2012 Grantmakers Information Technology Survey Report

Together the Technology Affinity Group (TAG) and Grants Managers Network (GMN) conducted an information technology survey of grantmaking organizations in July 2012. This survey serves as a follow?up to similar surveys TAG has conducted in collaboration with the Council on Foundation (The Council) in April 2003, July 2005, and June 2007, and then independently in 2010

2010 Grantmakers Information Technology Survey Report

In response to the desire for knowledge of how technology is used in the philanthropic sector, the Technology Affinity Group (TAG) conducted an information technology survey of grantmakers in July 2010. This survey serves as a follow?up to similar surveys TAG conducted in collaboration with the Council on Foundation (The Council) in April 2003, July 2005, and June2007, and is designed to help TAG better serve its members

Dissertation Completion Experience in Online CACREP-Accredited Counselor Education Programs: A Phenomenological Inquiry

In this qualitative phenomenological study, the purpose was to explore the experiences of recent online Council for the Accreditation of Counseling and Related Educational Programs (CACREP)-accredited counselor education and supervision (CES) graduates concerning their dissertation completion process. Past research had shown a dissertation noncompletion rate 10%–20% higher in distance education programs compared to traditional institutions. Participant recruitment was facilitated by criterion sampling and snowball sampling and included seven recent graduates of online CACREP-accredited CES programs. Semi-structured interviews were used to collect data. Data analysis conducted using Smith et al.’s six-step data analysis process yielded three significant themes: dissertation task engagement, stakeholder interaction, and impact of the environment. Implications of the findings extend to improvements in dissertation readiness and socialization, meaningful experiences, and dissertation completion rates

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

The HF-AF ENERGY Trial:Nicotinamide Riboside for the Treatment of Atrial Fibrillation in Heart Failure Patients

Background: The presence of atrial fibrillation (AF) in heart failure (HF) patients with reduced ejection fraction is common and associated with an increased risk of stroke, hospitalization and mortality. Recent research findings indicate that a reduction in nicotinamide adenine dinucleotide (NAD+) levels results in mitochondrial dysfunction, DNA damage and consequently cardiomyocyte impairment in experimental and clinical HF and AF. The HF-AF ENERGY trial aims to investigate the cardioprotective effects of the NAD+ precursor nicotinamide riboside (NR) treatment in ischemic heart disease patients diagnosed with AF. Study design: The HF-AF ENERGY trial is a prospective intervention study. The study consists of a (retrospective) 4 months observation period and a 4 months intervention period. The cardioprotective effect of NR on AF burden is investigated by remote monitoring software of implantable cardiac defibrillators (ICDs), which enables continuous atrial rhythm monitoring detection. Cardiac dimension and function are examined by echocardiography. Laboratory blood analysis is performed to determine mitochondrial function markers and energy metabolism. All the study parameters are assessed at two fixed time points (pre- and post-treatment). Pre- and post-treatment outcomes are compared to determine the effects of NR treatment on AF burden, mitochondrial function markers and energy metabolism. Conclusion: The HF-AF ENERGY trial investigates the cardioprotective effects of NR on AF burden and whether NR normalizes blood-based mitochondrial function markers and energy metabolites of the NAD metabolome in ischemic heart disease patients diagnosed with AF. The study outcomes elucidate whether NAD+ metabolism can be used as a future therapy for HF patients with AF.</p

Quantifying DNA Lesions and Circulating Free DNA:Diagnostic Marker for Electropathology and Clinical Stage of AF

Background: Atrial fibrillation (AF) persistence is associated with molecular remodeling that fuels electrical conduction abnormalities in atrial tissue. Previous research revealed DNA damage as a molecular driver of AF. Objectives: This study sought to explore the diagnostic value of DNA damage in atrial tissue and blood samples as an indicator of the prevalence of electrical conduction abnormalities and stage of AF. Methods: High-sensitivity long-run real-time PCR was performed on mitochondrial (ND1) and nuclear (P53) DNA from atrial tissue samples from paroxysmal (PAF), persistent (PeAF), and longstanding persistent (LS-PeAF) AF, and sinus rhythm (SR) patients (n = 83). PicoGreen assay and quantitative polymerase chain reaction were used on circulating free DNA (cfDNA) markers (total cfDNA, β-globin, ND1, and P53) in blood samples of 70 patients with AF or SR. High-resolution epicardial mapping of the atria (n = 48) was conducted to quantify electrical conduction abnormalities. Results: The number of DNA lesions gradually and significantly increased in PAF and PeAF and in patients with &lt;3 years of AF compared with SR. In SR, the quantity of nuclear DNA damage significantly correlated with the proportion of fractionated potentials. Mitochondrial DNA lesions correlated with slower conduction velocity and lower potential amplitudes in AF samples. Also, mitochondrial cfDNA levels decreased in patients with &gt;3 years of AF compared with &lt;3 years of AF (P = 0.004). Conclusions: The quantity of DNA lesions in atrial tissue samples is associated with atrial conduction abnormalities and stage of AF. Serum DNA damage markers discriminate short- from long-term AF. Therefore, the quantity of DNA damage may have diagnostic value in clinical AF management.</p