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  1. Article ; Online: The gut microbiome–Does stool represent right?

    Orly Levitan / Lanying Ma / Donato Giovannelli / Dawn B. Burleson / Peter McCaffrey / Ayin Vala / David A. Johnson

    Heliyon, Vol 9, Iss 3, Pp e13602- (2023)

    2023  

    Abstract: Many stool-based gut microbiome studies have highlighted the importance of the microbiome. However, we hypothesized that stool is a poor proxy for the inner-colonic microbiome and that studying stool samples may be inadequate to capture the true inner- ... ...

    Abstract Many stool-based gut microbiome studies have highlighted the importance of the microbiome. However, we hypothesized that stool is a poor proxy for the inner-colonic microbiome and that studying stool samples may be inadequate to capture the true inner-colonic microbiome. To test this hypothesis, we conducted prospective clinical studies with up to 20 patients undergoing an FDA-cleared gravity-fed colonic lavage without oral purgative pre-consumption. The objective of this study was to present the analysis of inner-colonic microbiota obtained non-invasively during the lavage and how these results differ from stool samples. The inner-colonic samples represented the descending, transverse, and ascending colon. All samples were analyzed for 16S rRNA and shotgun metagenomic sequences. The taxonomic, phylogenetic, and biosynthetic gene cluster analyses showed a distinctive biogeographic gradient and revealed differences between the sample types, especially in the proximal colon. The high percentage of unique information found only in the inner-colonic effluent highlights the importance of these samples and likewise the importance of collecting them using a method that can preserve these distinctive signatures. We proposed that these samples are imperative for developing future biomarkers, targeted therapeutics, and personalized medicine.
    Keywords Microbiome ; Gut microbiome ; Biogeography ; Bowel prep ; Colonoscopy ; Personalized medicine ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
    Subject code 500
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Sleep disruption due to nocturnal heartburn

    David A. Johnson / Amisha M. Parikh-Das / Evren Atillasoy / Hayk Davtyan / Leslie Shur / Andrea S. Blevins-Primeau / Nathaniel F. Watson

    Exploration of Medicine, Vol 4, Iss 6, Pp 1014-

    a review of the evidence and clinical implications

    2023  Volume 1025

    Abstract: Nocturnal heartburn (NHB) is a symptom that affects up to 25% of the general population and has been shown to cause sleep disruption that adversely affects quality of life and psychomotor performance. Few studies have evaluated the association between ... ...

    Abstract Nocturnal heartburn (NHB) is a symptom that affects up to 25% of the general population and has been shown to cause sleep disruption that adversely affects quality of life and psychomotor performance. Few studies have evaluated the association between occasional NHB and sleep disturbances; therefore, this connection may be underappreciated and left untreated by the primary care provider and patient, with potentially significant negative clinical consequences and effects on quality of life. This review sought to describe what is currently known about the interplay between occasional NHB and sleep disruption, and identify whether acid suppression therapy can improve symptoms of occasional NHB and associated sleep disruptions. The pathophysiology of heartburn-induced sleep disruption appears to follow a bidirectional cycle due to the normal physiologic changes that occur in the upper gastrointestinal tract during sleep and due to the potential for heartburn symptoms to cause sleep arousal. The majority of the identified studies suggested that pharmacologic interventions for acid reduction, including proton pump inhibitors or histamine type-2 receptor antagonists (H2RAs), improved objective and/or subjective sleep outcomes among individuals with gastroesophageal reflux disease (GERD) and NHB. Several studies specific to famotidine demonstrated that treatment with 10 mg or 20 mg reduced nighttime awakenings due to NHB. In conclusion, NHB symptoms can cause sleep dysfunction that can have a profound adverse downstream effect on quality of life, next-day functioning, and health-related outcomes. The current approach to managing occasional NHB is similar to that associated with GERD, highlighting the need for studies specific to the occasional heartburn population. Health care providers should investigate NHB as one of the potential causes of sleep complaints, and patients with heartburn should be questioned about sleep quality, recalled arousals, next-day vitality, early fatigue, and next-day functioning.
    Keywords heartburn ; gastroesophageal reflux disease ; reflux ; sleep ; nocturnal heartburn ; health related outcomes ; histamine 2 receptor antagonists ; sleep dysfunction ; Other systems of medicine ; RZ201-999
    Subject code 610
    Language English
    Publishing date 2023-12-01T00:00:00Z
    Publisher Open Exploration Publishing Inc.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: The Gestation and Growth of the Periodic Table

    David A. Johnson / Alan F. Williams

    CHIMIA, Vol 73, Iss

    2019  Volume 3

    Abstract: The development of ideas of chemical periodicity from Lavoisier to Mendeleyev's first periodic table of 1869 is surveyed. Although his first periodic table contained a number of errors and weaknesses, his remarkable predictions of the properties of ... ...

