863 resultados para Score metric
Resumo:
Exponential growth of genomic data in the last two decades has made manual analyses impractical for all but trial studies. As genomic analyses have become more sophisticated, and move toward comparisons across large datasets, computational approaches have become essential. One of the most important biological questions is to understand the mechanisms underlying gene regulation. Genetic regulation is commonly investigated and modelled through the use of transcriptional regulatory network (TRN) structures. These model the regulatory interactions between two key components: transcription factors (TFs) and the target genes (TGs) they regulate. Transcriptional regulatory networks have proven to be invaluable scientific tools in Bioinformatics. When used in conjunction with comparative genomics, they have provided substantial insights into the evolution of regulatory interactions. Current approaches to regulatory network inference, however, omit two additional key entities: promoters and transcription factor binding sites (TFBSs). In this study, we attempted to explore the relationships among these regulatory components in bacteria. Our primary goal was to identify relationships that can assist in reducing the high false positive rates associated with transcription factor binding site predictions and thereupon enhance the reliability of the inferred transcription regulatory networks. In our preliminary exploration of relationships between the key regulatory components in Escherichia coli transcription, we discovered a number of potentially useful features. The combination of location score and sequence dissimilarity scores increased de novo binding site prediction accuracy by 13.6%. Another important observation made was with regards to the relationship between transcription factors grouped by their regulatory role and corresponding promoter strength. Our study of E.coli ��70 promoters, found support at the 0.1 significance level for our hypothesis | that weak promoters are preferentially associated with activator binding sites to enhance gene expression, whilst strong promoters have more repressor binding sites to repress or inhibit gene transcription. Although the observations were specific to �70, they nevertheless strongly encourage additional investigations when more experimentally confirmed data are available. In our preliminary exploration of relationships between the key regulatory components in E.coli transcription, we discovered a number of potentially useful features { some of which proved successful in reducing the number of false positives when applied to re-evaluate binding site predictions. Of chief interest was the relationship observed between promoter strength and TFs with respect to their regulatory role. Based on the common assumption, where promoter homology positively correlates with transcription rate, we hypothesised that weak promoters would have more transcription factors that enhance gene expression, whilst strong promoters would have more repressor binding sites. The t-tests assessed for E.coli �70 promoters returned a p-value of 0.072, which at 0.1 significance level suggested support for our (alternative) hypothesis; albeit this trend may only be present for promoters where corresponding TFBSs are either all repressors or all activators. Nevertheless, such suggestive results strongly encourage additional investigations when more experimentally confirmed data will become available. Much of the remainder of the thesis concerns a machine learning study of binding site prediction, using the SVM and kernel methods, principally the spectrum kernel. Spectrum kernels have been successfully applied in previous studies of protein classification [91, 92], as well as the related problem of promoter predictions [59], and we have here successfully applied the technique to refining TFBS predictions. The advantages provided by the SVM classifier were best seen in `moderately'-conserved transcription factor binding sites as represented by our E.coli CRP case study. Inclusion of additional position feature attributes further increased accuracy by 9.1% but more notable was the considerable decrease in false positive rate from 0.8 to 0.5 while retaining 0.9 sensitivity. Improved prediction of transcription factor binding sites is in turn extremely valuable in improving inference of regulatory relationships, a problem notoriously prone to false positive predictions. Here, the number of false regulatory interactions inferred using the conventional two-component model was substantially reduced when we integrated de novo transcription factor binding site predictions as an additional criterion for