bluuebunny/crossref_metadata_2025 huggingface dataset:
AMPfret: synthetic nanosensor for cellular energy states
Authors: Crocker Hannah , Pelosse Martin , Schlattner Uwe , Berger Imre
Published: February 2020

Cellular energy is a cornerstone of metabolism and is crucial for human health and disease. Knowledge of the cellular energy states and the underlying regulatory mechanisms is therefore key to understanding cell physiology and to design therapeutic interventions. Cellular energy states are characterised by concentration ratios of adenylates, in particular ATP:ADP and ATP:AMP. We applied synthetic biology approaches to design, engineer and validate a genetically encoded nano-sensor for cellular energy state, AMPfret. It employs the naturally evolved energy sensing of eukaryotic cells provided by the AMP-activated protein kinase (AMPK). Our synthetic nano-sensor relies on fluorescence resonance energy transfer (FRET) to detect changes in ATP:ADP and ATP:AMP ratios both in vitro and in cells in vivo. Construction and iterative optimisation relied on ACEMBL, a parallelised DNA assembly and construct screening technology we developed, facilitated by a method we termed tandem recombineering (TR). Our approach allowed rapid testing of numerous permutations of the AMPfret sensor to identify the most sensitive construct, which we characterised and validated both in the test tube and within cells.
EXTraS discovery of an X-ray superflare from an L dwarf
Authors: De Luca Andrea , Stelzer Beate , Burgasser Adam J. , Pizzocaro Daniele , Ranalli Piero , Raetz Stefanie , Marelli Martino , Novara Giovanni , Vignali Cristian , Belfiore Andrea , Esposito Paolo , Franzetti Paolo , Fumana Marco , Gilli Roberto , Salvaterra Ruben , Tiengo Andrea
Published: February 2020

We present the first detection of an X-ray flare from an ultracool dwarf of spectral class L. The event was identified in the EXTraS database of XMM-Newton variable sources, and its optical counterpart, J0331−27, was found through a cross-match with the Dark Energy Survey Year 3 release. Next to an earlier four-photon detection of Kelu-1, J0331−27 is only the second L dwarf detected in X-rays, and much more distant than other ultracool dwarfs with X-ray detections (photometric distance of 240 pc). From an optical spectrum with the VIMOS instrument at the VLT, we determine the spectral type of J0331−27 to be L1. The X-ray flare has an energy of EX, F ∼ 2 × 1033 erg, placing it in the regime of superflares. No quiescent emission is detected, and from 2.5 Ms of XMM-Newton data we derive an upper limit of LX, qui <  1027 erg s−1. The flare peak luminosity (LX, peak = 6.3 × 1029 erg s−1), flare duration (τdecay ≈ 2400 s), and plasma temperature (≈16 MK) are similar to values observed in X-ray flares of M dwarfs. This shows that strong magnetic reconnection events and the ensuing plasma heating are still present even in objects with photospheres as cool as ∼2100 K. However, the absence of any other flares above the detection threshold of EX, F ∼ 2.5 × 1032 erg in a total of ∼2.5 Ms of X-ray data yields a flare energy number distribution inconsistent with the canonical power law dN/dE ∼ E−2, suggesting that magnetic energy release in J0331−27 – and possibly in all L dwarfs – takes place predominantly in the form of giant flares.
Copper/Silver Cocatalyzed Regioselective C5–H Functionalization of 8-Aminoquinoline Amides with 1,3-Dicarbonyl Compounds
Authors: Zhan Fuxu , Zhang Wei , Zhao Huaiqing
Published: February 2020

A copper/silver co-catalyzed cross-dehydrogenative coupling reaction is developed to achieve exclusively remote C5–H coupling of 8-aminoquinoline amides with the methylenic sp3 C–H bond of 1,3-dicarbonyl compounds. This protocol provides a highly regioselective synthetic route for the functionalization of 8-aminoquinoline amides at C5 under mild conditions. Preliminary experiments reveal that radicals may be involved in this catalytic transformation.
Gamma-ray beam produced by a plasma lens focused electron bunch
Authors: Hu Zhang-Hu , Wang Xiao-Juan , Hui De-Xuan , Zhao Quan-Tang , Cheng Rui , Zhao Yong-Tao , Zhang Zi-Min , Wang You-Nian
Published: February 2020

An accelerator electron bunch is focused and modulated in a plasma lens and then converted into a gamma-ray source using bremsstrahlung radiation in a dense material. In the linear regions with beam density much smaller than plasma density, a proper plasma density needs to be chosen to produce a high quality gamma-ray beam with a small spot size and low divergence, which can be applied in the radiograph of complex and dense objects with sub-millimeter resolution. As the bunch charge increases and bunch density approaches plasma density, micro-bunching of the bunch due to the nonuniform transverse wakefield and bunch energy chirp is observed, leading to a significant increase in gamma-ray beam divergence.
Wave propagation in elastic–plastic material with voids
Authors: Tomar S. K. , Kumar Suraj
Published: February 2020

