Open-source workflow approaches to passive acoustic monitoring of bats

The work was funded by grants to PTM from Carlsberg Semper Ardens Research Projects and the Independent Research Fund Denmark.The affordability, storage and power capacity of compact modern recording hardware have evolved passive acoustic monitoring (PAM) of animals and soundscapes into a non-invasive, cost-effective tool for research and ecological management particularly useful for bats and toothed whales that orient and forage using ultrasonic echolocation. The use of PAM at large scales hinges on effective automated detectors and species classifiers which, combined with distance sampling approaches, have enabled species abundance estimation of toothed whales. But standardized, user-friendly and open access automated detection and classification workflows are in demand for this key conservation metric to be realized for bats. We used the PAMGuard toolbox including its new deep learning classification module to test the performance of four open-source workflows for automated analyses of acoustic datasets from bats. Each workflow used a different initial detection algorithm followed by the same deep learning classification algorithm and was evaluated against the performance of an expert manual analyst. Workflow performance depended strongly on the signal-to-noise ratio and detection algorithm used: the full deep learning workflow had the best classification accuracy (≤67%) but was computationally too slow for practical large-scale bat PAM. Workflows using PAMGuard's detection module or triggers onboard an SM4BAT or AudioMoth accurately classified up to 47%, 59% and 34%, respectively, of calls to species. Not all workflows included noise sampling critical to estimating changes in detection probability over time, a vital parameter for abundance estimation. The workflow using PAMGuard's detection module was 40 times faster than the full deep learning workflow and missed as few calls (recall for both ~0.6), thus balancing computational speed and performance. We show that complete acoustic detection and classification workflows for bat PAM data can be efficiently automated using open-source software such as PAMGuard and exemplify how detection choices, whether pre- or post-deployment, hardware or software-driven, affect the performance of deep learning classification and the downstream ecological information that can be extracted from acoustic recordings. In particular, understanding and quantifying detection/classification accuracy and the probability of detection are key to avoid introducing biases that may ultimately affect the quality of data for ecological management.Publisher PDFPeer reviewe

Implications of porpoise echolocation and dive behaviour on passive acoustic monitoring

Funding: The post-doctoral position for J.D.J.M. was funded by a FNU – Danish Natural Science Research Council grant to P.T.M. This study was also funded by the German Federal Agency for Nature Conservation via the grants “Effects of underwater noise on marine vertebrates” (Cluster 7, Z1.2-53302/2010/14) and “Under Water Noise Effects—UWE” (Project No. FKZ 3515822000). The contribution by T.A.M. was funded under the ACCURATE project (U.S. Navy Living Marine Resources Program, Contract No. N3943019C2176) and CEAUL (funded by FCT—Fundação para a Ciência e a Tecnologia, Portugal, through Project No. UIDB/00006/2020).Harbour porpoises are visually inconspicuous but highly soniferous echolocating marine predators that are regularly studied using passive acoustic monitoring (PAM). PAM can provide quality data on animal abundance, human impact, habitat use, and behaviour. The probability of detecting porpoise clicks within a given area ( P ̂ ) is a key metric when interpreting PAM data. Estimates of P ̂ can be used to determine the number of clicks per porpoise encounter that may have been missed on a PAM device, which, in turn, allows for the calculation of abundance and ideally non-biased comparison of acoustic data between habitats and time periods. However, P ̂ is influenced by several factors, including the behaviour of the vocalising animal. Here, the common implicit assumption that changes in animal behaviour have a negligible effect on P ̂ between different monitoring stations or across time is tested. Using a simulation-based approach informed by acoustic biologging data from 22 tagged harbour porpoises, it is demonstrated that porpoise behavioural states can have significant (up to 3× difference) effects on P ̂ . Consequently, the behavioural state of the animals must be considered in analysis of animal abundance to avoid substantial over- or underestimation of the true abundance, habitat use, or effects of human disturbance.Publisher PDFPeer reviewe

