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  1. Article: Who Owns My Identity?

    Hill, T Patrick

    Journal of registry management

    2024  Volume 50, Issue 4, Page(s) 111–112

    MeSH term(s) Humans ; Ownership
    Language English
    Publishing date 2024-03-15
    Publishing country United States
    Document type Journal Article
    ISSN 1945-6123
    ISSN 1945-6123
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Data Sharing for The Common Good: An Ethical Obligation?

    Hill, T Patrick

    Journal of registry management

    2023  Volume 49, Issue 2, Page(s) 54–55

    MeSH term(s) Humans ; Moral Obligations ; Social Responsibility ; Information Dissemination ; Social Justice
    Language English
    Publishing date 2023-05-16
    Publishing country United States
    Document type Editorial
    ISSN 1945-6123
    ISSN 1945-6123
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Risk assessment in clinical trials: it don't mean an ethical thing if it ain't got that probability ring!

    Patrick Hill, T

    Ecancermedicalscience

    2014  Volume 8, Page(s) ed42

    Language English
    Publishing date 2014-09-03
    Publishing country England
    Document type Journal Article
    ISSN 1754-6605
    ISSN 1754-6605
    DOI 10.3332/ecancer.2014.ed42
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies.

    Tang, Li / Hill, Matthew C / Ellinor, Patrick T / Li, Min

    Genome biology

    2022  Volume 23, Issue 1, Page(s) 30

    Abstract: Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions, and the adoption of ChIP techniques to 3C-based protocols makes it possible to identify long-range interactions. To analyze ... ...

    Abstract Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions, and the adoption of ChIP techniques to 3C-based protocols makes it possible to identify long-range interactions. To analyze these large and complex datasets, computational methods are undergoing rapid and expansive evolution. Thus, a thorough evaluation of these analytical pipelines is necessary to identify which commonly used algorithms and processing pipelines need to be improved. Here we present a comprehensive benchmark framework, Bacon, to evaluate the performance of several computational methods. Finally, we provide practical recommendations for users working with HiChIP and/or ChIA-PET analyses.
    MeSH term(s) Benchmarking ; Chromatin/genetics ; Chromatin Immunoprecipitation Sequencing ; Chromosomes ; Pork Meat
    Chemical Substances Chromatin
    Language English
    Publishing date 2022-01-21
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1474-760X
    ISSN (online) 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-021-02597-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: MMCT-Loop: a mix model-based pipeline for calling targeted 3D chromatin loops.

    Tang, Li / Liao, Jiaqi / Hill, Matthew C / Hu, Jiaxin / Zhao, Yichao / Ellinor, Patrick T / Li, Min

    Nucleic acids research

    2024  Volume 52, Issue 5, Page(s) e25

    Abstract: Protein-specific Chromatin Conformation Capture (3C)-based technologies have become essential for identifying distal genomic interactions with critical roles in gene regulation. The standard techniques include Chromatin Interaction Analysis by Paired-End ...

    Abstract Protein-specific Chromatin Conformation Capture (3C)-based technologies have become essential for identifying distal genomic interactions with critical roles in gene regulation. The standard techniques include Chromatin Interaction Analysis by Paired-End Tag (ChIA-PET), in situ Hi-C followed by chromatin immunoprecipitation (HiChIP) also known as PLAC-seq. To identify chromatin interactions from these data, a variety of computational methods have emerged. Although these state-of-art methods address many issues with loop calling, only few methods can fit different data types simultaneously, and the accuracy as well as the efficiency these approaches remains limited. Here we have generated a pipeline, MMCT-Loop, which ensures the accurate identification of strong loops as well as dynamic or weak loops through a mixed model. MMCT-Loop outperforms existing methods in accuracy, and the detected loops show higher activation functionality. To highlight the utility of MMCT-Loop, we applied it to conformational data derived from neural stem cell (NSCs) and uncovered several previously unidentified regulatory regions for key master regulators of stem cell identity. MMCT-Loop is an accurate and efficient loop caller for targeted conformation capture data, which supports raw data or pre-processed valid pairs as input, the output interactions are formatted and easily uploaded to a genome browser for visualization.
    MeSH term(s) Chromatin/chemistry ; Chromatin/genetics ; Chromatin Immunoprecipitation/methods ; Chromosomes ; Genome ; Genomics/methods ; Genetic Techniques
    Chemical Substances Chromatin
    Language English
    Publishing date 2024-01-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkae029
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: Bacon

    Li Tang / Matthew C. Hill / Patrick T. Ellinor / Min Li

    Genome Biology, Vol 23, Iss 1, Pp 1-

    a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies

    2022  Volume 21

    Abstract: Abstract Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions, and the adoption of ChIP techniques to 3C-based protocols makes it possible to identify long-range interactions. To ... ...

    Abstract Abstract Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions, and the adoption of ChIP techniques to 3C-based protocols makes it possible to identify long-range interactions. To analyze these large and complex datasets, computational methods are undergoing rapid and expansive evolution. Thus, a thorough evaluation of these analytical pipelines is necessary to identify which commonly used algorithms and processing pipelines need to be improved. Here we present a comprehensive benchmark framework, Bacon, to evaluate the performance of several computational methods. Finally, we provide practical recommendations for users working with HiChIP and/or ChIA-PET analyses.
    Keywords Chromatin topology ; HiChIP ; ChIA-PET ; Looping ; Benchmark ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  7. Article ; Online: Integration and dosimetric validation of a dynamic collimation system for pencil beam scanning proton therapy.

