bluuebunny/crossref_metadata_2025 huggingface dataset:
Beam breakup simulations for the Mainz Energy recovering Superconducting Accelerator MESA
Authors: Stoll C P , Hug F
Published: December 2019

MESA is a two pass energy recovery linac (ERL) currently under construction at the Johannes Gutenberg-University in Mainz. MESA uses four 1.3 GHz TESLA type cavities with 12.5 MVm-1 of accelerating gradient in two modified ELBE type cryomodule with improved thermal connection of the HOM antennas and cw operation. In the first stage of MESA operation 1mA of beam current is foreseen, which will later be upgraded to 10 mA. One potential limit to maximum beam current in ERLs is the transverse beam breakup (BBU) instability induced by dipole Higher Order Modes (HOMs). These modes can be excited by bunches passing through the cavities off axis. Following bunches are then deflected by the HOMs, which results in even larger offsets for recirculated bunches. This feedback can even lead to beam loss. Simulation results for HOM spectra of a single TESLA cavity are available for example in [1]. It was possible to measure the HOM spectra in the cold, not tuned cavities at DESY and in the cold string tuned to the 1.3 GHz fundamental mode at Mainz. Results for the maximum beam current for MESA, limited by BBU, for the various HOM spectra are presented.
Experimental determination of proton hardness factors at several irradiation facilities
Authors: Allport P. , Bögelspacher F. , Bruce K. , Canavan R. , Dierlamm A. , Gonella L. , Knights P. , Mateu I. , Moll M. , Nikolopoulos K. , Phoenix B. , Price T. , Ram L. , Ravotti F. , Simpson-Allsop C. , Wood C.
Published: December 2019

The scheduled High Luminosity upgrade of the CERN Large Hadron Collider presents new challenges in terms of radiation hardness. As a consequence, campaigns to qualify the radiation hardness of detector sensors and components are undertaken worldwide. The effects of irradiation with beams of different particle species and energy, aiming to assess displacement damage in semiconductor devices, are communicated in terms of the equivalent 1 MeV neutron fluence, using the hardness factor for the conversion. In this work, the hardness factors for protons at three different kinetic energies have been measured by analysing the I–V and C–V characteristics of reverse biased diodes, pre- and post-irradiation. The sensors were irradiated at the MC40 Cyclotron of the University of Birmingham, the cyclotron at the Karlsruhe Institute of Technology, and the IRRAD proton facility at CERN, with the respective measured proton hardness factors being: 2.1± 0.5 for 24 MeV, 2.2 ± 0.4 for 23 MeV, and 0.62± 0.04 for 23 GeV. The hardness factors currently used in these three facilities are in agreement with the presented measurements.
Braiding properties of paired spin-singlet and non-Abelian hierarchy states
Authors: Tournois Yoran , Ardonne Eddy
Published: December 2019

We study explicit model wave functions describing the fundamental quasiholes in a class of non-Abelian fractional quantum Hall states. This class is a family of paired spin-singlet states with

internal degrees of freedom. We determine the braid statistics of the quasiholes by determining the monodromy of the explicit quasihole wave functions, that is how they transform under exchanges of quasihole coordinates. The statistics is shown to be the same as that of the quasiholes in the Read–Rezayi states, up to a phase. We also discuss the application of this result to a class of non-Abelian hierarchy wave functions.
Additive manufacturing of metal components – process-material interaction in different process chains
Authors: Hansen H N , Hattel J H , Pedersen D B , Mohanty S , Andersen S A , Nadimpalli V K , Klingaa C G , Dahmen T , Zhang Y
Published: December 2019

In this paper we describe metal additive manufacturing (AM) processes in general, and laser bed fusion processes in particular. The process characteristics are described, and the various modelling approaches demonstrated. The open AM architecture developed at DTU Mechanical Engineering is introduced, as well as an alternative process chain based on AM and subsequent injection moulding.
The ESRF dark-field x-ray microscope at ID06
Authors: Kutsal M , Bernard P , Berruyer G , Cook P K , Hino R , Jakobsen A C , Ludwig W , Ormstrup J , Roth T , Simons H , Smets K , Sierra J X , Wade J , Wattecamps P , Yildirim C , Poulsen H F , Detlefs C
Published: December 2019

We present an instrument for dark-field x-ray microscopy installed on beamline ID06 of the ESRF — the first of its kind. Dark-field x-ray microscopy uses full field illumination of the sample and provides three-dimensional (3D) mapping of micro-structure and lattice strain in crystalline matter. It is analogous to dark-field electron microscopy in that an objective lens magnifies diffracting features of the sample. The use of high-energy synchrotron x-rays, however, means that these features can be large and deeply embedded. 3D movies can be acquired with a time resolution of seconds to minutes. The field of view and spatial resolution can be adapted by simple reconfiguration of the x-ray objective lens, reaching spatial and angular resolution of 30-100 nm and 0.001°, respectively. The instrument furthermore allows pre-characterization of samples at larger length scales using 3DXRD or DCT, such that a region of interest (e.g. a single grain) can be selected for high-resolution studies without the need to dismount the sample. As examples of applications we show work on mapping the subgrains in plastically deformed iron and aluminum alloys, mapping domains and strain fields in ferroelectric crystals, and studies of biominerals. This ability to directly characterize complex, multi-scale phenomena in-situ is a key step towards formulating and validating multi-scale models that account for the entire heterogeneity of materials. As an outlook, we discuss future prospects for such multi-scale characterization by combining DFXM with 3DXRD/DCT, and coherent x-ray methods for coarser and finer length-scales, respectively.
Cold rolling behaviour of Cu with highly oriented nanotwins: the importance of local shear strain
Authors: Lu Q H , Bai J S , Cheng Z , Lu L
Published: December 2019

