The effects of aging on dopaminergic neurotransmission: a microPET study of [11C]-raclopride binding in the aged rodent brain

Rodent models are frequently used in aging research to investigate biochemical age effects and aid in the development of therapies for pathological and non-pathological age-related degenerative processes. In order to validate the use of animal models in aging research and pave the way for longitudinal intervention-based animal studies, the consistency of cerebral aging processes across species needs to be evaluated. The dopaminergic system seems particularly susceptible to the aging process, and one of the most consistent findings in human brain aging research is a decline in striatal D2-like receptor (D2R) availability, quantifiable by positron emission tomography (PET) imaging. In this study, we aimed to assess whether similar age effects can be discerned in rat brains, using in vivo molecular imaging with the radioactive compound [(11)C]-raclopride. We observed a robust decline in striatal [(11)C]-raclopride uptake in the aged rats in comparison to the young control group, comprising a 41% decrement in striatal binding potential. In accordance with human studies, these results indicate that substantial reductions in D2R availability can be measured in the aged striatal complex. Our findings suggest that rat and human brains exhibit similar biochemical alterations with age in the striatal dopaminergic system, providing support for the pertinence of rodent models in aging research.

Surveillance of norovirus infections in the state of Rio De Janeiro, Brazil 2005-2008

A 4-year (2005-2008) norovirus (NoV) surveillance study was conducted in the state of Rio Janeiro, Brazil, to demonstrate the role of these viruses in outbreaks and sporadic cases of acute gastroenteritis. A cohort of 1,687 fecal samples was obtained from patients with gastroenteritis; 324 were rotavirus-positive. Of the remainder 1,363 rotavirus-negative samples, 1,087 samples were tested for NoV RNA in this study. The study enrolled 267 outpatients from Municipal Public Health Centers and 820 inpatients, whose samples were obtained by active surveillance in Public Hospitals. Fecal samples were tested by reverse transcription (RT) followed by polymerase chain reaction (PCR) using the MON 431-434 set of degenerate primers for NoV GI and GII detection, and there were 35.1% (381/1,087) positive samples for NoV, consisting of 30.2% (248/820) and 49.8% (133/267) from inpatient and outpatient, respectively. Children infected by NoV had significantly more frequent mucus in feces, vomiting and fever. No seasonal pattern in NoV infections was observed in patients admitted to hospital; however, two peaks of NoV infections were observed from ambulatory cases, suggesting that there was an occurrence of outbreaks in those time periods. Molecular characterization revealed GII to be the most prevalent genogroup, totaling 96.3% (104/108) of all sequences analyzed, and GII.4 was the genotype detected most frequently (80.7%), followed by GII.6, 3, 14, 7, and 8. Two GI strains, GI.2 and GI.3, were also observed. The number of outbreaks and sporadic cases described in this study highlights the need to implement diagnosis of NoV in surveillance laboratories.

AIBench: a rapid application development framework for translational research in biomedicine

Applied research in both biomedical discovery and translational medicine today often requires the rapid development of fully featured applications containing both advanced and specific functionalities, for real use in practice. In this context, new tools are demanded that allow for efficient generation, deployment and reutilization of such biomedical applications as well as their associated functionalities. In this context this paper presents AIBench, an open-source Java desktop application framework for scientific software development with the goal of providing support to both fundamental and applied research in the domain of translational biomedicine. AIBench incorporates a powerful plug-in engine, a flexible scripting platform and takes advantage of Java annotations, reflection and various design principles in order to make it easy to use, lightweight and non-intrusive. By following a basic input-processing-output life cycle, it is possible to fully develop multiplatform applications using only three types of concepts: operations, data-types and views. The framework automatically provides functionalities that are present in a typical scientific application including user parameter definition, logging facilities, multi-threading execution, experiment repeatability and user interface workflow management, among others. The proposed framework architecture defines a reusable component model which also allows assembling new applications by the reuse of libraries from past projects or third-party software.