Constitutive relations and governing equations have been developed for an elastic–plastic material with voids having single slip-plane and direction. The plasticity of the material is considered through the dislocation of slip-plane. The propagation of unidirectional plane waves has been explored in an infinite elastic–plastic material with voids, and it has been found that there exist four basic waves consisting of three coupled elastic–plastic waves and a lone transverse wave. The speeds of propagation of all the coupled elastic–plastic waves are found to be affected by the plasticity and void parameters, in general, while the transverse wave is not affected by the plasticity and void parameters at all and travels with the speed of classical transverse waves. Out of the three coupled elastic–plastic waves, two waves are the counterpart of the waves existing in elastic materials with voids, while the third wave is new and has appeared due to the presence of plasticity in the material. One of the coupled elastic–plastic waves that is least affected by the plasticity faces a critical frequency, below which the wave is a nonpropagating wave. This critical frequency arises due to the presence of voids in the medium. The speed of various waves is computed for a specific model and the results that are obtained are presented graphically. At large frequencies, all the coupled elastic–plastic waves propagate with constant speeds, but at low frequencies, they propagate with speeds less than that of the longitudinal wave of classical elasticity. Several earlier known results have been recovered as special cases from the present formulation.
Ion beam production with an antenna type 2.45 GHz electron cyclotron resonance ion source
Authors: Liu Y. G. , Liu J. L. , Wu Q. , Sun L. T.
Published: February 2020

A very compact permanent magnet 2.45 GHz electron cyclotron resonance ion source has been designed and developed for various purposes. The microwave power is coupled into the plasma chamber using the coaxial antenna instead of the waveguide, the magnetic field is produced by two NdFeB permanent magnet rings, and the diameter of the source body is only 10 cm. The beam current under different conditions was measured. A maximum of 5.8 mA H+/H2+/H3+ mixed beam could be extracted from a 5.5 mm diameter extraction aperture.
Mechanics of randomly packed filaments—The “bird nest” as meta-material
Authors: Weiner N. , Bhosale Y. , Gazzola M. , King H.
Published: February 2020

Systems of randomly packed, macroscopic elements, from jammed spherical grains to tangled long filaments, represent a broad class of disordered meta-materials with a wide range of applications and manifestations in nature. A “bird nest” presents itself at an interface between hard round grains described by granular physics to long soft filaments, the center of textile material science. All of these randomly packed systems exhibit forms of self-assembly, evident through their robust packing statistics, and share a common elastoplastic response to oedometric compression. In reviewing packing statistics, mechanical response characterization, and consideration of boundary effects, we present a perspective that attempts to establish a link between the bulk and local behavior of a pile of sand and a wad of cotton, demonstrating the nest’s relationship with each. Finally, potential directions for impactful applications are outlined.
Thickness-dependent thermoelectric properties of evaporated ZnO:Al films assisted by RF atomic source
Authors: Liu Shiying , Piao Yongjun , Li Guojian , Lan Mingdi , Yuan Yi , Wang Qiang
Published: February 2020

Film thickness is very important in the preparation of film thermoelectric (TE) devices. To define the effect of the film thickness on the power factor and output power, the ZnO:Al films with thicknesses in the range of 100 nm–900 nm were prepared by thermal evaporation method assisted by radio frequency atomic source. The results show that the film thickness has no effect on the phase composition and the (002) preferred orientation of the wurtzite phase in the films. However, the grain size, surface particle size, and surface roughness increase with increasing film thickness. Transmittance significantly reduced for the 900 nm film. Meanwhile, the film thickness affects the carrier concentration and mobility through the defects and growth modes, so that the TE parameters of the films change with the film thickness. The 700 nm film has the highest power factor, and the maximum power factor is 627 μW m−1 K−2 at 560 K. The output power of the films increases as the increase of the temperature on the hot side and higher power factor results in higher output power. The maximum output power of the 700 nm film is 116.01 pW at temperature difference of 1 K. This indicates that film thickness, temperature difference, and power factor are the key factors affecting the film output power.
Numerical study on shock-accelerated gas rings
Authors: Wang Ge , Wang Yingnan , Li Dongdong , Guan Ben
Published: February 2020

The morphologies of shock-accelerated gas rings are presented numerically, based on which a straightforward circulation prediction approach is proposed. Sulfur hexafluoride (SF6) and helium (He) rings shocked in air are examined in the present study. The circulation prediction approach is derived from the direct linear superposition of the Samtaney and Zabusky model and the Yang, Kubota, and Zukoski model. We solved Euler equations using the fifth-order weighted essentially non-oscillatory scheme and third-order total variation diminishing Runge-Kutta scheme to demonstrate the complex shock–interface interactions. The numerical results show that, after the shock impact, the mass of the SF6 ring accumulates to its upstream part, while the mass of the He ring accumulates to its downstream part. The circulation prediction approach is found to be easy to implement and is proved reliable in predicting the total circulations of a series of SF6 rings under weak shock conditions.
Unified mechanisms for separation control around airfoil using plasma actuator with burst actuation over Reynolds number range of 103–106
Authors: Sato Makoto , Okada Koichi , Asada Kengo , Aono Hikaru , Nonomura Taku , Fujii Kozo
Published: February 2020

