REST-based sensor networks with OData

RESTful services gained a lot of attention recently, even in the enterprise world, which is traditionally more web-service centric. Data centric RESfFul services, as previously mainly known in web environments, established themselves as a second paradigm complementing functional WSDL-based SOA. In the Internet of Things, and in particular when talking about sensor motes, the Constraint Application Protocol (CoAP) is currently in the focus of both research and industry. In the enterprise world a protocol called OData (Open Data Protocol) is becoming the future RESTful data access standard. To integrate sensor motes seamlessly into enterprise networks, an embedded OData implementation on top of CoAP is desirable, not requiring an intermediary gateway device. In this paper we introduce and evaluate an embedded OData implementation. We evaluate the OData protocol in terms of performance and energy consumption, considering different data encodings, and compare it to a pure CoAP implementation. We were able to demonstrate that the additional resources needed for an OData/JSON implementation are reasonable when aiming for enterprise interoperability, where OData is suggested to solve both the semantic and technical interoperability problems we have today when connecting systems

Percutaneous access of the epicardial space for mapping ventricular and supraventricular arrhythmias in patients with and without prior cardiac surgery

There is a paucity of data on the success rates of achieving percutaneous epicardial access in different groups of patients.

Differences in access and patient outcomes across antiretroviral treatment clinics in the Free State province: a prospective cohort study

Objective. To assess differences in access to antiretroviral treatment (ART) and patient outcomes across public sector treatment facilities in the Free State province, South Africa. Design. Prospective cohort study with retrospective database linkage. We analysed data on patients enrolled in the treatment programme across 36 facilities between May 2004 and December 2007, and assessed percentage initiating ART and percentage dead at 1 year after enrolment. Multivariable logistic regression was used to estimate associations of facility-level and patient-level characteristics with both mortality and treatment status. Results. Of 44 866 patients enrolled, 15 219 initiated treatment within 1 year; 8 778 died within 1 year, 7 286 before accessing ART. Outcomes at 1 year varied greatly across facilities and more variability was explained by facility-level factors than by patient-level factors. The odds of starting treatment within 1 year improved over calendar time. Patients enrolled in facilities with treatment initiation available on site had higher odds of starting treatment and lower odds of death at 1 year compared with those enrolled in facilities that did not offer treatment initiation. Patients were less likely to start treatment if they were male, severely immunosuppressed (CD4 count ≤50 cells/μl), or underweight (<50 kg). Men were also more likely to die in the first year after enrolment. Conclusions. Although increasing numbers of patients started ART between 2004 and 2007, many patients died before accessing ART. Patient outcomes could be improved by decentralisation of treatment services, fast-tracking the most immunodeficient patients and improving access, especially for men.

Evaluating the Impact of the Number of Access Points in Mobile Robots Localization Using Artificial Neural Networks

Localization is information of fundamental importance to carry out various tasks in the mobile robotic area. The exact degree of precision required in the localization depends on the nature of the task. The GPS provides global position estimation but is restricted to outdoor environments and has an inherent imprecision of a few meters. In indoor spaces, other sensors like lasers and cameras are commonly used for position estimation, but these require landmarks (or maps) in the environment and a fair amount of computation to process complex algorithms. These sensors also have a limited field of vision. Currently, Wireless Networks (WN) are widely available in indoor environments and can allow efficient global localization that requires relatively low computing resources. However, the inherent instability in the wireless signal prevents it from being used for very accurate position estimation. The growth in the number of Access Points (AP) increases the overlap signals areas and this could be a useful means of improving the precision of the localization. In this paper we evaluate the impact of the number of Access Points in mobile nodes localization using Artificial Neural Networks (ANN). We use three to eight APs as a source signal and show how the ANNs learn and generalize the data. Added to this, we evaluate the robustness of the ANNs and evaluate a heuristic to try to decrease the error in the localization. In order to validate our approach several ANNs topologies have been evaluated in experimental tests that were conducted with a mobile node in an indoor space.

