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Book ; Online: (Table S1) Chronostratigraphic constrains for sediment core AND1-1B, supplementary data to: Naish, Tim R; Powell, Ross; Levy, R; Wilson, Gary S; Scherer, Reed P; Talarico, Franco; Krissek, Lawrence A; Niessen, Frank; Pompilio, Massimo; Wilson, Terry; Carter, Lionel; DeConto, Robert M; Huybers, P; McKay, R; Pollard, David; Ross, J; Winter, Diane M; Barrett, Peter J; Browne, G; Cody, R; Cowan, Ellen A; Crampton, J; Dunbar, Gavin B; Dunbar, N; Florindo, Fabio; Gebhardt, Andrea Catalina; Graham, IJ; Hannah, Mike J; Hansaraj, D; Harwood, David M; Helling, D; Henrys, Stuart; Hinnov, L; Kuhn, Gerhard; Kyle, Philip R; Läufer, Andreas L; Maffioli, P; Magens, Diana; Mandernack, Kevin W; McIntosh, WC; Millan, C; Morin, Roger H; Ohneiser, Christian; Paulsen, Timothy S; Persico, Davide; Raine, J Ian; Reed, J; Riesselman, C; Sagnotti, Leo; Schmitt, D R; Sjunneskog, C; Strong, P; Taviani, Marco; Vogel, Stefan; Wilch, T; Williams, Trevor (2009): Obliquity-paced Pliocene West Antarctic ice sheet oscillations. Nature, 458(7236), 322-329

Naish, Tim R / Krissek, Lawrence A / Levy, R / Niessen, Frank / Pompilio, Massimo / Powell, Ross / Scherer, Reed P / Talarico, Franco / Wilson, Gary S / al., et

2009

Abstract: ... from the upper 600 m of the AND-1B sediment core recovered from beneath the northwest part of the Ross ice shelf ... and atmospheric CO2 concentration was as high as ~400 p.p.m.v. (van der Burgh et al., 1993, doi:10 ... that simulates fluctuations in Antarctic ice volume of up to +7 m in equivalent sea level associated ...

Abstract	Thirty years after oxygen isotope records from microfossils deposited in ocean sediments confirmed the hypothesis that variations in the Earth's orbital geometry control the ice ages (Hays et al., 1976, doi:10.1126/science.194.4270.1121), fundamental questions remain over the response of the Antarctic ice sheets to orbital cycles (Raymo and Huybers, 2008, doi:10.1038/nature06589). Furthermore, an understanding of the behaviour of the marine-based West Antarctic ice sheet (WAIS) during the 'warmer-than-present' early-Pliocene epoch (~5-3 Myr ago) is needed to better constrain the possible range of ice-sheet behaviour in the context of future global warming (Solomon et al., 2007). Here we present a marine glacial record from the upper 600 m of the AND-1B sediment core recovered from beneath the northwest part of the Ross ice shelf by the ANDRILL programme and demonstrate well-dated, ~40-kyr cyclic variations in ice-sheet extent linked to cycles in insolation influenced by changes in the Earth's axial tilt (obliquity) during the Pliocene. Our data provide direct evidence for orbitally induced oscillations in the WAIS, which periodically collapsed, resulting in a switch from grounded ice, or ice shelves, to open waters in the Ross embayment when planetary temperatures were up to ~3° C warmer than today ( Kim and Crowley, 2000, doi:10.1029/1999PA000459) and atmospheric CO2 concentration was as high as ~400 p.p.m.v. (van der Burgh et al., 1993, doi:10.1126/science.260.5115.1788, Raymo et al., 1996, doi:10.1016/0377-8398(95)00048-8). The evidence is consistent with a new ice-sheet/ice-shelf model (Pollard and DeConto, 2009, doi:10.1038/nature07809) that simulates fluctuations in Antarctic ice volume of up to +7 m in equivalent sea level associated with the loss of the WAIS and up to +3 m in equivalent sea level from the East Antarctic ice sheet, in response to ocean-induced melting paced by obliquity. During interglacial times, diatomaceous sediments indicate high surface-water productivity, minimal summer sea ice and air temperatures above freezing, suggesting an additional influence of surface melt (Huybers, 2006, doi:10.1126/science.1125249) under conditions of elevated CO2.
Language	English
Dates of publication	2009-9999
Size	Online-Ressource
Publisher	PANGAEA - Data Publisher for Earth & Environmental Science
Publishing place	Bremen/Bremerhaven
Document type	Book ; Online
Note	This dataset is supplement to doi:10.1038/nature07867
DOI	10.1594/PANGAEA.769658
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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Book ; Online: Chronostratigraphy of sediment core CRP-2/2A (Table 1), supplementary data to: Wilson, Gary S; Bohaty, Steven M; Fielding, Christopher R; Florindo, Fabio; Hannah, Mike J; Harwood, David M; McIntosh, WC; Naish, Tim R; Roberts, Andrew P; Sagnotti, Leo; Scherer, Reed P; Strong, C Percy; Versub, KL; Villa, Giuliana; Watkins, David K; Webb, Peter-Noel; Woolfe, Ken (2000): Chronostratigraphy of CRP-2/2A, Victoria Land Basin, Antarctica. Terra Antartica, 7(4), 647-654

