Task-based Example Miner for Intelligent Tutoring Systems

Intelligent tutoring systems (ITS) aim to provide customized resources or feedback on a subject (commonly known as domain in ITS) to students in real-time, emulating the behavior of an actual teacher in a classroom. This thesis designs an ITS based on an instructional strategy called example-based learning (EBL), that focuses primarily on students devoting their time and cognitive capacity to studying worked-out examples so that they can enhance their learning and apply it to similar graded problems or tasks. A task is a graded problem or question that an ITS assigns to students (e.g. task T1 in C programming domain defined as “Write an assignment instruction in C that adds 2 integers”). A worked-out example refers to a complete solution of a problem or question in the domain. Existing ITS systems such as NavEx and PADS, that use EBL to teach their domain suffer from several limitations such as (1) methods used to extract knowledge from given tasks and worked-out examples require highly trained experts and are not easily applicable or extendable to other problem domains (e.g. Math), either due to use of manual knowledge extraction methods (such as Item Objective Consistency (IOC)) or highly complex automated methods (such as syntax tree generation) (2) recommended worked-out examples are not customized for assigned tasks and therefore are ineffective in improving student success rate

Reactivities Leading to Potential Chemical Repair of Sunlight-Induced DNA Damage: Mechanistic Studies of Cyclobutane Pyrimidine Dimer (CPD) Lesions under Alkaline Conditions

Indiana University-Purdue University Indianapolis (IUPUI)Cyclobutane pyrimidine dimers (CPD) are the predominant DNA lesions formed upon exposure of this biopolymer to sunlight. Given the potentially dire biological consequences of DNA lesions, there is a need to fully characterize their behavior, with an eye towards understanding their complete reactivity and as a possible means to detect and quantify their presence in the genome. The work described in this dissertation describes studies of the alkaline reactivity of CPD lesions generated within dinucleotide & polynucleotide strands. It was found that CPD-TpT is generally inert under alkaline conditions at room temperature, which is in agreement with earlier studies on alkaline hydrolysis of CPD-thymine and CPD-thymidine. However, a re-evaluation of the same reaction in the presence of 18O labelled water demonstrated that, similar to other UV-induced DNA lesions containing a saturated pyrimidine ring, CPD undergoes a water addition at the C4=O group of the nucleobase leading to the formation of a hemiaminal intermediate. This intermediate, however, does not lead to hydrolysis products and completely reverts to starting material under those same conditions. Moreover, the two C4=O groups present on 3′ and 5′-thymines in a CPD molecule show different chemical reactivities, with the 3′ C4=O group having greater affinity towards water addition as compared to the one on 5′ end, a fact reflected in different rates of exchange with the incoming nucleophile leading to the hemiaminal intermediate. The 18O labelling reaction was also investigated in CPD lesions generated within oligonucleotides to probe the cause of asymmetry between the 3′ vs 5′ C4=O groups; ultimately, it was determined that the asymmetric reactivity observed to occur between the two C4=O groups was an intrinsic property of the CPD molecule and did not arise as a result of asymmetry in a dinucleotide setting. In addition to the above studies, during the course of the investigation of the nucleophilic reactivity of CPD, a chemical reaction was observed leading to what appeared to be the rapid and total chemical reversal of CPD lesions to the original TpT (thymine-thymine dinucleotide)! This “repair” reaction occurred when CPD reacted with hydrazine, and appears facilitated by an inert atmosphere under which it rapidly proceeds to completion at room temperature

Comparative evaluation of different culture media for the isolation and identification of common urinary pathogens

Background: Urinary tracts infections (UTIs) are one of the most common infections encountered in hospital as well as community settings. There is continuous increase in incidence of this infection leading to more consumption of antimicrobial drugs. Urine cultures occupy most of the workload of routine microbiology laboratories in developing country like India. Accurate and rapid identification of pathogens is the primary responsibility of a clinical microbiology laboratory.Methods: Mid-stream urine and catheterized samples were collected. Cultures were plated on blood agar, MacConkey agar and cysteine lactose electrolyte deficient media and incubated overnight at 35°C-37°C in ambient air. Colonies on the MacConkey agar, CLED agar and blood agar were also identified. The final identification of the isolates was done using standard identification protocol.  Antimicrobial susceptibility was performed by Kirby- Bauer disc diffusion test according to the CLSI guidelines.Results: Out of 500 urine samples processed, 211 samples showed significant growth, 24 samples showed polymicrobial growth and 265 samples were reported sterile.  Out of these 211, 199 showed pure growth and 12 showed mixed growths. Out of 199 pure growths, 126 were gram negative bacilli, 56 were gram positive cocci and 17 were yeast. All the gram-negative bacilli grown on all the media but most of the gram-positive cocci and yeast were unable to grow on Mac-Conkey agar and blood agar but grew successfully on CLED agar.Conclusions: So, in resource constrain laboratories, CLED agar can be used as media of choice for isolation of common uropathogens because it is user friendly, cost effective and decreases work load of the laboratories