RIPK1 protects naive and regulatory T cells from TNFR1-induced apoptosis

The T cell population size is stringently controlled before, during, and after immune responses, as improper cell death regulation can result in autoimmunity and immunodeficiency. RIPK1 is an important regulator of peripheral T cell survival and homeostasis. However, whether different peripheral T cell subsets show a differential requirement for RIPK1 and which programmed cell death pathway they engage in vivo remains unclear. In this study, we demonstrate that conditional ablation of Ripk1 in conventional T cells (Ripk1ΔCD4) causes peripheral T cell lymphopenia, as witnessed by a profound loss of naive CD4+, naive CD8+, and FoxP3+ regulatory T cells. Interestingly, peripheral naive CD8+ T cells in Ripk1ΔCD4 mice appear to undergo a selective pressure to retain RIPK1 expression following activation. Mixed bone marrow chimeras revealed a competitive survival disadvantage for naive, effector, and memory T cells lacking RIPK1. Additionally, tamoxifen-induced deletion of RIPK1 in CD4-expressing cells in adult life confirmed the importance of RIPK1 in post-thymic survival of CD4+ T cells. Ripk1K45A mice showed no change in peripheral T cell subsets, demonstrating that the T cell lymphopenia was due to the scaffold function of RIPK1 rather than to its kinase activity. Enhanced numbers of Ripk1ΔCD4 naive T cells expressed the proliferation marker Ki-67+ despite the peripheral lymphopenia and single-cell RNA sequencing revealed T cell-specific transcriptomic alterations that were reverted by additional caspase-8 deficiency. Furthermore, Ripk1ΔCD4Casp8 ΔCD4 and Ripk1ΔCD4Tnfr1−/− double-knockout mice rescued the peripheral T cell lymphopenia, revealing that RIPK1-deficient naive CD4+ and CD8+ cells and FoxP3+ regulatory T cells specifically die from TNF- and caspase-8-mediated apoptosis in vivo. Altogether, our findings emphasize the essential role of RIPK1 as a scaffold in maintaining the peripheral T cell compartment and preventing TNFR1-induced apoptosis.</p

Recreational vessels without Automatic Identification System (AIS) dominate anthropogenic noise contributions to a shallow water soundscape

This study was funded by FNU and Semper Ardens Carlsberg Grants to P.T.M., and support from the Danish Environmental Protection Agency to J.T.Recreational boating is an increasing activity in coastal areas and its spatiotemporal overlap with key habitats of marine species pose a risk for negative noise impacts. Yet, recreational vessels are currently unaccounted for in vessel noise models using Automatic Identification System (AIS) data. Here we conduct a case study investigating noise contributions from vessels with and without AIS (non-AIS) in a shallow coastal area within the Inner Danish waters. By tracking vessels with theodolite and AIS, while recording ambient noise levels, we find that non-AIS vessels have a higher occurrence (83%) than AIS vessels, and that motorised recreational vessels can elevate third-octave band noise centred at 0.125, 2 and 16 kHz by 47–51 dB. Accordingly, these vessels dominated the soundscape in the study site due to their high numbers, high speeds and proximity to the coast. Furthermore, recreational vessels caused 49–85% of noise events potentially eliciting behavioural responses in harbour porpoises (AIS vessels caused 5–24%). We therefore conclude that AIS data would poorly predict vessel noise pollution and its impacts in this and other similar marine environments. We suggest to improve vessel noise models and impact assessments by requiring that faster and more powerful recreational vessels carry AIS-transmitters.Publisher PDFPeer reviewe

Effects of Butyrate Supplementation on Inflammation and Kidney Parameters in Type 1 Diabetes: A Randomized, Double-Blind, Placebo-Controlled Trial

Type 1 diabetes is associated with increased intestinal inflammation and decreased abundance of butyrate-producing bacteria. We investigated the effect of butyrate on inflammation, kidney parameters, HbA1c, serum metabolites and gastrointestinal symptoms in persons with type 1 diabetes, albuminuria and intestinal inflammation. We conducted a randomized placebo-controlled, double-blind, parallel clinical study involving 53 participants randomized to 3.6 g sodium butyrate daily or placebo for 12 weeks. The primary endpoint was the change in fecal calprotectin. Additional endpoints were the change in fecal short chain fatty acids, intestinal alkaline phosphatase activity and immunoglobulins, serum lipopolysaccharide, CRP, albuminuria, kidney function, HbA1c, metabolites and gastrointestinal symptoms. The mean age was 54 ± 13 years, and the median [Q1:Q3] urinary albumin excretion was 46 [14:121] mg/g. The median fecal calprotectin in the butyrate group was 48 [26:100] μg/g at baseline, and the change was −1.0 [−20:10] μg/g; the median in the placebo group was 61 [25:139] μg/g at baseline, and the change was −12 [−95:1] μg/g. The difference between the groups was not significant (p = 0.24); neither did we find an effect of butyrate compared to placebo on the other inflammatory markers, kidney parameters, HbA1c, metabolites nor gastrointestinal symptoms. Twelve weeks of butyrate supplementation did not reduce intestinal inflammation in persons with type 1 diabetes, albuminuria and intestinal inflammation