We conduct large-eddy simulations of separated airfoil flows with control by a dielectric-barrier-discharge plasma actuator over a wide range of Reynolds numbers. The Reynolds numbers based on the chord length (Re) are set at Re = 5.0 × 103, 1.0 × 104, 6.3 × 104, 2.6 × 105, and 1.6 × 106. These Reynolds numbers cover most of the conditions used in the previous studies on separation control by a plasma actuator. The burst frequency nondimensionalized by the chord length and freestream velocity (F+) is used as the computational parameter, and the effective burst actuation and control mechanisms at each Reynolds number condition are investigated. With regard to cases without the control, the flows separate near the leading edge in the laminar state at the Reynolds number range of 103–105, and a substantial turbulent separation occurs at the Reynolds number of 1.6 × 106. Separation control with a high burst frequency [F+ ≃ O(10)] can cause early flow reattachment through the promotion of turbulent transition of a separation shear-layer for Re = 6.3 × 104 and 2.6 × 105. Flow reattachment is mainly caused by momentum entrainment into the boundary layer by fine-scale turbulent vortices. On the other hand, the large-scale spanwise vortices play an important role at F+ = 1 for Re = 1.0 × 104 and 1.6 × 106. In these cases, the dynamics of the spanwise vortices show similar behavior and the pairing of these vortices significantly contributes to the separation control by increasing the momentum entrainment. The optimum value of F+ changes with a Reynolds number. In contrast, when a nondimensional burst frequency based on the characteristics of the separation shear-layer (Fθs) is considered, a high lift-to-drag ratio is found at Fθs≃O(10−2) for all Reynolds numbers. This demonstrates that one of the effective burst frequencies is closely related to the scale of the separation shear-layer, especially for the spanwise vortex shed from the separation shear-layer.
Coalescence of a soap film into a pool
Authors: Wei Yanju , Zhang Yajie , Yang Yajing , Zhang Jie , Deng Shengcai , Liu Shenghua
Published: February 2020

In this study, we investigate the transient process of tilted soap films coalescing onto a pool surface. Results show that the coalescence is actually a position-dependent pasting behavior. For the soap films with a tilt angle less than 20°, the merging process consists of four stages, namely, (I) acceleration, (II) balancing, (III) shock, and (IV) damping. In stage I, the contact angle increases following a simple equation relating to the position of the contact point and remains at 60° in stage II. Then, the film is suddenly accelerated and soon decelerated to produce a film inflation in stage III. Finally, the contact line gradually ceases at a certain position in stage IV. We establish persuasive theoretical expressions for the contact angle revolution of stages I and II and the criteria that lead to a shock in stage III.
Correlation transports at p-/n-types in electron metastable perovskite family of rare-earth nickelates
Authors: Chen Jinhao , Yan Fengbo , Hu Haiyang , Wang Jiaou , Jiang Yong , Chen Nuofu , Chen Jikun
Published: February 2020

It is important to achieve both donor and acceptor doping for correlated oxide semiconductors to cater for elementary device constructions, e.g., establishing a p-n junction and a thermal couple or a thermoelectric π-joint in correlated electronics. The perovskite family of rare-earth nickelates (ReNiO3) exhibits correlated transportation characters (e.g., metal to insulator transitions and thermistor transportations) dominated by electron conductions, as indicated by their negative thermopower for n-type materials. Herein, we demonstrate the presence of positive magnitude of thermopower as achieved in GdNiO3 single crystalline thin films, indicating a hole dominated transportation for p-type correlated semiconductors. Probing the Ni-L edge of GdNiO3 via near edge x-ray absorption fine structure indicates its distinguished intermediate acceptor energy states that are more easily occupied by the thermal excited valence band electrons. The hole-dominated transportation for GdNiO3 was further confirmed by its increased localization length and opposite sign in magnetoresistance, which are derived from the general tendency of ReNiO3, owing to the larger effective mass of holes compared to electrons. The discovery of p-types in GdNiO3 will further promote establishing ReNiO3-based elementary semiconductive devices in the field of correlated electronics.
Dielectric embedding GW for weakly coupled molecule-metal interfaces
Authors: Liu Zhen-Fei
Published: February 2020

Molecule-metal interfaces have a broad range of applications in nanoscale materials science. Accurate characterization of their electronic structures from first-principles is key in understanding material and device properties. The GW approach within many-body perturbation theory is the state-of-the-art and can in principle yield accurate quasiparticle energy levels and interfacial level alignments that are in quantitative agreement with experiments. However, the interfaces are large heterogeneous systems that are currently challenging for first-principles GW calculations. In this work, we develop a GW-based dielectric embedding approach for molecule-metal interfaces, significantly reducing the computational cost of direct GW without sacrificing the accuracy. To be specific, we perform explicit GW calculations only in the simulation cell of the molecular adsorbate, in which the dielectric effect of the metallic substrate is embedded. This is made possible via a real-space truncation of the substrate polarizability and the use of the interface plasma frequency in the adsorbate GW calculation. Here, we focus on the level alignment at weakly coupled molecule-metal interfaces, i.e., the energy difference between a molecular frontier orbital resonance and the substrate Fermi level. We demonstrate our method and assess a few GW-based approximations using two well-studied systems, benzene adsorbed on the Al (111) and on the graphite (0001) surfaces.
Longitudinal spatial hole burning in high-power semiconductor lasers: numerical analysis
Authors: Golovin V.S. , Shashkin I.S. , Slipchenko S.O. , Pikhtin N.A. , Kop’ev P.S.
Published: February 2020

Longitudinal spatial hole burning (LSHB) in high-power semiconductor lasers is analysed by numerically solving one-dimensional (1D) rate equations. Calculations are performed for GaAs-based lasers operating at a wavelength of 1.06 μm. It is shown that the LSHB-induced decrease in output power can be accounted for by two mechanisms: build-up of spontaneous recombination and decrease in slope efficiency, equivalent to a rise in internal optical loss. We analyse the influence of different laser chip parameters on the magnitude of the LSHB effect. In particular, it is shown that to suppress LSHB it is preferable to increase the optical confinement factor Γ. We examine the relationship between LSHB and other mechanisms capable of reducing the output power.
Variant forms of qualitative traits of indigenous chickens reared under extensive system in Tolon District, Ghana
Authors: Birteeb Peter T. , Boakye Thomas
Published: February 2020

Context
Rural chicken production in most developing countries is based mainly on scavenging systems with indigenous chickens that have not been properly characterised and classified into well-defined breeds.

