bluuebunny/crossref_metadata_2025 huggingface dataset:
Small islands and pandemic influenza: Potential benefits and limitations of travel volume reduction as a border control measure
Authors: Eichner Martin , Schwehm Markus , Wilson Nick , Baker Michael G
Published: September 2009

Background

Some island nations have explicit components of their influenza pandemic plans for providing travel warnings and restricting incoming travellers. But the potential value of such restrictions has not been quantified.

Methods

We developed a probabilistic model and used parameters from a published model (i.e., InfluSim) and travel data from Pacific Island Countries and Territories (PICTs).

Results

The results indicate that of the 17 PICTs with travel data, only six would be likely to escape a major pandemic with a viral strain of relatively low contagiousness (i.e., for R
0 = 1.5) even when imposing very tight travel volume reductions of 99% throughout the course of the pandemic. For a more contagious viral strain (R
0 = 2.25) only five PICTs would have a probability of over 50% to escape. The total number of travellers during the pandemic must not exceed 115 (for R
0 = 3.0) or 380 (for R
0 = 1.5) if a PICT aims to keep the probability of pandemic arrival below 50%.

Conclusion

These results suggest that relatively few island nations could successfully rely on intensive travel volume restrictions alone to avoid the arrival of pandemic influenza (or subsequent waves). Therefore most island nations may need to plan for multiple additional interventions (e.g., screening and quarantine) to raise the probability of remaining pandemic free or achieving substantial delay in pandemic arrival.
Gastric cancer mortality trends in Spain, 1976-2005, differences by autonomous region and sex
Authors: García-Esquinas Esther , Pérez-Gómez Beatriz , Pollán Marina , Boldo Elena , Fernández-Navarro Pablo , Lope Virginia , Vidal Enrique , López-Abente Gonzalo , Aragonés Nuria
Published: September 2009

Background

Gastric cancer is the second leading cause of oncologic death worldwide. One of the most noteworthy characteristics of this tumor's epidemiology is the marked decline reported in its incidence and mortality in almost every part of the globe in recent decades. This study sought to describe gastric cancer mortality time trends in Spain's regions for both sexes.

Methods

Mortality data for the period 1976 through 2005 were obtained from the Spanish National Statistics Institute. Cases were identified using the International Classification of Diseases 9th and 10th revision (codes 151 and C16, respectively). Crude and standardized mortality rates were calculated by geographic area, sex, and five-year period. Joinpoint regression analyses were performed to ascertain whether changes in gastric cancer mortality trends had occurred, and to estimate the annual percent change by sex and geographic area.

Results

Gastric cancer mortality decreased across the study period, with the downward trend being most pronounced in women and in certain regions situated in the interior and north of mainland Spain. Across the study period, there was an overall decrease of 2.90% per annum among men and 3.65% per annum among women. Generally, regions in which the rate of decline was sharpest were those that had initially registered the highest rates. However, the rate of decline was not constant throughout the study period: joinpoint analysis detected a shift in trend for both sexes in the early 1980s.

Conclusion

Gastric cancer mortality displayed in both sexes a downward trend during the study period, both nationally and regionally. The different trend in rates in the respective geographic areas translated as greater regional homogeneity in gastric cancer mortality by the end of the study period. In contrast, rates in women fell more than did those in men. The increasing differences between the sexes could indicate that some risk factors may be modifying the sex-specific pattern of this tumor.
Diagonal ear lobe crease in diabetic south Indian population: Is it associated with Diabetic Retinopathy?. Sankara Nethralaya Diabetic Retinopathy Epidemiology And Molecular-genetics Study (SN-DREAMS, Report no. 3)
Authors: Raman Rajiv , Rani Padmaja Kumari , Kulothungan Vaitheeswaran , Sharma Tarun
Published: September 2009

Background

To report the prevalence of ear lobe crease (ELC), a sign of coronary heart disease, in subjects (more than 40 years old) with diabetes and find its association with diabetic retinopathy.

Methods

Subjects were recruited from the Sankara Nethralaya Diabetic Retinopathy Epidemiology And Molecular-genetics Study (SN-DREAMS), a cross-sectional study between 2003 and 2006; the data were analyzed for the1414 eligible subjects with diabetes. All patients' fundi were photographed using 45° four-field stereoscopic digital photography. The diagnosis of diabetic retinopathy was based on the modified Klein classification. The presence of ELC was evaluated on physical examination.

Results

The prevalence of ELC, among the subjects with diabetes, was 59.7%. The ELC group were older, had longer duration of diabetes, had poor glycemic control and had a high socio-economic status compared to the group without ELC and the variables were statistically significant. There was no statistical difference in the prevalence of diabetic retinopathy in two groups. On multivariate analysis for any diabetic retinopathy, the adjusted OR for women was 0.69 (95% CI 0.51-0.93) (p = 0.014); for age >70 years, 0.49 (95% CI 0.26-0.89) (p = 0.024); for increasing duration of diabetes (per year increase), 1.11(95% CI 1.09-1.14) (p < 0.0001); and for poor glycemic control (per unit increase in glycosylated heamoglobin), 1.26 (95% CI 1.19-1.35) (p < 0.0001). For sight-threatening diabetic retinopathy, no variable was significant on multivariable analysis. In predicting any diabetic retinopathy, the presence of ELC had sensitivity of 60.4%, and specificity, 40.5%. The area under the ROC curve was 0.50 (95% CI 0.46-0.54) (p 0.02).

