ORE identifies extreme expression effects enriched for rare variants.

MOTIVATION: Non-coding rare variants (RVs) may contribute to Mendelian disorders but have been challenging to study due to small sample sizes, genetic heterogeneity and uncertainty about relevant non-coding features. Previous studies identified RVs associated with expression outliers, but varying outlier definitions were employed and no comprehensive open-source software was developed. RESULTS: We developed Outlier-RV Enrichment (ORE) to identify biologically-meaningful non-coding RVs. We implemented ORE combining whole-genome sequencing and cardiac RNAseq from congenital heart defect patients from the Pediatric Cardiac Genomics Consortium and deceased adults from Genotype-Tissue Expression. Use of rank-based outliers maximized sensitivity while a most extreme outlier approach maximized specificity. Rarer variants had stronger associations, suggesting they are under negative selective pressure and providing a basis for investigating their contribution to Mendelian disorders. AVAILABILITY AND IMPLEMENTATION: ORE, source code, and documentation are available at https://pypi.python.org/pypi/ore under the MIT license. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Patterns of cancer centre follow-up care for survivors of breast, colorectal, gynecologic, and prostate cancer.

BACKGROUND: Rising demand on cancer system resources, alongside mounting evidence that demonstrates the safety and acceptability of primary care-led follow-up care, has resulted in some cancer centres discharging patients back to primary care after treatment. At the same time, the ways in which routine cancer follow-up care is provided across Canada continue to vary widely. The objectives of the present study were to investigate patterns of routine follow-up care at a cancer centre for breast, colorectal, gynecologic, and prostate cancer survivors; factors associated with receipt of follow-up care at a cancer centre; and changes in follow-up care at a cancer centre over time. METHODS: We identified all people diagnosed in Nova Scotia with an invasive breast, colorectal, gynecologic, or prostate cancer between 1 January 2006 and 31 December 2013. We linked the resulting population-based dataset, at the patient level, to cancer centre or clinic data and to census data. We identified a nonmetastatic survivor cohort (n = 12,267) and developed decision rules to differentiate routine from non-routine visits during the follow-up care period (commencing 1 year after diagnosis). Descriptive statistics were computed to describe the patterns of routine follow-up care at a cancer centre. Negative binomial regression was used to examine factors associated with visits made and changes over time. RESULTS: Nearly half the survivors (48.4%) had at least 1 follow-up visit to the cancer centre, with variation by disease site (range: 30.2%-62.4%). Disease site and stage at diagnosis were associated with receipt of follow-up care at a cancer centre. For instance, compared with breast cancer survivors, survivors of gynecologic cancer had more visits [incidence rate ratio (irr): 1.48; 95% confidence interval (ci): 1.34 to 1.64], and survivors of colorectal cancer had fewer visits (irr: 0.45; 95% ci: 0.40 to 0.51). Year of diagnosis was associated with follow-up at a cancer centre, with each successive calendar year being associated with an 8% increase in visits made (irr: 1.08; 95% ci: 1.07 to 1.10). CONCLUSIONS: Despite evidence that follow-up care can be effectively and safely delivered in primary care, and despite intensifying demands on oncology services, many survivors continue to receive routine follow-up care at a cancer centre.

Cross-disciplinary research in cancer: an opportunity to narrow the knowledge-practice gap.

Health services researchers have consistently identified a gap between what is identified as "best practice" and what actually happens in clinical care. Despite nearly two decades of a growing evidence-based practice movement, narrowing the knowledge-practice gap continues to be a slow, complex, and poorly understood process. Here, we contend that cross-disciplinary research is increasingly relevant and important to reducing that gap, particularly research that encompasses the notion of transdisciplinarity, wherein multiple academic disciplines and non-academic individuals and groups are integrated into the research process. The assimilation of diverse perspectives, research approaches, and types of knowledge is potentially effective in helping research teams tackle real-world patient care issues, create more practice-based evidence, and translate the results to clinical and community care settings. The goals of this paper are to present and discuss cross-disciplinary approaches to health research and to provide two examples of how engaging in such research may optimize the use of research in cancer care.

