Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of incomplete multiple diagnostic tests, with an application in the colon cancer family registry study

Accurate diagnosis of a molecularly defined subtype of cancer is often an important step toward its effective control and treatment. For the diagnosis of some subtypes of a cancer, a gold standard with perfect sensitivity and specificity may be unavailable. In those scenarios, tumor subtype status is commonly measured by multiple imperfect diagnostic markers. Additionally, in many such studies, some subjects are only measured by a subset of diagnostic tests and the missing probabilities may depend on the unknown disease status. In this paper, we present statistical methods based on the EM algorithm to evaluate incomplete multiple imperfect diagnostic tests under a missing at random assumption and one missing not at random scenario. We apply the proposed methods to a real data set from the National Cancer Institute (NCI) colon cancer family registry on diagnosing microsatellite instability for hereditary non-polyposis colorectal cancer to estimate diagnostic accuracy parameters (i.e. sensitivities and specificities), prevalence, and potential differential missing probabilities for 11 biomarker tests. Simulations are also conducted to evaluate the small-sample performance of our methods.
Effective permittivity of composites with stratified particles

The effective electromagnetic, thermal and mechanical properties of heterogeneous media are commonly related to composition. Stratified composites are entities that are important in physics and engineering and are a class of compounds actively investigated for their dielectric properties. Such systems consist of composite inclusions of multicomponent materials embedded in a matrix of a distinct material. The effects of the volume fraction, permittivity and thickness of the various constituents on the complex effective permittivity of the heterostructures, in the quasistatic approximation, are reported. We use an exact numerical technique for the evaluation of the dielectric characteristics of three-component composites, arranged in a regular simple cubic lattice, which is based on the field calculation package PHI3D and a boundary integral equations solution scheme of Laplace's equation. `Exact' means that the correct properties are computed for the given microstructure and choice of individual component properties because all internal electric multipole interactions contributing to the polarization of the material medium are taken into account. The predictions of the Steeman and Maurer (dipolar) theory (Steeman P A M and Maurer F H J 1992 Colloid Polym. Sci. 270 1069) are compared with our numerical results where appropriate. An important feature, suggested by the results presented for stratified spheres and spheroids, is that any approach based solely on the dipole approximation must fail to predict the effective permittivity of dielectric heterostructures over the entire range of volume fraction of inclusions. The results discussed give motivation for the development of careful experiments which can be used to test the numerical simulations and to fabricate synthetic composite materials in which new electromagnetic properties can be obtained from the combination of several materials.
Metal-enhanced fluorescence from copper substrates

In this letter, the authors report the observation of metal-enhanced fluorescence emission from fluorophores deposited on copper (Cu) substrates. Different thicknesses of Cu particulate films (from 1 to 5nm) were deposited onto glass slides using thermal vapor deposition. Fluorophores positioned in close proximity to the Cu films show fluorescence enhancement as a function of the Cu thickness increases, reaching a maximum (2.5-fold) at ≈3nm. The findings strongly suggest that surface plasmons from Cu can radiate and therefore enhance a fluorophore’s spectral properties, similar to observations reported for both silver and gold nanoparticle deposited substrates.
Analysis and Optimal Design of Spherical Shells Under Axisymmetric Loads

In a companion paper the integral equations for a spherical shell have been developed. This paper is concerned with the engineering applications of the integral equation method. A structure is selected to demonstrate how to apply the method in shell analysis. Two different types of construction are used for the shell: one has constant thickness, the other, piecewise linearly varying thickness. The solutions so obtained are compared with the corresponding ones found by the finite element method. They are also compared against the theoretical solutions whenever possible. A good agreement is attained. The aforementioned shell is also subjected to optimal design. An exterior penalty function method is selected to minimize the weight of the shell with stress and displacement constraints. The integral equation method is used in the analytical phase. Acceptable results are obtained.
Site-Specific Antibody Conjugation with Payloads beyond Cytotoxins