acceptance in a case study of inference in the Fur regulon. This initial work was extended to a comparative study of the iron regulatory system across 20 Yersinia strains. This work revealed interesting, strain-specific difierences, especially between pathogenic and non-pathogenic strains. Such difierences were made clear through interactive visualisations using the TRNDifi software developed as part of this work, and would have remained undetected using conventional methods. This approach led to the nomination of the Yfe iron-uptake system as a candidate for further wet-lab experimentation due to its potential active functionality in non-pathogens and its known participation in full virulence of the bubonic plague strain. Building on this work, we introduced novel structures we have labelled as `regulatory trees', inspired by the phylogenetic tree concept. Instead of using gene or protein sequence similarity, the regulatory trees were constructed based on the number of similar regulatory interactions. While the common phylogentic trees convey information regarding changes in gene repertoire, which we might regard being analogous to `hardware', the regulatory tree informs us of the changes in regulatory circuitry, in some respects analogous to `software'. In this context, we explored the `pan-regulatory network' for the Fur system, the entire set of regulatory interactions found for the Fur transcription factor across a group of genomes. In the pan-regulatory network, emphasis is placed on how the regulatory network for each target genome is inferred from multiple sources instead of a single source, as is the common approach. The benefit of using multiple reference networks, is a more comprehensive survey of the relationships, and increased confidence in the regulatory interactions predicted. In the present study, we distinguish between relationships found across the full set of genomes as the `core-regulatory-set', and interactions found only in a subset of genomes explored as the `sub-regulatory-set'. We found nine Fur target gene clusters present across the four genomes studied, this core set potentially identifying basic regulatory processes essential for survival. Species level difierences are seen at the sub-regulatory-set level; for example the known virulence factors, YbtA and PchR were found in Y.pestis and P.aerguinosa respectively, but were not present in both E.coli and B.subtilis. Such factors and the iron-uptake systems they regulate, are ideal candidates for wet-lab investigation to determine whether or not they are pathogenic specific. In this study, we employed a broad range of approaches to address our goals and assessed these methods using the Fur regulon as our initial case study. We identified a set of promising feature attributes; demonstrated their success in increasing transcription factor binding site prediction specificity while retaining sensitivity, and showed the importance of binding site predictions in enhancing the reliability of regulatory interaction inferences. Most importantly, these outcomes led to the introduction of a range of visualisations and techniques, which are applicable across the entire bacterial spectrum and can be utilised in studies beyond the understanding of transcriptional regulatory networks.
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Reviews have criticised universities for not embedding sufficient praxis for preparing preservice teachers for the profession. The Teacher Education Done Differently (TEDD) project explored praxis development for preservice teachers within existing university coursework. This mixed-method investigation involved an analysis of multiple case studies with preservice teacher involvement in university programs, namely: Ed Start for practicum I (n=26), III (n=23), and IV (n=12); Move It Use It (Health and Physical Education program; n=38), Studies of Society and its Environment (SOSE, n=24), and Science in Schools (n=38). The project included preservice teachers teaching primary students at the campus site in gifted education (the B-GR8 program, n=22). The percentage range for preservice teacher agreement of their praxis development leading up to practicum I, III, and IV was between 91-100% with a high mean score range (4.26-5.00). Other university units had similar findings except for SOSE (i.e., percentage range: 10-86%; M range: 2.33-4.00; SD range: 0.55-1.32). Qualitative data presented an understanding of the praxis development leading to the conclusion that additional applied learning experiences as lead-up days for field experiences and as avenues for exploring the teaching of specific subject areas presented opportunities for enhancing praxis.
