Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-wide identification and characterization of DNA enhancers with a stacked multivariate fusion framework

Enhancers are short non-coding DNA sequences outside of the target promoter regions that can be bound by specific proteins to increase a gene’s transcriptional activity, which has a crucial role in the spatiotemporal and quantitative regulation of gene expression. However, enhancers do not have a specific sequence motifs or structures, and their scattered distribution in the genome makes the identification of enhancers from human cell lines particularly challenging. Here we present a novel, stacked multivariate fusion framework called SMFM, which enables a comprehensive identification and analysis of enhancers from regulatory DNA sequences as well as their interpretation. Specifically, to characterize the hierarchical relationships of enhancer sequences, multi-source biological information and dynamic semantic information are fused to represent regulatory DNA enhancer sequences. Then, we implement a deep learning–based sequence network to learn the feature representation of the enhancer sequences comprehensively and to extract the implicit relationships in the dynamic semantic information. Ultimately, an ensemble machine learning classifier is trained based on the refined multi-source features and dynamic implicit relations obtained from the deep learning-based sequence network. Benchmarking experiments demonstrated that SMFM significantly outperforms other existing methods using several evaluation metrics. In addition, an independent test set was used to validate the generalization performance of SMFM by comparing it to other state-of-the-art enhancer identification methods. Moreover, we performed motif analysis based on the contribution scores of different bases of enhancer sequences to the final identification results. Besides, we conducted interpretability analysis of the identified enhancer sequences based on attention weights of EnhancerBERT, a fine-tuned BERT model that provides new insights into exploring the gene semantic information likely to underlie the discovered enhancers in an interpretable manner. Finally, in a human placenta study with 4,562 active distal gene regulatory enhancers, SMFM successfully exposed tissue-related placental development and the differential mechanism, demonstrating the generalizability and stability of our proposed framework.
Charge transition levels of nitrogen dangling bonds at Si/SiO2 interfaces: A first-principles study

The defect levels of the nitrogen dangling bond at the Si/SiO2 interface are determined through a density-functional approach. The composition grading at the interface is modeled through crystalline and amorphous models of stoichiometric SiO2, nitrided SiO2, and substoichiometric silicon oxides. The relevant charge transition levels are first determined with respect to the band edges of the parent oxides within a semilocal density-functional scheme. Through the use of band edge shifts and band offsets previously obtained with hybrid functionals, the calculated defect levels are then positioned with respect to a band diagram of the Si/SiO2 interface which shows good agreement with the experimental one. We find that the 0/- charge transition level locates within the Si band gap. The level locates close to the Si valence band for nitrogen atoms in the stoichiometric oxide, but is found to rise across the silicon band gap as the environment of the nitrogen atoms becomes more silicon rich. The latter raise is accompanied by a stabilization of the incorporated nitrogen.
Pendellö/sung fringes in stroboscopic X‐ray section topography of weakly excited quartz resonators

The theory for slightly distorted crystals [Kato (1963). J. Phys. Soc. Jpn, 18, 1785-1791] is applied to the case of quartz AT-cut resonators to interpret stroboscopic section topographs. Features in the diffraction process such as ray trajectories, phase changes and intensities of diffracted waves are drawn from this theory. Furthermore, it is shown that extra Pendello/sung fringes appearing on section topographs with increasing acoustic vibration can be directly related to the vibration amplitude within a precision of about 0-3 A. Experimental images are compared with Kato's theoretical profiles and simulated images obtained by solving Takagi's [Acta Cryst. (1962), 15, 1311-1312] equations. The results lead to the conclusion that stroboscopic X-ray topography is a precise method to measure the vibration amplitude in weakly excited resonators.
Multi-Subband Effects on Performance Limit of Nanoscale MOSFETs

