bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insensitivity regions for deformation measurement on a dam
Authors: Fišerová Eva , Kubáček Lubomír 
Published: April 2009

AbstractDeformation measurement during the filling a dam can be modelled by a multivariate model. Multivariate models usually involve unknown parameters not only in the mean value of the observation matrix but also in the covariance matrix (variance components). The variance components must be estimated and plug‐in estimators for the mean value parameters can be used. To find statistical properties of plug‐in estimators is rather difficult. In some cases the sensitivity approach can be used. If we know that the true value of the variance components is with sufficiently high probability in so‐called insensitivity region, then the plug‐in estimator is almost the best linear unbiased estimator. The aim of the paper is to investigate this insensitivity regions, i.e. the region around the true value of variance components, where small changes of them are only of negligible influence on the mean value parameter estimators. The obtained results are applied on the problem of deformation measurement during the filling a dam. Copyright © 2009 John Wiley & Sons, Ltd.
Erosional unloading, hillslope geometry, and the height of the Cascade Range, Washington State, USA
Authors: Mitchell Sara , Montgomery David , Greenberg Harvey 
Published: April 2009

AbstractPeaks in the Cascade Range in northern Washington State are on average ∼800 m higher than in southern Washington. The influences of differential valley excavation and variations in hillslope length and average slope on these altitudinal trends were tested using a 3‐dimensional model for isostatic rock uplift and calculations of hillslope length and slope respectively. The magnitude of isostatic peak uplift calculated by the model is highly dependent on the flexural rigidity (D) and the related effective elastic thickness (Te) of the crust of this region. Crustal rigidity was constrained using published estimates and by estimating the depth of the seismogenic zone in the area (D > 1 × 1023 Nm and Te > 24 km). With these constraints, isostatic compensation due to differential erosion added < 700 m and 300 m, or < 25% overall, of height to peaks in the northern and southern Cascades, respectively. Deeper valley incision in the northern Cascades accounts for < 300 m of the 800 m difference in peak altitudes between north and south. Similarly, variation in valley spacing and slope account for < 350 m of the difference in mean altitude between northern and southern regions. Hence, at least several hundred m difference in altitude between the northern and southern regions of the Cascades in Washington must be due to tectonic, geologic, or geophysical factors rather than surficial and geomorphic effects like isostatic response to valley incision and hillslope geometry. Copyright © 2009 John Wiley & Sons, Ltd.
Differences in psychological morbidity among Australian and Chinese caregivers of persons with dementia in residential care
Authors: Wu Helen Zong Ying , Low Lee‐Fay , Xiao Shifu , Brodaty Henry 
Published: April 2009

AbstractObjectiveThe aim of the present study was to determine the effects of culture on caregiver psychological morbidity among informal caregivers of institutionalised persons with dementia in three different populations: (1) Shanghai, (2) Australian‐Chinese and (3) Australian mainstream (non‐Chinese).MethodsCaregivers and residents with dementia were recruited from (1) a dementia hospital in Shanghai, (2) three ethno‐specific Chinese nursing homes in Sydney and (3) four mainstream nursing homes in Sydney. Psychological morbidity was assessed using the Geriatric Depression Scale, mental health component (MHC) of the RAND‐36 Health Status Inventory and a guilt scale.ResultsThere were no significant differences between the three groups as measured by the guilt scale and MHC. Shanghai caregivers had higher mean depression scores than Australian‐Chinese caregivers (p < 0.001), who in turn had higher mean depression scores than Australian mainstream caregivers (p = 0.015). Higher depression scores were found to be inversely associated with the caregiver's education level and physical health status, and associated with increased frequency of nursing home visits, but not with levels of behavioural and psychological symptoms of dementia (BPSD).ConclusionLevels of depression in caregivers of institutionalised persons with dementia differ by culture and country of residence. Copyright © 2009 John Wiley & Sons, Ltd.
A model for intervention research in late‐life depression
Authors: Alexopoulos George S. , Bruce Martha L. 
Published: April 2009