Conclusion

The ELC was observed in nearly 60% of the urban south Indian population. However, the present study does not support the use of ELC as a screening tool for both any diabetic retinopathy and sight-threatening retinopathy.
Self-Rated Health in middle-aged and elderly Chinese: distribution, determinants and associations with cardio-metabolic risk factors
Authors: Haseli-Mashhadi Nazanin , Pan An , Ye Xingwang , Wang Jing , Qi Qibin , Liu Yong , Li Huaixing , Yu Zhijie , Lin Xu , Franco Oscar H
Published: September 2009

Background

Self-rated health (SRH) has been demonstrated to be an accurate reflection of a person's health and a valid predictor of incident mortality and chronic morbidity. We aimed to evaluate the distribution and factors associated with SRH and its association with biomarkers of cardio-metabolic diseases among middle-aged and elderly Chinese.

Methods

Survey of 1,458 men and 1,831 women aged 50 to 70 years, conducted in one urban and two rural areas of Beijing and Shanghai in 2005. SRH status was measured and categorized as good (very good and good) vs. not good (fair, poor and very poor). Determinants of SRH and associations with biomarkers of cardio-metabolic diseases were evaluated using logistic regression.

Results

Thirty two percent of participants reported good SRH. Males and rural residents tended to report good SRH. After adjusting for potential confounders, residence, physical activity, employment status, sleep quality and presence of diabetes, cardiovascular disease, and depression were the main determinants of SRH. Those free from cardiovascular disease (OR 3.68; 95%CI 2.39; 5.66), rural residents (OR 1.89; 95% CI 1.47; 2.43), non-depressed participants (OR 2.50; 95% CI 1.67; 3.73) and those with good sleep quality (OR 2.95; 95% CI 2.22; 3.91) had almost twice or over the chance of reporting good SRH compared to their counterparts. There were significant associations -and trend- between SRH and levels of inflammatory markers, insulin levels and insulin resistance.

Conclusion

Only one third of middle-aged and elderly Chinese assessed their health status as good or very good. Although further longitudinal studies are required to confirm our findings, interventions targeting social inequalities, lifestyle patterns might not only contribute to prevent chronic morbidity but as well to improve populations' perceived health.
Structural and functional characteristics of xenavidin, the first frog avidin from Xenopus tropicalis
Authors: Määttä Juha AE , Helppolainen Satu H , Hytönen Vesa P , Johnson Mark S , Kulomaa Markku S , Airenne Tomi T , Nordlund Henri R
Published: September 2009

Background

Avidins are proteins with extraordinarily high ligand-binding affinity, a property which is used in a wide array of life science applications. Even though useful for biotechnology and nanotechnology, the biological function of avidins is not fully understood. Here we structurally and functionally characterise a novel avidin named xenavidin, which is to our knowledge the first reported avidin from a frog.

Results

Xenavidin was identified from an EST sequence database forXenopus tropicalisand produced in insect cells using a baculovirus expression system. The recombinant xenavidin was found to be homotetrameric based on gel filtration analysis. Biacore sensor analysis, fluorescently labelled biotin and radioactive biotin were used to evaluate the biotin-binding properties of xenavidin - it binds biotin with high affinity though less tightly than do chicken avidin and bacterial streptavidin. X-ray crystallography revealed structural conservation around the ligand-binding site, while some of the loop regions have a unique design. The location of structural water molecules at the entrance and/or within the ligand-binding site may have a role in determining the characteristic biotin-binding properties of xenavidin.

Conclusion

The novel data reported here provide information about the biochemically and structurally important determinants of biotin binding. This information may facilitate the discovery of novel tools for biotechnology.
Quantitative data management in quality improvement collaboratives
Authors: van den Berg Mireille , Frenken Rianne , Bal Roland
Published: September 2009

Background

Collaborative approaches in quality improvement have been promoted since the introduction of the Breakthrough method. The effectiveness of this method is inconclusive and further independent evaluation of the method has been called for. For any evaluation to succeed, data collection on interventions performed within the collaborative and outcomes of those interventions is crucial. Getting enough data from Quality Improvement Collaboratives (QICs) for evaluation purposes, however, has proved to be difficult. This paper provides a retrospective analysis on the process of data management in a Dutch Quality Improvement Collaborative. From this analysis general failure and success factors are identified.

Discussion

This paper discusses complications and dilemma's observed in the set-up of data management for QICs. An overview is presented of signals that were picked up by the data management team. These signals were used to improve the strategies for data management during the program and have, as far as possible, been translated into practical solutions that have been successfully implemented.

The recommendations coming from this study are:

From our experience it is clear that quality improvement programs deviate from experimental research in many ways. It is not only impossible, but also undesirable to control processes and standardize data streams. QIC's need to be clear of data protocols that do not allow for change. It is therefore minimally important that when quantitative results are gathered, these results are accompanied by qualitative results that can be used to correctly interpret them.

Monitoring and data acquisition interfere with routine. This makes a database collecting data in a QIC an intervention in itself. It is very important to be aware of this in reporting the results. Using existing databases when possible can overcome some of these problems but is often not possible given the change objective of QICs.