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Background Heart failure (HF) remains a condition with high morbidity and mortality. We tested a telephone support strategy to reduce major events in rural and remote Australians with HF, who have limited healthcare access. Telephone support comprised an interactive telecommunication software tool (TeleWatch) with follow-up by trained cardiac nurses. Methods Patients with a general practice (GP) diagnosis of HF were randomised to usual care (UC) or UC and telephone support intervention (UC+I) using a cluster design involving 143 GPs throughout Australia. Patients were followed for 12 months. The primary end-point was the Packer clinical composite score. Secondary end-points included hospitalisation for any cause, death or hospitalisation, as well as HF hospitalisation. Results Four hundred and five patients were randomised into CHAT. Patients were well matched at baseline for key demographic variables. The primary end-point of the Packer Score was not different between the two groups (P=0.98), although more patients improved with UC+I. There were fewer patients hospitalised for any cause (74 versus 114, adjusted HR 0.67 [95% CI 0.50-0.89], p=0.006) and who died or were hospitalised (89 versus 124, adjusted HR 0.70 [95% CI 0.53 – 0.92], p=0.011), in the UC+I vs UC group. HF hospitalisations were reduced with UC+I (23 versus 35, adjusted HR 0.81 [95% CI 0.44 – 1.38]), although this was not significant (p=0.43). There were 16 deaths in the UC group and 17 in the UC+I group (p=0.43). Conclusions Although no difference was observed in the primary end-point of CHAT (Packer composite score), UC+I significantly reduced the number of HF patients hospitalised amongst a rural and remote cohort. These data suggest that telephone support may be an efficacious approach to improve clinical outcomes in rural and remote HF patients.
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People with Parkinson’s disease (PD) are at higher risk of malnutrition due to PD symptoms and pharmacotherapy side effects. Poorer outcomes are associated with higher amounts of weight loss (>5%) and lower levels of fat free mass. When pharmacotherapy is no longer effective for symptom control, deep-brain stimulation (DBS) surgery may be considered. People with PD scheduled for DBS surgery were recruited from a Brisbane neurological clinic (n=11 out of 16). The Scale for Outcomes of Parkinson’s disease –Autonomic (SCOPA-AUT), Modified Constipation Assessment Scale (MCAS), and a 3-day food diary were mailed to participants’ homes for completion prior to hospital admission. During admission, the Patient-Generated Subjective Global Assessment (PG-SGA), weight, height and body composition were assessed. Mean(±s.d.) PD duration from diagnosis and time since occurrence of PD symptoms was 9.0(±8.0) and 12(±8.8) years, respectively. Five participants reported unintentional weight loss (average loss of 15.6%). PD duration but not years since symptom onset significantly predicted PG-SGA scores (β=4.2, t(8)=2.7, p<.05). Both were positively correlated with PG-SGA score (r = .667, r=.587). On average, participants classified as well-nourished (SGA-A) (n=4) were younger, had shorter disease durations, lower PG-SGA scores, higher body mass (BMI) and fat free mass (FFMI) indices when compared to malnourished participants (SGA-B) (n=7). They also reported fewer non-motor symptoms on the SCOPA-AUT and MCAS. Three participants had previously received dietetic advice but not in relation to PD. These findings demonstrate that malnutrition remains unrecognised and untreated in this group despite unintentional weight loss and a high prevalence of malnutrition.
Resumo:
Objective: Malnutrition results in poor health outcomes, and people with Parkinson’s disease may be more at risk of malnutrition. However, the prevalence of malnutrition in Parkinson’s disease is not yet well defined. The aim of this study is to provide an estimate of the extent of malnutrition in community-dwelling people with Parkinson’s disease. Methods: This is a cross-sectional study of people with Parkinson’s disease residing within a 2 hour driving radius of Brisbane, Australia. The Subjective Global Assessment (SGA) and scored Patient Generated Subjective Global Assessment (PG-SGA) were used to assess nutritional status. Body weight, standing or knee height, mid-arm circumference and waist circumference were measured. Results: Nineteen (15%) of the participants were moderately malnourished (SGA-B). The median PG-SGA score of the SGA-B group was 8 (4 – 15), significantly higher than the SGA-A group, U=1860.5,p<.05. The symptoms most influencing intake were loss of appetite, constipation, early satiety and problems swallowing. Conclusions: As with other populations, malnutrition remains under-recognised and undiagnosed in people with Parkinson’s disease. Regular screening of nutritional status in people with Parkinson’s disease by health professionals with whom they have regular contact should occur to identify those who may benefit from further nutrition assessment and intervention.
