneau Donald J. , Sukhorukov Oleksandr , Brewer Jess H. , Mielke Steven L. , Truhlar Donald G. , Schatz George C. , Garrett Bruce C. , Peterson Kirk A. 
Published: November 2011

The neutral muonic helium atom 4Heμ, in which one of the electrons of He is replaced by a negative muon, may be effectively regarded as the heaviest isotope of the hydrogen atom, with a mass of 4.115 amu. We report details of the first muon spin rotation (μSR) measurements of the chemical reaction rate constant of 4Heμ with molecular hydrogen, 4Heμ + H2 → 4HeμH + H, at temperatures of 295.5, 405, and 500 K, as well as a μSR measurement of the hyperfine coupling constant of muonic He at high pressures. The experimental rate constants, kHeμ, are compared with the predictions of accurate quantum mechanical (QM) dynamics calculations carried out on a well converged Born–Huang (BH) potential energy surface, based on complete configuration interaction calculations and including a Born–Oppenheimer diagonal correction. At the two highest measured temperatures the agreement between the quantum theory and experiment is good to excellent, well within experimental uncertainties that include an estimate of possible systematic error, but at 295.5 K the quantum calculations for kHeμ are below the experimental value by 2.1 times the experimental uncertainty estimates. Possible reasons for this discrepancy are discussed. Variational transition state theory calculations with multidimensional tunneling have also been carried out for kHeμ on the BH surface, and they agree with the accurate QM rate constants to within 30% over a wider temperature range of 200–1000 K. Comparisons between theory and experiment are also presented for the rate constants for both the D + H2 and Mu + H2 reactions in a novel study of kinetic isotope effects for the H + H2 reactions over a factor of 36.1 in isotopic mass of the atomic reactant.
Friction mechanism of individual multilayered nanoparticles
Authors: Tevet Ofer , Von-Huth Palle , Popovitz-Biro Ronit , Rosentsveig Rita , Wagner H. Daniel , Tenne Reshef 
Published: November 2011

Inorganic nanoparticles of layered [two-dimensional (2D)] compounds with hollow polyhedral structure, known as fullerene-like nanoparticles (IF), were found to have excellent lubricating properties. This behavior can be explained by superposition of three main mechanisms: rolling, sliding, and exfoliation-material transfer (third body). In order to elucidate the tribological mechanism of individual nanoparticles in different regimes, in situ axial nanocompression and shearing forces were applied to individual nanoparticles using a high resolution scanning electron microscope. Gold nanoparticles deposited onto the IF nanoparticles surface served as markers, delineating the motion of individual IF nanoparticle. It can be concluded from these experiments that rolling is an important lubrication mechanism for IF-WS
2
in the relatively low range of normal stress (0.96±0.38 GPa). Sliding is shown to be relevant under slightly higher normal stress, where the spacing between the two mating surfaces does not permit free rolling of the nanoparticles. Exfoliation of the IF nanoparticles becomes the dominant mechanism at the high end of normal stress; above 1.2 GPa and (slow) shear; i.e., boundary lubrication conditions. It is argued that the
modus operandi
of the nanoparticles depends on their degree of crystallinity (defects); sizes; shape, and their mechanical characteristics. This study suggests that the rolling mechanism, which leads to low friction and wear, could be attained by improving the sphericity of the IF nanoparticle, the dispersion (deagglomeration) of the nanoparticles, and the smoothness of the mating surfaces.
An entirely specific type I A-kinase anchoring protein that can sequester two molecules of protein kinase A at mitochondria
Authors: Means Christopher K. , Lygren Birgitte , Langeberg Lorene K. , Jain Ankur , Dixon Rose E. , Vega Amanda L. , Gold Matthew G. , Petrosyan Susanna , Taylor Susan S. , Murphy Anne N. , Ha Taekjip , Santana Luis F. , Tasken Kjetil , Scott John D. 
Published: November 2011

