bluuebunny/crossref_metadata_2025 huggingface dataset:
SV40 large T antigen‐specific human T cell memory responses
Authors: Coleman Sharon , Gibbs Allen , Butchart Eric , Mason Malcolm D. , Jasani Bharat , Tabi Zsuzsanna
Published: June 2008

The continued presence of simian virus 40 (SV40), a monkey polyomavirus, in man is confirmed by the regular detection of SV40‐specific antibodies in 5–10% of children who are unlikely to have received contaminated polio‐vaccines. The aim of our experiments was to find cellular immunological evidence of SV40 infection in humans by testing memory T cell responses to SV40 large T antigen (Tag). As there is some indication that the virus may be present in malignant pleural mesothelioma (MPM) cells, we analyzed T cell responses in MPM patients and in healthy donors. The frequencies of responding T cells to overlapping Tag peptides were tested by cytokine flow cytometry. CD8+ T cells from 4 of 32 MPM patients responded (above twofold of control) to SV40 Tag peptides, while no positive responses were detected in 12 healthy donors. Within SV40 Tag we identified three 15 amino acid‐long immunogenic sequences and one 9 amino acid‐long T cell epitope (p138) (138FPSELLSFL146), the latter including a HLA‐B7‐restriction motif. T cell responses to p138 were SV40‐specific as T cells stimulated with p138 did not cross‐react with the corresponding sequences of Tag of human polyomaviruses BKV and JCV. Similarly, the relevant BKV and JCV Tag peptides did not generate T cell responses against SV40 TAg p138. Peptide‐stimulated T cells also killed SV40 Tag‐transfected target cells. This article demonstrates the presence, and provides a detailed analysis, of SV40‐specific T cell memory in man. J. Med. Virol. 80:1497–1504, 2008. © 2008 Wiley‐Liss, Inc.
Hepatitis B virus X mutations occurring naturally associated with clinical severity of liver disease among Korean patients with chronic genotype C infection
Authors: Kim Hyun‐Ju , Park Joo‐Hee , Jee Youngmee , Lee Seoung‐Ae , Kim Hong , Song Byung‐Cheol , Yang Soohyun , Lee Myunghee , Yoon Jung‐Hwan , Kim Yoon Jun , Lee Hyo‐Suk , Hwang Eung‐Soo , Kook Yoon‐Hoh , Kim Bum‐Joon
Published: June 2008

Few reports have detailed mutation frequencies and mutation patterns in the entire X region according to clinical status. The aims of this study were to elucidate the relationships between mutation patterns and their frequencies in the X region and clinical status in a Korean cohort and determine specific X mutation types, related closely with liver disease progression. All X mutations were determined by direct sequencing in 184 patients with different clinical features. Mutation rates in the X region in patients with more severe liver disease, hepatocellular carcinoma (HCC) (3.6%) or liver cirrhosis (4%) were always significantly higher than in patients with corresponding less severe forms, chronic hepatitis (2.9%) or asymptomatic carriers (2.1%), but no significant difference in mutation rates was found in terms of HBeAg serostatus. All five mutation types (V5M/L, P38S, H94Y, I127T/N, and K130M and V131I) affecting the six codons were found to be related significantly to clinical severity. Among these, two mutation types (V5M/L and K130M and V131I) were observed more frequently in HBeAg negative patients than in HBeAg positive patients. In conclusion, the results suggest that an accumulation of mutations in the X region contributes to disease progression in chronic patients, at least Korean patients with genotype C. Specific mutation types appears to be related more to severe liver diseases such as HCC or liver cirrhosis. In particular, a novel mutation type (V5M/L) discovered firstly during the present study was found to be associated significantly with HCC. J. Med. Virol. 80:1337–1343, 2008. © 2008 Wiley‐Liss, Inc.
The detection and characterization of hepatitis E virus in pig livers from retail markets of India
Authors: Kulkarni M.A. , Arankalle V.A.
Published: June 2008

The zoonotic transmission of Hepatitis E virus (HEV) is a well‐established fact and pigs are known reservoirs of the virus. The human and swine HEV from countries such as the USA, Japan and Taiwan, show a remarkable sequence identity. Swine liver samples from markets in Japan and US were shown to be HEV RNA positive. In contrast, in India, viruses belonging to different genotypes, that is, genotypes 1 and 4 circulate in humans and pigs respectively, at least for the last 20 years. To assess possible exposure of the Indian population to swine HEV, 240 pig liver samples were collected from retail markets of Pune, western India. Two (0.83%) samples were found positive for HEV RNA by nested RT‐PCR. Nucleotide sequence‐based phylogenetic analysis showed the presence of genotype 4 HEV with 90–91% similarity and clustering with Indian swine HEV sequences generated earlier. The data suggest the possibility of HEV infection in persons consuming infected pig liver. So far, it has not been possible to detect any type 4 HEV infection in humans. The absence of type 4 infections in humans may be attributed to cooking leading to the inactivation of the virus. J. Med. Virol. 80:1387–1390, 2008. © 2008 Wiley‐Liss, Inc.
Cross‐species infection of specific‐pathogen‐free pigs by a genotype 4 strain of human hepatitis E virus
Authors: Feagins A.R. , Opriessnig T. , Huang Y.W. , Halbur P.G. , Meng X.J.
Published: June 2008

