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Review of current methodological approaches for characterizing MicroRNAs in plants

International Journal of Plant Genomics 2009年第1期2009卷 262463页

作者： Unver, Turgay Namuth-Covert, Deana M. Budak, Hikmet Biological Sciences and Bioengineering Program Faculty of Engineering and Natural Sciences Sabanci University Orhanli Tuzla 34956 Istanbul Turkey Department of Agronomy and Horticulture University of Nebraska-Lincoln Lincoln NE United States

Advances in molecular biology have led to some surprising discoveries. One of these includes the complexities of RNA and its role in gene expression. One particular class of RNA called microRNA (miRNA) is the focus of this paper. We will first briefly look at some of the characteristics and biogenesis of miRNA in plant systems. The remainder of the paper will go into details of three different approaches used to identify and study miRNA. These include two reverse genetics approaches: computation (bioinformatics) and experimental, and one rare forward genetics approach. We also will summarize how to measure and quantify miRNAs, and how to detect their possible targets in plants. Strengths and weaknesses of each methodological approach are discussed. © 2009 Turgay Unver et al.

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Optimal dimensional synthesis of force feedback lower arm exoskeletons

Optimal dimensional synthesis of force feedback lower arm ex...

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IEEE/RAS-EMBS International Conference on Biomedical Robotics and Biomechatronics (BioRob)

作者： Ramazan Unal Volkan Patoglu Faculty of Engineering and Natural Sciences Mechatronics Program Sabanci University Istanbul Turkey

This paper presents multi-criteria design optimization of parallel mechanism based force feedback exoskeletons for human forearm and wrist. The optimized devices are aimed to be employed as a high fidelity haptic interfaces. Multiple design objectives are discussed and classified for the devices and the optimization problem to study the trade-offs between these criteria is formulated. Dimensional syntheses are performed for optimal global kinematic and dynamic performance, utilizing a Pareto front based framework, for two spherical parallel mechanisms that satisfy the ergonomic necessities of a human forearm and wrist. Two optimized mechanisms are compared and discussed in the light of multiple design criteria. Finally, kinematic structure and dimensions of an optimal exoskeleton are decided.

关键词： Force feedback Exoskeletons Design optimization Haptic interfaces Humans Kinematics Wrist Force sensors Parallel robots Ergonomics

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Estimating Response-Maximized Decision Rules With Applications to Breastfeeding (vol 104, pg 155, 2009)

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JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION 2009年第487期104卷 1292-1292页

作者： Moodie, Erica E. M. Platt, Robert W. Kramer, Michael S. [a] Erica E. M. Moodie is an Assistant Professor in the Department of Epidemiology & Biostatistics Health McGill University Montreal QC H3A 1A2 Canada . Robert W. Platt is an Associate Professor in the Department of Epidemiology & Biostatistics Health and the Department of Pediatrics at McGill University Montreal QC H3A 2K6 Canada . Dr. Platt is a Chercheur-boursier of the Fonds de recherche en santé du Québec (FRSQ). Michael S. Kramer is Professor in the Department of Pediatrics and the Department of Epidemiology & Biostatistics at McGill University Montreal QC H3H 1P3 Canada . Erica E. M. Moodie acknowledges funding through the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant Program and a University Faculty Award and an Operating Grant through the Canadian Institutes of Health Research (CIHR). Robert W. Platt's research is also supported by a Discovery Grant from NSERC and core funding to the Montreal Children's Hospital Research Institute from the FRSQ. The Promotion of Breastfeeding Intervention Trial was supported by grants from the Thrasher Research Fund the National Health Research and Development Program (Health Canada) UNICEF the European Regional Office of WHO and the CIHR. The authors would like to thank the associate editor David Banks and the two anonymous referees for their careful review of the manuscript and helpful suggestions.

To estimate the sequence of actions that optimizes response in a longitudinal setting, it is important to study the actions as part of a set of decision rules rather than in a series of single-action comparisons. We take as our motivating example the estimation of the set of decision rules for the duration of breastfeeding with a view to maximizing infant growth. Breastfeeding has many well-recognized beneficial effects on health and development. However observational evidence has suggested that breastfeeding is associated with reduced infant growth, although the long-term consequences for stature and adiposity remain controversial. The Promotion of Breastfeeding Intervention Trial (PROBIT) recruited 17,046 women in which hospitals and their affiliated polyclinics in Belarus were randomized to a breastfeeding promotion intervention or to standard care. In this article, we propose Structural Mean Models and estimate their parameters using G-estimation to obtain unbiased estimates of the effect of continued breastfeeding on infant growth (weight or length) at one year of age. We also implement a modified version of the G-estimation algorithm that is asymptotically unbiased; this is the first real-data application of the algorithm. Finally, we compare the decision rules implied by the G-estimates with the decision implied by a myopic optimization estimation approach, that is, we compare with decision rules that maximize response in the short-term. The breastfeeding regimes selected by each of the three models are optimal in the sense that specific criteria were optimized; the criteria considered here (maximizing weight or length) were chosen for simplicity, but may not lead to better overall health. We demonstrate in the context of a breastfeeding promotion intervention trial that optimal myopic decision strategies do not coincide with strategies that optimize a longer-term response. Please see the online supplements for a correction to this article.