Wilson, Gary S / Bohaty, Steven M / Fielding, Christopher R / Florindo, Fabio / Hannah, Mike J / Harwood, David M / McIntosh, WC / Naish, Tim R / Roberts, Andrew P / al., et

2000

Abstract: The 624.15 m glaciomarine sedimentary succession recovered in the CRP-2/2A drillcore comprises ... possible, all of which suggest that sediment accumulation rates averaged ~180 m/m.y. between unconformities ... straightforward and average sedimentation rates were much higher (>1000 m/m.y.). Between 306.65 mbsf and ...

Abstract	The 624.15 m glaciomarine sedimentary succession recovered in the CRP-2/2A drillcore comprises lower Oligocene (<c. 31 Ma) to lower Miocene (18.5 Ma) strata that are overlain by a thin succession of Pliocene and Pleistocene strata. The age model for the CRP-2/2A drillhole, as presented in this paper, is based on combined microfossil biostratigraphy. 40Ar/39Ar age on volcanic material, 87Sr/86Sr analyses on mollusc shells, and correlation of a magnetic polarity zonation to the magnetic polarity time scale (MPTS). Between 25.92 and 109.05 metres below sea floor (mbsf), several alternative correlations to the MPTS are possible, all of which suggest that sediment accumulation rates averaged ~180 <mark>m/m.y. between unconformities, although actual sedimentation rates may have been higher. Between 109.05 and 306.65 mbsf, the age model is straightforward and average sedimentation rates were much higher (>1000 m/m.y.). Between 306.65 mbsf and the bottom of the drillcore (624.15 mbsf), fewer datums are available to constrain the age model and unique correlation with the MPTS is not possible, although high average sediment accumulation rates are likely. A significant unconformity is identified at 306.65 mbsf, which may represent as much as 5 m.y. of missing time. Additional unconformities at 25.92 and 130.27 mbsf account for c. 16 and 2.5 m.y. of missing time, respectively. The Oligocene-lower Miocene interval documented in the CRP-2/2A drillcore spans about 13 million years, however, it is possible that more time is missing in sequence-bounding unconformities than is represented in the stratigraphic record recovered in the CRP-2/2A drillcore.
Language	English
Dates of publication	2000-9999
Size	Online-Ressource
Publisher	PANGAEA - Data Publisher for Earth & Environmental Science
Publishing place	Bremen/Bremerhaven
Document type	Book ; Online
Note	This dataset is supplement to hdl:10013/epic.28244.d001
DOI	10.1594/PANGAEA.189249
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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Article ; Online: Advances in COPD imaging using CT and MRI: linkage with lung physiology and clinical outcomes.

Elbehairy, Amany F / Marshall, Helen / Naish, Josephine H / Wild, Jim M / Parraga, Grace / Horsley, Alexander / Vestbo, Jørgen

The European respiratory journal

2024 Volume 63, Issue 5

Abstract: Recent years have witnessed major advances in lung imaging in patients with COPD. These include significant refinements in images obtained by computed tomography (CT) scans together with the introduction of new techniques and software that aim for ... ...

