Miracle-dz/UniFAR-FTUs huggingface dataset:
Biomarker Identification via a Factorization Machine-Based Neural Network With Binary Pairwise Encoding

Biomolecules, microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), play critical roles in diverse fundamental and vital biological processes. They can serve as disease biomarkers as their dysregulations could cause complex human diseases. Identifying those biomarkers is helpful with the diagnosis, treatment, prognosis, and prevention of diseases. In this study, we propose a factorization machine-based deep neural network with binary pairwise encoding, DFMbpe, to identify the disease-related biomarkers. First, to comprehensively consider the interdependence of features, a binary pairwise encoding method is designed to obtain the raw feature representations for each biomarker-disease pair. Second, the raw features are mapped into their corresponding embedding vectors. Then, the factorization machine is conducted to get the wide low-order feature interdependence, while the deep neural network is applied to obtain the deep high-order feature interdependence. Finally, two kinds of features are combined to get the final prediction results. Unlike other biomarker identification models, the binary pairwise encoding considers the interdependence of features even though they never appear in the same sample, and the DFMbpe architecture emphasizes both low-order and high-order feature interactions simultaneously. The experimental results show that DFMbpe greatly outperforms the state-of-the-art identification models on both cross-validation and independent dataset evaluation. Besides, three types of case studies further demonstrate the effectiveness of this model.
Simple cost‐effective larval injection method for dsRNA delivery to induce RNAi response in Helicoverpa armigera (Hübner)

Microinjection is considered as an effective method for dsRNA delivery in insects. It also facilitates the delivery of a precise quantity of dsRNA in the host insect, inducing an efficient RNAi response. However, the microinjection method needs prior optimization of several parameters like concentration of dsRNA, site of injection, developmental stage of insect etc. for inducing effective RNAi response. Moreover, sophisticated microinjection devices are largely expensive with high maintenance cost. The Old‐World bollworm, Helicoverpa armigera (Hübner) is known to be a detrimental polyphagous pest with widespread infestations across the globe. In the present study, we demonstrate a low‐cost and effective dsRNA delivery method for inducing RNAi response in H. armigera with the aid of basic insulin injection syringe and fabricated micropipette tip. In order to validate the RNAi response following dsRNA injection, we have selected three key genes from the chitin biosynthesis pathway of the insect. Besides these, argonaute 1 (ago1) was also used as an indicator gene for dsRNA‐mediated RNAi induction. Delivery of dsRNA using injection with insulin syringe caused significant upregulation of the ago1 gene in the insect irrespective of any of the three target genes concerned viz. HaNAGK (3.9 fold; p < 0.001), HaAGM (6.3 fold; p < 0.001) and HaUAP (5.9 fold; p < 0.01) respectively, as compared to control injected with nuclease‐free water. The dsRNA‐injected insects showed aberrant developmental symptoms typical of impeded chitin synthesis, eventually leading to anomalous ecdysis with substantial mortality (up to 69.04%), as compared to controls. The described protocol reduces insect injury, enabling easy restraining of larva and quick execution of dsRNA injection with efficient RNAi response.
SwaGrader: A Honest Effort Extracting, Modular Peer-Grading Tool

Massive open online courses pose a massive challenge for grading the answer scripts at a high accuracy. Peer grading is often viewed as a scalable solution to this challenge, which largely depends on the altruism of the peer graders. In this paper, we propose to demonstrate a tool designed for strategic peer-grading with the help of a structured and typical grading workflow. SwaGrader, a modular, secure and customizable (to any grading workflow) peer-grading tool enables the instructor to handle large courses (MOOCs and offline) with limited participation by teaching staff via a web-based application (extensible to any front-end framework based application) and a mechanism called TRUPEQA[1]. TRUPEQA (a) uses a constant number of instructor-graded answer-scripts to quantitatively measure the accuracies of the peer graders and corrects the scores accordingly, and (b) penalizes deliberate under-performing. We show that this mechanism is unique in its class to satisfy certain properties. Our human subject experiments show that TRUPEQA improves the grading quality over the mechanisms currently used in standard MOOCs. Our mechanism outperforms several standard peer grading techniques used in practice, even at times when the graders are non-manipulative.
On a Bivariate Pólya-Aeppli Distribution

