bluuebunny/crossref_metadata_2025 huggingface dataset:
Myths about new ultrahard phases: Why materials that are significantly superior to diamond in elastic moduli and hardness are impossible
Authors: Brazhkin Vadim V. , Solozhenko Vladimir L.
Published: April 2019

Reports published in the last 25 years on the synthesis of carbon-based materials significantly superior to diamond in hardness and elastic properties have been critically examined, and three groups of recently appearing myths have been analyzed. The first group concerns the possibility of producing materials with bulk moduli much higher than that of diamond. The second group concerns the “experimentally measured” hardness, which is significantly higher than that of diamond. Myths of the third group state that quantum confinement effects supposedly provide “theoretical” foundations for a several-fold increase in the hardness of covalent materials. The fundamental impossibility of synthesizing materials with elastic moduli noticeably exceeding those of diamond under normal conditions has been demonstrated. The problems relating to measuring hardness have been discussed; it was shown that the formation of obstacles for the motion of dislocations can allow an increase of the measured hardness of superhard materials by 20%–40%. It was demonstrated that other hypothetical ways for hardness increase, e.g., owing to quantum confinement, have no real physical grounds. The superior mechanical properties of diamond are due to reliably established physical laws. Accordingly, any statements on the possibility of obtaining materials with elastic characteristics and/or hardness several times higher than the corresponding values for diamond cannot be considered as scientifically reliable.
Simple low power nanosecond pulses from a continuous wave diode laser
Authors: McClymer J. P.
Published: April 2019

A low power continuous wave diode laser is rapidly modulated using the inherent propagation delay and finite slew rate of an inverter to create overlapping time transistor-transistor logic pulses to activate an AND gate to create sub-nanosecond laser pulses at user controller repetition rate up to 100 KHz.
Spin-selective AC Stark shifts in a charged quantum dot
Authors: Wilkinson T. A. , Cottrill D. J. , Cramlet J. M. , Maurer C. E. , Flood C. J. , Bracker A. S. , Yakes M. , Gammon D. , Flagg E. B.
Published: April 2019

A strong, far-detuned laser can shift the energy levels of an optically active quantum system via the AC Stark effect. We demonstrate that the polarization of the laser results in a spin-selective modification to the energy structure of a charged quantum dot, shifting one spin manifold but not the other. An additional shift occurs due to the Overhauser field of the nuclear spins, which are pumped into a partially polarized state. This mechanism offers a potentially rapid, reversible, and coherent control of the energy structure and polarization selection rules of a charged quantum dot.
Semi-polar (11–22) GaN epitaxial films with significantly reduced defect densities grown on m-plane sapphire using a sequence of two in situ SiNx interlayers
Authors: Xing Kun , Tseng Chiyao , Wang Liancheng , Chi Pingfeng , Wang Jiangtao , Chen Posung , Liang Huaguo
Published: April 2019

This letter reports an approach for growing semipolar (11–22) GaN films with significantly reduced defect densities on m-plane sapphire substrates by incorporating a sequence of two in situ SiNx layers. The first SiNx layer is deposited on an initial epitaxial GaN layer and acts as a nanomask for preventing the propagation of extended defects. The second SiNx layer is deposited just after subsequent epitaxial GaN overgrowth begins to form self-organized GaN islands, which encourages further GaN growth to initiate from the exposed island sidewalls while blocking the penetration of the remaining defects. X-ray rocking curve measurements show that our semipolar GaN films provide relatively low full width at half maximum values at 0.119° along both the [11–23] and [10–10] directions. Additionally, transmission electron microscopy analyses confirm that our semipolar GaN films provide a significantly reduced density of threading dislocations down to ∼6 × 108 cm−2, which is two orders of magnitude less than those of conventionally deposited films.
Clustering and Bellerophon state in Kuramoto model with second-order coupling
Authors: Li Xue , Zhang Jiameng , Zou Yong , Guan Shuguang
Published: April 2019

In this paper, clustering in the Kuramoto model with second-order coupling is investigated under the bimodal Lorentzian frequency distribution. By linear stability analysis and the Ott-Antonsen ansatz treatment, the critical coupling strength for the synchronization transition is obtained. The theoretical results are further verified by numerical simulations. It has been revealed that various synchronization paths, including the first- and second-order transitions as well as the multiple bifurcations, exist in this system with different parameters of frequency distribution. In certain parameter regimes, the Bellerophon states are observed and their dynamical features are fully characterized.
Analytical derivation of expressions for the specific heat of superfluid Fermi liquids with anisotropic spin-triplet p-wave pairing at finite temperatures
Authors: Tarasov A. N.
Published: April 2019

