A method for dense packing discovery

The problem of packing a system of particles as densely as possible is foundational in the field of discrete geometry and is a powerful model in the material and biological sciences. As packing problems retreat from the reach of solution by analytic constructions, the importance of an efficient numerical method for conducting \textit{de novo} (from-scratch) searches for dense packings becomes crucial. In this paper, we use the \textit{divide and concur} framework to develop a general search method for the solution of periodic constraint problems, and we apply it to the discovery of dense periodic packings. An important feature of the method is the integration of the unit cell parameters with the other packing variables in the definition of the configuration space. The method we present led to improvements in the densest-known tetrahedron packing which are reported in [arXiv:0910.5226]. Here, we use the method to reproduce the densest known lattice sphere packings and the best known lattice kissing arrangements in up to 14 and 11 dimensions respectively (the first such numerical evidence for their optimality in some of these dimensions). For non-spherical particles, we report a new dense packing of regular four-dimensional simplices with density $\phi=128/219\approx0.5845$ and with a similar structure to the densest known tetrahedron packing.Comment: 15 pages, 5 figure

Usefulness of primary care electronic networks to assess the incidence of chlamydia, diagnosed by general practitioners

Background: Chlamydia is the most common curable sexually transmitted infection (STI) in the Netherlands. The majority of chlamydia diagnoses are made by general practitioners (GPs). Baseline data from primary care will facilitate the future evaluation of the ongoing large population-based screening in the Netherlands. The aim of this study was to assess the usefulness of electronic medical records for monitoring the incidence of chlamydia cases diagnosed in primary care in the Netherlands. Methods. In the electronic records of two regional and two national networks, we identified chlamydia diagnoses by means of ICPC codes (International Classification of Primary Care), laboratory results in free text and the prescription of antibiotics. The year of study was 2007 for the two regional networks and one national network, for the other national network the year of study was 2005. We calculated the incidence of diagnosed chlamydia cases per sex, age group and degree of urbanization. Results: A large diversity was observed in the way chlamydia episodes were coded in the four different GP networks and how easily information concerning chlamydia diagnoses could be extracted. The overall incidence ranged from 103.2/100,000 to 590.2/100,000. Differences were partly related to differences between patient populations. Nevertheless, we observed similar trends in the incidence of chlamydia diagnoses in all networks and findings were in line with earlier reports. Conclusions: Electronic patient records, originally intended for individual patient care in general practice, can be an additional source of data for monitoring chlamydia incidence in primary care and can be of use in assessing the future impact of population-based chlamydia screening programs. To increase the usefulness of data we recommend more efforts to standardize registration by (specific) ICPC code and laboratory results across the existing GP networks

Load-Balancing for Parallel Delaunay Triangulations

Computing the Delaunay triangulation (DT) of a given point set in $\mathbb{R}^D$ is one of the fundamental operations in computational geometry. Recently, Funke and Sanders (2017) presented a divide-and-conquer DT algorithm that merges two partial triangulations by re-triangulating a small subset of their vertices - the border vertices - and combining the three triangulations efficiently via parallel hash table lookups. The input point division should therefore yield roughly equal-sized partitions for good load-balancing and also result in a small number of border vertices for fast merging. In this paper, we present a novel divide-step based on partitioning the triangulation of a small sample of the input points. In experiments on synthetic and real-world data sets, we achieve nearly perfectly balanced partitions and small border triangulations. This almost cuts running time in half compared to non-data-sensitive division schemes on inputs exhibiting an exploitable underlying structure.Comment: Short version submitted to EuroPar 201

DEVELOPMENT OF A FIELD EXPERIMENT OF CO 2 STORAGE IN COAL SEAMS IN THE UPPER SILESIAN BASIN OF POLAND (RECOPOL)

ABSTRACT In 2001 the RECOPOL project, which aims at the development of the first European field demonstration of CO 2 sequestration in subsurface coal seams, started. The required research, design and operation of the pilot field test is executed by an international consortium of research institutes, universities and industrial partners. A site was selected in the Silesian Basin in Poland where two CBM-wells are present at short distance from each other. One injection well will be drilled in between; drilling is scheduled in spring 2003. Injection is planned to start in the summer of 2003 and will continue until the end of 2004. Reservoir modelling shows that the distance between the injection well and the updip production well should be less than 200 m to increase the chance of breakthrough of CO 2 within the test period. Breakthrough is important for a thorough understanding of the process. After and during the injection period monitoring will be performed by direct measurements of CO 2 -concentration and by time lapse seismic monitoring

Dietary magnesium, not calcium, prevents vascular calcification in a mouse model for pseudoxanthoma elasticum

