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Article ; Online: Comparative Effectiveness of Single vs Repeated Rapid SARS-CoV-2 Antigen Testing Among Asymptomatic Individuals in a Workplace Setting.

Connor, Bradley A / Rogova, Marina / Garcia, Jefferson / Patel, Darshan / Couto-Rodriguez, Mara / Nagy-Szakal, Dorottya / Rendel, Michael

JAMA network open

2022 Volume 5, Issue 3, Page(s) e223073

MeSH term(s)	COVID-19/diagnosis ; COVID-19 Serological Testing ; Humans ; SARS-CoV-2 ; Workplace
Language	English
Publishing date	2022-03-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2574-3805
ISSN (online)	2574-3805
DOI	10.1001/jamanetworkopen.2022.3073
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Article ; Online: Monoclonal Antibody Therapy in a Vaccine Breakthrough SARS-CoV-2 Hospitalized Delta (B.1.617.2) Variant Case.

Connor, Bradley A / Couto-Rodriguez, Mara / Barrows, Joseph E / Gardner, Morgan / Rogova, Marina / O'Hara, Niamh B / Nagy-Szakal, Dorottya

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

2021 Volume 110, Page(s) 232–234

Abstract: We present two Delta (B.1.617.2) vaccine breakthrough individuals, a father and son living in separate households. The older, 63-year-old patient's symptoms were severe enough to require hospitalization. Despite having a high titer of anti-spike IgG in ... ...

Abstract	We present two Delta (B.1.617.2) vaccine breakthrough individuals, a father and son living in separate households. The older, 63-year-old patient's symptoms were severe enough to require hospitalization. Despite having a high titer of anti-spike IgG in his serum, his symptoms resolved within 24 hours following monoclonal antibody (bamlanivimab/etesevimab) therapy.
MeSH term(s)	Antibodies, Monoclonal/therapeutic use ; COVID-19 ; Humans ; Middle Aged ; SARS-CoV-2 ; Vaccines
Chemical Substances	Antibodies, Monoclonal ; Vaccines
Language	English
Publishing date	2021-07-13
Publishing country	Canada
Document type	Case Reports
ZDB-ID	1331197-9
ISSN	1878-3511 ; 1201-9712
ISSN (online)	1878-3511
ISSN	1201-9712
DOI	10.1016/j.ijid.2021.07.029
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Zs.A 4516: Show issues

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Article ; Online: Hyperlipasemia in Pediatric Inflammatory Bowel Diseases.

Ihekweazu, Faith D / Nagy-Szakal, Dorottya / Fishman, Douglas S / Kellermayer, Richard

Pancreas

2016 Volume 45, Issue 2, Page(s) e2–3

MeSH term(s)	Acute Disease ; Child ; Diagnosis, Differential ; Humans ; Inflammatory Bowel Diseases/blood ; Inflammatory Bowel Diseases/diagnosis ; Inflammatory Bowel Diseases/enzymology ; Lipase/blood ; Pancreatitis/blood ; Pancreatitis/diagnosis ; Pancreatitis/enzymology ; Retrospective Studies
Chemical Substances	Lipase (EC 3.1.1.3)
Language	English
Publishing date	2016-02
Publishing country	United States
Document type	Letter ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	632831-3
ISSN	1536-4828 ; 0885-3177
ISSN (online)	1536-4828
ISSN	0885-3177
DOI	10.1097/MPA.0000000000000513
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Zs.A 2160: Show issues

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Article ; Online: The remarkable capacity for gut microbial and host interactions.

Nagy-Szakal, Dorottya / Kellermayer, Richard

Gut microbes

2011 Volume 2, Issue 3, Page(s) 178–182

Abstract: The stunning complexity of the resident microbiota and the intricate pathways of microbial and host interactions provide a massive adaptive capacity for mammals. In this addendum we reflect on our recent publication on Toll-like receptor 2 deficiency ... ...

Abstract	The stunning complexity of the resident microbiota and the intricate pathways of microbial and host interactions provide a massive adaptive capacity for mammals. In this addendum we reflect on our recent publication on Toll-like receptor 2 deficiency related colonic mucosal epigenetic, immunologic and microbiomic changes. Our findings underscored the tremendous flexibility of the gut and its microbiota. This flexibility can provide means to overcome significant environmental or genetic challenges. In the meantime, the challenged intestinal system may become vulnerable to otherwise tolerable insults. In such instances, the fine-tuned mutualistic balance between the gut and its microflora may collapse leading to dysbiosis and disease. The ultimate challenge for biomedical research in these cases is to find optimal means for the restoration and maintenance of healthy host physiology.
MeSH term(s)	Adaptation, Physiological ; Animals ; Bacterial Physiological Phenomena ; Gastrointestinal Tract/microbiology ; Gastrointestinal Tract/physiology ; Humans ; Mammals/microbiology ; Mammals/physiology ; Metagenome ; Mice ; Mice, Knockout ; Symbiosis ; Toll-Like Receptor 2/genetics ; Toll-Like Receptor 2/metabolism
Chemical Substances	Toll-Like Receptor 2
Language	English
Publishing date	2011-05-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1949-0984
ISSN (online)	1949-0984
DOI	10.4161/gmic.2.3.16107
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Book ; Online: The Challenges and Opportunities in Creating an Early Warning System for Global Pandemics

