bluuebunny/crossref_metadata_2025_split huggingface dataset:
Live-Wires Using Path-Graphs
Authors: Hesser J. , König S. 
Published: March 2018

Summary

Objectives:
This article discusses our new Path-Graph approach for the interactive Live-Wire segmentation method in 2D applied to pre-segmented data. Furthermore, we examine whether or not the Live-Lane extension provides advantages in combination with pre-segmentation.

Methods:
We automatically over-segment the image data in a preprocessing step, using region growing with an automatic seed point generation. The Live-Wire algorithm is applied on this mosaic data by using the outlines of the homogeneous regions as the basis for graph building. We present a new definition of this underlying graph where the edges of the standard graphs are turning into vertices and the vertices of the new graph are defined by the edge connectivity in the standard graph. For better differentiation we name our new graph Path-Graph and the original defined graph Node-Graph.

Results:
The quality evaluation is done by comparing our segmentation results with existing model data. We show that using the Path-Graph as basis for the Live-Wire algorithm instead of the Node-Graph allows for a finer segmentation. We achieve a reduction of incorrectly classified pixels by 20.66 per cent and a decrease of the mean boundary deviation by 11.61 per cent. Since savings on cost tree calculations are compensated by additional computation time required to compute the Live-Lanes, a performance loss of 2.41 per cent is measured.

Conclusions:
Our redefinition of the underlying graph increases the quality of the Live-Wire segmentation. The Live-Lane extension in combination with pre-segmentation is not justified for our data.
Establishing an International Reference Image Database for Research and Development in Medical Image Processing
Authors: Prinz M. , Schneider S. , Sipilä O. , Spinnler K. , Vallée J.-P. , Leeuw I. , Vogl R. , Wittenberg T. , Zahlmann G. , Horsch A. 
Published: March 2018

Summary

Introduction:
The lack of comparability of evaluation results is one of the major obstacles of research and development in Medical Image Processing (MIP). The main reason for that is the usage of different image datasets with different quality, size and Gold standard.

Objectives:
Therefore, one of the goals of the Working Group on Medical Image Processing of the European Federation for Medical Informatics (EFMI WG MIP) is to develop first parts of a Reference Image Database.

Methods:
Kernel of the concept is to identify highly relevant medical problems with significant potential for improvement by MIP, and then to provide respective reference datasets. The EFMI WG MIP has primarily the role of a specifying group and an information broker, while the provider user relationships are defined by bilateral co-operation or license agreements.

Results:
An explorative database prototype has been implemented using the MySQL database software on the Web. Templates for provider user agreements have been worked out and already applied for own ‘pre-RID-MIP’ co-operations of the authors.

Discussion and Conclusion:
First steps towards a comprehensive reference image database have been done. Issues like funding, motivation, management, provision of Gold standards and evaluation guidelines are to be solved. Due to the interest from research groups and industry the efforts will be continued.
MRI-Based Individual 3D Region-of-Interest Atlases of the Human Brain
Authors: Kaiser H.-J. , Buell U. , Sabri O. , Wagenknecht G. 
Published: March 2018

Summary

Objectives:
Introduction of a new atlas-based method for analyzing functional data which takes into account the variability of individual human brains and the partial volume effects of functional emission computed tomography images in complex anatomical 3D regions, as well as describing the underlying multi-modal image processing principles.

Methods:
3D atlas extraction is done directly by automated segmentation of individual magnetic resonance images of the patient’s head. This is done in two steps: voxel-based classification of T1-weighted images for tissue differentiation (low-level processing) is followed by knowledge-based analysis of the classified images for extraction of 3D anatomical regions (high-level processing). For atlas-based quantification of co-registered functional images, 3D anatomical regions can be convoluted with an idealized point spread function of the emission computed tomography system, after which a partial volume-dependent threshold can be determined.

Results:
Quantitative evaluation studies, based on 50 realistic software head phantoms and 24 image data sets obtained from healthy subjects and patients, show low misclassification rates and stable results for the neural network-based classification approach (mean ± SD 3.587 ± 0.466%, range 2.726-4.927%) as well as for the adjustable parameters of the knowledge-based approach. Computation time is <5 min for classification, <1 min for most of the extraction algorithms. The influence of the partial volume-dependent threshold is shown for an activation study.

