Página 1 dos resultados de 354 itens digitais encontrados em 0.005 segundos

‣ Adaptive Approach for a Maximum Entropy Algorithm in Ecological Niche Modeling

RODRIGUES, E. S. C.; RODRIGUES, F. A.; ROCHA, R. L. A.; CORREA, P. L. P.
Fonte: IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC Publicador: IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC
Tipo: Artigo de Revista Científica
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This paper presents an Adaptive Maximum Entropy (AME) approach for modeling biological species. The Maximum Entropy algorithm (MaxEnt) is one of the most used methods in modeling biological species geographical distribution. The approach presented here is an alternative to the classical algorithm. Instead of using the same set features in the training, the AME approach tries to insert or to remove a single feature at each iteration. The aim is to reach the convergence faster without affect the performance of the generated models. The preliminary experiments were well performed. They showed an increasing on performance both in accuracy and in execution time. Comparisons with other algorithms are beyond the scope of this paper. Some important researches are proposed as future works.

‣ A Gazetteer for biodiversity data as a linked open data solution

Cardoso, Silvio Domingos; Serique, Kleberson Junio do Amaral; Amanqui, Flor Karina Mamani; Santos, J. L. Campos dos; Moreira, Dilvan de Abreu
Fonte: Università degli Studi di Parma; Università degli Studi di Modena e Reggio Emilia; Institute of Electrical and Electronics Engineers - IEEE; Parma Publicador: Università degli Studi di Parma; Università degli Studi di Modena e Reggio Emilia; Institute of Electrical and Electronics Engineers - IEEE; Parma
Tipo: Conferência ou Objeto de Conferência
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Biodiversity studies all life forms that we find in nature. The maintenance of biological diversity is importante because it is essential to life on Earth. The lack of accurate spatial geographic information in species occurrence data, especially from diversity rich regions (like the Amazon Forest), leads to problems in many conservation activities, such as systematic planning for the protection of endangered species. In this paper, we present a gazetteer (a geographical directory that associate name places to geographic coordinates) for biodiversity data that is available as an Linked Open Data resource (using a GeoSPARQL Endpoint) and show how it can be used to improve inaccurate geographic collection data. We compared the efficiency of our Gazetteer with three openly available resources, Geonames, WikiMapia and Wikipedia, and got a 10% better recall rate than these endpoints. We also used the Gazetteer to correct geographic data from a big record sample (327,000 occurrence records) from SpeciesLink and GBIF (two big open access repositories of biodiversity occurrence data). In this data set, we were able to add geographic coordinates to around 14% of records that did not have them before.; CAPES

‣ Editorial : special Issue contributed by the 10th International Chemical and Biological Engineering Conference - CHEMPOR 2008

Ferreira, E. C.; Mota, M.
Fonte: The Berkeley Electronic Press Publicador: The Berkeley Electronic Press
Tipo: Artigo de Revista Científica
Publicado em /05/2009 Português
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The 10th International Chemical and Biological Engineering Conference - CHEMPOR 2008, was held in Braga, Portugal, from the 4th to the 6th of September, 2008. The conference was jointly organized by the University of Minho, the “Ordem dos Engenheiros,” and the Institute for Biotechnology and Bioengineeing, with the support of “Sociedade Portuguesa de Qu´ımica” and “Sociedade Portuguesa de Biotecnologia”. The CHEMPOR series traditionally brings together both young and established researchers and end users to discuss recent developments in different areas of Chemical Engineering. The scope of this edition was extended to Biological Engineering research. One of the major core areas of the conference program was life quality, due to the importance that Chemical and Biological Engineering plays in this area. “Integration of Life Sciences & Engineering” and “Sustainable Process-Product Development through Green Chemistry” were two of the leading themes with papers addressing such important issues. This was complemented with additional leading themes including “Advancing the Chemical and Biological Engineering Fundamentals,” “Multi-Scale and/or Multi-Disciplinary Approach to Process-Product Innovation”...

