Repetitive project scheduling using genetic algorithms

Master'sMASTER OF ENGINEERIN

SPdb – a signal peptide database

BACKGROUND: The signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells. This transient, short peptide sequence functions like a postal address on an envelope by targeting proteins for secretion or for transfer to specific organelles for further processing. Understanding how signal peptides function is crucial in predicting where proteins are translocated. To support this understanding, we present SPdb signal peptide database , a repository of experimentally determined and computationally predicted signal peptides. RESULTS: SPdb integrates information from two sources (a) Swiss-Prot protein sequence database which is now part of UniProt and (b) EMBL nucleotide sequence database. The database update is semi-automated with human checking and verification of the data to ensure the correctness of the data stored. The latest release SPdb release 3.2 contains 18,146 entries of which 2,584 entries are experimentally verified signal sequences; the remaining 15,562 entries are either signal sequences that fail to meet our filtering criteria or entries that contain unverified signal sequences. CONCLUSION: SPdb is a manually curated database constructed to support the understanding and analysis of signal peptides. SPdb tracks the major updates of the two underlying primary databases thereby ensuring that its information remains up-to-date

Setting Up a Low-cost Lab Management System for a Multi-purpose Computing Laboratory Using Virtualisation Technology

Copyright issues: http://www.ascilite.org.au/ajet/about/ref/author-advice.html#copyright</a

Molecular characterisation of Haemoglobin Constant Spring and Haemoglobin Quong Sze with a combine-amplification refractory mutation system

Background: The interaction of the non-deletional α +- thalassaemia mutations Haemoglobin Constant Spring and Haemoglobin Quong Sze with the Southeast Asian double α-globin gene deletion results in non-deletional Haemoglobin H disease. Accurate detection of non-deletional Haemoglobin H disease, which is associated with severe phenotypes, is necessary as these mutations have been confirmed in the Malaysian population. Methods: DNA from two families with Haemoglobin H disease was extracted from EDTA-anticoagulated whole blood and subjected to molecular analysis for α-thalassaemia. A duplex polymerase chain reaction was used to detect the Southeast Asian α-globin gene deletion. Polymerase chain reaction-restriction fragment length polymorphism analysis was then carried out to determine the presence of Haemoglobin Constant Spring and Haemoglobin Quong Sze. A combine- amplification refractory mutation system protocol was optimised and implemented for the rapid and specific molecular characterisation of Haemoglobin Constant Spring and Haemoglobin Quong Sze in a single polymerase chain reaction. Results and Conclusions: The combine- amplification refractory mutation system for Haemoglobin Constant Spring and Haemoglobin Quong Sze, together with the duplex polymerase chain reaction, provides accurate pre- and postnatal diagnosis of non-deletional Haemoglobin H disease and allows detailed genotype analyses using minimal quantities of DNA

Fabrication of a highly selective and sensitive CrO4 sensor based on a N,N'Bis(salicylidene)ethylenediaminocobolt(II)hydrate.

In this work a membrane was prepared by use of N,N′Bis(salicylidene) ethylenediamino cobalt(II) hydrate (Co(SALEN)2) as an ion carrier, polyvinylchloride (PVC) as matrix, and 2-nitrophenyl octyl ether (2NPOE) as a plasticizer for an ion-selective electrode used in the measurement of CrO42-anions in solution. The amounts of (Co(SALEN)2) and PVC were optimized in the preparation of the membrane. The response of the electrode was Nernstian within the concentration range 1.0 × 10-6 to 1.0 × 10-1 M. This sensor displays a drift in Nernstian response for this anion changes with the amount of ionophore and PVC. The effects of various parameters such as pH, different anion interferences, the amounts of ionophore and PVC and time on response of the coated ion-selective electrode were investigated. The response of the fabricated electrode at concentration range from 1.0× 10-6 to 1.0× 10-1 M is linear with a Nernstian slope of -28.33 mV

High Prevalence of Alpha- and Beta-Thalassemia in the Kadazandusuns in East Malaysia: Challenges in Providing Effective Health Care for an Indigenous Group

