A reliable measure of similarity based on dependency for short time series: an application to gene expression networks

Background: Microarray techniques have become an important tool to the investigation of genetic relationships and the assignment of different phenotypes. Since microarrays are still very expensive, most of the experiments are performed with small samples. This paper introduces a method to quantify dependency between data series composed of few sample points. The method is used to construct gene co-expression subnetworks of highly significant edges. Results: The results shown here are for an adapted subset of a Saccharomyces cerevisiae gene expression data set with low temporal resolution and poor statistics. The method reveals common transcription factors with a high confidence level and allows the construction of subnetworks with high biological relevance that reveals characteristic features of the processes driving the organism adaptations to specific environmental conditions. Conclusion: Our method allows a reliable and sophisticated analysis of microarray data even under severe constraints. The utilization of systems biology improves the biologists ability to elucidate the mechanisms underlying celular processes and to formulate new hypotheses.

Analysis of Permeability and Morphology of Root Canal Dentin After Er,Cr:YSGG Laser Irradiation

Objective: The aim of this study was to evaluate the morphology and permeability of root canal walls irradiated with Er,Cr:YSGG laser after conventional endodontic treatment. Background: Laser irradiation can be used for dentinal tubule exposure, smear layer removal, and disinfection. Another potential, interesting application is as an adjunct to endodontic treatment, especially in the intracanal medication phase. Methods: Fifty-two single-rooted teeth had their crowns sectioned at the cementoenamel junction and were randomly divided into four groups (n = 13): G1: conventional preparation (CP) + irrigation with EDTA-T+rhodamine B dye solution associated with NDP (dexamethasone phosphate, paramonochlorophenol, polyethylenoglycol) (Rhod-NDP); G2: CP+EDTA-T + Er,Cr:YSGG laser irradiation 0.75W+Rhod-NDP; G3: CP + EDTA-T + Er,Cr:YSGG 1.5W+Rhod-NDP; G4: CP + EDTA-T + Er,Cr:YSGG 2.5W + Rhod-NDP. For the permeability analysis (n = 9), teeth were transversely cut and two slices of each third were selected. The images were analyzed by ImageLab software (Softium Informatica Ltda., Sao Paulo, SP, Brazil). Additional samples (n = 4) were examined by scanning electron microscopy. Results: Data were analyzed statistically using the Kruskal-Wallis and Student-Newman-Keuls tests for the following areas: apical third (H = 23.4651): G1 (14.25)(a), G2 (17.66)(ab), G3 (26.50)(b), G4 (39.58)(c); medium (H = 23.1611): G1 (14.16)(a), G2 (16.66)(ab), G3 (28.83)(b), G4 (38.33)(b); and cervical (H = 32.4810): G1 (9.66)(a), G2 (20.00)(ab), G3 (27.00)(b), G4 (41.33)(c), (p<0.01). Despite the irregular aspect of laser irradiation along the canal walls, the parameters of 1.5W and 2.5W allowed morphologic modifications that increased dentinal permeability. Conclusions: Irradiation with Er, Cr: YSGG laser could be effective in endodontic treatment for increasing dentinal permeability.

Effect of a Single Application of TiF(4) and NaF Varnishes and Solutions Combined with Nd:YAG Laser Irradiation on Enamel Erosion in Vitro

Objective: This in vitro study aimed to analyze the influence of neodymium-doped yttrium aluminum garnet (Nd:YAG) laser irradiation on the efficacy of titanium tetrafluoride (TiF(4)) and sodium fluoride (NaF) varnishes and solutions to protect enamel against erosion. Background data: The effect of Nd:YAG laser irradiation on NaF and AmF was analyzed; however, there is no available data on the interaction between Nd:YAG laser irradiation and TiF(4). Methods: Bovine enamel specimens were pre-treated with NaF varnish, TiF(4) varnish, NaF solution, TiF(4) solution, placebo varnish, Nd:YAG (84.9 J/cm(2)), Nd:YAG prior to or through NaF varnish, Nd:YAG prior to or through TiF(4) varnish, Nd:YAG prior to or through NaF solution, Nd:YAG prior to or through TiF(4) solution, and Nd:YAG prior to or through placebo varnish. Controls remained untreated. Ten specimens in each group were then subjected to an erosive demineralization (Sprite Zero, 4x90 s/day) and remineralization (artificial saliva, between the erosive cycles) cycling for 5 days. Enamel loss was measured profilometrically (mu m). Additionally, treated but non-eroded specimens were additionally analyzed by scanning electron microscope (SEM) (each group n-2). The data were statistically analyzed by ANOVA and Tukey's post-hoc test (p < 0.05). Results: Only TiF(4) varnish (1.8 +/- 0.6 mu m), laser prior to TiF(4) varnish (1.7 +/- 0.3 mu m) and laser prior to TiF(4) solution (1.4 +/- 0.3 mu m) significantly reduced enamel erosion compared to the control (4.1 +/- 0.6 mu m). SEM pictures showed that specimens treated with TiF(4) varnish presented a surface coating. Conclusions: Nd:YAG laser irradiation was not effective against enamel erosion and it did not have any influence on the efficacy of F, except for TiF(4) solution. On the other hand, TiF(4) varnish protected against enamel erosion, without the influence of laser irradiation.

