bluuebunny/crossref_metadata_2025 huggingface dataset:
Monetary policy and uncertainty in an empirical small open‐economy model
Authors: Justiniano Alejandro , Preston Bruce
Published: January 2010

This paper explores optimal policy design in an estimated model of three small open economies: Australia, Canada and New Zealand. Within a class of generalized Taylor rules, we show that to stabilize a weighted objective of output consumer price inflation and nominal interest variation optimal policy does not respond to the nominal exchange. This is despite the presence of local currency pricing and due, in large part, to observed exchange rate disconnect in these economies. Optimal policies that account for the uncertainty of model estimates, as captured by the parameters' posterior distribution, similarly exhibit a lack of exchange rate response. In contrast to Brainard (1967), the presence of parameter uncertainty can lead to more or less aggressive policy responses, depending on the model at hand. Copyright © 2010 John Wiley & Sons, Ltd.
Context‐dependent variability in the components of fish escape response: integrating locomotor performance and behavior
Authors: Domenici Paolo
Published: January 2010

Escape responses are used by most fish species in order to avoid predation. Escape responses include a number of behavioral and kinematic components, such as responsiveness, reaction distance, escape latency, directionality, and distance‐derived performance. All of these components can contribute to escape success. Work on the context‐dependent variability has focused on reaction distance, and suggests that this component is largely determined by the relative cost and benefits of escaping (economic hypothesis). For example, reaction distance was found to depend on many factors related to perceived risk and cost of escaping, such as the attack speed and size of the predators, the proximity to refuges, and engagement in other activities (e.g., feeding). Evidence from many behavioral, kinematic, and physiological studies suggest that performance in other components of the escape response is also not always maximized. For example, escape latencies may increase in the presence of schooling neighbors, and escape speed is higher in fish that have been subject to higher predation pressure. In addition, all escape components are further modulated by the effect of environmental factors. Variability in escape components can be interpreted by using both ultimate and proximate explanations, for example, the effect of stimulus strength on escape latency can be interpreted as the triggering neural threshold varying with stimulus strength (proximate explanation) and high intensity stimuli representing higher risk to the prey (ultimate explanation). An integrative approach is suggested for a full, ecologically relevant, assessment of escape performance in fish. J. Exp. Zool. 313A:59–79, 2010. © 2010 Wiley‐Liss, Inc.
Prenatal development of Crocodylus niloticus niloticus Laurenti, 1768
Authors: Peterka Miroslav , Yves Sire Jean , Hovorakova Maria , Prochazka Jan , Fougeirol Luc , Peterkova Renata , Viriot Laurent
Published: January 2010

Prenatal development in crocodilians represents a very interesting model for comparative studies. As the speed of prenatal development of crocodilians varies depending on incubation conditions, the staging of embryos and fetuses is a very important prerequisite for data correlation. To establish a background for future developmental studies on Crocodylus niloticus, we characterized its prenatal development in a collection comprising 169 animals during embryonic/incubation days 9–70. The characteristics included external morphology, head morphometry, and wet body weight determined before fixation. We documented the external morphology of prenatal Nile crocodiles in a large collection of photographs and described landmarks during the morphogenesis of the head, face and limbs. In the development of the facial processes (medial nasal, lateral nasal, maxillary), three phases could be distinguished: union, separation, reunion. At the free jaw margin, a regular series of prominences was present. The outer aspect of a prominence gave rise to a labial scale, the inner aspect to a tooth. In contrast to mammals (humans and mice), the hindlimbs of C. niloticus developed faster than the forelimbs. We also determined changes in basic measures of the head and of the wet body weight. Both morphological and morphometric characteristics showed an apparent inter‐individual variability among animals of the same age. This variability decreased among animals of a similar body weight (irrespective of their age). Body weight can be considered as the most representative and complex parameter for crocodile staging reflecting the overall growth of a whole embryo/fetus. J. Exp. Zool. (Mol. Dev. Evol.) 314B:353–368, 2010. © 2010 Wiley‐Liss, Inc.
The mesmerists inquire about “Oriental mind powers”: West meets East in the search for the universal trance
Authors: Schmit David T.
Published: January 2010