Aims
This study was conducted to identify the variant forms of qualitative phenotypic traits of local chickens in Tolon District, northern Ghana.

Methods
About 320 adult birds were sampled and data collected by using observation and a chicken colour chart. Traits included head shape; comb type, size and colour; feather distribution; and earlobe, eye, plumage, skin and shank colours. Chi-squared goodness of fit test was used to test whether variant phenotypes of each qualitative trait were equally distributed. The hypothesis of no associations between pairs of traits was tested by using Cramér’s V.

Key results
There were highly significant (P < 0.01) differences in the distributions of variant phenotypes of all traits. The main comb type observed was single (85.9%), followed by pea (8.8%) and rose (5.3%). A majority of birds had small combs (57.8%), although others had medium (28.4%) and large (13.8%) combs. Females had small to medium combs, whereas males had medium to large combs. A majority of the chickens had white earlobe colour (60.3%), followed by pied red and white (22.5%). Feather distributions observed were normal feathered (84.4%), naked neck (8.4%) and frizzled (7.2%). Five plumage colours were observed, although some were in combinations. White plumage was the most common (22.5%), followed by black (18.8%), with brown/ash the least common (0.03%). Community was significantly (P < 0.01) associated with comb type, size and colour, and eye, shank and skin colours. Also, comb size was significantly associated with sex and comb type.

Conclusions
Generally, local chickens exhibited heterogynous phenotypes for qualitative traits. Local chickens in the district could be described as normally feathered with wide variation in plumage colours and having mainly single comb type.

Implications
The knowledge of these variant phenotypes and their associations will serve as baseline information for the characterisation and conservation of local chicken types. It could also provide guidelines in selecting bird ecotypes and/or communities for breed improvement programs in the study area.
The Effects of Permanent Income Tax Cuts on Emigration from Israel
Authors: Blumkin Tomer , Margalioth Yoram , Strawczynski Michel
Published: February 2020

In this paper, we estimate the effect on emigration of the permanent income tax reductions implemented in Israel during the period 2004–2010. We find that emigration flows from Israel declined, especially for brackets that benefited from a larger tax reduction. We also find that the effect is stronger for younger workers than for older ones, a result consistent with the former group deriving expected tax benefits over a longer duration of time.
Identification and activity of the functional complex between hnRNPL and the pseudoexfoliation syndrome-associated lncRNA, LOXL1-AS1
Authors: Schmitt Heather M , Johnson William M , Aboobakar Inas F , Strickland Shelby , Gomez-Caraballo María , Parker Megan , Finnegan Laura , Corcoran David L , Skiba Nikolai P , Allingham R Rand , Hauser Michael A , Stamer W Daniel
Published: February 2020

Individuals with pseudoexfoliation (PEX) syndrome exhibit various connective tissue pathologies associated with dysregulated extracellular matrix homeostasis. PEX glaucoma is a common, aggressive form of open-angle glaucoma resulting from the deposition of fibrillary material in the conventional outflow pathway. However, the molecular mechanisms that drive pathogenesis and genetic risk remain poorly understood. PEX glaucoma-associated single-nucleotide polymorphisms are located in and affect activity of the promoter of LOXL1-AS1, a long non-coding RNA (lncRNA). Nuclear and non-nuclear lncRNAs regulate a host of biological processes, and when dysregulated, contribute to disease. Here we report that LOXL1-AS1 localizes to the nucleus where it selectively binds to the mRNA processing protein, heterogeneous nuclear ribonucleoprotein-L (hnRNPL). Both components of this complex are critical for the regulation of global gene expression in ocular cells, making LOXL1-AS1 a prime target for investigation in PEX syndrome and glaucoma.
Comparing National Approaches to the Study of Intelligence
Authors: Van Puyvelde Damien , Wirtz James J , Holeindre Jean-Vincent , Oudet Benjamin , Bar-Joseph Uri , Kotani Ken , Matei Florina Cristiana , Fernández Antonio M Díaz
Published: February 2020

This forum compares and contrasts national experiences in the development of intelligence studies from the perspective of seven countries: France, Japan, Israel, Romania, Spain, the United Kingdom, and the United States. The discussion is structured around a comparative framework that emphasizes five core dimensions that, we posit, are essential to the emergence of this subfield: access to relevant government information, institutionalization of research on intelligence and security in a higher education setting, periodic scientific meetings and networks, teaching and learning opportunities, and engagement between researchers and practitioners. The forum demonstrates how researchers working in different contexts and disciplines have overcome similar challenges to broaden our understanding of secret government practices.
Development and Validation of a Next-Generation Sequencing Panel for Syndromic and Nonsyndromic Hearing Loss
Authors: Butz Malinda , McDonald Amber , Lundquist Patrick A , Meyer Melanie , Harrington Sean , Kester Sarah , Stein Mariam I , Mistry Nipun A , Zimmerman Zuckerman Eric , Niu Zhiyv , Schimmenti Lisa , Hasadsri Linda , Boczek Nicole J
Published: February 2020

Background

Deafness and hearing loss are common conditions that can be seen independently or as part of a syndrome and are often mediated by genetic causes. We sought to develop and validate a hereditary hearing loss panel (HHLP) to detect single nucleotide variants (SNVs), insertions and deletions (indels), and copy number variants (CNVs) in 166 genes related to nonsyndromic and syndromic hearing loss.