OptFlux: an open-source software platform for in silico metabolic engineering

Background

Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications.

Results

OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using the methods of Flux Balance Analysis, Minimization of Metabolic Adjustment or Regulatory on/off Minimization of Metabolic flux changes, (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes.

OptFlux also contemplates several methods for model simplification and other pre-processing operations aimed at reducing the search space for optimization algorithms.

The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition of simulation results with the model graph.

Conclusions

The OptFlux software is freely available, together with documentation and other resources, thus bridging the gap from research in strain optimization algorithms and the final users. It is a valuable platform for researchers in the field that have available a number of useful tools. Its open-source nature invites contributions by all those interested in making their methods available for the community.

Given its plug-in based architecture it can be extended with new functionalities. Currently, several plug-ins are being developed, including network topology analysis tools and the integration with Boolean network based regulatory models.

Oxidative stress and mitochondrial dysfunction in atherosclerosis: mitochondria-targeted antioxidants as potential therapy

Chronic and acute overproduction of reactive oxygen species (ROS) under pathophysiologic conditions forms an integral part of the development of cardiovascular diseases (CVD), and in particular atherosclerosis. These ROS are released from different sources, such as xanthine oxidase, lipoxygenase, nicotinamide adenine dinucleotide phosphate oxidase, the uncoupling of nitric oxide synthase and, in particular, mitochondria. Endothelial dysfunction, characterized by a loss of nitric oxide (NO) bioactivity, occurs early on in the development of atherosclerosis, and determines future vascular complications. Although the molecular mechanisms responsible for mitochondria-mediated disease processes are not clear, oxidative stress seems to play an important role. In general, ROS are essential to cell function, but adequate levels of antioxidant defenses are required in order to avoid the harmful effects of excessive ROS production. Mitochondrial oxidative stress damage and dysfunction contribute to a number of cell pathologies that manifest themselves through a range of conditions. This review considers the process of atherosclerosis from a mitochondrial perspective, and assesses strategies for the targeted delivery of antioxidants to mitochondria that are currently under development. We will provide a summary of the following areas: the cellular metabolism of reactive oxygen species (ROS) and its role in pathophysiological processes such as atherosclerosis; currently available antioxidants and possible reasons for their efficacy and inefficacy in ameliorating oxidative stress-mediated diseases; and recent developments in mitochondrially-targeted antioxidants that concentrate on the matrix-facing surface of the inner mitochondrial membrane in order to protect against mitochondrial oxidative damage, and their therapeutic potential as a treatment for atherosclerosis.

@Note: a workbench for biomedical text mining

Biomedical Text Mining (BioTM) is providing valuable approaches to the automated curation of scientific literature. However, most efforts have addressed the benchmarking of new algorithms rather than user operational needs. Bridging the gap between BioTM researchers and biologists' needs is crucial to solve real-world problems and promote further research. We present @Note, a platform for BioTM that aims at the effective translation of the advances between three distinct classes of users: biologists, text miners and software developers. Its main functional contributions are the ability to process abstracts and full-texts; an information retrieval module enabling PubMed search and journal crawling; a pre-processing module with PDF-to-text conversion, tokenisation and stopword removal; a semantic annotation schema; a lexicon-based annotator; a user-friendly annotation view that allows to correct annotations and a Text Mining Module supporting dataset preparation and algorithm evaluation. @Note improves the interoperability, modularity and flexibility when integrating in-home and open-source third-party components. Its component-based architecture allows the rapid development of new applications, emphasizing the principles of transparency and simplicity of use. Although it is still on-going, it has already allowed the development of applications that are currently being used.

