Showing papers by "University of Jyväskylä published in 2014"

Performance of the ALICE experiment at the CERN LHC

Abstract: ALICE is the heavy-ion experiment at the CERN Large Hadron Collider. The experiment continuously took data during the first physics campaign of the machine from fall 2009 until early 2013, using proton and lead-ion beams. In this paper we describe the running environment and the data handling procedures, and discuss the performance of the ALICE detectors and analysis methods for various physics observables.

Tracking of physical activity from early childhood through youth into adulthood.

Abstract: PurposeThe aim of the study was to investigate the tracking of physical activity (PA) from preschool age to adulthood in six age cohorts of males and females.MethodsA random sample of 3596 boys and girls age 3–18 yr participated in the Cardiovascular Risks in Young Finns Study in 1980. The f

A synthesis of methane emissions from 71 northern, temperate, and subtropical wetlands

Abstract: Wetlands are the largest natural source of atmospheric methane. Here, we assess controls on methane flux using a database of approximately 19 000 instantaneous measurements from 71 wetland sites located across subtropical, temperate, and northern high latitude regions. Our analyses confirm general controls on wetland methane emissions from soil temperature, water table, and vegetation, but also show that these relationships are modified depending on wetland type (bog, fen, or swamp), region (subarctic to temperate), and disturbance. Fen methane flux was more sensitive to vegetation and less sensitive to temperature than bog or swamp fluxes. The optimal water table for methane flux was consistently below the peat surface in bogs, close to the peat surface in poor fens, and above the peat surface in rich fens. However, the largest flux in bogs occurred when dry 30-day averaged antecedent conditions were followed by wet conditions, while in fens and swamps, the largest flux occurred when both 30-day averaged antecedent and current conditions were wet. Drained wetlands exhibited distinct characteristics, e.g. the absence of large flux following wet and warm conditions, suggesting that the same functional relationships between methane flux and environmental conditions cannot be used across pristine and disturbed wetlands. Together, our results suggest that water table and temperature are dominant controls on methane flux in pristine bogs and swamps, while other processes, such as vascular transport in pristine fens, have the potential to partially override the effect of these controls in other wetland types. Because wetland types vary in methane emissions and have distinct controls, these ecosystems need to be considered separately to yield reliable estimates of global wetland methane release.

Gyrification from constrained cortical expansion

Abstract: The exterior of the mammalian brain—the cerebral cortex—has a conserved layered structure whose thickness varies little across species. However, selection pressures over evolutionary time scales have led to cortices that have a large surface area to volume ratio in some organisms, with the result that the brain is strongly convoluted into sulci and gyri. Here we show that the gyrification can arise as a nonlinear consequence of a simple mechanical instability driven by tangential expansion of the gray matter constrained by the white matter. A physical mimic of the process using a layered swelling gel captures the essence of the mechanism, and numerical simulations of the brain treated as a soft solid lead to the formation of cusped sulci and smooth gyri similar to those in the brain. The resulting gyrification patterns are a function of relative cortical expansion and relative thickness (compared with brain size), and are consistent with observations of a wide range of brains, ranging from smooth to highly convoluted. Furthermore, this dependence on two simple geometric parameters that characterize the brain also allows us to qualitatively explain how variations in these parameters lead to anatomical anomalies in such situations as polymicrogyria, pachygyria, and lissencephalia.