Percutaneous coronary interventions in Europe: prevalence, numerical estimates, and projections based on data up to 2004

AIMS: A registry mandated by the European Society of Cardiology collects data on trends in interventional cardiology within Europe. Special interest focuses on relative increases and ratios in new techniques and their distributions across Europe. We report the data through 2004 and give an overview of the development of coronary interventions since the first data collection in 1992. METHODS AND RESULTS: Questionnaires were distributed yearly to delegates of all national societies of cardiology represented in the European Society of Cardiology. The goal was to collect the case numbers of all local institutions and operators. The overall numbers of coronary angiographies increased from 1992 to 2004 from 684 000 to 2 238 000 (from 1250 to 3930 per million inhabitants). The respective numbers for percutaneous coronary interventions (PCIs) and coronary stenting procedures increased from 184 000 to 885 000 (from 335 to 1550) and from 3000 to 770 000 (from 5 to 1350), respectively. Germany was the most active country with 712 000 angiographies (8600), 249 000 angioplasties (3000), and 200 000 stenting procedures (2400) in 2004. The indication has shifted towards acute coronary syndromes, as demonstrated by rising rates of interventions for acute myocardial infarction over the last decade. The procedures are more readily performed and perceived safer, as shown by increasing rate of "ad hoc" PCIs and decreasing need for emergency coronary artery bypass grafting (CABG). In 2004, the use of drug-eluting stents continued to rise. However, an enormous variability is reported with the highest rate in Switzerland (70%). If the rate of progression remains constant until 2010 the projected number of coronary angiographies will be over three million, and the number of PCIs about 1.5 million with a stenting rate of almost 100%. CONCLUSION: Interventional cardiology in Europe is ever expanding. New coronary revascularization procedures, alternative or complementary to balloon angioplasty, have come and gone. Only stenting has stood the test of time and matured to the default technique. Facilitated access to PCI, more complete and earlier detection of coronary artery disease promise continued growth of the procedure despite the uncontested success of prevention.

Arterial access through the right subclavian artery in surgery of the aortic arch improves neurologic outcome and mid-term quality of life

BACKGROUND: We have shown that selective antegrade cerebral perfusion improves mid-term quality of life in patients undergoing surgical repair for acute type A aortic dissection and aortic aneurysms. The aim of the study was to assess the impact of continuous cerebral perfusion through the right subclavian artery on immediate outcome and quality of life. METHODS: Perioperative data of 567 consecutive patients who underwent surgery of the aortic arch using deep hypothermic circulatory arrest have been analyzed. Patients were divided into three groups, according to the management of cerebral protection. Three hundred eighty-seven patients (68.3%) had deep hypothermic circulatory arrest with pharmacologic protection with pentothal only, 91 (16.0%) had selective antegrade cerebral perfusion and pentothal, and 89 (15.7%) had continuous cerebral perfusion through the right subclavian artery and pentothal. All in-hospital data were assessed, and quality of life was analyzed prospectively 2.4 +/- 1.2 years after surgery with the Short Form-36 Health Survey Questionnaire. RESULTS: Major perioperative cerebrovascular injuries were observed in 1.1% of the patients with continuous cerebral perfusion through the right subclavian artery, compared with 9.8% with selective antegrade cerebral perfusion (p < 0.001) and 6.5% in the group with no antegrade cerebral perfusion (p = 0.007). Average quality of life after an arrest time between 30 and 50 minutes with continuous cerebral perfusion through the right subclavian artery was significantly better than selective antegrade cerebral perfusion (90.2 +/- 12.1 versus 74.4 +/- 40.7; p = 0.015). CONCLUSIONS: Continuous cerebral perfusion through the right subclavian artery improves considerably perioperative brain protection during deep hypothermic circulatory arrest. Irreversible perioperative neurologic complications can be significantly reduced and duration of deep hypothermic circulatory arrest can be extended up to 50 minutes without impairment in quality of life.

