Two unit analysis of Sri Lankan pygmy blue whale song over a decade

J.L.M.O. and S.L.N. were funded by the Office of Naval Research (Award No. N000141110619). D.V.H. was funded by the Office of Naval Research (Award No. N000141612364).Sri Lankan pygmy blue whale song consists of three repeated units: (1) low frequency pulsive unit, (2) frequency modulated (FM) upsweep, and (3) long tonal downsweep. The Unit 2 FM unit has up to three visible upsweeps with energy concentrated at approximately 40, 50, and 60 Hz, while the Unit 3 (∼100 Hz) tonal downsweep is the most distinct unit lasting 20–30 s. Spectral characteristics of the Units 2 and 3 song elements, along with ocean sound levels, were analyzed in the Indian Ocean from 2002 to 2013. The peak frequency of the tonal Unit 3 calls decreased from approximately 106.5 to 100.7 Hz over a decade corresponding to a 5.4% decrease. Over the same time period, the frequency content of the Unit 2 upsweeps did not change as dramatically with only a 3.1% change. Ambient sound levels in the vocalization bands did not exhibit equivalent patterns in amplitude trends. Analysis showed no increase in the ambient sound or compensated peak amplitude levels of the tonal downsweeps, eliminating the presence of a Lombard effect. Here it is proposed that each song unit may convey different information and thus may be responding to different selective pressures.PostprintPeer reviewe

Accommodating false positives within acoustic spatial capture–recapture, with variable source levels, noisy bearings and an inhomogeneous spatial density

Funding: Tiago Marques was partly supported by CEAUL (funded by FCT - Fundação para a Ciência e a Tecnologia, Portugal, through the project UIDB/00006/2020).Passive acoustic monitoring is a promising method for surveying wildlife populations that are easier to detect acoustically than visually. When animal vocalisations can be uniquely identified on an array of sensors, the potential exists to estimate population density through acoustic spatial capture–recapture (ASCR). However, sound classification is imperfect, and in some situations, a high proportion of sounds detected on just a single sensor (‘singletons’) are not from the target species. We present a case study of bowhead whale calls (Baleana mysticetus) collected in the Beaufort Sea in 2010 containing such false positives. We propose a novel extension of ASCR that is robust to false positives by truncating singletons and conditioning on calls being detected by at least two sensors. We allow for individual-level detection heterogeneity through modelling a variable sound source level, model inhomogeneous call spatial density, and include bearings with varying measurement error. We show via simulation that the method produces near-unbiased estimates when correctly specified. Ignoring source-level variation resulted in a strong negative bias, while ignoring inhomogeneous density resulted in severe positive bias. The case study analysis indicated a band of higher call density approximately 30 km from shore; 59.8% of singletons were estimated to have been false positives.Publisher PDFPeer reviewe

Conceptualising hepatitis C stigma: A thematic synthesis of qualitative research.

BACKGROUND: Stigma is an important element in the experience of living with chronic viral hepatitis B (HBV) and C (HCV), impacting healthcare access and uptake as well as health outcomes. Conceptualisations of stigma in research are, however, often assumed and implicit. This study aimed to synthesise and critically engage with the qualitative literature to provide an overarching conceptualisation of stigma as it pertains to viral hepatitis. METHODS: We critically reviewed qualitative literature that mobilised concepts or theories of stigma in relation to viral hepatitis. We searched seven electronic databases for peer-reviewed literature from 2000 to 2019. Given a dearth of conceptual literature on HBV stigma, we conducted a thematic analysis of concepts deployed to theorise stigma in relation to HCV. RESULTS: We found 13 studies that conceptualised stigma in relation to HCV, yet none for HBV. We synthesise the analytical findings of these studies and explore how HCV is theorised in relation to four themes: 'identity', 'embodiment', 'institutionalisation', and 'structuration'. Taken together, these themes illustrate the way in which HCV stigma manifests as the confluence of normative assumptions of socially unacceptable practices relating to HCV, such as injecting drug use and sexual behaviours; attitudes towards socially excluded populations; and fears of contracting a contagious and chronic illness. As such, operating within political, social, and economic systems, HCV stigma can act to silence the needs of those with HCV through misrecognising the multifaceted identities of individuals with HCV and structural determinants of health. Stigma, which is built and perpetuated by institutional arrangements, as well as in social processes and policies, shapes deservedness to, as well as engagements with, health and social care. CONCLUSION: While commonly employed as a framing concept, much research lacks explicit theoretical or critical engagement on how stigma is conceptualised. There is a tendency for qualitative, empirical research to focus on risk factors shaping individual behaviour change, rather than on risk contexts and socio-structural change. Approaches to address stigma in relation to HCV must consider how stigma operates throughout social processes and is embedded in systems of power and normalised in institutional operating systems

