Characterisation of chicken Campylobacter jejuni isolates using resolution optimised single nucleotide polymorphisms and binary gene markers

The principal objective of this study was to determine if Campylobacter jejuni genotyping methods based upon resolution optimised sets of single nucleotide polymorphisms (SNPs) and binary genetic markers were capable of identifying epidemiologically linked clusters of chicken-derived isolates. Eighty-eight C. jejuni isolates of known flaA RFLP type were included in the study. They encompassed three groups of ten isolates that were obtained at the same time and place and possessed the same flaA type. These were regarded as being epidemiologically linked. Twenty-six unlinked C. jejuni flaA type I isolates were included to test the ability of SNP and binary typing to resolve isolates that were not resolved by flaA RFLP. The remaining isolates were of different flaA types. All isolates were typed by real-time PCR interrogation of the resolution optimised sets of SNPs and binary markers. According to each typing method, the three epidemiologically linked clusters were three different clones that were well resolved from the other isolates. The 26 unlinked C. jejuni flaA type I isolates were resolved into 14 SNP-binary types, indicating that flaA typing can be unreliable for revealing epidemiological linkage. Comparison of the data with data from a fully typed set of isolates associated with human infection revealed that abundant lineages in the chicken isolates that were also found in the human isolates belonged to clonal complex (CC) -21 and CC-353, with the usually rare C-353 member ST-524 being especially abundant in the chicken collection. The chicken isolates selected to be diverse according to flaA were also diverse according to SNP and binary typing. It was observed that CC-48 was absent in the chicken isolates, despite being very common in Australian human infection isolates, indicating that this may be a major cause of human disease that is not chicken associated.

Development and Simulation of a Variable Rate Controller for an Air search and Air Sampling Unmanned Aerial System

This report describes the development and simulation of a variable rate controller for a 6-degree of freedom nonlinear model. The variable rate simulation model represents an off the shelf autopilot. Flight experiment involves risks and can be expensive. Therefore a dynamic model to understand the performance characteristics of the UAS in mission simulation before actual flight test or to obtain parameters needed for the flight is important. The control and guidance is implemented in Simulink. The report tests the use of the model for air search and air sampling path planning. A GUI in which a set of mission scenarios, in which two experts (mission expert, i.e. air sampling or air search and an UAV expert) interact, is presented showing the benefits of the method.

Normative values for corneal nerve morphology assessed using corneal confocal microscopy: A multinational normative data set

OBJECTIVE Corneal confocal microscopy is a novel diagnostic technique for the detection of nerve damage and repair in a range of peripheral neuropathies, in particular diabetic neuropathy. Normative reference values are required to enable clinical translation and wider use of this technique. We have therefore undertaken a multicenter collaboration to provide worldwide age-adjusted normative values of corneal nerve fiber parameters. RESEARCH DESIGN AND METHODS A total of 1,965 corneal nerve images from 343 healthy volunteers were pooled from six clinical academic centers. All subjects underwent examination with the Heidelberg Retina Tomograph corneal confocal microscope. Images of the central corneal subbasal nerve plexus were acquired by each center using a standard protocol and analyzed by three trained examiners using manual tracing and semiautomated software (CCMetrics). Age trends were established using simple linear regression, and normative corneal nerve fiber density (CNFD), corneal nerve fiber branch density (CNBD), corneal nerve fiber length (CNFL), and corneal nerve fiber tortuosity (CNFT) reference values were calculated using quantile regression analysis. RESULTS There was a significant linear age-dependent decrease in CNFD (-0.164 no./mm(2) per year for men, P < 0.01, and -0.161 no./mm(2) per year for women, P < 0.01). There was no change with age in CNBD (0.192 no./mm(2) per year for men, P = 0.26, and -0.050 no./mm(2) per year for women, P = 0.78). CNFL decreased in men (-0.045 mm/mm(2) per year, P = 0.07) and women (-0.060 mm/mm(2) per year, P = 0.02). CNFT increased with age in men (0.044 per year, P < 0.01) and women (0.046 per year, P < 0.01). Height, weight, and BMI did not influence the 5th percentile normative values for any corneal nerve parameter. CONCLUSIONS This study provides robust worldwide normative reference values for corneal nerve parameters to be used in research and clinical practice in the study of diabetic and other peripheral neuropathies.