关键词： Causal inference Confounding G-estimation Longitudinal data Optimal dynamic treatments regimes Structural Nested Mean Model

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Analog sliding mode controller for position tracking of piezoelectric actuators

Analog sliding mode controller for position tracking of piez...

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2007 Mediterranean Conference on Control and Automation, MED

作者： Yannier, S. Sabanovic, A. Sabanci University Faculty of Engineering and Natural Sciences Mechatronics Engineering Program Istanbul Turkey

ISBN: (纸本)142441282X

In this work, analog application for the sliding mode control (SMC) of piezoelectric actuators is presented. DSP application of the algorithm suffers from ADC and DAC conversions and faces speed limitations. Moreover, piezoelectric actuators are known to have very large bandwidth close to the DSP operation frequency. Therefore, with the direct analog application, improvement of the performance is expected and high frequency operation will be achieved. First an appropriate SMC is designed to have continuous control output and then experimental results for position tracking using DSP and analog application are presented for comparison. ©2007 IEEE.

关键词： Piezoelectric actuators

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Brachypodium genomics

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International Journal of Plant Genomics 2008年第unknown期2008卷 536104页

作者： Ozdemir, Bahar Sogutmaz Hernandez, Pilar Filiz, Ertugrul Budak, Hikmet Biological Science and Bioengineering Program Faculty of Engineering and Natural Sciences Sabanci University Orhanli 34956 Tuzla-Istanbul Turkey Institute for Sustainable Agriculture (IAS) Spanish National Research Council (CSIC) 14080 Cordoba Alameda del Obispo s/n Apartado 4084 Spain

Brachypodium distachyon (L.) Beauv. is a temperate wild grass species;its morphological and genomic characteristics make it a model system when compared to many other grass species. It has a small genome, short growth cycle, self-fertility, many diploid accessions, and simple growth requirements. In addition, it is phylogenetically close to economically important crops, like wheat and barley, and several potential biofuel grasses. It exhibits agricultural traits similar to those of these target crops. For cereal genomes, it is a better model than Arabidopsis thaliana and Oryza sativa (rice), the former used as a model for all flowering plants and the latter hitherto used as model for genomes of all temperate grass species including major cereals like barley and wheat. Increasing interest in this species has resulted in the development of a series of genomics resources, including nuclear sequences and BAC/EST libraries, together with the collection and characterization of other genetic resources. It is expected that the use of this model will allow rapid advances in generation of genomics information for the improvement of all temperate crops, particularly the cereals.

关键词： BRACHYPODIUM PLANT genomes PLANT breeding PLANT growth AGRICULTURAL productivity

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Optimization of Dry Powder Deposition parameters for the production of dielectric and magneto-dielectric composites

Optimization of Dry Powder Deposition parameters for the pro...

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Materials Science and Technology Conference and Exhibition, MS and T'07 - "Exploring Structure, Processing, and Applications Across Multiple Materials Systems"

作者： Nergiz, S. Kiziltas, G. Materials Science and Engineering Faculty of Engineering and Natural Sciences Sabanci University Istanbul Turkey Mechatronics Engineering Faculty of Engineering and Natural Sciences Sabanci University Istanbul Turkey

ISBN: (纸本)9781605601335

Spatially variable composites of Calcium Magnesium Titanates(CMT) with dielectric permittivity 15, 20 and 70 and commercial ferrite were produced by Dry Powder Deposition (DPD) method followed by cosintering at elevated temperatures. Thermogravimetric analysis of each constituent powder was used to analyze efficient removal of 1-3 % binder content of spray dried ferrite and CMT powders and achieve complete sintering of their textured composites. Smooth, monolithic dielectric and magneto-dielectric textured composites were obtained by cosintering at 1450 C for 4 hours that were compacted at 50 bar in a 12 *13 grid with 3 mm pixels and a thickness of 5mm. We reduced thermal mismatch effects of constituents observed at temperatures below 1450 C and prevented cracks and unwanted defects such as porosities in textured composites. Density measurements and SEM stressed that we finally obtained over >%98 dense ceramic constituents. Microstructural characterizations of pellets made of sintered constituent material were carried out by SEM. We present in this paper that textured monolithic dielectric and magneto-dielectric composites of various shades could be produced by DPD method which is an efficient way for production of spatially variable multimaterial dielectric substrates suitable for various antenna and filter applications. Copyright © 2007 MS&T'07®.

