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  1. AU="Craig J. McClain"
  2. AU="Esparza L.H.R."
  3. AU="Sánchez-Mendoza, Luz Marina"
  4. AU="Managh, Amy J"
  5. AU="Santer, Svetlana"
  6. AU="Svirin, Pavel"
  7. AU=Mause Sebastian F AU=Mause Sebastian F
  8. AU="Camacho, M R"
  9. AU="Thaprawat, Pariyamon"
  10. AU="Ng, Ying Ying"
  11. AU="Ramsden, Jeremy"
  12. AU="Maier, Alice"
  13. AU="Stoler, Robert"
  14. AU="Camp, Christina"
  15. AU="Morganti, Giulia"
  16. AU="Saini, Avneesh K"
  17. AU="Sansores-García, Leticia"
  18. AU="Vemulapalli, Krishna"
  19. AU=Beer Tomasz M
  20. AU="Maloney, Jillian"
  21. AU="Wallwork K."
  22. AU="Zhao, Shuoqi"
  23. AU="Brouwer, Marlies"
  24. AU="Diarrassouba, Assetou"
  25. AU="Kumar, Seema"
  26. AU="Díaz-Coello, S"
  27. AU="Madden, Richard C"
  28. AU="Walker, Andrew B"
  29. AU="Deol, Sundeep S"
  30. AU="Novo, Evlyn Márcia Moraes de Leão"

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  1. Artikel ; Online: Fifteen Years of Gene Set Analysis for High-Throughput Genomic Data

    Samarendra Das / Craig J. McClain / Shesh N. Rai

    Entropy, Vol 22, Iss 427, p

    A Review of Statistical Approaches and Future Challenges

    2020  Band 427

    Abstract: Over the last decade, gene set analysis has become the first choice for gaining insights into underlying complex biology of diseases through gene expression and gene association studies. It also reduces the complexity of statistical analysis and enhances ...

    Abstract Over the last decade, gene set analysis has become the first choice for gaining insights into underlying complex biology of diseases through gene expression and gene association studies. It also reduces the complexity of statistical analysis and enhances the explanatory power of the obtained results. Although gene set analysis approaches are extensively used in gene expression and genome wide association data analysis, the statistical structure and steps common to these approaches have not yet been comprehensively discussed, which limits their utility. In this article, we provide a comprehensive overview, statistical structure and steps of gene set analysis approaches used for microarrays, RNA-sequencing and genome wide association data analysis. Further, we also classify the gene set analysis approaches and tools by the type of genomic study, null hypothesis, sampling model and nature of the test statistic, etc. Rather than reviewing the gene set analysis approaches individually, we provide the generation-wise evolution of such approaches for microarrays, RNA-sequencing and genome wide association studies and discuss their relative merits and limitations. Here, we identify the key biological and statistical challenges in current gene set analysis, which will be addressed by statisticians and biologists collectively in order to develop the next generation of gene set analysis approaches. Further, this study will serve as a catalog and provide guidelines to genome researchers and experimental biologists for choosing the proper gene set analysis approach based on several factors.
    Schlagwörter gene set analysis ; microarrays ; RNA-sequencing ; genome wide association study ; competitive ; self-contained ; Science ; Q ; Astrophysics ; QB460-466 ; Physics ; QC1-999
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2020-04-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: Plasma Metabolomics Analysis of Polyvinyl Chloride Workers Identifies Altered Processes and Candidate Biomarkers for Hepatic Hemangiosarcoma and Its Development

    John J. Guardiola / Josiah E. Hardesty / Juliane I. Beier / Russell A. Prough / Craig J. McClain / Matthew C. Cave

    International Journal of Molecular Sciences, Vol 22, Iss 5093, p

    2021  Band 5093

    Abstract: Background: High-level occupational vinyl chloride (VC) exposures have been associated with hepatic hemangiosarcoma, which typically develops following a long latency period. Although VC is genotoxic, a more comprehensive mode of action has not been ... ...

