bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical relevance of decreased free protein S levels: results from a retrospective family cohort study involving 1143 relatives
Authors: Lijfering Willem M. , Mulder Rene , ten Kate Min Ki , Veeger Nic J. G. M. , Mulder Andre B. , van der Meer Jan
Published: October 2008

Conflicting data have been reported on the risk for venous thrombosis in subjects with low free protein S levels. We performed a post-hoc analysis in a single-center retrospective thrombophilic family cohort, to define the optimal free protein S level that can identify subjects at risk for venous thrombosis. Relatives (1143) were analyzed. Relatives with venous thrombosis (mean age 39 years) had lower free protein S levels than relatives without venous thrombosis (P < .001), which was most pronounced in the lowest quartile. Only relatives with free protein S levels less than the 5th percentile (< 41 IU/dL) or less than the 2.5th percentile (< 33 IU/dL) were at higher risk of first venous thrombosis compared with the upper quartile (> 91 IU/dL); annual incidence 1.20% (95% confidence interval [CI], 0.72–1.87) and 1.81% (95% CI, 1.01–2.99), respectively; adjusted hazard ratios 5.6, (95% CI, 2.7–11.5) and 11.3 (95% CI, 5.4–23.6). Recurrence rates were 12.12% (95 CI, 5.23–23.88) and 12.73% (95% CI, 5.12–26.22) per year; adjusted hazard ratios were 3.0 (95% CI, 1.03–8.5) and 3.4 (95% CI, 1.1–10.3). In conclusion, free protein S level can identify young subjects at risk for venous thrombosis in thrombophilic families, although the cutoff level lies far below the normal range in healthy volunteers.
CD40: Lord of the endothelial cell
Authors: Phipps Richard P.
Published: October 2008

CD40, a membrane-associated receptor, is a key activator of immune and vascular cells. In this issue of Blood, Pluvinet and colleagues reveal new features of human endothelial cells activated through CD40 that include inflammatory, thrombotic, and innate immune effects.
Background correction using dinucleotide affinities improves the performance of GCRMA
Authors: Gharaibeh Raad Z , Fodor Anthony A , Gibas Cynthia J
Published: October 2008

Background

High-density short oligonucleotide microarrays are a primary research tool for assessing global gene expression. Background noise on microarrays comprises a significant portion of the measured raw data, which can have serious implications for the interpretation of the generated data if not estimated correctly.

Results

We introduce an approach to calculate probe affinity based on sequence composition, incorporating nearest-neighbor (NN) information. Our model uses position-specific dinucleotide information, instead of the original single nucleotide approach, and adds up to 10% to the total variance explained (R2) when compared to the previously published model. We demonstrate that correcting for background noise using this approach enhances the performance of the GCRMA preprocessing algorithm when applied to control datasets, especially for detecting low intensity targets.

Conclusion

Modifying the previously published position-dependent affinity model to incorporate dinucleotide information significantly improves the performance of the model. The dinucleotide affinity model enhances the detection of differentially expressed genes when implemented as a background correction procedure in GeneChip preprocessing algorithms. This is conceptually consistent with physical models of binding affinity, which depend on the nearest-neighbor stacking interactions in addition to base-pairing.
Expression profiling of human glial precursors
Authors: Campanelli James T , Sandrock Robert W , Wheatley Will , Xue Haipeng , Zheng Jianhua , Liang Feng , Chesnut Jonathan D , Zhan Ming , Rao Mahendra S , Liu Ying
Published: October 2008

Background

We have generated gene expression databases for human glial precursors, neuronal precursors, astrocyte precursors and neural stem cells and focused on comparing the profile of glial precursors with that of other populations.

Results

A total of 14 samples were analyzed. Each population, previously distinguished from each other by immunocytochemical analysis of cell surface markers, expressed genes related to their key differentiation pathways. For the glial precursor cell population, we identified 458 genes that were uniquely expressed. Expression of a subset of these individual genes was validated by RT-PCR. We also report genes encoding cell surface markers that may be useful for identification and purification of human glial precursor populations.

Conclusion

We provide gene expression profile for human glial precursors. Our data suggest several signaling pathways that are important for proliferation and differentiation of human glial precursors. Such information may be utilized to further purify glial precursor populations, optimize media formulation, or study the effects of glial differentiation.
The lantibiotic mersacidin is a strong inducer of the cell wall stress response of Staphylococcus aureus
Authors: Sass Peter , Jansen Andrea , Szekat Christiane , Sass Vera , Sahl Hans-Georg , Bierbaum Gabriele
Published: October 2008

Background

The lantibiotic mersacidin is an antimicrobial peptide of 20 amino acids that is ribosomally produced by Bacillus sp. strain HIL Y-85,54728. Mersacidin acts by complexing the sugar phosphate head group of the peptidoglycan precursor lipid II, thereby inhibiting the transglycosylation reaction of peptidoglycan biosynthesis.

Results

Here, we studied the growth of Staphylococcus aureus in the presence of subinhibitory concentrations of mersacidin. Transcriptional data revealed an extensive induction of the cell wall stress response, which is partly controlled by the two-component regulatory system VraSR. In contrast to other cell wall-active antibiotics such as vancomycin, very low concentrations of mersacidin (0.15 × MIC) were sufficient for induction. Interestingly, the cell wall stress response was equally induced in vancomycin intermediately resistant S. aureus (VISA) and in a highly susceptible strain. Since the transcription of the VraDE ABC transporter genes was induced up to 1700-fold in our experiments, we analyzed the role of VraDE in the response to mersacidin. However, the deletion of the vraE gene did not result in an increased susceptibility to mersacidin compared to the wild type strain. Moreover, the efficacy of mersacidin was not affected by an increased cell wall thickness, which is part of the VISA-type resistance mechanism and functions by trapping the vancomycin molecules in the cell wall before they reach lipid II. Therefore, the relatively higher concentration of mersacidin at the membrane might explain why mersacidin is such a strong inducer of VraSR compared to vancomycin.