Physical Activity of Children: A Global Matrix of Grades Comparing 15 Countries

Abstract: The Active Healthy Kids Canada (AHKC) Report Card on Physical Activity for Children and Youth has been effective in powering the movement to get kids moving by influencing priorities, policies, and practice in Canada. The AHKC Report Card process was replicated in 14 additional countries from 5 continents using 9 common indicators (Overall Physical Activity, Organized Sport Participation, Active Play, Active Transportation, Sedentary Behavior, Family and Peers, School, Community and Built Environment, and Government Strategies and Investments), a harmonized process and a standardized grading framework. The 15 Report Cards were presented at the Global Summit on the Physical Activity of Children in Toronto on May 20, 2014. The consolidated findings are summarized here in the form of a global matrix of grades. There is a large spread in grades across countries for most indicators. Countries that lead in certain indicators lag in others. Overall, the grades for indicators of physical activity (PA) around the world are low/poor. Many countries have insufficient information to assign a grade, particularly for the Active Play and Family and Peers indicators. Grades for Sedentary Behaviors are, in general, better in low income countries. The Community and Built Environment indicator received high grades in high income countries and notably lower grades in low income countries. There was a pattern of higher PA and lower sedentary behavior in countries reporting poorer infrastructure, and lower PA and higher sedentary behavior in countries reporting better infrastructure, which presents an interesting paradox. Many surveillance and research gaps and weaknesses were apparent. International cooperation and cross-fertilization is encouraged to tackle existing challenges, understand underlying mechanisms, derive innovative solutions, and overcome the expanding childhood inactivity crisis.

Direct observation of a borane–silane complex involved in frustrated Lewis-pair-mediated hydrosilylations

Abstract: Perfluorarylborane Lewis acids catalyse the addition of silicon-hydrogen bonds across C=C, C=N and C=O double bonds. This 'metal-free' hydrosilylation has been proposed to occur via borane activation of the silane Si-H bond, rather than through classical Lewis acid/base adducts with the substrate. However, the key borane/silane adduct had not been observed experimentally. Here it is shown that the strongly Lewis acidic, antiaromatic 1,2,3-tris(pentafluorophenyl)-4,5,6,7-tetrafluoro-1-boraindene forms an observable, isolable adduct with triethylsilane. The equilibrium for adduct formation was studied quantitatively through variable-temperature NMR spectroscopic investigations. The interaction of the silane with the borane occurs through the Si-H bond, as evidenced by trends in the Si-H coupling constant and the infrared stretching frequency of the Si-H bond, as well as by X-ray crystallography and theoretical calculations. The adduct's reactivity with nucleophiles demonstrates conclusively the role of this species in metal-free 'frustrated-Lewis-pair' hydrosilylation reactions.

Signal amplification and transduction in phytochrome photosensors

Abstract: Sensory proteins must relay structural signals from the sensory site over large distances to regulatory output domains. Phytochromes are a major family of red-light-sensing kinases that control diverse cellular functions in plants, bacteria and fungi. Bacterial phytochromes consist of a photosensory core and a carboxy-terminal regulatory domain. Structures of photosensory cores are reported in the resting state and conformational responses to light activation have been proposed in the vicinity of the chromophore. However, the structure of the signalling state and the mechanism of downstream signal relay through the photosensory core remain elusive. Here we report crystal and solution structures of the resting and activated states of the photosensory core of the bacteriophytochrome from Deinococcus radiodurans. The structures show an open and closed form of the dimeric protein for the activated and resting states, respectively. This nanometre-scale rearrangement is controlled by refolding of an evolutionarily conserved 'tongue', which is in contact with the chromophore. The findings reveal an unusual mechanism in which atomic-scale conformational changes around the chromophore are first amplified into an angstrom-scale distance change in the tongue, and further grow into a nanometre-scale conformational signal. The structural mechanism is a blueprint for understanding how phytochromes connect to the cellular signalling network.

School burnout and engagement in the context of demands-resources model

Abstract: Background. A four-wave longitudinal study tested the demands–resources model in the school context. Aim. To examine the applicability of the demands–resources to the school context. Method. Data of 1,709 adolescents were gathered, once during the transition from comprehensive to post-comprehensive education, twice during post-comprehensive education, and once 2 years later. Results. The hypotheses were supported, path analysis showing that study demands were related to school burnout a year later, while study resources were related to schoolwork engagement. Self-efficacy was positively related to engagement and negatively to burnout. School burnout predicted schoolwork engagement negatively 1 year later. Engagement was positively related to life satisfaction 2 years later, while burnout was related to depressive symptoms. Finally, burnout mediated the relationship between study demands and mental health outcomes. Conclusions. The demands–resources model can usefully be applied to the school context, including the associations between school-related burnout and engagement among adolescents. The model comprises two processes, the energy-depleting process and the motivational process.