    Abstract Background: High-level occupational vinyl chloride (VC) exposures have been associated with hepatic hemangiosarcoma, which typically develops following a long latency period. Although VC is genotoxic, a more comprehensive mode of action has not been determined and diagnostic biomarkers have not been established. The purpose of this study is to address these knowledge gaps through plasma metabolomics. Methods: Plasma samples from polyvinyl chloride polymerization workers who developed hemangiosarcoma (cases, n = 15) and VC exposure-matched controls ( n = 17) underwent metabolomic analysis. Random forest and bioinformatic analyses were performed. Results: Cases and controls had similar demographics and routine liver biochemistries. Mass spectroscopy identified 606 known metabolites. Random forest analysis had an 82% predictive accuracy for group classification. 60 metabolites were significantly increased and 44 were decreased vs. controls. Taurocholate, bradykinin and fibrin degradation product 2 were up-regulated by greater than 80-fold. The naturally occurring anti-angiogenic phenol, 4-hydroxybenzyl alcohol, was down-regulated 5-fold. Top affected ontologies involved: (i) metabolism of bile acids, taurine, cholesterol, fatty acids and amino acids; (ii) inflammation and oxidative stress; and (iii) nicotinic cholinergic signaling. Conclusions: The plasma metabolome was differentially regulated in polyvinyl chloride workers who developed hepatic hemangiosarcoma. Ontologies potentially involved in hemangiosarcoma pathogenesis and candidate biomarkers were identified.
    Schlagwörter angiosarcoma ; vinyl chloride ; PVC ; liver cancer ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Thema/Rubrik (Code) 500
    Sprache Englisch
    Erscheinungsdatum 2021-05-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  3. Artikel ; Online: Analysis of sex differences in dietary copper-fructose interaction-induced alterations of gut microbial activity in relation to hepatic steatosis

    Ming Song / Fang Yuan / Xiaohong Li / Xipeng Ma / Xinmin Yin / Eric C. Rouchka / Xiang Zhang / Zhongbin Deng / Russell A. Prough / Craig J. McClain

    Biology of Sex Differences, Vol 12, Iss 1, Pp 1-

    2021  Band 16

    Abstract: Abstract Background Inadequate copper intake and increased fructose consumption represent two important nutritional problems in the USA. Dietary copper-fructose interactions alter gut microbial activity and contribute to the development of nonalcoholic ... ...

    Abstract Abstract Background Inadequate copper intake and increased fructose consumption represent two important nutritional problems in the USA. Dietary copper-fructose interactions alter gut microbial activity and contribute to the development of nonalcoholic fatty liver disease (NAFLD). The aim of this study is to determine whether dietary copper-fructose interactions alter gut microbial activity in a sex-differential manner and whether sex differences in gut microbial activity are associated with sex differences in hepatic steatosis. Methods Male and female weanling Sprague-Dawley (SD) rats were fed ad libitum with an AIN-93G purified rodent diet with defined copper content for 8 weeks. The copper content is 6 mg/kg and 1.5 mg/kg in adequate copper diet (CuA) and marginal copper diet (CuM), respectively. Animals had free access to either deionized water or deionized water containing 10% fructose (F) (w/v) as the only drink during the experiment. Body weight, calorie intake, plasma alanine aminotransferase, aspartate aminotransferase, and liver histology as well as liver triglyceride were evaluated. Fecal microbial contents were analyzed by 16S ribosomal RNA (16S rRNA) sequencing. Fecal and cecal short-chain fatty acids (SCFAs) were determined by gas chromatography-mass spectrometry (GC-MS). Results Male and female rats exhibit similar trends of changes in the body weight gain and calorie intake in response to dietary copper and fructose, with a generally higher level in male rats. Several female rats in the CuAF group developed mild steatosis, while no obvious steatosis was observed in male rats fed with CuAF or CuMF diets. Fecal 16S rRNA sequencing analysis revealed distinct alterations of the gut microbiome in male and female rats. Linear discriminant analysis (LDA) effect size (LEfSe) identified sex-specific abundant taxa in different groups. Further, total SCFAs, as well as, butyrate were decreased in a more pronounced manner in female CuMF rats than in male rats. Of note, the decreased SCFAs are concomitant with ...
    Schlagwörter Copper ; Fructose ; Gut microbiota ; Sex ; Nonalcoholic fatty liver disease ; Medicine ; R ; Physiology ; QP1-981
    Thema/Rubrik (Code) 590
    Sprache Englisch
    Erscheinungsdatum 2021-01-01T00:00:00Z
    Verlag BMC
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  4. Artikel ; Online: Microbiome data analysis with applications to pre-clinical studies using QIIME2

    Shesh N. Rai / Chen Qian / Jianmin Pan / Jayesh P. Rai / Ming Song / Juhi Bagaitkar / Michael Merchant / Matthew Cave / Nejat K. Egilmez / Craig J. McClain

    Genes and Diseases, Vol 8, Iss 2, Pp 215-

    Statistical considerations

    2021  Band 223

    Abstract: Diversity analysis and taxonomic profiles can be generated from marker-gene sequence data with the help of many available computational tools. The Quantitative Insights into Microbial Ecology Version 2 (QIIME2) has been widely used for 16S rRNA data ... ...