Pseudoxanthoma elasticum (PXE) is a heritable disorder characterized by ectopic calcification of connective tissue in skin, Bruch’s membrane of the eye, and walls of blood vessels. PXE is caused by mutations in the ABCC6 gene, but the exact etiology is still unknown. While observations on patients suggest that high calcium intake worsens the clinical symptoms, the patient organization PXE International has published the dietary advice to increase calcium intake in combination with increased magnesium intake. To obtain more data on this controversial issue, we examined the effect of dietary calcium and magnesium in the Abcc6−/− mouse, a PXE mouse model which mimics the clinical features of PXE. Abcc6−/− mice were placed on specific diets for 3, 7, and 12 months. Disease severity was measured by quantifying calcification of blood vessels in the kidney. Raising the calcium content in the diet from 0.5% to 2% did not change disease severity. In contrast, simultaneous increase of both calcium (from 0.5% to 2.0%) and magnesium (from 0.05% to 0.2%) slowed down the calcification significantly. Our present findings that increase in dietary magnesium reduces vascular calcification in a mouse model for PXE should stimulate further studies to establish a dietary intervention for PXE

Disorders of sex development: insights from targeted gene sequencing of a large international patient cohort

BACKGROUND: Disorders of sex development (DSD) are congenital conditions in which chromosomal, gonadal, or phenotypic sex is atypical. Clinical management of DSD is often difficult and currently only 13% of patients receive an accurate clinical genetic diagnosis. To address this we have developed a massively parallel sequencing targeted DSD gene panel which allows us to sequence all 64 known diagnostic DSD genes and candidate genes simultaneously. RESULTS: We analyzed DNA from the largest reported international cohort of patients with DSD (278 patients with 46,XY DSD and 48 with 46,XX DSD). Our targeted gene panel compares favorably with other sequencing platforms. We found a total of 28 diagnostic genes that are implicated in DSD, highlighting the genetic spectrum of this disorder. Sequencing revealed 93 previously unreported DSD gene variants. Overall, we identified a likely genetic diagnosis in 43% of patients with 46,XY DSD. In patients with 46,XY disorders of androgen synthesis and action the genetic diagnosis rate reached 60%. Surprisingly, little difference in diagnostic rate was observed between singletons and trios. In many cases our findings are informative as to the likely cause of the DSD, which will facilitate clinical management. CONCLUSIONS: Our massively parallel sequencing targeted DSD gene panel represents an economical means of improving the genetic diagnostic capability for patients affected by DSD. Implementation of this panel in a large cohort of patients has expanded our understanding of the underlying genetic etiology of DSD. The inclusion of research candidate genes also provides an invaluable resource for future identification of novel genes.Stephanie Eggers ... Elizabeth M. Thompson, Jennifer Couper, Anne Baxendale, Jozef Gecz ... et al

Concurrent Detection of Circulating Minor Histocompatibility Antigen-Specific CD8+ T Cells in SCT Recipients by Combinatorial Encoding MHC Multimers

Allogeneic stem cell transplantation (SCT) is a potentially curative treatment for patients with hematologic malignancies. Its therapeutic effect is largely dependent on recognition of minor histocompatibility antigens (MiHA) by donor-derived CD8+ T cells. Therefore, monitoring of multiple MiHA-specific CD8+ T cell responses may prove to be valuable for evaluating the efficacy of allogeneic SCT. In this study, we investigated the use of the combinatorial encoding MHC multimer technique to simultaneously detect MiHA-specific CD8+ T cells in peripheral blood of SCT recipients. Feasibility of this approach was demonstrated by applying dual-color encoding MHC multimers for a set of 10 known MiHA. Interestingly, single staining using a fluorochrome- and Qdot-based five-color combination showed comparable results to dual-color staining for most MiHA-specific CD8+ T cell responses. In addition, we determined the potential value of combinatorial encoding MHC multimers in MiHA identification. Therefore, a set of 75 candidate MiHA peptides was predicted from polymorphic genes with a hematopoietic expression profile and further selected for high and intermediate binding affinity for HLA-A2. Screening of a large cohort of SCT recipients resulted in the detection of dual-color encoded CD8+ T cells following MHC multimer-based T cell enrichment and short ex vivo expansion. Interestingly, candidate MiHA-specific CD8+ T cell responses for LAG3 and TLR10 derived polymorphic peptides could be confirmed by genotyping of the respective SNPs. These findings demonstrate the potency of the combinatorial MHC multimer approach in the monitoring of CD8+ T cell responses to known and potential MiHA in limited amounts of peripheral blood from allogeneic SCT recipients