Contemporary interest in Asian meditation raises questions about when Westerners began investigating these practices. A synopsis of Western‐originating scientific meditation research is followed by a brief introduction to mesmerism. Next, the unappreciated ways the mesmerists explored Oriental mind powers is recounted. How the mesmerists' cultural positioning, philosophy, and interest in mind—body practices facilitated their inquiries of Oriental medicine and Hindu contemplative practices is explored, followed by a consideration of why these investigations were unique for the era. The way this work subverted Western cultural imperialism is examined. A consideration of the historical continuities and discontinuities between the mesmerists' inquiries and twentieth‐century meditation research concludes the article. © 2010 Wiley Periodicals, Inc.
The individual and “the general situation”: The tension barometer and the race problem at the University of Chicago, 1947–1954
Authors: Gordon Leah N.
Published: January 2010

This article explains how social theories that posited white attitudes as the root of racial injustice gained traction in postwar social thought. Examining the production of a “tension barometer,” an attitude survey that scholars from the University of Chicago's Committee on Education, Training, and Research in Race Relations created to predict interracial violence, I chart vigorous debate over the nature and causes of racial oppression in the critical postwar decades. Available—and unavailable—social scientific frameworks, activists” interests, and emerging anticommunism, the Committee's history shows, created an environment where individualistic conceptions of the race problem won out, despite critique. © 2010 Wiley Periodicals, Inc.
Mice expressing the A53T mutant form of human alpha‐synuclein exhibit hyperactivity and reduced anxiety‐like behavior
Authors: Graham Dianca R. , Sidhu Anita
Published: January 2010

Genetic mutations associated with α‐synuclein (α‐Syn) are implicated in the pathogenesis of Parkinson's disease (PD). PD is primarily a movement disorder, but patients are known to experience anxiety and other mood disorders. In this study, we examined the effect of the hA53T mutation during development by analyzing the protein expression of norepinephrine (NET), serotonin (SERT), and dopamine (DAT) transporters in addition to assessing locomotor and anxiety‐like behavior. We observed significant decreases in DAT expression at 8 months in transgenic animals compared with normal and younger mice. We used the elevated plus maze, open‐field test, and rotarod apparatus to evaluate wild‐type and hA53T hemizygous mice at 2, 8, and 12 months of age. Our results showed that 12‐month‐old transgenic mice spend more time in the open arms and display a greater number of open entries of the elevated plus maze compared with wild‐type controls and younger mice. Open‐field test results showed that 12‐month‐old mice travel a greater distance overall and travel more in the inner zone than either wild‐type or younger mice. Rotarod testing showed that 8‐ and 12‐month‐old transgenic mice perform better than either wild‐type controls or younger mice. Overall, 8–12‐month‐old transgenic mice showed a trend toward reduced anxiety‐like behavior and increased hyperactivity. These results indicate a possible role of the A53T α‐Syn mutation in anxiety‐like and hyperactive behaviors in a PD mouse model, suggesting that these behaviors might be comorbid with this disease. © 2010 Wiley‐Liss, Inc.
Histological comparison of two different fractional photothermolysis devices operating at 1,550 nm
Authors: Thongsima Siremon , Zurakowski David , Manstein Dieter
Published: January 2010

Background

There are a wide variety of fractional resurfacing devices that are available and it is important to understand the tissue effect of different devices at different parameters to ensure a well‐controlled treatment. Thus, we have chosen to characterize and compare two different fractional laser devices, the Fraxel SR750 and SR1500 (re:store™) (Solta Medical, Hayward, CA). While the SR750 has a fixed focus spot diameter, the SR1500 features an internally controlled zoom optic allowing for an adjustable spot size.

Materials and Methods

Exposures were performed in vitro on human skin samples at 37°C. The exposures were performed for the SR750 at pulse energies between 6 and 40 mJ at 125 MTZ/cm2 with up to 20 passes, and for the SR1500 between 6 and 100 mJ, at Treatment Level 7 and 8 passes. The skin samples then were processed for serial frozen sectioning, stained with Nitro‐Blue‐Tetrazolium‐Chloride (NBTC) and lesion depth and width was determined.

Results

Mean lesion depth was significantly greater for lesions treated with the SR1500 laser compared to the SR750 at pulse energies of 6, 10, 30, and 40 mJ (P<0.001) with a borderline difference at 20 mJ. Mean lesion width was comparable for energies up to 20 mJ and relatively increased for the SR1500 for higher energies. The depth‐to‐width ratio (DWR) was in general higher for the SR1500, reaching significance at 6, 10, and 40 mJ.

