Data collapse, scaling functions, and analytical solutions of generalized growth models

We consider a nontrivial one-species population dynamics model with finite and infinite carrying capacities. Time-dependent intrinsic and extrinsic growth rates are considered in these models. Through the model per capita growth rate we obtain a heuristic general procedure to generate scaling functions to collapse data into a simple linear behavior even if an extrinsic growth rate is included. With this data collapse, all the models studied become independent from the parameters and initial condition. Analytical solutions are found when time-dependent coefficients are considered. These solutions allow us to perceive nontrivial transitions between species extinction and survival and to calculate the transition's critical exponents. Considering an extrinsic growth rate as a cancer treatment, we show that the relevant quantity depends not only on the intensity of the treatment, but also on when the cancerous cell growth is maximum.

Qualitative Analysis of the Interdisciplinary Interaction between Data Analysis Specialists and Novice Clinical Researchers

Background: The inherent complexity of statistical methods and clinical phenomena compel researchers with diverse domains of expertise to work in interdisciplinary teams, where none of them have a complete knowledge in their counterpart's field. As a result, knowledge exchange may often be characterized by miscommunication leading to misinterpretation, ultimately resulting in errors in research and even clinical practice. Though communication has a central role in interdisciplinary collaboration and since miscommunication can have a negative impact on research processes, to the best of our knowledge, no study has yet explored how data analysis specialists and clinical researchers communicate over time. Methods/Principal Findings: We conducted qualitative analysis of encounters between clinical researchers and data analysis specialists (epidemiologist, clinical epidemiologist, and data mining specialist). These encounters were recorded and systematically analyzed using a grounded theory methodology for extraction of emerging themes, followed by data triangulation and analysis of negative cases for validation. A policy analysis was then performed using a system dynamics methodology looking for potential interventions to improve this process. Four major emerging themes were found. Definitions using lay language were frequently employed as a way to bridge the language gap between the specialties. Thought experiments presented a series of ""what if'' situations that helped clarify how the method or information from the other field would behave, if exposed to alternative situations, ultimately aiding in explaining their main objective. Metaphors and analogies were used to translate concepts across fields, from the unfamiliar to the familiar. Prolepsis was used to anticipate study outcomes, thus helping specialists understand the current context based on an understanding of their final goal. Conclusion/Significance: The communication between clinical researchers and data analysis specialists presents multiple challenges that can lead to errors.

Work disability remains a major problem in rheumatoid arthritis in the 2000s: data from 32 countries in the QUEST-RA Study

Introduction: Work disability is a major consequence of rheumatoid arthritis (RA), associated not only with traditional disease activity variables, but also more significantly with demographic, functional, occupational, and societal variables. Recent reports suggest that the use of biologic agents offers potential for reduced work disability rates, but the conclusions are based on surrogate disease activity measures derived from studies primarily from Western countries. Methods: The Quantitative Standard Monitoring of Patients with RA (QUEST-RA) multinational database of 8,039 patients in 86 sites in 32 countries, 16 with high gross domestic product (GDP) (>24K US dollars (USD) per capita) and 16 low-GDP countries (<11K USD), was analyzed for work and disability status at onset and over the course of RA and clinical status of patients who continued working or had stopped working in high-GDP versus low-GDP countries according to all RA Core Data Set measures. Associations of work disability status with RA Core Data Set variables and indices were analyzed using descriptive statistics and regression analyses. Results: At the time of first symptoms, 86% of men (range 57%-100% among countries) and 64% (19%-87%) of women <65 years were working. More than one third (37%) of these patients reported subsequent work disability because of RA. Among 1,756 patients whose symptoms had begun during the 2000s, the probabilities of continuing to work were 80% (95% confidence interval (CI) 78%-82%) at 2 years and 68% (95% CI 65%-71%) at 5 years, with similar patterns in high-GDP and low-GDP countries. Patients who continued working versus stopped working had significantly better clinical status for all clinical status measures and patient self-report scores, with similar patterns in high-GDP and low-GDP countries. However, patients who had stopped working in high-GDP countries had better clinical status than patients who continued working in low-GDP countries. The most significant identifier of work disability in all subgroups was Health Assessment Questionnaire (HAQ) functional disability score. Conclusions: Work disability rates remain high among people with RA during this millennium. In low-GDP countries, people remain working with high levels of disability and disease activity. Cultural and economic differences between societies affect work disability as an outcome measure for RA.

