Cost-effective HPC clustering for computer vision applications

We will present a cost-effective and flexible realization of high performance computing (HPC) clustering and its potential in solving computationally intensive problems in computer vision. The featured software foundation to support the parallel programming is the GNU parallel Knoppix package with message passing interface (MPI) based Octave, Python and C interface capabilities. The implementation is especially of interest in applications where the main objective is to reuse the existing hardware infrastructure and to maintain the overall budget cost. We will present the benchmark results and compare and contrast the performances of Octave and MATLAB

Unsupervised segmentation of mitochondria using model-based spectral clustering

Segmentation of mitochondria in microscopic images represents a significant challenge that is motivated by the wide morphological and structural variations that are characteristic for this category of membrane enclosed sub cellular organelles. To address the drawbacks associated with manual mark-up procedures (which are common in current clinical evaluations), a recent direction of research investigate the application of statistical machine learning methods to mitochondria segmentation. Within this field of research the main issue was generated by the complexity of the training set that is able to describe the vast structural variation that is associated with mitochondria. To avoid this problem, in this paper we apply perceptual organization models such as Figure-Ground, Similarity, Proximity and Closure which target the identification of the closed membranes in EM images using multistage spectral clustering [1,2]. Our unsupervised mitochondria segmentation algorithm is outlined in Fig. 1. The first stage of the spectral clustering implements foreground segmentation with the similarity model S1 that aims to identify the dark contours that are given by the outer membrane of the mitochondrion. In the second stage, the foreground data is re-clustered with a different similarity model S2 to identify the inner membrane of the mitochondrion. The last stage involves a contour processing step that eliminates the pixels that are not consistent with the minimum distance between the inner and outer membranes of the mitochondrion. The algorithm has been tested on a suite of EM images provided by the American Society of Cell Biology and a number of experimental results are presented in Fig. 2

A Spiritual Call: Jeremiah’s Call to the Heart And the Stages of Spiritual Progression in Carmelite Spirituality

The aim of this study is first, to identify resonances between Jeremiah 1:10 and the three stages of the spiritual journey as defined by the Carmelites such as John of the Cross and Teresa of Avila (i.e., the stages known as purgative, illuminative and unitive) and then, in light of an in depth understanding of the spiritual senses attributed to Jeremiah 1:10 in its reception history, to evaluate the impact of Jer 1:10 upon the Carmelite conception of the spiritual journey. A comprehensive Word Study is undertaken of six task verbs from Jer 1:10, presented as three pairs: to root out (נתש) and to pull down (נחץ), to destroy (אבד) and to throw down (הרס), to build (בנה) and to plant (נטע). This analysis offers support for the alignment and resonances of the task verbs with the three stages of the spiritual journey. The Word Study also suggests that for the spiritual sense, the Hebrew text may provide a typology of a three-stage progression, in which two stages of purification (described by two pairs of negative task verbs) are necessary before the holiest and whole-hearted stage of unification is effected (described by the positive pair of task verbs). In addition, the repeated proximate position of task verbs to the themes of “turning” and “the heart” suggest that the verbs may work to turn the heart to the Lord, who continues to love his people despite their spiritual adultery and other sins. The evidence reviewed in the Word Study is supported by the reception history and indicates that Jer 1:10 may offer a significant and early spiritual model. This verse directly impacts upon Paul and Origen in the early era of Christianity. Based on Origen’s interpretation, it is possible that Jer 1:10 offers a biblical model for the tri-partite spiritual journey which precedes the conception of spiritual stages by Pseudo-Dionysius, who is often considered the originator of the purgative, illuminative and unitive concepts. In a number of ways, Origen’s spiritual interpretation seems to be carried through Christian tradition and may challenge oft-assumed Platonic or Neoplatonic sources of the spiritual journey. However, the impact of Jer 1:10 upon the Carmelites Saints John of the Cross and Teresa of Avila is diffuse and indirect. No direct citation or echo of Jer 1:10 has been identified in their writings. Nonetheless, like Origen’s interpretation of Jer 1:10, John recognizes successive stages of spiritual “destruction” (purgation and illumination) designed to open space in the soul for God, allowing for a third phase of “construction” (i.e., union). Jer 1:10 may offer insight into the earliest theological seeds of the spiritual journey, with echoes and resonances throughout the ages

Structural methods in subcellular image analysis

Mitochondria play a central role in cellular bioenergetics and in the regulation of apoptotic cell death. Mitochondrial morphology (shape and cristae architecture) is crucial to the understanding of apoptosis mechanisms and the subsequent development of therapies targeting age- and cancer-related diseases[1],[2]. There is a high demand in automated segmentation tools which can provide an objective quantitative information in a reasonable time frame[2]. The state of the art however is still dominated by manual segmentation tools[3]. Early attempts to address the challenges shown above are based on the machine learning framework[4]