Transapical access closure: the TA PLUG device

OBJECTIVES Percutaneous closure of the transapical (TA) access site for large-calibre devices is an unsolved issue. We report the first experimental data on the TA PLUG device for true-percutaneous closure following large apical access for transcatheter aortic valve implantation. METHODS The TA PLUG, a self-sealing full-core closure device, was implanted in an acute animal study in six pigs (60.2 ± 0.7 kg). All the pigs received 100 IU/kg of heparin. The targeted activated clotting time was left to normalize spontaneously. After accessing the left ventricular apex with a 39 French introducer, the closure plug device was delivered with a 33 French over-the-wire system under fluoroscopic guidance into the apex. Time to full haemostasis as well as rate of bleeding was recorded. Self-anchoring properties were assessed by haemodynamic push stress under adrenalin challenge. An additional feasibility study was conducted in four pigs (58.4 ± 1.1 kg) with full surgical exposure of the apex, and assessed device anchoring by pull-force measurements with 0.5 Newton (N) increments. All the animals were electively sacrified. Post-mortem analysis of the heart was performed and the renal embolic index assessed. RESULTS Of six apical closure devices, five were correctly inserted and fully deployed at the first attempt. One became blocked in the delivery system and was placed successfully at the second attempt. In all the animals, complete haemostasis was immediate and no leak was recorded during the 5-h observation period. Neither leak nor any device dislodgement was observed under haemodynamic push stress with repeated left ventricular peak pressure of up to 220 mmHg. In the feasibility study assessing pull-stressing, device migration occurred at a force of 3.3 ± 0.5 N corresponding to 247.5 mmHg. Post-mortem analyses confirmed full expansion of all devices at the intended target. No macroscopic damage was identified at the surrounding myocardium. The renal embolic index was zero. CONCLUSIONS True-percutaneous left ventricular apex closure following large access is feasible with the self-sealing TA PLUG. The device allows for immediate haemostasis and a reliable anchoring in the acute animal setting. This is the first report of a true-percutaneous closure for large-calibre transcatheter aortic valve implantation access.

The Virtual Skeleton Database: An Open Access Repository for Biomedical Research and Collaboration

Background: Statistical shape models are widely used in biomedical research. They are routinely implemented for automatic image segmentation or object identification in medical images. In these fields, however, the acquisition of the large training datasets, required to develop these models, is usually a time-consuming process. Even after this effort, the collections of datasets are often lost or mishandled resulting in replication of work. Objective: To solve these problems, the Virtual Skeleton Database (VSD) is proposed as a centralized storage system where the data necessary to build statistical shape models can be stored and shared. Methods: The VSD provides an online repository system tailored to the needs of the medical research community. The processing of the most common image file types, a statistical shape model framework, and an ontology-based search provide the generic tools to store, exchange, and retrieve digital medical datasets. The hosted data are accessible to the community, and collaborative research catalyzes their productivity. Results: To illustrate the need for an online repository for medical research, three exemplary projects of the VSD are presented: (1) an international collaboration to achieve improvement in cochlear surgery and implant optimization, (2) a population-based analysis of femoral fracture risk between genders, and (3) an online application developed for the evaluation and comparison of the segmentation of brain tumors. Conclusions: The VSD is a novel system for scientific collaboration for the medical image community with a data-centric concept and semantically driven search option for anatomical structures. The repository has been proven to be a useful tool for collaborative model building, as a resource for biomechanical population studies, or to enhance segmentation algorithms.

In vitro accuracy evaluation of image-guided robot system for direct cochlear access

HYPOTHESIS A previously developed image-guided robot system can safely drill a tunnel from the lateral mastoid surface, through the facial recess, to the middle ear, as a viable alternative to conventional mastoidectomy for cochlear electrode insertion. BACKGROUND Direct cochlear access (DCA) provides a minimally invasive tunnel from the lateral surface of the mastoid through the facial recess to the middle ear for cochlear electrode insertion. A safe and effective tunnel drilled through the narrow facial recess requires a highly accurate image-guided surgical system. Previous attempts have relied on patient-specific templates and robotic systems to guide drilling tools. In this study, we report on improvements made to an image-guided surgical robot system developed specifically for this purpose and the resulting accuracy achieved in vitro. MATERIALS AND METHODS The proposed image-guided robotic DCA procedure was carried out bilaterally on 4 whole head cadaver specimens. Specimens were implanted with titanium fiducial markers and imaged with cone-beam CT. A preoperative plan was created using a custom software package wherein relevant anatomical structures of the facial recess were segmented, and a drill trajectory targeting the round window was defined. Patient-to-image registration was performed with the custom robot system to reference the preoperative plan, and the DCA tunnel was drilled in 3 stages with progressively longer drill bits. The position of the drilled tunnel was defined as a line fitted to a point cloud of the segmented tunnel using principle component analysis (PCA function in MatLab). The accuracy of the DCA was then assessed by coregistering preoperative and postoperative image data and measuring the deviation of the drilled tunnel from the plan. The final step of electrode insertion was also performed through the DCA tunnel after manual removal of the promontory through the external auditory canal. RESULTS Drilling error was defined as the lateral deviation of the tool in the plane perpendicular to the drill axis (excluding depth error). Errors of 0.08 ± 0.05 mm and 0.15 ± 0.08 mm were measured on the lateral mastoid surface and at the target on the round window, respectively (n =8). Full electrode insertion was possible for 7 cases. In 1 case, the electrode was partially inserted with 1 contact pair external to the cochlea. CONCLUSION The purpose-built robot system was able to perform a safe and reliable DCA for cochlear implantation. The workflow implemented in this study mimics the envisioned clinical procedure showing the feasibility of future clinical implementation.