    Abstract Diversity analysis and taxonomic profiles can be generated from marker-gene sequence data with the help of many available computational tools. The Quantitative Insights into Microbial Ecology Version 2 (QIIME2) has been widely used for 16S rRNA data analysis. While many articles have demonstrated the use of QIIME2 with suitable datasets, the application to pre-clinical data has rarely been talked about. The issues involved in the pre-clinical data include the low-quality score and small sample size that should be addressed properly during analysis. In addition, there are few articles that discuss the detailed statistical methods behind those alpha and beta diversity significance tests that researchers are eager to find. Running the program without knowing the logic behind it is extremely risky. In this article, we first provide a guideline for analyzing 16S rRNA data using QIIME2. Then we will talk about issues in pre-clinical data, and how they could impact the outcome. Finally, we provide brief explanations of statistical methods such as group significance tests and sample size calculation.
    Schlagwörter 16S rRNA gene ; Alpha diversity ; ANOVA ; Beta diversity ; Bioinformatics ; Microbiome data ; Medicine (General) ; R5-920 ; Genetics ; QH426-470
    Thema/Rubrik (Code) 310
    Sprache Englisch
    Erscheinungsdatum 2021-03-01T00:00:00Z
    Verlag Elsevier
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  5. Artikel ; Online: Deficiency of Cathelicidin Attenuates High-Fat Diet Plus Alcohol-Induced Liver Injury through FGF21/Adiponectin Regulation

    Fengyuan Li / Jenny Chen / Yunhuan Liu / Zelin Gu / Mengwei Jiang / Lihua Zhang / Shao-Yu Chen / Zhongbin Deng / Craig J. McClain / Wenke Feng

    Cells, Vol 10, Iss 3333, p

    2021  Band 3333

    Abstract: Alcohol consumption and obesity are known risk factors of steatohepatitis. Here, we report that the deficiency of CRAMP (cathelicidin-related antimicrobial peptide—gene name: Camp ) is protective against a high-fat diet (HFD) plus acute alcohol (HFDE)- ... ...

    Abstract Alcohol consumption and obesity are known risk factors of steatohepatitis. Here, we report that the deficiency of CRAMP (cathelicidin-related antimicrobial peptide—gene name: Camp ) is protective against a high-fat diet (HFD) plus acute alcohol (HFDE)-induced liver injury. HFDE markedly induced liver injury and steatosis in WT mice, which were attenuated in Camp –/– mice. Neutrophil infiltration was lessened in the liver of Camp –/– mice. HFDE feeding dramatically increased epididymal white adipose tissue (eWAT) mass and induced adipocyte hypertrophy in WT mice, whereas these effects were attenuated by the deletion of Camp . Furthermore, Camp –/– mice had significantly increased eWAT lipolysis, evidenced by up-regulated expression of lipolytic enzymes, adipose triglyceride lipase (ATGL) and hormone-sensitive lipase (HSL). The depletion of Camp also increased uncoupling protein 1 (UCP1)-dependent thermogenesis in the brown adipose tissue (BAT) of mice. HFDE fed Camp –/– mice had elevated protein levels of fibroblast growth factor 21 (FGF21) in the eWAT, with an increased adiponectin production, which had been shown to alleviate hepatic fat deposition and inflammation. Collectively, we have demonstrated that Camp –/– mice are protected against HFD plus alcohol-induced liver injury and steatosis through FGF21/adiponectin regulation. Targeting CRAMP could be an effective approach for prevention/treatment of high-fat diet plus alcohol consumption-induced steatohepatitis.
    Schlagwörter cathelicidin ; HFD plus alcohol ; neutrophil ; FGF21/adiponectin ; adipose lipolysis ; Biology (General) ; QH301-705.5
    Sprache Englisch
    Erscheinungsdatum 2021-11-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel ; Online: Ileum Gene Expression in Response to Acute Systemic Inflammation in Mice Chronically Fed Ethanol

    Josiah E. Hardesty / Jeffrey B. Warner / Ying L. Song / Eric C. Rouchka / Craig J. McClain / Dennis R. Warner / Irina A. Kirpich

    International Journal of Molecular Sciences, Vol 22, Iss 4, p

    Beneficial Effects of Elevated Tissue n-3 PUFAs

    2021  Band 1582

    Abstract: Chronic alcohol consumption leads to disturbances in intestinal function which can be exacerbated by inflammation and modulated by different factors, e.g., polyunsaturated fatty acids (PUFAs). The mechanisms underlying these alterations are not well ... ...

