Miracle-dz/UniFAR-FTUs huggingface dataset:
Sterol regulatory element binding proteins: their role in the hypoxic response of cancer cells and their regulation by the Akt/mTORC1 pathway

Sterol regulatory element binding proteins (SREBPs) are transcription factors that regulate the expression of genes involved in fatty acid and cholesterol biosynthesis. It has been established that SREBPs are regulated downstream of the PI3-Kinase/Akt/ mTORC1 signalling axis, a pathway that is frequently hyper-activated in cancer. SREBP target genes are upregulated in some forms of human cancer and a role for lipid metabolism in tumourigenesis has been suggested. Glioblastoma multiforme (GBM) is a cancer type that is associated with hyperactivation of the PI3-kinase/Akt signalling pathway and frequently displays poorly oxygenated (hypoxic) regions. SREBP1 has been implicated in the tumourigenic potential of this cancer type. However, the exact role of SREBPs in tumourigenesis is not known. In oder to investigate the SREBP-transcriptional response in cancer cells, a gene expression microarry analysis was carried out. It was found that SREBPs regulate genes involved in a variety of cellular processes including lipid metabolism, cell cycle regulation, redox regulation and cellular stress response. In addition, the role of SREBPs in lipid metabolism in hypoxia was investigated. It was found that hypoxia leads to distinct changes in the expression of different SREBP isoforms and their target genes and is associated with a decrease in pyruvate-dependent lipid synthesis and increased lipid storage. SREBPs are regulated downstream of the Akt/mTORC1 pathway, although the exact mechanism of this regulation remains to be elucidated. Possible mechanisms by which Akt and mTORC1 regulate SREBPs were investigated. It was found that inhibition of mTORC1 differentially affects the expression of individual SREBP isoforms. The results described in this thesis also show that mTORC1 modulates the transcriptional activity of mature SREBP and may regulate its stability in a GSK3-independent manner.
Purification, surfactant stabilization, molecular weight studies, and divalent metal ion kinetics of dextransucrase from Leuconostoc mesenteroides NRRL B-512F

Dextransucrase (3 International Units/ml culture supernatant) was obtained by a modification of the method of Robyt and Walseth [J. F. Robyt and T. F. Walseth. Carbohydr. Res. 95-111 (1979)] from a nitrosoguanidine mutant of Leuconostoc mesenteroides NRRL B-512F selected for high dextransucrase production. Dialyzed, concentrated culture su­ pernatant (crude enzyme) was treated with immobilized dextranase and chromatographed on a column of Bio-Gel A—5m. The resulting, purified enzyme lost activity rapidly at 25° or on manipulation, as did the crude enzyme when diluted below 1 U/ml. Both enzyme preparations could be stabilized by low levels of high-molecular-weight dextran (e.g., 2 ug/ml), poly(ethylene glycol) (e.g., 10 wg/ml PEG 20,000), or nonionic detergents (e.g., 10 ug/ml Tween 80). The stabilizing capacity of poly(ethylene glycol) and of dextran increased, with molecular weight. Calcium had no stabilizing action in the absence of other additions, but reduced the inactivation that occurred in the presence of 5 mg/ml bovine serum albumin or high concentrations (>50 wg/ml) of Triton X-100. In summary, dextransucrase could be stabilized against activity losses caused by dilution or by thermal inactivation through the addition of low concentrations of nonionic polymers (dextran, PEG 20,000, methyl cellu­ lose) or of nonionic detergents at or slightly below their critical micelle concentrations.
Site-Specific Structure and Dynamics of Polyglutamine-Containing Amyloid Fibrils and the Caveolin Scaffolding Domain by Magic Angle Spinning Solid-State NMR

