bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential effects of resveratrol and its naturally occurring methylether analogs on cell cycle and apoptosis in human androgen‐responsive LNCaP cancer cells
Authors: Wang Thomas T. Y. , Schoene Norberta W. , Kim Young S. , Mizuno Cassia S. , Rimando Agnes M. 
Published: January 2010

AbstractStilbenes are phytoalexins that become activated when plants are stressed. These compounds exist in foods and are widely consumed. Resveratrol is a grape‐derived stilbene, which possesses a wide range of health‐promoting activities, including anticancer properties. Several other stilbenes structurally similar to resveratrol are also available in food, but their biological activities remain largely unknown. In this study, we compared the effects of resveratrol and its natural derivatives pterostilbene, trans‐resveratrol trimethylether, trans‐pinostilbene and trans‐desoxyrhapontigenin on androgen‐responsive human prostate cancer LNCaP cells. We found that these compounds exert differential effects on LNCaP cell growth, cell cycle and apoptosis. Trans‐resveratrol trimethylether appeared to be the most potent compound among the stilbenes tested. Treatment of LNCaP cells with trans‐resveratrol trimethylether resulted in G2/M blockage while other compounds, including resveratrol, induced G1/S arrest. Moreover, different from other compounds, trans‐resveratrol trimethylether induced apoptosis. At the molecular level, the effects of these compounds on cell cycle correlated with induction of the cyclin‐dependent kinase inhibitor 1A and B mRNA levels. Additionally, these compounds also inhibited both androgen‐ as well as estrogen‐mediated pathways. These results provide mechanistic information on how resveratrol and its methylether analogs may act to contribute to potential antiprostate cancer activity.
Clonal complex chromosome aberration in non‐ossifying fibroma
Authors: Brassesco María Sol , Valera Elvis Terci , Engel Edgard Eduard , Nogueira‐Barbosa Marcello Henrique , Becker Aline Paixão , Scrideli Carlos Alberto , Tone Luiz Gonzaga 
Published: January 2010

AbstractCytogenetic information of non‐ossifying fibromas (NOFs) is exceptionally limited. This fact relies, in part, on their benign nature but mainly because most cases evolve undetected or there is no need for surgical intervention. We report the case of a NOF arising in the left tibia of a 14‐year‐old male with an invariable clonal translocation. The karyotype was denoted as 42–46,XY,t(11;3;14)(q23;p21;p11). There are only two previous reported cases of clonally aberrant NOF. Records from additional cases will be essential to assess whether consistent karyotypic aberrations define this lesion. Pediatr Blood Cancer 2010;54:764–767. © 2010 Wiley‐Liss, Inc.
Fetal anatomic survey using three‐dimensional ultrasound in conjunction with first‐trimester nuchal translucency screening
Authors: Bhaduri Mousumi , Fong Katherine , Toi Ants , Tomlinson George , Okun Nan 
Published: January 2010

AbstractObjectiveTo determine the visualization rates of fetal anatomic structures by three‐dimensional ultrasound (3DUS) at 12–13 weeks of gestation.Study DesignThis was a prospective observational study of women presenting for nuchal translucency ultrasound. Five 3D volumes of the fetus were acquired transabdominally. Two investigators independently reviewed the stored volumes offline following a standardized protocol.ResultsOne hundred singleton fetuses were examined. The mean time for 3D volumes acquisition was 4.8 min; and for 3D review 17 min. Anatomic structures were seen as follows: cranium, lateral cerebral ventricles and abdominal wall 100%; stomach, vertebrae, upper and lower limbs ≥ 94%; face 71%, bladder 58%, both kidneys 39%, skin overlying spine 26% and heart 18%. Agreement between two observers ranged from 100% (for head, abdominal wall and lower limbs) to 43% (for visualization of skin overlying spine). A complete basic anatomic survey was achieved in 11.4% of the 12‐week fetuses and 33.3% of the 13‐week fetuses (p‐value = 0.038).ConclusionsFirst‐trimester transabdominal 3DUS was adequate for assessment of the head, abdominal wall, stomach, limbs and vertebral alignment. It was less effective for evaluating the heart and intactness of the skin over the spine. Copyright © 2010 John Wiley & Sons, Ltd.
Semi‐automatic tool to describe, store and compare proteomics experiments based on MIAPE compliant reports
Authors: Martínez‐Bartolomé Salvador , Medina‐Aunon J. Alberto , Jones Andrew R. , Albar Juan P. 
Published: January 2010