    Abstract The development of ideas of chemical periodicity from Lavoisier to Mendeleyev's first periodic table of 1869 is surveyed. Although his first periodic table contained a number of errors and weaknesses, his remarkable predictions of the properties of several then unknown elements, together with his capacity to adapt the table to new discoveries, slowly led to its general acceptance. The theory of atomic structure slowly developed to a point where it could rationalise the structure of the table which had, however, been established solely on the basis of experimental observations. Chemistry has played the central role, up to and including the final modification of Seaborg to introduce the actinides – although this had been foreseen by Alfred Werner! Finally we discuss the many physical forms in which the table has been presented.
    Keywords Actinides ; Lanthanides ; Mendeleyev ; Periodic table ; Chemistry ; QD1-999
    Language German
    Publishing date 2019-03-01T00:00:00Z
    Publisher Swiss Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Synthetic studies towards N-substituted 3-vinyl-4-piperidineacetic acid derivatives

    David A. Johnson / Gordon W. Gribble

    ARKIVOC, Vol 2019, Iss 5, Pp 178-

    2019  Volume 195

    Keywords Organic chemistry ; QD241-441
    Language English
    Publishing date 2019-03-01T00:00:00Z
    Publisher Arkat USA, Inc.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Gastrointestinal microbiome and coronavirus disease

    Kevin V. Houston / Ankit Patel / Michael Saadeh / Alejandra Vargas / Ana Rosa Vilela Sangay / Steve M. D'Souza / Byung Soo Yoo / David A. Johnson

    Exploration of Medicine, Vol 4, Iss 2, Pp 157-

    evidence of a bidirectional association

    2023  Volume 165

    Abstract: The gastrointestinal (GI) microbiome remains an emerging topic of study and the characterization and impact on human health and disease continue to be an area of great interest. Similarly, the coronavirus disease 2019 (COVID-19) pandemic has ... ...

    Abstract The gastrointestinal (GI) microbiome remains an emerging topic of study and the characterization and impact on human health and disease continue to be an area of great interest. Similarly, the coronavirus disease 2019 (COVID-19) pandemic has significantly impacted the healthcare system with active disease, lasting effects, and complications with the full impact yet to be determined. The most current evidence of the interaction between COVID-19 and the GI microbiome is reviewed, with a focus on key mediators and the microbiome changes associated with acute disease and post-acute COVID-19 syndrome (PACS).
    Keywords gastrointestinal microbiome ; dysbiosis ; coronavirus disease 2019 ; post-acute coronavirus disease 2019 syndrome ; long-haul coronavirus disease 2019 ; post infection irritable bowel syndrome ; Other systems of medicine ; RZ201-999
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher Open Exploration Publishing Inc.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: The impact of COVID-19 pandemic on diagnosis and management of gastrointestinal cancers

    Byung Soo Yoo / Ankit Patel / Kevin V. Houston / Alejandra Vargas / Ana Rosa Vilela Sangay / Steve M. D’Souza / David A. Johnson

    Exploration of Medicine, Vol 4, Iss 3, Pp 356-

    2023  Volume 362

    Abstract: Gastrointestinal (GI) cancer is one of the leading causes of death that affect many patients around the world. The coronavirus disease 2019 (COVID-19) pandemic significantly impacted our healthcare system in large that diagnosis and management of GI ... ...