Conclusion

We have characterized the lesion depth and width for the for two different Fractional Photothermolysis devices (SR750 vs. SR1500). The device with the adjustable spot size (SR1500 or Fraxel re:store™) provides generally deeper lesions at the same energy level. It remains to be shown whether increased lesion depth improves efficacy for certain clinical applications. Lasers Surg. Med. 42:32–37, 2010. © 2010 Wiley‐Liss, Inc.
Cathodic protection of XL 52 steel under the influence of sulfate reducing bacteria
Authors: Esquivel R. García , Olivares G. Zavala , Gayosso M. J. Hernández , Trejo A. Gayosso
Published: January 2010

The effect of sulfate reducing bacteria (SRB) upon the cathodic protection of XL 52 steel was determined, in order to identify if the potential value of −0.950 V versus copper/copper sulfate electrode is good enough to protect the metal surface. During the experiments, different operational parameters were monitored: hydrogen sulfide production, iron concentration, electrolyte alkalinity, microorganisms' population, as well as the metal surface damage. At the same time, the corrosion rate was determined using two electrochemical techniques: polarization resistance (PR) and electrochemical impedance spectroscopy (EIS). According to the results, it was observed that the protection potential of −0.950 V versus copper/copper sulfate electrode is not enough to control the microbiologically induced corrosion. This situation is reinforced by the fact that significant iron concentration was found in the electrolyte. The microbiological activity is not affected by the protection potential. On the contrary, the population growth is slightly strengthened. The alkalinity generated by the applied potential did not stop the SRB growth. A type of localized corrosion was developed during the experiments with microorganisms, even when the protection potential was applied to the system.
Synthesis and mechanical properties of nickel‐titania composite coatings
Authors: Lajevardi S. A. , Shahrabi T. , Hasannaeimi V.
Published: January 2010

Nickel‐titania composite coatings were prepared under direct current conditions by codeposition of nano titania particles (21 nm) and nickel from a nickel Watts type bath. Current density, concentration of titania particles, effect of agitation, and ultrasonic waves were investigated and the optimum values of these parameters for reaching to maximum vol% of titania particles in the coating were determined. Microhardness of these coatings was investigated by Vickers method and their morphological properties and chemical composition were studied by SEM and EDS analysis, respectively. The results showed that optimal values of current density, concentration of particles, and agitation rate exist that maximum percent of particles codeposited in the coating. Also it is demonstrated that using the ultrasonic waves dramatically decrease the agglomeration of particles in the coating.
On the role of deterioration of structures in their performance; with a focus on mining industry equipment and structures
Authors: Javaherdashti R. , Nikraz H.
Published: January 2010

Some examples of materials performance of civil materials such as steel and concrete in mining industry are considered. These examples are about structural steels (either as support for the structure or the equipment) and concrete structures. Also, it is mentioned that in mine sites that contain sulphide minerals, the formation of acid mine drainage (AMD) may also contribute to decreasing the integrity of civil and supportive structures. Using these examples, an effort has been made to emphasise that in order to extend the service life of structures in very aggressive environments such as those encountered in mining industry, a sound knowledge of deterioration and corrosion‐enhancing factors in addition to standardised application of measures against deterioration (such as painting) can be very applicative.
Simulation for fretting corrosion of tin‐coated copper contacts
Authors: Lee K. Y. , Jeong D. K. , Joo H. G. , Park Y. W.
Published: January 2010

The simulations of contact resistance variation under various oxide fractions are conducted. The copper oxide is assigned on the contact area with various fractions by the random distribution technique. The calculated contact resistance at each oxide area fraction is compared with the experimental result. The increase in contact resistance results in an increased oxide area fraction.
Characterization of New Amphiphilic Block Copolymers of N‐Vinyl Pyrrolidone and Vinyl Acetate, 1 – Analysis of Copolymer Composition, End Groups, Molar Masses and Molar Mass Distributions
Authors: Fandrich Nick , Falkenhagen Jana , Weidner Steffen M. , Pfeifer Dietmar , Staal Bastiaan , Thünemann Andreas F. , Laschewsky André
Published: January 2010

New amphiphilic block copolymers consisting of N‐vinyl pyrrolidone and vinyl acetate were synthesized via controlled radical polymerization using a reversible addition/fragmentation chain transfer (RAFT)/macromolecular design via the interchange of xanthates (MADIX) system. The synthesis was carried out in 1,4‐dioxane as process solvent. In order to get conclusions on the mechanism of the polymerization the molecular structure of formed copolymers was analysed by means of different analytical techniques. 13C NMR spectroscopy was used for the determination of the monomer ratios. End groups were analysed by means of matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry. This technique was also used to determine possible fragmentations of the RAFT end groups. By means of a combination of size exclusion chromatography, 13C NMR and static light scattering molar mass distributions and absolute molar masses could be analysed. The results clearly show a non‐ideal RAFT mechanism.

