Medical Image Data and Datasets in the Era of Machine Learning-Whitepaper from the 2016 C-MIMI Meeting Dataset Session.

At the first annual Conference on Machine Intelligence in Medical Imaging (C-MIMI), held in September 2016, a conference session on medical image data and datasets for machine learning identified multiple issues. The common theme from attendees was that everyone participating in medical image evaluation with machine learning is data starved. There is an urgent need to find better ways to collect, annotate, and reuse medical imaging data. Unique domain issues with medical image datasets require further study, development, and dissemination of best practices and standards, and a coordinated effort among medical imaging domain experts, medical imaging informaticists, government and industry data scientists, and interested commercial, academic, and government entities. High-level attributes of reusable medical image datasets suitable to train, test, validate, verify, and regulate ML products should be better described. NIH and other government agencies should promote and, where applicable, enforce, access to medical image datasets. We should improve communication among medical imaging domain experts, medical imaging informaticists, academic clinical and basic science researchers, government and industry data scientists, and interested commercial entities

Implementing a mobile diagnostic unit to increase access to imaging and laboratory services in western Kenya.

Access to basic imaging and laboratory services remains a major challenge in rural, resource-limited settings in sub-Saharan Africa. In 2016, the Academic Model Providing Access to Healthcare programme in western Kenya implemented a mobile diagnostic unit (MDU) outfitted with a generator-powered X-ray machine and basic laboratory tests to address the lack of these services at rural, low-resource, public health facilities. The objective of this paper is to describe the design, implementation, preliminary impact and operational challenges of the MDU in western Kenya. Since implementing the MDU at seven rural health facilities serving a catchment of over half a million people, over 4500 chest radiographs have been performed, with one or more abnormalities detected in approximately 30% of radiographs. We observed favorable feedback and uptake of MDU services by healthcare workers and patients. However, various operational challenges in the design and construction of the MDU and the transmission and reporting of radiographs in remote areas were encountered. Our experience supports the feasibility of deploying an MDU to increase access to basic radiology and laboratory services in rural, resource-limited settings

The real exchange rate and the structure of aggregate production

This paper proposes a new, production theory approach to the determination of the real exchange rate, which is defined as the relative price of traded to nontraded goods as is common in the international trade literature. Using a Translog real GDI function that describes the aggregate technology of an open economy as a starting point, the real exchange rate can be formally derived as a function of domestic excess savings, the terms of trade, relative factor endowments and technological progress. Empirical results for Switzerland suggest that the main drivers of the real exchange rate are the terms of trade, followed by relative factor endowments. Contrary to conventional wisdom, the Balassa-Samuelson effect does not seem to play a significant role in explaining the long-term real appreciation of the Swiss franc

A Platform for Innovation and Standards Evaluation: a Case Study from the OpenMRS Open-Source Radiology Information System

Open-source development can provide a platform for innovation by seeking feedback from community members as well as providing tools and infrastructure to test new standards. Vendors of proprietary systems may delay adoption of new standards until there are sufficient incentives such as legal mandates or financial incentives to encourage/mandate adoption. Moreover, open-source systems in healthcare have been widely adopted in low- and middle-income countries and can be used to bridge gaps that exist in global health radiology. Since 2011, the authors, along with a community of open-source contributors, have worked on developing an open-source radiology information system (RIS) across two communities-OpenMRS and LibreHealth. The main purpose of the RIS is to implement core radiology workflows, on which others can build and test new radiology standards. This work has resulted in three major releases of the system, with current architectural changes driven by changing technology, development of new standards in health and imaging informatics, and changing user needs. At their core, both these communities are focused on building general-purpose EHR systems, but based on user contributions from the fringes, we have been able to create an innovative system that has been used by hospitals and clinics in four different countries. We provide an overview of the history of the LibreHealth RIS, the architecture of the system, overview of standards integration, describe challenges of developing an open-source product, and future directions. Our goal is to attract more participation and involvement to further develop the LibreHealth RIS into an Enterprise Imaging System that can be used in other clinical imaging including pathology and dermatology

