bluuebunny/crossref_metadata_2025 huggingface dataset:
Mortui vivos docent [The dead teach the living]
Authors: Pidvalna Uliana , Mateshuk-Vatseba Lesya
Published: December 2019

Medical museums are a record of the history of the medical thought processes. The Anatomical museum of the Department of Normal Anatomy located in the Danylo Halytsky Lviv National Medical University was founded in 1894 by Professor Henryk Kadyi (1851–1912). The museum includes a number of unique objects and displays > 2,000 specimens. These medical artifacts include both normal anatomy and malformed artifacts. The museum is divided into three sections that are arranged according to the systems of the body and a method of preparing specimens. The vast array of preserved specimens represents comparative, developmental, gender, systemic, dynamic, plastic, and descriptive anatomy. Besides the Anatomical museum, the historical treasure is the Anatomical Theater, the oldest auditorium at the Danylo Halytsky Lviv National Medical University that preserved its authenticity. These educational places teach us not only about morphology, but also help us appreciate the beauty of the human body.
Rare Case of Pleomorphic Sarcoma of Oropharynx
Authors: Goel Sajal , Mittal Deepak K. , Sharma Pankaj , Khurana Nita
Published: December 2019

Introduction Pleomorphic sarcoma is the commonest soft tissue sarcoma of adult life. Less than 10% cases of this disease occur as primary in head and neck region. Although a case of pleomorphic sarcoma of lower extremity with metastasis to base of tongue had been reported earlier, a pleomorphic sarcoma arising from oropharynx is being reported for the first time.

Case Report A 75-year-old male chronic smoker was evaluated for complaints of dysphagia, change in voice, and multiple episodes of oral bleeding. He was found to have a locally advanced pleomorphic sarcoma of oropharynx. He was treated nonsurgically. He showed complete clinical and radiologic response. The disease-free survival is 12 months and overall survival is 74 months.

Conclusion This report highlights the importance of nonsurgical management of a case that would have otherwise needed surgery.
ACL Reconstruction in the Multiple Ligament Injured Knee
Authors: Marx Robert G. , Wolfe Isabel A.
Published: December 2019

Multiple ligament knee injuries are complex and can result from sports injuries or high energy trauma. The proper diagnosis and treatment of multiple ligament knee injuries are essential, and careful evaluation and planning are required to achieve successful outcomes. Anterior cruciate ligament (ACL) reconstruction in the multiple ligament injured knee is complicated by several factors, necessitating additional technical considerations. Patient selection, surgical timing, graft selection, and surgical technique require consideration specific to the ACL component of these injuries. We present a summary of the current knowledge with respect to the treatment of ACL injuries in the context of the multiple ligament injured knee.
Cardiac MRI in Evaluation of Dilated Cardiomyopathy
Authors: Rani Jyotsna , Ramakrishna Narayanan
Published: December 2019

Cardiac magnetic resonance imaging (MRI) plays an important role in the evaluation of dilated cardiomyopathy, and is the gold-standard technique in identifying the various etiological factors and differentiating one from the other. It not only helps in identifying the cause but also aids in monitoring the treatment response. The present article reviews the different MRI techniques available, recent advancements, and limitations in technology in the evaluation of patients with dilated cardiomyopathy in the present-day scenario.
Numerical simulations to study turbulent magnetic field amplification by nonlinear interaction of high-power laser and kinetic Alfvén waves in laboratory and astrophysical plasmas
Authors: Dewan Himani , Pathak Neha , Uma R. , Sharma R. P.
Published: December 2019

The model contouring the dynamics of transient nonlinear interaction between the high-frequency extraordinary-elliptically polarized laser (HFXPL) and low-frequency kinetic Alfvén wave (LFKAW) dynamics in the magnetized plasma is the focal point of the present investigation. The quasistatic ponderomotive force driven by the HFXPL pump induces density cavitation and humps in the low-frequency kinetic Alfvén wave. In order to study the intricate localized structures of HFXPL pump waves that evolve with time, the requisite dimensionless equations of the coupled system (HFXPL and LFKAW) are evaluated by using numerical methods in the nonlinear stage. The typical scale sizes of these structures in the early phase are ∼9 μm, and the typical time to grow is ∼10 ps. The ensemble-averaged magnetic power spectra are also presented, indicating energy cascade. The rendered investigations follow direct relevance to the experimental observations [Chatterjee et al., Rev. Sci. Instrum. 85, 013505 (2014); Romagnani et al., Phys. Rev. Lett. 122, 025001 (2019); Tzeferacos et al., Nat. Commun. 9, 591 (2018); Phys. Plasmas 24, 041404 (2017); Meinecke et al., Proc. Natl. Acad. Sci. 112, 8211 (2015); Nat. Phys. 10, 520–524 (2014); Mondal et al., Proc. Natl. Acad. Sci. 109, 8011 (2012); Chatterjee et al., Nat. Commun. 8, 15970 (2017)] and are imperative in understanding turbulence in astrophysical scenarios.
Dual beam modulated magneto-optical measurement setup
Authors: Acharya Shankar , Collier Brian , Geerts Wilhelmus
Published: December 2019