Multi-subband effects on the performance limit of metal oxide semiconductor field effect transistors (MOSFETs), which is represented by the ballistic MOSFET characteristics, is discussed for room temperature operation. A compact formula of the drain current of ballistic MOSFETs has been derived by the effective one-subband approximation. Consideration of the multi-subband effect, which requires a complicated self-consistent calculation, revises the result and provides a rigorous current value 20% smaller than the conventional estimation. The injection velocity ranges over a narrow region of 1.2–1.6×107 cm/s. It is equal to the thermal velocity in the weak inversion, but it increases in the strong inversion due to carrier degeneracy. A compact expression for predicting the saturation drain current is derived. The mechanism of current reduction due to the multi-subband effect is discussed.
A meta-heuristic satisfying tradeoff method for solving multiobjective combinatorial optimization problems-with application to flowshop scheduling

In this paper an effective meta-heuristic approach is proposed to realize a satisfying tradeoff method for solving multiobjective combinatorial optimization problems. Firstly, Pareto optimal solutions (individuals) are generated by using a genetic algorithm with the family elitist concept for a multiobjective combinatorial optimization problem. Then, we try to find a preferred solution of the decision maker based on the satisfying tradeoff method. In this paper a new meta-heuristic satisfying tradeoff method is proposed in which we do not need to solve a complex min-max problem in each iteration, but we try to find a min-max solution in the Pareto optimal solutions (individuals) generated by the genetic algorithm. We further revise the min-max solution by using a local search approach such as a simulated annealing method. As a numerical example a flowshop scheduling problem is included to verify the effectiveness of the method proposed in this paper.
Novel microstrip diplexer for ultra-wide-band (UWB) and wireless LAN (WLAN) bands

A new microstrip diplexer for ultra-wide-band (UWB) and wireless LAN (WLAN) bands is presented in this paper. The proposed structure integrates a multipole directional filter operating at WLAN band coupled to a UWB filter. The prototype is capable of processing the whole UWB region (from 3.1 to 10.6 GHz) with the WLAN band notch in one channel, and the passband WLAN band in other channel with a good selectivity due to the presence of transmission zeros at both sides of the WLAN band. The proposed diplexer is simple to fabricate, as it is designed using planar microstrip technology, and presents compact dimensions, making use of a low number of elements. Moreover, it presents the capacity of processing a narrow band (WLAN with 8% bandwidth) with a wide band (UWB). Simulated and measured results are presented with good agreement and the diplexer presents a good performance up to 15 GHz.
Pool Boiling Heat Transfer From Enhanced Surfaces to Dielectric Fluids

Pool boiling heat-transfer measurements were made using a 15.8 mm o.d. plain copper tube and three copper enhanced surfaces: a Union Carbide High Flux surface, a Hitachi Thermoexcell-E surface and a Wieland Gewa-T surface. The dielectric fluids were Freon-113 and Fluorinert FC-72, a perfluorinated organic compound manufactured to cool electronic equipment. Data were taken at atmospheric pressure, and at heat fluxes from 100 W/m/sup 2/ to 200,000 W/m/sup 2/. Prior to operation, each test surface was subjected to one of three aging procedures to observe the effect of surface past history upon boiling incipience. For Freon-113 the enhanced surfaces showed a two to tenfold increase in the heat-transfer coefficient when compared to a plain tube, whereas for FC-72 an increase of two to five was measured. The High Flux surface gave the best performance over the range of heat fluxes. The Gewa-T surface did not show as much of an enhancement at low fluxes as the other two surfaces, but at high fluxes its performance improved. In fact, it was the only surface tested which delayed the onset of film boiling with FC-72. The degree of superheat required to activate the enhanced surfaces was sensitive to both past history ofmore » the surface and to fluid properties. « less
ACTIVE METHODOLOGIES AND EVALUATIVE PORTFOLIOS: WHAT DO BRAZILIAN STUDIES SAY ABOUT THEIR RELATION

ABSTRACT: This qualitative research is an integrative systematic review of Brazil's scientific production, considering peer-reviewed articles in the educational field. It aimed to answer the question: what is the relationship between active methodologies and the use of portfolios as an assessment procedure? The objective was to investigate the relationship between theory and practice from a complex view of education. We collected data from the platforms of Capes, Scielo and Redalyc platforms. We initially found 115 articles, after treatment with inclusion and exclusion criteria, we obtained 25 publications for final analysis. We found that active methodologies and portfolios are primarily applied in health education in undergraduate degrees. We identified three central relations: legal, educational and pedagogical. Besides evaluation, the portfolio has a status of teaching-learning method and a reflexive attribute when connected to the problematization methodology. As an innovative perspective of the pedagogical practice, they are based on a concept of education based on the complexity paradigm allied to transformative education.
An atlas of confirmed and candidate supernova remnants in M33