Molecular and serological detection of A. centrale- and A. marginale-infected cattle grazing within an endemic area

A reverse line blot hybridization (RLB) one-stage nested PCR (nPCR) for Anaplasma centrale and a nested PCR for Anaplasma marginale were used to detect infected cattle grazing within an endemic region in Israel. A novel set of PCR primers and oligonucleotide probes based on a 16S ribosomal RNA gene was designed for RLB detection of both Anaplasma species, and the performance of the molecular assays compared. The immunofluorescent antibody test (IFA) was used to detect antibodies to both Anaplasma species, whereas, a highly sensitive and specific competitive enzyme-linked immunosorbent assay (cELISA) was used to detect antibodies in A. centrale-vaccinated cattle. The RLB and the nested PCR procedures showed bacteremia with sensitivity of 50 infected erythrocytes per milliliter. Up to 93% of the A. centrale vaccinates carried specific antibodies that were detected by cELISA, and up to 71% of the vaccinated cattle were found to be naturally infected with A. marginale according to the PCR and the RLB assays. Nevertheless, no severe outbreaks of A. marginale infection occurred among vaccinated herds in this endemic region. It appears that both, molecular tools and serology are useful for evaluation of the vaccine efficacy. In the light of wide natural field infection with A. marginale, strong recommendations to continue the A. centrale vaccination program regime will continue until a new generation of non-blood-based vaccine will be developed.

Set theoretic operations on polygons using the scan-grid approach

This paper describes an algorithm to compute the union, intersection and difference of two polygons using a scan-grid approach. Basically, in this method, the screen is divided into cells and the algorithm is applied to each cell in turn. The output from all the cells is integrated to yield a representation of the output polygon. In most cells, no computation is required and thus the algorithm is a fast one. The algorithm has been implemented for polygons but can be extended to polyhedra as well. The algorithm is shown to take O(N) time in the average case where N is the total number of edges of the two input polygons.

Bi-criteria single machine scheduling problem with a learning effect: Aneja-Nair method to obtain the set of optimal sequences

In this paper, we consider the bi-criteria single machine scheduling problem of n jobs with a learning effect. The two objectives considered are the total completion time (TC) and total absolute differences in completion times (TADC). The objective is to find a sequence that performs well with respect to both the objectives: the total completion time and the total absolute differences in completion times. In an earlier study, a method of solving bi-criteria transportation problem is presented. In this paper, we use the methodology of solvin bi-criteria transportation problem, to our bi-criteria single machine scheduling problem with a learning effect, and obtain the set of optimal sequences,. Numerical examples are presented for illustrating the applicability and ease of understanding.

Responses in carcass lean pH at 24 hours post-mortem in lines of Large White pigs selected for growth rate on a fixed ration over a set time

A restricted maximum likelihood analysis applied to an animal model showed no significant differences (P > 0.05) in pH value of the longissimus dorsi measured at 24 h post-mortem (pH24) between high and low lines of Large White pigs selected over 4 years for post-weaning growth rate on restricted feeding. Genetic and phenotypic correlations between pH24 and production and carcass traits were estimated using all performance testing records combined with the pH24 measurements (5.05-7.02) on slaughtered animals. The estimate of heritability for pH24 was moderate (0.29 ± 0.18). Genetic correlations between pH24 and production or carcass composition traits, except for ultrasonic backfat (UBF), were not significantly different from zero. UBF had a moderate, positive genetic correlation with pH24 (0.24 ± 0.33). These estimates of genetic correlations affirmed that selection for increased growth rate on restricted feeding is likely to result in limited changes in pH24 and pork quality since the selection does not put a high emphasis on reduced fatness.

Cognitive deficits and the Paced Auditory Serial Addition Test performance among patients with multiple sclerosis