A dual beam magneto-optical setup employing a dual axis photoelastic modulator (PEM) and an intensity-stabilized laser was designed and constructed. The beam transmitted through or reflected of the sample is split by a Wollaston prism into two orthogonal high-quality linearly polarized beams. Two photodetectors are used to measure the DC and 2ω components of each beam’s intensity. Theoretical calculations using Jones matrices show that the difference between the 2ω signals, i.e., ΔI2ω, is linearly proportional to the Kerr or Faraday rotation of the sample. Different from I2ω of a traditional single beam setup, the ΔI2ω does not contain an offset caused by the Fabry Perot interference in the PEM’s optical head, making the setup less sensitive for small sample movements and laser drifts including intensity, wavelength, and beam direction drifts all originating from mainly temperature fluctuations in the lab.
Stress-induced phase transformation in shape memory ceramic nanoparticles
Authors: Raut V. S. , Glen T. S. , Rauch H. A. , Yu H. Z. , Boles S. T.
Published: December 2019

Thermal treatment was observed to gradually transform the morphology of Ce0.12Zr0.88O2 (CZ) powder: transitioning from having round edges, to exhibiting clear facets, to particle growth, as a function of increasing treatment temperature. The effect of the morphological changes in the powder on the extent of stress-induced phase transformation upon mechanical compression is reported. The physical changes in the average particle size and the residual levels of monoclinic content (MC) post thermal treatment between 300 °C and 1550 °C are in line with the expectations. However, the extent of transformation upon compression is found to greatly depend on the thermal history of the powder, and generally, post compression, MC can be split into two regimes. Powders heat-treated below ∼1200 °C comprise regime 1, where post compression, MC increases as the preceding thermal processing temperature is increased. The increase in MC is despite the decreasing residual levels of the monoclinic phase in the CZ powder, which is caused by the thermal treatment. For the case of annealing above ∼1200 °C (comprising regime 2), stress-induced transformation becomes exceedingly difficult and the extent of the transformation is significantly reduced. The vital role played by the particle shape alone can be leveraged in the development of new applications of shape memory ceramics.
Systematic parameterization of heat-assisted magnetic recording switching probabilities and the consequences for the resulting SNR
Authors: Slanovc Florian , Vogler Christoph , Muthsam Olivia , Suess Dieter
Published: December 2019

The signal-to-noise ratio (SNR) of a bit series written with heat-assisted magnetic recording on granular media depends on a large number of different parameters. The choice of material properties is essential for the obtained switching probabilities of single grains and, therefore, for the written bits’ quality in terms of SNR. Studies where the effects of different material compositions on transition jitter and the switching probability are evaluated were done, but it is not obvious, how significant those improvements will finally change the received SNR. To investigate that influence, we developed an analytical model of the switching probability phase diagram, which contains independent parameters for, inter alia, transition width, switching probability, and curvature. Different values lead to corresponding bit patterns on granular media, where a reader model detects the resulting signal, which is finally converted to a parameter dependent SNR value. For grain diameters between 4 and 8 nm, we show an increase of ∼10dB for bit lengths between 4 and 12 nm, an increase of ∼9dB for maximum switching probabilities between 0.64 and 1.00, a decrease of ∼5dB for down-track-jitter parameters between 0 and 4 nm, a decrease of 1–3 dB for off-track-jitter parameters between 0 and 50 K, and an increase of ∼0.5dB for the reduced bit curvature. Those results are furthermore compared to the theoretical formulas for the SNR. We obtain a good agreement, even though we show slight deviations.
Functionalized graphene transistor for ultrasensitive detection of carbon quantum dots
Authors: Brndiarova Jana , Siffalovic Peter , Hulman Martin , Kalosi Anna , Bodik Michal , Skakalova Viera , Micusik Matej , Markovic Zoran , Majkova Eva , Frohlich Karol
Published: December 2019

Ubiquitous carbon nanomaterials have great potential for emerging technologies, but they also pose a threat to human health at the end of their lifecycle, especially when they are introduced into waste or ground waters. Graphene field-effect transistors (GFET) and real time in situ confocal Raman microscopy (CRM) were employed to detect a submonolayer of carbon quantum dots (CQDs) in water. An effective GFET channel was formed on exfoliated and chemical vapor deposited (CVD) graphene. The adsorption of CQDs was monitored by measuring conductance changes in GFETs. The graphene channel was functionalized with (3-aminopropyl) triethoxysilane (APTES), which allowed for easy observation of a shift in the charge neutrality point (CNP) when the graphene channel was exposed to CQDs. The affinity of the CQD’s carboxyl terminal groups to the aminofunctionalized channel enabled a highly sensitive CQD detection based on changes in the GFET conductivity. The adsorption of the CQDs induced a positive shift of the CNP with a limit of detection at concentrations of 239 ppm and 62 ppm for the exfoliated and CVD graphene, respectively. A supporting study of graphene functionalization and CQD adsorption was performed by real time in situ CRM, ellipsometry, and ex situ X-ray photoelectron spectroscopy.
Boundary layer transition over a foil using direct numerical simulation and large eddy simulation
Authors: Smith T. A. , Ventikos Y.
Published: December 2019

