Chicken skeletal muscle-associated macroarray for gene discovery

Macro- and microarrays are well-established technologies to determine gene functions through repeated measurements of transcript abundance. We constructed a chicken skeletal muscle-associated array based on a muscle-specific EST database, which was used to generate a tissue expression dataset of similar to 4500 chicken genes across 5 adult tissues (skeletal muscle, heart, liver, brain, and skin). Only a small number of ESTs were sufficiently well characterized by BLAST searches to determine their probable cellular functions. Evidence of a particular tissue-characteristic expression can be considered an indication that the transcript is likely to be functionally significant. The skeletal muscle macroarray platform was first used to search for evidence of tissue-specific expression, focusing on the biological function of genes/transcripts, since gene expression profiles generated across tissues were found to be reliable and consistent. Hierarchical clustering analysis revealed consistent clustering among genes assigned to 'developmental growth', such as the ontology genes and germ layers. Accuracy of the expression data was supported by comparing information from known transcripts and tissue from which the transcript was derived with macroarray data. Hybridization assays resulted in consistent tissue expression profile, which will be useful to dissect tissue-regulatory networks and to predict functions of novel genes identified after extensive sequencing of the genomes of model organisms. Screening our skeletal-muscle platform using 5 chicken adult tissues allowed us identifying 43 'tissue-specific' transcripts, and 112 co-expressed uncharacterized transcripts with 62 putative motifs. This platform also represents an important tool for functional investigation of novel genes; to determine expression pattern according to developmental stages; to evaluate differences in muscular growth potential between chicken lines, and to identify tissue-specific genes.

TCF7L2 variant genotypes and type 2 diabetes risk in Brazil: significant association, but not a significant tool for risk stratification in the general population

Background: Genetic polymorphisms of the TCF7L2 gene are strongly associated with large increments in type 2 diabetes risk in different populations worldwide. In this study, we aimed to confirm the effect of the TCF7L2 polymorphism rs7903146 on diabetes risk in a Brazilian population and to assess the use of this genetic marker in improving diabetes risk prediction in the general population. Methods: We genotyped the single nucleotide polymorphisms (SNP) rs7903146 of the TCF7L2 gene in 560 patients with known coronary disease enrolled in the MASS II (Medicine, Angioplasty, or Surgery Study) Trial and in 1,449 residents of Vitoria, in Southeast Brazil. The associations of this gene variant to diabetes risk and metabolic characteristics in these two different populations were analyzed. To access the potential benefit of using this marker for diabetes risk prediction in the general population we analyzed the impact of this genetic variant on a validated diabetes risk prediction tool based on clinical characteristics developed for the Brazilian general population. Results: SNP rs7903146 of the TCF7L2 gene was significantly associated with type 2 diabetes in the MASS-II population (OR = 1.57 per T allele, p = 0.0032), confirming, in the Brazilian population, previous reports of the literature. Addition of this polymorphism to an established clinical risk prediction score did not increased model accuracy (both area under ROC curve equal to 0.776). Conclusion: TCF7L2 rs7903146 T allele is associated with a 1.57 increased risk for type 2 diabetes in a Brazilian cohort of patients with known coronary heart disease. However, the inclusion of this polymorphism in a risk prediction tool developed for the general population resulted in no improvement of performance. This is the first study, to our knowledge, that has confirmed this recent association in a South American population and adds to the great consistency of this finding in studies around the world. Finally, confirming the biological association of a genetic marker does not guarantee improvement on already established screening tools based solely on demographic variables.