Hepatitis E virus (HEV) is an important pathogen. The animal strain of HEV, swine HEV, is related to human HEV. The genotype 3 swine HEV can infect humans and genotype 3 human HEV can infect pigs. The genotype 4 swine and human HEV strains are genetically related, but it is unknown whether genotype 4 human HEV can infect pigs. A swine bioassay was utilized in this study to determine whether genotype 4 human HEV can infect pigs. Fifteen, 4‐week‐old, specific‐pathogen‐free pigs were divided into three groups of five each. Group 1 pigs were each inoculated intravenously with PBS buffer as negative controls, group 2 pigs similarly with genotype 3 human HEV (strain US‐2), and group 3 pigs similarly with genotype 4 human HEV (strain TW6196E). Serum and fecal samples were collected at 0, 7, 14, 21, 28, 35, 42, 49, and 56 days postinoculation (dpi) and tested for evidence of HEV infection. All pigs were necropsied at 56 dpi. As expected, the negative control pigs remained negative. The positive control pigs inoculated with genotype 3 human HEV all became infected as evidenced by detection of HEV antibodies, viremia and fecal virus shedding. All five pigs in group 3 inoculated with genotype 4 human HEV also became infected: fecal virus shedding and viremia were detected variably from 7 to 56 dpi, and seroconversion occurred by 28 dpi. The data indicated that genotype 4 human HEV has an expanded host range, and the results have important implications for understanding the natural history and zoonosis of HEV. J. Med. Virol. 80:1379–1386, 2008. © 2008 Wiley‐Liss, Inc.
Virus load dynamics of individual CMV‐genotypes in lung transplant recipients with mixed‐genotype infections
Authors: Görzer Irene , Kerschner Heidrun , Jaksch Peter , Bauer Claudia , Seebacher Gernot , Klepetko Walter , Puchhammer‐Stöckl Elisabeth
Published: June 2008

Human cytomegalovirus (CMV) is a major cause of disease and transplant dysfunction in lung transplant recipients. Simultaneous emergence of more than one CMV‐genotype can occur, and appears to be disadvantageous for the patient. In this study, the dynamics of individual CMV‐genotypes in blood and lung was assessed within mixed CMV‐genotype populations emerging after lung transplantation. In 69 plasma and 76 bronchoalveolar lavage samples of 16 lung transplant recipients with mixed CMV‐genotype infections within the first year posttransplantation each of the major glycoprotein B (gB) and glycoprotein H (gH) genotypes was selectively quantified by genotype‐specific quantitative TaqMan assays. The data obtained revealed that individually different genotype dynamics occurred for the individual patients and that the relative levels of the genotypes to each other may change over time. The quantitative development was independent of the specific gB–gH‐genotype. In 10 of the 16 lung recipients the patient's individual genotype composition was the same in blood and lung. Genotype development during the follow‐up was influenced by antiviral treatment. These data show for the first time that the CMV load used as diagnostic tool after transplantation is not always a constant entity but reflects the sum of the individual CMV‐genotype dynamics developing over time. J. Med. Virol. 80:1405–1414, 2008. © 2008 Wiley‐Liss, Inc.
Follow‐up of a multi‐drug resistant HIV‐1 infected patient successfully treated with darunavir and etravirine
Authors: Audelin Anne Margrethe , Lebech Anne‐Mette , Petersen Ann Berith , Jørgensen Louise Bruun
Published: June 2008

A multi‐drug‐resistant, non‐compliant HIV‐1 patient was treated successfully with a combination of the drugs darunavir and etravirine for more than 8 months. The patient experienced an immunoreconstitution syndrome due to improved compliance. Examining previous resistance tests for this type of patient is valuable when assigning new medication. J. Med. Virol. 80:1319–1321, 2008. © 2008 Wiley‐Liss, Inc.
Oxidative behaviour of fresh‐cut ‘Fuji’ apples treated with stabilising substances
Authors: Larrigaudière Christian , Ubach Dolors , Soria Yolanda , Rojas‐Graü Ma Alejandra , Martín‐Belloso Olga
Published: June 2008

BACKGROUND:Although changes in the quality of fresh‐cut products treated with chemical stabilisers have been extensively described in the literature, very little is known about the physiology of these products. This work aims to describe the physiological aspect and particularly the effects of chemical preservatives on the oxidative behaviour of fresh‐cut apples.

RESULTS:Immediately after treatment, the samples treated with the anti‐browning agents (ascorbic acid + cysteine) exhibited a sharp increase in H2O2 levels (a five‐fold increase when compared to the other samples) and peroxidative damage, especially at the beginning of the storage period (two‐fold increase after 1 day). In line with this result, peroxidase (POX) activity decreased by 50% during the first day of storage, but no significant changes in superoxide dismutase (SOD) and catalase (CAT) activities were found between the different samples. H2O2 accumulation was not attributed to the action of cysteine but to a specific action of ascorbic acid, which mainly acted as a pro‐oxidant under these conditions.

CONCLUSION:The results presented in this work showed that ascorbic acid cause important oxidative damage in fresh‐cut Fuji apples. Alternatives are required to prevent detrimental loss of quality resulting from this oxidative action. Copyright © 2008 Society of Chemical Industry
Water‐Soluble Polymeric Thioxanthone Photoinitiator Containing Glucamine as Coinitiator
Authors: Jiang Xuesong , Yin Jie
Published: June 2008

A novel kind of water‐soluble polymeric photoinitiator was synthesized by introducing thioxanthone moieties and glucamine into the polymeric chain, as well as low‐molecular weight model compounds. The photochemical and photophysical properties of these photoinitiators were studied. PTX‐GA possesses a similar UV‐vis absorption, weaker fluorescence emission and a shorter lifetime of the TX triplet state (τ) as compared to TX‐MGA and TX‐PMAC/MDEA. ESR showed that in TX‐PMAC/MDEA the smallest number of radicals is generated. Photopolymerization of arylamide and methylene bisacryamide initiated by these photoinitiators shows that PTX‐GA is more effective than TX‐MGA and TX‐PMAC/MDEA.