Introducing a standardized spreadsheet to the teams is a very practical and helpful tool in collecting standardized data within a QIC. It is vital that the spreadsheets are handed out before baseline measurements start.
Increased expression of the oxidative pentose phosphate pathway and gluconeogenesis in anaerobically growing xylose-utilizing Saccharomyces cerevisiae
Authors: Runquist David , Hahn-Hägerdal Bärbel , Bettiga Maurizio
Published: September 2009

Background

Fermentation of xylose to ethanol has been achieved in S. cerevisiae by genetic engineering. Xylose utilization is however slow compared to glucose, and during anaerobic conditions addition of glucose has been necessary for cellular growth. In the current study, the xylose-utilizing strain TMB 3415 was employed to investigate differences between anaerobic utilization of glucose and xylose. This strain carried a xylose reductase (XYL1 K270R) engineered for increased NADH utilization and was capable of sustained anaerobic growth on xylose as sole carbon source. Metabolic and transcriptional characterization could thus for the first time be performed without addition of a co-substrate or oxygen.

Results

Analysis of metabolic fluxes showed that although the specific ethanol productivity was an order of magnitude lower on xylose than on glucose, product yields were similar for the two substrates. In addition, transcription analysis identified clear regulatory differences between glucose and xylose. Respiro-fermentative metabolism on glucose during aerobic conditions caused repression of cellular respiration, while metabolism on xylose under the same conditions was fully respiratory. During anaerobic conditions, xylose repressed respiratory pathways, although notably more weakly than glucose. It was also observed that anaerobic xylose growth caused up-regulation of the oxidative pentose phosphate pathway and gluconeogenesis, which may be driven by an increased demand for NADPH during anaerobic xylose catabolism.

Conclusion

Co-factor imbalance in the initial twp steps of xylose utilization may reduce ethanol productivity by increasing the need for NADP+ reduction and consequently increase reverse flux in glycolysis.
Spatial trends of breast and prostate cancers in the United States between 2000 and 2005
Authors: Mandal Rakesh , St-Hilaire Sophie , Kie John G , Derryberry DeWayne
Published: September 2009

Background

Breast cancer in females and prostate cancer in males are two of the most common cancers in the United States, and the literature suggests that they share similar features. However, it is unknown whether the occurrence of these two cancers at the county level in the United States is correlated. We analyzed Caucasian age-adjusted county level average annual incidence rates for breast and prostate cancers from the National Cancer Institute and State Cancer Registries to determine whether there was a spatial correlation between the two conditions and whether the two cancers had similar spatial patterns.

Results

There was a significant correlation between breast and prostate cancers by county (r = 0.332, p < 0.001). This relationship was more pronounced when we performed a geographically-weighted regression (GWR) analysis (r = 0.552) adjusting for county unemployment rates. There was variation in the parameter estimates derived with the GWR; however, the majority of the estimates indicted a positive association. The strongest relationship between breast and prostate cancer was in the eastern parts of the Midwest and South, and the Southeastern U.S. We also observed a north-south pattern for both cancers with our cluster analyses. Clusters of counties with high cancer incidence rates were more frequently found in the North and clusters of counties with low incidence rates were predominantly in the South.

Conclusion

Our analyses suggest breast and prostate cancers cluster spatially. This finding corroborates other studies that have found these two cancers share similar risk factors. The north-south distribution observed for both cancers warrants further research to determine what is driving this spatial pattern.
The rapamycin-regulated gene expression signature determines prognosis for breast cancer
Authors: Akcakanat Argun , Zhang Li , Tsavachidis Spiridon , Meric-Bernstam Funda
Published: September 2009

Background

Mammalian target of rapamycin (mTOR) is a serine/threonine kinase involved in multiple intracellular signaling pathways promoting tumor growth. mTOR is aberrantly activated in a significant portion of breast cancers and is a promising target for treatment. Rapamycin and its analogues are in clinical trials for breast cancer treatment. Patterns of gene expression (metagenes) may also be used to simulate a biologic process or effects of a drug treatment. In this study, we tested the hypothesis that the gene-expression signature regulated by rapamycin could predict disease outcome for patients with breast cancer.

Results

Colony formation and sulforhodamine B (IC50 < 1 nM) assays, and xenograft animals showed that MDA-MB-468 cells were sensitive to treatment with rapamycin. The comparison of in vitro and in vivo gene expression data identified a signature, termed rapamycin metagene index (RMI), of 31 genes upregulated by rapamycin treatment in vitro as well as in vivo (false discovery rate of 10%). In the Miller dataset, RMI did not correlate with tumor size or lymph node status. High (>75th percentile) RMI was significantly associated with longer survival (P = 0.015). On multivariate analysis, RMI (P = 0.029), tumor size (P = 0.015) and lymph node status (P = 0.001) were prognostic. In van 't Veer study, RMI was not associated with the time to develop distant metastasis (P = 0.41). In the Wang dataset, RMI predicted time to disease relapse (P = 0.009).

