Miracle-dz/UniFAR-FTUs huggingface dataset:
Minimum energy path for the nucleation of misfit dislocations in Ge/Si(0 0 1) heteroepitaxy

A possible mechanism for the formation of a 90° misfit dislocation at the Ge/Si(0 0 1) interface through homogeneous nucleation is identified from atomic scale calculations where a minimum energy path connecting the coherent epitaxial state and a final state with a 90° misfit dislocation is found using the nudged elastic band method. The initial path is generated using a repulsive bias activation procedure in a model system including 75 000 atoms. The energy along the path exhibits two maxima in the energy. The first maximum occurs as a 60° dislocation nucleates. The intermediate minimum corresponds to an extended 60° dislocation. The subsequent energy maximum occurs as a second 60° dislocation nucleates in a complementary, mirror glide plane, simultaneously starting from the surface and from the first 60° dislocation. The activation energy of the nucleation of the second dislocation is 30% lower than that of the first one showing that the formation of the second 60° dislocation is aided by the presence of the first one. The simulations represent a step towards unraveling the formation mechanism of 90° dislocations, an important issue in the design of growth procedures for strain released Ge overlayers on Si(1 0 0) surfaces, and more generally illustrate an approach that can be used to gain insight into the mechanism of complex nucleation paths of extended defects in solids.
COVID Seq as Laboratory Developed Test (LDT) for diagnosis of SARS-CoV-2 Variants of Concern (VOC)

Rapid classification and detection of SARS-CoV-2 variants have been critical in comprehending the virus's transmission dynamics. Clinical manifestation of the infection is influenced by comorbidities such as age, immune status, diabetes, and the infecting variant. Thus, clinical management may differ for new variants. For example, some monoclonal antibody treatments are variant-specific. Yet, an FDA-approved test for detecting the SARS-CoV-2 variant is unavailable. A laboratory-developed test (LDT) remains a viable option for reporting the infecting variant for clinical intervention or epidemiological purposes. Accordingly, we have validated the Illumina COVID-Seq assay as an LDT according to the guidelines prescribed by the College of American Pathologists (CAP) and Clinical Laboratory Improvement Amendments (CLIA). The limit of detection (LOD) of this test is Ct<30 (~15 viral copies) and >200X genomic coverage, and the test is 100% specific in the detection of existing variants. The test demonstrated 100% precision in inter-day, intra-day, and intra-laboratory reproducibility studies. It is also 100% accurate, defined by reference strain testing and split sample testing with other CLIA laboratories. Advanta Genetics LDT COVID Seq has been reviewed by CAP inspectors and is under review by FDA for Emergency Use Authorization.
LSP Squark Decays at the LHC and the Neutrino Mass Hierarchy

The existence of R-parity in supersymmetric models can be naturally explained as being a discrete subgroup of gauged baryon minus lepton number (B L). The most minimal supersymmetric B L model triggers spontaneousR-parity violation, while remaining consistent with proton stability. This model is well-motivated by string theory and makes several interesting, testable predictions. Furthermore,R-parity violation contributes to neutrino masses, thereby connecting the neutrino sector to the decay of the lightest supersymmetric particle (LSP). This paper analyzes the decays of third generation squark LSPs into a quark and a lepton. In certain cases, the branching ratios into charged leptons reveal information about the neutrino mass hierarchy, a current goal of experimental neutrino physics, as well as the 23 neutrino mixing angle. Furthermore, optimization of leptoquark searches for this scenario is discussed. Using currently available data, the lower bounds on the third generation squarks are computed.
Numerical analytic continuation: Answers to well-posed questions

We formulate the problem of numerical analytic continuation in a way that lets us draw meaningful conclusions about the properties of the spectral function based solely on the input data. Apart from ensuring consistency with the input data (within their error bars) and the a priori and a posteriori (conditional) constraints, it is crucial to reliably characterize the accuracy---or even ambiguity---of the output. We explain how these challenges can be met with two approaches: stochastic optimization with consistent constraints and the modified maximum entropy method. We perform illustrative tests for spectra with a double-peak structure, where we critically examine which spectral properties are accessible (second peak position and its spectral weight) and which ones are lost (second peak width/shape). For an important practical example, we apply our protocol to the Fermi polaron problem.
Spectroscopic and photometric analysis of the early-type spectroscopic binary HD 161853 in the centre of an H II region

