DNA for nano-bio scale computation of chemical formalisms using Higher Order Logic (HOL) and analysis using an interdisciplinary approach

Bio-molecular computing, 'computations performed by bio-molecules', is already challenging traditional approaches to computation both theoretically and technologically. Often placed within the wider context of ´bio-inspired' or 'natural' or even 'unconventional' computing, the study of natural and artificial molecular computations is adding to our understanding of biology, physical sciences and computer science well beyond the framework of existing design and implementation paradigms. In this introduction, We wish to outline the current scope of the field and assemble some basic arguments that, bio-molecular computation is of central importance to computer science, physical sciences and biology using HOL - Higher Order Logic. HOL is used as the computational tool in our R&D work. DNA was analyzed as a chemical computing engine, in our effort to develop novel formalisms to understand the molecular scale bio-chemical computing behavior using HOL. In our view, our focus is one of the pioneering efforts in this promising domain of nano-bio scale chemical information processing dynamics.

Comparing support vector machines and artificial neural networks in the recognition of steering angle for driving of mobile robots through paths in plantations

The use of mobile robots turns out to be interesting in activities where the action of human specialist is difficult or dangerous. Mobile robots are often used for the exploration in areas of difficult access, such as rescue operations and space missions, to avoid human experts exposition to risky situations. Mobile robots are also used in agriculture for planting tasks as well as for keeping the application of pesticides within minimal amounts to mitigate environmental pollution. In this paper we present the development of a system to control the navigation of an autonomous mobile robot through tracks in plantations. Track images are used to control robot direction by pre-processing them to extract image features. Such features are then submitted to a support vector machine and an artificial neural network in order to find out the most appropriate route. A comparison of the two approaches was performed to ascertain the one presenting the best outcome. The overall goal of the project to which this work is connected is to develop a real time robot control system to be embedded into a hardware platform. In this paper we report the software implementation of a support vector machine and of an artificial neural network, which so far presented respectively around 93% and 90% accuracy in predicting the appropriate route. (C) 2013 The Authors. Published by Elsevier B.V. Selection and peer review under responsibility of the organizers of the 2013 International Conference on Computational Science

Influence of the addition of chlorhexidine diacetate on bond strength of a high-viscosity glass ionomer cement to sound and artificial caries-affected dentin

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Natural and anthropogenic influence on soil erosion in a rural watershed in the Brazilian southeastern region

Human activities have been driven land cover, provoking acceleration of the erosive process and alteration on the soil characteristics. To explore the effects of human disturbance, we investigated the influences of natural and anthropogenic features on soil quality and soil erosion indicators (EI) within a Brazilian rural watershed located in Bauru Municipality, State of So Paulo. A pre-established set of soil EI was used to evaluate the influence of anthropogenic land cover categories on the presence and severity of erosion, related with spatial variations of soil attributes. On-site visits were carried out to measure the occurrence and the intensity of eleven separate EI values and to collect undisturbed topsoil samples for subsequent analyses. We registered 17 occurrences of EIs, distributed in ten locals. Occurrence and intensity of EIs were related to degree of sheet erosion. The EI qualities were more strongly associated with land cover management practices than to local topographic features. The occurrence of EIs and characteristics of soil and soil organic matter (SOM) were not significantly self-correlated. Although land cover class seems to influence soil properties and SOM attributes, we observed that the granulometric composition of the soils also contributes to the structural characteristics of the soil and consequently to the dynamic loss and gain of soil carbon. Sites covered with natural remnant vegetation (NRV) store 96.5 Mg ha(-1) of C and grassy and tilled soils stored more C than NRV, 100.1 and 142.4 Mg ha(-1), respectively. Due to the influence of soil texture over the soil C dynamic, we observe that in Bauru, pastured areas have high potential for sequestration of C if factors such as fire and/or erosion were avoided or effectively controlled. Results from this study show that human disturbance substantially affects soil properties within of southeastern region of Brazil.