Cytomegalovirus frequency in neonatal intrahepatic cholestasis determined by serology, histology, immunohistochemistry and PCR

AIM: To determine cytomegalovirus (CMV) frequency in neonatal intrahepatic cholestasis by serology, histological revision (searching for cytomegalic cells), immunohistochemistry, and polymerase chain reaction (PCR), and to verify the relationships among these methods. METHODS: The study comprised 101 non-consecutive infants submitted for hepatic biopsy between March 1982 and December 2005. Serological results were obtained from the patient's files and the other methods were performed on paraffin-embedded liver samples from hepatic biopsies. The following statistical measures were calculated: frequency, sensibility, specific positive predictive value, negative predictive value, and accuracy. RESULTS: The frequencies of positive results were as follows: serology, 7/64 (11%); histological revision, 0/84; immunohistochemistry, 1/44 (2%), and PCR, 6/77 (8%). Only one patient had positive immunohistochemical findings and a positive PCR. The following statistical measures were calculated between PCR and serology: sensitivity, 33.3%; specificity, 88.89%; positive predictive value, 28.57%; negative predictive value, 90.91%; and accuracy, 82.35%. CONCLUSION: The frequency of positive CMV varied among the tests. Serology presented the highest positive frequency. When compared to PCR, the sensitivity and positive predictive value of serology were low. (C) 2009 The WJG Press and Baishicleng. All rights reserved.

COOP/WONCA Charts as a Screen for Mental Disorders in Primary Care

PURPOSE most people with mental disorders receive treatment in primary care. The charts developed by the Dartmouth Primary Care Cooperative Research Network (COOP) and the World Organization of National Colleges, Academies, and Academic Associations of General Practitioners/Family Physicians (WONCA) have not yet been evaluated as a screen for these disorders, using a structured psychiatric interview by an expert or considering diagnoses other than depression. We evaluated the validity and feasibility of the COOP/WONCA Charts as a mental disorders screen by comparing them both with other questionnaires previously validated and with the assessment of a mental health specialist using a structured diagnostic interview. METHODS We trained community health workers and nurse assistants working in a collaborative mental health care model to administer the COOP/WONCA Charts, the 20-item Self-Reporting Questionnaire (SRQ-20), and the World Health Organization Five Well-Being Index (WHO-5) to 120 primary care patients. A psychiatrist blinded to the patients' results on these questionnaires administered the SCID, or Structured Clinical Interview for the DSM-IV (Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition). RESULTS The area under the receiver operating characteristic curve was at least 0.80 for single items, a 3-item combination, and the total score of the COOP/WONCA Charts, as well as for the SRQ-20 and the WHO-5, for screening both for all mental disorders and for depressive disorders. The accuracy, sensitivity, specificity, and positive and negative predictive values of these measures ranged between 0.77 and 0.92. Community health workers and nurse assistants rated the understandability, ease of use, and clinical relevance of all 3 questionnaires as satisfactory. CONCLUSIONS One-time assessment of patients with the COOP/WONCA Charts is a valid and feasible option for screening for mental disorders by primary care teams.

Esophageal Ulcer in Brazilian Patients with HIV: Prevalence and Comparative Analysis Among Diagnostic Methods

Esophageal ulcer (EU) represents an important comorbidity in AIDS. We evaluated the prevalence of EU, the accuracy of the endoscopic and histologic methods used to investigate viral EU in HIV-positive Brazilian patients and the numerical relevance of tissue sampling. A total of 399 HIV-positive patients underwent upper gastrointestinal (UGI) endoscopy. HIV-positive patients with EU determined by UGI endoscopy followed by biopsies were analyzed by the hematoxylin-eosin (HE) and immunohistochemical (IH) methods. EU was detected in 41 patients (mean age, 39.2 years; 23 males), with a prevalence of 10.27%. The median CD4 count was 49 cells/mm(3) (range, 1-361 cells/mm(3)) and the viral load was 58,869 copies per milliliter (range, 50-77,3290 copies per milliliter). UGI endoscopy detected 29 of 41 EU suggestive of cytomegalovirus (CMV) infection and 7 of 41 indicating herpes simplex virus (HSV) infection. HE histology confirmed 4 of 29 ulcers induced by CMV, 2 of 7 induced by HSV, and 1 of 7 induced by HSV plus CMV. IH for CMV and HSV confirmed the HE findings and detected one additional CMV-induced case. UGI endoscopy showed 100% sensitivity and 15% specificity for the diagnosis of EU due to CMV or HSV compared to HE and IH. HE proved to be an adequate method for etiologic evaluation, with 87% sensitivity and 100% specificity compared to IH. The number of samples did not influence the etiologic evaluation. The data support the importance of IH as a complementary method for HE in the diagnosis of EU of viral etiology.

