Generic Subsequence Matching Framework: Modularity, Flexibility, Efficiency

Subsequence matching has appeared to be an ideal approach for solving many problems related to the fields of data mining and similarity retrieval. It has been shown that almost any data class (audio, image, biometrics, signals) is or can be represented by some kind of time series or string of symbols, which can be seen as an input for various subsequence matching approaches. The variety of data types, specific tasks and their partial or full solutions is so wide that the choice, implementation and parametrization of a suitable solution for a given task might be complicated and time-consuming; a possibly fruitful combination of fragments from different research areas may not be obvious nor easy to realize. The leading authors of this field also mention the implementation bias that makes difficult a proper comparison of competing approaches. Therefore we present a new generic Subsequence Matching Framework (SMF) that tries to overcome the aforementioned problems by a uniform frame that simplifies and speeds up the design, development and evaluation of subsequence matching related systems. We identify several relatively separate subtasks solved differently over the literature and SMF enables to combine them in straightforward manner achieving new quality and efficiency. This framework can be used in many application domains and its components can be reused effectively. Its strictly modular architecture and openness enables also involvement of efficient solutions from different fields, for instance efficient metric-based indexes. This is an extended version of a paper published on DEXA 2012.Comment: This is an extended version of a paper published on DEXA 201

Effect of genotype on duodenal expression of nutrient transporter genes in dairy cows

peer-reviewedBackground Studies have shown clear differences between dairy breeds in their feed intake and production efficiencies. The duodenum is critical in the coordination of digestion and absorption of nutrients. This study examined gene transcript abundance of important classes of nutrient transporters in the duodenum of non lactating dairy cows of different feed efficiency potential, namely Holstein-Friesian (HF), Jersey (JE) and their F1 hybrid. Duodenal epithelial tissue was collected at slaughter and stored at -80°C. Total RNA was extracted from tissue and reverse transcribed to generate cDNA. Gene expression of the following transporters, namely nucleoside; amino acid; sugar; mineral; and lipid transporters was measured using quantitative real-time RT-PCR. Data were statistically analysed using mixed models ANOVA in SAS. Orthogonal contrasts were used to test for potential heterotic effects and spearman correlation coefficients calculated to determine potential associations amongst gene expression values and production efficiency variables. Results While there were no direct effects of genotype on expression values for any of the genes examined, there was evidence for a heterotic effect (P < 0.05) on ABCG8, in the form of increased expression in the F1 genotype compared to either of the two parent breeds. Additionally, a tendency for increased expression of the amino acid transporters, SLC3A1 (P = 0.072), SLC3A2 (P = 0.081) and SLC6A14 (P = 0.072) was also evident in the F1 genotype. A negative (P < 0.05) association was identified between the expression of the glucose transporter gene SLC5A1 and total lactational milk solids yield, corrected for body weight. Positive correlations (P < 0.05) were also observed between the expression values of genes involved in common transporter roles. Conclusion This study suggests that differences in the expression of sterol and amino acid transporters in the duodenum could contribute towards the documented differences in feed efficiency between HF, JE and their F1 hybrid. Furthermore, positive associations between the expression of genes involved in common transporter roles suggest that these may be co-regulated. The study identifies potential candidates for investigation of genetic variants regulating nutrient transport and absorption in the duodenum in dairy cows, which may be incorporated into future breeding programmes

Using stiffness to assess injury risk:comparison of methods for quantifying stiffness and their reliability in triathletes

Background: A review of the literature has indicated that lower body stiffness, defined as the extent to which the lower extremity joints resists deformation upon contact with the ground, may be a useful measure for assessing Achilles injury risk in triathletes. The nature of overuse injuries suggests that a variety of different movement patterns could conceivably contribute to the final injury outcome, any number and combination of which might be observed in a single individual. Measurements which incorporate both kinetics and kinematics (such as stiffness) of a movement may be better able to shed light on individuals at risk of injury, with further analysis then providing the exact mechanism of injury for the individual. Stiffness can be measured as vertical, leg or joint stiffness to model how the individual interacts with the environment upon landing. However, several issues with stiffness assessments limit the effectiveness of these measures to monitor athletes’ performance and/or injury risk. This may reflect the variety of common biomechanical stiffness calculations (dynamic, time, true leg and joint) that have been used to examine these three stiffness levels (vertical, leg and joint) across a variety of human movements (i.e. running or hopping) as well as potential issues with the reliability of these measures, especially joint stiffness. Therefore, the aims of this study were to provide a comparison of the various methods for measuring stiffness during two forms of human bouncing locomotion (running and hopping) along with the measurement reliability to determine the best methods to assess links with injury risk in triathletes. Methods: Vertical, leg and joint stiffness were estimated in 12 healthy male competitive triathletes on two occasions, 7 days apart, using both running at 5.0 ms−1 and hopping (2.2 Hz) tasks. Results: Inter-day reliability was good for vertical (ICC = 0.85) and leg (ICC = 0.98) stiffness using the time method. Joint stiffness reliability was poor when assessed individually. Reliability was improved when taken as the sum of the hip, knee and ankle (ICC = 0.86). The knee and ankle combination provided the best correlation with leg stiffness during running (Pearson’s Correlation = 0.82). Discussion: The dynamic and time methods of calculating leg stiffness had better reliability than the “true” method. The time and dynamic methods had the best correlation with the different combinations of joint stiffness, which suggests that they should be considered for biomechanical screening of triathletes. The knee and ankle combination had the best correlation with leg stiffness and is therefore proposed to provide the most information regarding lower limb mechanics during gait in triathletes

