Transformation and integration of heterogeneous health data in a privacy-preserving distributed learning infrastructure

Problem statement: A growing volume and variety of personal health data are being collected by different entities, such as healthcare providers, insurance companies, and wearable device manufacturers. Combining heterogeneous health data offers unprecedented opportunities to augment our understanding of human health and disease. However, a major challenge to research lies in the difficulty of accessing and analyzing health data that are dispersed in their format (e.g. CSV, XML), sources (e.g., medical records, laboratory data), representation (unstructured, structured), and governance (e.g., data collection and maintenance)[2]. Such considerations are crucial when we link and use personal health data across multiple legal entities with different data governance and privacy concerns

25 years of epidermal stem cell research.

This is a chronicle of concepts in the field of epidermal stem cell biology and a historic look at their development over time. The past 25 years have seen the evolution of epidermal stem cell science, from first fundamental studies to a sophisticated science. The study of epithelial stem cell biology was aided by the ability to visualize the distribution of stem cells and their progeny through lineage analysis studies. The excellent progress we have made in understanding epidermal stem cell biology is discussed in this article. The challenges we still face in understanding epidermal stem cells include defining molecular markers for stem and progenitor sub-populations, determining the locations and contributions of the different stem cell niches, and mapping regulatory pathways of epidermal stem cell proliferation and differentiation. However, our rapidly evolving understanding of epidermal stem cells has many potential uses that promise to translate into improved patient therapy

Robust selection of cancer survival signatures from high-throughput genomic data using two-fold subsampling

Identifying relevant signatures for clinical patient outcome is a fundamental task in high-throughput studies. Signatures, composed of features such as mRNAs, miRNAs, SNPs or other molecular variables, are often non-overlapping, even though they have been identified from similar experiments considering samples with the same type of disease. The lack of a consensus is mostly due to the fact that sample sizes are far smaller than the numbers of candidate features to be considered, and therefore signature selection suffers from large variation. We propose a robust signature selection method that enhances the selection stability of penalized regression algorithms for predicting survival risk. Our method is based on an aggregation of multiple, possibly unstable, signatures obtained with the preconditioned lasso algorithm applied to random (internal) subsamples of a given cohort data, where the aggregated signature is shrunken by a simple thresholding strategy. The resulting method, RS-PL, is conceptually simple and easy to apply, relying on parameters automatically tuned by cross validation. Robust signature selection using RS-PL operates within an (external) subsampling framework to estimate the selection probabilities of features in multiple trials of RS-PL. These probabilities are used for identifying reliable features to be included in a signature. Our method was evaluated on microarray data sets from neuroblastoma, lung adenocarcinoma, and breast cancer patients, extracting robust and relevant signatures for predicting survival risk. Signatures obtained by our method achieved high prediction performance and robustness, consistently over the three data sets. Genes with high selection probability in our robust signatures have been reported as cancer-relevant. The ordering of predictor coefficients associated with signatures was well-preserved across multiple trials of RS-PL, demonstrating the capability of our method for identifying a transferable consensus signature. The software is available as an R package rsig at CRAN (http://cran.r-project.org)

Analyzing Partitioned FAIR Health Data Responsibly

It is widely anticipated that the use of health-related big data will enable further understanding and improvements in human health and wellbeing. Our current project, funded through the Dutch National Research Agenda, aims to explore the relationship between the development of diabetes and socio-economic factors such as lifestyle and health care utilization. The analysis involves combining data from the Maastricht Study (DMS), a prospective clinical study, and data collected by Statistics Netherlands (CBS) as part of its routine operations. However, a wide array of social, legal, technical, and scientific issues hinder the analysis. In this paper, we describe these challenges and our progress towards addressing them.Comment: 6 pages, 1 figure, preliminary result, project repor