Mining Integrated Sequential Patterns From Multiple Databases

Existing work on multiple databases (MDBs) sequential pattern mining cannot mine frequent sequences to answer exact and historical queries from MDBs having different table structures. This article proposes the transaction id frequent sequence pattern (TidFSeq) algorithm to handle the difficult problem of mining frequent sequences from diverse MDBs. The TidFSeq algorithm transforms candidate 1-sequences to get transaction subsequences where candidate 1-sequences occurred as (1-sequence, itssubsequenceidlist) tuple or (1-sequence, position id list). Subsequent frequent i-sequences are computed using the counts of the sequence ids in each candidate i-sequence position id list tuples. An extended version of the general sequential pattern (GSP)-like candidate generates and a frequency count approach is used for computing supports of itemset (I-step) and separate (S-step) sequences without repeated database scans but with transaction ids. Generated patterns answer complex queries from MDBs. The TidFSeq algorithm has a faster processing time than existing algorithms

Breakdown of the blood-brain barrier during dengue virus infection of mice

A breakdown of the blood-brain barrier occurred in mice inoculated intracerebrally (i.c.) or intraperitoneally (i.p.) with dengue virus type 2 (DEN2). This resulted in leakage of protein-bound Evans blue dye and 51Cr-labelled erythrocytes into the brain tissue. The leakage increased with time after infection and coincided with an increase of a DEN2-induced cytokine, the cytotoxic factor (CF), in the spleens of such mice. The titres of virus in the brain increased exponentially in i.c. inoculated mice but the virus was not detected in brains of mice given DEN2 by the i.p. route. Similar breakdown of the blood-brain barrier also occurred in mice inoculated intravenously with CF; the damage was dose-dependent and the vascular integrity was restored during the 3 h period after inoculation. Treatment of mice with antihistamine drugs, blocking H1 or H2 receptors, decreased the DEN2-induced protein leakage by up to 50% in i.c. inoculated mice and up to 92% in those inoculated i.p. Indomethacin, a prostaglandin synthetase inhibitor, had no effect. In i.c. inoculated mice protein leakage was inhibited by about 60% by treatment with CF-specific (CFA) or DEN2-specific antisera (DEN2A) whereas protection was complete with the combined treatment with both antisera. On the other hand, in i.p. inoculated mice the inhibition of protein leakage was 80 to 89% with CFA. These findings show a breakdown of the blood-brain barrier leading to cerebral oedema during DEN2 infection which is mediated via the release of histamine by a virus-induced cytokine

Identification, purification and characterization of a receptor for dengue virus-induced macrophage cytotoxin (CF2) from murine T cells

Dengue type-2 virus infection in mice induces a subpopulation of T lymphocytes to produce a cytokine cytotoxic factor, which induces macrophages (MΦ ) to produce a biologically active cytotoxic cytokine, the MΦ cytotoxin (CF2). Previously we have identified the presence of intermediate-affinity receptors for CF2 on mouse peritoneal MΦ. The present study was undertaken to identify the CF2-receptors (CF2-R) on murine T cells followed by their purification and characterization. Receptor binding assay and Scatchard analysis revealed single, high-affinity (1.0309 nM) receptors for CF2 on T cells (22,000 receptors per cell). The binding of [125I]CF2 on murine T cells was saturable and specific. Furthermore, CF2-R was purified from normal mouse T cell plasma membrane by affinity chromatography followed by reversed-phase high-pressure liquid chromatography. The presence of CF2-R was confirmed by indirect dot-blot assay and its binding with [125I]CF2. The purified CF2-R is a 90-95-kDa protein as characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblot analysis. The chemical crosslinking of [125I]CF2 and its receptor complex showed a product of 100-110 kDa on different subpopulations of murine T cells. The pretreatment of target cells with anti-CF2-R antisera inhibited the cytotoxic activity of CF2 in a dose-dependent manner and thus confirmed the biological significance of CF2-R. Moreover, the presence of CF2-R was also identified on normal human peripheral blood mononuclear cells and T and B cells by crosslinking with [125I]CF2, thus revealing the possible role of CF2 and CF2-R in the immunopathogenesis of dengue virus disease