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This paper investigates the use of mel-frequency deltaphase (MFDP) features in comparison to, and in fusion with, traditional mel-frequency cepstral coefficient (MFCC) features within joint factor analysis (JFA) speaker verification. MFCC features, commonly used in speaker recognition systems, are derived purely from the magnitude spectrum, with the phase spectrum completely discarded. In this paper, we investigate if features derived from the phase spectrum can provide additional speaker discriminant information to the traditional MFCC approach in a JFA based speaker verification system. Results are presented which provide a comparison of MFCC-only, MFDPonly and score fusion of the two approaches within a JFA speaker verification approach. Based upon the results presented using the NIST 2008 Speaker Recognition Evaluation (SRE) dataset, we believe that, while MFDP features alone cannot compete with MFCC features, MFDP can provide complementary information that result in improved speaker verification performance when both approaches are combined in score fusion, particularly in the case of shorter utterances.
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OBJECTIVE: To determine the point at which differences in clinical assessment scores on physical ability, pain and overall condition are sufficiently large to correspond to a subjective perception of a meaningful difference from the perspective of the patient. METHODS: Forty patients with a diagnosis of rheumatoid arthritis participated in an evening of clinical assessment and one-on-one conversations with each other regarding their arthritic condition. The assessments included tender and swollen joint counts, clinician and patient global assessments, participant assessment of pain and the Health Assessment Questionnaire (HAQ) on physical ability. After each conversation, participants rated themselves relative to their conversational partner on physical ability, pain and overall condition. These subjective comparative ratings were compared to the differences of the individual clinical assessments. RESULTS: In total there were 120 conversations. Generally participants judged themselves as less disabled than others. They rated themselves as "somewhat better" than their conversation partner when they had a (mean) 7% better score on the HAQ, 6% less pain, and 9% better global assessment. In contrast, they rated themselves as "somewhat worse" when they had a (mean) 16% worse score on the HAQ, 16% more pain, and 29% worse global assessment. CONCLUSIONS: Patients view clinically important differences in an asymmetric manner. These results can provide guidance in interpreting results and planning clinical trials.
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BACKGROUND/OBJECTIVES: To describe the diet quality of a national sample of Australian women with a recent history of gestational diabetes mellitus (GDM) and determine factors associated with adherence to national dietary recommendations. SUBJECTS/METHODS: A postpartum lifestyle survey with 1499 Australian women diagnosed with GDM p3 years previously. Diet quality was measured using the Australian recommended food score (ARFS) and weighted by demographic and diabetes management characteristics. Multinominal logistic regression analysis was used to determine the association between diet quality and demographic characteristics, health seeking behaviours and diabetes-related risk factors. RESULTS: Mean (±s.d.) ARFS was 30.9±8.1 from a possible maximum score of 74. Subscale component scores demonstrated that the nuts/legumes, grains and fruits were the most poorly scored. Factors associated with being in the highest compared with the lowest ARFS quintile included age (odds ratio (OR) 5-year increase=1.40; 95% (confidence interval) CI:1.16–1.68), tertiary education (OR=2.19; 95% CI:1.52–3.17), speaking only English (OR=1.92; 95% CI:1.19–3.08), being sufficiently physically active (OR=2.11; 95% CI:1.46–3.05), returning for postpartum blood glucose testing (OR=1.75; 95% CI:1.23–2.50) and receiving riskreduction advice from a health professional (OR=1.80; 95% CI:1.24–2.60). CONCLUSIONS: Despite an increased risk of type 2 diabetes, women in this study had an overall poor diet quality as measured by the ARFS. Women with GDM should be targeted for interventions aimed at achieving a postpartum diet consistent with the guidelines for chronic disease prevention. Encouraging women to return for follow-up and providing risk reduction advice may be positive initial steps to improve diet quality, but additional strategies need to be identified.
