355 results on '"Clark ME"'
Search Results
2. Gene set enrichment analysis of the bronchial epithelium implicates contribution of cell cycle and tissue repair processes in equine asthma
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Tessier, L, Cote, O, Clark, ME, Viel, L, Diaz-Mendez, A, Anders, S, Bienzle, D, Tessier, L, Cote, O, Clark, ME, Viel, L, Diaz-Mendez, A, Anders, S, and Bienzle, D
- Abstract
Severe equine asthma is a chronic inflammatory condition of the lower airways similar to adult-onset asthma in humans. Exacerbations are characterized by bronchial and bronchiolar neutrophilic inflammation, mucus hypersecretion and airway constriction. In this study we analyzed the gene expression response of the bronchial epithelium within groups of asthmatic and non-asthmatic animals following exposure to a dusty hay challenge. After challenge we identified 2341 and 120 differentially expressed genes in asthmatic and non-asthmatic horses, respectively. Gene set enrichment analysis of changes in gene expression after challenge identified 587 and 171 significantly enriched gene sets in asthmatic and non-asthmatic horses, respectively. Gene sets in asthmatic animals pertained, but were not limited, to cell cycle, neutrophil migration and chemotaxis, wound healing, hemostasis, coagulation, regulation of body fluid levels, and the hedgehog pathway. Furthermore, transcription factor target enrichment analysis in the asthmatic group showed that transcription factor motifs with the highest enrichment scores for up-regulated genes belonged to the E2F transcription factor family. It is postulated that engagement of hedgehog and E2F pathways in asthmatic horses promotes dysregulated cell proliferation and abnormal epithelial repair. These fundamental lesions may prevent re-establishment of homeostasis and perpetuate inflammation.
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- 2018
3. Impaired response of the bronchial epithelium to inflammation characterizes severe equine asthma
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Tessier, L, Cote, O, Clark, ME, Viel, L, Diaz-Mendez, A, Anders, S, Bienzle, D, Tessier, L, Cote, O, Clark, ME, Viel, L, Diaz-Mendez, A, Anders, S, and Bienzle, D
- Abstract
BACKGROUND: Severe equine asthma is a naturally occurring lung inflammatory disease of mature animals characterized by neutrophilic inflammation, bronchoconstriction, mucus hypersecretion and airway remodeling. Exacerbations are triggered by inhalation of dust and microbial components. Affected animals eventually are unable of aerobic performance. In this study transcriptomic differences between asthmatic and non-asthmatic animals in the response of the bronchial epithelium to an inhaled challenge were determined. RESULTS: Paired endobronchial biopsies were obtained pre- and post-challenge from asthmatic and non-asthmatic animals. The transcriptome, determined by RNA-seq and analyzed with edgeR, contained 111 genes differentially expressed (DE) after challenge between horses with and without asthma, and 81 of these were upregulated. Genes involved in neutrophil migration and activation were in central location in interaction networks, and related gene ontology terms were significantly overrepresented. Relative abundance of specific gene products as determined by immunohistochemistry was correlated with differential gene expression. Gene sets involved in neutrophil chemotaxis, immune and inflammatory response, secretion, blood coagulation and apoptosis were overrepresented among up-regulated genes, while the rhythmic process gene set was overrepresented among down-regulated genes. MMP1, IL8, TLR4 and MMP9 appeared to be the most important proteins in connecting the STRING protein network of DE genes. CONCLUSIONS: Several differentially expressed genes and networks in horses with asthma also contribute to human asthma, highlighting similarities between severe human adult and equine asthma. Neutrophil activation by the bronchial epithelium is suggested as the trigger of the inflammatory cascade in equine asthma, followed by epithelial injury and impaired repair and differentiation. Circadian rhythm dysregulation and the sonic Hedgehog pathway were identified as potenti
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- 2017
4. Technical Basis for EPAʼs Proposed Regulation on the Cleanup of Sites Contaminated with Radioactivity
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Clark Me, Tsirigotis Pl, A. B. Wolbarst, D. Back, J. A. Mackinney, Ralston L, J. Mauro, Hull Hb, Doehnert M, Lailas N, J.W. Bartlett, D. Chan, Durman E, Anigstein R, Beres D, and Hay S
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Epidemiology ,Environmental remediation ,Health, Toxicology and Mutagenesis ,Radioactive waste ,complex mixtures ,Soil contamination ,Remedial action ,Regulatory Impact Analysis ,Public use ,Radioactive contamination ,Environmental science ,Radiology, Nuclear Medicine and imaging ,Technical management ,Environmental planning - Abstract
The US Environmental Protection Agency is proposing a regulation for the protection of the public and radioactive contamination at sites that are to be cleaned up and released for public use. The rule will apply to sites under the control of Federal agencies, and will impose limits on radiation doses to individuals living or working on a site following cleanup; it will thereby provide site owners and managers with uniform, consistent cleanup criteria for planning and carrying out remediation. This paper presents an overview of EPA`s approach to assessing some of the beneficial and adverse effects associated with various possible values for the annual dose limit. In particular, it discusses the method developed to determine how the choice of cleanup criterion affects (1) the time-integrated potential numbers of non-fatal and fatal radiogenic cancers averted among future populations, (2) the occurrence of radiogenic cancers among remediation workers and the public caused by the cleanup process itself, and (3) the volumes of contaminated soil that may require remediation. The analytic methods described here were used to provide input data and assumptions for the Regulatory Impact Analysis (RIA) that supports the proposed regulation; the RIA also considered non-radiological benefits and costs (i.e., publicmore » health, economic, and ecological) of the standards. 56 refs., 4 figs., 6 tabs.« less
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- 1996
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5. Diffuse contributions dominate over point sources of soluble nutrients in two sub-catchments of the Manawatu River, New Zealand
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Roygard, JKF, primary, McArthur, KJ, additional, and Clark, ME, additional
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- 2012
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6. Intraspecific interference among foraging blue crabs Callinectes sapidus:interactive effects of predator density and prey patch distribution
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Clark, ME, primary, Wolcott, TG, additional, Wolcott, DL, additional, and Hines, AH, additional
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- 1999
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7. An individual-based model of bay anchovy population dynamics in the mesohaline region of Chesapeake Bay
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Rose, KA, primary, Cowan, JH, additional, Clark, ME, additional, Houde, ED, additional, and Wang, SB, additional
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- 1999
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8. Mortality, size of the gonads, and ultrastructure of primordial germ cell in chick embryos treated with gamma-irradiation or injected with donor cells
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Maeda, T, primary, Clark, ME, additional, and Etches, RJ, additional
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- 1998
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9. Manipulation of blastodermal cells
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Etches, RJ, primary, Clark, ME, additional, Zajchowski, L, additional, Speksnijder, G, additional, Verrinder Gibbins, AM, additional, Kino, K, additional, Pain, B, additional, and Samarut, J, additional
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- 1997
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10. Production of chicken chimeras from injection of frozen-thawed blastodermal cells
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Kino, K, primary, Pain, B, additional, Leibo, SP, additional, Cochran, M, additional, Clark, ME, additional, and Etches, RJ, additional
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- 1997
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11. Opioid cessation and multidimensional outcomes after interdisciplinary chronic pain treatment.
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Murphy JL, Clark ME, and Banou E
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- 2013
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12. Pain and combat injuries in soldiers returning from Operations Enduring Freedom and Iraqi Freedom: implications for research and practice.
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Clark ME, Bair MJ, Buckenmaier CC III, Gironda RJ, and Walker RL
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Operation Enduring Freedom (OEF) and Operation Iraqi Freedom (OIF) have resulted in a growing number of seriously injured soldiers who are evacuated to the United States for comprehensive medical care. Trauma-related pain is an almost universal problem among these war-injured soldiers, and several military and Department of Veterans Affairs initiatives have been implemented to enhance pain care across the continuum of medical services. This article describes several innovative approaches for improving the pain care provided to OEF and OIF military personnel during acute stabilization, transport, medical-surgical treatment, and rehabilitation and presents summary data characterizing the soldiers, pain management services provided, and associated outcomes. We also identify some of the pain assessment, classification, and treatment challenges emerging from work with this population and provide recommendations for future research and practice priorities. [ABSTRACT FROM AUTHOR]
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- 2007
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13. Pain among veterans of Operation Enduring Freedom and Iraqi Freedom.
