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Book ; Online: Nd and Pb isotope data for DSDP and ODP sediments from the Bengal Fan, supplementary data to: Clift, Peter D; Shimizu, Nobumichi; Layne, Graham D; Blusztajn, Jerzy S; Gaedicke, Christoph; Schlüter, HU; Clark, MK; Amjad, Shahid (2001): Development of the Indus Fan and its significance for the erosional history of the Western Himalaya and Karakoram. Geological Society of America Bulletin, 113(8), 1039-1051

Clift, Peter D / Amjad, Shahid / Blusztajn, Jerzy S / Clark, MK / Gaedicke, Christoph / Layne, Graham D / Schlüter, HU / Shimizu, Nobumichi

2001

Abstract: Correlation of new multichannel seismic profiles across the upper Indus Fan and Murray Ridge with a dated industrial well on the Pakistan shelf demonstrates that ~40% of the Indus Fan predates the middle Miocene, and ~35% predates uplift of the Murray ... ...

Abstract	Correlation of new multichannel seismic profiles across the upper Indus Fan and Murray Ridge with a dated industrial well on the Pakistan shelf demonstrates that ~40% of the Indus Fan predates the middle Miocene, and ~35% predates uplift of the Murray Ridge (early Miocene, ~22 Ma). The Arabian Sea, in addition to the Makran accretionary complex, was therefore an important repository of sediment from the Indus River system during the Paleogene. Channel and levee complexes are most pronounced after the early Miocene, coincident with an increase in sedimentation rates. Middle Eocene sandstones from Deep Sea Drilling Project Site 224 on the Owen Ridge yield K-feldspars whose Pb isotopic composition, measured by in situ ion microprobe methods, indicates an origin in, or north of, the Indus suture zone. This observation requires that India-Asia collision had occurred by this time and that an Indus River system, feeding material from the suture zone into the basin, was active soon after collision. Pleistocene provenance was similar to that during the Eocene, albeit with greater contribution from the Karakoram. A mass balance of the erosional record on land with deposition in the fan and associated basins suggests that only ~40% of the Neogene sediment in the fan is derived from the Indian plate.
Language	English
Dates of publication	2001-9999
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:10.1130/0016-7606(2001)113<1039:DOTIFA>2.0.CO;2
DOI	10.1594/PANGAEA.717745
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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Article ; Online: Highly Dynamic Gene Family Evolution Suggests Changing Roles for PON Genes Within Metazoa.

Lucas, Sarah A M / Graham, Allie M / Presnell, Jason S / Clark, Nathan L

Genome biology and evolution

2023 Volume 15, Issue 2

Abstract: Change in gene family size has been shown to facilitate adaptation to different selective pressures. This includes gene duplication to increase dosage or diversification of enzymatic substrates and gene deletion due to relaxed selection. We recently ... ...

Abstract	Change in gene family size has been shown to facilitate adaptation to different selective pressures. This includes gene duplication to increase dosage or diversification of enzymatic substrates and gene deletion due to relaxed selection. We recently found that the PON1 gene, an enzyme with arylesterase and lactonase activity, was lost repeatedly in different aquatic mammalian lineages, suggesting that the PON gene family is responsive to environmental change. We further investigated if these fluctuations in gene family size were restricted to mammals and approximately when this gene family was expanded within mammals. Using 112 metazoan protein models, we explored the evolutionary history of the PON family to characterize the dynamic evolution of this gene family. We found that there have been multiple, independent expansion events in tardigrades, cephalochordates, and echinoderms. In addition, there have been partial gene loss events in monotremes and sea cucumbers and what appears to be complete loss in arthropods, urochordates, platyhelminths, ctenophores, and placozoans. In addition, we show the mammalian expansion to three PON paralogs occurred in the ancestor of all mammals after the divergence of sauropsida but before the divergence of monotremes from therians. We also provide evidence of a novel PON expansion within the brushtail possum. In the face of repeated expansions and deletions in the context of changing environments, we suggest a range of selective pressures, including pathogen infection and mitigation of oxidative damage, are likely influencing the diversification of this dynamic gene family across metazoa.
MeSH term(s)	Animals ; Vertebrates/genetics ; Proteins/genetics ; Gene Duplication ; Arthropods/genetics ; Mammals ; Evolution, Molecular
Chemical Substances	Proteins
Language	English
Publishing date	2023-01-31
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evad011
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: CD1a and bound lipids drive T-cell responses in human skin disease.

