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  1. Article: Transcriptomic biomarkers for predicting response to neoadjuvant treatment in oesophageal cancer.

    Lavery, Anita / Turkington, Richard C

    Gastroenterology report

    2021  Volume 8, Issue 6, Page(s) 411–424

    Abstract: Oesophageal cancer is a devastating disease with poor outcomes and is the sixth leading cause of cancer death worldwide. In the setting of resectable disease, there is clear evidence that neoadjuvant chemotherapy and chemoradiotherapy result in improved ... ...

    Abstract Oesophageal cancer is a devastating disease with poor outcomes and is the sixth leading cause of cancer death worldwide. In the setting of resectable disease, there is clear evidence that neoadjuvant chemotherapy and chemoradiotherapy result in improved survival. Disappointingly, only 15%-30% of patients obtain a histopathological response to neoadjuvant therapy, often at the expense of significant toxicity. There are no predictive biomarkers in routine clinical use in this setting and the ability to stratify patients for treatment could dramatically improve outcomes. In this review, we aim to outline current progress in evaluating predictive transcriptomic biomarkers for neoadjuvant therapy in oesophageal cancer and discuss the challenges facing biomarker development in this setting. We place these issues in the wider context of recommendations for biomarker development and reporting. The majority of studies focus on messenger RNA (mRNA) and microRNA (miRNA) biomarkers. These studies report a range of different genes involved in a wide variety of pathways and biological processes, and this is explained to a large extent by the different platforms and analysis methods used. Many studies are also vastly underpowered so are not suitable for identifying a candidate biomarker. Multiple molecular subtypes of oesophageal cancer have been proposed, although little is known about how these relate to clinical outcomes. We anticipate that the accumulating wealth of genomic and transcriptomic data and clinical trial collaborations in the coming years will provide unique opportunities to stratify patients in this poor-prognosis disease and recommend that future biomarker development incorporates well-designed retrospective and prospective analyses.
    Language English
    Publishing date 2021-01-08
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2710871-5
    ISSN 2052-0034
    ISSN 2052-0034
    DOI 10.1093/gastro/goaa065
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A rapid classification tool for deformities in Atlantic salmon (Salmo salar) embryos.

    Bartlett, Alanah D / Lavery, J Michelle / Nafziger, Jennifer / Cunjak, Richard A

    Journal of fish biology

    2022  Volume 101, Issue 1, Page(s) 317–322

    Abstract: Deformities in fish embryos are important for their survival in later life stages. However, a consistent way to refer to and classify salmonid embryo deformities does not exist. Expanding on reports of alevin deformities, we developed a classification ... ...

    Abstract Deformities in fish embryos are important for their survival in later life stages. However, a consistent way to refer to and classify salmonid embryo deformities does not exist. Expanding on reports of alevin deformities, we developed a classification tool for distinguishing the deformities observed in a collection of preserved Atlantic salmon (Salmo salar) embryos. Deformities were classified based on the deformed body part and a qualitative subtype. This classification tool uses external morphology, requires minimal equipment and can be applied from the first appearance of optic vesicles to hatch.
    MeSH term(s) Animals ; Salmo salar
    Language English
    Publishing date 2022-06-13
    Publishing country England
    Document type Journal Article
    ZDB-ID 410564-3
    ISSN 1095-8649 ; 0022-1112
    ISSN (online) 1095-8649
    ISSN 0022-1112
    DOI 10.1111/jfb.15112
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    In stock of ZB MED Bonn / Germany

    Z 4814: Show issues
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  3. Article ; Online: Bilateral linear red lines on the calves in an infant.

    Lavery, Michael J / Parslew, Richard

    Pediatric dermatology

    2019  Volume 36, Issue 6, Page(s) e108–e109

    MeSH term(s) Clothing/adverse effects ; Constriction ; Diagnosis, Differential ; Erythema/diagnosis ; Erythema/etiology ; Female ; Follow-Up Studies ; Humans ; Infant ; Leg/blood supply ; Leg Dermatoses/diagnosis ; Leg Dermatoses/etiology ; Risk Assessment
    Language English
    Publishing date 2019-04-01
    Publishing country United States
    Document type Case Reports ; Journal Article ; Review
    ZDB-ID 605539-4
    ISSN 1525-1470 ; 0736-8046
    ISSN (online) 1525-1470
    ISSN 0736-8046
    DOI 10.1111/pde.13935
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1882: 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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  4. Article ; Online: Internal Coordinate Normal Mode Analysis: A Strategy To Predict Protein Conformational Transitions.