Preparing a collection of radiology examinations for distribution and retrieval

OBJECTIVE: Clinical documents made available for secondary use play an increasingly important role in discovery of clinical knowledge, development of research methods, and education. An important step in facilitating secondary use of clinical document collections is easy access to descriptions and samples that represent the content of the collections. This paper presents an approach to developing a collection of radiology examinations, including both the images and radiologist narrative reports, and making them publicly available in a searchable database. MATERIALS AND METHODS: The authors collected 3996 radiology reports from the Indiana Network for Patient Care and 8121 associated images from the hospitals' picture archiving systems. The images and reports were de-identified automatically and then the automatic de-identification was manually verified. The authors coded the key findings of the reports and empirically assessed the benefits of manual coding on retrieval. RESULTS: The automatic de-identification of the narrative was aggressive and achieved 100% precision at the cost of rendering a few findings uninterpretable. Automatic de-identification of images was not quite as perfect. Images for two of 3996 patients (0.05%) showed protected health information. Manual encoding of findings improved retrieval precision. CONCLUSION: Stringent de-identification methods can remove all identifiers from text radiology reports. DICOM de-identification of images does not remove all identifying information and needs special attention to images scanned from film. Adding manual coding to the radiologist narrative reports significantly improved relevancy of the retrieved clinical documents. The de-identified Indiana chest X-ray collection is available for searching and downloading from the National Library of Medicine (http://openi.nlm.nih.gov/)

Examining the effect of peer helping in a coping skills intervention: a randomized controlled trial for advanced gastrointestinal cancer patients and their family caregivers

PURPOSE: At the end of life, spiritual well-being is a central aspect of quality of life for many patients and their family caregivers. A prevalent spiritual value in advanced cancer patients is the need to actively give. To address this need, the current randomized trial examined whether adding a peer helping component to a coping skills intervention leads to improved meaning in life and peace for advanced gastrointestinal cancer patients and their caregivers. Feasibility and acceptability outcomes were also assessed. METHODS: Advanced gastrointestinal cancer patients and caregivers (n = 50 dyads) were randomly assigned to a 5-session, telephone-based coping skills intervention or a peer helping + coping skills intervention. One or both dyad members had moderate-severe distress. Peer helping involved contributing to handouts on coping skills for other families coping with cancer. Patients and caregivers completed measures of meaning in life/peace, fatigue, psychological symptoms, coping self-efficacy, and emotional support. Patient pain and caregiver burden were also assessed. RESULTS: Small effects in favor of the coping skills group were found regarding meaning in life/peace at 1 and 5 weeks post-intervention. Other outcomes did not vary as a function of group assignment, with both groups showing small decreases in patient and caregiver fatigue and caregiver distress and burden. High recruitment and retention rates supported feasibility, and high participant satisfaction ratings supported acceptability. CONCLUSIONS: Although a telephone-based intervention is feasible and acceptable for this population, peer helping in the context of a coping skills intervention does not enhance spiritual well-being relative to coping skills alone

Creation and Curation of the Society of Imaging Informatics in Medicine Hackathon Dataset

In order to support innovation, the Society of Imaging Informatics in Medicine (SIIM) elected to create a collaborative computing experience called a "hackathon." The SIIM Hackathon has always consisted of two components, the event itself and the infrastructure and resources provided to the participants. In 2014, SIIM provided a collection of servers to participants during the annual meeting. After initial server setup, it was clear that clinical and imaging "test" data were also needed in order to create useful applications. We outline the goals, thought process, and execution behind the creation and maintenance of the clinical and imaging data used to create DICOM and FHIR Hackathon resources

Three cachexia phenotypes and the impact of fat-only loss on survival in FOLFIRINOX therapy for pancreatic cancer