AbstractThe Human Proteome Organization's Proteomics Standards Initiative aims to develop new standards for data representation and exchange. The Proteomics Standards Initiative has defined the Minimum Information About a Proteomics Experiment (MIAPE) guidelines that specify the information that should be reported with a published experiment. With the aim of promoting the implementation of standard reporting guidelines, we have developed a web tool that helps to generate and store MIAPE compliant reports describing gel electrophoresis and MS‐based experiments. The tool can be used in the reviewing phase of the proteomics publication process and can facilitate data interpretation through the comparison of related studies.
LysNDeNovo: An algorithm enabling de novo sequencing of Lys‐N generated peptides fragmented by electron transfer dissociation
Authors: van Breukelen Bas , Georgiou Alexandros , Drugan Madalina M. , Taouatas Nadia , Mohammed Shabaz , Heck Albert J. R. 
Published: January 2010

AbstractRecently, we introduced a novel proteomics method employing a metalloendopeptidase with Lys‐N specificity to produce proteolytic peptides. Fragmentation spectra generated by electron transfer dissociation, for a large proportion of the Lys‐N proteolytic peptides, were found to be dominated by extensive series of c‐type ions. Taking advantage of this unique spectral property, we developed an algorithm, LysNDeNovo, to facilitate de novo sequencing of these peptides. LysNDeNovo contains simple and naive heuristics to demonstrate a proof of concept, i.e. that Lys‐N peptide electron transfer dissociation spectra are perfectly suited for de novo interpretation. A stringent “golden” dataset of peptides identified by conventional database search algorithms was taken to validate the performance of LysNDeNovo. The results on this dataset indicate that LysNDeNovo was able to confidently identify a considerable proportion (42%), without requiring any prior genome or protein sequences. Results of similar quantity and quality could also be obtained on a much more extensive experimental dataset, illustrating the potential for higher throughput de novo sequencing using these methods.
Conformational analysis: Part 42. A modelling and LIS/NMR investigation of the conformations of some aromatic SO compounds
Authors: Abraham Raymond J. , Byrne Jonathan J. , Griffiths Lee , Sancassan Fernando 
Published: January 2010

AbstractA refined Lanthanide‐Induced‐Shift Analysis (LISA), in which both the paramagnetic and the diamagnetic lanthanide induced chemical shifts are normalised separately, is used with molecular mechanics (MMFF94) and ab initio (RHF/6‐31G, RHF/6‐311G** and B3LYP/6‐311G**) calculations to investigate the conformations of methyl para‐tolyl sulphoxide 1, sulphone 2 and sulphonate 3 and the conformational equilibria of methyl 2,4‐dimethylphenyl sulphoxide 4 and sulphone 5. In 1 acceptable agreement factors (AFs) in the LISA analysis were only obtained when the SO/phenyl dihedral angle was increased from that (10–15°) of the computed geometries to 30–40°. The calculated geometries for 2 had the methyl group orthogonal to the phenyl ring and gave good AF in the LISA analysis. In both compounds, the AF were in the order MMFF94 ≤ B3LYP < RHF with the larger basis sets giving better agreement than the limiting 6‐31G* function. In 3 all the geometries again had the methoxy group orthogonal to the phenyl ring but, while the ab initio geometries still gave good AFs, the MMFF94 structure gave an AF which was only just acceptable. The unsymmetrical compounds 4 and 5 display conformational equilibria. In 4 two energy minima were found, both with the SMe group orthogonal to the phenyl ring, with the SO oxygen cis or trans to the 2‐methyl group. The energy difference (cis–trans) was calculated as 1.6 kcal/mol (MMFF94), 2.7 (6‐31G*), 1.9 (6‐311G**) but −0.11 (DFT). The LISA analyses on the separate conformers gave poor agreement (ca. 3%) for the trans conformer but increasing the SO/Ph dihedral angle again gave an acceptable value (ca. 1.4%). Inclusion of even small amounts of the cis conformer in the LIS analysis gave poorer results. Thus, the LISA analysis confirms the MM and RHF prediction that the trans conformer is more stable and suggests that the conformer energy difference in solution is equal to or greater than the largest calculated value of 2.7 kcal/mol. In 5 all the calculations gave two mirror image conformations with the SMe orthogonal to the phenyl ring. The LISA analysis in this case is complicated by the fact that in the stable conformer the complexing oxygen atoms are not equivalent. This was resolved by considering both coordination sites in one Z‐matrix and varying the % coordination on each oxygen atom. This gave an acceptable AF of ca. 1.0% for all the geometries with ca. 2:1 coordination on the oxygen atoms trans and cis to the C2‐methyl. The difference in the geometries and conformer energies found by LISA for these molecules in solution compared to the theoretical values may be due to interactions with the chloroform solvent for these polar compounds. Copyright © 2010 John Wiley & Sons, Ltd.
Microfiltration isolation of human urinary exosomes for characterization by MS
Authors: Merchant Michael L. , Powell David W. , Wilkey Daniel W. , Cummins Timothy D. , Deegens Jeroen K. , Rood Ilse M. , McAfee K. Jill , Fleischer Cornelia , Klein Elias , Klein Jon B. 
Published: January 2010