A-kinase anchoring proteins (AKAPs) tether the cAMP-dependent protein kinase (PKA) to intracellular sites where they preferentially phosphorylate target substrates. Most AKAPs exhibit nanomolar affinity for the regulatory (RII) subunit of the type II PKA holoenzyme, whereas dual-specificity anchoring proteins also bind the type I (RI) regulatory subunit of PKA with 10–100-fold lower affinity. A range of cellular, biochemical, biophysical, and genetic approaches comprehensively establish that sphingosine kinase interacting protein (SKIP) is a truly type I-specific AKAP. Mapping studies located anchoring sites between residues 925–949 and 1,140–1,175 of SKIP that bind RI with dissociation constants of 73 and 774 nM, respectively. Molecular modeling and site-directed mutagenesis approaches identify Phe 929 and Tyr 1,151 as RI-selective binding determinants in each anchoring site. SKIP complexes exist in different states of RI-occupancy as single-molecule pull-down photobleaching experiments show that 41 ± 10% of SKIP sequesters two YFP-RI dimers, whereas 59 ± 10% of the anchoring protein binds a single YFP-RI dimer. Imaging, proteomic analysis, and subcellular fractionation experiments reveal that SKIP is enriched at the inner mitochondrial membrane where it associates with a prominent PKA substrate, the coiled-coil helix protein ChChd3.
Prophylactic effect of hot pack on symptoms of eccentric exercise‐induced muscle damage of the wrist extensors
Authors: Khamwong Peanchai , Nosaka Kazunori , Pirunsan Ubon , Paungmali Aatit 
Published: November 2011

AbstractThis study investigated whether hot pack treatment could provide prophylactic effects on muscle damage induced by eccentric exercise of the wrist extensors. Twenty‐eight healthy men (age 21±1 years, weight 65±16 kg, height 171±6 cm) were randomly placed into hot pack (n = 14) and control (n = 14) groups. All participants performed an exercise consisting of 300 maximal eccentric contractions of the wrist extensors of the non‐dominant arm using an isokinetic dynamometer. A hot pack was applied for 20 min to the wrist extensors of the exercised arm before the exercise for the hot pack group. The control group received no treatment before the exercise. Measured variables included pain intensity assessed by a visual analogue scale and a modified Likert's scale, cold thermal pain threshold, pressure pain threshold (PPT), range of motion in active wrist flexion (ROM‐AF) and extension (ROM‐AE), range of motion in passive wrist flexion (ROM‐PF) and extension (ROM‐PE), grip strength, and wrist extension strength. Changes in these variables before, immediately after, and 1 to 8 days following the exercise were compared between groups by a two‐way repeated measures ANOVA. All outcome measures from both groups (except for the cold thermal pain threshold of the hot pack group) demonstrated a significant change within the first 2–3 days following exercise. Significant differences between groups were only found at a single point in time for PPT, ROM‐PF, ROM‐PE and ROM‐AE, and the changes were smaller for the hot pack group in comparison to the control group. These results suggest that the prophylactic effects of hot pack treatment on eccentric exercise‐induced muscle damage of the wrist extensors are limited.
Feature-based classifiers for somatic mutation detection in tumour–normal paired sequencing data
Authors: Ding Jiarui , Bashashati Ali , Roth Andrew , Oloumi Arusha , Tse Kane , Zeng Thomas , Haffari Gholamreza , Hirst Martin , Marra Marco A. , Condon Anne , Aparicio Samuel , Shah Sohrab P. 
Published: November 2011

Abstract
Motivation: The study of cancer genomes now routinely involves using next-generation sequencing technology (NGS) to profile tumours for single nucleotide variant (SNV) somatic mutations. However, surprisingly few published bioinformatics methods exist for the specific purpose of identifying somatic mutations from NGS data and existing tools are often inaccurate, yielding intolerably high false prediction rates. As such, the computational problem of accurately inferring somatic mutations from paired tumour/normal NGS data remains an unsolved challenge.
Results: We present the comparison of four standard supervised machine learning algorithms for the purpose of somatic SNV prediction in tumour/normal NGS experiments. To evaluate these approaches (random forest, Bayesian additive regression tree, support vector machine and logistic regression), we constructed 106 features representing 3369 candidate somatic SNVs from 48 breast cancer genomes, originally predicted with naive methods and subsequently revalidated to establish ground truth labels. We trained the classifiers on this data (consisting of 1015 true somatic mutations and 2354 non-somatic mutation positions) and conducted a rigorous evaluation of these methods using a cross-validation framework and hold-out test NGS data from both exome capture and whole genome shotgun platforms. All learning algorithms employing predictive discriminative approaches with feature selection improved the predictive accuracy over standard approaches by statistically significant margins. In addition, using unsupervised clustering of the ground truth ‘false positive’ predictions, we noted several distinct classes and present evidence suggesting non-overlapping sources of technical artefacts illuminating important directions for future study.
Availability: Software called MutationSeq and datasets are available from http://compbio.bccrc.ca.
Contact: saparicio@bccrc.ca
Supplementary information: Supplementary data are available at Bioinformatics online.