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Macromol. Mater. Eng. 6/2008
Authors: Mittal Vikas , Matsko Nadejda B. , Butté Alessandro , Morbidelli Massimo
Published: June 2008

Cover: In the cover picture, the study of the PNIPAAM functionalization by ATRP polymerization of emulsion particles and monoliths is summarized. At the top, the functionalization of single particles is depicted: on the left, a TEM picture of the PNIPAAM brushes; on the right, their swelling behavior as a function of the temperature. At the bottom, the same characterization is shown for monolithic structures. Further details can be found in the article by V. Mittal, N. B. Matsko, A. Butté, and M. Morbidelli* on page 491.
Conducting Polypyrrole Conical Nanocontainers: Formation Mechanism and Voltage Switchable Property
Authors: Huang Jiyong , Quan Baogang , Liu Mingjie , Wei Zhixiang , Jiang Lei
Published: June 2008

Nanostructures with stimuli‐responsive properties are of great importance for the application of smart materials in nanotechnology. Unique hollow polypyrrole nanostructured arrays with a conical shape have been produced by a stepwise electropolymerization process. The polypyrrole conical nanocontainers exhibit a reversible switchable behavior between open and closed states, which is controlled by the movement of counter ions during electrically controlled reversible oxidation and reduction processes. The formation of conical nanocontainers is affected by the oleo‐wettability of the substrate. Conical nanocontainers can be formed on oleo‐phobic substrates in aqueous solution by using dopant‐stabilized pyrrole nanodroplets as the guiding template for the polymerization.

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Approximate transmission conditions through a weakly oscillating thin layer
Authors: Poignard Clair
Published: June 2008

We study the behavior of the electro‐quasistatic voltage potentials in a material composed by a bidimensional medium surrounded by a weakly oscillating thin layer and embedded in an ambient medium. We build approximate transmission conditions in order to replace the layer by these conditions on the boundary of the interior material. We deal with a weakly oscillating thin layer: the period of the oscillations is greater than the square root of the thinness. Our approach is essentially geometric and based on a suitable change of variable in the layer. This paper extends previous works (Méthodes asymptotiques pour le calcul de champs électromagnétiques dans des milieux à couche mince. Application aux cellules biologiques. Thesis, Université Lyon 1, France, November 2006; IEEE Trans. Magn. 2007. http://hal.archives‐ouvertes.fr/hal‐00165049/fr.) of the former author, in which the layer had constant thickness. Copyright © 2008 John Wiley & Sons, Ltd.
Arimoclomol at dosages up to 300 mg/day is well tolerated and safe in amyotrophic lateral sclerosis
Authors: Cudkowicz Merit E. , Shefner Jeremy M. , Simpson Elizabeth , Grasso Daniela , Yu Hong , Zhang Hui , Shui Amy , Schoenfeld David , Brown Robert H. , Wieland Scott , Barber Jack R.
Published: June 2008

Arimoclomol is an investigational drug for amyotrophic lateral sclerosis (ALS) that amplifies heat shock protein gene expression during cell stress. The objectives of the present study were to assess the safety, tolerability, and pharmacokinetics of arimoclomol in ALS. Eighty‐four participants with ALS received arimoclomol at one of three oral doses (25, 50, or 100 mg three times daily) or placebo. The primary outcome measure was safety and tolerability. A subset of 44 participants provided serum and cerebrospinal fluid (CSF) samples for pharmacokinetic analysis. Participants who completed 12 weeks of treatment could enroll in a 6‐month open‐label study. Arimoclomol at doses up to 300 mg/day was well tolerated and safe. Arimoclomol resulted in dose‐linear pharmacologic exposures and the half‐life did not change with continued treatment. Arimoclomol CSF levels increased with dose. Arimoclomol was shown to be safe, and it crosses the blood–brain barrier. Serum pharmacokinetic profiles support dosing of three times per day. An efficacy study in ALS is planned. Muscle Nerve, 2008
The correlation of voiding variables between non‐instrumented uroflowmetery and pressure‐flow studies in women with pelvic organ prolapse
Authors: Mueller Elizabeth , Wei John , Nygaard Ingrid , Brubaker Linda , Varner Ed , Visco Anthony , Cundiff Geoffrey W. , Weber Anne M. , Ghetti Chiara , Kreder Karl
Published: June 2008

Aims

To (1) correlate peak and maximum flow rates from non‐instrumented flow (NIF) and pressure‐flow studies (PFS) in women with pelvic organ prolapse (POP); (2) measure the impact of voided volume and degree of prolapse on correlations.

Methods

We compared four groups of women with stages II–IV POP. Groups 1 and 2 were symptomatically stress continent women participating in the colpopexy and urinary reduction efforts (CARE) trial; during prolapse reduction before sacrocolpopexy, Group 1 (n = 67) did not have and Group 2 (n = 84) had urodynamic stress incontinence (USI). Group 3 (n = 74) and Group 4 participants (n = 73), recruited specifically for this study, had stress urinary incontinence (SUI) symptoms. Group 3 planned sacrocolpopexy. Group 4 planned a different treatment option. Participants completed standardized uroflowmetry and pressure voiding studies.