Clinical information available to oncologists in surgically treated rectal cancer: room to improve.

INTRODUCTION: In rectal cancer, decisions about the use of adjuvant and neoadjuvant treatment rely on clinical information from a variety of sources. Currently, the quality and accuracy of the aggregate of this clinical information is unclear. The objectives of the present study were to evaluate the completeness and quality of clinical information available to oncologists managing rectal cancer. METHODS: All patients diagnosed with rectal cancer in Nova Scotia between 2001 and 2005 were identified through the provincial cancer registry. The registry was linked to other administrative databases to obtain demographic, diagnostic, and treatment data. Patients undergoing radiation oncology consultation were identified, and a standardized review of the cancer centre chart was performed on a random sample, stratified by year. RESULTS: For the 222 patients reviewed, the relevant endoscopy report was present in 113 cases (51%). The level of the tumour was documented in 75% of those reports, and colonoscopy completeness, in 81%. The relevant operative report was available in 192 cases (87%). Tumour level was described in 59% of those reports, and local extension, in 73%. Elements of total mesorectal excision were partially described in 97%. In pathology reports (10% of which were synoptic), we observed significant variability in the presence of important elements. Reporting of those elements was significantly better in the synoptic pathology reports. CONCLUSIONS: Clinical information related to adjuvant and neoadjuvant therapy decision-making in rectal cancer is often not available or incomplete. A synoptic reporting system in endoscopy, surgery, and pathology could potentially be a beneficial tool in rectal cancer care.

Dystrophin colocalizes with beta-spectrin in distinct subsarcolemmal domains in mammalian skeletal muscle.

Duchenne's muscular dystrophy (DMD) is caused by the absence or drastic decrease of the structural protein, dystrophin, and is characterized by sarcolemmal lesions in skeletal muscle due to the stress of contraction. Dystrophin has been localized to the sarcolemma, but its organization there is not known. We report immunofluorescence studies which show that dystrophin is concentrated, along with the major muscle isoform of beta-spectrin, in three distinct domains at the sarcolemma: in elements overlying both I bands and M lines, and in occasional strands running along the longitudinal axis of the myofiber. Vinculin, which has previously been found at the sarcolemma overlying the I bands and in longitudinal strands, was present in the same three structures as spectrin and dystrophin. Controls demonstrated that the labeling was intracellular. Comparison to labeling of the lipid bilayer and of the extracellular matrix showed that the labeling for spectrin and dystrophin is associated with the intact sarcolemma and is not a result of processing artifacts. Dystrophin is not required for this lattice-like organization, as similar domains containing spectrin but not dystrophin are present in muscle from the mdx mouse and from humans with Duchenne's muscular dystrophy. We discuss the possibility that dystrophin and spectrin, along with vinculin, may function to link the contractile apparatus to the sarcolemma of normal skeletal muscle.

The role of scientific evidence in decisions to adopt complex innovations in cancer care settings: a multiple case study in Nova Scotia, Canada.

BACKGROUND: Health care delivery and outcomes can be improved by using innovations (i.e., new ideas, technologies, and practices) supported by scientific evidence. However, scientific evidence may not be the foremost factor in adoption decisions and is rarely sufficient. The objective of this study was to examine the role of scientific evidence in decisions to adopt complex innovations in cancer care. METHODS: Using an explanatory, multiple case study design, we examined the adoption of complex innovations in five purposively sampled cases in Nova Scotia, Canada. Data were collected via documents and key informant interviews. Data analysis involved an in-depth analysis of each case, followed by a cross-case analysis to develop theoretically informed, generalizable knowledge on the role of scientific evidence in innovation adoption that may be applied to similar settings and contexts. RESULTS: The analyses identified key concepts alongside important caveats and considerations. Key concepts were (1) scientific evidence underpinned the adoption process, (2) evidence from multiple sources informed decision-making, (3) decision-makers considered three key issues when making decisions, and (4) champions were essential to eventual adoption. Caveats and considerations related to the presence of urgent problems and short-term financial pressures and minimizing risk. CONCLUSIONS: The findings revealed the different types of issues decision-makers consider while making these decisions and why different sources of evidence are needed in these processes. Future research should examine how different types of evidence are legitimized and why some types are prioritized over others.