Abstract	Recent years have witnessed major advances in lung imaging in patients with COPD. These include significant refinements in images obtained by computed tomography (CT) scans together with the introduction of new techniques and software that aim for obtaining the best image whilst using the lowest possible radiation dose. Magnetic resonance imaging (MRI) has also emerged as a useful radiation-free tool in assessing structural and more importantly functional derangements in patients with well-established COPD and smokers without COPD, even before the existence of overt changes in resting physiological lung function tests. Together, CT and MRI now allow objective quantification and assessment of structural changes within the airways, lung parenchyma and pulmonary vessels. Furthermore, CT and MRI can now provide objective assessments of regional lung ventilation and perfusion, and multinuclear MRI provides further insight into gas exchange; this can help in structured decisions regarding treatment plans. These advances in chest imaging techniques have brought new insights into our understanding of disease pathophysiology and characterising different disease phenotypes. The present review discusses, in detail, the advances in lung imaging in patients with COPD and how structural and functional imaging are linked with common resting physiological tests and important clinical outcomes.
MeSH term(s)	Humans ; Pulmonary Disease, Chronic Obstructive/diagnostic imaging ; Pulmonary Disease, Chronic Obstructive/physiopathology ; Magnetic Resonance Imaging/methods ; Tomography, X-Ray Computed/methods ; Lung/diagnostic imaging ; Lung/physiopathology ; Respiratory Function Tests
Language	English
Publishing date	2024-05-02
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	639359-7
ISSN	1399-3003 ; 0903-1936
ISSN (online)	1399-3003
ISSN	0903-1936
DOI	10.1183/13993003.01010-2023
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Article ; Online: Feasibility of dynamic T

Kim, Mina / Naish, Josephine H / Needleman, Sarah H / Tibiletti, Marta / Taylor, Yohn / O'Connor, James P B / Parker, Geoff J M

Magnetic resonance in medicine

2023 Volume 91, Issue 3, Page(s) 972–986

Abstract: Purpose: To demonstrate proof-of-concept of a T: Methods: We performed sequence-specific simulations for protocol optimisation and acquired free-breathing OE-MRI data from 16 healthy subjects using a dual-echo RF-spoiled gradient echo approach at 3T ... ...

Abstract	Purpose: To demonstrate proof-of-concept of a T Methods: We performed sequence-specific simulations for protocol optimisation and acquired free-breathing OE-MRI data from 16 healthy subjects using a dual-echo RF-spoiled gradient echo approach at 3T across two institutions. Non-linear registration and tissue density correction were applied. Derived metrics included percent signal enhancement (PSE), ∆R Results: Simulations and experimental data show negative contrast upon oxygen inhalation, due to substantial dominance of ∆R Conclusion: Our results demonstrate the feasibility of a T
MeSH term(s)	Humans ; Oxygen ; Reproducibility of Results ; Feasibility Studies ; Magnetic Resonance Imaging/methods ; Lung/diagnostic imaging
Chemical Substances	Oxygen (S88TT14065)
Language	English
Publishing date	2023-11-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	605774-3
ISSN	1522-2594 ; 0740-3194
ISSN (online)	1522-2594
ISSN	0740-3194
DOI	10.1002/mrm.29914
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Article ; Online: Independent component analysis (ICA) applied to dynamic oxygen-enhanced MRI (OE-MRI) for robust functional lung imaging at 3 T.

Needleman, Sarah H / Kim, Mina / McClelland, Jamie R / Naish, Josephine H / Tibiletti, Marta / O'Connor, James P B / Parker, Geoff J M

Magnetic resonance in medicine

2023 Volume 91, Issue 3, Page(s) 955–971

Abstract: Purpose: Dynamic lung oxygen-enhanced MRI (OE-MRI) is challenging due to the presence of confounding signals and poor signal-to-noise ratio, particularly at 3 T. We have created a robust pipeline utilizing independent component analysis (ICA) to ... ...

