Characterization of the metabolomic profile of renal cell carcinoma by high resolution magic angle spinning proton magnetic resonance spectroscopy.

Background: Renal cell carcinoma (RCC) is a metabolic disease, with subtypes exhibiting aberrations in different metabolic pathways. Metabolomics may offer greater sensitivity for revealing disease biology. We investigated the metabolomic profile of RCC using high-resolution magic angle spinning (HRMAS) proton magnetic resonance spectroscopy (HMRS).

Single-spoke binning: Reducing motion artifacts in abdominal radial stack-of-stars imaging.

Purpose: To increase the effectiveness of respiratory gating in radial stack-of-stars MRI, particularly when imaging at high spatial resolutions or with multiple echoes.

Methods: Free induction decay (FID) navigators were integrated into a three-dimensional gradient echo radial stack-of-stars pulse sequence. These navigators provided a motion signal with a high temporal resolution, which allowed single-spoke binning (SSB): each spoke at each phase encode step was sorted individually to the corresponding motion state of the respiratory signal.

Visualizing metabolomics data with R.

In communicating scientific results, convincing data visualization is of utmost importance. Especially in metabolomics, results based on large numbers of dimensions and variables necessitate particular attention in order to convey their message unambiguously to the reader; also, in the era of open science, traceability and reproducibility are becoming increasingly important. This article describes the use of the R programming language to visualize published metabolomics data resulting from ex vivo NMR spectroscopy and mass spectrometry experiments with a special focus on reproducibility, including example figures as well as associated R code for ease of reuse.

Patient-by-Patient Deep Transfer Learning for Drug-Response Profiling Using Confocal Fluorescence Microscopy of Pediatric Patient-Derived Tumor-Cell Spheroids.

Image-based phenotypic drug profiling is receiving increasing attention in drug discovery and precision medicine. Compared to classical end-point measurements quantifying drug response, image-based profiling enables both the quantification of drug response and characterization of disease entities and drug-induced cell-death phenotypes. Here, we aim to quantify image-based drug responses in patient-derived 3D spheroid tumor cell cultures, tackling the challenges of a lack of single-cell-segmentation methods and limited patient-derived material.

High Resolution Magic Angle Spinning Proton NMR Study of Alzheimer's Disease with Mouse Models.

Alzheimer's disease (AD) is a crippling condition that affects millions of elderly adults each year, yet there remains a serious need for improved methods of diagnosis. Metabolomic analysis has been proposed as a potential methodology to better investigate and understand the progression of this disease; however, studies of human brain tissue metabolomics are challenging, due to sample limitations and ethical considerations. Comprehensive comparisons of imaging measurements in animal models to identify similarities and differences between aging- and AD-associated metabolic changes should thus be tested and validated for future human non-invasive studies.

Functional Therapeutic Target Validation Using Pediatric Zebrafish Xenograft Models.

The survival rate among children with relapsed tumors remains poor, due to tumor heterogeneity, lack of directly actionable tumor drivers and multidrug resistance. Novel personalized medicine approaches tailored to each tumor are urgently needed to improve cancer treatment. Current pediatric precision oncology platforms, such as the INFORM (INdividualized Therapy FOr Relapsed Malignancies in Childhood) study, reveal that molecular profiling of tumor tissue identifies targets associated with clinical benefit in a subgroup of patients only and should be complemented with functional drug testing.

Screening human lung cancer with predictive models of serum magnetic resonance spectroscopy metabolomics.

The current high mortality of human lung cancer stems largely from the lack of feasible, early disease detection tools. An effective test with serum metabolomics predictive models able to suggest patients harboring disease could expedite triage patient to specialized imaging assessment. Here, using a training-validation-testing-cohort design, we establish our high-resolution magic angle spinning (HRMAS) magnetic resonance spectroscopy (MRS)-based metabolomics predictive models to indicate lung cancer presence and patient survival using serum samples collected prior to their disease diagnoses.

iTReX: Interactive exploration of mono- and combination therapy dose response profiling data.

