Miracle-dz/UniFAR-FTUs huggingface dataset:
Empirical Study of Protein Feature Representation on Deep Belief Networks Trained With Small Data for Secondary Structure Prediction

Protein secondary structure (SS) prediction is a classic problem of computational biology and is widely used in structural characterization and to infer homology. While most SS predictors have been trained on thousands of sequences, a previous approach had developed a compact model of training proteins that used a <bold>C</bold>-<bold>A</bold>lpha, C-<bold>B</bold>eta <bold>S</bold>ide Chain (<bold>CABS</bold>)-algorithm derived energy based feature representation. Here, the previous approach is extended to Deep Belief Networks (DBN). Deep learning methods are notorious for requiring large datasets and there is a wide consensus that training deep models from scratch on small datasets, works poorly. By contrast, we demonstrate a simple DBN architecture containing a single hidden layer, trained only on the CB513 dataset. Testing on an independent set of G Switch proteins improved the Q<inline-formula><tex-math notation="LaTeX">$_{3}$</tex-math><alternatives><mml:math><mml:msub><mml:mrow/><mml:mn>3</mml:mn></mml:msub></mml:math><inline-graphic xlink:href="rashid-ieq1-3168676.gif"/></alternatives></inline-formula> score of the previous compact model by almost 3%. The findings are further confirmed by comparison to several deep learning models which are trained on thousands of proteins. Finally, the DBN performance is also compared with <bold>P</bold>osition <bold>S</bold>pecific <bold>S</bold>coring <bold>M</bold>atrix (<italic>PSSM</italic>)-profile based feature representation. The importance of (i) structural information in protein feature representation and (ii) complementary small dataset learning approaches for detection of structural fold switching are demonstrated.
Modelling of grain refinement driven by negative grain boundary energy

Abstract Grain refinement can be described by the classical kinetic equation using a negative value of the specific grain boundary Gibbs energy. A respective overview is offered reporting according observations and simulations, particularly linked to grain boundary segregation. Classical grain growth model is used in the treatment of evolution of the distribution function during refinement. The adapted model requires defining nucleation rate of new grains, which significantly influences the kinetics of the system of grains. Moreover, a jump in the distribution function is allowed at a certain value of the grain radius RJ, which separates old grains from newly nucleated ones. Evolution equation for both the critical radius Rc and separation radius RJ (jump position) as well as for the dimension-free distribution (shape) function are derived. Illustrative examples for the evolution of the system parameters under various nucleation rates of newly generated grains are presented.
One dimensional graphene nanoscroll-wrapped MnO nanoparticles for high-performance lithium ion hybrid capacitors

Lithium ion hybrid capacitors (LIHCs) have high power density and high energy density. One of the biggest problems in LIHCs is the kinetics mismatch of a battery-type anode and capacitive cathode due to relatively slow Li+ reaction kinetics compared to fast ion adsorption/desorption behavior. Here, to address this challenge, an efficient strategy was proposed to prepare a one dimensional (1D) graphene nanoscroll wrapped MnO nanoparticle (GNS@MnO) material by a simple freeze-drying process followed by annealing treatment. The topological end-opening architecture of the GNS and the wrapping of graphene layers facilitate fast Li+ diffusion and electron transfer. As an anode material of lithium ion batteries (LIBs), the optimized GNS@MnO-600 electrode exhibits outstanding performance for Li+ ion storage with a high specific capacity of 437 mA h g−1 even at 5.0 A g−1. The constructed LIHC based on the GNS@MnO-600 anode and 3D framework activated carbon (3DFAC) with a high specific surface area delivered a high energy density of 197 W h kg−1 at 235 W kg−1. Even at a high power density of 23.5 kW kg−1, a high energy density of 114 W h kg−1 is still maintained, as well as a long cycling life (84.8% capacity retention after 3000 cycles). We believe that this highly efficient 1D GNS wrapping strategy provides a novel design concept for the construction of fast kinetics anode materials for LIBs and LIHCs.
Lateral Variations of Moho Depth and Average Crustal Properties Across the Taiwan Orogen From H‐V Stacking of P and S Receiver Functions

