Comparison of Energy Minimization Methods for 3-D Brain Tissue Classification

This paper presents 3-D brain tissue classificationschemes using three recent promising energy minimizationmethods for Markov random fields: graph cuts, loopybelief propagation and tree-reweighted message passing.The classification is performed using the well knownfinite Gaussian mixture Markov Random Field model.Results from the above methods are compared with widelyused iterative conditional modes algorithm. Theevaluation is performed on a dataset containing simulatedT1-weighted MR brain volumes with varying noise andintensity non-uniformities. The comparisons are performedin terms of energies as well as based on ground truthsegmentations, using various quantitative metrics.

Immunonutrition in gastrointestinal surgery.

Background: Patients undergoing major gastrointestinal surgery are at increased risk of developing complications. The use of immunonutrition (IN) in such patients is not widespread because the available data are heterogeneous, and some show contradictory results with regard to complications, mortality and length of hospital stay. Methods: Randomized controlled trials (RCTs) published between January 1985 and September 2009 that assessed the clinical impact of perioperative enteral IN in major gastrointestinal elective surgery were included in a meta-analysis. Results: Twenty-one RCTs enrolling a total of 2730 patients were included in the meta-analysis. Twelve were considered as high-quality studies. The included studies showed significant heterogeneity with respect to patients, control groups, timing and duration of IN, which limited group analysis. IN significantly reduced overall complications when used before surgery (odds ratio (OR) 0.48, 95 per cent confidence interval (c.i.) 0.34 to 0.69), both before and after operation (OR 0.39, 0.28 to 0.54) or after surgery (OR 0.46, 0.25 to 0.84). For these three timings of IN administration, ORs of postoperative infection were 0.36 (0.24 to 0.56), 0.41 (0.28 to 0.58) and 0.53 (0.40 to 0.71) respectively. Use of IN led to a shorter hospital stay: mean difference -2.12 (95 per cent c.i. -2.97 to -1.26) days. Beneficial effects of IN were confirmed when low-quality trials were excluded. Perioperative IN had no influence on mortality (OR 0.90, 0.46 to 1.76). Conclusion: Perioperative enteral IN decreases morbidity and hospital stay but not mortality after major gastrointestinal surgery; its routine use can be recommended.

Value and depreciation of mineral resources over the very long run: An empirical contrast of different methods

The paper contrasts empirically the results of alternative methods for estimating thevalue and the depreciation of mineral resources. The historical data of Mexico andVenezuela, covering the period 1920s-1980s, is used to contrast the results of severalmethods. These are the present value, the net price method, the user cost method andthe imputed income method. The paper establishes that the net price and the user costare not competing methods as such, but alternative adjustments to different scenariosof closed and open economies. The results prove that the biases of the methods, ascommonly described in the theoretical literature, only hold under the most restrictedscenario of constant rents over time. It is argued that the difference between what isexpected to happen and what actually did happen is for the most part due to a missingvariable, namely technological change. This is an important caveat to therecommendations made based on these models.

Exact and approximate stepdown methods for multiple hypothesis testing

Consider the problem of testing k hypotheses simultaneously. In this paper,we discuss finite and large sample theory of stepdown methods that providecontrol of the familywise error rate (FWE). In order to improve upon theBonferroni method or Holm's (1979) stepdown method, Westfall and Young(1993) make eective use of resampling to construct stepdown methods thatimplicitly estimate the dependence structure of the test statistics. However,their methods depend on an assumption called subset pivotality. The goalof this paper is to construct general stepdown methods that do not requiresuch an assumption. In order to accomplish this, we take a close look atwhat makes stepdown procedures work, and a key component is a monotonicityrequirement of critical values. By imposing such monotonicity on estimatedcritical values (which is not an assumption on the model but an assumptionon the method), it is demonstrated that the problem of constructing a validmultiple test procedure which controls the FWE can be reduced to the problemof contructing a single test which controls the usual probability of a Type 1error. This reduction allows us to draw upon an enormous resamplingliterature as a general means of test contruction.

Comparison of different methods for thin section EM analysis of Mycobacterium smegmatis.

Bacteria are generally difficult specimens to prepare for conventional resin section electron microscopy and mycobacteria, with their thick and complex cell envelope layers being especially prone to artefacts. Here we made a systematic comparison of different methods for preparing Mycobacterium smegmatis for thin section electron microscopy analysis. These methods were: (1) conventional preparation by fixatives and epoxy resins at ambient temperature. (2) Tokuyasu cryo-section of chemically fixed bacteria. (3) rapid freezing followed by freeze substitution and embedding in epoxy resin at room temperature or (4) combined with Lowicryl HM20 embedding and ultraviolet (UV) polymerization at low temperature and (5) CEMOVIS, or cryo electron microscopy of vitreous sections. The best preservation of bacteria was obtained with the cryo electron microscopy of vitreous sections method, as expected, especially with respect to the preservation of the cell envelope and lipid bodies. By comparison with cryo electron microscopy of vitreous sections both the conventional and Tokuyasu methods produced different, undesirable artefacts. The two different types of freeze-substitution protocols showed variable preservation of the cell envelope but gave acceptable preservation of the cytoplasm, but not lipid bodies, and bacterial DNA. In conclusion although cryo electron microscopy of vitreous sections must be considered the 'gold standard' among sectioning methods for electron microscopy, because it avoids solvents and stains, the use of optimally prepared freeze substitution also offers some advantages for ultrastructural analysis of bacteria.