In this article, we use the bivariate Poisson distribution obtained by the trivariate reduction method and compound it with a geometric distribution to derive a bivariate Pólya-Aeppli distribution. We then discuss a number of properties of this distribution including the probability generating function, correlation structure, probability mass function, recursive relations, and conditional distributions. The generating function of the tail probabilities is also obtained. Moment estimation of the parameters is then discussed and illustrated with a numerical example.
Converting Hybrid Potato Breeding Science into Practice

Research on diploid hybrid potato has made fast advances in recent years. In this review we give an overview of the most recent and relevant research outcomes. We define different components needed for a complete hybrid program: inbred line development, hybrid evaluation, cropping systems and variety registration. For each of these components the important research results are discussed and the outcomes and issues that merit further study are identified. We connect fundamental and applied research to application in a breeding program, based on the experiences at the breeding company Solynta. In the concluding remarks, we set hybrid breeding in a societal perspective, and we identify bottlenecks that need to be overcome to allow successful adoption of hybrid potato.
Design, Construction and Control of a Manipulator Driven by Pneumatic Artificial Muscles

This paper describes the design, construction and experimental testing of a single-joint manipulator arm actuated by pneumatic artificial muscles (PAMs) for the tasks of transporting and sorting work pieces. An antagonistic muscle pair is used in a rotational sense to produce a required torque on a pulley. The concept, operating principle and elementary properties of pneumatic muscle actuators are explained. Different conceptions of the system realizations are analyzed using the morphological-matrix conceptual design framework and top-rated solution was practically realized. A simplified, control-oriented mathematical model of the manipulator arm driven by PAMs and controlled with a proportional control valve is derived. The model is then used for a controller design process. Fluidic muscles have great potential for industrial applications and assembly automation to actuate new types of robots and manipulators. Their characteristics, such as compactness, high strength, high power-to-weight ratio, inherent safety and simplicity, are worthy features for advanced manipulation systems. The experiments were carried out on a practically realized manipulator actuated by a pair of muscle actuators set into an antagonistic configuration. The setup also includes an original solution for the subsystem to add work pieces in the working space of the manipulator.
Investigation of polarization-pinning mechanism in deep-line-etched vertical-cavity surface-emitting lasers

Recently, it has been shown that the etching of deep trenches in close proximity to GaAs vertical-cavity surface-emitting laser (VCSEL) apertures causes the linearly polarized TE emission to be pinned in a direction parallel to the line etch. In this letter, we show that etching introduces compressive strain or relaxes tensile strain through the creation of free interfaces. An anisotropic variation of strain is the origin of the polarization pinning effect. We report on the enhancement of polarization pinning by postannealing after etching. Photoluminescence and Raman measurements of the VCSEL wafer were taken before and after etching and annealing. The observed shift in the Fabry–Perot mode was used to model the strain, giving 4×108 dyn/cm2, or 0.05%, compressive strain perpendicular to the etch.
Pretile angle control of liquid crystal from homogeneous to homeotropic using photocurable prepolymer

We study pretilt angle control of liquid crystal from homogeneous to homeotropic using phase separation techniques of photocurable prepolymer by UV irradiation. Pretilt angle was controlled by changing the weight ratio of LC/photocurable prepolymer in homogeneous polyimide (PI) coated LC cell. Homogeneous alignment was observed in LC/photocurable prepolymer mixture of weight ratio of 99.9:0.1 after UV irradiation for 20 minutes. Tilted alignment was observed in weight ratio of 99.8:0.2. Finally homeotropic alignment was observed in weight ratio of over 99.7:0.3.
Reconciling float-based and tracer-based estimates of lateral diffusivities