    Abstract Chronic alcohol consumption leads to disturbances in intestinal function which can be exacerbated by inflammation and modulated by different factors, e.g., polyunsaturated fatty acids (PUFAs). The mechanisms underlying these alterations are not well understood. In this study, RNA-seq analysis was performed on ileum tissue from WT and fat-1 transgenic mice (which have elevated endogenous n-3 PUFAs). Mice were chronically fed ethanol (EtOH) and challenged with a single lipopolysaccharide (LPS) dose to induce acute systemic inflammation. Both WT and fat-1 mice exhibited significant ileum transcriptome changes following EtOH + LPS treatment. Compared to WT, fat-1 mice had upregulated expression of genes associated with cell cycle and xenobiotic metabolism, while the expression of pro-inflammatory cytokines and pro-fibrotic genes was decreased. In response to EtOH + LPS, fat-1 mice had an increased expression of genes related to antibacterial B cells (APRIL and IgA), as well as an elevation in markers of pro-restorative macrophages and γδ T cells that was not observed in WT mice. Our study significantly expands the knowledge of regulatory mechanisms underlying intestinal alterations due to EtOH consumption and inflammation and identifies the beneficial transcriptional effects of n-3 PUFAs, which may serve as a viable nutritional intervention for intestinal damage resulting from excessive alcohol consumption.
    Schlagwörter alcohol ; acute systemic inflammation ; polyunsaturated fatty acids ; intestine ; transcriptome ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Thema/Rubrik (Code) 610
    Sprache Englisch
    Erscheinungsdatum 2021-02-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  7. Artikel: Protein and Calorie Requirements Associated With the Presence of Obesity

    Dickerson, Roland N / Craig J. McClain / Jayshil J. Patel

    Nutrition in clinical practice. , v. 32, no. 1_suppl

    2017  

    Abstract: Obesity compounds the metabolic response to critical illness and increases the risk for overfeeding complications due to its comorbidities. Hypocaloric, high-protein nutrition therapy affords the hospitalized patient with obesity the opportunity to ... ...

    Abstract Obesity compounds the metabolic response to critical illness and increases the risk for overfeeding complications due to its comorbidities. Hypocaloric, high-protein nutrition therapy affords the hospitalized patient with obesity the opportunity to achieve net protein anabolism with a reduced risk of overfeeding complications. The intent of this review is to provide the theoretical framework for development of a hypocaloric high-protein regimen, scientific evidence to support this mode of therapy, and unique considerations for its use in specialized subpopulations. Macronutrient goals and practical suggestions for patient monitoring are given.
    Schlagwörter biochemical pathways ; comorbidity ; diet therapy ; high protein diet ; monitoring ; obesity ; overfeeding ; patients ; protein synthesis ; risk reduction
    Sprache Englisch
    Erscheinungsverlauf 2017-04
    Umfang p. 86S-93S.
    Erscheinungsort SAGE Publications
    Dokumenttyp Artikel
    ZDB-ID 645074-x
    ISSN 1941-2452 ; 0884-5336
    ISSN (online) 1941-2452
    ISSN 0884-5336
    DOI 10.1177/0884533617691745
    Datenquelle NAL Katalog (AGRICOLA)

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  8. Artikel ; Online: Interaction of Heavy Drinking Patterns and Depression Severity Predicts Efficacy of Quetiapine Fumarate XR in Lowering Alcohol Intake in Alcohol Use Disorder Patients

    Vatsalya Vatsalya / Maiying Kong / Luis M Marsano / Zimple Kurlawala / Kan V Chandras / Melanie L Schwandt / Vijay A Ramchandani / Craig J McClain

    Substance Abuse: Research and Treatment, Vol

    2020  Band 14

    Abstract: Background: Shared etiological pathways of dopamine and serotonin neurotransmission play a central role in heavy alcohol intake and exacerbation in the symptoms of depression. We investigated the treatment efficacy of Quetiapine fumarate extended release ...

