BraX-Ray: An X-Ray of the Brazilian Computer Science Graduate Programs

Research productivity assessment is increasingly relevant for allocation of research funds. On one hand, this assessment is challenging because it involves both qualitative and quantitative analysis of several characteristics, most of them subjective in nature. On the other hand, current tools and academic social networks make bibliometric data web-available to everyone for free. Those tools, especially when combined with other data, are able to create a rich environment from which information on research productivity can be extracted. In this context, our work aims at characterizing the Brazilian Computer Science graduate programs and the relationship among themselves. We (i) present views of the programs from different perspectives, (ii) rank the programs according to each perspective and a combination of them, (iii) show correlation between assessment metrics, (iv) discuss how programs relate to another, and (v) infer aspects that boost programs'' research productivity. The results indicate that programs with a higher insertion in the coauthorship network topology also possess a higher research productivity between 2004 and 2009.     

The Frequencies of IFNγ+IL2+TNFα+ PPD-Specific CD4+CD45RO+ T-Cells Correlate with the Magnitude of the QuantiFERON? Gold In-Tube Response in a Prospective Study of Healthy Indian Adolescents

Background

QuantiFERON-TB Gold In-Tube (QFT) is an IFNγ-release assay used in the diagnosis of Mycobacterium tuberculosis (MTB) infection. The risk of TB progression increases with the magnitude of the MTB-specific IFNγ-response. QFT reversion, also associated with low Tuberculin Skin Test responses, may therefore represent a transient immune response with control of M. tuberculosis infection. However, studies at the single cell level have suggested that the quality (polyfunctionality) of the T-cell response is more important than the quantity of cytokines produced.

Objective

To explore the quality and/or magnitude of mycobacteria-specific T-cell responses associated with QFT reversion and persistent QFT-positivity.

Methods

Multi-color flowcytometry on prospectively collected peripheral blood mononuclear cells was applied to assess mycobacteria-specific T-cell responses in 42 QFT positive Indian adolescents of whom 21 became QFT negative (reverters) within one year. Ten QFT consistent negatives were also included as controls.

Results

There was no difference in the qualitative PPD-specific CD4+ T-cell response between QFT consistent positives and reverters. However, compared with QFT consistent positives, reverters displayed lower absolute frequencies of polyfunctional (IFNγ+IL2+TNFα+) CD4+ T-cells at baseline, which were further reduced to the point where they were not different to QFT negative controls one year later. Moreover, absolute frequencies of these cells correlated well with the magnitude of the QFT-response.

Conclusion

Whereas specific polyfunctional CD4+ T-cells have been suggested to protect against TB progression, our data do not support that higher relative or absolute frequencies of PPD-specific polyfunctional CD4+ T-cells in peripheral blood can explain the reduced risk of TB progression observed in QFT reverters. On the contrary, absolute frequencies of these cells correlated with the QFT-response, suggesting that this readout reflects antigenic load.     

Contrasting Light Spectra Constrain the Macro and Microstructures of Scleractinian Corals

The morphological plasticity of scleractinian corals can be influenced by numerous factors in their natural environment. However, it is difficult to identify in situ the relative influence of a single biotic or abiotic factor, due to potential interactions between them. Light is considered as a major factor affecting coral skeleton morphology, due to their symbiotic relation with photosynthetic zooxanthellae. Nonetheless, most studies addressing the importance of light on coral morphological plasticity have focused on photosynthetically active radiation (PAR) intensity, with the effect of light spectra remaining largely unknown. The present study evaluated how different light spectra affect the skeleton macro- and microstructures in two coral species (Acropora formosa sensu Veron (2000) and Stylophora pistillata) maintained under controlled laboratory conditions. We tested the effect of three light treatments with the same PAR but with a distinct spectral emission: 1) T5 fluorescent lamps with blue emission; 2) Light Emitting Diodes (LED) with predominantly blue emission; and 3) Light Emitting Plasma (LEP) with full spectra emission. To exclude potential bias generated by genetic variability, the experiment was performed with clonal fragments for both species. After 6 months of experiment, it was possible to detect in coral fragments of both species exposed to different light spectra significant differences in morphometry (e.g., distance among corallites, corallite diameter, and theca thickness), as well as in the organization of their skeleton microstructure. The variability found in the skeleton macro- and microstructures of clonal organisms points to the potential pitfalls associated with the exclusive use of morphometry on coral taxonomy. Moreover, the identification of a single factor influencing the morphology of coral skeletons is relevant for coral aquaculture and can allow the optimization of reef restoration efforts.     

