bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Multi-resolution Approach for Content-based Image Retrieval on the Grid
Authors: Tweed T. , Miguet S. , Hassan K. 
Published: March 2018

Summary

Objectives:
Hospitals and medical centers are producing more and more data that need to be processed. Those data are confidential, heterogeneous, and limited to the geographic site where they have been produced. Unless properly anonymized, they cannot be distributed on wide area networks.

Methods:
Grid technologies allow the globalization of storage and processing resources, and enable large-scale experimentations on distributed data. They constitute a promising tool to treat the different data and analyze the knowledge they contain, while offering secured access and high-performance computing capacities to the different users. Our aim is to evaluate the possibilities of grid technologies for handling medical data.

Results and Conclusions:
In this paper, we focus on a breast cancer diagnosis assistance tool, based on distributed and incremental knowledge construction and a content-based image retrieval system. We analyze the different scenarios of uses of such a tool. We further propose an algorithm that indexes mammographic images for content-based query purposes. This algorithm is tested on images of different resolutions in order to reduce the indexation time and we analyze its performance with experiments on the grid.
The GENIUS Web Portal
Authors: Andronico G. , Falzone A. , Lo Re G. , Pulvirenti A. , Rodolico A. , Barbera R. 
Published: March 2018

Summary

Objective:
The development of computational Grids is making huge amounts of computing power and data storage available for a lot of scientific applications.At this stage of development, the use of the Grid is mainly based on Command Line Interface (CLI) tools that are not very friendly and can be considered an obstacle to the use of these powerful tools. The objective of this paper is to present a solution to this problem.

Methods:
To ease the access of new users to the grid the GENIUS (Grid Enabled web eNvironment for site Independent User job Submission) grid portal has been jointly developed by INFN and NICE within the context of both the Italian INFN Grid and the European DataGrid Projects. Here we devote particular care to the description of job creation and submission and the services for transparent access to user’s data and applications.

Results:
Using GENIUS, the obstacle of complicated CLI can be overtaken and simple web interfaces can be built for specific user communities and applications. Here we show examples in the field of bio-medical applications.

Conclusions:
The use of Grid can be made easy with the use of Grid portals such as GENIUS.
GPCALMA: a Grid-based Tool for Mammographic Screening
Authors: Bagnasco S. , Bottigli U. , Cheran S. C. , Delogu P. , Fantacci M. E. , Fauci F. , Forni G. , Lauria A. , Lopez Torres E. , Magro R. , Masala G. L. , Oliva P. , Palmiero R. , Ramello L. , Raso G. , Retico A. , Sitta M. , Stumbo S. , Tangaro S. , Zanon E. , Cerello P. 
Published: March 2018

Summary

Objectives:
The next generation of high energy physics (HEP) experiments requires a GRID approach to a distributed computing system: the key concept is the Virtual Organisation (VO), a group of distributed users with a common goal and the will to share their resources.

Methods:
A similar approach, applied to a group of hospitals that joined the GPCALMA project (Grid Platform for Computer Assisted Library for MAmmography), will allow common screening programs for early diagnosis of breast and, in the future, lung cancer. The application code makes use of neural networks for the image analysis and is useful in improving the radiologists' diagnostic performance. GRID services allow remote image analysis and interactive online diagnosis, with a potential for a relevant reduction of the delays presently associated with screening programs.

Results and Conclusions:
A prototype of the system, based on AliEn GRID Services [1], is already available, with a central server running common services [2] and several clients connecting to it. Mammograms can be acquired in any location; the related informatio required to select and access them at any time is stored in a common service called Data Catalogue, which can be queried by any client. Thanks to the PROOF facility [3], the result of a query can be used as input for analy-sis algorithms, which are executed on the nodes where the input images are stored,. The selected approach avoids data transfers for all the images with a negative diagnosis and allows an almost real time diagnosis for the set of images with high cancer probability.
Health Risk Appraisal Using Internet Technology
Authors: Yoshida K. , Suka M. 
Published: March 2018

Summary

Objective:
To develop a Web-based Health Risk Appraisal (HRA) system as a tool for health education based on personal health examination data.

Methods:
A Japanese health examination database was analyzed to develop models for HRA, which were designed to predict each of ten laboratory values in a year with and without lifestyle modifications. The HRA models were embedded into a server.

Results:
The Web-based HRA system has been introduced into a Japanese health care association having 37 branch centers. Following a health examination, an individual health education program using the Web-based HRA system is provided to a given client at each branch center or at a client’s office. A measured laboratory value and corresponding predicted laboratory values in a year with and without lifestyle modifications are displayed on the screen in forms of both numerical values and graphs. A trained nurse or another health care provider operates the system and explains the HRA result.