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Gironda RJ, Clark ME, Massengale JP, and Walker RL
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- 2006
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14. Development and validation of the Pain Outcomes Questionnaire-VA.
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Clark ME, Gironda RJ, and Young RW
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The development of effective pain treatment strategies requires the availability of precise and practical measures of treatment outcomes, the importance of which has been noted in the Veterans Health Administration's (VHA's) National Pain Initiative. This paper presents the results of a 5-year collaborative effort to develop and validate a comprehensive and efficient self-report measure of pain treatment outcomes. Two samples of veterans (957 total subjects) undergoing inpatient or outpatient pain treatment at six VHA facilities completed Pain Outcomes Questionnaire-VA (POQ-VA) items and several additional measures. We used a comprehensive, multistage analytic procedure to evaluate the psychometric properties of the instrument. Results provided strong support for the reliability, validity, and clinical use of the POQ-VA when used to evaluate the effectiveness of treatment for veterans experiencing chronic noncancer pain. [ABSTRACT FROM AUTHOR]
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- 2003
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15. Effect of endothelial shear stress on the progression of coronary artery disease, vascular remodeling, and in-stent restenosis in humans: in vivo 6-month follow-up study.
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Stone PH, Coskun AU, Kinlay S, Clark ME, Sonka M, Wahle A, Ilegbusi OJ, Yeghiazarians Y, Popma JJ, Orav J, Kuntz RE, Feldman CL, Stone, Peter H, Coskun, Ahmet U, Kinlay, Scott, Clark, Maureen E, Sonka, Milan, Wahle, Andreas, Ilegbusi, Olusegun J, and Yeghiazarians, Yerem
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- 2003
16. Morphology of the Achilles tendon in the newborn
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Clark Me
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Achilles tendon ,medicine.anatomical_structure ,business.industry ,Infant, Newborn ,Medicine ,Humans ,Morphology (biology) ,General Medicine ,Anatomy ,business ,Achilles Tendon - Published
- 1972
17. The structure of two distinct pancreatic amylase genes in mouse strain YBR
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Klintebaek Om, J. P. Hjorth, B.M. Mikkelsen, Janni Nielsen, Thomsen Kk, Gunna Christiansen, and Clark Me
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Pseudogene ,Mice, Inbred Strains ,Biochemistry ,DNA sequencing ,law.invention ,chemistry.chemical_compound ,Mice ,law ,Genetics ,Animals ,Amylase ,Amino Acid Sequence ,Cloning, Molecular ,Saliva ,Molecular Biology ,Peptide sequence ,Gene ,Pancreas ,Ecology, Evolution, Behavior and Systematics ,biology ,Base Sequence ,Chromosome Mapping ,General Medicine ,DNA Restriction Enzymes ,Molecular biology ,Isoenzymes ,chemistry ,Genes ,Amylases ,biology.protein ,Recombinant DNA ,DNA ,Heteroduplex - Abstract
The amylase complex on mouse chromosome 3 encodes both salivary and pancreatic amylase. It appears that one active gene is present for salivary amylase, whereas pancreatic amylase in some strains is coded by at least 4, and perhaps by more than 10, genes. Strain YBR is different from other strains in that it produces twice as much salivary amylase. Pancreatic amylase in YBR is present as two different protein forms, A beta and B beta, the sum of which amounts to only one-third of that in, for instance, strain A/J. YBR chromosomal DNA was cloned in phage gamma, followed by restriction and heteroduplex analysis of recombinant phages carrying amylase genes. Among 32 phage isolates, 5 carried parts of the salivary amylase sequence. The remaining phage isolates contained pancreatic amylase-like sequences and represented three nonoverlapping genomic regions, i.e., one of 34 kb containing a complete gene, PAN-II beta; another of 41 kb with a complete but different gene, PAN-I beta, plus a truncated gene, PAN-psi 1; and finally, one of 23 kb with another truncated gene, PAN-psi 2. Parts of the amino acid sequence of A beta and B beta have previously been determined, and we report here the sequencing of a 4-kb DNA fragment from Pan-II beta which establishes that this gene codes for B beta.
18. Morphology of the Achilles tendon in the newborn
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Clark, ME, primary
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- 1972
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19. Water intake and urine output of mice during chronic centrifugation
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Wunder, CC, primary, Meyer, FN, additional, Clark, ME, additional, and Bengele, HH, additional
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- 1971
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20. Myocardial vasculature: the third significant contributor to MR diffusion signals in the isolated rabbit heart
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Forder John R, Clark Melvin, and Hwang Min-Sig
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Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Published
- 2009
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21. A piece of my mind. No more apologies.
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Clark ME and Clark, Megan Elizabeth
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- 2012
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22. Understand appropriate long-term use of opioids--seventeen years and counting.
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Clark ME
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- 2008
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23. The GLBT Health Access Project: a state-funded effort to improve access to care.
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Clark ME, Landers S, Linde R, and Sperber J
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PROPRIETARY health facilities , *HEALTH services accessibility , *PUBLIC health administration , *PRIMARY health care , *LGBTQ+ people , *INTERPROFESSIONAL relations , *CULTURAL competence , *HEALTH planning - Abstract
The Gay, Lesbian, Bisexual, and Transgender (GLBT) Health Access Project is a unique public-private collaboration working to eliminate barriers to health care for the GLBT community, foster development of comprehensive, culturally appropriate health promotion policies and health care services for GLBT people and their families, and expand appropriate data collection on GLBT health. Funded by the Massachusetts Department of Public Health, the project developed community standards of practice for provision of quality health care services to GLBT clients. A health access training curriculum was developed and technical assistance was offered to health care providers implementing the standards, which cover personnel, clients' rights, intake and assessment, service delivery and planning, confidentiality, and community outreach and health promotion. Training participants (324 individuals from 89 agencies) reported positive though not statistically significant changes in attitude. [ABSTRACT FROM AUTHOR]
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- 2001
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24. The role for scientists in tackling food insecurity and climate change
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Beddington John R, Asaduzzaman Mohammed, Clark Megan E, Bremauntz Adrian, Guillou Marion D, Jahn Molly M, Lin Erda, Mamo Tekalign, Negra Christine, Nobre Carlos A, Scholes Robert J, Sharma Rita, Van Bo Nguyen, and Wakhungu Judi
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Agriculture ,Nutrition. Foods and food supply ,TX341-641 - Abstract
Abstract To adapt to climate change and ensure food security, major interventions are required to transform current patterns and practices of food production, distribution and consumption. The scientific community has an essential role to play in informing concurrent, strategic investments to establish climate-resilient agricultural production systems, minimize greenhouse gas emissions, make efficient use of resources, develop low-waste supply chains, ensure adequate nutrition, encourage healthy eating choices and develop a global knowledge system for sustainability. This paper outlines scientific contributions that will be essential to the seven policy recommendations for achieving food security in the context of climate change put forward by the Commission on Sustainable Agriculture and Climate Change. These include improved understanding of agriculture’s vulnerability to climate change, food price dynamics, food waste and consumption patterns and monitoring technologies as well as multidisciplinary investigation of regionally appropriate responses to climate change and food security challenges.
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- 2012
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25. Food price volatility and hunger alleviation – can Cannes work?
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Hajkowicz Stefan, Negra Christine, Barnett Paul, Clark Megan, Harch Bronwyn, and Keating Brian
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Food price volatility ,food security ,hunger alleviation ,policy responses ,G20 action plan ,Cannes Summit ,Agriculture ,Nutrition. Foods and food supply ,TX341-641 - Abstract
Abstract Recent years have seen global food prices rise and become more volatile. Price surges in 2008 and 2011 held devastating consequences for hundreds of millions of people and negatively impacted many more. Today one billion people are hungry. The issue is a high priority for many international agencies and national governments. At the Cannes Summit in November 2011, the G20 leaders agreed to implement five objectives aiming to mitigate food price volatility and protect vulnerable persons. To succeed, the global community must now translate these high level policy objectives into practical actions. In this paper, we describe challenges and unresolved dilemmas before the global community in implementing these five objectives. The paper describes recent food price volatility trends and an evaluation of possible causes. Special attention is given to climate change and water scarcity, which have the potential to impact food prices to a much greater extent in coming decades. We conclude the world needs an improved knowledge base and new analytical capabilities, developed in parallel with the implementation of practical policy actions, to manage food price volatility and reduce hunger and malnutrition. This requires major innovations and paradigm shifts by the global community.