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The objective of this research was to investigate the effect of suspension parameters on dynamic load-sharing of longitudinal-connected air suspensions of a tri-axle semi-trailer. A novel nonlinear model of a multi-axle semi-trailer with longitudinal-connected air suspension was formulated based on fluid mechanics and thermodynamics and was validated through test results. The effects of suspension parameters on dynamic load-sharing and road-friendliness of the semi-trailer were analyzed. Simulation results indicate that the road-friendliness metric DLC (Dynamic Load Coefficient), is generally in accordance with the load-sharing metric - DLSC (Dynamic Load Sharing Coefficient). When the static height or static pressure increases, the DLSC optimization ratio declines monotonically. The effect of employing larger air lines and connectors on the DLSC optimization ratio gives varying results as road roughness increases and as driving speed increases. The results also indicate that if the air line diameter is always assumed to be larger than the connector diameter, the influence of air line diameter on load-sharing is more significant than that of the connector.
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Background: The high rates of comorbid depression and substance use in young people have been associated with a range of adverse outcomes. Yet, few treatment studies have been conducted with this population. Objective: To determine if the addition of Motivational Interviewing and Cognitive Behaviour Therapy (MI/CBT) to standard alcohol and other drug (AOD) care improves the outcomes of young people with comorbid depression and substance use. Participants and Setting: Participants comprised 88 young people with comorbid depression (Kessler 10 score of > 17) and substance use (mainly alcohol/cannabis) seeking treatment at two youth AOD services in Melbourne, Australia. Sixty young people received MI/CBT in addition to standard care (SC) and 28 received SC alone. Outcomes Measures: Primary outcome measures were depressive symptoms and drug and alcohol use in the past month. Assessments were conducted at baseline, 3 and 6 months follow up. Results and Conclusions: The addition of MI/CBT to SC was associated with a significantly greater rate of change in depression, cannabis use, motivation to change substance use and social contact in the first 3 months. However, those who received SC had achieved similar improvements on these variables by 6 months follow up. All young people achieved significant improvements in functioning and quality of life variables over time, regardless of the treatment group. No changes in alcohol or other drug use were found in either group. The delivery of MI/CBT in addition to standard AOD care may offer accelerated treatment gains in the short-term.
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This paper analyses the expenditure patterns of 97 Australian international aid and development organisations, and examines the extent to which they disclose information about their expenditure in order to discharge their accountability. Not-for-profit (NFP) expenditure attracts media attention, with perceptions of excessive costs potentially damaging stakeholder trust in NFP organisations. This makes it important for organisations to be proactive in communicating their expenditure stories to stakeholders, rather than being judged on their performance by standardised expenditure metrics. By highlighting what it costs to ensure longer-term operational capability, NFP organisations will contribute to the discharge of their financial accountability and play a part in educating all stakeholders about the dangers of relying on a single metric.
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Introduction: Improving physical and cognitive functioning is a key objective of multi-disciplinary inpatient geriatric rehabilitation. Outcomes relevant to minimum functional ability required for older adults to successfully participate in the community have been reported. However, there has been little investigation reporting outcomes of older inpatients receiving multi-disciplinary rehabilitation being discharged home from geriatric rehabilitation units. This study aims to investigate characteristics and physical and cognitive outcomes of this cohort. Method: The Princess Alexandra Hospital Geriatric and Rehabilitation Unit is the largest rehabilitation unit in Queensland. Multidisciplinary health professionals enter admission and discharge functional and clinical outcomes along with demographic information into a purpose designed database for all patients. Data collected between 2005 and 2011 was analysed using descriptive statistics. Results: During the seven-year period, 4120 patients were admitted for rehabilitation; 2126 (52%) were female, mean age of 74 years (Standard Deviation 14). Primary reasons for admission were for reconditioning post medical illness or surgical admission (n = 1285, 31%), and 30% (n = 1233) admitted for orthopaedic reasons. Of these orthopaedic admissions, 6.6% (n = 82) were for elective surgery, and 46% (n = 565) were for fractured neck-of-femurs. 76% (n = 3130) of patients were discharged home, 13% (n = 552) to residential care facilities and 10% (n = 430) were discharged to an alternative hospital setting or passed away during their admission. Mean length of stay was 44 days (SD 39) Preliminary analysis of FIM outcomes shows a mean motor score of 53 (SD = 19) on admission which significantly improved to 71 (SD = 18) by discharge. There was no change on FIM cognitive score (28 (SD7) vs 29 (SD 6). Conclusion: Geriatric patients have significant functional limitations even on discharge from inpatient rehabilitation; though overall cognition is relatively intact. Orthopaedic conditions and general deconditioning from medical/surgical admissions are the main reasons for admission. The majority of people receiving rehabilitation are discharged home.
