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Article ; Online: mpwR: an R package for comparing performance of mass spectrometry-based proteomic workflows.

Kardell, Oliver / Breimann, Stephan / Hauck, Stefanie M

2023 Volume 39, Issue 6

Abstract: Summary: mpwR is an R package for a standardized comparison of mass spectrometry (MS)-based proteomic label-free workflows recorded by data-dependent or data-independent spectral acquisition. The user-friendly design allows easy access to compare the ... ...

Abstract	Summary: mpwR is an R package for a standardized comparison of mass spectrometry (MS)-based proteomic label-free workflows recorded by data-dependent or data-independent spectral acquisition. The user-friendly design allows easy access to compare the influence of sample preparation procedures, combinations of liquid chromatography (LC)-MS setups, as well as intra- and inter-software differences on critical performance measures across an unlimited number of analyses. mpwR supports outputs of commonly used software for bottom-up proteomics, such as ProteomeDiscoverer, Spectronaut, MaxQuant, and DIA-NN. Availability and implementation: mpwR is available as an open-source R package. Release versions can be accessed on CRAN (https://CRAN.R-project.org/package=mpwR) for all major operating systems. The development version is maintained on GitHub (https://github.com/okdll/mpwR) and full documentation with examples and workflow templates is provided via the package website (https://okdll.github.io/mpwR/).
MeSH term(s)	Proteomics/methods ; Workflow ; Mass Spectrometry/methods ; Software ; Chromatography, Liquid/methods
Language	English
Publishing date	2023-06-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btad358
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Article ; Online: The novel pre-rRNA detection workflow "Riboprobing" allows simple identification of undescribed RNA species.

Gerhalter, Magdalena / Kofler, Lisa / Zisser, Gertrude / Merl-Pham, Juliane / Hauck, Stefanie M / Bergler, Helmut

RNA (New York, N.Y.)

2024

Abstract: Ribosomes translate mRNA into proteins and are essential for every living organism. In eukaryotes both ribosomal subunits are rapidly assembled in a strict hierarchical order, starting in the nucleolus with transcription of a common precursor ribosomal ... ...

Abstract	Ribosomes translate mRNA into proteins and are essential for every living organism. In eukaryotes both ribosomal subunits are rapidly assembled in a strict hierarchical order, starting in the nucleolus with transcription of a common precursor ribosomal RNA (pre-rRNA). This pre-rRNA encodes three of the four mature rRNAs which are formed by several, consecutive endonucleolytic and exonucleolytic processing steps. Historically, Northern Blots are used to analyze the variety of different pre-rRNA species, only allowing rough length estimations. Although this limitation can be overcome with Primer Extension, both approaches often use radioactivity and are time consuming and costly. Here we present "Riboprobing" a reverse transcription-based workflow extended by linker ligation for easy and fast detection and characterization of various pre-rRNA species and their 5` as well as 3` ends. Using standard molecular biology lab equipment, our technique allows reliable discrimination of pre-rRNA species not resolved by Northern Blotting (e.g.: 27SA2, 27SA3 and 27SB). The method can be successfully used for analysis of total cell extracts as well as purified pre-ribosomes for a straightforward evaluation of the impact of mutant gene versions or inhibitors. In the course of method development, we identified and characterized a hitherto undescribed aberrant pre-rRNA, arising from LiCl inhibition. This pre-rRNA fragment spans from processing site A1 to E, forming a small RNP that is lacking most early joining assembly factors. This finding expands our knowledge of how the cell deals with severe pre-rRNA processing defects and demonstrates the strict requirement for the 5'ETS for the assembly process.
Language	English
Publishing date	2024-04-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.079912.123
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Article ; Online: Associations of Proteomics With Hypertension and Systolic Blood Pressure: KORA S4/F4/FF4 and KORA Age1/Age2 Cohort Studies.

