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.

Is sympathectomy at T4 level better than at T3 level for treating palmar hyperhidrosis?

Purpose: We compared the results from a video-assisted thoracoscopic sympathectomy (VTS) at the T4 denervation level with those from a VTS at the T3 level for the treatment of palmar hyperhydrosis (PH). Methods: Seventy patients with PH were prospectively followed for VTS at the T3 or T4 denervation levels for 6 months. The end points of this study were: absence of PH, compensatory hyperhydrosis (CH), and quality-of-life assessment. Results: Sixty-seven patients reported a complete resolution of PH after surgery. One failure occurred in the T3 group and 2 in the T4 group. When anhydrosis was obtained, we noticed totally dry hands in 26 patients in the T3 group and 6 patients in the T4 group. The other 27 patients in the T4 group and 8 in the T3 group maintained a small level of sweating and were also considered to be therapeutic successes. At 6 months, 25 patients in the T4 group had some degree of CH (71.42%) and all patients in the T3 group (100%), though the T4 group had a lower degree of severity of CH at the 6-month follow-up (P < 0.05). After the operation, quality of life was improved similarly in both groups. Conclusions: VTS at either the T3 or T4 level provides an effective treatment for PH. VTS at the T4 level is associated with a less severe form of CH. Despite the occurrence of CH, patients' quality of life is significantly improved following VTS at the T3 or T4 levels. For this reason, the T4 resection can now be used as a treatment for PH.

Comparison of the Effects of Electrical Field Stimulation and Low-Level Laser Therapy on Bone Loss in Spinal Cord-Injured Rats

Objective: This study investigated the effects of low-level laser therapy (LLLT) and electrical stimulation (ES) on bone loss in spinal cord-injured rats. Materials and Methods: Thirty-seven male Wistar rats were divided into four groups: standard control group (CG); spinal cord-injured control (SC); spinal cord-injured treated with laser (SCL; GaAlAs, 830 nm, CW, 30mW/cm, 250 J/cm(2)); and spinal cord-injured treated with electrical field stimulation (SCE; 1.5 MHz, 1: 4 duty cycles, 30 mW, 20 min). Biomechanical, densitometric, and morphometric analyses were performed. Results: SC rats showed a significant decrease in bone mass, biomechanical properties, and morphometric parameters (versus CG). SCE rats showed significantly higher values of inner diameter and internal and external areas of tibia diaphyses; and the SCL group showed a trend toward the same result (versus SC). No increase was found in either mechanical or densitometric parameters. Conclusion: We conclude that the mentioned treatments were able to initiate a positive bone-tissue response, maybe through stimulation of osteoblasts, which was able to determine the observed morphometric modifications. However, the evoked tissue response could not determine either biomechanical or densitometric modifications.

Decision theory applied to image quality control in radiology

Background: The present work aims at the application of the decision theory to radiological image quality control ( QC) in diagnostic routine. The main problem addressed in the framework of decision theory is to accept or reject a film lot of a radiology service. The probability of each decision of a determined set of variables was obtained from the selected films. Methods: Based on a radiology service routine a decision probability function was determined for each considered group of combination characteristics. These characteristics were related to the film quality control. These parameters were also framed in a set of 8 possibilities, resulting in 256 possible decision rules. In order to determine a general utility application function to access the decision risk, we have used a simple unique parameter called r. The payoffs chosen were: diagnostic's result (correct/incorrect), cost (high/low), and patient satisfaction (yes/no) resulting in eight possible combinations. Results: Depending on the value of r, more or less risk will occur related to the decision-making. The utility function was evaluated in order to determine the probability of a decision. The decision was made with patients or administrators' opinions from a radiology service center. Conclusion: The model is a formal quantitative approach to make a decision related to the medical imaging quality, providing an instrument to discriminate what is really necessary to accept or reject a film or a film lot. The method presented herein can help to access the risk level of an incorrect radiological diagnosis decision.

