Computational framework to support integration of biomolecular and clinical data within a translational approach

Background The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. Results We have implemented an extension of Chado – the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Conclusions Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different “omics” technologies with patient’s clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans webcite.

Effect of a low-level laser on bone regeneration after rapid maxillary expansion

Introduction: In this study, we evaluated the effects of a low-level laser on bone regeneration in rapid maxillary expansion procedures. Methods: Twenty-seven children, aged 8 to 12 years, took part in the experiment, with a mean age of 10.2 years, divided into 2 groups: the laser group (n=14), in which rapid maxillary expansion was performed in conjunction with laser use, and the no-laser group (n=13), with rapid maxillary expansion only. The activation protocol of the expansion screw was 1 full turn on the first day and a half turn daily until achieving overcorrection. The laser type used was a laser diode (TWIN Laser; MMOptics, Sao Carlos, Brazil), according to the following protocol: 780 nm wavelength, 40 mW power, and 10 J/cm(2) density at 10 points located around the midpalatal suture. The application stages were 1 (days 1-5 of activation), 2 (at screw locking, on 3 consecutive days), 3, 4, and 5 (7, 14, and 21 days after stage 2). Occlusal radiographs of the maxilla were taken with the aid of an aluminum scale ruler as a densitometry reference at different times: T1 (initial), T2 (day of locking), T3 (3-5 days after T2), T4 (30 days after T3), and T5 (60 days after T4). The radiographs were digitized and submitted to imaging software (Image Tool; UTHSCSA, San Antonio, Tex) to measure the optic density of the previously selected areas. To perform the statistical test, analysis of covariance was used, with the time for the evaluated stage as the covariable. In all tests, a significance level of 5% (P<0.05) was adopted. Results: From the evaluation of bone density, the results showed that the laser improved the opening of the midpalatal suture and accelerated the bone regeneration process. Conclusions: The low-level laser, associated with rapid maxillary expansion, provided efficient opening of the midpalatal suture and influenced the bone regeneration process of the suture, accelerating healing. (Am J Orthod Dentofacial Orthop 2012;141:444-50)

In Vitro Analysis of Bacterial Morphology by Atomic Force Microscopy of Low Level Laser Therapy 660, 830 and 904 nm

Objective: The objective of this study was to analyze the bacterial morphology by atomic force microscopy (AFM) after the application of low-level laser therapy (LLLT) in in vitro culture of Staphylococcus aureus ATCC 29213. Background data: Infections caused by S. aureus are among the highest occurring in hospitals and can often colonize pressure ulcers. LLLT is among the methods used to accelerate the healing of ulcers. However, there is no consensus on its effect on bacteria. Materials and methods: After being cultivated and seeded, the cultures were irradiated using wavelengths of 660, 830, and 904 nm at fluences of 0, 1, 2, 3, 4, 5, and 16 J/cm(2). Viable cells of S. aureus strain were counted after 24 h incubation. To analyze the occurrence of morphological changes, the topographical measurement of bacterial cells was analyzed using the AFM. Results: The overall assessment revealed that the laser irradiation reduced the S. aureus growth using 830 and 904 nm wavelengths; the latter with the greatest inhibition of the colony-forming units (CFU/mL) (331.1 +/- 38.19 and 137.38 +/- 21.72). Specifically with 660 nm, the statistical difference occurred only at a fluence of 3 J/cm(2). Topographical analysis showed small changes in morphological conformity of the samples tested. Conclusions: LLLT reduced the growth of S. aureus with 830 and 904 nm wavelengths, particularly with 904 nm at a fluence of 3 J/cm(2), where the greatest topographical changes of the cell structure occurred.

Low Level Laser Therapy as an Adjunctive Technique In the Management of Temporomandibular Disorders

The purpose of this study was to assess the effect of low level laser therapy on subjects with intra-articular temporomandibular disorders (IA-TMD), and to quantify and compare severity of signs and symptoms before, during, and after the laser applications. The sample consisted of 45 subjects randomly divided into three groups (G) of 15 subjects each: G-I: 15 individuals with IA-TMD submitted to an energy dose of 52.5 J/cm(2); G-II: dose of 105.0 J/cm(2); and G-III: placebo group (0 J/cm(2)). In all groups, the applications were performed on condylar points on the masseter and anterior temporalis muscles. Two weekly sessions were held for five weeks, totaling 10 applications. The assessed variables were: mandibular movements and painful symptoms evoked by muscle palpation. These variables were measured before starting the study, then immediately after the first, fifth, and tenth laser application, and finally, 32 days after completing the applications. The results showed that there were statistically significant differences for G-I and G-II at the level of 1% between the doses, as well as between assessments. Therefore, it was concluded that the use of low level laser increased the mean mandibular range of motion and reduced painful symptoms in the groups that received effective treatment, which did not occur in the placebo group.

