Cellular dynamic simulator: an event driven molecular simulation environment for cellular physiology.

In this paper, we present the Cellular Dynamic Simulator (CDS) for simulating diffusion and chemical reactions within crowded molecular environments. CDS is based on a novel event driven algorithm specifically designed for precise calculation of the timing of collisions, reactions and other events for each individual molecule in the environment. Generic mesh based compartments allow the creation / importation of very simple or detailed cellular structures that exist in a 3D environment. Multiple levels of compartments and static obstacles can be used to create a dense environment to mimic cellular boundaries and the intracellular space. The CDS algorithm takes into account volume exclusion and molecular crowding that may impact signaling cascades in small sub-cellular compartments such as dendritic spines. With the CDS, we can simulate simple enzyme reactions; aggregation, channel transport, as well as highly complicated chemical reaction networks of both freely diffusing and membrane bound multi-protein complexes. Components of the CDS are generally defined such that the simulator can be applied to a wide range of environments in terms of scale and level of detail. Through an initialization GUI, a simple simulation environment can be created and populated within minutes yet is powerful enough to design complex 3D cellular architecture. The initialization tool allows visual confirmation of the environment construction prior to execution by the simulator. This paper describes the CDS algorithm, design implementation, and provides an overview of the types of features available and the utility of those features are highlighted in demonstrations.

Studies to localize and characterize the isoform specific functional differences between cardiac and skeletal troponin C

Thin filament regulation of muscle contraction is a calcium dependent process mediated by the Tn complex. Calcium is released into the sarcomere and is bound by TnC. The subsequent conformation change in TnC is thought to begin a cascade of events that result in the activation of the actin-myosin ATPase. While the general events of this cascade are known, the molecular mechanisms of this signal transduction event are not. Recombinant DNA techniques, physiological and biochemical studies have been used to localize and characterize the structural domains of TnC that play a role in the calcium dependent signal transduction event that serves to trigger muscle contraction. The strategy exploited the observed functional differences between the isoforms of TnC to map regions of functional significance to the proteins. Chimeric cardiac-skeletal TnC proteins were generated to localize the domains of TnC that are required for maximal function in the myofibrilar ATPase assay. Characterization of these regions has yielded information concerning the molecular mechanism of muscle contraction. ^

Catastrophic Ice Shelf Breakup as the Source of Heinrich Event Icebergs

Heinrich layers of the glacial North Atlantic record abrupt widespread iceberg rafting of detrital carbonate and other lithic material at the extreme-cold culminations of Bond climate cycles. Both internal (glaciologic) and external ( climate) forcings have been proposed. Here we suggest an explanation for the iceberg release that encompasses external climate forcing on the basis of a new glaciological process recently witnessed along the Antarctic Peninsula: rapid disintegrations of fringing ice shelves induced by climate-controlled meltwater infilling of surface crevasses. We postulate that peripheral ice shelves, formed along the eastern Canadian seaboard during extreme cold conditions, would be vulnerable to sudden climate-driven disintegration during any climate amelioration. Ice shelf disintegration then would be the source of Heinrich event icebergs.

The 1452 or 1453 A.D. Kuwae Eruption Signal Derived from Multiple Ice Core Records: Greatest Volcanic Sulfate Event of the Past 700 Years

We combined 33 ice core records, 13 from the Northern Hemisphere and 20 from the Southern Hemisphere, to determine the timing and magnitude of the great Kuwae eruption in the mid-15th century. We extracted volcanic deposition signals by applying a high-pass loess filter to the time series and examining peaks that exceed twice the 31 year running median absolute deviation. By accounting for the dating uncertainties associated with each record, these ice core records together reveal a large volcanogenic acid deposition event during 1453 - 1457 A. D. The results suggest only one major stratospheric injection from the Kuwae eruption and confirm previous findings that the Kuwae eruption took place in late 1452 or early 1453, which may serve as a reference to evaluate and improve the dating of ice core records. The average total sulfate deposition from the Kuwae eruption was 93 kg SO4/km(2) in Antarctica and 25 kg SO4/km(2) in Greenland. The deposition in Greenland was probably underestimated since it was the average value of only two northern Greenland sites with very low accumulation rates. After taking the spatial variation into consideration, the average Kuwae deposition in Greenland was estimated to be 45 kg SO4/km(2). By applying the same technique to the other major eruptions of the past 700 years our result suggests that the Kuwae eruption was the largest stratospheric sulfate event of that period, probably surpassing the total sulfate deposition of the Tambora eruption of 1815, which produced 59 kg SO4/km(2) in Antarctica and 50 kg SO4/km(2) in Greenland.

