University of Amsterdam

About: University of Amsterdam is a education organization based out in Amsterdam, Noord-Holland, Netherlands. It is known for research contribution in the topics: Population & Context (language use). The organization has 59309 authors who have published 140894 publications receiving 5984137 citations. The organization is also known as: UvA & Universiteit van Amsterdam.

Molecular Dynamics Simulations

Abstract: Molecular Dynamics (MD) simulations are in many respects very similar to real experiments. In MD, first, sample is prepared, a model system consisting of N particles is selected, and then Newton's equations of motion are solved for the system until the properties of the system no longer change with time. To measure an observable quantity in a MD simulation, one must first of all be able to express this observable as a function of the positions and momenta of the particles in the system. The best introduction to MD simulations is to consider a simple program. To start the simulation, one should assign initial positions and velocities to all particles in the system. The particle positions should be chosen compatible with the structure that one is aiming to simulate. A good MD program requires a good algorithm to integrate Newton's equations of motion. Accuracy for large time steps is more important because the longer the time step that one can use, the fewer evaluations of the forces are needed per unit of simulation time. For most MD applications, Verlet-like algorithms are perfectly adequate. However, sometimes it is convenient to employ a higher-order algorithm.

Nitrogen deposition makes a minor contribution to carbon sequestration in temperate forests

Abstract: Humans have altered global nitrogen cycling such that more atmospheric N2 is being converted (‘fixed’) into biologically reactive forms by anthropogenic activities than by all natural processes combined1. In particular, nitrogen oxides emitted during fuel combustion and ammonia volatilized as a result of intensive agriculture have increased atmospheric nitrogen inputs (mostly NO3 and NH4) to temperate forests in the Northern Hemisphere2,3,4. Because tree growth in northern temperate regions is typically nitrogen-limited5, increased nitrogen deposition could have the effect of attenuating rising atmospheric CO2 by stimulating the accumulation of forest biomass. Forest inventories indicate that the carbon contents of northern forests have increased concurrently with nitrogen deposition since the 1950s6,7,8. In addition, variations in atmospheric CO2 indicate a globally significant carbon sink in northern mid-latitude forest regions9,10,11,12. It is unclear, however, whether elevated nitrogen deposition or other factors are the primary cause of carbon sequestration in northern forests. Here we use evidence from 15N-tracer studies in nine forests to show that elevated nitrogen deposition is unlikely to be a major contributor to the putative CO2 sink in forested northern temperature regions.

Biphasic kinetics of peripheral blood T cells after triple combination therapy in HIV-1 infection: a composite of redistribution and proliferation

Abstract: The origin of CD4+ T cells reappearing in the blood following antiretroviral therapy in human immunodeficiency virus type-1 (HIV-1) infection is still controversial. Here we show, using mathematical modeling, that redistribution of T cells to the blood can explain the striking correlation between the initial CD4+ and CD8+ memory T-cell repopulation and the observation that 3 weeks after the start of treatment memory CD4+ T-cell numbers reach a plateau. The increase in CD4+ T cells following therapy most likely is a composite of initial redistribution, accompanied by a continuous slow repopulation with newly produced naive T cells.

Using WordNet to measure semantic orientations of adjectives

Abstract: Current WordNet-based measures of distance or similarity focus almost exclusively on WordNet’s taxonomic relations. This effectively restricts their applicability to the syntactic categories of noun and verb. We investigate a graph-theoretic model of WordNet’s most important relation—synonymy—and propose measures that determine the semantic orientation of adjectives for three factors of subjective meaning. Evaluation against human judgments shows the effectiveness of the resulting measures.

Tokyo Guidelines 2018: diagnostic criteria and severity grading of acute cholecystitis (with videos).

Abstract: Although the diagnostic and severity grading criteria on the 2013 Tokyo Guidelines (TG13) are used worldwide as the primary standard for management of acute cholangitis (AC), they need to be validated through implementation and assessment in actual clinical practice. Here, we conduct a systematic review of the literature to validate the TG13 diagnostic and severity grading criteria for AC and propose TG18 criteria. While there is little evidence evaluating the TG13 criteria, they were validated through a large-scale case series study in Japan and Taiwan. Analyzing big data from this study confirmed that the diagnostic rate of AC based on the TG13 diagnostic criteria was higher than that based on the TG07 criteria, and that 30-day mortality in patients with a higher severity based on the TG13 severity grading criteria was significantly higher. Furthermore, a comparison of patients treated with early or urgent biliary drainage versus patients not treated this way showed no difference in 30-day mortality among patients with Grade I or Grade III AC, but significantly lower 30-day mortality in patients with Grade II AC who were treated with early or urgent biliary drainage. This suggests that the TG13 severity grading criteria can be used to identify Grade II patients whose prognoses may be improved through biliary drainage. The TG13 severity grading criteria may therefore be useful as an indicator for biliary drainage as well as a predictive factor when assessing the patient's prognosis. The TG13 diagnostic and severity grading criteria for AC can provide results quickly, are minimally invasive for the patients, and are inexpensive. We recommend that the TG13 criteria be adopted in the TG18 guidelines and used as standard practice in the clinical setting. Free full articles and mobile app of TG18 are available at: http://www.jshbps.jp/modules/en/index.php?content_id=47. Related clinical questions and references are also included.