Brazilian guidelines for the application of transcranial ultrasound as a diagnostic test for the confirmation of brain death

Neurosonological studies, specifically transcranial Doppler (TCD) and transcranial color-coded duplex (TCCD), have high level of specificity and sensitivity and they are used as complementary tests for the diagnosis of brain death (BD). A group of experts, from the Neurosonology Department of the Brazilian Academy of Neurology, created a task force to determine the criteria for the following aspects of diagnosing BD in Brazil: the reliability of TCD methodology; the reliability of TCCD methodology; neurosonology training and skills; the diagnosis of encephalic circulatory arrest; and exam documentation for BD. The results of this meeting are presented in the current paper.

Network-based high level data classification

Traditional supervised data classification considers only physical features (e. g., distance or similarity) of the input data. Here, this type of learning is called low level classification. On the other hand, the human (animal) brain performs both low and high orders of learning and it has facility in identifying patterns according to the semantic meaning of the input data. Data classification that considers not only physical attributes but also the pattern formation is, here, referred to as high level classification. In this paper, we propose a hybrid classification technique that combines both types of learning. The low level term can be implemented by any classification technique, while the high level term is realized by the extraction of features of the underlying network constructed from the input data. Thus, the former classifies the test instances by their physical features or class topologies, while the latter measures the compliance of the test instances to the pattern formation of the data. Our study shows that the proposed technique not only can realize classification according to the pattern formation, but also is able to improve the performance of traditional classification techniques. Furthermore, as the class configuration's complexity increases, such as the mixture among different classes, a larger portion of the high level term is required to get correct classification. This feature confirms that the high level classification has a special importance in complex situations of classification. Finally, we show how the proposed technique can be employed in a real-world application, where it is capable of identifying variations and distortions of handwritten digit images. As a result, it supplies an improvement in the overall pattern recognition rate.

Effect of topical clay application on the synthesis of collagen in skin: an experimental study

Background. Clay is often used in cosmetic treatments, although little is known about its action. Aim. To evaluate the effect of topical clay application on the histoarchitecture of collagen fibres in rat skin. Methods. Animals received a daily application of clay and retinoic acid (RA) 0.025% to the dorsal skin over 7 and 14 days, under vaporization at 37 degrees C for 40 min. Control skin was not vaporized. Samples from each region were excised, and stained with picrosirius red for collagen evaluation. Results. Seven days after clay treatment, an increase in the number of collagen fibres was observed in treated skin compared with control skin (51.74 +/- 1.28 vs. 43.39 +/- 1.79%, respectively, P < 0.01), whereas RA did not alter the collagen level (45.66 +/- 1.10%). Clay application over 14 days did not induce a further increase in skin collagen, whereas treatment with RA did (58.07 +/- 1.59%; P = 0.001 vs. control). Conclusion. Clay application promotes an increase in the number of collagen fibres, which may account for its beneficial effects.

Low-level laser therapy (LLLT) in human progressive-intensity running: effects on exercise performance, skeletal muscle status, and oxidative stress

The aim of this work was to evaluate the effects of low-level laser therapy (LLLT) on exercise performance, oxidative stress, and muscle status in humans. A randomized double-blind placebo-controlled crossover trial was performed with 22 untrained male volunteers. LLLT (810 nm, 200 mW, 30 J in each site, 30 s of irradiation in each site) using a multi-diode cluster (with five spots - 6 J from each spot) at 12 sites of each lower limb (six in quadriceps, four in hamstrings, and two in gastrocnemius) was performed 5 min before a standardized progressive-intensity running protocol on a motor-drive treadmill until exhaustion. We analyzed exercise performance (VO(2 max), time to exhaustion, aerobic threshold and anaerobic threshold), levels of oxidative damage to lipids and proteins, the activities of the antioxidant enzymes superoxide dismutase (SOD) and catalase (CAT), and the markers of muscle damage creatine kinase (CK) and lactate dehydrogenase (LDH). Compared to placebo, active LLLT significantly increased exercise performance (VO(2 max) p = 0.01; time to exhaustion, p = 0.04) without changing the aerobic and anaerobic thresholds. LLLT also decreased post-exercise lipid (p = 0.0001) and protein (p = 0.0230) damages, as well as the activities of SOD (p = 0.0034), CK (p = 0.0001) and LDH (p = 0.0001) enzymes. LLLT application was not able to modulate CAT activity. The use of LLLT before progressive-intensity running exercise increases exercise performance, decreases exercise-induced oxidative stress and muscle damage, suggesting that the modulation of the redox system by LLLT could be related to the delay in skeletal muscle fatigue observed after the use of LLLT.