Ogg, Graham S / Rossjohn, Jamie / Clark, Rachael A / Moody, D Branch

European journal of immunology

2023 Volume 53, Issue 10, Page(s) e2250333

Abstract: In addition to serving as the main physical barrier with the outside world, human skin is abundantly infiltrated with resident αβ T cells that respond differently to self, infectious, microbiome, and noxious stimuli. To study skin T cells during ... ...

Abstract	In addition to serving as the main physical barrier with the outside world, human skin is abundantly infiltrated with resident αβ T cells that respond differently to self, infectious, microbiome, and noxious stimuli. To study skin T cells during infection and inflammation, experimental biologists track T-cell surface phenotypes and effector functions, which are often interpreted with the untested assumption that MHC proteins and peptide antigens drive measured responses. However, a broader perspective is that CD1 proteins also activate human T cells, and in skin, Langerhans cells (LCs) are abundant antigen presenting cells that express extremely high levels of CD1a. The emergence of new experimental tools, including CD1a tetramers carrying endogenous lipids, now show that CD1a-reactive T cells comprise a large population of resident T cells in human skin. Here, we review studies showing that skin-derived αβ T cells directly recognize CD1a proteins, and certain bound lipids, such as contact dermatitis allergens, trigger T-cell responses. Other natural skin lipids inhibit CD1a-mediated T-cell responses, providing an entry point for the development of therapeutic lipids that block T-cell responses. Increasing evidence points to a distinct role of CD1a in type 2 and 22 T-cell responses, providing new insights into psoriasis, contact dermatitis, and other T-cell-mediated skin diseases.
MeSH term(s)	Humans ; T-Lymphocytes ; Skin ; Skin Diseases ; Dermatitis, Contact ; Lipids ; Antigens, CD1/metabolism
Chemical Substances	Lipids ; Antigens, CD1
Language	English
Publishing date	2023-08-11
Publishing country	Germany
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	120108-6
ISSN	1521-4141 ; 0014-2980
ISSN (online)	1521-4141
ISSN	0014-2980
DOI	10.1002/eji.202250333
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Article ; Online: Blastocystis.

Stensvold, Christen Rune / Tan, Kevin S W / Clark, C Graham

Trends in parasitology

2020 Volume 36, Issue 3, Page(s) 315–316

MeSH term(s)	Animals ; Blastocystis/classification ; Blastocystis/genetics ; Blastocystis/growth & development ; Blastocystis/physiology ; Blastocystis Infections/epidemiology ; Blastocystis Infections/parasitology ; Blastocystis Infections/transmission ; Humans
Language	English
Publishing date	2020-01-27
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2036227-4
ISSN	1471-5007 ; 1471-4922
ISSN (online)	1471-5007
ISSN	1471-4922
DOI	10.1016/j.pt.2019.12.008
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Article ; Online: Corrigendum: Neuro-PASC is characterized by enhanced CD4+ and diminished CD8+ T cell responses to SARSCoV-2 Nucleocapsid protein.

Visvabharathy, Lavanya / Hanson, Barbara A / Orban, Zachary S / Lim, Patrick H / Palacio, Nicole M / Jimenez, Millenia / Clark, Jeffrey R / Graham, Edith L / Liotta, Eric M / Tachas, George / Penaloza-MacMaster, Pablo / Koralnik, Igor J

Frontiers in immunology

2023 Volume 14, Page(s) 1275925

Abstract: This corrects the article DOI: 10.3389/fimmu.2023.1155770.]. ...

