Showing papers by "Bielefeld University published in 2016"

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.

Heavy-flavour and quarkonium production in the LHC era: from proton–proton to heavy-ion collisions

Abstract: This report reviews the study of open heavy-flavour and quarkonium production in high-energy hadronic collisions, as tools to investigate fundamental aspects of Quantum Chromodynamics, from the proton and nucleus structure at high energy to deconfinement and the properties of the Quark–Gluon Plasma. Emphasis is given to the lessons learnt from LHC Run 1 results, which are reviewed in a global picture with the results from SPS and RHIC at lower energies, as well as to the questions to be addressed in the future. The report covers heavy flavour and quarkonium production in proton–proton, proton–nucleus and nucleus–nucleus collisions. This includes discussion of the effects of hot and cold strongly interacting matter, quarkonium photoproduction in nucleus–nucleus collisions and perspectives on the study of heavy flavour and quarkonium with upgrades of existing experiments and new experiments. The report results from the activity of the SaporeGravis network of the I3 Hadron Physics programme of the European Union 7 $$\mathrm{th}$$ Framework Programme.

High-precision timing of 42 millisecond pulsars with the European Pulsar Timing Array

Abstract: We report on timing, flux density, and polarimetric observations of the transient magnetar and 5.54 s radio pulsar XTE J1810-197 using the GBT, Nancay, and Parkes radio telescopes beginning in early 2006, until its sudden disappearance as a radio source in late 2008. Repeated observations through 2016 have not detected radio pulsations again. The torque on the neutron star, as inferred from its rotation frequency derivative f-dot, decreased in an unsteady manner by a factor of 3 in the first year of radio monitoring. In contrast, during its final year as a detectable radio source, the torque decreased steadily by only 9%. The period-averaged flux density, after decreasing by a factor of 20 during the first 10 months of radio monitoring, remained steady in the next 22 months, at an average of 0.7+/-0.3 mJy at 1.4 GHz, while still showing day-to-day fluctuations by factors of a few. There is evidence that during this last phase of radio activity the magnetar had a steep radio spectrum, in contrast to earlier behavior. There was no secular decrease that presaged its radio demise. During this time the pulse profile continued to display large variations, and polarimetry indicates that the magnetic geometry remained consistent with that of earlier times. We supplement these results with X-ray timing of the pulsar from its outburst in 2003 up to 2014. For the first 4 years, XTE J1810-197 experienced non-monotonic excursions in f-dot by at least a factor of 8. But since 2007, its f-dot has remained relatively stable near its minimum observed value. The only apparent event in the X-ray record that is possibly contemporaneous with the radio shut-down is a decrease of ~20% in the hot-spot flux in 2008-2009, to a stable, minimum value. However, the permanence of the high-amplitude, thermal X-ray pulse, even after the radio demise, implies continuing magnetar activity.

The International Pulsar Timing Array: First Data Release

Abstract: The highly stable spin of neutron stars can be exploited for a variety of (astro)physical investigations. In particular, arrays of pulsars with rotational periods of the order of milliseconds can be used to detect correlated signals such as those caused by gravitational waves. Three such 'pulsar timing arrays' (PTAs) have been set up around the world over the past decades and collectively form the 'International' PTA (IPTA). In this paper, we describe the first joint analysis of the data from the three regional PTAs, i.e. of the first IPTA data set. We describe the available PTA data, the approach presently followed for its combination and suggest improvements for future PTA research. Particular attention is paid to subtle details (such as underestimation of measurement uncertainty and long-period noise) that have often been ignored but which become important in this unprecedentedly large and inhomogeneous data set. We identify and describe in detail several factors that complicate IPTA research and provide recommendations for future pulsar timing efforts. The first IPTA data release presented here (and available on-line) is used to demonstrate the IPTA's potential of improving upon gravitational-wave limits

Vacuolar compartmentalization as indispensable component of heavy metal detoxification in plants

Abstract: Plant cells orchestrate an array of molecular mechanisms for maintaining plasmatic concentrations of essential heavy metal (HM) ions, for example, iron, zinc and copper, within the optimal functional range. In parallel, concentrations of non-essential HMs and metalloids, for example, cadmium, mercury and arsenic, should be kept below their toxicity threshold levels. Vacuolar compartmentalization is central to HM homeostasis. It depends on two vacuolar pumps (V-ATPase and V-PPase) and a set of tonoplast transporters, which are directly driven by proton motive force, and primary ATP-dependent pumps. While HM non-hyperaccumulator plants largely sequester toxic HMs in root vacuoles, HM hyperaccumulators usually sequester them in leaf cell vacuoles following efficient long-distance translocation. The distinct strategies evolved as a consequence of organ-specific differences particularly in vacuolar transporters and in addition to distinct features in long-distance transport. Recent molecular and functional characterization of tonoplast HM transporters has advanced our understanding of their contribution to HM homeostasis, tolerance and hyperaccumulation. Another important part of the dynamic vacuolar sequestration syndrome involves enhanced vacuolation. It involves vesicular trafficking in HM detoxification. The present review provides an updated account of molecular aspects that contribute to the vacuolar compartmentalization of HMs.