Predictive values of aspartate aminotransferase and gamma-glutamyl transferase for the hepatic accumulation of copper in cattle and buffalo

Ten cattle and 10 buffalo were divided into 2 groups (control [n = 8] and experimental [n = 12]) that received daily administration of copper. Three hepatic biopsies and blood samples were performed on days 0, 45, and 105. The concentration of hepatic copper was determined by spectrophotometric atomic absorption, and the activities of aspartate aminotransferase (AST) and gamma-glutamyl transferase (GGT) were analyzed. Regression analyses were done to verify the possible existing relationship between enzymatic activity and concentration of hepatic copper. Sensitivity, specificity, accuracy, and positive and negative predictive values were determined. The serum activities of AST and GGT had coefficients of determination that were excellent predictive indicators of hepatic copper accumulation in cattle, while only GGT serum activity was predictive of hepatic copper accumulation in buffalo. Elevated serum GGT activity may be indicative of increased concentrations of hepatic copper even in cattle and buffalo that appear to be clinically healthy. Thus, prophylactic measures can be implemented to prevent the onset of a hemolytic crisis that is characteristic of copper intoxication.

Cost effectiveness of OptiMal (R) rapid diagnostic test for malaria in remote areas of the Amazon Region, Brazil

Background: In areas with limited structure in place for microscopy diagnosis, rapid diagnostic tests (RDT) have been demonstrated to be effective. Method: The cost-effectiveness of the Optimal (R) and thick smear microscopy was estimated and compared. Data were collected on remote areas of 12 municipalities in the Brazilian Amazon. Data sources included the National Malaria Control Programme of the Ministry of Health, the National Healthcare System reimbursement table, hospitalization records, primary data collected from the municipalities, and scientific literature. The perspective was that of the Brazilian public health system, the analytical horizon was from the start of fever until the diagnostic results provided to patient and the temporal reference was that of year 2006. The results were expressed in costs per adequately diagnosed cases in 2006 U. S. dollars. Sensitivity analysis was performed considering key model parameters. Results: In the case base scenario, considering 92% and 95% sensitivity for thick smear microscopy to Plasmodium falciparum and Plasmodium vivax, respectively, and 100% specificity for both species, thick smear microscopy is more costly and more effective, with an incremental cost estimated at US$ 549.9 per adequately diagnosed case. In sensitivity analysis, when sensitivity and specificity of microscopy for P. vivax were 0.90 and 0.98, respectively, and when its sensitivity for P. falciparum was 0.83, the RDT was more cost-effective than microscopy. Conclusion: Microscopy is more cost-effective than OptiMal (R) in these remote areas if high accuracy of microscopy is maintained in the field. Decision regarding use of rapid tests for diagnosis of malaria in these areas depends on current microscopy accuracy in the field.

