bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulatory versus coding signatures of natural selection in a candidate gene involved in the adaptive divergence of whitefish species pairs (Coregonus spp.)
Authors: Jeukens Julie , Bernatchez Louis 
Published: December 2011

AbstractWhile gene expression divergence is known to be involved in adaptive phenotypic divergence and speciation, the relative importance of regulatory and structural evolution of genes is poorly understood. A recent next‐generation sequencing experiment allowed identifying candidate genes potentially involved in the ongoing speciation of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis), such as cytosolic malate dehydrogenase (MDH1), which showed both significant expression and sequence divergence. The main goal of this study was to investigate into more details the signatures of natural selection in the regulatory and coding sequences of MDH1 in lake whitefish and test for parallelism of these signatures with other coregonine species. Sequencing of the two regions in 118 fish from four sympatric pairs of whitefish and two cisco species revealed a total of 35 single nucleotide polymorphisms (SNPs), with more genetic diversity in European compared to North American coregonine species. While the coding region was found to be under purifying selection, an SNP in the proximal promoter exhibited significant allele frequency divergence in a parallel manner among independent sympatric pairs of North American lake whitefish and European whitefish (C. lavaretus). According to transcription factor binding simulation for 22 regulatory haplotypes of MDH1, putative binding profiles were fairly conserved among species, except for the region around this SNP. Moreover, we found evidence for the role of this SNP in the regulation of MDH1 expression level. Overall, these results provide further evidence for the role of natural selection in gene regulation evolution among whitefish species pairs and suggest its possible link with patterns of phenotypic diversity observed in coregonine species.
Ligand Redox Non‐Innocence in Transition‐Metal σ‐Alkynyl and Related Complexes
Authors: Schauer Phil A. , Low Paul J. 
Published: December 2011

AbstractTransition‐metal σ‐alkynyl complexes are valuable functional materials that have found application as sructural units in the assembly of polymetallic arrays and large molecular structures, reagents for the transfer, oligomerisation or functionalisation of alkynes, magnetic or optical materials and putative components for use in a future molecular‐based electronics platform. Many σ‐alkynyl complexes are redox‐active, undergoing facile oxidation (reduction) at moderate potentials to generate radical cations (anions) in which the charge and spin density can be tuned from being largely metal‐centred to alkynyl ligand‐centred by variation of the nature of the metal, supporting ligands and alkynyl substituents. This review summarises the diverse chemical behaviour of metal‐supported σ‐alkynyl radicals, and some selected closely related systems, which can often be rationalised in terms of the distribution of electron‐spin density over the metal–alkynyl scaffold.
Electrocatalytic Oxidation of Some Hydrazine Compounds at Glassy Carbon Electrode Modified with Co‐Gluconate Complex
Authors: Casella Innocenzo G. , Contursi Michela 
Published: December 2011

AbstractCobalt oxyhydroxide modified glassy carbon electrodes (GC/Co) prepared by anodic electrodepostion in alkaline solution containing gluconate ions as ligand species have been characterized and proposed as sensing probes for the detection of hydrazine compounds. Under cyclic voltammetry and chronoamperometric conditions, the electrooxidation processes of hydrazines on the GC/Co are severely attenuated indicating strong and irreversible adsorption of the analyte on the electrode surface with subsequent formation of stable films with fouling effects on the catalytic sites. On the contrary, under flowing conditions the hydrazine compounds show well‐defined and reproducible peaks with good analytical performance. Flow injection analysis (FIA) carried out at constant applied potential of 0.3 V vs. Ag/AgCl (4 M KCl) and using a flowing stream of 0.1 M NaOH solution containing 50 µM Co2L22− as “on‐line” modifier, shows limits of detection (LODs) comprised between 0.5 µM for hydrazine and 2 µM for 1,2‐dimethyhydrazine. Regression analysis, shows linear ranges spanning over about three orders of magnitude above the detection limits with coefficients of correlation better than 0.96.
CCD‐Type Sodium Ion Image Sensor: Dynamic Observation of Ion‐Exchange Reactions of a Single Na‐Type Cation‐Exchange Resin Bead
Authors: Hattori Toshiaki , Yoshitomo Masaki , Mori Satoshi , Miyamoto Daichi , Kato Ryo , Sawada Kazuaki 
Published: December 2011