Conclusion

In conclusion, mersacidin appears to be a strong inducer of the cell wall stress response of S. aureus at very low concentrations, which reflects its general mode of action as a cell wall-active peptide as well as its use of a unique target site on lipid II. Additionally, mersacidin does not seem to be a substrate for the resistance transporter VraDE.
Alternative methods to analyse the impact of HIV mutations on virological response to antiviral therapy
Authors: Wittkop Linda , Commenges Daniel , Pellegrin Isabelle , Breilh Dominique , Neau Didier , Lacoste Denis , Pellegrin Jean-Luc , Chêne Geneviève , Dabis François , Thiébaut Rodolphe
Published: October 2008

Background

Principal component analysis (PCA) and partial least square (PLS) regression may be useful to summarize the HIV genotypic information. Without pre-selection each mutation presented in at least one patient is considered with a different weight. We compared these two strategies with the construction of a usual genotypic score.

Methods

We used data from the ANRS-CO3 Aquitaine Cohort Zephir sub-study. We used a subset of 87 patients with a complete baseline genotype and plasma HIV-1 RNA available at baseline and at week 12. PCA and PLS components were determined with all mutations that had prevalences >0. For the genotypic score, mutations were selected in two steps: 1) p-value < 0.01 in univariable analysis and prevalences between 10% and 90% and 2) backwards selection procedure based on the Cochran-Armitage Test. The predictive performances were compared by means of the cross-validated area under the receiver operating curve (AUC).

Results

Virological failure was observed in 46 (53%) patients at week 12. Principal components and PLS components showed a good performance for the prediction of virological response in HIV infected patients. The cross-validated AUCs for the PCA, PLS and genotypic score were 0.880, 0.868 and 0.863, respectively. The strength of the effect of each mutation could be considered through PCA and PLS components. In contrast, each selected mutation contributes with the same weight for the calculation of the genotypic score. Furthermore, PCA and PLS regression helped to describe mutation clusters (e.g. 10, 46, 90).

Conclusion

In this dataset, PCA and PLS showed a good performance but their predictive ability was not clinically superior to that of the genotypic score.
Extending the spectrum of Ellis van Creveld syndrome: a large family with a mild mutation in the EVCgene
Authors: Ulucan Hakan , Gül Davut , Sapp Julie C , Cockerham John , Johnston Jennifer J , Biesecker Leslie G
Published: October 2008

Background

Ellis-van Creveld (EvC) syndrome is characterized by short limbs, short ribs, postaxial polydactyly, dysplastic nails and teeth and is inherited in an autosomal recessive pattern. We report a family with complex septal cardiac defects, rhizomelic limb shortening, and polydactyly, without the typical lip, dental, and nail abnormalities of EvC. The phenotype was inherited in an autosomal recessive pattern, with one instance of pseudodominant inheritance.

Methods

Because of the phenotypic overlap with EvC, microsatellite markers were used to test for linkage to theEVC/EVC2locus. The results did not exclude linkage, so samples were sequenced for mutations.

Results

We identified a c.1868T>C mutation inEVC, which predicts p.L623P, and was homozygous in affected individuals.

Conclusion

We conclude that thisEVCmutation is hypomorphic and that such mutations can cause a phenotype of cardiac and limb defects that is less severe than typical EvC.EVCmutation analysis should be considered in patients with cardiac and limb malformations, even if they do not manifest typical EvC syndrome.
A pilot randomised controlled trial of the feasibility of using body scan and isometric exercises for reducing urge to smoke in a smoking cessation clinic
Authors: Al-Chalabi Lemees , Prasad Neha , Steed Lucy , Stenner Sarah , Aveyard Paul , Beach Jane , Ussher Michael
Published: October 2008

Background

The main cause of relapse in smokers attempting to quit is inability to resist urges to smoke. Pharmacotherapy ameliorates but does not entirely prevent urges to smoke when abstinent, so other methods to resist urges to smoke might be helpful. Exercise is effective, but aerobic exercise is often impractical when urges strike. Two techniques, body scan and isometric exercise, have been shown to reduce urge intensity and nicotine withdrawal symptoms in temporarily abstinent smokers. It is unclear whether they would be used or effective in typical smokers attempting to quit.

Methods

In a pilot trial set in a UK smoking cessation clinic, 20 smokers were randomised to receive emails containing .mp3 files and .pdf illustrations of the instructions for doing the body scan and isometric exercises. Twenty smokers received no other intervention, although all 40 were receiving weekly behavioural support and nicotine replacement therapy. Carbon monoxide confirmed abstinence, nicotine withdrawal symptoms, urges to smoke, and use of the techniques to resist urges were recorded weekly for four weeks after quit day.

Results

60–80% of quitters reported using the isometric exercises each week and 40–70% reported using the body scan to deal with urges. On average, these techniques were rated as 'slightly helpful' for controlling the urges. There were no large or significant differences in withdrawal symptoms or urge intensity between the two groups. The risk ratio and 95% confidence interval for exercises compared with controls for prolonged confirmed abstinence at four weeks was 0.82 (0.44–1.53). 81% of quitters intended to continue using isometric exercises and 25% body scan, while 81% and 50% respectively would recommend using these techniques to others trying to stop.

