A comprehensive view of Kara Sea polynya dynamics, sea-ice compactness and export from model and remote sensing data

The Shelf Seas of the Arctic are known for their large sea-ice production. This paper presents a comprehensive view of the Kara Sea sea-ice cover from high-resolution numerical modeling and space-borne microwave radiometry. As given by the latter the average polynya area in the Kara Sea takes a value of 21.2 x 10³ km² ± 9.1 x 10³ km² for winters (Jan.–Apr.) 1996/97 to 2000/01, being as high as 32.0 x 10³km² in 1999/2000 and below 12 x 10³ km² in 1998/99. Day-to-day variations of the Kara Sea polynya area can be as high as 50 x 10³ km². For the seasons 1996/ 97 to 2000/01 the modeled cumulative winter ice-volume flux out of the Kara Sea varied between 100 km³a¹ and 350 km³a¹. Modeled high (low) ice export coincides with a high (low) average and cumulative polynya area, and with a low (high) sea-ice compactness in the Kara Sea from remote sensing data, and with a high (low) sea-ice drift speed across its northern boundary derived from independent model data for the winters 1996/97 to 2000/0

Memristive behavior in a junctionless flash memory cell

We report charge storage based memristive operation of a junctionless thin film flash memory cell when it is operated as a two terminal device by grounding the gate. Unlike memristors based on nanoionics, the presented device mode, which we refer to as the flashristor mode, potentially allows greater control over the memristive properties, allowing rational design. The mode is demonstrated using a depletion type n-channel ZnO transistor grown by atomic layer deposition (ALD), with HfO2 as the tunnel dielectric, Al2O3 as the control dielectric, and non-stoichiometric silicon nitride as the charge storage layer. The device exhibits the pinched hysteresis of a memristor and in the unoptimized device, Roff/Ron ratios of about 3 are presented with low operating voltages below 5 V. A simplified model predicts Roff/Ron ratios can be improved significantly by adjusting the native threshold voltage of the devices. The repeatability of the resistive switching is excellent and devices exhibit 106s retention time, which can, in principle, be improved by engineering the gate stack and storage layer properties. The flashristor mode can find use in analog information processing applications, such as neuromorphic computing, where well-behaving and highly repeatable memristive properties are desirable. © 2015 AIP Publishing LLC

Impact of pro-domain stability of matrix metalloproteinase-8 on the outcome of sepsis

Citation: Berx, B., M. Dickey-Collas, M.D. Skogen, Y.-H. De Roeck, H. Klein, R. Barciela, R.M. Forster, E. Dombrowsky, M. Huret, M. Payne, Y. Sagarminaga, and C. Schrum. 2011. Does operational oceanography address the needs of fisheries and applied environmental scientists? Oceanography 24(1):166–171, doi:10.5670/oceanog.2011.14.Although many oceanographic data products are now considered operational, continued dialogue between data producers and their user communities is still needed. The fisheries and environmental science communities have often been criticized for their lack of multidisciplinarity, and it is not clear whether recent developments in operational oceanographic products are addressing these needs. The International Council for the Exploration of the Sea (ICES) Working Group on Operational Oceanographic products for Fisheries and Environment (WGOOFE) identified a potential mismatch between user requirements and the perception of requirements by the providers. Through a questionnaire (98 respondents), WGOOFE identified some of these issues. Although products of physical variables were in higher demand, several biological parameters scored in the top 10 rankings. Users placed specific focus on historic time series products with monthly or annual resolution and updating on similar time scales. A significant percentage requested access to numerical data rather than graphical output. While the outcomes of this survey challenge our views of operational oceanography, several initiatives are already attempting to close the gap between user requirements and products available

ProDy: Protein Dynamics Inferred from Theory and Experiments

Summary: We developed a Python package, ProDy, for structure-based analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations in heterogeneous datasets of structures experimentally resolved for a given biomolecular system, and for comparison of these variations with the theoretically predicted equilibrium dynamics. Datasets include structural ensembles for a given family or subfamily of proteins, their mutants and sequence homologues, in the presence/absence of their substrates, ligands or inhibitors. Numerous helper functions enable comparative analysis of experimental and theoretical data, and visualization of the principal changes in conformations that are accessible in different functional states. ProDy application programming interface (API) has been designed so that users can easily extend the software and implement new methods

Micro-CT Based Experimental Liver Imaging Using a Nanoparticulate Contrast Agent: A Longitudinal Study in Mice

BACKGROUND: Micro-CT imaging of liver disease in mice relies on high soft tissue contrast to detect small lesions like liver metastases. Purpose of this study was to characterize the localization and time course of contrast enhancement of a nanoparticular alkaline earth metal-based contrast agent (VISCOVER ExiTron nano) developed for small animal liver CT imaging. METHODOLOGY: ExiTron nano 6000 and ExiTron nano 12000, formulated for liver/spleen imaging and angiography, respectively, were intravenously injected in C57BL/6J-mice. The distribution and time course of contrast enhancement were analysed by repeated micro-CT up to 6 months. Finally, mice developing liver metastases after intrasplenic injection of colon carcinoma cells underwent longitudinal micro-CT imaging after a single injection of ExiTron nano. PRINCIPAL FINDINGS: After a single injection of ExiTron nano the contrast of liver and spleen peaked after 4-8 hours, lasted up to several months and was tolerated well by all mice. In addition, strong contrast enhancement of abdominal and mediastinal lymph nodes and the adrenal glands was observed. Within the first two hours after injection, particularly ExiTron nano 12000 provided pronounced contrast for imaging of vascular structures. ExiTron nano facilitated detection of liver metastases and provided sufficient contrast for longitudinal observation of tumor development over weeks. CONCLUSIONS: The nanoparticulate contrast agents ExiTron nano 6000 and 12000 provide strong contrast of the liver, spleen, lymph nodes and adrenal glands up to weeks, hereby allowing longitudinal monitoring of pathological processes of these organs in small animals, with ExiTron nano 12000 being particularly optimized for angiography due to its very high initial vessel contrast