Thirty emission nebulae in M33 have been discovered which, on the basis of strong forbidden S II compared with H-alpha, are almost certainly supernova remnants. The total number of known supernova remnants in M33 is now about 50. The cumulative number versus diameter relationship for the nebulae in the sample appears to show evidence of shock deceleration. The number of supernova remnants in M33 is consistent with a supernova rate of one per 26-300 yr. The observations are described and positions, diameters, line ratios, and images of the new candidates are presented, as well as 10 previously known and two suggested supernova remnants in M33 that were in the survey region. 57 refs.
Doubly-excited 1,3De resonance states of two-electron positive ions Li+ and Be2+ in Debye plasmas

We investigate the bound 1,3D states and the doubly-excited 1,3De resonance states of two-electron positive ions Li+ and Be2+ by employing correlated exponential wave functions. In the framework of the stabilization method, we are able to extract three series (2pnp, 2snd, 2pnf) of 1De resonances and two series (2pnp, 2snd) of 3De resonances below the N = 2 threshold. The 1,3De resonance parameters (resonance energies and widths) for Li+ and Be2+ along with the bound-excited 1s3d 1,3D state energies are reported for the first time as functions of the screening parameter. Accurate resonance energies and widths are also reported for Li+ and Be2+ in vacuum. For free-atomic cases, comparisons are made with the reported results and few resonance states are reported for the first time.
Tongue Image Texture Classification Based on Image Inpainting and Convolutional Neural Network

Tongue texture analysis is of importance to inspection diagnosis in traditional Chinese medicine (TCM), which has great application and irreplaceable value. The tough and tender classification for tongue image relies mainly on image texture of tongue body. However, texture discontinuity adversely affects the classification of the tough and tender tongue classification. In order to promote the accuracy and robustness of tongue texture analysis, a novel tongue image texture classification method based on image inpainting and convolutional neural network is proposed. Firstly, Gaussian mixture model is applied to separate the tongue coating and body. In order to exclude the interference of tongue coating on tough and tender tongue classification, a tongue body image inpainting model is built based on generative image inpainting with contextual attention to realize the inpainting of the tongue body image to ensure the continuity of texture and color change of tongue body image. Finally, the classification model of the tough and tender tongue inpainting image based on ResNet101 residual network is used to train and test. The experimental results show that the proposed method achieves better classification results compared with the existing methods of texture classification of tongue image and provides a new idea for tough and tender tongue classification.
Initial In-Flight Error Rates for 16-MB SRAM as Flying on the Double Asteroid Redirection Test (DART) Mission

In-flight static random access memory (SRAM) single bit error (SBE) rates are compared to a series of rate prediction methods in an effort to demonstrate methods for uncertainty propagation and reduction. Supplier ground test data are statistically processed via Monte Carlo methods and considering detailed 3-D spacecraft-level geometries. In-flight rates are considered for the UT8R4M39 SRAM flying in NASA’s Double Asteroid Redirection Test (DART) spacecraft avionics single board computer (SBC) prior to impacting the asteroid Dimorphos.
The potency and synergy of plant‐made monoclonal antibodies against the BA.5 variant of SARS‐CoV‐2

Variable region sequences for light chain (LC) and heavy chain (HC) of cilgavimab and tixagevimab from literature (Dong et al., 2021) were synthesized by GENEWIZ and were genetically fused to a human kappa constant sequence of the LC and a human gamma IgG1 constant sequence of HC (Lai et al., 2010). LC and HC genes were then cloned into a bean yellow dwarf virus (BeYDV)-based geminiviral vector and transiently expressed in N. benthamiana plants by agroinfiltration as described previously (Chen and Lai, 2014). 7D11 mAb were extracted and purified according to published protocols (Jugler et al., 2020). Briefly, mAb-expressing N. benthamiana leaves 7 days post infiltration were harvested and homogenized in extraction buffer (1X phosphate-buffered saline, pH 5.2 with 10 mg/mL Na-L-ascorbate, 2mM phenylmethylsulfonyl fluoride, and 1mM ethylenediaminetetraacetic acid). The pH of the homogenate was adjusted to 5.2 and then centrifuged several times. The supernatant was filtered through a 0.2-micron vacuum filter. The clarified protein extract was subsequently subjected to Protein A (MabSelect, Cytiva) chromatography according to the manufacture’s protocol prior to further analysis.
Representations of jointly stationary stochastic feedback processes