Cross-Canada differences in early-stage breast cancer treatment and acute-care use.

Background: Chemotherapy has improved outcomes in early-stage breast cancer, but treatment practices vary, and use of acute care is common. We conducted a pan-Canadian study to describe treatment differences and the incidence of emergency department visits (edvs), edvs leading to hospitalization (edvhs), and direct hospitalizations (hs) during adjuvant chemotherapy. Methods: The cohort consisted of women diagnosed with early-stage breast cancer (stages i-iii) during 2007-2012 in British Columbia, Manitoba, Ontario, or Nova Scotia who underwent curative surgery. Parallel provincial analyses were undertaken using linked clinical, registry, and administrative databases. The incidences of edvs, edvhs, and hs in the 6 months after treatment initiation were examined for patients treated with adjuvant chemotherapy. Results: The cohort consisted of 50,224 patients. The proportion of patients who received chemotherapy varied by province, with Ontario having the highest proportion (46.4%), and Nova Scotia, the lowest proportion (38.0%). Age, stage, receptor status, comorbidities, and geographic location were associated with receipt of chemotherapy in all provinces. Ontario had the highest proportion of patients experiencing an edv (36.1%), but the lowest proportion experiencing h (6.4%). Conversely, British Columbia had the lowest proportion of patients experiencing an edv (16.0%), but the highest proportion experiencing h (26.7%). The proportion of patients having an edvh was similar across provinces (13.9%-16.8%). Geographic location was associated with edvs, edvhs, and hs in all provinces. Conclusions: Intra- and inter-provincial differences in the use of chemotherapy and acute care were observed. Understanding variations in care can help to identify gaps and opportunities for improvement and shared learnings.

Response to dopamine hydrochloride in the hepatorenal syndrome.

Functional renal failure accompanying advanced cirrhosis of the liver carries a grave prognosis. Seven patients with the hepatorenal syndrome and five patients with decompensated cirrhosis of the liver without renal failure were studied by the xenon Xe 133 washout technique. Mean renal blood flow and its cortical component were decreased in both groups compared to normal transplant donors, but to a significantly greater degree in hepatorenal syndrome. In hepatorenal patients, intra-arterial infusion of subpresor doses of dopamine hydrochloride improved the angiographic appearance of the renal cortical vasculatrue and the cortical blood flow rate. Urine flow rate and glomerular filtration rate did not consistently improve with 12- to 24-hour intravenous infusions, although two patients survived, temporally related to the study. These patients had shown signs of liver function recovery.

Differential binding of the lectins Griffonia simplicifolia I and Lycopersicon esculentum to microvascular endothelium: organ-specific localization and partial glycoprotein characterization.

The lectins Griffonia simplicifolia I and Lycopersicon esculentum were used to assess the presence of endothelium-specific glycoproteins in the microvasculature of the rat myocardium, diaphragm and superficial cerebral cortex. Organs fixed by intravascular perfusion were processed to obtain semithin (0.5 micron) and thin (less than 0.1 micron) frozen sections that were reacted with biotinylated lectin followed by streptavidin conjugated to Texas Red, for semithin sections, or by streptavidin conjugated to 5-nm colloidal gold particles, for thin sections. Lycopersicon esculentum lectin exclusively labeled the endothelium of all small vessels in all three microvascular beds; it did not bind to components of either the parenchyma or the extracellular matrix. Griffonia simplicifolia I lectin exclusively labeled the endothelium of the entire microvasculature in the myocardium and diaphragm, but marked primarily pericytes in the cerebral microvasculature. It did not label any parenchymal or interstitial organ component. At the electron microscope level, the lectin Griffonia simplicifolia I labeling was associated with the plasmalemma proper and especially with plasmalemmal vesicles and their introits, and Lycopersicon esculentum lectin bound primarily to the luminal plasmalemma in the microvascular beds of the myocardium and diaphragm. In the cerebral cortex, labeling of the microvasculature was clearly different: Griffonia simplicifolia I bound primarily to pericytes and vascular smooth muscle cells whereas Lycopersicon esculentum labeled only the microvascular endothelium. Lysates prepared from the myocardium, diaphragm and cerebral cortex were processed through Griffonia simplicifolia I lectin affinity separation followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the fraction obtained. A number of putative endothelium-specific glycoproteins was detected and found to differ qualitatively and quantitatively from organ to organ. The most prominent polypeptide, approximately 97 kDa, was present in substantial amounts in the myocardium and diaphragm, but in considerably lower concentration in the cerebral cortex. The reverse applied for a approximately 55 kDa protein. The preferential distribution of the approximately 97 kDa protein parallels differences in Griffonia simplicifolia I lectin binding by fluorescence and electron microscopy on sections of the corresponding organs. The results provide further evidence for the existence of endothelial glycoproteins specific for different microvascular beds and possibly connected with local functional differentiations.