AbstractA new sodium ion image sensor containing a CCD‐type semiconductor and a plasticized PVC sodium ion selective membrane was developed. The output potential slope was linear for sodium ion concentrations from 10−1 to 10−5 M. The optimum membrane possessed a near Nernstian response and high selectivity to sodium ions. The sensor can take sodium ion images with a fast response, 0.2 s per image, allowing it to easily monitor the ion‐exchange reactions of a single Na‐type cation‐exchange resin bead. It was found that Na+‐Ba2+ ion‐exchange was faster than Na+‐Ca2+ ion‐exchange in the initial period.
Sediment modelling with fine temporal and spatial resolution for a hilly catchment
Authors: Elliott A. H. , Oehler F. , Schmidt J. , Ekanayake J. C. 
Published: December 2011

AbstractThe suitability of the physically based model SHETRAN for simulating sediment generation and delivery with a high degree of spatial (20 m) and temporal (sub‐hourly) resolution was assessed through application of the model to a 167‐km2 catchment leading to an estuary in New Zealand. By subdividing the catchment and conducting calculations on a computer cluster for a 6‐month hydrology initialisation period, it was possible to simulate a large rainfall event and its antecedent conditions in 24 h of computation time. The model was calibrated satisfactorily to catchment outlet flow and sediment flux for a large rainfall event in two subcatchments (~2 km2). Validation for a separate subcatchment was successful for flow (Nash–Sutcliff efficiency of 0.84) with a factor 2.1 over‐prediction for sediment load. Validation for sediment at full catchment scale using parameters from the subcatchment scale was good for flow but poor for sediment, with gross under‐estimation of the dominant stream sources of sediment. After recalibration at catchment scale, validation for a separate event gave good results for flow (Nash–Sutcliff efficiency of 0.93) and sediment load within a factor of two of measurements. An exploratory spatially explicit landslide model was added to SHETRAN, but it was not possible to test this fully because no landslides were observed in the study period. Application to climate change highlighted the non‐linear response to extreme rainfall. However, full exploration of land use and climate change and the evaluation of uncertainty were severely constrained by computational limitations. Subdivision of the catchment with separate stream routing is suggested as a way forward to overcome these limitations. Copyright © 2011 John Wiley & Sons, Ltd.
Phase Separation Dynamics of Aqueous Poly [(2‐ethoxy) ethoxy ethyl vinyl ether] Solutions as Explored using the Laser T‐Jump Technique Combined With Photometry
Authors: Tsuboi Yasuyuki , Kikuchi Kanae , Kitamura Noboru , Shimomoto Hiroaki , Kanaoka Shokyoku , Aoshima Sadahito 
Published: December 2011

AbstractPoly[(2‐ethoxy) ethoxy ethyl vinyl ether] (poly(EOEOVE)) is a representative thermoresponsive polymer in aqueous solution for which the time constants of the phase separation (PS) are determined with high accuracy. It is revealed that the PS dynamics of the polymer are entirely different from those of the poly(N‐isopropylacrylamide) (PNIPAM) system, which is an alternative representative thermoresponsive polymer. Poly(EOEOVE) exhibits complicated PS behavior that is described using double exponential functions. The PS of poly(EOEOVE) is much faster than the PS of PNIPAM in aqueous solutions and becomes faster with increasing concentration of the polymer. PS behavior that is particular to the present system is successfully understood within the framework of the aggregation mechanism.
On the strong stability of symplectic matrices
Authors: Dosso M. , Sadkane M. 
Published: December 2011

SUMMARYThe strong stability of a symplectic matrix is investigated from algorithmic and numerical viewpoints using a theory developed by S.K. Godunov. This theory is based on a different formulation of the Krein‐Gelfand‐Lidskii characterization of strong stability, better suited for numerical calculations. Copyright © 2011 John Wiley & Sons, Ltd.
Reactive murine lymph nodes uniquely permit parenchymal access for T cells that enter via the afferent lymphatics
Authors: Eidsmo Liv , Stock Angus T , Heath William R , Bedoui Sammy , Carbone Francis R 
Published: December 2011

