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MOTIVATION Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance(More)
This paper addresses the problem of simultaneous localization and mapping (SLAM) by a mobile robot. An incremental SLAM algorithm is introduced that is derived from multigrid methods used for solving partial differential equations. The approach improves on the performance of previous relaxation methods for robot mapping, because it optimizes the map at(More)
CHARMM27 is a widespread and popular force field for biomolecular simulation, and several recent algorithms such as implicit solvent models have been developed specifically for it. We have here implemented the CHARMM force field and all necessary extended functional forms in the GROMACS molecular simulation package, to make CHARMM-specific features(More)
In mountainous regions, climate warming is expected to shift species' ranges to higher altitudes. Evidence for such shifts is still mostly from revisitations of historical sites. We present recent (2001 to 2008) changes in vascular plant species richness observed in a standardized monitoring network across Europe's major mountain ranges. Species have moved(More)
A canal in the lower lip to function as a reservoir for snuff was surgically created in 150 male Sprague-Dawley rats. The animals were randomized into five groups of 30 each: Group I received snuff twice a day, 5 days a wk; Group II was painted with propylene glycol (solvent control) on the hard palate 3 times a wk during 4 wk; Group III underwent painting(More)
We investigated the association of urinary bladder cancer with genetic polymorphisms in the xeroderma pigmentosum complementation group C (XPC), group D (XPD) and group G (XPG), X-ray repair cross-complementing group 1 (XRCC1) and group 3 (XRCC3), Nijmegen breakage syndrome 1 (NBS1), cyclin D1, methylene-tetrahydrofolate reductase (MTHFR), NAD(P)H(More)
The atmospheric transport of polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) was compared by measuring concentrations in air and deposition on an island located in the central basin of the Baltic Sea. Median sigmaPBDE and sigmaPCB concentrations (gaseous + particle) were 8.6 and 7.4 pg m(-3), respectively. Airborne PCBs were(More)
The tumor promoting effects of snuff was studied in Lewis rats initiated with 4-nitroquinoline-N-oxide (4-NQO) and Sprague Dawley rats repeatedly inoculated with herpes simplex virus type 1 (HSV-1). The test substances were administered in a surgically created canal in the lower lips of the rats. There were 15 rats in each test group and 10 rats in the(More)
Biomolecular simulation is a core application on supercomputers, but it is exceptionally difficult to achieve the strong scaling necessary to reach biologically relevant timescales. Here, we present a new paradigm for parallel adaptive molecular dynamics and a publicly available implementation: Copernicus. This framework combines performance-leading(More)
OBJECTIVE To describe in detail the diagnosis and clinical course of an unselected population-based cohort of patients with newly diagnosed bladder neoplasms. MATERIAL AND METHODS A total of 538 patients registered in the Stockholm region with newly diagnosed primary bladder neoplasms (transitional cell carcinomas) in 1995 and 1996 were followed for at(More)