Targeting antioxidants to mitochondria: a potential new therapeutic strategy for cardiovascular diseases

Mitochondria produce large amounts of free radicals and play an important role in the life and death of a cell. Thus, mitochondrial oxidative damage and dysfunction contribute to a number of cell pathologies that manifest themselves through a range of conditions including ischemia-reperfusion injury, sepsis, diabetes, atherosclerosis and, consequently, cardiovascular diseases (CVD). In fact, endothelial dysfunction, characterized by a loss of nitric oxide (NO) bioactivity, occurs early on in the development of atherosclerosis, and determines future vascular complications. Although the molecular mechanisms responsible for mitochondria-mediated disease processes are not yet clear, oxidative stress seems to play an important role. This review considers the process of CVD from a mitochondrial perspective. Accordingly, strategies for the targeted delivery of antioxidants to mitochondria are being developed. In this review, we will provide a summary of the following areas: the cellular metabolism of reactive oxygen species (ROS) and its role in pathophysiological processes such as CVD; currently available antioxidants and possible reasons for their efficacy and inefficacy in ameliorating oxidative stress-mediated diseases; recent developments in mitochondrially-targeted antioxidants that concentrate on the matrix-facing surface of the inner mitochondrial membrane and therefore protect against mitochondrial oxidative damage, and their therapeutic potential for future treatment of CVDs. More pre-clinical and clinical studies, however, are necessary in order to evaluate the effectiveness and toxicity of mitochondrially-targeted antioxidants.

Association of Helicobacter species with hepatitis C cirrhosis with or without hepatocellular carcinoma

BACKGROUND AND AIMS

Recent studies have suggested that bacterial coinfection with Helicobacter species in patients already infected with hepatitis C virus (HCV) could be involved in the development of cirrhosis and hepatocellular carcinoma (HCC). A retrospective cross sectional study was performed in order to explore the association between Helicobacter species and HCV associated liver diseases.

METHODS

The presence of Helicobacter species was tested by polymerase chain reaction on liver samples from four groups of patients.

RESULTS

Helicobacter 16S rDNA was found in only 4.2% of liver samples from control patients (n=24) and in 3.5% of liver samples from patients with non-cirrhotic chronic hepatitis C (n=29) while it was found in 68.0% of liver samples from patients with HCV positive cirrhosis without HCC (n=25) as well as in 61.3% of cirrhotic liver samples from patients with HCV positive cirrhosis and HCC (n=31). In addition, when the HCC tumour tissue was tested (n=21), 90.5% of samples were positive. DNA from Helicobacter pylori- and Helicobacter pullorum-like organisms was found.

CONCLUSIONS

There is an association between the presence of Helicobacter species DNA in the liver and hepatitis C cirrhosis, with or without HCC. Indeed, the presence of these bacteria could be the result of structural changes in the liver. Alternatively, Helicobacter species could be a co-risk factor in HCV chronic liver diseases. This result warrants prospective studies to determine the possible causal role of these bacteria in the progression of chronic hepatitis C.

Atypical gastric presentation of strongyloidiasis in HIV-infected patient--case report

Strongyloides stercoralis is an intestinal helminth of systemic distribution, which, once in its host, has the ability to perpetuate itself through an autoinfection cycle, leading to chronic infection. In healthy hosts, the parasite usually does not cause any symptoms, or only mild symptoms that are limited mainly to the small intestine. However, in immunocompromised hosts, uncontrolled multiplication with massive infection may occur, causing hyperinfection syndrome or disseminated strongyloidiasis, which are both associated with high morbidity and mortality. There are few reports of gastric involvement, particularly presenting as ulcer in the stomach. We report a case of gastric ulcer caused by S. stercoralis in HIV-infected patient.

Radial endoscopic ultrasound and spiral computed tomography in the diagnosis and staging of periampullary tumors

BACKGROUND AND STUDY AIMS

The early detection and accurate staging of pancreatic and ampullary cancer is of utmost importance for the achievement of surgical radical treatment. The aim of this study was to assess prospectively the role of endoscopic ultrasonography (EUS) in detection and staging of pancreatic and ampullary cancer, comparing its results to those obtained with spiral computed tomography (SCT).