Analytical expressions for the specific heat of superfluid Fermi liquids (SFLs) with anisotropic spin-triplet p-wave pairing of the 3He-A type have been obtained based on a generalised Fermi-liquid approach both at the low temperatures of 0 < T ≪Tc0 (n) and near the temperature of the phase transition [Tc0 (n)] from a normal to a superfluid phase in the absence of a magnetic field. Apart from liquid 3He-A, we also study dense superfluid neutron matter (SNM) with anisotropic spin-triplet p-wave pairing (similar to 3He-A) at subnuclear (n < n0, where n0 = 0.17 fm–3 is the nuclear density) and supernuclear densities (n > n0) in view of generalised Skyrme forces (with additional terms depending on the density n). At 0 < T ≪Tc0 (n), we have obtained an asymptotic expansion for the specific heat CSNM(SFL)(T,n), in which, apart from the main term ∼ T 3 (known for 3He-A in the limit of T → 0) there is an additional correction term (∼ T5), which may reach several percent of the contribution from the main term to the decomposition of the specific heat of SNM (or SFLs). An analytical formula has also been derived for calculating the specific heat CSNM(SFL)(T,n) at temperatures near Tc0(n). The expressions obtained for the CSNM(T,n) functions (valid for an arbitrary parametrisation of the effective Skyrme interaction in neutron matter) have been defined for SNM with the generalised BSk21 parametrisation of Skyrme forces. In addition, dependency graphs were plotted for the specific heat CBSk21(t, y) in the reduced temperature range of 0 < t ≡ T/Tc0(n) ≪ 1 and at t ≲ 1 for dense SNM (at 0.1 ≤ y ≡ n/n0 ≤ 1.7). These results may be of interest for neutron star physics in connection with neutron star cooling (in the presence of neutron superfluidity with anisotropic spin-triplet p-wave Cooper pairing in the outer part of dense liquid neutron star cores).
The critical state of superconducting multilayered structures
Authors: Gavrilkin S. Yu. , Lykov A. N. , Tsvetkov A. Yu.
Published: April 2019

We propose a new method for calculating the dependence of the critical current on an external magnetic field, and the distribution of this current over the layers in superconducting multilayered structures. The method is based on a numerical solution of a system of nonlinear Ginzburg–Landau equations that describe the behavior of a superconducting plate carrying a transport current in a magnetic field, provided that it does not contain Abrikosov vortices. The way in which boundary conditions in the Ginzburg–Landau theory influence the critical state of superconducting layered structures is also considered. From a mathematical point of view, application of a general boundary condition to the system of Ginzburg–Landau equations leads to a change in the order parameter along the thickness of the thin superconducting plates. The physical nature of this phenomenon is explained by the proximity effect at the superconductor–normal metal (SN) interface, which leads to the suppression of the order parameter near the SN interface. The resulting calculated dependences of the plates’ critical current on the magnetic field strength applied parallel to the layers are used to determine the critical current of multilayer structures. It is assumed that the mutual influence of superconducting layers occurs only via the magnetic field that they create.
Comparison of Langmuir probe and laser Thomson scattering for plasma density and electron temperature measurements in HiPIMS plasma
Authors: Ryan Peter J. , Bradley James W. , Bowden Mark D.
Published: April 2019

The temporal evolution of plasma density and electron temperature in high power impulse magnetron sputtering discharges has been measured using the Langmuir probe and laser Thomson scattering techniques. Measurements were performed (nonsimultaneously) at two positions within the plasma, in the low magnetic field strength region on the discharge axis and in the high magnetic field strength region of the magnetic trap, for peak power densities of 450 W cm–2 and 900 W cm−2, respectively. The maximum plasma densities and temperatures were 6.9 × 1019 m−3 and 3.7 eV in the pulse-on time, and values decayed to 4.5 × 1017 m−3 and 0.1 eV at times up to 250 μs into the afterglow. The results indicate that although intrusive, the Langmuir probe can provide a good indication of electron properties in regions of different electron magnetization in the discharge.
A primary care programme to improve identification and stepped-care support of Asians with mental health and lifestyle issues
Authors: Shah Khalid , Corter Arden , Bird Amy , Goodyear-Smith Felicity
Published: April 2019

ABSTRACT
INTRODUCTIONAsians living in Western countries have a higher incidence of mental health and lifestyle issues, but are less likely to disclose these to health-care professionals due to stigma. Instead, they tend to present to primary care with somatic concerns.
AIMTo assess the feasibility and acceptability of a well-validated electronic screening and stepped-care support tool (eCHAT) to identify mental health and lifestyle issues among Asian patients.
METHODSA mixed-methods (interviews and survey) co-design approach explored patient and clinic staff perspectives on a translated version of eCHAT (AsiaCHAT). Recruitment was through a large primary care organisation with a high proportion of Asian patients. Of the 307 approached, 277 participated (92% acceptance rate).
RESULTSProblems of depression (n = 12) and anxiety (n = 69) were identified among patients, as were sexual health concerns (n = 22) among younger participants. Overall, participants and clinic staff rated AsiaCHAT as a useful and acceptable tool for disclosing and discussing patient concerns. Problems of finances, time constraints and competing demands made long-term implementation challenging.
DISCUSSIONAsiaCHAT is a promising tool for identifying mental health and lifestyle concerns among Asians presenting to primary care. The electronic screener supports patient and provider discussion of sensitive topics and the stepped-care support function helps direct care. Its flexible functionality means that there is potential to integrate it into busy clinic settings as well as online patient portals, and the programme aligns with current policy to improve Asian health in New Zealand.
Phospholipid membranes drive abdominal aortic aneurysm development through stimulating coagulation factor activity
Authors: Allen-Redpath Keith , Aldrovandi Maceler , Lauder Sarah N. , Gketsopoulou Anastasia , Tyrrell Victoria J. , Slatter David A. , Andrews Robert , Watkins W. John , Atkinson Georgia , McNeill Eileen , Gilfedder Anna , Protty Majd , Burston James , Johnson Sam R. C. , Rodrigues Patricia R. S. , Jones Dylan O. , Lee Regent , Handa Ashok , Channon Keith , Obaji Samya , Alvarez-Jarreta Jorge , Krönke Gerhard , Ackermann Jochen , Jenkins P. Vince , Collins Peter W. , O’Donnell Valerie B.
Published: April 2019

