bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mass spectrometry‐compatible silver staining of histones resolved on acetic acid‐urea‐Triton PAGE
Authors: Pramod Khare Satyajeet , Bharat Khade , Sanjay Gupta 
Published: April 2009

AbstractAcetic acid‐Urea‐Triton (AUT) PAGE is commonly used method to separate histone variants and their post‐translationally modified forms. Coomassie staining is the preferred method for protein visualization; however, its sensitivity is less than that of silver staining. Though silver staining of histones in AUT‐PAGE has been reported, the method is time‐consuming, dependent on prior staining by Amido black and has not been reported suitable for mass spectrometry. Here, we propose ‘SDS‐Silver’ method for rapid, sensitive and mass spectrometry‐compatible staining of histones resolved on AUT‐PAGE.
A proteomic‐based approach for the identification of immunodominant Cryptococcus neoformans proteins
Authors: Young Mattie , Macias Sandra , Thomas Derek , Wormley Floyd L. 
Published: April 2009

AbstractCryptococcus neoformans is an opportunistic fungal pathogen that can cause life‐threatening meningoencephalitis in immune compromised patients. Previous, studies in our laboratory have shown that prior exposure to an IFN‐γ‐producing C. neoformans strain (H99γ) elicits protective immunity against a second pulmonary C. neoformans challenge. Here, we characterized the antibody response produced in mice protected against experimental pulmonary C. neoformans infection compared to nonprotected mice. Moreover, we evaluated the efficacy of using serum antibody from protected mice to detect immunodominant C. neoformans proteins. Protected mice were shown to produce significantly more C. neoformans‐specific antibodies following a second experimental pulmonary cryptococcal challenge compared to nonprotected mice. Immunoblot analysis of C. neoformans proteins resolved by 2‐DE using serum from nonprotected mice failed to show any reactivity. In contrast, serum from protected mice was reactive with several cryptococcal protein spots. Analysis of these spots by capillary HPLC‐ESI‐MS/MS identified several cryptococcal proteins shown to be associated with the pathogenesis of cryptococcosis. Our studies demonstrate that mice immunized with C. neoformans strain H99γ produce antibodies that are immune reactive against specific cryptococcal proteins that may provide a basis for the development of immune based therapies that induce protective anticryptococcal immune responses.
Unique patterns of molecular profiling between human prostate cancer LNCaP and PC‐3 cells
Authors: Dozmorov Mikhail G. , Hurst Robert E. , Culkin Daniel J. , Kropp Bradley P. , Frank Mark Barton , Osban Jeanette , Penning Trevor M. , Lin Hsueh‐Kung 
Published: April 2009

AbstractBACKGROUNDHuman prostate cancer LNCaP and PC‐3 cell lines have been extensively used to study prostate cancer progression and to develop therapeutic agents. Although LNCaP and PC‐3 cells are generally assumed to represent early and late stages of prostate cancer, respectively, there is limited information regarding gene expression patterns between these two cell lines and its relationship to prostate cancer.METHODSComprehensive gene expression analysis was performed. Total RNA was isolated from cultured cells and hybridized to Illumina human BeadChips representing 24,526 transcripts. Bioinformatics analysis was applied to identify cell line specific genes as well as biological mechanisms, pathways, and functions related to the genes.RESULTSA total of 2,198 genes were differentially expressed between LNCaP and PC‐3 cells. Using a robust statistical analysis and high significance criteria, 115 and 188 genes were identified to be unique to LNCaP and PC‐3 cells, respectively. LNCaP cells maintained various metabolic pathways including a gene cluster that encodes UDP‐glucuronosyltransferases. Several transcription factors including Talα/β, GATA‐1, and c‐Myc/Max may be responsible for regulating LNCaP cell specific genes. By contrast, PC‐3 cells were characterized by their unique expression of cytoskeleton‐related genes and other genes including VEGFC, IL8, and TGFβ2.CONCLUSIONSThis study showed that LNCaP and PC‐3 cells represent two distinct prostate cancer cell lineages. LNCaP cells retain many prostate cell specific properties, whereas PC‐3 cells have acquired a more aggressive phenotype. Future studies for prostate cancer research need to consider similarities and differences between these two cells and their relationship to prostate cancer. Prostate 69:1077–1090, 2009. © 2009 Wiley‐Liss, Inc.
Optimizing molecular signatures for predicting prostate cancer recurrence
Authors: Sun Yijun , Goodison Steve 
Published: April 2009