Multiplexed Conformationally-Selective, Localized Gas-Phase Hydrogen Deuterium Exchange of Protein Ions Enabled by Transmission-Mode Electron Capture Dissociation

In this article, we present an approach for conformationally multiplexed localized hydrogen deuterium exchange (HDX) of gas-phase protein ions facilitated by ion mobility (IM) followed by electron capture dissociation (ECD). A quadrupole-ion mobility-time of flight instrument previously modified to enable ECD in transmission mode (without ion trapping) immediately following a mobility separation was further modified to allow for deuterated ammonia (ND3) to be leaked in after m/z selection. Collisional activation was minimized to prevent deuterium scrambling from giving structurally irrelevant results. This arrangement was demonstrated with the extensively studied protein folding models ubiquitin and cytochrome c. Ubiquitin was ionized from conditions that stabilize the native state and conditions that stabilize the partially-folded A-state. IM of deuterated ubiquitin 6+ ions allowed the separation of more compact conformers from more extended conformers. ECD of the separated subpopulations revealed that the more extended (later arriving) conformers had significant, localized differences in the amount of HDX observed. The 5+ charge state showed greater protection against HDX than the compact 6+ conformer, and the 11+ charge state, ionized from conditions that stabilize the A-state, showed much greater deuterium incorporation. The 7+ ions of cytochrome c ionized from aqueous conditions showed greater HDX with exterior and more unstructured regions of the protein, while interior, structured regions, especially those involved in heme binding, were more protected against exchange. These results, as well as potential future methods and experiments, are discussed herein

Important Factors in LEED\u27s Water Efficiency Strategies

This report identifies the important factors and the subsequent decisions which lead to identifying and incorporating water-saving strategies and the resulting credits for LEED certification. Furthermore, the report will try to demonstrate how the creation of a LEED’s measurement system, has led to a rise in new water saving technologies. Buildings can obtain certification by achieving LEED credits in categories consisting of: Sustainable Sites, Water Efficiency, Energy and Atmosphere, Materials and Resources, Indoor Environmental Quality and additional points for innovative design and regional priority. Data for the report was gathered through interviews with companies and individuals who had applied water efficiency strategies to meet LEED’s credit requirements

Data mining techniques for design of ITS student models

An Intelligent Tutoring System (ITS) is a computer system that provides a direct customized instruction or feedback to students while performing a task in a tutoring system without the intervention of a human. One of the modules of an ITS system is student module which helps to understand the student’s learning abilities. Several data mining techniques like association rule mining, clustering and mining using Bayesian networks have been proposed to design effective student models in ITS systems. This paper provides a comparative study of the various data mining techniques and tools that are used in student modeling. We also propose an example-driven approach that can integrate mined concept examples at different difficulty levels with the Bayesian networks in order to influence student learning

Clustering Examples in Web-based Tutoring Systems based on Relevance of Concepts

Web-based online tutoring systems (WOTS) have become extremely important and relevant in today\u27s world, especially with COVID-19 requiring schools, colleges and universities to offer alternate forms of delivery. Many studies have indicated that students find worked-out examples very useful, when they are performing a task or studying for final exams. WOTS certainly have the capability to host hundreds of such examples in their repositories, but presenting students with such repositories may cause cognitive overload on students and may force them to bear the responsibility of searching for the most relevant examples, when in need. This paper proposes an algorithm called CER (Clustering Examples based on Relevance) that organizes a collection of worked-out examples into coherent and relevant clusters-relevant to the learning concepts covered by them. When generating clusters, CER acknowledges not only the local relevance of a concept (using parameters such as mode) within a cluster but also its global relevance. The proposed algorithm CER is validated using Dunn\u27s index as the internal validity index-a score of 0.81 was achieved for CER. The external validity of CER was measured by comparing its results to a benchmark dataset that had properties of data that were common to the domain of CER