Conclusion

Isometric exercises, and to a lesser extent body scan, were popular and perceived as somewhat helpful by quitters. The trial showed that these techniques were used and a larger trial could now be developed to examine the influence of the methods on reducing urges to smoke and increasing abstinence.

Trial registration

ISRCTN70036823
DNA methylation-based biomarkers for early detection of non-small cell lung cancer: an update
Authors: Anglim Paul P , Alonzo Todd A , Laird-Offringa Ite A
Published: October 2008

Lung cancer is the number one cancer killer in the United States. This disease is clinically divided into two sub-types, small cell lung cancer, (10–15% of lung cancer cases), and non-small cell lung cancer (NSCLC; 85–90% of cases). Early detection of NSCLC, which is the more common and less aggressive of the two sub-types, has the highest potential for saving lives. As yet, no routine screening method that enables early detection exists, and this is a key factor in the high mortality rate of this disease. Imaging and cytology-based screening strategies have been employed for early detection, and while some are sensitive, none have been demonstrated to reduce lung cancer mortality. However, mortality might be reduced by developing specific molecular markers that can complement imaging techniques. DNA methylation has emerged as a highly promising biomarker and is being actively studied in multiple cancers. The analysis of DNA methylation-based biomarkers is rapidly advancing, and a large number of potential biomarkers have been identified. Here we present a detailed review of the literature, focusing on DNA methylation-based markers developed using primary NSCLC tissue. Viable markers for clinical diagnosis must be detectable in 'remote media' such as blood, sputum, bronchoalveolar lavage, or even exhaled breath condensate. We discuss progress on their detection in such media and the sensitivity and specificity of the molecular marker panels identified to date. Lastly, we look to future advancements that will be made possible with the interrogation of the epigenome.
Effects on hemodynamics and gas exchange of omega-3 fatty acid-enriched lipid emulsion in acute respiratory distress syndrome (ARDS): a prospective, randomized, double-blind, parallel group study
Authors: Sabater Joan , Masclans Joan Ramon , Sacanell Judit , Chacon Pilar , Sabin Pilar , Planas Merce
Published: October 2008

Introduction

We investigated the effects on hemodynamics and gas exchange of a lipid emulsion enriched with omega-3 fatty acids in patients with ARDS.

Methods

The design was a prospective, randomized, double-blind, parallel group study in our Intensive Medicine Department of Vall d'Hebron University Hospital (Barcelona-Spain). We studied 16 consecutive patients with ARDS and intolerance to enteral nutrition (14 men and 2 women; mean age: 58 ± 13 years; APACHE II score: 17.8 ± 2.3; Lung Injury Score: 3.1 ± 0.5; baseline PaO2/FiO2ratio: 149 ± 40). Patients were randomized into 2 groups: Group A (n = 8) received the study emulsion Lipoplus®20%, B.Braun Medical (50% MCT, 40% LCT, 10% ω-3); Group B (n = 8) received the control emulsion Intralipid®Fresenius Kabi (100% LCT). Lipid emulsions were administered during 12 h at a dose of 0.12 g/kg/h. Measurements of the main hemodynamic and gas exchange parameters were made at baseline (immediately before administration of the lipid emulsions), every hour during the lipid infusion, at the end of administration, and six hours after the end of administration lipid infusion.

Results

No statistically significant changes were observed in the different hemodynamic values analyzed. Likewise, the gas exchange parameters did not show statistically significant differences during the study. No adverse effect attributable to the lipid emulsions was seen in the patients analyzed.

Conclusion

The lipid emulsion enriched with omega-3 fatty acids was safe and well tolerated in short-term administration to patients with ARDS. It did not cause any significant changes in hemodynamic and gas exchange parameters.

Trial registration

ISRCTN63673813
Toxicity of CdSe Nanoparticles in Caco-2 Cell Cultures
Authors: Wang Lin , Nagesha Dattatri K , Selvarasah Selvapraba , Dokmeci Mehmet R , Carrier Rebecca L
Published: October 2008

Background

Potential routes of nanomaterial exposure include inhalation, dermal contact, and ingestion. Toxicology of inhalation of ultra-fine particles has been extensively studied; however, risks of nanomaterial exposure via ingestion are currently almost unknown. Using enterocyte-like Caco-2 cells as a small intestine epithelial model, the possible toxicity of CdSe quantum dot (QD) exposure via ingestion was investigated. Effect of simulated gastric fluid treatment on CdSe QD cytotoxicity was also studied.

Results

Commercially available CdSe QDs, which have a ZnS shell and poly-ethylene glycol (PEG) coating, and in-house prepared surfactant coated CdSe QDs were dosed to Caco-2 cells. Cell viability and attachment were studied after 24 hours of incubation. It was found that cytotoxicity of CdSe QDs was modulated by surface coating, as PEG coated CdSe QDs had less of an effect on Caco-2 cell viability and attachment. Acid treatment increased the toxicity of PEG coated QDs, most likely due to damage or removal of the surface coating and exposure of CdSe core material. Incubation with un-dialyzed in-house prepared CdSe QD preparations, which contained an excess amount of free Cd2+, resulted in dramatically reduced cell viability.

