ABCtoolbox: a versatile toolkit for approximate Bayesian computations

Background The estimation of demographic parameters from genetic data often requires the computation of likelihoods. However, the likelihood function is computationally intractable for many realistic evolutionary models, and the use of Bayesian inference has therefore been limited to very simple models. The situation changed recently with the advent of Approximate Bayesian Computation (ABC) algorithms allowing one to obtain parameter posterior distributions based on simulations not requiring likelihood computations. Results Here we present ABCtoolbox, a series of open source programs to perform Approximate Bayesian Computations (ABC). It implements various ABC algorithms including rejection sampling, MCMC without likelihood, a Particle-based sampler and ABC-GLM. ABCtoolbox is bundled with, but not limited to, a program that allows parameter inference in a population genetics context and the simultaneous use of different types of markers with different ploidy levels. In addition, ABCtoolbox can also interact with most simulation and summary statistics computation programs. The usability of the ABCtoolbox is demonstrated by inferring the evolutionary history of two evolutionary lineages of Microtus arvalis. Using nuclear microsatellites and mitochondrial sequence data in the same estimation procedure enabled us to infer sex-specific population sizes and migration rates and to find that males show smaller population sizes but much higher levels of migration than females. Conclusion ABCtoolbox allows a user to perform all the necessary steps of a full ABC analysis, from parameter sampling from prior distributions, data simulations, computation of summary statistics, estimation of posterior distributions, model choice, validation of the estimation procedure, and visualization of the results.

Deep brain stimulation of the globus pallidus internal improves symptoms of chorea-acanthocytosis

Chorea-acanthocytosis is a rare autosomal recessive disorder. To date, treatment is only symptomatic and supportive. Results from the few reports of chorea-acanthocytosis patients treated with deep brain stimulation (DBS) have been inconsistent. We present case reports for two patients with chorea-acanthocytosis who received DBS treatment and compare the outcomes with results from the literature. Both patients showed the typical clinical features of chorea-acanthocytosis with motor symptoms resistant to medical treatment. Chorea was significantly improved following low-frequency DBS treatment in both patients. However, dystonia was only mildly improved. Four chorea-acanthocytosis patients treated with DBS treatment have been reported in the literature. One patient had improvement with low-frequency DBS stimulation, while another two had improvement with higher-frequency DBS. One patient, however, did not improve with either low-frequency or high-frequency DBS. Bilateral DBS to the GPi can improve chorea and dystonia in some patients with intractable chorea-acanthocytosis. However, selection criteria for the most promising candidates must be defined, and the long-term benefits evaluated in clinical studies.

Chronic stimulation of the globus pallidus internus for treatment of non-dYT1 generalized dystonia and choreoathetosis: 2-year follow up

OBJECT: The authors studied the long-term efficacy of deep brain stimulation (DBS) of the posteroventral lateral globus pallidus internus up to 2 years postoperatively in patients with primary non-DYT1 generalized dystonia or choreoathetosis. The results are briefly compared with those reported for DBS in DYT1 dystonia (Oppenheim dystonia), which is caused by the DYT1 gene. METHODS: Enrollment in this prospective expanded pilot study was limited to adult patients with severely disabling, medically refractory non-DYT1 generalized dystonia or choreoathetosis. Six consecutive patients underwent follow-up examinations at defined intervals of 3 months, 1 year, and 2 years postsurgery. There were five women and one man, and their mean age at surgery was 45.5 years. Formal assessments included both the Burke-Fahn-Marsden dystonia scale and the recently developed Unified Dystonia Rating Scale. Two patients had primary generalized non-DYT1 dystonia, and four suffered from choreoathetosis secondary to infantile cerebral palsy. Bilateral quadripolar DBS electrodes were implanted in all instances, except in one patient with markedly asymmetrical symptoms. There were no adverse events related to surgery. The Burke-Fahn-Marsden scores in the two patients with generalized dystonia improved by 78 and 71% at 3 months, by 82 and 69% at 1 year, and by 78 and 70% at 2 years postoperatively. This was paralleled by marked amelioration of disability scores. The mean improvement in Burke-Fahn-Marsden scores in patients with choreoathetosis was 12% at 3 months, 29% at 1 year, and 23% at 2 years postoperatively, which was not significant. Two of these patients thought that they had achieved marked improvement at 2 years postoperatively, although results of objective evaluations were less impressive. In these two patients there was a minor but stable improvement in disability scores. All patients had an improvement in pain scores at the 2-year follow-up review. Medication was tapered off in both patients with generalized dystonia and reduced in two of the patients with choreoathetosis. All stimulation-induced side effects were reversible on adjustment of the DBS settings. Energy consumption of the batteries was considerably higher than in patients with Parkinson disease. CONCLUSIONS: Chronic pallidal DBS is a safe and effective procedure in generalized non-DYT1 dystonia, and it may become the procedure of choice in patients with medically refractory dystonia. Postoperative improvement of choreoathetosis is more modest and varied, and subjective ratings of outcome may exceed objective evaluations.

