bluuebunny/crossref_metadata_2025_split huggingface dataset:
Descriptive proteomic analysis shows protein variability between closely related clinical isolates of Mycobacterium tuberculosis
Authors: Mehaffy Carolina , Hess Ann , Prenni Jessica E. , Mathema Barun , Kreiswirth Barry , Dobos Karen M. 
Published: March 2010

AbstractThe use of isobaric tags such as iTRAQ allows the relative and absolute quantification of hundreds of proteins in a single experiment for up to eight different samples. More classical techniques such as 2‐DE can offer a complimentary approach for the analysis of complex protein samples. In this study, the proteomes of secreted and cytosolic proteins of genetically closely related strains of Mycobacterium tuberculosis were analyzed. Analysis of 2‐D gels afforded 28 spots with variations in protein abundance between strains. These were identified by MS/MS. Meanwhile, a rigorous statistical analysis of iTRAQ data allowed the identification and quantification of 101 and 137 proteins in the secreted and cytosolic fractions, respectively. Interestingly, several differences in protein levels were observed between the closely related strains BE, C28 and H6. Seven proteins related to cell wall and cell processes were more abundant in BE, while enzymes related to metabolic pathways (GltA2, SucC, Gnd1, Eno) presented lower levels in the BE strain. Proteins involved in iron and sulfur acquisition (BfrB, ViuB, TB15.3 and SseC2) were more abundant in C28 and H6. In general, iTRAQ afforded rapid identification of fine differences between protein levels such as those presented between closely related strains. This provides a platform from which the relevance of these differences can be assessed further using complimentary proteomic and biological modeling methods.
Validation of the FACT‐Gastric cancer quality of life questionnaire for use in Spanish‐speaking countries
Authors: Debb Scott M. , Arnold Benjamin , Perez Barbara , Cella David 
Published: March 2010

AbstractObjectives: The purpose of this study was to validate a universal Spanish translation of the Functional Assessment of Cancer Therapy‐Gastric Cancer (FACT‐Ga; Version 4) questionnaire for use in Spanish‐speaking countries.Methods: Translation of the FACT‐Ga from English to Spanish was accomplished by employing the Functional Assessment of Chronic Illness Therapy (FACIT) translation methodology, which utilizes a multinational team of translation experts. A single (universal) Spanish version of the questionnaire was developed for use with gastric cancer patients recruited from Argentina, Chile, Mexico, Peru, and Spain. Pretesting of the questionnaire was conducted using 75 cancer patients (15 from each country), who were also cognitively debriefed.Results: Statistical analysis yielded marginal results for the Peru and Spain samples, although when analyzing pooled data from all five countries, statistics were within expected ranges. Qualitative analysis indicated that there were negligible linguistic concerns that impacted a very small proportion of the items.Conclusion: The universal Spanish FACT‐Ga demonstrates content and linguistic validity, and is conceptually equivalent to its English source. It is a promising tool for use in evaluating the health‐related quality of life for Spanish‐speaking patients with gastrointestinal‐related cancers, given more research regarding universally derived reliability and validity statistics. Copyright © 2010 John Wiley & Sons, Ltd.
A systematic N‐terminal peptide quantitative labeling strategy for differential proteomic analysis
Authors: Liu Xin , Zhang Jiyang , Zheng Zhaobin , Yang Xing , Jia Wei , Li Lei , Gong Yan , Cai Yun , Zhu Yunping , He Fuchu , Ying Wantao , Qian Xiaohong 
Published: March 2010

AbstractPurpose: The purpose of this study is to develop a new systematic strategy for differential proteomic analysis.Experimental design: The new systematic strategy was developed by coupling the stable isotope‐coded N‐terminal acetyl labeling for guanidinated peptides with LTQ‐FT MS for accurate data acquisition, and an in‐house graphic user interface program called “MS‐based acetyl quantification” for automatic data processing.Results: The standard peptide mixture test showed that this method is easy and highly effective, with a linear dynamic range from 0.1 to 10 (R2 value >0.999 and slope error <5%), down to 25 fmol. Moreover, the range of quantitative ratios differing from the target value of 1.0 was statistically determined to be (0.6527, 1.5350) for the 99% confidence level in a fraction of plasma samples. The practicability of this method was further demonstrated in a pilot study on the differential proteomic analysis of cerebrospinal fluid, with the uncovering of 33 dysregulated proteins from different development stages.Conclusions and clinical Relevance: The outcome of the differential proteomic analysis of plasma protein and cerebrospinal fluid confirmed the whole strategy as a promising alternative for exploration of potential biomarker in complex clinical or biological samples.
Differentially expressed proteins of MCF‐7 human breast cancer cells affected by Zilongjin, a complementary Chinese herbal medicine
Authors: Tian Zhi‐Hua , Li Zheng‐Fu , Zhou Shao‐Bo , Liang Yun‐Yan , He Da‐Cheng , Wang Dai‐Shu 
Published: March 2010

