Relationship between global structural parameters and Enzyme Commission hierarchy: Implications for function prediction

In protein databases there is a substantial number of proteins structurally determined but without function annotation. Understanding the relationship between function and structure can be useful to predict function on a large scale. We have analyzed the similarities in global physicochemical parameters for a set of enzymes which were classified according to the four Enzyme Commission (EC) hierarchical levels. Using relevance theory we introduced a distance between proteins in the space of physicochemical characteristics. This was done by minimizing a cost function of the metric tensor built to reflect the EC classification system. Using an unsupervised clustering method on a set of 1025 enzymes, we obtained no relevant clustering formation compatible with EC classification. The distance distributions between enzymes from the same EC group and from different EC groups were compared by histograms. Such analysis was also performed using sequence alignment similarity as a distance. Our results suggest that global structure parameters are not sufficient to segregate enzymes according to EC hierarchy. This indicates that features essential for function are rather local than global. Consequently, methods for predicting function based on global attributes should not obtain high accuracy in main EC classes prediction without relying on similarities between enzymes from training and validation datasets. Furthermore, these results are consistent with a substantial number of studies suggesting that function evolves fundamentally by recruitment, i.e., a same protein motif or fold can be used to perform different enzymatic functions and a few specific amino acids (AAs) are actually responsible for enzyme activity. These essential amino acids should belong to active sites and an effective method for predicting function should be able to recognize them. (C) 2012 Elsevier Ltd. All rights reserved.

Comparative study of bone repair in mandibular body osteotomy between metallic and absorbable 2.0 mm internal fixation systems. Histological and histometric analysis in dogs: a pilot study

The objective of this study was to compare the bone repair along a mandibular body osteotomy stabilized with 2.0 mm absorbable and metallic systems. 12 male, adult mongrel dogs were divided into two groups (metallic and absorbable) and subjected to unilateral osteotomy between the mandibular third and fourth premolars, which was stabilized by applying two 4-hole plates. At 2 and 18 weeks, three dogs from each group were killed and the osteotomy sites were removed and divided equally into three parts: the upper part was labelled the tension third (TT), the lower part the compression third (CT), and the part between the TT and CT the intermediary third (IT). Regardless of the treatment system, union between the fragments was observed at 18 weeks and the CT showed more advanced stages of bone repair than the TT. Histometric analysis did not reveal any significant differences among the 3 parts or systems in the distance between bone fragments at 2 weeks. Although at 18 weeks the proportions of newly formed bone did not differ among TT, IT and CT, significantly enhanced bone formation was observed in all sections for the metallic group. The patterns of repair were distinct between treatments.

Suitability of distance metrics as indexes of home-range size in tropical rodent species

Estimators of home-range size require a large number of observations for estimation and sparse data typical of tropical studies often prohibit the use of such estimators. An alternative may be use of distance metrics as indexes of home range. However, tests of correlation between distance metrics and home-range estimators only exist for North American rodents. We evaluated the suitability of 3 distance metrics (mean distance between successive captures [SD], observed range length [ORL], and mean distance between all capture points [AD]) as indexes for home range for 2 Brazilian Atlantic forest rodents, Akodon montensis (montane grass mouse) and Delomys sublineatus (pallid Atlantic forest rat). Further, we investigated the robustness of distance metrics to low numbers of individuals and captures per individual. We observed a strong correlation between distance metrics and the home-range estimator. None of the metrics was influenced by the number of individuals. ORL presented a strong dependence on the number of captures per individual. Accuracy of SD and AD was not dependent on number of captures per individual, but precision of both metrics was low with numbers of captures below 10. We recommend the use of SD and AD instead of ORL and use of caution in interpretation of results based on trapping data with low captures per individual.

Morphodynamics of structurally controlled headland-bay beaches in southeastern Brazil: A review

This paper presents a comprehensive review on the interaction between hydrodynamic processes, beach morphology and sedimentology at large scale coastal behaviour along the coastline of Santa Catarina, between Laguna and Sao Francisco Island, a microtidal east coast swell environment with headland and bay geomorphologies. The parabolic bay shape equation has proven to be a convenient and practical tool for studying the stability of the headland-bay beaches, tombolos, and salients in Santa Catarina. The beaches exhibit different patterns of sediment removal as a function of the degree of beach curvature. In highly curved beaches, there is a well-developed shadow zone and a range of morphodynamic conditions, from a sheltered low-energy beach adjacent to the downdrift headland to a high-energy exposed beach on the straight end of the headland-bay beach. The less curved beaches instead, tend to show more uniform behaviour since they are directly exposed to incident waves. There is no obvious relationship between average wave height and mean grain size, showing the importance of sediment source to characterize the sedimentary distribution patterns in the study area. The analysis of beaches showed that beach morphodynamics and sequence profiles for a bay-headland coast in a microtidal east coast environment is a function of geological inheritance (e.g., distance between headlands and orientation, nearshore and inner shelf morphology, coastal plain morphology, and sediment source), and hydrodynamic factors (wave conditions, oceanic wave exposure and relative tidal range). (C) 2009 Elsevier B.V. All rights reserved.