    Abstract Background: Shared etiological pathways of dopamine and serotonin neurotransmission play a central role in heavy alcohol intake and exacerbation in the symptoms of depression. We investigated the treatment efficacy of Quetiapine fumarate extended release (XR) in lowering alcohol intake in alcohol use disorder (AUD) patients indicated by the shared alleviation of depression ratings and patterns of heavy drinking. Methods: Hundred and eight male and female heavy drinking AUD patients in the age range of 18 to 64 years. participated in a randomized clinical trial (RCT) to receive 12 weeks of quetiapine XR or placebo (N = 115). Participants were sub-grouped by the severity grading of depression using Montgomery-Asberg Depression Rating Scale (MADRS) (clinically relevant ⩾8 [CR], clinically non-relevant ⩽7 [CNR]) at baseline in both the groups. Drinking history and depression ratings were assessed at the patients’ visits. Results: Heavy drinking days (HDD) and total drinks (TD) were significantly fewer in CR patients at the treatment end. A true positive response in AUROC analysis supported the lowering of TD in CR patients. The number of drinking days (NDD) and average drinks per drinking day (AvgD) were lower in the CNR patients at treatment-end. Significant associations with increasing effect sizes were observed for all the heavy drinking measures (HDD, TD, NDD, and AvgD) and MADRS scores by the end of the treatment course. Conclusions: Baseline elevated depressive symptoms could likely predict the course of heavy alcohol drinking during the treatment, and efficacy outcome of a treatment. AUD patients with baseline clinically significant depression had a progressive lowering in heavy drinking markers significantly corresponding to the lowering of depression symptoms by the end of treatment with Quetiapine fumarate XR. ClinicalTrials.gov: NCT#0049862 ( https://clinicaltrials.gov/ct2/show/NCT00498628?term=litten&draw=2&rank=3 )
    Schlagwörter Public aspects of medicine ; RA1-1270
    Thema/Rubrik (Code) 150 ; 610
    Sprache Englisch
    Erscheinungsdatum 2020-09-01T00:00:00Z
    Verlag SAGE Publishing
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  9. Artikel ; Online: Differential role of MLKL in alcohol-associated and non–alcohol-associated fatty liver diseases in mice and humans

    Tatsunori Miyata / Xiaoqin Wu / Xiude Fan / Emily Huang / Carlos Sanz-Garcia / Christina K. Cajigas-Du Ross / Sanjoy Roychowdhury / Annette Bellar / Megan R. McMullen / Jaividhya Dasarathy / Daniela S. Allende / Joan Caballeria / Pau Sancho-Bru / Craig J. McClain / Mack Mitchell / Arthur J. McCullough / Svetlana Radaeva / Bruce Barton / Gyongyi Szabo /
    Srinivasan Dasarathy / Laura E. Nagy

    JCI Insight, Vol 7, Iss

    2022  Band 23

    Schlagwörter Medicine ; R
    Sprache Englisch
    Erscheinungsdatum 2022-12-01T00:00:00Z
    Verlag American Society for Clinical investigation
    Dokumenttyp Artikel ; Online
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  10. Artikel: Protein Requirements for Critically Ill Patients With Renal and Liver Failure

    Patel, Jayshil J / Craig J. McClain / Jill Hamilton-Reeves / Menaka Sarav / Ryan T. Hurt

    Nutrition in clinical practice. , v. 32, no. 1_suppl

    2017  

    Abstract: Diseases leading to critical illness induce proteolysis resulting in muscle wasting and negative nitrogen balance. Muscle wasting has been associated with poor intensive care unit (ICU)–related outcomes, including an increased risk for mortality. Acute ... ...

    Abstract Diseases leading to critical illness induce proteolysis resulting in muscle wasting and negative nitrogen balance. Muscle wasting has been associated with poor intensive care unit (ICU)–related outcomes, including an increased risk for mortality. Acute kidney injury (AKI) represents a common organ dysfunction associated with ICU-related disorders, such as sepsis, trauma, and respiratory failure. AKI and renal replacement therapy lead to amino acid loss. Decompensated liver cirrhosis (DLC) and acute liver failure (ALF) represent more severe forms of liver dysfunction leading to ICU admission. DLC and ALF are associated with proteolysis and amino acid loss. AKI, DLC, and ALF uniquely contribute to negative nitrogen balance. The purpose of this review is to outline proteolysis associated with critical illness; define specific protein abnormalities in AKI, DLC, and ALF; define protein requirements in AKI, DLC, and ALF; and discuss barriers associated with optimal protein supplementation in these disorders.
    Schlagwörter amino acids ; kidneys ; liver ; liver cirrhosis ; liver failure ; mortality ; muscles ; nitrogen balance ; patients ; protein supplements ; proteolysis ; sepsis (infection) ; therapeutics
    Sprache Englisch
    Erscheinungsverlauf 2017-04
    Umfang p. 101S-111S.
    Erscheinungsort SAGE Publications
    Dokumenttyp Artikel
    ZDB-ID 645074-x
    ISSN 1941-2452 ; 0884-5336
    ISSN (online) 1941-2452
    ISSN 0884-5336
    DOI 10.1177/0884533616687501
    Datenquelle NAL Katalog (AGRICOLA)

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