Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data

The Brain Imaging Data Structure (BIDS) is a specification for organizing, sharing, and archiving neuroimaging data and metadata in a reusable way. First developed for magnetic resonance imaging (MRI) datasets, the community-led specification evolved rapidly to include other modalities such as magnetoencephalography, positron emission tomography, and quantitative MRI (qMRI). In this work, we present an extension to BIDS for microscopy imaging data, along with example datasets. Microscopy-BIDS supports common imaging methods, including 2D/3D, ex/in vivo, micro-CT, and optical and electron microscopy. Microscopy-BIDS also includes comprehensible metadata definitions for hardware, image acquisition, and sample properties. This extension will facilitate future harmonization efforts in the context of multi-modal, multi-scale imaging such as the characterization of tissue microstructure with qMRI.

The Open Brain Consent: Informing research participants and obtaining consent to share brain imaging data

Having the means to share research data openly is essential to modern science. For human research, a key aspect in this endeavor is obtaining consent from participants, not just to take part in a study, which is a basic ethical principle, but also to share their data with the scientific community. To ensure that the participants' privacy is respected, national and/or supranational regulations and laws are in place. It is, however, not always clear to researchers what the implications of those are, nor how to comply with them. The Open Brain Consent (https://open-brain-consent.readthedocs.io) is an international initiative that aims to provide researchers in the brain imaging community with information about data sharing options and tools. We present here a short history of this project and its latest developments, and share pointers to consent forms, including a template consent form that is compliant with the EU general data protection regulation. We also share pointers to an associated data user agreement that is not only useful in the EU context, but also for any researchers dealing with personal (clinical) data elsewhere.

APPIAN: Automated Pipeline for PET Image Analysis

APPIAN is an automated pipeline for user-friendly and reproducible analysis of positron emission tomography (PET) images with the aim of automating all processing steps up to the statistical analysis of measures derived from the final output images. The three primary processing steps are coregistration of PET images to T1-weighted magnetic resonance (MR) images, partial-volume correction (PVC), and quantification with tracer kinetic modeling. While there are alternate open-source PET pipelines, none offers all of the features necessary for making automated PET analysis as reliably, flexibly and easily extendible as possible. To this end, a novel method for automated quality control (QC) has been designed to facilitate reliable, reproducible research by helping users verify that each processing stage has been performed as expected. Additionally, a web browser-based GUI has been implemented to allow both the 3D visualization of the output images, as well as plots describing the quantitative results of the analyses performed by the pipeline. APPIAN also uses flexible region of interest (ROI) definition—with both volumetric and, optionally, surface-based ROI—to allow users to analyze data from a wide variety of experimental paradigms, e.g., longitudinal lesion studies, large cross-sectional population studies, multi-factorial experimental designs, etc. Finally, APPIAN is designed to be modular so that users can easily test new algorithms for PVC or quantification or add entirely new analyses to the basic pipeline. We validate the accuracy of APPIAN against the Monte-Carlo simulated SORTEO database and show that, after PVC, APPIAN recovers radiotracer concentrations within 93–100% accuracy.

Resting state FDG-PET functional connectivity as an early biomarker of Alzheimer's disease using conjoint univariate and independent component analyses

Imaging cerebral glucose metabolism with positron emission tomography (PET) in Alzheimer's disease (AD) has allowed for improved characterisation of this pathology. Such patterns are typically analysed using either univariate or multivariate statistical techniques. In this work we combined voxel-based group analysis and independent component analysis to extract differential characteristic patterns from PET data of glucose metabolism in a large cohort of normal elderly controls and patients with AD. The patterns were used in conjunction with a support vector machine to discriminate between subjects with mild cognitive impairment (MCI) at risk or not of converting to AD. The method was applied to baseline fluoro-deoxyglucose (FDG)-PET images of subjects from the ADNI database. Our approach achieved improved early detection and differentiation of typical versus pathological metabolic patterns in the MCI population, reaching 80% accuracy (85% sensitivity and 75% specificity) when using selected regions. The method has the potential to assist in the advance diagnosis of Alzheimer's disease, and to identify early in the development of the disease those individuals at high risk of rapid cognitive decline who could be candidates for new therapeutic approaches.