Are They Different? Affect, Feeling, Emotion, Sentiment, and Opinion Detection in Text

Abstract: A major limitation in the automatic detection of affect, feelings, emotions, sentiments, and opinions in text is the lack of proper differentiation between these subjective terms and understanding of how they relate to one another. This lack of differentiation not only leads to inconsistency in terminology usage but also makes the subtleties and nuances expressed by the five terms difficult to understand, resulting in subpar detection of the terms in text. In light of such limitation, this paper clarifies the differences between these five subjective terms and reveals significant concepts to the computational linguistics community for their effective detection and processing in text.

Electron microscopy of gold nanoparticles at atomic resolution

Abstract: Structure determination of gold nanoparticles (AuNPs) is necessary for understanding their physical and chemical properties, but only one AuNP larger than 1 nanometer in diameter [a 102-gold atom NP (Au102NP)] has been solved to atomic resolution. Whereas the Au102NP structure was determined by x-ray crystallography, other large AuNPs have proved refractory to this approach. Here, we report the structure determination of a Au68NP at atomic resolution by aberration-corrected transmission electron microscopy, performed with the use of a minimal electron dose, an approach that should prove applicable to metal NPs in general. The structure of the Au68NP was supported by small-angle x-ray scattering and by comparison of observed infrared absorption spectra with calculations by density functional theory.

Error Estimates of Theoretical Models: a Guide

Abstract: This guide offers suggestions/insights on uncertainty quantification of nuclear structure models. We discuss a simple approach to statistical-error estimates, strategies to assess systematic errors, and show how to uncover inter-dependences by correlation analysis. The basic concepts are illustrated through simple examples. By providing theoretical error bars on predicted quantities and using statistical methods to study correlations between observables, theory can significantly enhance the feedback between experiment and nuclear modeling.

Technical design report for the upgrade of the ALICE inner tracking system

Abstract: ALICE (A Large Ion Collider Experiment) is studying the physics of strongly interacting matter, and in particular the properties of the Quark–Gluon Plasma (QGP), using proton–proton, proton–nucleus and nucleus–nucleus collisions at the CERN LHC (Large Hadron Collider). The ALICE Collaboration is preparing a major upgrade of the experimental apparatus, planned for installation in the second long LHC shutdown in the years 2018–2019. A key element of the ALICE upgrade is the construction of a new, ultra-light, high- resolution Inner Tracking System (ITS) based on monolithic CMOS pixel detectors. The primary focus of the ITS upgrade is on improving the performance for detection of heavy-flavour hadrons, and of thermal photons and low-mass di- electrons emitted by the QGP. With respect to the current detector, the new Inner Tracking System will significantly enhance the determination of the distance of closest approach to the primary vertex, the tracking efficiency at low transverse momenta, and the read-out rate capabilities. This will be obtained by seven concentric detector layers based on a 50 μm thick CMOS pixel sensor with a pixel pitch of about 30×30 μm2. This document, submitted to the LHCC (LHC experiments Committee) in September 2013, presents the design goals, a summary of the R&D activities, with focus on the technical implementation of the main detector components, and the projected detector and physics performance.

Engineering thermal conductance using a two-dimensional phononic crystal

Abstract: Controlling thermal transport is commonly achieved by introducing scattering centres. Here, the authors demonstrate that coherent band structure effects can also be used to control phonon transport, via the use of periodically nanostructured phononic crystals.

Hidden oscillations in mathematical model of drilling system actuated by induction motor with a wound rotor

Abstract: This work is devoted to the investigation of mathematical models of drilling systems described by ordinary differential equations. Here, we continue the study done by the researchers from Eindhoven where the two-mass mathematical model of a drilling system has been investigated (Mihajlovic et al. J. Dyn. Syst. Meas. Control 126(4): 709–720, 2004; de Bruin et al. Automatica 45(2): 405–415, 2009). The modified version of this model, which takes into account a full description of an induction motor, is studied. It is shown that such complex effects as hidden oscillations may appear in these kinds of systems. These effects may lead to drill string failures and breakdowns.