Effects of Low-Level Laser Therapy on Pain and Scar Formation After Inguinal Herniation Surgery: A Randomized Controlled Single-Blind Study

Objective: The aim of this study was to investigate the efficacy of an infrared GaAlAs laser operating with a wavelength of 830 nm in the postsurgical scarring process after inguinal-hernia surgery. Background: Low-level laser therapy (LLLT) has been shown to be beneficial in the tissue-repair process, as previously demonstrated in tissue culture and animal experiments. However, there is lack of studies on the effects of LLLT on postsurgical scarring of incisions in humans using an infrared 830-nm GaAlAs laser. Method: Twenty-eight patients who underwent surgery for inguinal hernias were randomly divided into an experimental group (G1) and a control group (G2). G1 received LLLT, with the first application performed 24 h after surgery and then on days 3, 5, and 7. The incisions were irradiated with an 830-nm diode laser operating with a continuous power output of 40 mW, a spot-size aperture of 0.08 cm(2) for 26 s, energy per point of 1.04 J, and an energy density of 13 J/cm(2). Ten points per scar were irradiated. Six months after surgery, both groups were reevaluated using the Vancouver Scar Scale (VSS), the Visual Analog Scale, and measurement of the scar thickness. Results: G1 showed significantly better results in the VSS totals (2.14 +/- 1.51) compared with G2 (4.85 +/- 1.87); in the thickness measurements (0.11 cm) compared with G2 (0.19 cm); and in the malleability (0.14) compared with G2 (1.07). The pain score was also around 50% higher in G2. Conclusion: Infra-red LLLT (830 nm) applied after inguinal-hernia surgery was effective in preventing the formation of keloids. In addition, LLLT resulted in better scar appearance and quality 6 mo postsurgery.

Real-Time PCR in HIV/Trypanosoma cruzi Coinfection with and without Chagas Disease Reactivation: Association with HIV Viral Load and CD4(+) Level

Background: Reactivation of chronic Chagas disease, which occurs in approximately 20% of patients coinfected with HIV/Trypanosoma cruzi (T. cruzi), is commonly characterized by severe meningoencephalitis and myocarditis. The use of quantitative molecular tests to monitor Chagas disease reactivation was analyzed. Methodology: Polymerase chain reaction (PCR) of kDNA sequences, competitive (C-) PCR and real-time quantitative (q) PCR were compared with blood cultures and xenodiagnosis in samples from 91 patients (57 patients with chronic Chagas disease and 34 with HIV/T. cruzi coinfection), of whom 5 had reactivation of Chagas disease and 29 did not. Principal Findings: qRT-PCR showed significant differences between groups; the highest parasitemia was observed in patients infected with HIV/T. cruzi with Chagas disease reactivation (median 1428.90 T. cruzi/mL), followed by patients with HIV/T. cruzi infection without reactivation (median 1.57 T. cruzi/mL) and patients with Chagas disease without HIV (median 0.00 T. cruzi/mL). Spearman's correlation coefficient showed that xenodiagnosis was correlated with blood culture, C-PCR and qRT-PCR. A stronger Spearman correlation index was found between C-PCR and qRT-PCR, the number of parasites and the HIV viral load, expressed as the number of CD4(+) cells or the CD4(+)/CD8(+) ratio. Conclusions: qRT-PCR distinguished the groups of HIV/T. cruzi coinfected patients with and without reactivation. Therefore, this new method of qRT-PCR is proposed as a tool for prospective studies to analyze the importance of parasitemia (persistent and/or increased) as a criterion for recommending pre-emptive therapy in patients with chronic Chagas disease with HIV infection or immunosuppression. As seen in this study, an increase in HIV viral load and decreases in the number of CD4(+) cells/mm(3) and the CD4(+)/CD8(+) ratio were identified as cofactors for increased parasitemia that can be used to target the introduction of early, pre-emptive therapy.