The complexity of the young Taiwan orogen mainly resulting from arc‐continent collision is manifold. As the Moho and crustal properties are crucial to unravel the still‐debated orogenic models, we adopt a H‐V stacking method jointly utilizing P and S receiver functions for simultaneously reliable determination of crustal thickness and average P‐ and S‐wave velocity, their ratio (Vp/Vs), and bulk sound speed (Vb) beneath 50 stations in Taiwan and offshore islands. Results indicate the Moho is inclined from ∼20 km in the north and west coastal areas to ∼47 km in the midwest of the Central Range (CR), and abruptly elevated >25 km at the eastern edge of the CR and adjacent collision suture zone. The uplifted Moho along with exclusively high Vp/Vs (2.1) suggest the subducted Eurasian crust may have been exhumed and compositionally modified by the accreted ophiolite complex of oceanic affinity during forearc basin closure. Our Moho mostly lies in the depths of the sharpest positive velocity gradient, a few to a dozen kilometers shallower than the Vp = 7.5 km/s isosurface assumed in the tomographic models. The unusually thin crust (∼20 km) with high Vp/Vs (1.9–2.0) is observed in the northern Taiwan volcanic zone, plausibly attributed to the post‐orogenic extensional thinning and induced melting in the sublithospheric mantle producing magmatic fluids trapped in the crust. Moreover, Vb apparently decreases from the coasts to the middle CR coinciding with the thickest crust, implying the crust under the central mountain range is more compressible and easily deformed/thickened by ongoing collisional compression.
Quantitative Index Construction of Website Influence: Taking China Private Universities as Example

Website influence is of great value to the brand promotion of private colleges and universities. This study collects the link index and traffic index data of private university websites in China, conducts relevant analysis, sorts out the relationship between link indicators and traffic indicators, and interprets the strategies of these indicators for brand promotion of private colleges and universities combined with case analysis.
Determination of the reference position in the near-infrared non-invasive blood glucose measurement in vivo

Position-based reference measurement method is taken as one of the most promising method in non-invasive measurement of blood glucose based on spectroscopic methodology. Selecting an appropriate source-detector separation as the reference position is important for deducting the influence of background change and reducing the loss of useful signals. Our group proposed a special source-detector separation named floating-reference position where the signal contains only background change, that is to say, the signal at this source-detector separation is uncorrelated with glucose concentration. The existence of floating-reference position has been verified in a three layer skin by Monte Carlo simulation and in the in vitro experiment. But it is difficult to verify the existence of floating-reference position on the human body because the interference is more complex during in vivo experiment. Aiming at this situation, this paper studies the determination of the best reference position on human body by collecting signals at several source-detector separations on the palm and measuring the true blood glucose levels during oral glucose tolerance test (OGTT) experiments of 3 volunteers. Partial least square (PLS) calibration model is established between the signals at every source-detector separation and its corresponding blood glucose levels. The results shows that the correlation coefficient (R) between 1.32 mm to 1.88 mm is lowest and they can be used as reference for background correction. The signal of this special position is important for improving the accuracy of near-infrared non-invasive blood glucose measurement.
SOCIAL MEDIA: AN IMPEDIMENT OR INSPIRATION TO IMPLEMENTATION OF DIGITAL LITERACY PROGRAMME IN KISII COUNTY, KENYA