AbstractObjectiveTo serve as a conceptual map of the role of new interventions designed to reduce the burden of late‐life depression.MethodsWe identified three needs to be addressed by intervention research: (1) the need for novel interventions given that the existing treatments leave many older adults depressed and disabled; (2) the need for procedures enabling community‐based agencies to offer interventions of known efficacy with fidelity; and (3) the need to increase access of depressed older adults to care.ResultsOur model orders novel interventions according to their role in serving depressed older adults and according to their position in the efficacy, effectiveness, implementation, and dissemination testing continuum. We describe three interventions designed by our institute to exemplify intervention research at different level of the model. A common element is that each intervention personalizes care both at the level of the individuals served and the level of community agencies providing care. To this end, each intervention is designed to accommodate the strengths and limitations of both patients and agencies and introduces changes in the patients' environment and community agencies needed in order to assimilate the new intervention.ConclusionsWe suggest that this model provides conceptual guidance on how to shorten the testing cycle and bring urgently needed novel treatments and implementation approaches to the community. While replication studies are important, propose that most of the support should be directed to those projects that take rational risks, and after adequate preliminary evidence, make the next step along the testing continuum. Copyright © 2009 John Wiley & Sons, Ltd.
Skeletal muscle glucose uptake during exercise: A focus on reactive oxygen species and nitric oxide signaling
Authors: Merry Troy L. , McConell Glenn K. 
Published: April 2009

AbstractLike insulin, muscle contraction (in vitro or in situ) and exercise increase glucose uptake into skeletal muscle. However, the contraction/exercise pathway of glucose uptake in skeletal muscle is an independent pathway to that of insulin. Indeed, skeletal muscle glucose uptake is normal during exercise in those who suffer from insulin resistance and diabetes. Thus, the pathway of contraction‐mediated glucose uptake into skeletal muscle provides an attractive potential target for pharmaceutical treatment and prevention of such conditions, especially as skeletal muscle is the major site of impaired glucose disposal in insulin resistance. The mechanisms regulating skeletal muscle glucose uptake during contraction have not been fully elucidated. Potential regulators include Ca2+ (via CaMK's and/or CaMKK), AMPK, ROS, and NO signaling, with some redundancy likely to be evident within the system. In this review, we attempt to briefly synthesize current evidence regarding the potential mechanisms involved in regulating skeletal muscle glucose uptake during contraction, focusing on ROS and NO signaling. While reading this review, it will become clear that this is an evolving field of research and that much more work is required to elucidate the mechanism(s) regulating skeletal muscle glucose uptake during contraction. © 2009 IUBMB IUBMB Life 61(5): 479–484, 2009
E2F1 transcription is induced by genotoxic stress through ATM/ATR activation
Authors: Carcagno Abel L. , Ogara María F. , Sonzogni Silvina V. , Marazita Mariela C. , Sirkin Pablo F. , Ceruti Julieta M. , Cánepa Eduardo T. 
Published: April 2009

AbstractE2F1, a member of the E2F family of transcription factors, plays a critical role in controlling both cell cycle progression and apoptotic cell death in response to DNA damage and oncogene activation. Following genotoxic stresses, E2F1 protein is stabilized by phosphorylation and acetylation driven to its accumulation. The aim of the present work was to examine whether the increase in E2F1 protein levels observed after DNA damage is only a reflection of an increase in E2F1 protein stability or is also the consequence of enhanced transcription of the E2F1 gene. The data presented here demonstrates that UV light and other genotoxics induce the transcription of E2F1 gene in an ATM/ATR dependent manner, which results in increasing E2F1 mRNA and protein levels. After genotoxic stress, transcription of cyclin E, an E2F1 target gene, was significantly induced. This induction was the result of two well‐differentiated effects, one of them dependent on de novo protein synthesis and the other on the protein stabilization. Our results strongly support a transcriptional effect of DNA damaging agents on E2F1 expression. The results presented herein uncover a new mechanism involving E2F1 in response to genotoxic stress. © 2009 IUBMB IUBMB Life, 61(5): 537–543, 2009
A semiparametric model for binary response and continuous outcomes under index heteroscedasticity
Authors: Klein Roger , Vella Francis 
Published: April 2009

