QUANTIFYING UNCERTAINTY IN GENOTYPE CALLS

Genome-wide association studies (GWAS) are used to discover genes underlying complex, heritable disorders for which less powerful study designs have failed in the past. The number of GWAS has skyrocketed recently with findings reported in top journals and the mainstream media. Mircorarrays are the genotype calling technology of choice in GWAS as they permit exploration of more than a million single nucleotide polymorphisms (SNPs)simultaneously. The starting point for the statistical analyses used by GWAS, to determine association between loci and disease, are genotype calls (AA, AB, or BB). However, the raw data, microarray probe intensities, are heavily processed before arriving at these calls. Various sophisticated statistical procedures have been proposed for transforming raw data into genotype calls. We find that variability in microarray output quality across different SNPs, different arrays, and different sample batches has substantial inuence on the accuracy of genotype calls made by existing algorithms. Failure to account for these sources of variability, GWAS run the risk of adversely affecting the quality of reported findings. In this paper we present solutions based on a multi-level mixed model. Software implementation of the method described in this paper is available as free and open source code in the crlmm R/BioConductor.

Evaluation of the chemical residue monitoring in animal-derived products in Switzerland

This paper evaluates whether the Swiss monitoring programme for foreign substances in animal products fulfils basic epidemiological quality requirements, and identifies possible sources of bias in the selection of samples. The sampling was analysed over a 4-year period (2002-05). The sampling frame in 37 participating abattoirs covered 51% of all slaughtered pigs, 73% of calves, 68% of beef and 36% of cows. The analysis revealed that some sub-populations as defined by the region of origin were statistically over-represented while others were under-represented. The programme that is in accordance with European Union requirements contained some relevant bias. Patterns of under-sampled regions characterized by management type differences were identified. This could lead to an underestimate of the number of contaminated animals within the programme. Although the current sampling was stratified and partially risk-based, its efficiency could be improved by adopting a more targeted approach.

The Other Side of the Doors: Butte & Beyond -- Congressman Pat Williams “In the Crucible of Change”

Pat Williams emerged from the Mining City of Butte, Montana with a sense of grassroots, people-oriented politics. His inherent belief in the power of ordinary citizens carried him through the Montana Legislature and into Congress for a record-setting period. The accomplishments of his long career partially obscured his innate progressive and populist instinct that is reflective of the period of “in the Crucible of Change.” This film addresses Pat’s early years when his progressive instincts and activities resulted in pushback from the giant Anaconda Company which had held Montana hostage for 75 years. Pat is joined for part of the film by former campaign staffer, and now prominent media consultant, Michael Fenenbock for reflections on Pat’s 1978 “Door-to-Door to Congress” campaign, which demonstrated the power of his belief in the people on the other side of the doors. Pat Williams (b. 1937) rose from teaching grade school in his hometown of Butte, MT, to serving for the longest number of consecutive terms (9 terms, 18 years) in the US House of Representatives of anyone in Montana history. Pat was a member of the National Guard and attended UM in Missoula and William Jewel College, graduating from the University of Denver. Pat also served in the Montana legislature for 2 terms (1966 & 1968 elections). In 1969. Pat helped his legislative seat-mate John Melcher get elected as Montana’s Eastern District Congressman in the Special Election that June. Pat went to Washington DC as Melcher’s Executive Assistant. Upon returning to Montana, Pat headed up the Montana offices of the innovative Mountain Plains Family Education Program. In 1974, Pat ran unsuccessfully for Montana’s Western District Congressional seat in a three-way race with former Congressman Arnold Olsen and state Legislator Max Baucus. After the drafting and passage of the 1972 Montana Constitution, Pat was named a member of Montana’s first-ever Reapportionment Commission. In 1978 he successfully ran for Congress, conducting a massive grass-roots door-to-door campaign of 1½ years, reaching 50,000 doors. In a hotly contested 6-way Democratic primary, Pat won going away and also handily won the general election. Pat served in Congress from January, 1979 until January of 1997, 14 years representing the Western District and 4 years representing the entire state. Upon his retirement from Congress, in 1997 Williams returned to Montana where has been an instructor at the University of Montana and Senior Fellow and Regional Policy Associate at the Center for the Rocky Mountain West. He is a former member of the Montana Board of Regents and serves on a number of national education-related boards. In Congress Pat was a Deputy Whip of the U.S. House of Representatives and sat on committees on: Budget, Natural Resources, Education and Labor, and Agriculture. Pat’s leadership helped pass trailblazing legislation to assist hard-working middle-class families and ensure opportunities for every child. Pat’s fingerprints are on many pieces of important legislation, including the College Middle Income Assistance Act, the Family and Medical Leave Act, the Toddlers and Childhood Disability Act, the Library Services and Construction Act, and the Museum Services Act. Pat successfully sponsored the Lee Metcalf Wilderness Area and the Rattlesnake Wilderness area, helped save the Bob Marshall Wilderness from oil and gas exploration, and helped ban geothermal energy drilling near the borders of Yellowstone National Park. As Chairman of The Post-Secondary Education Committee, he protected the National Endowment for the Arts from elimination, a remarkable undertaking during a very trying time for the Agency. Pat worked tirelessly with Tribal College Leaders to build Montana’s seven Tribal Colleges. He was also responsible for the legislation that created The American Conservation Corps, which became the Corporation for National Service, giving thousands of America’s young people a chance to serve their country and pursue higher education. Pat lives in Missoula with his wife Carol Griffith Williams, former Montana Senate Majority Leader. They have three children and five grandchildren.

