bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lung volumes and distribution of ventilation in survivors to congenital diaphragmatic hernia (CDH) during infancy
Authors: Dotta Andrea , Palamides Sabrina , Braguglia Annabella , Crescenzi Francesco , Ronchetti Maria Paola , Calzolari Flaminia , Iacobelli Barbara Daniela , Bagolan Pietro , Corchia Carlo , Orzalesi Marcello 
Published: May 2007

AbstractThe assessment of lung volumes, particularly functional residual capacity (FRC), is crucial for understanding lung development during infancy in CDH patients.AimTo evaluate changes in lung function during infancy in subjects with CDH treated with a “gentle ventilation” technique and delayed surgery strategy in the neonatal period.Methods13 CDH infants were studied twice and compared with a population of 28 healthy infants (HI). Tidal‐Volume (Vt), respiratory rate (RR) and time to peak expiratory flow/expiratory time ratio (tPTEF/Te) were measured with an ultrasonic flow meter; Compliance (Crs) and Resistance (Rrs) of the respiratory system were studied with the single occlusion technique; FRC and Lung Clearance Index (LCI), were assessed with the sulfur hexafluoride (SF6) wash‐in/wash‐out technique. The differences between the first (T1) and second (T2) measurement in the CDH group were assessed by the Student's t‐test for paired values. For each set of measurement (T1 and T2) the values were compared with HI by Student's t‐test.ResultsMean age at test was 7.5 ± 5.2 months for HI, 4.5 ± 2.5 at T1 and 11.9 ± 4.5 months at T2 for CDH infants. At T1 there were no significant differences between CDH infants and HI in Vt, Crs, and FRC, while tPTEF/te ratio was lower and RR, Rrs, and LCI were higher in CDH patients than in HI. At T2 Vt, Crs, and FRC remained normal in CDH patients as well as RR that, at this time was not different between CDH and healthy infants; tPTEF/te remained below and Rrs and LCI remained above normal ranges, indicating a persistent impairment in lower airways patency.ConclusionsLung function in infants with severe CDH is characterized by a persistent impairment in airways patency and significant inhomogeneity of ventilation, suggesting a peripheral bronchial obstruction even if the other lung function tests are within normal ranges. Pediatr Pulmonol. 2007; 42:600–604. © 2007 Wiley‐Liss, Inc.
Increased resistance to trail‐induced apoptosis in prostate cancer cells selected in the presence of bicalutamide
Authors: Mitterberger Michael , Neuwirt Hannes , Cavarretta Ilaria T. , Hobisch Alfred , Culig Zoran 
Published: May 2007

AbstractBACKGROUNDFollowing prolonged treatment with the non‐steroidal anti‐androgen bicalutamide (Casodex), LNCaP cells have become resistant to this drug. Previously, we found that the bicalutamide‐refractory subline LNCaP‐Bic acquires a growth advantage and does not respond to androgenic stimulation. In the present study, we have asked whether changes in response to the tumor‐selective apoptosis inducer TNF‐related apoptosis‐inducing ligand (TRAIL) occur in LNCaP‐Bic cells.METHODSLNCaP and LNCaP‐Bic cells were incubated with increasing concentrations of TRAIL and apoptosis rate was analyzed using FACS. Expression of death receptors (DR), adaptor protein Fas‐associated death domain (FADD), members of the Bcl‐2 family, and caspases were investigated by Western blot.RESULTSThe percentage of cells undergoing apoptosis was lower in LNCaP‐Bic in comparison to LNCaP cells. There were no major differences in death receptor expression between control LNCaP and bicalutamide‐selected cells. Surprisingly, treatment with TRAIL increased the levels of Bcl‐2 by 50% in LNCaP‐Bic cells. The ratio cleaved caspase/procaspase‐8 was substantially lower in LNCaP‐Bic cells.CONCLUSIONSReduced sensitivity to TRAIL‐induced apoptosis is a novel mechanism relevant to resistance to bicalutamide in prostate cancer. Inability of TRAIL to cause programmed cell death might be caused by multiple perturbations in the TRAIL‐signaling pathway. Prostate 67: 1194–1201, 2007. © 2007 Wiley‐Liss, Inc.
Antitumor activity of the histone deacetylase inhibitor MS‐275 in prostate cancer models
Authors: Qian David Z. , Wei Yong‐Feng , Wang Xiaofei , Kato Yukihiko , Cheng Linzhao , Pili Roberto 
Published: May 2007