We study the O-type star HD 161853, which has been noted as a probable double-lined spectroscopic binary system. We secured high-resolution spectra of HD 161853 during the past nine years. We separated the two components in the system and measured their respective radial velocities for the first time. We confirm that HD 161853 is an $\sim$1 Ma old binary system consisting of an O8 V star ($M_{\rm A,RV} \geq 22$ M$_\odot$) and a B1--3 V star ($M_{\rm B,RV} \geq 7.2$ M$_\odot$) at about 1.3 kpc. From the radial velocity curve, we measure an orbital period $P$ = 2.66765$\pm$0.00001 d and an eccentricity $e$ = 0.121$\pm$0.007. Its $V$-band light curve is constant within 0.014 mag and does not display eclipses, from which we impose a maximum orbital inclination $i=54$ deg. HD 161853 is probably associated with an H II region and a poorly investigated very young open cluster. In addition, we detect a compact emission region at 50 arcsec to HD 161853 in 22$\mu$m-WISE and 24$\mu$m-Spitzer images, which may be identified as a dust wave piled up by the radiation pressure of the massive binary system.
A DYNAMICAL STUDY OF THE BLACK HOLE X-RAY BINARY NOVA MUSCAE 1991

We present a dynamical study of the Galactic black hole binary system Nova Muscae 1991 (GS/GRS 1124–683). We utilize 72 high-resolution Magellan Echellette spectra and 72 strictly simultaneous V-band photometric observations; the simultaneity is a unique and crucial feature of this dynamical study. The data were taken on two consecutive nights and cover the full 10.4 hr orbital cycle. The radial velocities of the secondary star are determined by cross-correlating the object spectra with the best-match template spectrum obtained using the same instrument configuration. Based on our independent analysis of five orders of the echellette spectrum, the semi-amplitude of the radial velocity of the secondary is measured to be K 2 = 406.8 ± 2.7 ? > km s−1, which is consistent with previous work, while the uncertainty is reduced by a factor of 3. The corresponding mass function is f ( M ) = 3.02 ± 0.06 M ⊙ ? > . We have also obtained an accurate measurement of the rotational broadening of the stellar absorption lines ( v sin i = 85.0 ± 2.6 ? > km s−1), and hence the mass ratio of the system q = 0.079 ± 0.007 ? > . Finally, we have measured the spectrum of the non-stellar component of emission that veils the spectrum of the secondary. In a future paper, we will use our veiling-corrected spectrum of the secondary and accurate values of K2 and q to model multi-color light curves and determine the systemic inclination and the mass of the black hole.
High-velocity-dispersion cold gas in ULIRG Outflows - I. Direct simulations

ABSTRACT Observations have revealed cold gas with large velocity dispersions (ˇ 300 km/s)within the hot outows of ultra-luminous infrared galaxies (ULIRGs). This gas maytrace its origin to the Rayleigh-Taylor (RT) fragmentation of a super-bubble or mayarise on smaller scales. We model a ULIRG outow at two scales to recreate this gasin three-dimensional hydrodynamic simulations using FLASH. Although resolutionis limited, these models successfully produce cold gas in outows with large velocitydispersions. Our small-scale models produce this cold gas through RT fragmentationof the super-bubble wall, but the large-scale models produce the cold gas after hotbubbles fragment the disc’s gas into cold clouds which are then accelerated by thermalpressure, and supplemented by cooling within the outow. We produce simple mockspectra to compare these simulations to observed absorption spectra and nd line-widths of ˇ 250 km/s, agreeing with the lower end of observations.Key words: ISM: jets and outows, galaxies: starburst, line: formation, hydrody-namics
NUCLEOSYNTHESIS IN TWO-DIMENSIONAL DELAYED DETONATION MODELS OF TYPE Ia SUPERNOVA EXPLOSIONS