Transitional boundary layers over lifting bodies represent an important class of flows in many industrial applications, and accurately capturing the transition is crucial for the prediction of important phenomena such as lift, drag, and trailing-edge noise. In this study, we consider how large eddy simulations (LESs) can be used to capture the natural boundary layer transition and compare the results to fully resolved direct numerical simulations that provide a detailed picture of the transition and trailing edge flow. The ability of LES to capture the transition is considered by looking at different elements of the subfilter scale modeling and discretization. The behavior of the subfilter scale model is shown to be critical, and it must remain inactive during the early stages of transition to avoid erroneous predictions due to excessive dissipation. Dispersion errors, when present, can cause the natural transition mechanism to be bypassed at an earlier stage, which leads to higher levels of turbulent kinetic energy at the trailing edge.
Giant polarization charge density at lattice-matched GaN/ScN interfaces
Authors: Adamski Nicholas L. , Dreyer Cyrus E. , Van de Walle Chris G.
Published: December 2019

Rock-salt ScN is a semiconductor with a small lattice mismatch to wurtzite GaN. Within the modern theory of polarization, ScN has a nonvanishing formal polarization along the [111] direction. As a result, we demonstrate that an interface between (0001) GaN and (111) ScN exhibits a large polarization discontinuity of −1.358 Cm−2. Interfaces between ScN and wurtzite III-nitrides will exhibit a high-density electron gas at the (0001¯) GaN interface or a hole gas at the (0001) GaN interface, with carrier concentrations up to 8.5×1014 cm−2. The large polarization difference and small strain make ScN a desirable choice for polarization-enhanced tunnel junctions within the III-nitride materials system. The large sheet carrier densities may also be useful for contacts or current spreading layers.
A minimax approach to one-shot entropy inequalities
Authors: Anshu Anurag , Berta Mario , Jain Rahul , Tomamichel Marco
Published: December 2019

One-shot information theory entertains a plethora of entropic quantities, such as the smooth max-divergence, hypothesis testing divergence, and information spectrum divergence, that characterize various operational tasks in quantum information theory and are used to analyze their asymptotic behavior. Tight inequalities between these quantities are thus of immediate interest. In this note, we use a minimax approach (appearing previously, for example, in the proofs of the quantum substate theorem), to simplify the quantum problem to a commutative one, which allows us to derive such inequalities. Our derivations are conceptually different from previous arguments and in some cases lead to tighter relations. We hope that the approach discussed here can lead to progress in open problems in quantum Shannon theory and exemplify this by applying it to a simple case of the joint smoothing problem.
The biased disc of an electron cyclotron resonance ion source as a probe of instability-induced electron and ion losses
Authors: Tarvainen O. , Kronholm R. , Kalvas T. , Koivisto H. , Izotov I. , Skalyga V. , Toivanen V. , Maunoury L.
Published: December 2019

Electron Cyclotron Resonance Ion Source (ECRIS) plasmas are prone to kinetic instabilities resulting in loss of electron and ion confinement. It is demonstrated that the biased disk of an ECRIS can be used as a probe to quantify such instability-induced electron and ion losses occurring in less than 10 µs. The qualitative interpretation of the data is supported by the measurement of the energy spread of the extracted ion beams implying a transient plasma potential >1.5 kV during the instability. A parametric study of the electron losses combined with electron tracking simulations allows for estimating the fraction of electrons expelled in each instability event to be on the order of 10% of the total electron population.
Excited-state stability of quasi-two-dimensional metal halide perovskite films under optical and electrical excitations
Authors: Watanabe Satoru , Cheng Tai , Tumen-Ulzii Ganbaatar , Qin Chuanjiang , Matsushima Toshinori , Adachi Chihaya
Published: December 2019

Metal halide perovskites are promising as the emitter for efficient light-emitting diodes (LEDs). However, the operational stability of perovskite LEDs (Pe-LEDs) is still very low and, therefore, needs to be improved for future practical applications through the clarification of their basic degradation mechanisms. In this study, we investigated the stability of quasi-two-dimensional (q2D) perovskite films under three different conditions, i.e., carrier injection only, photoexcitation only, and photoexcitation in combination with carrier injection. As a result of the aforementioned comparison, we found that excited states (Wannier excitons) formed in q2D perovskite films by photoexcitation are relatively unstable. On the other hand, no degradation of q2D perovskite films was observed when electrons or holes were injected without the formation of excited states. The unstable excited states were associated with the change from the q2D phase to the three-dimensional phase and the formation of metallic lead working as an excited-state quencher in films. Furthermore, the excited-state stability became worse when the excited states and the charge carriers coexisted in films. This would be one of the reasons for the low stability of q2D Pe-LEDs under continuous electrical operation.
Low magnetic field effects on triplet pair annihilations at canonical orientations
Authors: Yago T.
Published: December 2019

Using the density operator formalism, a simple analytical model is developed to study low magnetic field effects on triplet pair annihilations in organic solids. Analysis is restricted to canonical orientations where two identical triplet molecules have the same orientation and the direction of the external magnetic field is parallel to one of the principle axes of the dipolar coupling tensor for a triplet. The analytical solution reveals that the low magnetic field effect in the triplet pair arises from the anisotropic dipole-dipole coupling in a triplet. In the presence of the dipole-dipole coupling, the spin quantization axis for each triplet gradually changes with the increase of the external magnetic field from zero field to high field. The low magnetic field effect reaches a maximum when the Zeeman splitting between the spin states matches a dipole-dipole coupling component orthogonal to the external magnetic field direction. The result is also discussed with the low magnetic field effect in the radical pair with one isotropic hyperfine coupling.
New method for dynamic mode decomposition of flows over moving structures based on machine learning (hybrid dynamic mode decomposition)
Authors: Naderi Mohammad Hossein , Eivazi Hamidreza , Esfahanian Vahid
Published: December 2019