In Vitro Evaluation of Enamel Erosion After Nd:YAG Laser Irradiation and Fluoride Application

Objective: Previous investigations have demonstrated improved enamel demineralization resistance after laser irradiation. Due to the possibility of a synergistic effect between laser and fluoride, this study investigated the effect of fluoridated agents and Nd:YAG irradiation separately and in combination on enamel resistance to erosion. Methods: One hundred bovine enamel blocks were randomly divided into 10 groups: G1, untreated (control); G2, acidic phosphate fluoride (APF) (1.23% F) for 4 min; G3, fluoride varnish for 6 h (NaF, 2.26%); G4, 0.5 W Nd: YAG laser (250 mm pulse width, 10 Hz, 35 J/cm(2), with uniform velocity for 30 sec in each application); G5, 0.75 W Nd:YAG laser (52.5 J/cm(2)); G6, 1.0 W Nd:YAG laser (70 J/cm(2)); G7, APF + 0.75 W Nd:YAG laser; G8, 0.75 W Nd:YAG laser + APF; G9, fluoride varnish + 0.75 W Nd:YAG laser; and G10, 0.75 W Nd:YAG laser + fluoride varnish. During 10 d the erosive cycle was conducted by immersion of the blocks in Sprite light for 1 min, followed by immersion in artificial saliva for 59 min. This procedure was consecutively repeated four times per day. In each day, during the remaining 20 h, the blocks were maintained in artificial saliva. The wear was evaluated by profilometry (days 5 and 10). Data were tested by two-way ANOVA and Bonferroni's tests (p < 0.05). Results: The mean wear at days 5 and 10 was, respectively: G1, 1.83 and 2.67 mu m; G2, 1.04 and 2.60 mu m; G3, 1.03 and 2.48 mu m; G4, 1.13 and 2.47 mu m; G5, 1.07 and 2.44 mu m; G6, 1.0 and 2.35 mu m; G7, 0.75 and 2.27 mu m; G8, 0.80 and 2.12 mu m; G9, 0.76 and 2.47 mu m; and G10, 1.09 and 2.46 mu m. At day 5, all the experimental groups presented significant lesser wear when compared to control group. However, at 10 d, only G7 and G8 were still different from control. Conclusions: The association between APF application and laser irradiation seems to be an alternative preventive measure against dental erosion.

Effect of Nd:YAG Irradiation and Fluoride Application on Dentine Resistance to Erosion in Vitro

