Miracle-dz/UniFAR-FTUs huggingface dataset:
Unraveling the complexity of biological processes from protein native dynamics to cell motility

Pavel I. Zhuravlev Unraveling the Complexity of Biological Processes from Protein Native Dynamics to Cell Motility in Molecular Simulations. (Under the direction of Dr. Garegin A. Papoian) This dissertation consists of two major parts. Both are dedicated to studying biological molecular processes with computer simulations, but differ in the scale of the studied processes. In one project we investigated the dynamics of cellular organelles involved in cell motility – the filopodia. The other project is zooming in to the scale of single molecule, elucidating the organization of protein molecule native state. Some motile cells use special fingerlike probes of their environment for guiding their motion called filopodia. They are bundles of parallel actin filaments protruding from the cell body and enveloped by cell’s membrane. They are highly dynamic, constantly growing an retracting, randomly, or in response to the change in the environment. These dynamics are governed by the cell’s regulatory proteins and by external chemical cues or mechanical obstacles. The previous models predicted that a filopodium grows to a stationary length of about 1 μm with miniscule fluctuations around. (i) We found that capping proteins (they attach to the barbed ends of actin filaments and stop polymerization) can induce macroscopic oscillation of filopodial length – the growth-retraction cycles. The retraction can be complete. This is the first model that predicts finite lifetimes for filopodia. The lifetimes are consistent with experimental observations. (ii) In the model, however, the maximal filopodial lengths of several microns
Seasonal heavy metal monitoring of water, sediment and common carp (Cyprinus carpio) in Aras Dam Lake of Iran

Heavy metal in aquatic ecosystems are monitored by measuring their concentrations in water, sediments and biota. In the presented study, cadmium, copper, lead, mercury, nickel, and zinc concentrations determined in water, sediment and tissues (liver and muscle) of Cyprinus carpio in Aras dam Lake of Iran, during spring, summer, autumn, and winter from 2016 to 2017. The concentration of Pb, Cd, Zn, Cu and Ni of samples were measured using inductively coupled plasma-optical emission spectroscopy. The concentration of Hg was analyzed using Atomic Absorption equipped with MHS 15 CVAAS. The trend in the metal mean concentrations of liver and muscle was Zn>Cu>Pb≈Ni>Cd>Hg, and water and sediment were Cu>Zn>Pb>Cd≈Ni>Hg. Heavy metals concentration was more in sediment than fish tissues and water. This results revealed that heavy metals accumulation of muscle was the highest in summer showing the most contaminated season. Whereas, winter had the lowest contamination in water (Cd،Hg, Cu, Pb, Ni, Zn), sediments (Hg, Cu, Zn, Pb, Ni), and the liver and muscle of fish (Cd, Zn, Ni, Cu). The amount of heavy metals was less or slightly higher than global standards (EPA, WHO).
RHEOLOGY AND FLOW OF MUCUS IN HUMAN BRONCHIAL EPITHELIAL CELL CULTURES

Yuan Jin: Rheology and Flow of Mucus in Human Bronchial Epithelial Cell Cultures (Under the direction of M. Gregory Forest) The propulsion of mucus in human airways toward the trachea by the collective and coordinated action of cilia, known as mucociliary clearance, remains an outstanding modeling and computational challenge. A model system for mucociliary clearance is provided by human bronchial epithelial (HBE) cell cultures that generate macroscopic mean rotational flow. We coarse grain the coordinated cilia propulsion into an imposed dynamic velocity condition on the flat base of a cylinder. A multi-mode Giseskus nonlinear viscoelastic constitutive model derived from rheological data of mucus is employed for the mucus layer. The full system of governing equations for the transient and stationary axisymmetric flow field and air-mucus interface is solved numerically. Our modeling is the first step toward a platform for several purposes: to test accuracy of the constitutive modeling of mucus; to build a faithful model of the cilia-mucus boundary condition; to simulate both the flow and stress fields throughout the mucus layer; to explore the linear and nonlinear viscoelastic behavior of the mucus flow; and to explore the advection-diffusion process of a drug concentration dropped at the surface of the cell culture, and illustrate how the absorption by the bottom plate varies versus the initial drop position and the diffusion coefficient.
Synthesis of Zinc Oxide Supported on Titanium Dioxide for Photocatalytic Oxidative Desulfurization of Dibenzothiophene