Percutaneous coronary revascularization in patients with formerly "refractory angina pectoris in end-stage coronary artery disease" - not "end-stage" after all

BACKGROUND: Patients with refractory angina pectoris in end-stage coronary artery disease represent a severe condition with a higher reduction of life-expectancy and quality of life as compared to patients with stable coronary artery disease. It was the purpose of this study to invasively re-evaluate highly symptomatic patients with formerly diagnosed refractory angina pectoris in end-stage coronary artery disease for feasible options of myocardial revascularization. METHODS: Thirty-four patients formerly characterized as having end stage coronary artery disease with refractory angina pectoris were retrospectively followed for coronary interventions. RESULTS: Of those 34 patients 21 (61.8%) were eventually revascularized with percutaneous interventional revascularization (PCI). Due to complex coronary morphology (angulation, chronic total occlusion) PCI demanded an above-average amount of time (66 +/- 42 minutes, range 25-206 minutes) and materials (contrast media 247 +/- 209 ml, range 50-750 ml; PCI guiding wires 2.0 +/- 1.4, range 1-6 wires). Of PCI patients 7 (33.3%) showed a new lesion as a sign of progression of atherosclerosis. Clinical success rate with a reduction to angina class II or lower was 71.4% at 30 days. Surgery was performed in a total of8 (23.5%) patients with a clinical success rate of 62.5%. Based on an intention-to-treat 2 patients of originally 8 (25%) demonstrated clinical success. Mortality during follow-up (1-18 months) was 4.8% in patients who underwent PCI, 25% in patients treated surgically and 25% in those only treated medically. CONCLUSION: The majority of patients with end-stage coronary artery disease can be treated effectively with conventional invasive treatment modalities. Therefore even though it is challenging and demanding PCI should be considered as a first choice before experimental interventions are considered.

Marker-Based Embodied Interaction for Handheld Augmented Reality Games

This article deals with embodied user interfaces for handheld augmented reality games, which consist of both physical and virtual components. We have developed a number of spatial interaction techniques that optically capture the device's movement and orientation relative to a visual marker. Such physical interactions in 3-D space enable manipulative control of mobile games. In addition to acting as a physical controller that recognizes multiple game-dependent gestures, the mobile device augments the camera view with graphical overlays. We describe three game prototypes that use ubiquitous product packaging and other passive media as backgrounds for handheld augmentation. The prototypes can be realized on widely available off-the-shelf hardware and require only minimal setup and infrastructure support.