AbstractPurpose: Zilongjin, a complementary Chinese herbal medicine, has been used to alleviate the adverse effects of chemotherapeutic drugs in cancer therapy. However, the mechanisms of anti‐cancer activity of Zilongjin are still largely unkonwn.Experimental design: First, the proteomic approach of combined 2‐DE and ESI‐MS/MS was used to investigate the effect of Zilongjin on the protein expression in MCF‐7 cells. Then, the differential expression of some proteins was confirmed by Western blot, cytoimmunofluoresecnce, and quantitative real‐time RT‐PCR analysis.Results: The identified proteins with differential expression, involved in such events as protein translation, cellular signal transduction, cytoskeleton formation and transportation, include seven downregulating proteins, such as Eukaryotic translation initiation factor 3 subunit I, Eukaryotic translation initiation factor 1A Y‐chromosomal, Ran‐specific GTPase‐activating protein, Ubiquitin‐conjugating enzyme E2 N, Tropomodulin‐3, Macrophage‐capping protein, and Tumor protein D52, as well as two upregulating proteins, HSP β‐1 and keratin18. Moreover, the differential expression of three proteins was confirmed.Conclusions and clinical relevance: (i) These results provide a new insight into the molecular mechanisms of Zilongjin on therapy for breast cancer. (ii) The application of the proteomic approaches will result in the more extended appreciation of Chinese medicine than those known at present.
Determination of Urea Nitrate and Guanidine Nitrate Vapor Pressures by Isothermal Thermogravimetry
Authors: Oxley Jimmie , Smith James L. , Brady Joe , Naik Sweta 
Published: March 2010

AbstractSince the bombing of Pan Am Flight 103 over Lockerbie, Scotland in 1988, detection of military explosives has received much attention. Only in the last few years has detection of improvised explosives become a priority. Many detection methods require that the particulate or vapor be available. Elsewhere we have reported the vapor pressures of peroxide explosives triacetone triperoxide (TATP), diacetone diperoxide (DADP), and 2,4,6‐trinitrotoluene (TNT). Herein we examine the vapor signatures of the nitrate salts of urea and guanidine (UN and GN, respectively), and compare them to ammonium nitrate (AN) and TATP using an isothermal thermo‐gravimetric method. The vapor signatures of the nitrate salts are assumed to be the vapor pressures of the neutral parent base and nitric acid. Studies were performed at elevated temperatures (80–120 °C for UN, 205–225 °C for GN, 100–160 °C for AN, and 40–59 °C for TATP), enthalpies of sublimation calculated and vapor pressures extrapolated to room temperature. Reported vapor pressure values (in Pa) are as follows: GN    ≪UN    <AN     ≪TATP 2.66×10−18  3.94×10−5  5.98×10−4  24.8
Characterization of cis elements of the probasin promoter necessary for prostate‐specific gene expression
Authors: Zhang JianFeng , Gao Nan , DeGraff David J. , Yu Xiuping , Sun Qian , Case Thomas C. , Kasper Susan , Matusik Robert J. 
Published: March 2010