Validity and responsiveness of the Rehabilitation Activities Profile (RAP) in patients with rheumatoid arthritis

Objective: To investigate the internal consistency, validity and responsiveness of the Rehabilitation Activities Profile (RAP; a rehabilitation tool structuring the multidisciplinary team care process) in patients with rheumatoid arthritis.

Methods: In 85 rheumatoid arthritis patients admitted to a rheumatology clinic the RAP was applied at admission, at discharge, and six weeks thereafter. Additional assessments included measures of physical and psychological functioning, disease activity and quality of life. The internal consistency of the RAP was determined with Cronbach's alpha. Associations between the RAP and other outcome measures were determined by Spearman rank correlation coefficients. Responsiveness measures included the standardized response mean (SRM), effect size (ES) and responsiveness ratio (RR).

Results: Cronbach's alpha of the RAP total score was 0.78. The RAP total score correlated significantly with all other outcome measures. The mean RAP total score improved from 15.2 to 13.2 at discharge (change -2.0; 95% confidence interval (CI) -3.4 to -0.7) and to 11.5 (change -3.7; 95% CI -3.9 to -1.5) six weeks thereafter. The responsiveness of the RAP total score was low (standardized response mean -0.34, effect size -0.30) to high (responsiveness ratio -0.87) at discharge and moderate (standardized response mean -0.54, effect size -0.55) to high (responsiveness ratio -1.56) six weeks thereafter.

Conclusions: The RAP appeared to be an internally consistent, valid and responsive measure to reflect limitations on the level of activities and participation in patients with rheumatoid arthritis admitted for multidisciplinary team care.

Can contextualization increase understanding during man-machine communication? A theory-driven study

The Internet offers unlimited possibilities for finding health information. However, the user is often faced with the problem of understanding it. Contextualization has a role to play in enhancing the user’s comprehension. We report on a study which addresses this issue, using a theoretical model of communication whose central theme is that of context. A randomized controlled experimental design was chosen, using as a test-bed the website SeniorGezond we had previously developed. The study was composed of a pre-test, the intervention with the website and a post-test. Participants (n=40) were randomly assigned to exposure or no exposure to contextualization with the website. Results show that contextualization increases understanding for non-knowledgeable users. Furthermore, the participant’s cognitive style was found to be a significant factor on understanding. We also found that participants bring their own contexts such as social context and psychological context to support their understanding.

The impact of the implementation of a rehabilitation tool on the contents of the communication during multidisciplinary team conferences in rheumatology

OBJECTIVE

Problems with multidisciplinary team conferences in health care include the exchange of too much (discipline-specific) information. The aim of this study was to investigate the effect of the implementation of a rehabilitation tool on the contents of communication during multidisciplinary team conferences in a rheumatology setting.

METHODS

All initial and follow-up team conferences of 25 consecutive patients with rheumatoid arthritis admitted to a day patient care ward were videotaped during a period before (period I) and after (period II) the introduction of a rehabilitation tool. The aims of the rehabilitation tool were to enhance discussions on the co-ordination of care rather than merely exchange of information. This was achieved by providing a framework for the setting and evaluation of common treatment goals and management strategies as well as accompanying electronic and printed records. For every team conference, the duration of time spent on three types of communication was recorded: (1) grounding regarding the patient's health status, (2) the making of practical arrangements by no more than two health professionals, and (3) the co-ordination of common treatment goals or management strategies. Comparisons of the proportions of time spent on the different types of communication between the two periods were done by means of the Mann-Whitney U-test.

RESULTS

Apart from the 25 initial team conferences in both periods, 86 and 71 follow-up team conferences were available in periods I and II, respectively. Regarding the initial team conferences, the proportion of time spent on grounding and practical arrangements was significantly smaller in period II than in period I. In addition, the proportion of time spent on common goals or management strategies was significantly greater in period II than in period I. For the follow-up team conferences, the proportion of time spent on practical arrangements was significantly smaller in period II, than in period I. Moreover, the proportions of time spent on the other types of communication did not differ significantly between the two periods.