AbstractBACKGROUNDThe derivation of molecular signatures indicative of disease status and predictive of subsequent behavior could facilitate the optimal choice of treatment for prostate cancer patients.METHODSIn this study, we conducted a computational analysis of gene expression profile data obtained from 79 cases, 39 of which were classified as having disease recurrence, to investigate whether advanced computational algorithms can derive more accurate prognostic signatures for prostate cancer.RESULTSAt the 90% sensitivity level, a newly derived prognostic genetic signature achieved 85% specificity. This is the first reported genetic signature to outperform a clinically used postoperative nomogram. Furthermore, a hybrid prognostic signature derived by combination of the nomogram and gene expression data significantly outperformed both genetic and clinical signatures, and achieved a specificity of 95%.CONCLUSIONSOur study demonstrates the feasibility of utilizing gene expression information for highly accurate prostate cancer prognosis beyond the current clinical systems, and shows that more advanced computational modeling of tissue‐derived microarray data is warranted before clinical application of molecular signatures is considered. Prostate 69:1119–1127, 2009. © 2009 Wiley‐Liss, Inc.
Locally range‐separated hybrids as linear combinations of range‐separated local hybrids
Authors: Henderson Thomas M. , Janesko Benjamin G. , Scuseria Gustavo E. , Savin Andreas 
Published: April 2009

AbstractRange‐separated hybrid density functionals, which incorporate different fractions of exact exchange at different interelectronic separations, offer substantial advantages over conventional global hybrid functionals. However, they generally use a fixed, system‐independent range‐separation parameter, which numerical experience and formal arguments both show to be a limiting approximation. Locally range‐separated hybrids, which instead use a position‐dependent range‐separation function, should overcome this limitation, but their implementation is nontrivial. Here, we present a method which in practice converts a locally range‐separated hybrid into a linear combination of range‐separated local hybrids. Thus, unlike our previous implementation of this locally range‐separated hybrid idea, we do not need to approximate the exchange hole, and we can take advantage of existing self‐consistent local hybrid implementations to carry out self‐consistent calculations using locally range‐separated hybrid functionals. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Relativistic adiabatic time‐dependent density functional theory using hybrid functionals and noncollinear spin magnetization
Authors: Bast Radovan , Jensen Hans Jørgen Aa. , Saue Trond 
Published: April 2009

AbstractWe report an implementation of adiabatic time‐dependent density functional theory based on the 4‐component relativistic Dirac–Coulomb Hamiltonian and a closed‐shell reference. The implementation includes noncollinear spin magnetization and full derivatives of functionals, including hybrid generalized gradient approximation (GGA) functionals. We avoid reducing the generalized eigenvalue problem to half the dimension involving the square of excitation energies since this may introduce spurious roots and also squares the matrix condition number. Rather we impose structure in terms of hermiticity and time reversal symmetry on trial vectors to obtain even better reductions in terms of memory and run time, and without invoking approximations. Further reductions are obtained by exploiting point group symmetries for D2h and subgroups in a symmetry scheme where symmetry reductions translate into reduction of algebra from quaternion to complex or real. For hybrid GGAs with noncollinear spin magnetization we derive a new computationally advantageous equation for the full second variational derivatives of such exchange‐correlation functionals. We apply our implementation to calculations on the ns2 → ns1np1 excitation energies in the Zn, Cd, and Hg atoms (n = 4–6) and (vertical) excitation energies of UO; and we test the performance of various functionals by comparison with experimental data (group 12 atoms) or higher‐level computational results (UO). The results indicate that the adiabatic local density approximation (ALDA) is a good approximation for some GGA functionals, but not all. Furthermore, the results also indicate that ALDA is an extremely bad approximation for hybrid functionals, unless one only employs ALDA for the pure DFT contribution to the exchange‐correlation kernel and retains the fraction of exact exchange; we denote this approximation ALDAh. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Building a wireless capturing tool for WiFi
Authors: Meng Ke , Xiao Yang , Vrbsky Susan V. 
Published: April 2009

