UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses.

https://bradleybiology.org/papers/pdf/2015/RobinsonEtAl2015.pdf

Integrative clinical genomics of advanced prostate cancer

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

https://air.unimi.it/bitstream/2434/586890/2/PIIS0092867418302290.pdf

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics.

https://minerva-access.unimelb.edu.au/bitstream/handle/11343/253538/PMC5957518.pdf

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer.

Magnetic resonance fingerprinting (MRF) is one novel fast quantitative imaging framework for simultaneous quantification of multiple parameters with pseudo-randomized acquisition patterns. The accuracy of the resulting multi-parameters is very important for clinical applications. In this paper, we derived signal evolutions from the anomalous relaxation using a fractional calculus. More specifically, we utilized time-fractional order extension of the Bloch equations to generate dictionary to provide more complex system descriptions for MRF applications. The representative results of phantom experiments demonstrated the good accuracy performance when applying the time-fractional order Bloch equations to generate dictionary entries in the MRF framework. The utility of the proposed method is also validated by in-vivo study.

Application of Time-Fractional Order Bloch Equation in Magnetic Resonance Fingerprinting

Localized prostate cancer develops very slowly in most men, with the androgen receptor (AR) and MYC transcription factors amongst the most well-characterized drivers of prostate tumorigenesis. Canonically, MYC up-regulation in luminal prostate cancer cells functions to oppose the terminally differentiating effects of AR. However, the effects of MYC up-regulation are pleiotropic and inconsistent with a poorly proliferative phenotype. Here we show that increased MYC expression and activity are associated with the down-regulation of MEIS1, a HOX-family transcription factor. Using RNA-seq to profile a series of human prostate cancer specimens laser capture microdissected on the basis of MYC immunohistochemistry, MYC activity and MEIS1 expression were inversely correlated. Knockdown of MYC expression in prostate cancer cells increased expression of MEIS1 and increased occupancy of MYC at the MEIS1 locus. Finally, we show in laser capture microdissected human prostate cancer samples and the prostate TCGA cohort that MEIS1 expression is inversely proportional to AR activity as well as HOXB13, a known interacting protein of both AR and MEIS1. Collectively, our data demonstrate that elevated MYC in a subset of primary prostate cancers functions in a negative role in regulating MEIS1 expression, and that this down-regulation may contribute to MYC-driven development and progression.

/pdf/meis1-down-regulation-by-myc-mediates-prostate-cancer-3yd6rtyb2q.pdf

MEIS1 down-regulation by MYC mediates prostate cancer development through elevated HOXB13 expression and AR activity

Should the involvement of skeletal muscle by prostatic adenocarcinoma be reported on biopsies

High peak RF amplitude and excessive specific absorption rate (SAR) are two critical concerns for hardware implementation and patient safety in scientific and clinical research for high field MRI using parallel transmissions (pTX). In this paper, we introduce a squeezing strategy to reduce peak RF amplitude and integrated RF power via direct reshaping of the k-space trajectory. In the existing peak RF / integrated RF power optimization methods gradient amplitude or slew rate is reduced, but the k-space trajectory remains unchanged. Unlike these traditional methods, we worked directly in the excitation k-space to reshape k-space traversal by a squeezing vector in order to achieve peak RF and total RF power optimization, using a particle swarm optimization algorithm. The squeezing strategy was applied to the conventional variable density spiral (CVDS) and the variable rate selective excitation (VERSE) trajectories, dubbed SVDS (squeezed variable density spiral) and SVERSE (squeezing trajectory with VERSE), respectively, for different excitation profiles of small or large tip angles. Pulse acceleration and off-resonance effects were evaluated for an 8-ch pTX via Bloch simulation. CVDS, VERSE, SVDS, and SVERSE pulses were implemented on a 3T scanner with a 2-ch pTX. Phantom and in vivo experiments were performed for reduced FOV (rFOV) imaging. The results show that SVDS pulses simultaneously reduce integrated RF power and peak RF by about 30% on average compared to CVDS pulses for a square pattern ( $80\times80$ mm2) with flip angles of 30°, 90°, and 180°. Compared with the VERSE method under the same peak RF constraints, the SVDS method reduces integrated RF power by an average of 20% for small tip excitations for profiles of slice, rectangular, square, and circle, and has slightly reduced excitation accuracy slightly (about 0.6%, from 6.8% to 7.4%). The SVERSE method shortens the duration of the VERSE pulse by 12.8% at large ti p angle (180°). Feasibility for rFOV imaging was demonstrated with phantom and in vivo experiments with squeezed pulses.

Squeezed Trajectory Design for Peak RF and Integrated RF Power Reduction in Parallel Transmission MRI

The invention discloses an ultra-short time of echo magnetic resonance fingerprint relaxation time measuring method. According to the method, semi-pulse excitation and semi-projection readout are adopted to shorten TE to achieve acquisition of an ultra-short T2 time signal; and image acquisition and reconstruction are based on a magnetic resonance fingerprint imaging technology. A TE change mode of sinusoidal fluctuation is introduced, so that the distinguishing capability of a magnetic resonance fingerprint signal to short T2 and ultra-short T2 tissues is improved, and simultaneous multi-parameter quantitative imaging of the short T2 and ultra-short T2 tissues and long T2 tissues is realized. The non-uniformity of a magnetic field is modulated into phase information of the fingerprint signal through the TE of the sinusoidal fluctuation; a B0 graph is directly reconstructed according to an amplitude modulation signal demodulation principle; and the phase change caused by a B0 field iscompensated in the fingerprint signal, so that the accuracy of signal recognition is improved. In magnetic resonance skeletal muscle system imaging, simultaneous quantitative measurement of T1, T2, PDand B0 of the bone (ultra-short T2) and muscle (long T2) tissues can be realized; and the method can also be used for imaging the brain and measuring the grey/white matter relaxation time and the skull structure.

Huihui Ye

Papers

Application of Time-Fractional Order Bloch Equation in Magnetic Resonance Fingerprinting

MEIS1 down-regulation by MYC mediates prostate cancer development through elevated HOXB13 expression and AR activity

Should the involvement of skeletal muscle by prostatic adenocarcinoma be reported on biopsies

Squeezed Trajectory Design for Peak RF and Integrated RF Power Reduction in Parallel Transmission MRI

Ultra-short time of echo magnetic resonance fingerprint relaxation time measuring method