Significance

Abdominal aortic aneurysm (AAA) is a disease of the abdominal aorta where inflammation causes damage and can ultimately lead to rupture. When this happens, uncontrolled internal bleeding can lead to death within minutes. Many aneurysms are not detected until they rupture, and for those that are, treatments to stop them progressing are limited. Here we used biophysics and genetically modified mice to show that a new family of lipids (fats) made by circulating blood cells promote AAA formation in the vessel wall because they directly regulate blood clotting. An approach that prevents AAA development was identified, based on intravenous administration of lipids. The studies provide insights into how AAA develops and may lead to novel therapies for this disease.
Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy
Authors: Mitra Jaba , Makurath Monika A. , Ngo Thuy T. M. , Troitskaia Alice , Chemla Yann R. , Ha Taekjip
Published: April 2019

Significance

G-quadruplex (GQ)–forming G4 DNA, made of four repeats of guanines, is implicated in many important processes. Telomeric GQs are being studied extensively as anticancer drug targets. Because many nucleic acid-processing enzymes can exert piconewton forces and can be functionally regulated by tension on DNA, we used a single-molecule instrument combining fluorescence with mechanical manipulation to study the dynamics of human telomeric DNA under physiological levels of tension. We observed extreme mechanical diversity with at least six different interconverting species that differ in mechanical responses. Such extreme mechanical diversity may induce differential interactions with helicases and polymerases and modulate processes such as replication and transcription. Our comparative analysis further revealed the effects of sequence changes and ionic conditions.
Cone photoreceptor classification in the living human eye from photostimulation-induced phase dynamics
Authors: Zhang Furu , Kurokawa Kazuhiro , Lassoued Ayoub , Crowell James A. , Miller Donald T.
Published: April 2019

Significance

The three spectral types of cone photoreceptors underlie color perception and are largely responsible for inherited and acquired color vision anomalies. In vivo mapping of the trichromatic cone mosaic by imaging provides the most direct and quantitative means to assess the role of photoreceptors in color vision, but remains challenging because cone reflections only weakly differentiate cone types. Here, we show a noninvasive light microscopy modality that reveals the cell’s spectral type, using the optical phase change that arises within the cell when stimulated with light. Our procedure is orders of magnitude faster and more accurate than prior approaches and makes in vivo cone classification promising for a much wider range of color vision applications.
Relative interfacial cleavage energetics of protein complexes revealed by surface collisions
Authors: Harvey Sophie R. , Seffernick Justin T. , Quintyn Royston S. , Song Yang , Ju Yue , Yan Jing , Sahasrabuddhe Aniruddha N. , Norris Andrew , Zhou Mowei , Behrman Edward J. , Lindert Steffen , Wysocki Vicki H.
Published: April 2019

Significance

There is a large gap between the number of protein complex structures currently solved and the number of functionally relevant structures. Mass spectrometry-based approaches for biomacromolecule structural characterization are growing, are beginning to fill critical gaps, and complement other structural biology tools. We have shown for several examples that collision of protein complex ions with a surface yields products that are reflective of substructure. We present here a computational model that predicts the relative appearance energy at which a globular protein complex dissociates. This appearance energy prediction can provide structural information when a high-resolution structure has not or cannot be obtained and in the future has potential to be used to select the best-fit candidate computational models, dramatically increasing the structural information obtained.
Hierarchy of clinical manifestations in SAVI N153S and V154M mouse models
Authors: Motwani Mona , Pawaria Sudesh , Bernier Jennifer , Moses Stephanie , Henry Kate , Fang Terry , Burkly Linda , Marshak-Rothstein Ann , Fitzgerald Katherine A.
Published: April 2019

Significance

STING is a key driver of monogenic interferonopathies that include STING-associated vasculopathy with onset in infancy (SAVI). Defining the molecular mechanisms and the contribution of individual cell types to disease could unveil new therapeutic targets for management of SAVI and related autoimmune diseases. Here we compare and contrast murine models representative of the two most common mutations and identify a hierarchy of lymphoid abnormalities that depend on T cell-intrinsic expression of the SAVI mutation. Although clinical manifestations result from hyperactivation of STING, they occur independently of type I interferon and necroptosis. These murine models facilitate a dissection of the role of STING in specific tissues and provide tools for evaluating STING inhibitors for the treatment of SAVI patients.
EXPANSIN A1-mediated radial swelling of pericycle cells positions anticlinal cell divisions during lateral root initiation
Authors: Ramakrishna Priya , Ruiz Duarte Paola , Rance Graham A. , Schubert Martin , Vordermaier Vera , Vu Lam Dai , Murphy Evan , Vilches Barro Amaya , Swarup Kamal , Moirangthem Kamaljit , Jørgensen Bodil , van de Cotte Brigitte , Goh Tatsuaki , Lin Zhefeng , Voβ Ute , Beeckman Tom , Bennett Malcolm J. , Gevaert Kris , Maizel Alexis , De Smet Ive
Published: April 2019