Localized Basis for Effective Lattice Hamiltonians: Lattice Wannier Functions

A systematic method is presented for constructing effective Hamiltonians for general phonon-related structural transitions. The key feature is the application of group theoretical methods to identify the subspace in which the effective Hamiltonian acts and construct for it localized basis vectors, which are the analogue of electronic Wannier functions. The results of the symmetry analysis for the perovskite, rocksalt, fluorite and A15 structures and the forms of effective Hamiltonians for the ferroelectric transition in $PbTiO_3$ and $BaTiO_3$, the oxygen-octahedron rotation transition in $SrTiO_3$, the Jahn-Teller instability in $La_{1-x}(Ca,Sr,Ba)_xMnO_3$ and the antiferroelectric transition in $PbZrO_3$ are discussed. For the oxygen- octahedron rotation transition in $SrTiO_3$, this method provides an alternative to the rotational variable approach which is well behaved throughout the Brillouin zone. The parameters appearing in the Wannier basis vectors and in the effective Hamiltonian, given by the corresponding invariant energy expansion, can be obtained for individual materials using first- principles density-functional-theory total energy and linear response techniques, or any technique that can reliably calculate force constants and distortion energies. A practical approach to the determination of these parameters is presented and the application to ferroelectric $PbTiO_3$ discussed.Comment: extensive revisions in presentation, 32 pages, Revtex, 7 Postscript figure

Model Analysis of Time Reversal Symmetry Test in the Caltech Fe-57 Gamma-Transition Experiment

The CALTECH gamma-transition experiment testing time reversal symmetry via the E2/M1 mulipole mixing ratio of the 122 keV gamma-line in Fe-57 has already been performed in 1977. Extending an earlier analysis in terms of an effective one-body potential, this experiment is now analyzed in terms of effective one boson exchange T-odd P-even nucleon nucleon potentials. Within the model space considered for the Fe-57 nucleus no contribution from isovector rho-type exchange is possible. The bound on the coupling strength phi_A from effective short range axial-vector type exchange induced by the experimental bound on sin(eta) leads to phi_A < 10^{-2}.Comment: 5 pages, RevTex 3.

Parent-worker relationships in child & family social work: a Belgian case study

The involvement of parents within child and family social work has become an important research topic during the past few decades. Within this research, a lot of attention is paid to partnership, which is recognised as a dominant concept in current thinking about the parent-worker relationship in present-day practice. The debate on parent-worker relationships, however, seems to be mainly focussed on the individual relationship between the parent and the social worker. Based on a historical analysis of policy documents on a Belgian child and family welfare service, this article offers a historical and sociopolitical contextualisation of the current debate on the parent-worker relationship. The analysis reveals that sociopolitical ideas about the responsibilities of the state, the community and the private family have induced a continuous reflection on which children and parents should be seen as the most appropriate clients for a particular service, as well as an ongoing development of diagnostic instruments to legitimise inclusion and exclusion of families within child and family social work. Consequences for parent-worker relationships in child and family social work are discussed, as well as some implications for future research on child and family social work practices

Characterization of port wine stain skin erythema and melanin content using cross-polarized diffuse reflectance imaging

Background and objectivesObjective methods to assess quantitatively port wine stain (PWS) blanching in response to laser therapy are needed to improve laser therapeutic outcome. Previous studies have attempted to assess objectively PWS color based on point measurement devices. To date, these approaches have typically been limited by a number of factors such as small test area and need for contact. To address these issues, a cross-polarized diffuse reflectance imaging system and color image analysis method has been developed to evaluate quantitatively erythema and melanin content in PWS skin.Study design/materials and methodsA cross-polarized diffuse reflectance system has been constructed to acquire high resolution digital images while minimizing artifacts such as glare, shadowing, and nonuniform illumination effects that can compromise image fidelity. Furthermore, an image analysis algorithm has also been developed to analyze normal and PWS skin in terms of CIEL*a*b* color space parameters. Using the algorithm, images of color space intensity, L*, and saturation, a*, indices have been calculated to extract quantitative metrics of melanin and erythema, respectively.ResultsCompared to the cross-polarized diffuse reflectance image, the a* index image enhanced the contrast in regions of high and low erythema and seems to have quasi correlation with the L* index image. In the presented PWS patient example, the relative a* index difference (Deltaa*) image showed less erythema in PWS skin after laser treatment when compared to pre-treatment values.ConclusionsOur cross-polarized imaging system and color image analysis method is a simple, noncontact technique that can indirectly provide quantitative measurement of erythema and melanin content in PWS skin