Promoting palliative care in the community: production of the primary palliative care toolkit by the European Association of Palliative Care Taskforce in primary palliative care

BACKGROUND A multidisciplinary European Association of Palliative Care Taskforce was established to scope the extent of and learn what facilitates and hinders the development of palliative care in the community across Europe. AIM To document the barriers and facilitators for palliative care in the community and to produce a resource toolkit that palliative care specialists, primary care health professionals or policymakers, service developers, educationalists and national groups more generally could use to facilitate the development of palliative care in their own country. DESIGN (1) A survey instrument was sent to general practitioners with knowledge of palliative care services in the community in a diverse sample of European countries. We also conducted an international systematic review of tools used to identify people for palliative care in the community. (2) A draft toolkit was then constructed suggesting how individual countries might best address these issues, and an online survey was then set up for general practitioners and specialists to make comments. Iterations of the toolkit were then presented at international palliative care and primary care conferences. RESULTS Being unable to identify appropriate patients for palliative care in the community was a major barrier internationally. The systematic review identified tools that might be used to help address this. Various facilitators such as national strategies were identified. A primary palliative care toolkit has been produced and refined, together with associated guidance. CONCLUSION Many barriers and facilitators were identified. The primary palliative care toolkit can help community-based palliative care services to be established nationally.

A versatile toolkit to produce sensitive FRET biosensors to visualize signaling in time and space

Genetically encoded, ratiometric biosensors based on fluorescence resonance energy transfer (FRET) are powerful tools to study the spatiotemporal dynamics of cell signaling. However, many biosensors lack sensitivity. We present a biosensor library that contains circularly permutated mutants for both the donor and acceptor fluorophores, which alter the orientation of the dipoles and thus better accommodate structural constraints imposed by different signaling molecules while maintaining FRET efficiency. Our strategy improved the brightness and dynamic range of preexisting RhoA and extracellular signal-regulated protein kinase (ERK) biosensors. Using the improved RhoA biosensor, we found micrometer-sized zones of RhoA activity at the tip of F-actin bundles in growth cone filopodia during neurite extension, whereas RhoA was globally activated throughout collapsing growth cones. RhoA was also activated in filopodia and protruding membranes at the leading edge of motile fibroblasts. Using the improved ERK biosensor, we simultaneously measured ERK activation dynamics in multiple cells using low-magnification microscopy and performed in vivo FRET imaging in zebrafish. Thus, we provide a construction toolkit consisting of a vector set, which enables facile generation of sensitive biosensors.

Distribution Map

Understanding large software systems is a challenging task, and to support it many approaches have been developed. Often, the result of these approaches categorize existing entities into new groups or associates them with mutually exclusive properties. In this paper we present the Distribution Map as a generic technique to visualize and analyze this type of result. Our technique is based on the notion of focus, which shows whether a property is well-encapsulated or cross-cutting, and the notion of spread, which shows whether the property is present in several parts of the system. We present a basic visualization and complement it with measurements that quantify focus and spread. To validate our technique we show evidence of applying it on the result sets of different analysis approaches. As a conclusion we propose that the Distribution Map technique should belong to any reverse engineering toolkit.

