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  1. Article ; Online: Evaluation of acoustic pattern recognition of nightingale (Luscinia megarhynchos) recordings by citizens

    Marcel Stehle / Mario Lasseck / Omid Khorramshahi / Ulrike Sturm

    Research Ideas and Outcomes, Vol 6, Iss , Pp 1-

    2020  Volume 9

    Abstract: Acoustic pattern recognition methods introduce new perspectives for species identification, biodiversity monitoring and data validation in citizen science but are rarely evaluated in real world scenarios. In this case study we analysed the performance of ...

    Abstract Acoustic pattern recognition methods introduce new perspectives for species identification, biodiversity monitoring and data validation in citizen science but are rarely evaluated in real world scenarios. In this case study we analysed the performance of a machine learning algorithm for automated bird identification to reliably identify common nightingales (Luscinia megarhynchos) in field recordings taken by users of the smartphone app Naturblick. We found that the performance of the automated identification tool was overall robust in our selected recordings. Although most of the recordings had a relatively low confidence score, a large proportion of the recordings were identified correctly.
    Keywords pattern recognition ; sound recognition ; species id ; Science ; Q
    Language English
    Publishing date 2020-02-01T00:00:00Z
    Publisher Pensoft Publishers
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Opportunities and limitations

    Denise Jäckel / Kim G Mortega / Ulrike Sturm / Ulrich Brockmeyer / Omid Khorramshahi / Silke L Voigt-Heucke

    PLoS ONE, Vol 16, Iss 6, p e

    A comparative analysis of citizen science and expert recordings for bioacoustic research.

    2021  Volume 0253763

    Abstract: Citizen science is an approach that has become increasingly popular in recent years. Despite this growing popularity, there still is widespread scepticism in the academic world about the validity and quality of data from citizen science projects. And ... ...

    Abstract Citizen science is an approach that has become increasingly popular in recent years. Despite this growing popularity, there still is widespread scepticism in the academic world about the validity and quality of data from citizen science projects. And although there might be great potential, citizen science is a rarely used approach in the field of bioacoustics. To better understand the possibilities, but also the limitations, we here evaluated data generated in a citizen science project on nightingale song as a case study. We analysed the quantity and quality of song recordings made in a non-standardized way with a smartphone app by citizen scientists and the standardized recordings made with professional equipment by academic researchers. We made comparisons between the recordings of the two approaches and among the user types of the app to gain insights into the temporal recording patterns, the quantity and quality of the data. To compare the deviation of the acoustic parameters in the recordings with smartphones and professional devices from the original song recordings, we conducted a playback test. Our results showed that depending on the user group, citizen scientists produced many to a lot of recordings of valid quality for further bioacoustic research. Differences between the recordings provided by the citizen and the expert group were mainly caused by the technical quality of the devices used-and to a lesser extent by the citizen scientists themselves. Especially when differences in spectral parameters are to be investigated, our results demonstrate that the use of the same high-quality recording devices and calibrated external microphones would most likely improve data quality. We conclude that many bioacoustic research questions may be carried out with the recordings of citizen scientists. We want to encourage academic researchers to get more involved in participatory projects to harness the potential of citizen science-and to share scientific curiosity and discoveries more directly with society.
    Keywords Medicine ; R ; Science ; Q
    Subject code 001
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: Identification of novel autoantigens via mass spectroscopy-based antibody-mediated identification of autoantigens (MS-AMIDA) using immune thrombocytopenic purpura (ITP) as a model disease

    Kamhieh-Milz, Julian / Abdulgabar Salama / Hatice Celik / Omid Khorramshahi / Reham Fadl Hassan Moftah / Viktor Sterzer

    Journal of proteomics. 2017 Mar. 22, v. 157

    2017  

    Abstract: Immune thrombocytopenic purpura (ITP) is one of the best characterized autoimmune diseases. Autoantibodies (AABs) against platelet antigens are considered as the diagnostic hallmark of ITP, but are detectable in only 50% of patients. We designed and ... ...

    Abstract Immune thrombocytopenic purpura (ITP) is one of the best characterized autoimmune diseases. Autoantibodies (AABs) against platelet antigens are considered as the diagnostic hallmark of ITP, but are detectable in only 50% of patients. We designed and applied a novel proteomic approach termed Mass Spectroscopy-based Antibody-Mediated Identification of Autoantigens (MS-AMIDA) for platelet antigens. Patients were separated into patients with classical AABs [ITP(+)] and patients without AABs [ITP(−)]. Altogether, 181 potential AAGs were found in ITP(+) and 135 AAGs in ITP(−), with 34 and 23 AAGs reproducibly found in two runs of MS-AMIDA. After subtracting identifiers from the controls, 57 AAGs in ITP(+) and 29 AAGs in ITP(+) remained, with 16 AAGs commonly found in ITP(+) and ITP(−) patients. Label-free quantification (LFQ) revealed 15 potential AAGs that are quantitatively stronger in ITP. Dot blot validation was performed on hexokinase 1 (HK1), E1 pyruvate dehydrogenase (E1-PDH), coagulation factor XIII, filamin A (FLNA), non-muscle myosin 9. Eleven patients were found to have anti-HK1 AABs, one patient had anti-E1-PDH AABs, and two patients had anti-FLNA AABs. Most antigens were of intracellular origin with significant association with actin-cytoskeleton and regulation of programmed cell death. In conclusion, novel AAGs for ITP were identified using MS-AMIDA.
    Keywords apoptosis ; autoantibodies ; autoantigens ; autoimmune diseases ; coagulation ; filamin ; hexokinase ; myosin ; patients ; pyruvate dehydrogenase (lipoamide) ; thrombocytopenic purpura
    Language English
    Dates of publication 2017-0322
    Size p. 59-70.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2400835-7
    ISSN 1876-7737 ; 1874-3919
    ISSN (online) 1876-7737
    ISSN 1874-3919
    DOI 10.1016/j.jprot.2017.01.012
    Database NAL-Catalogue (AGRICOLA)

