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  1. Book ; Online: Probabilistic and Non-Deterministic Event Data in Process Mining

    Pegoraro, Marco

    Embedding Uncertainty in Process Analysis Techniques

    2022  

    Abstract: Process mining is a subfield of process science that analyzes event data collected in databases called event logs. Recently, novel types of event data have become of interest due to the wide industrial application of process mining analyses. In this ... ...

    Abstract Process mining is a subfield of process science that analyzes event data collected in databases called event logs. Recently, novel types of event data have become of interest due to the wide industrial application of process mining analyses. In this paper, we examine uncertain event data. Such data contain meta-attributes describing the amount of imprecision tied with attributes recorded in an event log. We provide examples of uncertain event data, present the state of the art in regard of uncertainty in process mining, and illustrate open challenges related to this research direction.

    Comment: 12 pages, 4 figures, 4 tables, 16 references. arXiv admin note: text overlap with arXiv:2010.00334
    Keywords Computer Science - Artificial Intelligence
    Publishing date 2022-05-10
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Online: Process Mining on Uncertain Event Data

    Pegoraro, Marco

    2022  

    Abstract: With the widespread adoption of process mining in organizations, the field of process science is seeing an increase in the demand for ad-hoc analysis techniques of non-standard event data. An example of such data are uncertain event data: events ... ...

    Abstract With the widespread adoption of process mining in organizations, the field of process science is seeing an increase in the demand for ad-hoc analysis techniques of non-standard event data. An example of such data are uncertain event data: events characterized by a described and quantified attribute imprecision. This paper outlines a research project aimed at developing process mining techniques able to extract insights from uncertain data. We set the basis for this research topic, recapitulate the available literature, and define a future outlook.

    Comment: 2 pages, 1 figure, 2 tables, 9 references
    Keywords Computer Science - Artificial Intelligence
    Publishing date 2022-04-08
    Publishing country us
    Document type Book ; Online
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  3. Article ; Online: A role for DNA methylation in bumblebee morphogenesis hints at female-specific developmental erasure.

    Hunt, Ben J / Pegoraro, Mirko / Marshall, Hollie / Mallon, Eamonn B

    Insect molecular biology

    2024  

    Abstract: Epigenetic mechanisms, such as DNA methylation, are crucial factors in animal development. In some mammals, almost all DNA methylation is erased during embryo development and re-established in a sex- and cell-specific manner. This erasure and re- ... ...

    Abstract Epigenetic mechanisms, such as DNA methylation, are crucial factors in animal development. In some mammals, almost all DNA methylation is erased during embryo development and re-established in a sex- and cell-specific manner. This erasure and re-establishment is thought to primarily be a vertebrate-specific trait. Insects are particularly interesting in terms of development as many species often undergo remarkable morphological changes en route to maturity, that is, morphogenesis. However, little is known about the role of epigenetic mechanisms in this process across species. We have used whole-genome bisulfite sequencing to track genome-wide DNA methylation changes through the development of an economically and environmentally important pollinator species, the bumblebee Bombus terrestris (Hymenoptera:Apidae Linnaeus). We find overall levels of DNA methylation vary throughout development, and we find developmentally relevant differentially methylated genes throughout. Intriguingly, we have identified a depletion of DNA methylation in ovaries/eggs and an enrichment of highly methylated genes in sperm. We suggest this could represent a sex-specific DNA methylation erasure event. To our knowledge, this is the first suggestion of possible developmental DNA methylation erasure in an insect species. This study lays the required groundwork for functional experimental work to determine if there is a causal nature to the DNA methylation differences identified. Additionally, the application of single-cell methylation sequencing to this system will enable more accurate identification of if or when DNA methylation is erased during development.
    Language English
    Publishing date 2024-02-13
    Publishing country England
    Document type Journal Article
    ZDB-ID 33602-6
    ISSN 1365-2583 ; 0962-1075
    ISSN (online) 1365-2583
    ISSN 0962-1075
    DOI 10.1111/imb.12897
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  4. Article ; Online: Malaria in the 'Omics Era'.