Multiple sclerosis (MS) is a chronic, inflammatory disease of the central nervous system, characterized especially by myelin and axon damage. Cognitive impairment in MS is common but difficult to detect without a neuropsychological examination. Valid and reliable methods are needed in clinical practice and research to detect deficits, follow their natural evolution, and verify treatment effects. The Paced Auditory Serial Addition Test (PASAT) is a measure of sustained and divided attention, working memory, and information processing speed, and it is widely used in MS patients neuropsychological evaluation. Additionally, the PASAT is the sole cognitive measure in an assessment tool primarly designed for MS clinical trials, the Multiple Sclerosis Functional Composite (MSFC). The aims of the present study were to determine a) the frequency, characteristics, and evolution of cognitive impairment among relapsing-remitting MS patients, and b) the validity and reliability of the PASAT in measuring cognitive performance in MS patients. The subjects were 45 relapsing-remitting MS patients from Seinäjoki Central Hospital, Department of Neurology and 48 healthy controls. Both groups underwent comprehensive neuropsychological assessments, including the PASAT, twice in a one-year follow-up, and additionally a sample of 10 patients and controls were evaluated with the PASAT in serial assessments five times in one month. The frequency of cognitive dysfunction among relapsing-remitting MS patients in the present study was 42%. Impairments were characterized especially by slowed information processing speed and memory deficits. During the one-year follow-up, the cognitive performance was relatively stable among MS patients on a group level. However, the practice effects in cognitive tests were less pronounced among MS patients than healthy controls. At an individual level the spectrum of MS patients cognitive deficits was wide in regards to their characteristics, severity, and evolution. The PASAT was moderately accurate in detecting MS-associated cognitive impairment, and 69% of patients were correctly classified as cognitively impaired or unimpaired when comprehensive neuropsychological assessment was used as a "gold standard". Self-reported nervousness and poor arithmetical skills seemed to explain misclassifications. MS-related fatigue was objectively demonstrated as fading performance towards the end of the test. Despite the observed practice effect, the reliability of the PASAT was excellent, and it was sensitive to the cognitive decline taking place during the follow-up in a subgroup of patients. The PASAT can be recommended for use in the neuropsychological assessment of MS patients. The test is fairly sensitive, but less specific; consequently, the reasons for low scores have to be carefully identified before interpreting them as clinically significant.

In quest of a reliable and efficient computational test for detection of isomorphism in kinematic chains

The test based on comparison of the characteristic coefficients of the adjancency matrices of the corresponding graphs for detection of isomorphism in kinematic chains has been shown to fail in the case of two pairs of ten-link, simple-jointed chains, one pair corresponding to single-freedom chains and the other pair corresponding to three-freedom chains. An assessment of the merits and demerits of available methods for detection of isomorphism in graphs and kinematic chains is presented, keeping in view the suitability of the methods for use in computerized structural synthesis of kinematic chains. A new test based on the characteristic coefficients of the “degree” matrix of the corresponding graph is proposed for detection of isomorphism in kinematic chains. The new test is found to be successful in the case of a number of examples of graphs where the test based on characteristic coefficients of adjancency matrix fails. It has also been found to be successful in distinguishing the structures of all known simple-jointed kinematic chains in the categories of (a) single-freedom chains with up to 10 links, (b) two-freedom chains with up to 9 links and (c) three-freedom chains with up to 10 links.

An On-Line Algorithm for the Location of Cross Point Faults in Programmable Logic Arrays

An on-line algorithm is developed for the location of single cross point faults in a PLA (FPLA). The main feature of the valgorithm is the determination of a fault set corresponding to the response obtained for a failed test. For the apparently small number of faults in this set, all other tests are generated and a fault table is formed. Subsequently, an adaptive procedure is used to diagnose the fault. Functional equivalence test is carried out to determine the actual fault class if the adaptive testing results in a set of faults with identical tests. The large amount of computation time and storage required in the determination, a priori, of all the fault equivalence classes or in the construction of a fault dictionary are not needed here. A brief study of functional equivalence among the cross point faults is also made.

Test of the enemy release hypothesis: the native magpie moth prefers a native fireweed (Senecio pinnatifolius) to its introduced congener (S. madagascariensis).

The enemy release hypothesis predicts that native herbivores will either prefer or cause more damage to native than introduced plant species. We tested this using preference and performance experiments in the laboratory and surveys of leaf damage caused by the magpie moth Nyctemera amica on a co-occuring native and introduced species of fireweed (Senecio) in eastern Australia. In the laboratory, ovipositing females and feeding larvae preferred the native S. pinnatifolius over the introduced S. madagascariensis. Larvae performed equally well on foliage of S. pinnatifolius and S. madagascariensis: pupal weights did not differ between insects reared on the two species, but growth rates were significantly faster on S. pinnatifolius. In the field, foliage damage was significantly greater on native S. pinnatifolius than introduced S. madagascariensis. These results support the enemy release hypothesis, and suggest that the failure of native consumers to switch to introduced species contributes to their invasive success. Both plant species experienced reduced, rather than increased, levels of herbivory when growing in mixed populations, as opposed to pure stands in the field; thus, there was no evidence that apparent competition occurred.

