Baseband Detection of Bistatic Electron Spin Signals in Magnetic Resonance Force Microscopy (MRFM)

In single spin Magnetic Resonance Force Microscopy (MRFM), the objective is to detect the presence of an electron (or nuclear) spin in a sample volume by measuring spin-induced attonewton forces using a micromachined cantilever. In the OSCAR method of single spin MRFM, the spins are manipulated by an external rf field to produce small periodic deviations in the resonant frequency of the cantilever. These deviations can be detected by frequency demodulation followed by conventional amplitude or energy detection. In this paper, we present an alternative to these detection methods, based on optimal detection theory and Gibbs sampling. On the basis of simulations, we show that our detector outperforms the conventional amplitude and energy detectors for realistic MRFM operating conditions. For example, to achieve a 10% false alarm rate and an 80% correct detection rate our detector has an 8 dB SNR advantage as compared with the conventional amplitude or energy detectors. Furthermore, at these detection rates it comes within 4 dB of the omniscient matched-filter lower bound.Comment: 8 pages, 9 figures, revision of paper contains correction to a typo on the first page (introduction section

Towards Semantic Interoperability for IT Governance: An Ontological Approach

In today's IT-centric environment, businesses rely more heavily on IT technologies. Organizations are often obliged to satisfy different requirements demanded and imposed by customers, business partners and legal entities. With increasing regulatory requirements, various best practices and standards are phenomenally employed to benchmark organizational adherence to different regulations. In a heterogeneous, multi-regulated, multi-disciplined and global environment, corporations are often required to consult with multiple standards. Interoperability between the standards for heterogeneous compliance management in the forms of semantic data translation and data integration is subsequently required. Semantic translation between standards allows compliance efforts established on a standard to be based on another standard. On the other hand, semantic data integration enables an integrated view of multiple standards. We present in this paper an ontology-based approach to the semantic interoperability problem in the domain of IT governance

Near-Optimal Signal Detection for Finite-State Markov Signals with Application to Magnetic Resonance Force Microscopy

Detection of a finite-state Markov signal in additive white Gaussian noise (AWGN) can be done in an intuitive manner by applying an appropriate filter and using an energy detector. One might not expect this heuristic approach to signal detection to be optimal. However, in this paper, we show that for a certain type of finite-state Markov signal, namely, the discrete-time (DT) random telegraph, this filtered energy detector is approximately optimal under the following conditions of: symmetric transition probabilities, low signal-to-noise ratio (SNR), long observation time, and small probability of transition between two consecutive time instances. When these last three conditions hold, but the transition probabilities are not symmetric, we show that a variant of the filtered energy detector is approximately optimal. It is also shown, under low SNR conditions, that the likelihood ratio test (LRT) for a finite-state DT Markov signal in AWGN reduces to the matched filter statistic with the minimum mean-squared-error (MMSE) predictor signal values used in place of the known signal values. Using this result, we propose a general methodology for obtaining an approximation to the LRT of a finite-state DT Markov signal in AWGN. Specifically, instead of the conditional mean (also MMSE) estimators, affine estimators with lowest mean squared error are used. This work is relevant to magnetic resonance force microscopy, an emerging technology that uses ultrasensitive force sensing to detect magnetic resonance. Sensitivity down to the single spin level was demonstrated in a recent experiment.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/85833/1/Fessler44.pd

Carboxyl-terminal truncated HBx regulates a distinct microRNA transcription program in Hepatocellular carcinoma development

Background: The biological pathways and functional properties by which misexpressed microRNAs (miRNAs) contribute to liver carcinogenesis have been intensively investigated. However, little is known about the upstream mechanisms that deregulate miRNA expressions in this process. In hepatocellular carcinoma (HCC), hepatitis B virus (HBV) X protein (HBx), a transcriptional trans-activator, is frequently expressed in truncated form without carboxyl-terminus but its role in miRNA expression and HCC development is unclear. Methods: Human non-tumorigenic hepatocytes were infected with lentivirus-expressing full-length and carboxyl-terminal truncated HBx (Ct-HBx) for cell growth assay and miRNA profiling. Chromatin immunoprecipitation microarray was performed to identify the miRNA promoters directly associated with HBx. Direct transcriptional control was verified by luciferase reporter assay. The differential miRNA expressions were further validated in a cohort of HBV-associated HCC tissues using real-time PCR. Results: Hepatocytes expressing Ct-HBx grew significantly faster than the full-length HBx counterparts. Ct-HBx decreased while full-length HBx increased the expression of a set of miRNAs with growth-suppressive functions. Interestingly, Ct-HBx bound to and inhibited the transcriptional activity of some of these miRNA promoters. Notably, some of the examined repressed-miRNAs (miR-26a, -29c, -146a and -190) were also significantly down-regulated in a subset of HCC tissues with carboxyl-terminal HBx truncation compared to their matching non-tumor tissues, highlighting the clinical relevance of our data. Conclusion: Our results suggest that Ct-HBx directly regulates miRNA transcription and in turn promotes hepatocellular proliferation, thus revealing a viral contribution of miRNA deregulation during hepatocarcinogenesis. © 2011 Yip et al.published_or_final_versio

BRAF V600E Status Sharply Differentiates Lymph Node Metastasis-associated Mortality Risk in Papillary Thyroid Cancer