AbstractBACKGROUNDThe androgen‐regulated probasin (PB) promoter has been used extensively to target transgenes to the prostate in transgenic mice; however, limited data exist on the mechanism that dictates prostate‐specific gene expression. Tissue‐specific gene expression involves synergistic effects among transcription factors associated in a complex bound to cis‐acting DNA elements.METHODSUsing comprehensive linker scan mutagenesis, enzyme mobility shift and supershift assays, chromatin immunoprecipitation, and transgenic animal studies, we have extensively characterized the prostate‐specific PB promoter.RESULTSWe identified a series of nonreceptor transcription factors that are bound to the prostate‐specific rat PB promoter. These factors include several ubiquitously distributed proteins known to participate in steroid receptor‐mediated transcription. In addition, we identified two tissue‐specific DNA elements that are crucial in directing prostate‐specific PB expression, and confirmed the functional importance of both elements in transgenic animal studies. These two elements are functionally interchangeable and can be bound by multiple protein complexes, including the forkhead transcription factor FoxA1, a “pioneer factor” that has a restricted distribution to some cells type that are ectoderm and endoderm in origin. Using transgenic mice, we further demonstrate that the minimal PB promoter region (−244/−96 bp) that encompasses these tissue‐specific elements results in prostate‐specific gene expression in transgenic mice, contains androgen receptor and FoxA1‐binding sites, as well as ubiquitous transcription factor binding sites.CONCLUSIONWe propose that these sequence‐specific DNA‐binding proteins, including tissue‐restricted and ubiquitous factors, create the first level of transcriptional control, which responds to intracellular pathways that directs prostate‐specific gene expression. Prostate 70: 934–951, 2010. © 2010 Wiley‐Liss, Inc.
Association of caveolin‐1 and ‐2 genetic variants and post‐treatment serum caveolin‐1 with prostate cancer risk and outcomes
Authors: Langeberg Wendy J. , Tahir Salahaldin A. , Feng Ziding , Kwon Erika M. , Ostrander Elaine A. , Thompson Timothy C. , Stanford Janet L. 
Published: March 2010

AbstractBACKGROUNDCaveolin‐1 (cav‐1) is overexpressed by metastatic prostate cancer (PC) cells. Pre‐operative serum cav‐1 levels have been shown to be a prognostic marker for PC recurrence. This study evaluated the relationship between post‐treatment serum cav‐1 levels and single nucleotide polymorphisms (SNPs) in the cav‐1 and ‐2 genes with risk of PC, aggressive PC, PC recurrence or death.METHODSTwo case–control studies of PC among men in Washington State were combined for this analysis. Cases (n = 1,458) were diagnosed in 1993–1996 or 2002–2005 and identified via a SEER cancer registry. Age‐matched controls (n = 1,351) were identified via random digit dialing. Logistic regression was used to assess the relationship between exposures (19 haplotype‐tagging SNPs from all subjects and post‐treatment serum cav‐1 levels from a sample of 202 cases and 226 controls) and PC risk and aggressive PC. Cox proportional hazards regression was used to assess the relationship between exposures and PC recurrence and death.RESULTSRs9920 in cav‐1 was associated with an increased relative risk of overall PC (ORCT + CC = 1.37, 95% CI = 1.12, 1.68) and aggressive PC (ORCT + CC = 1.57, 95% CI = 1.20, 2.06), but not with PC recurrence or death. High post‐treatment serum cav‐1 levels were not associated with PC risk, aggressive PC, or PC‐specific death, but approached a significant inverse association with PC recurrence (hazard ratio = 0.69, 95% CI = 0.47, 1.00).CONCLUSIONSWe found modest evidence for an association with a variant in the cav‐1 gene and risk of overall PC and aggressive PC, which merits further study. We found no evidence that higher post‐treatment serum cav‐1 is associated with risk of aggressive PC or adverse PC outcomes. Prostate 70: 1020–1035, 2010. © 2010 Wiley‐Liss, Inc.
Optoelectronic properties simulation of hydrogenated microcrystalline silicon Schottky diode
Authors: Chahi Mokhtar , Bouhekka Ahmed , Sib Jamal Dine , Kebab Aissa , Bouizem Yahya , Chahed Larbi 
Published: March 2010

AbstractMicrocrystalline silicon has its own macroscopic characteristics which are different from each of the single phase characteristics. Hence, each phase of µc‐Si:H plays an important role in electronic transport. In this paper, we model a basic Schottky structure with a 1 µm thick, the device considered in our study is an alternance of amorphous and crystalline regions with different fractions (0 to 80%). The latest has a columns shape whose average size between 50 Å and 200 Å. The heterojunction physics is applied to the region of interfaces between the crystalline and the amorphous components. The numerical solution of the continuity and Poisson’s equations by Newton‐Raphson method let us to simulate the spectral response and the I(V) characteristic of µc‐Si:H Schottky diode under monochromatic illumination for the wavelength varying between 0.4µm and 1.2µm and under diverse bias voltage. We observe that the maximum of sensibility of microcrystalline diodes shifts towards higher energies compared with them of amorphous diodes, with normalised efficiency varying from 0.7 to 0.8 and the maximum position varies slightly with crystalline fraction and independently to the applied voltage (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
An investigation of rare earth chloride mixtures: combinatorial optimisation for AA2024‐t3 corrosion inhibition
Authors: Muster T. H. , Lau D. , Wrubel H. , Sherman N. , Hughes A. E. , Harvey T. G. , Markley T. , Alexander D. L. J. , Corrigan P. A. , White P. A. , Hardin S. G. , Glenn M. A. , Mardel J. , Garcia S. J. , Mol J. M. C. 
Published: March 2010