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- 2012
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26. Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: Carbon and energy flow contribute to the distinct biofilm growth state
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Clark Melinda E, He Zhili, Redding Alyssa M, Joachimiak Marcin P, Keasling Jay D, Zhou Jizhong Z, Arkin Adam P, Mukhopadhyay Aindrila, and Fields Matthew W
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continuously fed biofilm reactor, and compared to both batch and reactor planktonic populations. Results The functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenase as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from biofilm cells. Conclusions Even though both the planktonic and biofilm cells were oxidizing lactate and reducing sulfate, the biofilm cells were physiologically distinct compared to planktonic growth states due to altered abundances of genes/proteins involved in carbon/energy flow and extracellular structures. In addition, average expression values for multiple rRNA transcripts and respiratory activity measurements indicated that biofilm cells were metabolically more similar to exponential-phase cells although biofilm cells are structured differently. The characterization of physiological advantages and constraints of the biofilm growth state for sulfate-reducing bacteria will provide insight into bioremediation applications as well as microbially-induced metal corrosion.
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- 2012
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27. Perspectives on the ethical concerns and justifications of the 2006 Centers for Disease Control and Prevention HIV testing recommendations
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Waxman Michael J, Merchant Roland C, Celada M Teresa, and Clark Melissa A
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Medical philosophy. Medical ethics ,R723-726 - Abstract
Abstract Background In 2006, the Centers for Disease Control and Prevention (CDC) recommended three changes to HIV testing methods in US healthcare settings: (1) an opt-out approach, (2) removal of separate signed consent, and (3) optional HIV prevention counseling. These recommendations led to a public debate about their moral acceptability. Methods We interviewed 25 members from the fields of US HIV advocacy, care, policy, and research about the ethical merits and demerits of the three changes to HIV testing methods. We performed a qualitative analysis of the participant responses in the interviews and summarized the major themes. Results In general, arguments in favor of the methods were based upon their ultimate contribution to increasing HIV testing and permitting the consequent benefits of identifying those who are HIV infected and linking them to further care. Conclusions The prevailing theme of ethical concern focused on suspicions that the methods might not be properly implemented, and that further safeguards might be needed.
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- 2011
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28. Skin healing and scale regeneration in fed and unfed sea bream, Sparus auratus
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Canario Adelino VM, Clark Melody S, Bargelloni Luca, Milan Massimo, Costa Rita, Thorne Michael AS, Ferraresso Serena, Gregório Silvia F, Vieira Florbela A, and Power Deborah M
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Fish scales are an important reservoir of calcium and phosphorus and together with the skin function as an integrated barrier against environmental changes and external aggressors. Histological studies have revealed that the skin and scales regenerate rapidly in fish when they are lost or damaged. In the present manuscript the histological and molecular changes underlying skin and scale regeneration in fed and fasted sea bream (Sparus auratus) were studied using a microarray 3 and 7 days after scale removal to provide a comprehensive molecular understanding of the early stages of these processes. Results Histological analysis of skin/scales revealed 3 days after scale removal re-epithelisation and formation of the scale pocket had occurred and 53 and 109 genes showed significant up or down-regulation, respectively. Genes significantly up-regulated were involved in cell cycle regulation, cell proliferation and adhesion, immune response and antioxidant activities. 7 days after scale removal a thin regenerated scale was visible and only minor changes in gene expression occurred. In animals that were fasted to deplete mineral availability the expression profiles centred on maintaining energy homeostasis. The utilisation of fasting as a treatment emphasised the competing whole animal physiological requirements with regard to barrier repair, infection control and energy homeostasis. Conclusions The identification of numerous genes involved in the mitotic checkpoint and cell proliferation indicate that the experimental procedure may be useful for understanding cell proliferation and control in vertebrates within the context of the whole animal physiology. In response to skin damage genes of immune surveillance were up-regulated along with others involved in tissue regeneration required to rapidly re-establish barrier function. Additionally, candidate fish genes were identified that may be involved in cytoskeletal re-modelling, mineralization and stem cells, which are of potential use in aquaculture and fish husbandry, as they may impact on the ability of the fish to produce structural proteins, such as muscle, efficiently.
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- 2011
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29. Telephone and face to face methods of assessment of veteran's community reintegration yield equivalent results
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Clark Melissa A, Resnik Linda J, and Borgia Matthew
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Medicine (General) ,R5-920 - Abstract
Abstract Background The Community Reintegration of Service Members (CRIS) is a new measure of community reintegration developed to measure veteran's participation in life roles. It consists of three sub-scales: Extent of Participation (Extent), Perceived Limitations with Participation (Perceived), and Satisfaction with Participation (Satisfaction). Testing of the CRIS measure to date has utilized in-person administration. Administration of the CRIS measure by telephone, if equivalent to in-person administration, would be desirable to lower cost and decrease administrative burden. The purpose of this study was to test the equivalence of telephone and in-person mode of CRIS administration. Methods A convenience sample of 102 subjects (76% male, 24% female, age mean = 49 years, standard deviation = 8.3) were randomly assigned to received either telephone interview at Visit 1 and in-person interview at Visit 2, or in-person interview at Visit 1 and telephone interview a Visit 2. Both Visits were conducted within one week. Intraclass correlation coefficients, ICC (2,1), were used to evaluate correspondence between modes for both item scores and summary scores. ANOVAs with mode order as a covariate were used to test for presence of an ordering effect. Results ICCs (95%CI) for the subscales were 0.92 (0.88-0.94) for Extent, 0.85 (0.80-0.90) for Perceived, and 0.89 (0.84-0.93) for Satisfaction. No ordering effect was observed. Conclusion Telephone administration of the CRIS measure yielded equivalent results to in-person administration. Telephone administration of the CRIS may enable lower costs of administration and greater adoption.
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- 2011
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30. Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing
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Power Deborah M, Cardoso João CR, Vieira Florbela A, Thorne Michael AS, Clark Melody S, and Peck Lloyd S
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background The Antarctic clam, Laternula elliptica, is an infaunal stenothermal bivalve mollusc with a circumpolar distribution. It plays a significant role in bentho-pelagic coupling and hence has been proposed as a sentinel species for climate change monitoring. Previous studies have shown that this mollusc displays a high level of plasticity with regard to shell deposition and damage repair against a background of genetic homogeneity. The Southern Ocean has amongst the lowest present-day CaCO3 saturation rate of any ocean region, and is predicted to be among the first to become undersaturated under current ocean acidification scenarios. Hence, this species presents as an ideal candidate for studies into the processes of calcium regulation and shell deposition in our changing ocean environments. Results 454 sequencing of L. elliptica mantle tissue generated 18,290 contigs with an average size of 535 bp (ranging between 142 bp-5.591 kb). BLAST sequence similarity searching assigned putative function to 17% of the data set, with a significant proportion of these transcripts being involved in binding and potentially of a secretory nature, as defined by GO molecular function and biological process classifications. These results indicated that the mantle is a transcriptionally active tissue which is actively proliferating. All transcripts were screened against an in-house database of genes shown to be involved in extracellular matrix formation and calcium homeostasis in metazoans. Putative identifications were made for a number of classical shell deposition genes, such as tyrosinase, carbonic anhydrase and metalloprotease 1, along with novel members of the family 2 G-Protein Coupled Receptors (GPCRs). A membrane transport protein (SEC61) was also characterised and this demonstrated the utility of the clam sequence data as a resource for examining cold adapted amino acid substitutions. The sequence data contained 46,235 microsatellites and 13,084 Single Nucleotide Polymorphisms(SNPs/INDELS), providing a resource for population and also gene function studies. Conclusions This is the first 454 data from an Antarctic marine invertebrate. Sequencing of mantle tissue from this non-model species has considerably increased resources for the investigation of the processes of shell deposition and repair in molluscs in a changing environment. A number of promising candidate genes were identified for functional analyses, which will be the subject of further investigation in this species and also used in model-hopping experiments in more tractable and economically important model aquaculture species, such as Crassostrea gigas and Mytilus edulis.