Conclusion

Exposure to CdSe QDs resulted in cultured intestinal cell detachment and death; cytotoxicity depended largely, however, on the QD coating and treatment (e.g. acid treatment, dialysis). Experimental results generally indicated that Caco-2 cell viability correlated with concentration of free Cd2+ ions present in cell culture medium. Exposure to low (gastric) pH affected cytotoxicity of CdSe QDs, indicating that route of exposure may be an important factor in QD cytotoxicity.
Enhanced A3 adenosine receptor selectivity of multivalent nucleoside-dendrimer conjugates
Authors: Klutz Athena M , Gao Zhan-Guo , Lloyd John , Shainberg Asher , Jacobson Kenneth A
Published: October 2008

Background

An approach to use multivalent dendrimer carriers for delivery of nucleoside signaling molecules to their cell surface G protein-coupled receptors (GPCRs) was recently introduced.

Results

A known adenosine receptor (AR) agonist was conjugated to polyamidoamine (PAMAM) dendrimer carriers for delivery of the intact covalent conjugate to on the cell surface. Depending on the linking moiety, multivalent conjugates of theN6-chain elongated functionalized congener ADAC (N6-[4-[[[4-[[[(2-aminoethyl)amino]carbonyl]methyl]anilino]carbonyl]methyl]phenyl]-adenosine) achieved unanticipated high selectivity in binding to the cytoprotective human A3AR, a class A GPCR. The key to this selectivity of > 100-fold in both radioreceptor binding (Ki app= 2.4 nM) and functional assays (EC50= 1.6 nM in inhibition of adenylate cyclase) was maintaining a free amino group (secondary) in an amide-linked chain. Attachment of neutral amide-linked chains or thiourea-containing chains preserved the moderate affinity and efficacy at the A1AR subtype, but there was no selectivity for the A3AR. Since residual amino groups on dendrimers are associated with cytotoxicity, the unreacted terminal positions of this A3AR-selective G2.5 dendrimer were present as carboxylate groups, which had the further benefit of increasing water-solubility. The A3AR selective G2.5 dendrimer was also visualized binding the membrane of cells expressing the A3receptor but did not bind cells that did not express the receptor.

Conclusion

This is the first example showing that it is feasible to modulate and even enhance the pharmacological profile of a ligand of a GPCR based on conjugation to a nanocarrier and the precise structure of the linking group, which was designed to interact with distal extracellular regions of the 7 transmembrane-spanning receptor. This ligand tool can now be used in pharmacological models of tissue rescue from ischemia and to probe the existence of A3AR dimers.
Interleukin-1beta and tumor necrosis factor-alpha are expressed by different subsets of microglia and macrophages after ischemic stroke in mice
Authors: Clausen Bettina H , Lambertsen Kate L , Babcock Alicia A , Holm Thomas H , Dagnaes-Hansen Frederik , Finsen Bente
Published: October 2008

Background

Interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α) are expressed by microglia and infiltrating macrophages following ischemic stroke. Whereas IL-1β is primarily neurotoxic in ischemic stroke, TNF-α may have neurotoxic and/or neuroprotective effects. We investigated whether IL-1β and TNF-α are synthesized by overlapping or segregated populations of cells after ischemic stroke in mice.

Methods

We used flow cytometry and immunohistochemistry to examine cellular co-expression of IL-1β and TNF-α at 6, 12 and 24 hours after permanent middle cerebral artery occlusion in mice, validating the results by the use of bone marrow chimeric mice.

Results

We found that IL-1β and TNF-α were expressed in largely segregated populations of CD11b+CD45dimmicroglia and CD11b+CD45highmacrophages, with cells expressing both cytokines only rarely. The number of Gr1+granulocytes producing IL-1β or TNF-α was very low, and we observed no IL-1β- or TNF-α-expressing T cells or astrocytes.

Conclusion

Taken together, the results show that IL-1β and TNF-α are produced by largely segregated populations of microglia and macrophages after ischemic stroke in mice. Our findings provide evidence of a functional diversity among different subsets of microglia and macrophages that is potentially relevant to future design of anti-inflammatory therapies in stroke.
Partitioning the population attributable fraction for a sequential chain of effects
Authors: Mason Craig A , Tu Shihfen
Published: October 2008

Background

While the population attributable fraction (PAF) provides potentially valuable information regarding the community-level effect of risk factors, significant limitations exist with current strategies for estimating a PAF in multiple risk factor models. These strategies can result in paradoxical or ambiguous measures of effect, or require unrealistic assumptions regarding variables in the model. A method is proposed in which an overall or total PAF across multiple risk factors is partitioned into components based upon a sequential ordering of effects. This method is applied to several hypothetical data sets in order to demonstrate its application and interpretation in diverse analytic situations.

Results

The proposed method is demonstrated to provide clear and interpretable measures of effect, even when risk factors are related/correlated and/or when risk factors interact. Furthermore, this strategy not only addresses, but also quantifies issues raised by other researchers who have noted the potential impact of population-shifts on population-level effects in multiple risk factor models.

Conclusion

Combined with simple, unadjusted PAF estimates and an aggregate PAF based on all risk factors under consideration, the sequentially partitioned PAF provides valuable additional information regarding the
process
through which population rates of a disorder may be impacted. In addition, the approach can also be used to statistically control for confounding by other variables, while avoiding the potential pitfalls of attempting to separately differentiate direct and indirect effects.
DNA damage in preserved specimens and tissue samples: a molecular assessment
Authors: Zimmermann Juergen , Hajibabaei Mehrdad , Blackburn David C , Hanken James , Cantin Elizabeth , Posfai Janos , Evans Thomas C
Published: October 2008

The extraction of genetic information from preserved tissue samples or museum specimens is a fundamental component of many fields of research, including the Barcode of Life initiative, forensic investigations, biological studies using scat sample analysis, and cancer research utilizing formaldehyde-fixed, paraffin-embedded tissue. Efforts to obtain genetic information from these sources are often hampered by an inability to amplify the desired DNA as a consequence of DNA damage.