AbstractRare earth (lanthanides) cations have demonstrated exceptional activity as cathodic corrosion inhibitors for aluminium alloys (AAs). While Ce is generally regarded as the most active, there have been reports of synergistic interactions between mixtures of rare earths, which show increased inhibitive activity. In this study a combinatorial experimental approach was used to evaluate the corrosion inhibition of four rare earth chlorides (Ce, La, Pr, Nd) singly and as mixtures. The estimation of corrosion currents using both potentiodynamic scans and electrochemical impedance spectroscopy (EIS) provided the quantification of corrosion inhibition. The results were then modelled to determine the best predicted inhibition activity. A partial least squares (PLS) regression indicated that the optimal response directly correlated with the amount of Ce present. From the regression analysis, Ce alone demonstrated the best inhibition activity, with the optimum mixture predicted to contain 100% Ce. The addition of La, Pr or Nd, was not observed to improve the inhibition activity. This study represents one of the first applications of combinatorial design to a fundamental question of corrosion inhibition. Copyright © 2010 John Wiley & Sons, Ltd.
A metastasis or a second independent cancer? Evaluating the clonal origin of tumors using array copy number data
Authors: Ostrovnaya Irina , Olshen Adam B. , Seshan Venkatraman E. , Orlow Irene , Albertson Donna G. , Begg Colin B. 
Published: March 2010

AbstractWhen a cancer patient develops a new tumor it is necessary to determine if it is a recurrence (metastasis) of the original cancer, or an entirely new occurrence of the disease. This is accomplished by assessing the histo‐pathology of the lesions. However, there are many clinical scenarios in which this pathological diagnosis is difficult. Since each tumor is characterized by a distinct pattern of somatic mutations, a more definitive diagnosis is possible in principle in these difficult clinical scenarios by comparing the two patterns. In this article we develop and evaluate a statistical strategy for this comparison when the data are derived from array copy number data, designed to identify all of the somatic allelic gains and losses across the genome. First a segmentation algorithm is used to estimate the regions of allelic gain and loss. The correlation in these patterns between the two tumors is assessed, and this is complemented with more precise quantitative comparisons of each plausibly clonal mutation within individual chromosome arms. The results are combined to determine a likelihood ratio to distinguish clonal tumor pairs (metastases) from independent second primaries. Our data analyses show that in many cases a strong clonal signal emerges. Sensitivity analyses show that most of the diagnoses are robust when the data are of high quality. Copyright © 2010 John Wiley & Sons, Ltd.
Estimating long‐term effects of treatment from placebo‐controlled trials with an extension period, using virtual twins
Authors: Vittinghoff Eric , McCulloch Charles E. , Woo Claudine , Cummings Steven R. 
Published: March 2010

AbstractThe best information about the benefits of long‐term treatment is obtained from a long‐term placebo‐controlled trial. However, once efficacy has been demonstrated in relatively brief trials, it may not be possible to conduct long‐term placebo‐controlled trials, for ethical or practical reasons. This paper presents a method for estimating long‐term effects of a treatment from a placebo‐controlled trial in which some participants originally randomized to active‐treatment volunteer to continue on treatment during an extension study, but follow‐up of participants originally assigned to placebo ends with the trial, or they are crossed over to active treatment during the extension. We propose using data from the trial to project the outcomes for a ‘virtual twin’ for each active‐treatment volunteer under the counterfactual placebo condition, and using bootstrap methods for inference. The proposed method is validated using simulation, and applied to data from the Fracture Intervention Trial and its extension, FLEX. Copyright © 2010 John Wiley & Sons, Ltd.
Predictors of outcome at 2 years of age after early intrauterine growth restriction
Authors: Torrance H. L. , Bloemen M. C. T. , Mulder E. J. H. , Nikkels P. G. J. , Derks J. B. , De Vries L. S. , Visser G. H. A. 
Published: March 2010