Dynamic Mode Decomposition (DMD) is a data-driven reduced order method, which is known for its power to capture the basic features of dynamical systems. In fluid dynamics, modal analysis of unsteady fluid flows over moving structures is significant in terms of state estimation and control. However, the underlying algorithm of the DMD requires a fixed spatial domain, which is an obstacle for applying the DMD on the numerically investigated problems using dynamic meshes. In this study, a hybrid method called Hybrid Dynamic Mode Decomposition (HDMD) is presented for analysis of unsteady fluid flows over moving structures based on the DMD and machine learning. According to the assessment of several data interpolation methods, the K-nearest neighbor algorithm is employed for the interpolation of the numerical data from dynamic meshes at each time step to a single stationary grid. Three different case studies (rotating cylinder, oscillating airfoil, and Savonius wind turbine) are assessed to ensure the validity of the proposed method. Minimum mean R2 equal to 0.92 has been obtained for all of the mentioned cases, indicating the robustness of the HDMD algorithm for a variety of fluid flow simulations.
Vacuum ultraviolet photodissociation dynamics of CO2 near 133 nm: The spin-forbidden O(3Pj=2,1,0) + CO(X1Σ+) channel
Authors: Yu Shengrui , Yuan Daofu , Chen Wentao , Zhou Jiami , Yang Xueming , Wang Xingan
Published: December 2019

Understanding vacuum ultraviolet (VUV) photodissociation dynamics of CO2 is of considerable importance in the study of atmospheric chemistry and planetary chemistry. Yet, photodissociation dynamics of the spin-forbidden O(3Pj=2,1,0) + CO(X1Σ+) channel has not been clearly understood so far. Here, we study the O(3Pj) + CO(X1Σ+) dissociation processes in the VUV photodissociation of CO2 at the photolysis wavelengths between 129.02 and 134.67 nm by using the time-sliced velocity-mapped ion imaging technique. From the vibrational-resolved images of the O(3Pj=2,1,0) photofragment, the total kinetic energy releases, the CO(X1Σ+) cofragment vibrational state distributions, and the product angular distributions have been derived, respectively. The experimental observations show that the total kinetic energy releases for the three 3Pj spin-orbit states (j = 2, 1, 0) exhibit a broad CO(X1Σ+) vibrational energy distribution with significant inverted characteristics, especially at short photoexcitation wavelengths, indicating that the VUV photodissociation could take place in a relatively linear geometry of the triplet state, with one C–O bond extended and the other compressed. Furthermore, a notable photolysis wavelength dependent feature has also been found in the product angular distributions of all three spin-orbit channels (j = 2, 1, 0): Only the vibrational-state specific anisotropy parameter β values at 130.18 nm behave more anisotropic, while all those at other photolysis wavelengths are near the value β = 0.5 for O(3Pj=2,1) channels or β = 0.25 for the O(3Pj=0) channel, with small fluctuations. This anomalous phenomenon suggests that the different nonadiabatic interactions, such as singlet-triplet coupling, may play a key role in the formation of O(3Pj=2,1,0) + CO(X1Σ+) products, with strong photolysis wavelength dependence.
sp-hybridized carbon allotrope molecular structures: An ongoing challenge for density-functional approximations
Authors: Brémond Éric , Pérez-Jiménez Ángel José , Adamo Carlo , Sancho-García Juan Carlos
Published: December 2019

The recent synthesis of a C18 monocyclic ring constitutes a major breakthrough as a new all-carbon disclosed form. However, modern density functional theory approaches do not lead to the correct experimental polyynic structure and favor the cumulenic one instead. We demonstrate here that this serious drawback can be solved by recently developed range-separated nonempirical schemes, independently of which kind of functional is being applied (i.e., semilocal, hybrid, or double-hybrid).
Structural characterization of porous GaN distributed Bragg reflectors using x-ray diffraction
Authors: Griffin P. H. , Frentrup M. , Zhu T. , Vickers M. E. , Oliver R. A.
Published: December 2019

Porous GaN distributed Bragg reflectors (DBRs) provide strain-free, high-reflectivity structures with a wide range of applications across nitride optoelectronics. Structural characterization of porous DBRs is currently predominantly achieved by cross-sectional scanning electron microscopy (SEM), which is a destructive process that produces local data and has accuracy limited to around 3% by instrument calibration uncertainty. Here, we show that high-resolution x-ray diffraction (XRD) offers an alternative, nondestructive method for characterizing porous nitride structures. XRD scans of porous GaN DBRs show that despite the constant lattice parameter across the DBR layers, characteristic satellite peaks still arise, which are due to the interference between x-rays reflected from the porous and nonporous layers. By comparing the intensities and positions of the satellite peaks through diffraction patterns simulated from a kinematic model, the structural properties of the porous GaN DBRs can be analyzed. Using our method, we have measured a series of DBRs with stop bands from the blue wavelength region to the IR and compared their structural values with those from SEM data. Our results show that the XRD method offers improvements in the accuracy of determining layer thickness, although uncertainty for the value of porosity remains high. To verify the results gained from the XRD and SEM analysis, we modeled the optical reflectivity using the structural values of both methods. We found that the XRD method offered a better fit to the optical data. XRD, therefore, offers accurate, nondestructive characterization of porous DBR structures based on macroscale measurements and is suitable for full wafer analysis.
A novel micro-photogrammetric instrument for visualizing in 3D small objects applied to the quantitative study of the dissolution behavior of a pharmaceutical dosage form
Authors: D’Angelo Alessandra , Reading Mike , Antonijevic Milan
Published: December 2019

