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  1. Article ; Online: A retrospective of deaths related to migration along the southeasternmost land borders of Europe: an update encompassing the years 2015-22.

    Mavroudas, Sophia R / Pavlidis, Pavlos / Karakasi, Maria-Valeria

    Disasters

    2023  , Page(s) e12620

    Abstract: This study presents an update of forensic accounting of the numbers and demographics of migrants found deceased in the Evros region of Greece in the years from 2015-22. Compared to data from 2000-14, this update reflects the mounting number of border- ... ...

    Abstract This study presents an update of forensic accounting of the numbers and demographics of migrants found deceased in the Evros region of Greece in the years from 2015-22. Compared to data from 2000-14, this update reflects the mounting number of border-related deaths in the region, as well as the changing demographic trends associated with the migrants who perish crossing the Greek-Turkish border. Specifically, the paper documents a broadening of locations from which migrants originate, the increasing diversity of migrant death locations, and a shift in the leading causes of death. It contains important forensic accounting of the unique humanitarian crisis occurring along the Greek-Turkish land border while also providing an additional context for the global migration crisis. The data presented here offer insights into other forensic stakeholders impacted by the global migration crisis, with respect to what factors contribute to and detract from identification rates, and can help stakeholders make informed policy decisions.
    Language English
    Publishing date 2023-12-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 1482668-9
    ISSN 1467-7717 ; 0361-3666
    ISSN (online) 1467-7717
    ISSN 0361-3666
    DOI 10.1111/disa.12620
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  2. Article: Editorial: Scalable Bioinformatics: Methods, Software Tools, and Hardware Architectures.

    Alachiotis, Nikolaos / Low, Tze Meng / Pavlidis, Pavlos

    Frontiers in genetics

    2022  Volume 12, Page(s) 822986

    Language English
    Publishing date 2022-01-05
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2021.822986
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  3. Article ; Online: Balancing selection on genomic deletion polymorphisms in humans.

    Aqil, Alber / Speidel, Leo / Pavlidis, Pavlos / Gokcumen, Omer

    eLife

    2023  Volume 12

    Abstract: A key question in biology is why genomic variation persists in a population for extended periods. Recent studies have identified examples of genomic deletions that have remained polymorphic in the human lineage for hundreds of millennia, ostensibly owing ...

    Abstract A key question in biology is why genomic variation persists in a population for extended periods. Recent studies have identified examples of genomic deletions that have remained polymorphic in the human lineage for hundreds of millennia, ostensibly owing to balancing selection. Nevertheless, genome-wide investigation of ancient and possibly adaptive deletions remains an imperative exercise. Here, we demonstrate an excess of polymorphisms in present-day humans that predate the modern human-Neanderthal split (ancient polymorphisms), which cannot be explained solely by selectively neutral scenarios. We analyze the adaptive mechanisms that underlie this excess in deletion polymorphisms. Using a previously published measure of balancing selection, we show that this excess of ancient deletions is largely owing to balancing selection. Based on the absence of signatures of overdominance, we conclude that it is a rare mode of balancing selection among ancient deletions. Instead, more complex scenarios involving spatially and temporally variable selective pressures are likely more common mechanisms. Our results suggest that balancing selection resulted in ancient deletions harboring disproportionately more exonic variants with GWAS (genome-wide association studies) associations. We further found that ancient deletions are significantly enriched for traits related to metabolism and immunity. As a by-product of our analysis, we show that deletions are, on average, more deleterious than single nucleotide variants. We can now argue that not only is a vast majority of common variants shared among human populations, but a considerable portion of biologically relevant variants has been segregating among our ancestors for hundreds of thousands, if not millions, of years.
    MeSH term(s) Animals ; Humans ; Genome-Wide Association Study ; Hominidae/genetics ; Polymorphism, Genetic ; Genome ; Genomics ; Neanderthals/genetics ; Selection, Genetic
    Language English
    Publishing date 2023-01-10
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.79111
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  4. Article ; Online: Genome-wide scans for selective sweeps using convolutional neural networks.

    Zhao, Hanqing / Souilljee, Matthijs / Pavlidis, Pavlos / Alachiotis, Nikolaos

    Bioinformatics (Oxford, England)

    2023  Volume 39, Issue 39 Suppl 1, Page(s) i194–i203

    Abstract: Motivation: Recent methods for selective sweep detection cast the problem as a classification task and use summary statistics as features to capture region characteristics that are indicative of a selective sweep, thereby being sensitive to confounding ... ...