COMPARATIVE ANATOMICAL STUDY OF TWO SPECIES OF SEMELE FROM THAILAND (BIVALVIA: TELLINOIDEA)

An anatomical description of two semelids from Thailand is presented, based on samples from Kungkrabaen Bay, Gulf of Thailand. The species are Semele sinensis A. Adams, 1853, and S. carnicolor (Hanley, 1845), both with Indo-Pacific distributions. Morphology in these two species is typically tellinoidean, each with a long internal ligamental element (resilium), a distance between the inner fold of the mantle edge and the other two folds, long and branched gastric ducts to the digestive diverticula, and a stomach diverticulum located in the posterodorsal corner of the gastric chamber, projecting posteriorly. The main anatomical differentiation between the two species is in the character of the labial palps.

A note on permutation regularity

The existence of a small partition of a combinatorial structure into random-like subparts, a so-called regular partition, has proven to be very useful in the study of extremal problems, and has deep algorithmic consequences. The main result in this direction is the Szemeredi Regularity Lemma in graph theory. In this note, we are concerned with regularity in permutations: we show that every permutation of a sufficiently large set has a regular partition into a small number of intervals. This refines the partition given by Cooper (2006) [10], which required an additional non-interval exceptional class. We also introduce a distance between permutations that plays an important role in the study of convergence of a permutation sequence. (C) 2011 Elsevier B.V. All rights reserved.

Complex networks analysis of language complexity

Methods from statistical physics, such as those involving complex networks, have been increasingly used in the quantitative analysis of linguistic phenomena. In this paper, we represented pieces of text with different levels of simplification in co-occurrence networks and found that topological regularity correlated negatively with textual complexity. Furthermore, in less complex texts the distance between concepts, represented as nodes, tended to decrease. The complex networks metrics were treated with multivariate pattern recognition techniques, which allowed us to distinguish between original texts and their simplified versions. For each original text, two simplified versions were generated manually with increasing number of simplification operations. As expected, distinction was easier for the strongly simplified versions, where the most relevant metrics were node strength, shortest paths and diversity. Also, the discrimination of complex texts was improved with higher hierarchical network metrics, thus pointing to the usefulness of considering wider contexts around the concepts. Though the accuracy rate in the distinction was not as high as in methods using deep linguistic knowledge, the complex network approach is still useful for a rapid screening of texts whenever assessing complexity is essential to guarantee accessibility to readers with limited reading ability. Copyright (c) EPLA, 2012

Landscape changes in Serra do Japi: legal protection or scientific expectation?

The creation of new legally protected areas brings many conflicts that distance the real landscape from the expected according to environmental law or conservation researchers. In this study, we mapped and compared the changes in Serra da Japi (Sao Paulo State, Brazil) throughout 40 years with scenarios of legal protection and scientific expectation on forest conservation, to evaluate the distance between them. This may allow us to infer the direction of historical changes and assist in the debate among decision makers. The results showed that most legal requirements on forest protection in the current landscape have been met. The 1960s was the period when the forest cover was closest to the desirable conservation stage. Although the Serra do Japi has maintained large areas of forests during the entire study period, human interference increased with the expansion of reforestation and urban areas, and access roads were identified as a primary potential driving forces of change. In addition, habitat loss was observed in the landscape, which can represent the first phase of a sequence of modifications detrimental to the environmental conservation of this protected area, including decision changes to land use. In conclusion, the changes evolved toward conservation expectations, but not toward the forest configuration of scientific expectation.