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  4. Article: Secretome profiling of apheresis platelet supernatants during routine storage via antibody-based microarray

    Kamhieh-Milz, Julian / Abdulgabar Salama / Hatice Celik / Jörg D. Hoheisel / Kamran Movassaghi / Mohamed S.S. Alhamdani / Omid Khorramshahi / Sahime Keski / Shakhawan A. Mustafa / Viktor Sterzer

    Journal of proteomics. 2017 Jan. 06, v. 150

    2017  

    Abstract: Platelet storage lesions (PSLs) occur during platelet concentrate (PC) storage. Adverse transfusion reactions (ATRs) have been demonstrated to be more frequent in older PCs and removal of the supernatant prior to transfusion reduces their occurrence. ... ...

    Abstract Platelet storage lesions (PSLs) occur during platelet concentrate (PC) storage. Adverse transfusion reactions (ATRs) have been demonstrated to be more frequent in older PCs and removal of the supernatant prior to transfusion reduces their occurrence. Proteomic profiling of PC supernatants was thus performed to identify proteins associated with PSLs and ATRs. Twenty-four PCs were investigated daily from day 0 to day 9 for platelet pre-activation (PPA), platelet-derived extracellular vesicles (PEVs), and platelet function. Using antibody microarrays, 673 extracellular proteins were analysed in PC supernatants on days 0, 3, 5, 7, and 9. During 5days of storage, PPA and PEVs continuously increased (P<0.0001). Platelet function was observed to remain stable within the first 5days (P=0.1751) and decreased thereafter. Comparison of all time points to day 0 revealed the identification of 136 proteins that were significantly changed in abundance during storage, of which 72 were expressed by platelets. Network analysis identified these proteins to be predominantly associated with exosomes (P=4.61×10−8, n=45 genes) and two clusters with distinct functions were found with one being associated with haemostasis and the other with RNA binding. These findings may provide an explanation for ATRs.Changes in platelet concentrate (PC) supernatants during storage have been so far only poorly addressed and high abundant proteins burden the identification of quantitative changes in the secretome. We applied a high-throughput antibody microarray allowing for the sensitive quantification of 673 extracellular factors. PCs account for the highest number of adverse transfusion reactions (ATRs). ATRs have been demonstrated to be more frequent in older PCs and removal of the supernatant prior to transfusion reduces their occurrence. Comprehensive interpretation of the changing proteins in the secretome during platelet storage under blood banking conditions may help to identify mechanisms leading to the occurrence of adverse transfusion reactions.
    Keywords antibody microarrays ; blood platelets ; exosomes ; genes ; hemostasis ; microarray technology ; proteins ; proteomics ; RNA
    Language English
    Dates of publication 2017-0106
    Size p. 74-85.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2400835-7
    ISSN 1876-7737 ; 1874-3919
    ISSN (online) 1876-7737
    ISSN 1874-3919
    DOI 10.1016/j.jprot.2016.07.028
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Differentially Expressed MicroRNAs in Maternal Plasma for the Noninvasive Prenatal Diagnosis of Down Syndrome (Trisomy 21)

    Julian Kamhieh-Milz / Reham Fadl Hassan Moftah / Gürkan Bal / Matthias Futschik / Viktor Sterzer / Omid Khorramshahi / Martin Burow / Gundula Thiel / Annegret Stuke-Sontheimer / Rabih Chaoui / Sundrela Kamhieh-Milz / Abdulgabar Salama

    BioMed Research International, Vol

    2014  Volume 2014

    Abstract: Objectives. Most developmental processes are under the control of small regulatory RNAs called microRNAs (miRNAs). We hypothesize that different fetal developmental processes might be reflected by extracellular miRNAs in maternal plasma and may be ... ...

    Abstract Objectives. Most developmental processes are under the control of small regulatory RNAs called microRNAs (miRNAs). We hypothesize that different fetal developmental processes might be reflected by extracellular miRNAs in maternal plasma and may be utilized as biomarkers for the noninvasive prenatal diagnosis of chromosomal aneuploidies. In this proof-of-concept study, we report on the identification of extracellular miRNAs in maternal plasma of Down syndrome (DS) pregnancies. Methods. Using high-throughput quantitative PCR (HT-qPCR), 1043 miRNAs were investigated in maternal plasma via comparison of seven DS pregnancies with age and fetal sex matched controls. Results. Six hundred and ninety-five miRNAs were identified. Thirty-six significantly differentially expressed mature miRNAs were identified as potential biomarkers. Hierarchical cluster analysis of these miRNAs resulted in the clear discrimination of DS from euploid pregnancies. Gene targets of the differentially expressed miRNAs were enriched in signaling pathways such as mucin type-O-glycans, ECM-receptor interactions, TGF-beta, and endocytosis, which have been previously associated with DS. Conclusions. miRNAs are promising and stable biomarkers for a broad range of diseases and may allow a reliable, cost-efficient diagnostic tool for the noninvasive prenatal diagnosis of DS.
    Keywords Medicine ; R
    Subject code 500 ; 610
    Language English
    Publishing date 2014-01-01T00:00:00Z
    Publisher Hindawi Limited
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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