Objective: In this paper we evaluated the effect of two fluoridated agents and Nd:YAG irradiation separately and in combination on dentine resistance to erosion. Background Data: The morphological changes in dentin induced by laser treatment may reduce the progression of erosive lesions. Due to the possibility of a synergistic effect of laser with fluoride, this study was conducted. Materials and Methods: Eighty bovine dentine samples (4 x 4 mm) were randomly divided into eight groups, according to the following treatments: G1: untreated (control); G2: acidic phosphate fluoride gel (APF 1.23%) for 4 min; G3: fluoride varnish (NaF 2.26%) for 6 h; G4: 0.5 W Nd: YAG laser (250 mu sec pulse, 10 Hz, 35 J/cm(2), 30 sec); G5: 0.75 W Nd: YAG laser (52.5 J/cm(2)); G6: 1.0 W Nd: YAG laser (70 J/cm(2)); G7: APF + 0.75 W Nd: YAG laser; and G8: NaF + 0.75 W Nd: YAG laser. After the treatments, half of each dentine surface was protected with nail varnish. The samples were stored in artificial saliva (30 mL/sample) for 24 h and submitted to four erosive 1-min cycles. Between the erosive attacks, the blocks were maintained in artificial saliva for 59 min. The erosive wear was evaluated by profilometry. Results: The mean wear (+/- SD, mu m) was: G1: 1.20 +/- 0.20; G2: 0.47 +/- 0.06; G3: 0.81 +/- 0.11; G4: 1.47 +/- 0.32; G5: 1.52 +/- 0.24; G6: 1.49 +/- 0.30; G7: 0.49 +/- 0.11; and G8: 1.06 +/- 0.31 (Tukey's test, p < 0.05). Conclusions: Laser irradiation was not able to reduce dentine erosion. However, fluoride application was able to increase the dentine's resistance to erosion, and APF showed better results than fluoride varnish.

Application of Low-Level Laser Irradiation (LLLI) and rhBMP-2 in Critical Bone Defect of Ovariectomized Rats: Histomorphometric Evaluation

Objectives: The aim of this study was to evaluate the osteogenic potential of recombinant human bone morphogenetic protein-2 (rhBMP-2) and low-level laser irradiation (LLLI), isolated or combined in critical bone defects (5mm) in parietal bone using ovariectomized female rats as an experimental animal model. Materials and Methods: Forty-nine female Wistar rats, bilaterally ovariectomized (OVX), were divided into seven treatment groups of seven animals each: (I) laser in a single application, (II) 7 mu g of pure rhBMP-2, (III) laser and 7 mu g of pure rhBMP-2, (IV) 7 mu g of rhBMP-2/monoolein gel, (V) laser and 7 mu g of rhBMP-2/monoolein gel, (VI) laser and pure monoolein gel, and (VII) critical bone defect controls. The low-level laser source used was a gallium aluminum arsenide semiconductor diode laser device (lambda = 780 nm, D = 120 J/cm(2)). Results: Groups II and III presented higher levels of newly formed bone than all other groups with levels of 40.57% and 40.39%, respectively (p < 0.05). The levels of newly formed bone of groups I, IV, V, and VI were similar with levels of 29.67%, 25.75%, 27.75%, and 30.64%, respectively (p > 0.05). The area of new bone formation in group VII was 20.96%, which is significantly lower than groups I, II, III, and VI. Conclusions: It was concluded that pure rhBMP-2 and a single dose of laser application stimulated new bone formation, but the new bone formation area was significantly increased when only rhBMP-2 was used. Additionally, the laser application in combination with other treatments did not influence the bone formation area.

Low-Level Laser Intensity Application in Masseter Muscle for Treatment Purposes

Objective: This study evaluated with histochemical analysis how the number of laser applications can affect the masseter muscle. Background: In dentistry today, the laser is used in patients with temporomandibular disorders (TMDs), mainly for radiating pain in the masticatory muscles, whose origins may be associated with malocclusion, although the laser effects are not well understood on the cellular level. Materials and Methods: Thirty mice (HRS/J lineage) were randomly distributed into groups according to the number of laser applications (three, six, and 10). For each group of laser applications (experimental, n = 5), it was considered the control group (n = 5), which was not irradiated. All animals inhaled halothane (2-bromo-2-chloro-1, 1, 1-trifluoroethane, minimum 99%, Sigma Aldrich, India) before each laser irradiation performed on the left masseter muscle region, on alternate days with 20 J/cm(2), 40mW, for 20 sec. The muscle samples were collected for histochemical analysis with succinate dehydrogenase (SDH) enzyme 72 h after the last application. Results: (a) A decrease in area of light fibers type (35.91% +/- 6.9%; 32.08% +/- 6.3%, and 27.88% +/- 6.3%), according to the increase of laser applications (p < 0.05); (b) significant increase (p < 0.05) in the area of intermediate fibers, with an increase of laser application (11.08% +/- 3.9%; 16.52% +/- 5.7%, and 15.96% +/- 3.9%), although the increase with 10 applications was small; (c) area increase of dark fibers in the group with three laser applications (0.16% +/- 0.3%) (p < 0.05), and in groups with six and 10 laser applications, respectively (9.68% +/- 6.0% and 9.60% +/- 4.0%). Conclusions: The SDH enzyme activity revealed that the number of laser applications increases the metabolic pattern of the muscle fibers. A minimal difference in metabolic activity between six and 10 applications of a laser suggests that further analyses should be done to confirm that six applications are enough to produce the same clinical effects, thereby contributing data to professionals from different fields in regard to the cost-benefit ratio of this therapy.