Streaming Support for Data Intensive Cloud-Based Sequence Analysis

Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS) technology. Based on the concepts of “resources-on-demand” and “pay-as-you-go”, scientists with no or limited infrastructure can have access to scalable and cost-effective computational resources. However, the large size of NGS data causes a significant data transfer latency from the client’s site to the cloud, which presents a bottleneck for using cloud computing services. In this paper, we provide a streaming-based scheme to overcome this problem, where the NGS data is processed while being transferred to the cloud. Our scheme targets the wide class of NGS data analysis tasks, where the NGS sequences can be processed independently from one another. We also provide the elastream package that supports the use of this scheme with individual analysis programs or with workflow systems. Experiments presented in this paper show that our solution mitigates the effect of data transfer latency and saves both time and cost of computation.

Privacy Preserving Probabilistic Record Linkage (P3RL): a novel method for linking existing health-related data and maintaining participant confidentiality.

BACKGROUND Record linkage of existing individual health care data is an efficient way to answer important epidemiological research questions. Reuse of individual health-related data faces several problems: Either a unique personal identifier, like social security number, is not available or non-unique person identifiable information, like names, are privacy protected and cannot be accessed. A solution to protect privacy in probabilistic record linkages is to encrypt these sensitive information. Unfortunately, encrypted hash codes of two names differ completely if the plain names differ only by a single character. Therefore, standard encryption methods cannot be applied. To overcome these challenges, we developed the Privacy Preserving Probabilistic Record Linkage (P3RL) method. METHODS In this Privacy Preserving Probabilistic Record Linkage method we apply a three-party protocol, with two sites collecting individual data and an independent trusted linkage center as the third partner. Our method consists of three main steps: pre-processing, encryption and probabilistic record linkage. Data pre-processing and encryption are done at the sites by local personnel. To guarantee similar quality and format of variables and identical encryption procedure at each site, the linkage center generates semi-automated pre-processing and encryption templates. To retrieve information (i.e. data structure) for the creation of templates without ever accessing plain person identifiable information, we introduced a novel method of data masking. Sensitive string variables are encrypted using Bloom filters, which enables calculation of similarity coefficients. For date variables, we developed special encryption procedures to handle the most common date errors. The linkage center performs probabilistic record linkage with encrypted person identifiable information and plain non-sensitive variables. RESULTS In this paper we describe step by step how to link existing health-related data using encryption methods to preserve privacy of persons in the study. CONCLUSION Privacy Preserving Probabilistic Record linkage expands record linkage facilities in settings where a unique identifier is unavailable and/or regulations restrict access to the non-unique person identifiable information needed to link existing health-related data sets. Automated pre-processing and encryption fully protect sensitive information ensuring participant confidentiality. This method is suitable not just for epidemiological research but also for any setting with similar challenges.

PDB-Explorer: a web-based interactive map of the protein data bank in shape space

Background The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. Methods A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. Results The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. Conclusion A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3D-fingerprint for proteins and implemented in a web-based database exploration tool comprising an interactive color-coded map of the PDB chemical space and a nearest neighbor search tool. The PDB-Explorer website is freely available at www.​cheminfo.​org/​pdbexplorer and represents an unprecedented opportunity to interactively visualize and explore the structural diversity of the PDB.