Antifungals and acetylcholinesterase inhibitors from the stem bark of Croton heliotropiifolius

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The occurrence of UV filters in natural and drinking water in São Paulo State (Brazil)

Ultraviolet (UV) filters are widely used in the formulation of personal care products (PCPs) to prevent damage to the skin, lips, and hair caused by excessive UV radiation. Therefore, large amounts of these substances are released daily into the aquatic environment through either recreational activities or the release of domestic sewage. The concern regarding the presence of such substances in the environment and the exposure of aquatic organisms is based on their potential for bioaccumulation and their potential as endocrine disruptors. Although there are several reports regarding the occurrence and fate of UV filters in the aquatic environment, these compounds are still overlooked in tropical areas. In this study, we investigated the occurrence of the organic UV filters benzophenone-3 (BP-3), ethylhexyl salicylate (ES), ethylhexyl methoxycinnamate (EHMC), and octocrylene (OC) in six water treatment plants in various cities in Southeast Brazil over a period of 6 months to 1 year. All of the UV filters studied were detected at some time during the sampling period; however, only EHMC and BP-3 were found in quantifiable concentrations, ranging from 55 to 101 and 18 to 115 ng L(-1), respectively. Seasonal variation of BP-3 was most clearly noticed in the water treatment plant in Araraquara, São Paulo, where sampling was performed for 12 months. BP-3 was not quantifiable in winter but was quantifiable in summer. The levels of BP-3 were in the same range in raw, treated and chlorinated water, indicating that the compound was not removed by the water treatment process.

Shear strength of a natural and compacted tropical soil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estimation of deposit and spray distribution in hydro sensible paper and morning glory plant

Herbicides application success depends, besides product correct choice, the observation of environmental conditions and application quality. The work aimed to quantify the effects of surfactant addition in spraying solution, in natural and artificial targets, associated to different nozzle boom angles in relation to application offset, by using distinct evaluation methods. Two experiments were conducted at NuPAM-FCA/UNESP, Botucatu County, São Paulo State, constituted by ten treatments, in factorial scheme 2 × 5, corresponding to two spraying solutions conditions (absence or presence of Aterbane BRTM (0.25% v/v) adjuvant) and five angles of spray nozzle in relation to offset application (-30°, -15°, 90°, +15° and +30°). In Ipomea grandifolia leaves, the distribution and drops deposition of a tracer solution were evaluated by using scores visual and spectrophotometer process. In hydro sensible papers, volumetric medium diameter (VMD), density (cm2 ) and drops medium diameter, covered area (%) and application fees (L ha-1) were evaluated through e-SprinkleTM software. Aterbane BRTM (0.25% v/v) presence or absence, associated or no, to spray nozzles offset did not provide significant differences in I. grandifolia spray deposition. The use of artificial targets presented applicative technical limitations in relation to the use of natural ones as study matrix. Deposit and distribution variables esteem distinct behaviours, independent of target nature.

TGF-beta 1 modulates the homeostasis between MMPs and MMP inhibitors through p38 MAPK and ERK1/2 in highly invasive breast cancer cells

Background: Metastasis is the main factor responsible for death in breast cancer patients. Matrix metalloproteinases (MMPs) and their inhibitors, known as tissue inhibitors of MMPs (TIMPs), and the membrane-associated MMP inhibitor (RECK), are essential for the metastatic process. We have previously shown a positive correlation between MMPs and their inhibitors expression during breast cancer progression; however, the molecular mechanisms underlying this coordinate regulation remain unknown. In this report, we investigated whether TGF-beta 1 could be a common regulator for MMPs, TIMPs and RECK in human breast cancer cell models. Methods: The mRNA expression levels of TGF-beta isoforms and their receptors were analyzed by qRT-PCR in a panel of five human breast cancer cell lines displaying different degrees of invasiveness and metastatic potential. The highly invasive MDA-MB-231 cell line was treated with different concentrations of recombinant TGF-beta 1 and also with pharmacological inhibitors of p38 MAPK and ERK1/2. The migratory and invasive potential of these treated cells were examined in vitro by transwell assays. Results: In general, TGF-beta 2, T beta RI and T beta RII are over-expressed in more aggressive cells, except for T beta RI, which was also highly expressed in ZR-75-1 cells. In addition, TGF-beta 1-treated MDA-MB-231 cells presented significantly increased mRNA expression of MMP-2, MMP-9, MMP-14, TIMP-2 and RECK. TGF-beta 1 also increased TIMP-2, MMP-2 and MMP-9 protein levels but downregulated RECK expression. Furthermore, we analyzed the involvement of p38 MAPK and ERK1/2, representing two well established Smad-independent pathways, in the proposed mechanism. Inhibition of p38MAPK blocked TGF-beta 1-increased mRNA expression of all MMPs and MMP inhibitors analyzed, and prevented TGF-beta 1 upregulation of TIMP-2 and MMP-2 proteins. Moreover, ERK1/2 inhibition increased RECK and prevented the TGF-beta 1 induction of pro-MMP-9 and TIMP-2 proteins. TGF-beta 1-enhanced migration and invasion capacities were blocked by p38MAPK, ERK1/2 and MMP inhibitors. Conclusion: Altogether, our results support that TGF-beta 1 modulates the mRNA and protein levels of MMPs (MMP-2 and MMP-9) as much as their inhibitors (TIMP-2 and RECK). Therefore, this cytokine plays a crucial role in breast cancer progression by modulating key elements of ECM homeostasis control. Thus, although the complexity of this signaling network, TGF-beta 1 still remains a promising target for breast cancer treatment.