Lin, Jie-Sheng / Petrera, Agnese / Hauck, Stefanie M / Müller, Christian L / Peters, Annette / Thorand, Barbara

Hypertension (Dallas, Tex. : 1979)

2024 Volume 81, Issue 5, Page(s) 1156–1166

Abstract: Background: Hypertension, a complex condition, is primarily defined based on blood pressure readings without involving its pathophysiological mechanisms. We aimed to identify biomarkers through a proteomic approach, thereby enhancing the future ... ...

Abstract	Background: Hypertension, a complex condition, is primarily defined based on blood pressure readings without involving its pathophysiological mechanisms. We aimed to identify biomarkers through a proteomic approach, thereby enhancing the future definition of hypertension with insights into its molecular mechanisms. Methods: The discovery analysis included 1560 participants, aged 55 to 74 years at baseline, from the KORA (Cooperative Health Research in the Region of Augsburg) S4/F4/FF4 cohort study, with 3332 observations over a median of 13.4 years of follow-up. Generalized estimating equations were used to estimate the associations of 233 plasma proteins with hypertension and systolic blood pressure (SBP). For validation, proteins significantly associated with hypertension or SBP in the discovery analysis were validated in the KORA Age1/Age2 cohort study (1024 participants, 1810 observations). A 2-sample Mendelian randomization analysis was conducted to infer causalities of validated proteins with SBP. Results: Discovery analysis identified 49 proteins associated with hypertension and 99 associated with SBP. Validation in the KORA Age1/Age2 study replicated 7 proteins associated with hypertension and 23 associated with SBP. Three proteins, NT-proBNP (N-terminal pro-B-type natriuretic peptide), KIM1 (kidney injury molecule 1), and OPG (osteoprotegerin), consistently showed positive associations with both outcomes. Five proteins demonstrated potential causal associations with SBP in Mendelian randomization analysis, including NT-proBNP and OPG. Conclusions: We identified and validated 7 hypertension-associated and 23 SBP-associated proteins across 2 cohort studies. KIM1, NT-proBNP, and OPG demonstrated robust associations, and OPG was identified for the first time as associated with blood pressure. For NT-proBNP (protective) and OPG, causal associations with SBP were suggested.
MeSH term(s)	Humans ; Blood Pressure/physiology ; Cohort Studies ; Proteomics ; Hypertension ; Biomarkers ; Natriuretic Peptide, Brain ; Peptide Fragments
Chemical Substances	Biomarkers ; Natriuretic Peptide, Brain (114471-18-0) ; Peptide Fragments
Language	English
Publishing date	2024-03-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	423736-5
ISSN	1524-4563 ; 0194-911X ; 0362-4323
ISSN (online)	1524-4563
ISSN	0194-911X ; 0362-4323
DOI	10.1161/HYPERTENSIONAHA.123.22614
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Article: Unveiling Differential Responses of Granulocytes to Distinct Immunostimulants with Implications in Autoimmune Uveitis.

Degroote, Roxane L / Schmalen, Adrian / Hauck, Stefanie M / Deeg, Cornelia A

Biomedicines

2023 Volume 12, Issue 1

Abstract: The perception of circulating granulocytes as cells with a predetermined immune response mainly triggered by pathogens is evolving, recognizing their functional heterogeneity and adaptability, particularly within the neutrophil subset. The involvement of ...