Danko, David C. / Golden, James / Vorosmarty, Charles / Cak, Anthony / Corsi, Fabio / Mason, Christopher E. / Maciel-de-Freitas, Rafael / Nagy-Szakal, Dorottya / OHara, Niamh B.

2023

Abstract: The COVID-19 pandemic revealed that global health, social systems, and economies can be surprisingly fragile in an increasingly interconnected and interdependent world. Yet, during the last half of 2022, and quite remarkably, we began dismantling ... ...

Abstract	The COVID-19 pandemic revealed that global health, social systems, and economies can be surprisingly fragile in an increasingly interconnected and interdependent world. Yet, during the last half of 2022, and quite remarkably, we began dismantling essential infectious disease monitoring programs in several countries. Absent such programs, localized biological risks will transform into global shocks linked directly to our lack of foresight regarding emerging health risks. Additionally, recent studies indicate that more than half of all infectious diseases could be made worse by climate change, complicating pandemic containment. Despite this complexity, the factors leading to pandemics are largely predictable but can only be realized through a well-designed global early warning system. Such a system should integrate data from genomics, climate and environment, social dynamics, and healthcare infrastructure. The glue for such a system is community-driven modeling, a modern logistics of data, and democratization of AI tools. Using the example of dengue fever in Brazil, we can demonstrate how thoughtfully designed technology platforms can build global-scale precision disease detection and response systems that significantly reduce exposure to systemic shocks, accelerate science-informed public health policies, and deliver reliable healthcare and economic opportunities as an intrinsic part of the global sustainable development agenda.
Keywords	Quantitative Biology - Quantitative Methods ; Computer Science - Computers and Society
Publishing date	2023-02-01
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Human metastable epiallele candidates link to common disorders.

Harris, R Alan / Nagy-Szakal, Dorottya / Kellermayer, Richard

Epigenetics

2013 Volume 8, Issue 2, Page(s) 157–163

Abstract: Metastable epialleles (MEs) are mammalian genomic loci where epigenetic patterning occurs before gastrulation in a stochastic fashion leading to systematic interindividual variation within one species. Importantly, periconceptual nutritional influences ... ...

Abstract	Metastable epialleles (MEs) are mammalian genomic loci where epigenetic patterning occurs before gastrulation in a stochastic fashion leading to systematic interindividual variation within one species. Importantly, periconceptual nutritional influences may modulate the establishment of epigenetic changes, such as DNA methylation at MEs. Based on these characteristics, we exploited Infinium HumanMethylation450 BeadChip kits in a 2-tissue parallel screen on peripheral blood leukocyte and colonic mucosal DNA from 10 children without identifiable large intestinal disease. This approach led to the delineation of 1776 CpG sites meeting our criteria for MEs, which associated with 1013 genes. The list of ME candidates exhibited overlaps with recently identified human genes (including CYP2E1 and MGMT, where methylation has been associated with Parkinson disease and glioblastoma, respectively) in which perinatal DNA methylation levels where linked to maternal periconceptual nutrition. One hundred 18 (11.6%) of the ME candidates overlapped with genes where DNA methylation correlated (r > 0.871; p < 0.055) with expression in the colon mucosa of 5 independent control children. Genes involved in homophilic cell adhesion (including cadherin-associated genes) and developmental processes were significantly overrepresented in association with MEs. Additional filtering of gene expression-correlated MEs defined 35 genes, associated with 2 or more CpG sites within a 10 kb genomic region, fulfilling the ME criteria. DNA methylation changes at a number of these genes have been linked to various forms of human disease, including cancers, such as asthma and acute myeloid leukemia (ALOX12), gastric cancer (EBF3), breast cancer (NAV1), colon cancer and acute lymphoid leukemia (KCNK15), Wilms tumor (protocadherin gene cluster; PCDHAs) and colorectal cancer (TCERG1L), suggesting a potential etiologic role for MEs in tumorigenesis and underscoring the possible developmental origins of these malignancies. The presented compendium of ME candidates may accelerate our understanding of the epigenetic origins of common human disorders.
MeSH term(s)	Asthma/genetics ; Breast Neoplasms/genetics ; Colonic Neoplasms/genetics ; Colorectal Neoplasms/genetics ; CpG Islands ; DNA Methylation ; Epigenesis, Genetic ; Female ; Gene Expression ; Genetic Predisposition to Disease ; Humans ; Intestinal Mucosa/physiology ; Microtubule-Associated Proteins ; Nerve Growth Factors/genetics ; Nerve Growth Factors/metabolism ; Oligonucleotide Array Sequence Analysis/methods ; Potassium Channels, Tandem Pore Domain/genetics ; Potassium Channels, Tandem Pore Domain/metabolism ; Twins, Monozygotic/genetics
Chemical Substances	KCNK15 protein, human ; Microtubule-Associated Proteins ; NAV1 protein, human ; Nerve Growth Factors ; Potassium Channels, Tandem Pore Domain
Language	English
Publishing date	2013-01-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1559-2308
ISSN (online)	1559-2308
DOI	10.4161/epi.23438
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Article ; Online: Highly Sensitive Virome Capture Sequencing Technique VirCapSeq-VERT Identifies Partial Noncoding Sequences but no Active Viral Infection in Cutaneous T-Cell Lymphoma.