Morphological and molecular studies of Sphaerospermopsis torques-reginae (Cyanobacteria, Nostocales) from South American water blooms

Sphaerospermopsis torques-reginae (Komarek) Werner, Laughinghouse IV, Fiore & Sant'Anna comb. nov. was originally described as Anabaena torques-reginae Komarek from planktonic populations of Cuban eutrophic environments, characterized by twisted trichomes with spherical akinetes adjacent to the heterocytes. Recently, using molecular analyses, all planktonic Anabaena Bory ex Bornet & Flahault morphospecies were transferred into the genus Dolichospermum (Ralfs ex Bornet & Flahault) Wacklin el al., including Dolichospermum torques-reginae (Komarek) Wacklin et al. However, by a polyphasic characterization of strains of Anabaena reniformis Lemmermann and Aphanizomenon aphanizomenoides (Forti) Horecka & Komarek (=Anabaena aphanizomenoides Forti), these planktonic species were reclassified into Sphaerospermopsis Zapomelova et al. Our study's main objective was to characterize morphologically and molecularly cyanobacterial populations identified as Dolichospermum torques-reginae, observed in different aquatic ecosystems in South America. The 16S rRNA gene of two Dolichospermum torques-reginae strains (ITEP-024 and ITEP-026) was sequenced and phylogenetically analyzed for the first time. The morphological and phylogenetic analyses demonstrated the affiliation of the studied populations with the genus Sphaerospermopsis and, consequently, were denominated as Sphaerospermopsis torques-reginae. Furthermore, geographic distribution, ecology, and toxicity of the species are discussed. It was observed in different aquatic environments, natural and artificial, tropical and subtropical in Brazil, temperate in Argentina, and tropical in Colombia, suggesting a wide distribution in South America. It normally occurred in dense freshwater blooms, although it was also found in water with low salinity. Sphaerospermopsis torques-reginae toxic blooms have been reported in tropical water bodies in northeastern Brazil.

TGF-β1 modulates the homeostasis between MMPs and MMP inhibitors through p38 MAPK and ERK1/2 in highly invasive breast cancer cells

