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Article ; Online: Commentary: Cardiac surgery in COVID patients: Figuring it out as we go.

Clark, Sarah A / Teman, Nicholas R

The Journal of thoracic and cardiovascular surgery

2021 Volume 162, Issue 2, Page(s) e374–e375

MeSH term(s)	COVID-19 ; Cardiac Surgical Procedures/adverse effects ; Humans ; SARS-CoV-2 ; Thoracic Surgery
Language	English
Publishing date	2021-04-27
Publishing country	United States
Document type	Editorial ; Comment
ZDB-ID	3104-5
ISSN	1097-685X ; 0022-5223
ISSN (online)	1097-685X
ISSN	0022-5223
DOI	10.1016/j.jtcvs.2021.04.058
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Article: Structural basis for VLDLR recognition by eastern equine encephalitis virus.

Yang, Pan / Li, Wanyu / Fan, Xiaoyi / Pan, Junhua / Mann, Colin J / Varnum, Haley / Clark, Lars E / Clark, Sarah A / Coscia, Adrian / Smith, Katherine Nabel / Brusic, Vesna / Abraham, Jonathan

bioRxiv : the preprint server for biology

2023

Abstract: Alphaviruses are arthropod-borne enveloped RNA viruses that include several important human pathogens with outbreak potential. Among them, eastern equine encephalitis virus (EEEV) is the most virulent, and many survivors develop neurological sequelae, ... ...

Abstract	Alphaviruses are arthropod-borne enveloped RNA viruses that include several important human pathogens with outbreak potential. Among them, eastern equine encephalitis virus (EEEV) is the most virulent, and many survivors develop neurological sequelae, including paralysis and intellectual disability. The spike proteins of alphaviruses comprise trimers of heterodimers of their envelope glycoproteins E2 and E1 that mediate binding to cellular receptors and fusion of virus and host cell membranes during entry. We recently identified very-low density lipoprotein receptor (VLDLR) and apolipoprotein E receptor 2 (ApoER2), two closely related proteins that are expressed in the brain, as cellular receptors for EEEV and a distantly related alphavirus, Semliki forest virus (SFV)
Language	English
Publishing date	2023-11-14
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.11.14.567065
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Article ; Online: Rewiring of the Host Cell Metabolome and Lipidome during Lytic Gammaherpesvirus Infection Is Essential for Infectious-Virus Production.

Clark, Sarah A / Vazquez, Angie / Furiya, Kelsey / Splattstoesser, Madeleine K / Bashmail, Abdullah K / Schwartz, Haleigh / Russell, Makaiya / Bhark, Shun-Je / Moreno, Osvaldo K / McGovern, Morgan / Owsley, Eric R / Nelson, Timothy A / Sanchez, Erica L / Delgado, Tracie

Journal of virology

2023 Volume 97, Issue 6, Page(s) e0050623

Abstract: Oncogenic virus infections are estimated to cause ~15% of all cancers. Two prevalent human oncogenic viruses are members of the gammaherpesvirus family: Epstein-Barr virus (EBV) and Kaposi's sarcoma herpesvirus (KSHV). We use murine herpesvirus 68 (MHV- ... ...