AbstractWiFi is becoming increasingly prevalent nowadays, whether as a simple range extender for a home wired Ethernet interface or a wireless deployment throughout an enterprise. Wireless local area networks (WLANs) provide us with mobility, convenience, and low cost. At the same time, WiFi is unsafe and is more vulnerable than traditional Ethernet, so that anyone familiar with wireless networks can initiate an attack. One strategy to identify potentially malicious unauthorized users is through packet capturing. Although there are several software products available for packet capture, there is currently no paper in the literature that describes how to build a software tool to capture WiFi frames and its associated functions. In this paper, we present how we build our frame capture tool along with a set of implementation techniques for automatically capturing all the frames and analyzing an attack on a WiFi. In our research, we focus on the WiFi medium access control (MAC) layer for wireless network analysis. We also discuss what we learned and the limitations which we discovered when implementing the tool. Copyright © 2009 John Wiley & Sons, Ltd.
On the applicability of pushover analysis for seismic evaluation of medium‐ and high‐rise buildings
Authors: Huang Kai , Kuang J. S. 
Published: April 2009

AbstractThe assumption that the dynamic performance of structures is mainly determined from the corresponding single‐degree‐of‐freedom system in pushover analysis is generally valid for low‐rise structures, where the structural behaviour is dominated by the first vibration mode. However, higher modes of medium‐ and high‐rise structures will have significant effect on the dynamic characteristics. In this paper, the applicability of pushover analysis for seismic evaluation of medium‐to‐high‐rise shear‐wall structures is investigated. The displacements and internal forces of shear wall structures with different heights are determined by nonlinear response history analysis, where the shear walls are considered as multi‐degree‐of‐freedom systems and modelled by fibre elements. The results of the analysis are compared with those from the pushover procedure. It is shown that pushover analysis generally underestimates inter‐storey drifts and rotations, in particular those at upper storeys of buildings, and overestimates the peak roof displacement at inelastic deformation stage. It is shown that neglecting higher mode effects in the analysis will significantly underestimate the shear force and overturning moment. It is suggested that pushover analysis may not be suitable for analysing high‐rise shear‐wall or wall‐frame structures. New procedures of seismic evaluation for shear‐wall and wall‐frame structures based on nonlinear response history analysis should be developed. Copyright © 2009 John Wiley & Sons, Ltd.
Numerical studies on the application of tuned liquid dampers with screens to control seismic response of structures
Authors: Halabian A. M. , Torki M. 
Published: April 2009

AbstractTuned liquid damper (TLD) systems are nowadays increasingly being used as one of the economical and effective passive vibration absorbers. A TLD system consists of a water tank having the fundamental sloshing fluid frequency tuned to the frequency near to the natural frequency of structure. This research focuses on modelling tall buildings equipped with TLDs having inside screens subjected to strong ground motions. Strong excitation can cause wave‐breaking phenomenon and makes turbulent in shallow rectangular tanks which could also contribute to the additional damping due to TLDs. On the other hand, wire screens placed inside a liquid tank can play an important role in reducing the structural response due to increasing the inherent damping of the structure. Based on equalizing dissipated energies, a TLD equipped with internal screens can be modelled by equivalent amplitude‐dependent tuned mass damper (TMD). In this study, adopting this simple method, equations of motion for shear‐type buildings equipped with nonlinear amplitude‐dependent TMDs were developed. A complex modal analysis procedure was used to solve the governing equations. Coupling of TMD properties and structural response was solved with iteration on structural response and updating TMD properties. Performing a set of parametric studies on three proposed tall structures equipped with TLD subjected to different ground excitations showed that if the TLD is tuned to a frequency close to the natural frequency of the structure considering hardening behaviour of TLD, it could significantly reduce the seismic response (displacements and base shears) of the structures. Copyright © 2009 John Wiley & Sons, Ltd.
When circuits are printed, labels can talk ‐ New nanomaterials enable low cost flexible electronics
Authors: Arning Volker , Leenen Mark A.M. , Steiger Jürgen , Anselmann Ralf 
Published: April 2009