AbstractPurpose: The purpose of this study was to address the hypothesis that small vesicular urinary particles known as exosomes could be selectively microfiltered using low protein‐binding size exclusion filters, thereby simplifying their use in clinical biomarker discovery studies.Experimental design: We characterized a microfiltration approach using a low protein binding, hydrophilized polyvinylidene difluoride membrane to easily and efficiently isolate urinary exosomes from fresh, room temperature or 4°C urine, with a simultaneous depletion of abundant urinary proteins. Using LC‐MS, immunoblot analysis, and electron microscopy methods, we demonstrate this method to isolate intact exosomes and thereby enrich for a low abundant urinary proteome.Results: In comparison to other standard methods of exosome isolation including ultracentrifugation and nanofiltration, we demonstrate equivalent enrichment of the exosome proteome with reduced co‐purification of abundant urinary proteins.Conclusion and clinical relevance: In conclusion, we demonstrate a microfiltration isolation method that preserves the exosome structure, reduces contamination from higher abundant urinary proteins, and can be easily implemented into mass spectrometry analysis for biomarker discovery efforts or incorporation into routine clinical laboratory applications to yield higher sample throughput.
C‐peptide microheterogeneity in type 2 diabetes populations
Authors: Oran Paul E. , Jarvis Jason W. , Borges Chad R. , Nelson Randall W. 
Published: January 2010

AbstractPurpose: The purpose of this study was to investigate naturally occurring C‐peptide microheterogeneity in healthy and type 2 diabetes (T2D) populations.Experimental design: MS immunoassays capable of simultaneously detecting intact C‐peptide and variant forms were applied to plasma samples from 48 healthy individuals and 48 individuals diagnosed with T2D.Results: Common throughout the entire sample set were three previously unreported variations of C‐peptide. The relative contribution of one variant, subsequently identified as C‐peptide (3‐31), was found to be more abundant in the T2D population as compared to the healthy population. Dipeptidyl peptidase IV is suspected to be responsible for this particular cleavage product, which is consistent with the pathophysiology of T2D.Conclusions and clinical relevance: C‐peptide does not exist in the human body as a single molecular species. It is qualitatively more heterogeneous than previously thought. These results lay a foundation for future studies devoted to a comprehensive understanding of C‐peptide and its variants in healthy and diabetic populations.
Proteomic examination of Leishmania chagasi plasma membrane proteins: Contrast between avirulent and virulent (metacyclic) parasite forms
Authors: Yao Chaoqun , Li Yalan , Donelson John E. , Wilson Mary E. 
Published: January 2010