Computer-guided recognition of mitochondria in densely cluttered subcellular environments

Mitochondria are membrane enclosed organelles, on average approximately 300nm in diameter, which reside inside every living cell. Mitochondria play a central role in cellular bioenergetics and in the regulation of apoptotic (programmed) cell death. They contain a family of pro-apoptotic BCL-2 proteins that interact with anti-apoptotic proteins to induce apoptosis. The measurement of the morphological changes that mitochondria undergo during experimentally induced apoptosis is crucial to the understanding of apoptosis mechanisms and for the subsequent development of therapies targeting age and cancer-related diseases. From a computer vision perspective, the Transmission Electron Microscope (TEM) images represent extremely complex and dynamic environments and pose considerable challenges on the automated localization and segmentation of mitochondria. This is due, in part, to the variety of subcellular organisms and the deformable nature of their shapes and textures. Furthermore, mitochondrial morphology depends on the type of biological tissue and undergo changes during induced or naturally occurring biochemical processes. TEM images of mitochondria are able to capture the intrinsic structural elements that are caused by the inner membrane folding. This evidence suggests the feasibility of a feature-driven recognition approach.Therefore,our work is focused on the quantitative analysis of mitochondrial morphology and on the development of algorithms that perform the localization and segmentation of mitochondria in TEMimages.We report initial success on the extraction of specific localization markers for categories of mitochondria with ormal, lamellar and tubular morphology. Future work will focus on the development of shape segmentation algorithms

Evidence-Based Medicine Instruction in Integrative Medical School Curricula: A Tale of Two Libraries

Background: Many academic health sciences libraries have been moving towards active participation in the curriculum at their institutions.1 At the same time, many medical schools have completed, are working upon or are considering movement to an integrative curriculum, (the melding of basic sciences and clinical learning), based on suggested AAMC competencies.2We will discuss how libraries at two New England medical schools have successfully embraced roles in the their school’s curriculum, which are at different stages of adoption of new integrative curricula. Methods: The teaching of Evidence-Based Medicine (EBM) is an area ripe for collaboration between a medical school and its library. The libraries at both Harvard Medical School (HMS) and the University of Massachusetts Medical School (UMMS) now offer EBM instruction within their medical school curricula. HMS is refining its new integrative curriculum while UMMS is in the planning stages with implementation targeted for AY 2010. Teaching time, location within the curriculum, general content and methods between the programs at these two schools will be examined and compared. Results: UMMS conducts all of its EBM instruction within a traditional 3rd year clerkship format. HMS covers similar content online in a 1st year combined basic science/clinical course. However, the libraries at both institutions have successfully facilitated the incorporation of this important topic into required coursework. Reflection: Reflections on the following themes are included in the poster on: Staff and resources/workload Adding content into a packed curriculum Library expertise In person vs. online instruction Progressive versus single encounter instruction Conclusions: While at different phases of curriculum redesign, the academic libraries at UMMS and HMS have demonstrated the effectiveness of varied methods of teaching Evidence-Based Medicine within a medical school curriculum. 1Burrows, Suzetta, et al. Developing an evidence-based medicine and use of the biomedical literature component as a longitudinal theme of an outcomes-based medical school curriculum: year 1. Journal of the Medical Library Association 91.1 (2003):34-41. 2Association of American Medical Colleges. The Education of Medical Students: Ten Stories of Curriculum Change. New York: Milbank Memorial Funds, 2000. Presented at the Northeast Group on Educational Affairs (NEGEA) Regional Conference on May 2, 2009, in Hershey, Pennsylvania

Towards unsupervised segmentation in high-resolution medical nano-imaging

Recent advances in cellular and subcellular microscopy demonstrated its potential towards unraveling the mechanisms of various diseases at the molecular level. From a computer vision perspective nano-imaging is an inherently complex environment as can for example be seen from Fig.1(a,c). For the image analysis of intracellular organisms in high-resolution microscopy, new techniques which are capable of handling high-throughput data in a single pass and real time are of special interest. The additional emphasis is put therein on automated solutions which can provide the objective quantitative information in a reasonable time frame. The state-of-the-art is dominated by manual data annotation[1]and the early attempts to automate the segmentation are based on statistical machine-learning techniques[4]

Reducing weight and BMI following gestational diabetes: A systematic review and meta-analysis of digital and telemedicine interventions