The effect of a seven-week exercise program on golf swing performance and musculoskeletal measures

As most golf exercise studies have shown improved golf performance as a result of two or three sessions per week, the present study investigated the effects of a supervised exercise session performed once a week for seven weeks on golf swing variables and musculoskeletal screening measures. Professional Golfers Association of Australia International Golf Institute student golfers (n ¼ 43) with a mean standard deviation handicap of 8.6 8.3 participated in the study. Each golfer performed 10 musculoskeletal tests and a standardised 60-shot golf performance test (TrackMan, Vedbaek, Denmark) on separate days before and after the seven-week program. Significant improvements in a number of musculoskeletal tests (i.e. left leg bridging (6.6%), thoracic extension (62.5%), right thoracic rotation (23.3%), and right (20.8%) and left single leg squat (29.1%)) were observed (all p 0.024); however, no significant differences were observed for any golf swing variables. Future research investigating different training protocols may help to determine whether the type or frequency of training has the greatest influence on golf swing performance

Production of lectin-affinity matrices for process-scale glycoprotein purification

A selection of prokaryotic lectins with a variety of glycan specificities and affinities have been identified, cloned, expressed in Eschericia coli and characterised. The aims of this project are to: - express the lectins at 1L scale to produce sufficient quantities for immobilisation studies (~100 mg) - immobilisethelectinsonSepharose - evaluate lectin performance on column by monitoring their ability toreproducibly capture and elute glycoprotein glycoforms

Genetically enhanced recombinant lectins for glyco-selective analysis and purification

- Generation of a library of recombinant prokaryotic lectins (RPL’s) through random mutagenesis of the carbohydrate binding sites of bacterial lectins. - Characterisation of mutant lectins with respect to structure and specificity - Provision of mutant RPL’s with enhanced affinity and/or altered specificity, alongside wild-type RPL’s, for glycoprotein analysis and purificatio

The investigation of a recombinant GalNAc binding protein from bacillus thuringiensis as a tool for glycan analysis and detection

Changes in the structures of glycans on the surfaces of eukaryotic cells can be important biomarkers for developmental or disease states. Improved methods are needed for the detection and analysis of alterations in glycan structures. Carbohydrate binding proteins such as lectins have potential for the recognition of changes in glycan structure. Host-pathogen interactions frequently involve the recognition of host carbohydrates by proteins of bacteria or viruses. Many bacterial toxins have evolved to interact with host cell receptors or with a specific tissue due to lectin like properties. The toxins from Bacillus thuringiensis have been shown to have carbohydrate binding abilities, in particular N-Acetylgalactosamine (GalNAc) has been shown to inhibit the binding of the toxin Cry1Ac. GalNAc has been shown to be an important marker in many diseases such as breast cancer and colon carcinogenesis. Moreover, changes in GalNAc glycosylation have been identified in many disorders such as cystic fibrosis, neuromuscular disorders and nephropathy. Here we describe the purification of a GalNAc binding protein of bacterial origin that may have potential in the development of diagnostic assays

Exploitation of siderophores for the speciation of iron

Iron is essential for life. It acts as an electron donor/acceptor in metabolic processes facilitated by its variable valency. Although vital, it is toxic at high levels due to Fe2+ oxidation. Iron toxicity is a concern as it can affect growth and product yields in animal cell culture. Siderophores are high affinity Fe3+ chelators produced by microorganisms. This affinity gives them the potential to be used as a basis in platforms to detect and speciate iron in industrial cell culture. Rhizobactin 1021 is of interest due to its decanoic acid “tail” that is not involved in chelation which makes it an ideal target for immobilisation