Methods

We developed a custom-capture next-generation sequencing (NGS) reagent to detect all coding regions, ±10 flanking bp, for the 166 genes related to nonsyndromic and syndromic hearing loss. Our validation consisted of testing 52 samples to establish accuracy, reproducibility, and analytical sensitivity. In addition to NGS, supplementary methods, including multiplex ligation-dependent probe amplification, long-range PCR, and Sanger sequencing, were used to ensure coverage of regions that had high complexity or homology.

Results

We observed 100% positive and negative percentage agreement for detection of SNVs (n = 362), small indels (1–22 bp, n = 25), and CNVs (gains, n = 8; losses, n = 17). Finally, we showed that this assay was able to detect variants with a variant allele frequency ≥20% for SNVs and indels and ≥30% to 35% for CNVs.

Conclusions

We validated an HHLP that detects SNVs, indels, and CNVs in 166 genes related to syndromic and nonsyndromic hearing loss. The results of this assay can be utilized to confirm a diagnosis of hearing loss and related syndromic disorders associated with known causal genes.
Fuzzy swarm trajectory tracking control of unmanned aerial vehicle
Authors: Selma Boumediene , Chouraqui Samira , Abouaïssa Hassane
Published: February 2020

Accurate and precise trajectory tracking is crucial for unmanned aerial vehicles (UAVs) to operate in disturbed environments. This paper presents a novel tracking hybrid controller for a quadrotor UAV that combines the robust adaptive neuro-fuzzy inference system (ANFIS) and particle swarm optimization (PSO) algorithm. The ANFIS-PSO controller is implemented to govern the behavior of three degrees of freedom quadrotor UAV. The ANFIS controller allows controlling the movement of UAV to track a given trajectory in a 2D vertical plane. The PSO algorithm provides an automatic adjustment of the ANFIS parameters to reduce tracking error and improve the quality of the controller. The results showed perfect behavior for the control law to control a UAV trajectory tracking task. To show the effectiveness of the intelligent controller, simulation results are given to confirm the advantages of the proposed control method, compared with ANFIS and PID control methods.
An efficient controlled elitism non-dominated sorting genetic algorithm for multi-objective supplier selection under fuzziness
Authors: Hajipour Vahid , Tavana Madjid , Santos-Arteaga Francisco J , Alinezhad Alireza , Di Caprio Debora
Published: February 2020

Supplier selection and order allocation constitute vital strategic decisions that must be made by managers within supply chain management environments. In this paper, we propose a multi-objective fuzzy model for supplier selection and order allocation in a two-level supply chain with multi-period, multi-source, and multi-product characteristics. The supplier evaluation objectives considered in this model include cost, delay, and electronic-waste (e-waste) minimization, as well as coverage and weight maximization. A signal function is used to model the price discount offered by the suppliers. Triangular fuzzy numbers are used to deal with the uncertainty of delay and e-waste parameters while the fuzzy Technique for Order Performance by Similarity to Ideal Solution (TOPSIS) is used to obtain the weights of the suppliers. The resulting NP-hard problem, a Pareto-based meta-heuristic algorithm called controlled elitism non-dominated sorting genetic algorithm (CENSGA), is developed. The Non-dominated Sorting Genetic Algorithm (NSGA-II) and Multi-Objective Particle Swarm Optimization (MOPSO) are used to validate the applicability of the CENSGA algorithm and the Taguchi technique to tune the parameters of the algorithms. The results are analysed using graphical and statistical comparisons illustrating how the proposed CENSGA dominates NSGA-II and MOPSO in terms of mean ideal solution distance (MID) and spacing metrics.
Formation of planetary populations − II. Effects of initial disc size and radial dust drift
Authors: Alessi Matthew , Pudritz Ralph E , Cridland Alex J
Published: February 2020

Recent ALMA observations indicate that while a range of disc sizes exist, typical disc radii are small, and that radial dust drift affects the distribution of solids in discs. Here, we explore the consequences of these features in planet population synthesis models. A key feature of our model is planet traps – barriers to otherwise rapid type-I migration of forming planets – for which we include the ice line, heat transition, and outer edge of the dead zone. We find that the ice line plays a fundamental role in the formation of warm Jupiters. In particular, the ratio of super Earths to warm Jupiters formed at the ice line depends sensitively on the initial disc radius. Initial gas disc radii of ∼50 au results in the largest super Earth populations, while both larger and smaller disc sizes result in the ice line producing more gas giants near 1 au. This transition between typical planet class formed at the ice line at various disc radii confirms that planet formation is fundamentally linked to disc properties (in this case, disc size), and is a result that is only seen when dust evolution effects are included in our models. Additionally, we find that including radial dust drift results in the formation of more super Earths between 0.1 and 1 au, having shorter orbital radii than those produced in models where dust evolution effects are not included.
Ollier disease: the first report in Syria
Authors: Dhemesh Yaseen , Tawekji Talha , Abdul-Baki Mohammad-Nasan , Abi-Zamr Ghazal , Ali Sawssan
Published: February 2020

Ollier disease is a rare nonhereditary skeletal disorder, characterized by multiple enchondromas, which are noncancerous growth of cartilage. In this report, we present a case of Ollier disease in a 10-year-old Syrian boy. The patient presented with multiple boney masses on hands; he had a history of pathological fractures when he was 5, which caused crippling. We analyzed the clinical, radiographical and pathological characteristics of our patient, which helped us to reach the final diagnosis. Ollier disease is a benign bone tumor, but it has a risk of malignant transformation into chondrosarcoma. The aim of this report is to document the presence of Ollier disease in Syria to help other Syrian physicians considering this disease in the differential diagnosis if they face similar presentations.
Effect of Manual Upper Eyelid Elevation on Intraocular Pressure Measurement by Four Different Tonometers
Authors: Nakakura Shunsuke , Mori Etsuko , Fujio Yuki , Fujisawa Yasuko , Matsuya Kanae , Kobayashi Yui , Oogi Satomi , Shiraishi Miku , Tabuchi Hitoshi , Asaoka Ryo , Kiuchi Yoshiaki
Published: February 2020

SIGNIFICANCE

This study is the first to show that the manual upper eyelid elevation (manual UEE) that is commonly used to prevent disruption of the IOP measurement due to blinking or upper eyelid contact with the tip of the tonometer does not affect the IOP values.