Differential and specific labeling of epithelial and vascular endothelial cells of the rat lung by Lycopersicon esculentum and Griffonia simplicifolia I lectins.

In the rat lung, we found that the Lycopersicon esculentum (LEA) lectin specifically binds to the epithelium of bronchioles and alveoli whereas Griffonia simplicifolia I (GS-I) binds to the endothelium of alveolar capillaries. The differential binding affinity of these lectins was examined on semithin (approximately 0.5 microns) and thin (less than 0.1 (microns) frozen sections of rat lung lavaged to remove alveolar macrophages. On semithin frozen sections, LEA bound to epithelial cells lining bronchioles and the alveoli (type I, but not type II epithelial cells). On thin frozen sections, biotinylated Lycopersicon esculentum (bLEA)-streptavidin-gold conjugates were confined primarily to the luminal plasmalemma of type I cells. bGS-I-streptavidin-Texas Red was detected on the endothelial cells of alveolar capillaries and postcapillary venules but not on those of larger venules, veins or arterioles. By electron microscopy, GS-I-streptavidin-gold complexes were localized primarily to the luminal plasmalemma of thick and thin regions of the capillary endothelium. Neither lectin labeled type II alveolar cells, but both lectins labeled macrophages in the interstitia and in incompletely lavaged alveoli.

Adrenocorticotropin-cortisol axis abnormalities in hemodialysis patients.

The ACTH-cortisol axis was studied in 15 hemodialysis patients. Basal plasma cortisol concentrations were found to be elevated and ACTH to be in the high normal range. Cortisol responded normally to exogenous ACTH, but neither cortisol nor ACTH were suppressed in response to oral dexamethasone. 11-Deoxycortisol and ACTH concentrations did not rise normally in response to either oral or iv metyrapone. We conclude that standard testing of the ACTH-cortisol axis in dialysis patients yields results suggesting Cushing's syndrome.

Morphine and phenytoin binding to plasma proteins in renal and hepatic failure.

The binding of morphine and phenytoin to plasma proteins was examined in healthy subjects and in patients with renal and hepatic failure. In the uremic patients without hepatic failure, morphine binding was dependent on the concentration of total serum proteins and albumin, but not the severity of renal failure as measured by creatinine clearance. Binding of phenytoin, however, was dependent on the degree of renal failure and albumin concentration, but not on total serum protein concentration. Renal transplant in 1 patient restored the binding of both drugs to a value within the normal range. The combination of hypoalbuminemia and hyperbilirubinemia resulted in the greatest impairment to binding for both drugs. It is concluded that patients with uremia, jaundice, hypoalbuminemia, particularly in combination, are sensitive to usual clinical doses of morphine, at least in part, because of decreased binding to plasma proteins.

Do diuretics have antihypertensive properties independent of natriuresis?

