The calculation of acoustic indices to characterise acoustic recordings of the environment

This technical report describes the methods used to obtain a list of acoustic indices that are used to characterise the structure and distribution of acoustic energy in recordings of the natural environment. In particular it describes methods for noise reduction from recordings of the environment and a fast clustering algorithm used to estimate the spectral richness of long recordings.

Pedigree-free animal models : the relatedness matrix reloaded

Animal models typically require a known genetic pedigree to estimate quantitative genetic parameters. Here we test whether animal models can alternatively be based on estimates of relatedness derived entirely from molecular marker data. Our case study is the morphology of a wild bird population, for which we report estimates of the genetic variance-covariance matrices (G) of six morphological traits using three methods: the traditional animal model; a molecular marker-based approach to estimate heritability based on Ritland's pairwise regression method; and a new approach using a molecular genealogy arranged in a relatedness matrix (R) to replace the pedigree in an animal model. Using the traditional animal model, we found significant genetic variance for all six traits and positive genetic covariance among traits. The pairwise regression method did not return reliable estimates of quantitative genetic parameters in this population, with estimates of genetic variance and covariance typically being very small or negative. In contrast, we found mixed evidence for the use of the pedigree-free animal model. Similar to the pairwise regression method, the pedigree-free approach performed poorly when the full-rank R matrix based on the molecular genealogy was employed. However, performance improved substantially when we reduced the dimensionality of the R matrix in order to maximize the signal to noise ratio. Using reduced-rank R matrices generated estimates of genetic variance that were much closer to those from the traditional model. Nevertheless, this method was less reliable at estimating covariances, which were often estimated to be negative. Taken together, these results suggest that pedigree-free animal models can recover quantitative genetic information, although the signal remains relatively weak. It remains to be determined whether this problem can be overcome by the use of a more powerful battery of molecular markers and improved methods for reconstructing genealogies.

Reputation modelling in citizen science for environmental acoustic data analysis

Citizen Science projects are initiatives in which members of the general public participate in scientific research projects and perform or manage research-related tasks such as data collection and/or data annotation. Citizen Science is technologically possible and scientifically significant. However, as the gathered information is from the crowd, the data quality is always hard to manage. There are many ways to manage data quality, and reputation management is one of the common approaches. In recent year, many research teams have deployed many audio or image sensors in natural environment in order to monitor the status of animals or plants. The collected data will be analysed by ecologists. However, as the amount of collected data is exceedingly huge and the number of ecologists is very limited, it is impossible for scientists to manually analyse all these data. The functions of existing automated tools to process the data are still very limited and the results are still not very accurate. Therefore, researchers have turned to recruiting general citizens who are interested in helping scientific research to do the pre-processing tasks such as species tagging. Although research teams can save time and money by recruiting general citizens to volunteer their time and skills to help data analysis, the reliability of contributed data varies a lot. Therefore, this research aims to investigate techniques to enhance the reliability of data contributed by general citizens in scientific research projects especially for acoustic sensing projects. In particular, we aim to investigate how to use reputation management to enhance data reliability. Reputation systems have been used to solve the uncertainty and improve data quality in many marketing and E-Commerce domains. The commercial organizations which have chosen to embrace the reputation management and implement the technology have gained many benefits. Data quality issues are significant to the domain of Citizen Science due to the quantity and diversity of people and devices involved. However, research on reputation management in this area is relatively new. We therefore start our investigation by examining existing reputation systems in different domains. Then we design novel reputation management approaches for Citizen Science projects to categorise participants and data. We have investigated some critical elements which may influence data reliability in Citizen Science projects. These elements include personal information such as location and education and performance information such as the ability to recognise certain bird calls. The designed reputation framework is evaluated by a series of experiments involving many participants for collecting and interpreting data, in particular, environmental acoustic data. Our research in exploring the advantages of reputation management in Citizen Science (or crowdsourcing in general) will help increase awareness among organizations that are unacquainted with its potential benefits.