AbstractWhereas naïve T cells access the lymph nodes predominantly via the high endothelial venules, their effector counterparts can also enter via the afferent lymphatics. It is unclear if such cells are confined to the lymphatic spaces during their transit through the lymph node or whether they can access the lymphocyte‐ and dendritic cell‐rich parenchyma with its potentially stimulatory environment. We used a flank HSV inoculation model that featured neuronal‐mediated movement of virus to distinct areas of skin to study the lymphatic‐mediated transit of activated T cells between different skin‐draining lymph nodes. These experiments showed that activated T cells released from the brachial lymph node, draining the primary site of inoculation, entered the downstream axillary lymph node. These activated T cells accessed the subcapsular areas of the axillary lymph node via lymphatic vessels exiting the upstream brachial node regardless of whether the former drained skin that was associated with active infection. However, T cells remained within the sinusoidal network of the axillary lymph node unless it was directly associated with peripheral infection. Thus, activated T cells that enter a given lymph node using the afferent lymphatics do not have automatic access to the parenchyma unless it is a reactive node involved with peripheral inflammation or infection. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Salicylaldiminato nickel(II) catalysts with 5‐halo‐3‐methoxy groups for ethylene polymerization
Authors: Kolhatkar Nikhil A. , Monfette Amber M. , Lin Shuo , Miri Massoud J. 
Published: December 2011

AbstractTwo neutral salicylaldiminato methyl pyridine nickel(II) complexes were synthesized and evaluated for ethylene polymerization. Each catalyst bears a methoxy group in the 3‐position and a halogen atom in the 5‐position of the salicyl ligand, chlorine in case of catalyst 3a and bromine in 3b. Molecular structures of the catalysts were obtained by X‐ray crystallography. The resulting polymerization activities, for example, indicated by a maximum turnover frequency of 4,870 mol ethylene/(mol Ni × h) for 1‐h runs obtained with 3a, were higher than those of similar catalysts at comparable conditions reported in the literature. Catalyst 3a was slightly more active than catalyst 3b. The polymers are branched as measured by 1H NMR and 13C NMR. This was also reflected in the melting temperatures between 76 and 113 °C obtained by differential scanning calorimetry. By using gel permeation chromatography measurements, it was determined that the Mw of the polymers ranges between about 5,400 and 21,600 g/mol. In particular, the effect of the polymerization temperature on the catalyst activity, degree of branching, and molecular weight properties has been described. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Control of aggregate formation in poly(3‐hexylthiophene) by solvent, molecular weight, and synthetic method
Authors: Scharsich Christina , Lohwasser Ruth H. , Sommer Michael , Asawapirom Udom , Scherf Ullrich , Thelakkat Mukundan , Neher Dieter , Köhler Anna 
Published: December 2011

AbstractAggregate formation in poly(3‐hexylthiophene) depends on molecular weight, solvent, and synthetic method. The interplay of these parameters thus largely controls device performance. In order to obtain a quantitative understanding on how these factors control the resulting electronic properties of P3HT, we measured absorption in solution and in thin films as well as the resulting field effect mobility in transistors. By a detailed analysis of the absorption spectra, we deduce the fraction of aggregates formed, the excitonic coupling within the aggregates, and the conjugation length within the aggregates, all as a function of solvent quality for molecular weights from 5 to 19 kDa. From this, we infer in which structure the aggregated chains pack. Although the 5 kDa samples form straight chains, the 11 and 19 kDa chains are kinked or folded, with conjugation lengths that increase as the solvent quality reduces. There is a maximum fraction of aggregated chains (about 55 ± 5%) that can be obtained, even for poor solvent quality. We show that inducing aggregation in solution leads to control of aggregate properties in thin films. As expected, the field‐effect mobility correlates with the propensity to aggregation. Correspondingly, we find that a well‐defined synthetic approach, tailored to give a narrow molecular weight distribution, is needed to obtain high field effect mobilities of up to 0.01 cm2/Vs for low molecular weight samples (=11 kDa), while the influence of synthetic method is negligible for samples of higher molecular weight, if low molecular weight fractions are removed by extraction. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012
Lung function among infants born preterm, with or without bronchopulmonary dysplasia
Authors: Sanchez‐Solis Manuel , Garcia‐Marcos Luis , Bosch‐Gimenez Vicente , Pérez‐Fernandez Virginia , Pastor‐Vivero Maria D. , Mondéjar‐Lopez Pedro 
Published: December 2011