Conclusions:
This new method allows 3D atlas generation without the need to warp individual image data to an anatomical or statistical brain atlas. Going beyond the purely tissue-oriented approach, partial volume effects of emission computed tomography images can be analyzed in complex anatomical 3D regions.
Influenza-associated Excess Mortality from Monthly Total Mortality Data for Germany from 1947 to 2000
Authors: Stilianakis N. I. , Uphoff H. 
Published: March 2018

Summary

Objectives:
Death attributable to influenza is noted under various causes in the mortality statistics. Therefore, excess of total mortality is frequently used for the estimation of the entire impact of influenza on mortality. Various models for the estimation of the expected mortality are in use but are rather complex which hampers their routine use. A simple and hence transparent model was developed and applied to the total mortality in Germany from 1947 to 2000.

Methods:
The method is based on the pattern of the distribution of the mortality over the months. Additional trends over the time could be included with simple factors. In this manner the model was applicable over the total observation period.

Results:
The fit for the months where influenza was not epidemic was good and comparable to other models (R2 = 0.91). The estimated excess mortality is plausible and congruent with estimates based on other models.

Conclusion:
This method is applicable to long time series of any duration and obvious trends could be considered by simple factors in a readily identifiable and plausible way. Possible reductions in precision due to the consideration of a given monthly distribution pattern of the annual mortality seem tolerable with respect to the goodness of fit of the model. The estimation includes the pandemics of 1957/58 and 1968 to 1970.
Marfan Syndrome
Authors: Mátyás G. , Steinmann B. , Baumgartner D. , Baumgartner C. 
Published: March 2018

Summary

Objectives:
Marfan syndrome (MFS) is an autosomal dominant inherited connective tissue disorder caused by mutations in the fibrillin-1 (FBN1) gene with variable clinical manifestations in the cardiovascular, musculoskeletal and ocular systems.

Methods:
Data of molecular genetic analysis and a catalogue of clinical manifestations including aortic elastic parameters were mined in order to (i) assess aortic abnormality before and during medical treatment, and to (ii) identify novel correlations between the genotype and phenotype of the disease using hierarchical cluster analysis and logistic regression analysis. A score measure describing the similarity between a patient’s clinical symptoms and a characteristic phenotype class was introduced.

Results:
A probabilistic model for monitoring the loss of aortic elasticity was built on merely aortic parameters of 34 patients with classic MFS and 43 control subjects showing a sensitivity of 82% and a specificity of 96%. The clinical phenotypes of 100 individuals with classical or suspected MFS were clustered yielding four different phenotypic expressions. The highest correlation was found between FBN1 missense mutations, which manifested as ectopia lentis, skeletal major and skin minor criteria, and two out of four clustered phenotypes. The probability of the presence of a missense mutation in both phenotype classes is approximately 70%.

Conclusions:
Monitoring of aortic elastic properties during medical treatment may serve as additional criterion to indicate elective surgical interventions. Genotype-phenotype correlation may contribute to anticipate the clinical consequences of specific FBN1 mutations more comprehensively and may be helpful to identify MFS patients at risk at an early stage of disease.
Integration of Genomic Data in Electronic Health Records
Authors: Schmidt S. , Sax U. 
Published: March 2018

Summary

Objectives:
In this paper we give an overview about the challenge the postgenomic era poses on biomedical informaticists. The occurrence of new (genomic) data types necessitates new data models, new viewing metaphors and methods to deal with the disclosure of genomic data. We discuss integration issues when inferring phenotype and genotype data. Another challenge is to find the right phenotype to genotype data in order to get appropriate case numbers for sound clinical genotype-phenotype inference studies.

Methods:
Genomic data could be integrated in an Electronic Health Record (EHR) in several ways. We describe patient-centered and pointer-based integration strategies and the corresponding data types and data models. The inference mechanisms for the interpretation of raw data contain different agents. We describe vertical, horizontal and temporal agents.

Results:
We have to deal with several new data types, not being standardized for EHR integration. Genomic data tends to be more structured than phenotype data. Beyond the development of new data models, vertical, horizontal and temporal agents have to be developed in order to link genotype and phenotype. As the genomic EHR will contain very sensitive data, confidentiality and privacy concerns have to be addressed.

Conclusions:
Given the necessity to capture both environment and genomic state of a patient and their interaction, clinical information systems have to be redesigned. While genotyping seems to be automatable easily, this is not the case for clinical information. More integration work on terminologies and ontologies has to be done.
Why a System Awarded as “MIE ’99 Best Paper” Failed to Be Used and Hence to Affect Patient’s Health?
Authors: Mazzoleni M. C. 
Published: March 2018

Summary

Objective:
The failure of a promising system is described with the aim of identifying the errors and the unfavourable conditions that led to such a result.

Methods:
The system, based on the AHCPR guideline for pressure ulcers prevention and integrated into the already existing clinical information system, is aimed at supporting nurse’s activities for: the risk assessment of the inpatient at the beginning of the hospitalization; the prevention plan, customized to each specific patient; the work plan for each day for all the patients; the report of the non-compliances to the GL and of the workload of the nurses.