Abstract	Oncogenic virus infections are estimated to cause ~15% of all cancers. Two prevalent human oncogenic viruses are members of the gammaherpesvirus family: Epstein-Barr virus (EBV) and Kaposi's sarcoma herpesvirus (KSHV). We use murine herpesvirus 68 (MHV-68), which shares significant homology with KSHV and EBV, as a model system to study gammaherpesvirus lytic replication. Viruses implement distinct metabolic programs to support their life cycle, such as increasing the supply of lipids, amino acids, and nucleotide materials necessary to replicate. Our data define the global changes in the host cell metabolome and lipidome during gammaherpesvirus lytic replication. Our metabolomics analysis found that MHV-68 lytic infection induces glycolysis, glutaminolysis, lipid metabolism, and nucleotide metabolism. We additionally observed an increase in glutamine consumption and glutamine dehydrogenase protein expression. While both glucose and glutamine starvation of host cells decreased viral titers, glutamine starvation led to a greater loss in virion production. Our lipidomics analysis revealed a peak in triacylglycerides early during infection and an increase in free fatty acids and diacylglyceride later in the viral life cycle. Furthermore, we observed an increase in the protein expression of multiple lipogenic enzymes during infection. Interestingly, pharmacological inhibitors of glycolysis or lipogenesis resulted in decreased infectious virus production. Taken together, these results illustrate the global alterations in host cell metabolism during lytic gammaherpesvirus infection, establish essential pathways for viral production, and recommend targeted mechanisms to block viral spread and treat viral induced tumors.
MeSH term(s)	Animals ; Mice ; Glucose/metabolism ; Glutamine/metabolism ; Host Microbial Interactions ; Lipidomics ; Metabolome ; Nucleotides/metabolism ; Rhadinovirus/physiology ; Virus Replication/physiology ; Fatty Acids/metabolism ; Herpesviridae Infections/metabolism ; Herpesviridae Infections/virology
Chemical Substances	Glucose (IY9XDZ35W2) ; Glutamine (0RH81L854J) ; Nucleotides ; Fatty Acids
Language	English
Publishing date	2023-05-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/jvi.00506-23
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Article ; Online: Residue-level global and local ensemble-ensemble comparisons of protein domains.

Clark, Sarah A / Tronrud, Dale E / Karplus, P Andrew

Protein science : a publication of the Protein Society

2015 Volume 24, Issue 9, Page(s) 1528–1542

Abstract: Many methods of protein structure generation such as NMR-based solution structure determination and template-based modeling do not produce a single model, but an ensemble of models consistent with the available information. Current strategies for ... ...

Abstract	Many methods of protein structure generation such as NMR-based solution structure determination and template-based modeling do not produce a single model, but an ensemble of models consistent with the available information. Current strategies for comparing ensembles lose information because they use only a single representative structure. Here, we describe the ENSEMBLATOR and its novel strategy to directly compare two ensembles containing the same atoms to identify significant global and local backbone differences between them on per-atom and per-residue levels, respectively. The ENSEMBLATOR has four components: eePREP (ee for ensemble-ensemble), which selects atoms common to all models; eeCORE, which identifies atoms belonging to a cutoff-distance dependent common core; eeGLOBAL, which globally superimposes all models using the defined core atoms and calculates for each atom the two intraensemble variations, the interensemble variation, and the closest approach of members of the two ensembles; and eeLOCAL, which performs a local overlay of each dipeptide and, using a novel measure of local backbone similarity, reports the same four variations as eeGLOBAL. The combination of eeGLOBAL and eeLOCAL analyses identifies the most significant differences between ensembles. We illustrate the ENSEMBLATOR's capabilities by showing how using it to analyze NMR ensembles and to compare NMR ensembles with crystal structures provides novel insights compared to published studies. One of these studies leads us to suggest that a "consistency check" of NMR-derived ensembles may be a useful analysis step for NMR-based structure determinations in general. The ENSEMBLATOR 1.0 is available as a first generation tool to carry out ensemble-ensemble comparisons.
MeSH term(s)	Computational Biology/methods ; Crystallography, X-Ray ; Magnetic Resonance Spectroscopy/methods ; Models, Molecular ; Protein Conformation ; Protein Structure, Tertiary ; Proteins/chemistry
Chemical Substances	Proteins
Language	English
Publishing date	2015-09
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.2714
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Article ; Online: Multivalent IDP assemblies: Unique properties of LC8-associated, IDP duplex scaffolds.

