Showing papers by "University of Jyväskylä published in 2016"

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

A century of trends in adult human height

Abstract: Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.5–22.7) and 16.5 cm (13.3–19.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8–144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.

Electron-Ion Collider: The next QCD frontier: Understanding the glue that binds us all

Abstract: This White Paper presents the science case of an Electron-Ion Collider (EIC), focused on the structure and interactions of gluon-dominated matter, with the intent to articulate it to the broader nuclear science community. It was commissioned by the managements of Brookhaven National Laboratory (BNL) and Thomas Jefferson National Accelerator Facility (JLab) with the objective of presenting a summary of scientific opportunities and goals of the EIC as a follow-up to the 2007 NSAC Long Range plan. This document is a culmination of a community-wide effort in nuclear science following a series of workshops on EIC physics over the past decades and, in particular, the focused ten-week program on “Gluons and quark sea at high energies” at the Institute for Nuclear Theory in Fall 2010. It contains a brief description of a few golden physics measurements along with accelerator and detector concepts required to achieve them. It has been benefited profoundly from inputs by the users’ communities of BNL and JLab. This White Paper offers the promise to propel the QCD science program in the US, established with the CEBAF accelerator at JLab and the RHIC collider at BNL, to the next QCD frontier.

Neutrino Physics with JUNO

Abstract: The Jiangmen Underground Neutrino Observatory (JUNO), a 20 kton multi-purpose underground liquid scintillator detector, was proposed with the determination of the neutrino mass hierarchy (MH) as a primary physics goal. The excellent energy resolution and the large fiducial volume anticipated for the JUNO detector offer exciting opportunities for addressing many important topics in neutrino and astro-particle physics. In this document, we present the physics motivations and the anticipated performance of the JUNO detector for various proposed measurements. Following an introduction summarizing the current status and open issues in neutrino physics, we discuss how the detection of antineutrinos generated by a cluster of nuclear power plants allows the determination of the neutrino MH at a 3–4σ significance with six years of running of JUNO. The measurement of antineutrino spectrum with excellent energy resolution will also lead to the precise determination of the neutrino oscillation parameters ${\mathrm{sin}}^{2}{\theta }_{12}$, ${\rm{\Delta }}{m}_{21}^{2}$, and $| {\rm{\Delta }}{m}_{{ee}}^{2}| $ to an accuracy of better than 1%, which will play a crucial role in the future unitarity test of the MNSP matrix. The JUNO detector is capable of observing not only antineutrinos from the power plants, but also neutrinos/antineutrinos from terrestrial and extra-terrestrial sources, including supernova burst neutrinos, diffuse supernova neutrino background, geoneutrinos, atmospheric neutrinos, and solar neutrinos. As a result of JUNO's large size, excellent energy resolution, and vertex reconstruction capability, interesting new data on these topics can be collected. For example, a neutrino burst from a typical core-collapse supernova at a distance of 10 kpc would lead to ∼5000 inverse-beta-decay events and ∼2000 all-flavor neutrino–proton ES events in JUNO, which are of crucial importance for understanding the mechanism of supernova explosion and for exploring novel phenomena such as collective neutrino oscillations. Detection of neutrinos from all past core-collapse supernova explosions in the visible universe with JUNO would further provide valuable information on the cosmic star-formation rate and the average core-collapse neutrino energy spectrum. Antineutrinos originating from the radioactive decay of uranium and thorium in the Earth can be detected in JUNO with a rate of ∼400 events per year, significantly improving the statistics of existing geoneutrino event samples. Atmospheric neutrino events collected in JUNO can provide independent inputs for determining the MH and the octant of the ${\theta }_{23}$ mixing angle. Detection of the (7)Be and (8)B solar neutrino events at JUNO would shed new light on the solar metallicity problem and examine the transition region between the vacuum and matter dominated neutrino oscillations. Regarding light sterile neutrino topics, sterile neutrinos with ${10}^{-5}\,{{\rm{eV}}}^{2}\lt {\rm{\Delta }}{m}_{41}^{2}\lt {10}^{-2}\,{{\rm{eV}}}^{2}$ and a sufficiently large mixing angle ${\theta }_{14}$ could be identified through a precise measurement of the reactor antineutrino energy spectrum. Meanwhile, JUNO can also provide us excellent opportunities to test the eV-scale sterile neutrino hypothesis, using either the radioactive neutrino sources or a cyclotron-produced neutrino beam. The JUNO detector is also sensitive to several other beyondthe-standard-model physics. Examples include the search for proton decay via the $p\to {K}^{+}+\bar{ u }$ decay channel, search for neutrinos resulting from dark-matter annihilation in the Sun, search for violation of Lorentz invariance via the sidereal modulation of the reactor neutrino event rate, and search for the effects of non-standard interactions. The proposed construction of the JUNO detector will provide a unique facility to address many outstanding crucial questions in particle and astrophysics in a timely and cost-effective fashion. It holds the great potential for further advancing our quest to understanding the fundamental properties of neutrinos, one of the building blocks of our Universe.