Results

Subjects' median age was 61 years; median parity 3% and 80% had stage III or IV POP. Based on the Blaivas–Groutz nomogram, 49% of all women were obstructed. NIF and PFS peak and average flow rates had low correlations with one another (0.31, P < 0.001 and 0.35, P < 0.001, respectively). When NIF and PFS voided volumes were within 25% of each other, the peak and average flow rate correlations improved (0.52, P < 0.001 and 0.57, P < 0.001, respectively). As vaginal prolapse increased, correlations between NIF and PFS peak and average flow rates decreased.

Conclusion

Peak and average flow rates are highly dependent on voided volume in women with prolapse. As the prolapse stage increases, correlations between NIF and PFS variables decrease. Neurourol. Urodynam. 27:515–521, 2008. © 2008 Wiley‐Liss, Inc.
The significance of natural bladder filling by the production of urine during cystometry
Authors: Lee Sang Wook , Kim Jeong Hyun
Published: June 2008

Aims

Natural bladder filling by the production of urine could potentially influence the outcome of urodynamic investigations. In this prospective study, we determined the natural bladder filling rate during cystometry.

Methods

Between October 2005 and March 2006, we performed conventional urodynamic studies in 101 consecutive patients. We measured the exact volume infused during artificial filling, the volume voided and post‐void residual urine (PVR) after a pressure flow study to examine the difference between the measured bladder volume (voided volume plus PVR) and the infused volume. We also measured the exact time required for the urodynamic investigation. Finally, we analyzed the natural filling rates in 34 patients after excluding inadequate cases.

Results

The mean volume of artificial filling was 304.4 ml (SD ± 100.5 ml) and the mean measured volume consisting of the voided volume plus PVR was 337.2 ml (SD ± 106.5 ml). The mean total time was 24.2 min (range: 15.0–41.5 min) and the mean time for artificial filling was 7.2 min. The mean volume of natural filling and the mean rate of natural bladder filling were 32.8 ml (12.1% of artificial filling) and 1.4 ml/min, respectively.

Conclusions

Natural filling by the production of urine can affect the results of cystometry considerably, and should be considered when performing urodynamic investigations and interpreting the results. Because the effects can increase with the time required to conduct the investigation, effort should be made to decrease the total duration of urodynamic investigations. Neurourol. Urodynam. 27:772–774, 2008, © 2008 Wiley‐Liss, Inc.
The effect of chronic partial bladder outlet obstruction on corpus cavernosum smooth muscle and Rho‐kinase in rabbits
Authors: Lin Wei‐Yu , Mannikarottu Anita , Chichester Paul , Neuman Paul , Johnson Arnold , Pérez‐Martínez Francisco C. , Levin Robert M.
Published: June 2008

Aim

The goal of this study was to investigate the effect of different severities in bladder dysfunction on corpus cavernosum physiology, morphology and expression of Rho‐kinase in rabbits.

Methods

Male New Zealand rabbits were divided into control, 2 and 8 weeks of partial bladder outlet obstruction (PBOO) groups. Isolated cavernosal strips from all groups were precontracted with phenylephrine and the relaxant responses to electrical field stimulation (EFS), ATP, acetylcholine, and sodium nitroprusside (SNP) were determined. Histological and molecular studies were performed.

Results

Corpus cavernosum smooth muscle (CCSM) from 8 weeks obstruction rabbits showed significant decreases in the contractile response to phenylephrine and further decreased relaxation responses to EFS in comparison to 2 weeks group. Relaxation induced by ATP, acetylcholine, and SNP were all significantly diminished at both 2 and 8 weeks obstruction equally. The ratio of smooth muscle to collagen decreased at 2 weeks and further dropped at 8 weeks obstruction. Expression of both isoforms of Rho‐kinase were increased in both obstruction groups at 2 weeks obstruction and decreased significantly (from the 2 week obstructed values) at 8 weeks while remaining above control values.

Conclusion

The present study indicated that severe bladder dysfunction secondary to chronic PBOO induced significant physiological dysfunctions of CCSM as well as morphological changes. Activities of both ROK isoenzymes showed increases at 2‐ and 8‐week obstructions. Increase in Rho‐kinase expression/activity would be expected to make the CCSM more difficult to relax and also contribute to reduction of EFS‐induced relaxation of CCSM after chronic PBOO. Neurourol. Urodynam. 27:826–831, 2008, © 2008 Wiley‐Liss, Inc.
Urethral pressure reflectometry and pressure profilometry in healthy volunteers and stress urinary incontinent women
Authors: Klarskov Niels , Lose Gunnar
Published: June 2008

Aims

Urethral pressure reflectometry (UPR) is a novel reliable method for simultaneous measurement of pressure and cross‐sectional area in the female urethra. The aim of this study was to report values for UPR parameters in healthy and stress urinary incontinent (SUI) women and compare UPR with urethral pressure profilometry (UPP) parameters.

Methods

The study included 30 SUI women and 30 volunteers (23 “continent” and 7 “nearly continent”). The women were examined in the supine position both while relaxed and during squeezing, and upright position. The following UPR variables were measured; opening and closing pressure, opening and closing elastance, hysteresisabsolute and hysteresispercent. UPP with the perfusion technique was carried out with the women supine while relaxed and during squeezing. The maximum urethral pressure (MUP) and maximum urethral closure pressure (MUCP) were obtained.

Results

All parameters except the hysteresispercent were significantly decreased in the SUI group compared to the volunteers. The squeeze opening pressure increased in all women compared to the resting condition, while MUP and MUCP during squeeze increased in 78% and decreased in 22%. The separation between the continent and SUI women was better using the resting and squeezing opening pressure than the corresponding UPP parameters.