As antibody–drug conjugates have become a very important modality for cancer therapy, many site-specific conjugation approaches have been developed for generating homogenous molecules. The selective antibody coupling is achieved through antibody engineering by introducing specific amino acid or unnatural amino acid residues, peptides, and glycans. In addition to the use of synthetic cytotoxins, these novel methods have been applied for the conjugation of other payloads, including non-cytotoxic compounds, proteins/peptides, glycans, lipids, and nucleic acids. The non-cytotoxic compounds include polyethylene glycol, antibiotics, protein degraders (PROTAC and LYTAC), immunomodulating agents, enzyme inhibitors and protein ligands. Different small proteins or peptides have been selectively conjugated through unnatural amino acid using click chemistry, engineered C-terminal formylglycine for oxime or click chemistry, or specific ligation or transpeptidation with or without enzymes. Although the antibody protamine peptide fusions have been extensively used for siRNA coupling during early studies, direct conjugations through engineered cysteine or lysine residues have been demonstrated later. These site-specific antibody conjugates containing these payloads other than cytotoxic compounds can be used in proof-of-concept studies and in developing new therapeutics for unmet medical needs.
Accelerating Point-Voxel Representation of 3-D Object Detection for Automatic Driving

Current point-voxel fusion methods for 3-D object detection could not make full use of complementary information in the field of autonomous driving. Therefore, a novel two-stage 3-D object detection method, called accelerating point-voxel representation (APVR), is proposed. The advantages of point-based feature and voxel-based feature can be integrated into a single 3-D representation. Thereby, the proposed method retains more fine-grained information of an object while maintaining high efficiency. Specifically, the computational cost is reduced by adding offsets to query neighboring voxels of key-points. More fine-grained information can be obtained by calculating the matching probability between neighboring voxels and key-points. During the optimization of the prediction boxes, virtual grid points are set to capture the spatial information between key-points. The constraint of minimum enclosing rectangle is also added to optimize the directions of the prediction boxes. A large number of experiments on the KITTI, NuScenes, and Waymo datasets demonstrate great generalizability and portability of the proposed approach. The effectiveness and efficiency of APVR have been proved by comparisons with the state-of-the-art methods. APVR makes the real-time processing frame rate reach 40.4 Hz while ensuring high prediction accuracy.
The genome sequence of an erect bryozoan, Bugulina stolonifera (Ryland, 1960)

We present a genome assembly from a Bugulina stolonifera colony (an erect bryozoan; Bryozoa; Gymnolaemata; Cheilostomatida; Bugulidae). The genome sequence is 235 megabases in span. Most of the assembly (99.85%) is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial genome was also assembled and is 14.4 kilobases long.
Ultra-low loss hollow-core photonic crystal fibers at 589 nm for LGS-assisted AO

We are developing a hollow-core photonic crystal fiber to be used as a beam relay in pulsed sodium laser guide star systems with a target maximum attenuation of 30 dB/km, 20 dB/km as goal. In order to optimize the fiber geometry, we numerically model the light propagation using a finite-element solver that allows us to simultaneously optimize several structural parameters.
The thermodynamics of melting of simple substances

A review of the results of real and numerical experiments characterizing the thermodynamics of the melting of simple substances is given. With the examples of argon and sodium it is demonstrated that the qualitative trends in the behavior of the thermodynamic quantities along the melting curve are independent of the form of the interaction forces. The question of the form of the characteristic energy determining the melting or crystallization of a substance is analyzed. It is concluded that melting is the most general example of an order-disorder transition in coordinate space. The question of the nature of maxima in melting curves is discussed. The empirical relations of Lindemann and Simon are considered.
Forest-Fire-Risk Prediction Based on Random Forest and Backpropagation Neural Network of Heihe Area in Heilongjiang Province, China