Abstract Background Metastasis is the main factor responsible for death in breast cancer patients. Matrix metalloproteinases (MMPs) and their inhibitors, known as tissue inhibitors of MMPs (TIMPs), and the membrane-associated MMP inhibitor (RECK), are essential for the metastatic process. We have previously shown a positive correlation between MMPs and their inhibitors expression during breast cancer progression; however, the molecular mechanisms underlying this coordinate regulation remain unknown. In this report, we investigated whether TGF-β1 could be a common regulator for MMPs, TIMPs and RECK in human breast cancer cell models. Methods The mRNA expression levels of TGF-β isoforms and their receptors were analyzed by qRT-PCR in a panel of five human breast cancer cell lines displaying different degrees of invasiveness and metastatic potential. The highly invasive MDA-MB-231 cell line was treated with different concentrations of recombinant TGF-β1 and also with pharmacological inhibitors of p38 MAPK and ERK1/2. The migratory and invasive potential of these treated cells were examined in vitro by transwell assays. Results In general, TGF-β2, TβRI and TβRII are over-expressed in more aggressive cells, except for TβRI, which was also highly expressed in ZR-75-1 cells. In addition, TGF-β1-treated MDA-MB-231 cells presented significantly increased mRNA expression of MMP-2, MMP-9, MMP-14, TIMP-2 and RECK. TGF-β1 also increased TIMP-2, MMP-2 and MMP-9 protein levels but downregulated RECK expression. Furthermore, we analyzed the involvement of p38 MAPK and ERK1/2, representing two well established Smad-independent pathways, in the proposed mechanism. Inhibition of p38MAPK blocked TGF-β1-increased mRNA expression of all MMPs and MMP inhibitors analyzed, and prevented TGF-β1 upregulation of TIMP-2 and MMP-2 proteins. Moreover, ERK1/2 inhibition increased RECK and prevented the TGF-β1 induction of pro-MMP-9 and TIMP-2 proteins. TGF-β1-enhanced migration and invasion capacities were blocked by p38MAPK, ERK1/2 and MMP inhibitors. Conclusion Altogether, our results support that TGF-β1 modulates the mRNA and protein levels of MMPs (MMP-2 and MMP-9) as much as their inhibitors (TIMP-2 and RECK). Therefore, this cytokine plays a crucial role in breast cancer progression by modulating key elements of ECM homeostasis control. Thus, although the complexity of this signaling network, TGF-β1 still remains a promising target for breast cancer treatment.

Application of 137Cs and 210Pb radionuclides to determine sedimentation rates of recent sediments from admiraty Bay, Antarctica Peninsula

Studies about natural and artificial radionuclides in areas such as the Antarctic are key to understand natural and dynamic processes in marine environments. These studies are important to determine levels of radioactive elements and local sedimentation rates. Five marine sediment cores were collected in different points of Admiralty Bay, in the Antarctic Peninsula. The purpose of this study was to determine 137Cs, 226Ra and 210Pb and sedimentation rates at each site. 137Cs, 210Pb and 226Ra were assayed by gamma-counting through direct measurement of the peak at 661 keV, 47 keV and 609 keV, respectively. Sedimentation rates were obtained by 137Cs and 210Pb (CIC and CRS). The activities for 137Cs ranged from 0.84 to 7.09 Bq kg-1; to 226Ra from 6.77 to 31.07 Bq kg-1 and for 210Pb ranged from 1.10 to 36.90 Bq kg-1. The sedimentation rates obtained by the three models ranged from 0.11±0.01 cm y-1 to 0.46±0.05 cm y-1. The levels of 137Cs registered in this study, as well as in other studies in the Antarctic region indicate that global fallout is the main cause of artificial radionuclides present in this environment, since the Antarctic has not suffered a direct action of human activities that released radioactive elements. The possible grain size variations that occur in the studied points of Admiralty Bay may explain the differences found in the vertical distribution of radionuclides, because of the different values of sedimentation rates and respective dating determined in their profiles

The photosynthetic bacterial reaction center in native and artificial envirnoments: effects on light-induced electron transfer