Mobile Learning – Begriff, Modelle, Forschung

Der vorliegende Übersichtsartikel betrachtet Mobile Learning aus einer pädagogisch-psychologischen und didaktischen Perspektive. Mobile Learning (M-Learning), das seit Mitte der 1990er in unterschiedlichsten Kontexten Einzug in den Bildungssektor hielt, ist ein dynamisches und interdisziplinäres Feld. Dynamisch, weil M-Learning durch die rasche Entwicklung im Bereich der Informations- und Kommunikationstechnologie, wie kaum ein anderes Forschungsfeld, einem derart großen Wandel unterworfen ist. Interdisziplinär, weil durch das Zusammentreffen von mobiler Technik und Lernen auch unterschiedliche Fachdisziplinen betroffen sind. Die verschiedenen Sichtweisen und auch die Komplexität des Feldes haben dazu geführt, dass bis heute keine einheitliche Definition des Begriffs besteht. Ziel dieses Übersichtsartikels ist es, den aktuellen Forschungsstand aus didaktischer und pädagogisch-psychologischer Sicht aufzuzeigen. Dazu werden zunächst wichtige Komponenten des M-Learning-Begriffs herausgearbeitet und daran anschließend didaktisch bedeutsame theoretische Ansätze und Modelle vorgestellt sowie kritisch betrachtet. Basierend auf dieser theoretischen Ausgangslage wird dann ein Rahmen gezeichnet, der verdeutlichen soll, wo empirische Forschung aus didaktischer und pädagogisch-psychologischer Sicht ansetzen kann. Entsprechende empirische Studien werden ebenfalls vorgestellt, um einen Eindruck des aktuellen empirischen Forschungsstandes zu geben. Dies alles soll als Ausgangspunkt für den zukünftigen Forschungsbedarf dienen.

Against the Tide

In his most recent publication, Against the Tide: Critics of Digitalisation, Otto Peters brings together some of the most formidable and critical voices and compelling perspectives on the potential hazards of digitalization. The viewpoints presented range from personal, anthropological, and pedagogical to more scientific and technical, and arise from multiple disciplines. Peters has long been a respected scholar in the field of distance education, and while Peters’ earlier work has advocated the affordances of digitalization, this latest book is an abrupt shift to the darker side of digitalization. The assembly of critics Peters has gathered come from around the world and different walks of life: journalists, educators, scientists, philosophers, lawyers, mathematicians, and computer scientists, to name a few. Their one shared bond is a deep-seated belief that digitalization will have a profound and lasting impact on humankind – and not only in positive ways. ...

Astrocytes from the contused spinal cord inhibit oligodendrocyte differentiation of adult oligodendrocyte precursor cells by increasing the expression of bone morphogenetic proteins.

Promotion of remyelination is an important therapeutic strategy to facilitate functional recovery after traumatic spinal cord injury (SCI). Transplantation of neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) has been used to enhance remyelination after SCI. However, the microenvironment in the injured spinal cord is inhibitory for oligodendrocyte (OL) differentiation of NSCs or OPCs. Identifying the signaling pathways that inhibit OL differentiation in the injured spinal cord could lead to new therapeutic strategies to enhance remyelination and functional recovery after SCI. In the present study, we show that reactive astrocytes from the injured rat spinal cord or their conditioned media inhibit OL differentiation of adult OPCs with concurrent promotion of astrocyte differentiation. The expression of bone morphogenetic proteins (BMP) is dramatically increased in the reactive astrocytes and their conditioned media. Importantly, blocking BMP activity by BMP receptor antagonist, noggin, reverse the effects of active astrocytes on OPC differentiation by increasing the differentiation of OL from OPCs while decreasing the generation of astrocytes. These data indicate that the upregulated bone morphogenetic proteins in the reactive astrocytes are major factors to inhibit OL differentiation of OPCs and to promote its astrocyte differentiation. These data suggest that manipulation of BMP signaling in the endogenous or grafted NSCs or OPCs may be a useful therapeutic strategy to increase their OL differentiation and remyelination and enhance functional recovery after SCI.

Managing the risks of medical technology: Do hazard surveillance systems provide an early warning of medical device problems?

The Food and Drug Administration (FDA) is responsible for risk assessment and risk management in the post-market surveillance of the U.S. medical device industry. One of the FDA regulatory mechanisms, the Medical Device Reporting System (MDR) is an adverse event reporting system intended to provide the FDA with advance warning of device problems. It includes voluntary reporting for individuals, and mandatory reporting for device manufacturers. ^ In a study of alleged breast implant safety problems, this research examines the organizational processes by which the FDA gathers data on adverse events and uses adverse event reporting systems to assess and manage risk. The research reviews the literature on problem recognition, risk perception, and organizational learning to understand the influence highly publicized events may have on adverse event reporting. Understanding the influence of an environmental factor, such as publicity, on adverse event reporting can provide insight into the question of whether the FDA's adverse event reporting system operates as an early warning system for medical device problems. ^ The research focuses on two main questions. The first question addresses the relationship between publicity and the voluntary and mandatory reporting of adverse events. The second question examines whether government agencies make use of these adverse event reports. ^ Using quantitative and qualitative methods, a longitudinal study was conducted of the number and content of adverse event reports regarding breast implants filed with the FDA's medical device reporting system during 1985–1991. To assess variation in publicity over time, the print media were analyzed to identify articles related to breast implant failures. ^ The exploratory findings suggest that an increase in media activity is related to an increase in voluntary reporting, especially following periods of intense media coverage of the FDA. However, a similar relationship was not found between media activity and manufacturers' mandatory adverse event reporting. A review of government committee and agency reports on the FDA published during 1976–1996 produced little evidence to suggest that publicity or MDR information contributed to problem recognition, agenda setting, or the formulation of policy recommendations. ^ The research findings suggest that the reporting of breast implant problems to FDA may reflect the perceptions and concerns of the reporting groups, a barometer of the volume and content of media attention. ^