Forest fires are important factors that influence and restrict the development of forest ecosystems. In this paper, forest-fire-risk prediction was studied based on random forest (RF) and backpropagation neural network (BPNN) algorithms. The Heihe area of Heilongjiang Province is one of the key forest areas and forest-fire-prone areas in China. Based on daily historical forest-fire data from 1995 to 2015, daily meteorological data, topographic data and basic geographic information data, the main forest-fire driving factors were first analyzed by using RF importance characteristic evaluation and logistic stepwise regression. Then, the prediction models were established by using the two machine learning methods. Furthermore, the goodness of fit of the models was tested using the receiver operating characteristic test method. Finally, the fire-risk grades were divided by applying the kriging method. The results showed that 11 driving factors were significantly correlated with forest-fire occurrence, and days after the last rain, daily average relative humidity, daily maximum temperature, daily average water vapor pressure, daily minimum relative humidity and distance to settlement had a high correlation with the risk of forest-fire occurrence. The prediction accuracy of the two algorithms in regard to fire points was higher than that for nonfire points. The overall prediction accuracy and goodness of fit of the RF and BPNN algorithms were similar. The two methods were both suitable for forest-fire occurrence prediction. The high-fire-risk zones were mainly concentrated in the northwestern and central parts of the Heihe area.
Nernst effect in laser‐produced plasmas

A transverse magnetic field B is found to be convected by the electron heat flux qe because of the Nernst effect, i.e., with a velocity VT(∼2qe/3neTe). The mechanism is clarified by the two‐electron‐fluid model. In laser‐driven ablation the convection is toward the overdense region and B can be amplified by 10–100 times because ∇ ⋅ VT c/ωpe.
Propagation of light pulses in a laser amplifier

The problem of a light pulse propagating in a nonlinear laser medium is investigated. The electromagnetic field is treated classically and the active medium consists of thermally moving atoms which have two electronic states with independent decay constants ${\ensuremath{\gamma}}_{a}$ and ${\ensuremath{\gamma}}_{b}$ in addition to the decay constant ${\ensuremath{\gamma}}_{\mathrm{ab}}$ describing the phase memory. The self-consistency requirement that the field sustained by the polarized medium be equal to the field inducing the polarization leads to coupled equations of motion for the density matrix, and equations of propagation for the electromagnetic field. Although the theory is developed for a Doppler-broadened gaseous medium, it may also be applied to a solid medium with inhomogeneous broadening. A unified treatment is given encompassing a wide range of pulse durations from cw signals to psec pulses. Continuous pumping is allowed, as well as any amount of detuning of the carrier frequency of the pulse from the atomic resonance frequency. The three independent decay constants ${\ensuremath{\gamma}}_{a}$, ${\ensuremath{\gamma}}_{b}$, and ${\ensuremath{\gamma}}_{\mathrm{ab}}$ provide greater flexibility than that obtained by using $\frac{1}{{T}_{1}}$ and $\frac{1}{{T}_{2}}$. The equations are solved analytically in a few specialized cases and numerically in the general case. Flow charts for accomplishing the numerical integration are given. Among the special problems considered is the apparent paradox of pulses propagating faster than the velocity of light under circumstances described by Basov et al. It is shown that this contradiction with relativity arises from the use of an unphysical initial condition.
On the integral constraint of the pressure Poisson equation for incompressible flows

We illustrate, using analytical and numerical proofs, how a conservative discretisation of the pressure Poisson equation arising out of the discretisation of the incompressible Navier–Stokes equations (on a two-dimensional unstructured non-staggered grid) satisfies the integral constraint on the pressure boundary condition without any additional treatment. When discretised in a non-conservative manner, it is seen that the integral constraint is not exactly satisfied, but only to an order , where is an appropriate velocity scale. When solved using an iterative method, such as the Bi-Conjugate Stabilised method, it is proved that the vanishing sum of residuals on all points inclusive of the boundary is a consequence of this integral constraint. This result can then be used as a tool to identify whether the discrete integral constraint has been satisfied or not, especially when the pressure is solved as a Neumann problem.
Quasi-Optical Mode Converter Based on All-Dielectric Metamaterial for High-Order Mode Vacuum Electronics Devices

