Unifying Requirements and Code: an Example

Requirements and code, in conventional software engineering wisdom, belong to entirely different worlds. Is it possible to unify these two worlds? A unified framework could help make software easier to change and reuse. To explore the feasibility of such an approach, the case study reported here takes a classic example from the requirements engineering literature and describes it using a programming language framework to express both domain and machine properties. The paper describes the solution, discusses its benefits and limitations, and assesses its scalability.Comment: 13 pages; 7 figures; to appear in Ershov Informatics Conference, PSI, Kazan, Russia (LNCS), 201

The International Cancer Expert Corps: A Unique Approach for Sustainable Cancer Care in Low and Lower-Middle Income Countries

The growing burden of non-communicable diseases including cancer in low- and lower-middle income countries (LMICs) and in geographic-access limited settings within resource-rich countries requires effective and sustainable solutions. The International Cancer Expert Corps (ICEC) is pioneering a novel global mentorship–partnership model to address workforce capability and capacity within cancer disparities regions built on the requirement for local investment in personnel and infrastructure. Radiation oncology will be a key component given its efficacy for cure even for the advanced stages of disease often encountered and for palliation. The goal for an ICEC Center within these health disparities settings is to develop and retain a high-quality sustainable workforce who can provide the best possible cancer care, conduct research, and become a regional center of excellence. The ICEC Center can also serve as a focal point for economic, social, and healthcare system improvement. ICEC is establishing teams of Experts with expertise to mentor in the broad range of subjects required to establish and sustain cancer care programs. The Hubs are cancer centers or other groups and professional societies in resource-rich settings that will comprise the global infrastructure coordinated by ICEC Central. A transformational tenet of ICEC is that altruistic, human-service activity should be an integral part of a healthcare career. To achieve a critical mass of mentors ICEC is working with three groups: academia, private practice, and senior mentors/retirees. While in-kind support will be important, ICEC seeks support for the career time dedicated to this activity through grants, government support, industry, and philanthropy. Providing care for people with cancer in LMICs has been a recalcitrant problem. The alarming increase in the global burden of cancer in LMICs underscores the urgency and makes this an opportune time fornovel and sustainable solutions to transform cancer care globally

Differential gene expression and genomic patient stratification following left ventricular assist device support

AbstractObjectivesWe sought to determine whether mechanical unloading of the failing human heart with a left ventricular assist device (LVAD) results in significant changes in overall left ventricular gene expression.BackgroundMechanical circulatory support by LVAD in end-stage human heart failure (HF) can result in beneficial reverse remodeling of myocardial structure and function. The molecular mechanisms behind this salutary process are not well understood.MethodsLeft ventricular samples from six male patients were harvested during LVAD placement and subsequently at the time of explantation. Cardiac gene expression was determined using oligonucleotide microarrays.ResultsPaired ttest analysis revealed numerous genes that were regulated in a statistically significant fashion, including the downregulation of several previously studied genes. Further statistical analysis revealed that the overall gene expression profiles could significantly distinguish pre- and post-LVAD status. Interestingly, the data also identified two distinct groups among the pre-LVAD failing hearts, in which there was blind segregation of patients based on HF etiology. In addition to the substantial divergence in genomic profiles for these two HF groups, there were significant differences in their corresponding LVAD-mediated regulation of gene expression.ConclusionsSupport with an LVAD in HF induces significant changes in myocardial gene expression, as pre- and post-LVAD hearts demonstrate significantly distinct genomic footprints. Thus, reverse remodeling is associated with a specific pattern of gene expression. Moreover, we found that deoxyribonucleic acid microarray technology could distinguish, in a blind manner, patients with different HF etiologies. Expansion of this study and further development of these statistical methods may facilitate prognostic prediction of the individual patient response to LVAD support

Your Proof Fails? Testing Helps to Find the Reason

Applying deductive verification to formally prove that a program respects its formal specification is a very complex and time-consuming task due in particular to the lack of feedback in case of proof failures. Along with a non-compliance between the code and its specification (due to an error in at least one of them), possible reasons of a proof failure include a missing or too weak specification for a called function or a loop, and lack of time or simply incapacity of the prover to finish a particular proof. This work proposes a new methodology where test generation helps to identify the reason of a proof failure and to exhibit a counter-example clearly illustrating the issue. We describe how to transform an annotated C program into C code suitable for testing and illustrate the benefits of the method on comprehensive examples. The method has been implemented in STADY, a plugin of the software analysis platform FRAMA-C. Initial experiments show that detecting non-compliances and contract weaknesses allows to precisely diagnose most proof failures.Comment: 11 pages, 10 figure