Abstract	Purpose: Dynamic lung oxygen-enhanced MRI (OE-MRI) is challenging due to the presence of confounding signals and poor signal-to-noise ratio, particularly at 3 T. We have created a robust pipeline utilizing independent component analysis (ICA) to automatically extract the oxygen-induced signal change from confounding factors to improve the accuracy and sensitivity of lung OE-MRI. Methods: Dynamic OE-MRI was performed on healthy participants using a dual-echo multi-slice spoiled gradient echo sequence at 3 T and cyclical gas delivery. ICA was applied to each echo within a thoracic mask. The ICA component relating to the oxygen-enhancement signal was automatically identified using correlation analysis. The oxygen-enhancement component was reconstructed, and the percentage signal enhancement (PSE) was calculated. The lung PSE of current smokers was compared with nonsmokers; scan-rescan repeatability, ICA pipeline repeatability, and reproducibility between two vendors were assessed. Results: ICA successfully extracted a consistent oxygen-enhancement component for all participants. Lung tissue and oxygenated blood displayed the opposite oxygen-induced signal enhancements. A significant difference in PSE was observed between the lungs of current smokers and nonsmokers. The scan-rescan repeatability and the ICA pipeline repeatability were good. Conclusion: The developed pipeline demonstrated sensitivity to the signal enhancements of the lung tissue and oxygenated blood at 3 T. The difference in lung PSE between current smokers and nonsmokers indicates a likely sensitivity to lung function alterations that may be seen in mild pathology, supporting future use of our methods in patient studies.
MeSH term(s)	Humans ; Oxygen ; Reproducibility of Results ; Lung/diagnostic imaging ; Magnetic Resonance Imaging/methods
Chemical Substances	Oxygen (S88TT14065)
Language	English
Publishing date	2023-11-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	605774-3
ISSN	1522-2594 ; 0740-3194
ISSN (online)	1522-2594
ISSN	0740-3194
DOI	10.1002/mrm.29912
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Article ; Online: The formation and function of the neutrophil phagosome

Naish, Emily / Wood, Alexander J. T. / Stewart, Andrew P. / Routledge, Matthew / Morris, Andrew Conway / Chilvers, E. R. / Lodge, Katharine M.

Immunological Reviews 2023 Mar., v. 314, no. 1, p. 158-180

2023 , Page(s) 158–180

Abstract: Neutrophils are the most abundant circulating leukocyte and are crucial to the initial innate immune response to infection. One of their key pathogen‐eliminating mechanisms is phagocytosis, the process of particle engulfment into a vacuole‐like structure ...

Abstract	Neutrophils are the most abundant circulating leukocyte and are crucial to the initial innate immune response to infection. One of their key pathogen‐eliminating mechanisms is phagocytosis, the process of particle engulfment into a vacuole‐like structure called the phagosome. The antimicrobial activity of the phagocytic process results from a collaboration of multiple systems and mechanisms within this organelle, where a complex interplay of ion fluxes, pH, reactive oxygen species, and antimicrobial proteins creates a dynamic antimicrobial environment. This complexity, combined with the difficulties of studying neutrophils ex vivo, has led to gaps in our knowledge of how the neutrophil phagosome optimizes pathogen killing. In particular, controversy has arisen regarding the relative contribution and integration of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase‐derived antimicrobial agents and granule‐delivered antimicrobial proteins. Clinical syndromes arising from dysfunction in these systems in humans allow useful insight into these mechanisms, but their redundancy and synergy add to the complexity. In this article, we review the current knowledge regarding the formation and function of the neutrophil phagosome, examine new insights into the phagosomal environment that have been permitted by technological advances in recent years, and discuss aspects of the phagocytic process that are still under debate.
Keywords	NADP (coenzyme) ; antimicrobial properties ; neutrophils ; pH ; pathogens ; phagocytosis ; phagosomes ; reactive oxygen species
Language	English
Dates of publication	2023-03
Size	p. 158-180
Publishing place	John Wiley & Sons, Inc
Document type	Article ; Online
Note	REVIEW
ZDB-ID	391796-4
ISSN	1600-065X ; 0105-2896
ISSN (online)	1600-065X
ISSN	0105-2896
DOI	10.1111/imr.13173
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Article ; Online: Imaging human lung perfusion with contrast media: A meta-analysis.

