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.

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.

Evaluation of the Bond Strength Between a Composite Resin and Enamel Submitted to Bleaching Treatment and Etched with Er:YAG Laser

Background: The use of laser irradiation for dental surface treatment may increase tooth-composite bond strength. Its use on bleached teeth may decrease the waiting time between bleaching and restorative procedures. Objective: This study aimed to evaluate the bond strength between a composite resin and bovine enamel bleached with 35% hydrogen peroxide and etched with Er:YAG laser. Materials and Methods: Thirty bovine teeth were randomly divided into six groups (n = 5): G1, unbleached and restored 24 h after storage in artificial saliva, etching with 35% phosphoric acid (PA) (control); G2, unbleached and restored 24 h after storage in artificial saliva, etching with Er:YAG laser and 35% PA; G3, bleached and restored immediately afterward, etching with 35% PA; G4, bleached and restored 24 h after bleaching, etching with 35% PA; G5, bleached and restored immediately afterward, etching with Er:YAG and 35% PA laser; G6, bleached and restored 24 h after bleaching, etching with Er:YAG laser and 35% PA. Bond strength was quantitatively evaluated by microtensile test (1.0 mm/min). Data were submitted to statistical analysis using ANOVA and Tukey tests (alpha - 0.05). Results: Bond strength values (MPa) were G1, 26.17 +/- 4.44; G2, 28.87 +/- 3.94; G3, 17.25 +/- 4.58; G4, 21.93 +/- 5.02; G5, 16.69 +/- 2.31; and G6, 29.06 +/- 8.31. There was no statistically significant difference among groups G1, G2, and G6 (p - 0.119), which presented higher bond strength than group G4, followed by groups G3 and G5. Conclusion: Er:YAG irradiation of bleached surfaces may favor bonding procedures when performed 24 h after bleaching.

Influence of Aluminum Oxide Sandblasting Associated with Nd:YAG or Er:YAG Lasers on Shear Bond Strength of a Feldspathic Ceramic to Resin Cements

Objective: This in vitro study evaluated the influence of the surface pretreatment of a feldspathic ceramic on the shear bond strength of two different resin cements. Background Data: Although several conventional surface treatments have been used on feldspathic ceramic, few studies have investigated the effects of an alternative surface treatment, the association of aluminum oxide sandblasting with Nd:YAG and Er:YAG lasers. Methods: Sixty samples made of a feldspathic ceramic were divided into three groups (n = 20) and treated with (1) controlled-air abrasion with Al(2)O(3) + 10% hydrofluoric acid (HF), (2) Al(2)O(3) + Er:YAG laser, and (3) Al(2)O(3) + Nd:YAG laser. Afterward, silane (Dentsply) was applied on each treated surface. Each of the three main groups was divided into two subgroups (n = 10), where a different resin cement was employed for each subgroup. It was built a cylinder with resin cement (RelyX Arc) in subgroup (A) and with self-adhesive cement (RelyX U100) in subgroup (B). After 24 h at 37 degrees C, the prepared specimens were submitted to shear bond strength test and stereoscopic evaluation to determine the type of failure. Results: Bond strength mean values were not statistically significant for the surface treatment methods or resin cements. Conclusion: The null surface treatment proposed with aluminum oxide sandblasting associated with the Er:YAG or Nd:YAG laser and using cementation with self-adhesive cement can be an alternative bonding technique for feldspathic ceramic, since it was as effective as the conventional treatment with aluminum oxide sandblasting and hydrofluoric acid using the conventional resin cement.

Osler-Weber-Rendu Syndrome - Dental Implications

Osler-Weber-Rendu syndrome (OWRS) is a rare hereditary, autosomal dominant disease characterized by a local angiodysplasia. Its clinical characteristics are vascular hamartomas of the skin and oral mucosa, arteriovenous malformations in the lungs, liver, kidney and brain, and episodes of epistaxis. The oral lesions, which become apparent through hemorrhagic telangiectasia, may be the first sign of the disease. This is a case report of a 74-year-old woman whose diagnosis of OWRS was established by her dentist based on the presence of telangiectasia in the skin and oral mucosa, reports of frequent nosebleeds of unknown etiology and a family history of telangiectasia. Amputation of a lower limb and comorbidities, such as cardiopathy, nephropathy and rheumatic disorders, completed the profile. OWRS causes major vascular changes that can be diagnosed initially by a dentist. In this article, we describe the skills and knowledge that dentists need to monitor patients with OWRS properly.