AbstractThis paper formulates a likelihood‐based estimator for a double‐index, semiparametric binary response equation. A novel feature of this estimator is that it is based on density estimation under local smoothing. While the proofs differ from those based on alternative density estimators, the finite sample performance of the estimator is significantly improved. As binary responses often appear as endogenous regressors in continuous outcome equations, we also develop an optimal instrumental variables estimator in this context. For this purpose, we specialize the double‐index model for binary response to one with heteroscedasticity that depends on an index different from that underlying the ‘mean response’. We show that such (multiplicative) heteroscedasticity, whose form is not parametrically specified, effectively induces exclusion restrictions on the outcomes equation. The estimator developed exploits such identifying information. We provide simulation evidence on the favorable performance of the estimators and illustrate their use through an empirical application on the determinants, and affect, of attendance at a government‐financed school. Copyright © 2009 John Wiley & Sons, Ltd.
Force‐field parameters of the Ψ and Φ around glycosidic bonds to oxygen and sulfur atoms
Authors: Saito Minoru , Okazaki Isao 
Published: April 2009

AbstractThe Ψ and Φ torsion angles around glycosidic bonds in a glycoside chain are the most important determinants of the conformation of a glycoside chain. We determined force‐field parameters for Ψ and Φ torsion angles around a glycosidic bond bridged by a sulfur atom, as well as a bond bridged by an oxygen atom as a preparation for the next study, i.e., molecular dynamics free energy calculations for protein‐sugar and protein‐inhibitor complexes. First, we extracted the Ψ or Φ torsion energy component from a quantum mechanics (QM) total energy by subtracting all the molecular mechanics (MM) force‐field components except for the Ψ or Φ torsion angle. The Ψ and Φ energy components extracted (hereafter called “the remaining energy components”) were calculated for simple sugar models and plotted as functions of the Ψ and Φ angles. The remaining energy component curves of Ψ and Φ were well represented by the torsion force‐field functions consisting of four and three cosine functions, respectively. To confirm the reliability of the force‐field parameters and to confirm its compatibility with other force‐fields, we calculated adiabatic potential curves as functions of Ψ and Φ for the model glycosides by adopting the Ψ and Φ force‐field parameters obtained and by energetically optimizing other degrees of freedom. The MM potential energy curves obtained for Ψ and Φ well represented the QM adiabatic curves and also these curves' differences with regard to the glycosidic oxygen and sulfur atoms. Our Ψ and Φ force‐fields of glycosidic oxygen gave MM potential energy curves that more closely represented the respective QM curves than did those of the recently developed GLYCAM force‐field. © 2009 Wiley Periodicals, Inc., J Comput Chem, 2009
Conformational analysis of hydroxymatairesinol in aqueous solution with molecular dynamics
Authors: Sandberg Thomas , Hotokka Matti 
Published: April 2009

AbstractMolecular dynamics simulations were performed on the naturally occuring lignan hydroxymatairesinol (HMR) using the GROMACS software. The aim of this study was to explore the conformational behavior of HMR in aqueous solution adopting the TIP4P model. The topology of HMR was constructed by hand and HMR was modeled with the OPLS‐AA force field implemented in GROMACS. The five torsional angles in HMR were properly analyzed during the simulations. Correlations through certain patterns were observed between the angles. The determining property for the conformation preferred in aqueous solution was found to be the dipole moment and not the lowest energy in gas phase. The solvation effects on HMR was also studied by quantum chemical calculations applying the COnductorlike Screening MOdel (COSMO), the results of which were compared with results from a previous study using the Polarized Continuum Model (PCM). In the present work, COSMO was found to give more credible relative energies than PCM. © 2009 Wiley Periodicals, Inc., J Comput Chem, 2009
Adenovirus type 5 with modified hexons induces robust transgene‐specific immune responses in mice with pre‐existing immunity against adenovirus type 5
Authors: Abe Shinya , Okuda Kenji , Ura Takehiro , Kondo Asami , Yoshida Atsushi , Yoshizaki Shinji , Mizuguchi Hiroyuki , Klinman Dennis , Shimada Masaru 
Published: April 2009