For the explosion mechanism of Type Ia supernovae (SNe Ia), different scenarios have been suggested. In these, the propagation of the burning front through the exploding white dwarf (WD) star proceeds in different modes, and consequently imprints of the explosion model on the nucleosynthetic yields can be expected. The nucleosynthetic characteristics of various explosion mechanisms are explored based on three two-dimensional explosion simulations representing extreme cases: a pure turbulent deflagration, a delayed detonation following an approximately spherical ignition of the initial deflagration, and a delayed detonation arising from a highly asymmetric deflagration ignition. Apart from this initial condition, the deflagration stage is treated in a parameter-free approach. The detonation is initiated when the turbulent burning enters the distributed burning regime. This occurs at densities around 107 g cm−3—relatively low as compared to existing nucleosynthesis studies for one-dimensional spherically symmetric models. The burning in these multidimensional models is different from that in one-dimensional simulations as the detonation wave propagates both into unburned material in the high-density region near the center of a WD and into the low-density region near the surface. Thus, the resulting yield is a mixture of different explosive burning products, from carbon-burning products at low densities to complete silicon-burning products at the highest densities, as well as electron-capture products synthesized at the deflagration stage. Detailed calculations of the nucleosynthesis in all three models are presented. In contrast to the deflagration model, the delayed detonations produce a characteristic layered structure and the yields largely satisfy constraints from Galactic chemical evolution. In the asymmetric delayed detonation model, the region filled with electron capture species (e.g., 58Ni, 54Fe) is within a shell, showing a large off-set, above the bulk of 56Ni distribution, while species produced by the detonation are distributed more spherically.
COLD AND WARM ATOMIC GAS AROUND THE PERSEUS MOLECULAR CLOUD. II. THE IMPACT OF HIGH OPTICAL DEPTH ON THE HI COLUMN DENSITY DISTRIBUTION AND ITS IMPLICATION FOR THE HI-TO-H2 TRANSITION

We investigate the impact of high optical depth on the HI saturation observed in the Perseus molecular cloud by using Arecibo HI emission and absorption measurements toward 26 radio continuum sources. The spin temperature and optical depth of individual HI components are derived along each line of sight, enabling us to estimate the correction for high optical depth. We examine two different methods for the correction, Gaussian decomposition and isothermal methods, and find that they are consistent (maximum correction factor ∼1.2), likely due to the relatively low optical depth and insignificant contribution from the diffuse radio continuum emission for Perseus. We apply the correction to the optically thin HI column density on a pixel-by-pixel basis and find that the total HI mass increases by ∼10%. Using the corrected HI column density image and far-infrared data from the IRIS Survey, we then derive the H2 column density on ∼0.4 pc scales. For five dark and star-forming sub-regions, the HI surface density is uniform with &Sgr; HI ? > ∼ 7–9 M ⊙ ? > pc−2, in agreement with the minimum HI surface density required for shielding H2 against photodissociation. As a result, &Sgr; H 2 ? > / &Sgr; HI ? > and &Sgr; HI + &Sgr; H 2 ? > show a tight relation. Our results are consistent with predictions for H2 formation in steady state and chemical equilibrium and suggest that H2 formation is mainly responsible for the &Sgr; HI ? > saturation in Perseus. We also compare the optically thick HI with the observed “CO-dark” gas and find that the optically thick HI only accounts for ∼20% of the “CO-dark” gas in Perseus.
SR-GAN: Semantic Rectifying Generative Adversarial Network for Zero-shot Learning

The existing Zero-Shot learning (ZSL) methods may suffer from the vague class attributes that are highly overlapped for different classes. Unlike these methods that ignore the discrimination among classes, in this paper, we propose to classify unseen image by rectifying the semantic space guided by the visual space. First, we pre-train a Semantic Rectifying Network (SRN) to rectify semantic space with a semantic loss and a rectifying loss. Then, a Semantic Rectifying Generative Adversarial Network (SR-GAN) is built to generate plausible visual feature of unseen class from both semantic feature and rectified semantic feature. To guarantee the effectiveness of rectified semantic features and synthetic visual features, a pre-reconstruction and a post reconstruction networks are proposed, which keep the consistency between visual feature and semantic feature. Experimental results demonstrate that our approach significantly outperforms the state-of-the-arts on four benchmark datasets.
Development and implementation of an aspiration pneumonia cause investigation algorithm