Abstract	The perception of circulating granulocytes as cells with a predetermined immune response mainly triggered by pathogens is evolving, recognizing their functional heterogeneity and adaptability, particularly within the neutrophil subset. The involvement of these cells in the pathophysiology of autoimmune uveitis has become increasingly clear, yet their exact role remains elusive. We used an equine model for autoimmune-mediated recurrent pan-uveitis to investigate early responses of granulocytes in different inflammatory environments. For this purpose, we performed differential proteomics on granulocytes from healthy and diseased horses stimulated with IL8, LPS, or PMA. Compared to healthy horses, granulocytes from the recurrent uveitis model significantly changed the cellular abundance of 384 proteins, with a considerable number of specific changes for each stimulant. To gain more insight into the functional impact of these stimulant-specific proteome changes in ERU pathogenesis, we used Ingenuity Pathway Analysis for pathway enrichment. This resulted in specific reaction patterns for each stimulant, with IL8 predominantly promoting Class I MHC-mediated antigen processing and presentation, LPS enhancing processes in phospholipid biosynthesis, and PMA, clearly inducing neutrophil degranulation. These findings shed light on the remarkably differentiated responses of neutrophils, offering valuable insights into their functional heterogeneity in a T-cell-driven disease. Raw data are available via ProteomeXchange with identifier PXD013648.
Language	English
Publishing date	2023-12-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720867-9
ISSN	2227-9059
ISSN	2227-9059
DOI	10.3390/biomedicines12010019
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Article: Cathepsin S Is More Abundant in Serum of

Duda, Heidi C / von Toerne, Christine / Korbonits, Lucia / Didier, Andrea / Scholz, Armin M / Märtlbauer, Erwin / Hauck, Stefanie M / Deeg, Cornelia A

Metabolites

2024 Volume 14, Issue 4

Abstract: Mycobacterium ... ...

Abstract	Mycobacterium avium
Language	English
Publishing date	2024-04-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662251-8
ISSN	2218-1989
ISSN	2218-1989
DOI	10.3390/metabo14040215
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Article: Addition of inflammation-related biomarkers to the CAIDE model for risk prediction of all-cause dementia, Alzheimer's disease and vascular dementia in a prospective study.

Trares, Kira / Wiesenfarth, Manuel / Stocker, Hannah / Perna, Laura / Petrera, Agnese / Hauck, Stefanie M / Beyreuther, Konrad / Brenner, Hermann / Schöttker, Ben

Immunity & ageing : I & A

2024 Volume 21, Issue 1, Page(s) 23

Abstract: Background: It is of interest whether inflammatory biomarkers can improve dementia prediction models, such as the widely used Cardiovascular Risk Factors, Aging and Dementia (CAIDE) model.: Methods: The Olink Target 96 Inflammation panel was assessed ...

Abstract	Background: It is of interest whether inflammatory biomarkers can improve dementia prediction models, such as the widely used Cardiovascular Risk Factors, Aging and Dementia (CAIDE) model. Methods: The Olink Target 96 Inflammation panel was assessed in a nested case-cohort design within a large, population-based German cohort study (n = 9940; age-range: 50-75 years). All study participants who developed dementia over 20 years of follow-up and had complete CAIDE variable data (n = 562, including 173 Alzheimer's disease (AD) and 199 vascular dementia (VD) cases) as well as n = 1,356 controls were selected for measurements. 69 inflammation-related biomarkers were eligible for use. LASSO logistic regression and bootstrapping were utilized to select relevant biomarkers and determine areas under the curve (AUCs). Results: The CAIDE model 2 (including Apolipoprotein E (APOE) ε4 carrier status) predicted all-cause dementia, AD, and VD better than CAIDE model 1 (without APOE ε4) with AUCs of 0.725, 0.752 and 0.707, respectively. Although 20, 7, and 4 inflammation-related biomarkers were selected by LASSO regression to improve CAIDE model 2, the AUCs did not increase markedly. CAIDE models 1 and 2 generally performed better in mid-life (50-64 years) than in late-life (65-75 years) sub-samples of our cohort, but again, inflammation-related biomarkers did not improve their predictive abilities. Conclusions: Despite a lack of improvement in dementia risk prediction, the selected inflammation-related biomarkers were significantly associated with dementia outcomes and may serve as a starting point to further elucidate the pathogenesis of dementia.
Language	English
Publishing date	2024-04-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2168941-6
ISSN	1742-4933
ISSN	1742-4933
DOI	10.1186/s12979-024-00427-2
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Article ; Online: A Lysine Residue at the C-Terminus of MHC Class I Ligands Correlates with Low C-Terminal Proteasomal Cleavage Probability.

Schmalen, