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information technology [keywords]
- Clinical oncologic applications of PET/MRI: a new horizon. [REVIEW]
- Am J Nucl Med Mol Imaging 2014; 4(2):202-212.
Positron emission tomography/magnetic resonance imaging (PET/MRI) leverages the high soft-tissue contrast and the functional sequences of MR with the molecular information of PET in one single, hybrid imaging technology. This technology, which was recently introduced into the clinical arena in a few medical centers worldwide, provides information about tumor biology and microenvironment. Studies on indirect PET/MRI (use of positron emission tomography/computed tomography (PET/CT) images software fused with MRI images) have already generated interesting preliminary data to pave the ground for potential applications of PET/MRI. These initial data convey that PET/MRI is promising in neuro-oncology and head & neck cancer applications as well as neoplasms in the abdomen and pelvis. The pediatric and young adult oncology population requiring frequent follow-up studies as well as pregnant woman might benefit from PET/MRI due to its lower ionizing radiation dose. The indication and planning of therapeutic interventions and specifically radiation therapy in individual patients could be and to a certain extent are already facilitated by performing PET/MRI. The objective of this article is to discuss potential clinical oncology indications of PET/MRI.
- Bubble-free and pulse-free fluid delivery into microfluidic devices. [Journal Article]
- Biomicrofluidics 2014 Jan; 8(1):014102.
The bubble-free and pulse-free fluid delivery is critical to reliable operation of microfluidic devices. In this study, we propose a new method for stable bubble-free and pulse-free fluid delivery in a microfluidic device. Gas bubbles are separated from liquid by using the density difference between liquid and gas in a closed cavity. The pulsatile flow caused by a peristaltic pump is stabilized via gas compressibility. To demonstrate the proposed method, a fluidic chamber which is composed of two needles for inlet and outlet, one needle for a pinch valve and a closed cavity is carefully designed. By manipulating the opening or closing of the pinch valve, fluids fill up the fluidic chamber or are delivered into a microfluidic device through the fluidic chamber in a bubble-free and pulse-free manner. The performance of the proposed method in bubble-free and pulse-free fluid delivery is quantitatively evaluated. The proposed method is then applied to monitor the temporal variations of fluidic flows of rat blood circulating within a complex fluidic network including a rat, a pinch valve, a reservoir, a peristaltic pump, and the microfluidic device. In addition, the deformability of red blood cells and platelet aggregation are quantitatively evaluated from the information on the temporal variations of blood flows in the microfluidic device. These experimental demonstrations confirm that the proposed method is a promising tool for stable, bubble-free, and pulse-free supply of fluids, including whole blood, into a microfluidic device. Furthermore, the proposed method will be used to quantify the biophysical properties of blood circulating within an extracorporeal bypass loop of animal models.
- Slums' access to and coverage of primary health care services: a cross-sectional study in shiraz, a metropolis in southern iran. [Journal Article]
- Iran J Med Sci 2014 Mar; 39(2 Suppl):184-90.
Background:The United Nations has predicted that the population of slum dwellers will have grown from one billion people worldwide to 2 billion by 2030. This trend is also predictable in Iran. In the Iranian metropolis of Shiraz, more than 10% of the residents live in slum areas. There are several problems regarding the delivery of social services in these areas. The aim of this study was to evaluate slums dwellers' access to and coverage of health care.
Methods:This cross-sectional face-to-face study included 380 household of slum dwellers via stratified random sampling. Demographics, accessibility of health services, coverage of health care, and route of receiving health services were recorded through interviews.
Results:Approximately, 21.6% of the households had no physical access to health centers. The coverage rate of family planning programs for safe methods was 51.4% (95% CI: 48.86-53.9%). Vaccination coverage among children under 5 years old was 98% (95% CI: 97-99%). Furthermore, 34% of pregnant women had not received standard health care due to a lack of access to health centers.
Conclusion:Limited access to health services along with inadequate knowledge of slum residents about health care facilities was the main barrier to the utilization of the health care in the slums.
- Design and fabrication of a perpendicular magnetic tunnel junction based nonvolatile programmable switch achieving 40% less area using shared-control transistor structure. [JOURNAL ARTICLE]
- J Appl Phys 2014 May 7; 115(17):17B742.
A compact nonvolatile programmable switch (NVPS) using 90 nm CMOS technology together with perpendicular magnetic tunnel junction (p-MTJ) devices is fabricated for zero-standby-power field-programmable gate array. Because routing information does not change once it is programmed into an NVPS, high-speed read and write accesses are not required and a write-control transistor can be shared among all the NVPSs, which greatly simplifies structure of the NVPS. In fact, the effective area of the proposed NVPS is reduced by 40% compared to that of a conventional MTJ-based NVPS. The instant on/off behavior without external nonvolatile memory access is also demonstrated using the fabricated test chip.
- Intracellular performance of tailored nanoparticle tracers in magnetic particle imaging. [JOURNAL ARTICLE]
- J Appl Phys 2014 May 7; 115(17):17B306.