Conclusion:
The Web-based HRA system will be a practical tool for individual health education following health examination.
Evaluating Personal Health Care and Health Promotion Web Sites
Authors: Collen A. , Lang J. R. 
Published: March 2018

Summary

Objective:
An exemplary sample of web sites relevant to personal health care and health promotion was chosen and evaluated.

Methods:
Both quantitative and qualitative data were converged to assess and rank the sites on nine attributes.

Results:
The sites provided a definitive range of value and variety of presentations, health care and health promotion information, and services covering the virtual choices currently available to users of the Internet.

Conclusion:
Discussion focused on methodological approaches and issues of web site evaluation serving the public interest, health care, and health promotion.
Electronically Signed Documents in Health Care
Authors: Brandner R. , Bess A. , Schmücker P. , Bergh B. , Hollerbach A. 
Published: March 2018

Summary

Objectives:
Our objectives were to analyze and assess data formats for their suitability for conclusive and secure long-term archiving and to develop a concept for legally secure transformation of electronically signed documents that are not available in data formats appropriate for long-term archiving.

Methods:
On the basis of literature review and Internet searches we developed general evaluation criteria to assess data formats with regard to their suitability for conclusive and secure long-term archiving. The assessment of data formats refers to format specifications and available literature. For the analyses of the transformation of signed documents we analyzed legal requirements on the basis of laws and ordinances as well as technical requirements by means of literature reviews, Internet searches and technical specifications.

Results:
The following evaluation criteria are suited for this kind of assessment of data formats: transparency and standardization, stability, presentation and secuity According to our assessment the following data formats are most suitable for conclusive and secure long-term archiving: PDF for formatted and unstructured text documents, XML for markup languages, TIFF for images in general, DICOM for medical images and S/MIME for the storage of e-mail. To transform electronically signed documents we propose an elementary procedure and universal basic model in form of an XML schema definition that includes the necessary legal and technical information.

Conclusions:
If electronic documents are to replace paper-based documents in patient records, they have to conform to the criteria for secure long-term archiving. The analyzed data formats are to be extended by mechanisms to guarantee the long-term security of electronic signatures. To transform large quantities of documents in a legally secure way, our basic model has to be extended for automated procedures.
MorphoSaurus
Authors: Schulz S. , Hahn U. , Markó K. 
Published: March 2018

Summary

Objectives:
We propose an interlingua-based indexing approach to account for the particular challenges that arise in the design and implementation of cross-language document retrieval systems for the medical domain.

Methods:
Documents, as well as queries, are mapped to a language-independent conceptual layer on which retrieval operations are performed. We contrast this approach with the direct translation of German queries to English ones which, subsequently, are matched against English documents.

Results:
We evaluate both approaches, interlingua-based and direct translation, on a large medical document collection, the OHSUMED corpus. A substantial benefit for interlingua-based document retrieval using German queries on English texts is found, which amounts to 93% of the (monolingual) English baseline.

Conclusions:
Most state-of-the-art cross-language information retrieval systems translate user queries to the language(s) of the target documents. In contradistinction to this approach, translating both documents and user queries into a language-independent, concept-like representation format is more beneficial to enhance cross-language retrieval performance.
An Alternative Proposal for “Mixed Randomization” by Schulz and Grimes
Authors: Kundt G. 
Published: March 2018

Summary

Objective:
Randomization is an important part of clinical trials. Using permuted-block randomization for forcing equal group sizes potentially harms the unpredictability of treatment assignments. This can allow bias to creep into a trial. As an alternative, Schulz and Grimes suggest a “Mixed randomization” scheme which introduces more complexity to realize randomization. The objective of our research was to work out a model for randomization which is easier to handle than “Mixed randomization”, with an equal level of performance in unpredictability and balance.

Methods:
We analyzed a “Mixed randomization” procedure regarding the degree of unpredictability and balancing power and compared performance using permuted-block randomization with very large block size in a worst case scenario. Our work was done by the application of Blackwell-Hodges model for evaluation of the unpredictability of treatment assignments.

Results:
Regarding unpredictability, performance of permuted-block randomization with block size b = 36 was very similar to that of “Mixed randomization”. Regarding balancing power it was more favourable than “Mixed randomization”.