PURPOSE

We investigated whether manual UEE affects the IOP readings using three rebound tonometers (Icare TA01i, Icare PRO, and Icare ic100) and Goldmann applanation tonometry (GAT).

METHODS

One eye was measured for 101 patients (56 eyes of primary open-angle glaucoma patients and 45 healthy subjects). The IOPs were measured without and with manual UEE. Each IOP was measured twice; the measurement order using the tonometers was randomly selected. In addition, palpebral fissure height (distance between the upper and lower eyelids) was measured.

RESULTS

The IOPs without manual UEE were 12.1 ± 2.9, 13.3 ± 2.7, 11.7 ± 2.9, and 16.0 ± 3.2 mmHg (Icare TA01i, Icare PRO, Icare ic100, and GAT), and those with manual UEE were 12.3 ± 3.0, 13.3 ± 2.8, 11.7 ± 2.9, and 16.0 ± 3.3, respectively. No significant difference was found between the IOP without and with manual UEE (IOP difference; all, P > .50; paired t test). Multiple linear regression analyses revealed that palpebral fissure height did not affect IOP difference for any of the tonometers.

CONCLUSIONS

Simple manual UEE when measuring the IOP has little effect on the IOP obtained using all current rebound tonometers and GAT.
Assessing Corneal Speckle in Optical Coherence Tomography: A New Look at Glaucomatous Eyes
Authors: Iskander D. Robert , Kostyszak Małgorzata A. , Jesus Danilo A. , Majewska Małgorzata , Danielewska Monika E. , Krzyżanowska-Berkowska Patrycja
Published: February 2020

SIGNIFICANCE

Optical coherence tomography speckle is used here in an unconventional way as the indirect source of information on tissue microstructure. The study reveals that the corneal speckle of glaucoma suspects has a similar relationship between the parameters of scattering exhibited in glaucoma patients.

PURPOSE

The purpose of this study was to evaluate the potential of optical coherence tomography imaging of the cornea in early diagnosis of glaucoma.

METHODS

Corneas of 64 subjects of three groups, including 18 primary open-angle glaucoma patients, 24 glaucoma suspects with normal levels of IOP and uncompromised visual field, and 22 age-matched controls, were imaged with spectral optical coherence tomography. A central region of interest in each optical coherence tomography image visualizing the stroma was automatically extracted, and the intensity data within that region were fit with the generalized gamma distribution. Its parameters describe the scatterer cross section and scatterer density and indirectly assess corneal microstructure. In addition, subjects underwent measurements of IOP, visual field, Heidelberg Retinal Tomography, retinal nerve fiber layer thickness, and biometry. Group means of all parameters were tested for equality. Within each group of subjects, correlation was evaluated between the statistical parameters of the corneal speckle.

RESULTS

Glaucoma suspects had statistically significantly different IOP, visual field parameters, mean retinal fiber layer thickness, and central corneal thickness from those of glaucoma patients but not from those of the control group. The parameters of the corneal speckle were not significantly different between the groups, but they showed a markedly higher and statistically significant coefficient of determination for glaucoma patients and suspects than that for the control group (0.927 and 0.707 vs. 0.336).

CONCLUSIONS

The results indicate that glaucoma suspects have similar relationship between the corneal scatterer cross section and scatterer density to that exhibited in the glaucoma patients but markedly different from that of healthy controls.
Transfer of Sphingorhabdus marina, Sphingorhabdus litoris, Sphingorhabdus flavimaris and Sphingorhabdus pacifica corrig. into the novel genus Parasphingorhabdus gen. nov. and Sphingopyxis baekryungensis into the novel genus Novosphingopyxis gen. nov. within the family Sphingomonadaceae
Authors: Feng Guang-Da , Zhang Xian-Jiao , Yang Song-Zhen , Li An-Zhang , Yao Qing , Zhu Honghui
Published: February 2020

During a phylogenetic analysis of

Sphingorhabdus

and its closely related genera in the family

Sphingomonadaceae

, we found that the genus

Sphingorhabdus

and the species

Sphingopyxis baekryungensis

might not be properly assigned in the taxonomy. Phylogenetic, phenotypic and chemotaxonomic characterizations clearly showed that the genus

Sphingorhabdus

should be reclassified into two genera (Clade I and Clade II), for which the original genus name,

Sphingorhabdus

, is proposed to be retained only for Clade I, and a new genus named as Parasphingorhabdus gen. nov. is proposed for Clade II with four new combinations: Parasphingorhabdus marina comb. nov., Parasphingorhabdus litoris comb. nov., Parasphingorhabdus flavimaris comb. nov. and Parasphingorhabdus pacifica comb. nov. Moreover,

Sphingopyxis baekryungensis

should represent a novel genus in the family

Sphingomonadaceae

, for which the name Novosphingopyxis gen. nov. is proposed, with a combination of Novosphingopyxis baekryungensis comb. nov. The study provides a new insight into the taxonomy of closely related genera in the family