PATIENTS AND METHODS

Sixty-one patients with suspected pancreatic and ampullary tumors were included, 46 (75, 4%) of whom presented with obstructive jaundice. Patients underwent EUS and SCT within a 7-day period. Examiners were unaware of the previous imaging results, except conventional echography. Image interpretation was compared to surgical and histopathological findings.

RESULTS

Fifty-six (91, 8%) patients were surgically explored. Clinical follow-up and/or tissue diagnosis determined the correct diagnosis in the remaining five patients. Pancreatic cancer and ampullary cancer were observed in 29 (47, 6%) and 10 (16, 4%) patients, respectively. Chronic pancreatitis and choledocholithiasis were the most common diagnosis in patients with non-neoplastic disease. EUS was more effective than SCT for the definition of the final diagnosis in patients with obstructive jaundice (87.0 vs. 67.4%, p = 0.04). Both exams were equally effective for detecting pancreatic cancer but EUS predicted more accurately the involvement of portal-mesenteric axis by the tumor (87.0 vs. 67.4%, p = 0.04). EUS was particularly useful in the diagnosis of cancer of papilla of Vater.

CONCLUSION

In patients with pancreatic adenocarcinoma without unequivocal signs of distant metastatic disease, EUS is more accurate than SCT to predict venous involvement by the tumor. EUS is superior to SCT to detect ampullary adenocarcinoma. Both methods are equally ineffective to detect nodal involvement in pancreatic and ampullary cancer.

The role of adherence in tuberculosis HIV-positive patients treated in ambulatory regimen

Adherence to antituberculosis treatment, a major determinant of outcome, is of special concern in human immunodeficiency virus (HIV)-positive patients. However, tuberculosis death in HIV-positive patients remains higher than in HIV-negative patients, regardless of adherence. To assess determinants for an unfavourable tuberculosis outcome (defined as no cure or death), and determinants for nonadherence to antituberculosis treatment, 70 HIV-positive patients with tuberculosis referred to an outpatient centre were studied. Patient outcome was compared according to HIV risk factors, other opportunistic diseases, antiretroviral drugs use, current i.v. drugs use, a methadone programme participation, tuberculosis features, treatment characteristics and adherence. Adherent and non-adherent patient characteristics were also compared. An unfavourable outcome occurred in 22.9% of patients and 32.9% were nonadherent with therapy. Nonadherence was the only independent determinant for an unfavourable outcome. Adherence was independently associated with current i.v. drug use, treatment complications and use of methadone. This study confirms that human immunodeficiency virus-infected patients, treated as outpatients, have high rates of nonadherence and that adherence is the strongest determinant for tuberculosis outcome. Independently of the current use of drugs, a methadone programme improves adherence to treatment.

Effect of acute cold exposure on the expression of the adiponectin, resistin and leptin genes in rat white and brown adipose tissues

Leptin, adiponectin, and resistin are key hormones produced by adipose tissue. In the present study, we have examined the effects of acute cold exposure (18 h at 6 degrees C) on the expression of the genes encoding these hormones in both brown and white fat of rats. Acute cold exposure resulted in a significant (p < 0.001) increase in the level of UCP1 and metallothionein-1 mRNAs in brown adipose tissue, indicative of an activation of thermogenesis. Leptin mRNA was decreased (p < 0.001) in brown fat in the cold, and there was also a small but statistically significant (p < 0.05) decrease in adiponectin mRNA; resistin mRNA did not change significantly (p > 0.05). In white fat, the level of leptin mRNA also fell in the cold (p < 0.05), but there was no significant change (p > 0.05) in either adiponectin or resistin mRNA. The serum concentration of adiponectin was unchanged following acute cold exposure. We conclude that while leptin gene expression is inhibited by exposure to cold, there is no major effect on the expression of either the adiponectin or resistin genes in white or brown fat despite the cold-induced stimulation of sympathetic activity and fatty acid flux. Thus, adiponectin and resistin are unlikely to play a key role in the extensive metabolic adaptations to cold.