Protein assemblies and membrane associations play important roles in health and disease. Structural studies of these biological complexes are thus vital, but are often unfeasible by conventional tools in structural biology. Solid-state NMR (ssNMR) has made possible atomic-level structural studies of large, insoluble, and non-crystalline biological systems, such as amyloid fibrils and membrane proteins. Amyloid fibrils are associated with at least 20 human diseases, making structural aspects of their formation crucial to understanding their aggregation pathways. Huntington’s disease (HD) is caused by an expansion beyond a threshold of the polyglutamine (polyQ) domain in the Exon 1 of the huntingtin protein (htt). The 17-residue N-terminal segment of the Exon 1 (httNT) initiates the fibril aggregation and helps stabilize oligomers and fibrils. On the contrary, a polyPro segment C-terminal to the polyQ reduces fibril aggregation. In this thesis, magic-angle spinning (MAS) ssNMR was used to elucidate atomic-resolution structure and dynamics of the polyQ and its flanking domains in polyQ-containing amyloid-like fibrils. More than 25% of human proteins are membrane proteins. Caveolin-1 (Cav1) is a protein found associated with cholesterol-rich membranes that forms caveolae, curved cave-like invaginations in the plasma membrane, and is implicated in muscular diseases and cancers. The caveolin-scaffolding domain (CSD) of Cav1 is responsible for cholesterol-recognition and oligomerization to form the caveolae. In this thesis, MAS and static ssNMR are used to elucidate molecular structure of the CSD and its perturbation of the lipid bilayer in a cholesterol-rich lipid environment. These results allow for a more thorough understanding of the role of CSD in caveolae formation.
Dissecting the multiple roles of the Igf2r imprint control element

Genomische Pragung fuhrt zur monoallelischen Expression von Genen von einem elterlichen Allel und involviert epigenetische Mechanismen. Gepragte Gene treten meist in Clustern auf und jeder Cluster hat ein sogenanntes Imprintcontrolelement (ICE), welches die gepragte Expression aller Gene im Cluster reguliert. Der gepragte Igf2r Cluster am Mauschromosom 17 umfasst 430kb und enthalt drei maternal exprimierte proteincodierende Gene, Igf2r, Slc22a2 und Slc22a3 und eine paternal exprimierte nichtcodierende RNA (ncRNA), Airn, welche die gepragte Expression der proteincodierenden Gene reguliert. Am maternalen Allel ist das ICE DNA methyliert, am paternalen Allel hingegen unmethyliert. Man hat gezeigt, dass eine Deletion des ICE die gepragte Expression aller Gene im Igf2r Cluster aufhebt. In dieser Dissertation habe ich analysiert, ob das ICE eine weitere Rolle auf chromosomaler Ebene spielt und ob Elemente innherhalb des ICE verschiedene Rollen im Pragungsprozess spielen. DNA FISH Asynchronie ist ein Merkmal gepragter Cluster, der dahinterliegende Mechanismus ist jedoch noch nicht komplett aufgeklart. Im ersten Teil meiner Arbeit habe gezeigt, dass eine chromosomale Region von 3Mbp DNA-Fluoreszenz-in-situ-Hybridisierungs- (DNA FISH) Asynchronie aufweist. Diese Asynchronie wird jedoch weder vom ICE, noch von Airn oder der Igf2r Promoterregion kontrolliert. Weiters habe ich gefunden, dass diese DNA FISH Asynchronie weder aufgrund von Unterschieden in der Chromatinkompaktierung noch durch Unterschiede in der DNA Replikation wahrend der S-Phase zustande kommt. Im zweiten Teil meiner Arbeit habe ich den Effekt von zwei Subdeletionen des ICE auf verschiedene Aspekte der genomischen Pragung hin analysiert. Ich habe embryonale Stammzellen (ES Zellen) mit einer paternalen Deletion der tandem direkten Repeats oder der CpG Insel hergestellt und diese ES Zellen mit Hilfe eines in vitro Differenzierungssystems analysiert. Ich habe gezeigt, dass die tandem direkten Repeats die Lange von Airn und die Fahigkeit von Airn, gepragte Expression von Igf2r zu verursachen, regulieren, und die CpG Insel von Airn benotigt wird, um DNA Methylierung am paternalen Allel zu verhindern. Das zeigt, dass die CpG Insel, die abwarts vom Airn Promotor liegt, eine wichtige Rolle in der Transkription von Airn spielt.
Integration of Problem Based Learning (PBL) and Engineering is Elementary (EiE) to improve students’ creativity