The variability and predictors of quality of AIDS care services in Brazil

Background: Since establishing universal free access to antiretroviral therapy in 1996, the Brazilian Health System has increased the number of centers providing HIV/AIDS outpatient care from 33 to 540. There had been no formal monitoring of the quality of these services until a survey of 336 AIDS health centers across 7 Brazilian states was undertaken in 2002. Managers of the services were asked to assess their clinics according to parameters of service inputs and service delivery processes. This report analyzes the survey results and identifies predictors of the overall quality of service delivery. Methods: The survey involved completion of a multiple-choice questionnaire comprising 107 parameters of service inputs and processes of delivering care, with responses assessed according to their likely impact on service quality using a 3-point scale. K-means clustering was used to group these services according to their scored responses. Logistic regression analysis was performed to identify predictors of high service quality. Results: The questionnaire was completed by 95.8% (322) of the managers of the sites surveyed. Most sites scored about 50% of the benchmark expectation. K-means clustering analysis identified four quality levels within which services could be grouped: 76 services (24%) were classed as level 1 (best), 53 (16%) as level 2 (medium), 113 (35%) as level 3 (poor), and 80 (25%) as level 4 (very poor). Parameters of service delivery processes were more important than those relating to service inputs for determining the quality classification. Predictors of quality services included larger care sites, specialization for HIV/AIDS, and location within large municipalities. Conclusion: The survey demonstrated highly variable levels of HIV/AIDS service quality across the sites. Many sites were found to have deficiencies in the processes of service delivery processes that could benefit from quality improvement initiatives. These findings could have implications for how HIV/AIDS services are planned in Brazil to achieve quality standards, such as for where service sites should be located, their size and staffing requirements. A set of service delivery indicators has been identified that could be used for routine monitoring of HIV/AIDS service delivery for HIV/AIDS in Brazil (and potentially in other similar settings).

An assessment of population structure in eight breeds of cattle using a whole genome SNP panel

Background: Analyses of population structure and breed diversity have provided insight into the origin and evolution of cattle. Previously, these studies have used a low density of microsatellite markers, however, with the large number of single nucleotide polymorphism markers that are now available, it is possible to perform genome wide population genetic analyses in cattle. In this study, we used a high-density panel of SNP markers to examine population structure and diversity among eight cattle breeds sampled from Bos indicus and Bos taurus. Results: Two thousand six hundred and forty one single nucleotide polymorphisms ( SNPs) spanning all of the bovine autosomal genome were genotyped in Angus, Brahman, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black, Limousin and Nelore cattle. Population structure was examined using the linkage model in the program STRUCTURE and Fst estimates were used to construct a neighbor-joining tree to represent the phylogenetic relationship among these breeds. Conclusion: The whole-genome SNP panel identified several levels of population substructure in the set of examined cattle breeds. The greatest level of genetic differentiation was detected between the Bos taurus and Bos indicus breeds. When the Bos indicus breeds were excluded from the analysis, genetic differences among beef versus dairy and European versus Asian breeds were detected among the Bos taurus breeds. Exploration of the number of SNP loci required to differentiate between breeds showed that for 100 SNP loci, individuals could only be correctly clustered into breeds 50% of the time, thus a large number of SNP markers are required to replace the 30 microsatellite markers that are currently commonly used in genetic diversity studies.

Low-Level Laser Therapy on the Viability of Skin Flap in Rats Subjected to Deleterious Effect of Nicotine

Objective: The purpose of this study was to evaluate the effect of 830-nm laser in blocking the action of nicotine on the viability of skin flap. Background data: The authors have analyzed the deleterious effect of cigarette smoke or nicotine on the skin flap alone with evidence of increased skin necrosis in the flap. Materials and methods: Twenty-four Wistar-albino rats were divided into three groups of eight animals each: Group 1 (control), subjected to a surgical technique to obtain a flap for cranial base, laser irradiation simulation, and a subcutaneous injection of saline; Group 2, similar to Group 1, with subcutaneous injection of nicotine (2mg/kg/day) for a period of 1 week before and 1 week after surgery; and Group 3, similar to Group 2, with skin flaps subjected to a lambda 830-nm laser irradiation. The laser parameters used were: power 30 mW, beam area 0.07cm(2), irradiance 429 mW/cm(2), irradiation time 84 sec, total energy 2.52J, and energy density 36J/cm(2). The laser was used immediately after surgery and for 4 consecutive days, in one point at 2.5 cm of the flap cranial base. The areas of necrosis were examined by two macroscopic analyses: paper template and Mini-Mop (R). The pervious blood vessels were also counted. Results: The results were statistically analyzed by ANOVA and post-test contrast orthogonal method (multiple comparisons), showing that the laser decreased the area of necrosis in flaps subjected to nicotine, and consequently, increased the number of blood vessels (p < 0.05). Conclusions: The laser proved to be an effective way to decrease the area of necrosis in rats subjected to nicotine, making them similar to the control group.