Informacni a komunikacni technologie (IKT) způsobily revoluci ve způsobu fungovani různých odvětvi v rozvinutých i rozvojových zemich. Pronikly do modernich spolecnosti jako nastroje pro transformaci vzdělavacich systemů i podpory hospodařskeho rozvoje. Vytvařenim nových produktů a služeb a poskytnutim přistupu k informacim a odborným znalostem umožnily pokrok v zemědělstvi, zdravotnictvi a vzdělavani a propojeni komunit, ucitelů a studentů. Odvětvi vzdělavani v mnoha zemich plně zaclenilo IKT do oblasti výzkumu, výuky i uceni, což umožnilo rozvoj inovativnich způsobů uceni vhodných pro různe situace, ve kterých se žak nachazi. V pocatecni fazi zacleňovani IKT do výuky měli z tohoto procesu prospěch zejmena vysokoskolske instituce, nicmeně v posledni době z něj profituji i instituce nižsiho vzdělavani, vcetně zakladnich skol. V Keni je proces zacleňovani ICT do výuky na zakladnich skolach jednim ze stěžejnich programů vychazejicich z vize keňske vlady zajistit, aby byl každý jejich žak připraven na dnesni digitalni svět. Za timto ucelem byl na prvnim stupni keňských zakladnich skol, a zejmena v prvnich třidach, zaveden Program digitalni gramotnosti (DLP). Tato studie se zabýva předpokladanou jednoduchosti použiti a užitecnosti socialnich medii z pohledu ucitelů zakladnich skol v okrese Kisii v Keni a mirou uspěsnosti provaděni programu digitalniho uceni (DLP) těmito uciteli. Posuzovan byl nazor ucitelů na technologickou složitost socialnich medii, a to metodou výzkumneho setřeni. Metodou nahodneho, přiměřeneho a ucinneho výběru byl vybran vzorek 250 zakladnich skol a 276 ucitelů. Ucitelům nižsiho stupně zakladnich skol v ramci keňskeho vzdělavaciho systemu byly pomoci SAQ dotazniků (vyplňovaných respondentem) pokladany otazky ohledně toho, jak casto, s jakou lehkosti a s jakou intenzitou použivaji technologie socialnich medii, jako je Facebook, WhatsApp a Twitter. Ziskane výsledky ukazaly, že použivani aplikaci WhatsApp a Facebook výrazně ovlivňuje spolupraci a zapojeni ucitelů. Předpokladana jednoduchost použiti je zaroveň prediktorem předpokladane užitecnosti a obě tyto skutecnosti ovlivňuji miru, do jake ucitele socialni media využivaji pro vzdělavaci ucely. Snadný přistup ucitelů k internetu pomoci chytrých mobilnich telefonů jim umožnil spolu konverzovat a vzajemně komunikovat, vytvařet, upravovat a sdilet nove formy textoveho, vizualniho a zvukoveho obsahu. Ti, kteři internet použivali casto, se nasledně ve velke miře zapojili do snahy o zavedeni programu digitalniho uceni, s využitim nastroje pro ucitele Teacher Digital Device (TDD) a digitalniho výukoveho nastroje (LDD) pro žaky. Tento dokument dochazi k zavěru, že socialni media lze využit jako vzdělavaci nastroj, který ucitelům pomaha spolupracovat a zapojit se, a doporucuje, aby myslenku využiti socialnich medii pro výuku a uceni přijalo za svou i ministerstvo skolstvi.
Deep Understanding of Negative Gate Voltage Restriction for SiC mosfet Under Wide Temperature Range

In this letter, the origin and related physical insights of gate reliability issues under various Vgs and high temperatures (up to 300 °C) are revealed in-depth, through splitting MOS gate structure of silicon carbide (SiC) metal-oxide-semiconductor field-effect transistors (MOSFETs) into N-type JFET and P-type channel region under identical manufacturing processes and thermal budgets of SiC MOSFETs. From 25 to 300 °C, the safety limit of positive Vgs of SiC MOSFETs is mainly dependent on the gate oxide on the JFET surface, whereas that of negative Vgs is dependent on the gate oxide on the channel surface. The gate oxide on the channel surface is weaker than that on the JFET surface in terms of Fowler–Nordheim (F-N) tunneling, resulting in asymmetric safety Vgs of current SiC MOSFET. Moreover, when temperature ranges from 25 to 150 °C, the degradation of gate oxide under −15 V < Vgs < 25 V is caused by the hole or electron direct tunneling mechanism. However, when the temperature reaches 300 °C, the degradation of gate oxide under −5 V < Vgs < 10 V is caused by the hole or electron hopping conduction mechanism. Furthermore, the reliability of gate oxide is evaluated by the time-dependent dielectric breakdown measurement. The charge-to-breakdown (QBD) of gate oxide is severely degraded at 300 °C mainly due to the barrier height (${\it{ \Phi}}_{\rm B}$) degradation. These efforts can provide accurate weakness points of gate oxide under higher Vgs bias (particular for negative bias) and higher temperature (300 °C) for SiC MOSFETs, further helping use and design rugged converters with the fast-speed operation of SiC MOSFETs.
Topical nano-delivery of 5-fluorouracil: Preparation and characterization of water-in-oil nanoemulsion