This study aims to measure and analyze the creativity of high school students on Magnetic Induction topic through the application of Problem Based Learning (PBL) which are integrated with the Engineering is Elementary (EiE) approach. This quasi-experimental control group design formed research was conducted on students of Darul Imarah 1 Public High School. By using random sampling, grade twelve 2 was chosen as an experimental class and grade twelve 3 was chosen as control class. Student’s creativity was obtained through student’s answers to the Torrance Test of Creative Thinking (TTCT) creativity instrument for three aspects of creativity (elaboration, originality, and fluency). The result of t-test analysis of student’s creativity in the experimental class showed significant differences between both classes. The creativity of the experimental class students was found to be better than the control class for all three aspects of creativity. The result of this study has provided an evidence of empirical results that the models and approaches could increase student’s creativity, so active student learning approaches such as the PBL model have deserved to be used in teaching and learning process and are considered to be carried out in the High School Curriculum.
The Development of Tumor Neoantigen Vaccine Immunotherapy

Activating the immune system to fight against cancers has long been a goal in immunology and oncology studies. Recent clinical-trial data proved that boosting the activity of endogenous T cells to destroy cancer cells has great potential in controlling the progression of a variety of human malignancies. In essence, neoantigen is at the core of tumor immunology. Autologous T lymphocytes could distinguish tumor cells from normal cells by recognizing neoantigens, which are tumor specific. Neoantigens are derived from genome somatic mutations of tumors, and there are different approaches to predict and identify them with increasing accuracy. Neoantigens are tumor specific, which are ideal and attractive targets for tumor immunotherapies; many neoantigen-based clinical trials are being carried out around the world. In this review, we will discuss the recent advances of tumor neoantigen vaccine immunotherapy, and present the potential obstacle and future direction of this approach.
The Evolutionary History and Phylogeny of the Lithodinae (Decapoda: Anomura: Lithodidae)

The anomuran sub-family Lithodinae comprises a great diversity of morphological and ecological forms, whose global radiation has not been specifically addressed since the modern syntheses of plate tectonics, oceanography, species theory and cladistic systematics. The focus of this thesis was to investigate the origin and radiations of the deep-sea Lithodinae as a case study for interchanges between deep and shallow oceans in mobile benthic fauna. Molecular sequences were obtained from six genes (for 47 species belonging to 10 genera of Lithodidae) and different aspects of morphology were examined in order to identify nested monophyletic groups based on shared, derived characteristics. The hypothesis that lineage-specific temperature tolerances influence the distribution of deep- and shallow-water groups was tested by examining habitat alongside phylogeny. Lithodid ancestors are likely to have had a north Pacific, shallow-water distribution and planktotrophic larvae. Some shallow-water populations of Lithodidae are tied to locations north of 30°N because of the restricted thermal tolerance of pelagic larval stages; however, life-history changes allowed the subfamily Lithodinae to expand through the global deep sea, where they are now living at the frontier of their lower temperature threshold in the Southern Ocean. Phylogenies indicate the importance of large-scale dispersals within deep-sea groups, linked to the cold deep-water currents that connect the major oceans. The subfamily Lithodinae includes examples of at least two genera in which diverse morphologies have arisen within the deep ocean in the absence of discernable barriers to gene flow. Adult migration and larval dispersal partially explain the widespread occurrence of the Lithodidae, but this does not indicate that lithodids roam the ocean depths unconstrained by physical or chemical conditions. Climate change throughout the Cenozoic has substantially altered the marine environment and shaped the distribution and radiation of the extant Lithodidae. In the forthcoming years, measurable changes in ocean temperature, ocean currents and benthic habitat will affect the distribution of the lithodids and the communities they live in, as they have in the past.
Histopathological Analysis of Sealant Infiltration in White Spot Enamel Lesions (WSEL)