Telomeric expression sites are highly conserved in trypanosoma brucei

Subtelomeric regions are often under-represented in genome sequences of eukaryotes. One of the best known examples of the use of telomere proximity for adaptive purposes are the bloodstream expression sites (BESs) of the African trypanosome Trypanosoma brucei. To enhance our understanding of BES structure and function in host adaptation and immune evasion, the BES repertoire from the Lister 427 strain of T. brucei were independently tagged and sequenced. BESs are polymorphic in size and structure but reveal a surprisingly conserved architecture in the context of extensive recombination. Very small BESs do exist and many functioning BESs do not contain the full complement of expression site associated genes (ESAGs). The consequences of duplicated or missing ESAGs, including ESAG9, a newly named ESAG12, and additional variant surface glycoprotein genes (VSGs) were evaluated by functional assays after BESs were tagged with a drug-resistance gene. Phylogenetic analysis of constituent ESAG families suggests that BESs are sequence mosaics and that extensive recombination has shaped the evolution of the BES repertoire. This work opens important perspectives in understanding the molecular mechanisms of antigenic variation, a widely used strategy for immune evasion in pathogens, and telomere biology

A review of unmanned vehicles for the detection and monitoring of marine fauna

Recent technology developments have turned present-day unmanned systems into realistic alternatives to traditional marine animal survey methods. Benefits include longer survey durations, improved mission safety, mission repeatability, and reduced operational costs. We review the present status of unmanned vehicles suitable for marine animal monitoring conducted in relation to industrial offshore activities, highlighting which systems are suitable for three main monitoring types: population, mitigation, and focal animal monitoring. We describe the technical requirements for each of these monitoring types and discuss the operational aspects. The selection of a specific sensor/platform combination depends critically on the target species and its behaviour. The technical specifications of unmanned platforms and sensors also need to be selected based on the surrounding conditions of a particular offshore project, such as the area of interest, the survey requirements and operational constraints

Comparison of estimated 20-Hz pulse fin whale source levels from the tropical Pacific and Eastern North Atlantic Oceans to other recorded populations

D.H. was funded by the Office of Naval Research (Award: N00014-16-1-2364). J.M.O. was funded under Award: N00014-16-1-2860 also from the Office of Naval Research.Passive acoustic monitoring, mitigation, animal density estimation, and comprehensive understanding of the impact of sound on marine animals all require accurate information on vocalization source level to be most effective. This study focused on examining the uncertainty related to passive sonar equation terms that ultimately contribute to the variability observed in estimated source levels of fin whale calls. Differences in hardware configuration, signal detection methods, sample size, location, and time were considered in interpreting the variability of estimated fin whale source levels. Data from Wake Island in the Pacific Ocean and off Portugal in the Atlantic Ocean provided the opportunity to generate large datasets of estimated source levels to better understand sources of uncertainty leading to the observed variability with and across years. Average seasonal source levels from the Wake Island dataset ranged from 175 to 188 dB re 1 μPa m, while the 2007–2008 seasonal average detected off Portugal was 189 dB re 1 μPa m. Owing to the large inherent variability within and across this and other studies that potentially masks true differences between populations, there is no evidence to conclude that the source level of 20-Hz fin whale calls are regionally or population specific.Publisher PDFPeer reviewe

Assessing the carcinogenic potential of low-dose exposures to chemical mixtures in the environment: the challenge ahead.