Conclusions

UPR is a clinically reliable technique, which provides sound physiological parameters. The resting and squeezing opening pressures separate SUI from continent women better than the UPP parameters. The UPR parameters have the potential to provide a pathophysiologic subdivision of SUI and other dysfunctions. Neurourol. Urodynam. 27:807–812, 2008, © 2008 Wiley‐Liss, Inc.
Cetuximab inhibits thymidylate synthase in colorectal cells expressing epidermal growth factor receptor
Authors: Skvortsov Sergej , Sarg Bettina , Lindner Herbert , Lukas Peter , Hilbe Wolfgang , Zwierzina Heinz , Skvortsova Ira
Published: June 2008

The monoclonal antibody cetuximab directed against the epidermal growth factor receptor (EGFR) is an attractive agent for targeted therapy in advanced colorectal cancer (CRC), especially when combined with 5‐fluorouracil (5‐FU)‐based chemotherapy. However, the mechanisms of cetuximab activity as chemosensitizer remain poorly understood. Using proteome‐fluorescence‐based technology, we found that cetuximab is able to suppress the expression of thymidylate synthase (TS), which is involved in the mechanism of 5‐FU action. Caco‐2, HRT‐18, HT‐29, WiDr and SW‐480 CRC cells were found to express EGFR. SW‐620 was used as EGFR‐negative cell line. Only in EGFR‐expressing cells cetuximab is able to inhibit TS expression. Combined treatment with cetuximab and 5‐FU revealed a synergistic anti‐tumor response that is closely correlated with functional activity of EGFR/mitogen‐activated protein kinase (MAPK) pathway. Moreover, no correlation was seen between constitutive TS protein expression, level of cetuximab‐induced TS down‐regulation and response either to 5‐FU alone or in combination with cetuximab. We demonstrated that only EGFR expression with high functional activity of EGFR/MAPK pathway is important for the synergistic effects between cetuximab and 5‐FU in the investigated cell lines.
Performance characteristics of an FT MS‐based workflow for label‐free differential MS analysis of human plasma: standards, reproducibility, targeted feature investigation, and application to a model of controlled myocardial infarction
Authors: Sutton Jennifer , Richmond Tori , Shi Xu , Athanas Michael , Ptak Celeste , Gerszten Robert , Bonilla Leo
Published: June 2008

Proteomics is undergoing a rapid transformation from a qualitative global peptide sequencing discipline into a quantitative, reproducibility‐driven practice. Nowhere is this more evident than in the rapidly expanding field of protein biomarker discovery where the general goal is to uncover statistically robust patterns of differential expression between or among subjects/samples representing distinct biological/temporal states. This report presents the analytical characterization of a label‐free LC FT‐ICR‐MS workflow for differential proteomics analysis of human plasma. The key elements discussed include (i) methodologies for performing properly replicated experiments with highly reproducible sample preparation and analysis, including the use of internal standards to quantify variance at different steps in the process, (ii) a new methodology for performing sample re‐analysis that uses off‐line targeted robotic acquisition of complementary spectral data (e.g. ECD and/or IRMPD) to enhance the identification of differentially expressed peptides/proteins, and (iii) data processing pipelines capable of integrating the automatic statistical analysis of the label‐free (LC‐) MS signal, together with the intuitive and highly interactive curation and annotation of differential features using the output from standard sequence database search programs. We illustrate the application of the complete sample‐to‐annotated‐differential‐peptides (‐proteins) workflow by describing the acquisition and analysis of a large multidimensional dataset from patients undergoing a controlled myocardial infarction resulting in an experimental setup in which each patients serve as their own control. Furthermore, we discuss a couple illustrative examples of mid‐level proteins observed in this study whose plasma concentrations change consistently within and across patients, in a treatment‐ and time‐dependent fashion.
Protein profiling of formalin fixed paraffin embedded tissue: Identification of potential biomarkers for pediatric brainstem glioma
Authors: Nazarian Javad , Santi Mariarita , Hathout Yetrib , MacDonald Tobey J.
Published: June 2008

Little is known about the molecular characteristics of pediatric brainstem gliomas (BSG), which continue to have a dismal prognosis. Targeted molecular strategies are limited due to rarity of biopsy BSG specimen coupled with obstacles associated with the analyses of formalin‐fixed paraffin‐embedded (FFPE) autopsies. The objective of this study was to develop methodologies to successfully identify the proteome profile from these archived FFPE specimens. Peptides were extracted from both tumor and adjacent normal FFPE brainstem specimen and quantified using 18O proteolytic labeling strategy and LC‐MS/MS analysis. The ingenuity pathway analysis software was used to elucidate interactions amongst differentially expressed proteins. We identified 188 proteins of which 54 (29%) were found up‐regulated (≥1.5‐fold) in BSG compared to normal sections. Of these, 15 (28%) proteins have previously been reported as potential biomarkers for supratentorial malignant gliomas, while the rest appear to be exclusive to pediatric BSG. Because the majority of differentially expressed proteins are unique to BSG, we conclude that pediatric BSG is distinct from supratentorial gliomas. To the best of our knowledge, this is the first proteome profile of pediatric BSG, which may facilitate discovery of novel therapeutic targets for early diagnostics and improving prognostics.
Influence of variations in sample handling on SELDI‐TOF MS serum protein profiles for colorectal cancer
Authors: Engwegen Judith Y. M. N. , Alberts Marieke , Knol Jaco C. , Jimenez Connie R. , Depla Annekatrien C. T. M. , Tuynman Henriëtte , van Heukelem Henk A. , Snel Pleun , Smits Marianne E. , Cats Annemieke , Schellens Jan H. M. , Beijnen Jos H.
Published: June 2008