To clarify the deformation mechanism of nanotwinned materials under a complex stress state and large strain level, the microstructure evolution of pure Cu samples with high density of preferentially oriented nanotwins cold rolled to a strain up to 65% was systematically characterized by means of electron backscatter diffraction and transmission electron microscopy in this study. Heterogeneous deformation behavior was observed in nanotwinned Cu at different rolling strains. At a rolling strain of 15%, uniform deformation carried by the interactions between dislocations and twin boundaries dominate. At the same time, a small amount of strain localization in the direction ±45° respective to the rolling direction takes place, carried by detwinning and shear bands. As the rolling strain increased to 50%, detwinning becomes a dominant deformation mechanism and produces a large amount of coarse twin/matrix lamellae. A unique laminated structure with high angle lamellar boundaries (larger than 50° misorientation angle) and an average lamellar thickness of about 150 nm evolves from the coarse twin/matrix lamellae. As the rolling strain is increased up to 65%, an extensive laminated structures embedded with a few preserved twin blocks are prevalently formed. It is found that the local shear strain plays a critical role in the microstructure evolution of the nanotwinned Cu under cold rolling. When the local shear strains are so small as to be negligible, uniform deformation is sustained by interactions of dislocation/twin boundaries and the nanoscale twins survive. As the local shear strain increases up to 1, detwinning prevails and results in coarse twin/matrix lamellae. When the local shear strain is larger than 1, formation of shear bands composed of dislocation cells, sub-grains and fragments of twin lamellae instead of the detwinning process takes place, finally evolving into a laminated structure.
Quantification of local boundary migration in 2D/3D
Authors: Zhang Yubin
Published: December 2019

With the development of advanced electron and X-ray microscopy techniques, the local boundary migration during recrystallization and grain growth can be followed in 2D at a sample surface and/or in 3D inside bulk samples during in/ex situ annealing. The results show that locally boundaries migrate in a much more complex way than commonly imagined, for example by the development of local protrusions and retrusions and by migrating in a stop-go type of fashion. A quantitative analysis of the local boundary migration is essential for understanding this heterogeneous process. In this paper, methods for quantifying local boundary migration are summarized, including methods for quantification of local boundary migration velocities, misorientation (angle/axis pair) and plane normal of migrating/non-migrating boundaries, driving force (from both the energy stored in the deformation matrix and local boundary curvature), boundary mobility and activation energy. Through a quantitative analysis of both experimental and simulation data, local boundary migration is rationalized in several material systems during recrystallization and grain growth.
Integral mean curvature analysis of 3D grain growth: Linearity of dV/dt and grain volume
Authors: Patterson BR , DeHoff RT , Sahi CA , Sun J , Oddershede J , Bachmann F , Lauridsen E , Jensen D Juul
Published: December 2019

The volumetric growth rate of individual grains has been found to be directly proportional to the individual grain volume V as dV/dt = β(Vo
-V). This simple result is explained through the DeHoff relationship dV/dt = −kMs
between growth rate and the integral mean curvature of individual grains, M

s
, combined with the experimentally observed relationship between M

s
and grain volume, M

s
= α(Vo
-V). These relationships have now been observed consistently in both 3D grain growth simulations and experiments. This paper describes the relationships among these kinetic and geometric grain characteristics that provide this simple description of 3D grain growth.
Study of potential recrystallization nuclei in the cold-rolled microstructure of an electrical steel by electron backscatter diffraction
Authors: Hsu WC , Chang L , Kao PW
Published: December 2019

Strain induced boundary migration (SIBM) is widely recognized to be the main mechanism corresponding to recrystallization in metals of low or medium amount of deformation. The nucleation process in recrystallization of heavily deformed metals is, however, less understood for key issues such as how the nuclei are formed and where they are located. The evolution of texture from deformation to recrystallization cannot thus be explained well. In this study, an attempt was conducted to identify the potential recrystallization nuclei (PRN) in the cold-rolled microstructure of an electrical steel by electron backscatter diffraction (EBSD). This work demonstrates that the SIBM mechanism can be the main mechanism corresponding to recrystallization nucleation in a heavily deformed steel. The same area in both the cold-rolled and partially recrystallized states was analysed using EBSD to obtain the correlation between the recrystallized grains and the cold-rolled substructures. The deformed grains having high stored energy were first selected, followed by identifying substructures surrounded entirely or partly by high angle boundaries in these heavily deformed grains. The deformation induced grains having low intra-granular misorientation of 2° or less exhibit a very similar orientation distribution to that of the recrystallized grains and are proposed to be the PRN in subsequent recrystallization.
Microstructure and strength of weldment in Pt20Rh alloys dispersion-strengthened by ZrO2particles
Authors: Hu Faping , Wang Ziyang , Yu Tianbo , Yang Zonglun , Wei Guobing , Luo Xuan , Hansen Niels , Huang Xiaoxu , Xie Weidong
Published: December 2019