Integration and visualization of systems biology data in context of the genome

Background: High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results: The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions: Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment.

Novel Primate-Specific Genes, RMEL 1, 2 and 3, with Highly Restricted Expression in Melanoma, Assessed by New Data Mining Tool

Melanoma is a highly aggressive and therapy resistant tumor for which the identification of specific markers and therapeutic targets is highly desirable. We describe here the development and use of a bioinformatic pipeline tool, made publicly available under the name of EST2TSE, for the in silico detection of candidate genes with tissue-specific expression. Using this tool we mined the human EST (Expressed Sequence Tag) database for sequences derived exclusively from melanoma. We found 29 UniGene clusters of multiple ESTs with the potential to predict novel genes with melanoma-specific expression. Using a diverse panel of human tissues and cell lines, we validated the expression of a subset of three previously uncharacterized genes (clusters Hs.295012, Hs.518391, and Hs.559350) to be highly restricted to melanoma/melanocytes and named them RMEL1, 2 and 3, respectively. Expression analysis in nevi, primary melanomas, and metastatic melanomas revealed RMEL1 as a novel melanocytic lineage-specific gene up-regulated during melanoma development. RMEL2 expression was restricted to melanoma tissues and glioblastoma. RMEL3 showed strong up-regulation in nevi and was lost in metastatic tumors. Interestingly, we found correlations of RMEL2 and RMEL3 expression with improved patient outcome, suggesting tumor and/or metastasis suppressor functions for these genes. The three genes are composed of multiple exons and map to 2q12.2, 1q25.3, and 5q11.2, respectively. They are well conserved throughout primates, but not other genomes, and were predicted as having no coding potential, although primate-conserved and human-specific short ORFs could be found. Hairpin RNA secondary structures were also predicted. Concluding, this work offers new melanoma-specific genes for future validation as prognostic markers or as targets for the development of therapeutic strategies to treat melanoma.

New Epidemiological Data on Brazilian Spotted Fever in an Endemic Area of the State of Sao Paulo, Brazil

The present work evaluated rickettsial infection in dogs and their ticks in an area endemic for Brazilian spotted fever (BSF) in the metropolitan area of Sao Paulo, Brazil, where the tick Amblyomma aureolatum was presumed to be the vector of the disease. Ticks were collected on dogs from 185 houses, encompassing single infestations by Rhipicephalus sanguineus, Amblyomma aureolatum, Amblyomma longirostre, or Amblyomma sp. in dogs from 60 (32.4%), 77 (41.6%), 2 (1.1%), and 25 (13.5%) houses, respectively; 19 (10.3%) houses had dogs with mixed infestations by R. sanguineus and A. aureolatum; 1 (0.5%) house had dogs with infestations by A. aureolatum and A. longirostre; and 1 (0.5%) house had dogs with infestations by R. sanguineus and Amblyomma sp. Overall, A. aureolatum was present in dogs from 97 (52.4%) houses, and R. sanguineus in dogs from 80 (43.2%) houses. A total of 287 ticks (130 A. aureolatum and 157 R. sanguineus) infesting dogs from 98 houses were selected for testing by polymerase chain reaction (PCR) targeting rickettsial genes. Overall, 3.1% of the A. aureolatum ticks were infected by Rickettsia bellii, and 1.3% of the R. sanguineus were infected by Ricketttsii rickettsii. For serology, we selected 23 dogs living in and in the vicinity of the house where the R. rickettsii-infected ticks were collected. The indirect fluorescent antibody (IFA) test detected antibodies reactive with R. rickettsii in sera from 16 (69.6%) dogs, with titers ranging from 256 to 32,768. It is established that Amblyomma aureolatum is a vector of R. rickettsii in the Sao Paulo metropolitan area, but our results highlight for the first time in Brazil, a possible role of R. sanguineus in the epidemiology of R. rickettsii, corroborating previous findings in Mexico and the United States, where R. sanguineus has been implicated in the transmission of R. rickettsii to humans.

