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Article ; Online: Measuring and modeling diel oxygen dynamics in a shallow hypereutrophic estuary: Implications of low oxygen exposure on aquatic life.

Jarvis, Brandon M / Hagy, James D / Melendez, Wilson / Simmons, Cody W / Wan, Yongshan

2023 Volume 882, Page(s) 163474

Abstract: Hypoxia, or low dissolved oxygen (DO) is a common outcome of excess nitrogen and phosphorus delivered to coastal waterbodies. Shallow and highly productive estuaries are particularly susceptible to diel-cycling hypoxia, which can exhibit DO excursions ... ...

Abstract	Hypoxia, or low dissolved oxygen (DO) is a common outcome of excess nitrogen and phosphorus delivered to coastal waterbodies. Shallow and highly productive estuaries are particularly susceptible to diel-cycling hypoxia, which can exhibit DO excursions between anoxia (DO ≤1 mg L
MeSH term(s)	Humans ; Oxygen/analysis ; Estuaries ; Ecosystem ; Hypoxia ; Water
Chemical Substances	Oxygen (S88TT14065) ; Water (059QF0KO0R)
Language	English
Publishing date	2023-04-15
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2023.163474
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Article ; Online: Measuring and modeling diel oxygen dynamics in a shallow hypereutrophic estuary: Implications of low oxygen exposure on aquatic life

Jarvis, Brandon M. / Hagy, James D. / Melendez, Wilson / Simmons, Cody W. / Wan, Yongshan

Science of the Total Environment. 2023 July, v. 882 p.163474-

2023

Abstract	Hypoxia, or low dissolved oxygen (DO) is a common outcome of excess nitrogen and phosphorus delivered to coastal waterbodies. Shallow and highly productive estuaries are particularly susceptible to diel-cycling hypoxia, which can exhibit DO excursions between anoxia (DO ≤1 mg L⁻¹) and supersaturated concentrations within a day. Shallow estuaries exhibiting diel-cycling hypoxia are understudied relative to larger and deeper estuaries, with very few mechanistic models that can predict diel oxygen dynamics. We utilized continuous monitoring data and the Coastal Generalized Ecosystem Model (CGEM) coupled with an Environmental Fluid Dynamics Code (EFDC) hydrodynamic model to simulate diel DO dynamics in Weeks Bay, AL. Low oxygen conditions ranging from anoxia to DO ≤4 mg L⁻¹ were consistently observed and simulated in the lower water column for periods of minutes to >11 h. High frequency observations and model simulations also identified significant vertical gradients in near bottom DO that varied as much as 0.8 to 3.1 mg L⁻¹ within 0.4 m from the bottom. This spatiotemporal variability presents unique challenges to adequately quantify DO dynamics and the potential exposure of aquatic life to low oxygen conditions. Our results demonstrate the need for detailed measurements to adequately quantify the complex DO dynamics in shallow estuaries. We also demonstrate that simulation models can be successfully applied to evaluate diel oxygen dynamics in complex estuarine environments when calibrated with fine time scale data and effective parameterization of water column and benthic metabolic processes.
Keywords	aquatic organisms ; dissolved oxygen ; ecological models ; environment ; estuaries ; fluid mechanics ; hydrologic models ; hypoxia ; nitrogen ; oxygen ; phosphorus ; simulation models ; surface water ; Diel-cycling ; Primary production ; Respiration ; Simulation model ; Estuary
Language	English
Dates of publication	2023-07
Publishing place	Elsevier B.V.
Document type	Article ; Online
Note	Pre-press version
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2023.163474
Database	NAL-Catalogue (AGRICOLA)

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Article: Impacts of climate change on estuarine stratification and implications for hypoxia within a shallow subtropical system.

Duvall, Melissa S / Jarvis, Brandon M / Wan, Yongshan

Estuarine, coastal and shelf science

2023 Volume 279, Page(s) 1–14

Abstract: ... IR) and temperature (T), increased freshwater discharge (D), sea level rise (SLR), and wind ... intensification (W). Simulations showed that the impacts of climate change on modeled state variables varied over ...