A series of Pt20Rh alloys dispersion-strengthened by different volume fractions of ZrO2particles have been prepared by internal oxidation of Pt20Rh powder followed by consolidation and hot forging. The alloys were cold rolled to sheets, followed by annealing. The effects of welding on the microstructure and mechanical properties were also investigated. The microstructure of the rolled sheets showed a lamellar structure and the yield stress was significantly increased with increasing volume fraction of dispersion particles. After welding, the yield stress at room temperature was almost unchanged, although a small decrease was observed at 1000 °C. However, the work hardening capacity and ultimate tensile stress were significantly reduced in the welded sample due to grain coarsening and to increased pore density in the fusion zone.
In-situ neutron diffraction study on the deformation of a TRIP-assisted multi-phase steel composed of ferrite, austenite and martensite
Authors: Lavakumar A , Park M H , Gao S , Shibata A , Okitsu Y , Gong W , Harjo S , Tsuji N
Published: December 2019

Multi-phase steels showing transformation induced plasticity (TRIP), can exhibit an excellent combination of high strength and good ductility by the aid of martensitic transformation during deformation. Even though TRIP-assisted multi-phase steels have been widely used in industry, the role of each phase in the enhancement of mechanical properties is still unclear given their complicated microstructures. In order to understand better the nature of the TRIP effect, the mechanical interaction between different phases at the micro-scale should be clarified. In the present study, the mechanical behavior of a transformation induced plasticity (TRIP) assisted multi-phase steel, has been characterized by in-situ neutron diffraction during tensile testing. The result of strain partitioning between the different phases obtained from the in-situ neutron analysis revealed that the martensite phase took much more elastic strain than the ferrite and retained austenite phases, which suggests that the work hardening behavior in the present steel is affected by the higher load borne by deformation-induced martensite.
2D/3D local strain analysis of layered metal composites with a strength-ductility synergy
Authors: Li D Y , Huang M , Xia Y P , Xu C , Gan W M , Geng L , Fan G H
Published: December 2019

A long-standing question is why layered structures can overcome the strength-ductility trade-off and achieve synergy in this relationship. In this paper, layered Ti/Al, Ti/Ti metal materials are taken as examples to investigate the influence of a heterogeneous layered structure on their deformation behavior from a viewpoint of the local strain. In-situ neutron diffraction, DIC and synchrotron radiation tomography were performed to obtain lattice strain evolution (elastic stage), local strain evolution (plastic stage), and crack initiation and propagation (fracture stage), respectively. It is found that strain delocalization is the key to achieving a strength-ductility synergy in layered materials, and that layered structures can influence the local strains from start to failure, which improves strain compatibility between the component layers. In-situ tracking of local strains based on 2D/3D characterization methods during entire deformation process deepens our understanding of the deformation behavior of layered materials.
Grain size effect on deformation mechanisms in Mg-3Gd
Authors: Luo X , Luo J Q , Feng Z Q , Hu F P , Yu T , Berggreen C , Wu G L , Hansen N , Huang X
Published: December 2019

Mg-3Gd (wt. %) samples were prepared by accumulative roll-bonding (ARB) and subsequent annealing to produce samples with average grain sizes in a wide range from 3.3 μm to 45.1 μm. These samples were tensile tested at room temperature. Dislocation structures and deformation twins in the tested tensile samples were characterized by transmission electron microscopy. Dislocations with different types of Burgers vector were identified based on two-beam diffraction contrast experiments. The results revealed that deformation twins and  dislocations are dominant in coarse-grained samples while  and  dislocations characterize the fine grain deformation structure. The transition of deformation mechanisms and its implications for microstructural design and property optimization are discussed.
Comparison of local stress and strain in a heterogeneouslycompressed AA 1050 ring by electron microscopy, microhardness and finite element modelling
Authors: Nielsen C V , Hansen N , Zhang X
Published: December 2019

An investigation comparing the local stress and strain in a centimeter-scale heterogeneously-compressed AA 1050 ring under nearly full sticking conditions has been carried out. Three complementary techniques were used, covering multiple length scales from nanometers to tens of millimeters, namely electron microscopy (electron backscatter diffraction), microhardness, and finite element modelling. To underpin the present findings on the centimeter-scale heterogeneous structure, the same techniques were applied in an analysis of the homogeneous microstructure resulting from compression of cylinders of the same original hot-extruded AA 1050 material. The analyses support the idea that the local-region microstructure in a heterogeneous structure evolves in accordance with universal mechanisms and principles established for the deformation microstructure of polycrystalline metals.
Local residual stress in partially recrystallized iron characterized using high resolution electron backscatter diffraction
Authors: Wang T , Jensen D Juul , Godfrey A , Zhang Y
Published: December 2019