Conclusion:
Results of Schulz and Grimes are very important as they emphasized that mildly unequal sample sizes of therapy groups don’t cause problems. But the suggested scheme of “Mixed randomization” to a large extent adds complexity and we do not believe that this proposal is very feasible. Basically, we rather recommend the use of only one restricted randomization procedure in the best way. This can be permuted-block randomization with optimum choice of a large block size.
A Decision-support System for Real-time Risk Assessment of Airborne Spread of the Foot-and-Mouth Disease Virus
Authors: Fuchs K. , Rubel F. 
Published: March 2018

Summary

Objectives:
The application of epidemic models during the first days following the confirmation of a virus outbreak should significantly contribute to minimize its costs. Here we describe the first version of a decision-support system for the calculation of the airborne spread of a virus and its application to foot-and-mouth disease (FMD). The goal is to provide geographical maps depicting infection risk for various animal species to support the national health authorities.

Methods:
The major tool of the decision-support system is a specific epidemic (or atmospheric) model: A so-called Gaussian dispersion model to calculate 3-dimensional virus plumes. Additional tools providing input data and visualizing the output are: A veterinary data base of geo-referenced premises, a geographical information system (GIS), and, as an external part running at the National Weather Service, a numerical weather prediction (NWP) model. To demonstrate the features of the decision-support system a pilot study in Styria, Austria, has been performed simulating an artificial FMD outbreak.

Results:
One result of this simulation experiment is the determination of neighboring premises at which animals are at risk to be infected. Particular attention has been turned to cattle, sheep and swine. Using actual hourly NWP data from April 25, 2003, and a source of ten swine excreting a virus, cattle have been estimated to be at risk downwind 1,000-12,000 m, sheep 200-1,300 m, and swines 70-330 m.

Conclusions:
A system for real-time risk assessment of the airborne spread of a virus, applied to FMD, was introduced. Due to the forcing of the Gaussian dispersion model with NWP data, it is designed to run in both analysis and forecast mode. The system was applied for the first time during the Austrian real-time exercise on FMD, instructed by the European Union, in November 2004.
Scoring and Staging Systems Using Cox Linear Regression Modeling and Recursive Partitioning
Authors: Lee J. W. , Um S. H. , Lee J. B. , Mun J. , Cho H. 
Published: March 2018

Summary

Objectives:
Scoring and staging systems are used to determine the order and class of data according to predictors. Systems used for medical data, such as the Child-Turcotte-Pugh scoring and staging systems for ordering and classifying patients with liver disease, are often derived strictly from physicians’ experience and intuition. We construct objective and data-based scoring/staging systems using statistical methods.

Methods:
We consider Cox linear regression modeling and recursive partitioning techniques for censored survival data. In particular, to obtain a target number of stages we propose cross-validation and amalgamation algorithms. We also propose an algorithm for constructing scoring and staging systems by integrating local Cox linear regression models into recursive partitioning, so that we can retain the merits of both methods such as superior predictive accuracy, ease of use, and detection of interactions between predictors. The staging system construction algorithms are compared by cross-validation evaluation of real data.

Results:
The data-based cross-validation comparison shows that Cox linear regression modeling is somewhat better than recursive partitioning when there are only continuous predictors, while recursive partitioning is better when there are significant categorical predictors. The proposed local Cox linear recursive partitioning has better predictive accuracy than Cox linear modeling and simple recursive partitioning.

Conclusions:
This study indicates that integrating local linear modeling into recursive partitioning can significantly improve prediction accuracy in constructing scoring and staging systems.
The M2DM Project
Authors: Bellazzi R. , Stefanelli M. , Ferrari P. , De Cata P. , Gazzaruso C. , Fratino P. , D’Annunzio G. , Hernando E. , Gomez E.J. , Larizza C. 
Published: March 2018

Summary

Objectives:
This paper presents a multi-access service for the management of diabetes mellitus patients and the results of its assessment in two Italian clinical sites.

Methods:
The service was evaluated for one year in order to prove the advantages of these kind of systems from different points of view. In this paper the clinical, usability and technical outcomes are presented.

Results:
The evaluation results show that, thanks to the high flexibility of the implemented service, the tele-medicine management of diabetes patients is feasible, well accepted by patients and clinically effective. However, in Italy the problem of quantifying the reimbursement rate of telematic services and the impact they have on the organization are factors that may hamper their introduction in routine clinical practice.

Conclusions:
The evaluation study showed that the telemedicine intervention has been satisfactory both for physicians because it allows to constantly monitor the patients’ blood glucose level and for patients because it strengthens their motivation to self-monitor the metabolic situation.
Success and Failure Factors in the Regional Health Information System Design Process
Authors: Karimaa E. , Nykänen P. 
Published: March 2018

Summary

Objectives:
To identify success and failure factors in the design process of a regional health information system.