On the growth and form of cortical convolutions

Abstract: A 3D-printed fetal brain undergoes constrained expansion to reproduce the shape of the human cerebral cortex. The soft gels of the model swell in solvent, mimicking cortical growth and revealing the mechanical origin of the brain’s folded geometry.

Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein.

Abstract: A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction.

EPPS16: Nuclear parton distributions with LHC data

Abstract: We introduce a global analysis of collinearly factorized nuclear parton distribution functions (PDFs) including, for the first time, data constraints from LHC proton-lead collisions. In comparison to our previous analysis, EPS09, where data only from charged-lepton-nucleus deep inelastic scattering (DIS), Drell-Yan (DY) dilepton production in proton-nucleus collisions and inclusive pion production in deuteron-nucleus collisions were the input, we now increase the variety of data constraints to cover also neutrino-nucleus DIS and low-mass DY production in pion-nucleus collisions. The new LHC data significantly extend the kinematic reach of the data constraints. We now allow much more freedom for the flavour dependence of nuclear effects than in other currently available analyses. As a result, especially the uncertainty estimates are more objective flavour by flavour. The neutrino DIS plays a pivotal role in obtaining a mutually consistent behaviour for both up and down valence quarks, and the LHC dijet data clearly constrain gluons at large momentum fraction. Mainly for insufficient statistics, the pion-nucleus DY and heavy gauge boson production in proton-lead collisions impose less visible constraints. The outcome - a new set of next-to-leading order nuclear PDFs called EPPS16 - is made available for applications in high-energy nuclear collisions.

Atomically Precise Alkynyl-Protected Metal Nanoclusters as a Model Catalyst: Observation of Promoting Effect of Surface Ligands on Catalysis by Metal Nanoparticles.

Abstract: Metal nanoclusters whose surface ligands are removable while keeping their metal framework structures intact are an ideal system for investigating the influence of surface ligands on catalysis of metal nanoparticles. We report in this work an intermetallic nanocluster containing 62 metal atoms, Au34Ag28(PhC≡C)34, and its use as a model catalyst to explore the importance of surface ligands in promoting catalysis. As revealed by single-crystal diffraction, the 62 metal atoms in the cluster are arranged as a four-concentric-shell Ag@Au17@Ag27@Au17 structure. All phenylalkynyl (PA) ligands are linearly coordinated to the surface Au atoms with staple "PhC≡C-Au-C≡CPh" motif. Compared with reported thiolated metal nanoclusters, the surface PA ligands on Au34Ag28(PhC≡C)34 are readily removed at relatively low temperatures, while the metal core remains intact. The clusters before and after removal of surface ligands are used as catalysts for the hydrolytic oxidation of organosilanes to silanols. It is, for the first time, demonstrated that the organic-capped metal nanoclusters work as active catalysts much better than those with surface ligands partially or completely removed.

Event-by-event fluctuations in a perturbative QCD + saturation + hydrodynamics model: Determining QCD matter shear viscosity in ultrarelativistic heavy-ion collisions

Abstract: This paper introduces an event-by-event perturbative QCD plus saturation framework for the initial state of high-energy heavy-ion collisions and evolves the matter using dissipative fluid dynamics. The results favor a ratio of shear viscosity-to-entropy density that has a minimum near a temperature of 150 MeV, in line with theoretical expectations.

Plasmonic twinned silver nanoparticles with molecular precision

Abstract: Determining the structures of nanoparticles at atomic resolution is vital to understand their structure–property correlations. Large metal nanoparticles with core diameter beyond 2 nm have, to date, eluded characterization by single-crystal X-ray analysis. Here we report the chemical syntheses and structures of two giant thiolated Ag nanoparticles containing 136 and 374 Ag atoms (that is, up to 3 nm core diameter). As the largest thiolated metal nanoparticles crystallographically determined so far, these Ag nanoparticles enter the truly metallic regime with the emergence of surface plasmon resonance. As miniatures of fivefold twinned nanostructures, these structures demonstrate a subtle distortion within fivefold twinned nanostructures of face-centred cubic metals. The Ag nanoparticles reported in this work serve as excellent models to understand the detailed structure distortion within twinned metal nanostructures and also how silver nanoparticles can span from the molecular to the metallic regime. The structure of nanoparticles strongly influences their properties. Here, the authors use single crystal X-ray diffraction to resolve the crystal structures of Ag136 and Ag374nanoparticles, enabling the observation of local structure distortion and the lower size limit of surface plasmon resonance.