Randomised controlled trial of an automated, interactive telephone intervention (TLC Diabetes) to improve type 2 diabetes management : Baseline findings and six-month outcomes

Background: Effective self-management of diabetes is essential for the reduction of diabetes-related complications, as global rates of diabetes escalate. Methods: Randomised controlled trial. Adults with type 2 diabetes (n = 120), with HbA1c greater than or equal to 7.5 %, were randomly allocated (4 × 4 block randomised block design) to receive an automated, interactive telephone-delivered management intervention or usual routine care. Baseline sociodemographic, behavioural and medical history data were collected by self-administered questionnaires and biological data were obtained during hospital appointments. Health-related quality of life (HRQL) was measured using the SF-36. Results: The mean age of participants was 57.4 (SD 8.3), 63 % of whom were male. There were no differences in demographic, socioeconomic and behavioural variables between the study arms at baseline. Over the six-month period from baseline, participants receiving the Australian TLC (Telephone-Linked Care) Diabetes program showed a 0.8 % decrease in geometric mean HbA1c from 8.7 % to 7.9 %, compared with a 0.2 % HbA1c reduction (8.9 % to 8.7 %) in the usual care arm (p = 0.002). There was also a significant improvement in mental HRQL, with a mean increase of 1.9 in the intervention arm, while the usual care arm decreased by 0.8 (p = 0.007). No significant improvements in physical HRQL were observed. Conclusions: These analyses indicate the efficacy of the Australian TLC Diabetes program with clinically significant post-intervention improvements in both glycaemic control and mental HRQL. These observed improvements, if supported and maintained by an ongoing program such as this, could significantly reduce diabetes-related complications in the longer term. Given the accessibility and feasibility of this kind of program, it has strong potential for providing effective, ongoing support to many individuals with diabetes in the future.

Effects of acute multinutrient supplementation on rugby union game performance and recovery

Purpose: To investigate the effects of an acute multinutrient supplement on game-based running performance, peak power output, anaerobic by-products, hormonal profiles, markers of muscle damage, and perceived muscular soreness before, immediately after, and 24 h following competitive rugby union games. Methods: Twelve male rugby union players ingested either a comprehensive multinutrient supplement (SUPP), [RE-ACTIVATE:01], or a placebo (PL) for 5 d. Participants then performed a competitive rugby union game (with global positioning system tracking), with associated blood draws and vertical jump assessments pre, immediately post and 24 h following competition. Results: SUPP ingestion resulted in moderate to large effects for augmented 1st half very high intensity running (VHIR) mean speed (5.9 ± 0.4 vs 4.8 ± 2.3 m·min–1; d= 0.93). Further, moderate increases in 2nd half VHIR distance (137 ± 119 vs 83 ± 89 m; d= 0.73) and VHIR mean speed (5.9 ± 0.6 v 5.3 ± 1.7 m·min–1; d= 0.56) in SUPP condition were also apparent. Postgame aspartate aminotransferase (AST; 44.1 ± 11.8 vs 37.0 ± 3.2 UL; d= 1.16) and creatine kinase (CK; 882 ± 472 vs. 645 ± 123 UL; d= 0.97) measures demonstrated increased values in the SUPP condition, while AST and CK values correlated with 2nd half VHIR distance (r= –0.71 and r= –0.76 respectively). Elevated C-reactive protein (CRP) was observed postgame in both conditions; however, it was significantly blunted with SUPP (P= .05). Conclusions: These findings suggest SUPP may assist in the maintenance of VHIR during rugby union games, possibly via the buffering qualities of SUPP ingredients. However, correlations between increased work completed at very high intensities and muscular degradation in SUPP conditions, may mask any anticatabolic properties of the supplement.

Effects of acute multi-nutrient supplementation on rugby union match performance and recovery