The structure and dynamics of Abell 1942

Aims. We present a dynamical analysis of the galaxy cluster Abell 1942 based on a set of 128 velocities obtained at the European Southern Observatory. Methods. Data on individual galaxies are presented and the accuracy of the determined velocities as some properties of the cluster are discussed. We have also made use of publicly available Chandra X-ray data. Results. We obtained an improved mean redshift value z = 0.22513 +/- 0.0008 and velocity dispersion sigma = 908(139)(+147) km s(-1). Our analysis indicates that inside a radius of similar to 1.5 h(70)(-1) Mpc (similar to 7 arcmin) the cluster is well relaxed, without any remarkable features and the X-ray emission traces the galaxy distribution fairly well. Two possible optical substructures are seen at similar to 5 arcmin from the centre in the northwest and the southwest directions, but are not confirmed by the velocity field. These clumps are, however, kinematically bound to the main structure of Abell 1942. X-ray spectroscopic analysis of Chandra data resulted in a temperature kT = 5.5+/-0.5 keV and metal abundance Z = 0.33 +/- 0.15 Z(circle dot). The velocity dispersion corresponding to this temperature using the T(X-sigma) scaling relation is in good agreement with the measured galaxy velocities. Our photometric redshift analysis suggests that the weak lensing signal observed to the south of the cluster and previously attributed to a ""dark clump"" is produced by background sources, possibly distributed as a filamentary structure.

The metal content of bulge field stars from FLAMES-GIRAFFE spectra - I. Stellar parameters and iron abundances

Aims. We determine the iron distribution function (IDF) for bulge field stars, in three different fields along the Galactic minor axis and at latitudes b = -4 degrees, b = -6 degrees, and b = -12 degrees. A fourth field including NGC 6553 is also included in the discussion. Methods. About 800 bulge field K giants were observed with the GIRAFFE spectrograph of FLAMES@VLT at spectral resolution R similar to 20 000. Several of them were observed again with UVES at R similar to 45 000 to insure the accuracy of the measurements. The LTE abundance analysis yielded stellar parameters and iron abundances that allowed us to construct an IDF for the bulge that, for the first time, is based on high-resolution spectroscopy for each individual star. Results. The IDF derived here is centered on solar metallicity, and extends from [Fe/H] similar to -1.5 to [Fe/H] similar to + 0.5. The distribution is asymmetric, with a sharper cutoff on the high-metallicity side, and it is narrower than previously measured. A variation in the mean metallicity along the bulge minor axis is clearly between b = -4 degrees and b = -6 degrees ([Fe/H] decreasing similar to by 0.6 dex per kpc). The field at b = -12 degrees. is consistent with the presence of a gradient, but its quantification is complicated by the higher disk/bulge fraction in this field. Conclusions. Our findings support a scenario in which both infall and outflow were important during the bulge formation, and then suggest the presence of a radial gradient, which poses some challenges to the scenario in which the bulge would result solely from the vertical heating of the bar.

New constraints on the chemical evolution of the solar neighbourhood and Galactic disc(s) Improved astrophysical parameters for the Geneva-Copenhagen Survey

We present a re-analysis of the Geneva-Copenhagen survey, which benefits from the infrared flux method to improve the accuracy of the derived stellar effective temperatures and uses the latter to build a consistent and improved metallicity scale. Metallicities are calibrated on high-resolution spectroscopy and checked against four open clusters and a moving group, showing excellent consistency. The new temperature and metallicity scales provide a better match to theoretical isochrones, which are used for a Bayesian analysis of stellar ages. With respect to previous analyses, our stars are on average 100 K hotter and 0.1 dex more metal rich, which shift the peak of the metallicity distribution function around the solar value. From Stromgren photometry we are able to derive for the first time a proxy for [alpha/Fe] abundances, which enables us to perform a tentative dissection of the chemical thin and thick disc. We find evidence for the latter being composed of an old, mildly but systematically alpha-enhanced population that extends to super solar metallicities, in agreement with spectroscopic studies. Our revision offers the largest existing kinematically unbiased sample of the solar neighbourhood that contains full information on kinematics, metallicities, and ages and thus provides better constraints on the physical processes relevant in the build-up of the Milky Way disc, enabling a better understanding of the Sun in a Galactic context.