Recent synchrotron measurements have shown the presence of local residual stress within nearly defect-free grains in partially recrystallized samples. A detailed quantification of such local stress is very important for understanding local boundary migration during recrystallization and for tailoring the microstructure of materials. In this study, we utilize high resolution electron backscatter diffraction (HR-EBSD, Wilkinson’s method) to investigate the local residual stress in recrystallized grains in a sample of partially recrystallized iron. The effects of reference selection on the strain distribution are also discussed.
Investigation of plastic yielding in near-micrometer grain size aluminum using synchrotron microdiffraction
Authors: Zhang C.L. , Godfrey A , Gao W.Q. , Zhang Y.B. , Wu G.L. , Liu W. , Xu R.Q. , Jensen D. Juul
Published: December 2019

The onset of plastic yielding has been studied in samples of aluminum with near-micrometer average grain size using in situ tensile loading combined with synchrotron radiation. A white-beam Laue 3D micro-diffraction technique was used allowing the collection of diffraction signal from a volume with a resolution of 1 μm in all three dimensions. The orientation data obtained from the micro-diffraction are used to estimate the local variation in geometrically necessary dislocation density, and correction factors are suggested for voxels where neighbors are missing in either one or two dimensions. The results demonstrate a considerable heterogeneity in deformation in the early stages of plastic deformation.
Design of control system for cover washing machine in the automotive manufacturing industry
Authors: Ardi Syahril , Pratama Fariz Risky
Published: December 2019

In this paper, it discusses research conducted in the automotive manufacturing industry. In this case that is in the process of manufacturing the two-wheeled vehicle parts cover. In manufacturing the cover parts includes several processes, namely: Melting, Casting, Finishing, Machining, Painting, and Assembling. The washing process is the process of cleaning the chips and coolants that attach to the part, namely by spraying water and wind. The previous washing process used a manual method, namely by dipping the part in a container filled with water and then spraying it clean free of coolant. This method still has drawbacks, namely that there are still coolant marks left in the part. Coolant that has been attached to the part will be difficult to clean when it has dried. We conduct research by designing a cover washing machine that is integrated with the PLC (Programmable Logic Controller). In this case, the control system has 60 Input-Output, consisting of 36 inputs and 24 outputs. This machine construction uses the Rotary Table principle, so that the operator’s work becomes more effective. In addition, the results reduce the amount of rejection in the painting process by 5% and increase the amount of production from 400 pieces per day to 700 pieces per day.
Sampled-data control of pan-tilt platform using discrete-time high gain observer
Authors: Ullah Hameed , Malik Fahad Mumtaz , Saeed Anjum , Ali Akbar Zeeshan , Hussain Sajjad
Published: December 2019

In this paper we have presented the design of sampled-data control algorithm for Pan-tilt platform using Discrete-time High Gain Observer (DHGO). The Pan-Tilt platform is a 2-axis serial robotic manipulator having a nonlinear dynamic model. The design of the control algorithm is carried out in 2 steps. In 1st steps, a continuous time state feedback control law based on feedback linearization is designed which is subsequently discretized. In the second stage, the states of the system are estimated using DHGO. To evaluate the performance of the suggested algorithm extensive simulations are carried out in Matlab Simulink.
Parametric synthesis of a robust PID-controller for interval control system with aperiodic transient process
Authors: Ezangina T A , Gayvoronskiy S A , Khozhaev I V
Published: December 2019

The paper is dedicated to a problem of synthesizing a PID-controller, which provides and aperiodical transient process of desired duration in a control system of the third order with interval parametric uncertainty. To solve the problem, a new method of synthesis was developed. It is based on a decomposing a characteristic polynomial of a considered system in two multipliers: dominant polynomial, which determines allocation of a dominant pole and, consequently, quality of a transient process in a considered system, and non-dominant polynomial, which determines allocation of all other system poles. In order to provide a desired allocation of system poles, parameters of a PID-controller are divided to unrestricted ones and dependent ones. The research resulted in algebraic expressions for calculating dependent parameters of a PID-controller and a system of inequalities for finding its unrestricted parameter. Developed method of a PID-controller parametric synthesis allows placing an interval real dominant pole according to desired control quality and placing all other poles of a system in a desired part of a complex plane to provide necessary degree of a robust pole domination.
Comparative study of three robust observers for automotive damper force estimation
Authors: Pham Thanh-Phong , Sename Olivier , Dugard Luc
Published: December 2019

This paper aims at comparing three robust observers used to estimate the damping force of electrorheological (ER) dampers in a vehicle suspension system. Firstly, a nonlinear quarter-car model, augmented with a first-order dynamical nonlinear damper model, is developed. The first two methods are designed considering the nonlinearity as an unknown input and minimizing the effect of the unknown input disturbances (including a nonlinearity term, the measurement noise and the unknown road profile) on the estimation errors, by using an H2
and H∞
criterion, respectively. The latter method aims at minimizing only the effects of measurement noises and road profiles on the state variable estimation errors by using a H∞
criterion, while the nonlinearity is bounded through a Lipschitz condition. For implementation issue, two low-cost sensors signals (two accelerometers data from the sprung mass and the unsprung mass) are considered as inputs for the observer designs. Then, the observers are implemented in real-time on the INOVE test bench from GIPSA-lab (1/5-scaled real vehicle) to assess and compare experimentally the performances of the approaches. Both simulations and experimental results demonstrate a better effectiveness of the latter observer in terms of the ability of estimating the damper force in real-time despite the nonlinearity, the measurement noises and the road disturbances.
Characterization of damages in materials by computer-aided tap testing
Authors: Oral Imran
Published: December 2019