    Frezza, Elisa / Lavery, Richard

    The journal of physical chemistry. B

    2019  Volume 123, Issue 6, Page(s) 1294–1301

    Abstract: We analyze the capacity of normal mode analysis in internal coordinates' space to generate large-amplitude structural deformations that can describe the conformational changes occurring upon the binding of proteins to other species. We also analyze how ... ...

    Abstract We analyze the capacity of normal mode analysis in internal coordinates' space to generate large-amplitude structural deformations that can describe the conformational changes occurring upon the binding of proteins to other species. We also analyze how many modes need to be studied to capture a given transition and whether a combination of two modes is better than using a single mode. The technique is tested on known unbound-to-bound structural transitions for a set of single- or multidomain proteins. The results suggest that this approach is a promising way to generate structures for protein docking or for more refined molecular dynamics simulations.
    MeSH term(s) Animals ; Escherichia coli K12/chemistry ; Mice ; Models, Chemical ; Protein Conformation ; Proteins/chemistry ; Saccharomyces cerevisiae/chemistry
    Chemical Substances Proteins
    Language English
    Publishing date 2019-02-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.8b11913
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  5. Book ; Online: Chapter 4 The Oceanography and Marine Ecology of Ningaloo, A World Heritage Area

    Vanderklift, Mathew A. / Babcock, Russell C. / Barnes, Peter B. / Cresswell, Anna K. / Feng, Ming / Haywood, Michael D. E. / Holmes, Thomas H. / Lavery, Paul S. / Pillans, Richard D. / Smallwood, Claire B. / Thomson, Damian P. / Tucker, Anton D. / Waples, Kelly / Wilson, Shaun K.

    2020  

    Keywords Marine biology ; Volume, Todd, Swearer, Smith, S, Russell, Review, P, OMBAR, Oceanography, Marine, L, I, Hawkins, Firth, Evans, Biology, Bates,B, Annual, Allcock
    Size 1 Online-Ressource
    Publisher Taylor and Francis
    Document type Book ; Online
    Note English[eng] ; Open Access
    HBZ-ID HT021027040
    ISBN 9780367524722 ; 0367524724
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  6. Article ; Online: Response to: 'Unified definition of relapse-free survival should be used for evaluating survival benefit in oesophageal adenocarcinoma' by Li.

    Lavery, Anita / Blayney, Jaine K / Turkington, Richard C

    Gut

    2020  Volume 70, Issue 3, Page(s) 626

    MeSH term(s) Adenocarcinoma ; Esophageal Neoplasms ; Humans
    Language English
    Publishing date 2020-06-30
    Publishing country England
    Document type Letter ; Comment
    ZDB-ID 80128-8
    ISSN 1468-3288 ; 0017-5749
    ISSN (online) 1468-3288
    ISSN 0017-5749
    DOI 10.1136/gutjnl-2020-322096
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 160: 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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  7. Article ; Online: A Superficial Acral Fibromyxoma Presenting as an Exquisitely Painful Lesion on the Finger.

    Lavery, Michael J / Vasile, Cristina / Bakshi, Arti / Azurdia, Richard M

    Skinmed

    2021  Volume 19, Issue 5, Page(s) 399–400

    MeSH term(s) Fibroma/diagnosis ; Fibroma/pathology ; Fingers/pathology ; Humans ; Upper Extremity/pathology
    Language English
    Publishing date 2021-10-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2171125-2
    ISSN 1751-7125 ; 1540-9740
    ISSN (online) 1751-7125
    ISSN 1540-9740
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6041: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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  8. Article ; Online: Fully 3D Printed Tin Selenide (SnSe) Thermoelectric Generators with Alternating

    Burton, Matthew Richard / Howells, Geraint / Mehraban, Shahin / McGettrick, James D / Lavery, Nicholas / Carnie, Matthew J

    ACS applied energy materials

    2023  Volume 6, Issue 10, Page(s) 5498–5507

    Abstract: Tin selenide (SnSe) has attracted much attention in the field of thermoelectrics since the discovery of the record figure of merit ( ...

    Abstract Tin selenide (SnSe) has attracted much attention in the field of thermoelectrics since the discovery of the record figure of merit (
    Language English
    Publishing date 2023-05-03
    Publishing country United States
    Document type Journal Article
    ISSN 2574-0962
    ISSN (online) 2574-0962
    DOI 10.1021/acsaem.3c00576
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  9. Article ; Online: An overview of acute gastrointestinal side effects of systemic anti-cancer therapy and their management.