High throughput screening methods, measuring the sensitivity and resistance of tumor cells to drug treatments have been rapidly evolving. Not only do these screens allow correlating response profiles to tumor genomic features for developing novel predictors of treatment response, but they can also add evidence for therapy decision making in precision oncology. Recent analysis methods developed for either assessing single agents or combination drug efficacies enable quantification of dose-response curves with restricted symmetric fit settings.

CT-based attenuation correction of whole-body radiotherapy treatment positioning devices in PET/MRI hybrid imaging.

Objective: To implement computed tomography (CT)-based attenuation maps of radiotherapy (RT) positioning hardware and radiofrequency (RF) coils to enable hybrid positron emission tomography/magnetic resonance imaging (PET/MRI)-based RT treatment planning.

Materials And Methods: The RT positioning hardware consisted of a flat RT table overlay, coil holders for abdominal scans, coil holders for head and neck scans and an MRI compatible hip and leg immobilization device. CT images of each hardware element were acquired on a CT scanner.

Efficacy of Endoactivator, CanalBrush, and passive ultrasonic irrigation in the removal of calcium hydroxide paste with iodoform and p-chlorophenol from root canals.

Aims: We evaluated and compared EndoActivator, CanalBrush, and passive ultrasonic irrigation (PUI) in the removal of calcium hydroxide and calcium hydroxide with iodoform and p-chlorophenol paste (Calcipast Forte) from artificial standardized grooves in the apical third of root canals.

Materials And Methods: A total of 34 mandibular premolars were prepared and then split longitudinally. A standardized groove was prepared in the apical part of both segments.

Algorithms for joint activity-attenuation estimation from positron emission tomography scatter.

Background: Attenuation correction in positron emission tomography remains challenging in the absence of measured transmission data. Scattered emission data may contribute missing information, but quantitative scatter-to-attenuation (S2A) reconstruction needs to input the reconstructed activity image. Here, we study S2A reconstruction as a building block for joint estimation of activity and attenuation.

Magnetic Resonance Spectroscopy-based Metabolomic Biomarkers for Typing, Staging, and Survival Estimation of Early-Stage Human Lung Cancer.

Low-dose CT has shown promise in detecting early stage lung cancer. However, concerns about the adverse health effects of radiation and high cost prevent its use as a population-wide screening tool. Effective and feasible screening methods to triage suspicious patients to CT are needed.

Metabolomic prostate cancer fields in HRMAS MRS-profiled histologically benign tissue vary with cancer status and distance from cancer.

In this article, we review the state of the field of high resolution magic angle spinning MRS (HRMAS MRS)-based cancer metabolomics since its beginning in 2004; discuss the concept of cancer metabolomic fields, where metabolomic profiles measured from histologically benign tissues reflect patient cancer status; and report our HRMAS MRS metabolomic results, which characterize metabolomic fields in prostatectomy-removed cancerous prostates. Three-dimensional mapping of cancer lesions throughout each prostate enabled multiple benign tissue samples per organ to be classified based on distance from and extent of the closest cancer lesion as well as the Gleason score (GS) of the entire prostate. Cross-validated partial least squares-discriminant analysis separations were achieved between cancer and benign tissue, and between cancer tissue from prostates with high (≥4 + 3) and low (≤3 + 4) GS.

Numerical algorithms for scatter-to-attenuation reconstruction in PET: empirical comparison of convergence, acceleration, and the effect of subsets.

Unlabelled: The use of scattered coincidences for attenuation correction of positron emission tomography (PET) data has recently been proposed. For practical applications, convergence speeds require further improvement, yet there exists a trade-off between convergence speed and the risk of non-convergence. In this respect, a maximum-likelihood gradient-ascent (MLGA) algorithm and a two-branch back-projection (2BP), which was previously proposed, were evaluated.

Comparison of intracoronal bleaching methods on teeth discolored by different antibiotic pastes.

Aim: To compare the bleaching efficacy of sodium perborate with different activation methods on crowns discolored by two different antibiotic pastes.

Materials And Methods: Eighty-five extracted human incisors were prepared to size #30 using ProTaper rotary instruments. After chemomechanical preparation and irrigation procedures, the specimens received triple antibiotic paste (TAP, n = 40), minocycline paste (MP, n = 40), or calcium hydroxide (n = 5, control group) and coronally sealed with temporary filling material.