Lateral diffusivities are computed from synthetic particles and tracers advected by a velocity field derived from sea-surface height measurements from the South Pacific, in a region west of Drake Passage. Three different estimates are compared: (1) the tracer-based "effective diffusivity" of Nakamura (1996), (2) the growth of the second moment of a cloud of tracer and (3) the single- and two-particle Lagrangian diffusivities. The effective diffusivity measures the cross-stream component of eddy mixing, so this article focuses on the meridional diffusivities for the others, as the mean flow (the ACC) is zonally oriented in the region. After an initial transient of a few weeks, the effective diffusivity agrees well with the meridional diffusivity estimated both from the tracer cloud and from the particles. This proves that particleand tracer-based estimates of eddy diffusivities are equivalent, despite recent claims to the contrary. Convergence among the three estimates requires that the Lagrangian diffusivities be estimated using their asymptotic values, not their maximum values. The former are generally much lower than the latter in the presence of a mean flow. Sampling the long-time asymptotic behavior of Lagrangian diffusivities requires very large numbers of floats in field campaigns. For example, it is shown that hundreds of floats would be necessary to estimate the vertical and horizontal variations in eddy diffusivity in a sector of the Pacific Southern Ocean.
State-transition-matrix optimization for reconfiguration manoeuvres of formation-flying satellites

The on-orbit reconfiguration of a pair of formation-flying satellites in low Earth orbit is studied in the presence of J2–J6 gravitational perturbations. A methodology for determining a robust and accurate impulsive thrusting scheme is developed with the aim of minimizing reconfiguration overshoot errors and fuel expenditure (Δ V). The method uses a state transition matrix based on the Hill–Clohessy–Wiltshire linear equations of relative motion and the analytical solution to the state-space model to solve for a pair of impulsive thrusts. The manoeuvre is then propagated through a fully nonlinear orbital simulator with the thrusts implemented non-impulsively. A Sequential Quadratic Programming optimizer adjusts the inputs to the linear state transition matrix to produce impulses that, when applied in the high-fidelity orbital propagator, mitigates the Δ V of the manoeuvre while maintaining acceptable overshoot errors.
Seismic Performance Assessment of Low-Rise Unreinforced and Confined Brick Masonry School Buildings Using the Applied Element Method

Masonry buildings are generally vulnerable to seismic action, as evidenced extensively in past earthquakes. In order to improve their seismic performance, several modifications have been introduced, such as reinforcing or confining the masonry. This paper presents a seismic analysis and fragility assessment procedure for non-engineered masonry building typologies, employing the applied element method (AEM). Compared to buildings with stiff diaphragms, the conventional pushover-based procedure is challenging for the seismic assessment of masonry buildings with flexible diaphragms, due to the lack of a global box-like behaviour. This study first presents a novel and validated method for nonlinear pushover analysis, independent of the type of diaphragm action on the building, by applying incremental ground acceleration and by considering suitable engineering demand parameters for the assessment of lateral capacity. Based on the failure mechanisms, a seismic performance assessment and fragility evaluation approach is then proposed, for reliable accounting of both the in-plane and out-of-plane failure modes. Finally, the proposed methodology is applied to a number of unreinforced and confined masonry school buildings with different seismic detailing levels, as often found in the Himalayan belt and beyond.
Chylous Ascites After Gastric Cancer Surgery: Risk Factors and Treatment Results

Purpose Although chylous ascites is a frequent complication of radical gastrectomy for gastric cancer, proper diagnostic criteria and optimal treatment strategies have not been established. This study aimed to identify the clinical features of chylous ascites and evaluate the treatment outcomes. Materials and Methods We retrospectively analyzed the data of patients who underwent radical gastrectomy between 2013 and 2019. Diagnosis was made when milky fluid or elevated triglyceride levels (≥100 mg/dL) appeared in the drains without a preceding infection. The clinical features, risk factors, and treatment outcomes were assessed according to the initial treatment modalities for fasting and non-fasting groups. Results Among the 7,388 patients who underwent radical gastrectomy for gastric cancer, 156 (2.1%) experienced chylous ascites. The median length of hospital stay was longer in patients with chylous ascites than in those without (median [interquartile range]: 8.0 [6.0–12.0] vs. 6.0 [5.0–8.0], P<0.001). Low body mass index (adjusted odds ratio [aOR]=0.9; P<0.001), advanced gastric cancer (aOR=1.51, P=0.024), open surgery (reference: laparoscopic surgery; aOR=1.87, P=0.003), and extent of surgical resection (reference: subtotal gastrectomy, total gastrectomy, aOR=1.5, P=0.029; proximal gastrectomy, aOR=2.93, P=0.002) were associated with the occurrence of chylous ascites. The fasting group (n=12) was hospitalized for a longer period than the non-fasting group (n=144) (15.0 [12.5–19.5] vs. 8.0 [6.0–10.0], P<0.001). There was no difference in grade III complication rate (16.7% vs. 4.2%, P=0.117) or readmission rate (16.7% vs. 11.1%, P=0.632) between the groups. Conclusions A fat-controlled diet and medication without fasting provided adequate initial treatment for chylous ascites after radical gastrectomy for gastric cancer.
Comparative Analysis of Rote Learning on High and Low Achievers in Graduate and Undergraduate Programs