Clark, Sarah A / Jespersen, Nathan / Woodward, Clare / Barbar, Elisar

FEBS letters

2015 Volume 589, Issue 19 Pt A, Page(s) 2543–2551

Abstract: A wide variety of subcellular complexes are composed of one or more intrinsically disordered proteins (IDPs) that are multivalent, flexible, and characterized by dynamic binding of diverse partner proteins. These multivalent IDP assemblies, of broad ... ...

Abstract	A wide variety of subcellular complexes are composed of one or more intrinsically disordered proteins (IDPs) that are multivalent, flexible, and characterized by dynamic binding of diverse partner proteins. These multivalent IDP assemblies, of broad functional diversity, are classified here into five categories distinguished by the number of IDP chains and the arrangement of partner proteins in the functional complex. Examples of each category are summarized in the context of the exceptional molecular and biological properties of IDPs. One type - IDP duplex scaffolds - is considered in detail. Its unique features include parallel alignment of two IDP chains, formation of new self-associated domains, enhanced affinity for additional bivalent ligands, and ubiquitous binding of the hub protein LC8. For two IDP duplex scaffolds, dynein intermediate chain IC and nucleoporin Nup159, these duplex features, together with the inherent flexibility of IDPs, are central to their assembly and function. A new type of IDP-LC8 interaction, distributed binding of LC8 among multiple IDP recognition sites, is described for Nup159 assembly.
MeSH term(s)	Animals ; Cytoplasmic Dyneins/chemistry ; Cytoplasmic Dyneins/metabolism ; Entropy ; Humans ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/metabolism ; Models, Molecular ; Protein Binding ; Protein Multimerization ; Protein Structure, Tertiary
Chemical Substances	Intrinsically Disordered Proteins ; DYNLL1 protein, human (EC 3.6.1.-) ; Cytoplasmic Dyneins (EC 3.6.4.2)
Language	English
Publishing date	2015-09-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1016/j.febslet.2015.07.032
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Article ; Online: SARS-CoV-2 evolution in an immunocompromised host reveals shared neutralization escape mechanisms.

Clark, Sarah A / Clark, Lars E / Pan, Junhua / Coscia, Adrian / McKay, Lindsay G A / Shankar, Sundaresh / Johnson, Rebecca I / Brusic, Vesna / Choudhary, Manish C / Regan, James / Li, Jonathan Z / Griffiths, Anthony / Abraham, Jonathan

Cell

2021 Volume 184, Issue 10, Page(s) 2605–2617.e18

Abstract: Many individuals mount nearly identical antibody responses to SARS-CoV-2. To gain insight into how the viral spike (S) protein receptor-binding domain (RBD) might evolve in response to common antibody responses, we studied mutations occurring during ... ...

Abstract	Many individuals mount nearly identical antibody responses to SARS-CoV-2. To gain insight into how the viral spike (S) protein receptor-binding domain (RBD) might evolve in response to common antibody responses, we studied mutations occurring during virus evolution in a persistently infected immunocompromised individual. We use antibody Fab/RBD structures to predict, and pseudotypes to confirm, that mutations found in late-stage evolved S variants confer resistance to a common class of SARS-CoV-2 neutralizing antibodies we isolated from a healthy COVID-19 convalescent donor. Resistance extends to the polyclonal serum immunoglobulins of four out of four healthy convalescent donors we tested and to monoclonal antibodies in clinical use. We further show that affinity maturation is unimportant for wild-type virus neutralization but is critical to neutralization breadth. Because the mutations we studied foreshadowed emerging variants that are now circulating across the globe, our results have implications to the long-term efficacy of S-directed countermeasures.
MeSH term(s)	Antibodies, Neutralizing ; Antibodies, Viral/immunology ; COVID-19/genetics ; COVID-19/immunology ; Evolution, Molecular ; Female ; HEK293 Cells ; Humans ; Immune Evasion/immunology ; Immunocompromised Host ; Immunoglobulin Fab Fragments/immunology ; Male ; Protein Domains ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/immunology
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Immunoglobulin Fab Fragments ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-03-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2021.03.027
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Article: Multivalent IDP assemblies: Unique properties of LC8-associated, IDP duplex scaffolds