Can type of school be used as an alternative indicator of socioeconomic status in dental caries studies? A cross-sectional study

Background: Despite the importance of collecting individual data of socioeconomic status (SES) in epidemiological oral health surveys with children, this procedure relies on the parents as respondents. Therefore, type of school (public or private schools) could be used as an alternative indicator of SES, instead of collecting data individually. The aim of this study was to evaluate the use of the variable type of school as an indicator of socioeconomic status as a substitute of individual data in an epidemiological survey about dental caries in Brazilian preschool children. Methods: This study followed a cross-sectional design, with a random sample of 411 preschool children aged 1 to 5 years, representative of Catalao, Brazil. A calibrated examiner evaluated the prevalence of dental caries and parents or guardians provided information about several individual socioeconomic indicators by means of a semi-structured questionnaire. A multilevel approach was used to investigate the association among individual socioeconomic variables, as well as the type of school, and the outcome. Results: When all significant variables in the univariate analysis were used in the multiple model, only mother's schooling and household income (individual socioeconomic variables) presented significant associations with presence of dental caries, and the type of school was not significantly associated. However, when the type of school was used alone, children of public school presented significantly higher prevalence of dental caries than those enrolled in private schools. Conclusions: The type of school used as an alternative indicator for socioeconomic status is a feasible predictor for caries experience in epidemiological dental caries studies involving preschool children in Brazilian context.

New methodology to assess activity status of occlusal caries in primary teeth using laser fluorescence device

An in vivo study was conducted to verify the ability of laser fluorescence (LF) to assess the activity status of occlusal caries in primary teeth, using different air-drying times. Occlusal sites (707) were examined using LF (DIAGNOdent) after air-drying for 3 s and 15 s, and the difference between readings (DIF15 s-3 s) was calculated. For concurrent validation of LF, visual criteria-Nyvad (NY) and Lesion Activity Assessment associated with the International Caries Detection and Assessment System (LAA-ICDAS)-were the reference standards for lesion activity. Histological exam using a pH-indicator dye (0.1% methyl red) was performed in 46 exfoliated/extracted teeth for criterion validation. LF readings and DIF15 s-3 s were compared using Kruskall-Wallis and Mann-Whitney tests. Receiver operating characteristic analyses were performed and validity parameters calculated, considering the caries activity assessment. Using NY, active lesions (3 s: 30.0 +/- 29.3; 15 s: 34.2 +/- 30.6) presented higher LF readings than inactive lesions (3 s: 17.0 +/- 16.3; 15 s: 19.2 +/- 17.3; p <0.05), different from LAA-ICDAS. Active cavitated caries resulted in higher LF readings (3 s: 50.3 +/- 3.5; 15 s: 54.7 +/- 30.2) than inactive cavitated caries (3 s: 19.9 +/- 16.3; 15 s: 22.8 +/- 16.8). Therefore, LF can distinguish cavitated active and inactive lesions classified by NY, but not by LAA-ICDAS; however, this difference might be related to the visual system rather than to LF. The air-drying time could be an alternative to improve the caries activity assessment; however, longer air-drying time is suggested to be tested subsequently. (C) 2010 Society of Photo-Optical Instrumentation Engineers. [DOI: 10.1117/1.3463007]

A Paradigm Shift in Predoctoral Dental Curricula in Brazil: Evaluating the Process of Change

In 2002, the Brazilian Ministry of Education approved the official curricular guidelines for undergraduate courses in Brazil to be adopted by the nation's 188 dental schools. In 2005-06, the Brazilian Dental Education Association (BDEA) promoted workshops in forty-eight of the schools to verify the degree of transformation of the curriculum based on these guidelines. Among the areas analyzed were course philosophy (variables were v1: knowledge production based on the needs of the Brazilian Public Health System [BPHS]; v2: health determinants; and v3: postgraduate studies and permanent education); pedagogical skills (v4: curricular structure; v5: changes in pedagogic and didactic skills; and v6: course program orientation); and dental practice scenarios (v7: diversity of the scenarios for training/learning; v8: academic health care centers opened to the BPHS; and v9: participation of students in health care delivery for the population). The subjects consisted of faculty members (n=711), students (n=228), and employees (n=14). The results showed an incipient degree of curriculum transformation. The degree of innovation was statistically different depending on the type of university (public or private) for variables I, 2, 4, 5, 6, and 7. Private schools reported a higher level of innovation than public institutions. Resistance to transforming the dental curriculum according to the official guidelines may be linked to an ideological conception that supports the private practice model, continues to have faculty members direct all classroom activities, and prevents students from developing an understanding of professional practice as targeted towards the oral health needs of all segments of society.