A survey was conducted to study the preferred learning strategies; that is, surface learning or deep learning of undergraduate and graduate male and female students and the impact of the preferred strategy on their academic performance. Both learning strategies help university students to get good scores in their examinations to meet the demands of industry in workforce. Quantitative research method was used to determine the impact of learning strategy on academic achievements. The R-SPQ2F questionnaire was sent to 103 students through Google forms and hard copies through snowball sampling technique. The results show that rote learning and academic performance are inversely related to each other. In high achievers, deep learning is significant as compared to low achievers. Furthermore, comparative analysis of learning styles on males and females showed that both preferred deep learning strategy equally. Learning strategy is not related to education level of students because there is no difference among preferred learning strategies of graduate and undergraduate students.
Self-Adaptive Fault Feature Extraction of Rolling Bearings Based on Enhancing Mode Characteristic of Complete Ensemble Empirical Mode Decomposition with Adaptive Noise

Originally, a rolling bearing, as a key part in rotating machinery, is a cyclic symmetric structure. When a fault occurs, it disrupts the symmetry and influences the normal operation of the rolling bearing. To accurately identify faults of rolling bearing, a novel method is proposed, which is based enhancing the mode characteristics of complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN). It includes two parts: the first is the enhancing decomposition of CEEMDAN algorithm, and the second is the identified method of intrinsic information mode (IIM) of vibration signal. For the first part, the new mode functions (CIMFs) are obtained by combing the adjacent intrinsic mode functions (IMFs) and performing the corresponding Fast Fourier Transform (FFT) to strengthen difference feature among IMFs. Then, probability density function (PDF) is used to estimate FFT of each CIMF to obtain overall information of frequency component. Finally, the final intrinsic mode functions (FIMFs) are obtained by proposing identified method of adjacent PDF based on geometrical similarity (modified Hausdorff distance (MHD)). FIMFs indicate the minimum amount of mode information with physical meanings and avoid interference of spurious mode in original CEEMDAN decomposing. Subsequently, comprehensive evaluate index (Kurtosis and de-trended fluctuation analysis (DFA)) is proposed to identify IIM in FIMFs. Experiment results indicate that the proposed method demonstrates superior performance and can accurately extract characteristic frequencies of rolling bearing.
The influence of an MgO nanolayer on the planar Hall effect in NiFe films

The Planar Hall Effect (PHE) in NiFe films was studied using MgO as the buffer and capping layer to reduce the shunt effect. The thermal annealing was found to be effective in increasing the sensitivity. The sensitivity of the magnetic field reached as high as 865 V/AT in a MgO (3 nm)/NiFe (5 nm)/MgO(3 nm)/Ta(3 nm) structure after annealing at 500 °C for 2 h, which is close to the sensitivity of semiconductor Hall Effect (HE) sensors. X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD) and high-resolution transmission electron microscopy (HRTEM) were used to study the sample. The results show that the top crystallization of MgO and NiFe (111) texture were improved by proper annealing. The smooth and clear bottom MgO/NiFe and top NiFe/MgO interface is evident from our data. In addition, the shunt current of Ta was decreased. These combined factors facilitate the improvement of the sensitivity of the magnetic field.
Thermo-chemo-mechanics of ASR expansion in concrete structures