Conclusion

Rapamycin-regulated gene expression signature predicts clinical outcome in breast cancer. This supports the central role of mTOR signaling in breast cancer biology and provides further impetus to pursue mTOR-targeted therapies for breast cancer treatment.
Blockage of transdifferentiation from fibroblast to myofibroblast in experimental ovarian cancer models
Authors: Yao Qin , Qu Xun , Yang Qifeng , Good David A , Dai Shuzhen , Kong Beihua , Wei Ming Q
Published: September 2009

Background

Tumour stromal myofibroblasts can promote tumour invasion. As these cells are genetically more stable than cancer cells, there has been enormous interest in developing targeted molecular therapies against them. Chloride intracellular channel 4 (CLIC4) and reactive oxygen species (ROS) have been linked with promoting stromal cell transdifferentiation in various cancers, but little is known of their roles in ovarian cancer. In this study, we examined the functional roles that both CLIC4 and ROS play in the process of ovarian cancer cell-stimulated or TGF-β1 induced fibroblast-to-myofibroblast transdifferentiation. We also examine whether it is possible to reverse such a process, with the aim of developing novel therapies against ovarian cancer by targeting activated transdifferentiated myofibroblasts.

Results

We demonstrate that TGF-β1 induced or CMSKOV3 activate transdifferentiated myofibroblasts (fibroblasts). These fibroblasts mimic "reactive" stromal myofibroblasts and demonstrate significant up-regulation of CLIC4 expression and increased level of ROS production. Blocking the production of ROS with an antioxidant consequently reduces the expression of CLIC4, and is accompanied by disappearance of α-smooth-muscle actin (α-SMA), a myofibroblast marker, suggesting ROS acts as a signalling molecule that promotes and enhances CLIC4 activities in the myofibroblast transdifferentiaton process. Down-regulation of CLIC4 with a generic agent or specific siRNA both significantly reduces the expression of factors related to the phenotypes and functions of myofibroblasts, such as α-SMA, hepatocyte growth factor (HGF) and vascular endothelial growth factor (VEGF), thus reversing the myofibroblast phenotype back to fibroblasts. These results convincingly show that ROS and CLIC4 are responsible for TGF-β1 induced fibroblast-to-myofibroblast transdifferentiaton and down-regulation of both is sufficient to block transdifferentiated myofibroblasts.

Conclusion

Molecular targeting of ROS and CLIC4 has the potential to develop novel therapies for ovarian cancer.
2-DE analysis indicates that Acinetobacter baumannii displays a robust and versatile metabolism
Authors: Soares Nelson C , Cabral Maria P , Parreira José R , Gayoso Carmen , Barba Maria J , Bou Germán
Published: September 2009

Background

Acinetobacter baumannii is a nosocomial pathogen that has been associated with outbreak infections in hospitals. Despite increasing awareness about this bacterium, its proteome remains poorly characterised, however recently the complete genome of A. baumannii reference strain ATCC 17978 has been sequenced. Here, we have used 2-DE and MALDI-TOF/TOF approach to characterise the proteome of this strain.

Results

The membrane and cytoplasmatic protein extracts were analysed separately, these analyses revealed the reproducible presence of 239 and 511 membrane and cytoplamatic protein spots, respectively. MALDI-TOF/TOF characterisation identified a total of 192 protein spots (37 membrane and 155 cytoplasmatic) and revealed that the identified membrane proteins were mainly transport-related proteins, whereas the cytoplasmatic proteins were of diverse nature, although mainly related to metabolic processes.

Conclusion

This work indicates that A. baumannii has a versatile and robust metabolism and also reveal a number of proteins that may play a key role in the mechanism of drug resistance and virulence. The data obtained complements earlier reports of A. baumannii proteome and provides new tools to increase our knowledge on the protein expression profile of this pathogen.
c-Myc affects mRNA translation, cell proliferation and progenitor cell function in the mammary gland
Authors: Stoelzle Tina , Schwarb Patrick , Trumpp Andreas , Hynes Nancy E
Published: September 2009

Background

The oncoprotein c-Myc has been intensely studied in breast cancer and mouse mammary tumor models, but relatively little is known about the normal physiological role of c-Myc in the mammary gland. Here we investigated functions of c-Myc during mouse mammary gland development using a conditional knockout approach.

Results

Generation of c-myc

fl/fl
mice carrying the mammary gland-specific WAPiCre transgene resulted in c-Myc loss in alveolar epithelial cells starting in mid-pregnancy. Three major phenotypes were observed in glands of mutant mice. First, c-Myc-deficient alveolar cells had a slower proliferative response at the start of pregnancy, causing a delay but not a block of alveolar development. Second, while milk composition was comparable between wild type and mutant animals, milk production was reduced in mutant glands, leading to slower pup weight-gain. Electron microscopy and polysome fractionation revealed a general decrease in translational efficiency. Furthermore, analysis of mRNA distribution along the polysome gradient demonstrated that this effect was specific for mRNAs whose protein products are involved in milk synthesis. Moreover, quantitative reverse transcription-polymerase chain reaction analysis revealed decreased levels of ribosomal RNAs and ribosomal protein-encoding mRNAs in mutant glands. Third, using the mammary transplantation technique to functionally identify alveolar progenitor cells, we observed that the mutant epithelium has a reduced ability to repopulate the gland when transplanted into NOD/SCID recipients.

Conclusion

We have demonstrated that c-Myc plays multiple roles in the mouse mammary gland during pregnancy and lactation. c-Myc loss delayed, but did not block proliferation and differentiation in pregnancy. During lactation, lower levels of ribosomal RNAs and proteins were present and translation was generally decreased in mutant glands. Finally, the transplantation studies suggest a role for c-Myc in progenitor cell proliferation and/or survival.

