Biology subjects

Bick, A.

Publications and source records attributed to Bick, A..

9 recordsLinked to original sources

bioRxiv2024

National-scale acoustic monitoring of avian biodiversity and phenology

Billions of birds migrate annually, triggered by endogenous behaviors but also by ecoclimatic drivers which are shifting with climate change. These dynamics play out over huge spatiotemporal scales, making monitoring of phenology challenging with traditional biodiversity survey approaches. In this study, over a complete spring migration season (April through June), we collected 37,429 hours of audio from 28 networked sensors in forests across Norway using a nationwide passive acoustic monitoring (PAM) system. We applied an open-source detection algorithm to automatically classify bird vocalizations; through expert validation we found the algorithm classified 57 species (14 full migrants) with at least 80% precision. Using these automated detections, we developed regional arrival curves for three common migratory passerines: Willow Warbler, Common Chiffchaff, and Spotted Flycatcher. We then demonstrate that PAM detections can be used to train audio species distribution models that map how species vocalization probability changes across Norway during spring migration. Lastly, we discuss how PAM can complement existing manual surveys to support the design and implementation of effective policy and conservation measures.

ecology↗

bioRxiv2023

Automatic vocalisation detection delivers reliable, multi-faceted, and global avian biodiversity monitoring

Tracking biodiversity and its dynamics at scale is essential if we are to solve global environmental challenges. Detecting animal vocalisations in passively recorded audio data offers a highly automatable, inexpensive, and taxonomically broad way to monitor biodiversity. However, uptake is slow due to the expertise and labour required to label new data and fine-tune algorithms for each deployment. In this study, we applied an off-the-shelf bird vocalisation detection model, BirdNET, to 152,376 hours of audio comprising of datasets from Norway, Taiwan, Costa Rica, and Brazil. We manually listened to a subset of detections for each species in each dataset and found precisions of over 80% for 89 of the 139 species (100% for 57 species). Whilst some species were reliably detected across multiple datasets, the performance of others was dataset specific. By filtering out unreliable detections, we could extract species and community level insight on diel (Brazil) and seasonal (Taiwan) temporal scales, as well as landscape (Costa Rica) and national (Norway) spatial scales. Our findings demonstrate that, with a relatively fast validation step, a single vocalisation detection model can deliver multi-faceted community and species level insight across highly diverse datasets; unlocking the scale at which acoustic monitoring can deliver immediate applied impact.

ecology↗

bioRxiv2022

Is there an accurate and generalisable way to use soundscapes to monitor biodiversity?

Acoustic monitoring has the potential to deliver biodiversity insight on vast scales. Whilst autonomous recording networks are being deployed across the world, existing analytical techniques struggle with generalisability. This limits the insight that can be derived from audio recordings in regions without ground-truth calibration data. By calculating 128 learned features and 60 soundscape indices of audio recorded during 8,023 avifaunal point counts from diverse ecosystems, we investigated the generalisability of soundscape approaches to biodiversity monitoring. Within each dataset, we found univariate correlations between several acoustic features and avian species richness, but features behaved unpredictably across datasets. Training a machine learning model on compound indices, we could predict species richness within datasets. However, models were uninformative when applied to datasets not used for training. We found that changes in soundscape features were correlated with changes in avian communities across all datasets. However, there were cases where avian communities changed without an associated shift in soundscapes. Our results suggest that there are no common hallmarks of biodiverse soundscapes across ecosystems. Therefore, soundscape monitoring should only be used when high quality ground-truth data exists for the region of interest, and in conjunction with more targeted and accurate in-person ecological surveys. By better understanding how to use interpret data reliably, we hope to unlock the scale at which acoustic monitoring can be used to deliver true impact for land managers and scientists monitoring biodiversity around the world. SummaryWhilst eco-acoustic monitoring has the potential to deliver biodiversity insight on vast scales, existing analytical approaches behave unpredictably across studies. We collated 8,023 audio recordings with paired manual avifaunal point counts to investigate whether soundscapes could be used to monitor biodiversity across diverse ecosystems. We found that neither univariate indices nor machine learning models were predictive of species richness across datasets, but soundscape change was consistently indicative of community change. Our findings indicate that there are no common features of biodiverse soundscapes, and that soundscape monitoring should be used cautiously and in conjunction with more reliable in-person ecological surveys.

ecology↗

bioRxiv2022

Mosaic chromosomal alterations in blood across ancestries via whole-genome sequencing