Clark, Sarah A / Nathan Jespersen / Clare Woodward / Elisar Barbar

Federation of European Biochemical Societies FEBS letters. 2015 Sept. 14, v. 589, no. 19

2015

Abstract	A wide variety of subcellular complexes are composed of one or more intrinsically disordered proteins (IDPs) that are multivalent, flexible, and characterized by dynamic binding of diverse partner proteins. These multivalent IDP assemblies, of broad functional diversity, are classified here into five categories distinguished by the number of IDP chains and the arrangement of partner proteins in the functional complex. Examples of each category are summarized in the context of the exceptional molecular and biological properties of IDPs. One type – IDP duplex scaffolds – is considered in detail. Its unique features include parallel alignment of two IDP chains, formation of new self-associated domains, enhanced affinity for additional bivalent ligands, and ubiquitous binding of the hub protein LC8. For two IDP duplex scaffolds, dynein intermediate chain IC and nucleoporin Nup159, these duplex features, together with the inherent flexibility of IDPs, are central to their assembly and function. A new type of IDP–LC8 interaction, distributed binding of LC8 among multiple IDP recognition sites, is described for Nup159 assembly.
Keywords	dynein ATPase ; functional diversity ; ligands ; proteins
Language	English
Dates of publication	2015-0914
Size	p. 2543-2551.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1016/j.febslet.2015.07.032
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Article: Molecular basis for a germline-biased neutralizing antibody response to SARS-CoV-2.

Clark, Sarah A / Clark, Lars E / Pan, Junhua / Coscia, Adrian / McKay, Lindsay G A / Shankar, Sundaresh / Johnson, Rebecca I / Griffiths, Anthony / Abraham, Jonathan

bioRxiv : the preprint server for biology

2020

Abstract: The SARS-CoV-2 viral spike (S) protein mediates attachment and entry into host cells and is a major target of vaccine and drug design. Potent SARS-CoV-2 neutralizing antibodies derived from closely related antibody heavy chain genes (IGHV3-53 or 3-66) ... ...

Abstract	The SARS-CoV-2 viral spike (S) protein mediates attachment and entry into host cells and is a major target of vaccine and drug design. Potent SARS-CoV-2 neutralizing antibodies derived from closely related antibody heavy chain genes (IGHV3-53 or 3-66) have been isolated from multiple COVID-19 convalescent individuals. These usually contain minimal somatic mutations and bind the S receptor-binding domain (RBD) to interfere with attachment to the cellular receptor angiotensin-converting enzyme 2 (ACE2). We used antigen-specific single B cell sorting to isolate S-reactive monoclonal antibodies from the blood of a COVID-19 convalescent individual. The seven most potent neutralizing antibodies were somatic variants of the same IGHV3-53-derived antibody and bind the RBD with varying affinity. We report X-ray crystal structures of four Fab variants bound to the RBD and use the structures to explain the basis for changes in RBD affinity. We show that a germline revertant antibody binds tightly to the SARS-CoV-2 RBD and neutralizes virus, and that gains in affinity for the RBD do not necessarily correlate with increased neutralization potency, suggesting that somatic mutation is not required to exert robust antiviral effect. Our studies clarify the molecular basis for a heavily germline-biased human antibody response to SARS-CoV-2.
Keywords	covid19
Language	English
Publishing date	2020-11-13
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.11.13.381533
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Article ; Online: Outcomes of surgical mitral valve replacement: A benchmark to assess transcatheter technologies.

Chancellor, William Z / Hunter Mehaffey, J / Clark, Sarah A / Hawkins, Robert B / Beller, Jared P / Rich, Jeffery B / Speir, Alan M / Quader, Mohammed / Yarboro, Leora T / Ailawadi, Gorav

Journal of cardiac surgery

2020 Volume 36, Issue 1, Page(s) 69–73

Abstract: Background: Clinical trials are underway to evaluate the safety and efficacy of transcatheter mitral valve replacement in intermediate and high surgical risk patients. We analyzed outcomes of surgical mitral valve replacement in a regional consortium to ...

