What can we learn from antique ornithology?

Ornithology has a venerable history. Worldwide, birds are both culturally important and one of the most salient reminders of the natural world, and beyond their regular appearances in folklore, literature and art they were among the first subjects of natural history from the classical world to the Renaissance. The study of birds remained a fixture of inquiry through the scientific revolution: Philosophical Transactions of the Royal Society, the oldest scientific journal still published, included ornithological method papers in its very first volume (Boyle 1666), and as scientific practice developed ornithological research kept pace. A growing interest in the diversity and systematics of birds ultimately led to the formation of dedicated ornithological societies and journals in the second half of the nineteenth century. First were the Society of German Ornithologists (Deutsche Ornithologen-Gesellschaft) in 1850 and the British Ornithologists’ Union in 1858; their respective journals ‘Journal für Ornithologie’ (now ‘Journal of Ornithology’) and ‘Ibis’ followed in 1853 and 1859. In America, the American Ornithologists’ Union was founded in 1883 with its journal ‘Auk’ beginning the same year, followed by the Wilson Ornithological Society (1886) and Cooper Ornithological Club (1893) and their journals shortly thereafter. The Royal Australasian Ornithologists’ Union (now part of BirdLife Australia) was founded in 1901, along with its journal ‘Emu’. Amazingly, all these publications are still extant, and digital versions of much of their content are now available back to their first issues. In common with other branches of science, ornithological research has exploded in recent decades, and with this plethora of new work, it is tempting to disregard the older corpus of knowledge, under the assumption that it has either been superseded or is too far removed from modern practice to be useful. However, with over 10 000 extant bird species worldwide and the avifauna of many regions still rarely studied, we would encourage the ornithological community to not overlook earlier literature. In this note, we illustrate the potential interest and value of older studies using three diverse articles published in a single journal issue 100 years ago: volume nineteen of Emu

Experimental evidence for phonemic contrasts in a nonhuman vocal system

The ability to generate new meaning by rearranging combinations of meaningless sounds is a fundamental component of language. Although animal vocalizations often comprise combinations of meaningless acoustic elements, evidence that rearranging such combinations generates functionally distinct meaning is lacking. Here, we provide evidence for this basic ability in calls of the chestnut-crowned babbler (Pomatostomus ruficeps), a highly cooperative bird of the Australian arid zone. Using acoustic analyses, natural observations, and a series of controlled playback experiments, we demonstrate that this species uses the same acoustic elements (A and B) in different arrangements (AB or BAB) to create two functionally distinct vocalizations. Specifically, the addition or omission of a contextually meaningless acoustic element at a single position generates a phoneme-like contrast that is sufficient to distinguish the meaning between the two calls. Our results indicate that the capacity to rearrange meaningless sounds in order to create new signals occurs outside of humans. We suggest that phonemic contrasts represent a rudimentary form of phoneme structure and a potential early step towards the generative phonemic system of human language

Cohort Profile: Antiretroviral Therapy Cohort Collaboration (ART-CC)

The advent of effective combination antiretroviral therapy (ART) in 1996 resulted in fewer patients experiencing clinical events, so that some prognostic analyses of individual cohort studies of human immunodeficiency virus-infected individuals had low statistical power. Because of this, the Antiretroviral Therapy Cohort Collaboration (ART-CC) of HIV cohort studies in Europe and North America was established in 2000, with the aim of studying the prognosis for clinical events in acquired immune deficiency syndrome (AIDS) and the mortality of adult patients treated for HIV-1 infection. In 2002, the ART-CC collected data on more than 12,000 patients in 13 cohorts who had begun combination ART between 1995 and 2001. Subsequent updates took place in 2004, 2006, 2008, and 2010. The ART-CC data base now includes data on more than 70 000 patients participating in 19 cohorts who began treatment before the end of 2009. Data are collected on patient demographics (e.g. sex, age, assumed transmission group, race/ethnicity, geographical origin), HIV biomarkers (e.g. CD4 cell count, plasma viral load of HIV-1), ART regimen, dates and types of AIDS events, and dates and causes of death. In recent years, additional data on co-infections such as hepatitis C; risk factors such as smoking, alcohol and drug use; non-HIV biomarkers such as haemoglobin and liver enzymes; and adherence to ART have been collected whenever available. The data remain the property of the contributing cohorts, whose representatives manage the ART-CC via the steering committee of the Collaboration. External collaboration is welcomed. Details of contacts are given on the ART-CC website (www.art-cohort-collaboration.org