AbstractBackgroundAdenovirus type 5 (Ad5) is widely used as a vehicle for vaccine delivery in the treatment of infectious disease and cancer. However, the efficacy of Ad5 vectors has been limited in humans because exposure to Ad5 infections results in most adults having neutralizing antibodies against Ad5. To overcome this limitation, the hexon epitope present in the fifth hypervariable region of Ad5 was modified.MethodsTo evaluate the ability of Ad5 vectors encoding the HIV env protein to induce Ag‐specific immune responses in the face of pre‐existing anti‐Ad5 immunity, mice were administrated intramuscularly with the Ad‐Luc vector, and then vaccinated with parental or hexon‐modified Ad5 vectors (Ad‐HisHIV, Ad‐END/AAAHIV or Ad‐HIV) at week 8. HIV‐specific cell‐mediated immune responses were detected through a combination of tetramer assays and intracellular cytokine staining from weeks 8–23.ResultsThe hexon‐modified Ad vector was able to escape from anti‐Ad5 neutralizing antibody, and mice with the modified vector generated significantly lower individual neutralizing antibody than those immunized with the parental vector. Furthermore, mice with pre‐existing anti‐Ad immunity immunized with the modified vector generated significantly stronger cell‐mediated anti‐env responses than those immunized with the parental vector.ConclusionsThese data demonstrate that Ad5 vector with hexon modification reduce their sensitivity to pre‐existing anti‐Ad immunity and improve their clinical utility. Copyright © 2009 John Wiley & Sons, Ltd.
Molecular recognition properties of tartrates and metal‐tartrates in solution and gas phase
Authors: Wijeratne Aruna B. , Schug Kevin A. 
Published: April 2009

AbstractSolution phase and gas phase chiral molecular recognition properties of tartrates (salts or esters of tartaric acid) and metal tartrates (binuclear tartrato(4‐)‐metal‐bridged complexes) are reviewed in conjunction with their applications in enantiomeric separation science and their mass spectrometric chiral discrimination properties.
Monolithic silica capillary columns having immobilized lectins and surface bound polar functionalities for lectin affinity and normal phase nano‐LC and CEC of glycoconjugates, respectively
Authors: Zhong Hengwen , El Rassi Ziad 
Published: April 2009

AbstractIn this report, monolithic silica‐based capillary columns were produced by the sol–gel process and subsequently silanized with γ‐glycidoxypropyltrimethoxysilane to form on the surface of the monolith a reactive γ‐glycidoxypropylsilyl sublayer to which an interactive top layer can be covalently attached. The interactive top layer consisted of either an immobilized lectin or polar cyano functions to perform lectin affinity chromatography (LAC) of glycoproteins or normal phase chromatography (NPC) of glycans, respectively. Two lectins were immobilized, namely Con A and wheat germ agglutinin (WGA) due to their utility in LAC of a wide range of glycoconjugates. On the other hand, 1H‐imidazole‐4,5‐dicarbonitrile was covalently attached to the silica monolith to yield polar silica monolith referred to as 2CN–OH monolith. The two lectin monolithic columns were evaluated in Nano‐LC with standard glycoproteins over a wide range of conditions and proved useful in capturing the glycoforms bearing the pertinent saccharidic motifs for interaction with the given lectin. The 2CN–OH monolithic columns were effective in the profiling of glycans derived from glycoproteins in both NP‐CEC and NP‐Nano‐LC with NP‐CEC offering enhanced separation when compared to NP‐Nano‐LC.
SwissPIT: An workflow‐based platform for analyzing tandem‐MS spectra using the Grid
Authors: Quandt Andreas , Masselot Alexandre , Hernandez Patricia , Hernandez Céline , Maffioletti Sergio , Appel Ron D. , Lisacek Frederique 
Published: April 2009

