Free Technology Academy : a Joint Venture of Free Software and OER

The decision to publish educational materials openly and under free licenses brings up the challenge of doing it in a sustainable way. Some lessons can be learned from the business models for production, maintenance and distribution of Free and Open Source Software. The Free Technology Academy (FTA) has taken on these challenges and has implemented some of these models. We briefly review the FTA educational programme, methodologies and organisation, and see to which extent these models are proving successful in the case of the FTA.

Free-breathing 3 T magnetic resonance t(2)-mapping of the heart.

OBJECTIVES: This study sought to establish an accurate and reproducible T(2)-mapping cardiac magnetic resonance (CMR) methodology at 3 T and to evaluate it in healthy volunteers and patients with myocardial infarct. BACKGROUND: Myocardial edema affects the T(2) relaxation time on CMR. Therefore, T(2)-mapping has been established to characterize edema at 1.5 T. A 3 T implementation designed for longitudinal studies and aimed at guiding and monitoring therapy remains to be implemented, thoroughly characterized, and evaluated in vivo. METHODS: A free-breathing navigator-gated radial CMR pulse sequence with an adiabatic T(2) preparation module and an empirical fitting equation for T(2) quantification was optimized using numerical simulations and was validated at 3 T in a phantom study. Its reproducibility for myocardial T(2) quantification was then ascertained in healthy volunteers and improved using an external reference phantom with known T(2). In a small cohort of patients with established myocardial infarction, the local T(2) value and extent of the edematous region were determined and compared with conventional T(2)-weighted CMR and x-ray coronary angiography, where available. RESULTS: The numerical simulations and phantom study demonstrated that the empirical fitting equation is significantly more accurate for T(2) quantification than that for the more conventional exponential decay. The volunteer study consistently demonstrated a reproducibility error as low as 2 ± 1% using the external reference phantom and an average myocardial T(2) of 38.5 ± 4.5 ms. Intraobserver and interobserver variability in the volunteers were -0.04 ± 0.89 ms (p = 0.86) and -0.23 ± 0.91 ms (p = 0.87), respectively. In the infarction patients, the T(2) in edema was 62.4 ± 9.2 ms and was consistent with the x-ray angiographic findings. Simultaneously, the extent of the edematous region by T(2)-mapping correlated well with that from the T(2)-weighted images (r = 0.91). CONCLUSIONS: The new, well-characterized 3 T methodology enables robust and accurate cardiac T(2)-mapping at 3 T with high spatial resolution, while the addition of a reference phantom improves reproducibility. This technique may be well suited for longitudinal studies in patients with suspected or established heart disease.

A discrete forest in a continuous landscape : investigating interactions between natural resource management and sustainable development