AbstractObjectiveBoth healthy preterm infants and those with bronchopulmonary dysplasia (BPD) have poor lung function during childhood and adolescence, although there is no evidence whether prematurity alone explains the reduction in lung function found in BPD infants. Our study seeks to know if lung function, measured in infancy by means of rapid thoracic compression with raised volume technique, is different between preterm infants with and without BPD.MethodsLung function was measured in 43 preterm infants with BPD and in 32 preterm infants without BPD at a chronological age range of 2–28 months. Forced vital capacity (FVC), forced expiratory volume at 0.5 sec, and forced expiratory flows at 50, 75, 85%, and 25–75% of FVC were obtained from maximal expiratory volume curves by means of rapid thoracic compression with raised volume technique. Maximal flow at functional residual capacity was measured using rapid thoracic compression at tidal volume. Multiple regression analysis and generalized least squares (GLS) random‐effects regression model were used to control for variables such as gender, weeks of gestation, age, birth weight, and tobacco smoke exposure. A sub‐analysis was performed in infants born at 28+ weeks of gestation.ResultsBPD was associated to significantly lower flows (regression coefficients: −0.51, −0.54, −57, −0.53, and −0.82, respectively for FEF50, FEF75, FEF85, FEF25–75). This association was driven by males and maintained in the subgroup of infants born at 28+ weeks of gestation.ConclusionBPD is associated with an additional decrease of lung function during the first 2 years of life in infants born preterm. Pediatr Pulmonol. 2012; 47:674–681. © 2011 Wiley Periodicals, Inc.
The Sensitivity of Lung Disease Surrogates in Detecting Chest CT Abnormalities in Children With Cystic Fibrosis
Authors: Sanders Don B. , Li Zhanhai , Rock Michael J. , Brody Alan S. , Farrell Philip M. 
Published: December 2011

AbstractRationaleChest CT scans detect structural abnormalities in children with cystic fibrosis (CF), even when pulmonary function tests (PFTs) are normal. The use of chest CT is limited in clinical practice, because of concerns over expense, increased resource utilization, and radiation exposure. Quantitative chest radiography scores are useful in detecting mild lung disease, but whether they are sensitive to the presence of CT scan abnormalities has not been evaluated.ObjectiveTo determine in a cross‐sectional study if quantitative chest radiography is a more sensitive marker of chest CT abnormalities than other lung disease surrogates.MethodsBrody chest CT scores were calculated for 81 children enrolled in the Wisconsin CF Neonatal Screening Project. We determined the sensitivity for Wisconsin (WCXR) and Brasfield (BCXR) chest radiography scores, PFTs, positive cultures forP. aeruginosa(PA), and parental report of symptoms to detect a Brody score worse than the median score for study participants.Measurements and Main ResultsThe mean FEV1for the study population was 91% predicted. Abnormal WCXR and BCXR scores had the highest sensitivity to detect a chest CT score worse than the median; abnormal PFTs, parental report of symptoms, and the presence of PA had much lower sensitivity (P < 0.001).ConclusionsIn this cross sectional study, quantitative chest radiography has excellent sensitivity to detect an abnormal chest CT and may have a role in monitoring lung disease progression in children with CF. Pediatr Pulmonol. 2012; 47:567–573. © 2011 Wiley Periodicals, Inc.
Validating the vitality strategy for fighting drug resistance
Authors: Singh Nidhi , Frushicheva Maria P. , Warshel Arieh 
Published: December 2011