Five new fast radio bursts from the HTRU high-latitude survey at Parkes: First evidence for two-component bursts

Abstract: The detection of five new fast radio bursts (FRBs) found in the 1.4-GHz High Time Resolution Universe high-latitude survey at Parkes, is presented. The rate implied is 7(-3)(+5) x 10(3) (95 per cent) FRBs sky(-1) d(-1) above a fluence of 0.13 Jy ms for an FRB of 0.128 ms duration to 1.5 Jy ms for 16 ms duration. One of these FRBs has a two-component profile, in which each component is similar to the known population of single component FRBs and the two components are separated by 2.4 +/- 0.4 ms. All the FRB components appear to be unresolved following deconvolution with a scattering tail and accounting for intrachannel smearing. The two-component burst, FRB 121002, also has the highest dispersion measure (1629 pc cm(-3)) of any FRB to-date. Many of the proposed models to explain FRBs use a single high-energy event involving compact objects (such as neutron-star mergers) and therefore cannot easily explain a two-component FRB. Models that are based on extreme versions of flaring, pulsing, or orbital events, however, could produce multiple component profiles. The compatibility of these models and the FRB rate implied by these detections is discussed.

Timing analysis for 20 millisecond pulsars in the Parkes Pulsar Timing Array

Abstract: We present timing models for 20 millisecond pulsars in the Parkes Pulsar Timing Array. The precision of the parameter measurements in these models has been improved over earlier results by using longer data sets and modelling the non-stationary noise. We describe a new noise modelling procedure and demonstrate its effectiveness using simulated data. Our methodology includes the addition of annual dispersion measure (DM) variations to the timing models of some pulsars. We present the first significant parallax measurements for PSRs J1024-0719, J1045-4509, J1600-3053, J1603-7202, and J1730-2304, as well as the first significant measurements of some post-Keplerian orbital parameters in six binary pulsars, caused by kinematic effects. Improved Shapiro delay measurements have resulted in much improved pulsar mass measurements, particularly for PSRs J0437-4715 and J1909-3744 with M-p = 1.44 +/- 0.07 and 1.47 +/- 0.03 M-circle dot, respectively. The improved orbital period-derivative measurement for PSR J0437-4715 results in a derived distance measurement at the 0.16 per cent level of precision, D = 156.79 +/- 0.25 pc, one of the most fractionally precise distance measurements of any star to date.

moveHMM: an R package for the statistical modelling of animal movement data using hidden Markov models

Abstract: Summary Due to the substantial progress in tracking technology, recent years have seen an explosion in the amount of movement data being collected. This has led to a huge demand for statistical tools that allow ecologists to draw meaningful inference from large tracking data sets. The class of hidden Markov models (HMMs) matches the intuitive understanding that animal movement is driven by underlying behavioural modes and has proven to be very useful for analysing movement data. For data that involve a regular sampling unit and negligible measurement error, these models usually are sufficiently flexible to capture the complex correlation structure found in movement data, yet are computationally inexpensive compared to alternative methods. The R package moveHMM allows ecologists to process GPS tracking data into series of step lengths and turning angles, and to fit an HMM to these data, allowing, in particular, for the incorporation of environmental covariates. The package includes assessment and visualization tools for the fitted model. We illustrate the use of moveHMM using (simulated) movement of the legendary wild haggis Haggis scoticus. Our findings illustrate the role our software, and movement modelling in general, can play in conservation and management by illuminating environmental constraints.

CMB Anomalies after Planck

Abstract: Several unexpected features have been observed in the microwave sky at large angular scales, both by WMAP and by Planck. Among those features is a lack of both variance and correlation on the largest angular scales, alignment of the lowest multipole moments with one another and with the motion and geometry of the solar system, a hemispherical power asymmetry or dipolar power modulation, a preference for odd parity modes and an unexpectedly large cold spot in the Southern hemisphere. The individual p-values of the significance of these features are in the per mille to per cent level, when compared to the expectations of the best-fit inflationary ACDM model. Some pairs of those features are demonstrably uncorrelated, increasing their combined statistical significance and indicating a significant detection of CMB features at angular scales larger than a few degrees on top of the standard model. Despite numerous detailed investigations, we still lack a clear understanding of these large-scale features, which seem to imply a violation of statistical isotropy and scale invariance of inflationary perturbations. In this contribution we present a critical analysis of our current understanding and discuss several ideas of how to make further progress.

Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ

Abstract: Super-resolved structured illumination microscopy (SR-SIM) is an important tool for fluorescence microscopy. SR-SIM microscopes perform multiple image acquisitions with varying illumination patterns, and reconstruct them to a super-resolved image. In its most frequent, linear implementation, SR-SIM doubles the spatial resolution. The reconstruction is performed numerically on the acquired wide-field image data, and thus relies on a software implementation of specific SR-SIM image reconstruction algorithms. We present fairSIM, an easy-to-use plugin that provides SR-SIM reconstructions for a wide range of SR-SIM platforms directly within ImageJ. For research groups developing their own implementations of super-resolution structured illumination microscopy, fairSIM takes away the hurdle of generating yet another implementation of the reconstruction algorithm. For users of commercial microscopes, it offers an additional, in-depth analysis option for their data independent of specific operating systems. As a modular, open-source solution, fairSIM can easily be adapted, automated and extended as the field of SR-SIM progresses.

Corynebacterium glutamicum Metabolic Engineering with CRISPR Interference (CRISPRi)

Abstract: Corynebacterium glutamicum is an important organism for the industrial production of amino acids. Metabolic pathways in this organism are usually engineered by conventional methods such as homologous recombination, which depends on rare double-crossover events. To facilitate the mapping of gene expression levels to metabolic outputs, we applied CRISPR interference (CRISPRi) technology using deactivated Cas9 (dCas9) to repress genes in C. glutamicum. We then determined the effects of target repression on amino acid titers. Single-guide RNAs directing dCas9 to specific targets reduced expression of pgi and pck up to 98%, and of pyk up to 97%, resulting in titer enhancement ratios of l-lysine and l-glutamate production comparable to levels achieved by gene deletion. This approach for C. glutamicum metabolic engineering, which only requires 3 days, indicates that CRISPRi can be used for quick and efficient metabolic pathway remodeling without the need for gene deletions or mutations and subsequent selection.

Thermophilic archaea activate butane via alkyl-coenzyme M formation

Abstract: The anaerobic formation and oxidation of methane involve unique enzymatic mechanisms and cofactors, all of which are believed to be specific for C1-compounds. Here we show that an anaerobic thermophilic enrichment culture composed of dense consortia of archaea and bacteria apparently uses partly similar pathways to oxidize the C4 hydrocarbon butane. The archaea, proposed genus 'Candidatus Syntrophoarchaeum', show the characteristic autofluorescence of methanogens, and contain highly expressed genes encoding enzymes similar to methyl-coenzyme M reductase. We detect butyl-coenzyme M, indicating archaeal butane activation analogous to the first step in anaerobic methane oxidation. In addition, Ca. Syntrophoarchaeum expresses the genes encoding β-oxidation enzymes, carbon monoxide dehydrogenase and reversible C1 methanogenesis enzymes. This allows for the complete oxidation of butane. Reducing equivalents are seemingly channelled to HotSeep-1, a thermophilic sulfate-reducing partner bacterium known from the anaerobic oxidation of methane. Genes encoding 16S rRNA and methyl-coenzyme M reductase similar to those identifying Ca. Syntrophoarchaeum were repeatedly retrieved from marine subsurface sediments, suggesting that the presented activation mechanism is naturally widespread in the anaerobic oxidation of short-chain hydrocarbons.

Tuning of Redox Regulatory Mechanisms, Reactive Oxygen Species and Redox Homeostasis under Salinity Stress.

Abstract: Soil salinity is a crucial environmental constraint which limits biomass production at many sites on a global scale. Saline growth conditions cause osmotic and ionic imbalances, oxidative stress and perturb metabolism, e.g., the photosynthetic electron flow. The plant ability to tolerate salinity is determined by multiple biochemical and physiological mechanisms protecting cell functions, in particular by regulating proper water relations and maintaining ion homeostasis. Redox homeostasis is a fundamental cell property. Its regulation includes control of reactive oxygen species (ROS) generation, sensing deviation from and readjustment of the cellular redox state. All these redox related functions have been recognized as decisive factors in salinity acclimation and adaptation. This review focuses on the core response of plants to overcome the challenges of salinity stress through regulation of ROS generation and detoxification systems and to maintain redox homeostasis. Emphasis is given to the role of NADH oxidase (RBOH), alternative oxidase (AOX), the plastid terminal oxidase (PTOX) and the malate valve with the malate dehydrogenase isoforms under salt stress. Overwhelming evidence assigns an essential auxiliary function of ROS and redox homeostasis to salinity acclimation of plants.