AbstractElectronics and printing are two very powerful technologies that we encounter many times on a daily basis. Both technologies are very efficient and optimized for their purpose but have distinctive limitations. Printed information is unbeatable when it comes to production efficiency and cost, but once the information has been printed it cannot be changed. Electronics on the other hand is very powerful in the handling of changing information, but the associated costs of the electronics make it often too expensive for the integration into simple day‐to‐day products. If the advantages of printing and electronics are successfully combined, a new technological field with a potential market size of several billion euros will be created. In this article, the basic principles of printing and electronics are explained and ways for the realization of electronics by printing are outlined. A short overview will be given on the material classes which are currently investigated for use in printed circuits.
Open fractures of the tibia in the pediatric population: A systematic review
Authors: Baldwin Keith D. , Babatunde Oladapo M. , Russell Huffman G. , Hosalkar Harish S. 
Published: April 2009

Purpose The management of open fractures of the tibia in a pediatric population represents a challenge to the clinician. Several case series over the course of many years have been performed describing the results of treating these injuries. It remains unclear, however, whether there is a preferred modality of treatment for these injuries, if a more severe injury confers a greater risk of infection, and if time to union is affected by Gustilo type, although trends seem to exist. The purpose of this study was to assemble the available data to determine (1) the risk of infection and time to union of various subtypes of open tibia fractures in children and (2) the changes in treatment pattern over the past three decades. Methods A systematic review of the available literature was performed. Frequency weighted mean union times were used to compare union times for different types of open fractures. Mantel Haentzel cumulative odds ratios were used to compare infection risk between different types of open fractures. Linear regression by year was used to determine treatment practices over time. Results No significant change in practice patterns was found for type I and III fractures, although type II fractures were more likely to be treated closed in the later years of the study compared to the earlier years. Type III fractures conferred a 3.5- and 2.3-fold greater odds of infection than type I and type II fractures, respectively. There was no significant difference in odds of infection between type I and II fractures. There was a significant delay in mean time to union between type I and type II fractures, and between type II and type III fractures. Conclusions With the exception of type II fractures, the philosophy of treatment of open fractures of the tibia has not significantly changed over the past three decades. Closed treatment or internal fixation are both viable options for type II fractures based on their relatively low incidence of infection. This study also demonstrates a strong relationship between Gustillo sub-types and odds of infection in this population. Not surprisingly, union rates are also delayed with increasing injury severity.
Decreased activity of desaturase 5 in association with obesity and insulin resistance aggravates declining long-chainn-3 fatty acid status in Cree undergoing dietary transition
Authors: Zhou Yuan E. , Kubow Stan , Dewailly Eric , Julien Pierre , Egeland Grace M. 
Published: April 2009

Emerging evidence shows that desaturase 5 (Δ5), the key regulator in the synthesis of highly unsaturated long-chain fatty acids (HUFA), is modulated by factors including adiposity, diet and insulin resistance. We explored the association of these factors in a cross-sectional study within a high-risk Cree population. Anthropometric measures and fasting blood glucose and insulin were analysed. Δ5 was estimated as the 20 : 4n-6:20 : 3n-6 ratio in erythrocyte membranes. The setting of the present study was the Mistissini community in the Cree Territory of Québec, Canada with ninety-eight female and sixty-eight male subjects aged 20–88 years. Obesity (BMI ≥ 30 kg/m2) was prevalent across age groups. Δ5 was inversely associated with BMI (Spearman's correlation coefficient (rs) − 0·175;P = 0·03) and positively associated with age (rs0·593;P < 0·0001), which was driven by age-related increases in dietary intake ofn-3 fatty acids and decreases in 20 : 3n-6. Homeostasis model assessment of insulin resistance (HOMA-IR) was significantly inversely associated with Δ5 in age-adjusted linear regression analyses in normoglycaemic individuals (β − 2·110 (se0·566);P < 0·001), whereas no association was observed among glucose-intolerant individuals (interaction termP = 0·03). In contrast, there were no significant interactions indicating differences in the slope for each of the adiposity measures in their associations with Δ5. The present study indicates that the dietary transition of reduced consumption of fish among younger Cree may compound the effects of obesity and emerging insulin resistance which, in turn, could reduce bioavailability of HUFAn-3 (through reduced Δ5 activity). Also, the study suggests that disease progression is an important consideration when evaluating correlates of Δ5 activity in observational studies.
Reconstructing Fossil Sub-structures of the Galactic Disk: Clues from Abundance Patterns of Old Open Clusters and Moving Groups
Authors: De Silva G. M. , Freeman K. C. , Bland-Hawthorn J. 
Published: April 2009