Abstract	Vertical density stratification often plays an important role in the formation and expansion of coastal hypoxic zones through its effect on near-bed circulation and vertical oxygen flux. However, the impact of future climate change on estuarine circulation is widely unknown. Here, we developed and calibrated a three-dimensional hydrodynamic model for Pensacola Bay, a shallow subtropical estuary in the northeastern Gulf of Mexico. Model simulations based on years 2013-2017 were applied to examine changes in salinity, temperature, and density under future climate scenarios, including increased radiative forcing (IR) and temperature (T), increased freshwater discharge (D), sea level rise (SLR), and wind intensification (W). Simulations showed that the impacts of climate change on modeled state variables varied over time with external forcing conditions. The model demonstrated the potential for sea level rise and increased freshwater discharge to episodically increase vertical density gradients in the Bay. However, increased wind forcing destabilized vertical gradients, at times reducing the spatial extent and duration of stable stratification. For time periods with low freshwater discharge, moderate increases in wind speed (10%) can destabilize density gradients strengthened by increased discharge (10%) and sea level rise (0.48 m). In contrast, destruction of strong density gradients that form near the mid-Bay channel following flood events requires stronger wind forcing. These results highlight the importance of considering natural variability in freshwater and wind forcing, as well as local phenomena that are generally unresolved by global climate models.
Language	English
Publishing date	2023-09-07
Publishing country	England
Document type	Journal Article
ISSN	0272-7714
ISSN	0272-7714
DOI	10.1016/j.ecss.2022.108146
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Book: Bennett & Brachman's hospital infections

Jarvis, William R.

2007

Title variant	Bennett and Brachman's hospital infections ; Hospital infections
Author's details	ed. William R. Jarvis
Keywords	Cross Infection / prevention & control ; Cross Infection / etiology ; Nosocomial infections ; Nosocomial infections/Prevention
Subject code	614.44
Language	English
Size	XIV, 832 S., 26cm
Edition	5. ed.
Publisher	Wolters Kluwer/Lippincott Williams & Wilkins
Publishing place	Philadelphia, Pa. u.a.
Publishing country	United States
Document type	Book
Note	Includes bibliographical references and index. - Previous ed.: published as Hospital infections. 1998. - Formerly CIP
Old title	Frühere Aufl. u.d.T. Hospital infections
HBZ-ID	HT015715466
ISBN	978-0-7817-6383-7 ; 0-7817-6383-5
Database	Catalogue ZB MED Medicine, Health

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Article: Exploring changing attitudes to non-invasive liver fibrosis tests in secondary care pathways: comparison of two national surveys.

Abeysekera, Kushala W M / Srivastava, Ankur / Rowe, Ian / Jarvis, Helen / Ryder, Stephen D / Yeoman, Andrew / Dillon, John F / Rosenberg, William

Frontline gastroenterology

2023 Volume 14, Issue 6, Page(s) 483–490

Abstract: Introduction: The increasing availability of non-invasive tests (NITs) has created the opportunity to explore their use in improving risk stratification of advanced liver disease. The study aimed to determine the attitudes and practices among UK ... ...

Abstract	Introduction: The increasing availability of non-invasive tests (NITs) has created the opportunity to explore their use in improving risk stratification of advanced liver disease. The study aimed to determine the attitudes and practices among UK secondary care specialists, focusing primarily on attitudes to fibrosis assessment and the use of NITs. Methods: Two web-based surveys were circulated, first between 2014 and 2015 (survey 1), and again in 2021 (survey 2). The surveys were promoted via the British Society of Gastroenterology, the British Association for the Study of the Liver and using Twitter. Results: In survey 1, 215 healthcare professionals (HCPs) completed the online survey. 112 HCPs completed survey 2. 71 acute UK trusts were represented in survey 1 compared with 60 trusts in survey 2. Between the two surveys, the proportion of HCPs performing fibrosis assessment in all or nearly all cases rose from 45.1% to 74.1% (χ Conclusion: Between 2014 and 2021, the role of NITs in fibrosis assessment has risen substantially, as has the proportion of clinicians using NITs in clinical pathways to assess risk of liver disease. Poor access to NITs remains the predominant barrier.
Language	English
Publishing date	2023-06-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2521857-8
ISSN	2041-4137
ISSN	2041-4137
DOI	10.1136/flgastro-2023-102415
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Article ; Online: Progress is impossible without change: understanding the evolving nomenclature of steatotic liver disease and its effect on hepatology practice.

Brennan, Paul N / Tavabie, Oliver D / Li, Wenhao / Marjot, Thomas / Corless, Lynsey / Fallowfield, Jonathan A / Jarvis, Helen / Mansour, Dina / McPherson, Stuart / Rosenberg, William / Rockell, Karen / Tomlinson, Jeremy / Yeoman, Andrew / Tsochatzis, Emmanuel A / Dillon, John F / Alazawi, William / Abeysekera, Kushala W M

The lancet. Gastroenterology & hepatology

2024

Abstract: The American, European, and Latin American liver societies have proposed a change in the nomenclature we use to describe alcohol-related liver disease and non-alcoholic fatty liver disease. Additionally, a term encompassing both is now advocated: ... ...