[Surgery for Parkinson's disease]

Surgery for Parkinson's Disease (PD) is being increasingly used. The main reason for this renewal in surgical treatment for PD is the "deep brain stimulation" (DBS) that replaced the previously used stereotactic lesions in most centers. DBS allows a focal specific electrical stimulation of basal ganglia target instead of an irreversible lesion. Mainly bilateral DBS of the nucleus subthalamicus is now an established surgical treatment for PD. But DBS of the Globus pallidus internus and of the thalamus should still be considered in selected patients. DBS is an efficient treatment for motor complication of PD that can no longer be controlled by drug treatment. Dyskinesia, bradykinesia, tremor and rigor can be improved by DBS and the medication can be reduced. It is still unclear, however, how the improvement in motor symptoms affects quality of life in the long term. Furthermore, patients with severe cognitive and psychiatric symptoms as well as patients with severe axial symptoms should not be operated since these symptoms may worsen after surgery.

Long-term pallidal deep brain stimulation in patients with advanced Parkinson disease: 1-year follow-up study

OBJECT: The goal of this study was to investigate the efficacy of long-term deep brain stimulation (DBS) of the posteroventral lateral globus pallidus internus (GPi) accomplished using a single-contact monopolar electrode in patients with advanced Parkinson disease (PD). METHODS: Sixteen patients suffering from severe PD and levodopa-induced side effects such as dyskinesias and on-off fluctuations were enrolled in a prospective study protocol. There were six women and 10 men and their mean age at surgery was 65 years. All patients underwent implantation of a monopolar electrode in the posteroventral lateral GPi. Initially, nine patients received unilateral stimulation. Three of these patients underwent contralateral surgery at a later time. Ten patients received bilateral stimulation (contemporaneous bilateral surgery was performed in seven patients and staged bilateral surgery in the three patients who had received unilateral stimulation initially). Formal assessments were performed during both off-medication and on-medication (levodopa) periods preoperatively, and at 3 and 12 months postoperatively. There were no serious complications related to surgery or to DBS. Two transient adverse events occurred: in one patient a small pallidal hematoma developed, resulting in a prolonged micropallidotomy effect, and in another patient a subcutaneous hemorrhage occurred at the site of the pacemaker. In patients who received unilateral DBS, the Unified Parkinson's Disease Rating Scale activities of daily living (ADL) score during the off-levodopa period decreased from 30.8 at baseline to 20.4 at 3 months (34% improvement) and 20.6 at 12 months (33% improvement) postoperatively. The motor score during the off period improved from 57.2 at baseline to 35.2 at 3 months (38% improvement) and 35.3 at 12 months (38% improvement) postoperatively. Bilateral DBS resulted in a reduction in the ADL score during the off period from 34.9 at baseline to 22.3 at 3 months (36% improvement) and 22.9 at 12 months (34% improvement). The motor score for the off period changed from 63.4 at baseline to 40.3 at 3 months (36% improvement) and 37.5 at 12 months (41% improvement). In addition, there were significant improvements in patients' symptoms during the on period and in on-off motor fluctuations. CONCLUSIONS: Pallidal DBS accomplished using a monopolar electrode is a safe and effective procedure for treatment of advanced PD. Compared with pallidotomy, the advantages of pallidal DBS lie in its reversibility and the option to perform bilateral surgery in one session. Comparative studies in which DBS is applied to other targets are needed.

