Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of Domain- and Genotype-Specific Models to Infer Post-Transcriptional Regulation of Segmentation Gene Expression in Drosophila

Unlike transcriptional regulation, the post-transcriptional mechanisms underlying zygotic segmentation gene expression in early Drosophila embryo have been insufficiently investigated. Condition-specific post-transcriptional regulation plays an important role in the development of many organisms. Our recent study revealed the domain- and genotype-specific differences between mRNA and the protein expression of Drosophila hb, gt, and eve genes in cleavage cycle 14A. Here, we use this dataset and the dynamic mathematical model to recapitulate protein expression from the corresponding mRNA patterns. The condition-specific nonuniformity in parameter values is further interpreted in terms of possible post-transcriptional modifications. For hb expression in wild-type embryos, our results predict the position-specific differences in protein production. The protein synthesis rate parameter is significantly higher in hb anterior domain compared to the posterior domain. The parameter sets describing Gt protein dynamics in wild-type embryos and Kr mutants are genotype-specific. The spatial discrepancy between gt mRNA and protein posterior expression in Kr mutants is well reproduced by the whole axis model, thus rejecting the involvement of post-transcriptional mechanisms. Our models fail to describe the full dynamics of eve expression, presumably due to its complex shape and the variable time delays between mRNA and protein patterns, which likely require a more complex model. Overall, our modeling approach enables the prediction of regulatory scenarios underlying the condition-specific differences between mRNA and protein expression in early embryo.
EFFECT OF STAINING METHOD ON THE EFFICIENCY OF PROTEIN ELECTROPHORESIS IN QUANTIFYING RESISTANCE OF FLAX TO POWDERY MILDEW DISEASE

Seed proteins of ten flax genotypes, having different levels of susceptibility to powdery mildew (PM), were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Gels were stained with Coomassie Brilliant Blue R-250 (CBB) or silver nitrate (SN). Data for PM severity and amounts of protein fractions were entered into a computerized stepwise multiple regression. Using the predictors supplied by stepwise regression, a two-factor model was constructed to predict PM severity when the gel was stained with CBB. This model showed that PM severity differences were due largely to the protein fractions nos. 24 and 3, which accounted for 76.18% of the total variation in severity ratings. On staining the gel with SN, a five-factor model was constructed. This model showed that PM severity differences were due to largely to the protein fractions nos. 36, 22, 32, 2, and 21, which accounted for 96.03% of the total variation in PM severity. These results indicate that the SN regression model was superior, compared with that of CBB, in predicting PM severity from banding patterns. This superiority was attributed to the higher R value of the model. Therefore, SDSPAGE of proteins and staining with SN may provide a supplementary assay to field trials to distinguish between PM resistant or susceptible genotypes quantitatively.
A KNOWLEDGE-BASED APPROACH TO MINE VENTILATION PLANNING IN YUGOSLAV MINING PRACTICE

Ventilation system analysis is a complex process based on the calculation and analysis of numerous parameters. These problems can be successfully solved by the SimVent numerical package, but a full understanding and use of the obtained results require the involvement of an experienced specialist in the ventilation field. The solution was found in the creation of a hybrid system INVENTS, whose knowledge base represents a formalization of the expert knowledge in the mine ventilation field. In this paper, we present the design methodology of the hybrid system INVENTS, as well as system structure and user interface.
Human navigation by sound

Discusses the development of electronic travel aids for the blind, considering in particular the use of IF and US devices. Problems associated with focusing, resolution and ranging are discussed and three methods of modulation are considered-pulse modulation, pulse repetition modulation and frequency modulation. Methods used for information processing and display are also discussed. As examples, the Sonic Guide (an FM ultrasonic aid) and the Sonic Pathfinder (a prototype pulse echo ultrasonic aid) are described
Application of EFDC Model in Preventing Water Quality Deterioration through Water Circulation