AbstractPurpose: About two million new cases of leishmaniasis with 50 000 associated deaths occur worldwide each year. Promastigotes of the causative Leishmania spp. develop from the procyclic stage to the highly virulent metacyclic stage within the sand fly vector. We hypothesized that proteins important for promastigote virulence might be uniquely represented in the plasma membrane of metacyclic, but not procyclic, promastigotes.Experimental design: Procyclic (logarithmic) promastigotes and purified metacyclic promastigotes from stationary phase cultures of Leishmania chagasi were used to prepare membrane preparations either by surface biotinylation‐streptavidin affinity separation or by octyl glucoside detergent extraction.Results: These membrane fractions were enriched over 130‐ and 250‐fold, respectively, as estimated by Western blotting for the plasma membrane's major surface protease. Hundreds or dozens of proteins were identified by LC‐MS/MS in the surface biotinylation or detergent extraction, respectively. Confocal microscopy suggested the difference between the lists was due to the fact that proteins localized both on the surface membrane and within the flagellar pocket were accessible to surface biotinylation, whereas only proteins on the membrane were obtained by detergent extraction. Using detergent extraction, we found different proteins were present in membranes of the procyclic stage compared to metacyclic stage promastigotes. Several dozen were stage specific.Conclusions and clinical relevance: These data provide a foundation for identifying virulence factors in the plasma membranes of Leishmania spp. promastigotes during metacyclogenesis.
Proteome of human endometrium: Identification of differentially expressed proteins in proliferative and secretory phase endometrium
Authors: Rai Priyanka , Kota Venkatesh , Sundaram Curam Sreenivasacharlu , Deendayal Mamta , Shivaji Sisinthy 
Published: January 2010

AbstractPurpose: To exploit the potential of proteomics to identify and study additional yet‐unidentified important proteins present in human endometrium.Experimental design: The proteome of human endometrium would be established using 2‐DE and MALDI and the data analyzed to identify differential protein expression in the proliferative and secretory phase of the menstrual cycle using PDQuest software and MALDI.Results: In the present work, 2‐DE of human endometrium protein led to the resolution of over 200 spots. Subsequent MALDI analysis of 215 spots allowed the identification of 194 proteins. A total of 57 out of the 215 spots were found to be differentially expressed, out of which 49 could be identified using MALDI. These differentially expressed proteins included structural proteins, molecular chaperones, signaling proteins, metabolic proteins, proteins related to immunity, RNA biogenesis, protein biosynthesis and others. The differential expressions of seven representative proteins in secretory and proliferative phase endometrium tissue were confirmed by immunoblot analysis.Conclusion and clinical relevance: This study establishes the 2‐D proteome of human endometrium represented by 194 identified protein spots. The present data provides an important clue towards determining the function of these proteins with respect to endometrium related diseases.
Radiation inactivation of galactose oxidase, a monomeric enzyme with a stable free radical
Authors: Kempner Ellis S. , Whittaker James W. , Miller Jay H. 
Published: January 2010

AbstractTo determine the radiation sensitivity of galactose oxidase, a 68 kDa monomeric enzyme containing a mononuclear copper ion coordinated with an unusually stable cysteinyl‐tyrosine (Cys‐Tyr) protein free radical. Both active enzyme and reversibly rendered inactive enzyme were irradiated in the frozen state with high‐energy electrons. Surviving polypeptides and surviving enzyme activity were analyzed by radiation target theory giving the radiation sensitive mass for each property. In both active and inactive forms, protein monomer integrity was lost with a single radiation interaction anywhere in the polypeptide, but enzymatic activity was more resistant, yielding target sizes considerably smaller than that of the monomer. These results suggest that the structure of galactose oxidase must make its catalytic activity unusually robust, permitting the enzymatic properties to survive in molecules following cleavage of the polymer chain. Radiation target size for loss of monomers yielded the mass of monomers indicating a polypeptide chain cleavage after a radiation interaction anywhere in the monomer. Loss of enzymatic activity yielded a much smaller mass indicating a robust structure in which catalytic activity could be expressed in cleaved polypeptides.
Amino acid interaction preferences in proteins
Authors: Nath Jha Anupam , Vishveshwara Saraswathi , Banavar Jayanth R. 
Published: January 2010

AbstractUnderstanding the key factors that influence the interaction preferences of amino acids in the folding of proteins have remained a challenge. Here we present a knowledge‐based approach for determining the effective interactions between amino acids based on amino acid type, their secondary structure, and the contact based environment that they find themselves in the native state structure as measured by their number of neighbors. We find that the optimal information is approximately encoded in a 60 × 60 matrix describing the 20 types of amino acids in three distinct secondary structures (helix, beta strand, and loop). We carry out a clustering scheme to understand the similarity between these interactions and to elucidate a nonredundant set. We demonstrate that the inferred energy parameters can be used for assessing the fit of a given sequence into a putative native state structure.
Fourier transform photocurrent measurement of thin silicon films on rough, conductive and opaque substrates
Authors: Holovský Jakub , Dagkaldiran Űmit , Remeš Zdeněk , Purkrt Adam , Ižák Tibor , Poruba Aleš , Vaněček Milan 
Published: January 2010