Purpose: To prepare and characterize a water-in-oil nanoemulsion of 5-fluorouracil (5FU) for enhanced skin penetration. Methods: Nanoemulsions of 5FU were prepared using Capyrol (propylene glycol monocaprylate). Transcutol (highly purified diethylene glycol monoethyl ether) and polyethylene glycol (PEG) 400 as oil, surfactant and co-surfactant, respectively. The optimized formulations were subjected to heating - cooling cycling, centrifugation and freeze - thaw cycling to assess their stability. Particle size distribution and zeta potential of the nanoemulsions were evaluated. Furthermore, in vitro and in vivo skin permeation studies were carried out on the formulations in a rat model. Skin irritation studies were also performed on rats to assess the irritation potential of the formulations. The 1 % w/v of Carbopol 934 gel loaded with 1 % 5FU was used as control (FU gel). Results: The results showed that the mean droplet size of the nanoemulsions was ~100 nm with a zeta potential of ± 15. Significant increase in permeability was also observed for the nanoemulsion formulations compared with control. The steady-state flux (Jss), enhancement ratio and permeability coefficient (Kp) for optimized nanoemulsion formulation were significantly (p < 0.05) higher than those of the conventional gel (control). Both in vitro and in vivo skin retention results indicate higher drug release from the nanoemulsion (292.45 μg/cm 2 ) than for control (121.42 μg/cm 2 ). Mean irritation index for the nanoemulsion was significantly lower than for control. Conclusion: The results suggest that a water-in-oil nanoemulsion is safe and can potentially be used to promote skin penetration of 5FU following topical application on the skin for the treatment of some skin diseases. Keywords: Nanoemulsion, Controlled release, 5-Fluorouracil, Skin penetration, Skin irritation
Development of technology for meat products enriched with essential trace elements

One of the directions of development of food components in the composition of meat products is proposed to use bee products as a source of vitamins, macro-, micronutrients, enzymes, hormones, amino acids, etc. the chemical composition and therapeutic and preventive properties of bee pollen have been Studied. The article presents the results of research on dried whole-muscle snack foods-jerks enriched with bee pollen. The formulation and technology of jerky has been developed. The operation modes of drying the product, which are in the range of 45-47 ° C, are justified, which allow preserving the activity of enzymes, hormones, and vitamins. The total chemical composition of the product, energy value, active acidity, water activity, vitamin and mineral composition of individual indicators were determined.
Research on Power Harmonic Noise Suppression Method Based on Genetic Algorithm for Urban TEM Data

In recent years, ground accidents are constantly occurring in the process of urban underground space development. TEM provides effective technical support for the rational development and safe operation of urban underground space as a flexible and low-cost geophysical method. However, the interference of human electromagnetic noise is serious in the urban environment, especially the power frequency harmonic noise has wide frequency band distribution, as it is difficult to suppress it quickly and effectively, resulting in low accuracy of the extracted secondary field signal and large inversion error. Aiming at the problem of power frequency harmonic noise interference, this paper proposes a noise suppression method based on genetic algorithm. Through the optimization algorithm, the feature matching segment in the reference noise is quickly searched, and it is self-adaptive offset with the power frequency harmonic noise in the signal. The simulation results show that the method can obtain higher signal-to-noise ratio when collecting less sample data. Furthermore, it is proved that this method of this paper has the characteristics of fast noise suppression and no signal loss.
Numerical investigation of the growth kinetics for macromolecular microsphere composite hydrogel based on the TDGL equation

We present results of a detailed numerical investigation of the phase separation kinetic process of the macromolecular microsphere composite (MMC) hydrogel. Based on the Flory-Huggins-de Gennes-like reticular free energy, we use the time-dependent Ginzburg–Landau (TDGL) mesoscopic model (called MMC-TDGL model) to simulate the phase separation process. Domain growth is investigated through the pair correlation function. Then we obtain the time-dependent characteristic domain size, which reflects the growth kinetics of the MMC hydrogel. The results indicate that the growth law based on the MMC-TDGL equation is consistent with the modified Lifshitz–Slyozov theory.
GREEN COMMUNITY EMPOWERMENT BUSINESS MODEL TO RECOGNIZE SOLO GREEN CITY: A CASE STUDY