BACKGROUND: By the traditional definition of unintended weight loss, cachexia develops in ~80% of patients with pancreatic ductal adenocarcinoma (PDAC). Here, we measure the longitudinal body composition changes in patients with advanced PDAC undergoing 5-fluorouracil, leucovorin, irinotecan, and oxaliplatin therapy. METHODS: We performed a retrospective review of 53 patients with advanced PDAC on 5-fluorouracil, leucovorin, irinotecan, and oxaliplatin as first line therapy at Indiana University Hospital from July 2010 to August 2015. Demographic, clinical, and survival data were collected. Body composition measurement by computed tomography (CT), trend, univariate, and multivariate analysis were performed. RESULTS: Among all patients, three cachexia phenotypes were identified. The majority of patients, 64%, had Muscle and Fat Wasting (MFW), while 17% had Fat-Only Wasting (FW) and 19% had No Wasting (NW). NW had significantly improved overall median survival (OMS) of 22.6 months vs. 13.0 months for FW and 12.2 months for MFW (P = 0.02). FW (HR = 5.2; 95% confidence interval = 1.5-17.3) and MFW (HR = 1.8; 95% confidence interval = 1.1-2.9) were associated with an increased risk of mortality compared with NW. OMS and risk of mortality did not differ between FW and MFW. Progression of disease, sarcopenic obesity at diagnosis, and primary tail tumours were also associated with decreased OMS. On multivariate analysis, cachexia phenotype and chemotherapy response were independently associated with survival. Notably, CT-based body composition analysis detected tissue loss of >5% in 81% of patients, while the traditional definition of >5% body weight loss identified 56.6%. CONCLUSIONS: Distinct cachexia phenotypes were observed in this homogeneous population of patients with equivalent stage, diagnosis, and first-line treatment. This suggests cellular, molecular, or genetic heterogeneity of host or tumour. Survival among patients with FW was as poor as for MFW, indicating adipose tissue plays a crucial role in cachexia and PDAC mortality. Adipose tissue should be studied for its mechanistic contributions to cachexia

Learning to Verify the Heap

Abstract. We present a data-driven verification framework to automatically prove memory safety and functional correctness of heap programs. For this, we introduce a novel statistical machine learning technique that maps observed program states to (possibly disjunctive) separation logic formulas describing the invariant shape of (possibly nested) data structures at relevant program locations. We then attempt to verify these predictions using a theorem prover, where counterexamples to a predicted invariant are used as additional input to the shape predictor in a refinement loop. After obtaining valid shape invariants, we use a second learning algorithm to strengthen them with data invariants, again employing a refinement loop using the underlying theorem prover. We have implemented our techniques in Cricket, an extension of the GRASShopper verification tool. Cricket is able to automatically prove memory safety and correctness of implementations of a variety of classical heap-manipulating programs such as insertionsort, quicksort and traversals of nested data structures

Evaluation der Ökomassnahmen: Bereich Biodiversität

1993 führte der Bund ökologische Direktzahlungen ein; seit 1999 ist die Erbringung des ökologischen Leistungsnachweises (ÖLN) durch die Landwirtschaftsbetriebe die Voraussetzung zum Bezug von Direktzahlungen. Heute werden 97 % der landwirtschaftlichen Nutzfläche nach den Regeln des ÖLN bewirtschaftet. Die wichtigste Massnahme des ÖLN, welche einen Einfluss auf die Biodiversität hat, ist, dass die Betriebe 7 % ihrer landwirtschaftlichen Nutzfläche (LN) als ökologische Ausgleichsflächen (öAF) auszuweisen haben (bei Spezialkulturen 3,5 %). Weitere Anforderungen des ÖLN (ausgeglichene Nährstoffbilanz, geregelte Fruchtfolge, Bodenschutz, gezielter Einsatz von Pflanzenschutzmitteln, tiergerechte Haltung der Nutztiere) können ebenfalls einen Einfluss haben, stehen jedoch weniger im Vordergrund