The EFDC model is applied to predict the flow field of two typical circulating water body impacted by both pump driven current and wind-driven current. The result demonstrates that there exists strong effect between pump driven current and wind-driven current. The wind can effectively reduce the area of low velocity zone of pump drive current as well as the power consumption of pump. And the increased high velocity area could better inhibit the algae growth and thus prevents degradation of water quality.
A Real Time Optimizer for Security Dispatch

As power systems have evolved in size and complexity so has the need for sophisticated and comprehensive real time control and dispatch techniques. Solutions presented in this paper are intended for on-line applications and are further designed to accommodate "network" as well as "nonnetwork" (e.g., environmental) and interacting operating restrictions. The paper reviews the criteria for the constrained optimization of real power; discusses practical approaches towards implementation; presents numerical results of tests on a large network model including the effects of convergence, external equivalents, and reference bus locations; proposes extensions to include reactive power dispatch and contingency constraints
Multi-Branch-CNN: classification of ion channel interacting peptides using parallel convolutional neural networks

Ligand peptides that have high affinity for ion channels are critical for regulating ion flux across the plasma membrane. These peptides are now being considered as potential drug candidates for many diseases, such as cardiovascular disease and cancers. There are several studies to identify ion channel interacting peptides computationally, but, to the best of our knowledge, none of them published available tools for prediction. To provide a solution, we present Multi-branch-CNN, a parallel convolutional neural networks (CNNs) method for identifying three types of ion channel peptide binders (sodium, potassium, and calcium). Our experiment shows that the Multi-Branch-CNN method performs comparably to thirteen traditional ML algorithms (TML13) on the test sets of three ion channels. To evaluate the predictive power of our method with respect to novel sequences, as is the case in real-world applications, we created an additional test set for each ion channel, called the novel-test set, which has little or no similarities to the sequences in either the sequences of the train set or the test set. In the novel-test experiment, Multi-Branch-CNN performs significantly better than TML13, showing an improvement in accuracy of 6%, 14%, and 15% for sodium, potassium, and calcium channels, respectively. We confirmed the effectiveness of Multi-Branch-CNN by comparing it to the standard CNN method with one input branch (Single-Branch-CNN) and an ensemble method (TML13-Stack). To facilitate applications, the data sets, script files to reproduce the experiments, and the final predictive models are freely available at https://github.com/jieluyan/Multi-Branch-CNN.
Green Water Investigation for a Containership

Abstract The occurrence of deck wetness for ships with forward speed is predicted using a non-linear strip method in both regular and irregular head seas. The approach is validated with experimental data for the container ship model S-175. Once green water has taken place, a simplified model of green water flow on deck is simulated using CFD. Loads on deck and a vertical wall downstream are validated as well.
Fabrication Techniques for PDMS Dome-Shaped Membrane Using Soft Lithography Process

The dome-shaped membrane is very important part of the micro/nano devices. The dome-shaped with the thickness of 150 μm and a radius of 3.2 mm was fabricated using the soft lithography process. The Polydimethylsiloxane (PDMS) was selected as a material because it deformable and suitable to implement as a membrane. Soft lithography is based on pattern transfer using a mold that is patterning the substrate material. In this paper, two techniques were suggested to fabricate the dome-shaped membrane which are reflow technique and stamping technique. The comparison was made for both techniques using a Scanning Electron Microscope (SEM) and it seems the stamping technique has an advantage where the uniform thickness of the dome-shaped membrane can be achieved. The discussion on the temperature effect of a stamping technique shows that the suitable temperature to harden the PDMS is in temperature room where the bubbles can be eliminated under this temperature.
An Expert System Applied in Construction Water Quality Monitoring