Relationship between maxillary and mandibular base lengths and dental crowding in patients with complete Class II malocclusions

Objective: To verify the relationship between maxillary and mandibular effective lengths and dental crowding in patients with Class II malocclusions. Materials and Methods: The sample comprised 80 orthodontic patients with complete Class II malocclusions in the permanent dentition (47 male, 33 female) who were divided into two groups according to the amount of mandibular tooth-arch size discrepancy. The maxillary and mandibular effective lengths (Co-A and Co-Gn) and tooth-arch size discrepancies were measured on the initial cephalograms and dental casts, respectively. Intergroup comparisons of apical base lengths were performed with independent t-tests. Correlation between base length and dental crowding was examined by means of Pearson's correlation coefficient (P < .05). Results: Patients with Class II malocclusion and moderate to severe crowding had significantly smaller maxillary and mandibular effective lengths than subjects with the same malocclusion and slight mandibular crowding. A weak inverse correlation was also found between maxillary and mandibular effective lengths and the severity of dental crowding. Conclusion: Decreased maxillary and mandibular effective lengths constitute an important factor associated with dental crowding in patients with complete Class II malocclusion. (Angle Orthod. 2011;81:217-221.)

Increased Occurrence of Dental Anomalies Associated with Second-Premolar Agenesis

Objective: To evaluate the prevalence of dental anomalies in patients with agenesis of second premolars and compare the findings with the prevalence of these anomalies in the general population. Materials and Methods: A Brazilian sample of 203 patients aged 8 to 22 years was selected. All patients presented agenesis of at least one second premolar. Panoramic and periapical radiographs and dental casts were used to analyze the presence of other associated dental anomalies, including agenesis of other permanent teeth, ectopia of unerupted permanent teeth, infraocclusion of deciduous molars, microdontia of maxillary lateral incisors, and supernumerary teeth. The occurrence of these anomalies was compared with occurrence data previously reported for the general population. Statistical testing was performed using the chi-square test (P < .05) and the odds ratio. Results: The sample with agenesis of at least one second premolar presented a significantly increased prevalence rate of permanent tooth agenesis (21%), excluding third molars. Among the sample segment aged 14 years or greater (N = 77), occurrence of third-molar agenesis (48%) exceeded twice its normal frequency. Significant increases in occurrence of microdontia of maxillary lateral incisors (20.6%), infraocclusion of deciduous molars (24.6%), and distoangulation of mandibular second premolars (7.8%) were observed. Palatally displaced canine anomaly was also significantly elevated (8.1%). Conclusion: The results provide evidence that agenesis of other permanent teeth, microdontia, deciduous molar infraocclusion, and certain dental ectopias are the products of the same genetic mechanisms that cause second-premolar agenesis. (Angle Orthod. 2009;79:436-441.)

Effects of Low-Level Laser Therapy and Orthodontic Tooth Movement on Dental Pulps in Rats

Objectives: To describe the microscopic pulpal reactions resulting from orthodontically induced tooth movement associated with low-level laser therapy (LLLT) in rats. Materials and Methods: Forty-five young male Wistar rats were randomly assigned to three groups. In group I (n = 20), the maxillary right first molars were submitted to orthodontic movement with placement of a coil spring. In group II (n = 20), the teeth were submitted to orthodontic movement plus LLLT at 4 seconds per point (buccal, palatal, and mesial) with a GaAlAs diode laser source (830 nm, 100 mW, 18 J/cm(2)). Group III (n = 5) served as a control (no orthodontic movement or LLLT). Groups I and 11 were divided into four subgroups according to the time elapsed between the start of tooth movement and sacrifice (12 hours, 24 hours, 3 days, and 7 days). Results: Up until the 3-day period, the specimens in group I presented a thicker odontoblastic layer, no cell-free zone of Weil, pulp core with differentiated mesenchymal and defense cells, and a high concentration of blood vessels. In group II, at the 12- and 24-hour time points, the odontoblastic layer was disorganized and the cell-free zone of Weil was absent, presenting undifferentiated cells, intensive vascularization with congested capillaries, and scarce defense cells in the cell-rich zone. In groups I and II, pulpal responses to the stimuli were more intense in the area underneath the region of application of the force or force/laser. Conclusions: The orthodontic-induced tooth movement and LLLT association showed reversible hyperemia as a tissue response to the stimulus. LLLT leads to a faster repair of the pulpal tissue due to orthodontic movement. (Angle Orthod. 2010;80:116-122.)

Three-dimensional finite element thermal analysis of dental tissues irradiated with Er,Cr:YSGG laser

In the present study, a finite element model of a half-sectioned molar tooth was developed in order to understand the thermal behavior of dental hard tissues (both enamel and dentin) under laser irradiation. The model was validated by comparing it with an in vitro experiment where a sound molar tooth was irradiated by an Er,Cr:YSGG pulsed laser. The numerical tooth model was conceived to simulate the in vitro experiment, reproducing the dimensions and physical conditions of the typical molar sound tooth, considering laser energy absorption and calculating the heat transfer through the dental tissues in three dimensions. The numerical assay considered the same three laser energy densities at the same wavelength (2.79 mu m) used in the experiment. A thermographic camera was used to perform the in vitro experiment, in which an Er, Cr: YSGG laser (2.79 mu m) was used to irradiate tooth samples and the infrared images obtained were stored and analyzed. The temperature increments in both the finite element model and the in vitro experiment were compared. The distribution of temperature inside the tooth versus time plotted for two critical points showed a relatively good agreement between the results of the experiment and model. The three dimensional model allows one to understand how the heat propagates through the dentin and enamel and to relate the amount of energy applied, width of the laser pulses, and temperature inside the tooth. (C) 2008 American Institute of Physics. [DOI: 10.1063/1.2953526]