AbstractFourier transform photocurrent spectroscopy (FTPS) is used as an inspection method for hydrogenated amorphous silicon (a‐Si:H) thin films deposited on aluminium foil and aluminium foil coated with rough SnO2. These structures are part of roll‐to‐roll solar cell fabrication process. Measurement technique utilizes transparent electrode in a sandwich arrangement. An elaborate calculation procedure is used to correct the measurement for the optical effects in order to obtain spectra of optical absorption coefficient. Correction procedure is based partly on analytical formulae and partly on Monte‐Carlo simulations. Quality of thin a‐Si:H layers deposited by PECVD on glass and aluminium foil with and without rough layer of SnO2 were compared. Positive effect of aluminium and SnO2 on layer quality and effect of bandgap shift was observed.
Reporting cumulative proportion of subjects with an adverse event based on data from multiple studies
Authors: Chuang‐Stein Christy , Beltangady Mohan 
Published: January 2010

AbstractExperience has shown us that when data are pooled from multiple studies to create an integrated summary, an analysis based on naïvely‐pooled data is vulnerable to the mischief of Simpson's Paradox. Using the proportions of patients with a target adverse event (AE) as an example, we demonstrate the Paradox's effect on both the comparison and the estimation of the proportions. While meta analytic approaches have been recommended and increasingly used for comparing safety data between treatments, reporting proportions of subjects experiencing a target AE based on data from multiple studies has received little attention. In this paper, we suggest two possible approaches to report these cumulative proportions. In addition, we urge that regulatory guidelines on reporting such proportions be established so that risks can be communicated in a scientifically defensible and balanced manner. Copyright © 2010 John Wiley & Sons, Ltd.
A Dirichlet reputation system in reliable routing of wireless ad hoc network
Authors: Yang Li , Cemerlic Alma , Cui Xiaohui 
Published: January 2010

AbstractAd hoc networks are very helpful in situations when no fixed network infrastructure is available, such as natural disasters and military conflicts. In such a network, all wireless nodes are equal peers simultaneously serving as both senders and routers for other nodes. Therefore, how to route packets through reliable paths becomes a fundamental problems when behaviors of certain nodes deviate from wireless ad hoc routing protocols. We proposed a novel Dirichlet reputation model based on Bayesian inference theory which evaluates reliability of each node in terms of packet delivery. Our system offers a way to predict and select a reliable path through combination of first‐hand observation and second‐hand reputation reports. We also proposed moving window mechanism which helps to adjust ours responsiveness of our system to changes of node behaviors. We integrated the Dirichlet reputation into routing protocol of wireless ad hoc networks. Our extensive simulation indicates that our proposed reputation system can improve good throughput of the network and reduce negative impacts caused by misbehaving nodes. Copyright © 2010 John Wiley & Sons, Ltd.
Enhanced correlation power analysis attack against trusted systems
Authors: Li Huiyun , Wu Keke , Yu Fengqi 
Published: January 2010

AbstractPower analysis attacks pose a serious threat to the security of many trusted systems. The principle of power analysis attacks is based on the assumption that the power consumption of an electronic device is proportional to the Hamming weight (HW) of the data being processed. However, this power model is defective as it is deviated from the CMOS circuit power consumption theory where power consumption is largely dependent on the switching ability, i.e., the Hamming distance (HD) of the data being processed. This paper presents an HD power analysis model which emulates Hamming distance based on probability distribution of HW, thus conjointly achieving better feasibility and accuracy. The experiment of CPA analysis on smart card chips running DES (Data Encryption Standard) and AES (Advanced Encryption Standard) encryption demonstrates that the proposed model can achieve 10% ∼ 18% better results compared to the existing HW model, which suggests higher success rate of discerning the secret key from the trusted systems. Copyright © 2010 John Wiley & Sons, Ltd.