Abstract	[This corrects the article DOI: 10.3389/fimmu.2023.1155770.].
Language	English
Publishing date	2023-08-24
Publishing country	Switzerland
Document type	Published Erratum
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1275925
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Article ; Online: Synchronous retreat of Thwaites and Pine Island glaciers in response to external forcings in the presatellite era.

Clark, Rachel W / Wellner, Julia S / Hillenbrand, Claus-Dieter / Totten, Rebecca L / Smith, James A / Miller, Lauren E / Larter, Robert D / Hogan, Kelly A / Graham, Alastair G C / Nitsche, Frank O / Lehrmann, Asmara A / Lepp, Allison P / Kirkham, James D / Fitzgerald, Victoria T / Garcia-Barrera, Georgina / Ehrmann, Werner / Wacker, Lukas

Proceedings of the National Academy of Sciences of the United States of America

2024 Volume 121, Issue 11, Page(s) e2211711120

Abstract: Today, relatively warm Circumpolar Deep Water is melting Thwaites Glacier at the base of its ice shelf and at the grounding zone, contributing to significant ice retreat. Accelerating ice loss has been observed since the 1970s; however, it is unclear ... ...

Abstract	Today, relatively warm Circumpolar Deep Water is melting Thwaites Glacier at the base of its ice shelf and at the grounding zone, contributing to significant ice retreat. Accelerating ice loss has been observed since the 1970s; however, it is unclear when this phase of significant melting initiated. We analyzed the marine sedimentary record to reconstruct Thwaites Glacier's history from the early Holocene to present. Marine geophysical surveys were carried out along the floating ice-shelf margin to identify core locations from various geomorphic settings. We use sedimentological data and physical properties to define sedimentary facies at seven core sites. Glaciomarine sediment deposits reveal that the grounded ice in the Amundsen Sea Embayment had already retreated to within ~45 km of the modern grounding zone prior to ca. 9,400 y ago. Sediments deposited within the past 100+ y record abrupt changes in environmental conditions. On seafloor highs, these shifts document ice-shelf thinning initiating at least as early as the 1940s. Sediments recovered from deep basins reflect a transition from ice proximal to slightly more distal conditions, suggesting ongoing grounding-zone retreat since the 1950s. The timing of ice-shelf unpinning from the seafloor for Thwaites Glacier coincides with similar records from neighboring Pine Island Glacier. Our work provides robust new evidence that glacier retreat in the Amundsen Sea was initiated in the mid-twentieth century, likely associated with climate variability.
Language	English
Publishing date	2024-02-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2211711120
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Article ; Online: High Incidence of Acute Kidney Injury Following Antibiotic-Loaded Spacer Insertion for Periprosthetic Joint Infection: An Updated Review of the Literature.

Thomas, Terence L / Kothari, Purab D / Baker, Colin M / Tarabichi, Saad / Clark, Sean C / Goh, Graham S

The Journal of arthroplasty

2023 Volume 39, Issue 2, Page(s) 549–558.e3

Abstract: Background: The use of antibiotic-impregnated cement during 2-stage revision arthroplasty for periprosthetic joint infection poses a risk of renal complications following spacer insertion. This systematic review aimed to investigate the rate of acute ... ...