Tarinakontekstin vaikutus sanojen muistamiseen kompleksisessa työmuistitehtävässä

Objectives. The sentence span task is a complex working memory span task used for estimating total working memory capacity for both processing (sentence comprehension) and storage (remembering a set of words). Several traditional models of working memory suggest that performance on these tasks relies on phonological short-term storage. However, long-term memory effects as well as the effects of expertise and strategies have challenged this view. This study uses a working memory task that aids the creation of retrieval structures in the form of stories, which have been shown to form integrated structures in longterm memory. The research question is whether sentence and story contexts boost memory performance in a complex working memory task. The hypothesis is that storage of the words in the task takes place in long-term memory. Evidence of this would be better recall for words as parts of sentences than for separate words, and, particularly, a beneficial effect for words as part of an organized story. Methods. Twenty stories consisting of five sentences each were constructed, and the stimuli in all experimental conditions were based on these sentences and sentence-final words, reordered and recombined for the other conditions. Participants read aloud sets of five sentences that either formed a story or not. In one condition they had to report all the last words at the end of the set, in another, they memorised an additional separate word with each sentence. The sentences were presented on the screen one word at a time (500 ms). After the presentation of each sentence, the participant verified a statement about the sentence. After five sentences, the participant repeated back the words in correct positions. Experiment 1 (n=16) used immediate recall, experiment 2 (n=21) both immediate recall and recall after a distraction interval (the operation span task). In experiment 2 a distracting mental arithmetic task was presented instead of recall in half of the trials, and an individual word was added before each sentence in the two experimental conditions when the participants were to memorize the sentence final words. Subjects also performed a listening span task (in exp.1) or an operation span task (exp.2) to allow comparison of the estimated span and performance in the story task. Results were analysed using correlations, repeated measures ANOVA and a chi-square goodness of fit test on the distribution of errors. Results and discussion. Both the relatedness of the sentences (the story condition) and the inclusion of the words into sentences helped memory. An interaction showed that the story condition had a greater effect on last words than separate words. The beneficial effect of the story was shown in all serial positions. The effects remained in delayed recall. When the sentences formed stories, performance in verification of the statements about sentence context was better. This, as well as the differing distributions of errors in different experimental conditions, suggest different levels of representation are in use in the different conditions. In the story condition, the nature of these representations could be in the form of an organized memory structure, a situation model. The other working memory tasks had only few week correlations to the story task. This could indicate that different processes are in use in the tasks. The results do not support short-term phonological storage, but instead are compatible with the words being encoded to LTM during the task.

Guaiac versus immunochemical tests: Faecal occult blood test screening for colorectal cancer in a rural community

Objective: To describe patient participation and clinical performance in a colorectal cancer (CRC) screening program utilising faecal occult blood test (FOBT). Methods: A community-based intervention was conducted in a small, rural community in north Queensland, 2000/01. One of two FOBT kits – guaiac (Hemoccult-ll) or immunochemical (Inform) – was assigned by general practice and mailed to participants (3,358 patients aged 50–74 years listed with the local practices). Results: Overall participation in FOBT screening was 36.3%. Participation was higher with the immunochemical kit than the guaiac kit (OR=1.9, 95% Cl 1.6-2.2). Women were more likely to comply with testing than men (OR=1.4, 95% Cl 1.2-1.7), and people in their 60s were less likely to participate than those 70–74 years (OR=0.8, 95% Cl 0.6-0.9). The positivity rate was higher for the immunochemical (9.5%) than the guaiac (3.9%) test (χ2=9.2, p=0.002), with positive predictive values for cancer or adenoma of advanced pathology of 37.8% (95% Cl 28.1–48.6) for !nform and 40.0% (95% Cl 16.8–68.7) for Hemoccult-ll. Colonoscopy follow-up was 94.8% with a medical complication rate of 2–3%. Conclusions: An immunochemical FOBT enhanced participation. Higher positivity rates for this kit did not translate into higher false-positive rates, and both test types resulted in a high yield of neoplasia. Implications: In addition to type of FOBT, the ultimate success of a population-based screening program for CRC using FOBT will depend on appropriate education of health professionals and the public as well as significant investment in medical infrastructure for colonoscopy follow-up.

Validating economic and environmental sustainability of a short-term summer forage legume in dryland wheat cropping systems in south-west Queensland.

