BAYESIAN NONPARAMETRIC CROSS-STUDY VALIDATION OF PREDICTION METHODS

We consider comparisons of statistical learning algorithms using multiple data sets, via leave-one-in cross-study validation: each of the algorithms is trained on one data set; the resulting model is then validated on each remaining data set. This poses two statistical challenges that need to be addressed simultaneously. The first is the assessment of study heterogeneity, with the aim of identifying a subset of studies within which algorithm comparisons can be reliably carried out. The second is the comparison of algorithms using the ensemble of data sets. We address both problems by integrating clustering and model comparison. We formulate a Bayesian model for the array of cross-study validation statistics, which defines clusters of studies with similar properties and provides the basis for meaningful algorithm comparison in the presence of study heterogeneity. We illustrate our approach through simulations involving studies with varying severity of systematic errors, and in the context of medical prognosis for patients diagnosed with cancer, using high-throughput measurements of the transcriptional activity of the tumor’s genes

Efficient CPP-mediated Cre protein delivery to developing and adult CNS tissues

<p>Abstract</p> <p>Background</p> <p>Understanding and manipulating gene function in physiological conditions is a major objective for both fundamental and applied research. In contrast to other experimental settings, which use either purely genetic or gene delivery (viral or non-viral) strategies, we report here a strategy based on direct protein delivery to central nervous system (CNS) tissues. We fused Cre recombinase with cell-penetrating peptides and analyzed the intracellular biological activity of the resulting chimerical proteins when delivered into cells endowed with Cre-mediated reporter gene expression.</p> <p>Results</p> <p>We show that active Cre enzymatic conjugates are readily internalized and exert their enzymatic activity in the nucleus of adherent cultured cells. We then evaluated this strategy in organotypic cultures of neural tissue explants derived from reporter mice carrying reporter "floxed" alleles. The efficacy of two protocols was compared on explants, either by direct addition of an overlying drop of protein conjugate or by implantation of conjugate-coated beads. In both cases, delivery of Cre recombinase resulted in genomic recombination that, with the bead protocol, was restricted to discrete areas of embryonic and adult neural tissues. Furthermore, delivery to adult brain tissue resulted in the transduction of mature postmitotic populations of neurons.</p> <p>Conclusion</p> <p>We provide tools for the spatially restricted genetic modification of cells in explant culture. This strategy allows to study lineage, migration, differentiation and death of neural cells. As a proof-of-concept applied to CNS tissue, direct delivery of Cre recombinase enabled the selective elimination of an interneuron subpopulation of the spinal cord, thereby providing a model to study early events of neurodegenerative processes. Thus our work opens new perspectives for both fundamental and applied cell targeting protocols using proteic cargoes which need to retain full bioactivity upon internalisation, as illustrated here with the oligomeric Cre recombinase.</p

Freeze/thaw stress induces organelle remodeling and membrane recycling in cryopreserved human mature oocytes

Purpose: Our aim was to evaluate the ultrastructure of human metaphase II oocytes subjected to slow freezing and fixed after thawing at different intervals during post-thaw rehydration. Methods: Samples were studied by light and transmission electron microscopy. Results: We found that vacuolization was present in all cryopreserved oocytes, reaching a maximum in the intermediate stage of rehydration. Mitochondria-smooth endoplasmic reticulum (M-SER) aggregates decreased following thawing, particularly in the first and intermediate stages of rehydration, whereas mitochondria-vesicle (MV) complexes augmented in the same stages. At the end of rehydration, vacuoles and MV complexes both diminished and M-SER aggregates increased again. Cortical granules (CGs) were scarce in all cryopreserved oocytes, gradually diminishing as rehydration progressed. Conclusions: This study also shows that such a membrane remodeling is mainly represented by a dynamic process of transition between M-SER aggregates and MV complexes, both able of transforming into each other. Vacuoles and CG membranes may take part in the membrane recycling mechanism

Cross-study validation for the assessment of prediction algorithms

Motivation: Numerous competing algorithms for prediction in high-dimensional settings have been developed in the statistical and machine-learning literature. Learning algorithms and the prediction models they generate are typically evaluated on the basis of cross-validation error estimates in a few exemplary datasets. However, in most applications, the ultimate goal of prediction modeling is to provide accurate predictions for independent samples obtained in different settings. Cross-validation within exemplary datasets may not adequately reflect performance in the broader application context. Methods: We develop and implement a systematic approach to ‘cross-study validation’, to replace or supplement conventional cross-validation when evaluating high-dimensional prediction models in independent datasets. We illustrate it via simulations and in a collection of eight estrogen-receptor positive breast cancer microarray gene-expression datasets, where the objective is predicting distant metastasis-free survival (DMFS). We computed the C-index for all pairwise combinations of training and validation datasets. We evaluate several alternatives for summarizing the pairwise validation statistics, and compare these to conventional cross-validation. Results: Our data-driven simulations and our application to survival prediction with eight breast cancer microarray datasets, suggest that standard cross-validation produces inflated discrimination accuracy for all algorithms considered, when compared to cross-study validation. Furthermore, the ranking of learning algorithms differs, suggesting that algorithms performing best in cross-validation may be suboptimal when evaluated through independent validation. Availability: The survHD: Survival in High Dimensions package (http://www.bitbucket.org/lwaldron/survhd) will be made available through Bioconductor. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Quantum Zeno and anti-Zeno effects in surface diffusion of interacting adsorbates

Surface diffusion of interacting adsorbates is here analyzed within the context of two fundamental phenomena of quantum dynamics, namely the quantum Zeno effect and the anti-Zeno effect. The physical implications of these effects are introduced here in a rather simple and general manner within the framework of non-selective measurements and for two (surface) temperature regimes: high and very low (including zero temperature). The quantum intermediate scattering function describing the adsorbate diffusion process is then evaluated for flat surfaces, since it is fully analytical in this case. Finally, a generalization to corrugated surfaces is also discussed. In this regard, it is found that, considering a Markovian framework and high surface temperatures, the anti-Zeno effect has already been observed, though not recognized as such.Comment: 17 pages, 1 figur

Neurofibroma plexiforme de cólon transverso : relato de caso

Tumores neurogênicos de cólon são raros na população geral, mas podem ocorrer em 11 a 25% dos pacientes com doença de von Recklinghausen. Apresentamos o caso de uma paciente de 24 anos de idade com neurofibroma plexiforme 'do intestino grosso cuja manifestação inicial caracterizou-se por aparecimento de massa no hipocôndrio e flanco esquerdos. A paciente não apresentava, ao exame físico, sinais de neurofibromatose.Neurogenic colon tumors are rare in the general population but may occur in 11 to 25% of von Recklinghausen's disease patients. This is a case report of a 24 years old patient with large bowel plexiform neurofibroma whose initial manifestations was a left upper quadrant and flank mass. On physical exam, the patient did not show signals of neurofibromatosis