    Abstract Motivation: Recent methods for selective sweep detection cast the problem as a classification task and use summary statistics as features to capture region characteristics that are indicative of a selective sweep, thereby being sensitive to confounding factors. Furthermore, they are not designed to perform whole-genome scans or to estimate the extent of the genomic region that was affected by positive selection; both are required for identifying candidate genes and the time and strength of selection.
    Results: We present ASDEC (https://github.com/pephco/ASDEC), a neural-network-based framework that can scan whole genomes for selective sweeps. ASDEC achieves similar classification performance to other convolutional neural network-based classifiers that rely on summary statistics, but it is trained 10× faster and classifies genomic regions 5× faster by inferring region characteristics from the raw sequence data directly. Deploying ASDEC for genomic scans achieved up to 15.2× higher sensitivity, 19.4× higher success rates, and 4× higher detection accuracy than state-of-the-art methods. We used ASDEC to scan human chromosome 1 of the Yoruba population (1000Genomes project), identifying nine known candidate genes.
    MeSH term(s) Humans ; Genomics ; Neural Networks, Computer
    Language English
    Publishing date 2023-06-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btad265
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    Zs.A 2374: Show issues Location:
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  5. Article ; Online: Death by compaction in a robotic dumpster.

    Karakasi, Maria-Valeria / Nikolaidis, Ioannis / Pavlidis, Pavlos

    Journal of forensic sciences

    2023  Volume 68, Issue 4, Page(s) 1386–1392

    Abstract: Robotic waste management automation systems are increasingly utilized around the globe as a user-friendly, ecological and hygienic alternative to waste disposal, simultaneously reducing the volume and frequency of waste collection. The present paper aims ...

    Abstract Robotic waste management automation systems are increasingly utilized around the globe as a user-friendly, ecological and hygienic alternative to waste disposal, simultaneously reducing the volume and frequency of waste collection. The present paper aims to report a case of death by compaction in an automated robotic waste management system and review relevant literature on compactor-related fatalities. The unusual fatal accident involved a 37-year-old male citizen who deliberately entered the robotic dumpster to retrieve his accidentally discarded medication. Upon entering the robotic chamber, the compaction system was automatically activated, although all safety measures were in full operation. This paper highlights the lack of standardized reporting on compactor-related mortality, which however is of importance both in terms of its social impact and public safety. These deaths occur rarely, in scattered areas of the globe, associated with various situations (e.g., occupational fatalities, homeless people, infanticide) and trash compactors of different types, technology, age, maintenance quality, warning signage and safety interlocks. In all previously reported fatalities, the technology involved was considerably older (as in conventional waste containers, garbage compaction trucks, chute-fed compactors in buildings, etc.). The case described in the present report is a rare event in both literature and international news coverage as it encompasses a fully automated technology intended for unsupervised, direct use by the public being located in public spaces where all citizens can interact with it. The aim of this report is to raise awareness and improve knowledge about safety parameters so that similar incidents can be avoided in the future.
    MeSH term(s) Male ; Humans ; Adult ; Refuse Disposal ; Robotic Surgical Procedures ; Waste Management ; Garbage ; Environment
    Language English
    Publishing date 2023-05-02
    Publishing country United States
    Document type Case Reports
    ZDB-ID 219216-0
    ISSN 1556-4029 ; 0022-1198
    ISSN (online) 1556-4029
    ISSN 0022-1198
    DOI 10.1111/1556-4029.15264
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  6. Article ; Online: Safety and efficacy of ovarian tissue autotransplantation: A systematic literature review.

    Giovannopoulou, Eirini / Karakasi, Maria-Valeria / Kouroupi, Maria / Giatromanolaki, Alexandra / Tsikouras, Panagiotis / Pavlidis, Pavlos

    Folia medica

    2024  Volume 65, Issue 3, Page(s) 362–370

    Abstract: Ovarian tissue autotransplantation is an innovative fertility preservation technique that has provoked ongoing investigations. The purpose of the present study was to assess the safety and reproductive performance of ovarian tissue autotransplantation. ... ...

    Abstract Ovarian tissue autotransplantation is an innovative fertility preservation technique that has provoked ongoing investigations. The purpose of the present study was to assess the safety and reproductive performance of ovarian tissue autotransplantation. This review is conducted according to PRISMA guidelines. Seven studies met the inclusion criteria. A total of 3427 patients underwent ovarian tissue cryopreservation and 205 received an autotransplantation. Tissue retrieval was mainly performed by laparoscopy and only one major complication occurred. Transplantations were predominantly performed by open procedures and data on safety were insufficient. A total of 295 autotransplantations were analyzed, resulting in 104 pregnancies. Sixty-five pregnancies led to live births, while nine were ongoing at that time. A pregnancy rate (PR) of 50.7% and a live-birth rate (LBR) of 32.7% were observed. Natural conception accounted for 46.3% of live births. No birth deficits were recorded. Ovarian tissue autotransplantation seems to be a safe procedure with acceptable pregnancy rates.
    MeSH term(s) Pregnancy ; Female ; Humans ; Ovary/surgery ; Transplantation, Autologous ; Fertility Preservation/methods ; Cryopreservation/methods
    Language English
    Publishing date 2024-02-14
    Publishing country Bulgaria
    Document type Systematic Review ; Journal Article
    ZDB-ID 300275-5
    ISSN 1314-2143 ; 0430-8638 ; 0204-8043
    ISSN (online) 1314-2143
    ISSN 0430-8638 ; 0204-8043
    DOI 10.3897/folmed.65.e89198
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  7. Article ; Online: Of dogs and men.