DESCRIPTION OF ADULTS AND NYMPH, AND REDESCRIPTION OF THE LARVA, OF ORNITHODOROS MARINKELLEI (ACARI: ARGASIDAE), WITH DATA ON ITS PHYLOGENETIC POSITION

The argasid tick Ornithodoros marinkellei Kohls, Clifford, and Jones, 1969 was described 4 decades ago based on larval specimens collected from bats (Pteronotus spp.) in Colombia and Panama. Thereafter, larval O. marinkellei parasitizing bats were reported from Venezuela, Guyana, and Brazil. Herein, we describe the adults and nymph, and redescribe the larva of O. marinkellei based on specimens recently collected in the western Brazilian Amazon region. In contrast to all other known adult argasids, the idiosoma of both males and females of O. marinkellei is covered with sclerotized plaques. The idiosoma of the nymph of O. marinkellei is entirely micromamillated, and differs from the adults by the absence of plaques. The larva of O. marinkellei is morphologically similar to the larvae of the 2 other species belonging to the subgenus Subparmatus, i.e., Ornithodoros viguerasi Cooley and Kohls, 1941 and Ornithodoros mormoops Kohls, Clifford, and Jones, 1969. Because of the long and narrow dorsal plate, the larva of O. marinkellei is readily distinguished from O. viguerasi and O. mormoops. Comparison of our larvae from Brazil with O. marinkellei paratype specimens from Colombia confirmed their taxonomic identification. However, a few morphological differences, particularly in the size of the gnathosoma, were observed. Further studies are necessary to clarify whether O. marinkellei is a complex of different species, or a single species represented by morphologically polymorphic, and geographically distinct populations. Partial mitochondrial 16S rDNA gene sequences were generated for O. marinkellei specimens from Brazil, and compared with available homologous sequences in GenBank. Phylogenetic analyses revealed O. marinkellei to be distinct from the remaining argasid species available in GenBank, including other bat-associated tick species that are found in sympatry with O. marinkellei in the Neotropical region.

Nd:YAG Laser Improves Biocompatibility of Human Dental Root Surfaces

Objective: Our goal was to compare the in vivo biocompatibility of dental root surfaces submitted to four different treatments after tooth avulsion followed by implantation into rat subcutaneous tissue. Background Data: Dental root surface preparation prior to replanting teeth remains a challenge for endodontists. Root surface changes made by Nd:YAG irradiation could be an alternative preparation. Methods: Forty-eight freshly extracted human dental roots were randomly divided into four treatment groups prior to implantation into rat subcutaneous tissue: G1, dry root, left in the environment up to 3 h; G2, the same treatment as G1, followed by a soaking treatment in a 2.4% sodium fluoride solution (pH 5.5); G3, root soaked in physiologic saline after avulsion for 72 h; G4, the same treatment as G1, followed by Nd:YAG laser irradiation (2.0 W, 20 Hz, 100 mJ, and 124.34 J/cm(2)). The animals were sacrificed 1, 7, and 45 d later. Histological and scanning electron microscopy analyses were done. Results: All dental roots were involved and in intimate contact with connective tissue capsules of variable thicknesses. Differences were observed in the degree of inflammation and in connective tissue maturation. In G3 the inflammatory infiltrate was maintained for 45 d, whereas the Nd:YAG laser irradiation (G4) led to milder responses. The overall aspects of the root surfaces were similar, except by the irradiated roots, where fusion and resolidification of the root surface covering the dentinal tubules were observed. Conclusion: Nd:YAG laser irradiation improves the biocompatibility of dental root and thus could be an alternative treatment of dental root prior to replantation.

Morphologic changes and removal of debris on apical dentin surfaces after Nd : YAG laser and diode laser irradiation

Objective: To verify the effects of laser energy on intracanal dentin surfaces, by analyzing the morphologic changes and removal of debris in the apical third of 30 extracted human teeth, prepared and irradiated with the Nd:YAG laser and diode laser. Background Data: Lasers have been widely used in endodontics. The morphologic changes in dentin walls caused by Nd: YAG and diode laser irradiation could improve apical seals and cleanliness. Materials and Methods: The protocol used for Nd: YAG laser irradiation was 1.5 W, 100 mJ, and 15 Hz, in pulsed mode, and for diode laser was 2.5 W in continuous mode. Each specimen was irradiated four times at a speed of 2 mm/sec with a 20-sec interval between applications. Five calibrated examiners scored the morphologic changes and debris removal on a 4-point scale. Results: In analyzing the scores, there were no statistically significant differences between the two types of laser for either parameter, according to Kruskal-Wallis testing at p = 0.05. The SEM images showed fusion and resolidification of the dentin surface, with partial removal of debris on the specimens irradiated with the Nd: YAG laser and the diode laser, compared with controls. Conclusion: Both lasers promote morphologic changes and debris removal. These alterations of the dentin surface appeared to be more evident in the Nd: YAG laser group, but the diode laser group showed more uniform changes.

