| 1. |
- Groenen, M. A., et al.
(författare)
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Analyses of pig genomes provide insight into porcine demography and evolution
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 491:7424, s. 393-398
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Tidskriftsartikel (refereegranskat)abstract
- For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
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| 2. |
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| 3. |
- Fairley, Jacqueline A., et al.
(författare)
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Wavelet analysis for detection of phasic electromyographic activity in sleep : of mother wavelet and dimensionality reduction
- 2014
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Ingår i: Computers in Biology and Medicine. - : Elsevier. - 0010-4825 .- 1879-0534. ; 48:1, s. 77-84
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Tidskriftsartikel (refereegranskat)abstract
- Phasic electromyographic (EMG) activity during sleep is characterized by brief muscle twitches (duration 100-500. ms, amplitude four times background activity). High rates of such activity may have clinical relevance. This paper presents wavelet (WT) analyses to detect phasic EMG, examining both Symlet and Daubechies approaches. Feature extraction included 1. s epoch processing with 24 WT-based features and dimensionality reduction involved comparing two techniques: principal component analysis and a feature/variable selection algorithm. Classification was conducted using a linear classifier. Valid automated detection was obtained in comparison to expert human judgment with high (>90%) classification performance for 11/12 datasets
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| 4. |
- Mesher, David, et al.
(författare)
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Population-level effects of human papillomavirus vaccination programs on infections with nonvaccine genotypes
- 2016
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Ingår i: Emerging Infectious Diseases. - : Centers for Disease Control and Prevention (CDC). - 1080-6040 .- 1080-6059. ; 22:10, s. 1732-1740
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Tidskriftsartikel (refereegranskat)abstract
- We analyzed human papillomavirus (HPV) prevalences during prevaccination and postvaccination periods to consider possible changes in nonvaccine HPV genotypes after introduction of vaccines that confer protection against 2 high-risk types, HPV16 and HPV18. Our meta-analysis included 9 studies with data for 13,886 girls and women ≤19 years of age and 23,340 women 20–24 years of age. We found evidence of cross-protection for HPV31 among the younger age group after vaccine introduction but little evidence for reductions of HPV33 and HPV45. For the group this same age group, we also found slight increases in 2 nonvaccine high-risk HPV types (HPV39 and HPV52) and in 2 possible high-risk types (HPV53 and HPV73). However, results between age groups and vaccines used were inconsistent, and the increases had possible alternative explanations; consequently, these data provided no clear evidence for type replacement. Continued monitoring of these HPV genotypes is important.
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| 5. |
- Aken, Bronwen L., et al.
(författare)
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The Ensembl gene annotation system
- 2016
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Ingår i: Database. - : Oxford University Press (OUP). - 1758-0463.
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Tidskriftsartikel (refereegranskat)abstract
- The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.
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| 6. |
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| 7. |
- Karvelis, Petros, et al.
(författare)
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Semi-automated annotation of phasic electromyographic activity
- 2014
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Konferensbidrag (refereegranskat)abstract
- Recent research on manual/visual identification of phasic muscle activity utilizing the phasic electromyographic metric (PEM) in human polysomnograms (PSGs) cites evidence that PEM is a potentially reliable quantitative metric to assist in distinguishing between neurodegenerative disorder populations and age-matched controls. However, visual scoring of PEM activity is time consuming-preventing feasible implementation within a clinical setting. Therefore, here we propose an assistive/semi-supervised software platform designed and tested to automatically identify and characterize PEM events in a clinical setting that will be extremely useful for sleep physicians and technicians. The proposed semi-automated approach consists of four levels: A) Signal Parsing, B) Calculation of quantitative features on candidate PEM events, C) Classification of PEM and non-PEM events using a linear classifier, and D) Post-processing/Expert feedback to correct/remove automated misclassifications of PEM and Non-PEM events. Performance evaluation of the designed software compared to manual labeling is provided for electromyographic (EMG) activity from the PSG of a control subject. Results indicate that the semi-automated approach provides an excellent benchmark that could be embedded into a clinical decision support system to detect PEM events that would be used in neurological disorder identification and treatment.
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| 8. |
- Kong, Fabian Y. S., et al.
(författare)
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Optimisation of treatments for oral Neisseria gonorrhoeae infection : Pharmacokinetics Study (STI-PK project) - study protocol for non-randomised clinical trial
- 2022
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Ingår i: BMJ Open. - : BMJ Publishing Group Ltd. - 2044-6055. ; 12:11
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Tidskriftsartikel (refereegranskat)abstract
- INTRODUCTION: Neisseria gonorrhoeae infections are common and incidence increasing. Oropharyngeal infections are associated with greater treatment failure compared with other sites and drive transmission to anogenital sites through saliva. Gonococcal resistance is increasing and new treatments are scarce, therefore, clinicians must optimise currently available and emerging treatments in order to have efficacious therapeutic options. This requires pharmacokinetic data from the oral cavity/oropharynx, however, availability of such information is currently limited.METHODS AND ANALYSIS: Healthy male volunteers (participants) recruited into the study will receive single doses of either ceftriaxone 1 g, cefixime 400 mg or ceftriaxone 500 mg plus 2 g azithromycin. Participants will provide samples at 6-8 time points (treatment regimen dependent) from four oral sites, two oral fluids, one anorectal swab and blood. Participants will complete online questionnaires about their medical history, sexual practices and any side effects experienced up to days 5-7. Saliva/oral mucosal pH and oral microbiome analysis will be undertaken. Bioanalysis will be conducted by liquid chromatography-mass spectrometry. Drug concentrations over time will be used to develop mathematical models for optimisation of drug dosing regimens and to estimate pharmacodynamic targets of efficacy.ETHICS AND DISSEMINATION: This study was approved by Royal Melbourne Hospital Human Research Ethics Committee (60370/MH-2021). The study results will be submitted for publication in peer-reviewed journals and reported at conferences. Summary results will be sent to participants requesting them. All data relevant to the study will be included in the article or uploaded as supplementary information.TRIAL REGISTRATION NUMBER: ACTRN12621000339853.
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