Parallel Graph Partitioning for Complex Networks

Processing large complex networks like social networks or web graphs has recently attracted considerable interest. In order to do this in parallel, we need to partition them into pieces of about equal size. Unfortunately, previous parallel graph partitioners originally developed for more regular mesh-like networks do not work well for these networks. This paper addresses this problem by parallelizing and adapting the label propagation technique originally developed for graph clustering. By introducing size constraints, label propagation becomes applicable for both the coarsening and the refinement phase of multilevel graph partitioning. We obtain very high quality by applying a highly parallel evolutionary algorithm to the coarsened graph. The resulting system is both more scalable and achieves higher quality than state-of-the-art systems like ParMetis or PT-Scotch. For large complex networks the performance differences are very big. For example, our algorithm can partition a web graph with 3.3 billion edges in less than sixteen seconds using 512 cores of a high performance cluster while producing a high quality partition -- none of the competing systems can handle this graph on our system.Comment: Review article. Parallelization of our previous approach arXiv:1402.328

Transcriptional regulation of prostate kallikrein-like genes by androgen.

Using gene-specific synthetic oligonucleotides the expression and regulation of kallikrein-like genes in the human prostatic cancer cell line LNCaP were studied. Prostate-specific antigen (PSA) and human glandular kallikrein (hGK-1) together constitute a subfamily of serine proteases exclusively produced in the human prostate. RNA analysis revealed that both genes are expressed in LNCaP cells with PSA basal levels being 2-fold higher than hGK-1 levels. Both mRNAs are induced over a period of 24 h in the presence of 3.3 nM of the synthetic androgen mibolerone. Stimulation of PSA RNA is about 5- fold,whereas hGK-1 stimulation is less pronounced. Nuclear run-on analysis revealed that androgen induction of kallikrein-like genes in LNCaP cells is a rapid event (c3 h) occurring at the level of transcription initiation. Treatment of cells with cycloheximide demonstrates that, while PSA/hGK-1 basal transcription strictly depends on continuous protein synthesis, transcriptional induction by androgen does not. This suggests the direct involvement of the androgen receptor in the induction process independent of additional labile protein factors necessary for kallikrein basal transcription. A binding motif is present in the PSA and hGK-1 promoters, closely resembling the consensus sequence for steroidresponsive elements. The androgen antagonist cyproterone acetate was also able to stimulate transcription of kallikrein-like genes in LNCaP cells. In contrast, androgen-dependent transcriptional suppression of the protooncogene c-myc was strongly counteracted by cyproterone acetate. Thus, antiandrogens act differentially on androgen-regulated prostate-specific (PSA, hGK-1) and growthrelated (c-myc) gene expression in LNCaP cells

Longitudinal qualitative exploration of cancer information-seeking experiences across the disease trajectory: the INFO-SEEK protocol

Introduction Α substantial corpus of literature has sought to describe the information-seeking behaviour of patients with cancer. Yet, available evidence comes mainly from cross-sectional studies, which provide ‘snapshots’ of patients’ information needs and information-seeking styles at a single time point. Only a few longitudinal studies currently exist; however, these are quantitative in nature and, despite successfully documenting changes in patients’ information needs throughout the clinical course of cancer, they have failed to provide an evidence-based interpretation of the causes and consequences of change. The goal of this study is threefold: First, we wish to provide a holistic understanding of how cancer information-seeking behaviour may evolve across different stages of the patient journey. Second, we will seek to elucidate the contextual and intervening conditions that may affect possible changes in information seeking. Third, we will attempt to identify what the consequences of these changes are, while heightening their implications for clinical practice and policy. Methods and analysis We will carry out a longitudinal qualitative study, based on face-to-face, in-depth interviews with approximately 25 individuals diagnosed with cancer. Patients will be recruited from 2 oncology hospitals located in Ticino, Switzerland, and will be interviewed at 3 different time points: (1) within 2 weeks after receiving the cancer diagnosis; (2) within 2 weeks after their initial treatment; and (3) 6 months after their initial treatment. All interviews will be recorded and transcribed verbatim. A grounded theory approach will be used for the analysis of the data. Ethics and dissemination The study protocol has been approved by the Ethics Committee of Canton Ticino (CE 2813). Participation in the study will be voluntary, and confidentiality and anonymity ensured. Prior to study participation, patients will be asked to provide signed informed consent. Findings will be disseminated in international peer-reviewed journals and presented in relevant conferences

Stress correlations of dislocations in a double-pileup configuration: a continuum dislocation density approach – complas XII

Dislocation motion in the crystal lattice of materials is the basis for macroscopic plasticity. While continuum models for describing the role of dislocations in plasticity have existed for decades, only recently have the mathematical tools become available to describe ensembles of moving, oriented lines. These tools have allowed for the creation of a Continuum Dislocation Dynamics (CDD) theory describing a second-order dislocation density tensor, a higher order analog of the classical dislocation density tensor, and its evolution in time. In order to reduce the computational complexity of the theory, a simplified theory has also been developed, which more readily allows for a numerical implementation, useful for describing larger systems of dislocations. In order to construct a self-consistent implementation, several issues have to be resolved including calculation of the stress field of a system of dislocations, coarse graining, and boundary values. The present work deals with the implementation including treatment of the near- and far-field stresses caused by the dislocation density tensor as well as boundary value considerations. The implementation is then applied to a few simple benchmark problems, notably the double pileup of dislocations in 1D. Applications to more general problems are considered, as well as comparisons with analytical solutions to classical dislocation problems. Focus is placed on problems where analytical solutions as well as simulations of discrete dislocations are known which act, along with experimental results, as the basis of comparison to determine the validity of the results