The tap test is an easy and effective way of characterization of flaws and damages in different materials (especially honeycomb sandwich composites). When the tapping is carried out systematically to cover an area, the measured impact duration can be used for generating a “scan image” of the tapped area. Such an instrumented tap test and imaging system can be used for the detection of flaws and damages, for the evaluation of repaired areas and for the verification of normal reinforced substructures. In this study, the images of intact and damaged aluminum honeycomb sandwich composite, pine board and poplar board samples were obtained by using Computer Aided Tap Tester (CATT) system in the electric and magnetic field and also without any field. As a result of the tests made, it has been figured out that the tests made in the electric field and the magnetic field increased the quality of the images for damages. Also, it has been found out that the CATT system is quite successful in detecting damage of honeycomb sandwich composite materials.
Rational curves on prime Fano threefolds of index 1
Authors: Lehmann Brian , Tanimoto Sho
Published: December 2019

We study the moduli spaces of rational curves on prime Fano threefolds of index 1. For general threefolds of most genera we compute the dimension and the number of irreducible components of these moduli spaces. Our results confirm Geometric Manin’s Conjecture in these examples and show the enumerativity of certain Gromov-Witten invariants.
Genome reconstruction and haplotype phasing using chromosome conformation capture methodologies
Authors: Xu Zhichao , Dixon Jesse R
Published: December 2019

Genomic analysis of individuals or organisms is predicated on the availability of high-quality reference and genotype information. With the rapidly dropping costs of high-throughput DNA sequencing, this is becoming readily available for diverse organisms and for increasingly large populations of individuals. Despite these advances, there are still aspects of genome sequencing that remain challenging for existing sequencing methods. This includes the generation of long-range contiguity during genome assembly, identification of structural variants in both germline and somatic tissues, the phasing of haplotypes in diploid organisms and the resolution of genome sequence for organisms derived from complex samples. These types of information are valuable for understanding the role of genome sequence and genetic variation on genome function, and numerous approaches have been developed to address them. Recently, chromosome conformation capture (3C) experiments, such as the Hi-C assay, have emerged as powerful tools to aid in these challenges for genome reconstruction. We will review the current use of Hi-C as a tool for aiding in genome sequencing, addressing the applications, strengths, limitations and potential future directions for the use of 3C data in genome analysis. We argue that unique features of Hi-C experiments make this data type a powerful tool to address challenges in genome sequencing, and that future integration of Hi-C data with alternative sequencing assays will facilitate the continuing revolution in genomic analysis and genome sequencing.
GABAC: an arithmetic coding solution for genomic data
Authors: Voges Jan , Paridaens Tom , Müntefering Fabian , Mainzer Liudmila S , Bliss Brian , Yang Mingyu , Ochoa Idoia , Fostier Jan , Ostermann Jörn , Hernaez Mikel
Published: December 2019

Motivation

In an effort to provide a response to the ever-expanding generation of genomic data, the International Organization for Standardization (ISO) is designing a new solution for the representation, compression and management of genomic sequencing data: the Moving Picture Experts Group (MPEG)-G standard. This paper discusses the first implementation of an MPEG-G compliant entropy codec: GABAC. GABAC combines proven coding technologies, such as context-adaptive binary arithmetic coding, binarization schemes and transformations, into a straightforward solution for the compression of sequencing data.

Results

We demonstrate that GABAC outperforms well-established (entropy) codecs in a significant set of cases and thus can serve as an extension for existing genomic compression solutions, such as CRAM.

Availability and implementation

The GABAC library is written in C++. We also provide a command line application which exercises all features provided by the library. GABAC can be downloaded from https://github.com/mitogen/gabac.

Supplementary information

Supplementary data are available at Bioinformatics online.
pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm
Authors: Labudová Dominika , Hon Jiří , Lexa Matej
Published: December 2019

Motivation

G-quadruplex is a DNA or RNA form in which four guanine-rich regions are held together by base pairing between guanine nucleotides in coordination with potassium ions. G-quadruplexes are increasingly seen as a biologically important component of genomes. Their detection in vivo is problematic; however, sequencing and spectrometric techniques exist for their in vitro detection. We previously devised the pqsfinder algorithm for PQS identification, implemented it in C++ and published as an R/Bioconductor package. We looked for ways to optimize pqsfinder for faster and user-friendly sequence analysis.

Results

We identified two weak points where pqsfinder could be optimized. We modified the internals of the recursive algorithm to avoid matching and scoring many sub-optimal PQS conformations that are later discarded. To accommodate the needs of a broader range of users, we created a website for submission of sequence analysis jobs that does not require knowledge of R to use pqsfinder.

Availability and implementation

https://pqsfinder.fi.muni.cz, https://bioconductor.org/packages/pqsfinder.