AbstractBACKGROUNDHistone deacetylase (HDAC) inhibitors represent a novel class of therapeutic agents with antitumor activity currently in clinical development. In this study, we tested the biological effects of the HDAC inhibitor MS‐275 in various pre‐clinical prostate cancer models both in'vitro and in vivo.METHODSIn vitro cell proliferation XTT assay and protein expression analysis by Western blot were performed. In vivo tumor growth assessment in subcutaneous, orthotopic, and transgenic mouse models were conducted.RESULTSMS‐275 significantly upregulated histone H3 acetylation and p21 gene expression in human prostate cancer cell lines. MS‐275 exerted growth arrest in PC‐3 and LNCaP cells, and induced cell death in DU‐145 cells. Prostate specific antigen protein levels were increased by MS‐275 in LAPC4 cell line. In vivo, MS‐275 inhibited the growth of DU‐145, LNCaP, and PC‐3 in subcutaneous xenografts. MS‐275 had also a significant inhibition of PC‐3 cells growth in a mouse intratibial model. Molecular analysis showed increased histone acetylation and p21 expression in tumor samples from MS‐275‐treated mice. In transgenic adenocarcinoma of mouse prostate (TRAMP) mice, long‐term treatment of MS‐275 slowed the progression of prostate carcinomas with significant reduction in cell proliferation.CONCLUSIONSTaken together, these data support the clinical testing of MS‐275 for the treatment of prostate cancer. Prostate 67: 1182–1193, 2007. © 2007 Wiley‐Liss, Inc.
From coarse‐grain to all‐atom: Toward multiscale analysis of protein landscapes
Authors: Heath Allison P. , Kavraki Lydia E. , Clementi Cecilia 
Published: May 2007

AbstractMultiscale methods are becoming increasingly promising as a way to characterize the dynamics of large protein systems on biologically relevant time‐scales. The underlying assumption in multiscale simulations is that it is possible to move reliably between different resolutions. We present a method that efficiently generates realistic all‐atom protein structures starting from the Cα atom positions, as obtained for instance from extensive coarse‐grain simulations. The method, a reconstruction algorithm for coarse‐grain structures (RACOGS), is validated by reconstructing ensembles of coarse‐grain structures obtained during folding simulations of the proteins src‐SH3 and S6. The results show that RACOGS consistently produces low energy, all‐atom structures. A comparison of the free energy landscapes calculated using the coarse‐grain structures versus the all‐atom structures shows good correspondence and little distortion in the protein folding landscape. Proteins 2007. © 2007 Wiley‐Liss, Inc.
FLIPDock: Docking flexible ligands into flexible receptors
Authors: Zhao Yong , Sanner Michel F. 
Published: May 2007

AbstractConformational changes of biological macromolecules when binding with ligands have long been observed and remain a challenge for automated docking methods. Here we present a novel protein–ligand docking software called FLIPDock (Flexible LIgand–Protein Docking) allowing the automated docking of flexible ligand molecules into active sites of flexible receptor molecules. In FLIPDock, conformational spaces of molecules are encoded using a data structure that we have developed recently called the Flexibility Tree (FT). While the FT can represent fully flexible ligands, it was initially designed as a hierarchical and multiresolution data structure for the selective encoding of conformational subspaces of large biological macromolecules. These conformational subspaces can be built to span a range of conformations important for the biological activity of a protein. A variety of motions can be combined, ranging from domains moving as rigid bodies or backbone atoms undergoing normal mode‐based deformations, to side chains assuming rotameric conformations. In addition, these conformational subspaces are parameterized by a small number of variables which can be searched during the docking process, thus effectively modeling the conformational changes in a flexible receptor. FLIPDock searches the variables using genetic algorithm‐based search techniques and evaluates putative docking complexes with a scoring function based on the AutoDock3.05 force‐field.In this paper, we describe the concepts behind FLIPDock and the overall architecture of the program. We demonstrate FLIPDock's ability to solve docking problems in which the assumption of a rigid receptor previously prevented the successful docking of known ligands. In particular, we repeat an earlier cross docking experiment and demonstrate an increased success rate of 93.5%, compared to original 72% success rate achieved by AutoDock over the 400 cross‐docking calculations. We also demonstrate FLIPDock's ability to handle conformational changes involving backbone motion by docking balanol to an adenosine‐binding pocket of protein kinase A. Proteins 2007. © 2007 Wiley‐Liss, Inc.
SIMPLE estimate of the free energy change due to aliphatic mutations: Superior predictions based on first principles
Authors: Bueno Marta , Camacho Carlos J. , Sancho Javier 
Published: May 2007