Extraversion and short-term memory for chromatic stimuli: an event-related potential analysis.

The present study investigated extraversion-related individual differences in visual short-term memory (VSTM) functioning. Event related potentials were recorded from 50 introverts and 50 extraverts while they performed a VSTM task based on a color-change detection paradigm with three different set sizes. Although introverts and extraverts showed almost identical hit rates and reaction times, introverts displayed larger N1 amplitudes than extraverts independent of color change or set size. Extraverts also showed larger P3 amplitudes compared to introverts when there was a color change, whereas no extraversion-related difference in P3 amplitude was found in the no-change condition. Our findings provided the first experimental evidence that introverts' greater reactivity to punctuate physical stimulation, as indicated by larger N1 amplitude, also holds for complex visual stimulus patterns. Furthermore, P3 amplitude in the change condition was larger for extraverts than introverts suggesting higher sensitivity to context change. Finally, there were no extraversion-related differences in P3 amplitude dependent on set size. This latter finding does not support the resource allocation explanation as a source of differences between introverts and extraverts.

Vulnerability Following a Critical Life Event: Temporary Crisis or Chronic Distress? A Psychological Controversy, Methodological Considerations, and Empirical Evidence

This contribution deals with psychological vulnerability resulting from marital breakup after a long-term relationship. Despite the existing vast body of consolidated knowledge on divorce and psychological adaptation, there are still several controversies concerning the vulnerabilizing impact of marital breakup. One major issue refers to the question of whether vulnerability after marital breakup is a temporary crisis or rather a chronic strain. In this chapter we want to present two possible methodological options to tackle this question: First, comparing a sample of almost 1000 middle-aged persons, who were married on average 19 years, and who experienced a marital split within the last 5 years (4 time groups), with a group of age-matched married controls with regard to various indicators of psychological vulnerability (such as depression and hopelessness). Second, comparing within the divorced group the most vulnerable individuals (in terms of depression, hopelessness, life satisfaction) with those who were the least affected, regarding intra-personal resources (personality, resilience), divorce circumstances, post-divorce situation, and socio-economic resources. The study results underline the vulnerabilizing impact of marital breakup, but at the same time they reveal individual differences in psychological adaptation especially due to personality, new partnership, economic resources, and last but not least due to time. Furthermore our data strongly suggest that there is not a generalized psychological vulnerability after marital breakup, but that the emotional dimensions such as depression or feelings of not overcoming the loss are more affected than the more cognitive ones such as life satisfaction.

Mechanistic aspects of mRNA targeting for nonsense-mediated mRNA decay in human cells