Aim: To determine the effects of an acute multi-nutrient supplement on physiological, performance and recovery responses to intermittent-sprint running and muscular damage during rugby union matches. Methods: Using a randomised, double-blind, cross-over design, twelve male rugby union players ingested either 75 g of a comprehensive multi-nutrient supplement (SUPP), [Musashi] or 1 g of a taste and carbohydrate matched placebo (PL) for 5 days pre-competition. Competitive rugby union game running performance was then measured using 1 Hz GPS data (SPI10, SPI elite, GPSports), in addition to associated blood draws, vertical jump assessments and ratings of perceived muscular soreness (MS) pre, immediately post and 24 h post-competition. Baseline (BL) GPS data was collected during six competition rounds preceding data collection. Results: No significant differences were observed between supplement conditions for all game running, vertical jump, and ratings of perceived muscular soreness. However, effect size analysis indicated SUPP ingestion increased 1st half very high intensity running (VHIR) mean speed (d = 0.93) and 2nd half relative distance (m/min) (d = 0.97). Further, moderate increases in 2nd half VHIR distance (d = 0.73), VHIR m/min (d = 0.70) and VHIR mean speed (d = 0.56) in SUPP condition were also apparent. Moreover, SUPP demonstrated significant increases in 2nd half dist m/min, total game dist m/min and total game HIR m/min compared with BL data (P < 0.05). Further, large ES increases in VHIR time (d = 0.88) and moderate increases in 2nd half HIR m/min (d = 0.65) and 2nd half VHIR m/min (d = 0.74) were observed between SUPP and BL. Post-game aspartate aminotransferase (AST) (d = 1.16) and creatine kinase (CK) (d = 0.97) measures demonstrated increased ES values with SUPP, while AST and CK values correlated with 2nd half VHIR distance (r = −0.71 and r = −0.76 respectively). Elevated c-reactive protein (CRP) was observed post-game in both conditions, however was significantly blunted with SUPP (P = 0.05). Additionally, pre-game (d = 0.98) and post-game (d = 0.96) increases in cortisol (CORT) were apparent with SUPP. No differences were apparent between conditions for pH, lactate, glucose, HCO3, vertical jump assessments and MS (P > 0.05). Conclusion: These findings suggest SUPP may assist in the maintenance of VHIR speeds and distances covered during rugby union games, possibly via the buffering qualities of SUPP ingredients (i.e. caffeine, creatine, bicarbonate). While the mechanisms for these findings are unclear, the similar pH between conditions despite additional VHIR during SUPP may support this conclusion. Finally, correlations between increased work completed at very high intensities and muscular degradation in SUPP conditions, may mask any anti-catabolic properties of supplementation.

Referral patterns and proximity to palliative care inpatient services by level of socio-economic disadvantage : a national study using spatial analysis

Background: A range of health outcomes at a population level are related to differences in levels of social disadvantage. Understanding the impact of any such differences in palliative care is important. The aim of this study was to assess, by level of socio-economic disadvantage, referral patterns to specialist palliative care and proximity to inpatient services. Methods: All inpatient and community palliative care services nationally were geocoded (using postcode) to one nationally standardised measure of socio-economic deprivation – Socio-Economic Index for Areas (SEIFA; 2006 census data). Referral to palliative care services and characteristics of referrals were described through data collected routinely at clinical encounters. Inpatient location was measured from each person’s home postcode, and stratified by socio-economic disadvantage. Results: This study covered July – December 2009 with data from 10,064 patients. People from the highest SEIFA group (least disadvantaged) were significantly less likely to be referred to a specialist palliative care service, likely to be referred closer to death and to have more episodes of inpatient care for longer time. Physical proximity of a person’s home to inpatient care showed a gradient with increasing distance by decreasing levels of socio-economic advantage. Conclusion: These data suggest that a simple relationship of low socioeconomic status and poor access to a referral-based specialty such as palliative care does not exist. Different patterns of referral and hence different patterns of care emerge.

A strong quantitative trait locus for wing length on chromosome 2 in a wild population of great reed warblers

Wing length is a key character for essential behaviours related to bird flight such as migration and foraging. In the present study, we initiate the search for the genes underlying wing length in birds by studying a long-distance migrant, the great reed warbler (Acrocephalus arundinaceus). In this species wing length is an evolutionary interesting trait with pronounced latitudinal gradient and sex-specific selection regimes in local populations. We performed a quantitative trait locus (QTL) scan for wing length in great reed warblers using phenotypic, genotypic, pedigree and linkage map data from our long-term study population in Sweden. We applied the linkage analysis mapping method implemented in GRIDQTL (a new web-based software) and detected a genome-wide significant QTL for wing length on chromosome 2, to our knowledge, the first detected QTL in wild birds. The QTL extended over 25 cM and accounted for a substantial part (37%) of the phenotypic variance of the trait. A genome scan for tarsus length (a bodysize-related trait) did not show any signal, implying that the wing-length QTL on chromosome 2 was not associated with body size. Our results provide a first important step into understanding the genetic architecture of avian wing length, and give opportunities to study the evolutionary dynamics of wing length at the locus level. This journal is© 2010 The Royal Society.