Heterogeneity in outcomes of treated HIV-positive patients in Europe and North America: relation with patient and cohort characteristics

Background HIV cohort collaborations, which pool data from diverse patient cohorts, have provided key insights into outcomes of antiretroviral therapy (ART). However, the extent of, and reasons for, between-cohort heterogeneity in rates of AIDS and mortality are unclear. Methods We obtained data on adult HIV-positive patients who started ART from 1998 without a previous AIDS diagnosis from 17 cohorts in North America and Europe. Patients were followed up from 1 month to 2 years after starting ART. We examined between-cohort heterogeneity in crude and adjusted (age, sex, HIV transmission risk, year, CD4 count and HIV-1 RNA at start of ART) rates of AIDS and mortality using random-effects meta-analysis and meta-regression. Results During 61 520 person-years, 754/38 706 (1.9%) patients died and 1890 (4.9%) progressed to AIDS. Between-cohort variance in mortality rates was reduced from 0.84 to 0.24 (0.73 to 0.28 for AIDS rates) after adjustment for patient characteristics. Adjusted mortality rates were inversely associated with cohorts' estimated completeness of death ascertainment [excellent: 96-100%, good: 90-95%, average: 75-89%; mortality rate ratio 0.66 (95% confidence interval 0.46-0.94) per category]. Mortality rate ratios comparing Europe with North America were 0.42 (0.31-0.57) before and 0.47 (0.30-0.73) after adjusting for completeness of ascertainment. Conclusions Heterogeneity between settings in outcomes of HIV treatment has implications for collaborative analyses, policy and clinical care. Estimated mortality rates may require adjustment for completeness of ascertainment. Higher mortality rate in North American, compared with European, cohorts was not fully explained by completeness of ascertainment and may be because of the inclusion of more socially marginalized patients with higher mortality ris

Impact of Risk Factors for Specific Causes of Death in the First and Subsequent Years of Antiretroviral Therapy Among HIV-Infected Patients

Among HIV-infected patients who initiated antiretroviral therapy (ART), patterns of cause-specific death varied by ART duration and were strongly related to age, sex, and transmission risk group. Deaths from non-AIDS malignancies were much more frequent than those from cardiovascular diseas

Impact of risk factors for specific causes of death in the first and subsequent years of antiretroviral therapy among HIV-infected patients.

BACKGROUND: Patterns of cause-specific mortality in individuals infected with human immunodeficiency virus type 1 (HIV-1) are changing dramatically in the era of antiretroviral therapy (ART). METHODS: Sixteen cohorts from Europe and North America contributed data on adult patients followed from the start of ART. Procedures for coding causes of death were standardized. Estimated hazard ratios (HRs) were adjusted for transmission risk group, sex, age, year of ART initiation, baseline CD4 count, viral load, and AIDS status, before and after the first year of ART. RESULTS: A total of 4237 of 65 121 (6.5%) patients died (median, 4.5 years follow-up). Rates of AIDS death decreased substantially with time since starting ART, but mortality from non-AIDS malignancy increased (rate ratio, 1.04 per year; 95% confidence interval [CI], 1.0-1.1). Higher mortality in men than women during the first year of ART was mostly due to non-AIDS malignancy and liver-related deaths. Associations with age were strongest for cardiovascular disease, heart/vascular, and malignancy deaths. Patients with presumed transmission through injection drug use had higher rates of all causes of death, particularly for liver-related causes (HRs compared with men who have sex with men: 18.1 [95% CI, 6.2-52.7] during the first year of ART and 9.1 [95% CI, 5.8-14.2] thereafter). There was a persistent role of CD4 count at baseline and at 12 months in predicting AIDS, non-AIDS infection, and non-AIDS malignancy deaths. Lack of viral suppression on ART was associated with AIDS, non-AIDS infection, and other causes of death. CONCLUSIONS: Better understanding of patterns of and risk factors for cause-specific mortality in the ART era can aid in development of appropriate care for HIV-infected individuals and inform guidelines for risk factor management

Cohort profile: Antiretroviral Therapy Cohort Collaboration (ART-CC).

