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Search Results: 1 - 10 of 461863 matches for " Ikbal A. Ince "
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The Salivary Secretome of the Tsetse Fly Glossina pallidipes (Diptera: Glossinidae) Infected by Salivary Gland Hypertrophy Virus
Henry M. Kariithi,Ikbal A. Ince,Sjef Boeren,Adly M. M. Abd-Alla,Andrew G. Parker,Serap Aksoy,Just M. Vlak ,Monique M. van Oers
PLOS Neglected Tropical Diseases , 2011, DOI: 10.1371/journal.pntd.0001371
Abstract: Background The competence of the tsetse fly Glossina pallidipes (Diptera; Glossinidae) to acquire salivary gland hypertrophy virus (SGHV), to support virus replication and successfully transmit the virus depends on complex interactions between Glossina and SGHV macromolecules. Critical requisites to SGHV transmission are its replication and secretion of mature virions into the fly's salivary gland (SG) lumen. However, secretion of host proteins is of equal importance for successful transmission and requires cataloging of G. pallidipes secretome proteins from hypertrophied and non-hypertrophied SGs. Methodology/Principal Findings After electrophoretic profiling and in-gel trypsin digestion, saliva proteins were analyzed by nano-LC-MS/MS. MaxQuant/Andromeda search of the MS data against the non-redundant (nr) GenBank database and a G. morsitans morsitans SG EST database, yielded a total of 521 hits, 31 of which were SGHV-encoded. On a false discovery rate limit of 1% and detection threshold of least 2 unique peptides per protein, the analysis resulted in 292 Glossina and 25 SGHV MS-supported proteins. When annotated by the Blast2GO suite, at least one gene ontology (GO) term could be assigned to 89.9% (285/317) of the detected proteins. Five (~1.8%) Glossina and three (~12%) SGHV proteins remained without a predicted function after blast searches against the nr database. Sixty-five of the 292 detected Glossina proteins contained an N-terminal signal/secretion peptide sequence. Eight of the SGHV proteins were predicted to be non-structural (NS), and fourteen are known structural (VP) proteins. Conclusions/Significance SGHV alters the protein expression pattern in Glossina. The G. pallidipes SG secretome encompasses a spectrum of proteins that may be required during the SGHV infection cycle. These detected proteins have putative interactions with at least 21 of the 25 SGHV-encoded proteins. Our findings opens venues for developing novel SGHV mitigation strategies to block SGHV infections in tsetse production facilities such as using SGHV-specific antibodies and phage display-selected gut epithelia-binding peptides.
Morphological, Anatomical and Palynological Properties of Some Turkish Veronica L. Species (Scrphulariaceae)
Ayse Kaplan,Asli Hasanoglu,Ikbal Agah Ince
International Journal of Botany , 2007,
Abstract: In this study, pollen and seed morphology, leaf and stem anatomy of four Veronica L. species (Scrophulariaceae) one of which is endemic (V. multifida) belonging to four Sections [V. persica (Sect. Pocilla), V. beccabunga (Sect. Beccabunga), V. officinalis and V. multifida (Sect. Veronica)] grown in Turkey have been studied on light and scanning electron microscopy. Different and similar features of these species were described.
Open-source software for studying neural codes
Robin A. A. Ince
Quantitative Biology , 2012,
Abstract: In this chapter we first outline some of the popular computing environments used for analysing neural data, followed by a brief discussion of 'software carpentry', basic tools and skills from software engineering that can be of great use to computational scientists. We then introduce the concept of open-source software and explain some of its potential benefits for the academic community before giving a brief directory of some freely available open source software packages that address various aspects of the study of neural codes. While there are many commercial offerings that provide similar functionality, we concentrate here on open source packages, which in addition to being available free of charge, also have the source code available for study and modification.