Previous studies have described techniques for improved DNA extraction from such samples or focused on the effect of damaging agents – such as light, oxygen or formaldehyde – on free nucleotides.

We present ongoing work to characterize lesions in DNA samples extracted from preserved specimens. The extracted DNA is digested to single nucleosides with a combination of DNase I, Snake Venom Phosphodiesterase, and Antarctic Phosphatase and then analyzed by HPLC-ESI-TOF-MS.

We present data for moth specimens that were preserved dried and pinned with no additional preservative and for frog tissue samples that were preserved in either ethanol, or formaldehyde, or fixed in formaldehyde and then preserved in ethanol. These preservation methods represent the most common methods of preserving animal specimens in museum collections. We observe changes in the nucleoside content of these samples over time, especially a loss of deoxyguanosine. We characterize the fragmentation state of the DNA and aim to identify abundant nucleoside lesions. Finally, simple models are introduced to describe the DNA fragmentation based on nicks and double-strand breaks.
Prescription profile of potentially aristolochic acid containing Chinese herbal products: an analysis of National Health Insurance data in Taiwan between 1997 and 2003
Authors: Hsieh Shu-Ching , Lin I-Hsin , Tseng Wei-Lum , Lee Chang-Hsing , Wang Jung-Der
Published: October 2008

Background

Some Chinese herbal products (CHPs) may contain aristolochic acid (AA) or may be adulterated by the herbs suspected of containing AA which is nephrotoxic and carcinogenic. This study aims to identify the risk and the prescription profile of AA-containing CHPs (AA-CHPs) in Taiwan.

Methods

A longitudinal analysis was conducted on a randomly sampled cohort of 200,000 patients using the data from the National Health Insurance (NHI) in Taiwan between 1997 and 2003.

Results

During the 7-year study period, 78,644 patients were prescribed with AA-CHPs; most patients were females, or middle-aged, or both. A total of 526,867 prescriptions were made to use 1,218 licensed AA-CHPs. Over 85% of the AA-exposed patients took less than 60 g of AA-herbs; however, about 7% were exposed to a cumulated dose of over 100 g of Radix et Rhizoma Asari (Xixin), Caulis Akebiae (Mutong) or Fructus Aristolochiae (Madouling). Patients of respiratory and musculoskeletal diseases received most of the AA-CHP prescriptions. The most frequently prescribed AA-CHPs Shujing Huoxie Tang, Chuanqiong Chadiao San and Longdan Xiegan Tang, containing Radix Stephaniae Tetrandrae, Radix et Rhizoma Asari and Caulis Akebiae, respectively.

Conclusion

About one-third of people in Taiwan have been prescribed with AA-CHPs between 1997 and 2003. Although the cumulated doses were not large, further actions should be carried out to ensure the safe use of AA-CHPs.
Laparoscopic pyeloplasty for ureteropelvic junction obstruction of the lower moiety in a completely duplicated collecting system: a case report
Authors: Stravodimos Konstantinos G. , Anastasiou Ioannis , Adamakis Ioannis , Kapetanakis Theodoros , Koritsiadis Georgios , Constantinides Constantinos
Published: October 2008

Introduction

There are only a few reports on laparoscopic pyeloplasty in kidney abnormalities and only one case for laparoscopic pyeloplasty in a duplicated system. Increasing experience in laparoscopic techniques allows proper treatment of such anomalies. However, its feasibility in difficult cases with altered kidney anatomy such as that of duplicated renal pelvis still needs to be addressed.

Case presentation

We present a case of a 22-year-old white Caucasian female patient with ureteropelvic junction obstruction of the lower ureter of a completely duplicated system that was managed with laparoscopic pyeloplasty. Crossing vessels were identified and transposed. The procedure was carried out successfully and the patient's symptoms subsided. Follow-up studies demonstrated complete resolution of the obstruction.

Conclusion

Since laparoscopic pyeloplasty is still an evolving procedure, its feasibility in complex cases of kidney anatomic abnormalities is herein further justified.
Comparing the xylose reductase/xylitol dehydrogenase and xylose isomerase pathways in arabinose and xylose fermenting Saccharomyces cerevisiae strains
Authors: Bettiga Maurizio , Hahn-Hägerdal Bärbel , Gorwa-Grauslund Marie F
Published: October 2008

Background

Ethanolic fermentation of lignocellulosic biomass is a sustainable option for the production of bioethanol. This process would greatly benefit from recombinant Saccharomyces cerevisiae strains also able to ferment, besides the hexose sugar fraction, the pentose sugars, arabinose and xylose. Different pathways can be introduced in S. cerevisiae to provide arabinose and xylose utilisation. In this study, the bacterial arabinose isomerase pathway was combined with two different xylose utilisation pathways: the xylose reductase/xylitol dehydrogenase and xylose isomerase pathways, respectively, in genetically identical strains. The strains were compared with respect to aerobic growth in arabinose and xylose batch culture and in anaerobic batch fermentation of a mixture of glucose, arabinose and xylose.