Sample handling can have a profound effect on serum protein profiles, challenging results obtained with archived sera under non‐standardized sample collection. Here, we evaluate the influence of variations in sample handling on previous serum protein profiles for colorectal cancer (CRC) (Engwegen et al.,. World J. Gastroenterol. 2006, 12, 1536–1544). Sera were prospectively obtained from individuals with an indication for colonoscopy (n = 150: 65 controls, 52 adenomatous polyps, 29 CRC, 4 unknown), as well as from normal volunteers (n = 8). Protein profiles were acquired by SELDI‐TOF MS on CM10 chips at pH 5. We assessed the influence of storage temperature, type of collection tube, coagulation temperature and freeze‐thaw cycles on the serum protein profile. Several peptides occurred only in samples stored at –20°C, indicating proteolytic degradation during storage. One was a previous CRC biomarker candidate, an N‐terminal albumin fragment (m/z 3087), and two others complement C3f and a fragment thereof (m/z 2022 and 1863). Overall differences in protein profiles were also seen for different collection tubes, coagulation temperature and freeze‐thaw cycles. However, three of five of our previously defined CRC biomarker candidates are stable to variations in the sample handling protocol, justifying their further validation in prospective studies.
Myofilament proteins: From cardiac disorders to proteomic changes
Authors: Yuan Chao , Solaro R. John
Published: June 2008

Myofilament proteins of the cardiac sarcomere house the molecular machinery responsible for generating tension and pressure. Release of intracellular Ca2+ triggers myofilament tension generation and shortening, but the response to Ca2+ is modulated by changes in key regulatory proteins. We review how these proteomic changes are essential to adaptive physiological regulation of cardiac output and become maladaptive in cardiac disorders. We also review the essentials of proteomic techniques used to study myofilament protein changes, including degradation, isoform expression, phosphorylation and oxidation. Selected proteomic studies illustrate the applications of these approaches.
Nitric oxide‐mediated protein modification in cardiovascular physiology and pathology
Authors: Gödecke Axel , Schrader Jürgen , Reinartz Michael
Published: June 2008

Nitric oxide (NO) is a key regulator of cardiovascular functions including the control of vascular tone, anti‐inflammatory properties of the endothelium, cardiac contractility, and thrombocyte activation and aggregation. Numerous experimental data support the view that NO not only acts via cyclic guanosine monophosphate (cGMP)‐dependent mechanisms but also modulates protein function by nitrosation, nitrosylation, glutathiolation, and nitration, respectively. To understand how NO regulates all of these diverse biological processes on the molecular level a comprehensive assessment of NO‐mediated cGMP‐dependent and independent targets is required. Novel proteomic approaches allow the simultaneous identification of large quantities of proteins modified in an NO‐dependent manner and thereby will considerably deepen our understanding of the role NO plays in cardiovascular physiology and pathophysiology.
A multi‐tracers analysis of sources and transfers of particulate organic matter in a tropical reservoir (Petit Saut, French Guiana)
Authors: de Junet Alexis , Abril Gwenaël , Guérin Frédéric , Billy Isabelle , de Wit Rutger
Published: June 2008

We measured the organic carbon (OC) content, the isotopic composition, the C/N ratios and the photosynthetic pigment composition of suspended matter, sediments, sediments traps and epiphytic and epilithic biofilms at the tropical Sinnamary River system (French Guiana). Our sampling included the mid‐stream reservoir lake (Petit Saut) and the estuary on the Atlantic coast. These tracers were complementary and allowed identifying different sources of particulate organic matter (POM) in the system. We found a δ13C–C/N signature of POM close to that of soils and litters collected in the surrounding forest, both for water column and sediment at the upstream station as well as for the sediment in a littoral zone of the reservoir, which thus indicated a terrestrial origin. Plankton communities at the centre of the reservoir were dominated by Chlorophyceae (chlorophyll a (Chl a), chlorophyll b (Chl b) and lutein) in the oxic epilimnion and by anoxygenic phototrophic bacteria, namely Chlorobiaceae (bacteriochlorophyll d (BChl d) and bacteriochlorophyll c (BChl c)) at and below the oxycline (6 m depth). In addition, this planktonic material was slightly 13C‐depleted due to a contribution of methanotrophic bacteria. Phytoplankton and bacterioplankton were the major source of settling material collected in the traps at all depths in the centre of the reservoir. In the traps, POM was subject to intense degradation, as revealed by C/N and isotopic data and by the presence of pheopigments. In the river downstream of the dam, Chl b, lutein, BChl c and d originating from the reservoir progressively decreased downstream as the result of mineralization. At the estuarine mouth, fucoxanthin showed the presence of diatoms and the δ13C‐C/N signature matched that of POM carried by the Amazonian coastal mobile mud belt. By analysing sedimentation rates in the reservoir and its outflow into the river, we were able to provide a first estimates of POM transfers in this system during the sampling period. Copyright © 2008 John Wiley & Sons, Ltd.
Nitrate removal in the hyporheic zone of a salmon river in Alaska
Authors: Pinay Gilles , O'Keefe Thomas C. , Edwards Richard T. , Naiman Robert J.
Published: June 2008