Abstract	The American, European, and Latin American liver societies have proposed a change in the nomenclature we use to describe alcohol-related liver disease and non-alcoholic fatty liver disease. Additionally, a term encompassing both is now advocated: steatotic liver disease, which includes metabolic dysfunction associated steatotic liver disease (MASLD) and MASLD with greater alcohol consumption (MetALD). These classifications offer increased relevance for clinicians, researchers, and patients alike. In this Viewpoint, we discuss the basis for this nomenclature shift and how it was developed. We also explore the challenges that will be faced in the adoption of such change. The proposed change seeks to banish stigma associated with phrasing such as alcoholic and fatty. However stigma, particularly related to the term fatty, is culturally nuanced, and reflects different entities depending on location. If such a change is internationally accepted, there will be wide-reaching effects on practitioners in primary care and metabolic medicine, and on patients. We discuss those effects and the opportunities the nomenclature change could offer, particularly for patients with alcohol and metabolic risk factors who represent a group previously ignored by clinical trials.
Language	English
Publishing date	2024-02-27
Publishing country	Netherlands
Document type	Journal Article ; Review
ISSN	2468-1253
ISSN (online)	2468-1253
DOI	10.1016/S2468-1253(23)00453-3
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Article ; Online: Promise and peril: how health system reforms impacted public health in three Canadian provinces.

Jarvis, Tamika / Smith, Robert W / Sandhu, Harman Singh / Mac-Seing, Muriel / O'Neill, Meghan / Rosella, Laura / Allin, Sara / Pinto, Andrew D

Canadian journal of public health = Revue canadienne de sante publique

2023 Volume 114, Issue 5, Page(s) 714–725

Abstract: Objectives: Several Canadian provinces and territories have reformed their health systems by centralizing power, resources, and responsibilities. Our study explored motivating factors and perceived impacts of centralization reforms on public health ... ...

Abstract	Objectives: Several Canadian provinces and territories have reformed their health systems by centralizing power, resources, and responsibilities. Our study explored motivating factors and perceived impacts of centralization reforms on public health systems and essential operations. Methods: A multiple case study design was used to examine three Canadian provinces that have undergone, or are in the process of undergoing, health system reform. Semi-structured interviews were conducted with 58 participants within public health at strategic and operational levels, from Alberta, Ontario, and Québec. Data were analyzed using a thematic analytical approach to iteratively conceptualize and refine themes. Results: Three major themes were developed to describe the context and impacts of health system centralization reforms on public health: (1) promising "value for money" and consolidating authority; (2) impacting intersectoral and community-level collaboration; and (3) deprioritizing public health operations and contributing to workforce precarity. Centralization highlighted concerns about the prioritization of healthcare sectors. Some core public health functions were reported to operate more efficiently, with less duplication of services, and improvements in program consistency and quality, particularly in Alberta. Reforms were also reported to have diverted funding and human resources away from core essential functions, and diminished the public health workforce. Conclusion: Our study highlighted that stakeholder priorities and a limited understanding about public health systems influenced how reforms were implemented. Our findings support calls for modernized and inclusive governance, stable public health funding, and investment in the public health workforce, which may help inform future reforms.
MeSH term(s)	Humans ; Public Health ; Ontario ; Quebec ; Alberta ; Health Care Reform
Language	English
Publishing date	2023-07-06
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	417262-0
ISSN	1920-7476 ; 0008-4263
ISSN (online)	1920-7476
ISSN	0008-4263
DOI	10.17269/s41997-023-00785-2
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Article ; Online: Assessing the strengths and limitations of quantitative micromorphometry for the forensic examination of small arms propellant towards brand identification.

Jarvis, Casey M / Kress, Devin / Hanka, Janean / Moorehead, Wayne / Hietpas, Jack

Forensic science international

2023 Volume 353, Page(s) 111880

Abstract: Smalls arms propellants (SAP) also known as canister powders are readily accessible and cost-effective materials that firearms enthusiasts can acquire for the legitimate assembly of ammunition. These attributes also make SAPs advantageous for the ... ...

Abstract	Smalls arms propellants (SAP) also known as canister powders are readily accessible and cost-effective materials that firearms enthusiasts can acquire for the legitimate assembly of ammunition. These attributes also make SAPs advantageous for the construction of improvised explosive devices (IEDs). Thus, there is a need to develop robust metrics for the characterization of propellants to provide investigative leads as well as for comparisons between known and recovered residues. The goal of this research was to investigate the utility of a high-throughput, non-destructive, and low-cost quantitative automated image analysis routine for the characterization and discrimination of SAP. For this project, 204 one-pound canisters of smokeless propellant (powder) were acquired from local and online sources. These samples represent nine manufacturers and 154 unique brands. From this set, five brands were selected to assess the intra- and inter-lot variability. Eight parameters, which encompass size- and shape-dependent metrics were measured for each sample. A total of ∼85,000 granules (∼680,000 measurements) were analyzed using linear discriminant analysis. A detailed assessment of the variables shows that the size-dependent metrics provide the greatest amount of sample discrimination. Overall accuracy of the method to correctly classify a test subset of data to the brand level is ∼84.72%. The results from this study provide a framework in which to interpret smokeless propellant micromorphometry in the context of intelligence purposes for initial stages of criminal investigations, and for traditional comparisons between known and unknown samples.
Language	English
Publishing date	2023-11-04
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	424042-x
ISSN	1872-6283 ; 0379-0738
ISSN (online)	1872-6283
ISSN	0379-0738
DOI	10.1016/j.forsciint.2023.111880
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Article ; Online: Structure-Toxicity Relationship in Intermediate Fibrils from α-Synuclein Condensates.