AbstractThe bioinformatics revolution of the last decade has been instrumental in the development of empirical potentials to quantitatively estimate protein interactions for modeling and design. Although computationally efficient, these potentials hide most of the relevant thermodynamics in 5‐to‐40 parameters that are fitted against a large experimental database. Here, we revisit this longstanding problem and show that a careful consideration of the change in hydrophobicity, electrostatics, and configurational entropy between the folded and unfolded state of aliphatic point mutations predicts 20–30% less false positives and yields more accurate predictions than any published empirical energy function. This significant improvement is achieved with essentially no free parameters, validating past theoretical and experimental efforts to understand the thermodynamics of protein folding. Our first principle analysis strongly suggests that both the solute–solute van der Waals interactions in the folded state and the electrostatics free energy change of exposed aliphatic mutations are almost completely compensated by similar interactions operating in the unfolded ensemble. Not surprisingly, the problem of properly accounting for the solvent contribution to the free energy of polar and charged group mutations, as well as of mutations that disrupt the protein backbone remains open. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Pactolus I‐domain: Functional switching of the Rossmann fold
Authors: Sen Mehmet , Legge Glen B. 
Published: May 2007

AbstractMurine Pactolus is a neutrophil‐specific single chain glycoprotein that plays a role as an apoptosis marker for macrophages. The extracellular region of the protein shows strong sequence similarities to integrin β‐subunits. Critical sequence modifications differentiate its function when compared to the integrin family. We show experimentally that Pactolus I‐domain does not bind divalent metal ions, indicating that ligand binding is not mediated through a metal ion‐dependent adhesion site (MIDAS). NMR data was used to map secondary structure and the strand pairing within the β‐sheet to confirm an overall Rossmann fold topology. Homology modeling enhanced by the NMR data was used to determine the overall structure, with two key loop insertions/deletions (insertion 2 and SDL) that distinguish the Pactolus I‐domain from the integrin α I‐domain and β I‐domains. NMR peak exchange broadening is observed due to dimerization, correlating to the β I‐domain and β propeller heterodimerization region within the integrin headpiece. Two unique N‐linked glycosylation sites (Asn151 and Asn230) within this region disrupt dimerization and may account for why Pactolus is not found to associate with an α‐subunit. These changes in quaternary structure, ligand binding loops, glycosylation, and metal sites illustrate how evolution has rapidly and effectively altered key aspects of the integrin β‐subunit to derive a protein of novel function on an existing protein scaffold. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Ranking the factors that contribute to protein β‐sheet folding
Authors: Parisien Marc , Major François 
Published: May 2007

AbstractThe formation of β‐sheet domains in proteins involves five energetically important factors: the formation of networks of hydrogen bonds and hydrophobic faces, and the residue propensities, or preferences, to be found at the edges of the β‐sheet, to adopt the extended conformation, and to make contact with other residues. These relative energy contributions define a potential energy function. Here, we show how optimizing this potential energy function reveals the formation of hydrophobic faces as the utmost factor. The potential energy function was optimized to minimize the Z‐scores of the native topologies among the exhaustive sets of over 400 different β‐sheets. These results corroborate with experimental data that showed the environment of a protein is an important modulator of β‐sheet folding. The contact propensities were found to be the least important, which could explain the poor predictive power of β‐strand alignment methods based on pair‐wise contact matrices. Proteins 2007. © 2007 Wiley‐Liss, Inc.
The relationship between N‐gram patterns and protein secondary structure
Authors: Vries John K. , Liu Xiong , Bahar Ivet 
Published: May 2007