Localization of DJ-1 mRNA in the mouse brain

DJ-1 is mutated in autosomal recessive, early onset Parkinson's disease but the exact localization of the DJ-1 gene product in the mammalian brain is largely unknown. We aimed to evaluate the DJ-1 mRNA expression pattern in the mouse brain. Serial coronal sections of brains of five male and five female adult mice were investigated by using in situ hybridization with a DJ-1 specific 35S-labeled oligonucleotide probe. Hybridized sections were analyzed after exposure to autoradiography films and after coating with a photographic emulsion. DJ-1 was heterogeneously expressed throughout the mouse central nervous system. A high expression of DJ-1 mRNA was detected in neuronal and non-neuronal populations of several structures of the motor system such as the substantia nigra, the red nucleus, the caudate putamen, the globus pallidus, and the deep nuclei of the cerebellum. Furthermore, DJ-1 mRNA was also highly expressed in non-motor structures including the hippocampus, the olfactory bulb, the reticular nucleus of the thalamus, and the piriform cortex. The high expression of DJ-1 mRNA in brain regions involved in motor control is compatible with the occurrence of parkinsonian symptoms after DJ-1 mutations. However, expression in other regions indicates that a dysfunction of DJ-1 may contribute to additional clinical features in patients with a DJ-1 mutation.

EC Electronic Communications and Competition Law

Telecommunications have developed at an incredible speed over the last couple of decades. The decreasing size of our phones and the increasing number of ways in which we can communicate are barely the only result of this (r)evolutionary development. The latter has indeed multiple implications. The change of paradigm for telecommunications regulation, epitomised by the processes of liberalisation and reregulation, was not sufficient to answer all regulatory questions pertinent to communications. Today, after the transition from monopoly to competition, we are faced perhaps with an even harder regulatory puzzle, since we must figure out how to regulate a sector that is as dynamic and as unpredictable as electronic communications have proven to be, and as vital and fundamental to the economy and to society at large. The present book addresses the regulatory puzzle of contemporary electronic communications and suggests the outlines of a coherent model for their regulation. The search for such a model involves essentially deliberations on the question "Can competition law do it all?", since generic competition rules are largely seen as the appropriate regulatory tool for the communications domain. The latter perception has been the gist of the 2002 reform of the European Community (EC) telecommunications regime, which envisages a withdrawal of sectoral regulation, as communications markets become effectively competitive and ultimately bestows the regulation of the sector upon competition law only. The book argues that the question of whether competition law is the appropriate tool needs to be examined not in the conventional contexts of sector specific rules versus competition rules or deregulation versus regulation but in a broader governance context. Consequently, the reader is provided with an insight into the workings and specific characteristics of the communications sector as network-bound, converging, dynamic and endowed with a special societal role and function. A thorough evaluation of the regulatory objectives in the communications environment contributes further to the comprehensive picture of the communications industry. Upon this carefully prepared basis, the book analyses the communications regulatory toolkit. It explores the interplay between sectoral communications regulation, competition rules (in particular Article 82 of the EC Treaty) and the rules of the World Trade Organization (WTO) relevant to telecommunications services. The in-depth analysis of multilevel construct of EC communications law is up-to-date and takes into account important recent developments in the EC competition law in practice, in particular in the field of refusal to supply and tying, of the reform of the EC electronic communications framework and new decisions of the WTO dispute settlement body, such as notably the Mexico-Telecommunications Services Panel Report. Upon these building elements, an assessment of the regulatory potential of the EC competition rules is made. The conclusions drawn are beyond the scope of the current situation of EC electronic communications and the applicable law and explore the possible contours of an optimal regulatory framework for modern communications. The book is of particular interest to communications and antitrust law experts, as well as policy makers, government agencies, consultancies and think-tanks active in the field. Experts on other network industries (such as electricity or postal communications) can also profit from the substantial experience gathered in the communications sector as the most advanced one in terms of liberalisation and reregulation.

A Skull-Stripping Filter for ITK

Skull-stripping (or brain extraction) is an important pre-processing step in neuroimage analysis. This document describes a skull-stripping filter implemented using the Insight Toolkit ITK, which we named itk::StripTsImageFilter. It is a composite filter based on existing ITK classes. The filter has been implemented with usability, robustness, speed and versatility in mind, rather than accuracy. This makes it useful for many pre-processing tasks in neuroimage analysis. This paper is accompanied by the source code, input data and a testing environment.

