GLORIA

GEOMAR Library Ocean Research Information Access

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2021
    In:  BMC Bioinformatics Vol. 22, No. 1 ( 2021-12)
    In: BMC Bioinformatics, Springer Science and Business Media LLC, Vol. 22, No. 1 ( 2021-12)
    Abstract: Traditional methods for single-variant genome-wide association study (GWAS) incur a substantial multiple-testing burden because of the need to test for associations with a vast number of single-nucleotide polymorphisms (SNPs) simultaneously. Further, by ignoring more complex joint effects of nearby SNPs within a given region, these methods fail to consider the genomic context of an association with the outcome. Results To address these shortcomings, we present a more powerful method for GWAS, coined ‘Wavelet Screening’ (WS), that greatly reduces the number of tests to be performed. This is achieved through the use of a sliding-window approach based on wavelets to sequentially screen the entire genome for associations. Wavelets are oscillatory functions that are useful for analyzing the local frequency and time behavior of signals. The signals can then be divided into different scale components and analyzed separately. In the current setting, we consider a sequence of SNPs as a genetic signal, and for each screened region, we transform the genetic signal into the wavelet space. The null and alternative hypotheses are modeled using the posterior distribution of the wavelet coefficients. WS is enhanced by using additional information from the regression coefficients and by taking advantage of the pyramidal structure of wavelets. When faced with more complex genetic signals than single-SNP associations, we show via simulations that WS provides a substantial gain in power compared to both the traditional GWAS modeling and another popular regional association test called SNP-set (Sequence) Kernel Association Test (SKAT). To demonstrate feasibility, we applied WS to a large Norwegian cohort (N=8006) with genotypes and information available on gestational duration. Conclusions WS is a powerful and versatile approach to analyzing whole-genome data and lends itself easily to investigating various omics data types. Given its broader focus on the genomic context of an association, WS may provide additional insight into trait etiology by revealing genes and loci that might have been missed by previous efforts.
    Type of Medium: Online Resource
    ISSN: 1471-2105
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2041484-5
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 2
    Online Resource
    Online Resource
    Wiley ; 2020
    In:  Methods in Ecology and Evolution Vol. 11, No. 3 ( 2020-03), p. 403-417
    In: Methods in Ecology and Evolution, Wiley, Vol. 11, No. 3 ( 2020-03), p. 403-417
    Abstract: Ecoacoustics has the potential to provide a large amount of information about the abundance of many animal species at a relatively low cost. Acoustic recording units are widely used in field data collection, but the facilities to reliably process the data recorded – recognizing calls that are relatively infrequent, and often significantly degraded by noise and distance to the microphone – are not well‐developed yet. We propose a call detection method for continuous field recordings that can be trained quickly and easily on new species, and degrades gracefully with increased noise or distance from the microphone. The method is based on the reconstruction of the sound from a subset of the wavelet nodes (elements in the wavelet packet decomposition tree). It is intended as a preprocessing filter, therefore we aim to minimize false negatives: false positives can be removed in subsequent processing, but missed calls will not be looked at again. We compare our method to standard call detection methods, and also to machine learning methods (using as input features either wavelet energies or Mel‐Frequency Cepstral Coefficients) on real‐world noisy field recordings of six bird species. The results show that our method has higher recall (proportion detected) than the alternative methods: 87% with 85% specificity on 〉 53 hr of test data, resulting in an 80% reduction in the amount of data that needed further verification. It detected 〉 60% of calls that were extremely faint (far away), even with high background noise. This preprocessing method is available in our AviaNZ bioacoustic analysis program and enables the user to significantly reduce the amount of subsequent processing required (whether manual or automatic) to analyse continuous field recordings collected by spatially and temporally large‐scale monitoring of animal species. It can be trained to recognize new species without difficulty, and if several species are sought simultaneously, filters can be run in parallel.
    Type of Medium: Online Resource
    ISSN: 2041-210X , 2041-210X
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2528492-7
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 3
    Online Resource
    Online Resource
    Acoustical Society of America (ASA) ; 2021
    In:  The Journal of the Acoustical Society of America Vol. 150, No. 4 ( 2021-10-01), p. 2469-2478
    In: The Journal of the Acoustical Society of America, Acoustical Society of America (ASA), Vol. 150, No. 4 ( 2021-10-01), p. 2469-2478
    Abstract: Long-term soundscape recordings are useful for a variety of applications, most notably in bioacoustics. However, the processing of such data is currently limited by the ability to efficiently and reliably detect the target sounds, which are often sparse and overshadowed by environmental noise. This paper proposes a sound detector based on changepoint theory applied to a wavelet representation of the sound. In contrast to existing methods, in this framework, theoretical analysis of the detector's performance and optimality for downstream applications can be made. The relevant statistical and algorithmic developments to support these claims are presented. The method is then tested on a real task of detecting two bird species in acoustic surveys. Compared to commonly used alternatives, the proposed method consistently produced a lower false alarm rate and improved the survey efficiency as measured by the precision of the inferred population size. Finally, it is demonstrated how the method can be combined with a simple classifier to detect cat sounds in domestic recordings, which is an example from the Detection and Classification of Acoustic Scenes and Events (DCASE) 2018 workshop. The resulting performance is comparable to the state-of-the-art deep learning models and requires much less training data.
