Biexponential diffusion decay in formalin-fixed prostate tissue: Preliminary findings

Magnetic resonance microimaging was used to measure diffusion decay over an extended b-factor range in a formalin-fixed normal prostate sample and a Gleason pattern 3+4 cancer tissue sample. The coefficients of biexponential fits to diffusion decay data from 1600 voxels of dimension 160 x 160 x 160 mu m3 in each sample were correlated with underlying epithelial and stromal compartment partial volumes estimated from high-resolution apparent diffusion coefficient (ADC) data (40 x 40 x 40 mu m3 voxels) from the same tissue. In the normal tissue sample, the signal fractions of the low and high ADC components of the biexponential fits correlated linearly with partial volumes of epithelial tissue (R2 = 0.6) and stromal tissue (R2 = 0.5), respectively. Similar but weaker correlations were observed in the cancer sample. Epithelium-containing high spatial resolution voxels appeared to be composed of similar to 60% low ADC and similar to 40% high ADC component. Stromal voxels appeared to be composed of similar to 20% low ADC and similar to 80% high ADC component. This preliminary report suggests that distinctly different diffusion properties in microscopically adjacent cell types contribute to the multiexponential diffusion decay phenomenon in prostate tissue. Magn Reson Med, 2012. (c) 2011 Wiley Periodicals, Inc

Deep Weighted Averaging Classifiers

Recent advances in deep learning have achieved impressive gains in classification accuracy on a variety of types of data, including images and text. Despite these gains, however, concerns have been raised about the calibration, robustness, and interpretability of these models. In this paper we propose a simple way to modify any conventional deep architecture to automatically provide more transparent explanations for classification decisions, as well as an intuitive notion of the credibility of each prediction. Specifically, we draw on ideas from nonparametric kernel regression, and propose to predict labels based on a weighted sum of training instances, where the weights are determined by distance in a learned instance-embedding space. Working within the framework of conformal methods, we propose a new measure of nonconformity suggested by our model, and experimentally validate the accompanying theoretical expectations, demonstrating improved transparency, controlled error rates, and robustness to out-of-domain data, without compromising on accuracy or calibration.Comment: 13 pages, 8 figures, 5 tables, added DOI and updated to meet ACM formatting requirements, In Proceedings of FAT* (2019

Attentional differences in a driving hazard perception task in adults with autism spectrum disorders

The current study explored attentional processing of social and non social stimuli in ASD within the context of a driving hazard perception task. Participants watched videos of road scenes and detected hazards while their eye movements were recorded. Although individuals with ASD demonstrated relatively good detection of driving hazards, they were slower to orient to hazards. Greater attentional capture in the time preceding the hazards’ onset was associated with lower verbal IQ. The findings suggest that individuals with ASD may distribute and direct their attention diferently when identifying driving hazards

Plasma Metabolomics Implicates Modified Transfer RNAs and Altered Bioenergetics in the Outcomes of Pulmonary Arterial Hypertension.

BACKGROUND: Pulmonary arterial hypertension (PAH) is a heterogeneous disorder with high mortality. METHODS: We conducted a comprehensive study of plasma metabolites using ultraperformance liquid chromatography mass spectrometry to identify patients at high risk of early death, to identify patients who respond well to treatment, and to provide novel molecular insights into disease pathogenesis. RESULTS: Fifty-three circulating metabolites distinguished well-phenotyped patients with idiopathic or heritable PAH (n=365) from healthy control subjects (n=121) after correction for multiple testing (P<7.3e-5) and confounding factors, including drug therapy, and renal and hepatic impairment. A subset of 20 of 53 metabolites also discriminated patients with PAH from disease control subjects (symptomatic patients without pulmonary hypertension, n=139). Sixty-two metabolites were prognostic in PAH, with 36 of 62 independent of established prognostic markers. Increased levels of tRNA-specific modified nucleosides (N2,N2-dimethylguanosine, N1-methylinosine), tricarboxylic acid cycle intermediates (malate, fumarate), glutamate, fatty acid acylcarnitines, tryptophan, and polyamine metabolites and decreased levels of steroids, sphingomyelins, and phosphatidylcholines distinguished patients from control subjects. The largest differences correlated with increased risk of death, and correction of several metabolites over time was associated with a better outcome. Patients who responded to calcium channel blocker therapy had metabolic profiles similar to those of healthy control subjects. CONCLUSIONS: Metabolic profiles in PAH are strongly related to survival and should be considered part of the deep phenotypic characterization of this disease. Our results support the investigation of targeted therapeutic strategies that seek to address the alterations in translational regulation and energy metabolism that characterize these patients