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Self‐management rehabilitation and health‐related quality of life in Parkinson's disease: A randomized controlled trial
Authors: Tickle‐Degnen Linda , Ellis Terry , Saint‐Hilaire Marie H. , Thomas Cathi A. , Wagenaar Robert C.
Published: January 2010

The purpose of this randomized controlled trial was to determine whether increasing hours of self‐management rehabilitation had increasing benefits for health‐related quality of life (HRQOL) in Parkinson's disease beyond best medical treatment, whether effects persisted at 2 and 6 months of follow‐up, and whether targeted compared with nontargeted HRQOL domains responded more to rehabilitation. Participants on best medication therapy were randomly assigned to one of three conditions for 6 weeks intervention: 0 hours of rehabilitation; 18 hours of clinic group rehabilitation plus 9 hours of attention control social sessions; and 27 hours of rehabilitation, with 18 in clinic group rehabilitation and 9 hours of rehabilitation designed to transfer clinic training into home and community routines. Results (N = 116) showed that at 6 weeks, there was a beneficial effect of increased rehabilitation hours on HRQOL measured with the Parkinson's Disease Questionnaire‐39 summary index (F(1,112) = 6.48, η = 0.23, CI = 0.05–0.40, P = 0.01). Benefits persisted at follow‐up. The difference between 18 and 27 hours was not significant. Clinically relevant improvement occurred at a greater rate for 18 and 27 hours (54% improved) than for 0 hours (18% improved), a significant 36% difference in rates (95% CI = 20–52% difference). Effects were largest in two targeted domains: communication and mobility. More concerns with mobility and activities of daily living at baseline predicted more benefit from rehabilitation. © 2010 Movement Disorder Society
Mild parkinsonian signs are associated with increased risk of dementia in a prospective, population‐based study of elders
Authors: Louis Elan D. , Tang Ming X. , Schupf Nicole
Published: January 2010

There is some evidence that mild parkinsonian signs (MPSs) are associated with increased risk of dementia, suggesting that MPS could be an early biomarker for dementia. Our aims, in a new cohort, were to determine whether (1) baseline MPS are a predictor of incident dementia and (2) there is an interaction between MPS and other baseline risk factors for dementia (i.e., the presence of both together greatly elevates the risk of dementia) was the objective. In a prospective, longitudinal study of community‐dwelling elders in northern Manhattan, NY, Parkinsonian signs were rated with an abbreviated Unified Parkinson's Disease Rating Scale. Risk of incident dementia was assessed using Cox proportional hazards models. There were 1,851 participants (mean follow‐up = 3.7 years). Participants with baseline MPS were twice as likely to develop dementia as participants without MPS: 16.3% versus 7.7%, unadjusted hazards ratio (HR) = 2.24 (P< 0.001), adjusted HR = 1.98 (P < 0.001). MPS were divided into three subtypes: adjusted HRaxial dysfunction = 2.45 (P < 0.001), adjusted HRtremor = 2.38 (P = 0.006), and adjusted HRrigidity = 1.16 (P = 0.58). When MPS were treated as a continuous variable, the adjusted HR = 1.15 (P = 0.001). There were no interactions between MPS and other baseline risk factors for dementia, including gender, education, race, family history of dementia, stroke, and apolipoprotein E‐e4. Baseline MPS seems to be a predictor of incident dementia. These motor signs might, therefore, serve as a useful biomarker for emerging dementia. © 2010 Movement Disorder Society
Clinical experience with the lateral septocutaneous superior gluteal artery perforator flap for autologous breast reconstruction
Authors: Rad Ariel N. , Flores Jaime I. , Prucz Roni B. , Stapleton Sahael M. , Rosson Gedge D.
Published: January 2010