Summary Forests are key ecosystems of the earth and associated with a large range of functions. Many of these functions are beneficial to humans and are referred to as ecosystem services. Sustainable development requires that all relevant ecosystem services are quantified, managed and monitored equally. Natural resource management therefore targets the services associated with ecosystems. The main hypothesis of this thesis is that the spatial and temporal domains of relevant services do not correspond to a discrete forest ecosystem. As a consequence, the services are not quantified, managed and monitored in an equal and sustainable manner. The thesis aims were therefore to test this hypothesis, establish an improved conceptual approach and provide spatial applications for the relevant land cover and structure variables. The study was carried out in western Switzerland and based primarily on data from a countrywide landscape inventory. This inventory is part of the third Swiss national forest inventory and assesses continuous landscape variables based on a regular sampling of true colour aerial imagery. In addition, land cover variables were derived from Landsat 5 TM passive sensor data and land structure variables from active sensor data from a small footprint laserscanning system. The results confirmed the main hypothesis, as relevant services did not scale well with the forest ecosystem. Instead, a new conceptual approach for sustainable management of natural resources was described. This concept quantifies the services as a continuous function of the landscape, rather than a discrete function of the forest ecosystem. The explanatory landscape variables are therefore called continuous fields and the forest becomes a dependent and function-driven management unit. Continuous field mapping methods were established for land cover and structure variables. In conclusion, the discrete forest ecosystem is an adequate planning and management unit. However, monitoring the state of and trends in sustainability of services requires them to be quantified as a continuous function of the landscape. Sustainable natural resource management iteratively combines the ecosystem and gradient approaches. Résumé Les forêts sont des écosystèmes-clés de la terre et on leur attribue un grand nombre de fonctions. Beaucoup de ces fonctions sont bénéfiques pour l'homme et sont nommées services écosystémiques. Le développement durable exige que ces services écosystémiques soient tous quantifiés, gérés et surveillés de façon égale. La gestion des ressources naturelles a donc pour cible les services attribués aux écosystèmes. L'hypothèse principale de cette thèse est que les domaines spatiaux et temporels des services attribués à la forêt ne correspondent pas à un écosystème discret. Par conséquent, les services ne sont pas quantifiés, aménagés et surveillés d'une manière équivalente et durable. Les buts de la thèse étaient de tester cette hypothèse, d'établir une nouvelle approche conceptuelle de la gestion des ressources naturelles et de préparer des applications spatiales pour les variables paysagères et structurelles appropriées. L'étude a été menée en Suisse occidentale principalement sur la base d'un inventaire de paysage à l'échelon national. Cet inventaire fait partie du troisième inventaire forestier national suisse et mesure de façon continue des variables paysagères sur la base d'un échantillonnage régulier sur des photos aériennes couleur. En outre, des variables de couverture ? terrestre ont été dérivées des données d'un senseur passif Landsat 5 TM, ainsi que des variables structurelles, dérivées du laserscanning, un senseur actif. Les résultats confirment l'hypothèse principale, car l'échelle des services ne correspond pas à celle de l'écosystème forestier. Au lieu de cela, une nouvelle approche a été élaborée pour la gestion durable des ressources naturelles. Ce concept représente les services comme une fonction continue du paysage, plutôt qu'une fonction discrète de l'écosystème forestier. En conséquence, les variables explicatives de paysage sont dénommées continuous fields et la forêt devient une entité dépendante, définie par la fonction principale du paysage. Des méthodes correspondantes pour la couverture terrestre et la structure ont été élaborées. En conclusion, l'écosystème forestier discret est une unité adéquate pour la planification et la gestion. En revanche, la surveillance de la durabilité de l'état et de son évolution exige que les services soient quantifiés comme fonction continue du paysage. La gestion durable des ressources naturelles joint donc l'approche écosystémique avec celle du gradient de manière itérative.

WePreserve 2009: DPE/Planets/CASPAR/nestor Joint Training Event: The Preservation challenge: basic concepts and practical applications (Barcelona, 23-27 març 2009)

Reseña del congreso WePreserve 2009 que tuvo lugar los pasados 23 al 27 de marzo en Barcelona, organizadopor la Facultad de Biblioteconomía y Documentación de la Universitat de Barcelona, con la colaboración del Institut d'Estudis Catalans, la Biblioteca de Catalunya y el Consorci de Biblioteques de Barcelona. El seminario 2009 WePreserve se celebra anualmente desde el año 2007 y participan todas las figuras de referencia europeas en materia de investigación en sistemas y metodologías que garantizan la preservación digital de los documentos: Digital Preservation Europe (DPE), Preservation and Long-term Access Through Networked Services (Planets), Cultural Artistic and Scientific Knowledge for Preservation, Access and Retrieval (CASPAR), y Network of expertise in Digital long-term preservation (nestor).

Disparate activation of the coronary sinus and inferior left atrium during atrial tachycardia after persistent atrial fibrillation ablation: prevalence, pitfalls, and impact on mapping.