A search for thermally emitting isolated neutron stars in the 2XMMp catalogue

The relatively large number of nearby radio-quiet and thermally emitting isolated neutron stars (INSs) discovered in the ROSAT All-Sky Survey, dubbed the ""Magnificent Seven"", suggests that they belong to a formerly neglected major component of the overall INS population. So far, attempts to discover similar INSs beyond the solar vicinity failed to confirm any reliable candidate. The good positional accuracy and soft X-ray sensitivity of the EPIC cameras onboard the XMM-Newton satellite allow us to efficiently search for new thermally emitting INSs. We used the 2XMMp catalogue to select sources with no catalogued candidate counterparts and with X-ray spectra similar to those of the Magnificent Seven, but seen at greater distances and thus undergoing higher interstellar absorptions. Identifications in more than 170 astronomical catalogues and visual screening allowed us to select fewer than 30 good INS candidates. In order to rule out alternative identifications, we obtained deep ESO-VLT and SOAR optical imaging for the X-ray brightest candidates. We report here on the optical follow-up results of our search and discuss the possible nature of 8 of our candidates. A high X-ray-to-optical flux ratio together with a stable flux and soft X-ray spectrum make the brightest source of our sample, 2XMM J104608.7-594306, a newly discovered thermally emitting INS. The X-ray source 2XMM J010642.3+005032 has no evident optical counterpart and should be further investigated. The remaining X-ray sources are most probably identified with cataclysmic variables and active galactic nuclei, as inferred from the colours and flux ratios of their likely optical counterparts. Beyond the finding of new thermally emitting INSs, our study aims at constraining the space density of this Galactic population at great distances and at determining whether their apparently high density is a local anomaly or not.

AUTOMATED DETERMINATION OF [Fe/H] AND [C/Fe] FROM LOW-RESOLUTION SPECTROSCOPY

We develop an automated spectral synthesis technique for the estimation of metallicities ([Fe/H]) and carbon abundances ([C/Fe]) for metal-poor stars, including carbon-enhanced metal-poor stars, for which other methods may prove insufficient. This technique, autoMOOG, is designed to operate on relatively strong features visible in even low- to medium-resolution spectra, yielding results comparable to much more telescope-intensive high-resolution studies. We validate this method by comparison with 913 stars which have existing high-resolution and low- to medium-resolution to medium-resolution spectra, and that cover a wide range of stellar parameters. We find that at low metallicities ([Fe/H] less than or similar to -2.0), we successfully recover both the metallicity and carbon abundance, where possible, with an accuracy of similar to 0.20 dex. At higher metallicities, due to issues of continuum placement in spectral normalization done prior to the running of autoMOOG, a general underestimate of the overall metallicity of a star is seen, although the carbon abundance is still successfully recovered. As a result, this method is only recommended for use on samples of stars of known sufficiently low metallicity. For these low- metallicity stars, however, autoMOOG performs much more consistently and quickly than similar, existing techniques, which should allow for analyses of large samples of metal-poor stars in the near future. Steps to improve and correct the continuum placement difficulties are being pursued.

Both accurate and precise gf-values for Fe II lines

We present a new set of oscillator strengths for 142 Fe II lines in the wavelength range 4000-8000 angstrom. Our gf-values are both accurate and precise, because each multiplet was globally normalized using laboratory data ( accuracy), while the relative gf-values of individual lines within a given multiplet were obtained from theoretical calculations ( precision). Our line list was tested with the Sun and high-resolution (R approximate to 10(5)), high-S/N (approximate to 700-900) Keck+HIRES spectra of the metal-poor stars HD 148816 and HD 140283, for which line-to-line scatter (sigma) in the iron abundances from Fe II lines as low as 0.03, 0.04, and 0.05 dex are found, respectively. For these three stars the standard error in the mean iron abundance from Fe II lines is negligible (sigma(mean) <= 0.01 dex). The mean solar iron abundance obtained using our gf-values and different model atmospheres is A(Fe) = 7.45(sigma = 0.02).