CCL5/RANTES is a key chemoattractant released by degenerative intervertebral discs in organ culture.

Release of chemotactic factors in response to tissue damage has been described for different musculoskeletal tissues, including the intervertebral disc (IVD). This study investigated the chemoattractants that are released by induced degenerative IVDs and may be involved in recruiting mesenchymal stem cells (MSCs). Bovine caudal discs were cultured within a bioreactor and loaded under conditions that mimicked physiological or degenerative settings. Between days 4-6, medium was replaced by PBS, which was subsequently used for proteomic, ELISA and immunoprecipitation analyses of secreted chemokines and cytokines. A Boyden chamber assay was used to observe human MSC migration towards native and chemokine depleted media. Gene expression levels of chemokine receptors in human MSCs were analysed, and CCL5 was localised in bovine and human IVD by immunohistochemistry. Proteomic analysis revealed the presence of CCL5 and CXCL6 within conditioned media. Higher concentrations of CCL5 were found in the degenerative media, and a relationship was found between interleukin-1β and CCL5 concentration. Chemokine immunoprecipitation showed that MSCs had a significantly reduced chemotactic migration towards CCL5-immunoprecipitated and CCL5/CXCL6 co-immunoprecipitated media, whilst CXCL6 depletion did not change MSC chemotaxis. MSCs showed a significant increase in mRNA expression of the CCL5 receptors, CCR1 and CCR4, upon culture in degenerative media. Furthermore, CCL5 was identified in bovine and human disc tissue by immunohistochemistry. Hence, CCL5 may be a key chemoattractant that is produced and released by the intervertebral disc cells. Therefore, these factors could be used to enhance stem/progenitor cell mobilisation in regenerative therapies for early stages of disc degeneration.

Endothelial progenitor cells as a biological marker of peripheral artery disease.

The role of endothelial progenitor cells (EPCs) in peripheral artery disease (PAD) remains unclear. We hypothesized that EPC mobilization and function play a central role in the development of endothelial dysfunction and directly influence the degree of atherosclerotic burden in peripheral artery vessels. The number of circulating EPCs, defined as CD34(+)/KDR(+) cells, were assessed by flow cytometry in 91 subjects classified according to a predefined sample size of 31 non-diabetic PAD patients, 30 diabetic PAD patients, and 30 healthy volunteers. Both PAD groups had undergone endovascular treatment in the past. As a functional parameter, EPC colony-forming units were determined ex vivo. Apart from a broad laboratory analysis, a series of clinical measures using the ankle-brachial index (ABI), flow-mediated dilatation (FMD) and carotid intima-media thickness (cIMT) were investigated. A significant reduction of EPC counts and proliferation indices in both PAD groups compared to healthy subjects were observed. Low EPC number and pathological findings in the clinical assessment were strongly correlated to the group allocation. Multivariate statistical analysis revealed these findings to be independent predictors of disease appearance. Linear regression analysis showed the ABI to be a predictor of circulating EPC number (p=0.02). Moreover, the functionality of EPCs was correlated by linear regression (p=0.017) to cIMT. The influence of diabetes mellitus on EPCs in our study has to be considered marginal in already disease-affected patients. This study demonstrated that EPCs could predict the prevalence and severity of symptomatic PAD, with ABI as the determinant of the state of EPC populations in disease-affected groups.