The use of resin sealants has shown partial infiltration of White-Spot Enamel Lesions in vitro (WSEL). The aim of the present study was to perform a morphological evaluation of natural WSEL when infiltrated using a commercially available sealant (Concise, 3MESPE). 20 bicuspids extracted for orthodontic reasons from patients ranging 18 to 30 years old, which had WSEL, were used in this study. The patients agreed to donate their teeth by signing a written consent. Every WSEL was assessed microscopically (Stereo Zeiss Axiscop) and then photographed (ProScope HR microscope). Prior to applying the sealant the lesion was etched using phosphoric acid at 37 % (3M-ESPE, St Paul, MN, USA.) for 30 seconds, washed for 40 seconds and then air-dried. The sealant was marked with rhodamine B (1mg/ml) and was applied according to the manufacturer directions. A specimen of approximately 100 mm was obtained for every WSEL by cutting perpendicularly through the lesion (Isomet 1000, Buehler Co.) and grinding (600 grit). The specimens were evaluated using: clear camp, polarized light, and epifluorescence microscopy. Images were taken of each specimen for every microscopic evaluation using a slide film (Kodak Ektachrome film 400 ASA). The images were digitalized by scanning at 1200 dpi resolution (Epson Filmscan 200) and then saved as JPEG and TIFF files. The sealant infiltration into The WSEL was assessed by means of analysis, processing and digital superimposing using Adobe Photoshop 7.0 and Matrox Inspector 1.07. It was concluded that the sealant infiltrated the whole body zone of the lesion. The depth of penetration of sealants into White Spot Enamel Lesion plays an important role in the control of caries lesion progression. KEYS WORDS: histopathological analysis, sealant, white-spot enamel lesion, microscopy
Optimization approach on using fishing strategy

A novel optimization means of using the strategy of fisher’fishing is introduced in this paper.Three search technologies which are called moving search,reducing search and speeding search are used in this optimization approach.In the beginning,some points are randomly distributed over the grabbling domain,and every point of them is regarded as a"fisher". Then every"fisher"of them is used to search"himself"optimum points or global optimum solution through"his"moving search,reducing search and speeding search independently.The results of this experiment indicate that the optimization algorithm shows its better efficiency of searching the global optimum solution.So the optimization approach is effective and feasible.
Docking Unit Joining Omni Wheel Robot and Mobile Robot

This research realizes a docking unit joining omni wheel robot and mobile robot. The omni wheel robot cannot move on rough ground. In order to move on rough ground, a mobile robot that can move with the omni wheel robot is required. The docking unit aims at a unit that can be used without remodeling omni wheel robot. The docking unit realized by this research can store the fixed part of the omni wheel robot. When omni wheel robot is mounted, the mounting surface is flat because the fixed parts are stored, and the omni wheel robot can be mounted by sliding. As a result, we designed a mechanism to connect the fixed parts to store the parts that fix the omni wheel robot. And the fixed parts with the mechanism were made.
An Efficient Directory Entry Lookup Cache With Prefix-Awareness for Mobile Devices

Modern mobile devices, such as smartphones, maintain a directory cache (DCache) to accelerate directory and file accesses. However, the original DCache recursively walks through all the components of a path name for each directory entry (dentry) lookup operation, leading to low lookup efficiency. In this article, we first investigate intrinsic characteristics of dentry lookup operations in smartphones and make several interesting findings: 1) file path lookup operations are called frequently (up to 104 times per second) by mobile applications; 2) file path lookup operations present high temporal and spatial locality; and 3) the latency of a file path lookup is linear to the depth of the path name. Based on our findings, we further propose an efficient directory entry lookup cache architecture, named dynamic skipping cache (DS-Cache), which adopts an ASCII-based hash table to simplify the path lookup complexity. In DS-Cache, a dynamic skip lookup algorithm is proposed to skip the common prefixes of different accessing paths. A rename algorithm and a delete algorithm are designed to promise the consistence of DS-Cache and the backend file system. We also design a prefix-aware cache replacement scheme to optimize the DS-Cache hit ratio. We have implemented and deployed DS-Cache on a Google Nexus 6P smartphone. The experimental results show that we can significantly reduce the latency of invoking system calls by up to 81%, and further reduce the completion time of real-world mobile applications by up to 67%.
A BIO-HYBRID PLATFORM USING THIN-FILM-TRANSISTOR ARRAYS AND A BIOMIMETIC NEURAL NETWORK