Computational Multiaxial Fatigue Modelling for Notched Components*  [PDF]
Ayhan Ince
Modeling and Numerical Simulation of Material Science (MNSMS) , 2013, DOI: 10.4236/mnsms.2013.33A003
Abstract: Fatigue failures of driveline and suspension notched components for ground vehicles under multiaxial loading conditions are common, since most of those components are subjected to complex multiaxial loadings in service. A computational fatigue analysis methodology has been proposed here for performing multiaxial fatigue life prediction for notched components using analytical and numerical methods. The proposed multiaxial fatigue analysis methodology consists of an elastic-plastic stress/strain model and a multiaxial fatigue damage parameter. Results of the proposed multiaxial fatigue analysis methodology are compared to sets of experimental data published in the literature to verify the prediction capability of the elastic-plastic stress/strain model and the multiaxial fatigue damage parameter. Based on the comparison between calculated results and experimental data, it is found that the multiaxial elastic-plastic stress/strain model correlates well with experimental strain data for SAE 1070 steel notched shafts subjected to several non-proportional load paths. In addition, the proposed fatigue damage parameter is found to correlate reasonably well with experimental fatigue data of SAE 1045 steel notched shafts subjected to proportional and non-proportional loadings.
Amorphous Silicon Single-Junction Thin-Film Solar Cell Exceeding 10% Efficiency by Design Optimization
Mohammed Ikbal Kabir,Seyed A. Shahahmadi,Victor Lim,Saleem Zaidi
International Journal of Photoenergy , 2012, DOI: 10.1155/2012/460919
Abstract:
Effects of Globalization on Lowland and Upland Villages in Anatolia: Case Study on Serpil and Akbelenli Villages
A. Tolunay,A. Akyol,Y. Ince
Journal of Applied Sciences , 2009,
Abstract: This study investigates the effects of globalization on rural communities and was conducted in two villages, one upland and the other lowland, located in Turkey`s Western Mediterranean region. These are namely the villages of Serpil and Akbelenli, both located in E irdir District of Isparta Province. The Rapid Rural Appraisal (RRA) technique was utilized throughout the study and included such tools as interviews, observations and secondary data analysis. The results emerging from the study indicate that globalization has had varying effects on upland and lowland villages. In the village of Serpil, a low basin, (1) resources are sufficient for the rural community to live on; (2) there is no issue of migration either to or from the village due to rural poverty; (3) modern communication tools are widely used in the village; (4) villagers are in close contact with the outside world through the use of the internet; (5) villagers take fairly good advantage of the beneficial consequences of globalization. On the other hand, in the village of Akbelenli, a high basin, (1) resources are not adequate to provide subsistence to the uplands villagers; (2) the younger generation is relocating to cities and rural areas become gradually abandoned; (3) modern mass media and computer tools are not utilized due to rural poverty; (4) opportunities that globalization provides for gathering information are not taken advantage of; (5) at its present state, the rural community is unable to attain a basic grip on the information age. The primary reason why these two villages are different from each other has to do with the fact that their geographic locations and the amount of resources available to the villagers are so distinct. Therefore, in Turkey, actions aimed at rural development should be taken in consideration of this distinction between upland and lowland villages.
Amorphous Silicon Single-Junction Thin-Film Solar Cell Exceeding 10% Efficiency by Design Optimization
Mohammed Ikbal Kabir,Seyed A. Shahahmadi,Victor Lim,Saleem Zaidi,Kamaruzzaman Sopian,Nowshad Amin
International Journal of Photoenergy , 2012, DOI: 10.1155/2012/460919
Abstract: The conversion efficiency of a solar cell can substantially be increased by improved material properties and associated designs. At first, this study has adopted AMPS-1D (analysis of microelectronic and photonic structures) simulation technique to design and optimize the cell parameters prior to fabrication, where the optimum design parameters can be validated. Solar cells of single junction based on hydrogenated amorphous silicon (a-Si:H) have been analyzed by using AMPS-1D simulator. The investigation has been made based on important model parameters such as thickness, doping concentrations, bandgap, and operating temperature and so forth. The efficiency of single junction a-Si:H can be achieved as high as over 19% after parametric optimization in the simulation, which might seem unrealistic with presently available technologies. Therefore, the numerically designed and optimized a-SiC:H/a-SiC:H-buffer/a-Si:H/a-Si:H solar cells have been fabricated by using PECVD (plasma-enhanced chemical vapor deposition), where the best initial conversion efficiency of 10.02% has been achieved ( ?V, ?mA/cm2 and ) for a small area cell (0.086?cm2). The quantum efficiency (QE) characteristic shows the cell’s better spectral response in the wavelength range of 400?nm–650?nm, which proves it to be a potential candidate as the middle cell in a-Si-based multijunction structures. 