INTRODUCTION: Persistent atrial fibrillation (AF) ablation may lead to partial disconnection of the coronary sinus (CS). As a result, disparate activation sequences of the local CS versus contiguous left atrium (LA) may be observed during atrial tachycardia (AT). We aimed to evaluate the prevalence of this phenomenon and its impact on activation mapping. METHODS: AT occurring after persistent AF ablation were investigated in 74 consecutive patients. Partial CS disconnection during AT was suspected when double potentials with disparate activation sequences were observed on the CS catheter. Endocardial mapping facing CS bipoles was performed to differentiate LA far-field from local CS potentials. RESULTS: A total of 149 ATs were observed. Disparate LA-CS activations were apparent in 20 ATs after magnifying the recording scale (13%). The most common pattern (90%) was distal to proximal endocardial LA activation against proximal to distal CS activation, the latter involving the whole CS or its distal part. Perimitral macroreentry was more common when disparate LA-CS activations were observed (67% vs 29%; P = 0.002). Partial CS disconnection also resulted in "pseudo" mitral isthmus (MI) block during LA appendage pacing in 20% of patients as local CS activation was proximal to distal despite distal to proximal activation of the contiguous LA. CONCLUSION: Careful analysis of CS recordings during AT following persistent AF ablation often reveals disparate patterns of activation. Recognizing when endocardial LA activation occurs in the opposite direction to the more obvious local CS signals is critical to avoid misleading interpretations during mapping of AT and evaluation of MI block.

Large-Area Photo-Mosaics Using Global Alignment and Navigation Data

Seafloor imagery is a rich source of data for the study of biological and geological processes. Among several applications, still images of the ocean floor can be used to build image composites referred to as photo-mosaics. Photo-mosaics provide a wide-area visual representation of the benthos, and enable applications as diverse as geological surveys, mapping and detection of temporal changes in the morphology of biodiversity. We present an approach for creating globally aligned photo-mosaics using 3D position estimates provided by navigation sensors available in deep water surveys. Without image registration, such navigation data does not provide enough accuracy to produce useful composite images. Results from a challenging data set of the Lucky Strike vent field at the Mid Atlantic Ridge are reported

Dix erreurs a ne pas commettre lors de la prise en charge d'une prothèse articulaire infectée en orthopédie [Ten errors to avoid while dealing with infected total joint arthroplasties].

Infections after total joint arthroplasty are rare but come with severe consequences. Timely, adequate and standardized treatment beginning at the onset of symptoms will have a major impact on the handling of this dreaded complication. In absences of clear guidelines, errors are often committed, with occasionally severe consequences for the patient. In this article, the 10 most frequent errors starting with diagnostics till antibiotic and surgical treatment will be discussed.

Positive contrast visualization of nitinol devices using susceptibility gradient mapping.

MRI visualization of devices is traditionally based on signal loss due to T(2)* effects originating from local susceptibility differences. To visualize nitinol devices with positive contrast, a recently introduced postprocessing method is adapted to map the induced susceptibility gradients. This method operates on regular gradient-echo MR images and maps the shift in k-space in a (small) neighborhood of every voxel by Fourier analysis followed by a center-of-mass calculation. The quantitative map of the local shifts generates the positive contrast image of the devices, while areas without susceptibility gradients render a background with noise only. The positive signal response of this method depends only on the choice of the voxel neighborhood size. The properties of the method are explained and the visualizations of a nitinol wire and two stents are shown for illustration.

Monocular-based 3-D seafloor reconstruction and ortho-mosaicing by piecewise planar representation

Photo-mosaicing techniques have become popular for seafloor mapping in various marine science applications. However, the common methods cannot accurately map regions with high relief and topographical variations. Ortho-mosaicing borrowed from photogrammetry is an alternative technique that enables taking into account the 3-D shape of the terrain. A serious bottleneck is the volume of elevation information that needs to be estimated from the video data, fused, and processed for the generation of a composite ortho-photo that covers a relatively large seafloor area. We present a framework that combines the advantages of dense depth-map and 3-D feature estimation techniques based on visual motion cues. The main goal is to identify and reconstruct certain key terrain feature points that adequately represent the surface with minimal complexity in the form of piecewise planar patches. The proposed implementation utilizes local depth maps for feature selection, while tracking over several views enables 3-D reconstruction by bundle adjustment. Experimental results with synthetic and real data validate the effectiveness of the proposed approach