AbstractAn n‐gram pattern (NP{n,m}) in a protein sequence is a set of n residues and m wildcards in a window of size n+m. Each window of n+m amino acids is associated with a collection of NP{n,m} patterns based on the combinatorics of n+m objects taken m at a time. NP{n,m} patterns that are shared between sequences reflect evolutionary relationships. Recently the authors developed an alignment‐independent protein classification algorithm based on shared NP{4,2} patterns that compared favorably to PSI‐BLAST. Theoretically, NP{4,2} patterns should also reflect secondary structure propensity since they contain all possible n‐grams for 1 ≤ n ≤ 4 and a window of 6 residues is wide enough to capture periodicities in the 2 ≤ n ≤ 5 range. This sparked interest in differentiating the information content in NP{4,2} patterns related to evolution from the content related to local propensity. The probability of α‐, β‐, and coil components was determined for every NP{4,2} pattern over all the chains in the Protein Data Bank (PDB). An algorithm exclusively based on the Z‐values of these distributions was developed, which accurately predicted 71–76% of α‐helical segments and 62–67% of β‐sheets in rigorous jackknife tests. This provided evidence for the strong correlation between NP{4,2} patterns and secondary structure. By grouping PDB chains into subsets with increasing levels of sequence identity, it was also possible to separate the evolutionary and local propensity contributions to the classification process. The results showed that information derived from evolutionary relationships was more important for β‐sheet prediction than α‐helix prediction. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Pest management programmes in vineyards using male mating disruption
Authors: Harari Ally R , Zahavi Tirtza , Gordon Dvora , Anshelevich Leonid , Harel Miriam , Ovadia Shmulik , Dunkelblum Ezra 
Published: May 2007

AbstractIsraeli vine growers have been reluctant to adopt the mating disruption technique for control of the European vine moth, Lobesia botrana Den. & Schiff. Since the chemically controlled honeydew moth, Cryptoblabes gnidiella Mill., coexists with the European vine moth, growers have maintained that the use of mating disruption would fail to bring about a significant reduction in pesticide use. In this study, the efficacy of mating disruption techniques against C. gnidiella was tested, as well as the effect of these methods on pesticide use and damage to clusters when the method was employed against both of the pests in wine grapes. Comparisons were made between plots treated with (1) L. botrana mating disruption pheromone, (2) L. botrana and C. gnidiella mating disruption pheromones and (3) control plots. A significant difference in the number of clusters infested with the developmental stages of the moths was seen between pheromone‐treated plots and controls, while no such difference was observed between plots treated with one versus two pheromones. A similar pattern was observed in the number of insecticide applications; the greatest number of applications was used in control plots, followed by plots treated with L. botrana mating disruption pheromone and by plots treated with pheromones against both pests, in which no pesticides were applied. Copyright © 2007 Society of Chemical Industry
Toxicity of insecticides to the sweetpotato whitefly (Hemiptera: Aleyrodidae) and its natural enemies
Authors: Bacci Leandro , Crespo André LB , Galvan Tederson L , Pereira Eliseu JG , Picanço Marcelo C , Silva Gerson A , Chediak Mateus 
Published: May 2007

AbstractEfficient chemical control is achieved when insecticides are active against insect pests and safe to natural enemies. In this study, the toxicity of 17 insecticides to the sweetpotato whitefly, Bemisia tabaci (Gennadius), and the selectivity of seven insecticides to natural enemies of this insect pest were evaluated. To determine the insecticide toxicity, B. tabaci adults were exposed to abamectin, acephate, acetamiprid, cartap, imidacloprid, malathion, methamidophos, bifenthrin, cypermethrin, deltamethrin, esfenvalerate, fenitrothion, fenpropathrin, fenthion, phenthoate, permethrin and trichlorphon at 50 and 100% of the field rate (FR), and to water (untreated control). To determine the insecticide selectivity, adults of Encarsia sp., Acanthinus sp., Discodon sp. and Lasiochilus sp. were exposed to abamectin, acephate, acetamiprid, cartap, imidacloprid, malathion and methamidophos at 50 and 100% FR, and to water. Groups of each insect species were exposed to kale leaves preimmersed in each treatment under laboratory conditions. Mortality of exposed individuals was recorded 24 h after treatment. Cartap and imidacloprid at 50 and 100% FR and abamectin and acetamiprid at 100% FR showed insecticidal activity to B. tabaci adults. Abamectin at 50 and 100% FR was the least insecticidal compound to the natural enemies Acanthinus sp., Discodon sp. and Lasiochilus sp. The present results suggest that abamectin at 100% FR may decrease B. tabaci field populations but can still be harmless to predators. Implications of these results within an integrated pest management context are discussed. Copyright © 2007 Society of Chemical Industry
A review of name‐based ethnicity classification methods and their potential in population studies
Authors: Mateos Pablo 
Published: May 2007