Chen, Serene W / Barritt, Joseph D / Cascella, Roberta / Bigi, Alessandra / Cecchi, Cristina / Banchelli, Martina / Gallo, Angelo / Jarvis, James A / Chiti, Fabrizio / Dobson, Christopher M / Fusco, Giuliana / De Simone, Alfonso

Journal of the American Chemical Society

2024 Volume 146, Issue 15, Page(s) 10537–10549

Abstract: The aberrant aggregation of α-synuclein (αS) into amyloid fibrils is associated with a range of highly debilitating neurodegenerative conditions, including Parkinson's disease. Although the structural properties of mature amyloids of αS are currently ... ...

Abstract	The aberrant aggregation of α-synuclein (αS) into amyloid fibrils is associated with a range of highly debilitating neurodegenerative conditions, including Parkinson's disease. Although the structural properties of mature amyloids of αS are currently understood, the nature of transient protofilaments and fibrils that appear during αS aggregation remains elusive. Using solid-state nuclear magnetic resonance (ssNMR), cryogenic electron microscopy (cryo-EM), and biophysical methods, we here characterized intermediate amyloid fibrils of αS forming during the aggregation from liquid-like spherical condensates to mature amyloids adopting the structure of pathologically observed aggregates. These transient amyloid intermediates, which induce significant levels of cytotoxicity when incubated with neuronal cells, were found to be stabilized by a small core in an antiparallel β-sheet conformation, with a disordered N-terminal region of the protein remaining available to mediate membrane binding. In contrast, mature amyloids that subsequently appear during the aggregation showed different structural and biological properties, including low levels of cytotoxicity, a rearranged structured core embedding also the N-terminal region, and a reduced propensity to interact with the membrane. The characterization of these two fibrillar forms of αS, and the use of antibodies and designed mutants, enabled us to clarify the role of critical structural elements endowing intermediate amyloid species with the ability to interact with membranes and induce cytotoxicity.
MeSH term(s)	Humans ; alpha-Synuclein/genetics ; alpha-Synuclein/toxicity ; alpha-Synuclein/chemistry ; Parkinson Disease/metabolism ; Amyloid/chemistry ; Neurodegenerative Diseases ; Protein Conformation, beta-Strand
Chemical Substances	alpha-Synuclein ; Amyloid
Language	English
Publishing date	2024-04-03
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.3c14703
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Article ; Online: Single-Input Multi-Output U-Net for Automated 2D Foetal Brain Segmentation of MR Images.

Rampun, Andrik / Jarvis, Deborah / Griffiths, Paul D / Zwiggelaar, Reyer / Scotney, Bryan W / Armitage, Paul A

Journal of imaging

2021 Volume 7, Issue 10

Abstract: In this work, we develop the Single-Input Multi-Output U-Net (SIMOU-Net), a hybrid network for foetal brain segmentation inspired by the original U-Net fused with the holistically nested edge detection (HED) network. The SIMOU-Net is similar to the ... ...

Abstract	In this work, we develop the Single-Input Multi-Output U-Net (SIMOU-Net), a hybrid network for foetal brain segmentation inspired by the original U-Net fused with the holistically nested edge detection (HED) network. The SIMOU-Net is similar to the original U-Net but it has a deeper architecture and takes account of the features extracted from each side output. It acts similar to an ensemble neural network, however, instead of averaging the outputs from several independently trained models, which is computationally expensive, our approach combines outputs from a single network to reduce the variance of predications and generalization errors. Experimental results using 200 normal foetal brains consisting of over 11,500 2D images produced Dice and Jaccard coefficients of 94.2 ± 5.9% and 88.7 ± 6.9%, respectively. We further tested the proposed network on 54 abnormal cases (over 3500 images) and achieved Dice and Jaccard coefficients of 91.2 ± 6.8% and 85.7 ± 6.6%, respectively.
Language	English
Publishing date	2021-10-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2824270-1
ISSN	2313-433X ; 2313-433X
ISSN (online)	2313-433X
ISSN	2313-433X
DOI	10.3390/jimaging7100200
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