    Abstract Gastrointestinal (GI) cancer is one of the leading causes of death that affect many patients around the world. The coronavirus disease 2019 (COVID-19) pandemic significantly impacted our healthcare system in large that diagnosis and management of GI cancer have suffered with a reduction in cancer screening. This review will describe the current practices of cancer screening during COVID-19 pandemic and summarize how each GI cancer (esophageal, gastric, colorectal, and hepatocellular cancers) has been affected by COVID-19. World widely there has been a decreasing trend in screening, diagnosis, and management of GI cancers during the COVID-19 pandemic. Many healthcare institutions are now observing the effect of this change and implementing practice variations to adapt to the pandemic.
    Keywords covid-19 pandemic ; gastrointestinal cancer ; gastric cancer ; cancer screening ; mortality ; prognosis ; Other systems of medicine ; RZ201-999
    Subject code 610
    Language English
    Publishing date 2023-06-01T00:00:00Z
    Publisher Open Exploration Publishing Inc.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Differential Effect of Light and Dark Period Sleep Fragmentation on Composition of Gut Microbiome and Inflammation in Mice

    Larry D. Sanford / Laurie L. Wellman / Richard P. Ciavarra / Edward C. Oldfield / Rouzbeh Shams / Jennifer L. Copare / David A. Johnson

    Life, Vol 11, Iss 1283, p

    2021  Volume 1283

    Abstract: Bi-directional interactions amongst the gut microbiota, immune system, and brain function are thought to be critical mediators of health and disease. The role sleep plays in mediating these interactions is not known. We assessed the effects of sleep ... ...

    Abstract Bi-directional interactions amongst the gut microbiota, immune system, and brain function are thought to be critical mediators of health and disease. The role sleep plays in mediating these interactions is not known. We assessed the effects of sleep fragmentation (SF) on the microbiota–gut–brain axis. Male C57BL/6NCrl mice (4 to 5 per cage, fed standard lab chow) experienced SF via mechanical stimulation at 2 min intervals during the light (SF) and dark (DD, dark disturbances) periods. Home cage (HC) controls were undisturbed. After 10 days, fecal samples were collected at light onset, midday, light offset, and midnight. Samples were also collected after 10 days without SF. Subsequently, the mice were randomized across groups and allowed 20 additional days of recovery followed by 10 days of SF or DD. To assess effects on the microbiota, 16S rRNA sequencing was used, and mesenteric lymph nodes (MLNs) and cortex and medial prefrontal cortex were analyzed using cytokine arrays. SF and DD produced significant alterations in the microbiota compared to HC, and DD had greater impact than SF on some organisms. SF produced marked suppression in MLNs of chemokines that regulate inflammation (CCL3, CCL4 and their receptor CCR5) and maintain the immune mucosal barrier (Cxcl13) at the same time that cortical cytokines (IL-33) indicated neuroinflammation. DD effects on immune responses were similar to HC. These data suggest that SF alters the microbiome and suppresses mucosal immunity at the same time that mediators of brain inflammation are upregulated. The translational implications for potential application to clinical care are compelling.
    Keywords chemokine ; cytokine ; immune system ; microbiome ; neuroinflammation ; Science ; Q
    Subject code 610
    Language English
    Publishing date 2021-11-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article: Stereoselective One-Pot Deconjugation, Aldol, and Stabilized Peterson Olefination of α-Trialkylsilyl-β-alkyl-α,β-Unsaturated Esters

    Probasco, Michael S / David A. Johnson / Michael P. Jennings

    Organic letters. 2019 Feb. 20, v. 21, no. 5

    2019  

    Abstract: A stereoselective reaction process including a one-pot deconjugation, aldol, and stabilized Peterson olefination of α-trialkylsilyl-β-alkyl-α,β-unsaturated esters coupled with aliphatic aldehydes is described. This sequential procedure afforded tri-and ... ...

    Abstract A stereoselective reaction process including a one-pot deconjugation, aldol, and stabilized Peterson olefination of α-trialkylsilyl-β-alkyl-α,β-unsaturated esters coupled with aliphatic aldehydes is described. This sequential procedure afforded tri-and disubstituted conjugated diene ester products with dr values of 12–20:1 for the newly established alkene moieties in modest to good isolated yields.
    Keywords aldehydes ; chemical reactions ; esters ; moieties ; stereoselectivity
    Language English
    Dates of publication 2019-0220
    Size p. 1379-1383.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1523-7052
    DOI 10.1021/acs.orglett.9b00069
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: Treatment with clopidogrel and proton pump inhibitors in combination

    David A. Johnson / Danial E. Baker

    Open Journal of Internal Medicine, Vol 01, Iss 03, Pp 45-

    a review of emerging evidence

    2011  Volume 55

    Abstract: Proton pump inhibitors often are prescribed in combination with clopidogrel to decrease risk of gastrointestinal bleeding after acute coronary syndrome. Clopidogrel is a prodrug that has to be metabolized in the liver to generate the active metabolite. ... ...