[Context]: How lymph node metastasis (LNM)-associated mortality risk is affected by BRAF V600E in papillary thyroid cancer (PTC) remains undefined. [Objective]: To study whether BRAF V600E affected LNM-associated mortality in PTC. [Design, Setting, and Participants]: We retrospectively analyzed the effect of LNM on PTC-specific mortality with respect to BRAF status in 2638 patients (2015 females and 623 males) from 11 centers in 6 countries, with median age of 46 [interquartile range (IQR) 35-58] years and median follow-up time of 58 (IQR 26-107) months. [Results]: Overall, LNM showed a modest mortality risk in wild-type BRAF patients but a strong one in BRAF V600E patients. In conventional PTC (CPTC), LNM showed no increased mortality risk in wild-type BRAF patients but a robustly increased one in BRAF V600E patients; mortality rates were 2/659 (0.3%) vs 4/321 (1.2%) in non-LNM vs LNM patients (P = 0.094) with wild-type BRAF, corresponding to a hazard ratio (HR) (95% CI) of 4.37 (0.80-23.89), which remained insignificant at 3.32 (0.52-21.14) after multivariate adjustment. In BRAF V600E CPTC, morality rates were 7/515 (1.4%) vs 28/363 (7.7%) in non-LNM vs LNM patients (P < 0.001), corresponding to an HR of 4.90 (2.12-11.29) or, after multivariate adjustment, 5.76 (2.19-15.11). Adjusted mortality HR of coexisting LNM and BRAF V600E vs absence of both was 27.39 (5.15-145.80), with Kaplan-Meier analyses showing a similar synergism. [Conclusions]: LNM-associated mortality risk is sharply differentiated by the BRAF status in PTC; in CPTC, LNM showed no increased mortality risk with wild-type BRAF but a robust one with BRAF mutation. These results have strong clinical relevance.This work was supported partly by the following funding at the individual participating centers: Polish National Center of Research and Development MILESTONE Project—molecular diagnostics and imaging in individualized therapy for breast, thyroid and prostate cancer, grant No. STRATEGMED2/267398/4/ NCBR/2015 (Poland, AC, BJ); Grants No. PID2019-105303RB-I00 (AEI from MICINN), GCB14142311CRES (AECC Foundation), and B2017/BMD-3724 TIRONET2-CM (Spain; PS and GR-E); Grant No. AZV 16-32665A and MH CZ-DRO (Institute of Endocrinology-EU, 00023761) (Czech Republic; BB, VS); NIH/ National Institute on Aging Grant No. 5R03AG042334-02 (LY); and grants from the Qingdao Science and Technology Project for People’s Livelihood No.13-1-3-58-nsh (China; FW) and the Innovative Platform Project of Qingdao No.12-1-2-15-jch (China; YW)

Glioma Through the Looking GLASS: Molecular Evolution of Diffuse Gliomas and the Glioma Longitudinal AnalySiS Consortium

Adult diffuse gliomas are a diverse group of brain neoplasms that inflict a high emotional toll on patients and their families. The Cancer Genome Atlas (TCGA) and similar projects have provided a comprehensive understanding of the somatic alterations and molecular subtypes of glioma at diagnosis. However, gliomas undergo significant cellular and molecular evolution during disease progression. We review the current knowledge on the genomic and epigenetic abnormalities in primary tumors and after disease recurrence, highlight the gaps in the literature, and elaborate on the need for a new multi-institutional effort to bridge these knowledge gaps and how the Glioma Longitudinal AnalySiS Consortium (GLASS) aims to systemically catalog the longitudinal changes in gliomas. The GLASS initiative will provide essential insights into the evolution of glioma toward a lethal phenotype, with the potential to reveal targetable vulnerabilities, and ultimately, improved outcomes for a patient population in need

Genome-wide association meta-analysis of corneal curvature identifies novel loci and shared genetic influences across axial length and refractive error

Corneal curvature, a highly heritable trait, is a key clinical endophenotype for myopia - a major cause of visual impairment and blindness in the world. Here we present a trans-ethnic meta-analysis of corneal curvature GWAS in 44,042 individuals of Caucasian and Asian with replication in 88,218 UK Biobank data. We identified 47 loci (of which 26 are novel), with population-specific signals as well as shared signals across ethnicities. Some identified variants showed precise scaling in corneal curvature and eye elongation (i.e. axial length) to maintain eyes in emmetropia (i.e. HDAC11/FBLN2 rs2630445, RBP3 rs11204213); others exhibited association with myopia with little pleiotropic effects on eye elongation. Implicated genes are involved in extracellular matrix organization, developmental process for body and eye, connective tissue cartilage and glycosylation protein activities. Our study provides insights into population-specific novel genes for corneal curvature, and their pleiotropic effect in regulating eye size or conferring susceptibility to myopia.</p

Genome-wide association meta-analysis of corneal curvature identifies novel loci and shared genetic influences across axial length and refractive error

Abstract: Corneal curvature, a highly heritable trait, is a key clinical endophenotype for myopia - a major cause of visual impairment and blindness in the world. Here we present a trans-ethnic meta-analysis of corneal curvature GWAS in 44,042 individuals of Caucasian and Asian with replication in 88,218 UK Biobank data. We identified 47 loci (of which 26 are novel), with population-specific signals as well as shared signals across ethnicities. Some identified variants showed precise scaling in corneal curvature and eye elongation (i.e. axial length) to maintain eyes in emmetropia (i.e. HDAC11/FBLN2 rs2630445, RBP3 rs11204213); others exhibited association with myopia with little pleiotropic effects on eye elongation. Implicated genes are involved in extracellular matrix organization, developmental process for body and eye, connective tissue cartilage and glycosylation protein activities. Our study provides insights into population-specific novel genes for corneal curvature, and their pleiotropic effect in regulating eye size or conferring susceptibility to myopia