ETYK III-vaihe (Tasavallan Presidentin esittämä Suomen puheenvuoro 31.7.1975 = Conference on Security and Co-operation in Europe = main speech of Finland delivered by President Urho Kekkonen July 31, 1975)

Puhe

Methods for integration site distribution analyses in animal cell genomes.

The question of where retroviral DNA becomes integrated in chromosomes is important for understanding (i) the mechanisms of viral growth, (ii) devising new anti-retroviral therapy, (iii) understanding how genomes evolve, and (iv) developing safer methods for gene therapy. With the completion of genome sequences for many organisms, it has become possible to study integration targeting by cloning and sequencing large numbers of host-virus DNA junctions, then mapping the host DNA segments back onto the genomic sequence. This allows statistical analysis of the distribution of integration sites relative to the myriad types of genomic features that are also being mapped onto the sequence scaffold. Here we present methods for recovering and analyzing integration site sequences.

Isolating DNA from sexual assault cases: a comparison of standard methods with a nuclease-based approach.

AbstractText BACKGROUND: Profiling sperm DNA present on vaginal swabs taken from rape victims often contributes to identifying and incarcerating rapists. Large amounts of the victim's epithelial cells contaminate the sperm present on swabs, however, and complicate this process. The standard method for obtaining relatively pure sperm DNA from a vaginal swab is to digest the epithelial cells with Proteinase K in order to solubilize the victim's DNA, and to then physically separate the soluble DNA from the intact sperm by pelleting the sperm, removing the victim's fraction, and repeatedly washing the sperm pellet. An alternative approach that does not require washing steps is to digest with Proteinase K, pellet the sperm, remove the victim's fraction, and then digest the residual victim's DNA with a nuclease. METHODS: The nuclease approach has been commercialized in a product, the Erase Sperm Isolation Kit (PTC Labs, Columbia, MO, USA), and five crime laboratories have tested it on semen-spiked female buccal swabs in a direct comparison with their standard methods. Comparisons have also been performed on timed post-coital vaginal swabs and evidence collected from sexual assault cases. RESULTS: For the semen-spiked buccal swabs, Erase outperformed the standard methods in all five laboratories and in most cases was able to provide a clean male profile from buccal swabs spiked with only 1,500 sperm. The vaginal swabs taken after consensual sex and the evidence collected from rape victims showed a similar pattern of Erase providing superior profiles. CONCLUSIONS: In all samples tested, STR profiles of the male DNA fractions obtained with Erase were as good as or better than those obtained using the standard methods.

Relação dos Estagiários e seus Orientadores com as TIC: um Estudo Realizado no Ano Letivo 2011/2012 no Departamento de Ciências Sociais e Humanas da Universidade de Cabo Verde

No contexto das atividades de formação de professores ao nível da Universidade Pública de Cabo Verde (Uni-CV), constatamos que existem algumas dificuldades associadas ao funcionamento dos estágios pedagógicos, que consideramos poderem ser superadas com recurso às tecnologias de informação e comunicação (TIC). Entendemos que o estágio curricular constitui uma das etapas decisivas para os futuros docentes de ensino secundário no país, garantindo-lhes a oportunidade de contato com estratégias de trabalho atuais e inovadoras para esses contextos. Esta comunicação enquadra-se num processo de investigação-ação que pretende dinamizar as metodologias de trabalho com os estagiários e seus orientadores no Departamento de Ciências Sociais e Humanas no campus do Palmarejo da Uni-CV. Para tal, pretende-se recorrer à dinamização de um espaço virtual na Moodle, de forma a superar algumas das dificuldades previamente identificadas. Os dados aqui apresentados resultam de um diagnóstico de necessidades de formação e representam uma breve avaliação das condições existentes para o acompanhamento dos estágios pedagógicos através de um ambiente online, onde se constatou que os estagiários e seus orientadores, além de serem utilizadores e terem bons conhecimentos das TIC, gostariam de poder contar com um espaço virtual que os apoiasse ao longo de todo o estágio.

Dynamic graphics of parametrically linked multivariate methods used in compositional data analysis

Many multivariate methods that are apparently distinct can be linked by introducing oneor more parameters in their definition. Methods that can be linked in this way arecorrespondence analysis, unweighted or weighted logratio analysis (the latter alsoknown as "spectral mapping"), nonsymmetric correspondence analysis, principalcomponent analysis (with and without logarithmic transformation of the data) andmultidimensional scaling. In this presentation I will show how several of thesemethods, which are frequently used in compositional data analysis, may be linkedthrough parametrizations such as power transformations, linear transformations andconvex linear combinations. Since the methods of interest here all lead to visual mapsof data, a "movie" can be made where where the linking parameter is allowed to vary insmall steps: the results are recalculated "frame by frame" and one can see the smoothchange from one method to another. Several of these "movies" will be shown, giving adeeper insight into the similarities and differences between these methods.

