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Search Results: 1 - 10 of 301 matches for " Sarit Aviel-Ronen "
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Large fragment Bst DNA polymerase for whole genome amplification of DNA from formalin-fixed paraffin-embedded tissues
Sarit Aviel-Ronen, Chang Qi Zhu, Bradley P Coe, Ni Liu, Spencer K Watson, Wan L Lam, Ming Tsao
BMC Genomics , 2006, DOI: 10.1186/1471-2164-7-312
Abstract: We amplified genomic DNA of five FFPE samples of normal human lung tissue with the large fragment of Bst DNA polymerase. Using quantitative PCR, the copy number of 7 genes was evaluated in both amplified and original DNA samples. Four neuroblastoma xenograft samples derived from cell lines with known N-myc gene copy number were also evaluated, as were 7 samples of non-small cell lung cancer (NSCLC) tumors with known Skp2 gene amplification. In addition, we compared the array comparative genomic hybridization (CGH)-based genome profiles of two NSCLC samples before and after Bst MDA. A median 990-fold amplification of DNA was achieved. The DNA amplification products had a very high molecular weight (> 23 Kb). When the gene content of the amplified samples was compared to that of the original samples, the representational distortion was limited to threefold. Array CGH genome profiles of amplified and non-amplified FFPE DNA were similar.Large fragment Bst DNA polymerase is suitable for WGA of DNA extracted from FFPE tissues, with an expected maximal representational distortion of threefold. Amplified DNA may be used for the detection of gene copy number changes by quantitative realtime PCR and genome profiling by array CGH.With growing interest in the genomic characteristics of various human tumors and a steep increase in the availability of genomic tests for both clinical and research purposes, the amount of genomic DNA available from biological samples may limit the practicality of genomic analysis. Having been used for decades, formalin-fixed paraffin-embedded (FFPE) tissues comprise the most common form of human tissue samples archives. Therefore, it is desirable to establish a whole genome amplification (WGA) method specifically for DNA extracted from FFPE tissues. Two main approaches for WGA have been developed: thermocycling protocols and isothermal amplification methods.Several thermocycling protocols have been used, including the degenerate oligonucleotide prim
Quantitative image analysis of immunohistochemical stains using a CMYK color model
Nhu-An Pham, Andrew Morrison, Joerg Schwock, Sarit Aviel-Ronen, Vladimir Iakovlev, Ming-Sound Tsao, James Ho, David W Hedley
Diagnostic Pathology , 2007, DOI: 10.1186/1746-1596-2-8
Abstract: We adapted a Cyan/Magenta/Yellow/Key (CMYK) model for automated computer image analysis to quantify IHC stains in hematoxylin counterstained histological sections.The spectral characteristics of the chromogens AEC, DAB and NovaRed as well as the counterstain hematoxylin were first determined using CMYK, Red/Green/Blue (RGB), normalized RGB and Hue/Saturation/Lightness (HSL) color models. The contrast of chromogen intensities on a 0–255 scale (24-bit image file) as well as compared to the hematoxylin counterstain was greatest using the Yellow channel of a CMYK color model, suggesting an improved sensitivity for IHC evaluation compared to other color models. An increase in activated STAT3 levels due to growth factor stimulation, quantified using the Yellow channel image analysis was associated with an increase detected by Western blotting. Two clinical image data sets were used to compare the Yellow channel automated method with observer-dependent methods. First, a quantification of DAB-labeled carbonic anhydrase IX hypoxia marker in 414 sections obtained from 138 biopsies of cervical carcinoma showed strong association between Yellow channel and positive color selection results. Second, a linear relationship was also demonstrated between Yellow intensity and visual scoring for NovaRed-labeled epidermal growth factor receptor in 256 non-small cell lung cancer biopsies.The Yellow channel image analysis method based on a CMYK color model is independent of observer biases for threshold and positive color selection, applicable to different chromogens, tolerant of hematoxylin, sensitive to small changes in IHC intensity and is applicable to simple automation procedures. These characteristics are advantageous for both basic as well as clinical research in an unbiased, reproducible and high throughput evaluation of IHC intensity.Immunohistochemistry (IHC) for the evaluation of antigen expression as well as higher resolution methodologies for cytogenetic analysis are standard
Genomic Deregulation of the E2F/Rb Pathway Leads to Activation of the Oncogene EZH2 in Small Cell Lung Cancer
Bradley P. Coe, Kelsie L. Thu, Sarit Aviel-Ronen, Emily A. Vucic, Adi F. Gazdar, Stephen Lam, Ming-Sound Tsao, Wan L. Lam
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0071670
Abstract: Small cell lung cancer (SCLC) is a highly aggressive lung neoplasm with extremely poor clinical outcomes and no approved targeted treatments. To elucidate the mechanisms responsible for driving the SCLC phenotype in hopes of revealing novel therapeutic targets, we studied copy number and methylation profiles of SCLC. We found disruption of the E2F/Rb pathway was a prominent feature deregulated in 96% of the SCLC samples investigated and was strongly associated with increased expression of EZH2, an oncogene and core member of the polycomb repressive complex 2 (PRC2). Through its catalytic role in the PRC2 complex, EZH2 normally functions to epigenetically silence genes during development, however, it aberrantly silences genes in human cancers. We provide evidence to support that EZH2 is functionally active in SCLC tumours, exerts pro-tumourigenic functions in vitro, and is associated with aberrant methylation profiles of PRC2 target genes indicative of a “stem-cell like” hypermethylator profile in SCLC tumours. Furthermore, lentiviral-mediated knockdown of EZH2 demonstrated a significant reduction in the growth of SCLC cell lines, suggesting EZH2 has a key role in driving SCLC biology. In conclusion, our data confirm the role of EZH2 as a critical oncogene in SCLC, and lend support to the prioritization of EZH2 as a potential therapeutic target in clinical disease.