Photocatalytic oxidative desulfurization (PODS) has received much attention due to low energy consumption and high efficiency, as well as simple and pollution-free operation. In this study, zinc oxide supported on titanium dioxide (ZnO/TiO2) catalysts were prepared via a simple electrochemical method. The presence of anatase phase TiO2 and wurtzite ZnO was confirmed by X-ray diffraction (XRD) analysis while band gap energies were determined by UV-Vis diffuse reflectance spectroscopy (UV-Vis DRS). The photocatalytic activity was tested for desulfurization of 100 mg/L dibenzothiophene (DBT). The highest desulfurization rate (2.20 × 10-3 mM/min) was achieved using 1 g/L of 10 wt% ZnO/TiO2 after 2 hr under UV irradiation.
Ant colony and particle swarm optimization algorithm-based solution to multi-mode resource-constrained project scheduling problem

A hybrid of ant colony and particle swarm optimization algorithms is proposed to solve the multi-mode resource-constrained project scheduling problems.The hybrid is formulated in a form of hierarchical structure.The ant colony algorithm is performed at the master level to select activity mode,while the particle swarm algorithm is carried out at the slave level to schedule activities without violating the result from the master level.Then,the transfer probabilities of ant,the selective probability for modes and the selective probability for activities are designed in order to distribute resource equably and minimize the makespan of project.Furthermore,the main parameters in the algorithm are optimized with the benchmark problems from PSPLIB.The simulation results and comparison with others' validate the effectiveness of the proposed algorithm.
Fault diagnosis of mechanical systems based on electrical supply characteristics

Induction motors are the main workhorses of industry. Condition monitoring (CM) of motor based systems plays an important role in the early detection of possible defects, averting adverse operational and financial effects caused by unexpected breakdowns. Limited information has been found which explores the diagnostic abilities of voltage and motor current signals from motors with variable speed drives (VSDs), which are increasingly used in industry to obtain better dynamic response, higher efficiency and lower energy consumption. This study addresses the gap identified by carrying out a systematic review of the monitoring of mechanical systems using induction motors with sensorless VSDs. Specifically, existing techniques often prove ineffective for common internal and external faults that develop in Induction motors. The primary aim is to extract accurate diagnostic information from the power supply parameters of a VSD to monitor IM driven systems for early diagnosis of both mechanical and electrical faults. This thesis examines the effectiveness of both motor current and voltage signals using spectrum analysis for detecting broken rotor bar(s) and/or shaft misalignment and gear oil viscosity changes with different degrees of severities under sensorless control (close) modes. The results are obtained from common spectrum analysis applied to signals from a laboratory experimental setup operating under different speeds and loads. Evaluation of the results shows that the faults cause an increase in sideband amplitudes, which can be observed in both the current and voltage signals under the sensorless control mode. In addition, combined faults cause an additional increase in the sideband amplitudes and this increase can be observed in both the current and voltage signals. The voltage signals show greater change compared with the current signals because the VSD adapts the voltage supply source to compensate for changes in the system dynamics. Furthermore, this study also presents a model of an induction motorfed by a variable speed drive (VSD), as an approach to simulate broken rotor bars and shaft misalignments to give an in-depth understanding of fault signatures. The model was validated with experimental results in both current and voltage signals, with good agreement. The model confirmed that BRB causes a shift and increase in the amplitudes of the sidebands with the amplitudes of the rotor frequency components increased due to shaft misalignment.
Development of Character and Life Skills through Islamic Methods of Teaching Acquired Science Subjects at Islamic International Schools in Malaysia