Supplementary information

Supplementary data are available at Bioinformatics online.
A neurophysiological model of speech production deficits in fragile X syndrome
Authors: Schmitt Lauren M , Wang Jun , Pedapati Ernest V , Thurman Angela John , Abbeduto Leonard , Erickson Craig A , Sweeney John A
Published: December 2019

Fragile X syndrome is the most common inherited intellectual disability and monogenic cause of autism spectrum disorder. Expressive language deficits, especially in speech production, are nearly ubiquitous among individuals with fragile X, but understanding of the neurological bases for these deficits remains limited. Speech production depends on feedforward control and the synchronization of neural oscillations between speech-related areas of frontal cortex and auditory areas of temporal cortex. Interaction in this circuitry allows the corollary discharge of intended speech generated from an efference copy of speech commands to be compared against actual speech sounds, which is critical for making adaptive adjustments to optimize future speech. We aimed to determine whether alterations in coherence between frontal and temporal cortices prior to speech production are present in individuals with fragile X and whether they relate to expressive language dysfunction. Twenty-one participants with full-mutation fragile X syndrome (aged 7–55 years, eight females) and 20 healthy controls (matched on age and sex) completed a talk/listen paradigm during high-density EEG recordings. During the talk task, participants repeated pronounced short vocalizations of ‘Ah’ every 1–2 s for a total of 180 s. During the listen task, participants passively listened to their recordings from the talk task. We compared pre-speech event-related potential activity, N1 suppression to speech sounds, single trial gamma power and fronto-temporal coherence between groups during these tasks and examined their relation to performance during a naturalistic language task. Prior to speech production, fragile X participants showed reduced pre-speech negativity, reduced fronto-temporal connectivity and greater frontal gamma power compared to controls. N1 suppression during self-generated speech did not differ between groups. Reduced pre-speech activity and increased frontal gamma power prior to speech production were related to less intelligible speech as well as broader social communication deficits in fragile X syndrome. Our findings indicate that coordinated pre-speech activity between frontal and temporal cortices is disrupted in individuals with fragile X in a clinically relevant way and represents a mechanism contributing to prominent speech production problems in the disorder.
Two distinct prions in fatal familial insomnia and its sporadic form
Authors: Takeuchi Atsuko , Mohri Shirou , Kai Hideaki , Tamaoka Akira , Kobayashi Atsushi , Mizusawa Hidehiro , Iwasaki Yasushi , Yoshida Mari , Shimizu Hiroshi , Murayama Shigeo , Kuroda Shigetoshi , Morita Masanori , Parchi Piero , Kitamoto Tetsuyuki
Published: December 2019

Fatal familial insomnia is a genetic prion disease, which is associated with the aspartic acid to asparagine substitution at codon 178 of the prion protein gene. Although the hallmark pathological feature is thalamic and olivary degeneration, there is a patient with an atypical fatal familial insomnia without the hallmark feature. The cause of the pathological variability is unclear. We analysed a Japanese fatal familial insomnia kindred and compared one atypical clinicopathological fatal familial insomnia phenotype case and typical fatal familial insomnia phenotype cases with transmission studies using multiple lines of knock-in mice and with protein misfolding cyclic amplification. We also analysed the transmissibility and the amplification properties of sporadic fatal insomnia. Transmission studies revealed that the typical fatal familial insomnia with thalamic and olivary degeneration showed successful transmission only using knock-in mice expressing human–mouse chimeric prion protein gene. The atypical fatal familial insomnia with spongiform changes showed successful transmission only using knock-in mice expressing bank vole prion protein gene. Two sporadic fatal insomnia cases with thalamic and olivary degeneration showed the same transmissibility as the typical fatal familial insomnia phenotype. Interestingly, one sporadic fatal insomnia case with thalamic/olivary degeneration and spongiform changes showed transmissibility of both the typical and atypical fatal familial insomnia phenotypes. Protein misfolding cyclic amplification could amplify both typical fatal familial insomnia cases and sporadic fatal insomnia cases but not the atypical fatal familial insomnia phenotype or other sporadic Creutzfeldt–Jakob disease subtypes. In addition to clinical findings and neuropathological features, the transmission properties and the amplification properties were different between the typical and atypical fatal familial insomnia phenotypes. It is suggested that two distinct prions were associated with the diversity in the fatal familial insomnia phenotype, and these two prions could also be detected in sporadic fatal insomnia.
Cardiovascular effects of glucagon-like peptide 1 receptor agonists: from mechanistic studies in humans to clinical outcomes
Authors: Heuvelman Valerie D , Van Raalte Daniël H , Smits Mark M
Published: December 2019