    Pavlidis, Pavlos / Somel, Mehmet

    Science (New York, N.Y.)

    2020  Volume 370, Issue 6516, Page(s) 522–523

    MeSH term(s) Animals ; Dogs ; Humans ; Male
    Keywords covid19
    Language English
    Publishing date 2020-10-29
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.abe7823
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  8. Article ; Online: Cronos: A Machine Learning Pipeline for Description and Predictive Modeling of Microbial Communities Over Time.

    Litos, Aristeidis / Intze, Evangelia / Pavlidis, Pavlos / Lagkouvardos, Ilias

    Frontiers in bioinformatics

    2022  Volume 2, Page(s) 866902

    Abstract: Microbial time-series analysis, typically, examines the abundances of individual taxa over time and attempts to assign etiology to observed patterns. This approach assumes homogeneous groups in terms of profiles and response to external effectors. These ... ...

    Abstract Microbial time-series analysis, typically, examines the abundances of individual taxa over time and attempts to assign etiology to observed patterns. This approach assumes homogeneous groups in terms of profiles and response to external effectors. These assumptions are not always fulfilled, especially in complex natural systems, like the microbiome of the human gut. It is actually established that humans with otherwise the same demographic or dietary backgrounds can have distinct microbial profiles. We suggest an alternative approach to the analysis of microbial time-series, based on the following premises: 1) microbial communities are organized in distinct clusters of similar composition at any time point, 2) these intrinsic subsets of communities could have different responses to the same external effects, and 3) the fate of the communities is largely deterministic given the same external conditions. Therefore, tracking the transition of communities, rather than individual taxa, across these states, can enhance our understanding of the ecological processes and allow the prediction of future states, by incorporating applied effects. We implement these ideas into Cronos, an analytical pipeline written in R. Cronos' inputs are a microbial composition table (e.g., OTU table), their phylogenetic relations as a tree, and the associated metadata. Cronos detects the intrinsic microbial profile clusters on all time points, describes them in terms of composition, and records the transitions between them. Cluster assignments, combined with the provided metadata, are used to model the transitions and predict samples' fate under various effects. We applied Cronos to available data from growing infants' gut microbiomes, and we observe two distinct trajectories corresponding to breastfed and formula-fed infants that eventually converge to profiles resembling those of mature individuals. Cronos is freely available at https://github.com/Lagkouvardos/Cronos.
    Language English
    Publishing date 2022-08-09
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2673-7647
    ISSN (online) 2673-7647
    DOI 10.3389/fbinf.2022.866902
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  9. Article: Neuropsychological Assessment of a Patient Diagnosed with Major Depression and Huntington's Disease.

    Theofilidis, Antonios / Karakasi, Maria-Valeria / Pavlidis, Pavlos / Nimatoudis, Ioannis

    Psychiatria Danubina

    2022  Volume 34, Issue 3, Page(s) 511–513

    MeSH term(s) Humans ; Huntington Disease/diagnosis ; Huntington Disease/psychology ; Depression ; Depressive Disorder, Major/diagnosis ; Neuropsychological Tests
    Language English
    Publishing date 2022-10-18
    Publishing country Croatia
    Document type Journal Article
    ZDB-ID 1067580-2
    ISSN 0353-5053
    ISSN 0353-5053
    DOI 10.24869/psyd.2022.511
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  10. Article: Contact Endoscopic Surface Vascular and Epithelial Morphology in Leukoplakia and Carcinoma of the Vocal Cords: Vascular and morphological changes of vocal folds in leukoplakia and cancer.

    Pavlidis, Pavlos / Tseriotis, Vasileios Spyridon / Matthias, Christopher / Katsikari, Ioulia / Chatzinikolaou, Aimilios / Gouveris, Haralampos

    Indian journal of otolaryngology and head and neck surgery : official publication of the Association of Otolaryngologists of India

    2023  Volume 76, Issue 1, Page(s) 462–468

    Abstract: ... ...

    Abstract Purpose
    Language English
    Publishing date 2023-09-20
    Publishing country India
    Document type Journal Article
    ZDB-ID 1471137-0
    ISSN 0973-7707 ; 2231-3796 ; 0019-5421
    ISSN (online) 0973-7707
    ISSN 2231-3796 ; 0019-5421
    DOI 10.1007/s12070-023-04183-5
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