A scalable application server on Beowulf clusters : a thesis presented in partial fulfilment of the requirement for the degree of Master of Information Science at Albany, Auckland, Massey University, New Zealand

Application performance and scalability of a large distributed multi-tiered application is a core requirement for most of today's critical business applications. I have investigated the scalability of a J2EE application server using the standard ECperf benchmark application in the Massey Beowulf Clusters namely the Sisters and the Helix. My testing environment consists of Open Source software: The integrated JBoss-Tomcat as the application server and the web server, along with PostgreSQL as the database. My testing programs were run on the clustered application server, which provide replication of the Enterprise Java Bean (EJB) objects. I have completed various centralized and distributed tests using the JBoss Cluster. I concluded that clustering of the application server and web server will effectively increase the performance of the application running on them given sufficient system resources. The application performance will scale to a point where a bottleneck has occurred in the testing system, the bottleneck could be any resources included in the testing environment: the hardware, software, network and the application that is running. Performance tuning for a large-scale J2EE application is a complicated issue, which is related to the resources available. However, by carefully identifying the performance bottleneck in the system with hardware, software, network, operating system and application configuration. I can improve the performance of the J2EE applications running in a Beowulf Cluster. The software bottleneck can be solved by changing the default settings, on the other hand, hardware bottlenecks are harder unless more investment are made to purchase higher speed and capacity hardware

Investigation and validation of algorithms for estimating land surface temperature from Sentinel-3 SLSTR data

Land surface temperature (LST) is an important indicator of global ecological environment and climate change. The Sea and Land Surface Temperature Radiometer (SLSTR) onboard the recently launched Sentinel-3 satellites provides high-quality observations for estimating global LST. The algorithm of the official SLSTR LST product is a split-window algorithm (SWA) that implicitly assumes and utilizes knowledge of land surface emissivity (LSE). The main objective of this study is to investigate alternative SLSTR LST retrieval algorithms with an explicit use of LSE. Seventeen widely accepted SWAs, which explicitly utilize LSE, were selected as candidate algorithms. First, the SWAs were trained using a comprehensive global simulation dataset. Then, using simulation data as well as in-situ LST, the SWAs were evaluated according to their sensitivity and accuracy: eleven algorithms showed good training accuracy and nine of them exhibited low sensitivity to uncertainties in LSE and column water vapor content. Evaluation based on two global simulation datasets and a regional simulation dataset showed that these nine SWAs had similar accuracy with negligible systematic errors and RMSEs lower than 1.0 K. Validation based on in-situ LST obtained for six sites further confirmed the similar accuracies of the SWAs, with the lowest RMSE ranges of 1.57–1.62 K and 0.49−0.61 K for Gobabeb and Lake Constance, respectively. While the best two SWAs usually yielded good accuracy, the official SLSTR LST generally had lower accuracy. The SWAs identified and described in this study may serve as alternative algorithms for retrieving LST products from SLSTR data

Development of a new barcode-based, multiplex-PCR, next-generation-sequencing assay and data processing and analytical pipeline for multiplicity of infection detection of Plasmodium falciparum.

BACKGROUND Simultaneous infection with multiple malaria parasite strains is common in high transmission areas. Quantifying the number of strains per host, or the multiplicity of infection (MOI), provides additional parasite indices for assessing transmission levels but it is challenging to measure accurately with current tools. This paper presents new laboratory and analytical methods for estimating the MOI of Plasmodium falciparum. METHODS Based on 24 single nucleotide polymorphisms (SNPs) previously identified as stable, unlinked targets across 12 of the 14 chromosomes within P. falciparum genome, three multiplex PCRs of short target regions and subsequent next generation sequencing (NGS) of the amplicons were developed. A bioinformatics pipeline including B4Screening pathway removed spurious amplicons to ensure consistent frequency calls at each SNP location, compiled amplicons by SNP site diversity, and performed algorithmic haplotype and strain reconstruction. The pipeline was validated by 108 samples generated from cultured-laboratory strain mixtures in different proportions and concentrations, with and without pre-amplification, and using whole blood and dried blood spots (DBS). The pipeline was applied to 273 smear-positive samples from surveys conducted in western Kenya, then providing results into StrainRecon Thresholding for Infection Multiplicity (STIM), a novel MOI estimator. RESULTS The 24 barcode SNPs were successfully identified uniformly across the 12 chromosomes of P. falciparum in a sample using the pipeline. Pre-amplification and parasite concentration, while non-linearly associated with SNP read depth, did not influence the SNP frequency calls. Based on consistent SNP frequency calls at targeted locations, the algorithmic strain reconstruction for each laboratory-mixed sample had 98.5% accuracy in dominant strains. STIM detected up to 5 strains in field samples from western Kenya and showed declining MOI over time (q < 0.02), from 4.32 strains per infected person in 1996 to 4.01, 3.56 and 3.35 in 2001, 2007 and 2012, and a reduction in the proportion of samples with 5 strains from 57% in 1996 to 18% in 2012. CONCLUSION The combined approach of new multiplex PCRs and NGS, the unique bioinformatics pipeline and STIM could identify 24 barcode SNPs of P. falciparum correctly and consistently. The methodology could be applied to field samples to reliably measure temporal changes in MOI