A Turbo Drive for the Global Reduction of Energy-Related CO2 Emissions
Aviel Verbruggen
Sustainability , 2011, DOI: 10.3390/su3040632
Abstract: The Copenhagen Accord performed a seizure in the COP ungainly crawl. The Accord’s urgent combat against climate change and deep cuts in emissions require a policy reversal, ending the zero sum games on pledged caps, creating clarity on immediate marching directions and eliciting worldwide action by today’s operational institutes at all levels. For reducing energy-related CO 2 emissions, all turbo drive components are available. First the global 2 °C ceiling needs translation into, by country, marching directions and indicative future paths of their national average CO 2 emissions per person. The latter intensity indicator is the product of three driving intensities: wealth per person, energy used for wealth production, and CO 2 emissions of energy use, all observed annually for virtually all countries in the world. Second, parties should commit to nearby year improvements on the three driving intensities. Third, transfers from rich to poor countries depend on ability to pay and on ability to spend, and on countries’ mitigation progress. The approach dissolves main barriers to mitigation progress, like: outdated emissions baselines; illusory global instruments; bureaucratic MRV (monitoring, reporting and verification) concepts; blocked graduation of parties; unclear transfer mechanisms. In revamping the jammed COP rituals, UNFCCC now leaves operations to established global institutes and mainly to the parties acting in common resolve, stimulated and verified by a lightweight, transparent global framework.
A Note on the Expectation Value of Time  [PDF]
Yigal Ronen
Journal of Modern Physics (JMP) , 2016, DOI: 10.4236/jmp.2016.76047
Abstract: In this note, the expectation value of time based on quantum mechanics formalism is derived. It is found that the expectation value of time does not depend on space.
Security Considerations for Remote Electronic Voting over the Internet
Aviel D. Rubin
Computer Science , 2001,
Abstract: This paper discusses the security considerations for remote electronic voting in public elections. In particular, we examine the feasibility of running national federal elections over the Internet. The focus of this paper is on the limitations of the current deployed infrastructure in terms of the security of the hosts and the Internet itself. We conclude that at present, our infrastructure is inadequate for remote Internet voting.
On the Application of Probabilistic Hydrometeorological Simulation of Soil Moisture across Different Stations in India  [PDF]
Sarit Kumar Das, Rajib Maity
Journal of Geoscience and Environment Protection (GEP) , 2014, DOI: 10.4236/gep.2014.23021
Abstract:

An application of a proposed hydrometeorological approach for probabilistic simulation of soil moisture is carried out. The time series of in-situ soil moisture and meteorological variables at monthly scale from a few monitoring stations having different soil-hydrologic properties across India are utilized. Preliminary investigation with both precipitation and near-surface air-tempera- ture as meteorological variables to establish that the strength of association between soil moisture and precipitation is more significant as compared to that between soil moisture and temperature. Precipitation-based probabilistic estimation of soil moisture using the proposed hydrometeorological approach is tested with in-situ observed soil moisture, CPC model output and with soil moisture data of the Climate Change Initiative (CCI) project. The parameter of the developed model is linked to the soil-hydrologic characteristics through Hydrologic Soil Group (HSG) classification. Higher values of model parameter (dependence parameter (θ) for the selected copula) correspond to HSG A and B having higher soil porosity, whereas, lower values correspond to HSG B and C having lower soil porosity.