Lifestyle factors are responsible for a considerable portion of cancer incidence worldwide, but credible estimates from the World Health Organization and the International Agency for Research on Cancer (IARC) suggest that the fraction of cancers attributable to toxic environmental exposures is between 7% and 19%. To explore the hypothesis that low-dose exposures to mixtures of chemicals in the environment may be combining to contribute to environmental carcinogenesis, we reviewed 11 hallmark phenotypes of cancer, multiple priority target sites for disruption in each area and prototypical chemical disruptors for all targets, this included dose-response characterizations, evidence of low-dose effects and cross-hallmark effects for all targets and chemicals. In total, 85 examples of chemicals were reviewed for actions on key pathways/mechanisms related to carcinogenesis. Only 15% (13/85) were found to have evidence of a dose-response threshold, whereas 59% (50/85) exerted low-dose effects. No dose-response information was found for the remaining 26% (22/85). Our analysis suggests that the cumulative effects of individual (non-carcinogenic) chemicals acting on different pathways, and a variety of related systems, organs, tissues and cells could plausibly conspire to produce carcinogenic synergies. Additional basic research on carcinogenesis and research focused on low-dose effects of chemical mixtures needs to be rigorously pursued before the merits of this hypothesis can be further advanced. However, the structure of the World Health Organization International Programme on Chemical Safety 'Mode of Action' framework should be revisited as it has inherent weaknesses that are not fully aligned with our current understanding of cancer biology

Processing of spatial-frequency altered faces in schizophrenia: Effects of illness phase and duration

Low spatial frequency (SF) processing has been shown to be impaired in people with schizophrenia, but it is not clear how this varies with clinical state or illness chronicity. We compared schizophrenia patients (SCZ, n534), first episode psychosis patients (FEP, n522), and healthy controls (CON, n535) on a gender/facial discrimination task. Images were either unaltered (broadband spatial frequency, BSF), or had high or low SF information removed (LSF and HSF conditions, respectively). The task was performed at hospital admission and discharge for patients, and at corresponding time points for controls. Groups were matched on visual acuity. At admission, compared to their BSF performance, each group was significantly worse with low SF stimuli, and most impaired with high SF stimuli. The level of impairment at each SF did not depend on group. At discharge, the SCZ group performed more poorly in the LSF condition than the other groups, and showed the greatest degree of performance decline collapsed over HSF and LSF conditions, although the latter finding was not significant when controlling for visual acuity. Performance did not change significantly over time for any group. HSF processing was strongly related to visual acuity at both time points for all groups. We conclude the following: 1) SF processing abilities in schizophrenia are relatively stable across clinical state; 2) face processing abnormalities in SCZ are not secondary to problems processing specific SFs, but are due to other known difficulties constructing visual representations from degraded information; and 3) the relationship between HSF processing and visual acuity, along with known SCZ- and medication-related acuity reductions, and the elimination of a SCZ-related impairment after controlling for visual acuity in this study, all raise the possibility that some prior findings of impaired perception in SCZ may be secondary to acuity reductions

Fin whale density and distribution estimation using acoustic bearings derived from sparse arrays

D.V.H. and L.T. were funded by the Office of Naval Research (Grant Nos. N00014-14-1-0394 and N00014-16-1-2364). J.L.M.O. and J.A.V. were funded under Grant Nos. N00014-14-1-0397 and N00014-16-1-2860 also from the Office of Naval Research.Passive acoustic monitoring of marine mammals is common, and it is now possible to estimate absolute animal density from acoustic recordings. The most appropriate density estimation method depends on how much detail about animals' locations can be derived from the recordings. Here, a method for estimating cetacean density using acoustic data is presented, where only horizontal bearings to calling animals are estimable. This method also requires knowledge of call signal-to-noise ratios, as well as auxiliary information about call source levels, sound propagation, and call production rates. Results are presented from simulations, and from a pilot study using recordings of fin whale (Balaenoptera physalus) calls from Comprehensive Nuclear-Test-Ban Treaty Organization (CTBTO) hydrophones at Wake Island in the Pacific Ocean. Simulations replicating different animal distributions showed median biases in estimated call density of less than 2%. The estimated average call density during the pilot study period (December 2007-February 2008) was 0.02 calls hr-1 km2 (coefficient of variation, CV: 15%). Using a tentative call production rate, estimated average animal density was 0.54 animals/1000 km2 (CV: 52%). Calling animals showed a varied spatial distribution around the northern hydrophone array, with most detections occurring at bearings between 90 and 180 degrees.PostprintPeer reviewe