Women with past gestational diabetes mellitus (GDM) are at risk of subsequent type 2 diabetes and adverse cardiovascular events. Digital and telemedicine interventions targeting weight loss and reductions in body mass index (BMI) may help reduce risk for women with GDM. The aim was to compare the effectiveness of digital or telemedicine intervention with usual care. Randomized controlled trials (RCTs) were identified in Embase, Medline, CINAHL, PsycINFO and the Cochrane Library. Included trials recruited women with prior GDM but without pre-existing diabetes, and tested a digital or telemedicine intervention with or without an in-person component. Data extraction was carried out independently by two authors. The search yielded 898 citations. Eighteen articles reporting 15 trials were included, of which 8 tested digital interventions. Reported outcomes included weight, BMI, fasting plasma glucose and waist circumference. None of the included trials reported type 2 diabetes incidence or cardiovascular risk. Data were pooled using a random-effects model. The point estimate favored the intervention but was non-significant for both BMI (−0.90 kg/m2, 95% CI −1.89 to 0.09; p=0.08) and weight (−1.83 kg, 95% CI −4.08 to 0.42, p=0.11). Trials evaluating digital and telemedicine interventions identified clinically relevant, but non-significant improvements in BMI and weight compared with control. No trials assessed type 2 diabetes occurrence as an outcome. More well-designed RCTs with adequate power and long-term follow-up are needed to identify the impact of these interventions on type 2 diabetes occurrence

The Landscape of Inappropriate Laboratory Testing: A 15-Year Meta-Analysis

Background: Laboratory testing is the single highest-volume medical activity and drives clinical decision-making across medicine. However, the overall landscape of inappropriate testing, which is thought to be dominated by repeat testing, is unclear. Systematic differences in initial vs. repeat testing, measurement criteria, and other factors would suggest new priorities for improving laboratory testing. Methods: A multi-database systematic review was performed on published studies from 1997–2012 using strict inclusion and exclusion criteria. Over- vs. underutilization, initial vs. repeat testing, low- vs. high-volume testing, subjective vs. objective appropriateness criteria, and restrictive vs. permissive appropriateness criteria, among other factors, were assessed. Results: Overall mean rates of over- and underutilization were 20.6% (95% CI 16.2–24.9%) and 44.8% (95% CI 33.8–55.8%). Overutilization during initial testing (43.9%; 95% CI 35.4–52.5%) was six times higher than during repeat testing (7.4%; 95% CI 2.5–12.3%; P for stratum difference <0.001). Overutilization of low-volume tests (32.2%; 95% CI 25.0–39.4%) was three times that of high-volume tests (10.2%; 95% CI 2.6–17.7%; P<0.001). Overutilization measured according to restrictive criteria (44.2%; 95% CI 36.8–51.6%) was three times higher than for permissive criteria (12.0%; 95% CI 8.0–16.0%; P<0.001). Overutilization measured using subjective criteria (29.0%; 95% CI 21.9–36.1%) was nearly twice as high as for objective criteria (16.1%; 95% CI 11.0–21.2%; P = 0.004). Together, these factors explained over half (54%) of the overall variability in overutilization. There were no statistically significant differences between studies from the United States vs. elsewhere (P = 0.38) or among chemistry, hematology, microbiology, and molecular tests (P = 0.05–0.65) and no robust statistically significant trends over time. Conclusions: The landscape of overutilization varies systematically by clinical setting (initial vs. repeat), test volume, and measurement criteria. Underutilization is also widespread, but understudied. Expanding the current focus on reducing repeat testing to include ordering the right test during initial evaluation may lead to fewer errors and better care

Libraries in Medical Education (LIME): A Special Interest Group of NEGEA

Purpose: Health science librarians play key roles in medical education by providing curriculum-integrated information skills instruction; by assisting faculty with research; by purchasing and maintaining collections of information resources; by participating in the development of standards and guidelines for educational outcomes; and by creating and managing libraries conducive to education. A group of medical librarians from northeastern medical schools proposed Libraries in Medical Education (LIME) Special Interest Group (SIG) to benefit all NEGEA (Northeast Group on Educational Affairs) members. The SIG will promote communication and collaboration between librarians and NEGEA members on research and curricular initiatives; enhance librarians knowledge and skills of current trends and issues of interest to the medical education community; recognize librarians as valued components of the medical education team; and increase the professional knowledge and skills of NEGEA members through programming delivered at annual meetings by librarians. Methods: In 2006, medical librarians drafted and submitted a proposal to become an official LIME SIG. Librarians have successfully implemented special interest groups within professional organizations. The Libraries in Medical Education SIG instituted within the Central Group on Education Affairs and the active Libraries/Educational Resources Section of American Association of Colleges of Pharmacy (AACP) served as models. Results: In 2007, the LIME was officially accepted by NEGEA as a special interest group. Conclusion: An enthusiastic LIME-SIG group looks forward to an exciting future of collaboration. Presented at the Northeast Group for Educational Affairs Annual Educational Retreat held in Stony Brook, NY, on June 8, 2007