Pacific boreal streams and riparian zones are believed to receive significant N loads that are derived from the ocean in the form of decaying sockeye salmon (Oncorhynchus nerka). Using a small stream in south‐central Alaska we examined whether the associated riparian forest could take up the pulse of marine‐derived nitrogen (MDN) entering the hyporheic zone from spawning and dying sockeye salmon. We evaluate the relative importance of riparian uptake and denitrification in nitrate‐N removal in hyporheic sediment. We found that maximum biological removal of nitrate peaked within 1 h of water entering the hyporheic zone, decreasing exponentially with subsurface flow duration. Plant and microbial uptake reached 14 µg NO‐N L−1 min−1and denitrification reached 4 µg NO‐N L−1 min−1during the initial 2 h of transit time. Our results reinforce the hypothesis that MDN from Pacific salmon can be transferred to riparian zone via hyporheic flow. Most nitrate‐N removal along hyporheic flow paths is by plant and microbial uptake (the respective contributions could not be determined). Denitrifying bacteria are present and active in the hyporheic zones of this well‐oxygenated Alaskan stream but their contribution to the nitrate‐N removal is small compared to plant and microbial uptake in such nitrate‐N poor environment. Copyright © 2008 John Wiley & Sons, Ltd.
The effects of flow reduction rates on fish stranding in British Columbia, Canada
Authors: Irvine Robyn L. , Oussoren Trevor , Baxter James S. , Schmidt Dana C.
Published: June 2008

Juvenile fish can strand in pools or in interstitial spaces when the water elevation drops in regulated rivers due to flow reductions. Three years of summer and winter experiments on the Columbia and Kootenay Rivers (Canada) assessed the effect of the rate of change in water level (ramping rate) on the probability of pool and interstitial stranding for juvenile (<100 mm) fish. The factors of wetted history of the site, time of day, natural fish density and the occurrence of a conditioning reduction prior to the operational reduction were also examined for their effect on stranding. Experimental net pens were constructed to test these factors in situ in the varial zones of the two rivers. Linear models with plausible additive combinations of the potential explanatory factors and a null model were fitted to the logistically transformed data and ranked using the second‐order Akaike Information Criterion (AICc). The null model was the top ranked model for the interstitial stranding analyses, highlighting that none of the factors tested were significant variables in predicting the probability of stranding. Natural fish density, wetted history of the site, ramping rate and the presence of a conditioning reduction were variables included in the top three ranking models for the pool stranding analyses. Probability of pool stranding in summer was reduced by the occurrence of a conditioning reduction prior to the operational reduction. Higher natural fish density, longer periods of wetted history and higher ramping rates all led to higher probabilities of pool stranding. Copyright © 2008 John Wiley & Sons, Ltd.
Estimating HIV incidence in the United States from HIV/AIDS surveillance data and biomarker HIV test results
Authors: Karon John M. , Song Ruiguang , Brookmeyer Ron , Kaplan Edward H. , Hall H. Irene
Published: June 2008

The development of an human immunodeficiency virus (HIV) test that detects recent infection has enabled the U.S. Centers for Disease Control and Prevention (CDC) to estimate annual HIV incidence (number of new infections per year, not per person at risk) in the United States from data on new HIV and acquired immunodeficiency syndrome (AIDS) diagnoses reported to HIV/AIDS surveillance. We developed statistical procedures to estimate the probability that an infected person will be detected as recently infected, accounting for individuals choosing whether and how frequently to seek HIV testing, variation of testing frequency, the reporting of test results only for infected persons, and infected persons who never had an HIV‐negative test. The incidence estimate is the number of persons detected as recently infected divided by the estimated probability of detection. We used simulation to show that, under the assumptions we make, our procedures have acceptable bias and correct confidence interval coverage. Because data on the biomarker for recent infection or on testing history were missing for many persons, we used multiple imputation to apply our models to surveillance data. CDC has used these procedures to estimate HIV incidence in the United States. Copyright © 2008 John Wiley & Sons, Ltd.
Explaining racial disparities in HIV/AIDS incidence among women in the U.S.: A systematic review
Authors: Tillerson Kristen
Published: June 2008

Surveillance data indicate that HIV incidence among Black women is more than 20 times that among White women and more than 4 times that among Hispanic women. Several studies have examined HIV risk factors by race/ethnicity including high‐risk sex, drug use, inconsistent disclosure of same‐sex behavior by male partners, and sexually transmitted diseases (STDs). We formed these risk factors into four hypotheses that attempt to explain the higher incidence of HIV infection among Black women. We further conducted a literature review by searching three online databases for studies published between 1985 and 2006 addressing the four hypotheses.

Literature suggests that Black women are no more likely to have unprotected sex, have multiple sexual partners, or use drugs than women of other racial/ethnic groups. However, some studies suggest that Black women are more likely to have risky sex partners and STDs. We also found that Black men are less likely to disclose their same‐sex behavior to female partners.

These four hypotheses are insufficient in explaining the greater burden of HIV among Black women. Future investigations should continue to explore these and other social and behavioral factors such as poverty, health‐care access, and receptivity to prevention messages to explain racial/ethnic disparities in HIV incidence. Copyright © 2008 John Wiley & Sons, Ltd.
Bayesian latent class models with conditionally dependent diagnostic tests: A case study
Authors: Menten Joris , Boelaert Marleen , Lesaffre Emmanuel
Published: June 2008