To ascertain whether diuretics have an antihypertensive effect independent of natriuresis, 12 stable patients on maintenance hemodialysis underwent a crossover evaluation with hydrochlorothiazide, 50 mg daily, metolazone, 5 mg daily, or placebo in 4-wk treatment periods for 6 mo. Compliance was assured by pill counts and serum drug concentrations. All patients had daily urine less than 100 ml. Pre- and postdialysis blood pressure, body weight, plasma volume, and plasma renin activity were monitored. Over the 6-mo study period there were no statistically significant changes in any parameter related to diuretic therapy. It is concluded that a functioning kidney with the ability to respond to diuretics with a natriuresis is necessary for the antihypertensive action of diuretics. Direct vascular effects of diuretics to lower peripheral resistance could not be demonstrated in this unique patient population.

Gentamicin binding to serum and plasma proteins.

Gentamicin binding to serum proteins was studied by equilibrium dialysis at 37 degrees C and pH 7.4 in the presence of both physiologic and adjusted concentrations of ionized calcium and magnesium. The percentage of bound drug was inversely related to the concentration of these two divalent cations, raning from 27% bound with no calcium and magnesium present to 17% bound in the presence of four times physiologic concentrations. No significant difference in the extent of drug-protein binding was noted in a comparison of sera from healthy and uremic subjects. Heparin also was found to affect gentamicin binding. Increasing heparin concentration in serum increased apparent gentamicin-protein binding to 34% in the presence of physiologic amounts of calcium and magnesium. Buffered heparin solutions without plasma proteins bound up to 65% of total drug concentration. Gentamicin-protein binding may have implications regarding pharmacokinetics and renal cortical uptake.

Effect of milk constituents on hepatic cholesterol-genesis.

Two preparations active in reducing hepatic cholesterol biosynthesis were isolated from bovine skim milk. One of the inhibitors was in the dialysate and was identified as orotic acid (OA). The other inhibitor, present in the retentate, was not identified. Orotic acid appears to act by inhibiting cholesterol biosynthesis before the formation of mevalonate, whereas the retentate inhibitor exerts its effect beyond the formation of mevalonate in the biosynthetic pathway. Human milk also inhibited the incorporation of both labeled acetate and mevalonate into cholesterol by rat liver. Orotic acid was not detectable in human milk samples employed in this study. Administration of [6-14C]orotate to rats revealed its conversion to uracil in the liver. Subsequent work demonstrated that uracil had inhibitory activity on hepatic cholesterol biosynthesis similar to that of orotate when incubated with rat liver slices.

Pathogenesis of renal failure due to aminoglycosides and contrast media used in roentgenography.

The etiology of acute renal failure has changed in recent years due to the recognition of drug nephrotoxicity as a more common cause. In this communication we emphasize recent information concerning the pathophysiology of nephrotoxic acute renal failure produced by aminoglycoside antibiotics and the contrast media used in roentgenography. The aminoglycosides are excreted primarily by glomerular filtration; however, net tubular reabsorption and renal parenchymal accumulation do occur. The exact mechanism of uptake is not clear, but the luminal membrane seems primarily involved. The pathogenesis of nephrotoxicity, although probably linked to cortical accumulation, is complex since experimental animals recover from gentamicin-induced renal failure despite continued administration of the drug. Knowledge of the precise cellular mechanisms of injury awaits further studies. Histologic damage is usually limited to proximal tubular necrosis and, clinically, the renal failure is nonoliguric. Although reports of the contrast media used in roentgenography producing acute renal failure have increased, the pathogenesis is unclear. Evidence supporting various theories is reviewed.

Natural history of asymptomatic coronary arteriographic lesions in diabetic patients with end-stage renal disease.

Arteriosclerotic heart disease is a major cause of death in insulin-requiring juvenile diabetic patients treated for end-stage renal disease. Eleven consecutive diabetic patients without clinical evidence of coronary artery disease underwent complete cardiac evaluations, including coronary arteriography, as part of transplant recipient work-ups. Seven were women and four were men; their mean age was 32 (21 to 50 years). Angiographically, every patient had multifocal atherosclerotic coronary disease. Four of seven patients tested had positive-stress electrocardiograms. In this group of patients followed for a mean of 19.8 months, eight died. Of these deaths, six were due to coronary heart disease and another due to a stroke. In two patients who became clinically symptomatic, serial angiograms revealed progressive disease of the coronary circulation; in one case, despite normal renal allograft function and serum lipid levels. The mode of end-stage renal disease treatment, serum lipids or blood pressure control could not be linked to mortality. It is concluded that arteriosclerotic heart disease is common in diabetic patients with end-stage renal disease even when angina is absent. The natural history in this high risk population is an important consideration in the selection of patients for end-stage renal disease treatment.