Mosaic mutations in blood are common with increasing age and are prognostic markers for cancer, cardiovascular dysfunction and other diseases. This group of acquired mutations include megabase-scale mosaic chromosomal alterations (mCAs). These large mutations have mainly been surveyed using SNP array data from individuals of European (EA) or Japanese genetic ancestry. To gain a better understanding of mCA rates and associated risk factors in genetically diverse populations, we surveyed whole genome sequencing data from 67,390 individuals, including 20,132 individuals of African ancestry (AA), and 7,608 of Hispanic ancestry (HA) with deep (30X) whole genome sequencing data from the NHLBI Trans Omics for Precision Medicine (TOPMed) program. We adapted an existing mCA calling algorithm for application to WGS data, and observed higher sensitivity with WGS data, compared with array-based data, in uncovering mCAs at low mutant cell fractions. As in previous reports, we observed a strong association with age and a non-uniform distribution of mCAs across the genome. The presence of autosomal (but not chromosome X) mCAs was associated with an increased risk of both lymphoid and myeloid malignancies. After adjusting for age, we found that individuals of European ancestry have the highest rates of autosomal mCAs, mirroring the higher rate of leukemia in this group. Our analysis also uncovered higher rates of chromosome X mCAs in AA and HA compared to EA, again after adjusting for age. Germline variants in ATM and MPL showed strong associations with mCAs in cis, including ancestry specific variants. And rare variant gene-burden analysis confirmed the association of putatively protein altering variants in ATM and MPL with mCAs in cis. Individual rare variants in DCPS, ADM17, PPP1R16B, and TET2 were all associated with autosomal mCAs and rare variants in OR4C16 were associated with chromosome X mCAs in females. There was significant enrichment of co-occurrence of CHIP mutations and mCAs both altering cancer associated genes TET2, DNMT3A, JAK2, CUX1, and TP53. Overall, our study demonstrates that rates of mCAs differ across populations and that rare inherited germline variants are strongly associated with mCAs across genetically diverse populations. These results strongly motivate further studies of mCAs in under-represented populations to better understand the causes and consequences of this class of somatic variation.

genomics↗

bioRxiv2022

Development and Validation of the Vanderbilt PRS-KS, an Instrument to Quantify Polygenic Risk Score Knowledge

PurposeAs polygenic risk scores (PRS) enter clinical practice, healthcare providers and the publics comprehension of PRS results are of great importance, yet poorly understood. We present the Vanderbilt Polygenic Risk Scores Knowledge Score (Vanderbilt PRS-KS), a tool to quantify PRS knowledge. MethodsThe Vanderbilt PRS-KS was developed by a team of genetic counselors and physicians to cover key conceptual facts pertaining to PRSs. We recruited (n=500) individuals with demographics representative of a U.S. sample and graduate-level healthcare students (n=74) at a large academic medical center to participate in this validation study. We evaluated the Vanderbilt PRS-KSs psychometric properties using confirmatory factor analysis (CFA) and item response theory (IRT). ResultsThe 7-item Vanderbilt PRS-KS correlated to a single latent construct on CFA ({Lambda}=0.31-0.61). The scale showed promising reliability (Cronbachs =0.66) with IRT summed scores of [≥]2 to [≤]5, demonstrating reliability > 0.70. The Vanderbilt PRS-KS significantly correlated with genetic knowledge and applied PRS knowledge (r=0.55, r=0.29), and graduate-level healthcare students had significantly higher scores compared to the representative sample (p<0.01). ConclusionsThe Vanderbilt PRS-KS is a rigorously validated measure to quantify PRS knowledge.

genetics↗

bioRxiv2021

Autoantibodies against Progranulin and IL-1 receptor antagonist in critically ill COVID-19

STRUCTURED ABSTRACTHyperinflammation is frequently observed in patients with severe COVID-19. Inadequate and defective IFN type I responses against SARS-CoV-2, associated with autoantibodies in a proportion of patients, lead to severe courses of disease. In addition, hyperactive responses of the humoral immune system have been described. In the current study we investigated a possible role of neutralizing autoantibodies against antiinflammatory mediators. Plasma from adult patients with severe and critical COVID-19 was screened by ELISA for antibodies against PGRN, IL-1-Ra, IL-10, IL-18BP, IL-22BP, IL-36-Ra, CD40, IFN-2, IFN-{gamma}, IFN-{omega} and serpinB1. Autoantibodies were characterized and the antigens were analyzed for immunogenic alterations. In a discovery cohort with severe to critical COVID-19 high titers of PGRN-autoantibodies were detected in 11 of 30 (36.7%), and of IL-1-Ra-autoantibodies in 14 of 30 (46.7%) patients. In a validation cohort of 64 patients with critical COVID-19 high-titer PGRN-Abs were detected in 25 (39%) and IL-1-Ra-Abs in 32 of 64 patients (50%). PGRN-Abs and IL-1-Ra-Abs belonged to IgM and several IgG subclasses. In separate cohorts with non-critical COVID-19, PGRN-Abs and IL-1-Ra-Abs were detected in low frequency (i.e. in < 5% of patients) and at low titers. Neither PGRN-nor IL-1-Ra-Abs were found in 40 healthy controls vaccinated against SARS-CoV-2 or 188 unvaccinated healthy controls. PGRN-Abs were not cross-reactive against SARS-CoV-2 structural proteins nor against IL-1-Ra. Plasma levels of both free PGRN and free IL-1-Ra were significantly decreased in autoantibody-positive patients compared to Ab-negative and non-COVID-19 controls. In vitro PGRN-Abs from patients functionally reduced PGRN-dependent inhibition of TNF- signaling, and IL-1-Ra-Abs from patients reduced IL-1-Ra- or anakinra-dependent inhibition of IL-1{beta} signaling. The pSer81 hyperphosphorylated PGRN isoform was exclusively detected in patients with high-titer PGRN-Abs; likewise, a hyperphosphorylated IL-1-Ra isoform was only found in patients with high-titer IL-1-Ra-Abs. Thr111 was identified as the hyperphophorylated amino acid of IL-1-Ra. In longitudinally collected samples hyperphosphorylated isoforms of both PGRN and IL-1-Ra emerged transiently, and preceded the appearance of autoantibodies. In hospitalized patients, the presence of IL-1-Ra-Abs or IL-1-Ra-Abs in combination with PGRN-Abs was associated with a higher morbidity and mortality. To conclude, neutralizing autoantibodies to IL-1-Ra and PGRN occur in a significant portion of patients with critical COVID-19, with a concomitant decrease in circulating free PGRN and IL-1-Ra, indicative of a misdirected, proinflammatory autoimmune response. The break of self-tolerance is likely caused by atypical hyperphosphorylated isoforms of both antigens, whose appearances precede autoantibody induction. Our data suggest that these immunogenic secondary modifications are induced by the SARS-CoV-2-infection itself or the inflammatory environment evoked by the infection and predispose for a critical course of COVID-19.