Edwards, Lucy / Waterton, John C / Naish, Josephine / Short, Christopher / Semple, Thomas / Jm Parker, Geoff / Tibiletti, Marta

European journal of radiology

2023 Volume 164, Page(s) 110850

Abstract: Purpose: To pool and summarise published data of pulmonary blood flow (PBF), pulmonary blood volume (PBV) and mean transit time (MTT) of the human lung, obtained with perfusion MRI or CT to provide reliable reference values of healthy lung tissue. In ... ...

Abstract	Purpose: To pool and summarise published data of pulmonary blood flow (PBF), pulmonary blood volume (PBV) and mean transit time (MTT) of the human lung, obtained with perfusion MRI or CT to provide reliable reference values of healthy lung tissue. In addition, the available data regarding diseased lung was investigated. Methods: PubMed was systematically searched to identify studies that quantified PBF/PBV/MTT in the human lung by injection of contrast agent, imaged by MRI or CT. Only data analysed by 'indicator dilution theory' were considered numerically. Weighted mean (wM), weighted standard deviation (wSD) and weighted coefficient of variance (wCoV) were obtained for healthy volunteers (HV), weighted according to the size of the datasets. Signal to concentration conversion method, breath holding method and presence of 'pre-bolus' were noted. Results: PBV was obtained from 313 measurements from 14 publications (wM: 13.97 ml/100 ml, wSD: 4.21 ml/100 ml, wCoV 0.30). MTT was obtained from 188 measurements from 10 publications (wM: 5.91 s, wSD: 1.84 s wCoV 0.31). PBF was obtained from 349 measurements from 14 publications (wM: 246.26 ml/100 ml ml/min, wSD: 93.13 ml/100 ml ml/min, wCoV 0.38). PBV and PBF were higher when the signal was normalised than when it was not. No significant differences were found for PBV and PBF between breathing states or between pre-bolus and no pre-bolus. Data for diseased lung were insufficient for meta-analysis. Conclusion: Reference values for PBF, MTT and PBV were obtained in HV. The literature data are insufficient to draw strong conclusions regarding disease reference values.
MeSH term(s)	Humans ; Contrast Media ; Lung/diagnostic imaging ; Lung/blood supply ; Pulmonary Circulation/physiology ; Magnetic Resonance Imaging/methods ; Perfusion
Chemical Substances	Contrast Media
Language	English
Publishing date	2023-04-27
Publishing country	Ireland
Document type	Systematic Review ; Meta-Analysis ; Journal Article
ZDB-ID	138815-0
ISSN	1872-7727 ; 0720-048X
ISSN (online)	1872-7727
ISSN	0720-048X
DOI	10.1016/j.ejrad.2023.110850
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Article: Medical management of Crohn's disease: a `holding operation'.

Naish, J M

Proceedings of the Royal Society of Medicine

2010 Volume 59, Issue 3, Page(s) 196

Language	English
Publishing date	2010-10-04
Publishing country	England
Document type	Journal Article
ZDB-ID	209243-8
ISSN	0035-9157
ISSN	0035-9157
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Article ; Online: Growth differentiation factor-15 in patients with or at risk of heart failure but before first hospitalisation.

Bradley, Joshua / Schelbert, Erik B / Bonnett, Laura J / Lewis, Gavin A / Lagan, Jakub / Orsborne, Christopher / Brown, Pamela Frances / Black, Nicholas / Naish, Josephine H / Williams, Simon G / McDonagh, Theresa / Schmitt, Matthias / Miller, Christopher A

Heart (British Cardiac Society)

2024 Volume 110, Issue 3, Page(s) 195–201

Abstract: Objective: Identification of patients at risk of adverse outcome from heart failure (HF) at an early stage is a priority. Growth differentiation factor (GDF)-15 has emerged as a potentially useful biomarker. This study sought to identify determinants of ...