Results

The specific aerobic arabinose growth rate was identical, 0.03 h-1, for the xylose reductase/xylitol dehydrogenase and xylose isomerase strain. The xylose reductase/xylitol dehydrogenase strain displayed higher aerobic growth rate on xylose, 0.14 h-1, and higher specific xylose consumption rate in anaerobic batch fermentation, 0.09 g (g cells)-1 h-1 than the xylose isomerase strain, which only reached 0.03 h-1 and 0.02 g (g cells)-1h-1, respectively. Whereas the xylose reductase/xylitol dehydrogenase strain produced higher ethanol yield on total sugars, 0.23 g g-1 compared with 0.18 g g-1 for the xylose isomerase strain, the xylose isomerase strain achieved higher ethanol yield on consumed sugars, 0.41 g g-1 compared with 0.32 g g-1 for the xylose reductase/xylitol dehydrogenase strain. Anaerobic fermentation of a mixture of glucose, arabinose and xylose resulted in higher final ethanol concentration, 14.7 g l-1 for the xylose reductase/xylitol dehydrogenase strain compared with 11.8 g l-1 for the xylose isomerase strain, and in higher specific ethanol productivity, 0.024 g (g cells)-1 h-1 compared with 0.01 g (g cells)-1 h-1 for the xylose reductase/xylitol dehydrogenase strain and the xylose isomerase strain, respectively.

Conclusion

The combination of the xylose reductase/xylitol dehydrogenase pathway and the bacterial arabinose isomerase pathway resulted in both higher pentose sugar uptake and higher overall ethanol production than the combination of the xylose isomerase pathway and the bacterial arabinose isomerase pathway. Moreover, the flux through the bacterial arabinose pathway did not increase when combined with the xylose isomerase pathway. This suggests that the low activity of the bacterial arabinose pathway cannot be ascribed to arabitol formation via the xylose reductase enzyme.
A global transcriptional view of apoptosis in human T-cell activation
Authors: Wang Min , Windgassen Dirk , Papoutsakis Eleftherios T
Published: October 2008

Background

T-cell activation is an essential step of immune response. The process of proper T-cell activation is strictly monitored and regulated by apoptosis signaling. Yet, regulation of apoptosis, an integral and crucial facet during the process of T-cell activation, is not well understood.

Methods

In this study, a Gene-Ontology driven global gene expression analysis coupled with protein abundance and activity assays identified genes and pathways associated with regulation of apoptosis in primary human CD3+ T cells and separately CD4+ and CD8+ T cells.

Results

We identified significantly regulated apoptotic genes in several protein families, such as BCL2 proteins, CASPASE proteins, and TNF receptors, and detailed their transcriptional kinetics during the T-cell activation process. Transcriptional patterns of a few select genes (BCL2A1, BBC3 and CASP3) were validated at the protein level. Many of these apoptotic genes are involved in NF-κB signaling pathway, including TNFRSF10A, TNFRSF10B, TRAF4, TRAF1, TRAF3, and TRAF6. Upregulation of NF-κB and IκB family genes (REL, RELA, and RELB, NFKBIA, NFKBIE and NFKB1) at 48 to 96 hours, supported by the increase of phosphorylated RELA (p65), suggests that the involvement of the NF-κB complex in the process of T-cell proliferation is not only regulated at the protein level but also at the transcriptional level. Examination of genes involved in MAP kinase signalling pathway, important in apoptosis, suggests an induction of p38 and ERK1 cascades in T-cell proliferation (at 48 to 96 hours), which was explored using phosphorylation assays for p38 (MAPK14) and ERK1 (MAPK3). An immediate and short-lived increase of AP-1 activity measured by DNA-binding activity suggests a rapid and transient activation of p38 and/or JNK cascades upon T-cell activation.

Conclusion

This comparative genome-scale, transcriptional analysis of T-cell activation in the CD4+ and CD8+ subsets and the mixed CD3+ population identified many apoptosis genes not previously identified in the context of T-cell activation. Furthermore, it provided a comprehensive temporal analysis of the transcriptional program of apoptosis associated with T-cell activation.
A role of p38 mitogen-activated protein kinase in adenosine A1 receptor-mediated synaptic depotentiation in area CA1 of the rat hippocampus
Authors: Liang Ying-Ching , Huang Chiung-Chun , Hsu Kuei-Sen
Published: October 2008

Background

Although long-term potentiation (LTP) of synaptic strength is very persistent, current studies have provided evidence that various manipulations or pharmacological treatment when applied shortly after LTP induction can reverse it. This kind of reversal of synaptic strength is termed as depotentiation and may have a function to increase the flexibility and storage capacity of neuronal networks. Our previous studies have demonstrated that an increase in extracellular levels of adenosine and subsequent activation of adenosine A1 receptors are important for the induction of depotentiation; however, the signaling downstream of adenosine A1 receptors to mediate depotentiation induction remains elusive.

Results

We confirm that depotentiation induced by low-frequency stimulation (LFS) (2 Hz, 10 min, 1200 pulses) was dependent on adenosine A1 receptor activation, because it was mimicked by bath-applied adenosine A1 receptor agonist N
6-cyclopentyladenosine (CPA) and was inhibited by the selective adenosine A1 receptor antagonist 8-cyclopentyl-1,3-dipropylxanthine (DPCPX). Pretreatment of the hippocampal slices with the selective p38 mitogen-activated protein kinase (MAPK) inhibitors, 4-(4-fluorophenyl)-2-(4-methylsulfinylphenyl]-5-(4-pyrudyl)-1H-imidazole (SB203580) or trans-1-(4-hydroxycyclohexyl)-4-(fluorophenyl)-5-(2-methoxypyrimidin-4-yl)imidazole (SB239063), prevented the induction of depotentiation by LFS and CPA. In agreement with electrophysiological observation, both LFS- and CPA-induced depotentiation are associated with an increase in p38 MAPK activation, which are blocked by DPCPX or SB203580 application.