Significance

Organ formation is an essential process in plants and animals, driven by cell division and cell identity establishment. Root branching where lateral roots form along the primary root axis increases the root system and aids the capture of water and nutrients. We have discovered that tight control of the cell width is necessary to coordinate asymmetric cell divisions in cells that give rise to a new lateral root organ. Although biomechanical processes have been shown to play a role in plant organogenesis, including lateral root formation, our data give mechanistic insights into cell size control during lateral root initiation.
Erosion–corrosion resistance of a β-Ta2O5 nanocrystalline coating in two-phase fluid impingement environments
Authors: Xu Jiang , Peng Shuang , Jiang Shuyun , Munroe Paul , Xie Zong-Han
Published: April 2019

In this study, a β-Ta2O5 coating was deposited onto a Ti–6Al–4V substrate using a double-cathode glow discharge plasma technique. The hardness and elastic modulus values of the β-Ta2O5 coating were almost 4 times and 1.8 times greater than that of the Ti–6Al–4V substrate, respectively. Potentiodynamic polarisation curves indicated that the current densities of the β-Ta2O5 coated sample are least one order of magnitude less than that observed for the uncoated substrate under a solid/liquid slurry flow. Electrochemical impedance spectroscopy results showed that the resistance values for the β-Ta2O5 coating are of the order of 106 Ω cm2, and at the same erosion time, the resistance value for the β-Ta2O5 coating is one order of magnitude greater than that of the Ti–6Al–4V.
Effect of strain on cavity development during Al–Zn–Mg–Cu alloy superplastic flow
Authors: Li Guangyu , Ding Hua , Wang Jian , Zhang Wenjing , Zhang Ning , Hou Hongliang
Published: April 2019

Cavitation behaviour has been investigated in an Al–Zn–Mg–Cu alloy with an average grain size of 10 µm during superplastic deformation. The superplastic tensile tests were interrupted at different true strains at 530°C and 3 × 10−4 s−1. The results showed that cavity nucleation occurred above a critical strain in the optimum loading condition. It was easy for cavities to form at the triple junction due to the stress concentration caused by cooperative grain boundary sliding. Since the tensile stress was higher in the middle of the sample, the cavities were arranged in a straight line parallel to the tensile axis in the centre of the sample. A more appropriate cavity growth equation considering the critical strain was proposed to describe the cavitation behaviour.
Expectation propagation for Poisson data
Authors: Zhang Chen , Arridge Simon , Jin Bangti
Published: April 2019

The Poisson distribution arises naturally when dealing with data involving counts, and it has found many applications in inverse problems and imaging. In this work, we develop an approximate Bayesian inference technique based on expectation propagation for approximating the posterior distribution formed from the Poisson likelihood function and a Laplace type prior distribution, e.g. the anisotropic total variation prior. The approach iteratively yields a Gaussian approximation, and at each iteration, it updates the Gaussian approximation to one factor of the posterior distribution by moment matching. We derive explicit update formulas in terms of one-dimensional integrals, and also discuss stable and efficient quadrature rules for evaluating these integrals. The method is showcased on two-dimensional PET images.
Many-body perturbation theory calculations using the yambo code
Authors: Sangalli D , Ferretti A , Miranda H , Attaccalite C , Marri I , Cannuccia E , Melo P , Marsili M , Paleari F , Marrazzo A , Prandini G , Bonfà P , Atambo M O , Affinito F , Palummo M , Molina-Sánchez A , Hogan C , Grüning M , Varsano D , Marini A
Published: April 2019

yambo is an open source project aimed at studying excited state properties of condensed matter systems from first principles using many-body methods. As input, yambo requires ground state electronic structure data as computed by density functional theory codes such as Quantum ESPRESSO and Abinit. yambo’s capabilities include the calculation of linear response quantities (both independent-particle and including electron–hole interactions), quasi-particle corrections based on the GW formalism, optical absorption, and other spectroscopic quantities. Here we describe recent developments ranging from the inclusion of important but oft-neglected physical effects such as electron–phonon interactions to the implementation of a real-time propagation scheme for simulating linear and non-linear optical properties. Improvements to numerical algorithms and the user interface are outlined. Particular emphasis is given to the new and efficient parallel structure that makes it possible to exploit modern high performance computing architectures. Finally, we demonstrate the possibility to automate workflows by interfacing with the yambopy and AiiDA software tools.
Rangeland vegetation dynamics in the Altai mountain region of Mongolia, Russia, Kazakhstan and China: effects of climate, topography, and socio-political context for livestock herding practices
Authors: Iegorova Liza V , Gibbs James P , Mountrakis Giorgos , Bastille-Rousseau Guillaume , Paltsyn Mikhail Yu , Ayatkhan Atay , Baylagasov Leonid V , Robertus Yury V , Chelyshev Andrey V
Published: April 2019