‣ Book of abstracts of the 10th International Chemical and Biological Engineering Conference : CHEMPOR 2008

Ferreira, E. C.; Mota, M.
Fonte: Universidade do Minho. Departamento de Engenharia Biológica Publicador: Universidade do Minho. Departamento de Engenharia Biológica
Tipo: Livro
Publicado em /09/2008 Português
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This book contains the extended abstracts presented at the 10th International Chemical and Biological Engineering Conference - CHEMPOR 2008, held in Braga, Portugal, over 3 days, from the 4th to the 6th of September, 2008. Previous editions took place in Lisboa (1975, 1889, 1998), Braga (1978), Póvoa de Varzim (1981), Coimbra (1985, 2005), Porto (1993), and Aveiro (2001). The conference was jointly organized by the University of Minho, “Ordem dos Engenheiros”, and the IBB - Institute for Biotechnology and Bioengineering with the usual support of the “Sociedade Portuguesa de Química” and, by the first time, of the “Sociedade Portuguesa de Biotecnologia”. Thirty years elapsed since CHEMPOR was held at the University of Minho, organized by T.R. Bott, D. Allen, A. Bridgwater, J.J.B. Romero, L.J.S. Soares and J.D.R.S. Pinheiro. We are fortunate to have Profs. Bott, Soares and Pinheiro in the Honor Committee of this 10th edition, under the high Patronage of his Excellency the President of the Portuguese Republic, Prof. Aníbal Cavaco Silva. The opening ceremony will confer Prof. Bott with a “Long Term Achievement” award acknowledging the important contribution Prof. Bott brought along more than 30 years to the development of the Chemical Engineering science...

‣ Pre-Columbian agricultural landscapes, ecosystem engineers, and self-organized patchiness in Amazonia

McKey, Doyle; Rostain, Stéphen; Iriarte, José; Glaser, Bruno; Birk, Jago Jonathan; Holst, Irene; Renard, Delphine
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
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The scale and nature of pre-Columbian human impacts in Amazonia are currently hotly debated. Whereas pre-Columbian people dramatically changed the distribution and abundance of species and habitats in some parts of Amazonia, their impact in other parts is less clear. Pioneer research asked whether their effects reached even further, changing how ecosystems function, but few in-depth studies have examined mechanisms underpinning the resilience of these modifications. Combining archeology, archeobotany, paleoecology, soil science, ecology, and aerial imagery, we show that pre-Columbian farmers of the Guianas coast constructed large raised-field complexes, growing on them crops including maize, manioc, and squash. Farmers created physical and biogeochemical heterogeneity in flat, marshy environments by constructing raised fields. When these fields were later abandoned, the mosaic of well-drained islands in the flooded matrix set in motion self-organizing processes driven by ecosystem engineers (ants, termites, earthworms, and woody plants) that occur preferentially on abandoned raised fields. Today, feedbacks generated by these ecosystem engineers maintain the human-initiated concentration of resources in these structures. Engineer organisms transport materials to abandoned raised fields and modify the structure and composition of their soils...

‣ Turbidity suppression from the ballistic to the diffusive regime in biological tissues using optical phase conjugation

McDowell, Emily J.; Cui, Meng; Vellekoop, Ivo M.; Senekerimyan, Vahan; Yaqoob, Zahid; Yang, Changhuei
Fonte: Society of Photo-Optical Instrumentation Engineers Publicador: Society of Photo-Optical Instrumentation Engineers
Tipo: Artigo de Revista Científica
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We describe the amplitude and resolution trends of the signals acquired by turbidity suppression through optical phase conjugation (TSOPC) with samples that span the ballistic and diffusive scattering regimes. In these experiments, the light field scattered through a turbid material is written into a hologram, and a time-reversed copy of the light field is played back through the sample. In this manner, the wavefront originally incident on the sample is reconstructed. We examine a range of scattering samples including chicken breast tissue sections of increasing thickness and polyacrylamide tissue-mimicking phantoms with increasing scattering coefficients. Our results indicate that only a small portion of the scattered wavefront (<0.02%) must be collected to reconstruct a TSOPC signal. Provided the sample is highly scattering, all essential angular information is contained within such small portions of the scattered wavefront due to randomization by scattering. A model is fitted to our results, describing the dependence of the TSOPC signal on other measurable values within the system and shedding light on the efficiency of the phase conjugation process. Our results describe the highest level of scattering that has been phase conjugated in biological tissues to date.

‣ Effect of photobleaching on calibration model development in biological Raman spectroscopy

Barman, Ishan; Kong, Chae-Ryon; Singh, Gajendra P.; Dasari, Ramachandra R.
Fonte: Society of Photo-Optical Instrumentation Engineers (SPIE) Publicador: Society of Photo-Optical Instrumentation Engineers (SPIE)
Tipo: Artigo de Revista Científica
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A major challenge in performing quantitative biological studies using Raman spectroscopy lies in overcoming the influence of the dominant sample fluorescence background. Moreover, the prediction accuracy of a calibration model can be severely compromised by the quenching of the endogenous fluorophores due to the introduction of spurious correlations between analyte concentrations and fluorescence levels. Apparently, functional models can be obtained from such correlated samples, which cannot be used successfully for prospective prediction. This work investigates the deleterious effects of photobleaching on prediction accuracy of implicit calibration algorithms, particularly for transcutaneous glucose detection using Raman spectroscopy. Using numerical simulations and experiments on physical tissue models, we show that the prospective prediction error can be substantially larger when the calibration model is developed on a photobleaching correlated dataset compared to an uncorrelated one. Furthermore, we demonstrate that the application of shifted subtracted Raman spectroscopy (SSRS) reduces the prediction errors obtained with photobleaching correlated calibration datasets compared to those obtained with uncorrelated ones.