See related minireview by Evan et al: http://jbiol.com/content/8/8/77
Two matched filters and the evolution of mating signals in four species of cricket
Authors: Kostarakos Konstantinos , Hennig Matthias R , Römer Heiner
Published: September 2009

Background

Male field crickets produce pure-tone calling songs to attract females. Receivers are expected to have evolved a "matched filter" in the form of a tuned sensitivity for this frequency. In addition, the peripheral directionality of field crickets is sharply tuned as a result of a pressure difference receiver. We studied both forms of tuning in the same individuals of four species of cricket, where Gryllus bimaculatus and G. campestris are largely allopatric, whereas Teleogryllus oceanicus and T. commodus occur also sympatrically.

Results

The sharpness of the sensitivity filter is highest for T. commodus, which also exhibits low interindividual variability. Individual receivers may also vary strongly in the best frequency for directional hearing. In G. campestris, such best frequencies occur even at frequencies outside the range of carrier frequencies of males. Contrary to the predictions from the "matched filter hypothesis", in three of the four species the frequency optima of the two involved filters are not matched to each other, and the mismatch can amount to 1.2 kHz. The mean carrier frequency of the male population is between the frequency optima of both filters in three species. Only in T. commodus we found a match between both filters and the male carrier frequency.

Conclusion

Our results show that a mismatch between the sensitivity and directionality tuning is not uncommon in crickets, and an observed match (T. commodus) appears to be the exception rather than the rule. The data suggests that independent variation of both filters is possible. During evolution each sensory task may have been driven by independent constraints, and may have evolved towards its own respective optimum.
Induction of cell-cell fusion by ectromelia virus is not inhibited by its fusion inhibitory complex
Authors: Erez Noam , Paran Nir , Maik-Rachline Galia , Politi Boaz , Israely Tomer , Schnider Paula , Fuchs Pinhas , Melamed Sharon , Lustig Shlomo
Published: September 2009

Background

Ectromelia virus, a member of the Orthopox genus, is the causative agent of the highly infectious mousepox disease. Previous studies have shown that different poxviruses induce cell-cell fusion which is manifested by the formation of multinucleated-giant cells (polykaryocytes). This phenomenon has been widely studied with vaccinia virus in conditions which require artificial acidification of the medium.

Results

We show that Ectromelia virus induces cell-cell fusion under neutral pH conditions and requires the presence of a sufficient amount of viral particles on the plasma membrane of infected cells. This could be achieved by infection with a replicating virus and its propagation in infected cells (fusion "from within") or by infection with a high amount of virus particles per cell (fusion "from without"). Inhibition of virus maturation or inhibition of virus transport on microtubules towards the plasma membrane resulted in a complete inhibition of syncytia formation. We show that in contrast to vaccinia virus, Ectromelia virus induces cell-cell fusion irrespectively of its hemagglutination properties and cell-surface expression of the orthologs of the fusion inhibitory complex, A56 and K2. Additionally, cell-cell fusion was also detected in mice lungs following lethal respiratory infection.

Conclusion

Ectromelia virus induces spontaneous cell-cell fusion in-vitro and in-vivo although expressing an A56/K2 fusion inhibitory complex. This syncytia formation property cannot be attributed to the 37 amino acid deletion in ECTV A56.
Use of dried blood samples for monitoring hepatitis B virus infection
Authors: Lira Rosalia , Maldonado-Rodriguez Angelica , Rojas-Montes Othon , Ruiz-Tachiquin Martha , Torres-Ibarra Rocio , Cano-Dominguez Carlos , Valdez-Salazar Hilda , Gomez-Delgado Alejandro , Muñoz Onofre , Alvarez-Muñoz Ma-Teresa
Published: September 2009

Background

Hepatitis B virus (HBV) infection is a problem in several regions of the world with limited resources. Blood samples dried on filter paper (DBS) have been successfully used to diagnose and monitor several infectious diseases. In Mexico there is an urgent need for an affordable and easy sampling method for viral load (VL) testing and monitoring of chronic HBV infection. The purpose of this work was to validate the utility of DBS samples for monitoring HBV infection in patients from Mexico City.

Methods

Matched samples of plasma and DBS on filter paper from 47 HBV infected patients from the Instituto Mexicano del Seguro Social (IMSS), were included. To evaluate the DNA stability and purity from DBS stored at different temperature conditions, samples from ten patients were stored at 4 degree, 25 degree, and 37 degree C for 7 days. After DBS elution and DNA extraction, the purity of these samples was determined measuring the O.D. rate 260/280. The DBS utility for molecular studies was assessed with PCR assays to amplify a 322 bp fragment from the "a" determinant region of the HBV "S" gene. The VL from all samples was determined to evaluate the correlation between plasma and DBS matched samples.

Results

The quality of the DNA from DBS specimen is not adversely affected by storage at 4 degree, 25 degree and 37 degree C for up 7 days. Statistical ANOVA analyses did not show any significant difference. The same amplification efficiency was observed between DNA templates from samples stored at different temperatures. The Pearson correlation between the VL from DBS and plasma matched samples was 0.93 (p = 0.01). The SD was 1.48 for DBS vs.1.32 for Plasma, and an average of log10copies/mL of 5.32 vs. 5.53. ANOVA analysis did not show any statistically significant difference between the analyzed groups (p = 0.92).