    Type of Medium: Online Resource
    ISSN: 0001-4966 , 1520-8524
    RVK:
    Language: English
    Publisher: Acoustical Society of America (ASA)
    Publication Date: 2021
    detail.hit.zdb_id: 1461063-2
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 4
    In: Annals of Epidemiology, Elsevier BV, ( 2023-9)
    Type of Medium: Online Resource
    ISSN: 1047-2797
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
    detail.hit.zdb_id: 2003468-4
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 5
    In: Nature Metabolism, Springer Science and Business Media LLC, Vol. 4, No. 3 ( 2022-03-21), p. 344-358
    Type of Medium: Online Resource
    ISSN: 2522-5812
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2933873-6
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 6
    Online Resource
    Online Resource
    Wiley ; 2022
    In:  Methods in Ecology and Evolution Vol. 13, No. 9 ( 2022-09), p. 2005-2017
    In: Methods in Ecology and Evolution, Wiley, Vol. 13, No. 9 ( 2022-09), p. 2005-2017
    Abstract: Sound recordings are used in various ecological studies, including wildlife monitoring by acoustic surveys. Such surveys often require automatic detection of target sound events in the large amount of data produced. However, current processing methods, especially those relying on sound intensity for detection, are severely impacted by wind, which causes transient intensity peaks. The rapid dynamics of this noise invalidate standard noise estimators, and no satisfactory method for dealing with wind exists in bioacoustics, where simple training and generalization between conditions are important. We estimate the transient noise level by fitting short‐term spectrum models to a wavelet packet representation. This estimator is then combined with log‐spectral subtraction to stabilize the background level. The resulting adjusted wavelet series can be analysed by standard detectors. We use real data from long‐term acoustic monitoring to tune this workflow, demonstrate its denoising capabilities and test the improved detection in two population surveys of birds. The proposed short‐term estimator was more effective than standard (constant) noise estimates in both denoising and detection tasks. In the surveys, the noise‐robust workflow greatly reduced the number of false alarms. As a result, the survey efficiency (precision of the estimated call density) improved for both species. In contrast to existing methods, the proposed estimator can adjust for transient broadband noises without requiring additional hardware or extensive tuning to each species. It improved the detection workflow based on very little training data, making it particularly attractive for detection of rare species or general soundscape analysis.
    Type of Medium: Online Resource
    ISSN: 2041-210X , 2041-210X
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2528492-7
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 7
    In: Nature Genetics, Springer Science and Business Media LLC, Vol. 55, No. 4 ( 2023-04), p. 559-567
    Abstract: The timing of parturition is crucial for neonatal survival and infant health. Yet, its genetic basis remains largely unresolved. We present a maternal genome-wide meta-analysis of gestational duration ( n  = 195,555), identifying 22 associated loci (24 independent variants) and an enrichment in genes differentially expressed during labor. A meta-analysis of preterm delivery (18,797 cases, 260,246 controls) revealed seven associated loci and large genetic similarities with gestational duration. Analysis of the parental transmitted and nontransmitted alleles ( n  = 136,833) shows that 15 of the gestational duration genetic variants act through the maternal genome, whereas 7 act both through the maternal and fetal genomes and 2 act only via the fetal genome. Finally, the maternal effects on gestational duration show signs of antagonistic pleiotropy with the fetal effects on birth weight: maternal alleles that increase gestational duration have negative fetal effects on birth weight. The present study provides insights into the genetic effects on the timing of parturition and the complex maternal–fetal relationship between gestational duration and birth weight.
    Type of Medium: Online Resource
    ISSN: 1061-4036 , 1546-1718
    RVK:
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 1494946-5
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 8
    In: Nature Genetics, Springer Science and Business Media LLC, Vol. 55, No. 7 ( 2023-07), p. 1250-1250
    Type of Medium: Online Resource
    ISSN: 1061-4036 , 1546-1718
    RVK:
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 1494946-5
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 9
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2023
    In:  Human Molecular Genetics Vol. 32, No. 14 ( 2023-07-04), p. 2399-2407
    In: Human Molecular Genetics, Oxford University Press (OUP), Vol. 32, No. 14 ( 2023-07-04), p. 2399-2407
    Abstract: Preterm birth is a major burden to neonatal health worldwide, determined in part by genetics. Recently, studies discovered several genes associated with this trait or its continuous equivalent—gestational duration. However, their effect timing, and thus clinical importance, is still unclear. Here, we use genotyping data of 31 000 births from the Norwegian Mother, Father and Child cohort (MoBa) to investigate different models of the genetic pregnancy ‘clock’. We conduct genome-wide association studies using gestational duration or preterm birth, replicating known maternal associations and finding one new fetal variant. We illustrate how the interpretation of these results is complicated by the loss of power when dichotomizing. Using flexible survival models, we resolve this complexity and find that many of the known loci have time-varying effects, often stronger early in pregnancy. The overall polygenic control of birth timing appears to be shared in the term and preterm, but not very preterm, periods and exploratory results suggest involvement of the major histocompatibility complex genes in the latter. These findings show that the known gestational duration loci are clinically relevant and should help design further experimental studies.
    Type of Medium: Online Resource
    ISSN: 0964-6906 , 1460-2083
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1474816-2
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 10
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2021
    In:  Environmental and Ecological Statistics Vol. 28, No. 3 ( 2021-09), p. 587-608
    In: Environmental and Ecological Statistics, Springer Science and Business Media LLC, Vol. 28, No. 3 ( 2021-09), p. 587-608
    Type of Medium: Online Resource
    ISSN: 1352-8505 , 1573-3009
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2000906-9
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...