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- 2010
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31. Surviving the cold: molecular analyses of insect cryoprotective dehydration in the Arctic springtail Megaphorura arctica (Tullberg)
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Popović Željko D, Hillyard Guy, Burns Gavin, Purać Jelena, Thorne Michael AS, Clark Melody S, Grubor-Lajšić Gordana, and Worland M Roger
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Insects provide tractable models for enhancing our understanding of the physiological and cellular processes that enable survival at extreme low temperatures. They possess three main strategies to survive the cold: freeze tolerance, freeze avoidance or cryoprotective dehydration, of which the latter method is exploited by our model species, the Arctic springtail Megaphorura arctica, formerly Onychiurus arcticus (Tullberg 1876). The physiological mechanisms underlying cryoprotective dehydration have been well characterised in M. arctica and to date this process has been described in only a few other species: the Antarctic nematode Panagrolaimus davidi, an enchytraied worm, the larvae of the Antarctic midge Belgica antarctica and the cocoons of the earthworm Dendrobaena octaedra. There are no in-depth molecular studies on the underlying cold survival mechanisms in any species. Results A cDNA microarray was generated using 6,912 M. arctica clones printed in duplicate. Analysis of clones up-regulated during dehydration procedures (using both cold- and salt-induced dehydration) has identified a number of significant cellular processes, namely the production and mobilisation of trehalose, protection of cellular systems via small heat shock proteins and tissue/cellular remodelling during the dehydration process. Energy production, initiation of protein translation and cell division, plus potential tissue repair processes dominate genes identified during recovery. Heat map analysis identified a duplication of the trehalose-6-phosphate synthase (TPS) gene in M. arctica and also 53 clones co-regulated with TPS, including a number of membrane associated and cell signalling proteins. Q-PCR on selected candidate genes has also contributed to our understanding with glutathione-S-transferase identified as the major antioxdidant enzyme protecting the cells during these stressful procedures, and a number of protein kinase signalling molecules involved in recovery. Conclusion Microarray analysis has proved to be a powerful technique for understanding the processes and genes involved in cryoprotective dehydration, beyond the few candidate genes identified in the current literature. Dehydration is associated with the mobilisation of trehalose, cell protection and tissue remodelling. Energy production, leading to protein production, and cell division characterise the recovery process. Novel membrane proteins, along with aquaporins and desaturases, have been identified as promising candidates for future functional analyses to better understand membrane remodelling during cellular dehydration.
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- 2009
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32. Discovering genes associated with dormancy in the monogonont rotifer Brachionus plicatilis
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Kube Michael, Clark Melody S, Thorne Michael AS, Denekamp Nadav Y, Reinhardt Richard, and Lubzens Esther
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Microscopic monogonont rotifers, including the euryhaline species Brachionus plicatilis, are typically found in water bodies where environmental factors restrict population growth to short periods lasting days or months. The survival of the population is ensured via the production of resting eggs that show a remarkable tolerance to unfavorable conditions and remain viable for decades. The aim of this study was to generate Expressed Sequence Tags (ESTs) for molecular characterisation of processes associated with the formation of resting eggs, their survival during dormancy and hatching. Results Four normalized and four subtractive libraries were constructed to provide a resource for rotifer transcriptomics associated with resting-egg formation, storage and hatching. A total of 47,926 sequences were assembled into 18,000 putative transcripts and analyzed using both Blast and GO annotation. About 28–55% (depending on the library) of the clones produced significant matches against the Swissprot and Trembl databases. Genes known to be associated with desiccation tolerance during dormancy in other organisms were identified in the EST libraries. These included genes associated with antioxidant activity, low molecular weight heat shock proteins and Late Embryonic Abundant (LEA) proteins. Real-time PCR confirmed that LEA transcripts, small heat-shock proteins and some antioxidant genes were upregulated in resting eggs, therefore suggesting that desiccation tolerance is a characteristic feature of resting eggs even though they do not necessarily fully desiccate during dormancy. The role of trehalose in resting-egg formation and survival remains unclear since there was no significant difference between resting-egg producing females and amictic females in the expression of the tps-1 gene. In view of the absence of vitellogenin transcripts, matches to lipoprotein lipase proteins suggest that, similar to the situation in dipterans, these proteins may serve as the yolk proteins in rotifers. Conclusion The 47,926 ESTs expand significantly the current sequence resource of B. plicatilis. It describes, for the first time, genes putatively associated with resting eggs and will serve as a database for future global expression experiments, particularly for the further identification of dormancy related genes.
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- 2009
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33. Differential response effects of data collection mode in a cancer screening study of unmarried women ages 40–75 years: A randomized trial
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Rakowski William, Armstrong Gene F, Rogers Michelle L, Clark Melissa A, and Kviz Frederick J
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Medicine (General) ,R5-920 - Abstract
Abstract Background Little is known about the impact of data collection method on self-reported cancer screening behaviours, particularly among hard-to-reach populations. The purpose of this study is to examine the effects of data collection mode on response to indicators of cancer screenings by unmarried middle-aged and older women. Methods Three survey methods were evaluated for collecting data about mammography and Papanicolaou (hereafter, Pap) testing among heterosexual and sexual minority (e.g., lesbian and bisexual) women. Women ages 40–75 were recruited from June 2003 – June 2005 in Rhode Island. They were randomly assigned to receive: Self-Administered Mailed Questionnaire [SAMQ; N = 202], Computer-Assisted Telephone Interview [CATI; N = 200], or Computer-Assisted Self-Interview [CASI; N = 197]. Logistic regression models were computed to assess survey mode differences for 13 self-reported items related to cancer screenings, adjusting for age, education, income, race, marital status, partner gender, and recruitment source. Results Compared to women assigned to CATI, women assigned to SAMQ were less likely to report two or more years between most recent mammograms (CATI = 23.2% vs. SAMQ = 17.7%; AOR = 0.5, 95% CI = 0.3 – 0.8) and women assigned to CASI were slightly less likely to report being overdue for mammography (CATI = 16.5% vs. CASI = 11.8%; AOR = 0.5, 95% CI = 0.3 – 1.0) and Pap testing (CATI = 14.9% vs. CASI = 10.0%; AOR = 0.5, 95% CI = 0.2 – 1.0). There were no other consistent mode effects. Conclusion Among participants in this sample, mode of data collection had little effect on the reporting of mammography and Pap testing behaviours. Other measures such as efficiency and cost-effectiveness of the mode should also be considered when determining the most appropriate form of data collection for use in monitoring indicators of cancer detection and control.
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- 2008
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34. Surviving extreme polar winters by desiccation: clues from Arctic springtail (Onychiurus arcticus) EST libraries
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Kube Michael, Grubor-Lajšić Gordana, Purać Jelena, Thorne Michael AS, Clark Melody S, Reinhardt Richard, and Worland M Roger
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Ice, snow and temperatures of -14°C are conditions which most animals would find difficult, if not impossible, to survive in. However this exactly describes the Arctic winter, and the Arctic springtail Onychiurus arcticus regularly survives these extreme conditions and re-emerges in the spring. It is able to do this by reducing the amount of water in its body to almost zero: a process that is called "protective dehydration". The aim of this project was to generate clones and sequence data in the form of ESTs to provide a platform for the future molecular characterisation of the processes involved in protective dehydration. Results Five normalised libraries were produced from both desiccating and rehydrating populations of O. arcticus from stages that had previously been defined as potentially informative for molecular analyses. A total of 16,379 EST clones were generated and analysed using Blast and GO annotation. 40% of the clones produced significant matches against the Swissprot and trembl databases and these were further analysed using GO annotation. Extraction and analysis of GO annotations proved an extremely effective method for identifying generic processes associated with biochemical pathways, proving more efficient than solely analysing Blast data output. A number of genes were identified, which have previously been shown to be involved in water transport and desiccation such as members of the aquaporin family. Identification of these clones in specific libraries associated with desiccation validates the computational analysis by library rather than producing a global overview of all libraries combined. Conclusion This paper describes for the first time EST data from the arctic springtail (O. arcticus). This significantly enhances the number of Collembolan ESTs in the public databases, providing useful comparative data within this phylum. The use of GO annotation for analysis has facilitated the identification of a wide variety of ESTs associated with a number of different biochemical pathways involved in the dehydration and recovery process in O. arcticus.