Conclusion

The results provide strong evidence that the isolation and quantification of DNA-HBV from DBS is a viable alternative for patient monitoring, and molecular characterization of the virus variants circulating in Mexico.
Multipathogen infections in hospitalized children with acute respiratory infections
Authors: Peng Dan , Zhao Dongchi , Liu Jingtao , Wang Xia , Yang Kun , Xicheng Hong , Li Yang , Wang Fubing
Published: September 2009

Background

To explore the epidemiologic and clinical features of, and interactions among, multipathogen infections in hospitalized children with acute respiratory tract infection (ARTI). A prospective study of children admitted with ARTI was conducted. Peripheral blood samples were analyzed by indirect immunofluorescence to detect respiratory agents including respiratory syncytial virus; adenovirus; influenza virus (Flu) types A and B; parainfluenza virus (PIV) types 1, 2, and 3; chlamydia pneumonia; and mycoplasma pneumonia. A medical history of each child was taken.

Results

Respiratory agents were detected in 164 (51.9%) of 316 children with ARTI. A single agent was identified in 50 (15.8%) children, and multiple agents in 114 (36.1%). Flu A was the most frequently detected agent, followed by Flu B. Coinfection occurred predominantly in August and was more frequent in children between 3 and 6 years of age. A significantly higher proportion of Flu A, Flu B, and PIV 1 was detected in samples with two or more pathogens per sample than in samples with a single pathogen.

Conclusion

Our study suggests that there is a high occurrence of multipathogen infections in children admitted with ARTI and that coinfection is associated with certain pathogens.
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling
Authors: Wittmann Dominik M , Krumsiek Jan , Saez-Rodriguez Julio , Lauffenburger Douglas A , Klamt Steffen , Theis Fabian J
Published: September 2009

Background

The understanding of regulatory and signaling networks has long been a core objective in Systems Biology. Knowledge about these networks is mainly of qualitative nature, which allows the construction of Boolean models, where the state of a component is either 'off' or 'on'. While often able to capture the essential behavior of a network, these models can never reproduce detailed time courses of concentration levels.

Nowadays however, experiments yield more and more quantitative data. An obvious question therefore is how qualitative models can be used to explain and predict the outcome of these experiments.

Results

In this contribution we present a canonical way of transforming Boolean into continuous models, where the use of multivariate polynomial interpolation allows transformation of logic operations into a system of ordinary differential equations (ODE). The method is standardized and can readily be applied to large networks. Other, more limited approaches to this task are briefly reviewed and compared. Moreover, we discuss and generalize existing theoretical results on the relation between Boolean and continuous models. As a test case a logical model is transformed into an extensive continuous ODE model describing the activation of T-cells. We discuss how parameters for this model can be determined such that quantitative experimental results are explained and predicted, including time-courses for multiple ligand concentrations and binding affinities of different ligands. This shows that from the continuous model we may obtain biological insights not evident from the discrete one.

Conclusion

The presented approach will facilitate the interaction between modeling and experiments. Moreover, it provides a straightforward way to apply quantitative analysis methods to qualitatively described systems.
Puncture mechanics of cnidarian cnidocysts: a natural actuator
Authors: Oppegard Shawn C , Anderson Peter A , Eddington David T
Published: September 2009

Background

Cnidocysts isolated from cnidarian organisms are attractive as a drug-delivery platform due to their fast, efficient delivery of toxins. The cnidocyst could be utilized as the means to deliver therapeutics in a wearable drug-delivery patch. Cnidocysts have been previously shown to discharge upon stimulation via electrical, mechanical, and chemical pathways. Cnidocysts isolated from the Portuguese Man O' War jellyfish (Physalia physalis) are attractive for this purpose because they possess relatively long threads, are capable of puncturing through hard fish scales, and are stable for years.

Results

As a first step in using cnidocysts as a functional component of a drug delivery system, the puncture mechanics of the thread were characterized. Tentacle-contained cnidocysts were used as a best-case scenario due to physical immobilization of the cnidocysts within the tentacle. Ex vivo tentacle-contained cnidocysts from Physalia possessed an elastic modulus puncture threshold of approximately 1-2 MPa, based on puncture tests of materials with a gamut of hardness. Also, a method for inducing discharge of isolated cnidocysts was found, utilizing water as the stimulant. Preliminary lectin-binding experiments were performed using fluorophore-conjugated lectins as a possible means to immobilize the isolated cnidocyst capsule, and prevent reorientation upon triggering. Lectins bound homogeneously to the surface of the capsule, suggesting the lectins could be used for cnidocyst immobilization but not orientation.