Seeing a single molecule vibrate through time-resolved coherent anti-Stokes Raman scattering

Abstract: The vibrations of the chemical bonds of a single molecule are observed by employing time-resolved coherent anti-Stokes Raman scattering. A gold nanoantenna is used to enhance the signal from the molecule.

Nanomolar Pyrophosphate Detection in Water and in a Self-Assembled Hydrogel of a Simple Terpyridine-Zn2+ Complex

Abstract: A simple terpyridine-Zn(II) complex is shown to act as an efficient and highly selective fluorescent sensor for pyrophosphate in water at physiological pH. The sensor complex showed an unprecedented fluorescence response (∼500 fold increase) and a record nanomolar sensitivity (detectable fluorescent response at 20 nM and LOD ∼ 0.8 nM). It has successfully been used to stain and record confocal fluorescence microscopy images of HeLa cells. Moreover, the complex was found to self-assemble into a hydrogel which was subsequently used to coat disposable paper strips for easy, low-cost detection of pyrophosphate.

Upgrade of the ALICE Experiment Letter Of Intent

Abstract: ALICE (A Large Ion Collider Experiment) is studying the physics of strongly interacting matter, and in particular the properties of the Quark–Gluon Plasma (QGP), using proton–proton, proton–nucleus and nucleus–nucleus collisions at the CERN LHC (Large Hadron Collider). The ALICE Collaboration is preparing a major upgrade of the experimental apparatus, planned for installation in the second long LHC shutdown in the years 2018–2019. These plans are presented in the ALICE Upgrade Letter of Intent, submitted to the LHCC (LHC experiments Committee) in September 2012. In order to fully exploit the physics reach of the LHC in this field, high-precision measurements of the heavy-flavour production, quarkonia, direct real and virtual photons, and jets are necessary. This will be achieved by an increase of the LHC Pb–Pb instant luminosity up to 6×1027 cm−2s−1 and running the ALICE detector with the continuous readout at the 50 kHz event rate. The physics performance accessible with the upgraded detector, together with the main detector modifications, are presented.

Unravelling biodiversity, evolution and threats to conservation in the Sahara‐Sahel

Abstract: Deserts and arid regions are generally perceived as bare and rather homogeneous areas of low diversity. The Sahara is the largest warm desert in the world and together with the arid Sahel displays high topographical and climatic heterogeneity, and has experienced recent and strong climatic oscillations that have greatly shifted biodiversity distribution and community composition. The large size, remoteness and long-term political instability of the Sahara-Sahel, have limited knowledge on its biodiversity. However, over the last decade, there have been an increasing number of published scientific studies based on modern geomatic and molecular tools, and broad sampling of taxa of these regions. This review tracks trends in knowledge about biodiversity patterns, processes and threats across the Sahara-Sahel, and anticipates needs for biodiversity research and conservation. Recent studies are changing completely the perception of regional biodiversity patterns. Instead of relatively low species diversity with distribution covering most of the region, studies now suggest a high rate of endemism and larger number of species, with much narrower and fragmented ranges, frequently limited to micro-hotspots of biodiversity. Molecular-based studies are also unravelling cryptic diversity associated with mountains, which together with recent distribution atlases, allows identifying integrative biogeographic patterns in biodiversity distribution. Mapping of multivariate environmental variation (at 1 km × 1 km resolution) of the region illustrates main biogeographical features of the Sahara-Sahel and supports recently hypothesised dispersal corridors and refugia. Micro-scale water-features present mostly in mountains have been associated with local biodiversity hotspots. However, the distribution of available data on vertebrates highlights current knowledge gaps that still apply to a large proportion of the Sahara-Sahel. Current research is providing insights into key evolutionary and ecological processes, including causes and timing of radiation and divergence for multiple taxa, and associating the onset of the Sahara with diversification processes for low-mobility vertebrates. Examples of phylogeographic patterns are showing the importance of allopatric speciation in the Sahara-Sahel, and this review presents a synthetic overview of the most commonly hypothesised diversification mechanisms. Studies are also stressing that biodiversity is threatened by increasing human activities in the region, including overhunting and natural resources prospection, and in the future by predicted global warming. A representation of areas of conflict, landmines, and natural resources extraction illustrates how human activities and regional insecurity are hampering biodiversity research and conservation. Although there are still numerous knowledge gaps for the optimised conservation of biodiversity in the region, a set of research priorities is provided to identify the framework data needed to support regional conservation planning.