In the assessment of the accuracy of diagnostic tests for infectious diseases, the true disease status of the subjects is often unknown due to the lack of a gold standard test. Latent class models with two latent classes, representing diseased and non‐diseased subjects, are often used to analyze this type of data. In its basic format, latent class analysis requires the observed outcomes to be statistically independent conditional on the disease status. In most diagnostic settings, this assumption is highly questionable. During the last decade, several methods have been proposed to estimate latent class models with conditional dependence between the test results. A class of flexible fixed and random effects models were described by Dendukuri and Joseph in a Bayesian framework. We illustrate these models using the analysis of a diagnostic study of three field tests and an imperfect reference test for the diagnosis of visceral leishmaniasis. We show that, as observed earlier by Albert and Dodd, different dependence models may result in similar fits to the data while resulting in different inferences. Given this problem, selection of appropriate latent class models should be based on substantive subject matter knowledge. If several clinically plausible models are supported by the data, a sensitivity analysis should be performed by describing the results obtained from different models and using different priors. Copyright © 2008 John Wiley & Sons, Ltd.
Testing for genetic association: A powerful score test
Authors: El Galta R. , Stijnen T. , Houwing‐Duistermaat J. J.
Published: June 2008

To study the association between a candidate gene and a complex genetic disease, Pearson's χ2 statistic can be applied to an m × 2 contingency table, where the m categories correspond to m haplotypes or marker alleles. For m>2, two alternative approaches for Pearson's χ2 can be followed, which are more powerful if one haplotype or marker allele is associated. For the first approach, various 2 × 2 tables are formed by combining various categories and the maximum of the corresponding chi‐square statistics is considered as the final statistic. The second approach takes the average over the possible associated categories by writing down an overall likelihood. For the latter approach, we propose a new score statistic, which gives more weight to haplotypes or marker alleles that are common. Since the disease allele is often not observed, the power of the various statistics depends on both the linkage disequilibrium pattern and the frequencies of the associated haplotype or marker allele in the cases and the controls. We heuristically compare various statistics within the two approaches and present the results of a simulation that compares the performance of all considered statistics. Finally, we apply the statistics to a case–control study on the association between COL2A1 gene and radiographic osteoarthritis. Our conclusion is that overall the new proposed score statistic has good power. Copyright © 2008 John Wiley & Sons, Ltd.
Understanding a lack of trust in Global Software Teams: a multiple‐case study
Authors: Moe Nils Brede , Šmite Darja
Published: June 2008

Many organizations have turned towards globally distributed software development (GSD) in their quest for cheap, higher‐quality software that has a short development cycle. However, this kind of development has often been reported as being problematic and complex to manage. There are indications that trust is a fundamental factor in determining the success or failure of GSD projects. This article studies the key factors that cause a lack of trust and the effect of lacking trust and present data from four projects in which problems with trust were experienced. We found the key factors to be poor socialization and socio‐cultural fit, increased monitoring, inconsistency and disparities in work practices, reduction of and unpredictability in communication; and a lack of face‐to‐face meetings, language skills, conflict handling, and cognitive‐based trust. The effect of lacking trust was a decrease in productivity, quality, information exchange and feedback, morale among the employees, and an increase in relationship conflicts. In addition, the employees tended to self‐protect, to prioritize individual goals over group goals, and to doubt negative feedback from the manager. Further, the managers increased monitoring, which reduced the level of trust even more. These findings have implications for software development managers and practitioners involved in GSD. Copyright © 2008 John Wiley & Sons, Ltd.
Effect of Inorganic Phosphates on the Adhesion of Mono‐phosphorylated Cornstarch to Fibers
Authors: Zhu Zhifeng , Cheng Zheqiong
Published: June 2008

The influences of inorganic phosphates, as residuals and/or impurities within starch, on the adhesion of acid‐treated cornstarch phosphates to cotton and polyester fibers were investigated for warp sizing. The phosphate impurities considered included sodium dihydrogenphosphate, sodium hydrogenphosphate, sodium pyrophosphate, and pentasodium triphosphate. The starches with a phosphate degree of substitution (DS) range of 0.004‐0.021 were phosphorylated by heating acid‐treated cornstarch at 125°C for 90 min in a solid‐state reaction with pentasodium triphosphate. The adhesion was evaluated in terms of the breaking strength and work‐to‐break of slightly sized rovings. It was found that the phosphorylation improves the adhesion to both fibers even at a low phosphorylation extent. The phosphate impurities within starch have an adverse effect and reduce the adhesion to both fibers. The adverse effect depends on the type and level of the phosphates, decreasing in the series NaH2PO4 > Na2HPO4 > Na4P2O7 ≈ Na5P3O10. The adhesion enhances as the DS increases and as the free phosphate content decreases. Furthermore, the adverse effect can be offset by the phosphate modification of starch.
Classification of Rice Starch Amylose Content from Rheological Changes of Starch Paste after Cold Recrystallization
Authors: Tukomane Tuangporn , Varavinit Saiyavit
Published: June 2008

Following storage at 4°C for 24 h (recrystallization) rice starch pastes with low and medium amylose content exhibited a lower increase in consistency index, shear stress and Casson plastic viscosities than pastes with high amylose content. On the other hand, high amylose rice starch showed a higher degree of retrogradation than rice starch of lower amylose content.
Influence of Octenyl Succinate Rice Starch on Rheological Properties of Gelatinized Rice Starch before and after Retrogradation
Authors: Tukomane Tuangporn , Varavinit Saiyavit
Published: June 2008

Steady‐shear rheological properties, including the consistency index from the power law, the yield stress and Casson plastic viscosity from the Casson's model were employed in the study of retrogradation of native rice starch, octenyl succinate (OS) rice starch and blends containing up to 80% OS rice starch. After cold storage at 4°C for 24 h, presence of OS rice starch reduced retrogradation of rice starch mixtures as indicated by reduction of measured retrogradation parameters based on the three abovementioned rheological properties.