Type 2 diabetes mellitus (T2DM) is currently one of the most prevalent diseases, with as many as 415 million patients worldwide. T2DM is characterized by elevated blood glucose levels and is often accompanied by several comorbidities, such as cardiovascular disease. Treatment of T2DM is focused on reducing glucose levels by either lifestyle changes or medical treatment. One treatment option for T2DM is based on the gut-derived hormone glucagon-like peptide 1 (GLP-1). GLP-1 reduces blood glucose levels by stimulating insulin secretion, however, it is rapidly degraded, and thereby losing its glycaemic effect. GLP-1 receptor agonists (GLP-1RAs) are immune to degradation, prolonging the glycaemic effect. Lately, GLP-1RAs have spiked the interest of researchers and clinicians due to their beneficial effects on cardiovascular disease. Preclinical and clinical data have demonstrated that GLP-1 receptors are abundantly present in the heart and that stimulation of these receptors by GLP-1 has several effects. In this review, we will discuss the effects of GLP-1RA on heart rate, blood pressure, microvascular function, lipids, and inflammation, as measured in human mechanistic studies, and suggest how these effects may translate into the improved cardiovascular outcomes as demonstrated in several trials.
Long-term follow-up analysis of a highly characterized arrhythmogenic cardiomyopathy cohort with classical and non-classical phenotypes–a real-world assessment of a novel prediction model: does the subtype really matter
Authors: Casella Michela , Gasperetti Alessio , Gaetano Fassini , Busana Mattia , Sommariva Elena , Catto Valentina , Sicuso Rita , Rizzo Stefania , Conte Edoardo , Mushtaq Saima , Andreini Daniele , Di Biase Luigi , Carbucicchio Corrado , Natale Andrea , Basso Cristina , Tondo Claudio , Dello Russo Antonio
Published: December 2019

Aims

To provide long-term outcome data on arrhythmogenic cardiomyopathy (ACM) patients with non-classical forms [left dominant ACM (LD-ACM) and biventricular ACM (Bi-ACM)] and an external validation of a recently proposed algorithm for ventricular arrhythmia (VA) prediction in ACM patients.

Methods and results

Demographic, clinical, and outcome data were retrieved from all ACM patients encountered at our institution. Patients were classified according to disease phenotype (R-ACM; Bi-ACM; LD-ACM). Overall and by phenotype long-term survival were calculated; the novel Cadrin-Tourigny et al. algorithm was used to calculate the a priori predicted VA risk, and it was compared with the observed outcome to test its reliability. One hundred and one patients were enrolled; three subgroups were defined (R-ACM, n = 68; Bi-ACM, n = 14; LD-ACM, n = 19). Over a median of 5.41 (2.59–8.37) years, the non-classical form cohort experienced higher rates of VAs than the classical form [5-year freedom from VAs: 0.58 (0.43–0.78) vs. 0.76 (0.66–0.89), P = 0.04]. The Cadrin-Tourigny et al. predictive model adequately described the overall cohort risk [mean observed-predicted risk difference (O-PRD): +6.7 (−4.3, +17.7) %, P = 0.19]; strafing by subgroup, excellent goodness-of-fit was demonstrated for the R-ACM subgroup (mean O-PRD, P = 0.99), while in the Bi-ACM and LD-ACM ones the real observed risk appeared to be underestimated [mean O-PRD: −20.0 (−1.1, −38.9) %, P < 0.0001; −22.6 (−7.8, −37.5) %, P < 0.0001, respectively].

Conclusion

Non-classical ACM forms appear more prone to VAs than classical forms. The novel prediction model effectively predicted arrhythmic risk in the classical R-ACM cohort, but seemed to underestimate it in non-classical forms.
Anaplerotic reactions active during growth of Saccharomyces cerevisiae on glycerol
Authors: Xiberras Joeline , Klein Mathias , Prosch Celina , Malubhoy Zahabiya , Nevoigt Elke
Published: December 2019

Anaplerotic reactions replenish TCA cycle intermediates during growth. In Saccharomyces cerevisiae, pyruvate carboxylase and the glyoxylate cycle have been experimentally identified to be the main anaplerotic routes during growth on glucose (C6) and ethanol (C2), respectively. The current study investigates the importance of the two isoenzymes of pyruvate carboxylase (PYC1 and PYC2) and one of the key enzymes of the glyoxylate cycle (ICL1) for growth on glycerol (C3) as a sole carbon source. As the wild-type strains of the CEN.PK family are unable to grow in pure synthetic glycerol medium, a reverse engineered derivative showing a maximum specific growth rate of 0.14 h−1 was used as the reference strain. While the deletion of PYC1 reduced the maximum specific growth rate by about 38%, the deletion of PYC2 had no significant impact, neither in the reference strain nor in the pyc1Δ mutant. The deletion of ICL1 only marginally reduced growth of the reference strain but further decreased the growth rate of the pyc1 deletion strain by 20%. Interestingly, the triple deletion (pyc1Δ pyc2Δ icl1Δ) did not show any growth. Therefore, both the pyruvate carboxylase and the glyoxylate cycle are involved in anaplerosis during growth on glycerol.
Yoga, Health-Related Quality of Life and Mental Well-Being: A Re-analysis of a Meta-analysis Using the Quality Effects Model
Authors: Kelley George A , Kelley Kristi S
Published: December 2019

Background

Provide robust and practically relevant information regarding the association between yoga, health-related quality-of-life (HRQOL), and mental well-being (MWB) in older adults.