The role of magnetic reconnection on jet/accretion disk systems

Context. It was proposed earlier that the relativistic ejections observed in microquasars could be produced by violent magnetic reconnection episodes at the inner disk coronal region (de Gouveia Dal Pino & Lazarian 2005). Aims. Here we revisit this model, which employs a standard accretion disk description and fast magnetic reconnection theory, and discuss the role of magnetic reconnection and associated heating and particle acceleration in different jet/disk accretion systems, namely young stellar objects (YSOs), microquasars, and active galactic nuclei (AGNs). Methods. In microquasars and AGNs, violent reconnection episodes between the magnetic field lines of the inner disk region and those that are anchored in the black hole are able to heat the coronal/disk gas and accelerate the plasma to relativistic velocities through a diffusive first-order Fermi-like process within the reconnection site that will produce intermittent relativistic ejections or plasmons. Results. The resulting power-law electron distribution is compatible with the synchrotron radio spectrum observed during the outbursts of these sources. A diagram of the magnetic energy rate released by violent reconnection as a function of the black hole (BH) mass spanning 10(9) orders of magnitude shows that the magnetic reconnection power is more than sufficient to explain the observed radio luminosities of the outbursts from microquasars to low luminous AGNs. In addition, the magnetic reconnection events cause the heating of the coronal gas, which can be conducted back to the disk to enhance its thermal soft X-ray emission as observed during outbursts in microquasars. The decay of the hard X-ray emission right after a radio flare could also be explained in this model due to the escape of relativistic electrons with the evolving jet outburst. In the case of YSOs a similar magnetic configuration can be reached that could possibly produce observed X-ray flares in some sources and provide the heating at the jet launching base, but only if violent magnetic reconnection events occur with episodic, very short-duration accretion rates which are similar to 100-1000 times larger than the typical average accretion rates expected for more evolved (T Tauri) YSOs.

The BRAzilian Seismographic Integrated Systems (BRASIS): infrastructure and data management

In geophysics and seismology, raw data need to be processed to generate useful information that can be turned into knowledge by researchers. The number of sensors that are acquiring raw data is increasing rapidly. Without good data management systems, more time can be spent in querying and preparing datasets for analyses than in acquiring raw data. Also, a lot of good quality data acquired at great effort can be lost forever if they are not correctly stored. Local and international cooperation will probably be reduced, and a lot of data will never become scientific knowledge. For this reason, the Seismological Laboratory of the Institute of Astronomy, Geophysics and Atmospheric Sciences at the University of Sao Paulo (IAG-USP) has concentrated fully on its data management system. This report describes the efforts of the IAG-USP to set up a seismology data management system to facilitate local and international cooperation.

Modeling Two-Oscillator Circadian Systems Entrained by Two Environmental Cycles

Several experimental studies have altered the phase relationship between photic and non-photic environmental, 24 h cycles (zeitgebers) in order to assess their role in the synchronization of circadian rhythms. To assist in the interpretation of the complex activity patterns that emerge from these ""conflicting zeitgeber'' protocols, we present computer simulations of coupled circadian oscillators forced by two independent zeitgebers. This circadian system configuration was first employed by Pittendrigh and Bruce (1959), to model their studies of the light and temperature entrainment of the eclosion oscillator in Drosophila. Whereas most of the recent experiments have restricted conflicting zeitgeber experiments to two experimental conditions, by comparing circadian oscillator phases under two distinct phase relationships between zeitgebers (usually 0 and 12 h), Pittendrigh and Bruce compared eclosion phase under 12 distinct phase relationships, spanning the 24 h interval. Our simulations using non-linear differential equations replicated complex non-linear phenomena, such as ""phase jumps'' and sudden switches in zeitgeber preferences, which had previously been difficult to interpret. Our simulations reveal that these phenomena generally arise when inter-oscillator coupling is high in relation to the zeitgeber strength. Manipulations in the structural symmetry of the model indicated that these results can be expected to apply to a wide range of system configurations. Finally, our studies recommend the use of the complete protocol employed by Pittendrigh and Bruce, because different system configurations can generate similar results when a ""conflicting zeitgeber experiment'' incorporates only two phase relationships between zeitgebers.