The work presented here proposes an innovative approach to 3D chemical mapping of solid formulations by microphotogrammetry. We present details of a novel microphotogrammetry apparatus and the first results for the application of photogrammetry to the dissolution analysis of solid pharmaceutical dosage forms. Unlike other forms of optical imaging, microphotogrammetry allows a true 3D model to be constructed that includes direct observation of the sides of the sample rather than only top-down topographic imaging. Volume and structural changes are assessed quantitatively and related to chemical analysis by high performance liquid chromatography. The recently introduced method of chemical identification by dissolution analysis, or chemical imaging by dissolution analysis, is employed for the first time to obtain tomographic images of the dissolution process.
Unveiling dimensions of stability in complex ecological networks
Authors: Domínguez-García Virginia , Dakos Vasilis , Kéfi Sonia
Published: December 2019

Understanding the stability of ecological communities is a matter of increasing importance in the context of global environmental change. Yet it has proved to be a challenging task. Different metrics are used to assess the stability of ecological systems, and the choice of one metric over another may result in conflicting conclusions. Although each of the multitude of metrics is useful for answering a specific question about stability, the relationship among metrics is poorly understood. Such lack of understanding prevents scientists from developing a unified concept of stability. Instead, by investigating these relationships we can unveil how many dimensions of stability there are (i.e., in how many independent components stability metrics can be grouped), which should help build a more comprehensive concept of stability. Here we simultaneously measured 27 stability metrics frequently used in ecological studies. Our approach is based on dynamical simulations of multispecies trophic communities under different perturbation scenarios. Mapping the relationships between the metrics revealed that they can be lumped into 3 main groups of relatively independent stability components: early response to pulse, sensitivities to press, and distance to threshold. Selecting metrics from each of these groups allows a more accurate and comprehensive quantification of the overall stability of ecological communities. These results contribute to improving our understanding and assessment of stability in ecological communities.
Pressure-induced topological phase transition in noncentrosymmetric elemental tellurium
Authors: Ideue Toshiya , Hirayama Motoaki , Taiko Hiroaki , Takahashi Takanari , Murase Masayuki , Miyake Takashi , Murakami Shuichi , Sasagawa Takao , Iwasa Yoshihiro
Published: December 2019

Significance

Topological Weyl semimetal, which is a gapless semimetallic phase protected by symmetry, generally appears by band gap closing in noncentrosymmetric semiconductors. So far, there have been only a limited number of reports of such a topological phase transition so that many basic aspects have remained unexplored. Here we report potential signatures of the topological phase transition under pressure in elemental tellurium with noncentrosymmetric chiral crystal structure. Our result represents that elemental tellurium can be one of the model systems for the topological phase transition from a semiconductor to a Weyl semimetal, opening the avenue for studying the topological phase transition by the external field and resultant topological properties.
On asymptotic charges in 3D gravity
Authors: Bergshoeff Eric A , Merbis Wout , Townsend Paul K
Published: December 2019

A variant of the ADT method for the determination of gravitational charges as integrals at infinity is applied to ‘Chern–Simons-like’ theories of 3D gravity, and the result is used to find the mass and angular momentum of the BTZ black hole considered as a solution of a variety of massive 3D gravity field equations. The results agree with many obtained previously by other methods, including our own results for ‘Minimal Massive Gravity’, but they disagree with others, including recently reported results for ‘Exotic Massive Gravity’. We also find the central charges of the asymptotic conformal symmetry algebra for the generic 3D gravity model with AdS vacuum and discuss implications for black hole thermodynamics.
An accurate instrument for emissivity measurements by direct and indirect methods
Authors: Zhu Chengxi , Hobbs Matthew J , Willmott Jon R
Published: December 2019

Emissivity is a quantity essential to consider when assessing the measurement uncertainty in non-contact temperature measurements. This paper presents a new instrument for measuring emissivity of opaque materials from 200 °C to 450 °C in the spectral range of 2.1 to 2.5 µm. These ranges are ideal for measuring the temperature of metals, such as aluminium, during manufacture or heat-treating processes. The instrument consists of a pair of hemispherical cups coated with Vantablack® and gold respectively, a custom designed radiation thermometer, and a hot plate. This instrument enables both the direct and the indirect methods for measuring emissivity of materials. Use of two identical cups allowed for quantitative analysis of the uncertainty of the instrument to determine the most suitable emissivity measurement range. The expanded uncertainty of the instrument was lower than 0.058 (k  =  2) over the entire measuring temperature range. Studies were undertaken using different materials with emissivities ranging from 0.06 to 1. These included aluminium alloy 6082, stainless steel 304, and HiE-Coat 840M paint. Relative uncertainty analysis indicated that the indirect method was more accurate for measuring low-emissivity materials, whereas the direct method was more suitable for all other materials. Our instrument, with experimentally determined measurement uncertainty, aims to offer accurate emissivity references for use in radiation thermometry applications.
Gravity and warped time—clarifying conceptual confusions in general relativity
Authors: Kersting Magdalena , Toellner Richard , Blair David , Burman Ron
Published: December 2019