The present study set out to test the hypothesis through field and simulation studies that the incorporation of short-term summer legumes, particularly annual legume lablab (Lablab purpureus cv. Highworth), in a fallow-wheat cropping system will improve the overall economic and environmental benefits in south-west Queensland. Replicated, large plot experiments were established at five commercial properties by using their machineries, and two smaller plot experiments were established at two intensively researched sites (Roma and St George). A detailed study on various other biennial and perennial summer forage legumes in rotation with wheat and influenced by phosphorus (P) supply (10 and 40 kg P/ha) was also carried out at the two research sites. The other legumes were lucerne (Medicago sativa), butterfly pea (Clitoria ternatea) and burgundy bean (Macroptilium bracteatum). After legumes, spring wheat (Triticum aestivum) was sown into the legume stubble. The annual lablab produced the highest forage yield, whereas germination, establishment and production of other biennial and perennial legumes were poor, particularly in the red soil at St George. At the commercial sites, only lablab-wheat rotations were experimented, with an increased supply of P in subsurface soil (20 kg P/ha). The lablab grown at the commercial sites yielded between 3 and 6 t/ha forage yield over 2-3 month periods, whereas the following wheat crop with no applied fertiliser yielded between 0.5 to 2.5 t/ha. The wheat following lablab yielded 30% less, on average, than the wheat in a fallow plot, and the profitability of wheat following lablab was slightly higher than that of the wheat following fallow because of greater costs associated with fallow management. The profitability of the lablab-wheat phase was determined after accounting for the input costs and additional costs associated with the management of fallow and in-crop herbicide applications for a fallow-wheat system. The economic and environmental benefits of forage lablab and wheat cropping were also assessed through simulations over a long-term climatic pattern by using economic (PreCAPS) and biophysical (Agricultural Production Systems Simulation, APSIM) decision support models. Analysis of the long-term rainfall pattern (70% in summer and 30% in winter) and simulation studies indicated that ~50% time a wheat crop would not be planted or would fail to produce a profitable crop (grain yield less than 1 t/ha) because of less and unreliable rainfall in winter. Whereas forage lablab in summer would produce a profitable crop, with a forage yield of more than 3 t/ha, ~90% times. Only 14 wheat crops (of 26 growing seasons, i.e. 54%) were profitable, compared with 22 forage lablab (of 25 seasons, i.e. 90%). An opportunistic double-cropping of lablab in summer and wheat in winter is also viable and profitable in 50% of the years. Simulation studies also indicated that an opportunistic lablab-wheat cropping can reduce the potential runoff+drainage by more than 40% in the Roma region, leading to improved economic and environmental benefits.

Kinnasneulatekniikan verkko-oppimateriaalin kehittäminen ja neulalla neulomisen taidon kehittyminen

The purpose of the study was to develop a functional web-based learning material for the learning of the nålbinding technique. The study of the research topic was already begun in my pedagogical thesis in 2008 by considering the demands on pedagogic material for the teaching of the technique. This study falls into the field of qualitative design research which was carried out through three stages. In the study three methods of usability testing, i.e. expert analysis, the informants’ thinking aloud and interviews, were used as research methods. At the first stage of the study the first version of the learning material was created. This was done on the basis of theoretical knowledge, the demands set on learning materials as clarified in previous studies, on the basis of previously created learning materials for the learning of the nålbinding technique as well as with the help of two experts on the technique. At the second stage, the learning material was developed on the basis of expert analysis and another version of the material was created. At the third stage, usability testing was carried out on the material. At this stage two informants used the material, practiced stitching with the nålbinding needle and thought aloud while doing so. In the usability testing the Morae –programme was used to record the events on the screen, the actions of the informants and their spoken out thoughts. The Morae –programme was also used when analysing the recordings. After the testing, the informants practised stitching independently and in a few weeks time they were interviewed. The interviews were aimed at finding out the informants’ opinions on the future development of the material. On the basis of the informants’ independent attempts at using the nålbinding technique, the development of their skills after the testing was also discussed at the interviews. The development of the learning material will continue after this study on the basis of the usability testing and the interviews. The web-based learning material was created for the website Käspaikka in the address www.kaspaikka.fi/kinnasneula. By creating a multimodal learning material the dual-coding theory by Paivio was taken into consideration. According to the theory, several methods of presentation help a learner to restore information in his/her memory. The independent construction of the learner’s knowledge, i.e. learning according to the principles of the constructivist learning theory, was also supported by creating a logical navigation system, by linking interrelated topics to one another and by presenting the topics in several different forms. In the test situations the learning material was judged to work well when practising stitching with the nålbinding needle. Both informants learned the basics of the nålbinding technique even though their respective learning strategies were quite different. In the usability testing illogicalities and shortcomings were still noticed in the learning material which will still be further developed in the future.