The Use of Virtual Reality in Motor Learning: A Multiple Pilot Study Review  [PDF]
Einat Yanovich, Omri Ronen
Advances in Physical Education (APE) , 2015, DOI: 10.4236/ape.2015.53023
Abstract: In recent years, technological improvements have allowed for the creation of V.R. environments for different uses, especially in the training of pilots, astronauts, medical staff, soldiers, and athletes. In regards to physical activity, V.R. is currently being used in two main fields: Exergaming and Rehabilitation. The purpose of this article is to investigate the use of this technology as a means of demonstrating and learning motor abilities in many types of populations and situations. Three studies were done using V.R. In all three of them healthy participants were assigned to a control or test group. These studies were done using two main V.R. systems designed for motor learning: Timocco and IREX. Study 1 tested bi-lateral transfer in the upper limbs; Study 2 tested the differences in improvement using V.R. between internal and extrinsic focus of attention; Study 3 tested differences in different learning strategies in motor tasks—massed practice vs. distributed practice. Study 1 found significant differences between control and test groups; Study 2 did not find that external focus of attention was superior as expected but found a stronger correlation between tests at different days; Study 3 found no significant improvements (p > 0.05) for each group. In conclusion, V.R. can be an effective means of teaching and training basic motor skills, sometimes even superior to “real-life” because of the highly modifiable environment and difficulty in the comfort of one’s clinic or home.
Attentional networks in developmental dyscalculia
Sarit Askenazi, Avishai Henik
Behavioral and Brain Functions , 2010, DOI: 10.1186/1744-9081-6-2
Abstract: Fourteen university students that were diagnosed as suffering from developmental dyscalculia--intelligence and reading abilities in the normal range and no indication of attention-deficit hyperactivity disorder--and 14 matched controls were tested using the attention networks test - interactions. All participants were given preliminary tests to measure mathematical abilities, reading, attention and intelligence.The results revealed deficits in the alerting network--a larger alerting effect--and in the executive function networks--a larger congruity effect in developmental dyscalculia participants. The interaction between the alerting and executive function networks was also modulated by group. In addition, developmental dyscalculia participants were slower to respond in the non-cued conditions.These results imply specific attentional deficits in pure developmental dyscalculia. Namely, those with developmental dyscalculia seem to be deficient in the executive function and alertness networks. They suffer from difficulty in recruiting attention, in addition to the deficits in numerical processing.Developmental dyscalculia is generally defined as a disorder in mathematical abilities presumed to be due to a specific impairment in brain function [1,2]. Developmental dyscalculia is supposed to be a unique deficit that is not caused by a reading disorder (dyslexia), attentional disorder (ADHD/ADD- attention-deficit disorder) or general intelligence (IQ) problems. The present study aims to examine attention in developmental dyscalculia by employing a recently designed test of three attentional networks and their interactions [3].Children with developmental dyscalculia fail in a wide range of numerical tasks. For example, they present difficulties in retrieval of arithmetical facts [4-8], in using arithmetical procedures [e.g., [7]], and in solving arithmetical operations in general [9]. Recently, studies on developmental dyscalculia concentrated on basic numerical processing
Engineering of near IR fluorescent albumin nanoparticles for in vivo detection of colon cancer
Cohen Sarit,Margel Shlomo
Journal of Nanobiotechnology , 2012, DOI: 10.1186/1477-3155-10-36
Abstract: Background The use of near-infrared (NIR) fluorescence imaging techniques has gained great interest for early detection of cancer because water and other intrinsic biomolecules display negligible absorption or autofluorescence in this region. Novel fluorescent nanoparticles with potential to improve neoplasm detection sensitivity may prove to be a valuable tool in early detection of colon tumors. Methods The present study describes the synthesis and use of NIR fluorescent albumin nanoparticles as a diagnostic tool for detection of colon cancer. These fluorescent nanoparticles were prepared by a precipitation process of human serum albumin (HSA) in aqueous solution in the presence of a carboxylic acid derivative of the NIR dye IR-783 (CANIR). Tumor-targeting ligands such as peanut agglutinin (PNA), anti-carcinoembryonic antigen antibodies (anti-CEA) and tumor associated glycoprotein-72 monoclonal antibodies (anti-TAG-72) were covalently conjugated to the albumin nanoparticles via the surface carboxylate groups by using the carbodiimide activation method. Results and discussion Leakage of the encapsulated dye into PBS containing 4% HSA or human bowel juice was not detected. This study also demonstrates that the encapsulation of the NIR fluorescent dye within the HSA nanoparticles reduces the photobleaching of the dye significantly. Specific colon tumor detection in a mouse model was demonstrated for PNA, anti-CEA and anti-TAG-72 conjugated NIR fluorescent HSA nanoparticles. These bioactive NIR fluorescent albumin nanoparticles also detected invisible tumors that were revealed as pathological only subsequent to histological analysis. Conclusions These results may suggest a significant advantage of NIR fluorescence imaging using NIR fluorescent nanoparticles over regular colonoscopy. In future work we plan to broaden this study by encapsulating cancer drugs, such as paclitaxel and doxorubicin, within these biodegradable NIR fluorescent HSA nanoparticles, in order to use them for both detection as well as therapy of colon cancer and others.
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