In recent years, general relativity (GR) and gravitational-wave astronomy have emerged both as active fields of research and as popular topics in physics classrooms. Teachers can choose from an increasing number of modern instructional models to introduce students to relativistic ideas. However, the true potential of an instructional model can only be unleashed if teachers know about its scope and limitations and how the model relates to key concepts of the theory. GR is a conceptually rich theory and many relativistic concepts entail subtleties that often elude non-experts. Building on the recent introduction of a digital warped-time model (Kersting 2019 Phys. Educ. 54 035008), this article identifies three potentially confusing concepts in GR. We present three pedagogical pathways to address these concepts and supplement our considerations with quantitative treatments accessible at the upper secondary school level. By interlacing pedagogical and content-specific perspectives, we aim to support teachers who wish to deepen their knowledge of relativistic phenomena. At the same time, we offer specific instructional strategies to make successful use of the warped-time model. Our perspectives contribute to an on-going re-evaluation of practices in modern physics education that can offer new impetus to the physics teaching community beyond the learning domain of relativity.
Erosion and cathodic arc plasma of Nb–Al cathodes: composite versus intermetallic
Authors: Zöhrer Siegfried , Golizadeh Mehran , Koutná Nikola , Holec David , Anders André , Franz Robert
Published: December 2019

Many properties of cathodic arcs from single-element cathodes show a correlation to the cohesive energy of the cathode material. For example, the burning voltage, the erosion rate, or, to a lesser extent, plasma properties like electron temperatures or average ion energy and charge states. For multi-element cathodes, various phases with different cohesive energies can initially be present in the cathode, or form due to arc exposure, complicating the evaluation of such correlations. To test the influence of morphology and phase composition of multi-element cathodes on cathodic arc properties, a Nb–Al cathode model system was used that includes: pure Nb and Al cathodes; intermetallic Nb3Al, Nb2Al and NbAl3 cathodes; and three composite Nb–Al cathodes with atomic ratios corresponding to the stoichiometric ratios of the intermetallic phases. Pulsed cathodic arc plasmas from these cathodes were examined using a mass-per-charge and energy-per-charge analyzer, showing that charge-state-resolved ion energy distributions of plasmas from the intermetallic and corresponding composite cathodes are nearly identical. An examination of converted layers of eroded cathodes using x-ray diffraction and scanning electron microscopy indicates the formation of a surface layer with similar phase composition for intermetallic and their corresponding composite cathode types. The average arc voltages do not follow the trend of cohesive energies of Nb, Al and intermetallic Nb–Al phases, which have been calculated using density functional theory. Possible reasons for this effect are discussed based on the current knowledge of multi-element arc cathodes and their arc plasma available in literature.
Magnetostriction of helimagnets in the skyrmion crystal phase
Authors: Wang Shasha , Hu Yangfan , Tang Jin , Wei Wensen , Cong Junzhuang , Sun Young , Du Haifeng , Tian Mingliang
Published: December 2019

We solve the magnetostriction strains for B20 helimagnets in the skyrmion crystal phase. By taking MnSi as an example, we reproduce its temperature–magnetic field (T–B) phase diagrams within a thermodynamic potential incorporating magnetoelastic interactions. The calculation shows that the normal strain ε
33 undergoes a sudden jump through a conical-skyrmion phase transition at any temperature. The corresponding experimental measurements for MnSi agree quantitatively well with the calculation.
Theoretical investigation of the applicability of the Meservey–Tedrow technique to the surface states of topological insulators
Authors: Götte Matthias , Dahm Thomas
Published: December 2019

The spin polarization of topological surface states is of high interest for possible applications in spintronics. At present, the only technique capable to measure the surface state spin texture is spin and angle resolved photoemission spectroscopy (SARPES). However, values reported by SARPES differed strongly. An established technique to measure the spin polarization of ferromagnetic materials is the so-called Meservey–Tedrow technique, which is based on spin dependent tunneling from a superconducting electrode to a ferromagnet. Here, we theoretically investigate how the Meservey–Tedrow technique can be adapted to topological insulators. We demonstrate that with a specific device geometry it is possible to determine the in-plane component of the spin polarization of topological surface states. More complex device geometries can access the full momentum dependence of the spin polarization. We also show that it is possible to extract the spin-flip scattering rate of surface electrons with the same devices.
Siegel modular forms of degree three and invariants of ternary quartics
Authors: Lercier Reynald , Ritzenthaler Christophe
Published: December 2019

We determine the structure of the graded ring of Siegel modular forms of degree 3. It is generated by 19 modular forms, among which we identify a homogeneous system of parameters with 7 forms of weights

4
4

,

12
12

,

12
12

,

14
14

,

18
18

,

20
20

and

30
30

. We also give a complete dictionary between the Dixmier-Ohno invariants of ternary quartics and the above generators.
Classification of exterior and proper fibrations
Authors: García-Calcines J. , García-Díaz P. , Murillo A.
Published: December 2019

As in the classical setting, we classify a large class of exterior fibrations in the based exterior homotopy category. More precisely, the fibration sequences

F
→
E
→
X

F\to E\to X

of path-connected based exterior CW-complexes are in bijective correspondence with the based exterior homotopy classes of maps from