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The higher education sector is undergoing a number of significant changes, the implications of which have yet to emerge. One such change is the increasing reliance by higher education providers on the revenue generated by full fee paying international students to fund their operating expenses. The report by the Victorian Ombudsman, Investigation into how Universities Deal with International Students ('Victorian Ombudsman's Report') tabled in the Victorian Parliament on 27 October 2011, provides evidence that Australian higher education providers may be failing to meet their legal obligations to international students. The Victorian Ombudsman's Report is the result of an investigation into four Victorian universities teaching international students with a focus on accounting and nursing schools. The report contains evidence that the universities were admitting students with scores below, or at the lower end of, the International English Language Testing System ('IELTS') score considered acceptable. Alternatively, they were relying upon their own language testing admission standards and not on an independent test like the IELTS test. While the universities provided English language support services for their international students after they had been admitted, the Ombudsman was concerned that the universities 'have not dedicated sufficient resources to meet the level of need amongst international students'.
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Food preferences have been identified as a key determinant of children’s food acceptance and consumption. The aim of this study was to identify factors that influence children’s liking for fruits, vegetables and non-core foods. Participants were Australian mothers (median age at delivery=31 years, 18-46 years) and their two-year-old children (M=25 months, SD=1 month; 52% female) allocated to the control group (N=230) of the NOURISH RCT. The effects of repeated exposure to new foods, maternal food preferences and child food neophobia on toddlers’ liking of vegetables, fruits and non-core foods and the proportion never tried were examined via hierarchical regression models; adjusting for key maternal (age, BMI, education) and child covariates (birth weight Z-score, gender), duration of breastfeeding and age of introduction to solids. Maternal preferences corresponded with child preferences. Food neophobia among toddlers was associated with liking fewer vegetables and fruits, and trying fewer vegetables. Number of repeated exposures to new food was not significantly associated with food liking at this age. Results highlight the need to: (i) encourage parents to offer a wide range of foods, regardless of their own food preferences, and (ii) provide parents with guidance on managing food neophobia.
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miRDeep and its varieties are widely used to quantify known and novel micro RNA (miRNA) from small RNA sequencing (RNAseq). This article describes miRDeep*, our integrated miRNA identification tool, which is modeled off miRDeep, but the precision of detecting novel miRNAs is improved by introducing new strategies to identify precursor miRNAs. miRDeep* has a user-friendly graphic interface and accepts raw data in FastQ and Sequence Alignment Map (SAM) or the binary equivalent (BAM) format. Known and novel miRNA expression levels, as measured by the number of reads, are displayed in an interface, which shows each RNAseq read relative to the pre-miRNA hairpin. The secondary pre-miRNA structure and read locations for each predicted miRNA are shown and kept in a separate figure file. Moreover, the target genes of known and novel miRNAs are predicted using the TargetScan algorithm, and the targets are ranked according to the confidence score. miRDeep* is an integrated standalone application where sequence alignment, pre-miRNA secondary structure calculation and graphical display are purely Java coded. This application tool can be executed using a normal personal computer with 1.5 GB of memory. Further, we show that miRDeep* outperformed existing miRNA prediction tools using our LNCaP and other small RNAseq datasets. miRDeep* is freely available online at http://www.australianprostatecentre.org/research/software/mirdeep-star
