27,226 research outputs found
First-principles study of high conductance DNA sequencing with carbon nanotube electrodes
Rapid and cost-effective DNA sequencing at the single nucleotide level might
be achieved by measuring a transverse electronic current as single-stranded DNA
is pulled through a nano-sized pore. In order to enhance the electronic
coupling between the nucleotides and the electrodes and hence the current
signals, we employ a pair of single-walled close-ended (6,6) carbon nanotubes
(CNTs) as electrodes. We then investigate the electron transport properties of
nucleotides sandwiched between such electrodes by using first-principles
quantum transport theory. In particular we consider the extreme case where the
separation between the electrodes is the smallest possible that still allows
the DNA translocation. The benzene-like ring at the end cap of the CNT can
strongly couple with the nucleobases and therefore both reduce conformational
fluctuations and significantly improve the conductance. The optimal molecular
configurations, at which the nucleotides strongly couple to the CNTs, and which
yield the largest transmission, are first identified. Then the electronic
structures and the electron transport of these optimal configurations are
analyzed. The typical tunneling currents are of the order of 50 nA for voltages
up to 1 V. At higher bias, where resonant transport through the molecular
states is possible, the current is of the order of several A. Below 1 V
the currents associated to the different nucleotides are consistently
distinguishable, with adenine having the largest current, guanine the
second-largest, cytosine the third and finally thymine the smallest. We further
calculate the transmission coefficient profiles as the nucleotides are dragged
along the DNA translocation path and investigate the effects of configurational
variations. Based on these results we propose a DNA sequencing protocol
combining three possible data analysis strategies.Comment: 12 pages, 17 figures, 3 table
Multi-Estimator Full Left Ventricle Quantification through Ensemble Learning
Cardiovascular disease accounts for 1 in every 4 deaths in United States.
Accurate estimation of structural and functional cardiac parameters is crucial
for both diagnosis and disease management. In this work, we develop an ensemble
learning framework for more accurate and robust left ventricle (LV)
quantification. The framework combines two 1st-level modules: direct estimation
module and a segmentation module. The direct estimation module utilizes
Convolutional Neural Network (CNN) to achieve end-to-end quantification. The
CNN is trained by taking 2D cardiac images as input and cardiac parameters as
output. The segmentation module utilizes a U-Net architecture for obtaining
pixel-wise prediction of the epicardium and endocardium of LV from the
background. The binary U-Net output is then analyzed by a separate CNN for
estimating the cardiac parameters. We then employ linear regression between the
1st-level predictor and ground truth to learn a 2nd-level predictor that
ensembles the results from 1st-level modules for the final estimation.
Preliminary results by testing the proposed framework on the LVQuan18 dataset
show superior performance of the ensemble learning model over the two base
modules.Comment: Jiasha Liu, Xiang Li and Hui Ren contribute equally to this wor
Long-term power-law fluctuation in Internet traffic
Power-law fluctuation in observed Internet packet flow are discussed. The
data is obtained by a multi router traffic grapher (MRTG) system for 9 months.
The internet packet flow is analyzed using the detrended fluctuation analysis.
By extracting the average daily trend, the data shows clear power-law
fluctuations. The exponents of the fluctuation for the incoming and outgoing
flow are almost unity. Internet traffic can be understood as a daily periodic
flow with power-law fluctuations.Comment: 10 pages, 8 figure
Vitamin C Prevents Hypogonadal Bone Loss
Epidemiologic studies correlate low vitamin C intake with bone loss. The genetic deletion of enzymes involved in de novo vitamin C synthesis in mice, likewise, causes severe osteoporosis. However, very few studies have evaluated a protective role of this dietary supplement on the skeleton. Here, we show that the ingestion of vitamin C prevents the low-turnover bone loss following ovariectomy in mice. We show that this prevention in areal bone mineral density and micro-CT parameters results from the stimulation of bone formation, demonstrable in vivo by histomorphometry, bone marker measurements, and quantitative PCR. Notably, the reductions in the bone formation rate, plasma osteocalcin levels, and ex vivo osteoblast gene expression 8 weeks post-ovariectomy are all returned to levels of sham-operated controls. The study establishes vitamin C as a skeletal anabolic agent. © 2012 Zhu et al
Metabolomics defines complex patterns of dyslipidaemia in juvenile-sle patients associated with inflammation and potential cardiovascular disease risk
Cardiovascular disease (CVD) is a leading cause of mortality in patients with juvenile-onset systemic lupus erythematosus (JSLE) associated with atherosclerosis. The interplay between dyslipidaemia and inflammation—mechanisms that drive atherosclerosis—were investigated retro-spectively in adolescent JSLE patients using lipoprotein-based serum metabolomics in patients with active and inactive disease, compared to healthy controls (HCs). Data was analysed using machine learning, logistic regression, and linear regression. Dyslipidaemia in JSLE patients was characterised by lower levels of small atheroprotective high-density lipoprotein subsets compared to HCs. These changes were exacerbated by active disease and additionally associated with significantly higher atherogenic very-low-density lipoproteins (VLDL) compared to patients with low disease activity. Atherogenic lipoprotein subset expression correlated positively with clinical and serological markers of JSLE disease activity/inflammation and was associated with disturbed liver function, and elevated expression of T-cell and B-cell lipid rafts (cell signalling platforms mediating immune cell activa-tion). Finally, exposing VLDL/LDL from patients with active disease to HC lymphocytes induced a significant increase in lymphocyte lipid raft activation compared to VLDL/LDL from inactive patients. Thus, metabolomic analysis identified complex patterns of atherogenic dyslipidaemia in JSLE patients associated with inflammation. This could inform lipid-targeted therapies in JSLE to improve cardiovascular outcomes
Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks
Image registration is a gateway technology for Developmental Systems Biology, enabling computational analysis of related datasets within a shared coordinate system. Many registration tools rely on landmarks to ensure that datasets are correctly aligned; yet suitable landmarks are not present in many datasets. Atlas Toolkit is a Fiji/ImageJ plugin collection offering elastic group-wise registration of 3D morphological datasets, guided by segmentation of the interesting morphology. We demonstrate the method by combinatorial mapping of cell signalling events in the developing eyes of chick embryos, and use the integrated datasets to predictively enumerate Gene Regulatory Network states
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