Problem statement: An untoward environmental impact of urban growth in Malaysia has been deterioration in a number of watercourses due to severe siltation and other pollutants from the construction site. Water quality monitoring is a plan for decision makers to take into account the adverse impacts of construction activities on the receiving water bodies. It is also a process for collecting the construction water quality monitoring, baseline data and standard level. Approach: In recent years, expert systems have been used extensively in different applications areas including environmental studies. In this study, expert system software -CWQM- developed by using Microsoft Visual Basic was introduced. CWQM to be used for water quality monitoring during construction activities was designed based on the legal process in Malaysia. Results: According to the water quality monitoring regulation enacted in Malaysia, construction activities require mandatory water quality monitoring plans duly approved by Department of Environment before staring activities. CWQM primarily aims to provide educational and support system for water quality monitoring engineers and decision-makers during construction activities. It displays water quality monitoring plan in report form, water sampling location in GIS format and water quality monitoring data in graph. Conclusion: When the use of CWQM in construction water quality monitoring becomes widespread, it is highly possible that it will be benefited in terms of having more accurate and objective decisions on construction projects which are mainly focused on reducing the stormwater pollution.
IL-33/ST2 Axis Deficiency Exacerbates Hepatic Pathology by Regulating Treg and Th17 Cells in Murine Schistosomiasis Japonica

Purpose Schistosoma japonicum-infected IL-33 and ST2 gene deficiency (IL-33−/− and ST2−/−, respectively) mice were used to explore the role of the IL-33/ST2 axis in liver pathology targeting regulatory T cells (Treg)/T helper 17 cells (Th17). Materials and Methods Each mouse was infected percutaneously with 20 S. japonicum cercariae. Hepatic mass index (HMI), liver egg granulomas, hepatic fibrosis biomarkers and serum levels of alanine aminotransferase (ALT) were investigated. Treg and Th17 frequency was determined by flow cytometry. Expressions of Foxp3, ST2, TGF-β1, IL-10, RORγt, and IL-17A were measured via quantitative real-time polymerase chain reaction (qRT-PCR). Concentrations of TGF-β1, IL-10 and IL-17A were tested with ELISA. In vitro experiments, mRNA expressions of Foxp3, TGF-β1, IL-10, Atg5, Beclin-1 and p62 associated with polarization of Treg by recombinant mouse IL-33 (rmIL-33) were detected by qRT-PCR. Results An increased expression of IL-33/ST2 was shown in S. japonicum-infected mice. Deficiency of IL-33 or ST2 gene led to an aggravated liver pathology, which was evidenced by elevated hepatic granuloma volume, HMI and ALT levels and fibrosis, which was demonstrated by increased hepatic collagen deposition in the infected mice. Injection of rmIL-33 into the infected IL-33−/− mice strongly abrogated the liver pathology and fibrosis, whereas no detectable effect with injecting rmIL-33 into the infected ST2−/− mice. Furthermore, depletion of the IL-33/ST2 axis inhibited Treg, accompanied by increased Th17. rmIL-33 treatment upregulated Treg and downregulated Th17 in the infected IL-33−/− mice, while no effect in the infected ST2−/− mice. rmIL-33 led to elevated expressions of Atg5, Beclin-1 and inhibited expression of p62 in expansion of Treg. Conclusion The IL-33/ST2 axis plays a protective role in S. japonicum infected mice, which is closely related to increasing Treg responses as well as suppressing Th17 responses. Expansion of Treg by IL-33 may be associated with its regulation of autophagy.
Explaining the performance of talented youth speed skaters