Anderson, Mary E / Nagy-Szakal, Dorottya / Jain, Komal / Patrone, Christina C / Frattini, Mark G / Lipkin, W Ian / Geskin, Larisa J

The Journal of investigative dermatology

2018 Volume 138, Issue 7, Page(s) 1671–1673

MeSH term(s)	Aged ; Aged, 80 and over ; Carcinogenesis/genetics ; Contig Mapping ; Female ; Genome, Viral/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Leukocytes, Mononuclear/virology ; Male ; Middle Aged ; Nucleic Acids/genetics ; Nucleic Acids/isolation & purification ; Sezary Syndrome/blood ; Sezary Syndrome/genetics ; Sezary Syndrome/virology ; Skin Neoplasms/blood ; Skin Neoplasms/genetics ; Skin Neoplasms/virology ; Viruses/genetics ; Viruses/isolation & purification
Chemical Substances	Nucleic Acids
Language	English
Publishing date	2018-02-07
Publishing country	United States
Document type	Letter
ZDB-ID	80136-7
ISSN	1523-1747 ; 0022-202X
ISSN (online)	1523-1747
ISSN	0022-202X
DOI	10.1016/j.jid.2018.01.024
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Article ; Online: Fecal Microbiota Transplantation Commonly Failed in Children With Co-Morbidities.

Kellermayer, Richard / Wu, Qinglong / Nagy-Szakal, Dorottya / Queliza, Karen / Ihekweazu, Faith D / Bocchini, Claire E / Magee, Abria R / Oezguen, Numan / Spinler, Jennifer K / Hollister, Emily B / Shulman, Robert J / Versalovic, James / Luna, Ruth Ann / Savidge, Tor C

Journal of pediatric gastroenterology and nutrition

2021 Volume 74, Issue 2, Page(s) 227–235

Abstract: Objectives: Fecal microbiota transplantation (FMT) is arguably the most effective treatment for recurrent Clostridioides difficile infection (rCDI). Clinical reports on pediatric FMT have not systematically evaluated microbiome restoration in patients ... ...

Abstract	Objectives: Fecal microbiota transplantation (FMT) is arguably the most effective treatment for recurrent Clostridioides difficile infection (rCDI). Clinical reports on pediatric FMT have not systematically evaluated microbiome restoration in patients with co-morbidities. Here, we determined whether FMT recipient age and underlying co-morbidity influenced clinical outcomes and microbiome restoration when treated from shared fecal donor sources. Methods: Eighteen rCDI patients participating in a single-center, open-label prospective cohort study received fecal preparation from a self-designated (single case) or two universal donors. Twelve age-matched healthy children and four pediatric ulcerative colitis (UC) cases from an independent serial FMT trial, but with a shared fecal donor were examined as controls for microbiome restoration using 16S rRNA gene sequencing of longitudinal fecal specimens. Results: FMT was significantly more effective in rCDI recipients without underlying chronic co-morbidities where fecal microbiome composition in post-transplant responders was restored to levels of healthy children. Microbiome reconstitution was not associated with symptomatic resolution in some rCDI patients who had co-morbidities. Significant elevation in Bacteroidaceae, Bifidobacteriaceae, Lachnospiraceae, Ruminococcaceae, and Erysipelotrichaceae was consistently observed in pediatric rCDI responders, while Enterobacteriaceae decreased, correlating with augmented complex carbohydrate degradation capacity. Conclusion: Recipient background disease was a significant risk factor influencing FMT outcomes. Special attention should be taken when considering FMT for pediatric rCDI patients with underlying co-morbidities.
MeSH term(s)	Child ; Clostridioides difficile ; Clostridium Infections/therapy ; Fecal Microbiota Transplantation ; Feces ; Humans ; Morbidity ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Recurrence ; Treatment Outcome
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2021-10-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	603201-1
ISSN	1536-4801 ; 0277-2116
ISSN (online)	1536-4801
ISSN	0277-2116
DOI	10.1097/MPG.0000000000003336
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Article ; Online: Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights.