Abstract Stable constant linear closed-loop systems relating an input vector u to an output vector u and vice versa produce a jointly stationary (y, u)-procoss. On the other hand it is often natural to split up a stationary vector random process z into component vectors yand u, and to examine the closed-loop relations between y and u. This paper presents a number of new results on the spectral factorization and the closed-loop representation of a jointly stationary vector (y, u)-proccss. Conditions are derived on the closed-loop models for the joint process model to bo oE minimal degree, stable and minimum-phase. Relations between different joint process models producing the same spectrum φyu(z)are established.
Heat Transfer Performance of Gel Foam Layer with Nanoparticles Doping under a Radiative Heat Flux

The risk of fire in the chemical industry’s production process is fatal. Gel foam has been widely employed in petroleum storage tanks, oil pools, and other petrochemical equipment for fire extinguishing and thermal protection. Recently, nanoparticles have been doped into gel foam to enhance thermal stability and insulation. However, heat transfer behaviors of the gel foam layer containing nanoparticles are still missing. In this study, a numerical heat transfer model of a gel foam layer containing silica nanoparticles under a radiative heat flux was established. Through simulation, the changes in foam thickness and temperature distribution were analyzed. The effects of the maximum heating temperature, initial gas content, nanoparticle size, and concentration on the thermal insulation behavior of the gel foam layer were systematically studied. The results showed that the thermal stability and insulation performance of the three-phase gel foam layer decreased with the increase in the initial gas content and particle size. Increasing the nanoparticle concentration could enhance the foam’s thermal stability and insulation performance. The results provide guidance for a designing gel foam with high thermal protection performance.
Three-dimensional numerical investigation of hybrid nanofluids in chain microchannel under electrohydrodynamic actuator

Abstract Energy efficiency enhancement methods have received considerable attention within the industry and scientific community, owing to the rising concern of global energy sustainability. The present article attempts to scrutinize the effects of electrohydrodynamics and nanofluids on the rate of heat transfer and fluid flow in the 3-D chain microchannels. Improved heat exchangers (e.g., chain microchannel) would have a key role in increasing of the performance of such systems since they provide efficient thermal management needed for more robust computational power. To date, analysis of electrohydrodynamics and nanofluids in the chain microchannel was not comprehensively discussed. Here, steady-state, laminar, and three-dimensional chain microchannel are numerically modeled based on a control volume method in Fluent. Results show that by increasing the volume fraction of nanoparticles, the viscosity of the nanofluid increases leading to an increase in pressure drops. Moreover, Nusselt at Re = 125, 250, 500 and 1000 for hybrid nanofluid ( ) is 1.206, 1.541, 2.075 and 2.707, respectively which, in turn, depicts surging by 22.94%, 24.17%, 24.70% and 24.707% in comparison to water, respectively. In addition, at low Reynolds number (0.416 the lower Reynolds results in decreasing of percentage of pressure drop. Meanwhile, imposing electrohydrodynamic (V = 30 KV) at Re= 125, 250, 500 and 1000 leads to increasing by 23%, 22%, 20% and 18% of Nusselt number in comparison to absence of electric field, respectively. It means that the considered effect of the increasing the Nusselt number at lower Reynolds number is more effective. Moreover, heat transfer rises with augmentation of supplied voltage and Reynolds number. Highlights Using active (electrohydrodynamics and hybrid nanofluid) and passive (3-D chain microchannel) methods to enhance heat transfer rate. Adding two additional equations (including and V) in Fluent With Using UDS (User Defined Scalar). Writing UDM to achieve E ( ) as well as UDF to solve source terms ( E and Considering the charge convection term ( ) in the electric current density ( owing to used fluids (water and nanofluids) in this article, whilst it is negligible for air. Investigation of effects of different types of nanofluid and their concentration as well as impacts of adding electrode and its voltages. Imposing electrohydrodynamic (V = 30 KV) at Re= 125, 250, 500 and 1000 leads to increasing by 23%, 22%, 20% and 18% of Nusselt number in comparison to absence of electric field, respectively.
Lumbar Multifidus Morphology in Youth Competitive Alpine Skiers and Associated Sex, Age, Biological Maturation, Trunk Stability, and Back Complaints