Results:
The system was abandoned after a short period. The reported reasons for the abandonment were: too strict constraints in the work-plan and the mandatory updating of the tasks at the end of each shift (both executed and not); the double writing activity, on paper first and afterward on the workstation.The first complaint was almost unrecoverable and not related to the system from the implementation point of view. Portable notebooks and wireless connections to the LAN could have been a solution for the second problem. Simultaneously a portable device at the bed side could have benefited many other features of the clinical information system. We proposed to quantify the added value, if any, due to making the information system available as close as possible to the points on the wards where information are both generated and used. The proposal was rejected.

Conclusions:
In our experience in a hospital setting, closing the gap among the medical informatics minority, the health professionals and the hospital management, through their collaborative responsibilities and participation in the decision-making process, can make the difference between the success and the failure of a good computer-based solution.
Advanced EHR Architectures–Promises or Reality
Authors: Blobel B. G. M. E. 
Published: March 2018

Summary

Objectives:
Forming the informational reflection of the patients and their care, the Electronic Health Record (EHR) is the core application of any complex health information system or health network. Such an ideally lifelong history file must be reliable, flexible, adaptable to new concepts and technologies, and robust, to allow for sharing knowledge over its lifetime. A sophisticated architecture must be chosen for meeting this challenge.

Methods:
An advanced EHR architecture for designing and implementing future-proof EHR systems must be a model of generic properties required for any Electronic Patient Record to provide communicable, comprehensive, useful, effective, and legally binding records that preserve their integrity over the time, independent of platforms and systems as well as of national special-ties. The resulting approach is based on the ISO Reference Model – Open Distributed Processing.

Results:
Based on advanced architectural principles introduced in the paper, a new generation of EHR systems has been designed and implemented for demonstrating the feasibility of the approach. This result is presented and evaluated regarding the achievements and problems using the component-based paradigm of model-driven health information system architectures.

Conclusions:
The future-proof EHR approach that has been established has been shortly evaluated. Advantages regarding flexibility, reliability, and portability of policy-driven, highly secure, role-dependent applications have to be considered in the light of performance as well as of the availability of network and application services.
The Gießen Tumor Documentation System (GTDS) – Review and Perspectives
Authors: Dudeck J. , Altmann U. 
Published: March 2018

Summary

Objectives:
GTDS is a documentation system used by more than 40 German hospital cancer registries. This paper discusses the factors that contributed to its success concerning design, development, and routine use.

Methods:
Success is measured in terms of the system‘s financial independence of public grants and its successful use by the registries. Success factors are presented in a descriptive way covering the topics of development (tools and development team) as well as system‘s functionality and user support. The description of the system’s use and user satisfaction was collected in a user survey conducted in 1999.

Results:
GTDS has become the main tool in hospital cancer registries in Germany and remarkably contributed to their success. A comprehensive data network between hospital cancer registries and population-based cancer registries has especially been established in the new states. After the first years of routine use the registries produce valuable data analyses on the basis of common tools. Under specific conditions physicians use the system directly for treatment management. The system succeeded to be financed by support contracts for continuous development which indicates generally good user acceptance. Close interaction between users and developers is important to meet user requirements during development and maintenance.

Conclusion:
Important success factors are the strong ministry‘s support including initial sponsoring and introduction of support contracts, the comprehensive functionality as well as flexibility and broad user support which allow the adaptation to different environments.
Semantic Interoperability
Authors: Engel K. , Pharowe P. , Blobel B. G. M. E. 
Published: March 2018

Summary

Objectives:
To meet the challenge for high quality and efficient care, highly specialized and distributed healthcare establishments have to communicate and co-operate in a semantically interoperable way. Information and communication technology must be open, flexible, scalable, knowledge-based and service-oriented as well as secure and safe.

Methods:
For enabling semantic interoperability, a unified process for defining and implementing the architecture, i.e. structure and functions of the cooperating systems’ components, as well as the approach for knowledge representation, i.e. the used information and its interpretation, algorithms, etc. have to be defined in a harmonized way. Deploying the Generic Component Model, systems and their components, underlying concepts and applied constraints must be formally modeled, strictly separating platform-independent from platform-specific models.

Results:
As HL7 Version 3 claims to represent the most successful standard for semantic interoperability, HL7 has been analyzed regarding the requirements for model-driven, service-oriented design of semantic interoperable information systems, thereby moving from a communication to an architecture paradigm. The approach is compared with advanced architectural approaches for information systems such as OMG’s CORBA 3 or EHR systems such as GEHR/openEHR and CEN EN 13606 Electronic Health Record Communication.