Abstract	Background: The use of antibiotic-impregnated cement during 2-stage revision arthroplasty for periprosthetic joint infection poses a risk of renal complications following spacer insertion. This systematic review aimed to investigate the rate of acute kidney injury (AKI) following antibiotic-loaded spacer insertion and to identify risk factors associated with this complication. Methods: A systematic review was performed using PubMed, Cochrane Central, and Scopus databases. All clinical studies that documented renal complications following antibiotic-loaded spacer insertion for periprosthetic knee (total knee arthroplasty [TKA]) or hip (total hip arthroplasty [THA]) infection were included. Articles that combined THA and TKA outcomes were also included and labeled "THA + TKA." Descriptive statistics were analyzed when data were available. Results: There were 24 studies (9 THA, 7 TKA, 8 THA + TKA) included. The mean incidences of spacer-related AKI across THA, TKA, and THA + TKA cohorts were 4.2 (range, 0 to 10%), 14 (range, 0 to 19%), and 27% (range, 0 to 35%), respectively. The most common patient-related risk factors for AKI were underlying chronic kidney disease or high baseline creatinine, low preoperative hemoglobin, and blood transfusion requirement. Spacer-related risk factors included high antibiotic dosage (>3.6 g/cement batch) and antibiotic type. While most recovered without complication, select patients required hemodialysis for acute management (2 THA, 18 THA + TKA) and/or developed chronic kidney disease (8 TKA, 8 THA). Conclusion: The rate of AKI following spacer insertion was high and likely under-reported in the literature. Surgeons should be cognizant of this devastating complication and should closely monitor at-risk patients for AKI following antibiotic-loaded spacer insertion.
MeSH term(s)	Humans ; Anti-Bacterial Agents ; Incidence ; Prosthesis-Related Infections/drug therapy ; Prosthesis-Related Infections/epidemiology ; Prosthesis-Related Infections/etiology ; Reoperation/adverse effects ; Arthroplasty, Replacement, Hip/adverse effects ; Arthritis, Infectious/etiology ; Acute Kidney Injury/chemically induced ; Acute Kidney Injury/epidemiology ; Renal Insufficiency, Chronic/complications ; Retrospective Studies
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2023-08-26
Publishing country	United States
Document type	Systematic Review ; Journal Article
ZDB-ID	632770-9
ISSN	1532-8406 ; 0883-5403
ISSN (online)	1532-8406
ISSN	0883-5403
DOI	10.1016/j.arth.2023.08.055
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Article ; Online: Unraveling the Ultrafast Photochemical Dynamics of Nitrobenzene in Aqueous Solution.

Lau, Nicholas A / Ghosh, Deborin / Bourne-Worster, Susannah / Kumar, Rhea / Whitaker, William A / Heitland, Jonas / Davies, Julia A / Karras, Gabriel / Clark, Ian P / Greetham, Gregory M / Worth, Graham A / Orr-Ewing, Andrew J / Fielding, Helen H

Journal of the American Chemical Society

2024 Volume 146, Issue 15, Page(s) 10407–10417

Abstract: ... find that hydrogen bonding between nitrobenzene and surrounding water molecules slows the S ...

Abstract	Nitroaromatic compounds are major constituents of the brown carbon aerosol particles in the troposphere that absorb near-ultraviolet (UV) and visible solar radiation and have a profound effect on the Earth's climate. The primary sources of brown carbon include biomass burning, forest fires, and residential burning of biofuels, and an important secondary source is photochemistry in aqueous cloud and fog droplets. Nitrobenzene is the smallest nitroaromatic molecule and a model for the photochemical behavior of larger nitroaromatic compounds. Despite the obvious importance of its droplet photochemistry to the atmospheric environment, there have not been any detailed studies of the ultrafast photochemical dynamics of nitrobenzene in aqueous solution. Here, we combine femtosecond transient absorption spectroscopy, time-resolved infrared spectroscopy, and quantum chemistry calculations to investigate the primary steps following the near-UV (λ ≥ 340 nm) photoexcitation of aqueous nitrobenzene. To understand the role of the surrounding water molecules in the photochemical dynamics of nitrobenzene, we compare the results of these investigations with analogous measurements in solutions of methanol, acetonitrile, and cyclohexane. We find that vibrational energy transfer to the aqueous environment quenches internal excitation, and therefore, unlike the gas phase, we do not observe any evidence for formation of photoproducts on timescales up to 500 ns. We also find that hydrogen bonding between nitrobenzene and surrounding water molecules slows the S
Language	English
Publishing date	2024-04-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.3c13826
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Article ; Online: Disordered interfaces of alkaline aluminate salt hydrates provide glimpses of Al