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- 2007
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35. Persistence of duplicated PAC1 receptors in the teleost, Sparus auratus
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Clark Melody S, Elgar Greg, Louro Bruno, de Vet Edwin CJM, Cardoso João CR, and Power Deborah M
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Evolution ,QH359-425 - Abstract
Abstract Background: Duplicated genes are common in vertebrate genomes. Their persistence is assumed to be either a consequence of gain of novel function (neofunctionalisation) or partitioning of the function of the ancestral molecule (sub-functionalisation). Surprisingly few studies have evaluated the extent of such modifications despite the numerous duplicated receptor and ligand genes identified in vertebrate genomes to date. In order to study the importance of function in the maintenance of duplicated genes, sea bream (Sparus auratus) PAC1 receptors, sequence homologues of the mammalian receptor specific for PACAP (Pituitary Adenylate Cyclase-Activating Polypeptide), were studied. These receptors belong to family 2 GPCRs and most of their members are duplicated in teleosts although the reason why both persist in the genome is unknown. Results: Duplicate sea bream PACAP receptor genes (sbPAC1A and sbPAC1B), members of family 2 GPCRs, were isolated and share 77% amino acid sequence identity. RT-PCR with specific primers for each gene revealed that they have a differential tissue distribution which overlaps with the distribution of the single mammalian receptor. Furthermore, in common with mammals, the teleost genes undergo alternative splicing and a PAC1Ahop1 isoform has been characterised. Duplicated orthologous receptors have also been identified in other teleost genomes and their distribution profile suggests that function may be species specific. Functional analysis of the paralogue sbPAC1s in Cos7 cells revealed that they are strongly stimulated in the presence of mammalian PACAP27 and PACAP38 and far less with VIP (Vasoactive Intestinal Peptide). The sbPAC1 receptors are equally stimulated (LOGEC50 values for maximal cAMP production) in the presence of PACAP27 (-8.74 ± 0.29 M and -9.15 ± 0.21 M, respectively for sbPAC1A and sbPAC1B, P > 0.05) and PACAP38 (-8.54 ± 0.18 M and -8.92 ± 0.24 M, respectively for sbPAC1A and sbPAC1B, P > 0.05). Human VIP was found to stimulate sbPAC1A (-7.23 ± 0.20 M) more strongly than sbPAC1B (-6.57 ± 0.14 M, P < 0.05) and human secretin (SCT), which has not so far been identified in fish genomes, caused negligible stimulation of both receptors. Conclusion: The existence of functionally divergent duplicate sbPAC1 receptors is in line with previously proposed theories about the origin and maintenance of duplicated genes. Sea bream PAC1 duplicate receptors resemble the typical mammalian PAC1, and PACAP peptides were found to be more effective than VIP in stimulating cAMP production, although sbPAC1A was more responsive for VIP than sbPAC1B. These results together with the highly divergent pattern of tissue distribution suggest that a process involving neofunctionalisation occurred after receptor duplication within the fish lineage and probably accounts for their persistence in the genome. The characterisation of further duplicated receptors and their ligands should provide insights into the evolution and function of novel protein-protein interactions associated with the vertebrate radiation.
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- 2007
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36. Comparison of patient comprehension of rapid HIV pre-test fundamentals by information delivery format in an emergency department setting
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Clark Melissa A, Gee Erin M, Merchant Roland C, Mayer Kenneth H, Seage George R, and DeGruttola Victor G
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Public aspects of medicine ,RA1-1270 - Abstract
Abstract Background Two trials were conducted to compare emergency department patient comprehension of rapid HIV pre-test information using different methods to deliver this information. Methods Patients were enrolled for these two trials at a US emergency department between February 2005 and January 2006. In Trial One, patients were randomized to a no pre-test information or an in-person discussion arm. In Trial Two, a separate group of patients were randomized to an in-person discussion arm or a Tablet PC-based video arm. The video, "Do you know about rapid HIV testing?", and the in-person discussion contained identical Centers for Disease Control and Prevention-suggested pre-test information components as well as information on rapid HIV testing with OraQuick®. Participants were compared by information arm on their comprehension of the pre-test information by their score on a 26-item questionnaire using the Wilcoxon rank-sum test. Results In Trial One, 38 patients completed the no-information arm and 31 completed the in-person discussion arm. Of these 69 patients, 63.8% had twelve years or fewer of formal education and 66.7% had previously been tested for HIV. The mean score on the questionnaire for the in-person discussion arm was higher than for the no information arm (18.7 vs. 13.3, p ≤ 0.0001). In Trial Two, 59 patients completed the in-person discussion and 55 completed the video arms. Of these 114 patients, 50.9% had twelve years or fewer of formal education and 68.4% had previously been tested for HIV. The mean score on the questionnaire for the video arm was similar to the in-person discussion arm (20.0 vs. 19.2; p ≤ 0.33). Conclusion The video "Do you know about rapid HIV testing?" appears to be an acceptable substitute for an in-person pre-test discussion on rapid HIV testing with OraQuick®. In terms of adequately informing ED patients about rapid HIV testing, either form of pre-test information is preferable than for patients to receive no pre-test information.
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- 2007
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37. Correlates of women's cancer screening and contraceptive knowledge among female emergency department patients
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Bock Beth C, Gee Erin M, Merchant Roland C, Becker Bruce M, and Clark Melissa A
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Gynecology and obstetrics ,RG1-991 ,Public aspects of medicine ,RA1-1270 - Abstract
Abstract Background Lack of knowledge regarding preventive health services for women might impede campaigns to expand these services in the emergency department setting. For 18–55-year-old English-speaking women visiting an urban emergency department, we aimed to: (1) Ascertain their knowledge regarding the applicability, purpose, and recommended intervals of three women's cancer screening and three contraceptive methods; and (2) Determine if patient age, race/ethnicity, medical insurance status, and current or recent usage of these methods are associated with greater or lesser knowledge about them. Methods Emergency department-based survey on recent or current usage and knowledge about Pap smears, breast self-examinations, mammograms, condoms, birth control, and emergency contraception. Analyses included calculation of summary statistics and creation of multivariable logistic regression models. Results Of 1,100 patients eligible for the study, 69.9% agreed to participate. Most of the participants were < age 35, white, single (never married and no partner), Catholic, and had private medical insurance. Participant's recent or current usage of a particular cancer screening or contraceptive method varied by type of method: Pap smear within the past year (69.1%), breast self-exam within the past month (45.5%), mammogram within the past year (65.7% for women age 45–55), condom usage during every episode of sexual intercourse (15.4%), current usage of birth control pills (17.8%), and ever use of emergency contraception (9.3%). The participants correctly answered 87.9% of all survey questions about condoms, 82.5% about birth control pills, 78.5% about breast self-exams, 52.9% about Pap smears, 35.4% about mammograms, and 25.0% about emergency contraception. In multivariable logistic regression models, survey participants who had private medical insurance and those who recently or currently used a given screening or contraceptive method had a greater odds of correctly answering all questions about each cancer screening or contraceptive method. Conclusion Although these female ED patients demonstrated strong knowledge on some women's cancer screening and contraceptive methods, there were several areas of knowledge deficit. Women without private medical insurance and those who have not used a particular cancer screening or contraceptive method demonstrated less knowledge. Reduced knowledge about women's cancer screening and contraceptive methods should be considered during clinical encounters and when instituting or evaluating emergency department-based initiatives that assess the need for these methods.