Proteomic Analysis of Gastrocnemius Muscle in Rats with Streptozotocin-Induced Diabetes and Chronically Exposed to Fluoride

Administration of high doses of fluoride (F) can alter glucose homeostasis and lead to insulin resistance (IR). This study determined the profile of protein expression in the gastrocnemius muscle of rats with streptozotocin-induced diabetes that were chronically exposed to F. Male Wistar rats (60 days old) were randomly distributed into two groups of 18 animals. In one group, diabetes was induced through the administration of streptozotocin. Each group (D-diabetic and ND-non-diabetic) was further divided into 3 subgroups each of which was exposed to a different F concentration via drinking water (0 ppm, 10 ppm or 50 ppm F, as NaF). After 22 days of treatment, the gastrocnemius muscle was collected and submitted to proteomic analysis (2D-PAGE followed by LC-MS/MS). Protein functions were classified by the GO biological process (ClueGO v2.0.7+Clupedia v1.0.8) and protein-protein interaction networks were constructed (PSICQUIC, Cytoscape). Quantitative intensity analysis of the proteomic data revealed differential expression of 75 spots for ND0 vs. D0, 76 for ND10 vs.D10, 58 spots for ND50 vs. D50, 52 spots for D0 vs. D10 and 38 spots for D0 vs. D50. The GO annotations with the most significant terms in the comparisons of ND0 vs. D0, ND10 vs. D10, ND50 vs. D50, D0 vs. D10 and D0 vs. D50, were muscle contraction, carbohydrate catabolic processes, generation of precursor metabolites and energy, NAD metabolic processes and gluconeogenesis, respectively. Analysis of subnetworks revealed that, in all comparisons, proteins with fold changes interacted with GLUT4. GLUT4 interacting proteins, such as MDH and the stress proteins HSPB8 and GRP78, exhibited decreased expression when D animals were exposed to F. The presence of the two stress proteins indicates an increase in IR, which might worsen diabetes. Future studies should evaluate whether diabetic animals treated with F have increased IR, as well as which molecular mechanisms are involved.     

Poor Clinical Outcomes for HIV Infected Children on Antiretroviral Therapy in Rural Mozambique: Need for Program Quality Improvement and Community Engagement

Introduction

Residents of Zambézia Province, Mozambique live from rural subsistence farming and fishing. The 2009 provincial HIV prevalence for adults 15–49 years was 12.6%, higher among women (15.3%) than men (8.9%). We reviewed clinical data to assess outcomes for HIV-infected children on combination antiretroviral therapy (cART) in a highly resource-limited setting.

Methods

We studied rates of 2-year mortality and loss to follow-up (LTFU) for children <15 years of age initiating cART between June 2006–July 2011 in 10 rural districts. National guidelines define LTFU as >60 days following last-scheduled medication pickup. Kaplan-Meier estimates to compute mortality assumed non-informative censoring. Cumulative LTFU incidence calculations treated death as a competing risk.

Results

Of 753 children, 29.0% (95% CI: 24.5, 33.2) were confirmed dead by 2 years and 39.0% (95% CI: 34.8, 42.9) were LTFU with unknown clinical outcomes. The cohort mortality rate was 8.4% (95% CI: 6.3, 10.4) after 90 days on cART and 19.2% (95% CI: 16.0, 22.3) after 365 days. Higher hemoglobin at cART initiation was associated with being alive and on cART at 2 years (alive: 9.3 g/dL vs. dead or LTFU: 8.3–8.4 g/dL, p<0.01). Cotrimoxazole use within 90 days of ART initiation was associated with improved 2-year outcomes Treatment was initiated late (WHO stage III/IV) among 48% of the children with WHO stage recorded in their records. Marked heterogeneity in outcomes by district was noted (p<0.001).

Conclusions

We found poor clinical and programmatic outcomes among children taking cART in rural Mozambique. Expanded testing, early infant diagnosis, counseling/support services, case finding, and outreach are insufficiently implemented. Our quality improvement efforts seek to better link pregnancy and HIV services, expand coverage and timeliness of infant diagnosis and treatment, and increase follow-up and adherence.     

“Stop Ne(c)king around”: How interactomics contributes to functionally characterize Nek family kinases

Aside from Polo and Aurora, a third but less studied kinase family involved in mitosis regulation is the never in mitosis-gene A(NIMA)-related kinases(Neks). The founding member of this family is the sole member NIMA of Aspergillus nidulans, which is crucial for the initiation of mitosis in that organism. All 11 human Neks have been functionally assigned to one of the three core functions established for this family in mammals:(1) centrioles/mitosis;(2) primary ciliary function/ciliopathies; and(3) DNA damage response(DDR). Recent findings, especially on Nek 1 and 8, showed however, that several Neks participate in parallel in at least two of these contexts: primary ciliary function and DDR. In the core section of this in-depth review, we report the current detailed functional knowledge on each of the 11 Neks. In the discussion, we return to the cross-connections among Neks and point out how our and other groups' functional and interactomics studies revealed that most Neks interact with protein partners associated with two if not all three of the functional contexts. We then raise the hypothesis that Neks may be the connecting regulatory elements that allow the cell to fine tune and synchronize the cellular events associated with these three core functions. The new and exciting findings on the Nek family open new perspectives and should allow the Neks to finally claim the attention they deserve in the field of kinases and cell cycle biology.     