Islamic Schools strive to achieve educational excellence while integrating religious values into their curriculum. Yet, what makes an Islamic school really “Islamic” is not just the content of the curriculum, but also the teaching methods employed by the teachers who are teaching religious and non-religious subjects which affect the whole implementation of the integrated curriculum. The aim of this paper is to investigate the potential benefits of using Quranic and Prophetic Teaching Methods (QPTMs) in non-religious classes on developing the characters of students. Semi-structured one-on-one interviews were conducted with 6 teachers teaching non-religious subjects in Islamic international schools in Malaysia. The interviews were transcribed and the data collected was analyzed by the researchers. The study analysis revealed that teachers of non-religious subjects in Islamic international schools believe that QPTMs contribute to students’ character development by inculcating characteristics and life skills. The findings of the study can draw the attention of integrated curriculum developers to the impact of including the QPTMs in teaching non-religious subjects in the inculcation of Islamic morals and developing the characters of the students. Key words: Islamic education, moral education, character development, teaching methods, integrated curriculum
USING FEED ADDITIVES FOR BETTER UTILIZATION OF PHOSPHORUS AND NITROGEN IN BROILERS FEEDS

One hundred fifty Arbor Acers broiler chicks were distributed into five groups to study effects of using sodium formate, formic acid, Lactobacillus acidophilus and beta mannanase enzyme, in broiler feeds, on production performance, carcass traits, blood parameters, tibia properties and economic efficiency. Each group of birds, was divided into three replicates of ten chicks. The control group was fed basal (starter, grower and finisher) with no additives (T1), while other groups were offered basal diets supplemented with 2g sodium formate/kg (T2); 2 ml formic acid / kg (T3); 1g Lactobacillus acidophilus/ kg (T4) and 0.3 g beta mannanase/ kg (T5), respectively. The results indicated that all production performance parameters: initial and final body weight, daily body weight gain, daily feed intake and feed conversion ratio, were not significantly affected by treatments throughout experimental period. Also, data of carcass, indicated that treatments had no significant effects compared with control group. Plasma total protein, uric acid, calcium, phosphorus and activity of alkaline phosphatase, were significantly different within groups. Tibia bone parameters: breaking force, density, robusticity index, Seedor index, were not significantly affected by treatments. Economical evaluation showed that, relative economic efficiency, was improved with chicks fed (T2) or (T3) diets, while those fed (T4) or (T5) diets, recorded lower values. It could be concluded that, supplementation of basal diets with sodium formate or formic acid enhanced economic efficiency of broiler chickens, without affecting performance or carcass traits.
Using robot-based practices to develop an activity that incorporated the 6E model to improve elementary school students’ learning performances

ABSTRACT This study used robot-based practices to develop an activity that incorporated the 6E model. The sixth-grade students learned interdisciplinary knowledge about how to use Arduino electronic components, microcontrollers, and hands-on tools to make a “Crab Robot. ” In addition, the students learned how to use Scratch programming language to control the robot and complete the “Crab Robot Crossing the Road” task. The study implemented a quasi-experimental design to examine whether the students who learned the robot-based activity using the 6E model acquired better learning motivation, learning performance, computational thinking ability, and hands-on ability than those who learned the activity through lectures. This study adopted purposive sampling to select 70 sixth-grade students from four classes, which were divided into the experimental group (6E model) and the control group (lectures). The experiment was conducted over a period of 18 weeks (for a total duration of 1,440 minutes). The results from the pretests-posttests showed that both groups of students improved their learning motivation, learning performance, computational thinking ability, and hands-on ability; however, the experimental group’s scores were significantly better. More importantly, this study provides a pedagogy manuscript for instructors who want to teach mechatronics programs and programming design education.
Optical limiting properties of BODIPY dyes substituted with styryl or vinylene groups on the nanosecond timescale