In this thesis we focussed on the characterization of the reaction center (RC) protein purified from the photosynthetic bacterium Rhodobacter sphaeroides. In particular, we discussed the effects of native and artificial environment on the light-induced electron transfer processes. The native environment consist of the inner antenna LH1 complex that copurifies with the RC forming the so called core complex, and the lipid phase tightly associated with it. In parallel, we analyzed the role of saccharidic glassy matrices on the interplay between electron transfer processes and internal protein dynamics. As a different artificial matrix, we incorporated the RC protein in a layer-by-layer structure with a twofold aim: to check the behaviour of the protein in such an unusual environment and to test the response of the system to herbicides. By examining the RC in its native environment, we found that the light-induced charge separated state P+QB - is markedly stabilized (by about 40 meV) in the core complex as compared to the RC-only system over a physiological pH range. We also verified that, as compared to the average composition of the membrane, the core complex copurifies with a tightly bound lipid complement of about 90 phospholipid molecules per RC, which is strongly enriched in cardiolipin. In parallel, a large ubiquinone pool was found in association with the core complex, giving rise to a quinone concentration about ten times larger than the average one in the membrane. Moreover, this quinone pool is fully functional, i.e. it is promptly available at the QB site during multiple turnover excitation of the RC. The latter two observations suggest important heterogeneities and anisotropies in the native membranes which can in principle account for the stabilization of the charge separated state in the core complex. The thermodynamic and kinetic parameters obtained in the RC-LH1 complex are very close to those measured in intact membranes, indicating that the electron transfer properties of the RC in vivo are essentially determined by its local environment. The studies performed by incorporating the RC into saccharidic matrices evidenced the relevance of solvent-protein interactions and dynamical coupling in determining the kinetics of electron transfer processes. The usual approach when studying the interplay between internal motions and protein function consists in freezing the degrees of freedom of the protein at cryogenic temperature. We proved that the “trehalose approach” offers distinct advantages with respect to this traditional methodology. We showed, in fact, that the RC conformational dynamics, coupled to specific electron transfer processes, can be modulated by varying the hydration level of the trehalose matrix at room temperature, thus allowing to disentangle solvent from temperature effects. The comparison between different saccharidic matrices has revealed that the structural and dynamical protein-matrix coupling depends strongly upon the sugar. The analyses performed in RCs embedded in polyelectrolyte multilayers (PEM) structures have shown that the electron transfer from QA - to QB, a conformationally gated process extremely sensitive to the RC environment, can be strongly modulated by the hydration level of the matrix, confirming analogous results obtained for this electron transfer reaction in sugar matrices. We found that PEM-RCs are a very stable system, particularly suitable to study the thermodynamics and kinetics of herbicide binding to the QB site. These features make PEM-RC structures quite promising in the development of herbicide biosensors. The studies discussed in the present thesis have shown that, although the effects on electron transfer induced by the native and artificial environments tested are markedly different, they can be described on the basis of a common kinetic model which takes into account the static conformational heterogeneity of the RC and the interconversion between conformational substates. Interestingly, the same distribution of rate constants (i.e. a Gamma distribution function) can describe charge recombination processes in solutions of purified RC, in RC-LH1 complexes, in wet and dry RC-PEM structures and in glassy saccharidic matrices over a wide range of hydration levels. In conclusion, the results obtained for RCs in different physico-chemical environments emphasize the relevance of the structure/dynamics solvent/protein coupling in determining the energetics and the kinetics of electron transfer processes in a membrane protein complex.

Context detection and abstraction in smart environments

Context-aware computing is currently considered the most promising approach to overcome information overload and to speed up access to relevant information and services. Context-awareness may be derived from many sources, including user profile and preferences, network information, sensor analysis; usually context-awareness relies on the ability of computing devices to interact with the physical world, i.e. with the natural and artificial objects hosted within the "environment”. Ideally, context-aware applications should not be intrusive and should be able to react according to user’s context, with minimum user effort. Context is an application dependent multidimensional space and the location is an important part of it since the very beginning. Location can be used to guide applications, in providing information or functions that are most appropriate for a specific position. Hence location systems play a crucial role. There are several technologies and systems for computing location to a vary degree of accuracy and tailored for specific space model, i.e. indoors or outdoors, structured spaces or unstructured spaces. The research challenge faced by this thesis is related to pedestrian positioning in heterogeneous environments. Particularly, the focus will be on pedestrian identification, localization, orientation and activity recognition. This research was mainly carried out within the “mobile and ambient systems” workgroup of EPOCH, a 6FP NoE on the application of ICT to Cultural Heritage. Therefore applications in Cultural Heritage sites were the main target of the context-aware services discussed. Cultural Heritage sites are considered significant test-beds in Context-aware computing for many reasons. For example building a smart environment in museums or in protected sites is a challenging task, because localization and tracking are usually based on technologies that are difficult to hide or harmonize within the environment. Therefore it is expected that the experience made with this research may be useful also in domains other than Cultural Heritage. This work presents three different approaches to the pedestrian identification, positioning and tracking: Pedestrian navigation by means of a wearable inertial sensing platform assisted by the vision based tracking system for initial settings an real-time calibration; Pedestrian navigation by means of a wearable inertial sensing platform augmented with GPS measurements; Pedestrian identification and tracking, combining the vision based tracking system with WiFi localization. The proposed localization systems have been mainly used to enhance Cultural Heritage applications in providing information and services depending on the user’s actual context, in particular depending on the user’s location.