Using virtual reality to teach special populations how to cope in crisis: the case of a virtual earthquake

The unique characteristics of special populations such as pre-school children and Down syndrome kids in crisis and their distorted self-image were never studied before, because of the difficulty of crisis reproduction. This study proposes a VR setting that tries to model some special population's behaviour in the time of crises and offers them a training scenario. The sample population consisted of 30 pre-school children and 20 children with Down syndrome. The VR setting involved a high-speed PC, a VPL EyePhone 1, a MR toolkit, a vibrations plate, a motion capture system and other sensors. The system measured and modelled the typical behaviour of these special populations in a Virtual Earthquake scenario with sight and sound and calculated a VR anthropomorphic model that reproduced their behaviour and emotional state. Afterwards one group received an emotionally enhanced VR self-image as feedback for their training, one group received a plain VR self-image and another group received verbal instructions. The findings strongly suggest that the training was a lot more biased by the emotionally enhanced VR self-image than the other approaches. These findings could highlight the special role of the self-image to therapy and training and the interesting role of imagination to emotions, motives and learning. Further studies could be done with various scenarios in order to measure the best-biased behaviour and establish the most natural and affective VR model. This presentation is going to highlight the main findings and some theories behind them.

EC Electronic Communications and Competition Law

Telecommunications have developed at an incredible speed over the last couple of decades. The decreasing size of our phones and the increasing number of ways in which we can communicate are barely the only result of this (r)evolutionary development. The latter has indeed multiple implications. The change of paradigm for telecommunications regulation, epitomised by the processes of liberalisation and reregulation, was not sufficient to answer all regulatory questions pertinent to communications. Today, after the transition from monopoly to competition, we are faced perhaps with an even harder regulatory puzzle, since we must figure out how to regulate a sector that is as dynamic and as unpredictable as electronic communications have proven to be, and as vital and fundamental to the economy and to society at large. The present book addresses the regulatory puzzle of contemporary electronic communications and suggests the outlines of a coherent model for their regulation. The search for such a model involves essentially deliberations on the question "Can competition law do it all?", since generic competition rules are largely seen as the appropriate regulatory tool for the communications domain. The latter perception has been the gist of the 2002 reform of the European Community (EC) telecommunications regime, which envisages a withdrawal of sectoral regulation, as communications markets become effectively competitive and ultimately bestows the regulation of the sector upon competition law only. The book argues that the question of whether competition law is the appropriate tool needs to be examined not in the conventional contexts of sector specific rules versus competition rules or deregulation versus regulation but in a broader governance context. Consequently, the reader is provided with an insight into the workings and specific characteristics of the communications sector as network-bound, converging, dynamic and endowed with a special societal role and function. A thorough evaluation of the regulatory objectives in the communications environment contributes further to the comprehensive picture of the communications industry. Upon this carefully prepared basis, the book analyses the communications regulatory toolkit. It explores the interplay between sectoral communications regulation, competition rules (in particular Article 82 of the EC Treaty) and the rules of the World Trade Organization (WTO) relevant to telecommunications services. The in-depth analysis of multilevel construct of EC communications law is up-to-date and takes into account important recent developments in the EC competition law in practice, in particular in the field of refusal to supply and tying, of the reform of the EC electronic communications framework and new decisions of the WTO dispute settlement body, such as notably the Mexico-Telecommunications Services Panel Report. Upon these building elements, an assessment of the regulatory potential of the EC competition rules is made. The conclusions drawn are beyond the scope of the current situation of EC electronic communications and the applicable law and explore the possible contours of an optimal regulatory framework for modern communications. The book is of particular interest to communications and antitrust law experts, as well as policy makers, government agencies, consultancies and think-tanks active in the field. Experts on other network industries (such as electricity or postal communications) can also profit from the substantial experience gathered in the communications sector as the most advanced one in terms of liberalisation and reregulation.

Typology of the Tools of EC Communications Regulation

The present article is an abridged version of a chapter to the book EC Electronic Communications and Competition Law (London: Cameron May 2007). It explores in a neutral manner the pros and cons of the currently applied toolkit of European Community communications law, i.e. the generic competition law rules and the sector specific regulatory framework. A number of criteria are introduced and these tools are then tested as to their efficiency and efficacy.