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- 2007
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38. Evolution of secretin family GPCR members in the metazoa
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Clark Melody S, Vieira Florbela A, Pinto Vanda C, Cardoso João CR, and Power Deborah M
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Evolution ,QH359-425 - Abstract
Abstract Background Comparative approaches using protostome and deuterostome data have greatly contributed to understanding gene function and organismal complexity. The family 2 G-protein coupled receptors (GPCRs) are one of the largest and best studied hormone and neuropeptide receptor families. They are suggested to have arisen from a single ancestral gene via duplication events. Despite the recent identification of receptor members in protostome and early deuterostome genomes, relatively little is known about their function or origin during metazoan divergence. In this study a comprehensive description of family 2 GPCR evolution is given based on in silico and expression analyses of the invertebrate receptor genes. Results Family 2 GPCR members were identified in the invertebrate genomes of the nematodes C. elegans and C. briggsae, the arthropods D. melanogaster and A. gambiae (mosquito) and in the tunicate C. intestinalis. This suggests that they are of ancient origin and have evolved through gene/genome duplication events. Sequence comparisons and phylogenetic analyses have demonstrated that the immediate gene environment, with regard to gene content, is conserved between the protostome and deuterostome receptor genomic regions. Also that the protostome genes are more like the deuterostome Corticotrophin Releasing Factor (CRF) and Calcitonin/Calcitonin Gene-Related Peptide (CAL/CGRP) receptors members than the other family 2 GPCR members. The evolution of family 2 GPCRs in deuterostomes is characterised by acquisition of new family members, with SCT (Secretin) receptors only present in tetrapods. Gene structure is characterised by an increase in intron number with organismal complexity with the exception of the vertebrate CAL/CGRP receptors. Conclusion The family 2 GPCR members provide a good example of gene duplication events occurring in tandem with increasing organismal complexity during metazoan evolution. The putative ancestral receptors are proposed to be more like the deuterostome CAL/CGRP and CRF receptors and this may be associated with their fundamental role in calcium regulation and the stress response, both of which are essential for survival.
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- 2006
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39. In vitro cytotoxicity of Manville Code 100 glass fibers: Effect of fiber length on human alveolar macrophages
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Jones William, Baron Paul, Deye Gregory J, Clark Melissa P, Ameredes Bill T, Calhoun William J, Zeidler-Erdely Patti C, Blake Terri, and Castranova Vincent
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Toxicology. Poisons ,RA1190-1270 ,Industrial hygiene. Industrial welfare ,HD7260-7780.8 - Abstract
Abstract Background Synthetic vitreous fibers (SVFs) are inorganic noncrystalline materials widely used in residential and industrial settings for insulation, filtration, and reinforcement purposes. SVFs conventionally include three major categories: fibrous glass, rock/slag/stone (mineral) wool, and ceramic fibers. Previous in vitro studies from our laboratory demonstrated length-dependent cytotoxic effects of glass fibers on rat alveolar macrophages which were possibly associated with incomplete phagocytosis of fibers ≥ 17 μm in length. The purpose of this study was to examine the influence of fiber length on primary human alveolar macrophages, which are larger in diameter than rat macrophages, using length-classified Manville Code 100 glass fibers (8, 10, 16, and 20 μm). It was hypothesized that complete engulfment of fibers by human alveolar macrophages could decrease fiber cytotoxicity; i.e. shorter fibers that can be completely engulfed might not be as cytotoxic as longer fibers. Human alveolar macrophages, obtained by segmental bronchoalveolar lavage of healthy, non-smoking volunteers, were treated with three different concentrations (determined by fiber number) of the sized fibers in vitro. Cytotoxicity was assessed by monitoring cytosolic lactate dehydrogenase release and loss of function as indicated by a decrease in zymosan-stimulated chemiluminescence. Results Microscopic analysis indicated that human alveolar macrophages completely engulfed glass fibers of the 20 μm length. All fiber length fractions tested exhibited equal cytotoxicity on a per fiber basis, i.e. increasing lactate dehydrogenase and decreasing chemiluminescence in the same concentration-dependent fashion. Conclusion The data suggest that due to the larger diameter of human alveolar macrophages, compared to rat alveolar macrophages, complete phagocytosis of longer fibers can occur with the human cells. Neither incomplete phagocytosis nor length-dependent toxicity was observed in fiber-exposed human macrophage cultures. In contrast, rat macrophages exhibited both incomplete phagocytosis of long fibers and length-dependent toxicity. The results of the human and rat cell studies suggest that incomplete engulfment may enhance cytotoxicity of fiber glass. However, the possibility should not be ruled out that differences between human versus rat macrophages other than cell diameter could account for differences in fiber effects.
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- 2006
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40. Speaking out.
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Clark ME, Morrison C, and Worthington JL
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- 1984
41. Preliminary evaluation of reliability and criterion validity of Actiwatch-Score.
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Gironda RJ, Lloyd J, Clark ME, and Walker RL
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The restoration of normal physical activity is a primary objective of most chronic pain rehabilitative interventions, yet few clinically practical objective measures of activation exist. Actigraphy is one technology that promises to fill this void in the field of pain outcomes assessment. This study evaluates the measurement properties of one of several commercially available actigraphs: the Actiwatch-Score (AW-S). We conducted separate trials to examine concordance between units when worn concurrently at the same and different body sites and to compare the AW-S to a validated optical three-dimensional motion-tracking system. The data indicate that the AW-S has excellent interunit reliability and good criterion validity, but its intersite reliability varies with activity type. These results suggest that this device, and those like it, warrants further investigation and is likely to yield valuable data regarding the optimal application of this technology. [ABSTRACT FROM AUTHOR]
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- 2007
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42. Band Visibility in High-Resolution Optical Coherence Tomography Assessed With a Custom Review Tool and Updated, Histology-Derived Nomenclature.
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Goerdt L, Swain TA, Kar D, McGwin G, Berlin A, Clark ME, Owsley C, Sloan KR, and Curcio CA
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- Humans, Adult, Aged, Young Adult, Male, Female, Retina diagnostic imaging, Aged, 80 and over, Middle Aged, Reproducibility of Results, Tomography, Optical Coherence methods, Terminology as Topic, Macular Degeneration pathology, Macular Degeneration diagnostic imaging, Aging
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Purpose: For structure-function research at the transition of aging to age-related macular degeneration, we refined the current consensus optical coherence tomography (OCT) nomenclature and evaluated a novel review software for investigational high-resolution OCT imaging (HR-OCT; <3 µm axial resolution)., Method: Volume electron microscopy, immunolocalizations, histology, and investigational devices informed a refined OCT nomenclature for a custom ImageJ-based review tool to assess retinal band visibility. We examined effects on retinal band visibility of automated real-time averaging (ART) 9 and 100 (11 eyes of 10 healthy young adults), aging (10 young vs 22 healthy aged), and age-related macular degeneration (AMD; 22 healthy aged, 17 early (e)AMD, 15 intermediate (i)AMD). Intrareader reliability was assessed., Results: Bands not included in consensus nomenclature are now visible using HR-OCT: inner plexiform layer (IPL) 1-5, outer plexiform layer (OPL) 1-2, outer segment interdigitation zone 1-2 (OSIZ, including hyporeflective outer segments), and retinal pigment epithelium (RPE) 1-5. Cohen's kappa was 0.54-0.88 for inner and 0.67-0.83 for outer retinal bands in a subset of 10 eyes. IPL-3-5 and OPL-2 visibility benefitted from increased ART. OSIZ-2 and RPE-1,2,3,5 visibility was worse in aged eyes than in young eyes. OSIZ-1-2, RPE-1, and RPE-5 visibility decreased in eAMD and iAMD compared to healthy aged eyes., Conclusions: We reliably identified 28 retinal bands using a novel review tool for HR-OCT. Image averaging improved inner retinal band visibility. Aging and AMD development impacted outer retinal band visibility., Translational Significance: Detailed knowledge of anatomic structures visible on OCT will enhance precision in research, including AI training and structure-function analyses.
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- 2024
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43. A content analysis of parents' reflections on pathogenic and uncertain pediatric oncology germline sequencing results.