All-dielectric metamaterials (ADMs) have recently attracted much attention due to their ability to achieve wavefront control with high power capability. In this article, an investigation on quasi-optical mode converter (QOC) based on ADM for high-order vacuum electronics devices (VEDs) is presented. Specifically, four ADM QOCs are designed to convert the cylindrical waveguide TE01, TE21, TE31, and TM01 modes into linear polarized Gaussian beams at 35 GHz. Electromagnetic simulations show that the Gaussian mode contents of the output waves from four mode converters are all over 94% with high polarization contents. Furthermore, a Ka-band ADM mode converter with the input mode of circular waveguide TE01 mode is fabricated and measured. Experimental results show that the output fields with scalar Gaussian content over 90% can be obtained at 30–38.85 GHz, corresponding to a relative bandwidth of 25.3% around 35 GHz. The maximum scalar Gaussian mode content of 99.18% is observed at 34.56 GHz in the experiment. The investigation opens new avenues toward high-order mode conversion technology based on ADM.
The parameters of atmospheric turbidity

The methods for evaluating the atmospheric turbidity parameters, introduced by the present author in 1929–30, are subjected to a critical examination. A method first suggested by M. Herovanu (1959) is here simplified and expanded, and used for deriving the named parameters in adherence to a procedure described by the present author in a previous paper in this journal (1961). The procedure is applied to the pyrheliometric observations at Potsdam in 1932–36, published by Hoelper (1939) A comparison between the frequency distribution of the coefficient of wave-length dependence α at the high level station Davos and the low level station Potsdam gives results which are discussed in detail. In all the figures of the present paper, where the turbidity coefficients occur, they are multiplied by 10 3 . DOI: 10.1111/j.2153-3490.1964. tb00144.x
Population distribution, aggregation sites and seasonal occurrence of Australia’s western population of the grey nurse shark Carcharias taurus

: Western Australia (WA) is host to a genetically discrete population of grey nurse sharks Carcharias taurus , listed by the IUCN as Near Threatened based on mean annual catch rates prior to protection within Australian waters in 1997. Only one small aggregation has been documented in WA to date with little data available on population dynamics, or spatial and temporal distribution along the WA coastline. We analysed C. taurus data from 16 years (2006−2021) of diver observations (2347 sightings) and commercial fisheries bycatch records (574 sharks), finding evidence of 4 new aggregation sites. Sightings at Shark Cave, a popular dive site near Perth, were related to water temperature and time of year (non-linear), with sightings per unit effort generally higher during the warmer months of summer and autumn (20−22°C). Evidence of fishing injuries was found on 17% of all C. taurus photo-tagged at Shark Cave. Strong site philopatry was apparent at most sites, and included a male shark that returned for 12 consecutive years to the Exmouth Navy Pier. This study confirms the range of Australia’s western population of C. tau-rus from near the South Australia/WA border, north to Shark Bay, with distribution ex tending further north along the coast when sea temperatures are lower (May−December). The beneficial role of citizen science in large observation studies such as this one is supported. However, while this research greatly increases the C. taurus knowledge base in WA, a large information deficit still exists. The identification and assessment of further aggregation sites is recommended, underpinning future management and protection measures for this iconic species.
Recent Advances in Yttrium Iron Garnet Films: Methodologies, Characterization, Properties, Applications, and Bibliometric Analysis for Future Research Directions