AbstractObjectiveTo examine the relative importance of antenatal and perinatal variables on short‐ and long‐term outcome of preterm growth restricted fetuses with umbilical artery (UA) Doppler abnormalities.MethodsThis was a cohort study of 180 neonates with birth weight < 10th percentile, gestational age at delivery < 34 weeks and abnormal Doppler ultrasound examination of the UA. Various antenatal and perinatal variables were studied in relation to short‐ and long‐term outcome.ResultsNeonatal and overall mortality (up to 2 years of age) were predicted by low gestational age at delivery. Neonatal mortality was additionally predicted by absent or reversed UA end‐diastolic flow, while the presence of severe neonatal complications and placental villitis were additional predictors of both infant (between 28 days and 1 year of postnatal life) and overall mortality. Placental villitis was found to be the only predictor of necrotizing enterocolitis. Low gestational age at delivery, male sex, abnormal cardiotocography, absent or reversed UA end‐diastolic flow and the HELLP syndrome predicted respiratory distress syndrome. Abnormal neurodevelopmental outcome at 2 years was predicted by low birth weight (< 2.3rd percentile), fetal acidosis (UA pH < 7.00), and placental villitis.ConclusionLess advanced gestation at delivery remains an important predictor of short‐term outcome in growth‐restricted fetuses. In addition, the presence of placental villitis may aid neonatologists in the early identification of infants at increased risk of necrotizing enterocolitis, death and abnormal neurodevelopment at 2 years of age. Abnormal neurodevelopment was related to low weight and acidosis at birth, indicating that the severity of malnutrition and fetal acidosis affect long‐term outcome. Copyright © 2010 ISUOG. Published by John Wiley & Sons, Ltd.
On the constitutive modeling of reinforced rubber in a broad frequency domain
Authors: Suwannachit A. , Nackenhorst U. 
Published: March 2010

AbstractA constitutive model for the numerical simulation of rubber behavior in a wide frequency range is presented. The combination between the well known Simo's viscoelastic model and a pseudo‐elastic approach enables for the modeling of inelastic effects at low frequencies, such as nonlinear elasticity, hysteretic behavior, and damage (Mullins effect). The constitutive formulation is derived in detail with an aim of the finite element implementation. Because mechanical response at high frequencies is usually characterized by complex modulus, the developed viscoelastic damage model is extended to high‐frequency analysis. A key idea is the decomposition of the deformation gradient into linear and nonlinear part. The nonlinear part is associated with inelastic deformations established at low frequencies, while the linear contribution plays an important role for dynamic analysis at high frequencies. As a result, the steady‐state response of rubber at a certain static deformation is evaluated and consequently leads to the numerical solution for complex modulus. The computational efficiency of the proposed model can be seen from a good agreement with experimental data.
Interfacial Composition, Structural and Thermodynamic Parameters of Water/(Surfactant+n‐Butanol)/n‐Heptane Water‐in‐Oil Microemulsion Formation in Relation to the Surfactant Chain Length
Authors: De Mrinmoy , Bhattacharya Subhash C. , Moulik Satya P. , Panda Amiya K. 
Published: March 2010

AbstractInterfacial behavior, structural and thermodynamic parameters of a water/(surfactant+nbutanol)/n‐heptane water‐in‐oil (w/o) microemulsion have been investigated using the dilution technique at different temperatures, and [water]/[surfactant] mole ratios. The cationic surfactants used were alkyltrimethyl ammonium bromides (CnTAB, n = 10, 14 and 16) while the nonionic surfactants were polyoxyethylene (20) sorbitan monoalkanoates (polysorbate), viz., palmitate (PS 40), stearate (PS 60) and oleate (PS 80). The distribution of cosurfactant between the oil–water interface and the bulk oil at the threshold level of stability, and the thermodynamics of transfer of the cosurfactant from the bulk oil to the interface were evaluated. Structural parameters such as the dimensions, population density and effective water pool radius of the dispersed water droplets in the oil phase and the interfacial population of the surfactant and cosurfactant have been evaluated in terms of the surfactant chain length.
Microemulsions with Mixed Nonionic Surfactants and Flavor Oil
Authors: Fanun Monzer 
Published: March 2010

AbstractThe microemulsion systems composed of water/sucrose laurate/ethoxylated mono‐di‐glyceride/peppermint oil were formulated and characterized using electrical conductivity and small‐angle X‐ray scattering. The solubilization capacity of water in the oil is dependent on the surfactant mixing ratio. A static percolation phenomenon was observed in these systems and the water volume fraction percolation threshold was determined. A progressive transformation of water‐in‐oil to bicontinuous microemulsions, occurring upon dilution with water was revealed for equal amounts of sucrose laurate and ethoxylated mono‐di‐glyceride in the microemulsions. The periodicity, that is a characteristic length for the domain size of the microemulsions, increases linearly with the increase in the water volume fraction, whereas the correlation length, that is also a characteristic length for the domain size, increases with the increase in the water volume fraction up to a certain value then decreases.