Abstract	Background: Clinical trials are underway to evaluate the safety and efficacy of transcatheter mitral valve replacement in intermediate and high surgical risk patients. We analyzed outcomes of surgical mitral valve replacement in a regional consortium to provide benchmark data for emerging alternative therapies. Methods: All patients undergoing mitral replacement with a Society of Thoracic Surgeons predicted risk of mortality (STS PROM) in a regional consortium from 2001 to 2017 were analyzed. Patients with endocarditis were excluded. Patients were stratified by STS PROM into low (<4%), moderate (4%-8%), and high risk (>8%) cohorts. Mortality, postoperative complications, and resource utilization were evaluated for each group. Results: A total of 1611 patients were analyzed including 927 (58%) low, 370 (23%) moderate, and 314 (20%) high-risk patients. The mean STS PROM was 2%, 5.6%, and 15.4% for each group. Mortality was adequately predicted for all groups while the most common complications included prolonged ventilation, reoperation, and renal failure. Higher risk patients had longer intensive care unit and hospital lengths of stay (2 vs. 3 vs. 5 days, p < .0001 and 7 vs. 8 vs. 10 days, p < .0001) and higher total hospital costs ($38,029 vs. $45,075 vs. $59,171 p < .0001). Conclusions: Mitral valve replacement is associated with acceptable morbidity and mortality, particularly for low and intermediate-risk patients. These outcomes also serve as a benchmark with which to compare forthcoming results of transcatheter mitral valve replacement trials.
MeSH term(s)	Aortic Valve Stenosis/surgery ; Benchmarking ; Heart Valve Prosthesis Implantation ; Humans ; Mitral Valve/surgery ; Reoperation ; Retrospective Studies ; Risk Factors ; Transcatheter Aortic Valve Replacement ; Treatment Outcome
Language	English
Publishing date	2020-11-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	639059-6
ISSN	1540-8191 ; 0886-0440
ISSN (online)	1540-8191
ISSN	0886-0440
DOI	10.1111/jocs.15157
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Article ; Online: VLDLR and ApoER2 are receptors for multiple alphaviruses.

Clark, Lars E / Clark, Sarah A / Lin, ChieYu / Liu, Jianying / Coscia, Adrian / Nabel, Katherine G / Yang, Pan / Neel, Dylan V / Lee, Hyo / Brusic, Vesna / Stryapunina, Iryna / Plante, Kenneth S / Ahmed, Asim A / Catteruccia, Flaminia / Young-Pearse, Tracy L / Chiu, Isaac M / Llopis, Paula Montero / Weaver, Scott C / Abraham, Jonathan

Nature

2021 Volume 602, Issue 7897, Page(s) 475–480

Abstract: Alphaviruses, like many other arthropod-borne viruses, infect vertebrate species and insect vectors separated by hundreds of millions of years of evolutionary history. Entry into evolutionarily divergent host cells can be accomplished by recognition of ... ...

Abstract	Alphaviruses, like many other arthropod-borne viruses, infect vertebrate species and insect vectors separated by hundreds of millions of years of evolutionary history. Entry into evolutionarily divergent host cells can be accomplished by recognition of different cellular receptors in different species, or by binding to receptors that are highly conserved across species. Although multiple alphavirus receptors have been described
MeSH term(s)	Animals ; LDL-Receptor Related Proteins ; Ligands ; Mice ; Mosquito Vectors ; Receptors, LDL ; Semliki forest virus/metabolism ; Sindbis Virus/physiology
Chemical Substances	LDL-Receptor Related Proteins ; Ligands ; Receptors, LDL ; VLDL receptor ; low density lipoprotein receptor-related protein 8
Language	English
Publishing date	2021-12-20
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-021-04326-0
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