‣ Multispectral fluorescence imaging to assess pH in biological specimens

Hight, Matthew R.; Nolting, Donald D.; McKinley, Eliot T.; Lander, Adam D.; Wyatt, Shelby K.; Gonyea, Mark; Zhao, Ping; Manning, H. Charles
Fonte: Society of Photo-Optical Instrumentation Engineers (SPIE) Publicador: Society of Photo-Optical Instrumentation Engineers (SPIE)
Tipo: Artigo de Revista Científica
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Simple, quantitative assays to measure pH in tissue could improve the study of complicated biological processes and diseases such as cancer. We evaluated multispectral fluorescence imaging (MSFI) to quantify extracellular pH (pHe) in dye-perfused, surgically-resected tumor specimens with commercially available instrumentation. Utilizing a water-soluble organic dye with pH-dependent fluorescence emission (SNARF-4F), we used standard fluorimetry to quantitatively assess the emission properties of the dye as a function of pH. By conducting these studies within the spectroscopic constraints imposed by the appropriate imaging filter set supplied with the imaging system, we determined that correction of the fluorescence emission of deprotonated dye was necessary for accurate determination of pH due to suboptimal excitation. Subsequently, employing a fluorimetry-derived correction factor (CF), MSFI data sets of aqueous dye solutions and tissuelike phantoms could be spectrally unmixed to accurately quantify equilibrium concentrations of protonated (HA) and deprotonated (A−) dye and thus determine solution pH. Finally, we explored the feasibility of MSFI for high-resolution pHe mapping of human colorectal cancer cell-line xenografts. Data presented suggest that MSFI is suitable for quantitative determination of pHe in ex vivo dye-perfused tissue...

‣ Biological approaches for addressing the grand challenge of providing access to clean drinking water

Riley, Mark R; Gerba, Charles P; Elimelech, Menachem
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Publicado em 31/03/2011 Português
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The U.S. National Academy of Engineering (NAE) recently published a document presenting "Grand Challenges for Engineering". This list was proposed by leading engineers and scientists from around the world at the request of the U.S. National Science Foundation (NSF). Fourteen topics were selected for these grand challenges, and at least seven can be addressed using the tools and methods of biological engineering. Here we describe how biological engineers can address the challenge of providing access to clean drinking water. This issue must be addressed in part by removing or inactivating microbial and chemical contaminants in order to properly deliver water safe for human consumption. Despite many advances in technologies this challenge is expanding due to increased pressure on fresh water supplies and to new opportunities for growth of potentially pathogenic organisms.

‣ Photoacoustic tomography of foreign bodies in soft biological tissue

Cai, Xin; Kim, Chulhong; Pramanik, Manojit; Wang, Lihong V.
Fonte: Society of Photo-Optical Instrumentation Engineers (SPIE) Publicador: Society of Photo-Optical Instrumentation Engineers (SPIE)
Tipo: Artigo de Revista Científica
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In detecting small foreign bodies in soft biological tissue, ultrasound imaging suffers from poor sensitivity (52.6%) and specificity (47.2%). Hence, alternative imaging methods are needed. Photoacoustic (PA) imaging takes advantage of strong optical absorption contrast and high ultrasonic resolution. A PA imaging system is employed to detect foreign bodies in biological tissues. To achieve deep penetration, we use near-infrared light ranging from 750 to 800 nm and a 5-MHz spherically focused ultrasonic transducer. PA images were obtained from various targets including glass, wood, cloth, plastic, and metal embedded more than 1 cm deep in chicken tissue. The locations and sizes of the targets from the PA images agreed well with those of the actual samples. Spectroscopic PA imaging was also performed on the objects. These results suggest that PA imaging can potentially be a useful intraoperative imaging tool to identify foreign bodies.