CONCLUSION

The implementation of a rehabilitation tool including a computer application increased the proportion of time spent on the discussion of common treatment goals or management strategies during initial but not during follow-up team conferences in a day patient rheumatology clinic.

Anatomical and radiological evidence for the iliolumbar vein as an inferior lumbar venous system

The purpose of this work was to study an inferior lumbar venous system, which turned out to be the vertical component of the iliolumbar vein as defined in early works by Bourgery and Jacob, though there is a terminological ambiguity between the iliolumbar vein and the ascending lumbar vein in the literature. However, the iliolumbar vein is most commonly defined as a vein draining the fourth and fifth lumbar vertebral segments. Cadaver studies, including one injection-corrosion, and in vivo venograms were analyzed by visual inspection and measurements. Whether the injection was made via the axillary or the saphenous veins, the inferior lumbar vein was always filled, demonstrating that it is part of the vertebral venous system. An interruption or a plexiform shape of the venous system at the level of the third lumbar vertebra, and an increase in caliber as this vein runs downwards, allowed differentiating the inferior lumbar vein from the ascending lumbar vein. The inferior lumbar vein and the superior iliac vein drained into the iliac veins, either external or internal iliac vein, but typically into the common iliac vein, separately or with a single common trunk. This common trunk was observed in 92% of the dissected cases on the right side and in 46% on the left, whereas it was seen in 50% of the radiological studies on the right side and 52% on the left. Consequently, the inferior lumbar vein was the main component of the iliolumbar vein, and as such should be differentiated from the ascending lumbar vein.

[3D reconstruction of anterior internal vertebral venous plexus of a human fetus: a feasibility study]

Anterior internal vertebral venous plexus have been studied extensively due to their clinical importance in diseases of the spine and obstruction of the inferior vena cava. The aim of this feasibility study was to reconstruct in 3D the lower thoracic area of the anterior epidural space of a 69 mm (crown-rump) human fetus from the Rouvière Collection, circa 1927. Forty slices (spaced by 40 microm) at the level of the tenth and eleventh thoracic vertebrae, and their lower adjacent intervertebral discs, were reconstructed in 3D using the commercial software SURFdriver. In a preliminary study, we had found that the structures of the epidural space are already formed at this stage of development, and that they are comparable to the adult stage (2002). Reconstruction of the microscopic slices in 3D allowed to better visualize spatially the structures of the venous plexus and their anatomical relationships. This technique could be used as a complement to the classically used histological studies.

Pilot study of the development of a theory-based instrument to evaluate the communication process during multidisciplinary team conferences in rheumatology

BACKGROUND

Coordinated teams with multidisciplinary team conferences are generally seen as a solution to the management of complex health conditions. However, problems regarding the process of communication during team conferences are reported, such as the absence of a common language or viewpoint and the exchange of irrelevant or repeated information. To determine the outcome of interventions aimed at improving communication during team conferences, a reliable and valid assessment method is needed.

AIM

To investigate the feasibility of a theory-based measurement instrument for assessing the process of the communication during multidisciplinary team conferences in rheumatology.

METHOD

An observation instrument was developed based on communication theory. The instrument distinguishes three types of communication: (I) grounding activities, (II) coordination of non-team activities, and (III) coordination of team activities. To assess the process of communication during team conferences in a rheumatology clinic with inpatient and day patient facilities, team conferences were videotaped. To determine the inter-rater reliability, in 20 conferences concerning 10 patients with rheumatoid arthritis admitted to the inpatient unit, the instrument was applied by two investigators independently. Content validity was determined by analysing and comparing the results of initial and follow-up team conferences of 25 consecutive patients with rheumatoid arthritis admitted to the day patient unit (Wilcoxon signed rank test).