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Howard Sharp KM, Clark ME, Jurbergs N, Ouma A, Harrison L, Taylor L, Hamilton K, McGee RB, Nuccio R, Hines-Dowell S, Gattuso JS, Pritchard M, Mandrell B, Tercyak KP, Johnson LM, and Nichols KE
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- Humans, Female, Male, Child, Adult, Adolescent, Genetic Testing, Child, Preschool, Genetic Predisposition to Disease, Uncertainty, Emotions, Adaptation, Psychological, Middle Aged, Genetic Counseling psychology, Parents psychology, Neoplasms genetics, Neoplasms psychology, Germ-Line Mutation
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Germline genomic sequencing is increasingly integrated into pediatric cancer care, with pathogenic cancer-predisposing variants identified among 5-18% of affected children and variants of uncertain significance (VUS) in up to 70%. Given the potential medical implications for children and their families, parents' psychosocial responses to learning results are important to understand. Parents of children with cancer who learned their children's germline pathogenic or VUS results following paired tumor and germline genomic sequencing described their cognitive and affective responses to results in an open-ended write-in question after disclosure (M = 10 months post-disclosure; range = 1-28). Responses were coded and categorized using content analysis, then compared across results using chi-square and Fisher's exact test. Parents of children with pathogenic (n = 9), VUS (n = 52), and pathogenic plus VUS results (n = 9) described negative emotions, positive reactions, mixed emotions (i.e., positive and negative emotions), and neutral reactions. Negative emotions were described significantly more frequently with pathogenic results than VUS only (χ
2 = 5.19; p = .02), with peace of mind and empowerment only described for those with VUS. Parents also described approach(es) to coping (e.g., faith, plan of action) and reactions specific to the uncertainty of VUS (e.g., disappointment at no explanation for cancer etiology). A subset with VUS described decreasing worry/distress with increased understanding of results, whereas others displayed misconceptions regarding VUS. Screening for emotional adjustment is warranted for parents of children with cancer receiving pathogenic germline results, and screening for understanding is warranted with VUS. Findings highlight the importance of pre-and posttest genetic counseling., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)- Published
- 2024
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44. Acute ocular hypertension in the living human eye: Model description and initial cellular responses to elevated intraocular pressure.
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Girkin CA, Strickland RG, Somerville MM, Anne Garner M, Grossman GH, Blake A, Kumar N, Ianov L, Fazio MA, Clark ME, and Gross AK
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- Humans, Glial Fibrillary Acidic Protein metabolism, Male, Retina physiopathology, Acute Disease, Female, Middle Aged, Adult, Immunohistochemistry, Intraocular Pressure physiology, Ocular Hypertension physiopathology, Ocular Hypertension metabolism, Optic Disk metabolism
- Abstract
This initial methods study presents the initial immunohistochemical and transcriptomic changes in the optic nerve head and retina from three research-consented brain-dead organ donors following prolonged and transient intraocular pressure (IOP) elevation. In this initial study, research-consented brain-dead organ donors were exposed to unilateral elevation of IOP for 7.5 h (Donor 1), 30 h (Donor 2), and 1 h (Donor 3) prior to organ procurement. Optic nerve tissue and retinal tissue was obtained following organ procurement for immunohistological and transcriptomic analysis. Optic nerve sections in Donor 1 exposed to 7.5-hours of unilateral sub-ischemic IOP elevation demonstrated higher levels of protein expression of the astrocytic marker, glial fibrillary acidic protein (GFAP), within the lamina cribrosa with greatest expression inferior temporally in the treated eye compared to control. Spatial transcriptomic analysis performed on optic nerve head tissues from Donor 2 exposed to 30 h of unilateral IOP elevation demonstrated differential transcription of mRNA across laminar and scleral regions. Immunohistochemistry of retinal sections from Donor 2 exhibited higher GFAP and IBA1 expression in the treated eye compared with control, but this was not observed in Donor 3, which was exposed to only 1-hour of IOP elevation. While there were no differences in GFAP protein expression in the retina following the 1-hour IOP elevation in Donor 3, there were higher levels of transcription of GFAP in the inner nuclear layer, and CD44 in the retinal ganglion cell layer, indicative of astrocytic and Müller glial reactivity as well as an early inflammatory response, respectively. We found that transcriptomic differences can be observed across treated and control eyes following unilateral elevation of IOP in brain dead organ donors. The continued development of this model affords the unique opportunity to define the acute mechanotranscriptomic response of the optic nerve head, evaluate the injury and repair mechanisms in the retina in response to IOP elevation, and enable correlation of in vivo imaging and functional testing with ex vivo cellular responses for the first time in the living human eye., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)
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- 2024
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45. Outer Retinal Thinning is Associated With Brain Atrophy in Early Age-Related Macular Degeneration.
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Jiang Y, Swain T, Gim N, Blazes M, Donald CM, Rokem A, Owen JP, Balu N, Clark ME, Goerdt L, McGwin G, Hunt D, Curcio CA, Levendovszky SR, Trittschuh EH, Owsley C, and Lee CS
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- Humans, Female, Cross-Sectional Studies, Male, Aged, Aged, 80 and over, Brain pathology, Brain diagnostic imaging, Retina pathology, Retina diagnostic imaging, Macular Degeneration diagnosis, Tomography, Optical Coherence methods, Magnetic Resonance Imaging, Atrophy
- Abstract
Purpose: Both retinal changes and age-related macular degeneration (AMD) have been shown to be associated with Alzheimer's disease and related dementias (ADRD). In AMD, the outer retina is impacted significantly and early, but little is known about its association with cognition or changes in brain morphometry. This study investigates the relationship between retinal and brain morphometry in older adults with early and intermediate AMD., Design: Cross-sectional study., Methods: Adults ≥70 years with normal, early, and intermediate AMD were recruited from Callahan Eye Hospital Clinics at the University of Alabama at Birmingham. Participants underwent cognitive testing, optical coherence tomography, and magnetic resonance imaging. Associations of retinal layer thickness with brain volume and thickness of specific brain regions were evaluated utilizing multivariable linear regression. The relevance of retinal thickness variables in brain volumetrics was quantified using least absolute shrinkage and selection operator regression models. Correlations between demographic variables, cognitive scores, and brain morphometry were evaluated., Results: Participants with thinner outer retina had significantly smaller hippocampus (β = 0.019, P = .022), lower occipital cortex regions of interest (occipital ROIs) thickness (β = 5.68, P = .020), and lower cortical thickness in ADRD-related brain regions (β = 7.72, P = .006). People with thinner total retina had significantly lower occipital ROIs (β = 3.19, P = .009) and ADRD-related brain region (β = 3.94, P = .005) thickness. Outer retinal thickness in the outer Early Treatment of Diabetic Retinopathy Study ring was the most frequently reported retinal variable associated with brain morphometry on least absolute shrinkage and selection operator regression. Total gray matter volume showed positive correlations with education (Pearson's r = 0.30, P = .022)., Conclusions: In older adults with normal retinal aging and early and intermediate AMD, thinner outer retina had specific associations with brain regions primarily involved in vision and cognition, such as lower hippocampal volume and lower thickness of the occipital ROIs and brain regions known to show early structural changes in dementia., (Copyright © 2024 Elsevier Inc. All rights reserved.)
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- 2025
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46. Analysis of bigmouth buffalo Ictiobus cyprinellus spawning phenology in Minnesota reveals 50-year recruitment failure and conservation concern.
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Lackmann AR, Seybold S, Bielak-Lackmann ES, Ford W, Butler MG, and Clark ME
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- Animals, Female, Male, Minnesota, Seasons, Reproduction physiology, Conservation of Natural Resources
- Abstract
The bigmouth buffalo Ictiobus cyprinellus (Catostomidae) is a freshwater fish native to North America that is known for its longevity. During the 1970s, the bigmouth buffalo was recorded as declining in Canada, Minnesota, and North Dakota and became a protected species in Canada. In the USA, population declines are exacerbated by wasteful recreational bowfishing, lack of fisheries management, and overall lack of knowledge. However, recent studies have revealed the exceptional lifespan of bigmouth buffalo, their negligible senescence, slow growth, delayed maturity, and episodic recruitment. Yet little is known about the spawning phenology of bigmouth buffalo, nor their age demographics in east central Minnesota. In this 2021-2023 study of bigmouth buffalo from Rice Lake National Wildlife Refuge we found that 99.7% (389 of 390) of the extant population hatched prior to 1972 despite annual spawning in Rice Lake. Moreover, recruitment success declined significantly since water control measures were established (1953). We found males arrive to spawning grounds with females but depart later, that both the midpoint and duration of spawn significantly vary across years, and that more massive females of the same age range invest disproportionately more in ovaries. Extensive post-spawn seining revealed bigmouth buffalo young-of-the-year in low numbers, but by mid-to-late summer they were no longer evident having likely succumbed to predation. Overall, these findings thoroughly reveal one of the oldest populations of vertebrate currently known (median age of 79 years as of 2024) and expose the stark vulnerability of a bigmouth buffalo population for which substantial recruitment has not occurred for more than six decades. Multiple lines of evidence indicate that the long-lived bigmouth buffalo is vulnerable, that a precautionary approach is immediately needed, and that the unlimited and unregulated kill-fishery be closed., (© 2024. The Author(s).)