‣ Time-reversed ultrasonically encoded optical focusing in biological tissue

Lai, Puxiang; Xu, Xiao; Liu, Honglin; Wang, Lihong V.
Fonte: Society of Photo-Optical Instrumentation Engineers Publicador: Society of Photo-Optical Instrumentation Engineers
Tipo: Artigo de Revista Científica
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We report an experimental investigation of time-reversed ultrasonically encoded optical focusing in biological tissue. This technology combines the concepts of optical phase conjugation and ultrasound modulation of diffused coherent light. The ultrasonically encoded (or tagged) diffused light from a tissue sample is collected in reflection mode and interferes with a reference light in a photorefractive crystal (used as a phase conjugation mirror) to form a hologram. Then a time-reversed copy of the tagged light is generated and traces back the original trajectories to the ultrasonic focus inside the tissue sample. With our current setup, we can achieve a maximum penetration depth of 5 mm in a chicken breast sample and image optical contrasts within a tissue sample with a spatial resolution approximately equaling 1/2 of the ultrasound focal diameter.

‣ Open source software for electric field Monte Carlo simulation of coherent backscattering in biological media containing birefringence

Radosevich, Andrew J.; Rogers, Jeremy D.; Çapoğlu, İlker R.; Mutyal, Nikhil N.; Pradhan, Prabhakar; Backman, Vadim
Fonte: Society of Photo-Optical Instrumentation Engineers Publicador: Society of Photo-Optical Instrumentation Engineers
Tipo: Artigo de Revista Científica
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We present an open source electric field tracking Monte Carlo program to model backscattering in biological media containing birefringence, with computation of the coherent backscattering phenomenon as an example. These simulations enable the modeling of tissue scattering as a statistically homogeneous continuous random media under the Whittle-Matérn model, which includes the Henyey-Greenstein phase function as a special case, or as a composition of discrete spherical scatterers under Mie theory. The calculation of the amplitude scattering matrix for the above two cases as well as the implementation of birefringence using the Jones N-matrix formalism is presented. For ease of operator use and data processing, our simulation incorporates a graphical user interface written in MATLAB to interact with the underlying C code. Additionally, an increase in computational speed is achieved through implementation of message passing interface and the semi-analytical approach. Finally, we provide demonstrations of the results of our simulation for purely scattering media and scattering media containing linear birefringence.

‣ Teaching the principle of biological optimization

Johnson, Arthur T
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Publicado em 20/02/2013 Português
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Among the important principles in biology that should be taught in biological engineering educational programs is the principle of optimization, what it means, why it is important, and how it comes about. This material can be presented at numerous levels throughout the curriculum. Understanding of this principle can lead biological engineers to expect it in many, if not all, biological system applications. Understanding optimization in biological systems can help understand the predictive power of evolutionary principles and what to expect from living things incorporated in designs.

‣ Biological imaging with coherent Raman scattering microscopy: a tutorial

Alfonso-García, Alba; Mittal, Richa; Lee, Eun Seong; Potma, Eric O.
Fonte: Society of Photo-Optical Instrumentation Engineers Publicador: Society of Photo-Optical Instrumentation Engineers
Tipo: Artigo de Revista Científica
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Coherent Raman scattering (CRS) microscopy is gaining acceptance as a valuable addition to the imaging toolset of biological researchers. Optimal use of this label-free imaging technique benefits from a basic understanding of the physical principles and technical merits of the CRS microscope. This tutorial offers qualitative explanations of the principles behind CRS microscopy and provides information about the applicability of this nonlinear optical imaging approach for biological research.

‣ Tools and reference standards supporting the engineering and evolution of synthetic biological systems

Kelly, Jason R. (Jason Robert)
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 168 p.
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Biological engineers have constructed a number of multi-part synthetic biological systems that conduct logical operations on input signals, produce oscillatory output signals, store memory, or produce desired products. However, very few of these genetically-encoded systems worked as originally designed. The typical process of constructing a functional system involves a period of tuning the system properties to find a functional variant. This tuning process has been optimized and applied with great success to the engineering of individual biological parts by directed evolution. For instance, researchers developing improved enzymes, transcriptional promoters, and fluorescent proteins have generated large libraries of variants and screened these libraries to find individual mutants that met desired performance specifications. In this thesis, I address some of the bottlenecks preventing the application of directed evolution to more complex devices and systems. First, I describe an input / output screening plasmid that was designed to enable screening of higher-order genetic devices based on the equilibrium response of the device. This plasmid includes two fluorescent reporters and an inducible promoter to enable screening of device libraries across a range of inputs. Second...