RESULTS

The inter-rater reliability was excellent with the intra-class correlation coefficients being >0.98 for both types I and III communications in 10 initial and 10 follow-up conferences (type II was not observed). An analysis of an additional 25 initial and 86 follow-up team conferences showed that time spent on grounding (type I) made up the greater part of the contents of communication (87% S.D. 14 and 60% S.D. 29 in initial and follow-up conferences, respectively), which is significantly more compared to time spent on co-ordination (p<0.001 and 0.02 for categories II and III, respectively). Moreover, significantly less time spent was spent on grounding in follow-up as compared to initial team conferences, whereas the time spent on coordination (type III) increased (both p-values<0.001).

CONCLUSION

This theory-based measurement instrument for describing and evaluating the communication process during team conferences proved to be reliable and valid in this pilot study. Its usefulness to detect changes in the communication process, e.g. after implementing systems for re-structuring team conferences mediated by ICT applications, should be further examined.

The impact of structuring multidisciplinary team conferences mediated by ICT in the treatment of patients with rheumatic diseases

Communication processes are pervasive in the daily practice of health professionals. Reorganizing these daily practices by introducing ICT, inevitably effects one or more communication processes. Understanding exactly what these effects are, is a major problem in designing and implementing ICT-applications. In this paper we present an analysis of these effects, based on a theory of communication processes. The concept of 'decoupling' is pivotal in our analysis. Based on the identified effects, and some preconditions that have to be met in order for these effects to take place, we derive a number of guidelines for reorganizing communication processes by means of applying ICT. The application of these quidelines will be demonstrated and discussed in the context of the reorganization of a team conference at the Rehabilitation Clinic of the Rheumatology Department of the Leiden University Medical Center (RCRD/LUMC), a multidisciplinary team care setting.

The impact of ICT on communication in healthcare

Communication processes are pervasive in the daily practice of health professionals. Reorganizing these daily practices by introducing ICT, inevitably effects one or more communication processes. Understanding exactly what these effects are, is a major problem in designing and implementing ICT-applications. In this paper we present an analysis of these effects, based on a theory of communication processes. The concept of 'decoupling' is pivotal in our analysis. Based on the identified effects, and some preconditions that have to be met in order for these effects to take place, we derive a number of guidelines for reorganizing communication processes by means of applying ICT. The application of these guidelines will be demonstrated and discussed in the context of the reorganization of a team conference at the Rehabilitation Clinic of the Rheumatology Department of the Leiden University Medical Center (RCRD/LUMC).

15O Radioactivity clearance is faster after intracarotid bolus injection of 15O-labeled oxyhemoglobin than after 15O-water injection

The authors tested the hypothesis that the oxygen content of brain tissue is negligible by injecting an intracarotid bolus of 15O-labeled tracer into rats. Under the hypothesis, the clearance rates of 15O radioactivity from the brain after injections of both 15O-labeled water (H(2)15O) and 15O-labeled oxyhemoglobin (HbO15O) should be identical. However, the logarithmic slope of the 15O radioactivity curve after HbO15O injection (0.494 +/- 0.071 min-1) was steeper than that after H(2)15O injection (0.406 +/- 0.038 min-1) (P<0.001, n = 13), where the time range used in the comparison was between 60 and 120 seconds after the injection. A possible interpretation of this result is that nonmetabolized O15O may dwell in the brain tissue for a finite period of time before it is eventually metabolized or returned to the blood stream unaltered. These findings contradict assumptions made by models currently used to measure cerebral oxygen metabolism.

Improving the quality of communication in healthcare

In this paper we present an assessment instrument for evaluating the quality of communication processes in health care. This instrument is based on communication theory, and does not only indicate the level of quality, but also explains it. This makes it also useful as a design tool in reorganising communication processes, in order to make them more effective. Such a tool is highly needed when Information and Communication Technology is applied in health care to support communication between professionals. The instrument is demonstrated for a case in multidisciplinary team care.