Conclusion

Cnidocysts were found to puncture materials up to 1 MPa in hardness, can be discharged in a dry state using water as a stimulant, and bind homogeneously to lectins, a potential means of immobilization. The information gained from this preliminary work will aid in determining the materials and design of the patch that could be used for drug delivery.
Management of synchronous adenocarcinoma of the esophago-gastric junction and ampulla of Vater: case report of a surgically challenging condition
Authors: Jayaprakash Namita , O'Kelly Fardod , Lim Kheng Tian , Reynolds John Vincent
Published: September 2009

We report herein a case of a synchronous presentation of an adenocarcinoma of esophagago-gastric junction type II and an ampullary tumor that was treated by combined Whipple's pancreaticoduodenectomy, total gastrectomy and esophagectomy. The magnitude of this operation was safely achieved with meticulous surgical techniques and perioperative care without any major short or long term complications. Patient returned to a good quality of life at six-month follow up with no further gastrointestinal symptoms or evidence of disease recurrence.
Candidate metastasis suppressor genes uncovered by array comparative genomic hybridization in a mouse allograft model of prostate cancer
Authors: Yi Yajun , Nandana Srinivas , Case Thomas , Nelson Colleen , Radmilovic Tatjana , Matusik Robert J , Tsuchiya Karen D
Published: September 2009

Background

The purpose of this study was to identify candidate metastasis suppressor genes from a mouse allograft model of prostate cancer (NE-10). This allograft model originally developed metastases by twelve weeks after implantation in male athymic nude mice, but lost the ability to metastasize after a number of in vivo passages. We performed high resolution array comparative genomic hybridization on the metastasizing and non-metastasizing allografts to identify chromosome imbalances that differed between the two groups of tumors.

Results

This analysis uncovered a deletion on chromosome 2 that differed between the metastasizing and non-metastasizing tumors. Bioinformatics filters were employed to mine this region of the genome for candidate metastasis suppressor genes. Of the 146 known genes that reside within the region of interest on mouse chromosome 2, four candidate metastasis suppressor genes (Slc27a2, Mall, Snrpb, and Rassf2) were identified. Quantitative expression analysis confirmed decreased expression of these genes in the metastasizing compared to non-metastasizing tumors.

Conclusion

This study presents combined genomics and bioinformatics approaches for identifying potential metastasis suppressor genes. The genes identified here are candidates for further studies to determine their functional role in inhibiting metastases in the NE-10 allograft model and human prostate cancer.
Synovial tissues concentrate secreted APRIL
Authors: Gabay Cem , Krenn Veit , Bosshard Carine , Seemayer Christian Alexander , Chizzolini Carlo , Huard Bertrand
Published: September 2009

Introduction

A proliferation-inducing ligand (APRIL) from the TNF family, owing to its role in the generation and survival of plasma cells (PCs), is currently targeted for rheumatoid arthritis (RA) treatment. However, little is known about APRIL expression in RA lesions, hampering our understanding of the way APRIL may modulate this autoimmune disease.

Methods

We performed immunological staining of human normal, non-RA and RA synovial tissues with a pair of antibodies specifically recognizing APRIL-producing cells and secreted APRIL.

Results

We detected significant amounts of secreted APRIL in normal synovium mostly concentrated around blood vessels and at the lining layer, but no cells producing APRIL. Meanwhile, we observed that blood neutrophils constitutively secrete APRIL, indicating that blood APRIL may diffuse into the synovium via its fenestrated vessels. Synovium from non-RA and RA patients retained similarly secreted APRIL, but in this case APRIL-producing cells, including neutrophils and macrophages, were present in the tissue. Notably, PCs - when present in RA synovium - accumulated in areas of APRIL retention, spreading from blood vessels towards the lining layer.

Conclusions

PCs accumulate in synovial zones rich in secreted APRIL, consistent with a pro-survival role of APRIL for PCs in RA. The concentration of APRIL by normal synovium indicates that this tissue may constitute a proper environment for PCs even before RA onset.
High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans
Authors: Ramani Arun K , Nelson Andrew C , Kapranov Philipp , Bell Ian , Gingeras Thomas R , Fraser Andrew G
Published: September 2009

Background

While many genome sequences are complete, transcriptomes are less well characterized. We used both genome-scale tiling arrays and massively parallel sequencing to map the Caenorhabditis elegans transcriptome across development. We utilized this framework to identify transcriptome changes in animals lacking the nonsense-mediated decay (NMD) pathway.

Results

We find that while the majority of detectable transcripts map to known gene structures, >5% of transcribed regions fall outside current gene annotations. We show that >40% of these are novel exons. Using both technologies to assess isoform complexity, we estimate that >17% of genes change isoform across development. Next we examined how the transcriptome is perturbed in animals lacking NMD. NMD prevents expression of truncated proteins by degrading transcripts containing premature termination codons. We find that approximately 20% of genes produce transcripts that appear to be NMD targets. While most of these arise from splicing errors, NMD targets are enriched for transcripts containing open reading frames upstream of the predicted translational start (uORFs). We identify a relationship between the Kozak consensus surrounding the true start codon and the degree to which uORF-containing transcripts are targeted by NMD and speculate that translational efficiency may be coupled to transcript turnover via the NMD pathway for some transcripts.

Conclusions

We generated a high-resolution transcriptome map for C. elegans and used it to identify endogenous targets of NMD. We find that these transcripts arise principally through splicing errors, strengthening the prevailing view that splicing and NMD are highly interlinked processes.
Role of Anthracyclines in the Treatment of Early Breast Cancer
Authors: Gianni Luca , Norton Larry , Wolmark Norman , Suter Thomas M. , Bonadonna Gianni , Hortobagyi Gabriel N.
Published: September 2009

Purpose

To review data relating to anthracyclines in the adjuvant treatment of early breast cancer.