Nuclear energy density optimization: Shell structure

Abstract: Background: Nuclear density functional theory is the only microscopical theory that can be applied throughout the entire nuclear landscape. Its key ingredient is the energy density functional.Purpose: In this work, we propose a new parametrization unedf2 of the Skyrme energy density functional.Methods: The functional optimization is carried out using the pounders optimization algorithm within the framework of the Skyrme Hartree-Fock-Bogoliubov theory. Compared to the previous parametrization unedf1, restrictions on the tensor term of the energy density have been lifted, yielding a very general form of the energy density functional up to second order in derivatives of the one-body density matrix. In order to impose constraints on all the parameters of the functional, selected data on single-particle splittings in spherical doubly-magic nuclei have been included into the experimental dataset.Results: The agreement with both bulk and spectroscopic nuclear properties achieved by the resulting unedf2 parametrization is comparable with unedf1. While there is a small improvement on single-particle spectra and binding energies of closed shell nuclei, the reproduction of fission barriers and fission isomer excitation energies has degraded. As compared to previous unedf parametrizations, the parameter confidence interval for unedf2 is narrower. In particular, our results overlap well with those obtained in previous systematic studies of the spin-orbit and tensor terms.Conclusions: unedf2 can be viewed as an all-around Skyrme EDF that performs reasonably well for both global nuclear properties and shell structure. However, after adding new data aiming to better constrain the nuclear functional, its quality has improved only marginally. These results suggest that the standard Skyrme energy density has reached its limits, and significant changes to the form of the functional are needed.

Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser.

Abstract: We describe a method to measure ultrafast protein structural changes using time-resolved wide-angle X-ray scattering at an X-ray free-electron laser. We demonstrated this approach using multiphoton excitation of the Blastochloris viridis photosynthetic reaction center, observing an ultrafast global conformational change that arises within picoseconds and precedes the propagation of heat through the protein. This provides direct structural evidence for a 'protein quake': the hypothesis that proteins rapidly dissipate energy through quake-like structural motions.

Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge

Abstract: Ewald summation, which has become the de facto standard for computing electrostatic interactions in biomolecular simulations, formally requires that the simulation box is neutral. For non-neutral systems, the Ewald algorithm implicitly introduces a uniform background charge distribution that effectively neutralizes the simulation box. Because a uniform distribution of counter charges typically deviates from the spatial distribution of counterions in real systems, artifacts may arise, in particular in systems with an inhomogeneous dielectric constant. Here, we derive an analytical expression for the effect of using an implicit background charge instead of explicit counterions, on the chemical potential of ions in heterogeneous systems, which (i) provides a quantitative criterium for deciding if the background charge offers an acceptable trade-off between artifacts arising from sampling problems and artifacts arising from the homogeneous background charge distribution, and (ii) can be used to correct this artifact in certain cases. Our model quantifies the artifact in terms of the difference in charge density between the non-neutral system with a uniform neutralizing background charge and the real neutral system with a physically correct distribution of explicit counterions. We show that for inhomogeneous systems, such as proteins and membranes in water, the artifact manifests itself by an overstabilization of ions inside the lower dielectric by tens to even hundreds kilojoules per mole. We have tested the accuracy of our model in molecular dynamics simulations and found that the error in the calculated free energy for moving a test charge from water into hexadecane, at different net charges of the system and different simulation box sizes, is correctly predicted by the model. The calculations further confirm that the incorrect distribution of counter charges in the simulation box is solely responsible for the errors in the PMFs.

Too Fit To Fracture: exercise recommendations for individuals with osteoporosis or osteoporotic vertebral fracture

Abstract: Summary A consensus process was conducted to develop exercise recommendations for individuals with osteoporosis or vertebral fractures. A multicomponent exercise program that includes balance and resistance training is recommended.