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.)

Continental passive microwave-based rainfall estimation algorithm: Application to the Amazon Basin

This paper presents a new statistical algorithm to estimate rainfall over the Amazon Basin region using the Tropical Rainfall Measuring Mission (TRMM) Microwave Imager (TMI). The algorithm relies on empirical relationships derived for different raining-type systems between coincident measurements of surface rainfall rate and 85-GHz polarization-corrected brightness temperature as observed by the precipitation radar (PR) and TMI on board the TRMM satellite. The scheme includes rain/no-rain area delineation (screening) and system-type classification routines for rain retrieval. The algorithm is validated against independent measurements of the TRMM-PR and S-band dual-polarization Doppler radar (S-Pol) surface rainfall data for two different periods. Moreover, the performance of this rainfall estimation technique is evaluated against well-known methods, namely, the TRMM-2A12 [ the Goddard profiling algorithm (GPROF)], the Goddard scattering algorithm (GSCAT), and the National Environmental Satellite, Data, and Information Service (NESDIS) algorithms. The proposed algorithm shows a normalized bias of approximately 23% for both PR and S-Pol ground truth datasets and a mean error of 0.244 mm h(-1) ( PR) and -0.157 mm h(-1)(S-Pol). For rain volume estimates using PR as reference, a correlation coefficient of 0.939 and a normalized bias of 0.039 were found. With respect to rainfall distributions and rain area comparisons, the results showed that the formulation proposed is efficient and compatible with the physics and dynamics of the observed systems over the area of interest. The performance of the other algorithms showed that GSCAT presented low normalized bias for rain areas and rain volume [0.346 ( PR) and 0.361 (S-Pol)], and GPROF showed rainfall distribution similar to that of the PR and S-Pol but with a bimodal distribution. Last, the five algorithms were evaluated during the TRMM-Large-Scale Biosphere-Atmosphere Experiment in Amazonia (LBA) 1999 field campaign to verify the precipitation characteristics observed during the easterly and westerly Amazon wind flow regimes. The proposed algorithm presented a cumulative rainfall distribution similar to the observations during the easterly regime, but it underestimated for the westerly period for rainfall rates above 5 mm h(-1). NESDIS(1) overestimated for both wind regimes but presented the best westerly representation. NESDIS(2), GSCAT, and GPROF underestimated in both regimes, but GPROF was closer to the observations during the easterly flow.

Automated supervised classification of variable stars in the CoRoT programme Method and application to the first four exoplanet fields

Aims. In this work, we describe the pipeline for the fast supervised classification of light curves observed by the CoRoT exoplanet CCDs. We present the classification results obtained for the first four measured fields, which represent a one-year in-orbit operation. Methods. The basis of the adopted supervised classification methodology has been described in detail in a previous paper, as is its application to the OGLE database. Here, we present the modifications of the algorithms and of the training set to optimize the performance when applied to the CoRoT data. Results. Classification results are presented for the observed fields IRa01, SRc01, LRc01, and LRa01 of the CoRoT mission. Statistics on the number of variables and the number of objects per class are given and typical light curves of high-probability candidates are shown. We also report on new stellar variability types discovered in the CoRoT data. The full classification results are publicly available.

Mimicking nanoribbon behavior using a graphene layer on SiC

We propose a natural way to create quantum-confined regions in graphene in a system that allows large-scale device integration. We show, using first-principles calculations, that a single graphene layer on a trenched region of [000 (1) over bar] SiC mimics (i) the energy bands around the Fermi level and (ii) the magnetic properties of free-standing graphene nanoribbons. Depending on the trench direction, either zigzag or armchair nanoribbons are mimicked. This behavior occurs because a single graphene layer over a SiC surface loses the graphenelike properties, which are restored solely over the trenches, providing in this way a confined strip region.