Troubling stories of the end of occupy : feminist narratives of betrayal at occupy Glasgow

This article offers a feminist take on the question of why Occupy camps closed down, in the form of a narrative analysis of interviews from participants in Occupy Glasgow. In response to the emergence of an activist discourse emphasising the role of external forces in camp closure and the existence of a longer-term legacy in terms of individual and community politicisation, I build here on feminist interventions that point instead to serious internal problems within the camps and thus to a more limited legacy. Interrogating the plotting, characterisation and denouement of interviewee narratives, I show that feminist participants in Occupy Glasgow characterise the trajectory of the camp as a tragedy, attribute responsibility for the camp’s demise to co-campers and sometimes to themselves, and present the outcome of Occupy Glasgow as limited, and in some cases even traumatic. This raises serious questions about the culmination and outcomes of Occupy in Glasgow and more generally, and indicates the extent of the hard work remaining if future mobilisation against neoliberal austerity is to be more inclusive and sustainable. The article closes by considering the theoretical implications for the wider question of why movements come to an end

The Use of Experimental Structures to Model Protein Dynamics

The number of solved protein structures submitted in the Protein Data Bank (PDB) has increased dramatically in recent years. For some specific proteins, this number is very high—for example, there are over 550 solved structures for HIV-1 protease, one protein that is essential for the life cycle of human immunodeficiency virus (HIV) which causes acquired immunodeficiency syndrome (AIDS) in humans. The large number of structures for the same protein and its variants include a sample of different conformational states of the protein. A rich set of structures solved experimentally for the same protein has information buried within the dataset that can explain the functional dynamics and structural mechanism of the protein. To extract the dynamics information and functional mechanism from the experimental structures, this chapter focuses on two methods—Principal Component Analysis (PCA) and Elastic Network Models (ENM). PCA is a widely used statistical dimensionality reduction technique to classify and visualize high-dimensional data. On the other hand, ENMs are well-established simple biophysical method for modeling the functionally important global motions of proteins. This chapter covers the basics of these two. Moreover, an improved ENM version that utilizes the variations found within a given set of structures for a protein is described. As a practical example, we have extracted the functional dynamics and mechanism of HIV-1 protease dimeric structure by using a set of 329 PDB structures of this protein. We have described, step by step, how to select a set of protein structures, how to extract the needed information from the PDB files for PCA, how to extract the dynamics information using PCA, how to calculate ENM modes, how to measure the congruency between the dynamics computed from the principal components (PCs) and the ENM modes, and how to compute entropies using the PCs. We provide the computer programs or references to software tools to accomplish each step and show how to use these programs and tools. We also include computer programs to generate movies based on PCs and ENM modes and describe how to visualize them

On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm

N-Acetyl-L-Glutamate Kinase (NAGK) is the structural paradigm for examining the catalytic mechanisms and dynamics of amino acid kinase family members. Given that the slow conformational dynamics of the NAGK (at the microseconds time scale or slower) may be rate-limiting, it is of importance to assess the mechanisms of the most cooperative modes of motion intrinsically accessible to this enzyme. Here, we present the results from normal mode analysis using an elastic network model representation, which shows that the conformational mechanisms for substrate binding by NAGK strongly correlate with the intrinsic dynamics of the enzyme in the unbound form. We further analyzed the potential mechanisms of allosteric signalling within NAGK using a Markov model for network communication. Comparative analysis of the dynamics of family members strongly suggests that the low-frequency modes of motion and the associated intramolecular couplings that establish signal transduction are highly conserved among family members, in support of the paradigm sequence→structure→dynamics→function © 2010 Marcos et al

Season of birth and handedness in Serbian high school students

<p>Abstract</p> <p>Background</p> <p>Although behavioural dominance of the right hand in humans is likely to be under genetic control, departures from this population norm, i.e. left- or non-right-handedness, are believed to be influenced by environmental factors. Among many such environmental factors including, for example, low birth weight, testosterone level, and maternal age at birth, season of birth has occasionally been investigated. The overall empirical evidence for the season of birth effect is mixed.</p> <p>Methods</p> <p>We have investigated the effect of season of birth in an epidemiologically robust sample of randomly selected young people (n = 977), all born in the same year. A Kolmogorov-Smirnov type statistical test was used to determine season of birth.</p> <p>Results</p> <p>Neither the right-handed nor the non-right-handed groups demonstrated birth asymmetry relative to the normal population birth distribution. There was no between-group difference in the seasonal distribution of birth when comparing the right-handed to the non-right-handed groups.</p> <p>Conclusion</p> <p>The present study failed to provide support for a season of birth effect on atypical lateralisation of handedness in humans.</p