CATCH across Texas: Building a model for the diffusion of effective school-based health promotion programs

The impact of health promotion programs is related to both program effectiveness and the extent to which the program is implemented among the target population. The purpose of this dissertation was to describe the development and evaluation of a school-based program diffusion intervention designed to increase the rate of dissemination and adoption of the Child and Adolescent Trial for Cardiovascular Health, or CATCH program (recently renamed the Coordinated Approach to Child Health). ^ The first study described the process by which schools across the state of Texas spontaneously began to adopt the CATCH program after it was tested and proven effective in a multi-site randomized efficacy trial. A survey of teachers and administrator representatives of all schools on record that purchased the CATCH program, but were not involved in the efficacy trial, was used to find out who brought CATCH into the schools, how they garnered support for its adoption, why they decided to adopt the program, and what was involved in deciding to adopt. ^ The second study described how the Intervention Mapping framework guided the planning, development and implementation of a program for the diffusion of CATCH. An iterative process was used to integrate theory, literature, the experience of project staff and data from the target population into a meaningful set of program determinants and performance objectives. Proximal program objectives were specified and translated into both media and interpersonal communication strategies for program diffusion. ^ The third study assessed the effectiveness of the diffusion program in a case-comparison design. Three of the twenty Education Service Center regions in Texas were chosen, selected based on similar demographic criteria, and were followed for adoption of the CATCH curriculum. One of these regions received the full media and interpersonal channel intervention; a second received a reduced media-only intervention, and a third received no intervention. Results suggested the use of the interpersonal channels with media follow-up is an effective means to facilitate program dissemination and adoption. The media-alone condition was not effective in facilitating program adoption. ^

Is low parental education associated with congenital heart defects?

Objective. The purpose of this study was to determine if there are associations between low parental education and congenital heart defects. ^ Methods. This was a cross-sectional study of 281,262 live born singletons, 1765 of whom were identified by the Texas Birth Defects Monitoring Division (TBDMD) as having heart defects without known chromosomal anomalies. Data on the specific diagnoses of these infants were linked to their corresponding birth certificates. Only infants born between January 1, 1995 and December 31, 1997, whose mothers resided in the Texas public health regions under surveillance by the TBDMD were included in the study. The number of years of schooling of the most educated parent was used to calculate crude, stratified and adjusted odds ratios. ^ Results. An increase in the likelihood of having an infant with any type of congenital heart defect was found among parents with less than 16 years of education, compared to those with 16 or more years of schooling. The association became more marked with increasing paternal age, and was found among whites and Hispanics but not among blacks. Statistically significant associations with low parental education were found for ventricular septal defects, transposition of the great vessels and miscellaneous heart and vessel defects. Among whites, there was an inverse association between parental education and likelihood of having an infant with a severe ASD. This association was not found among non-whites. The suggestion of an association between low parental education and tetralogy of Fallot, was also found, but was not statistically significant. Parents with ≥16 years of education had a greater likelihood of having an infant with severe endocardial cushion lesions or total anomalous pulmonary return than less well educated parents. ^ Conclusion. This study suggests that parental education is associated with certain types of heart defects, especially among whites and Hispanics. ^

Constructed Response Answers in a Multiple-Choice Universe

A scheme is introduced which allows computer readable multiple choice forms used in traditional examinations to be employed for constructed response items.

A review of the effects of Transcendental Meditation on cardiovascular disease

Cardiovascular disease (CVD) is the single greatest cause of death in the United States, accounting for nearly 2400 deaths each day. It is estimated that 79.4 million American adults have some form of the disease, and CVD mortality rates are greater than those of cancer, chronic lower respiratory diseases, accidents and diabetes mellitus combined. Psychosocial stress is a nontraditional risk factor for CVD, and can contribute to the clustering of traditional risk factors as well as to vascular manifestations of the disease. The Transcendental Meditation (TM) technique has been researched as a cost effective intervention aimed at decreasing psychosocial stress. This literature review attempts to analyze randomized controlled clinical trials of TM on cardiovascular disease outcomes. Eleven studies met inclusion criteria and are described below, with statistically significant positive outcomes observed in each study. Studies are grouped by primary outcome reported in the categories of cardiovascular function, blood pressure, and exercise tolerance. The TM intervention significantly decreased insulin resistance, heart rate variability, and carotid intima media thickness and improved exercise tolerance compared to control groups. Seven studies also reported significant decreases in blood pressure among hypertensive and normotensive subjects. Five studies focused solely on African American subjects, a population that has disproportionately higher rates of CVD and hypertension, and found significant improvements in CVD outcomes. Further research is recommended to establish the efficacy of TM on CVD outcomes. Future trials should include larger sample populations, wider ethnic distributions of subjects, and longer follow-up to ascertain the impact of this particular stress reduction technique on cardiovascular disease.^