    Smith, Padraic / Lavery, Anita / Turkington, Richard C

    Best practice & research. Clinical gastroenterology

    2020  Volume 48-49, Page(s) 101691

    Abstract: Treatment-related acute gastrointestinal toxicities are a common and often debilitating hurdle encountered in the treatment of cancer patients. While the introduction of targeted therapies such as tyrosine kinase inhibitors has led to improvements in ... ...

    Abstract Treatment-related acute gastrointestinal toxicities are a common and often debilitating hurdle encountered in the treatment of cancer patients. While the introduction of targeted therapies such as tyrosine kinase inhibitors has led to improvements in survival outcomes, their use has also been complicated by a high frequency of clinically important adverse effects. Gastrointestinal toxicities such as nausea, vomiting, diarrhoea and hepatotoxicity represent potentially serious adverse events that may necessitate dose reductions, treatment interruptions and cessation of treatment. An improved knowledge of the incidence, pathophysiology, management and prophylaxis of these toxicities is crucial in order to reduce patient morbidity and mortality. In this review, we discuss the main gastrointestinal toxicities associated with chemotherapy and targeted therapies in oncology, outlining their incidence, pathophysiology and expert management guidelines.
    MeSH term(s) Antineoplastic Agents/adverse effects ; Drug-Related Side Effects and Adverse Reactions/drug therapy ; Drug-Related Side Effects and Adverse Reactions/etiology ; Gastrointestinal Diseases/chemically induced ; Gastrointestinal Diseases/therapy ; Humans ; Neoplasms/complications ; Risk Factors
    Chemical Substances Antineoplastic Agents
    Language English
    Publishing date 2020-10-14
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2048181-0
    ISSN 1532-1916 ; 1521-6918
    ISSN (online) 1532-1916
    ISSN 1521-6918
    DOI 10.1016/j.bpg.2020.101691
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    In stock of ZB MED Cologne/Königswinter

    Se 1098: Show issues Location:
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  10. Article ; Online: Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties.

    Corsi, Flavia / Lavery, Richard / Laine, Elodie / Carbone, Alessandra

    PLoS computational biology

    2020  Volume 16, Issue 2, Page(s) e1007624

    Abstract: Interactions between proteins and nucleic acids are at the heart of many essential biological processes. Despite increasing structural information about how these interactions may take place, our understanding of the usage made of protein surfaces by ... ...

    Abstract Interactions between proteins and nucleic acids are at the heart of many essential biological processes. Despite increasing structural information about how these interactions may take place, our understanding of the usage made of protein surfaces by nucleic acids is still very limited. This is in part due to the inherent complexity associated to protein surface deformability and evolution. In this work, we present a method that contributes to decipher such complexity by predicting protein-DNA interfaces and characterizing their properties. It relies on three biologically and physically meaningful descriptors, namely evolutionary conservation, physico-chemical properties and surface geometry. We carefully assessed its performance on several hundreds of protein structures and compared it to several machine-learning state-of-the-art methods. Our approach achieves a higher sensitivity compared to the other methods, with a similar precision. Importantly, we show that it is able to unravel 'hidden' binding sites by applying it to unbound protein structures and to proteins binding to DNA via multiple sites and in different conformations. It is also applicable to the detection of RNA-binding sites, without significant loss of performance. This confirms that DNA and RNA-binding sites share similar properties. Our method is implemented as a fully automated tool, [Formula: see text], freely accessible at: http://www.lcqb.upmc.fr/JET2DNA. We also provide a new dataset of 187 protein-DNA complex structures, along with a subset of 82 associated unbound structures. The set represents the largest body of high-resolution crystallographic structures of protein-DNA complexes, use biological protein assemblies as DNA-binding units, and covers all major types of protein-DNA interactions. It is available at: http://www.lcqb.upmc.fr/PDNAbenchmarks.
    MeSH term(s) Algorithms ; Biological Evolution ; DNA/metabolism ; DNA-Binding Proteins/metabolism ; Machine Learning ; Proteins/metabolism
    Chemical Substances DNA-Binding Proteins ; Proteins ; DNA (9007-49-2)
    Language English
    Publishing date 2020-02-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1007624
    Database MEDical Literature Analysis and Retrieval System OnLINE

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