The diagnostic criteria of aspiration pneumonia have not been established, and it remains an underdiagnosed entity. Diagnosis and cause investigation is essential in improving the management of aspiration pneumonia. The Japanese Respiratory Society Guidelines for the Management of Pneumonia in Adults (JRS Guidelines) show a list of risk factors for aspiration pneumonia. We developed an algorithm to aid physicians in evaluating these possible underlying factors and guide their management with a focus on aspiration pneumonia. The algorithm was developed based on the JRS Guidelines. The algorithm suggested dysphagia screening, pneumococcal and influenza vaccination, and other preventative measures for pneumonia. The algorithm was implemented in the acute setting of a general hospital among older patients admitted with pneumonia. Their outcomes were compared with a historical control group constituting similar patients from the previous year. Forty patients with pneumonia were assessed with the algorithm group, and 44 patients were included in the control group. In the algorithm group, significantly more cases (95.0% vs. 15.9%, p < 0.01) underwent early screening for a swallowing disorder. Two patients in the algorithm group were diagnosed with a new condition causing aspiration pneumonia, as opposed to none in the control group. Drugs with a potential risk for aspiration were identified and discontinued in 27.5% of the patients in the algorithm group and 4.5% in the control group. In conclusion, an aspiration pneumonia cause investigation algorithm translating the JRS guideline approach into practice enhanced the rate of swallow screening and preventative measures for aspiration.
Differences in Rural Built Environment Perceptions Across Demographic and Social Environment Characteristics

The benefits of physical activity to health and obesity prevention are well established. However, attributes of the built environment influence participation in physical activity. The purpose of this study is to assess differences in perceptions of neighborhood walkability across demographic characteristics and social environment factors among rural residents. In a telephone survey, adult respondents (N = 448) across nine rural counties in a southeastern state answered questions about perceived neighborhood walkability, demographic characteristics, and their neighborhood social environment. Study recruitment for a convenience sample occurred through collaborations with local community organizations. Prevalence of destinations and barriers were estimated according to demographic and neighborhood social environment characteristics. Multiple logistic regression models assessed the association of demographic and neighborhood social environment characteristics with neighborhood walkability and calculated adjusted prevalence. Relaxing places to walk were the most often reported destinations (62.0%), followed by retail destinations (45.7%), and communal destinations (42.6%). Traffic was the most reported barrier to safe walking (40.4%), followed by animals (37.5%), and crime (30.5%). Perceptions of retail and communal destinations varied by age and race. Perceptions of traffic and crime as barriers varied by race, weight status, and income. Community belonging and social cohesion were associated with lower perceptions of barriers. Study findings present demographic characteristics and social environment attributes as key factors that shape perceived neighborhood walkability. Findings can help inform programmatic efforts and environmental change strategies to improve walking in rural areas.
The void galaxy survey: Star formation properties

We study the star formation properties of 59 void galaxies as part of the Void Galaxy Survey (VGS). Current star formation rates are derived from H alpha and recent star formation rates from near-UV imaging. In addition, infrared 3.4, 4.6, 12 and 22 mu m Wide field Infrared Survey Explorer emission is used as star formation and mass indicator. Infrared and optical colours show that the VGS sample displays a wide range of dust and metallicity properties. We combine these measurements with stellar and Hi masses to measure the specific SFRs (SFR/M,) and star formation efficiencies (SFR/M-HI). We compare the star formation properties of our sample with galaxies in the more moderate density regions of the cosmic web, 'the field'. We find that specific SFRs of the VGS galaxies as a function of stellar and HI mass are similar to those of the galaxies in these field regions. Their SFR alpha is slightly elevated than the galaxies in the field for a given total HI mass. In the global star formation picture presented by Kennicutt Schmidt, VGS galaxies fall into the regime of low average star formation and correspondingly low HI surface density. Their mean SFR alpha/M-HI and SFR alpha/M-star are of the order of 10(-9,9) yr(-1). We conclude that while the large-scale underdense environment must play some role in galaxy formation and growth through accretion, we find that even with respect to other galaxies in the more mildly underdense regions, the increase in star formation rate is only marginal.
Directional and Singular Surface Plasmon Generation in Chiral and Achiral Nanostructures Demonstrated by Leakage Radiation Microscopy