A Graph-Based Semantics Workbench for Concurrent Asynchronous Programs

A number of novel programming languages and libraries have been proposed that offer simpler-to-use models of concurrency than threads. It is challenging, however, to devise execution models that successfully realise their abstractions without forfeiting performance or introducing unintended behaviours. This is exemplified by SCOOP---a concurrent object-oriented message-passing language---which has seen multiple semantics proposed and implemented over its evolution. We propose a "semantics workbench" with fully and semi-automatic tools for SCOOP, that can be used to analyse and compare programs with respect to different execution models. We demonstrate its use in checking the consistency of semantics by applying it to a set of representative programs, and highlighting a deadlock-related discrepancy between the principal execution models of the language. Our workbench is based on a modular and parameterisable graph transformation semantics implemented in the GROOVE tool. We discuss how graph transformations are leveraged to atomically model intricate language abstractions, and how the visual yet algebraic nature of the model can be used to ascertain soundness.Comment: Accepted for publication in the proceedings of FASE 2016 (to appear

Utilization of a labeled tracking oligonucleotide for visualization and quality control of spotted 70-mer arrays

BACKGROUND: Spotted 70-mer oligonucleotide arrays offer potentially greater specificity and an alternative to expensive cDNA library maintenance and amplification. Since microarray fabrication is a considerable source of data variance, we previously directly tagged cDNA probes with a third fluorophore for prehybridization quality control. Fluorescently modifying oligonucleotide sets is cost prohibitive, therefore, a co-spotted Staphylococcus aureus-specific fluorescein-labeled "tracking" oligonucleotide is described to monitor fabrication variables of a Mycobacterium tuberculosis oligonucleotide microarray. RESULTS: Significantly (p < 0.01) improved DNA retention was achieved printing in 15% DMSO/1.5 M betaine compared to the vendor recommended buffers. Introduction of tracking oligonucleotide did not effect hybridization efficiency or introduce ratio measurement bias in hybridizations between M. tuberculosis H37Rv and M. tuberculosis mprA. Linearity between the mean log Cy3/Cy5 ratios of genes differentially expressed from arrays either possessing or lacking the tracking oligonucleotide was observed (R(2 )= 0.90, p < 0.05) and there were no significant differences in Pearson's correlation coefficients of ratio data between replicates possessing (0.72 ± 0.07), replicates lacking (0.74 ± 0.10), or replicates with and without (0.70 ± 0.04) the tracking oligonucleotide. ANOVA analysis confirmed the tracking oligonucleotide introduced no bias. Titrating target-specific oligonucleotide (40 μM to 0.78 μM) in the presence of 0.5 μM tracking oligonucleotide, revealed a fluorescein fluorescence inversely related to target-specific oligonucleotide molarity, making tracking oligonucleotide signal useful for quality control measurements and differentiating false negatives (synthesis failures and mechanical misses) from true negatives (no gene expression). CONCLUSIONS: This novel approach enables prehybridization array visualization for spotted oligonucleotide arrays and sets the stage for more sophisticated slide qualification and data filtering applications

Hospital variation in missed nursing care

Quality of nursing care across hospitals is variable, and this variation can result in poor patient outcomes. One aspect of quality nursing care is the amount of necessary care that is omitted. This article reports on the extent and type of nursing care missed and the reasons for missed care. The MISSCARE Survey was administered to nursing staff (n = 4086) who provide direct patient care in 10 acute care hospitals. Missed nursing care patterns as well as reasons for missing care (labor resources, material resources, and communication) were common across all hospitals. Job title (ie, registered nurse vs nursing assistant), shift worked, absenteeism, perceived staffing adequacy, and patient work loads were significantly associated with missed care. The data from this study can inform quality improvement efforts to reduce missed nursing care and promote favorable patient outcomes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/94115/1/Hospital variation in missed nursing care.pd

The early childhood generalized trust belief scale

The study was designed to develop and evaluate the Early Childhood Generalized Trust Belief Scale (ECGTBS) as a method of assessing 5-to-8-year-olds’ generalized trust. Two hundred and eleven (103 male and 108 female) children (mean age 6 years and 2 months at Time 1) completed the ECGTBS twice over a year. A subsample of participants completed the ECGTBS after two weeks to assess the scale’s test-retest reliability. Exploratory and confirmatory factor analyses confirmed that the ECGTBS assessed the expected three factors: reliability, emotional trust, and honesty with item-pairs loading most strongly on their corresponding factor. However, the ECGTBS demonstrated low to modest internal consistency and test-retest reliability which indicates a need for further development of this instrument. As evidence for the convergent validity of the ECGTBS, the reliability and emotional trust items were associated with the children’s trust in classmates at Time 2. Concurrent asymmetric quadratic relationships indicated the importance of midrange generalized trust. Specifically, children with very high generalized trust experienced greater loneliness and children with very low generalized trust had fewer friendships than children with midrange trust