Graham, Trent R / Pouvreau, Maxime / Gorniak, Rafal / Wang, Hsiu-Wen / Nienhuis, Emily T / Miller, Quin R S / Liu, Jian / Prange, Micah P / Schenter, Gregory K / Pearce, Carolyn I / Rosso, Kevin M / Clark, Aurora E

Journal of colloid and interface science

2023 Volume 637, Page(s) 326–339

Abstract: Hypothesis: The precipitation and dissolution of aluminum-bearing mineral phases in aqueous systems often proceed via changes in both aluminum coordination number and connectivity, complicating molecular-scale interpretation of the transformation ... ...

Abstract	Hypothesis: The precipitation and dissolution of aluminum-bearing mineral phases in aqueous systems often proceed via changes in both aluminum coordination number and connectivity, complicating molecular-scale interpretation of the transformation mechanism. Here, the thermally induced transformation of crystalline sodium aluminum salt hydrate, a phase comprised of monomeric octahedrally coordinated aluminate which is of relevance to industrial aluminum processing, has been studied. Because intermediate aluminum coordination states during melting have not previously been detected, it is hypothesized that the transition to lower coordinated aluminum ions occurs within ahighly disordered quasi-two-dimensional phase at the solid-solution interface. Experiments and simulations: In situ X-ray diffraction (XRD), Raman and Findings: In contrast to classical dissolution, aluminum coordination change proceeds through a dynamically stabilized ensemble of intermediate states in a disordered layer at the solid-solution interface. In both melting and dissolution of NSA, octahedral, monomeric aluminum transition through an intermediate of pentahedral coordination. The intermediate dehydroxylates to form tetrahedral aluminate (Al(OH)
Language	English
Publishing date	2023-01-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	241597-5
ISSN	1095-7103 ; 0021-9797
ISSN (online)	1095-7103
ISSN	0021-9797
DOI	10.1016/j.jcis.2023.01.003
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Article ; Online: Neuro-PASC is characterized by enhanced CD4+ and diminished CD8+ T cell responses to SARS-CoV-2 Nucleocapsid protein.

Frontiers in immunology

2023 Volume 14, Page(s) 1155770

Abstract: Introduction: Many people with long COVID symptoms suffer from debilitating neurologic post-acute sequelae of SARS-CoV-2 infection (Neuro-PASC). Although symptoms of Neuro-PASC are widely documented, it is still unclear whether PASC symptoms impact ... ...

Abstract	Introduction: Many people with long COVID symptoms suffer from debilitating neurologic post-acute sequelae of SARS-CoV-2 infection (Neuro-PASC). Although symptoms of Neuro-PASC are widely documented, it is still unclear whether PASC symptoms impact virus-specific immune responses. Therefore, we examined T cell and antibody responses to SARS-CoV-2 Nucleocapsid protein to identify activation signatures distinguishing Neuro-PASC patients from healthy COVID convalescents. Results: We report that Neuro-PASC patients exhibit distinct immunological signatures composed of elevated CD4 Discussion: We conclude that these data provide new insight into the impact of virus-specific cellular immunity on the pathogenesis of long COVID and pave the way for the rational design of predictive biomarkers and therapeutic interventions.
MeSH term(s)	Humans ; CD4-Positive T-Lymphocytes ; CD8-Positive T-Lymphocytes ; COVID-19/immunology ; Interleukin-6 ; Post-Acute COVID-19 Syndrome/immunology ; SARS-CoV-2
Chemical Substances	Interleukin-6 ; nucleocapsid phosphoprotein, SARS-CoV-2
Language	English
Publishing date	2023-05-29
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1155770
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