Influence of low-level laser associated with osteogenic proteins recombinant human BMP-2 and Hevea brasiliensis on bone repair in Wistar rats

This study analyzed the newly formed bone tissue after application of recombinant human BMP-2 (rhBMP-2) and P-1 (extracted from Hevea brasiliensis) proteins, 2 weeks after the creation of a critical bone defect in male Wistar rats treated or not with a low-intensity laser (GaAlAs 780 nm, 60 mW of power, and energy density dose of 30 J/cm2). The animals were divided into two major groups: (1) bone defect plus low-intensity laser treatment and (2) bone defect without laser irradiation. The following subgroups were also analyzed: (a) 5 mu g of pure rhBMP-2; (b) 5 mu g of pure P-1 fraction; (c) 5 mu g of rhBMP-2/monoolein gel; (d) 5 mu g of P-1 fraction/monoolein gel; (e) pure monoolein gel. Comparisons of the groups receiving laser treatment with those that did not receive laser irradiation show differences in the areas of new bone tissue. The group treated with 5 mu g of rhBMP-2 and laser irradiation was not significantly different (P >0.05) than the nonirradiated group that received the same treatment. The irradiated, rhBMP-2/monoolein gel treatment group showed a lower area of bone formation than the nonirradiated, rhBMP-2/gel monoolein treatment group (P < 0.001). The area of new bone tissue in the other nonirradiated and irradiated groups was not significantly different (P > 0.05). Furthermore, the group that received the 5 mu g of rhBMP-2 application showed the greatest bone formation. We conclude that the laser treatment did not interfere with the area of new bone tissue growth and that the greatest stimulus for bone formation involved application of the rhBMP-2 protein. Microsc. Res. Tech. 2011. (c) 2011 Wiley Periodicals, Inc.

Low-level laser therapy (808 nm) reduces inflammatory response and oxidative stress in rat tibialis anterior muscle after cryolesion

Background and Objective Muscle regeneration is a complex phenomenon, involving coordinated activation of several cellular responses. During this process, oxidative stress and consequent tissue damage occur with a severity that may depend on the intensity and duration of the inflammatory response. Among the therapeutic approaches to attenuate inflammation and increase tissue repair, low-level laser therapy (LLLT) may be a safe and effective clinical procedure. The aim of this study was to evaluate the effects of LLLT on oxidative/nitrative stress and inflammatory mediators produced during a cryolesion of the tibialis anterior (TA) muscle in rats. Material and Methods Sixty Wistar rats were randomly divided into three groups (n?=?20): control (BC), injured TA muscle without LLLT (IC), injured TA muscle submitted to LLLT (IRI). The injured region was irradiated daily for 4 consecutive days, starting immediately after the lesion using a AlGaAs laser (continuous wave, 808?nm, tip area of 0.00785?cm2, power 30?mW, application time 47?seconds, fluence 180?J/cm2; 3.8?mW/cm2; and total energy 1.4?J). The animals were sacrificed on the fourth day after injury. Results LLLT reduced oxidative and nitrative stress in injured muscle, decreased lipid peroxidation, nitrotyrosine formation and NO production, probably due to reduction in iNOS protein expression. Moreover, LLLT increased SOD gene expression, and decreased the inflammatory response as measured by gene expression of NF-k beta and COX-2 and by TNF-a and IL-1 beta concentration. Conclusion These results suggest that LLLT could be an effective therapeutic approach to modulate oxidative and nitrative stress and to reduce inflammation in injured muscle. Lasers Surg. Med. 44: 726735, 2012. (c) 2012 Wiley Periodicals, Inc.

Effect of low-level laser therapy on pain levels in patients with temporomandibular disorders: a systematic review

Temporomandibular disorders (TMD) are characterized by the presence of temporomandibular joint (TMJ) and/or masticatory muscle pain and dysfunction. Low-level laser is presented as an adjuvant therapeutic modality for the treatment of TMD, especially when the presence of inflammatory pain is suspected. Objective: To systematically review studies that investigated the effect of low level laser therapy (LLLT) on the pain levels in individuals with TMD. Material and Methods: The databases Scopus, embase, ebsco and PubMed were reviewed from January/2003 to October/2010 with the following keywords: laser therapy, low-level laser therapy, temporomandibular joint disorders, temporomandibular joint dysfunction syndrome, temporomandibular joint, temporomandibular, facial pain and arthralgia, with the inclusion criteria for intervention studies in humans. exclusion criteria adopted were intervention studies in animals, studies that were not written in english, Spanish or Portuguese, theses, monographs, and abstracts presented in scientific events. Results: After a careful review, 14 studies fit the criteria for inclusion, of which, 12 used a placebo group. As for the protocol for laser application, the energy density used ranged from 0.9 to 105 J/cm², while the power density ranged from 9.8 to 500 mW. The number of sessions varied from 1 to 20 and the frequency of applications ranged from daily for 10 days to 1 time per week for 4 weeks. A reduction in pain levels was reported in 13 studies, with 9 of these occurring only in the experimental group, and 4 studies reporting pain relief for both the experimental group and for the placebo. Conclusion: Most papers showed that LLLT seemed to be effective in reducing pain from TMD. However, the heterogeneity of the standardization regarding the parameters of laser calls for caution in interpretation of these results. Thus, it is necessary to conduct further research in order to obtain a consensus regarding the best application protocol for pain relief in patients with TMD.