Discriminating between climate- and human-induced variation in rangeland quality poses a major challenge for developing policy to sustain herder livelihoods and alleviate herder poverty. We contrasted changes in rangeland vegetation cover across a region—the Altai Mountains of central Asia (China, Kazakhstan, Russia and Mongolia)—that juxtaposes strongly contrasting social, political and economic conditions across a community of herders of shared cultural background (all of Kazakh origin). Our analysis focused on a satellite-derived vegetation index (Normalized Difference Vegetation Index—NDVI) from the Advanced Very High Resolution Radiometer sensor during the period 1982–2013, which included the breakup of the Soviet Union in 1990 and heralded a transition away from pervasive state control on herding practices in many parts of the region. Grassland cover increased with decreasing elevation and increasing precipitation. Grassland also decreased under increased livestock density but was largely unresponsive to the dramatic changes that occurred in the sociopolitical context for grazing practices. Average NDVI values and duration of growing season were greater after the Soviet Union’s collapse across the region, trends that precipitation and temperature data indicate were most likely driven by a changing climate. We conclude that rangeland policy development to assure sustainability of herder livelihoods in the Altai Mountain region should focus on climate change adaptation measures rather than modifying herders’ grazing practices.
The service-stock trap: analysis of the environmental impacts and productivity of the service sector in Hungary
Authors: Dombi Mihály
Published: April 2019

Urbanization and the emerging share of the service sector in economic output may support the sustainability transition due to lower material input and emissions, while further accelerating the economic growth at the same time. Nevertheless, there are significant barriers to the transition. In this study, the service sector of Hungary and its four commercial sub-sectors have been analyzed with regard to their material requirement (input flows and stock) and greenhouse gas emissions (GHG) emissions utilizing EXIOBASE v3. General policy implications are also provided with special regard to costs, possible taxes and productivity of resources. The share of direct and indirect GHG emissions and material input generated by the sector was stable and moderate. A permanently improving trend is present in GHG, and material input intensity. Material stock accumulation in the service sector (capital stock), however, shows an ascending trend, and it has increased from 42% in 1995 to be 55% in 2015. Material input productivity of investments into services has increased until the economic crisis, then it starts to decline or stagnate; while overall stock productivity has decreased in two sub-sectors, and slow improvement was observable in sub-sectors of transportation and information and communication technology (ICT). Stock productivity of ICT and machinery capital stock was decreased dramatically in all sub-sectors. Four economic sub-sectors of the commercial services analyzed in this study have increased their capital stock from 130 to 288 Mt between 2000 and 2015. The exponential trend in material stock accumulation is an environmental issue with rising scientific concern and awareness, since it constitutes the basis of crucial waste management, resource scarcity and resource use challenges in the future. The current study indicates general reinforcement of the environmental pressure of material stock accumulation by the service sector. This phenomena was defined as the ‘service-stock trap’, which refers to the sign of a trade-off between the descending flow-type environmental impacts and ascending impacts of capital stock accumulation during the economic transition towards a service-based economy. As a promising way out of the trap, the resource tax was discussed in detail, which seems to be suitable for forming investment decisions of the business actors.
Ten years of AoB PLANTS the open access journal for plant scientists: inception and progress since 2009
Authors: Jackson Michael B
Published: April 2019

AoB PLANTS is a not-for-profit, open access, plant science journal and one of three peer-reviewed journals owned and managed by the Annals of Botany Company. This article explains events and thinking that led to the starting of AoB PLANTS and how the unique features of the Journal came to be formalized prior to its launch in September 2009. The article also describes how the Journal’s management developed over the first 10 years and summarizes the Journal’s achievements in a decade where open access journals have proliferated despite subscription journals continuing to dominate the publishing of peer-reviewed botanical science.
Figure and caption extraction from biomedical documents
Authors: Li Pengyuan , Jiang Xiangying , Shatkay Hagit
Published: April 2019

Motivation

Figures and captions convey essential information in biomedical documents. As such, there is a growing interest in mining published biomedical figures and in utilizing their respective captions as a source of knowledge. Notably, an essential step underlying such mining is the extraction of figures and captions from publications. While several PDF parsing tools that extract information from such documents are publicly available, they attempt to identify images by analyzing the PDF encoding and structure and the complex graphical objects embedded within. As such, they often incorrectly identify figures and captions in scientific publications, whose structure is often non-trivial. The extraction of figures, captions and figure-caption pairs from biomedical publications is thus neither well-studied nor yet well-addressed.

Results

We introduce a new and effective system for figure and caption extraction, PDFigCapX. Unlike existing methods, we first separate between text and graphical contents, and then utilize layout information to effectively detect and extract figures and captions. We generate files containing the figures and their associated captions and provide those as output to the end-user.

We test our system both over a public dataset of computer science documents previously used by others, and over two newly collected sets of publications focusing on the biomedical domain. Our experiments and results comparing PDFigCapX to other state-of-the-art systems show a significant improvement in performance, and demonstrate the effectiveness and robustness of our approach.

Availability and implementation

Our system is publicly available for use at: https://www.eecis.udel.edu/~compbio/PDFigCapX. The two new datasets are available at: https://www.eecis.udel.edu/~compbio/PDFigCapX/Downloads
Impact of 10-Valent Pneumococcal Conjugate Vaccine Introduction on Pneumococcal Carriage and Antibiotic Susceptibility Patterns Among Children Aged <5 Years and Adults With Human Immunodeficiency Virus Infection: Kenya, 2009–2013
Authors: Kobayashi Miwako , Bigogo Godfrey , Kim Lindsay , Mogeni Ondari D , Conklin Laura M , Odoyo Arthur , Odiembo Herine , Pimenta Fabiana , Ouma Dominic , Harris Aaron M , Odero Kennedy , Milucky Jennifer L , Ouma Alice , Aol George , Audi Allan , Onyango Clayton , Cosmas Leonard , Jagero Geofrey , Farrar Jennifer L , da Gloria Carvalho Maria , Whitney Cynthia G , Breiman Robert F , Lessa Fernanda C
Published: April 2019

Background

Kenya introduced 10-valent pneumococcal conjugate vaccine (PCV10) among children <1 year in 2011 with catch-up vaccination among children 1–4 years in some areas. We assessed changes in pneumococcal carriage and antibiotic susceptibility patterns in children <5 years and adults.