Ultrastructural analysis of root canal dentine irradiated with 980-nm diode laser energy at different parameters

Objective: The purpose of this in vitro study was to investigate using the scanning electron microscope (SEM) the ultrastructural morphological changes of the radicular dentine surface after irradiation with 980-nm diode laser energy at different parameters and angles of incidence. Background Data: There have been limited reports on the effects of diode laser irradiation at 980 nm on radicular dentin morphology. Materials and Methods: Seventy-two maxillary canines were sectioned and roots were biomechanically prepared using K3 rotary instruments. The teeth were irrigated with 2 mL of distilled water between files and final irrigation was performed with 10 mL of distilled water. The teeth were then randomly divided into five groups (n = 8 each) according to their diode laser parameters: Group 1: no irradiation (control); group 2: 1.5 W/continuous wave (CW) emission (the manufacturer's parameters); group 3: 1.5 W/100 Hz; group 4: 3 W/CW; and group 5: 3 W/100 Hz. Laser energy was applied with helicoid movements (parallel to the canal walls) for 20 sec. Eight additional teeth for each group were endodontically prepared and split longitudinally and irradiation was applied perpendicularly to the root surface. Results: Statistical analysis showed no difference between the root canal thirds irradiated with the 980-nm diode laser, and similar results between the parameters 1.5 W/CW and 3 W/100 Hz (p > 0.05). Conclusion: When considering different output powers and delivery modes our results showed that changes varied from smear layer removal to dentine fusion.

Developmental Potential of Bovine Hand-Made Clone Embryos Reconstructed by Aggregation or Fusion with Distinct Cytoplasmic Volumes

Animal cloning has been associated with developmental abnormalities, with the level of heteroplasmy caused by the procedure being one of its potential limiting factors. The aim of this study was to determine the effect of the fusion of hemicytoplasts or aggregation of hemiembryos, varying the final cytoplasmic volume, on development and cell density of embryos produced by hand-made cloning (HMC), parthenogenesis or by in vitro fertilization (IVF). One or two enucleated hemicytoplasts were paired and fused with one skin somatic cell. Activated clone and zona-free parthenote embryos and hemiembryos were in vitro cultured in the well-of-the-well (WOW) system, being allocated to one of six experimental groups, on a per WOW basis: single clone or parthenote hemiembryos (1 x 50%); aggregation of two (2 x 50%), three (3 x 50%), or four (4 x 50%) clone or parthenote hemiembryos; single clone or parthenote embryos (1 x 100%); or aggregation of two clone or parthenote embryos (2 x 100%). Control zona-intact parthenote or IVF embryos were in vitro cultured in four-well dishes. Results indicated that the increase in the number of aggregated structures within each WOW was followed by a linear increase in cleavage, blastocyst rate, and cell density. The increase in cytoplasmic volume, either by fusion or by aggregation, had a positive effect on embryo development, supporting the establishment of pregnancies and the birth of a viable clone calf after transfer to recipients. However, embryo aggregation did not improve development on a hemicytoplast basis, except for the aggregation of two clone embryos.

Fast ray-tracing algorithm for circumstellar structures (FRACS) II. Disc parameters of the B[e] supergiant CPD-57 degrees 2874 from VLTI/MIDI data

Context. B[e] supergiants are luminous, massive post-main sequence stars exhibiting non-spherical winds, forbidden lines, and hot dust in a disc-like structure. The physical properties of their rich and complex circumstellar environment (CSE) are not well understood, partly because these CSE cannot be easily resolved at the large distances found for B[e] supergiants (typically greater than or similar to 1 kpc). Aims. From mid-IR spectro-interferometric observations obtained with VLTI/MIDI we seek to resolve and study the CSE of the Galactic B[e] supergiant CPD-57 degrees 2874. Methods. For a physical interpretation of the observables (visibilities and spectrum) we use our ray-tracing radiative transfer code (FRACS), which is optimised for thermal spectro-interferometric observations. Results. Thanks to the short computing time required by FRACS (<10 s per monochromatic model), best-fit parameters and uncertainties for several physical quantities of CPD-57 degrees 2874 were obtained, such as inner dust radius, relative flux contribution of the central source and of the dusty CSE, dust temperature profile, and disc inclination. Conclusions. The analysis of VLTI/MIDI data with FRACS allowed one of the first direct determinations of physical parameters of the dusty CSE of a B[e] supergiant based on interferometric data and using a full model-fitting approach. In a larger context, the study of B[e] supergiants is important for a deeper understanding of the complex structure and evolution of hot, massive stars.