Methods

Data were derived from a recent meta-analysis of 12 randomized controlled yoga trials representing 752 adults ≥60 years of age. Standardized mean difference effect sizes (ESs) were pooled using the recently developed quality effects model and 95% compatibility intervals (CI). Small-study effects were examined using the Doi plot and Luis Furuya-Kanamori (LFK) index. Sensitivity and cumulative meta-analyses were conducted as well as percentile improvement, number needed to treat (NNT), and number to benefit. The grading of recommendations assessment, development, and evaluation (GRADE) instrument was used to assess the strength of the evidence.

Results

Yoga was associated with improvements in both HRQOL (ES = 0.51, 95% CI, 0.25–0.77, I2 = 63.1%) and MWB (ES = 0.39, 95% CI, 0.15–0.63, I2 =56.2%). Percentile improvements were 19.5 for HRQOL and 15.3 for MWB whereas the NNT was 4 for HRQOL and 5 for MWB. An estimated 378,222 and 302,578 U.S. yoga-practicing adults ≥65 years of age could potentially improve their HRQOL and MWB, respectively. Major asymmetry suggestive of small-study effects was observed for MWB but not HRQOL. Further examination for asymmetry revealed that greater improvements in MWB were associated with more (151 vs. 68) minutes of yoga per week (p = .007). Overall strength of evidence was considered “high” for HRQOL and “moderate” for MWB.

Conclusions

Yoga is associated with improvements in HRQOL and MWB among older adults, with approximately 150 minutes or more per week possibly optimal.
Accessible and reproducible mass spectrometry imaging data analysis in Galaxy
Authors: Föll Melanie Christine , Moritz Lennart , Wollmann Thomas , Stillger Maren Nicole , Vockert Niklas , Werner Martin , Bronsert Peter , Rohr Karl , Grüning Björn Andreas , Schilling Oliver
Published: December 2019

Background

Mass spectrometry imaging is increasingly used in biological and translational research because it has the ability to determine the spatial distribution of hundreds of analytes in a sample. Being at the interface of proteomics/metabolomics and imaging, the acquired datasets are large and complex and often analyzed with proprietary software or in-house scripts, which hinders reproducibility. Open source software solutions that enable reproducible data analysis often require programming skills and are therefore not accessible to many mass spectrometry imaging (MSI) researchers.

Findings

We have integrated 18 dedicated mass spectrometry imaging tools into the Galaxy framework to allow accessible, reproducible, and transparent data analysis. Our tools are based on Cardinal, MALDIquant, and scikit-image and enable all major MSI analysis steps such as quality control, visualization, preprocessing, statistical analysis, and image co-registration. Furthermore, we created hands-on training material for use cases in proteomics and metabolomics. To demonstrate the utility of our tools, we re-analyzed a publicly available N-linked glycan imaging dataset. By providing the entire analysis history online, we highlight how the Galaxy framework fosters transparent and reproducible research.

Conclusion

The Galaxy framework has emerged as a powerful analysis platform for the analysis of MSI data with ease of use and access, together with high levels of reproducibility and transparency.
A Dignified Death for All: How a Relational Conceptualisation of Dignity Strengthens the Case for Legalising Assisted Dying in England and Wales
Authors: Reichstein Angelika
Published: December 2019

Criminalising assisted dying is irreconcilable with human dignity and condemns a small number of individuals to significant suffering. Human rights law requires the protection of privacy, but States are given some flexibility in terms of balancing the right to respect for private life with the need to safeguard life itself. The recurring cases of suffering individuals who seek legal recognition of a right to die demonstrate the need for legal change to make the law more compassionate. After introducing conflicting definitions of dignity and the human rights conflict behind a right to die, this article engages with a new idea, which strengthens the claim for the legalisation of assisted dying: relational dignity. While the permissibility of assistance to die is a global issue, this article will specifically focus on England and Wales.
Self-Contracted Curves in Spaces With Weak Lower Curvature Bound
Authors: Lebedeva Nina , Ohta Shin-ichi , Zolotov Vladimir
Published: December 2019

We show that bounded self-contracted curves are rectifiable in metric spaces with weak lower curvature bound in a sense we introduce in this article. This class of spaces is wide and includes, for example, finite-dimensional Alexandrov spaces of curvature bounded below and Berwald spaces of nonnegative flag curvature. (To be more precise, our condition is regarded as a strengthened doubling condition and holds also for a certain class of metric spaces with upper curvature bound.) We also provide the non-embeddability of large snowflakes into (balls in) metric spaces in the same class. We follow the strategy of the last author’s previous paper based on the small rough angle condition, where spaces with upper curvature bound are considered. Here we apply this strategy to spaces with lower curvature bound.
Endofunctors and Poincaré–Birkhoff–Witt Theorems
Authors: Dotsenko Vladimir , Tamaroff Pedro
Published: December 2019

We determine what appears to be the bare-bones categorical framework for Poincaré–Birkhoff–Witt (PBW)-type theorems about universal enveloping algebras of various algebraic structures. Our language is that of endofunctors; we establish that a natural transformation of monads enjoys a PBW property only if that transformation makes its codomain a free right module over its domain. We conclude with a number of applications to show how this unified approach proves various old and new PBW-type theorems. In particular, we prove a PBW-type result for universal enveloping dendriform algebras of pre-Lie algebras, answering a question of Loday.