Conclusion

These results suggest that activation of adenosine A1 receptor and in turn triggering p38 MAPK signaling may contribute to the LFS-induced depotentiation at hippocampal CA1 synapses.
Effect of anti-CD52 antibody alemtuzumab on ex-vivo culture of umbilical cord blood stem cells
Authors: Lim Che K , Sun Li , Feng Qi , Law Ping , Chua Wei T , Lim Shy N , Hwang William YK
Published: October 2008

Background

Excessive maturation of hematopoietic cells leads to a reduction of long-term proliferative capability during cord blood (CB) expansion. In this study, we report the effects of anit-CD52 (Alemtuzumab, Campath) on both short- and long-term ex vivo expansion of CB hematopoietic stem cells (HSC) by evaluating the potential role of Alemtuzumab in preserving the repopulating capability in CB HSC and nonlymphoid progenitors.

Methods

Ex vivo expansion experiments were carried out using freshly purified CB CD34+ cells in StemSpan™ SFEM medium in the presence of stem cell factor, Flt3-Ligand and thrombopoietin at 50 ng/ml. Alemtuzumab (10 μg/ml) was used to deplete CD52+ cells during the cultures. Flow cytometry was used to monitor CB HSC and their differentiation. Colony forming unit (CFU) assays and long term culture-initiating cell (LTC-IC) assays were performed on cells obtained from day 0 (before culture) and day 14 after cultures. Secondary cultures was performed using CD34+ cells isolated at 35 days from primary cultures and further cultured in StemSpan™ SFEM medium for another 14 days to confirm the long term effect of alemtuzumab in liquid cultures.

Results

Compared to cytokines alone, addition of alemtuzumab resulted in a significant increase in total nucleated cells, absolute CD34+ cells, myeloid and megakaryocytic progenitors, multi-lineage and myeloid CFU and LTC-IC.

Conclusion

The results from current study suggested that the use of alemtuzumab for ex vivo expansion of CBHSC maybe advantageous. Our findings may improve current technologies for CBHSC expansion and increase the availability of CB units for transplantation. However, in vivo studies using animal models are likely needed in further studies to test the hematopoietic effects using such expanded CB products.
Dermoid cyst of the mandibula: a case report
Authors: Menditti Dardo , Laino Luigi , Ferrara Nicola , Baldi Alfonso
Published: October 2008

Background

Dermoid cysts are rare congenital lesions derived from pluripotential cells.

Case Presentation

We present a case of a female patient aged 30 years presenting for a lesion of the mandibula incidentally seen on a routine panoramic radiograph obtained for dental care. The instrumental, clinical and histological characteristics of the lesion are reported. Finally, a bibliographic revision of this pathology at the level of the oral cavity is reported.

Conclusion

Dermoid cysts must be considered in the differential diagnosis of mandibula's lesions.
Melanoma in-situ arising in seborrheic keratosis: a case report
Authors: Repertinger Susan , Wang Jeff , Adickes Edward , Sarma Deba P
Published: October 2008

Background

Seborrheic keratosis is a very common benign skin tumor in man. Melanoma is rare but is the most dreaded of all malignant skin tumors. A melanoma arising in a seborrheic keratosis is distinctly rare. We are reporting such a case occurring in an 86-year-old man.

Case presentation

An-86-year-old male with a history of multiple actinic keratoses and seborrheic keratoses of the head and trunk presented with a mid-back skin lesion. The lesion was poorly circumscribed, flat, and gray, with a pink-tan, well-circumscribed scaly nodule within it. The biopsied lesion was composed of the usual features of hyperkeratotic seborrheic keratosis, but with focal atypical melanocytic proliferation with nesting along the dermal-epidermal junction. We interpreted this lesion as a melanoma in-situ arising within a seborrheic keratosis.

Conclusion

It is not uncommon for many physicians to remove a typical seborrheic keratosis without a confirmatory microscopic confirmation. We urge that all such lesions be examined by the pathologist to avoid missing another concomitant malignant lesion such as melanoma which needs adequate resection and close follow-up.
Cowden syndrome. Managing multiple skeletal metastases of different origin: a case report
Authors: Angoules Antonios , Tsapakis Evangelia Maria , Polyzois Ioannis , Gamie Zakareya , Rankine James Julian , Tsiridis Eleftherios
Published: October 2008

Background

Cowden Syndrome is a rare autosomal dominant multiple hamartomatous condition, characterised by both benign and malignant tumours affecting multiple systems.

Case presentation

We present a 47-year-old female patient with thigh pain that was diagnosed with Cowden syndrome 20 years ago and developed multiple and different skeletal metastases which became resistant to radio-chemotherapy. A percutaneous plate fixation of the distal femur with an intralesional excision and cementoplasty of the metastasis was performed initially. This was combined with a cemented total hip arthroplasty using an Exeter long revision stem and a cementoplasty of the femoral canal for the proximal lesions.