Liquid–liquid extraction of fermentation inhibiting compounds in lignocellulose hydrolysate

Several compounds that are formed or released during hydrolysis of lignocellulosic biomass inhibit the fermentation of the hydrolysate. The use of a liquid extractive agent is suggested as a method for removal of these fermentation inhibitors. The method can be applied before or during the fermentation. For a series of alkanes and alcohols, partition coefficients were measured at low concentrations of the inhibiting compounds furfural, hydroxymethyl furfural, vanillin, syringaldehyde, coniferyl aldehyde, acetic acid, as well as for ethanol as the fermentation product. Carbon dioxide production was measured during fermentation in the presence of each organic solvent to indicate its biocompatibility. The feasibility of extractive fermentation of hydrolysate was investigated by ethanolic glucose fermentation in synthetic medium containing several concentrations of furfural and vanillin and in the presence of decanol, oleyl alcohol and oleic acid. Volumetric ethanol productivity with 6 g/L vanillin in the medium increased twofold with 30% volume oleyl alcohol. Decanol showed interesting extractive properties for most fermentation inhibiting compounds, but it is not suitable for in situ application due to its poor biocompatibility. Biotechnol. Bioeng. 2009;102: 1354–1360. © 2008 Wiley Periodicals, Inc.     

Cross immunity with Haemaphysalis longicornis glutathione S-transferase reduces an experimental Rhipicephalus (Boophilus) microplus infestation

Recombinant Glutathione S-transferase of Haemaphysalis longicornis (rGST-Hl) was expressed in Escherichia coli, purified by affinity chromatography and used in the immunization of cattle. Western blot analysis showed positive antibody response in cattle immunized with rGST-Hl. The tests also showed that immunized bovine sera recognize native Rhipicephalus microplus proteins in different tissue extracts. Furthermore, the vaccine potential of rGST-Hl was investigated against infestation of Hereford cattle by R. microplus. Vaccination of cattle with rGST-Hl conferred partial cross-protection immunity against R. microplus. Considering the effect on number of engorged ticks, egg laying capacity and egg fertility, the overall efficacy of vaccination was of 57%, as compared with control group.     

Determination of the critical micelle concentration of surfactants using the fluorescent probe N-phenyl-1-naphthylamine

The fluorescence quantum yield of N-phenyl-1-naphthylamine (NPN) increases about 10-fold and the wavelength of maximum fluorescence emission is blue-shifted when this molecule partitions into the apolar core of micellar structures from the aqueous phase. This property allowed the utilization of NPN as a fluorescent indicator of micelle formation by 14 different surfactants belonging to the families of alkyltrimethylammonium halides, alkylsulfates, alkylbetaines, alkylglucosides, and bile salts. The critical micelle concentrations (CMCs) determined with NPN agreed well with literature values. In this work NPN was used at a concentration of 10(-6) M which allowed determination of CMCs in the range between approximately 10(-5) and greater than 10(-2) M. With high-sensitivity instrumentation considerably lower NPN concentrations can be used and consequently considerably lower CMCs can be rapidly and accurately determined.     

Light-break experiments and photoperiodic time measurement in the spider mite Tetranychus urticae

To explain photoperiodic induction of diapause in the spider mite Tetranychus urticae (Acarina: Tetranychidae) a theoretical model was developed, consisting of two components, viz. a “clock” and a photoperiodic “counter” mechanism. The clock executes photoperiodic time measurement according to hourglass kinetics; the counter accumulates the photoperiodic information contained in a number of successive $\text{light}\text{dark}$ cycles by adding up the number of “long” and “short” nights experienced by the developmental stages of the mites sensitive to the photoperiod. The influence of the circadian system on photoperiodic induction is interpreted as an inhibitory effect exerted on the expression of the photoperiodic response; this effect is encountered only in certain photoperiodic regimes, where the circadian system and the photoperiod are out of “resonance” with each other. This “hourglass timer oscillator counter model”, devised to give a theoretical explanation of photoperiodic time measurement, the summation of photoperiodic information, and the influence of the circadian system on photoperiodic induction, proved to be consistent with experimental results obtained with T. urticae in both symmetrical and asymmetrical “skeleton” photoperiods, the latter based on diel as well as non-diel $\text{light}\text{dark}$ cycles.