关键词： Dielectric materials

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Analog sliding mode controller for position tracking of piezoelectric actuators

Analog sliding mode controller for position tracking of piez...

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Mediterranean Conference on Control and Automation (MED)

作者： S. Yannier A. Sabanovic Faculty of Engineering and Natural Sciences Mechatronics Engineering Program Sabanci University Istanbul Turkey

关键词： Sliding mode control Piezoelectric actuators Digital signal processing Open loop systems Atomic force microscopy Bandwidth Frequency Aerospace materials Hysteresis Capacitive sensors

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Correlation Between Defective NK Activity and Low Expression of CD16, NKp44 and NKG2D in Beta Thalassemia Patients

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Blood 2008年第11期112卷 5425-5425页

作者： Belkis Atasever Serap Erdem Kuruca Zeynep Karakas Batu Erman Arzu Ergen Turgay Isbir Physiology Department Istanbul University Istanbul Faculty of Medicine Istanbul Turkey Pediatrics Department Istanbul University Istanbul Faculty of Medicine Istanbul Turkey Faculty of Engineering and Natural Sciences Biological Sciences & Bioengineering Program Sabanci University Istanbul Turkey Department of Molecular Medicine Istanbul University Institute of Experimental Medicine Istanbul Turkey

Beta thalassemia patients have a major global impact on health and mortality and are characterized by absence of beta globin chain production. In most patients, multiple blood transfusions can induce differences of immune response Therefore, they are often associated with bone marrow expansion and immunodeficiency in terms of lymphocyte subsets and cytokine levels in the peripheral blood and presence of alloantibodies. We have previously shown that children with beta thalassemia major have had decreased NK cells. natural killer (NK) cells are lymphocyte subpopulations that are important effectors of innate immune responses against infectious pathogens and tumor cells. The cytotoxic activity of NK cells is regulated by the equilibrium between positive and negative signals from multiple receptors expressed on their cell surface; signals that can trigger the cytolytic machinery as well as cytokine or chemokine secretion. The activator receptors of NK cells are natural cytotoxicity receptors (NCR) and NKG2D. NCR are represented by NKp46, NKp44, and NKp30. These receptors, upon engagement by their specific ligands, induce a strong activation of NK-mediated cytotoxic activity. NKp44, a triggering receptor selectively expressed by activated NK cells. NK cells can make cytolytic function by regulating pro-inflammatory cytokines as IFN-gamma, TNF-alpha and IL10. This study was carried out to investigate details NK cell function of 27 transfusion-dependent children with beta thalassemia. Data from 18 age- and sex-balanced children served as controls. For this purpose, we analyzed their cytolytic function against K562 cells in both pure NK cells (CD56 + CD16 + CD3 − ) and PBMC. Before and after the assessment of NK activity, we have examined the levels of NK activating receptors expressed on NK cells. The expression levels of the activation receptors (NKp30, NKp44, NKG2D) on CD56 + CD16 + CD3 − NK cells was quantified by multicolour immunofluorescent analysis using flow cytome

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Optimization of broaching design

Optimization of broaching design

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IIE Annual Conference and Expo 2007 - Industrial engineering's Critical Role in a Flat World

作者： Özelkan, Ertunga C. Öztürk, Özkan Budak, Erhan Engineering Management Program Center for Lean Logistics and Engineered Systems University of North Carolina at Charlotte Charlotte NC 28223 United States Department of Mechanical Engineering Center for Precision Metrology University of North Carolina at Charlotte Charlotte NC 28223 United States Faculty of Engineering and Natural Sciences Sabanci University Istanbul Turkey

Broaching is one of the most recognized machining processes that can yield high productivity and high quality when applied properly. One big disadvantage of broaching is that all process parameters, except cutting speed, are built into the broaching tools. Therefore, it is not possible to modify the cutting conditions during the process once the tool is manufactured. Optimal design of broaching tools has a significant impact to increase the productivity and to obtain high quality products. In this paper, an optimization model for broaching design is presented. The model results in a non-linear non-convex optimization problem. Analysis of the model structure indicates that the model can be decomposed into smaller problems. The model is applied on a turbine disc broaching problem which is considered as one of the most complex broaching operations.

关键词： Machining

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Sliding mode control application to nano positioners

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Lecture Notes in Control and Information sciences 2006年 334卷 395-421页

作者： Sabanovic, Asif Abidi, Khalid Önal, Çaǧdaş Sabanci University Faculty of Engineering Natural Sciences Mechatronics Program Turkey

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