Protocol for implementation of family health history collection and decision support into primary care using a computerized family health history system

<p>Abstract</p> <p>Background</p> <p>The CDC's Family History Public Health Initiative encourages adoption and increase awareness of family health history. To meet these goals and develop a personalized medicine implementation science research agenda, the Genomedical Connection is using an implementation research (T3 research) framework to develop and integrate a self-administered computerized family history system with built-in decision support into 2 primary care clinics in North Carolina.</p> <p>Methods/Design</p> <p>The family health history system collects a three generation family history on 48 conditions and provides decision support (pedigree and tabular family history, provider recommendation report and patient summary report) for 4 pilot conditions: breast cancer, ovarian cancer, colon cancer, and thrombosis. All adult English-speaking, non-adopted, patients scheduled for well-visits are invited to complete the family health system prior to their appointment. Decision support documents are entered into the medical record and available to provider's prior to the appointment. In order to optimize integration, components were piloted by stakeholders prior to and during implementation. Primary outcomes are change in appropriate testing for hereditary thrombophilia and screening for breast cancer, colon cancer, and ovarian cancer one year after study enrollment. Secondary outcomes include implementation measures related to the benefits and burdens of the family health system and its impact on clinic workflow, patients' risk perception, and intention to change health related behaviors. Outcomes are assessed through chart review, patient surveys at baseline and follow-up, and provider surveys. Clinical validity of the decision support is calculated by comparing its recommendations to those made by a genetic counselor reviewing the same pedigree; and clinical utility is demonstrated through reclassification rates and changes in appropriate screening (the primary outcome).</p> <p>Discussion</p> <p>This study integrates a computerized family health history system within the context of a routine well-visit appointment to overcome many of the existing barriers to collection and use of family history information by primary care providers. Results of the implementation process, its acceptability to patients and providers, modifications necessary to optimize the system, and impact on clinical care can serve to guide future implementation projects for both family history and other tools of personalized medicine, such as health risk assessments.</p

Annual report for active IDOT wetland compensation and hydrologic monitoring sites, September 1, 2002 to September 1, 2003

Contract Number IDOT SW WIP FY04 to Illinois Department of TransportationOpe

Annual report for active IDOT wetland compensation and hydrologic monitoring sites : September 1, 2001 to September 1, 2002

Illinois Department of Transportation, Bureau of Design and Environment, Wetlands Unit, Contract Number IDOT SW WIP FY03 ANTCOpe

Vaccinia virus protein C16 acts intracellularly to modulate the host response and promote virulence

The vaccinia virus (VACV) strain Western Reserve C16 protein has been characterized and its effects on virus replication and virulence have been determined. The C16L gene is present in the inverted terminal repeat and so is one of the few VACV genes that are diploid. The C16 protein is highly conserved between different VACV strains, and also in the orthopoxviruses variola virus, ectromelia virus, horsepox virus and cowpox virus. C16 is a 37.5 kDa protein, which is expressed early during infection and localizes to the cell nucleus and cytoplasm of infected and transfected cells. The loss of the C16L gene had no effect on virus growth kinetics but did reduce plaque size slightly. Furthermore, the virulence of a virus lacking C16L (vΔC16) was reduced in a murine intranasal model compared with control viruses and there were reduced virus titres from 4 days post-infection. In the absence of C16, the recruitment of inflammatory cells in the lung and bronchoalveolar lavage was increased early after infection (day 3) and more CD4+ and CD8+ T cells expressed the CD69 activation marker. Conversely, late after infection with vΔC16 (day 10) there were fewer T cells remaining, indicating more rapid clearance of infection. Collectively, these data indicate that C16 diminishes the immune response and is an intracellular immunomodulator