Effect of Low-Level Laser Therapy on Malondialdehyde Concentration in Random Cutaneous Flap Viability

Objective: The aim of this study was to assess the effects of 830 and 670 nm laser on malondialdehyde (MDA) concentration in random skin-flap survival. Background Data: Low-level laser therapy (LLLT) has been reported to be successful in stimulating the formation of new blood vessels and activating superoxide-dismutase delivery, thus helping the inhibition of free-radical action and consequently reducing necrosis. Materials and Methods: Thirty Wistar rats were used and divided into three groups, with 10 rats in each one. A random skin flap was raised on the dorsum of each animal. Group 1 was the control group; group 2 received 830 nm laser radiation; and group 3 was submitted to 670 nm laser radiation. The animals underwent laser therapy with 36 J/cm(2) energy density immediately after surgery and on the 4 days subsequent to surgery. The application site of the laser radiation was 1 point, 2.5 cm from the flap's cranial base. The percentage of the skin-flap necrosis area was calculated 7 days postoperative using the paper-template method, and a skin sample was collected immediately after as a way of determining the MDA concentration. Results: Statistically significant differences were found between the necrosis percentages, with higher values seen in group 1 compared with groups 2 and 3. Groups 2 and 3 did not present statistically significant differences (p > 0.05). Group 3 had a lower concentration of MDA values compared to the control group (p < 0.05). Conclusion: LLLT was effective in increasing the random skin-flap viability in rats, and the 670 nm laser was efficient in reducing the MDA concentration.

Low-Level Laser Therapy in Burning Mouth Syndrome Patients: A Pilot Study

Objective: The aim of this study was to investigate the effect of low-level laser therapy (LLLT) on the treatment of burning mouth syndrome (BMS). In addition, the laser effect was compared on the different affected oral sites. Materials and Methods: Eleven subjects with a total of 25 sites (tongue, lower lip, upper lip, and palate) affected by a burning sensation were selected. The affected areas were irradiated once a week for three consecutive weeks with an infrared laser (lambda = 790 nm). The probe was kept in contact with the tissue, and the mucosal surface was scanned during the irradiation. The exposure time was calculated based on the fluence of 6 J/cm(2), the output power of 120 mW, and the area to be treated. Burning intensity was recorded through a visual analog scale before and after the treatment and at the 6-week follow-up. The percentage of the improvement in symptoms was also obtained. Results: Burning intensity at the end of the laser therapy was statistically lower than at the beginning (p < 0.01). Patients reported an 80.4% reduction in the intensity of symptoms after laser treatment. There was no statistical difference between the end of the treatment and the 6-week follow-up, except for the tongue site. Conclusion: Under the investigated parameters, infrared LLLT proved to be a valuable alternative for BMS treatment, providing a significant and lasting reduction in symptoms.

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.)

Observational evidences on the modulation of the South American Low Level Jet east of the Andes according the ENSO variability

The differences on the phase and wavelength of the quasi-stationary waves over the South America generated by El Nino (EN) and La Nina (LN) events seem to affect the daily evolution of the South American Low Level Jet east of the Andes (SALLJ). For the austral summer period of 1977 2004 the SALLJ episodes detected according to Bonner criterion 1 show normal to above-normal frequency in EN years, and in LN years the episodes show normal to below-normal frequency. During EN and LN years the SALLJ episodes were associated with positive rainfall anomalies over the La Plata Basin, but more intense during LN years. During EN years the increase in the SALLJ cases were associated to intensification of the Subtropical Jet (SJ) around 30 degrees S and positive Sea Level Pressure (SLP) anomalies over the western equatorial Atlantic and tropical South America, particularly over central Brazil. This favored the intensification of the northeasterly trade winds over the northern continent and it channeled by the Andes mountain to the La Plata Basin region where negative SLP are found. The SALLJ cases identified during the LN events were weaker and less frequent when compared to those for EN years. In this case the SJ was weaker than in EN years and the negative SLP anomalies over the tropical continent contributed to the inversion of the northeasterly trade winds. Also a southerly flow anomaly was generated by the geostrophic balance due to the anomalous blocking over southeast Pacific and the intense cyclonic transient over the southern tip of South America. As result the warm tropical air brought by the SALLJ encounters the cold extratropical air from the southerly winds over the La Plata basin. This configuration can increase the conditional instability over the La Plata basin and may explain the more intense positive rainfall anomalies in SALLJ cases during LN years than in EN years.