The results of recent studies on the optical limiting properties of BODIPY dyes at 532 and 1064 nm are described and compared. The optical limiting properties of novel 1,7-dimethyl-3,5-di-4-dihydroxyborylstyryl- and 3,5,7-tristyryl-1-methyl-BODIPY dyes were studied in CH2Cl2 and C6H6 and polystyrene thin films using the open aperture Z-scan technique at 532 nm with nanosecond laser pulses to provide an example of how the effective nonlinear absorption coefficient, the third order susceptibility, hyperpolarizability and limiting thresholds can be calculated.
Nonlinear Dielectric Effect in the Vicinity of Solid–Liquid Phase Transition of 1-Decanol

A motivation to perform the non-linear dielectric effect (NDE) experiments in the vicinity of freezing-melting region of 1-decanol was the intention to observe a pre-transition anomaly in supercooled liquid, similar to that announced already for nitrobenzene. In the case of 1-decanol the pre-transition effects were not observed, but we found interesting NDE behaviors in the solid state approaching the melting temperature. To our best knowledge, it is the first time when NDE effect was measured in the solid state close to solid-liquid phase transition. In our opinion, the observed behaviors could be interpreted as an effect of appearing of the rotator phase and premelting.
Automatic Recovery Estimation of Degraded Soils by Artificial Neural Networks in Function of Chemical and Physical Attributes in Brazilian Savannah Soil

ABSTRACT The Oxisols is predominant in 54% of Brazilian territories and characterized by high weathering, relatively low chemical properties, and adequate structure. This study aimed to analyze the Oxisols through an Artificial Neural Network (ANN) with the purpose of estimating its recovery in function to soil chemical and physical attributes. The chemical attributes considered were: pH, cation exchange capacity (CEC), base saturation (V%), phosphorus (P), magnesium (Mg2+), and potassium (K+) and for the physical attributes, bulk density, soil porosity and soil resistance to penetration. The ANN used in this study is the Multilayer Perceptron (MLP), composed of three layers, input, intermediate and the output and with backpropagation training algorithm (supervised training). The intermediate layer is composed by 10 neurons and the layer of exit by 1 neuron, which has a function of informing the levels of chemical recovery (high, medium and low chemical attributes of the soil) and soil physics (recovered, partially recovered or not recovered). From the results obtained by ANN showed that the network reached an adequate training, with low mean square error (MSE). Therefore, ANN is a powerful and automatic alternative for the recovery estimation of degraded soils.
Intravital assessment of angioarchitecture in rat hepatocellular nodules using in vivo fluorescent microscopy.

Background To prospectively evaluate the stepwise changes that occur in intra-nodular microvessels and microcirculation during the carcinogenesis process of hepatocellular nodules by using in vivo fluorescent microscopy, and to compare these with pathological changes. Methods Forty-five 10-week-old male Wistar rats received drinking water containing N-nitrosomorpholine at 10 mg/100 mL for 18weeks to develop multiple hepatocellular carcinomas (HCC) and dysplastic nodules (DN) in the liver; meanwhile, the non-lesion liver tissues become fibrotic. The microvascular morphological change and hemodynamic change of two lesion areas (HCC or DN) and one non-lesion area in each rat were observed with in vivo fluorescent microscope. After in vivo microscopy, 90 nodules and 45 non-lesion liver tissues that were observed were removed for pathological study. The microvessel density (MVD), branch density (BD), and cell density (CD) of these lesions were compared with the Kruskal-Wallis test and Mann-Whitney test, with an overall statistical significance of 0.05. Results The intra-nodular microvessels appeared tortuous, with irregular branching and abrupt diameter changes to form irregular convoluted networks in the HCC. This was distinctly different from the appearance of DN and non-lesion liver parenchyma. The MVD and BD of HCC were less than that of the DN and non-lesion liver parenchyma (P<0.01), and the BD of DN was also less than that of the non-lesion liver parenchyma (P<0.05). However, the MVD of the DN was similar to that of the non-lesion liver parenchyma (P>0.05). The CD of HCC was more than that of the DN and non-lesion liver parenchyma (P<0.05), and the CD of DN was also more than that of the non-lesion liver parenchyma (P<0.05). Conclusions Concurrent with the carcinogenesis process of the hepatocellular nodule, both the intra-nodular microvascular morphology and hemodynamics were stepwise changed, and the number of the intravascular lumen of intranodular microvessels decreased due to the infiltration and compression of intra-nodular parenchymal cells.
Development of Android Comic Media for the Chapter of Newton’s Gravity to Map Learning Motivation of Students