Conclusion

A meticulous approach to her complex metastatic disease resulted in successful palliative prophylactic reconstructive surgery that improved her quality of life, allowing her independent pain free walking for 12 months.
Novel image analysis approach for quantifying expression of nuclear proteins assessed by immunohistochemistry: application to measurement of oestrogen and progesterone receptor levels in breast cancer
Authors: Rexhepaj Elton , Brennan Donal J , Holloway Peter , Kay Elaine W , McCann Amanda H , Landberg Goran , Duffy Michael J , Jirstrom Karin , Gallagher William M
Published: October 2008

Introduction

Manual interpretation of immunohistochemistry (IHC) is a subjective, time-consuming and variable process, with an inherent intra-observer and inter-observer variability. Automated image analysis approaches offer the possibility of developing rapid, uniform indicators of IHC staining. In the present article we describe the development of a novel approach for automatically quantifying oestrogen receptor (ER) and progesterone receptor (PR) protein expression assessed by IHC in primary breast cancer.

Methods

Two cohorts of breast cancer patients (n = 743) were used in the study. Digital images of breast cancer tissue microarrays were captured using the Aperio ScanScope XT slide scanner (Aperio Technologies, Vista, CA, USA). Image analysis algorithms were developed using MatLab 7 (MathWorks, Apple Hill Drive, MA, USA). A fully automated nuclear algorithm was developed to discriminate tumour from normal tissue and to quantify ER and PR expression in both cohorts. Random forest clustering was employed to identify optimum thresholds for survival analysis.

Results

The accuracy of the nuclear algorithm was initially confirmed by a histopathologist, who validated the output in 18 representative images. In these 18 samples, an excellent correlation was evident between the results obtained by manual and automated analysis (Spearman's ρ = 0.9, P < 0.001). Optimum thresholds for survival analysis were identified using random forest clustering. This revealed 7% positive tumour cells as the optimum threshold for the ER and 5% positive tumour cells for the PR. Moreover, a 7% cutoff level for the ER predicted a better response to tamoxifen than the currently used 10% threshold. Finally, linear regression was employed to demonstrate a more homogeneous pattern of expression for the ER (R = 0.860) than for the PR (R = 0.681).

Conclusions

In summary, we present data on the automated quantification of the ER and the PR in 743 primary breast tumours using a novel unsupervised image analysis algorithm. This novel approach provides a useful tool for the quantification of biomarkers on tissue specimens, as well as for objective identification of appropriate cutoff thresholds for biomarker positivity. It also offers the potential to identify proteins with a homogeneous pattern of expression.
Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes
Authors: Boekhorst Jos , van Breukelen Bas , Heck Albert JR , Snel Berend
Published: October 2008

Background

Reversible phosphorylation of proteins is involved in a wide range of processes, ranging from signaling cascades to regulation of protein complex assembly. Little is known about the structure and evolution of phosphorylation networks. Recent high-throughput phosphoproteomics studies have resulted in the rapid accumulation of phosphopeptide datasets for many model organisms. Here, we exploit these novel data for the comparative analysis of phosphorylation events between different species of eukaryotes.

Results

Comparison of phosphoproteomics datasets of six eukaryotes yields an overlap ranging from approximately 700 sites for human and mouse (two large datasets of closely related species) to a single site for fish and yeast (distantly related as well as two of the smallest datasets). Some conserved events appear surprisingly old; those shared by plant and animals suggest conservation over the time scale of a billion years. In spite of the hypothesized incomprehensive nature of phosphoproteomics datasets and differences in experimental procedures, we show that the overlap between phosphoproteomes is greater than expected by chance and indicates increased functional relevance. Despite the dynamic nature of the evolution of phosphorylation, the relative overlap between the different datasets is identical to the phylogeny of the species studied.

Conclusion

This analysis provides a framework for the generation of biological insights by comparative analysis of high-throughput phosphoproteomics datasets. We expect the rapidly growing body of data from high-throughput mass spectrometry analysis to make comparative phosphoproteomics a powerful tool for elucidating the evolutionary and functional dynamics of reversible phosphorylation.
Chlamydia trachomatisdiversity viewed as a tissue-specific coevolutionary arms race
Authors: Nunes Alexandra , Nogueira Paulo J , Borrego Maria J , Gomes João P
Published: October 2008

Background

The genomes of pathogens are thought to have evolved under selective pressure provided by the host in a coevolutionary arms race (the 'Red Queen's Hypothesis'). Traditionally, adaptation by pathogens is thought to rely not on whole chromosome dynamics but on gain/loss of specific genes, yielding differential abilities to infect distinct tissues. Thus, it is not known whether distinct host organs differently shape the genome of the same pathogen. We tested this hypothesis using Chlamydia trachomatis as model species, looking at 15 serovars that infect different organs: eyes, genitalia and lymph nodes.

Results

We analyzed over 51,000 base pairs from all serovars using various phylogenetic approaches and a non-phylogenetic indel-based algorithm to study the evolution of individual and concatenated loci. This survey comprised about 33% of all single nucleotide polymorphisms in C. trachomatis chromosomes. We present a model in which genome evolution indeed correlates with the cell type (epithelial versus lymph cells) and organ (eyes versus genitalia) that a serovar infects, illustrating an adaptation to physiologically distinct niches, and discarding genetic drift as the dominant evolutionary driving force. We show that radiation of serovars occurred primarily by accumulation of single nucleotide polymorphisms in intergenomic regions, housekeeping genes, and genes encoding hypothetical and cell envelope proteins. Furthermore, serovar evolution also correlates with ecological success, as the two most successful serovars showed a parallel evolution.

Conclusion

We identified a single nucleotide polymorphism-based tissue-specific arms race for strains in the same species, reflecting global chromosomal dynamics. Studying such tissue-specific arms race scenarios is crucial for understanding pathogen-host interactions during the course of infectious diseases, in order to dissect pathogen biology and develop preventive and therapeutic strategies.