This research investigated whether it is possible to explain the performance of talented youth speed skaters between the age of 15 to 20 years. Multidimensional performance characteristics were compared with the speed skating performance on separate distances (500 m, 1.000 m, 1.500 m and 3.000 m) and the allround performance, in the season of 2009-2010. Eight athletes from the Dutch national youth speed skating team (18-19 year old), along with 20 talented athletes from the Dutch district teams (15- 17 year old) were included. Multidimensional performance characteristics consisted of anthropometrical, physiological, technical and psychological characteristics. Partial correlations were calculated between each performance characteristic and the speed skating performance, while controlling for gender and age. For the 500 m, jump height, measured as a squat jump (r=-.664) and countermovement jump (r=-.619), and the technique of the speed skaters (r=-.500) was found to be an explanation of the performance. For the 1.000 m this was only jump height, measured as a squat jump (r=-.555) and countermovement jump (r=-.491). The speed skating performance on the longer distances (1.500 m and 3.000 m) were found to be significantly related with evaluation (r=-.420 and r=-.481) and anaerobic power (r=.409 with the 3.000 m). The allround speed skating performance was significantly related with jump height, measured as a squat jump (r=-.406) and related with the technique (r=-.541). It can be concluded that explaining the performance of talented youth speed skaters is difficult. Nevertheless, this study reveals that jump height and technique seem to be important prerequisites for almost all distances.
EFFECT OF MONOSODIUM GLUTAMATE ON THE POST-NATAL DEVELOPMENT OF THE RETINA OF ALBINO RAT

to detect the early and delayed effects of monosodium glutamate on the retina of neonatal albino rats by using histological and ultra structural techniques. A total number of 24 animals aged 2 days postnatal were used in this study. Twelve animals were used as controls and injected with saline. The other 12 animals were treated subcutaneously with 4mg/gm body weight monosodium glutamate from the 2 nd to the 18 th day postnatal. The retina of six treated animals was examined in the next day after the last dose of treatment to detect the early effect of monosodium glutamate administration. The retina of the remaining six of the treated animals was examined later on at the age of 2 months to detect the delayed effect of monosodium glutamate. The semi-thin sections showed significant reduction in the thickness of different layers of the retina of the treated groups as compared with the control. This reduction was more marked in the treated 2 months age group as compared with the treated 19 days age group. This reduction in the thickness was detected by using statistical analysis using student t-test. On the ultra structural level manifestation of degeneration and cell death are observed in the treated groups. These include distortion in the shapes and dimensions of the cells and nuclei, marked vacuolization of the cytoplasm and destruction of the cell organelles. These monosodium glutamate induced ultra structural changes were prominent in the inner nuclear layer as well as in the ganglionic cell layer. Also these changes were more obvious in the older animals. It is concluded that monosodium glutamate has a toxic effect on different layers of the retina. This effect was more marked in the inner nuclear and ganglionic cell layers. In addition the late effect was more marked than the early effect. regions immediately temporal to the nerve head (central regions) were taken. Semi-thin sections (1 micron) and ultra-thin sections (0.07 microns) were done using ultra-microtome. Semi-thin sections were stained by toluidine blue and examined by light microscopy. Thickness of different layers of the retina was measured by using camera Lucida. Data for each group was presented in the mean ± standard deviation. Statistical analysis was done using student t-test. Ultra-thin sections were stained by uranyl acetate
Solution of Load-Flow Problems by Partitioning Systems into Trees

This paper presents a method of calculating load flows by partitioning a system into subsystems of tree form, for which the node-voltage equations can be solved very efficiently by optimally ordered Gaussian elimination. The solution for the complete system is then obtained by coupling direct solutions for the trees by a blockiterative method. Results comparing the block method with the accelerated Gauss-Seidel method show that the block method is considerably faster.
Six Sigma quality: a structured review and implications for future research

Purpose – This paper aims to clarify emerging aspects and trends of Six Sigma literature over 17 years, from 1992 to 2008.Design/methodology/approach – The literature on Six Sigma from 417 referred journal articles in business and management disciplines, information systems and computer science, engineering, healthcare, etc. were systematically analyzed based on a scheme that consists of four distinct dimensions: publication year and journal, major themes, research type, and application sector (i.e. manufacturing vs service). Findings – A number of key findings emerged: Six Sigma research is growing rapidly, covering various disciplines and domains with a great focus on Six Sigma tools and techniques; empirical research is dominant with more emphasis on case study approach; and the growing gap between manufacturing‐ and service‐focused articles implies the return of Six Sigma to manufacturing as its initial base. Although a large volume of literature is available on Six Sigma, the topic is still under deve.
Optimization of a 3.6-THz quantum cascade laser for real-time imaging with a microbolometer focal plane array