This research was designed to map students’s learning motivation by developing comic physics media. This study used the ADDIE development model. The subjects tried in this study were students in one senior high school in Yogyakarta at the grade of 10th science. Data collection instruments were in the form of students’ motivation observation sheets and students’ learning motivation questionnaire. The data obtained were analyzed quantitatively. The results showed that (1) Android-based physics comic media on the Newton’s Gravity chapter was an innovation in the world of education that utilized TPACK (Technological Pedagogical Content Knowledge). (2) Comic media can be and are suitable for use in physics learning for senior high school, and (3) comic media can be used to map the learning motivation of high school students.
Automatic deployment and reproducibility of workflow on the Cloud using container virtualization

Cloud computing is a service-oriented approach to distributed computing that has many attractive features, including on-demand access to large compute resources. One type of cloud applications are scientific workflows, which are playing an increasingly important role in building applications from heterogeneous components. Workflows are increasingly used in science as a means to capture, share, and publish computational analysis. Clouds can offer a number of benefits to workflow systems, including the dynamic provisioning of the resources needed for computation and storage, which has the potential to dramatically increase the ability to quickly extract new results from the huge amounts of data now being collected. However, there are increasing number of Cloud computing platforms, each with different functionality and interfaces. It therefore becomes increasingly challenging to define workflows in a portable way so that they can be run reliably on different clouds. As a consequence, workflow developers face the problem of deciding which Cloud to select and more importantly for the long-term how to avoid vendor lock-in. A further issue that has arisen with workflows is that it is common for them to stop being executable a relatively short time after they were created. This can be due to the external resources required to execute a workflow such as data and services becoming unavailable. It can also be caused by changes in the execution environment on which the workflow depends, such as changes to a library causing an error when a workflow service is executed. This ”workflow decay” issue is recognised as an impediment to the reuse of workflows and the reproducibility of their results. It is becoming a major problem, as the reproducibility of science is increasingly dependent on the reproducibility of scientific workflows. In this thesis we presented new solutions to address these challenges. We propose a new approach to workflow modelling that offers a portable and re-usable description of the workflow using the TOSCA specification language. Our approach addresses portability by allowing workflow components to be systematically specified and automatically
Detecting non-tree-like signal using multiple tree topologies

Recent applications of phylogenetic methods to historical linguistics have been criticized for assuming a tree structure in which ancestral languages differentiate and split up into daughter languages, while language evolution is inherently non-tree-like (François 2014; Blench 2015: 32–33). This article attempts to contribute to this debate by discussing the use of the multiple topologies method (Pagel & Meade 2006a) implemented in BayesPhylogenies (Pagel & Meade 2004). This method is applied to lexical datasets from four different language families: Austronesian (Gray, Drummond & Greenhill 2009), Sinitic (Ben Hamed & Wang 2006), Indo-European (Bouckaert et al. 2012), and Japonic (Lee & Hasegawa 2011). Evidence for multiple topologies is found in all families except, surprisingly, Austronesian. It is suggested that reticulation may arise from a number of processes, including dialect chain break-up, borrowing (both shortly after language splits and later on), incomplete lineage sorting, and characteristics of lexical datasets. It is shown that the multiple topologies method is a useful tool to study the dynamics of language evolution.