    Abstract Proton pump inhibitors often are prescribed in combination with clopidogrel to decrease risk of gastrointestinal bleeding after acute coronary syndrome. Clopidogrel is a prodrug that has to be metabolized in the liver to generate the active metabolite. Both medications are metabolized largely by the CYP2C19 enzyme; therefore, concerns exist that a drug-drug interaction during concomitant treatment with clopidogrel and a proton pump inhibitor may result in reduction of platelet inhibition. We have reviewed observational and randomized control studies that have evaluated the potential influence of proton pump inhibitors on the platelet inhibitory effect of clopidogrel, along with cardiovascular outcomes. We also have summarized regulatory and academic guidelines for treatment of patients in which concomitant therapy with clopidogrel and proton pump inhibitors may be indicated. Confounding issues, including differential effects of individual proton pump inhibitors on the pharmacodynamics of clopidogrel and variation in clopidogrel metabolism mediated by CYP2C19 gene polymorphisms, also are discussed.
    Keywords Proton Pump Inhibitors ; Clopidogrel ; Dual Antiplatelet Therapy ; Drug-Drug Interaction ; Gastrointestinal Bleeding ; Myocardial Infarction ; Percutaneous Coronary Intervention ; Internal medicine ; RC31-1245 ; Medicine ; R ; DOAJ:Internal medicine ; DOAJ:Medicine (General) ; DOAJ:Health Sciences
    Subject code 610
    Language English
    Publishing date 2011-12-01T00:00:00Z
    Publisher Scientific Research Publishing
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Discrimination of Methionine Sulfoxide and Sulfone by Human Neutrophil Elastase

    Darren Leahy / Cameron Grant / Alex Jackson / Alex Duff / Nicholas Tardiota / Jessica Van Haeften / Xingchen Chen / Jonathan M. Peake / Michael D. Kruppa / Eliot T. Smith / David A. Johnson / William B. Lott / Jonathan M. Harris

    Molecules, Vol 26, Iss 5344, p

    2021  Volume 5344

    Abstract: Human neutrophil elastase (HNE) is a uniquely destructive serine protease with the ability to unleash a wave of proteolytic activity by destroying the inhibitors of other proteases. Although this phenomenon forms an important part of the innate immune ... ...

    Abstract Human neutrophil elastase (HNE) is a uniquely destructive serine protease with the ability to unleash a wave of proteolytic activity by destroying the inhibitors of other proteases. Although this phenomenon forms an important part of the innate immune response to invading pathogens, it is responsible for the collateral host tissue damage observed in chronic conditions such as chronic obstructive pulmonary disease (COPD), and in more acute disorders such as the lung injuries associated with COVID-19 infection. Previously, a combinatorially selected activity-based probe revealed an unexpected substrate preference for oxidised methionine, which suggests a link to oxidative pathogen clearance by neutrophils. Here we use oxidised model substrates and inhibitors to confirm this observation and to show that neutrophil elastase is specifically selective for the di-oxygenated methionine sulfone rather than the mono-oxygenated methionine sulfoxide. We also posit a critical role for ordered solvent in the mechanism of HNE discrimination between the two oxidised forms methionine residue. Preference for the sulfone form of oxidised methionine is especially significant. While both host and pathogens have the ability to reduce methionine sulfoxide back to methionine, a biological pathway to reduce methionine sulfone is not known. Taken together, these data suggest that the oxidative activity of neutrophils may create rapidly cleaved elastase “super substrates” that directly damage tissue, while initiating a cycle of neutrophil oxidation that increases elastase tissue damage and further neutrophil recruitment.
    Keywords human neutrophil elastase ; peptide aldehyde ; substrate guided inhibitor design ; methionine oxidation ; methionine sulfone ; substrate selectivity ; Organic chemistry ; QD241-441
    Subject code 540
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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