AbstractThe long term goal of large-scale chemical tagging is to use stellar elemental abundances as a tracer of dispersed substructures of the Galactic disk. The identification of such lost stellar aggregates and the exploration of their chemical properties will be key in understanding the formation and evolution of the disk. Present day stellar structures such as open clusters and moving groups are the ideal testing grounds for the viability of chemical tagging, as they are believed to be the remnants of the original larger star-forming aggregates. Until recently, high accuracy elemental abundance studies of open clusters and moving groups having been lacking in the literature. In this paper we examine recent high resolution abundance studies of open clusters to explore the various abundance trends and reasses the prospects of large-scale chemical tagging.
Nasal mucosal expression of the leukotriene and prostanoid pathways in seasonal and perennial allergic rhinitis
Authors: Westergren V. S. , Wilson S. J. , Penrose J. F. , Howarth P. H. , Sampson A. P. 
Published: April 2009

SummaryBackgroundLeukotrienes (LTs) and prostanoids are potent pro‐inflammatory and vasoactive lipid mediators implicated in airway disease, but their cellular sources in the nasal airway in naturally occurring allergic rhinitis (AR) are unclear.ObjectiveTo quantify cellular expression of enzymes of the 5‐lipoxygenase (5‐LO) and cyclooxygenase (COX) pathways by immunohistochemistry in nasal biopsies from patients with symptomatic perennial AR (PAR,n=13) and seasonal AR (SAR,n=14) and from normal subjects (n=12).MethodsEnzymes of the 5‐LO pathway (5‐LO, FLAP, LT A4hydrolase, LTC4synthase) and the COX pathway (COX‐1, COX‐2, prostaglandin D2synthase) were immunostained in glycol methacrylate resin‐embedded inferior turbinate biopsy specimens, quantified in the lamina propria and epithelium, and co‐localized to leucocyte markers bycamera lucida.ResultsIn the lamina propria of PAR biopsies, median counts of cells expressing FLAP were fourfold higher than in normal biopsies (Mann–Whitney,P=0.014), and also tended to be higher than in SAR biopsies (P=0.06), which were not different from normal. PAR biopsies showed threefold more cells immunostaining for LTC4synthase compared with SAR biopsies (P=0.011) but this was not significant compared with normal biopsies (P=0.2). These changes were associated with ninefold more eosinophils (P=0.0005) with no differences in other leucocytes. There were no significant differences in the lamina propria in immunostaining for 5‐LO, LTA4hydrolase, COX‐1, COX‐2 or PGD2synthase. Within the epithelium, increased expression of COX‐1 was evident in PAR biopsies (P=0.014) and SAR biopsies (P=0.037), associated with more intra‐epithelial mast cells in both rhinitic groups (P<0.02).ConclusionsIn the nasal biopsies of PAR subjects, increased expression of regulatory enzymes of the cysteinyl‐LT biosynthetic pathway was associated with lamina propria infiltration by eosinophils. Seasonal rhinitis biopsies shared only some of these changes, consistent with transient disease. Increased intra‐epithelial mast cells and epithelial COX‐1 expression in both rhinitic groups may generate modulatory prostanoids.