Design of efficient and elastic storage in the cloud

Ph.DDOCTOR OF PHILOSOPH

LogBase: A Scalable Log-structured Database System in the Cloud

Numerous applications such as financial transactions (e.g., stock trading) are write-heavy in nature. The shift from reads to writes in web applications has also been accelerating in recent years. Write-ahead-logging is a common approach for providing recovery capability while improving performance in most storage systems. However, the separation of log and application data incurs write overheads observed in write-heavy environments and hence adversely affects the write throughput and recovery time in the system. In this paper, we introduce LogBase - a scalable log-structured database system that adopts log-only storage for removing the write bottleneck and supporting fast system recovery. LogBase is designed to be dynamically deployed on commodity clusters to take advantage of elastic scaling property of cloud environments. LogBase provides in-memory multiversion indexes for supporting efficient access to data maintained in the log. LogBase also supports transactions that bundle read and write operations spanning across multiple records. We implemented the proposed system and compared it with HBase and a disk-based log-structured record-oriented system modeled after RAMCloud. The experimental results show that LogBase is able to provide sustained write throughput, efficient data access out of the cache, and effective system recovery.Comment: VLDB201

Stability of twin circular tunnels in cohesive-frictional soil using the node-based smoothed finite element method (NS-FEM)

This paper presents an upper bound limit analysis procedure using the node-based smoothed finite element method (NS-FEM) and second order cone programming (SOCP) to evaluate the stability of twin circular tunnels in cohesive-frictional soils subjected to surcharge loading. At first stage, kinematically admissible displacement fields of the tunnel problems are approximated by NS-FEM using triangular elements (NS-FEM-T3). Next, commercial software Mosek is employed to deal with the optimization problems, which are formulated as second order cone. Collapse loads as well as failure mechanisms of plane strain tunnels are obtained directly by solving the optimization problems. For twin circular tunnels, the distance between centers of two parallel tunnels is the major parameter used to determine the stability. In this study, the effects of mechanical soil properties and the ratio of tunnel diameter and the depth to the tunnel stability are investigated. Numerical results are verified with those available to demonstrate the accuracy of the proposed method

SYNTHESIS OF STARCH MODIFIED MONTMORILLONITE AS AN EFFECTIVE ADSORBENT FOR Pb (II) REMOVAL FROM WATER

The adsorbent is prepared by the montmorillonite co-modification with starch for the removal of Pb (II) ions from aqueous solution. The Fourier-transformed infrared (FTIR), X-ray diffraction (XRD) spectroscopies were used to determine the structure and characteristics of the adsorbent. The main factors affecting the removal of Pb (II) ions were investigated, including the effect of pH, contact time, adsorbent dosage and the initial concentration of Pb (II). Batch process can be used for adsorption and equilibrium studies. The experimental data were fitted using Freundlich and Langmuir adsorption models. The Langmuir isotherm best fitted the experimental data with R2 0.99 and maximum Pb (II) adsorption capacity of 21.5 mg/g indicated monolayer adsorption. Kinetic studies using pseudo-first-order and pseudo-second-order rate models showed that the process complied well with the pseudo second-order rate model

Giant compound odontoma of the mandible in an adolescent

Abstract Odontomas are one type of benign odontogenic hamartoma that includes the compound and complex odontoma. They are generally reported not to exceed 3 cm in diameter. Odontomas with a diameter exceeding 3 cm are considered giant odontomas. An accurate diagnosis of odontomas cannot be made during the clinical examination. The majority of compound odontoma is diagnosed most commonly during radiographic screening. It should be done in coordination with a histological examination after surgical treatment. We report a case of giant compound odontoma of the mandible in a young boy. The tumor is treated by surgical excision under general anesthesia

Pedagogical Challenges in Online Teaching: A Qualitative Study on Vietnamese University Teachers of Social Sciences