This research aims to investigate how local government of Surakarta developing green businesses to realise Solo Green City, as the answer of environmental sustainability issue. We elaborate the Green Business Model as a strategy to enhance communities participation in green projects. Schaltegger et al. (2012) explained that green business is a sistematical approach to develop both business and sustainable environment. We applied the qualitative method in this study. We did interview two groups of respondents, policy makers and green business practitioners. Policy makers are Regional Planning Agency (Bappeda) as macro planner and Environmental Agency and Agricurtural; Food Security and Fishery Agency as implementers. On the other hand, we interviewed businessmen of decorative plants, hidroponic community, organic vegetables village, and go green souvenirs sellers as practitioners. It can be concluded that from several green business activities, the community empowerment is the most influential movement to establish Solo Green City. The success project such as Organic Vegetables Village in Mojosongo is the result from collaboration of NGO Rumah Zakat with local community. The project was supervised under Environmental Agency as pilot project of the climate villages. The model that we developed will be submitted to the local government as policy recommendation
Engineering the large pocket of an (S)-selective transaminase for asymmetric synthesis of (S)-1-amino-1-phenylpropane

Amine transaminases offer an environmentally benign chiral amine asymmetric synthesis route. However, their catalytic efficiency towards bulky chiral amine asymmetric synthesis is limited by the natural geometric structure of the small pocket, representing a great challenge for industrial applications. Here, we rationally engineered the large binding pocket of an (S)-selective ω-transaminase BPTA from Paraburkholderia phymatum to relieve the inherent restriction caused by the small pocket and efficiently transform the prochiral aryl alkyl ketone 1-propiophenone with a small substituent larger than the methyl group. Based on combined molecular docking and dynamic simulation analyses, we identified a non-classical substrate conformation, located in the active site with steric hindrance and undesired interactions, to be responsible for the low catalytic efficiency. By relieving the steric barrier with W82A, we improved the specific activity by 14-times compared to WT. A π–π stacking interaction was then introduced by M78F and I284F to strengthen the binding affinity with a large binding pocket to balance the undesired interactions generated by F44. T440Q further enhanced the substrate affinity by providing a more hydrophobic and flexible environment close to the active site entry. Finally, we constructed a quadruple variant M78F/W82A/I284F/T440Q to generate the most productive substrate conformation. The 1-propiophenone catalytic efficiency of the mutant was enhanced by more than 470-times in terms of kcat/KM, and the conversion increased from 1.3 to 94.4% compared with that of WT, without any stereoselectivity loss (ee > 99.9%). Meanwhile, the obtained mutant also showed significant activity improvements towards various aryl alkyl ketones with a small substituent larger than the methyl group ranging between 104- and 230-fold, demonstrating great potential for the efficient synthesis of enantiopure aryl alkyl amines with steric hindrance in the small binding pocket.
Beyond the State of the Art of Electric Vehicles: A Fact-Based Paper of the Current and Prospective Electric Vehicle Technologies

Today, there are many recent developments that focus on improving the electric vehicles and their components, particularly regarding advances in batteries, energy management systems, autonomous features and charging infrastructure. This plays an important role in developing next electric vehicle generations, and encourages more efficient and sustainable eco-system. This paper not only provides insights in the latest knowledge and developments of electric vehicles (EVs), but also the new promising and novel EV technologies based on scientific facts and figures—which could be from a technological point of view feasible by 2030. In this paper, potential design and modelling tools, such as digital twin with connected Internet-of-Things (IoT), are addressed. Furthermore, the potential technological challenges and research gaps in all EV aspects from hard-core battery material sciences, power electronics and powertrain engineering up to environmental assessments and market considerations are addressed. The paper is based on the knowledge of the 140+ FTE counting multidisciplinary research centre MOBI-VUB, that has a 40-year track record in the field of electric vehicles and e-mobility.