A large area 100 channel Picosec Micromegas detector with sub 20 ps time resolution

The PICOSEC Micromegas precise timing detector is based on a Cherenkov radiator coupled to a semi-transparent photocathode and a Micromegas amplification structure. The first proof of concept single-channel small area prototype was able to achieve time resolution below 25 ps. One of the crucial aspects in the development of the precise timing gaseous detectors applicable in high-energy physics experiments is a modular design that enables large area coverage. The first 19-channel multi-pad prototype with an active area of approximately 10 cm$^2$ suffered from degraded timing resolution due to the non-uniformity of the preamplification gap. A new 100 cm$^2$ detector module with 100 channels based on a rigid hybrid ceramic/FR4 Micromegas board for improved drift gap uniformity was developed. Initial measurements with 80 GeV/c muons showed improvements in timing response over measured pads and a time resolution below 25 ps. More recent measurements with a new thinner drift gap detector module and newly developed RF pulse amplifiers show that the resolution can be enhanced to a level of 17~ps. This work will present the development of the detector from structural simulations, design, and beam test commissioning with a focus on the timing performance of a thinner drift gap detector module in combination with new electronics using an automated timing scan method

Towards robust PICOSEC Micromegas precise timing detectors

The PICOSEC Micromegas (MM) detector is a precise timing gaseous detector consisting of a Cherenkov radiator combined with a photocathode and a MM amplifying structure. A 100-channel non-resistive PICOSEC MM prototype with 10x10 cm^2 active area equipped with a Cesium Iodide (CsI) photocathode demonstrated a time resolution below 18 ps. The objective of this work is to improve the PICOSEC MM detector robustness aspects; i.e. integration of resistive MM and carbon-based photocathodes; while maintaining good time resolution. The PICOSEC MM prototypes have been tested in laboratory conditions and successfully characterised with 150 GeV/c muon beams at the CERN SPS H4 beam line. The excellent timing performance below 20 ps for an individual pad obtained with the 10x10 cm^2 area resistive PICOSEC MM of 20 MOhm/sq showed no significant time resolution degradation as a result of adding a resistive layer. A single-pad prototype equipped with a 12 nm thick Boron Carbide (B4C) photocathode presented a time resolution below 35 ps; opening up new possibilities for detectors with robust photocathodes. The results made the concept more suitable for the experiments in need of robust detectors with good time resolution

Comparative genomics reveals insights into avian genome evolution and adaptation

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Facile and Efficient Atomic Hydrogenation Enabled Black TiO2_2 with Enhanced Photo‐Electrochemical Activity via a Favorably Low‐Energy‐Barrier Pathway

Black TiO₂ has demonstrated a great potential for a variety of renewable energy technologies. However, its practical application is heavily hindered due to lack of efficient hydrogenation methods and a deeper understanding of hydrogenation mechanisms. Here, a simple and straightforward hot wire annealing (HWA) method is presented to prepare black TiO₂ (H–TiO₂) nanorods with enhanced photo‐electrochemical (PEC) activity by means of atomic hydrogen [H]. Compared to conventional molecular hydrogen approaches, the HWA shows remarkable effectiveness without any detrimental side effects on the device structure, and simultaneously the photocurrent density of H–TiO₂ reaches 2.5 mA cm⁻² (at 1.23 V vs reversible hydrogen electrode (RHE)). Due to the controllable and reproducible [H] flux, the HWA can be developed as a standard hydrogenation method for black TiO₂. Meanwhile, the relationships between the wire temperatures, structural, optical, and photo‐electrochemical properties are systematically investigated to verify the improved PEC activity. Furthermore, the density functional theory (DFT) study provides a comprehensive insight not only into the highly efficient mechanism of the HWA approach but also its favorably low‐energy‐barrier hydrogenation pathway. The findings will have a profound impact on the broad energy applications of H–TiO₂ and contribute to the fundamental understanding of its hydrogenation

Metastable Interwoven Mesoporous Metal–Organic Frameworks

Three isostructural interwoven 3,4-connected mesoporous metal–organic frameworks of pto-a topology (<b>UTSA-28-Cu</b>, <b>UTSA-28-Zn</b>, and <b>UTSA-28-Mn</b>) were synthesized and structurally characterized. Because of their metastable nature, their gas sorption properties are highly dependent on the metal ions and activation profiles. The most stable, <b>UTSA-28a-Cu</b>, exhibits promising gas storage and separation capacities