A survey of serendipity in recommender systems

Abstract: We summarize most efforts on serendipity in recommender systems.We compare definitions of serendipity in recommender systems.We classify the state-of-the-art serendipity-oriented recommendation algorithms.We review methods to assess serendipity in recommender systems.We provide the future directions of serendipity in recommender systems. Recommender systems use past behaviors of users to suggest items. Most tend to offer items similar to the items that a target user has indicated as interesting. As a result, users become bored with obvious suggestions that they might have already discovered. To improve user satisfaction, recommender systems should offer serendipitous suggestions: items not only relevant and novel to the target user, but also significantly different from the items that the user has rated. However, the concept of serendipity is very subjective and serendipitous encounters are very rare in real-world scenarios, which makes serendipitous recommendations extremely difficult to study. To date, various definitions and evaluation metrics to measure serendipity have been proposed, and there is no wide consensus on which definition and evaluation metric to use. In this paper, we summarize most important approaches to serendipity in recommender systems, compare different definitions and formalizations of the concept, discuss serendipity-oriented recommendation algorithms and evaluation strategies to assess the algorithms, and provide future research directions based on the reviewed literature.

Organocatalytic Domino Oxa-Michael/1,6-Addition Reactions: Asymmetric Synthesis of Chromans Bearing Oxindole Scaffolds.

Abstract: An asymmetric organocatalytic domino oxa-Michael/1,6-addition reaction of ortho-hydroxyphenyl-substituted para-quinone methides and isatin-derived enoates has been developed. In the presence of 5 mol % of a bifunctional thiourea organocatalyst, this scalable domino reaction affords 4-phenyl-substituted chromans bearing spiro-connected oxindole scaffolds and three adjacent stereogenic centers in good to excellent yields (up to 98 %) and with very high stereoselectivities (up to >20:1 d.r., >99 % ee).

A meta-analysis of distributed leadership from 2002 to 2013 : Theory development, empirical evidence and future research focus

Abstract: This article provides a meta-analysis of research conducted on distributed leadership from 2002 to 2013. It continues the review of distributed leadership commissioned by the English National College for School Leadership (NCSL) (Distributed Leadership: A Desk Study, Bennett et al., 2003), which identified two gaps in the research during the 1996–2002 period. The review found that the studies had been unable to conceptualise distributed leadership or empirically outline its application. The two research gaps identified by Bennett et al. (2003) constitute the focus of the present review, which attempts to determine whether recent research has been able to fill these gaps. Based on the findings of the present meta-analysis, the authors recommend directions for future studies on distributed leadership.

Fundamental movement skills: an important focus

Abstract: Purpose: Recent international conference presentations have critiqued the promotion of fundamental movement skills (FMS) as a primary pedagogical focus. Presenters have called for a debate about the importance of, and rationale for teaching FMS, and this letter is a response to that call. The authors of this letter are academics who actively engage in FMS research. Method: We have answered a series of contentions about the promotion of FMS using the peer reviewed literature to support our perspective. Results: We define what we mean by FMS, discuss the context of what skills can be considered fundamental, discuss how the development of these skills is related to broader developmental health contexts, and recommend the use of different pedagogical approaches when teaching FMS. Conclusions: We conclude the promotion of FMS is an important focus in Physical Education (PE) and sport and provide future research questions for investigation.

Physical exercise increases adult hippocampal neurogenesis in male rats provided it is aerobic and sustained

Abstract: Key points Aerobic exercise, such as running, enhances adult hippocampal neurogenesis (AHN) in rodents. Little is known about the effects of high-intensity interval training (HIT) or of purely anaerobic resistance training on AHN. Here, compared with a sedentary lifestyle, we report a very modest effect of HIT and no effect of resistance training on AHN in adult male rats. We found the most AHN in rats that were selectively bred for an innately high response to aerobic exercise that also run voluntarily and increase maximal running capacity. Our results confirm that sustained aerobic exercise is key in improving AHN. Abstract Aerobic exercise, such as running, has positive effects on brain structure and function, such as adult hippocampal neurogenesis (AHN) and learning. Whether high-intensity interval training (HIT), referring to alternating short bouts of very intense anaerobic exercise with recovery periods, or anaerobic resistance training (RT) has similar effects on AHN is unclear. In addition, individual genetic variation in the overall response to physical exercise is likely to play a part in the effects of exercise on AHN but is less well studied. Recently, we developed polygenic rat models that gain differentially for running capacity in response to aerobic treadmill training. Here, we subjected these low-response trainer (LRT) and high-response trainer (HRT) adult male rats to various forms of physical exercise for 6–8 weeks and examined the effects on AHN. Compared with sedentary animals, the highest number of doublecortin-positive hippocampal cells was observed in HRT rats that ran voluntarily on a running wheel, whereas HIT on the treadmill had a smaller, statistically non-significant effect on AHN. Adult hippocampal neurogenesis was elevated in both LRT and HRT rats that underwent endurance training on a treadmill compared with those that performed RT by climbing a vertical ladder with weights, despite their significant gain in strength. Furthermore, RT had no effect on proliferation (Ki67), maturation (doublecortin) or survival (bromodeoxyuridine) of new adult-born hippocampal neurons in adult male Sprague–Dawley rats. Our results suggest that physical exercise promotes AHN most effectively if the exercise is aerobic and sustained, especially when accompanied by a heightened genetic predisposition for response to physical exercise.