Thalassemia can lead to severe transfusion-dependent anemia, and it is the most common genetic disorder in Malaysia. This paper aims to determine the prevalence of thalassemia in the Kadazandusuns, the largest indigenous group in Sabah, East Malaysia. α- and β-thalassemia were confirmed in 33.6% and 12.8%, of the individuals studied respectively. The high prevalence of α- and β-thalassemia in the Kadazandusuns indicates that thalassemia screening, genetic counseling, and prenatal diagnosis should be included as part of their healthcare system. This preliminary paper serves as a baseline for further investigations into the health and genetic defects of the major indigenous population in Sabah, East Malaysia

Lasting DNA Damage and Aberrant DNA Repair Gene Expression Profile Are Associated with Post-Chronic Cadmium Exposure in Human Bronchial Epithelial Cells

Cadmium (Cd) is a widespread environmental pollutant and carcinogen. Although the exact mechanisms of Cd-induced carcinogenesis remain unclear, previous acute/chronic Cd exposure studies have shown that Cd exerts its cytotoxic and carcinogenic effects through multiple mechanisms, including interference with the DNA repair system. However, the effects of post-chronic Cd exposure remain unknown. Here, we establish a unique post-chronic Cd-exposed human lung cell model (the CR0 cells) and investigate the effects of post-chronic Cd exposure on the DNA repair system. We found that the CR0 cells retained Cd-resistant property even though it was grown in Cd-free culture medium for over a year. The CR0 cells had lasting DNA damage due to reduced DNA repair capacity and an aberrant DNA repair gene expression profile. A total of 12 DNA repair genes associated with post-chronic Cd exposure were identified, and they could be potential biomarkers for identifying post-chronic Cd exposure. Clinical database analysis suggests that some of the DNA repair genes play a role in lung cancer patients with different smoking histories. Generally, CR0 cells were more sensitive to chemotherapeutic (cisplatin, gemcitabine, and vinorelbine tartrate) and DNA damaging (H2O2) agents, which may represent a double-edged sword for cancer prevention and treatment. Overall, we demonstrated for the first time that the effects of post-chronic Cd exposure on human lung cells are long-lasting and different from that of acute and chronic exposures. Findings from our study unveiled a new perspective on Cd-induced carcinogenesis-the post-chronic exposure of Cd. This study encourages the field of post-exposure research which is crucial but has long been ignored

MultiRes Attention Deep Learning Approach for Abdominal Fat Compartment Segmentation and Quantification

Global increase in obesity has led to alarming rise in co-morbidities leading to deteriorated quality of life. Obesity phenotyping benefits profiling and management of the condition but warrants accurate quantification of fat compartments. Manual quantification MR scans are time consuming and laborious. Hence, many studies rely on semi/automatic methods for quantification of abdominal fat compartments. We propose a MultiRes-Attention U-Net with hybrid loss function for segmentation of different abdominal fata compartments namely (i) Superficial subcutaneous adipose tissue (SSAT), (ii) Deep subcutaneous adipose tissue (DSAT), and (iii) Visceral adipose tissue (VAT) using abdominal MR scans. MultiRes block, ResAtt-Path, and attention gates can handle shape, scale, and heterogeneity in the data. Dataset involved MR scans from 190 community-dwelling older adults (mainly Chinese, 69.5% females) with mean age—67.85 ± 7.90 years), BMI 23.75 ± 3.65 kg/m2. Twenty-six datasets were manually segmented to generate the ground truth. Data augmentations were performed using MR data acquisition variations. Training and validation were performed on 105 datasets, while testing was conducted on 25 datasets. Median Dice scores were 0.97 for SSAT & DSAT and 0.96 for VAT, and mean Hausdorff distance was <5 mm for all the three fat compartments. Further, MultiRes-Attention U-Net was tested on a new 190 datasets (unseen during training; upper & lower abdomen scans with different resolution), which yielded accurate results. MultiRes-Attention U-Net significantly improved the performance over MultiResUNet, showed excellent generalization and holds promise for body-profiling in large cohort studies