The critical nature of the alkali-silica reaction (ASR) on premature concrete deterioration requires the quantitative assessment, in time and space, of the chemomechanical impact of ASR expansion on the dimensional stability of concrete structures. In particular, the coupled problem of heat diffusion and ASR kinetics can be critical, as the ASR is a thermoactivated chemical reaction. The quantitative analysis of these coupled effects on both material and structural level is the main objective of this paper. Starting from the governing micromechanisms of ASR expansions, a chemoelastic model is developed that accounts for ASR kinetics and the swelling pressure exerted by the ASR reaction products on the skeleton. This chemoelastic model is a first-order engineering approach to capture timescale and magnitude of ASR expansion. It is shown that the realistic prediction of ASR structural effects requires the consideration of two timescales: (1) a latency time associated with the dissolution of reactive silica; and (2) a characteristic time associated with the ASR product formation. In addition, a dimensional analysis of the governing equations reveals that the ASR deterioration of “massive” concrete structures is driven by the simultaneous activation of heat diffusion and reaction kinetics within a surface layer defined by a characteristic ASR heat diffusion length. In turn, in “slender” structures, it is the simultaneous activation of moisture diffusion and ASR kinetics that drives the surface layer delamination. This is illustrated through finite-element case studies of ASR effects in structures of different dimensions: a concrete gravity dam and a bridge box girder.
Signal Amplification by the trans-Cleavage Activity of CRISPR-Cas Systems: Kinetics and Performance

ACCESS Metrics & More Article Recommendations ■ CONTENTS Functional Basics of Cas12 and Cas13 208 Nuclease Activity of Cas12a 208 Nuclease Activity of Cas13a 208 Quantitative Determination of trans-Cleavage Kinetics of Cas Enzymes 209 trans-Cleavage Kinetics of Cas12 and Cas13 212 trans-Cleavage Kinetics of Cas12 and Its Contributing Factors 212 trans-Cleavage Kinetics of Cas13 and Its Contributing Factors 212 Nucleic Acid Detection Sensitivity Achieved by trans-Cleavage Activity of Cas Enzymes 213 Relations between the trans-Cleavage Kinetics and the Limit of Detection 213 Prediction of Performance Aided by Machine Learning 214 Challenges of trans-Cleavage and Signal Amplification in Live Cells 214 Concluding Remarks and Perspectives 214 Author Information 215 Corresponding Author 215 Authors 215 Notes 215 Biographies 215 Acknowledgments 215 References 216
Generalization of Einstein's principle of equivalence so as to embrace the field equations of gravitation.

It is shown that the apparent impossibility of deriving Einstein's field equations of gravitation in a way similar to that used by him in deriving the equations of particle motion and electromagnetism–being a direct generalization of his famous imaginary experiment of a box falling freely in a gravitational field–may be overcome by using the quantal vacuum with its fluctuations instead of the vacuum of ordinary physics with its absolute emptiness. Thus, the Dirac equation with gravitation, thereby used, appears, in contrast to the ordinary view, as the prototype of interaction theory based on general principles, one of them being a generalized principle of equivalence.
The Cosmic Microwave Background Quadrupole in a Polarized Light

The low quadrupole of the cosmic microwave background (CMB), measured by the Cosmic Background Explorer (COBE) and confirmed by the Wilkinson Microwave Anisotropy Probe (WMAP), has generated much discussion recently. We point out that the well-known correlation between temperature and polarization anisotropies of the CMB further constrains the low-multipole anisotropy data. This correlation originates from the fact that the low-multipole polarization signal is sourced by the CMB quadrupole as seen by free electrons during the relatively recent cosmic history. Consequently, the large-angle temperature anisotropy data make restrictive predictions for the large-angle polarization anisotropy, which depend primarily on the optical depth for electron scattering after cosmological recombination, τ. We show that if current cosmological models for the generation of large-angle anisotropy are correct and the COBE/WMAP data are not significantly contaminated by non-CMB signals, then the observed C amplitude on the largest scales is discrepant at the ~99.8% level with the observed C for the concordant ΛCDM model with τ = 0.10. Using τ = 0.17, the preferred WMAP model-independent value, the discrepancy is at the level of 98.5%.