Design

This is a report from a seminar in which the future of anthracyclines in the adjuvant treatment of breast cancer was considered. In particular, the question of whether anthracyclines should now be discarded and replaced by taxanes was addressed.

Results

Accumulating data from large randomized trials indicate that genetic markers may have a role in predicting sensitivity to cytotoxic drugs. However, no reliable, validated test is available for predicting sensitivity to anthracyclines in particular. Topoisomerase IIα amplification and/or deletion, especially in conjunction with human epidermal growth factor receptor-2 amplification, has been proposed to fulfill this role but more data are needed. Currently, only one published trial has shown that a taxane-based regimen may be superior to an anthracycline-based regimen, but several trials indicate that combinations including both anthracyclines and taxanes may be better still. Further studies aimed at optimizing anthracyclines and taxanes in combination, and integrating biologic agents, seem to be the way forward. There is no validated test that can determine whether anthracyclines can be of greater benefit than other agents for individual patients.

Conclusion

Anthracyclines have been extensively tested in clinical trials spanning several decades; currently, there are insufficient data to recommend replacing them in the adjuvant treatment of breast cancer.
Targeted High-Resolution Ultrasound Is Not an Effective Substitute for Sentinel Lymph Node Biopsy in Patients With Primary Cutaneous Melanoma
Authors: Sanki Amira , Uren Roger F. , Moncrieff Marc , Tran Kayla L. , Scolyer Richard A. , Lin Hui-Yi , Thompson John F.
Published: September 2009

Purpose

To reassess traditional ultrasound descriptors of sentinel lymph node (SLN) metastases, to determine the minimum cross-sectional area (CSA) of an SLN metastasis detectable by ultrasound (US), and to establish whether targeted, high-resolution US of SLNs identified by lymphoscintigraphy before initial melanoma surgery can be used as a substitute for excisional SLN biopsy.

Methods

US was performed on SLNs identified in 871 lymph node fields in 716 patients. SLN biopsy was performed within 24 hours of lymphoscintigraphy and US examination. The CSA of each SLN metastatic deposit was determined sonographically and histologically.

Results

The sensitivity of targeted US in the detection of positive SLNs was 24.3% (95% CI, 19.5% to 28.7%), and the specificity was 96.8% (95% CI, 95.9% to 97.7%). The sensitivity was highest for neck SLNs (45.8%) and improved with greater Breslow thickness. The median histologic CSA of the SLN metastatic deposits was 0.39 mm2 (12.75 mm2 for US true-positive results and 0.22 mm2 for US false-negative results). True-positive, US-detected SLNs had significantly greater CSAs (t test P < .001) than undetected SLN metastases and were more likely to be spherical in cross-section. More than two sonographic descriptors of SLN metastases or rounding of the node alone were factors highly suggestive of a melanoma deposit.

Conclusion

US is not an appropriate substitute for SLN biopsy, but it is of value in preoperative SLN assessment and postoperative monitoring.
Randomized Phase II/III Trial Assessing Gemcitabine/ Carboplatin and Methotrexate/Carboplatin/Vinblastine in Patients With Advanced Urothelial Cancer “Unfit” for Cisplatin-Based Chemotherapy: Phase II—Results of EORTC Study 30986
Authors: De Santis Maria , Bellmunt Joaquim , Mead Graham , Kerst J. Martijn , Leahy Michael , Maroto Pablo , Skoneczna Iwona , Marreaud Sandrine , de Wit Ronald , Sylvester Richard
Published: September 2009

Purpose

There is no standard treatment for patients with advanced urothelial cancer who are ineligible (“unfit”) for cisplatin-based chemotherapy (CHT). To compare the activity and safety of two CHT combinations in this patient group, a randomized phase II/III trial was conducted by the EORTC (European Organisation for Research and Treatment of Cancer). We report here the phase II results of the study.

Patients and Methods

CHT-naïve patients with measurable disease and impaired renal function (30 mL/min < glomerular filtration rate [GFR] < 60 mL/min) and/or performance status (PS) 2 were randomly assigned to receive either GC (gemcitabine 1,000 mg/m2 on days 1 and 8 and carboplatin area under the serum concentration-time curve [AUC] 4.5) for 21 days or M-CAVI (methotrexate 30 mg/m2 on days 1, 15, and 22; carboplatin AUC 4.5 on day 1; and vinblastine 3 mg/m2 on days 1, 15, and 22) for 28 days. End points of response and severe acute toxicity (SAT) were evaluated with respect to treatment group, renal function, PS, and Bajorin risk groups.

Results

Three of 178 patients who were ineligible or did not start treatment were excluded. SAT was reported in 13.6% of patients on GC and in 23% on M-CAVI. Overall response rates were 42% (37 of 88) for GC and 30% (26 of 87) for M-CAVI. Patients with PS 2 and GFR less than 60 mL/min and patients in Bajorin risk group 2 showed a response rate of only 26% and 20% and an SAT rate of 26% and 25%, respectively.

Conclusion

Both combinations are active in this group of unfit patients. However, patients with PS 2 and GFR less than 60 mL/min do not benefit from combination CHT. Alternative treatment modalities should be sought in this subgroup of poor-risk patients.