AbstractThe current challenge in designing effective drugs against HIV‐1 is to find novel candidates with high potency, but with a lower susceptibility to mutations associated with drug resistance. Trying to address this challenge, we developed in our previous study (Ishikita and Warshel, Angew Chem Int Ed Engl 2008; 47:697–700) a novel computational strategy for fighting drug resistance by predicting the likely moves of the virus through constraints on binding and catalysis. This has been based on calculating the ratio between the vitality values ((Ki kcat/KM)mutant/(Ki kcat/KM)wild‐type) and using it as a guide for predicting the moves of the virus. The corresponding calculations of the binding affinity, Ki , were carried out using the semi‐macroscopic version of the protein dipole Langevin dipole (PDLD/S) in its linear response approximation (LRA) in its β version (PDLD/S‐LRA/β). We also calculate the proteolytic efficiency, kcat/KM, by evaluating the transition state (TS) binding free energies using the PDLD/S‐LRA/β method. Here we provide an extensive validation of our strategy by calculating the vitality of six existing clinical and experimental drug candidates. It is found that the computationally determined vitalities correlate reasonably well with those derived from the corresponding experimental data. This indicates that the calculated vitality may be used to identify mutations that would be most effective for the survival of the virus. Thus, it should be possible to use our approach in screening for mutations that would provide the most effective resistance to any proposed antiviral drug. This ability should be very useful in guiding the design of drug molecules that will lead to the slowest resistance. Proteins 2012; © 2011 Wiley Periodicals, Inc.
Molecular insight into substrate recognition by human cytosolic sialidase NEU2
Authors: Mozzi Alessandra , Mazzacuva Pietro , Zampella Giuseppe , Forcella Matilde Emma , Fusi Paola Alessandra , Monti Eugenio 
Published: December 2011

AbstractSialidases or neuramidases are glycoside hydrolases removing terminal sialic acid residues from sialo‐glycoproteins and sialo‐glycolipids. Viral neuraminidases (NAs) have been extensively characterized and represent an excellent target for antiviral therapy through the synthesis of a series of competitive inhibitors that block the release of newly formed viral particles from infected cells. The human cytosolic sialidase NEU2 is the only mammalian enzyme structurally characterized and represents a valuable model to study the specificity of novel NA inhibitory drugs. Moreover, the availability of NEU2 3D structure represents a pivotal step toward the characterization of the molecular basis of natural substrates recognition by the enzyme. In this perspective, we have carried out a study of molecular docking of NEU2 active site using natural substrates of increasing complexity. Moreover, selective mutations of the residues putatively involved into substrate(s) interaction/recognition have been performed, and the resulting mutant enzymes have been preliminary tested for their catalytic activity and substrate specificity. We found that Q270 is involved in the binding of the disaccharide α(2,3) sialyl‐galactose, whereas K45 and Q112 bind the distal glucose of the trisaccharide α(2,3) sialyl‐lactose, corresponding to the oligosaccharide moiety of GM3 ganglioside. In addition, E218, beside D46, is proved to be a key catalytic residue, being, together with Y334, the second member of the nucleophile pair required for the catalysis. Overall, our results point out the existence of a dynamic network of interactions that are possibly involved in the recognition of the glycans bearing sialic acid. Proteins 2012; © 2011 Wiley Periodicals, Inc.
The effects of rigid motions on elastic network model force constants
Authors: Lezon Timothy R. 
Published: December 2011

AbstractElastic network models provide an efficient way to quickly calculate protein global dynamics from experimentally determined structures. The model's single parameter, its force constant, determines the physical extent of equilibrium fluctuations. The values of force constants can be calculated by fitting to experimental data, but the results depend on the type of experimental data used. Here, we investigate the differences between calculated values of force constants and data from NMR and X‐ray structures. We find that X‐ray B factors carry the signature of rigid‐body motions, to the extent that B factors can be almost entirely accounted for by rigid motions alone. When fitting to more refined anisotropic temperature factors, the contributions of rigid motions are significantly reduced, indicating that the large contribution of rigid motions to B factors is a result of over‐fitting. No correlation is found between force constants fit to NMR data and those fit to X‐ray data, possibly due to the inability of NMR data to accurately capture protein dynamics. Proteins 2012; © 2011 Wiley Periodicals, Inc.