Experimental contrast-associated nephropathy and its clinical implications.

Acute renal failure after contrast media injection has been recognized for at least 35 years but the exact mechanism responsible for the renal injury remains an enigma. The clinical characteristics of contrast-induced nephropathy (CAN) are well-known although more recently the nonoliguric presentation has occurred at an increased frequency--in 70 to 90% of cases. For nonoliguric presentation of CAN, one can expect an asymptomatic increase in serum creatinine, the mean peak occurring at 4.2 days. If oliguric, the fractional excretion of sodium will be less than 1% and resistant to either fluid challenge or loop diuretics. Preexisting renal insufficiency, with or without diabetes mellitus, increases the risk of CAN 6- to 10-fold but recovery is expected, with less than 10% of all patients requiring dialytic support. Despite the growing body of published reports, the lack of a suitable animal model to evaluate various proposed mechanisms of renal injury has compromised our ability to devise a technique for preventing CAN. A popular scheme has been proposed to describe the possible sequence by which ischemia or nephrotoxins, or both, induce acute renal failure. In particular, a vascular mechanism (i.e., ischemia), is an appealing explanation for CAN since acute changes in renal hemodynamics after contrast media injection have been confirmed by several animal experiments. Unlike other vascular beds in which contrast media induce acute vasoconstriction followed by vasodilatation, the initial effect on the renal circulation is acute vasodilatation, followed by progressive vasoconstriction, increasing renal vascular resistance and a concomitant decrease in both renal blood flow and glomerular filtration rate.(ABSTRACT TRUNCATED AT 250 WORDS)

Contrast-associated nephropathy.

Contrast nephropathy can be defined as an acute impairment of renal function that follows exposure to radiocontrast materials and for which alternative explanations for renal impairment have been eliminated. Based on reported studies, the incidence of contrast associated nephropathy (CAN) varies from 0 to 22%. This wide variation can be traced to differences in study design and the criteria used to designate significant renal impairment. Irrespective of the exact incidence, 2 defined risk factors have been identified: preexisting renal disease and diabetes mellitus. Whereas preexisting renal insufficiency is the single most influential risk factor for CAN, when diabetes coexists the incidence approaches 100%. The clinical presentation of CAN is distinct, having a temporal relation between the performance of the contrast study in the high-risk patient and the onset of an increase in serum creatinine levels within the next 24 hours. Serum creatinine values greater than 50% of baseline or rising 1 mg/dl or more is diagnostic. The peak serum creatinine level occurs within 3 to 5 days of the contrast study and oliguria is associated in approximately 30% of the cases. Monitoring serum creatinine is the most useful clinical procedure in high-risk patients after angiography. At least 5 potential pathophysiologic mechanisms of CAN have been proposed: interference with renal perfusion, altered glomerular perm-selectivity, direct tubular injury, intraluminal obstruction, and immunologic mechanisms. Support for each mechanism, either singularly or in combination, can be found in published reports; however, none has achieved universal acceptance. The single most important clinical axiom regarding the prevention and management of CAN is, "Always use the least invasive diagnostic procedure available."(ABSTRACT TRUNCATED AT 250 WORDS)

Renal consequences of valvular heart disease.

Three aspects of potential renal involvement in patients with valvular heart disease are discussed. These include (1) disturbances in renal salt and water handling and their implications with respect to diuretic management; (2) the hemodynamic effects of angiographic contrast agents with identification of potentially dangerous effects on the kidneys; and (3) the histologic patterns of bacterial endocarditis in the kidney and their similarity to those of immunologically mediated disease.