    Pegoraro, Mirko / Weedall, Gareth D

    Genes

    2021  Volume 12, Issue 6

    Abstract: Genomics has revolutionised the study of the biology of parasitic diseases. The first Eukaryotic parasite to have its genome sequenced was the malaria ... ...

    Abstract Genomics has revolutionised the study of the biology of parasitic diseases. The first Eukaryotic parasite to have its genome sequenced was the malaria parasite
    MeSH term(s) Epigenome ; Genome, Protozoan ; Humans ; Malaria/parasitology ; Plasmodium falciparum/genetics ; Plasmodium falciparum/metabolism ; Polymorphism, Genetic
    Language English
    Publishing date 2021-05-30
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes12060843
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  5. Article: Malaria in the ‘Omics Era’

    Pegoraro, Mirko / Weedall, Gareth D.

    Genes. 2021 May 30, v. 12, no. 6

    2021  

    Abstract: Genomics has revolutionised the study of the biology of parasitic diseases. The first Eukaryotic parasite to have its genome sequenced was the malaria parasite Plasmodium falciparum. Since then, Plasmodium genomics has continued to lead the way in the ... ...

    Abstract Genomics has revolutionised the study of the biology of parasitic diseases. The first Eukaryotic parasite to have its genome sequenced was the malaria parasite Plasmodium falciparum. Since then, Plasmodium genomics has continued to lead the way in the study of the genome biology of parasites, both in breadth—the number of Plasmodium species’ genomes sequenced—and in depth—massive-scale genome re-sequencing of several key species. Here, we review some of the insights into the biology, evolution and population genetics of Plasmodium gained from genome sequencing, and look at potential new avenues in the future genome-scale study of its biology.
    Keywords Plasmodium falciparum ; evolution ; genomics ; malaria ; parasites ; population genetics
    Language English
    Dates of publication 2021-0530
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes12060843
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  6. Article ; Online: Febrile sepsis: first report of human disease due to

    Vecchia, Ilaria Dalla / Fasan, Daniele / Pegoraro, Manuela / Benedetti, Paolo

    Access microbiology

    2023  Volume 5, Issue 6

    Abstract: Introduction: Paenibacillus: Case presentation: A 57-year-old female patient was referred to our Unit after a 2 month history of remittent fever. Upon admission, a septic state and bacteraemia were revealed; : Conclusion: The patient did not ... ...

    Abstract Introduction: Paenibacillus
    Case presentation: A 57-year-old female patient was referred to our Unit after a 2 month history of remittent fever. Upon admission, a septic state and bacteraemia were revealed;
    Conclusion: The patient did not report any previous episode of infection. Most of the well-known risk factors to
    Language English
    Publishing date 2023-06-23
    Publishing country England
    Document type Case Reports
    ISSN 2516-8290
    ISSN (online) 2516-8290
    DOI 10.1099/acmi.0.000580.v3
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  7. Article ; Online: Imaging-based representation and stratification of intra-tumor heterogeneity via tree-edit distance.

    Cavinato, Lara / Pegoraro, Matteo / Ragni, Alessandra / Ieva, Francesca

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 19607

    Abstract: Personalized medicine is the future of medical practice. In oncology, tumor heterogeneity assessment represents a pivotal step for effective treatment planning and prognosis prediction. Despite new procedures for DNA sequencing and analysis, non-invasive ...

    Abstract Personalized medicine is the future of medical practice. In oncology, tumor heterogeneity assessment represents a pivotal step for effective treatment planning and prognosis prediction. Despite new procedures for DNA sequencing and analysis, non-invasive methods for tumor characterization are needed to impact on daily routine. On purpose, imaging texture analysis is rapidly scaling, holding the promise to surrogate histopathological assessment of tumor lesions. In this work, we propose a tree-based representation strategy for describing intra-tumor heterogeneity of patients affected by metastatic cancer. We leverage radiomics information extracted from PET/CT imaging and we provide an exhaustive and easily readable summary of the disease spreading. We exploit this novel patient representation to perform cancer subtyping according to hierarchical clustering technique. To this purpose, a new heterogeneity-based distance between trees is defined and applied to a case study of prostate cancer. Clusters interpretation is explored in terms of concordance with severity status, tumor burden and biological characteristics. Results are promising, as the proposed method outperforms current literature approaches. Ultimately, the proposed method draws a general analysis framework that would allow to extract knowledge from daily acquired imaging data of patients and provide insights for effective treatment planning.
    MeSH term(s) Male ; Humans ; Positron Emission Tomography Computed Tomography/methods ; Prognosis ; Prostatic Neoplasms/diagnostic imaging ; Prostatic Neoplasms/pathology ; Tumor Burden
    Language English
    Publishing date 2022-11-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-23752-2
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  8. Article: Nucleotide Variation in