Nagy-Szakal, Dorottya / Couto-Rodriguez, Mara / Wells, Heather L / Barrows, Joseph E / Debieu, Marilyne / Butcher, Kristin / Chen, Siyuan / Berki, Agnes / Hager, Courteny / Boorstein, Robert J / Taylor, Mariah K / Jonsson, Colleen B / Mason, Christopher E / O'Hara, Niamh B

Microbiology spectrum

2021 Volume 9, Issue 2, Page(s) e0019721

Abstract: The emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic variants that may alter viral fitness highlights the urgency of widespread next-generation sequencing (NGS) surveillance. To profile genetic variants of the ... ...

Abstract	The emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic variants that may alter viral fitness highlights the urgency of widespread next-generation sequencing (NGS) surveillance. To profile genetic variants of the entire SARS-CoV-2 genome, we developed and clinically validated a hybridization capture SARS-CoV-2 NGS assay, integrating novel methods for panel design using double-stranded DNA (dsDNA) biotin-labeled probes, and built accompanying software. This test is the first hybrid capture-based NGS assay given Food and Drug Administration (FDA) emergency use authorization for detection of the SARS-CoV-2 virus. The positive and negative percent agreement (PPA and NPA, respectively) were defined in comparison to the results for an orthogonal real-time reverse transcription polymerase chain reaction (RT-PCR) assay (PPA and NPA, 96.7 and 100%, respectively). The limit of detection was established to be 800 copies/ml with an average fold enrichment of 46,791. Furthermore, utilizing the research-use-only analysis to profile the variants, we identified 55 novel mutations, including 11 in the functionally important spike protein. Finally, we profiled the full nasopharyngeal microbiome using metagenomics and found overrepresentation of 7 taxa and evidence of macrolide resistance in SARS-CoV-2-positive patients. This hybrid capture NGS assay, coupled with optimized software, is a powerful approach to detect and comprehensively map SARS-CoV-2 genetic variants for tracking viral evolution and guiding vaccine updates.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; COVID-19/pathology ; Drug Resistance, Bacterial/genetics ; Genetic Variation/genetics ; Genome, Viral/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Limit of Detection ; Macrolides/pharmacology ; Metagenomics/methods ; Microbiota/genetics ; Nasopharynx/microbiology ; RNA, Viral/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification
Chemical Substances	Anti-Bacterial Agents ; Macrolides ; RNA, Viral
Language	English
Publishing date	2021-09-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2165-0497
ISSN (online)	2165-0497
DOI	10.1128/Spectrum.00197-21
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Article ; Online: Bacteroides ovatus

Ihekweazu, Faith D / Fofanova, Tatiana Y / Queliza, Karen / Nagy-Szakal, Dorottya / Stewart, Christopher J / Engevik, Melinda A / Hulten, Kristina G / Tatevian, Nina / Graham, David Y / Versalovic, James / Petrosino, Joseph F / Kellermayer, Richard

Gut microbes

2019 Volume 10, Issue 4, Page(s) 504–520

Abstract: Background and ... ...

Abstract	Background and aims
MeSH term(s)	Animals ; Bacteria/classification ; Bacteria/growth & development ; Bacteroides/classification ; Bacteroides/growth & development ; Bacteroides/physiology ; Colitis/chemically induced ; Colitis/pathology ; Colitis/therapy ; Dextran Sulfate/toxicity ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Feces/microbiology ; Gastrointestinal Tract/microbiology ; Gastrointestinal Tract/pathology ; Inflammation/prevention & control ; Male ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics ; Survival Analysis ; Treatment Outcome
Chemical Substances	RNA, Ribosomal, 16S ; Dextran Sulfate (9042-14-2)
Language	English
Publishing date	2019-01-21
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1949-0984
ISSN (online)	1949-0984
DOI	10.1080/19490976.2018.1560753
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