Use cases and DEMO: aligning functional features of ICT-infrastructure to business processes

OBJECTIVES

The proper alignment of functional features of the ICT-infrastructure to business processes is a major challenge in health care organisations. This alignment takes into account that the organisational structure not only shapes the ICT-infrastructure, but that the inverse also holds. To solve the alignment problem, relevant features of the ICT-infrastructure should be derived from the organisational structure and the influence of this envisaged ICT to the work practices should be pointed out. The objective of our study was to develop a method to solve this alignment problem.

METHODS

In a previous study we demonstrated the appropriateness of the business process modelling methodology Dynamic Essential Modelling of Organizations (DEMO). A proven and widely used modelling language for expressing functional features is Unified Modelling Language (UML). In the context of a specific case study at the University Medical Centre Utrecht in the Netherlands we investigated if the combined use of DEMO and UML could solve the alignment problem.

RESULTS AND CONCLUSION

The study demonstrated that the DEMO models were suited as a starting point in deriving system functionality by using the use case concept of UML. Further, the case study demonstrated that in using this approach for the alignment problem, insight is gained into the mutual influence of ICT-infrastructure and organisation structure: (a) specification of independent, re-usable components-as a set of related functionalities-is realised, and (b) a helpful representation of the current and future work practice is provided for in relation to the envisaged ICT support.

Communication support: a challenge for ICT in health care

Communication makes up a very important part of the daily practice of health professionals. Current trends in health care indicate that this will even increase. However, the explicit application of Information and Communication Technologies (ICT) in order to support communication is relatively rare. This leaves a great potential of ICT in health care unused. The clinical informatics group at the Leiden University Medical Centre has established a research program which aims at eliciting, analysing, and specifying requirements for communication supporting ICT-applications in health care. Several research projects are part of this program already. Two of these, that focus on supporting a specific kind of health professional/client communication, are discussed in this paper against the background of the research program.

Integration of information systems: assessing its quality

Due to organizational and technological changes the need for integrating information systems within healthcare institutions, has increased enormously. Although the technical means for systems integration have definitely matured, integration methodologies are still in their infancy. Two important questions regarding systems integration are hardly ever addressed in a systematic way: how to derive integration requirements, and how to check whether the requirements are met in a given integrated system. These two questions must be answered if we want to assess or improve the quality of integration of a given set of systems. In this article we present a nine-step method for deriving integration requirements from a business process model, and we assess the quality of integration of a given integrated system against these requirements. The method is demonstrated by elaborating two case studies from the health care domain.

Sensorimotor organization in patients who have undergone hemispherectomy: a study with (15)O-water PET and somatosensory evoked potentials

To identify cortical structures that subserve residual motor and sensory function in patients with congenital hemiparesis due to a porencephalic cyst, we examined, using [(15)O]H2O, PET and somatosensory evoked potentials (SEPs) in three patients with left-sided hemiparesis who had undergone hemispherectomy. Motor stimulation of the affected hand produced ipsilateral activation in the premotor area in all patients, the SMA in two patients, and SII in two patients. Vibrotactile stimulation resulted in activation of the ipsilateral SII in all subjects. Median nerve stimulation of the affected hand produced ipsilateral long-latency SEPs in fronto-centro-parietal areas, whereas stimulation of the non-affected hand produced normal early cortical potentials in the contralateral hemisphere. Our results suggest that residual function in the paretic hand is warranted through non-primary motor and sensory areas, and higher order associative areas in the intact hemisphere.

A process view of medical practice by modeling communicative acts

The need of an electronic patient record with a process view on medical care is widely acknowledged. Characteristics of DEMO (Dynamic Essential Modeling of Organizations) suggest that with this methodology an adequate process view of medical practice can be obtained. In applying DEMO to the care process of the emergency department at the University Medical Centre Utrecht, it was investigated if DEMO fulfilled our expectations. This practical application showed that DEMO yields an adequate process view by a clear and comprehensible view of the core processes, responsibilities, co-ordination of activities, and a clear description of causal and conditional relations between activities.