In this paper, we describe the implementation of leakage radiation microscopy to probe the chirality of plasmonic nanostructures. We demonstrate experimentally spin-driven directional coupling as well as vortex generation of surface plasmon polaritons (SPPs) by nanostructures built with T-shaped and Λ-shaped apertures. Using this far-field method, quantitative inspections, including directivity and extinction ratio measurements, are achieved via polarization analysis in both image and Fourier planes. To support our experimental findings, we develop an analytical model based on a multidipolar representation of Λ- and T-shaped aperture plasmonic couplers, allowing a theoretical explanation of both directionality and singular SPP formation. Furthermore, the roles of symmetry breaking and phases are emphasized in this work. This quantitative characterization of spin–orbit interactions paves the way for developing new directional couplers for subwavelength routing.
QED-based Optical Bloch Equations without electric dipole approximation: A model for a two-level atom interacting with a monochromatic X-ray laser beam

We derive a set of optical Bloch equations (OBEs) directly from the minimal-coupling Hamiltonian density of the bound-state quantum electrodynamics (bound-state QED). Such optical Bloch equations are beyond the former widely-used ones due to that there is no electric dipole approximation (EDA) on the minimal-coupling Hamiltonian density of the bound-state QED. Then our optical Bloch equations can describe a two-level atom interacting with a monochromatic light of arbitrary wavelength, which are suitable to study the spectroscopy and the Rabi oscillations of two-level atoms in X-ray laser beams since that the wavelength of X-ray is close to an atom to make the electric dipole approximation (EDA) invalid.
Comparison of global DNA methylation analysis by whole genome bisulfite sequencing and the Infinium Mouse Methylation BeadChip using fresh and fresh-frozen mouse epidermis

ABSTRACT Until recently, studying the murine methylome was restricted to sequencing-based methods. In this study we compared the global DNA methylation levels of hairless mouse epidermis using the recently released Infinium Mouse Methylation BeadChip from Illumina and whole genome bisulphite sequencing (WGBS). We also studied the effect of sample storage conditions by using fresh and fresh-frozen epidermis. The DNA methylation levels of 123,851 CpG sites covered by both the BeadChip and WGBS were compared. DNA methylation levels obtained with WGBS and the BeadChip were strongly correlated (Pearson correlation r = 0.984). We applied a threshold of 15 reads for the WGBS methylation analysis. Even at a threshold of 10 reads, we observed no substantial difference in DNA methylation levels compared with that obtained with the BeadChip. The DNA methylation levels from the fresh and the fresh-frozen samples were strongly correlated when analysed with both the BeadChip (r = 0.999) and WGBS (r = 0.994). We conclude that the two methods of analysis generally work equally well for studies of DNA methylation of mouse epidermis and find that fresh and fresh-frozen epidermis can generally be used equally well. The choice of method will depend on the specific study’s aims and the available resources in the laboratory.
What parents want in an autism diagnostic report: An interview-based study of parents accessing a neurodevelopmental assessment service

Diagnostic reports are a key outcome of autism assessment services. However, there is limited evidence regarding what key stakeholders, including families, want to see in reports. In this project, 30 parents whose young person had recently received a diagnosis of autism from a Neurodevelopmental Assessment Service in the North East of England took part in a telephone-based interview to explore what they want from a report. Interviews were analysed using thematic analysis. Ten key recommendations for reports were identified. Parents indicated that they want a detailed, balanced, sensitively written report. They highlighted that reports needed to be accessible and clearly structured. In this respect, it might be helpful to include a parent-driven summary of key points at the top, clear signposting of the structure of the report, and a description of what happened in the assessment process. Parents also valued practical, personalised recommendations based on the young person’s strengths and difficulties. Future research might explore perspectives on reports in families accessing other services, in other client groups (e.g., families of pre-schoolers diagnosed with autism), and with different stakeholders, including schools, referrers and autistic people.