‣ Engineering phosphorylation-dependent post-translational protein devices

Sutton, Samantha C. (Samantha Carol)
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 127 p.
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One goal underlying synthetic biology is to develop standard biological parts that can be reliably assembled into devices encoding higher-order functions. Here, I developed a framework for engineering post-translational devices, which are devices whose inner workings are modulated by non-covalent protein interactions and covalent protein modifications. To test the framework, I designed a scaffold for engineering post-translational devices in yeast, the Phospholocator, that can be used to assemble peptide parts in order to produce devices that couple upstream kinase activity to regulated nuclear translocation. I used the Phospholocator to design, build, and characterize a Phospholocator device, the Cdc28-Phospholocator, whose location is regulated by the activity of cyclin-dependent kinase Cdc28. I next engineered and tested a Fus3-Phospholocator device, whose location is regulated by the activity of the mitogen-activated protein kinase Fus3, in order to demonstrate that the Phospholocator scaffold supports the engineering of many post-translational devices. I used the Cdc28-Phospholocator to follow Cdc28 activity levels throughout the yeast cell cycle, thereby illustrating the utility of the Cdc28-Phospholocator as a tool for biological inquiry. To implement more complex functions...

‣ Polarized light Monte Carlo analysis of birefringence-induced depolarization in biological tissues

Ortega Quijano, Noé; Fanjul Vélez, Félix; Salas García, Irene; Arce Diego, José Luis
Fonte: The Optical Society (OSA)-; SPIE Society of Photo-Optical Instrumentation Engineers Publicador: The Optical Society (OSA)-; SPIE Society of Photo-Optical Instrumentation Engineers
Tipo: info:eu-repo/semantics/conferenceObject; publishedVersion
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In this work we analyze the impact of linear birefringence on biological tissues depolarization, which is essential for correctly interpreting experimental results. Our approach is based on the polarized light Monte Carlo method in transmission. We present a comparative analysis of light depolarization in biological tissues with different values of linear birefringence and particle sizes, in order to evaluate its impact on the calculated parameters.

‣ Numerical modeling of light propagation in biological tissues: time-resolved 3D simulations based on light diffusion model and FDTD solution of Maxwell’s equations

Ortega Quijano, Noé; Romanov, Oleg G.; Fanjul Vélez, Félix; Salas García, Irene; Tolstik, Alexei L.; Arce Diego, José Luis
Fonte: SPIE Society of Photo-Optical Instrumentation Engineers-; The Optical Society (OSA) Publicador: SPIE Society of Photo-Optical Instrumentation Engineers-; The Optical Society (OSA)
Tipo: info:eu-repo/semantics/conferenceObject; publishedVersion
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In this work, optical propagation through turbid media is analyzed by FDTD simulation. In particular, the method is applied to biological tissues. Continuous light propagation in turbid media has been widely studied, but pulsed light propagation has received less interest due to its complexity. Therefore, in this work we focus on pulsed light. FDTD method is applied to several media with optical parameters in the typical range of those observed in biological tissues. We perform an analysis of the variations of pulsed light propagation as a function of the scatterers characteristics (namely size, concentration, and optical contrast). The results are compared with those obtained by the use of the diffusion approximation. The potential of the FDTD method over the diffusion model is given by its high accuracy, its capacity to perform time-resolved simulations, and the fact that it carries all the information about the phase and coherence of the wavefront. The results of this work can be applied to a wide range of areas of interest like the timeresolved study of ultrashort light pulses propagation, the optimization of optical penetration depth, the coherence properties of pulsed light, and the effect of modified wavefronts in light propagation.

‣ Grand challenges for biological engineering

Yoon, Jeong-Yeol; Riley, Mark R
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Publicado em 22/09/2009 Português
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Biological engineering will play a significant role in solving many of the world's problems in medicine, agriculture, and the environment. Recently the U.S. National Academy of Engineering (NAE) released a document "Grand Challenges in Engineering," covering broad realms of human concern from sustainability, health, vulnerability and the joy of living. Biological engineers, having tools and techniques at the interface between living and non-living entities, will play a prominent role in forging a better future. The 2010 Institute of Biological Engineering (IBE) conference in Cambridge, MA, USA will address, in part, the roles of biological engineering in solving the challenges presented by the NAE. This letter presents a brief outline of how biological engineers are working to solve these large scale and integrated problems of our society.

‣ Large-scale Dynamical Models and Estimation for Permeation in Biological Membrane Ion Channels

Krishnamurthy, Vikram; Chung, Shin-Ho
Fonte: Institute of Electrical and Electronics Engineers (IEEE Inc) Publicador: Institute of Electrical and Electronics Engineers (IEEE Inc)
Tipo: Artigo de Revista Científica
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Biological ion channels are water-filled angstrom-unit (1 angstrom unit=10-10 m)sized pores formed by proteins in the cell membrane. They are responsible for regulating the flow of ions into and out of a cell and hence they control all electrical activiti