Magnetic Particle Imaging (MPI) is a quantitative mass-sensitive, tracer-based imaging technique, with potential applications in various cellular imaging applications. The spatial resolution of MPI, in the first approximation, improves by decreasing the full width at half maximum (FWHM) of the field-derivative of the magnetization, dm/dH of the nanoparticle (NP) tracers. The FWHM of dm/dH depends critically on NPs' size, size distribution, and their environment. However, there is limited information on the MPI performance of the NPs after their internalization into cells. In this work, 30 to 150 μg of the iron oxide NPs were incubated in a lysosome-like acidic buffer (0.2 ml, 20 mM citric acid, pH 4.7) and investigated by vibrating sample magnetometry, magnetic particle spectroscopy, transmission electron microscopy, and dynamic light scattering (DLS). The FWHM of the dm/dH curves of the NPs increased with incubation time and buffer to NPs ratio, consistent with a decrease in the median core size of the NPs from ∼20.1 ± 0.98 to ∼18.5 ± 3.15 nm. Further, these smaller degraded NPs formed aggregates that responded to the applied field by hysteretic reversal at higher field values and increased the FWHM. The rate of core size decrease and aggregation were inversely proportional to the concentration of the incubated NPs, due to their slower biodegradation kinetics. The results of this model experiment show that the MPI performance of the NPs in the acidic environments of the intracellular organelles (i.e., lysosomes and endosomes) can be highly dependent on their rate of internalization, residence time, and degradation.
- Defining functional DNA elements in the human genome. [JOURNAL ARTICLE]
- Proc Natl Acad Sci U S A 2014 Apr 21.
With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. The resulting genome-wide data reveal sites of biochemical activity with high positional resolution and cell type specificity that facilitate studies of gene regulation and interpretation of noncoding variants associated with human disease. However, the biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Here, we review the strengths and limitations of biochemical, evolutionary, and genetic approaches for defining functional DNA segments, potential sources for the observed differences in estimated genomic coverage, and the biological implications of these discrepancies. We also analyze the relationship between signal intensity, genomic coverage, and evolutionary conservation. Our results reinforce the principle that each approach provides complementary information and that we need to use combinations of all three to elucidate genome function in human biology and disease.
- aLFQ: An R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data. [JOURNAL ARTICLE]
- Bioinformatics 2014 Apr 20.
The determination of absolute quantities of proteins in biological samples is necessary for multiple types of scientific inquiry. While relative quantification has been commonly used in proteomics, few proteomic datasets measuring absolute protein quantities have been reported to date. Various technologies have been applied using different types of input data, e.g. ion intensities or spectral counts, as well as different absolute normalization strategies. To date, a user friendly and transparent software supporting large-scale absolute protein quantification has been lacking.We present a bioinformatics tool, termed aLFQ, which supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/ MS proteomics data, together with validation algorithms enabling automated data analysis and error estimation.aLFQ is written in R and freely available under the GPLv3 from CRAN (http://www.cran.r-project.org). Instructions and example data are provided in the R-package. The raw data can be obtained from the PeptideAtlas raw data repository (PASS00321).firstname.lastname@example.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
- MRMPROBS Suite for metabolomics using large-scale MRM assays. [JOURNAL ARTICLE]
- Bioinformatics 2014 Apr 20.
We developed new software environment for the metabolome analysis of large-scale multiple reaction monitoring (MRM) assays. It supports the data format of four major mass spectrometer (MS) vendors and mzML common data format. This program provides a process pipeline from the raw-format import to high-dimensional statistical analyses. The novel aspect is GUI-based visualization to perform peak quantification, to interpolate missing values and to normalize peaks interactively based on quality control samples. Together with the software platform, the MRM standard library of 301 metabolites with 775 transitions is also available, which contributes to the reliable peak identification by using retention time and ion abundances.MRMPROBS is available for Windows OS under the creative-commons by-attribution license at http://email@example.com SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.
- Translation of etiology into evidence-based prevention: The life skills program IPSY. [Journal Article]
- New Dir Youth Dev 2014 Mar; 2014(141):83-94.
IPSY (Information + Psychosocial Competence = Protection) is a universal life skills program aiming at the promotion of generic intra- and interpersonal life skills, substance specific skills (for example, resistance skills), school bonding, knowledge, and the prevention of substance misuse with a focus on alcohol and tobacco in youth. This program is based on the WHO's life skills approach as well as on theories and empirical findings concerning the development of substance misuse during early adolescence. IPSY is implemented by teachers over three years of schooling (grades 5-7 in Germany). Guided by models of translational research dealing with conditions of a successful translation of etiological findings into evidence-based prevention programs, the chapter highlights the results of a more than ten-year research program focusing on the development and evaluation of the IPSY program. Findings on long-term general effects, mediators and moderators of program effectiveness, and cross-cultural transferability of the program to other European countries are summarized and discussed in light of dissemination issues.
- Performance of Protein Disorder Prediction Programs on Amino Acid Substitutions. [JOURNAL ARTICLE]
- Hum Mutat 2014 Apr 21.
Many proteins contain intrinsically disordered regions, which may be crucial for function, but on the other hand be related to the pathogenicity of variants. Prediction programs have been developed to detect disordered regions from sequences and used to predict the consequences of variants, although, their performance for this task has not been assessed. We tested the performance of protein disorder prediction programs in detecting changes to disorder caused by amino acid substitutions. We assessed the quality of 29 protein disorder predictors and versions with 101 amino acid substitutions, whose effects have been experimentally validated. Disorder predictors detected the true positives at most with 6% success rate and true negatives with 34% rate for variants. The corresponding rates for the wild type forms are 7 and 90%. The analysis revealed that disorder programs cannot reliably predict the effects of substitutions, consequently the tested methods, and possibly similar programs, cannot be recommended for variant analysis without other information indicating to the relevance of disorder. These results inspired us to develop a new method, PON-Diso (http://structure.bmc.lu.se/PON-Diso), for disorder related amino acid substitutions. With 50% success rate for independent test set and 70.5% rate in cross validation it outperforms the evaluated methods. This article is protected by copyright. All rights reserved.