Directed Abelian algebras and their application to stochastic models

With each directed acyclic graph (this includes some D-dimensional lattices) one can associate some Abelian algebras that we call directed Abelian algebras (DAAs). On each site of the graph one attaches a generator of the algebra. These algebras depend on several parameters and are semisimple. Using any DAA, one can define a family of Hamiltonians which give the continuous time evolution of a stochastic process. The calculation of the spectra and ground-state wave functions (stationary state probability distributions) is an easy algebraic exercise. If one considers D-dimensional lattices and chooses Hamiltonians linear in the generators, in finite-size scaling the Hamiltonian spectrum is gapless with a critical dynamic exponent z=D. One possible application of the DAA is to sandpile models. In the paper we present this application, considering one- and two-dimensional lattices. In the one-dimensional case, when the DAA conserves the number of particles, the avalanches belong to the random walker universality class (critical exponent sigma(tau)=3/2). We study the local density of particles inside large avalanches, showing a depletion of particles at the source of the avalanche and an enrichment at its end. In two dimensions we did extensive Monte-Carlo simulations and found sigma(tau)=1.780 +/- 0.005.

Synergistic interaction between gold nanoparticles and nickel phthalocyanine in layer-by-layer (LbL) films: evidence of constitutional dynamic chemistry (CDC)

The concept of constitutional dynamic chemistry (CDC) based on the control of non-covalent interactions in supramolecular structures is promising for having a large impact on nanoscience and nanotechnology if adequate nanoscale manipulation methods are used. In this study, we demonstrate that the layer-by-layer (LbL) technique may be used to produce electroactive electrodes with ITO coated by tetrasulfonated nickel phthalocyanine (NiTsPc) alternated with poly(allylamine hydrochloride) (PAH) incorporating gold nanoparticles (AuNP), in which synergy has been achieved in the interaction between the nanoparticles and NiTsPc. The catalytic activity toward hydrogen peroxide (H(2)O(2)) in multilayer films was investigated using cyclic voltammetry, where oxidation of H(2)O(2) led to increased currents in the PAH-AuNP/NiTsPc films for the electrochemical processes associated with the phthalocyanine ring and nickel at 0.52 and 0.81 V vs. SCE, respectively, while for PAH/NiTsPc films (without AuNP) only the first redox process was affected. In control experiments we found out that the catalytic activity was not solely due to the presence of AuNP, but rather to the nanoparticles inducing NiTsPc supramolecular structures that favored access to their redox sites, thus yielding strong charge transfer. The combined effects of NiTsPc and AuNP, which could only be observed in nanostructured LbL films, point to another avenue to pursue within the CDC paradigm.

Application of electron paramagnetic resonance Spectroscopy for validation of the novel (AN plus DN) solvent polarity scale

Based on solvation studies of polymers, the sum (1: 1) of the electron acceptor (AN) and electron donor (DN) values of solvents has been proposed as an alternative polarity scale. To test this, the electron paramagnetic resonance isotropic hyperfine splitting constant, a parameter known to be dependent on the polarity/proticity of the medium, was correlated with the (AN+DN) term using three paramagnetic probes. The linear regression coefficient calculated for 15 different solvents was approximately 0.9, quite similar to those of other well-known polarity parameters, attesting to the validity of the (AN+DN) term as a novel ""two-parameter"" solvent polarity scale.

Hybrid layer-by-layer assembly based on animal and vegetable structural materials: multilayered films of collagen and cellulose nanowhiskers

Layer-by-layer (LBL) assembly was used to combine crystalline rod-like nanoparticles obtained from a vegetable source, cellulose nanowhiskers (CNWs), with collagen, the main component of skin and connective tissue found exclusively in animals. The film growth of the multilayered collagen/CNW was monitored by UV-Vis spectroscopy and ellipsometry measurements, whereas the film morphology and surface roughness were characterized by SEM and AFM. UV-Vis spectra showed the deposition of the same amount of collagen, 5 mg m(-2), in each dipping cycle. Ellipsometry data showed an increment in thickness with the number of layers, and the average thickness of each bilayer was found to be 8.6 nm. The multilayered bio-based nanocomposites were formed by single layers of densely packed CNWs adsorbed on top of each thin collagen layer where the hydrogen bonding between collagen amide groups and OH groups of the CNWs plays a mandatory role in the build-up of the thin films. The approach used in this work represents a potential strategy to mimic the characteristics of natural extracellular matrix (ECM) which can be used for applications in the biomedical field.