Due to recent advances in communication systems, dielectric and magnetic ceramics (ferrites) are attractive for use in devices. Spinel-type ferrites were the first material utilized in microwave devices; however, yttrium iron garnet (YIG) has low dielectric losses and is exploited in many applications. Owing to its high Faraday rotation, YIG films are utilized in magneto-optical applications. This study intends to examine the research trends and scientific research progress on highly cited papers discussing YIG films published between 2012 and 2022 using a bibliometric method. A comprehensive review of 100 scientific papers about YIG was performed from the Scopus database. The assessment of these highly cited papers was highlighted based on the following factors: publication trends and performance, limitations/research gaps, keywords, sub-fields, methodology journal evaluations, document type evaluation, issues, difficulties, solutions, and applications as well as guiding future YIG research. The majority of publications (99%) comprise experimental analysis, whereas 1% provide a based state-of-the-art overview. Ninety-one percent of articles focused on magnetization characterization. This bibliometric survey indicates that YIG film research is an expanding and developing field. The results of the data analysis can be utilized to improve the researchers’ understanding of YIG research and to encourage additional study in this area.
The evolution of small‐scale structures in homogeneous isotropic turbulence

Using direct numerical simulations of homogeneous isotropic turbulence, the temporal evolution of small‐scale vorticity and passive scalar structures has been examined. Visualization of small‐scale vorticity structures indicates a process where vortex sheets may roll up into intense vortex tubes through a Kelvin–Helmholtz‐type instability. The ability of these vortex structures to mix a passive scalar has also been examined. The regions of intense scalar gradient form sheets which are found to occur in regions of persistent straining flow, such as between neighboring vortex structures of approximately equal circulation. The magnitude of vorticity of these structures is usually not large, as persistent straining is most commonly found in connection with regions of moderate vorticity. Scalar gradient sheets are also found between low intensity regions of antiparallel vorticity, which are also observed to produce persistent straining.
Image enhancement of restored motion blurred images

Motion blurred images could be restored by Super-Resolution arithmetic which took the angle calculated by Radon transformation of the spectrum of original images and the extent calculated by autocorrelation as parameters necessarily even though the blur of images was very severity. Unfortunately the noise of blurred images would be amplified while we captured useful information, which influenced the observation of restored images seriously. An enhancement arithmetic was proposed in this discourse to improve the quality of the low signal-noise ratio images obtained through restoration arithmetic. The main purpose of the arithmetic was to eliminate unwanted noises and remain desired signals. The arithmetic was based on the principle of the least square error method, which fitted discrete pixels to continuous piecewise curves. The interval of each row and column was subdivided into several subintervals to predigest the fitting of pixels. Then a curve was used to fit the pixels within the subinterval. A weighting technique with a linear weighting factor was proposed to merge two adjacent lines together. A series of experiments were carried out to research the effects of the arithmetic, and the signal-noise ratio showed that the proposed arithmetic could achieve high quality enhancement images.
Development of a high-speed real-time PCR system for rapid and precise nucleotide recognition

Polymerase chain reaction (PCR) is a common method used to create copies of a specific target region of a DNA sequence and to produce large quantities of DNA. A few DNA molecules, which act as templates, are rapidly amplified by PCR into many billions of copies. PCR is a key technology in genome-based biological analysis, revolutionizing many life science fields such as medical diagnostics, food safety monitoring, and countermeasures against bioterrorism. Thus, many applications have been developed with the thermal cycling. For these PCR applications, one of the most important key factors is reduction in the data acquisition time. To reduce the acquisition time, it is necessary to decrease the temperature transition time between the high and low ends as much as possible. We have developed a novel rapid real-time PCR system based on rapid exchange of media maintained at different temperatures. This system consists of two thermal reservoirs and a reaction chamber for PCR observation. The temperature transition was achieved within 0.3 sec, and good thermal stability was achieved during thermal cycling with rapid exchange of circulating media. This system allows rigorous optimization of the temperatures required for each stage of the PCR processes. Resulting amplicons were confirmed by electrophoresis. Using the system, rapid DNA amplification was accomplished within 3.5 min, including initial heating and complete 50 PCR cycles. It clearly shows that the device could allow us faster temperature switching than the conventional conduction-based heating systems based on Peltier heating/cooling.