Component-based development for supporting workflows in hospitals

Changing requirements for health care information systems force the development of an open, modular architecture in which components can be integrated. This offers a flexible means for integrating different (heterogeneous) systems used by different users. Selecting the components to integrate, and determining the 'right way' to integrate them, necessitates a shift in focus towards the business process to be supported. The realization of such an open, modular architecture is a difficult task. It consists of breaking down existing systems in required components and integrating these and other components. Many authors on component-based development strategies focus attention on the technological issues of component integration (do we use CORBA, DCOM/OLE, or EDI?). This paper presents an approach for determining the required components, and the way they have to be integrated, based on an analysis of the business process to be supported, and the information systems currently used.

Constructing an enterprise viewpoint: evaluation of four business modelling techniques

Business process modelling is presented as an important first step in the process of designing a distributed system by integrating pre-existing components. The elements describing a business process are derived from the ODP-enterprise viewpoint language. One of the viewpoints distinguished in the Open Distributed Processing standard is the enterprise viewpoint. This viewpoint describes the organizational context in which the distributed system to be constructed will be used. In this paper we will review four business modelling techniques and their suitability for expressing the enterprise viewpoint is evaluated.

Integrating information systems in medicine: a reference model for middleware

This paper addresses the problem of integrating healthcare information systems, from a technological viewpoint. We propose to take the concept of an ¿integration service' as an elementary concept in discussing the problem of integration. We then propose a taxonomy for grouping integration services according to their functionality and their domain specificity. The use of this taxonomy for decomposing an integration problem into (less complex) sub-problems is demonstrated. Finally, a sequence of steps to be taken in solving an integration problem is discussed.

L-arginine infusion increases basal but not activated cerebral blood flow in humans

Nitric oxide is a potent vasodilator. Infusion of its precursor, L-arginine, results in increased cerebral blood flow (CBF) in experimental animals. We examined the effects of L-arginine infusion on CBF in humans using positron emission tomography and the quantitative H2(15)O method. Six subjects received 500 ml of 0.9% NaCl solution, and six subjects received an infusion of L-arginine (16.7 mg/kg/min; 500 mg/kg). Before and after the i.v. infusion, paired CBF measurements were performed at baseline and with vibrotactile stimulation of the right hand. In scans performed without vibrotactile stimulation, mean whole-brain CBF increased from 34.9 +/- 3.7 ml 100 g-1 min-1 to 38.2 +/- 4.4 ml 100 g-1 min-1. (9.5%; p < 0.005) after L-arginine infusion. The temporal pattern of CBF changes differed from that of plasma growth hormone and insulin levels and of arterial pH. In contrast, in the saline group, mean whole-brain CBF did not change significantly (35.8 +/- 5.9 ml 100 g-1 min-1 to 35.9 +/- 6.4 ml 100 g-1 min-1; 0.3%). Vibrotactile stimulation produced significant focal increases in CBF, which were unaffected by L-arginine infusion. L-arginine infusion was associated with an increase in plasma L-citrulline, a byproduct of nitric oxide synthesis.

Supporting shared care for diabetes patients. The synapses solution

In this paper we discuss the construction of a Federated Health Care Record server within the context of the European R&D project Synapses. We describe the system using the five ODP viewpoints. From an analysis of the business process to be supported by the distributed system (the shared care for diabetes patients) requirements for the server are derived.

Migration towards a component based HIS architecture

Changing requirements for health care information systems force the development of an open, modular architecture in which components can be integrated. This offers a flexible means for integrating different (heterogeneous) systems used by different users. Migration towards such an open, modular architecture is a difficult task. It consists of breaking down existing systems in components and integrating these components. Many authors on migration strategies focus attention on the ordering of the steps to be taken without detailing how these steps were arrived at. This paper presents a more rigorous approach for deriving a migration strategy.

The complexity of transactions: a means for assessing interoperability

Interoperability seems to be a major focal point of the activities within the Informatics Society in general, and the Medical Informatics society in particular. In both Europe and the USA standardization efforts are pursued in order to enable interoperability. However, even if the technical requirements are met, interoperability is sometimes not feasible because the message exchange needed is too complex. This complexity is influenced by at least three factors: the volume of the data to be exchanged, the functionality of the information exchange, and the communication standard adopted.