INTRODUCTION Neurons and cardiac cells exhibit electrical activity, which is usually measured in-vitro using MultiElectrode-Array (MEA) devices [1]. This work proposes a bio-hybrid platform which interfaces and evaluates with a biomimetic neural network new types of MEAs, made by Thin-Film-Transistor technology. Actually, it is the only technology, recently used for biological applications [2], which makes possible to reach around two orders of magnitude in term of density of sensing areas compared to MEAs. By combining a biomimetic device to this development, the authors investigated how neural biomimetic signals are sensed by the TFT array device, as a preliminary investigation before interfacing with biological cells.
A rule‐based self‐regulated learning assistance scheme to facilitate personalized learning with adaptive scaffoldings: A case study for learning computer software

Many studies indicate that most students find it difficult to learn effectively in computer‐based learning environments because of a lack of self‐regulated learning (SRL) abilities. Therefore, based on the design approach of the rule‐based system, this paper proposes a rule‐based self‐regulated learning assistance scheme (SRL‐RuAS) to intelligently facilitate personalized learning with SRL‐based adaptive scaffolding support for learning computer software. In the SRL‐RuAS scheme, SRL‐based adaptive scaffolding strategies (SRL‐AS) are defined according to SRL behaviors, the subject knowledge is formatted using the concept ontology technique, the relations of learning resources and the portfolio of students are modeled by the proposed learning analysis data model, and the learning analysis rules of adaptive scaffolding are defined according to SRL‐AS. Consequently, an intelligent learning environment with SRL‐RuAS can intelligently give learning support to actively assist students in understanding the learning status and guiding learning improvement. Hence, the learning process with SRL‐based assistance is able to improve learning motivation and effectiveness. Experimental results of a case study for learning computer software show that the SRL‐RuAS scheme is beneficial for learning achievement and the satisfaction of students, and its scaffolding strategies and application domain can thus be manageable and extended because of the rule‐based system design.
The lifecycle of a research tutorial: From concept to implementation and beyond

Abstract In 2016, the University of Maryland Global Campus Library began a redesign of its core information literacy tutorial in response to substantive curricular changes, the technological obsolescence of an older tutorial, and an improving understanding of student needs based on an analysis of reference questions received. This article describes the design process, with an emphasis on best practices and directions for future research.
Extending Abstract Interpretation to Dependency Analysis of Database Applications

Dependency information (data- and/or control-dependencies) among program variables and program statements is playing crucial roles in a wide range of software-engineering activities, e.g., program slicing, information flow security analysis, debugging, code-optimization, code-reuse, code-understanding. Most existing dependency analyzers focus on mainstream languages and they do not support database applications embedding queries and data-manipulation commands. The first extension to the languages for relational database management systems, proposed by Willmor et al. in 2004, suffers from the lack of precision in the analysis primarily due to its syntax-based computation and flow insensitivity. Since then no significant contribution is found in this research direction. This paper extends the Abstract Interpretation framework for static dependency analysis of database applications, providing a semantics-based computation tunable with respect to precision. More specifically, we instantiate dependency computation by using various relational and non-relational abstract domains, yielding to a detailed comparative analysis with respect to precision and efficiency. Finally, we present a prototype <inline-formula><tex-math notation="LaTeX">$\sf{ semDDA}$</tex-math><alternatives><mml:math><mml:mi mathvariant="sans-serif">semDDA</mml:mi></mml:math><inline-graphic xlink:href="jana-ieq1-2861707.gif"/></alternatives></inline-formula>, a <bold>sem</bold>antics-based <bold>D</bold>atabase <bold>D</bold>ependency <bold>A</bold>nalyzer integrated with various abstract domains, and we present experimental evaluation results to establish the effectiveness of our approach. We show an improvement of the precision on an average of 6 percent in the interval, 11 percent in the octagon, 21 percent in the polyhedra and 7 percent in the powerset of intervals abstract domains, as compared to their syntax-based counterpart, for the chosen set of Java Server Page (JSP)-based open-source database-driven web applications as part of the GotoCode project.