Background: The lumbar multifidus (LMF), as a dynamic stabilizer of the lumbar spine, may play an important role in the prevention of overuse-related back complaints. Hypothesis: LMF morphology is associated with trunk stability and differs between symptomatic and asymptomatic skiers. Study Design: Cohort study. Level of Evidence: Level 3. Methods: A total of 85 youth skiers (28 females, mean age, 14.7 ± 0.7 years; 57 males, mean age, 14.9 ± 0.5 years) underwent anthropometric assessments, an estimation of biological maturation, a magnetic resonance imaging- and ultrasound-based examination of LMF morphology, and a biomechanical quantification of deadbug bridging stabilization performance. Athletes were categorized as symptomatic if they had registered at least 1 significant overuse-related back complaint episode in the 12 months before the main examination. Results: Male skiers showed a greater LMF size (ie, anatomical cross-sectional area [ACSA]) than female skiers, except for vertebral body L5, where no difference was found (8.8 ± 1.8 cm2 vs 8.3 ± 1.4 cm2, P = 0.18). Conversely, female skiers displayed longer fascicles than male skiers (5.8 ± 0.8 cm vs 5.4 ± 0.8 cm, P = 0.03). Skiers aged under 16 years (U16) skiers had greater values for LMF size and fascicle length than U15 skiers. Maturity offset was associated with L5 LMF size (R2 = 0.060, P = 0.01), fascicle length (R2 = 0.038, P = 0.04), and muscle thickness (R2 = 0.064, P = 0.02). L5 LMF size was associated with trunk stability (R2 = 0.068, P = 0.01). Asymptomatic skiers showed on average a 12.8% greater value for L5 LMF size compared with symptomatic skiers (P = 0.04). Conclusion: There are sex- and age-related differences in LMF morphology in youth competitive alpine skiers. Moreover, the ACSA at the level of the lumbar vertebral body L5 undergoes changes during biological maturation, shows a small, but significant association with trunk stability, and differs between symptomatic and asymptomatic skiers with back complaints. Clinical Relevance: The observed association of muscle structure (ie, L5 LMF ACSA) with functional aspects (ie, trunk stabilization capacity) and clinical representation (ie, overuse-related back complaints) further highlights the important role of the multifidus muscle for training and injury prevention in youth competitive alpine skiers around the growth spurt.
Surface EMG Statistical and Performance Analysis of Targeted-Muscle-Reinnervated (TMR) Transhumeral Prosthesis Users in Home and Laboratory Settings

A pattern-recognition (PR)-based myoelectric control system is the trend of future prostheses development. Compared with conventional prosthetic control systems, PR-based control systems provide high dexterity, with many studies achieving >95% accuracy in the last two decades. However, most research studies have been conducted in the laboratory. There is limited research investigating how EMG signals are acquired when users operate PR-based systems in their home and community environments. This study compares the statistical properties of surface electromyography (sEMG) signals used to calibrate prostheses and quantifies the quality of calibration sEMG data through separability indices, repeatability indices, and correlation coefficients in home and laboratory settings. The results demonstrate no significant differences in classification performance between home and laboratory environments in within-calibration classification error (home: 6.33 ± 2.13%, laboratory: 7.57 ± 3.44%). However, between-calibration classification errors (home: 40.61 ± 9.19%, laboratory: 44.98 ± 12.15%) were statistically different. Furthermore, the difference in all statistical properties of sEMG signals is significant (p < 0.05). Separability indices reveal that motion classes are more diverse in the home setting. In summary, differences in sEMG signals generated between home and laboratory only affect between-calibration performance.