The nonsense-mediated mRNA decay (NMD) pathway is best known as a translation-coupled quality control system that recognizes and degrades aberrant mRNAs with ORF-truncating premature termination codons (PTCs), but a more general role of NMD in posttranscriptional regulation of gene expression is indicated by transcriptome-wide mRNA profilings that identified a plethora of physiological mRNAs as NMD substrates. We try to decipher the mechanism of mRNA targeting to the NMD pathway in human cells. Recruitment of the conserved RNA-binding helicase UPF1 to target mRNAs has been reported to occur through interaction with release factors at terminating ribosomes, but evidence for translation-independent interaction of UPF1 with the 3’ untranslated region (UTR) of mRNAs has also been reported. We have transcriptome-wide determined the UPF1 binding sites by individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) in human cells, untreated or after inhibiting translation. We detected a strongly enriched association of UPF1 with 3’ UTRs in undisturbed, translationally active cells. After translation inhibition, a significant increase in UPF1 binding to coding sequence (CDS) was observed, indicating that UPF1 binds RNA before translation and gets displaced from the CDS by translating ribosomes. This suggests that the decision to trigger NMD occurs after association of UPF1 with mRNA, presumably through activation of RNA-bound UPF1 by aberrant translation termination. In a second recent study, we re-visited the reported restriction of NMD in mammals to the ‘pioneer round of translation’, i.e. to cap-binding complex (CBC)-bound mRNAs. The limitation of mammalian NMD to early rounds of translation would indicate a – from an evolutionary perspective – unexpected mechanistic difference to NMD in yeast and plants, where PTC-containing mRNAs seem to be available to NMD at each round of translation. In contrast to previous reports, our comparison of decay kinetics of two NMD reporter genes in mRNA fractions bound to either CBC or the eukaryotic initiation factor 4E (eIF4E) in human cells revealed that NMD destabilizes eIF4E-bound transcripts as efficiently as those associated with CBC. These results corroborate an emerging unified model for NMD substrate recognition, according to which NMD can ensue at every aberrant translation termination event.

Measurement of the distributions of event-by-event flow harmonics in lead-lead collisions at = 2.76 TeV with the ATLAS detector at the LHC

The distributions of event-by-event harmonic flow coefficients v_n for n=2-4 are measured in sqrt(s_NN)=2.76 TeV Pb+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using charged particles with transverse momentum pT> 0.5 GeV and in the pseudorapidity range |eta|<2.5 in a dataset of approximately 7 ub^-1 recorded in 2010. The shapes of the v_n distributions are described by a two-dimensional Gaussian function for the underlying flow vector in central collisions for v_2 and over most of the measured centrality range for v_3 and v_4. Significant deviations from this function are observed for v_2 in mid-central and peripheral collisions, and a small deviation is observed for v_3 in mid-central collisions. It is shown that the commonly used multi-particle cumulants are insensitive to the deviations for v_2. The v_n distributions are also measured independently for charged particles with 0.51 GeV. When these distributions are rescaled to the same mean values, the adjusted shapes are found to be nearly the same for these two pT ranges. The v_n distributions are compared with the eccentricity distributions from two models for the initial collision geometry: a Glauber model and a model that includes corrections to the initial geometry due to gluon saturation effects. Both models fail to describe the experimental data consistently over most of the measured centrality range.

Characterisation and mitigation of beam-induced backgrounds observed in the ATLAS detector during the 2011 proton-proton run

This paper presents a summary of beam-induced backgrounds observed in the ATLAS detector and discusses methods to tag and remove background contaminated events in data. Trigger-rate based monitoring of beam-related backgrounds is presented. The correlations of backgrounds with machine conditions, such as residual pressure in the beam-pipe, are discussed. Results from dedicated beam-background simulations are shown, and their qualitative agreement with data is evaluated. Data taken during the passage of unpaired, i.e. non-colliding, proton bunches is used to obtain background-enriched data samples. These are used to identify characteristic features of beam-induced backgrounds, which then are exploited to develop dedicated background tagging tools. These tools, based on observables in the Pixel detector, the muon spectrometer and the calorimeters, are described in detail and their efficiencies are evaluated. Finally an example of an application of these techniques to a monojet analysis is given, which demonstrates the importance of such event cleaning techniques for some new physics searches.

Does World Natural Heritage status trigger sustainable regional development efforts?

Today, there are over 200 World Natural Heritage (WNH) sites. Although the original aim of the World Heritage (WH) Convention was to spark off concerted international efforts to preserve sites of outstanding and universal value, today a multitude of expectations rests on WNH sites in terms of conservation, tourism, management and regional development. This paper identifies the effects of WNH status on sustainable regional development and the driving factors behind these effects. The results are based on a global survey of WNH sites and qualitative interviews with key WNH personnel. The paper shows that WNH status can be an important trigger for sustainable regional development, but its effectiveness depends on a number of intricately interwoven ‘soft’ success factors. Clearer policies and management guidelines, as envisaged by UNESCO, are crucial to achieving a balance between conservation and development.