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BACKGROUND: We present a C++ class library for Monte Carlo simulation of molecular systems, including proteins in solution. The design is generic and highly modular, enabling multiple developers to easily implement additional features. The statistical mechanical methods are documented by extensive use of code comments that - subsequently - are collected to automatically build a web-based manual. R
Isotropic chiral media can be modelled in several ways. We show that when realizing such a medium from spiral inclusions with real permittivities and permeabilities in a periodic structure, a modified Drude–Born–Fedorov model is obtained. This model equals the original Born model for small wave vectors, but the strength of the chirality depends on the propagation direction. The effective parameter
New drugs are urgently needed for the treatment of tropical and subtropical parasitic diseases, such as African sleeping sickness. Chagas' disease, leishmaniasis and malaria. Enzymes in polyamine biosynthesis and thiol metabolism, as well as polyamine transporters, are potential drug targets within these organisms. In the present review, the current knowledge of unique properties of polyamine meta
Background: Cancer of unknown primary (CUP) is diagnosed at a metastatic stage but no diagnostic effort is spared to find the primary cancers because these will guide the treatment. Consequently, the diagnostic work-up for CUP is more comprehensive than for any other cancer, resulting in detection of second cancers unrelated to CUP. We want to use the detection rate of second cancers as a measure
Drawing on his anthropological field work in Bolivia in the midst of profound social and political change, the author examines the attitudes of various interlocutors toward knowledge, and in particular the important differences between “hegemonic theories of knowledge and indigenous epistemologies, between propositional and non-propositional knowledge, between knowledge of the world and knowledge
More reliable and faster prediction methods are needed to interpret enormous amounts of data generated by sequencing and genome projects. We have developed a new computational tool, PON-P2, for classification of amino acid substitutions in human proteins. The method is a machine learning-based classifier and groups the variants into pathogenic, neutral and unknown classes, on the basis of random f
Background Peripheral arterial disease (PAD) may cause occlusions (blockages) in the main arteries of lower limbs. One treatment option is bypass surgery using autologous (the patient's own tissue) vein graft or prosthetic (artificial) graft. A number of factors influence occlusion rates in these patients, including the material used. To prevent graft occlusion patients are usually treated with an
THE HUNTINGTON cluster (USNM 536849; Fig. 1) measures 4.1 mm in total length and is comprised of five elements of the maxillary apparatus; the first and second pair of maxillae (right and left MI and MII) and the basal plate (Bp) fitted into the bight of the right MI (for descriptive terminology for ramphoprionids, see Kielan-Jaworowska, 1966; Eriksson, 2001; Fig. 2). Both the MI are broken and la
We propose a new method to determine magnetic fields, by using the magnetic-field-induced electric dipole transition 3p(4) 3d D-4(7/2) -> 3p(5) P-3/2 in Fe9+ ions. This ion has a high abundance in astrophysical plasma and is therefore well suited for direct measurements of even rather weak fields in, e.g., solar flares. This transition is induced by an external magnetic field and its rate is propo
We present a search for a light (mass < 2 GeV) boson predicted by Hidden Valley supersymmetric models that decays into a final state consisting of collimated muons or electrons, denoted "lepton-jets". The analysis uses 5 fb(-1) of root s = 7 TeV proton-proton collision data recorded by the ATLAS detector at the Large Hadron Collider to search for the following signatures: single lepton-jets with a
Let mu be a finite positive measure on the closed disk (D) over bar in the complex plane, let 1 <= t < infinity, and let P-t(mu) denote the closure of the analytic polynomials in L-t(mu). We suppose that D is the set of analytic bounded point evaluations for P-t(mu), and that P-t(mu) contains no nontrivial characteristic functions. It is then known that the restriction of mu to partial derivative
We have implemented intraprocedural control-flow and data-flow analysis of Java source code in a declarative manner, using reference attribute grammars augmented with circular attributes and collection attributes. Our implementation is built on top of the JastAdd Extensible Java Compiler and we have run the analyses on medium-sized Java programs. We show how the analyses can be built using sma
The temperature degradation in terahertz quantum cascade lasers is investigated with the focus on the role acoustic phonon scattering. A self-energy describing the electron-acoustic phonon interaction is derived and used to study the importance in transport and optical properties. We observe a strong degradation of the gain peak with temperature. Despite the very small coupling to electrons, the e
Background: Auditory event-related potentials (AERPs) can be used as indices of neural information processing. Altered AERPs have been reported in children and young adults with frontal lobe infarction. Aim: To test the hypothesis that perinatal brain injury affects cortical auditory processing. Methods: We assessed AERPs at term. 6 and 12 months of age in preterm infants [n = 9. median gestationa
Pseudocoordination is a construction where two verbs or VPs appear to be conjoined by what looks like the conjunction och ‘and’. In my paper I focus on pseudocoordination with gå ‘walk, go’ as Verb 1, in particular cases where this has been claimed to give rise to a “surprise effect” (Wiklund 2005, 2008). I set out from the assumption that Verb 1 in pseudocoordination is a light verb, which, follo
Popular Abstract in Swedish Fysisk inaktivitet och fetma är ett växande hälsoproblem i hela världen. Tre olika grupper av individer med ett brett spektrum av glukostolerans ingick i avhandlingen. Arbetskapacitet har studerats i en grupp friska fysiskt inaktiva medelålders män med normal glukostolerans i studie I och II. Hos en grupp äldre män med normal glukostolerans (NGT), nedsatt glukostoleranPhysical inactivity and obesity is a growing health problem world wide. Three different samples with a wide range of glucose tolerance were included in the thesis to represent a wider population. The exercise capacity was studied in one group of healthy sedentary middle aged men with normal glucose tolerance in study I and II. In a group of elderly men with normal glucose tolerance (NGT), impaire
The paper compares PM10 concentrations in railroad environments with EU air quality standards and characterizes particle concentrations and particle properties in relation to train traffic. The results show that PM10 concentrations in ground-level railroad environments do not exceed the EU directive 24-h limit value, while on the platforms of the two subterranean stations PM10 concentrations were