Real-time imaging in the terahertz (THz) spectral range was achieved using a 3.6-THz quantum cascade laser (QCL) and an uncooled, 160×120 pixel microbolometer camera fitted with a picarin lens. Noise equivalent temperature difference of the camera in the 1-5 THz frequency range was calculated to be at least 3 K, confirming the need for external THz illumination when imaging in this frequency regime. After evaluating the effects of various operating parameters on laser performance, the QCL found to perform optimally at 1.9 A in pulsed mode with a 300 kHz repetition rate and 10-20% duty cycle; average output power was approximately 1 mW. Under this scheme, a series of metallic objects were imaged while wrapped in various obscurants. Single-frame and extended video recordings demonstrate strong contrast between metallic materials and those of plastic, cloth, and paper - supporting the viability of this imaging technology in security screening applications. Thermal effects arising from Joule heating of the laser were found to be the dominant issue affecting output power and image quality; these effects were mitigated by limiting laser pulse widths to 670 ns and operating the system under closed-cycle refrigeration at a temperature of 10 K.
Improving Deep Reinforcement Learning for Financial Trading Using Deep Adaptive Group-Based Normalization

Deep Reinforcement Learning methods have provided powerful tools to train profitable agents for financial trading. However, the noisy and non-stationary nature of financial data often requires carefully designed and tuned input normalization schemes, since otherwise the agents are unable to consistently perform profitable trades. To overcome this limitation, in this work we propose a deep adaptive input normalization approach specifically designed to train DRL agents for financial trading directly using the raw price as input, without any additional pre-processing. The proposed method consists of two trainable neural layers that are designed to perform adaptive normalization, i.e., normalize the input observations after (implicitly) identifying the distribution that was used for generating them. Furthermore, instead of normalizing the whole input at once, the proposed approach performs group-based normalization, which allows for better capturing fine variations in the price trends. Despite being simple to implement and apply, the proposed method can lead to enormous improvements over existing the normalization methods, as demonstrated through the experiments conducted on two challenging FOREX currency pairs.
Modifying an unstructured Roe solver for large eddy simulation

© 2015 American Institute of Aeronautics and Astronautics Inc. All rights reserved. With the ever increasing availability of computing power, attention is being turned to large eddy simulation as a design tool at the component level. To maintain integration with pre-existing design processes based on solving the Reynolds Averaged Navier-Stokes equations, legacy RANS codes are being pressed into service with minimal adaptation to perform large eddy simulations. Often, these legacy RANS solvers are based around the approximate Riemann solver of Roe. It is shown here that the Roe scheme is not ideally suited to large eddy simulations, and may require excessive user care to extract worthwhile information — a process not always possible within design timeframes. A different discretisation scheme, which is shown to conserve kinetic energy, but which also shares some of the favourable structural behaviour of Roe’s is implemented, and is then tested on a range of geometries, both canonical and industrial. One of the advantages of this approach is its ability to eliminate the smoothing terms which have a strong deleterious affect on the LES performance of Roe. This allows explicit subgrid models to be sensibly applied. The new scheme, with explicit turbulence modelling, is found to outperform the Roe scheme for LES in all of the test cases.
z-transform analysis of nonuniformly sampled digital filters

The paper presents a z transform analysis of digital filters operated with nonuniform sample periods. The analysis is applicable to filters using a mean-square definition of transfer function, e. g. moving-target-indicator filters, and also to conventional digital filters. The evaluation of the frequency response of such filters using the analytic results of the paper leads to considerable savings in computation time over direct simulation methods. Nonuniform sampling of conventional digital filters is shown to result in a reduction of the effective Nyquist frequency, although, within this limited frequency range, additional control of the frequency response is possible for certain filters. A pole-zero diagram may be drawn for a nonuniformly sampled filter, and allows comparisons to be made with the corresponding uniformly sampled case.