    Nelson, Nicholas P / Culberson, Wesley S / Hyer, Daniel E / Geoghegan, Theodore J / Patwardhan, Kaustubh A / Smith, Blake R / Flynn, Ryan T / Gutiérrez, Alonso N / Boland, Thibault / Hill, Patrick M

    Biomedical physics & engineering express

    2023  Volume 9, Issue 6

    Abstract: Objective. ...

    Abstract Objective.
    MeSH term(s) Proton Therapy/methods ; Radiotherapy Planning, Computer-Assisted/methods ; Radiotherapy Dosage ; Phantoms, Imaging ; Radiometry
    Language English
    Publishing date 2023-10-25
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2057-1976
    ISSN (online) 2057-1976
    DOI 10.1088/2057-1976/ad02ff
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Nerve blocks for occipital headaches: A systematic review and meta-analysis.

    Evans, Adam G / Joseph, Kardeem S / Samouil, Marc M / Hill, Dorian S / Ibrahim, Maryo M / Assi, Patrick E / Joseph, Jeremy T / Kassis, Salam Al

    Journal of anaesthesiology, clinical pharmacology

    2023  Volume 39, Issue 2, Page(s) 170–180

    Abstract: Migraine surgeons have identified six "trigger sites" where cranial nerve compression may trigger a migraine. This study investigates the change in headache severity and frequency following nerve block of the occipital trigger site. This PRISMA-compliant ...

    Abstract Migraine surgeons have identified six "trigger sites" where cranial nerve compression may trigger a migraine. This study investigates the change in headache severity and frequency following nerve block of the occipital trigger site. This PRISMA-compliant systematic review of five databases searched from database inception through May 2020 is registered under the PROSPERO ID: CRD42020199369. Only randomized controlled trials utilizing injection treatments for headaches with pain or tenderness in the occipital scalp were included. Pain severity was scored from 0 to 10. Headache frequency was reported as days per week. Included were 12 RCTs treating 586 patients of mean ages ranging from 33.7 to 55.8 years. Meta-analyses of pain severity comparing nerve blocks to baseline showed statistically significant reductions of 2.88 points at 5 to 20 min, 3.74 points at 1 to 6 weeks, and 1.07 points at 12 to 24 weeks. Meta-analyses of pain severity of nerve blocks compared with treatment groups of neurolysis, pulsed radiofrequency, and botulinum toxin type A showed similar headache pain severity at 1 to 2 weeks, and inferior improvements compared with the treatment groups after 2 weeks. Meta-analyses of headache frequency showed statistically significant reductions at 1 to 6-week follow-ups as compared with baseline and at 1 to 6 weeks as compared with inactive control injections. The severity and frequency of occipital headaches are reduced following occipital nerve blocks. This improvement is used to predict the success of migraine surgery. Future research should investigate spinous process injections with longer follow-up.
    Language English
    Publishing date 2023-04-25
    Publishing country India
    Document type Journal Article ; Review
    ZDB-ID 1401760-x
    ISSN 0970-9185
    ISSN 0970-9185
    DOI 10.4103/joacp.JOACP_62_21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4830: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
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  9. Article ; Online: Investigating aperture-based approximations to model a focused dynamic collimation system for pencil beam scanning proton therapy.

    Nelson, Nicholas P / Culberson, Wesley S / Hyer, Daniel E / Smith, Blake R / Flynn, Ryan T / Hill, Patrick M

    Biomedical physics & engineering express

    2022  Volume 8, Issue 2

    Abstract: ... ...

    Abstract Purpose
    MeSH term(s) Monte Carlo Method ; Phantoms, Imaging ; Proton Therapy ; Radiotherapy Dosage ; Radiotherapy Planning, Computer-Assisted/methods
    Language English
    Publishing date 2022-02-18
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 2057-1976
    ISSN (online) 2057-1976
    DOI 10.1088/2057-1976/ac525f
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Dosimetric delivery validation of dynamically collimated pencil beam scanning proton therapy.

    Nelson, Nicholas P / Culberson, Wesley S / Hyer, Daniel E / Geoghegan, Theodore J / Patwardhan, Kaustubh A / Smith, Blake R / Flynn, Ryan T / Yu, Jen / Gutiérrez, Alonso N / Hill, Patrick M

    Physics in medicine and biology

    2023  Volume 68, Issue 5

    Abstract: ... ...

    Abstract Objective
    MeSH term(s) Radiotherapy Planning, Computer-Assisted/methods ; Proton Therapy/methods ; Radiotherapy Dosage ; Phantoms, Imaging ; Monte Carlo Method
    Language English
    Publishing date 2023-02-20
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 208857-5
    ISSN 1361-6560 ; 0031-9155
    ISSN (online) 1361-6560
    ISSN 0031-9155
    DOI 10.1088/1361-6560/acb6cd
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 199: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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