Correlation test to assess low-level processing of high-density oligonucleotide microarray data

Background  

There are currently a number of competing techniques for low-level processing of oligonucleotide array data. The choice of technique has a profound effect on subsequent statistical analyses, but there is no method to assess whether a particular technique is appropriate for a specific data set, without reference to external data.     

SNP haplotype tagging from DNA pools of two individuals

Background  

DNA pooling is a technique to reduce genotyping effort while incurring only minor losses in accuracy of allele frequency estimates for single nucleotide polymorphism (SNP) markers.     

Chromato-panning: an efficient new mode of identifying suitable ligands from phage display libraries

Background  

Phage Display technology is a well established technique for high throughput screening of affinity ligands. Here we describe a new compact chromato-panning procedure for selection of suitable binders from a phage peptide display library.     

Extraction of average neck flexion angle during swallowing in neutral and chin-tuck positions

Background  

A common but debated technique in the management of swallowing difficulties is the chin tuck swallow, where the neck is flexed forward prior to swallowing. Natural variations in chin tuck angles across individuals may contribute to the differential effectiveness of the technique.     

Probabilistic principal component analysis for metabolomic data

Background  

Data from metabolomic studies are typically complex and high-dimensional. Principal component analysis (PCA) is currently the most widely used statistical technique for analyzing metabolomic data. However, PCA is limited by the fact that it is not based on a statistical model.     

A novel functional module detection algorithm for protein-protein interaction networks

Background  

The sparse connectivity of protein-protein interaction data sets makes identification of functional modules challenging. The purpose of this study is to critically evaluate a novel clustering technique for clustering and detecting functional modules in protein-protein interaction networks, termed STM.     

Improving Detection Accuracy of Lung Cancer Serum Proteomic Profiling via Two-Stage Training Process

Background  

Surface-Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (SELDI-TOF-MS) is a frequently used technique for cancer biomarker research. The specificity of biomarkers detected by SELDI can be influenced by concomitant inflammation. This study aimed to increase detection accuracy using a two-stage analysis process.     

Selective control of primer usage in multiplex one-step reverse transcription PCR

Background  

Multiplex RT-PCR is a valuable technique used for pathogen identification, disease detection and relative quantification of gene expression. The simplification of this protocol into a one-step procedure saves time and reagents. However, intensive PCR optimization is often required to overcome competing undesired PCR primer extension during the RT step.     

Isolation of bacteria-containing phagosomes by magnetic selection

Background  

There is a growing awareness of the importance of intracellular events in determining the outcome of infectious disease. To improve the understanding of such events, like phagosome maturation, we set out to develop a versatile technique for phagosome isolation that is rapid and widely applicable to different pathogens.     

Selection strategy and the design of hybrid oligonucleotide primers for RACE-PCR: cloning a family of toxin-like sequences from <Emphasis Type="Italic">Agelena orientalis</Emphasis>

Background  

the use of specific but partially degenerate primers for nucleic acid hybridisations and PCRs amplification of known or unknown gene families was first reported well over a decade ago and the technique has been used widely since then.     

Extended morphological processing: a practical method for automatic spot detection of biological markers from microscopic images

Background  

A reliable extraction technique for resolving multiple spots in light or electron microscopic images is essential in investigations of the spatial distribution and dynamics of specific proteins inside cells and tissues. Currently, automatic spot extraction and characterization in complex microscopic images poses many challenges to conventional image processing methods.     

PyMix - The Python mixture package - a tool for clustering of heterogeneous biological data

Background  

Cluster analysis is an important technique for the exploratory analysis of biological data. Such data is often high-dimensional, inherently noisy and contains outliers. This makes clustering challenging. Mixtures are versatile and powerful statistical models which perform robustly for clustering in the presence of noise and have been successfully applied in a wide range of applications.     

A rolling-gliding wear simulator for the investigation of tribological material pairings for application in total knee arthroplasty

Background  

Material wear testing is an important technique in the development and evaluation of materials for use in implant for total knee arthroplasty. Since a knee joint induces a complex rolling-gliding movement, standardised material wear testing devices such as Pin-on-Disc or Ring-on-Disc testers are suitable to only a limited extent because they generate pure gliding motion only.     

Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis

Background  

Genome-wide identification of specific oligonucleotides (oligos) is a computationally-intensive task and is a requirement for designing microarray probes, primers, and siRNAs. An artificial neural network (ANN) is a machine learning technique that can effectively process complex and high noise data. Here, ANNs are applied to process the unique subsequence distribution for prediction of specific oligos.     

Temperature limited fed-batch technique for control of proteolysis in <Emphasis Type="Italic">Pichia pastoris</Emphasis> bioreactor cultures

Background  

A temperature limited fed-batch (TLFB) technique is described and used for Pichia pastoris Mut⁺ strain cultures and compared with the traditional methanol limited fed-batch (MLFB) technique. A recombinant fusion protein composed of a cellulose-binding module (CBM) from Neocallimastix patriciarum cellulase 6A and lipase B from Candida antarctica (CALB), was produced and secreted by this strain.     

Does measuring early basal serum follicular lutinising hormone assist in predicting In vitro fertilization (IVF)/Intracytoplasmic sperm injection (ICSI) outcome?

Background  

The aim was to examine the correlation of early follicular serum lutinising hormone (LH) and the clinical outcome of assisted reproduction technique (ART).     

Diagnostic polymorphisms in the mitochondrial cytochrome b gene allow discrimination between cattle,sheep, goat,roe buck and deer by PCR-RFLP

Background  

As an alternative to direct DNA sequencing of PCR products, random PCR-RFLP is an efficient technique to discriminate between species. The PCR-RFLP-method is an inexpensive tool in forensic science, even if the template is degraded or contains only traces of DNA from various species.