Recovery of the star formation history of the LMC from the VISTA survey of the Magellanic system

The VISTA near infrared survey of the Magellanic System (VMC) will provide deep YJK(s) photometry reaching stars in the oldest turn-off point throughout the Magellanic Clouds (MCs). As part of the preparation for the survey, we aim to access the accuracy in the star formation history (SFH) that can be expected from VMC data, in particular for the Large Magellanic Cloud (LMC). To this aim, we first simulate VMC images containing not only the LMC stellar populations but also the foreground Milky Way (MW) stars and background galaxies. The simulations cover the whole range of density of LMC field stars. We then perform aperture photometry over these simulated images, access the expected levels of photometric errors and incompleteness, and apply the classical technique of SFH-recovery based on the reconstruction of colour-magnitude diagrams (CMD) via the minimisation of a chi-squared-like statistics. We verify that the foreground MW stars are accurately recovered by the minimisation algorithms, whereas the background galaxies can be largely eliminated from the CMD analysis due to their particular colours and morphologies. We then evaluate the expected errors in the recovered star formation rate as a function of stellar age, SFR(t), starting from models with a known age-metallicity relation (AMR). It turns out that, for a given sky area, the random errors for ages older than similar to 0.4 Gyr seem to be independent of the crowding. This can be explained by a counterbalancing effect between the loss of stars from a decrease in the completeness and the gain of stars from an increase in the stellar density. For a spatial resolution of similar to 0.1 deg(2), the random errors in SFR(t) will be below 20% for this wide range of ages. On the other hand, due to the lower stellar statistics for stars younger than similar to 0.4 Gyr, the outer LMC regions will require larger areas to achieve the same level of accuracy in the SFR( t). If we consider the AMR as unknown, the SFH-recovery algorithm is able to accurately recover the input AMR, at the price of an increase of random errors in the SFR(t) by a factor of about 2.5. Experiments of SFH-recovery performed for varying distance modulus and reddening indicate that these parameters can be determined with (relative) accuracies of Delta(m-M)(0) similar to 0.02 mag and Delta E(B-V) similar to 0.01 mag, for each individual field over the LMC. The propagation of these errors in the SFR(t) implies systematic errors below 30%. This level of accuracy in the SFR(t) can reveal significant imprints in the dynamical evolution of this unique and nearby stellar system, as well as possible signatures of the past interaction between the MCs and the MW.

Proper motions of thermally emitting isolated neutron stars measured with Chandra

The remarkable astrometric capabilities of the Chandra Observatory offer the possibility to measure proper motions of X-ray sources with an unprecedented accuracy in this wavelength range. We recently completed a proper motion survey of three of the seven thermally emitting radio-quiet isolated neutron stars (INSs) discovered in the ROSAT all-sky survey. These INSs (RXJ0420.0-5022, RXJ0806.4-4123 and RXJ1308.6+2127) either lack an optical counterpart or have one so faint that ground based or space born optical observations push the current possibilities of the instrumentation to the limit. Pairs of ACIS observations were acquired 3 to 5 years apart to measure the displacement of the sources on the X-ray sky using as a reference the background of extragalactic or remote Galactic X-ray sources. We derive 2 sigma upper limits of 123 mas yr(-1) and 86 mas yr(-1) on the proper motion of RXJ0420.0-5022 and RXJ0806.4-4123, respectively. RXJ1308.6+2127 exhibits a very significant displacement (similar to 9 sigma) yielding mu = 220 +/- 25 mas yr(-1), the second fastest measured among all ROSAT-discovered INSs. The source is probably moving away rapidly from the Galactic plane at a speed which precludes any significant accretion of matter from the interstellar medium. Its transverse velocity of similar to 740 (d/700 pc) km s(-1) might be the largest of all ROSAT INSs and its corresponding spatial velocity lies among the fastest recorded for neutron stars. RXJ1308.6+2127 is thus a middle-aged (age similar to 1 My) high velocity cooling neutron star. We investigate its possible origin in nearby OB associations or from a field OB star. In most cases, the flight time from birth place appears significantly shorter than the characteristic age derived from spin down rate. Overall, the distribution in transverse velocity of the ROSAT INSs is not statistically different from that of normal radio pulsars.