Schistosomiasis risk mapping in the state of Minas Gerais, Brazil, using a decision tree approach, remote sensing data and sociological indicators

Schistosomiasis mansoni is not just a physical disease, but is related to social and behavioural factors as well. Snails of the Biomphalaria genus are an intermediate host for Schistosoma mansoni and infect humans through water. The objective of this study is to classify the risk of schistosomiasis in the state of Minas Gerais (MG). We focus on socioeconomic and demographic features, basic sanitation features, the presence of accumulated water bodies, dense vegetation in the summer and winter seasons and related terrain characteristics. We draw on the decision tree approach to infection risk modelling and mapping. The model robustness was properly verified. The main variables that were selected by the procedure included the terrain's water accumulation capacity, temperature extremes and the Human Development Index. In addition, the model was used to generate two maps, one that included risk classification for the entire of MG and another that included classification errors. The resulting map was 62.9% accurate.

Properties of ideal composite knots.

The shortest tube of constant diameter that can form a given knot represents the 'ideal' form of the knot. Ideal knots provide an irreducible representation of the knot, and they have some intriguing mathematical and physical features, including a direct correspondence with the time-averaged shapes of knotted DNA molecules in solution. Here we describe the properties of ideal forms of composite knots-knots obtained by the sequential tying of two or more independent knots (called factor knots) on the same string. We find that the writhe (related to the handedness of crossing points) of composite knots is the sum of that of the ideal forms of the factor knots. By comparing ideal composite knots with simulated configurations of knotted, thermally fluctuating DNA, we conclude that the additivity of writhe applies also to randomly distorted configurations of composite knots and their corresponding factor knots. We show that composite knots with several factor knots may possess distinct structural isomers that can be interconverted only by loosening the knot.

Genetic polymorphisms in folate pathway enzymes, DRD4 and GSTM1 are related to temporomandibular disorder

BACKGROUND Temporomandibular disorder (TMD) is a multifactorial syndrome related to a critical period of human life. TMD has been associated with psychological dysfunctions, oxidative state and sexual dimorphism with coincidental occurrence along the pubertal development. In this work we study the association between TMD and genetic polymorphisms of folate metabolism, neurotransmission, oxidative and hormonal metabolism. Folate metabolism, which depends on genes variations and diet, is directly involved in genetic and epigenetic variations that can influence the changes of last growing period of development in human and the appearance of the TMD. METHODS A case-control study was designed to evaluate the impact of genetic polymorphisms above described on TMD. A total of 229 individuals (69% women) were included at the study; 86 were patients with TMD and 143 were healthy control subjects. Subjects underwent to a clinical examination following the guidelines by the Research Diagnostic Criteria for Temporomandibular Disorders (RDC/TMD). Genotyping of 20 Single Nucleotide Polymorphisms (SNPs), divided in two groups, was performed by multiplex minisequencing preceded by multiplex PCR. Other seven genetic polymorphisms different from SNPs (deletions, insertions, tandem repeat, null genotype) were achieved by a multiplex-PCR. A chi-square test was performed to determine the differences in genotype and allelic frequencies between TMD patients and healthy subjects. To estimate TMD risk, in those polymorphisms that shown significant differences, odds ratio (OR) with a 95% of confidence interval were calculated. RESULTS Six of the polymorphisms showed statistical associations with TMD. Four of them are related to enzymes of folates metabolism: Allele G of Serine Hydoxymethyltransferase 1 (SHMT1) rs1979277 (OR = 3.99; 95%CI 1.72, 9.25; p = 0.002), allele G of SHMT1 rs638416 (OR = 2.80; 95%CI 1.51, 5.21; p = 0.013), allele T of Methylentetrahydrofolate Dehydrogenase (MTHFD) rs2236225 (OR = 3.09; 95%CI 1.27, 7.50; p = 0.016) and allele A of Methionine Synthase Reductase (MTRR) rs1801394 (OR = 2.35; 95CI 1.10, 5.00; p = 0.037). An inflammatory oxidative stress enzyme, Gluthatione S-Tranferase Mu-1(GSTM1), null allele (OR = 2.21; 95%CI 1.24, 4.36; p = 0.030) and a neurotransmission receptor, Dopamine Receptor D4 (DRD4), long allele of 48 bp-repeat (OR = 3.62; 95%CI 0.76, 17.26; p = 0.161). CONCLUSIONS Some genetic polymorphisms related to folates metabolism, inflammatory oxidative stress, and neurotransmission responses to pain, has been significantly associated to TMD syndrome.