Abstract	Objective: Identification of patients at risk of adverse outcome from heart failure (HF) at an early stage is a priority. Growth differentiation factor (GDF)-15 has emerged as a potentially useful biomarker. This study sought to identify determinants of circulating GDF-15 and evaluate its prognostic value, in patients at risk of HF or with HF but before first hospitalisation. Methods: Prospective, longitudinal cohort study of 2166 consecutive patients in stage A-C HF undergoing cardiovascular magnetic resonance and measurement of GDF-15. Multivariable linear regression investigated determinants of GDF-15. Cox proportional hazards modelling, Net Reclassification Improvement and decision curve analysis examined its incremental prognostic value. Primary outcome was a composite of first hospitalisation for HF or all-cause mortality. Median follow-up was 1093 (939-1231) days. Results: Major determinants of GDF-15 were age, diabetes and N-terminal pro-B-type natriuretic peptide, although despite extensive phenotyping, only around half of the variability of GDF-15 could be explained (R Conclusion: In patients at risk of HF, or with HF but before first hospitalisation, GDF-15 provides unique information and is highly predictive of hospitalisation for HF or all-cause mortality, leading to more accurate risk stratification that can improve clinical decision making. Trial registration number: NCT02326324.
MeSH term(s)	Humans ; Prospective Studies ; Growth Differentiation Factor 15 ; Longitudinal Studies ; Heart Failure/diagnosis ; Heart Failure/therapy ; Prognosis ; Biomarkers
Chemical Substances	Growth Differentiation Factor 15 ; Biomarkers
Language	English
Publishing date	2024-01-10
Publishing country	England
Document type	Journal Article
ZDB-ID	1303417-0
ISSN	1468-201X ; 1355-6037
ISSN (online)	1468-201X
ISSN	1355-6037
DOI	10.1136/heartjnl-2023-322857
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Article ; Online: Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis.

Fernandes, Joiselle B / Naish, Matthew / Lian, Qichao / Burns, Robin / Tock, Andrew J / Rabanal, Fernando A / Wlodzimierz, Piotr / Habring, Anette / Nicholas, Robert E / Weigel, Detlef / Mercier, Raphael / Henderson, Ian R

Genome biology

2024 Volume 25, Issue 1, Page(s) 30

Abstract: Background: Centromeres load kinetochore complexes onto chromosomes, which mediate spindle attachment and allow segregation during cell division. Although centromeres perform a conserved cellular function, their underlying DNA sequences are highly ... ...

Abstract	Background: Centromeres load kinetochore complexes onto chromosomes, which mediate spindle attachment and allow segregation during cell division. Although centromeres perform a conserved cellular function, their underlying DNA sequences are highly divergent within and between species. Despite variability in DNA sequence, centromeres are also universally suppressed for meiotic crossover recombination, across eukaryotes. However, the genetic and epigenetic factors responsible for suppression of centromeric crossovers remain to be completely defined. Results: To explore the centromere-proximal meiotic recombination landscape, we map 14,397 crossovers against fully assembled Arabidopsis thaliana (A. thaliana) genomes. A. thaliana centromeres comprise megabase satellite repeat arrays that load nucleosomes containing the CENH3 histone variant. Each chromosome contains a structurally polymorphic region of ~3-4 megabases, which lack crossovers and include the satellite arrays. This polymorphic region is flanked by ~1-2 megabase low-recombination zones. These recombination-suppressed regions are enriched for Gypsy/Ty3 retrotransposons, and additionally contain expressed genes with high genetic diversity that initiate meiotic recombination, yet do not crossover. We map crossovers at high-resolution in proximity to CEN3, which resolves punctate centromere-proximal hotspots that overlap gene islands embedded in heterochromatin. Centromeres are densely DNA methylated and the recombination landscape is remodelled in DNA methylation mutants. We observe that the centromeric low-recombining zones decrease and increase crossovers in CG (met1) and non-CG (cmt3) mutants, respectively, whereas the core non-recombining zones remain suppressed. Conclusion: Our work relates the genetic and epigenetic organization of A. thaliana centromeres and flanking pericentromeric heterochromatin to the zones of crossover suppression that surround the CENH3-occupied satellite repeat arrays.
MeSH term(s)	Arabidopsis/genetics ; DNA Methylation ; Heterochromatin ; Centromere ; Meiosis
Chemical Substances	Heterochromatin
Language	English
Publishing date	2024-01-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-024-03163-4
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