Transcatheter aortic valve implantation with a self-expanding nitinol bioprosthesis: Prediction of the Need for Permanent Pacemaker Using Simple Baseline and Procedural Characteristics

Objective: To ascertain incidence and predictors of new permanent pacemaker (PPM) following transcatheter aortic valve implantation (TAVI) with the self-expanding aortic bioprosthesis. Background: TAVI with the Medtronic Corevalve (MCV) Revalving System (Medtronic, Minneapolis, MN) has been associated with important post-procedural conduction abnormalities and frequent need for PPM. Methods: Overall, 73 consecutive patients with severe symptomatic AS underwent TAVI with the MCV at two institutions; 10 patients with previous pacemaker and 3 patients with previous aortic valve replacement were excluded for this analysis. Clinical, echocardiographic, and procedural data were collected prospectively in a dedicated database. A standard 12-lead ECG was recorded in all patients at baseline, after the procedure and predischarge. Decision to implant PPM was taken according to current guidelines. Logistic multivariable modeling was applied to identify independent predictors of PPM at discharge. Results: Patients exhibited high-risk features as evidenced by advanced age (mean = 82.1 +/- 6.2 years) and high surgical scores (logistic EuroSCORE 23.0 +/- 12.8%, STS score 9.4 +/- 6.9%). The incidence of new PPM was 28.3%. Interventricular septum thickness and logistic Euroscore were the baseline independent predictors of PPM. When procedural variables were included, the independent predictors of PPM were interventricular septum thickness (OR 0.52; 95% CI 0.320.85) and the distance between noncoronary cusp and the distal edge of the prosthesis (OR 1.37; 95% CI 1.031.83). Conclusions: Conduction abnormalities are frequently observed after TAVI with self-expandable bioprosthesis and definitive pacing is required in about a third of the patients, with a clear association with depth of implant and small interventricular septum thickness. (c) 2011 Wiley Periodicals, Inc.

A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

Background: The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. Results: The mapping population parents ('IAC66-6' and 'TUC71-7') contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization. Conclusions: Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposonscIvana_1 (similar to 60) copies in the sugarcane genome, confirming previously reported molecular results. In addition, this research possibly will have indirect implications in crop economics e. g., productivity enhancement via QTL studies, as the mapping population parents differ in response to an important fungal disease.

Cortical mapping with navigated transcranial magnetic stimulation in low-grade glioma surgery

Transcranial magnetic stimulation (TMS) is a promising method for both investigation and therapeutic treatment of psychiatric and neurologic disorders and, more recently, for brain mapping. This study describes the application of navigated TMS for motor cortex mapping in patients with a brain tumor located close to the precentral gyrus. Materials and methods: In this prospective study, six patients with low-grade gliomas in or near the precentral gyrus underwent TMS, and their motor responses were correlated to locations in the cortex around the lesion, generating a functional map overlaid on three-dimensional magnetic resonance imaging (MRI) scans of the brain. To determine the accuracy of this new method, we compared TMS mapping with the gold standard mapping with direct cortical electrical stimulation in surgery. The same navigation system and TMS-generated map were used during the surgical resection procedure. Results: The motor cortex could be clearly mapped using both methods. The locations corresponding to the hand and forearm, found during intraoperative mapping, showed a close spatial relationship to the homotopic areas identified by TMS mapping. The mean distance between TMS and direct cortical electrical stimulation (DES) was 4.16 +/- 1.02 mm (range: 2.56-5.27 mm). Conclusion: Preoperative mapping of the motor cortex with navigated TMS prior to brain tumor resection is a useful presurgical planning tool with good accuracy.

Population divergence of Melipona scutellaris (Hymenoptera: Meliponina) in two restricted areas in Bahia, Brazil

Melipona scutellaris Latreille has great economic and ecological importance, especially because it is a pollinator of native plant species. Despite the importance of this species, there is little information about the conservation status of their populations. The objective of this study was to assess the diversity in populations of M. scutellaris coming from a Semideciduous Forest Fragment and an Atlantic Forest Fragment in the Northeast Brazil, through geometric morphometric analysis of wings in worker bees. In each area, worker bees were collected from 10 colonies, 10 workers per colony. To assess the diversity on the right wings of worker bees, 15 landmarks were plotted and the measures were used in analysis of variance and multivariate analysis, principal component analysis, discriminant analysis and clustering analysis. There were significant differences in the shape of the wing venation patterns between colonies of two sites (Wilk's lambda = 0.000006; p < 0.000001), which is probably due to the geographical distance between places of origin which impedes the gene flow between them. It indicates that inter and intrapopulation morphometric variability exists (p < 0.000001) in M. scutellaris coming from two different biomes, revealing the existence of diversity in these populations, which is necessary for the conservation of this bee species.