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- 2024
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47. Genomic profiling of pediatric hematologic malignancies and diagnosis of cancer predisposition syndromes: tumoronly versus paired tumor-normal sequencing.
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Newman H, Clark ME, Wong D, Wu J, Brodeur GM, Hunger SP, Tasian SK, Olson T, Warren JT, Teachey DT, Bona K, Schubert J, Golenberg N, Patel M, Denenberg EH, Fanning EA, Chen J, Luke T, Charles S, Gallo D, Cao K, Fu W, Fan Z, Surrey LF, Wertheim G, Luo M, MacFarland SP, Li MM, and Zhong Y
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- Humans, Child, Male, Genomics methods, Female, Adolescent, Child, Preschool, Neoplastic Syndromes, Hereditary genetics, Neoplastic Syndromes, Hereditary diagnosis, Gene Expression Profiling, High-Throughput Nucleotide Sequencing, Hematologic Neoplasms genetics, Hematologic Neoplasms diagnosis, Genetic Predisposition to Disease
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- 2024
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48. Investigating the effect of reduced temperatures on the efficacy of rhabdovirus-based viral vector platforms.
- Author
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Kakish JE, Mehrani Y, Kodeeswaran A, Geronimo K, Clark ME, van Vloten JP, Karimi K, Mallard BA, Meng B, Bridle BW, and Knapp JP
- Subjects
- Humans, Animals, Vesiculovirus physiology, Vesiculovirus genetics, Oncolytic Virotherapy methods, Cell Line, Genetic Vectors genetics, Cell Line, Tumor, Temperature, Cold Temperature, Rhabdoviridae physiology, Rhabdoviridae genetics, Virus Replication, Oncolytic Viruses physiology, Oncolytic Viruses genetics
- Abstract
Rhabdoviral vectors can induce lysis of cancer cells. While studied almost exclusively at 37 °C, viruses are subject to a range of temperatures in vivo , including temperatures ≤31 °C. Despite potential implications, the effect of temperatures <37 °C on the performance of rhabdoviral vectors is unknown. We investigated the effect of low anatomical temperatures on two rhabdoviruses, vesicular stomatitis virus (VSV) and Maraba virus (MG1). Using a metabolic resazurin assay, VSV- and MG1-mediated oncolysis was characterized in a panel of cell lines at 28, 31, 34 and 37 °C. The oncolytic ability of both viruses was hindered at 31 and 28 °C. Cold adaptation of both viruses was attempted as a mitigation strategy. Viruses were serially passaged at decreasing temperatures in an attempt to induce mutations. Unfortunately, the cold-adaptation strategies failed to potentiate the oncolytic activity of the viruses at temperatures <37 °C. Interestingly, we discovered that viral replication was unaffected at low temperatures despite the abrogation of oncolytic activity. In contrast, the proliferation of cancer cells was reduced at low temperatures. Equivalent oncolytic effects could be achieved if cells at low temperatures were treated with viruses for longer times. This suggests that rhabdovirus-mediated oncolysis could be compromised at low temperatures in vivo where therapeutic windows are limited.
- Published
- 2024
- Full Text
- View/download PDF
49. Extent and Topography of Subretinal Drusenoid Deposits Associate With Rod-Mediated Vision in Aging and AMD: ALSTAR2 Baseline.
- Author
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Goerdt L, Amjad M, Swain TA, McGwin G, Clark ME, Owsley C, Sloan KR, Curcio CA, and Kar D
- Subjects
- Humans, Female, Aged, Male, Middle Aged, Aging physiology, Aged, 80 and over, Fluorescein Angiography methods, Deep Learning, Tomography, Optical Coherence methods, Retinal Drusen diagnosis, Retinal Drusen physiopathology, Dark Adaptation physiology, Retinal Rod Photoreceptor Cells physiology, Retinal Rod Photoreceptor Cells pathology, Macular Degeneration physiopathology, Macular Degeneration diagnosis, Visual Acuity physiology
- Abstract
Purpose: In AMD, rod-mediated dark adaptation (RMDA) at 5° eccentricity is slower in eyes with subretinal drusenoid deposits (SDDs) than in eyes without. Here we quantified SDD burden using supervised deep learning for comparison to vision and photoreceptor topography., Methods: In persons ≥60 years from the Alabama Study on Early Age-Related Macular Degeneration 2, normal, early AMD, and intermediate AMD eyes were classified by the AREDS nine-step system. A convolutional neural network was trained on 55°-wide near-infrared reflectance images for SDD segmentation. Trained graders annotated ground truth (SDD yes/no). Predicted and true datasets agreed (Dice coefficient, 0.92). Inference was manually proofread using optical coherence tomography. The mean SDD area (mm2) was compared among diagnostic groups (linear regression) and to vision (age-adjusted Spearman correlations). Fundus autofluorescence images were used to mask large vessels in SDD maps., Results: In 428 eyes of 428 persons (normal, 218; early AMD, 120; intermediate AMD, 90), the mean SDD area differed by AMD severity (P < 0.0001): 0.16 ± 0.87 (normal), 2.48 ± 11.23 (early AMD), 11.97 ± 13.33 (intermediate AMD). Greater SDD area was associated with worse RMDA (r = 0.27; P < 0.0001), mesopic (r = -0.13; P = 0.02) and scotopic sensitivity (r = -0.17; P < 0.001). SDD topography peaked at 5° superior, extended beyond the Early Treatment of Diabetic Retinopathy Study grid and optic nerve, then decreased., Conclusions: SDD area is associated with degraded rod-mediated vision. RMDA 5° (superior retina) probes where SDD is maximal, closer to the foveal center than the rod peak at 3 to 6 mm (10.4°-20.8°) superior and the further eccentric peak of rod:cone ratio. Topographic data imply that factors in addition to rod density influence SDD formation.
- Published
- 2024
- Full Text
- View/download PDF
50. Repeatability of Rod-Mediated Dark Adaptation Testing in Normal Aging and Early and Intermediate Age-Related Macular Degeneration.
- Author
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Owsley C, Swain TA, McGwin G Jr, Bernard MM, Clark ME, and Curcio CA
- Subjects
- Humans, Aged, Male, Female, Reproducibility of Results, Aged, 80 and over, Middle Aged, Vision Tests, Dark Adaptation physiology, Retinal Rod Photoreceptor Cells physiology, Aging physiology, Visual Acuity physiology, Macular Degeneration physiopathology, Macular Degeneration diagnosis
- Abstract
Purpose: The vulnerability of rod photoreceptors in aging and early and intermediate age-related macular degeneration (AMD) has been well documented. Rod-mediated dark adaptation (RMDA) is a measure of the recovery of light sensitivity in rod photoreceptors following a bright light. Delays in RMDA during early and intermediate AMD have been widely reported. For RMDA's promise as an outcome for trials targeted at early and intermediate AMD to be realized, excellent test-retest reliability, its repeatability, must be established., Methods: Test-retest performance in a commonly used RMDA test based on the rod intercept time metric (RIT) was evaluated in participants with early and intermediate AMD and with normal retinal aging with testing approximately 2 weeks apart. The test target was placed at 5° eccentricity superior to the foveal center, an area with maximal rod loss in aging and AMD. Disease severity was identified by a trained and masked grader of fundus photographs using both the AREDS 9-step and Beckman classification systems. Bland-Altman plots and intra-class correlation coefficients (ICC) evaluated repeatability., Results: The analysis sample consisted of 37 older adults (mean age 76 years, standard deviation 5), with approximately one-third of the sample in each of three groups - normal aging, early AMD, and intermediate AMD. For the total sample, the ICC was 0.98. For individual AMD groups for both AREDS 9-step and Beckman classifications, the ICCs were also very high ranging from 0.82 to 0.99., Conclusion: We demonstrated that RMDA testing using the RIT metric has excellent repeatability when target location is at 5° in studying older adults from normal aging to intermediate AMD, suggesting the reliable use of this functional measure in trials.
- Published
- 2024
- Full Text
- View/download PDF
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