X
X

to a universal exterior CW-complex

Y
F

Y_F

. As a result we classify proper fibrations between CW-complexes.
ImPLoc: a multi-instance deep learning model for the prediction of protein subcellular localization based on immunohistochemistry images
Authors: Long Wei , Yang Yang , Shen Hong-Bin
Published: December 2019

Motivation

The tissue atlas of the human protein atlas (HPA) houses immunohistochemistry (IHC) images visualizing the protein distribution from the tissue level down to the cell level, which provide an important resource to study human spatial proteome. Especially, the protein subcellular localization patterns revealed by these images are helpful for understanding protein functions, and the differential localization analysis across normal and cancer tissues lead to new cancer biomarkers. However, computational tools for processing images in this database are highly underdeveloped. The recognition of the localization patterns suffers from the variation in image quality and the difficulty in detecting microscopic targets.

Results

We propose a deep multi-instance multi-label model, ImPLoc, to predict the subcellular locations from IHC images. In this model, we employ a deep convolutional neural network-based feature extractor to represent image features, and design a multi-head self-attention encoder to aggregate multiple feature vectors for subsequent prediction. We construct a benchmark dataset of 1186 proteins including 7855 images from HPA and 6 subcellular locations. The experimental results show that ImPLoc achieves significant enhancement on the prediction accuracy compared with the current computational methods. We further apply ImPLoc to a test set of 889 proteins with images from both normal and cancer tissues, and obtain 8 differentially localized proteins with a significance level of 0.05.

Availability and implementation

https://github.com/yl2019lw/ImPloc.

Supplementary information

Supplementary data are available at Bioinformatics online.
LIMES: a tool for comparing species partition
Authors: Ducasse Jacques , Ung Visotheary , Lecointre Guillaume , Miralles Aurélien
Published: December 2019

Motivation

Species delimitation (SD) is on the verge of becoming a fully fledged research field in systematics, but the variety of available approaches tends to result in significant—sometimes striking—incongruences, when tested comparatively with a given taxonomic sampling.

Results

We present LIMES, an automatic calculation tool which qualitatively compares species partitions obtained by distinct SD approaches, regardless of their respective theoretical backgrounds, and even in absence of reference topology. The program implements four different previously published indexes, and allows their automated calculation.

Availability and implementation

LIMES is freely downloadable at www.limes.cnrs.fr.

Supplementary information

Supplementary data are available at Bioinformatics online.
Measurement Models in Social Work Research: A Data-Based Illustration of Four Confirmatory Factor Models and Their Conceptual Application
Authors: Cimino Andrea N , Killian Michael O , Von Ende Adam K , Segal Elizabeth A
Published: December 2019

Confirmatory factor analysis (CFA) is a valuable tool for social work researchers to examine validity of measurements and other latent constructs. Best practice recommendations are to specify and evaluate the fit of multiple models, balancing plausibility, parsimony and quantitative indices. However, little attention has been given to the conceptual and theoretical implications of CFA model variations. This article offers a brief report on the state of CFA modelling published in social work research and presents a data-based illustration of four CFA models of a measure of empathy including a single-factor, correlated factors, higher order and bifactor models. We present results from each model and describe the models’ conceptual application with substantive explanation and theoretical application to the measurement of empathy. Syntax for all models in Mplus, R, Stata and EQS programmes are provided for reference. As familiarity with CFA and latent variable modelling methods grows, researchers must understand the theory-based implications of varying measurement models and test which model best represents their data and explain their conceptual application.
Temporal DNA methylation pattern and targeted therapy in colitis-associated cancer
Authors: Li Junshu , Su Xiaolan , Dai Lei , Chen Na , Fang Chao , Dong Zhexu , Fu Jiamei , Yu Yan , Wang Wenshuang , Zhang Hantao , Wang Huiling , Ji Yanhong , Liu Yi , Cheng Lin , Shi Gang , Zhang Shuang , Yang Yang , Deng Hongxin
Published: December 2019

DNA methylation plays a crucial role in the pathogenesis of various diseases, including colorectal cancer (CRC). However, the global and temporal DNA methylation pattern during initiation and progression of colitis-associated cancer (CAC) are still unknown, including the potential therapeutic strategy of targeting methylation for CAC. In the present study, the global DNA methylation pattern was determined at different time points during CAC using DNA methylation sequencing, followed by the Starburst plot integrating alterations and potential functional prediction analysis. After demonstrating the regulatory role of DNA methyltransferases (DNMTs) on the expression of hub-genes in CRC cells, DNMT inhibitors were administered to treat CAC mice. Our results indicated that 811 genes were hypermethylated at different time points during initiation and progression of CAC. Genes that were downregulated and hypermethylated during CAC, including hub-genes BAD and inositol polyphosphate phosphatase-like 1 (INPPL1), were involved in MAPK signaling pathways, kit receptor signaling pathways, apoptosis and EGF/EGFR signaling pathways. Upregulated DNMTs (DNMT1, DNMT3A and DNMT3B) mediated downregulation and hypermethylation of BAD and INPPL1 in CAC and CRC cells. Low doses of DNMT inhibitors (decitabine (DAC) and azacitidine (AZA)) exerted efficient antitumor effects in CAC, accompanied with upregulation of BAD and INPPL1 expression, and apoptosis induction. In summary, the present study demonstrates the temporal DNA methylation pattern during CAC and provides a novel therapeutic strategy for treating this disease.
Subclinical Vascular Disease in Children With Human Immunodeficiency Virus in Uganda Is Associated With Intestinal Barrier Dysfunction
Authors: Dirajlal-Fargo Sahera , Albar Zainab , Bowman Emily , Labbato Danielle , Sattar Abdus , Karungi Christine , Longenecker Chris T , Nazzinda Rashida , Funderburg Nicholas , Kityo Cissy , Musiime Victor , McComsey Grace A
Published: December 2019

Background

The risk of cardiovascular disease (CVD) and its mechanisms in children living with perinatally acquired HIV (PHIV) in sub-Saharan Africa has been understudied.