Sphingomonadaceae

.
Predicting human health from biofluid-based metabolomics using machine learning
Authors: Evans Ethan D. , Duvallet Claire , Chu Nathaniel D. , Oberst Michael K. , Murphy Michael A. , Rockafellow Isaac , Sontag David , Alm Eric J.
Published: February 2020

Biofluid-based metabolomics enables the profiling of thousands of molecules and has the potential to provide highly accurate, minimally invasive diagnostics for a range of health conditions. However, typical metabolomics studies focus on only a few statistically significant features. We study the applicability of machine learning for health state-prediction across 35 human mass spectrometry-based metabolomics studies. Models trained on all features outperform those using only significant features and frequently provide high predictive performance across nine health states, despite disparate experimental conditions and disease contexts. Combining data from different experimental settings (e.g. sample type, instrument, chromatography) within a study minimally alters predictive performance, suggesting information overlap between different methods. Using only non-significant features, we still often obtain high predictive performance. To facilitate further advances, we provide all data online. This work highlights the applicability of biofluid-based metabolomics with data-driven analysis for health state diagnostics.
DNA methylation aging clocks and pancreatic cancer risk: Pooled analysis of three prospective nested case-control studies
Authors: Chung Mei , Ruan Mengyuan , Zhao Naisi , Koestler Devin C. , De Vivo Immaculata , Kelsey Karl T. , Michaud Dominique S.
Published: February 2020

Structured Abstract

Background

Pancreatic cancer is projected to become the second leading cause of cancer-related death by 2030 in the United States. DNA methylation (DNAm) age may reflect age-related variations in the biological changes and abnormalities related to cancer development.

Method

We conducted a pooled analysis using prediagnostic blood samples of pancreatic cancer cases and matched controls selected from the Nurses’ Health Study (NHS), the Physician’s Health Study (PHS), and the Health Professionals Follow-up Study (HPFS). We used three DNAm aging clocks (Hannum, Horvath, and PhenoAge) to estimate subjects’ DNAm age, epigenetic age acceleration (AA) and intrinsic epigenetic age acceleration (IEAA) metrics. We performed conditional logistic regression and multivariable Cox proportional hazard regression to examine associations between six AA and IEAA metrics and risk of pancreatic cancer and survival, respectively.

Results

A total of 393 incidence pancreatic cancer cases and 431 matched controls from the NHS, PHS, and HPFS cohorts were included in this analysis. The medians of all three epigenetic AA and three IEAA metrics were consistently above zero (indicating accelerated age) among cases, while they were below zero (indicating decelerated age) among the matched controls. Comparing participants in the highest quartile of age acceleration metrics, the pancreatic cancer risks were significantly increased by 67% to 83% for Hannum and PhenoAge AA or IEAA metrics with minimal of 7- to 9-years accelerated ages. Except for Hovarth AA and IEAA metrics, there were significant dose-response trends, such that higher age accelerations were associated with higher pancreatic cancer risk, but the relationships were nonlinear. Stratified analyses showed heterogeneous associations, varying by participants’ characteristics and by epigenetic AA or IEAA metrics. As time to diagnosis increased, the ORs of pancreatic cancer for the Hannum AA and Horvath AA or IEAA metrics trended upwards, while the ORs for the PhenoAge AA or IEAA and Hannum IEAA metrics trended downward. Overall, we observed no significant association between pancreatic cancer survival and any of the prediagnostic epigenetic AA or IEAA metrics.

Conclusion

Our results indicate DNAm age acceleration is associated with an increased risk of pancreatic cancer in a nonlinear, dose-response manner. Epigenetic IEAA metrics may be a useful addition to current methods for pancreatic cancer risk prediction.
Direct Measurement of Rates of Asymptomatic Infection and Clinical Care-Seeking for Seasonal Coronavirus
Authors: Shaman Jeffrey , Galanti Marta
Published: February 2020

The pandemic potential of the novel coronavirus (nCoV) that emerged in Wuhan, China, during December 2019 is strongly tied to the number and contagiousness of undocumented human infections. Here we present findings from a proactive longitudinal sampling study of acute viral respiratory infections that documents rates of asymptomatic infection and clinical care seeking for seasonal coronavirus. We find that the majority of infections are asymptomatic by most symptom definitions and that only 4% of individuals experiencing a seasonal coronavirus infection episode sought medical care for their symptoms. These numbers indicate that a very high percentage of seasonal coronavirus infections are undocumented and provide a reference for understanding the spread of the emergent nCoV.
A large cross-ancestry meta-analysis of genome-wide association studies identifies 69 novel risk loci for primary open-angle glaucoma and includes a genetic link with Alzheimer’s disease
Authors: Gharahkhani Puya , Jorgenson Eric , Hysi Pirro , Khawaja Anthony P. , Pendergrass Sarah , Han Xikun , Ong Jue Sheng , Hewitt Alex W. , Segre Ayellet , Igo Robert P. , Choquet Helene , Qassim Ayub , Josyula Navya S , Cooke Bailey Jessica N. , Bonnemaijer Pieter , Iglesias Adriana , Siggs Owen M. , Young Terri , Vitart Veronique , Thiadens Alberta A.H.J. , Karjalainen Juha , Uebe Steffen , Melles Ronald B. , Nair K. Saidas , Luben Robert , Simcoe Mark , Amersinghe Nishani , Cree Angela J. , Hohn Rene , Poplawski Alicia , Chen (CUHK) Li Jia , Cheng Ching-Yu , Vithana Eranga Nishanthie ,   NEIGHBORHOOD consortium,   ANZRAG consortium,   Biobank Japan project,   FinnGen study,   UK Biobank Eye and Vision Consortium,   GIGA study group,   23andMe Research Team, Tamiya Gen , Shiga Yukihiro , Yamamoto Masayuki , Nakazawa Toru , Rouhana John , Currant Hannah , Birney Ewan , Wang Xin , Auton Adam , Ashaye Adeyinka , Olawoye Olusola , Williams Susan E. , Akafo Stephen , Ramsay Michele , Hashimoto Kazuki , Kamatani Yoichito , Akiama Masato , Momozawa Yukihide , Foster Paul J. , Khaw Peng T. , Morgan James E. , Strouthidis Nicholas G. , Kraft Peter , Kang Jae Hee , Pui Pang (CUHK) Calvin Chi , Pasutto Francesca , Mitchell Paul , Lotery Andrew J. , Palotie Aarno , van Duijn Cornelia , Haines Jonathan , Hammond Chris , Pasquale Louis R. , Klaver Caroline C.W. , Hauser Michael , Khor Chiea Chuen , Mackey David A. , Kubo Michiaki , Aung Tin , Craig Jamie , MacGregor Stuart , Wiggs Janey
Published: February 2020