SPITZER OBSERVATIONS OF A1763. II. CONSTRAINING THE NATURE OF ACTIVITY IN THE CLUSTER-FEEDING FILAMENT WITH VLA AND XMM-NEWTON DATA

The A1763 superstructure at z = 0.23 contains the first galaxy filament to be directly detected using mid-infrared observations. Our previous work has shown that the frequency of starbursting galaxies, as characterized by 24 mu m emission is much higher within the filament than at either the center of the rich galaxy cluster, or the field surrounding the system. New Very Large Array and XMM-Newton data are presented here. We use the radio and X-ray data to examine the fraction and location of active galaxies, both active galactic nuclei (AGNs) and starbursts (SBs). The radio far-infrared correlation, X-ray point source location, IRAC colors, and quasar positions are all used to gain an understanding of the presence of dominant AGNs. We find very few MIPS-selected galaxies that are clearly dominated by AGN activity. Most radio-selected members within the filament are SBs. Within the supercluster, three of eight spectroscopic members detected both in the radio and in the mid-infrared are radio-bright AGNs. They are found at or near the core of A1763. The five SBs are located further along the filament. We calculate the physical properties of the known wide angle tail (WAT) source which is the brightest cluster galaxy of A1763. A second double lobe source is found along the filament well outside of the virial radius of either cluster. The velocity offset of the WAT from the X-ray centroid and the bend of the WAT in the intracluster medium are both consistent with ram pressure stripping, indicative of streaming motions along the direction of the filament. We consider this as further evidence of the cluster-feeding nature of the galaxy filament.

HR Del REMNANT ANATOMY USING TWO-DIMENSIONAL SPECTRAL DATA AND THREE-DIMENSIONAL PHOTOIONIZATION SHELL MODELS

The HR Del nova remnant was observed with the IFU-GMOS at Gemini North. The spatially resolved spectral data cube was used in the kinematic, morphological, and abundance analysis of the ejecta. The line maps show a very clumpy shell with two main symmetric structures. The first one is the outer part of the shell seen in H alpha, which forms two rings projected in the sky plane. These ring structures correspond to a closed hourglass shape, first proposed by Harman & O'Brien. The equatorial emission enhancement is caused by the superimposed hourglass structures in the line of sight. The second structure seen only in the [O III] and [N II] maps is located along the polar directions inside the hourglass structure. Abundance gradients between the polar caps and equatorial region were not found. However, the outer part of the shell seems to be less abundant in oxygen and nitrogen than the inner regions. Detailed 2.5-dimensional photoionization modeling of the three-dimensional shell was performed using the mass distribution inferred from the observations and the presence of mass clumps. The resulting model grids are used to constrain the physical properties of the shell as well as the central ionizing source. A sequence of three-dimensional clumpy models including a disk-shaped ionization source is able to reproduce the ionization gradients between polar and equatorial regions of the shell. Differences between shell axial ratios in different lines can also be explained by aspherical illumination. A total shell mass of 9 x 10(-4) M(circle dot) is derived from these models. We estimate that 50%-70% of the shell mass is contained in neutral clumps with density contrast up to a factor of 30.

The B0.5IVe CoRoT target HD 49330 I. Photometric analysis from CoRoT data

Context. Be stars undergo outbursts producing a circumstellar disk from the ejected material. The beating of non-radial pulsations has been put forward as a possible mechanism of ejection. Aims. We analyze the pulsational behavior of the early B0.5IVe star HD 49330 observed during the first CoRoT long run towards the Galactical anticenter (LRA1). This Be star is located close to the lower edge of the beta Cephei instability strip in the HR diagram and showed a 0.03 mag outburst during the CoRoT observations. It is thus an ideal case for testing the aforementioned hypothesis. Methods. We analyze the CoRoT light curve of HD 49330 using Fourier methods and non-linear least square fitting. Results. In this star, we find pulsation modes typical of beta Cep stars (p modes) and SPB stars (g modes) with amplitude variations along the run directly correlated with the outburst. These results provide new clues about the origin of the Be phenomenon as well as strong constraints on the seismic modelling of Be stars.