Methods

During 2009–2013, we performed annual cross-sectional pneumococcal carriage surveys in 2 sites: Kibera (children <5 years) and Lwak (children <5 years, adults). Only Lwak had catch-up vaccination. Nasopharyngeal and oropharyngeal (adults only) swabs underwent culture for pneumococci; isolates were serotyped. Antibiotic susceptibility testing was performed on isolates from 2009 and 2013; penicillin nonsusceptible pneumococci (PNSP) was defined as penicillin-intermediate or -resistant. Changes in pneumococcal carriage by age (<1 year, 1–4 years, adults), site, and human immunodeficiency virus (HIV) status (adults only) were calculated using modified Poisson regression, with 2009–2010 as baseline.

Results

We enrolled 2962 children (2073 in Kibera, 889 in Lwak) and 2590 adults (2028 HIV+, 562 HIV−). In 2013, PCV10-type carriage was 10.3% (Lwak) to 14.6% (Kibera) in children <1 year and 13.8% (Lwak) to 18.7% (Kibera) in children 1–4 years. This represents reductions of 60% and 63% among children <1 year and 52% and 60% among children 1–4 years in Kibera and Lwak, respectively. In adults, PCV10-type carriage decreased from 12.9% to 2.8% (HIV+) and from 11.8% to 0.7% (HIV−). Approximately 80% of isolates were PNSP, both in 2009 and 2013.

Conclusions

PCV10-type carriage declined in children <5 years and adults post–PCV10 introduction. However, PCV10-type and PNSP carriage persisted in children regardless of catch-up vaccination.
GIDB: a knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal cancer
Authors: Wang Ying , Wang Yueqian , Wang Shuangkuai , Tong Yuantao , Jin Ling , Zong Hui , Zheng Rongbin , Yang Jinxuan , Zhang Zeyu , Ouyang En , Zhou Mengyan , Zhang Xiaoyan
Published: April 2019

Gastrointestinal (GI) cancer is common, characterized by high mortality, and includes oesophagus, gastric, liver, bile duct, pancreas, rectal and colon cancers. The insufficient specificity and sensitivity of biomarkers is still a key clinical hindrance for GI cancer diagnosis and successful treatment. The emergence of `precision medicine’, `basket trial’ and `field cancerization’ concepts calls for an urgent need and importance for the understanding of how organ system cancers occur at the molecular levels. Knowledge from both the literature and data available in public databases is informative in elucidating the molecular alterations underlying GI cancer. Currently, most available cancer databases have not offered a comprehensive discovery of gene-disease associations, molecular alterations and clinical information by integrated text mining and data mining in GI cancer. We develop GIDB, a panoptic knowledge database that attempts to automate the curation of molecular signatures using natural language processing approaches and multidimensional analyses. GIDB covers information on 8730 genes with both literature and data supporting evidence, 248 miRNAs, 58 lncRNAs, 320 copy number variations, 49 fusion genes and 2381 semantic networks. It presents a comprehensive database, not only in parallelizing supporting evidence and data integration for signatures associated with GI cancer but also in providing the timeline feature of major molecular discoveries. It highlights the most comprehensive overview, research hotspots and the development of historical knowledge of genes in GI cancer. Furthermore, GIDB characterizes genomic abnormalities in multilevel analysis, including simple somatic mutations, gene expression, DNA methylation and prognosis. GIDB offers a user-friendly interface and two customizable online tools (Heatmap and Network) for experimental researchers and clinicians to explore data and help them shorten the learning curve and broaden the scope of knowledge. More importantly, GIDB is an ongoing research project that will continue to be updated and improve the automated method for reducing manual work.
Intragenomic heterogeneity of intergenic ribosomal DNA spacers in Cucurbita moschata is determined by DNA minisatellites with variable potential to form non-canonical DNA conformations
Authors: Matyášek Roman , Kuderová Alena , Kutílková Eva , Kučera Marek , Kovařík Aleš
Published: April 2019

The intergenic spacer (IGS) of rDNA is frequently built of long blocks of tandem repeats. To estimate the intragenomic variability of such knotty regions, we employed PacBio sequencing of the Cucurbita moschata genome, in which thousands of rDNA copies are distributed across a number of loci. The rRNA coding regions are highly conserved, indicating intensive interlocus homogenization and/or high selection pressure. However, the IGS exhibits high intragenomic structural diversity. Two repeated blocks, R1 (300–1250 bp) and R2 (290–643 bp), account for most of the IGS variation. They exhibit minisatellite-like features built of multiple periodically spaced short GC-rich sequence motifs with the potential to adopt non-canonical DNA conformations, G-quadruplex-folded and left-handed Z-DNA. The mutual arrangement of these motifs can be used to classify IGS variants into five structural families. Subtle polymorphisms exist within each family due to a variable number of repeats, suggesting the coexistence of an enormous number of IGS variants. The substantial length and structural heterogeneity of IGS minisatellites suggests that the tempo of their divergence exceeds the tempo of the homogenization of rDNA arrays. As frequently occurring among plants, we hypothesize that their instability may influence transcription regulation and/or destabilize rDNA units, possibly spreading them across the genome.
A Micro-Scale Approach to Ethnic Minority Concentration in the Residential Environment and Voting for the Radical Right in The Netherlands
Authors: Janssen Heleen J , van Ham Maarten , Kleinepier Tom , Nieuwenhuis Jaap
Published: April 2019