We conducted a large multi-ethnic meta-analysis of genome-wide association studies for primary open-angle glaucoma (POAG) on a total of 34,179 cases vs 349,321 controls, and identified 127 independent risk loci, almost doubling the number of known loci for POAG. The majority of loci have broadly consistent effect across European, Asian and African ancestries. We identify a link, both genome-wide and at specific loci, between POAG and Alzheimer’s disease. Gene expression data and bioinformatic functional analyses provide further support for the functional relevance of the POAG risk genes. Several drug compounds target these risk genes and may be potential candidates for developing novel POAG treatments.
The use of simultaneous SEEG and MEG in localising seizure onset zone
Authors: Vivekananda Umesh , Cao Chunyan , Liu Wei , Zhang Jing , Rugg-Gunn Fergus , Walker Matthew C , Litvak Vladimir , Sun Bomin , Zhan Shikun
Published: February 2020

Objectives

Both Magnetoencephalography (MEG) and stereo-electroencephalography (SEEG) are used in presurgical epilepsy assessment, with contrasting advantages and limitations. It is not known whether combined recording using both modalities can maintain inherent advantages whilst overcoming these limitations e.g. recording from deep brain sources whilst preserving good spatial resolution.

Methods

24 adult and paediatric patients who underwent SEEG study for pre-surgical evaluation of focal drug-resistant epilepsy, were recorded using simultaneous SEEG-MEG, of which 14 had abnormal interictal activity during recording. The 14 patients were divided into two groups; those with presumed superficial (n=7) and deep (n=7) brain interictal activity.

Results

There was no significant difference between SEEG and MEG in identifying superficial spikes (p=0.135) and SEEG was significantly better at detecting deep spikes (p=0.002). Mean distance across patients between SEEG channel with highest average spike amplitude and MEG dipole was 26.6+/-3.6 mm for superficial sources, and 21.5 +/- 2.04 mm for deep sources, even though for some of the latter (n=4) no MEG spikes were detected and MEG dipole was fitted to a SEEG interictal activity triggered average. Removal of MEG dipole was associated with 1 year seizure freedom in 5/6 patients with superficial source, and 4/6 patients with deep source.

Conclusions

Although SEEG has greater sensitivity in identifying interictal activity from deeper sources, an MEG source can be localised using SEEG information, thereby providing useful whole brain context to SEEG and potential role in epilepsy surgery planning.
High Risk Infants who are Low Dose Tolerant after Peanut Oral Food Challenges
Authors: Lin Adora , Uygungil Burcin , Robbins Karen , Ackerman Olivia , Sharma Hemant
Published: February 2020

Background

Early peanut (PN) introduction may prevent peanut allergy in at-risk children. Little data exists regarding early introduction for infants with large skin prick tests (SPT) or high peanut IgE levels, who are not often offered oral food challenges (OFC).

Objective

To retrospectively assess tolerance of a low dose (1 gram) of peanut in infants at risk for peanut allergy, including highest-risk infants (HRI) with SPT wheal >7mm.

Methods

We reviewed PN OFCs performed over a two-year period at our pediatric allergy center. Low-dose PN OFC was offered to all infants considered at risk for PN allergy, regardless of peanut SPT or IgE results. Dosing was escalated after OFC at home.

Results

Of infants with SPT wheal <=4 mm (n=30), 29 (97%) were low-dose-tolerant. Of those with SPT >4 mm (n=40), 25 (63%) were low-dose-tolerant, and Ara h2 IgE was significantly lower compared to non-tolerant individuals (median 0.62 versus 6.49 kU/L, p<0.05). Among HRI with SPT >7mm (n=22), 12 (55%) were tolerant, with median SPT 9mm (range 8-11mm), PN-IgE 1.1 kU/L (0.3-10.7 kU/L) and Ara h2 1.6 kU/L (0-9.57 kU/L). Age, sex, race, eczema, and egg sensitization did not affect tolerance regardless of SPT size. After 3-6 months, most infants tolerant at OFC were gradually able to consume larger doses of PN.

Conclusion

Many infants with PN-SPT >4mm are tolerant of low-dose peanut, and Ara h 2 IgE may be predictive for clinical tolerance among these infants. Low-dose PN-OFC with gradual updosing may help prevent PN allergy in a greater number of at-risk infants.