European Pulsar Timing Array Limits on Continuous Gravitational Waves from Individual Supermassive Black Hole Binaries

Abstract: We have searched for continuous gravitational wave (CGW) signals produced by individually resolvable, circular supermassive black hole binaries (SMBHBs) in the latest European Pulsar Timing Array (EPTA) data set, which consists of ultraprecise timing data on 41-ms pulsars. We develop frequentist and Bayesian detection algorithms to search both for monochromatic and frequency-evolving systems. None of the adopted algorithms show evidence for the presence of such a CGW signal, indicating that the data are best described by pulsar and radiometer noise only. Depending on the adopted detection algorithm, the 95 per cent upper limit on the sky-averaged strain amplitude lies in the range 6 × 10−15 10^9M⊙ out to a distance of about 25 Mpc, and with Mc > 10^10M⊙ out to a distance of about 1Gpc (z ≈ 0.2). We show that state-of-the-art SMBHB population models predict <1 per cent probability of detecting a CGW with the current EPTA data set, consistent with the reported non-detection. We stress, however, that PTA limits on individual CGW have improved by almost an order of magnitude in the last five years. The continuing advances in pulsar timing data acquisition and analysis techniques will allow for strong astrophysical constraints on the population of nearby SMBHBs in the corning years.

Critical analysis of the current treatment guidelines for complex ptsd in adults.

Abstract: According to current treatment guidelines for Complex PTSD (cPTSD), psychotherapy for adults with cPTSD should start with a “stabilization phase.” This phase, focusing on teaching self-regulation strategies, was designed to ensure that an individual would be better able to tolerate trauma-focused treatment. The purpose of this paper is to critically evaluate the research underlying these treatment guidelines for cPTSD, and to specifically address the question as to whether a phase-based approach is needed. As reviewed in this paper, the research supporting the need for phase-based treatment for individuals with cPTSD is methodologically limited. Further, there is no rigorous research to support the views that: (1) a phase-based approach is necessary for positive treatment outcomes for adults with cPTSD, (2) front-line trauma-focused treatments have unacceptable risks or that adults with cPTSD do not respond to them, and (3) adults with cPTSD profit significantly more from trauma-focused treatments when preceded by a stabilization phase. The current treatment guidelines for cPTSD may therefore be too conservative, risking that patients are denied or delayed in receiving conventional evidence-based treatments from which they might profit.

KNN Classifier with Self Adjusting Memory for Heterogeneous Concept Drift

Abstract: Data Mining in non-stationary data streams is gaining more attentionrecently, especially in the context of Internet of Things and Big Data. It is a highly challenging task, since the fundamentally different typesof possibly occurring drift undermine classical assumptions such asi.i.d. data or stationary distributions. Available algorithms are either struggling with certain forms of drift or require a priori knowledge in terms of a task specific setting. We propose the Self Adjusting Memory (SAM) model for the k Nearest Neighbor (kNN) algorithm since kNN constitutes a proven classifier within the streaming setting. SAM-kNN can deal with heterogeneous concept drift, i.e different drift types and rates, using biologically inspiredmemory models and their coordination. It can be easilyapplied in practice since an optimization of the meta parameters is not necessary. The basic idea is to construct dedicated models for thecurrent and former concepts and apply them according tothe demands of the given situation. An extensive evaluation on various benchmarks, consisting of artificial streamswith known drift characteristics as well as real world datasets is conducted. Thereby, we explicitly add new benchmarks enabling a precise performance evaluation on multiple types of drift. The highly competitive results throughout all experiments underline the robustness of SAM-kNN as well as its capabilityto handle heterogeneous concept drift.

A blue-light photoreceptor mediates the feedback regulation of photosynthesis

Abstract: In plants and algae, light serves both as the energy source for photosynthesis and a biological signal that triggers cellular responses via specific sensory photoreceptors. Red light is perceived by bilin-containing phytochromes and blue light by the flavin-containing cryptochromes and/or phototropins (PHOTs), the latter containing two photosensory light, oxygen, or voltage (LOV) domains. Photoperception spans several orders of light intensity, ranging from far below the threshold for photosynthesis to values beyond the capacity of photosynthetic CO2 assimilation. Excess light may cause oxidative damage and cell death, processes prevented by enhanced thermal dissipation via high-energy quenching (qE), a key photoprotective response. Here we show the existence of a molecular link between photoreception, photosynthesis, and photoprotection in the green alga Chlamydomonas reinhardtii. We show that PHOT controls qE by inducing the expression of the qE effector protein LHCSR3 (light-harvesting complex stress-related protein 3) in high light intensities. This control requires blue-light perception by LOV domains on PHOT, LHCSR3 induction through PHOT kinase, and light dissipation in photosystem II via LHCSR3. Mutants deficient in the PHOT gene display severely reduced fitness under excessive light conditions, indicating that the sensing, utilization, and dissipation of light is a concerted process that plays a vital role in microalgal acclimation to environments of variable light intensities.