Evaluation of plastic deformation ability of Cu/Ni/W metallic multilayers

Plastic deformation behavior of Cu/Ni/Wmetallicmultilayers with individual layer thickness ranging from 5 nm to 300 nm is investigated by nanoindentation testing. The experimental results reveal that the composite still exhibits indentation-induced plastic deformation instability and the loss of strain hardening ability at the nanometer scale even if the composite contains two kinds of layer interfaces (face centered cubic(FCC)/FCC and FCC/ body centered cubic) simultaneously. Plastic deformation behavior of the nanolayered material was evaluated and analyzed.

The birds of the Bush Heritage, Cravens Peak Reserve

Bird communities were studied in two subregional areas of Cravens Peak, the Toko Plains and the Simpson-Strzelecki Dunefields, using the point counts method. A total of 42 2ha 20 minute surveys, 46 five-hundred metre radius area surveys and 170 5km drive through area surveys were conducted and observations made. Bird species were identified, counted and recorded. The data were compared in the two subregions and, as a whole, considering species groups according to land system on which the ecosystem occurs, the specific ecosystem and according to their general feeding habits (insectivore, omnivore, frugivore, granivore, nectarivore and carnivore). Species richness and species relative abundance were compared using Simpson’s Diversity Index and the data revealed that species are distributed largely on the basis of habitat. In general, areas with a greater number of vegetation strata recorded greater species diversity. Overall, the Tall Open Acacia georginae Shrubland on alluvial floodplains has a greater diversity of birds in a 2ha area (0.87, Simpson’s Index of Diversity 1-D) compared to the other survey sites.

Birds : indicators of environmental repair in oil affected coastlines

Bird coastal communities were studied along Bribie Island and Moreton Island, two islands within Moreton Bay, Brisbane, Queensland, Australia, using the point counts method. A total of 128 five-hundred metre radius area surveys and 81 beach drive surveys were conducted and observations made over four seasons. Bird species were identified, counted and recorded. The data was compared between the two islands and, between sites on each island as oil-spill affected sites to non-oil spill affected sites. Species such as waders, shorebirds, terns/gulls and raptors were identified as species at most risk from an oil spill and the data was selected to look mainly at these species. The data indicated that sites affected by the oil spill contained 50% less oil-affected species than sites not affected by the oil spill. Bribie Island held on average 5 species per site in the oil affected sites compared to 12 species in non-oil affected sites. This same trend was observed on Moreton Island which held 6 species compared to 14 species. Bird data will continue to be counted over several years to determine whether the observed data is a true reflection of the affects of an oil spill on the habitat of shorebirds.

A practical comparison of manual and autonomous methods for acoustic monitoring

1. Autonomous acoustic recorders are widely available and can provide a highly efficient method of species monitoring, especially when coupled with software to automate data processing. However, the adoption of these techniques is restricted by a lack of direct comparisons with existing manual field surveys. 2. We assessed the performance of autonomous methods by comparing manual and automated examination of acoustic recordings with a field-listening survey, using commercially available autonomous recorders and custom call detection and classification software. We compared the detection capability, time requirements, areal coverage and weather condition bias of these three methods using an established call monitoring programme for a nocturnal bird, the little spotted kiwi(Apteryx owenii). 3. The autonomous recorder methods had very high precision (>98%) and required <3% of the time needed for the field survey. They were less sensitive, with visual spectrogram inspection recovering 80% of the total calls detected and automated call detection 40%, although this recall increased with signal strength. The areal coverage of the spectrogram inspection and automatic detection methods were 85% and 42% of the field survey. The methods using autonomous recorders were more adversely affected by wind and did not show a positive association between ground moisture and call rates that was apparent from the field counts. However, all methods produced the same results for the most important conservation information from the survey: the annual change in calling activity. 4. Autonomous monitoring techniques incur different biases to manual surveys and so can yield different ecological conclusions if sampling is not adjusted accordingly. Nevertheless, the sensitivity, robustness and high accuracy of automated acoustic methods demonstrate that they offer a suitable and extremely efficient alternative to field observer point counts for species monitoring.