immunology↗

bioRxiv2020

Analysis of cardiac magnetic resonance imaging traits in 29,000 individuals reveals shared genetic basis with dilated cardiomyopathy

Dilated cardiomyopathy (DCM) is an important cause of heart failure and the leading indication for heart transplantation. Many rare genetic variants have been associated with DCM, but common variant studies of the disease have yielded few associated loci. As structural changes in the heart are a defining feature of DCM, we conducted a genome-wide association study (GWAS) of cardiac magnetic resonance imaging (MRI)-derived left ventricular measurements in 29,041 UK Biobank participants. 26 novel loci were associated with cardiac structure and function. These loci were found near 17 genes previously shown to cause Mendelian cardiomyopathies. A polygenic score of left ventricular end systolic volume was associated with incident DCM in previously disease-free individuals (hazard ratio = 1.54 per one standard deviation increase in the polygenic score, P = 2.1x10-16). Even among carriers of truncating mutations in TTN, the polygenic score influenced the size and function of the heart. These results further implicate common genetic polymorphisms in DCM pathogenesis.

genomics↗

bioRxiv2019

A missense variant in Mitochondrial Amidoxime Reducing Component 1 gene and protection against liver disease

Analyzing 5770 all-cause cirrhosis cases and 572,850 controls from seven cohorts, we identify a missense variant in the Mitochondrial Amidoxime Reducing Component 1 gene (MARC1 p.A165T) that associates with protection from all-cause cirrhosis (OR 0.88, p=2.1*10-8). This same variant also associates with lower levels of hepatic fat on computed tomographic imaging and lower odds of physician-diagnosed fatty liver as well as lower blood levels of alanine transaminase (-0.012 SD, 1.4*10-8), alkaline phosphatase (-0.019 SD, 6.6*10-9), total cholesterol (-0.037 SD, p=1*10-18) and LDL cholesterol (-0.035 SD, p=7.3*10-16). Carriers of rare protein-truncating variants in MARC1 had lower liver enzyme levels, cholesterol levels, and reduced odds of liver disease (OR 0.19, p= 0.04) suggesting that deficiency of the MARC1 enzyme protects against cirrhosis.

genomics↗

bioRxiv2018

Human Subthalamic Nucleus Selectively Decreases its Response to the Go-Signal in a Motor Inhibition Context

To better understand the mechanism of movement facilitation and inhibition in the subthalamic nucleus (STN), we recorded subthalamic multiunit activity intra-operatively while parkinsonian patients (n=43 patients, 173 sites) performed increasingly complex oddball paradigms: auditory ( None-Go, n=7, 28), simple movement ( All-Go, n=7, 26) and movement inhibition ( Go-NoGo, n=29, 119) tasks. To enable physiological sampling of the different subthalamic nucleus domains in both hemispheres, each patient performed one of the oddball paradigms several times.\n\nThe human STN responded mainly to movement-involving tasks: movement execution at the motor STN and movement planning at the limbic-associative STN. In the limbic-associative STN, responses to the inhibitory cue (deviant tone) in the movement inhibition task were not significantly different from the simple movement task. However, responses to the go cue (frequent tone) were significantly reduced. The reduction was mainly in the negative component of the evoked response amplitude. Successful movement inhibition was correlated with higher baseline activity before the inhibitory cue.\n\nWe suggest that the STN adapts to movement inhibition context by selectively decreasing the amplitude of neuronal activity. Thus, the STN enables movement inhibition not by increasing responses to the inhibitory cue but by reducing responses to the release cue. The negative component of the evoked response probably facilitates movement and a higher baseline activity enables successful inhibition of movement. These discharge modulations were found in the ventromedial, non-motor domain of the STN and therefore suggest a significant role of the associative-limbic domains in movement planning and in global movement regulation.

neuroscience↗