The advent of effective combination antiretroviral therapy (ART) in 1996 resulted in fewer patients experiencing clinical events, so that some prognostic analyses of individual cohort studies of human immunodeficiency virus-infected individuals had low statistical power. Because of this, the Antiretroviral Therapy Cohort Collaboration (ART-CC) of HIV cohort studies in Europe and North America was established in 2000, with the aim of studying the prognosis for clinical events in acquired immune deficiency syndrome (AIDS) and the mortality of adult patients treated for HIV-1 infection. In 2002, the ART-CC collected data on more than 12,000 patients in 13 cohorts who had begun combination ART between 1995 and 2001. Subsequent updates took place in 2004, 2006, 2008, and 2010. The ART-CC data base now includes data on more than 70,000 patients participating in 19 cohorts who began treatment before the end of 2009. Data are collected on patient demographics (e.g. sex, age, assumed transmission group, race/ethnicity, geographical origin), HIV biomarkers (e.g. CD4 cell count, plasma viral load of HIV-1), ART regimen, dates and types of AIDS events, and dates and causes of death. In recent years, additional data on co-infections such as hepatitis C; risk factors such as smoking, alcohol and drug use; non-HIV biomarkers such as haemoglobin and liver enzymes; and adherence to ART have been collected whenever available. The data remain the property of the contributing cohorts, whose representatives manage the ART-CC via the steering committee of the Collaboration. External collaboration is welcomed. Details of contacts are given on the ART-CC website (www.art-cohort-collaboration.org)

Engesser et al. Dryad

Files include data and values used to generate figure

Responses to calls with and without reciprocal element exchange.

<p>Behavioural responses of functional relevance remained similar between (A) natural flight calls and switched-element flight calls comprising prompt call elements (natural versus switched-element comparisons: look out: χ²₁ = 0.02, <i>p</i> = 0.9; hop/fly: χ²₁ = 0.2, <i>p</i> = 0.6; look nest: χ²₁ = 0.03, <i>p</i> = 0.9) and (B) natural prompt calls and switched-element prompt calls using the two flight call elements (natural versus switched-element comparisons: look out: χ²₁ = 0.2, <i>p</i> = 0.6; hop/fly: χ²₁ = 1.3, <i>p</i> = 0.3; look nest: χ²₁ = 0.01, <i>p</i> = 0.9). (C) Behavioural responses to switched-element flight and switched-element prompt calls differed significantly or showed a non-significant tendency to do so (switched-element flight versus switched-element prompt call comparisons: look out: χ²₁ = 5.7, <i>p</i> = 0.02; hop/fly: χ²₁ = 3.2, <i>p</i> = 0.09; look nest: χ²₁ = 10.0, <i>p</i> = 0.002). Analyses were conducted as above (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002171#pbio.1002171.g003" target="_blank">Fig 3</a>) except that in (A) and (B) (which are shown separately for clarity) stimulus type (natural versus switched-element) and its interaction with call type were added as additional fixed effects, while in (C), natural flight and prompt calls were replaced with switched-element ones. All figures show back-transformed predicted means (±SE).</p

Responses to natural playbacks.

<p>Proportion of time spent engaged in three behaviours of functional relevance differed significantly during the playbacks of the two call types (see text). Figure shows back-transformed predicted means (± standard error [SE]) generated from three Generalized Linear Mixed Models (GLMM), in which the time engaged in each of the three activities (looking out of the aviary, in movement [hopping/flying], and looking at the nest) were fitted as three independent response terms. In each case, response terms were fitted to a binomial error structure with logit link function, time spent in camera view was fitted as the binomial denominator, call type (natural flight versus natural prompt) was fitted as a two-level factor, and individual identity nested within group identity were fitted as random terms.</p