Methods

Mean common carotid artery intima-media thickness (IMT) and pulse-wave velocity (PWV) were evaluated in 101 PHIV and 96 HIV-negative (HIV−) children. PHIV were on ART, with HIV-1 RNA levels ≤400 copies/mL. We measured plasma and cellular markers of monocyte activation, T-cell activation, oxidized lipids, and gut integrity.

Results

Overall median (interquartile range, Q1–Q3) age was 13 (11–15) years and 52% were females. Groups were similar by age, sex, and BMI. Median ART duration was 10 (8–11) years. PHIV had higher waist–hip ratio, triglycerides, and insulin resistance (P ≤ .03). Median IMT was slightly thicker in PHIVs than HIV− children (1.05 vs 1.02 mm for mean IMT and 1.25 vs 1.21 mm for max IMT; P < .05), while PWV did not differ between groups (P = .06). In univariate analyses, lower BMI and oxidized LDL, and higher waist–hip ratio, hsCRP, and zonulin correlated with thicker IMT in PHIV (P ≤ .05). After adjustment for age, BMI, sex, CD4 cell count, triglycerides, and separately adding sCD163, sCD14, and hsCRP, higher levels of intestinal permeability as measured by zonulin remained associated with IMT (β = 0.03 and 0.02, respectively; P ≤ .03).

Conclusions

Our study shows that African PHIV have evidence of CVD risk and structural vascular changes despite viral suppression. Intestinal intestinal barrier dysfunction may be involved in the pathogenesis of subclinical vascular disease in this population.
High-resolution genome-wide analysis is essential for the identification of ambiguous Aeromonas strains
Authors: de Melo Beatriz Souza Toscano , Mendes-Marques Carina Lucena , Campos Túlio de Lima , Almeida Alzira Maria Paiva de , Leal Nilma Cintra , Xavier Danilo Elias
Published: December 2019

Aeromonads are mainly opportunistic pathogens; however, many species are emerging as important human pathogens. Therefore, monitoring these bacteria and their accurate characterization of its species is highly important. Aeromonas Aer593 strain was recovered from a diarrhoea outbreak and did not group with any previously described Aeromonas species by housekeeping gene sequencing. To clarify the taxonomic position of Aer593, its genome was sequenced and analysed by multilocus phylogenetic analysis (MLPA), in silico DNA–DNA hybridization (isDDH), average nucleotide identity (ANI) and core genome-based phylogenetic analyzes. The MLPA with the housekeeping genes gyrB, rpoD, recA, dnaJ, gyrA and dnaX ranked the Aer593 isolate into an independent branch suggesting that it could represent a new species. However, the identity percentages of Aer593 to A. caviae strains using robust genomic analysis by isDDH and ANI were at least 81.3% and 97.8%, respectively, defining Aer593 as A. caviae. Multilocus sequence typing (MLST) presented an exact match against only a single allele (groL96) and the novel ST648 was assigned for this strain. The core genome-based phylogenetic analyses with a total of 863 orthologous genes also grouped the Aer593 isolate with A. caviae reference strains. These findings warn about the possibility of misidentification of some Aeromonas strains by MLPA and show that high-resolution genome-wide analysis is essential for the correct identification of ambiguous Aeromonas strains.
Mortality and Obesity Among U.S. Older Adults: The Role of Polygenic Risk
Authors: Vinneau Justin M , Huibregtse Brooke M , Laidley Thomas M , Goode Joshua A , Boardman Jason D
Published: December 2019

Objectives

To examine the relationship between obesity and mortality as a function of polygenic risk for obesity among older U.S. adults.

Method

Using data from the 1994–2014 Health and Retirement Study in conjunction with genome-wide data, we evaluated the risk of mortality as a function of obesity classification, an individual’s polygenic risk score (PGS) for obesity, and their interaction, stratified by sex. We conducted our analyses using cox proportional hazard models.

Results

Among those with an average PGS for obesity (8,143 [68.8%]), obese I (hazard ratio [HR] = 0.79, p = .336) adults show no difference in their risk for mortality and obese II/III (HR = 3.17, p = .000) adults present higher risk of mortality relative to non-obese adults. The interaction of obesity classification and PGS suggests that obese II/III respondents with low PGS in the total sample (HR = 2.71, p = .006) and among women (HR = 3.02, p = .023) are at significantly higher risk of death when compared to obese II/III respondents with average or high PGS.

Discussion

We posit that these findings suggest that the pathway to obesity, in this case, more socio-behavioral rather than genetic, may influence subsequent risk of death in older adults. We suggest that practitioners and population researchers be mindful of these pathways as to better identify and understand mortality risk.