In recent years, online teaching has gained significant traction in higher education institutions across the globe, primarily due to the widespread impact of the Covid-19 pandemic. Before the pandemic, online teaching was mainly associated with distance learning which aims to provide further education for in-service learners. In this context, our study aims to explore the pedagogical obstacles encountered by Vietnamese university teachers when implementing online teaching in social sciences. Employing qualitative research methods, such as snowball sampling and semi-structured in-depth interviews, the researchers gathered data from 23 university teachers specializing in social sciences across 12 public and private universities in Ho Chi Minh City, Vietnam. The findings of this investigation shed light on various pedagogical barriers that impede the teaching process, encompassing aspects such as lesson plan preparation, lecture delivery (limited interactions, teaching methods and activities, students’ distraction and passive participation, managing virtual classrooms), student assessment, and overall teaching ineffectiveness. This study contributes to the existing literature on contextualized online instructions in higher education, specifically focusing on the social sciences domain. Furthermore, the discussion delves into the critical points, providing a comprehensive understanding of the challenges faced by educators in the online teaching landscape

AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance

We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best practice analysis pipeline allowing researchers to perform comprehensive analysis of a collection of samples directly from raw sequencing data with a single command line. The analysis results in a report showing the genome structure, genome annotations, antibiotic resistance and virulence profile for each sample. The pan-genome of all samples of the collection is analyzed to identify core- and accessory-genes. Phylogenies of the whole genome as well as all gene clusters are also generated. The toolkit provides a web-based visualization dashboard allowing researchers to interactively examine various aspects of the analysis results. Availability: AMRViz is implemented in Python and NodeJS, and is publicly available under open source MIT license at https://github.com/amromics/amrviz

Efficient inference of large prokaryotic pangenomes with PanTA

Pangenome inference is an indispensable step in bacterial genomics, yet its scalability poses a challenge due to the rapid growth of genomic collections. This paper presents PanTA, a software package designed for constructing pangenomes of large bacterial datasets, showing unprecedented efficiency levels multiple times higher than existing tools. PanTA introduces a novel mechanism to construct the pangenome progressively without rebuilding the accumulated collection from scratch. The progressive mode is shown to consume orders of magnitude less computational resources than existing solutions in managing growing datasets. The software is open source and is publicly available at https://github.com/amromics/panta and at 10.6084/m9.figshare.23724705

AMRomics: a scalable workflow to analyze large microbial genome collections

Whole genome analysis for microbial genomics is critical to studying and monitoring antimicrobial resistance strains. The exponential growth of microbial sequencing data necessitates a fast and scalable computational pipeline to generate the desired outputs in a timely and cost-effective manner. Recent methods have been implemented to integrate individual genomes into large collections of specific bacterial populations and are widely employed for systematic genomic surveillance. However, they do not scale well when the population expands and turnaround time remains the main issue for this type of analysis. Here, we introduce AMRomics, an optimized microbial genomics pipeline that can work efficiently with big datasets. We use different bacterial data collections to compare AMRomics against competitive tools and show that our pipeline can generate similar results of interest but with better performance. The software is open source and is publicly available at https://github.com/amromics/amromics under an MIT license

10-Year Cardiovascular Risk in Hypertensive Patients: Insights from Central Vietnam Using WHO 2019 Chart

Background: Assessing the 10-year cardiovascular disease (CVD) risk is crucial for effective prevention and management. Despite its significance, information is limited on CVD risk among hypertensive patients in primary care in Central Vietnam. We conducted this study to estimate 10-year CVD risk in primary care settings and explore its associated risk factors, using the 2019 WHO CVD risk chart. Methods and Results: This cross-sectional study collected socio-demographic and clinical data through a standardized questionnaire. Cardiovascular risk was estimated using the WHO CVD risk charts for Southeast Asia. The prevalence of low, moderate, and high CVD risk was 52.1%, 38.9%, and 9.0%, respectively. Notably, men had significantly higher rates of moderate (48.6%) and high (17.6%) CVD risk than women (31.4 and 2.4%, respectively) (P=0.000). Age was a significant factor, with an increasing prevalence of moderate and high CVR as age advanced. Specifically, the 50-59 age group had a moderate risk of 18.6%, rising to 69.9% in the 70-74 age group. High CVD risk increased from 0.6% to 27.6% in the same age groups. Lower educational levels were associated with a higher proportion of moderate CVD risk. Smoking and excessive alcohol consumption were linked to elevated CVD risks (25.0% and 30.0%, respectively), surpassing those without these behaviors. Similar trends were observed for individuals with diabetes, high total cholesterol, and high blood pressure. Conclusion: Approximately one-tenth of hypertensive patients face a high risk of developing CVDs within the next 10 years. A comprehensive approach, encompassing behavioral changes and the management of metabolic risk factors, is essential to reduce CVD risk effectively