AbstractSeveral approaches have been proposed to classify populations into ethnic groups using people's names, as an alternative to ethnicity self‐identification information when this is not available. These methodologies have been developed, primarily in the public health and population genetics literature in different countries, in isolation from and with little participation from demographers or social scientists. The objective of this paper is to bring together these isolated efforts and provide a coherent comparison, a common methodology and terminology in order to foster new research and applications in this promising and multidisciplinary field. A systematic review has been conducted of the most representative studies that develop new name‐based ethnicity classifications, extracting methodological commonalities, achievements and shortcomings; 13 studies met the inclusion criteria and all followed a very similar methodology to create a name reference list with which to classify populations into a few most common ethnic groups. The different classifications' sensitivity varies between 0.67 and 0.95, their specificity between 0.80 and 1, their positive predicted value between 0.70 and 0.96, and their negative predicted value between 0.96 and 1.Name‐based ethnicity classification systems have a great potential to overcome data scarcity issues in a wide variety of key topics in population studies, as is proved by the 13 papers analysed. Their current limitations are mainly due to a restricted number of names and a partial spatio‐temporal coverage of the reference population data‐sets used to produce name reference lists. Improved classifications with extensive population coverage and higher classification accuracy levels will be achieved by using population registers with wider spatio‐temporal coverage. Furthermore, there is a requirement for such new classifications to include all of the potential ethnic groups present in a society, and not just one or a few of them. Copyright © 2007 John Wiley & Sons, Ltd.
Application of microsize light‐emitting diode structure for monolithic optoelectronic integrated circuits
Authors: Moon S. Y. , Yonezu H. , Furukawa Y. , Morisaki Y. , Yamada S. , Wakahara A. 
Published: May 2007

AbstractA Si/III–V–N alloys/Si structure was grown on a Si substrate by solid‐source molecular beam epitaxy (SSMBE) with an rf plasma nitrogen source and electron‐beam (EB) evaporator. A two‐dimensional (2D) growth mode was maintained during the growth of all layers. High‐resolution X‐ray diffraction (HRXRD) revealed that the structure had a small lattice mismatch to the Si substrate. InGaPN/GaPN double‐heterostructure (DH) light‐emitting diodes (LEDs) were fabricated on Si/III–V–N alloys/Si structure. The various sized LEDs were fabricated to put into the MOSFET for monolithic optoelectronic integrated circuits (OEIC). The luminescence properties of LEDs were evaluated by electroluminescence (EL). A double emission peak from all LED samples was observed at about 642 nm and 695 nm at room temperature (RT). As injection current increased, the emission peak wavelength changed from the peak wavelength of the InGaPN layer to that of the GaPN layer, likely due to carrier overflow of the active layer. A simplified fabrication process for the microsize LED of the unit circuit was proposed. The LEDs with emission areas from 5 × 5 μm2 to 20 × 20 μm2 were fabricated. The LED with an emission area of 5 × 5 μm2 can be applied to an optical device of a monolithic OEIC. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Fabrication of surface‐oxidized GaN crystallites for UV electroluminescent devices
Authors: Honda Tohru , Baba Taichi , Watanabe Makiko , Okuhata Takashi 
Published: May 2007

AbstractThe cathodoluminescence (CL) of GaN crystallites with and without surface oxide layers is reported. The CL intensity of the coated GaN crystallites is higher than that of the crystallites without oxide layers although the shapes of the coated GaN crystallites are similar to those of uncoated GaN crystallites. The surface coating with gallium oxide is effective for the reduction of surface recombination in GaN crystallites. Electroluminescent devices (ELDs) using GaN crystallites covered with gallium oxides were fabricated. UV light emission was observed from the GaN‐based ELDs at RT. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)