Conclusion:
HL7 Version 3 is maturing towards an architectural approach for semantic interoperability. Despite current differences, there is a close collaboration between the teams involved guaranteeing a convergence between competing approaches.
The Semantics of Procedures and Diseases in SNOMED® CT
Authors: Hanser S. , Hahn U. , Rogers J. , Schulz S. 
Published: March 2018

Summary

Objectives:
SNOMED® CT is emerging as a reference terminology for the entire health care process. It claims to be founded on logic-based modelling principles. In this article, we analyze a special encoding scheme for diseases and procedures in SNOMED® CT, the so-called relationship groups (RGs), which had been devised to avoid ambiguities in definitions.

Methods:
We reformulate SNOMED® CT’s relationship groups in the format of description logics in order to check whether RGs serve the needs they were designed for.

Results:
We show that a considerable proportion of relationship groups represent hidden mereological relations. We also report discrepancies encountered between the defined semantics of many SNOMED® CT terms and their intuitive meaning, as well as inconsistencies detected between the definition of various complex composed terms and the definition of their top-level parents.

Conclusions:
We formulate recommendations for improving SNOMED® CT by replacing most occurrences of relation groups by formally more adequate “part-of” relations.
A Simple Method to Estimate Tobacco-related Lung Cancer Deaths Based on Smoking Prevalence Data
Authors: Winkler V. , Gbangou A. , Kouyate B. , Becher H. 
Published: March 2018

Summary

Objective:
Tobacco is the major cause of cancer and a relevant risk factor for several other chronic diseases. Due to the epidemiological transition in developing countries with overall increasing life expectancy there is an increasing relevance of chronic diseases to the total burden of diseases. Furthermore, there are indications for a rise in the consumption of tobacco products in developing countries. Since in Africa data on smoking prevalence are scarce and cancer diagnosis is often imprecise or missing, it is difficult to estimate the current and future number of cancer cases attributable to tobacco smoking. In this paper, we present an approach to estimate the effects of smoking on lung cancer in selected developing countries in Africa.

Methods:
We combined data on smoking prevalence from different African countries with estimates on age-specific lung cancer rates in smokers and non-smokers from industrialized countries and data on age and sex distribution in African countries. We perform a sensitivity analysis to evaluate the effect of the assumptions necessary for the procedure.

Results:
If the smoking prevalence in African countries will remain on the current level, we estimate age-specific lung cancer rates lower than those in Germany. Despite the relatively small proportion of adults aged 50 and more which is the age when most cancer cases occur, there is an appreciable number of deaths from lung cancer that could be prevented when smoking prevalence could be reduced. Depending on assumptions we estimate up about 50,000 lung cancer deaths per year in Africa, most of which could be prevented.

Conclusions:
Efforts for smoking prevalence reduction are much more needed in the developing world. Better and more comprehensive data on smoking are needed for more precise estimates.
Are KISS Data Representative of German Intensive Care Units?
Authors: Schoop R. , Beyersmann J. , Schumacher M. , Zuschneid I. , Rücker G. 
Published: March 2018

Summary

Objectives:
Data collected within the German nosocomial infection surveillance system KISS are recommended as reference data for judging nosocomial infection rates in German intensive care units (ICUs). It is unknown whether the KISS data tend to under- or overestimate the true infection incidence rates. In this article, methodological aspects of the SIR1 study on the incidence of nosocomial infections are discussed, with the aim of estimating unbiased incidence rates of nosocomial infections in interdisciplinary German ICUs and examining whether the KISS data are representative.

Methods:
We discuss the following methodological issues: 1) Sample size estimation. 2) Stratified random sampling of German ICUs. 3) Investigation of seasonal effects. 4) Statistical modeling of incidence rates using a negative binomial regression model. 5) Comparison of weighted incidence rates with the standardized rate ratio (SRR).

Results:
Random sampling proved difficult to realize in practice since many ICUs refused to participate, particularly those in small hospitals. Analysis was adjusted for hospital size. No seasonal trends were found in the KISS data. Due to marked differences between ICUs, the number of infections is over-dispersed compared to a Poisson model, so negative binomial regression was used. Fifty ICUs were observed for two consecutive months each, corresponding to 21,832 patient days, during which 262 infections occurred. Infections were more frequent in large hospitals. The incidence rates provided by the SIR study are on average (SRR) 1.89 (1.63-2.20) times as large as those estimated by the KISS system.

Conclusion:
For estimating nosocomial infection incidence rates, random sampling and statistical modeling of over-dispersion were successfully performed. The study provides evidence that the KISS surveillance system tends to underestimate the true incidence rates of nosocomial infections in German ICUs.