Existing empirical research on the link between ethnic minority concentration in residential environments and voting for the radical right is inconclusive, mainly due to major differences between studies in the spatial scale at which minority concentration is measured. We examined whether the presence of non-western ethnic minorities in the residential environment, measured at four spatial scales, is related to individuals’ intention to vote for the Dutch Party for Freedom (Dutch acronym PVV). We combined individual level survey data and register data, and we used multi-level structural equation models to examine possible mediation by anti-immigrant attitudes and political dissatisfaction. The models show different effects at different scales. At the micro scale (100 by 100 meter grids) we find a curvilinear effect: individuals with 30–50 per cent non-western minorities in their direct living environment are most likely to report to vote for the PVV. At higher spatial scales (up to municipal level) we find that the higher the proportion of non-western minorities, the more likely individuals are to report to vote for the PVV. These effects can however not be explained by anti-immigrant attitudes or political dissatisfaction. We even find that at the micro scale the presence of non-western minorities is related to less anti-immigrant attitudes.
The effect of implantable cardioverter-defibrillator in patients with diabetes and non-ischaemic systolic heart failure
Authors: Rørth Rasmus , Thune Jens Jakob , Nielsen Jens C , Haarbo Jens , Videbæk Lars , Korup Eva , Signorovitch James , Bruun Niels E , Eiskjær Hans , Hassager Christian , Svendsen Jesper Hastrup , Høfsten Dan E , Torp-Pedersen Christian , Pehrson Steen , Køber Lars , Kristensen Søren L
Published: April 2019

Aims

Implantable cardioverter-defibrillator (ICD) implantation reduce the risk of sudden cardiac death, but not all-cause death in patients with non-ischaemic systolic heart failure (HF). Whether co-existence of diabetes affects ICD treatment effects is unclear.

Methods and results

We examined the effect of ICD implantation on risk of all-cause death, cardiovascular death, and sudden cardiac death (SCD) according to diabetes status at baseline in the Danish Study to Assess the Efficacy of ICDs in Patients with Non-ischaemic Systolic Heart Failure on Mortality (DANISH) trial. Outcomes were analysed by use of cumulative incidence curves and Cox regressions models. Of the 1116 patients enrolled, 211 (19%) had diabetes at baseline. Patients with diabetes were more obese, had worse kidney function and more were in New York Heart Association Class III/IV. The risk of device infections and other complications in the ICD group was similar among patients with and without diabetes (6.1% vs. 4.6% P = 0.54). Irrespective of treatment group, diabetes was associated with higher risk of all-cause death, cardiovascular death, and SCD. The treatment effect of ICD in patients with diabetes vs. patients without diabetes was hazard ratio (HR) = 0.92 (0.57–1.50) vs. HR = 0.85 (0.63–1.13); Pinteraction = 0.60 for all-cause mortality, HR = 0.99 (0.58–1.70) vs. HR = 0.70 (0.48–1.01); Pinteraction = 0.25 for cardiovascular death, and HR = 0.81 (0.35–1.88) vs. HR = 0.40 (0.22–0.76); Pinteraction = 0.16 for sudden cardiac death.

Conclusion

Among patients with non-ischaemic systolic HF, diabetes was associated with higher incidence of all-cause mortality, primarily driven by cardiovascular mortality including SCD. Treatment effect of ICD therapy was not significantly modified by diabetes which might be due to lack of power.
A cellular model of Brugada syndrome with SCN10A variants using human-induced pluripotent stem cell-derived cardiomyocytes
Authors: El-Battrawy Ibrahim , Albers Sebastian , Cyganek Lukas , Zhao Zhihan , Lan Huan , Li Xin , Xu Qiang , Kleinsorge Mandy , Huang Mengying , Liao Zhenxing , Zhong Rujia , Rudic Boris , Müller Jonas , Dinkel Hendrik , Lang Siegfried , Diecke Sebastian , Zimmermann Wolfram-Hubertus , Utikal Jochen , Wieland Thomas , Borggrefe Martin , Zhou Xiaobo , Akin Ibrahim
Published: April 2019

Aims

Brugada syndrome (BrS) is associated with a pronounced risk to develop sudden cardiac death (SCD). Up to 21% of patients are related to mutations in SCN5A. Studies identified SCN10A as a contributor of BrS. However, the investigation of the human cellular phenotype of BrS in the presence of SCN10A mutations remains lacking. The objective of this study was to establish a cellular model of BrS in presence of SCN10A mutations using human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs).

Methods and results

Dermal fibroblasts obtained from a BrS patient suffering from SCD harbouring the SCN10A double variants (c.3803G>A and c.3749G>A) and three independent healthy control subjects were reprogrammed to hiPSCs. Human-induced pluripotent stem cells were differentiated into cardiomyocytes (hiPSC-CMs).The hiPSC-CMs from the BrS patient showed a significantly reduced peak sodium channel current (INa) and a significantly reduced ATX II (sea anemone toxin, an enhancer of late INa) sensitive as well as A-887826 (a blocker of SCN10A channel) sensitive late sodium channel current (INa) when compared with the healthy control hiPSC-CMs, indicating loss-of-function of sodium channels. Consistent with reduced INa the action potential amplitude and upstroke velocity (Vmax) were significantly reduced, which may contribute to arrhythmogenesis of BrS. Moreover, Ajmaline effects on action potentials were stronger in BrS-hiPSC-CMs than in healthy control cells. This is in agreement with the higher susceptibility of patients to sodium channel blocking drugs in unmasking BrS.