    Pegoraro, Mirko / Sayegh Rezek, Emily / Fishman, Bettina / Tauber, Eran

    Frontiers in physiology

    2022  Volume 13, Page(s) 781380

    Abstract: Cryptochrome (CRY) is a conserved protein associated with the circadian clock in a broad range of organisms, including plants, insects, and mammals. ... ...

    Abstract Cryptochrome (CRY) is a conserved protein associated with the circadian clock in a broad range of organisms, including plants, insects, and mammals. In
    Language English
    Publishing date 2022-02-17
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2564217-0
    ISSN 1664-042X
    ISSN 1664-042X
    DOI 10.3389/fphys.2022.781380
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  9. Article ; Online: Microdosimetric Measurements in Gamma and neutron Fields with a Tissue Equivalent Proportional Counter Based on a Gas Electron Multiplier.

    De Nardo, L / Dal Corso, F / Pegoraro, M

    Radiation protection dosimetry

    2017  Volume 175, Issue 2, Page(s) 260–266

    Abstract: A multi-element tissue-equivalent proportional counter (TEPC), based on a single gas electron multiplier (GEM) foil of standard geometry, has been constructed with 16 cylindrical sensitives volumes. In this article, the design of this novel counter is ... ...

    Abstract A multi-element tissue-equivalent proportional counter (TEPC), based on a single gas electron multiplier (GEM) foil of standard geometry, has been constructed with 16 cylindrical sensitives volumes. In this article, the design of this novel counter is described and first microdosimetric measurements are presented. To study the response of the GEM-TEPC to both low and high linear energy transfer radiation fields, the microdosimetric spectra due to a 137Cs gamma-ray source and to fast neutrons from 7Li(d,n)8Be reaction have been measured using pure propane gas at low pressure, in order to simulate a tissue site of about 1 µm equivalent size. The comparison with spectra measured with a spherical TEPC and with a mini-TEPC demonstrates promising properties for application of the GEM-TEPC for microdosimetric applications.
    Language English
    Publishing date 2017-06-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 225912-6
    ISSN 1742-3406 ; 0144-8420
    ISSN (online) 1742-3406
    ISSN 0144-8420
    DOI 10.1093/rpd/ncw294
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    Zs.A 2009: Show issues Location:
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  10. Article ; Online: Adaptation of

    Deppisch, Peter / Prutscher, Johanna M / Pegoraro, Mirko / Tauber, Eran / Wegener, Christian / Helfrich-Förster, Charlotte

    Journal of biological rhythms

    2022  Volume 37, Issue 2, Page(s) 185–201

    Abstract: Circadian clocks help animals to be active at the optimal time of the day whereby for most species the daily light-dark cycle is the most important zeitgeber for their circadian clock. In this respect, long arctic summer days are particularly challenging ...

    Abstract Circadian clocks help animals to be active at the optimal time of the day whereby for most species the daily light-dark cycle is the most important zeitgeber for their circadian clock. In this respect, long arctic summer days are particularly challenging as light is present almost 24 h per day, and continuous light makes the circadian clocks of many animals arrhythmic. This is especially true for the fruit fly,
    MeSH term(s) Alleles ; Animals ; Circadian Rhythm/genetics ; Cryptochromes ; Drosophila/physiology ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/physiology ; Light ; Photoperiod
    Chemical Substances Cryptochromes ; Drosophila Proteins
    Language English
    Publishing date 2022-03-18
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 896387-3
    ISSN 1552-4531 ; 0748-7304
    ISSN (online) 1552-4531
    ISSN 0748-7304
    DOI 10.1177/07487304221082448
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    Zs.A 2872: Show issues Location:
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