Methods:
A constructive evaluation study including interviews, observations, usability study and document analysis.

Results:
Modelling was found to be a key element for the successful implementation of a health information system. The developed service chain model helped to define use cases and to implement seamless service chains. User participation in the design process was a success factor resulting in good user acceptance and signs of positive impacts on work practices. Evaluation study also helped system developers to guide the system’s further development. An important failure factor identified was the lack of semantic interoperability of the system components.

Conclusions:
The results emphasize the socio-technical nature of health information systems. The starting point for development should be thorough insight into the health care work practices where the information systems are to be used. Successful system design should start from modelling of work processes, data and information flows and definition of concepts and their relations. Health informatics as a scientific discipline provides theories and models for the design and development process.
An Experience of Microbiological Data Sharing
Authors: Nappo A. , Giacomini M. 
Published: March 2018

Summary

Objectives:
The control of infections and their resistance to antibiotics in hospitals is a matter of vital importance in the follow-up of transplant patients. This project has the purpose of translating microbiological reports from an obsolete file structure to a system which could guarantee a more correct and quick transmission of data, a system of storage which reduces the possibility of errors, a smoother manipulation, consultation and updating of data and, at least, a simple way to compute the cost of analysis, based on the costs determined by the national’s DRG.

Methods:
The proposed solution is a semiautomatic interface which translates these data into a relational database on a daily basis, interprets the requests coming from external centers and produces reports. The prospective to use this tool for several centers indicates to us the need to choose an HL7 output for the interface.

Results:
A prototype version of this program was installed in February 2004. In this period, routine work has been recorded with an average of 6.5 samples per day, with a maximum of 23 samples. Moreover, historical data from 1998 has been translated. The main source of errors in these data was due to patient identification problems with an average occurrence of 4.06% in the virology section and of 4.16% in the microbiological division.

Conclusions:
A complete reorganization of the system would be desirable but at the moment it is not realistic because of obvious budget problems. The proposed approach, mainly the HL7 interface, seems to be a reasonable compromise.
Reproducible Statistical Analysis in Microarray Profiling Studies
Authors: Ruschhaupt M. , Huber W. , Mansmann U. 
Published: March 2018

Summary

Objectives:
Microarrays are a recent biotechnology that offers the hope of improved cancer classification. A number of publications presented clinically promising results by combining this new kind of biological data with specifically designed algorithmic approaches. But, reproducing published results in this domain is harder than it may seem.

Methods:
This paper presents examples, discusses the problems hidden in the published analyses and demonstrates a strategy to improve the situation which is based on the vignette technology available from the R and Bioconductor projects.

Results:
The tool of a compendium is discussed to achieve reproducible calculations and to offer an extensible computational framework. A compendium is a document that bundles primary data, processing methods (computational code), derived data, and statistical output with textual documentation and conclusions. It is interactive in the sense that it allows for the modification of the processing options, plugging in new data, or inserting further algorithms and visualizations.

Conclusions:
Due to the complexity of the algorithms, the size of the data sets, and the limitations of the medium printed paper it is usually not possible to report all the minutiae of the data processing and statistical computations. The technique of a compendium allows a complete critical assessment of a complex analysis.
Gaining Insight from Flexible Models
Authors: Pitha J. , Podrapska I. , Poledne R. , Valenta Z. 
Published: March 2018

Summary

Objectives:
We present results from a secondary prevention trial of coronary heart disease (CHD) in the Czech male population from northern Bohemia with the history of myocardial infarction (MI) and high prevalence of metabolic syndrome. We compare several approaches to analyzing survival data from our study in terms of respective model assumptions.

Methods:
While both the Cox and Weibull survival regression models assume proportionality of the hazard functions over time, in many instances this assumption appears incompatible with the data at hand. Gray’s implementation of flexible models using penalized splines allows for a more realistic assessment of the covariate effects which may vary over time.

Results:
Gray’s model results revealed a steady decline in the age-adjusted intervention effect over time, which remained significant until about 2.7 years of follow-up. This was in contrast with the results obtained from the Cox and Weibull models which suggested an overall risk reduction due to intervention during the total follow-up of 6.7 years. Survival estimates based on the Cox and Gray models are shown for the two treatment groups and selected sample quantiles of the age distribution for illustration.

Conclusions:
Gray’s time-varying coefficients model facilitated a more realistic assessment of the intervention effect. Using suitable historical controls with MI history the effect of intervention was found to gradully diminish over time.