MLAA-based attenuation correction of flexible hardware components in hybrid PET/MR imaging.

Background: Accurate PET quantification demands attenuation correction (AC) for both patient and hardware attenuation of the 511 keV annihilation photons. In hybrid PET/MR imaging, AC for stationary hardware components such as patient table and MR head coil is straightforward, employing CT-derived attenuation templates. AC for flexible hardware components such as MR-safe headphones and MR radiofrequency (RF) surface coils is more challenging.

Attenuation correction in emission tomography using the emission data--A review.

The problem of attenuation correction (AC) for quantitative positron emission tomography (PET) had been considered solved to a large extent after the commercial availability of devices combining PET with computed tomography (CT) in 2001; single photon emission computed tomography (SPECT) has seen a similar development. However, stimulated in particular by technical advances toward clinical systems combining PET and magnetic resonance imaging (MRI), research interest in alternative approaches for PET AC has grown substantially in the last years. In this comprehensive literature review, the authors first present theoretical results with relevance to simultaneous reconstruction of attenuation and activity.

Scattered PET data for attenuation-map reconstruction in PET/MRI.

Purpose: In hybrid medical imaging devices combining positron emission tomography (PET) with magnetic resonance imaging, PET attenuation correction remains challenging. Known approaches to estimating attenuation (μ-)maps from PET emission data, especially maximum-likelihood reconstruction of activity and attenuation (MLAA), take into account true coincidences only and exhibit two kinds of ambiguities: First, the attenuation sinogram can only be determined up to a constant offset (sinogram ambiguity). Second, the attenuation sinogram is unknown outside of the support of the activity sinogram and does not completely define a μ-map (image-space ambiguity).

Knowledge and attitudes of Turkish endodontists towards digital radiology and cone beam computed tomography.

Introduction: The aim of this study was to assess the knowledge and attitudes of Turkish endodontists toward digital radiological imaging (DRI) and cone-beam computed tomography (CBCT).

Materials And Methods: One hundred and fifty questionnaires were distributed. Questionnaires were given to a sample of endodontists and PhD students in endodontics who attended the 11 th International Congress of the Turkish Endodontic Society in Istanbul in 2012.

Sensitivity encoded silicon photomultiplier--a new sensor for high-resolution PET-MRI.

Detectors for simultaneous positron emission tomography and magnetic resonance imaging in particular with sub-mm spatial resolution are commonly composed of scintillator crystal arrays, readout via arrays of solid state sensors, such as avalanche photo diodes (APDs) or silicon photomultipliers (SiPMs). Usually a light guide between the crystals and the sensor is used to enable the identification of crystals which are smaller than the sensor elements. However, this complicates crystal identification at the gaps and edges of the sensor arrays.

Study-parameter impact in quantitative 90-Yttrium PET imaging for radioembolization treatment monitoring and dosimetry.

A small positron-generating branch in 90-Yttrium ((90)Y) decay enables post-therapy dose assessment in liver cancer radioembolization treatment. The aim of this study was to validate clinical (90)Y positron emission tomography (PET) quantification, focusing on scanner linearity as well as acquisition and reconstruction parameter impact on scanner calibration. Data from three dedicated phantom studies (activity range: 55.

Challenges and current methods for attenuation correction in PET/MR.

Quantitative PET imaging requires an attenuation map to correct for attenuation. In stand-alone PET or PET/CT, the attenuation map is usually derived from a transmission scan or CT image, respectively. In PET/MR, these methods will most likely not be used.

MRI-based attenuation correction for hybrid PET/MRI systems: a 4-class tissue segmentation technique using a combined ultrashort-echo-time/Dixon MRI sequence.

Unlabelled: Accurate γ-photon attenuation correction (AC) is essential for quantitative PET/MRI as there is no simple relation between MR image intensity and attenuation coefficients. Attenuation maps (μ-maps) can be derived by segmenting MR images and assigning attenuation coefficients to the compartments. Ultrashort-echo-time (UTE) sequences have been used to separate cortical bone and air, and the Dixon technique has enabled differentiation between soft and adipose tissues.