Conclusion

Patient-specific hiPSC-CMs are able to recapitulate single-cell phenotype features of BrS with SCN10A mutations and may provide novel opportunities to further elucidate the cellular disease mechanism.
Chromosome-scale genome assembly of kiwifruit Actinidia eriantha with single-molecule sequencing and chromatin interaction mapping
Authors: Tang Wei , Sun Xuepeng , Yue Junyang , Tang Xiaofeng , Jiao Chen , Yang Ying , Niu Xiangli , Miao Min , Zhang Danfeng , Huang Shengxiong , Shi Wei , Li Mingzhang , Fang Congbing , Fei Zhangjun , Liu Yongsheng
Published: April 2019

Background

Kiwifruit (Actinidia spp.) is a dioecious plant with fruits containing abundant vitamin C and minerals. A handful of kiwifruit species have been domesticated, among which Actinidiaeriantha is increasingly favored in breeding owing to its superior commercial traits. Recently, elite cultivars from A. eriantha have been successfully selected and further studies on their biology and breeding potential require genomic information, which is currently unavailable.

Findings

We assembled a chromosome-scale genome sequence of A. eriantha cultivar White using single-molecular sequencing and chromatin interaction map–based scaffolding. The assembly has a total size of 690.6 megabases and an N50 of 21.7 megabases. Approximately 99% of the assembly were in 29 pseudomolecules corresponding to the 29 kiwifruit chromosomes. Forty-three percent of the A. eriantha genome are repetitive sequences, and the non-repetitive part encodes 42,988 protein-coding genes, of which 39,075 have homologues from other plant species or protein domains. The divergence time between A. eriantha and its close relative Actinidia chinensis is estimated to be 3.3 million years, and after diversification, 1,727 and 1,506 gene families are expanded and contracted in A. eriantha, respectively.

Conclusions

We provide a high-quality reference genome for kiwifruit A. eriantha. This chromosome-scale genome assembly is substantially better than 2 published kiwifruit assemblies from A. chinensis in terms of genome contiguity and completeness. The availability of the A. eriantha genome provides a valuable resource for facilitating kiwifruit breeding and studies of kiwifruit biology.
Estimating age composition for multiple years when there are gaps in the ageing data: the case of western Atlantic bluefin tuna
Authors: Ailloud Lisa E , Lauretta Matthew V , Walter John F , Hoenig John M
Published: April 2019

Age–length key (ALK) methods generally perform well when length samples and age samples are representative of the underlying population. It is unclear how well these methods perform when lengths are representative but age samples are sparse (i.e. age samples are small or missing in many years, and some length groups do not have any age observations). With western Atlantic bluefin tuna, the available age data are sparse and have been, for the most part, collected opportunistically. We evaluated two methods capable of accommodating sparse age data: a novel hybrid ALK (combining forward ALKs and cohort slicing) and the combined forward-inverse ALK. Our goal was to determine if the methods performed better than cohort slicing, which has traditionally been used to obtain catch-at-age for Atlantic bluefin tuna, given the data limitations outlined above. Simulation results indicated that the combined forward-inverse ALK performed much better than the other methods. When applied to western Atlantic bluefin tuna data, the combined forward-inverse ALK approach was able to track cohorts and identified an inconsistency in the ageing of some samples.
Early Measles Vaccination During an Outbreak in the Netherlands: Short-Term and Long-Term Decreases in Antibody Responses Among Children Vaccinated Before 12 Months of Age
Authors: Brinkman Iris D , de Wit Jelle , Smits Gaby P , ten Hulscher Hinke I , Jongerius Maria C , Abreu Taymara C , van der Klis Fiona R M , Hahné Susan J M , Koopmans Marion P G , Rots Nynke Y , van Baarle Debbie , van Binnendijk Robert S
Published: April 2019

Background

The majority of infants will not be protected by maternal antibodies until their first measles vaccination, between 12 and 15 months of age. This provides incentive to reduce the age at measles vaccination, but immunological consequences are insufficiently understood, and long-term effects are largely unknown.

Methods

A total of 79 infants who received early measles vaccination between 6 and 12 months age and a second dose at 14 months of age were compared to 44 children in a control group who received 1 dose at 14 months of age. Measles virus–specific neutralizing antibody concentrations and avidity were determined up to 4 years of age.

Results

Infants who first received measles vaccination before 12 months of age had a long-term decrease in the concentration and avidity of measles virus–specific neutralizing antibodies, compared with infants in the control group. For 11.1% of children with a first dose before 9 months of age, antibody levels at 4 years of age had dropped below the cutoff for clinical protection.

Conclusions

Early measles vaccination provides immediate protection in the majority of infants but yields a long-term decrease in neutralizing antibody responses, compared to vaccination at a later age. Additional vaccination at 14 months of age does not improve this. Over the long term, this may result in an increasing number of children susceptible to measles.