Fanconi-Bickel syndrome and autosomal recessive proximal tubulopathy with hypercalciuria (ARPTH) are allelic variants caused by GLUT2 mutations.

CONTEXT: Many inherited disorders of calcium and phosphate homeostasis are unexplained at the molecular level. OBJECTIVE: The objective of the study was to identify the molecular basis of phosphate and calcium abnormalities in two unrelated, consanguineous families. PATIENTS: The affected members in family 1 presented with rickets due to profound urinary phosphate-wasting and hypophosphatemic rickets. In the previously reported family 2, patients presented with proximal renal tubulopathy and hypercalciuria yet normal or only mildly increased urinary phosphate excretion. METHODS: Genome-wide linkage scans and direct nucleotide sequence analyses of candidate genes were performed. Transport of glucose and phosphate by glucose transporter 2 (GLUT2) was assessed using Xenopus oocytes. Renal sodium-phosphate cotransporter 2a and 2c (Npt2a and Npt2c) expressions were evaluated in transgenically rescued Glut2-null mice (tgGlut2-/-). RESULTS: In both families, genetic mapping and sequence analysis of candidate genes led to the identification of two novel homozygous mutations (IVS4-2A>G and R124S, respectively) in GLUT2, the gene mutated in Fanconi-Bickel syndrome, a rare disease usually characterized by renal tubulopathy, impaired glucose homeostasis, and hepatomegaly. Xenopus oocytes expressing the [R124S]GLUT2 mutant showed a significant reduction in glucose transport, but neither wild-type nor mutant GLUT2 facilitated phosphate import or export; tgGlut2-/- mice demonstrated a profound reduction of Npt2c expression in the proximal renal tubules. CONCLUSIONS: Homozygous mutations in the facilitative glucose transporter GLUT2, which cause Fanconi-Bickel syndrome, can lead to very different clinical and biochemical findings that are not limited to mild proximal renal tubulopathy but can include significant hypercalciuria and highly variable degrees of urinary phosphate-wasting and hypophosphatemia, possibly because of the impaired proximal tubular expression of Npt2c.

Management of severe pediatric subglottic stenosis with glottic involvement.

OBJECTIVE: We sought to describe our experience in the management of complex glotto-subglottic stenosis in the pediatric age group. METHODS: Between 1978 and 2008, 33 children with glotto-subglottic stenosis underwent partial cricotracheal resection, and they form the focus of this study. They were compared with 67 children with isolated subglottic stenosis (no glottic involvement). The outcomes measured were need for revision open surgical intervention, delayed decannulation (>6 months), and operation-specific and overall decannulation rates. Fisher's exact test was used for comparison of outcomes. RESULTS: Results of preoperative evaluation showed Myer-Cotton grade III or IV stenosis in 32 (97%) patients and grade II stenosis in 1 patient. All patients with glotto-subglottic stenosis were treated with partial cricotracheal resection and simultaneous repair of the glottic pathology. Bilateral fixed vocal cords were seen in 19 (58%) of 33 patients, bilateral restricted abduction was seen in 7 (21%) of 33 patients, and unilateral fixed vocal cord was seen in 7 (21%) of 33 patients. Ten patients underwent single-stage partial cricotracheal resection with excision of interarytenoid scar tissue. The endotracheal tube was kept for a mean period of 7 days as a stent. Twenty-three patients underwent extended partial cricotracheal resection with LT-Mold (Bredam S.A., St. Sulpice, Switzerland) or T-tube stenting. The overall decannulation rate included 26 (79%) patients, and the operation-specific decannulation rate included 20 (61%) patients. CONCLUSIONS: Glotto-subglottic stenosis is a complex laryngeal injury associated with delayed decannulation and decreased overall and operation-specific decannulation rates when compared with those after subglottic stenosis without glottic involvement after partial cricotracheal resection.

Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine.

Nowadays, genome-wide association studies (GWAS) and genomic selection (GS) methods which use genome-wide marker data for phenotype prediction are of much potential interest in plant breeding. However, to our knowledge, no studies have been performed yet on the predictive ability of these methods for structured traits when using training populations with high levels of genetic diversity. Such an example of a highly heterozygous, perennial species is grapevine. The present study compares the accuracy of models based on GWAS or GS alone, or in combination, for predicting simple or complex traits, linked or not with population structure. In order to explore the relevance of these methods in this context, we performed simulations using approx 90,000 SNPs on a population of 3,000 individuals structured into three groups and corresponding to published diversity grapevine data. To estimate the parameters of the prediction models, we defined four training populations of 1,000 individuals, corresponding to these three groups and a core collection. Finally, to estimate the accuracy of the models, we also simulated four breeding populations of 200 individuals. Although prediction accuracy was low when breeding populations were too distant from the training populations, high accuracy levels were obtained using the sole core-collection as training population. The highest prediction accuracy was obtained (up to 0.9) using the combined GWAS-GS model. We thus recommend using the combined prediction model and a core-collection as training population for grapevine breeding or for other important economic crops with the same characteristics.