AbstractThe identification and characterization of peptides from MS/MS data represents a critical aspect of proteomics. It has been the subject of extensive research in bioinformatics resulting in the generation of a fair number of identification software tools. Most often, only one program with a specific and unvarying set of parameters is selected for identifying proteins. Hence, a significant proportion of the experimental spectra do not match the peptide sequences in the screened database due to inappropriate parameters or scoring schemes. The Swiss protein identification toolbox (swissPIT) project provides the scientific community with an expandable multitool platform for automated in‐depth analysis of MS data also able to handle data from high‐throughput experiments. With swissPIT many problems have been solved: The missing standards for input and output formats (A), creation of analysis workflows (B), unified result visualization (C), and simplicity of the user interface (D). Currently, swissPIT supports four different programs implementing two different search strategies to identify MS/MS spectra. Conceived to handle the calculation‐intensive needs of each of the programs, swissPIT uses the distributed resources of a Swiss‐wide computer Grid (http://www.swing‐grid.ch).
Experimental annotation of channel catfish virus by probabilistic proteogenomic mapping
Authors: Kunec Dusan , Nanduri Bindu , Burgess Shane C. 
Published: April 2009

AbstractExperimental identification of expressed proteins by proteomics constitutes the most reliable approach to identify genomic location and structure of protein‐coding genes and substantially complements computational genome annotation. Channel catfish herpesvirus (CCV) is a simple comparative model for understanding herpesvirus biology and the evolution of the Herpesviridae. The canonical CCV genome has 76 predicted ORF and only 12 of these have been confirmed experimentally. We describe a modification of a statistical method, which assigns significance measures, q‐values, to peptide identifications based on 2‐D LC ESI MS/MS, real‐decoy database searches and SEQUEST XCorr and ΔCn scores. We used this approach to identify CCV proteins expressed during its replication in cell culture, to determine protein composition of mature virions and, consequently, to refine the canonical CCV genome annotation. To complement trypsin, we used partial proteinase K digestion, which yielded greater proteome coverage. At FDR <5%, for peptide identifications, we identified 25/76 previously predicted ORF using trypsin and 31/76 using proteinase K. Furthermore, we identified 17 novel protein‐coding regions (7 potential ATG‐initiated ORF). Most of these novel ORF encode small proteins (<100 amino acids). Directed, strand‐specific reverse transcription real‐time PCR confirmed RNA expression from 6/7 novel ATG‐initiated ORF investigated.
Quantum dots laser desorption/ionization MS: multifunctional CdSe quantum dots as the matrix, concentrating probes and acceleration for microwave enzymatic digestion for peptide analysis and high resolution detection of proteins in a linear MALDI‐TOF MS
Authors: Shrivas Kamlesh , Kailasa Suresh Kumar , Wu Hui‐Fen 
Published: April 2009

AbstractWe report the first use of functionalized cadmium selinide quantum dots (CdSe QDs) with 11‐mercaptoundecanoic acid (MUA) as the matrix for the selective ionization of proteins with high resolution and rapid analysis of amino acids and peptides by using quantum dots laser desorption/ionization mass spectrometry (QDLDI‐MS). The mercaptocarboxylic groups of CdSe QDs have been known to be an effective affinity probe to interact with the biomolecules at low abundance level. Using these QDs as the matrix, sensitivity of the method was greatly enhanced and the LOQ of peptides was found to be 100 pM with RSD <10%. The QDLDI‐MS is capable for the selective ionization of insulin, lysozyme and myoglobin with high resolution, which is not observed with sinapic acid (SA) as the matrix. The QDLDI‐MS technique offers many advantages for the analysis of amino acids, peptides and proteins with regard to simplicity, rapidity, sensitivity and the mass spectra were generated in the presence of signal suppressors such as urea and Trition X‐100. In addition, the CdSe QDs have been successfully applied as preconcentrating probes for the analysis of digested peptides in lysozyme from chicken egg white by microwave‐assisted enzymatic digestion. This indicates that the QDs are able to absorb radiation from microwave and their ability to trap peptides from microwave‐digested lysozyme. These results demonstrate that the CdSe QDs are promising candidates for the selective ionization of the analytes with an accurate platform to the rapid screening of biomolecules.