Leprosy reactions: the effect of gender and household contacts

Various host-related factors have been reported as relevant risk factors for leprosy reactions. To support a new hypothesis that an antigenic load in local tissues that is sufficient to trigger the immune response may come from an external supply of Mycobacterium leprae organisms, the prevalence of reactional leprosy was assessed against the number of household contacts. The number of contacts was ascertained at diagnosis in leprosy patients coming from an endemic area of Brazil. The prevalence of reactions (patients with reactions/total patients) was fitted by binomial regression and the risk difference (RD) was estimated with a semi-robust estimation of variance as a measure of effect. Five regression models were fitted. Model 1 included only the main exposure variable "number of household contacts"; model 2 included all four explanatory variables ("contacts", "fertile age", "number of skin lesions" and "bacillary index") that were found to be associated with the outcome upon univariate analysis; models 3-5 contained various combinations of three predictors. Male and female patients were analyzed separately. In females, household contacts were a significant predictor for leprosy reactions in model 1 [crude RD = 0.06; 95% confidence interval (CI) = 0.01; 0.12] and model 5 (RD = 0.05; CI = 0.02; 0.09), which included contacts, bacillary index and skin lesions as predictors. Other models were unsatisfactory because the joint presence of fertile age and bacillary index was a likely source of multicollinearity. No significant results were obtained for males. The likely interpretation of our findings might suggest that in female patients, leprosy reactions may be triggered by an external spreading of M. leprae by healthy carrier family members. The small number of observations is an obvious limitation of our study which requires larger confirmatory studies.

Mapping the proteome of Leishmania Viannia parasites using two-dimensional polyacrylamide gel electrophoresis and associated technologies.

In this study we have demonstrated the potential of two-dimensional electrophoresis (2DE)-based technologies as tools for characterization of the Leishmania proteome (the expressed protein complement of the genome). Standardized neutral range (pH 5-7) proteome maps of Leishmania (Viannia) guyanensis and Leishmania (Viannia) panamensis promastigotes were reproducibly generated by 2DE of soluble parasite extracts, which were prepared using lysis buffer containing urea and nonidet P-40 detergent. The Coomassie blue and silver nitrate staining systems both yielded good resolution and representation of protein spots, enabling the detection of approximately 800 and 1,500 distinct proteins, respectively. Several reference protein spots common to the proteomes of all parasite species/strains studied were isolated and identified by peptide mass spectrometry (LC-ES-MS/MS), and bioinformatics approaches as members of the heat shock protein family, ribosomal protein S12, kinetoplast membrane protein 11 and a hypothetical Leishmania-specific 13 kDa protein of unknown function. Immunoblotting of Leishmania protein maps using a monoclonal antibody resulted in the specific detection of the 81.4 kDa and 77.5 kDa subunits of paraflagellar rod proteins 1 and 2, respectively. Moreover, differences in protein expression profiles between distinct parasite clones were reproducibly detected through comparative proteome analyses of paired maps using image analysis software. These data illustrate the resolving power of 2DE-based proteome analysis. The production and basic characterization of good quality Leishmania proteome maps provides an essential first step towards comparative protein expression studies aimed at identifying the molecular determinants of parasite drug resistance and virulence, as well as discovering new drug and vaccine targets.