Virtual birding : extending an environmental pastime into the virtual world for citizen science

This paper investigates engaging experienced birders, as volunteer citizen scientists, to analyze large recorded audio datasets gathered through environmental acoustic monitoring. Although audio data is straightforward to gather, automated analysis remains a challenging task; the existing expertise, local knowledge and motivation of the birder community can complement computational approaches and provide distinct benefits. We explored both the culture and practice of birders, and paradigms for interacting with recorded audio data. A variety of candidate design elements were tested with birders. This study contributes an understanding of how virtual interactions and practices can be developed to complement existing practices of experienced birders in the physical world. In so doing this study contributes a new approach to engagement in e-science. Whereas most citizen science projects task lay participants with discrete real world or artificial activities, sometimes using extrinsic motivators, this approach builds on existing intrinsically satisfying practices.

Community response to disasters in Indonesia : Gotong Royong; a double edged-sword

Indonesia is a country spread across wide-ranging archipelago, located in South East Asia between two oceans, the Indian and the Pacific. Indonesia is well known as an active tectonic region because it lies on top of three major active tectonic plates: the Eurasian in the North, the Indian Ocean-Australian in the South, and the Pacific plate in the East. The southern and eastern part of the country features a range of volcanic arcs, volcanic mountains, and lowlands with 500 young volcanoes, of which 128 are active and thus representing 15% of the world’s active volcanoes. In the period 2002-2007, approximately 1782 disasters occurred, with hundreds of thousands of lives lost and billions of rupiah in losses incurred: (Floods - 1183 instances, cyclones - 272 instances, and landslides - 252 instances). Of these, the 2004 Aceh tsunami and the 2006 central Java earthquake (impacting predominantly city and suburbs of Yogyakarta) were the most significant. Even so, disaster management experts believe lessons learnt from the two major natural disasters needs to be formalised into laws and institutions before another disaster occurs, regardless of the type of natural disaster – i.e. Volcano eruption or landslide; as opposed to tsunami or earthquake. Following in the wake of disasters occurring in Yogyakarta, many of its community members responded by banding together as one, with the determination of rebuilding its villages and cities through the spirit of ‘gotong royong’. The idea of social interaction; in particular as a collective, consensual, and cooperative nation; has predominantly formed the ideological basis of Indonesia’s societal nature. Many Indonesian terms cohere to this ideology, such as: ‘koperasi” (cooperatives as the basis of economic interactions), ‘musyawarah’ (consensual nature in decision making), and ‘gotong royong’ (mutual assistance). ‘Gotong royong’ has become a key cultural operator in Indonesia, in particular In Jogjakarta. Appropriately so as ‘gotong royong’ is depicted from the traditional Javanese village, where labour is accomplished through reciprocal exchange and the villagers are motivated by a general ethos of selfishness and concern for the common good. The culture of ‘gotong royong’ promotes positive values such as social harmony and mutual reciprocation in disaster-affected areas provides the necessary spirit needed to endure the hardships and for all involved. While gotong royong emphasises the positive notions of mutual family support and deep community level activity there is a potential for contrast against government lead disaster response and recovery management activities especially in settings where sporadic governance mechanisms exist and transparency and accountability in the recovery process of public infrastructure assets have been questioned. This paper thus questions whether Gotong Royong is a double-edged sword, and explores the potential marriage of community values and governance mechanisms for future disaster management planning and practice.

Single-nucleotide polymorphism alleles in the insulin receptor gene are associated with typical migraine

We have identified a migraine locus on chromosome 19p13.3/2 using linkage and association analysis. We isolated 48 single-nucleotide polymorphisms within the locus, of which we genotyped 24 in a Caucasian population comprising 827 unrelated cases and 765 controls. Five single-nucleotide polymorphisms within the insulin receptor gene showed significant association with migraine. This association was independently replicated in a case-control population collected separately. We used experiments with insulin receptor RNA and protein to investigate functionality for the migraine-associated single-nucleotide polymorphisms. We suggest possible functions for the insulin receptor in migraine pathogenesis.