Effects of Butyrate Supplementation on Inflammation and Kidney Parameters in Type 1 Diabetes: A Randomized, Double-Blind, Placebo-Controlled Trial

Type 1 diabetes is associated with increased intestinal inflammation and decreased abundance of butyrate-producing bacteria. We investigated the effect of butyrate on inflammation, kidney parameters, HbA1c, serum metabolites and gastrointestinal symptoms in persons with type 1 diabetes, albuminuria and intestinal inflammation. We conducted a randomized placebo-controlled, double-blind, parallel clinical study involving 53 participants randomized to 3.6 g sodium butyrate daily or placebo for 12 weeks. The primary endpoint was the change in fecal calprotectin. Additional endpoints were the change in fecal short chain fatty acids, intestinal alkaline phosphatase activity and immunoglobulins, serum lipopolysaccharide, CRP, albuminuria, kidney function, HbA1c, metabolites and gastrointestinal symptoms. The mean age was 54 ± 13 years, and the median [Q1:Q3] urinary albumin excretion was 46 [14:121] mg/g. The median fecal calprotectin in the butyrate group was 48 [26:100] μg/g at baseline, and the change was −1.0 [−20:10] μg/g; the median in the placebo group was 61 [25:139] μg/g at baseline, and the change was −12 [−95:1] μg/g. The difference between the groups was not significant (p = 0.24); neither did we find an effect of butyrate compared to placebo on the other inflammatory markers, kidney parameters, HbA1c, metabolites nor gastrointestinal symptoms. Twelve weeks of butyrate supplementation did not reduce intestinal inflammation in persons with type 1 diabetes, albuminuria and intestinal inflammation

Effects of Butyrate Supplementation on Inflammation and Kidney Parameters in Type 1 Diabetes : A Randomized, Double-Blind, Placebo-Controlled Trial

Type 1 diabetes is associated with increased intestinal inflammation and decreased abundance of butyrate-producing bacteria. We investigated the effect of butyrate on inflammation, kidney parameters, HbA1c, serum metabolites and gastrointestinal symptoms in persons with type 1 diabetes, albuminuria and intestinal inflammation. We conducted a randomized placebo-controlled, double-blind, parallel clinical study involving 53 participants randomized to 3.6 g sodium butyrate daily or placebo for 12 weeks. The primary endpoint was the change in fecal calprotectin. Additional endpoints were the change in fecal short chain fatty acids, intestinal alkaline phosphatase activity and immunoglobulins, serum lipopolysaccharide, CRP, albuminuria, kidney function, HbA1c, metabolites and gastrointestinal symptoms. The mean age was 54 +/- 13 years, and the median [Q1:Q3] urinary albumin excretion was 46 [14:121] mg/g. The median fecal calprotectin in the butyrate group was 48 [26:100] mu g/g at baseline, and the change was -1.0 [-20:10] mu g/g; the median in the placebo group was 61 [25:139] mu g/g at baseline, and the change was -12 [-95:1] mu g/g. The difference between the groups was not significant (p = 0.24); neither did we find an effect of butyrate compared to placebo on the other inflammatory markers, kidney parameters, HbA1c, metabolites nor gastrointestinal symptoms. Twelve weeks of butyrate supplementation did not reduce intestinal inflammation in persons with type 1 diabetes, albuminuria and intestinal inflammation.Peer reviewe

Spatial and temporal variability of ambient underwater sound in the Baltic Sea

During last decades, anthropogenic underwater sound and its chronic impact on marine species have been recognised as an environmental protection challenge. At the same time, studies on the spatial and temporal variability of ambient sound, and how it is affected by biotic, abiotic and anthropogenic factors are lacking. This paper presents analysis of a large-scale and long-term underwater sound monitoring in the Baltic Sea. Throughout the year 2014, sound was monitored in 36 Baltic Sea locations. Selected locations covered different natural conditions and ship traffic intensities. The 63 Hz, 125 Hz and 2 kHz one-third octave band sound pressure levels were calculated and analysed. The levels varied significantly from one monitoring location to another. The annual median sound pressure level of the quietest and the loudest location differed almost 50 dB in the 63 Hz one-third octave band. Largest difference in the monthly medians was 15 dB in 63 Hz one-third octave band. The same monitoring locations annual estimated probability density functions for two yearly periods show strong similarity. The data variability grows as the averaging time period is reduced. Maritime traffic elevates the ambient sound levels in many areas of the Baltic Sea during extensive time periods