Centrality Dependence of the Charged-Particle Multiplicity Density at Midrapidity in Pb-Pb Collisions at sNN =5.02 TeV

Abstract: The pseudorapidity density of charged particles, dNch/dη, at midrapidity in Pb-Pb collisions has been measured at a center-of-mass energy per nucleon pair of √sNN=5.02 TeV. For the 5% most central collisions, we measure a value of 1943 ± 54. The rise in dNch/dη as a function of √sNN p is steeper than that observed in proton-proton collisions and follows the trend established by measurements at lower energy. The increase of dNch/dη as a function of the average number of participant nucleons, ⟨Npart⟩, calculated in a Glauber model, is compared with the previous measurement at √sNN=2.76 TeV. A constant factor of about 1.2 describes the increase in dNch/dη from √sNN=2.76 to 5.02 TeV for all centrality classes, within the measured range of 0%–80% centrality. The results are also compared to models based on different mechanisms for particle production in nuclear collisions.

Photo-stability of CsPbBr3 perovskite quantum dots for optoelectronic application

Abstract: Due to their superior photoluminescence (PL) quantum yield (QY) and tunable optical band gap, all-inorganic CsPbBr3 perovskite quantum dots (QDs) have attracted intensive attention for the application in solar cells, light emitting diodes (LED), photodetectors and laser devices. In this scenario, the stability of such materials becomes a critical factor to be revealed. We hereby investigated the long-term stability of as-synthesized CsPbBr3 QDs suspended in toluene at various environmental conditions. We found light illumination would induce drastic photo-degradation of CsPbBr3 QDs. The steady-state spectroscopy, transmission electron microscopy (TEM), and X-ray diffraction (XRD) verified that CsPbBr3 QDs tend to aggregate to form larger particles under continuous light soaking. In addition, decreasing PL QY of the QDs during light soaking indicates the formation of trap sites. Our work reveals that the main origin of instability in CsPbBr3 QDs and provides reference to engineer such QDs towards optimal device application.

Asymmetric Synthesis of Chiral Bimetallic [Ag28Cu12(SR)24]4- Nanoclusters via Ion Pairing

Abstract: In this work, a facile ion-pairing strategy for asymmetric synthesis of optically active negatively charged chiral metal nanoparticles using chiral ammonium cations is demonstrated. A new thiolated chiral three-concentric-shell cluster, [Ag28Cu12(SR)24]4–, was first synthesized as a racemic mixture and characterized by single-crystal X-ray structure determination. Mass spectrometric measurements revealed relatively strong ion-pairing interactions between the anionic nanocluster and ammonium cations. Inspired by this observation, the as-prepared racemic mixture was separated into enantiomers by employing chiral quaternary ammonium salts as chiral resolution agents. Subsequently, direct asymmetric synthesis of optically active enantiomers of [Ag28Cu12(SR)24]4– was achieved by using appropriate chiral ammonium cations (such as N-benzylcinchoninium vs N-benzylcinchonidinium) in the cluster synthesis. These simple strategies, ion-pairing enantioseparation and direct asymmetric synthesis using chiral counterion...

Using latent variable models to identify large networks of species‐to‐species associations at different spatial scales

Abstract: Summary We present a hierarchical latent variable model that partitions variation in species occurrences and co-occurrences simultaneously at multiple spatial scales. We illustrate how the parameterized model can be used to predict the occurrences of a species by using as predictors not only the environmental covariates, but also the occurrences of all other species, at all spatial scales. We leverage recent progress in Bayesian latent variable models to implement a computationally effective algorithm that enables one to consider large communities and extensive sampling schemes. We exemplify the framework with a community of 98 fungal species sampled in c. 22 500 dead wood units in 230 plots in 29 beech forests. The networks identified by correlations and partial correlations were consistent, as were networks for natural and managed forests, but networks at different spatial scales were dissimilar. Accounting for the occurrences of the other species roughly doubled the predictive powers of the models compared to accounting for environmental covariates only .