1. Introduction The performance of solar photovoltaic cells depends on its design, material properties, and fabrication technology. Photovoltaic (PV) researchers present improved cells over the period of time, although the overall process is quite complex, expensive, and time consuming. Numerical simulation is the best approach for solar cell researchers, which help to find out an optimized structure with good fitted parameters. As a result fabrication complexity, costs, and time reduce significantly. The major objectives of numerical modeling and simulation in solar cell research are testing the validity of proposed physical structures, geometry on cell performance, and fitting of modeling output to experimental results. The numerical modeling has become indispensable tools for designing a high-efficiency solar cell. Numerical modeling is increasingly used to obtain insight into the details of the physical operation of thin-film solar cells. Over the years, several modeling tools specific to thin-film PV devices have been developed. A number of these tools have been reached in a mature status and are available to the PV community. A driving force for the development is the complicated structure of
Analysis of Slow (Theta) Oscillations as a Potential Temporal Reference Frame for Information Coding in Sensory Cortices
Christoph Kayser ,Robin A. A. Ince,Stefano Panzeri
PLOS Computational Biology , 2012, DOI: 10.1371/journal.pcbi.1002717
Abstract: While sensory neurons carry behaviorally relevant information in responses that often extend over hundreds of milliseconds, the key units of neural information likely consist of much shorter and temporally precise spike patterns. The mechanisms and temporal reference frames by which sensory networks partition responses into these shorter units of information remain unknown. One hypothesis holds that slow oscillations provide a network-intrinsic reference to temporally partitioned spike trains without exploiting the millisecond-precise alignment of spikes to sensory stimuli. We tested this hypothesis on neural responses recorded in visual and auditory cortices of macaque monkeys in response to natural stimuli. Comparing different schemes for response partitioning revealed that theta band oscillations provide a temporal reference that permits extracting significantly more information than can be obtained from spike counts, and sometimes almost as much information as obtained by partitioning spike trains using precisely stimulus-locked time bins. We further tested the robustness of these partitioning schemes to temporal uncertainty in the decoding process and to noise in the sensory input. This revealed that partitioning using an oscillatory reference provides greater robustness than partitioning using precisely stimulus-locked time bins. Overall, these results provide a computational proof of concept for the hypothesis that slow rhythmic network activity may serve as internal reference frame for information coding in sensory cortices and they foster the notion that slow oscillations serve as key elements for the computations underlying perception.
Applications of Information Theory to Analysis of Neural Data
Simon R. Schultz,Robin A. A. Ince,Stefano Panzeri
Quantitative Biology , 2015, DOI: 10.1007/978-1-4614-7320-6_280-1
Abstract: Information theory is a practical and theoretical framework developed for the study of communication over noisy channels. Its probabilistic basis and capacity to relate statistical structure to function make it ideally suited for studying information flow in the nervous system. It has a number of useful properties: it is a general measure sensitive to any relationship, not only linear effects; it has meaningful units which in many cases allow direct comparison between different experiments; and it can be used to study how much information can be gained by observing neural responses in single trials, rather than in averages over multiple trials. A variety of information theoretic quantities are commonly used in neuroscience - (see entry "Definitions of Information-Theoretic Quantities"). In this entry we review some applications of information theory in neuroscience to study encoding of information in both single neurons and neuronal populations.
Estimating Information-Theoretic Quantities
Robin A. A. Ince,Simon R. Schultz,Stefano Panzeri
Quantitative Biology , 2015, DOI: 10.1007/978-1-4614-7320-6_140-1
Abstract: Information theory is a practical and theoretical framework developed for the study of communication over noisy channels. Its probabilistic basis and capacity to relate statistical structure to function make it ideally suited for studying information flow in the nervous system. It has a number of useful properties: it is a general measure sensitive to any relationship, not only linear effects; it has meaningful units which in many cases allow direct comparison between different experiments; and it can be used to study how much information can be gained by observing neural responses in single trials, rather than in averages over multiple trials. A variety of information theoretic quantities are in common use in neuroscience - (see entry "Summary of Information-Theoretic Quantities"). Estimating these quantities in an accurate and unbiased way from real neurophysiological data frequently presents challenges, which are explained in this entry.
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