Background: Superior gluteal artery perforator (SGAP) flaps are a useful adjunct for autologous microvascular breast reconstruction. However, limitations of short pedicle length, complex anatomy, and donor site deformity make it an unpopular choice. Our goals were to define the anatomic characteristics of SGAPs in cadavers, and report preliminary clinical and radiographic results of using the lateral septocutaneous perforating branches of the superior gluteal artery (LSGAP) as the basis for a modified gluteal flap. Methods: We performed 12 cadaveric dissections and retrospectively reviewed 12 consecutive breast reconstruction patients with gluteal flaps (19 flaps: 9 LSGAP, 10 traditional SGAP) over a 12‐month period. The LSGAP flap was converted to traditional SGAP in 53% of flaps because of dominance of a traditional intramuscular perforator. Preoperative 3D computed tomography angiography (CTA) and cadaveric dissections were used to define anatomy. Anatomic, demographic, radiographic, perioperative, and outcomes data were analyzed. Mean follow‐up was 4 ± 3.4 months (range 4 weeks to 10 months). Results: Compared with the pedicle in the SGAP flap, the mean pedicle length in the LSGAP flap was 1.54 times longer by CTA, 2.05 times longer by cadaver dissection, and 2.36 times longer by intraoperative bilateral measurement. These differences were statistically significant (P < 0.001). Clinically, 100% of the flaps survived. Conclusions: LSGAP flap reconstruction is advantageous, when feasible, because of the septocutaneous pedicle dissection and gain in pedicle length that make microsurgical anastomoses easier without compromising gluteus function. © 2010 Wiley‐Liss, Inc. Microsurgery 30:339–347, 2010.
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

Stilbenes 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

Cytogenetic 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

Objective

To determine the visualization rates of fetal anatomic structures by three‐dimensional ultrasound (3DUS) at 12–13 weeks of gestation.

Study Design

This 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.

Results

One 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).

Conclusions

First‐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

The 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

Recently, 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

A 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

Purpose: 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

Purpose: 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

Purpose: 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

Purpose: 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

To 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

Understanding 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

Fourier 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

Experience 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

Ad 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

Power 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.
DSA‐Mesh: a distributed security architecture for wireless mesh networks
Authors: Martignon Fabio , Paris Stefano , Capone Antonio
Published: January 2010

Wireless Mesh Networks (WMNs) have emerged recently as a technology for next‐generation wireless networking. They consist of mesh routers and clients, where mesh routers are almost static and form the backbone of WMNs. WMNs provide network access for both mesh and conventional clients.

In this paper, we propose DSA‐Mesh, a fully distributed security architecture that provides access control for mesh routers as well as a key distribution scheme that supports layer‐2 encryption to ensure security and data confidentiality of all communications that occur in the backbone of the WMN.

DSA‐Mesh exploits the routing capabilities of mesh routers: after connecting to the access network as generic wireless clients, new mesh routers authenticate to a key management service (consisting of several servers) implemented using threshold cryptography, and obtain a temporary key that is used both to prove their credentials to neighbor nodes and to encrypt all the traffic transmitted on wireless backbone links.

A key feature in the design of DSA‐Mesh is its independence from the underlying wireless technology used by network nodes to form the backbone. Furthermore, DSA‐Mesh enables seamless mobility of mesh routers. Since it is completely distributed, DSA‐Mesh permits to deploy automatically and incrementally large WMNs, while increasing, at the same time, the robustness of the system by eliminating the single point of failure typical of centralized architectures.

DSA‐Mesh has been implemented in Network Simulator, and extensive simulations have been performed in large‐scale network scenarios, comparing it to a static key approach and to a centralized architecture where a single key server is deployed. Numerical results show that our proposed architecture considerably increases the WMN security and reliability, with a negligible impact on the network performance, thus representing an effective solution for wireless mesh networking. Copyright © 2010 John Wiley & Sons, Ltd.
Nonstationarity
Authors: Yang Wei , Zurbenko Igor
Published: January 2010

The definition of stationary time series was first provided followed by a few examples of nonstationary time series. Statistical methods to analyze nonstationary time series was then reviewed in two categories: parametric methods and nonparametric methods. Focus was given to nonparametric methods. Spectral analysis of time series with seasonal components was discussed as a special case. Copyright © 2010 John Wiley & Sons, Inc.

This article is categorized under:

Data: Types and Structure > Time Series, Stochastic Processes, and Functional Data