Buccal Bone Plate Remodeling After Immediate Implant Placement With and Without Synthetic Bone Grafting and Flapless Surgery: Radiographic Study in Dogs

Recent studies in animals have shown pronounced resorption of the buccal bone plate after immediate implantation. The use of flapless surgical procedures prior to the installation of immediate implants, as well as the use of synthetic bone graft in the gaps represent viable alternatives to minimize buccal bone resorption and to favor osseointegration. The aim of this study was to evaluate the healing of the buccal bone plate following immediate implantation using the flapless approach, and to compare this process with sites in which a synthetic bone graft was or was not inserted into the gap between the implant and the buccal bone plate. Lower bicuspids from 8 dogs were bilaterally extracted without the use of flaps, and 4 implants were installed in the alveoli in each side of the mandible and were positioned 2.0 mm from the buccal bone plate (gap). Four groups were devised: 2.0-mm subcrestal implants (3.3 x 8 mm) using bone grafts (SCTG), 2.0-mm subcrestal implants without bone grafts (SCCG), equicrestal implants (3.3 x 10 mm) with bone grafts (EGG), and equicrestal implants without bone grafts (ECCG). One week following the surgical procedures, metallic prostheses were installed, and within 12 weeks the dogs were sacrificed. The blocks containing the individual implants were turned sideways, and radiographic imaging was obtained to analyze the remodeling of the buccal bone plate. In the analysis of the resulting distance between the implant shoulder and the bone crest, statistically significant differences were found in the SCTG when compared to the ECTG (P = .02) and ECCG (P = .03). For mean value comparison of the resulting linear distance between the implant surface and the buccal plate, no statistically significant difference was found among all groups (P > .05). The same result was observed in the parameter for presence or absence of tissue formation between the implant surface and buccal plate. Equicrestally placed implants, in this methodology, presented little or no loss of the buccal bone. The subcrestally positioned implants presented loss of buccal bone, even though synthetic bone graft was used. The buccal bone, however, was always coronal to the implant shoulder.

Microsurgical Anatomy of the Optic Radiation and Related Fibers in 3-Dimensional Images

BACKGROUND: The fiber dissection technique provides unique 3-dimensional anatomic knowledge of the white matter. OBJECTIVE: To examine the optic radiation anatomy and its important relationship with the temporal stem and to discuss its findings in relation to the approaches to temporal lobe lesions. METHODS: We studied 40 cerebral hemispheres of 20 brains that had been fixed in formalin solution for 40 days. After removal of the arachnoid membrane, the hemispheres were frozen, and the Klingler technique was used for dissection under magnification. Stereoscopic 3-dimensional images of the dissection were obtained for illustration. RESULTS: The optic radiations are located deep within the superior and middle temporal gyri, always above the inferior temporal sulcus. The mean distance between the cortical surface and the lateral edge of the optic radiation was 21 mm. Its fibers are divided into 3 bundles after their origin. The mean distance between the anterior tip of the temporal horn and the Meyer loop was 4.5 mm, between the temporal pole and the anterior border of the Meyer loop was 28.4 mm, and between the limen insulae and the Meyer loop was 10.7 mm. The mean distance between the lateral geniculate body and the lateral margin of the central bundle of the optic radiation was 17.4 mm. CONCLUSION: The white matter fiber dissection reveals the tridimensional intrinsic architecture of the brain, and its knowledge regarding the temporal lobe is particularly important for the neurosurgeon, mostly because of the complexity of the optic radiation and related fibers.

INFLUENCE OF CORTICAL BONE THICKNESS ON THE ULTRASOUND VELOCITY

Objective: An experimental in vitro study was carried out to evaluate the influence of cortical bone thickness on ultrasound propagation velocity. Methods: Sixty bone plates were used, made from bovine femurs, with thickness ranging from 1 to 6 mm (10 of each). The ultrasound velocity measurements were performed using a device specially designed for this purpose, in an underwater acoustic tank and with direct contact using contact gel. The transducers were positioned in two ways: on opposite sides, with the bone between them, for the transverse measurement; and parallel to each other, on the same side of the bone plates, for the axial measurements. Results: In the axial transmission mode, the ultrasound velocity speed increased with cortical bone thickness, regardless of the distance between the transducers, up to a thickness of 5 mm, then remained constant thereafter. There were no changes in velocity when the transverse measures were made. Conclusion: Ultrasound velocity increased with cortical bone thickness in the axial transmission mode, until the thickness surpasses the wavelength, after which point it remained constant. Level of Evidence: Experimental Study.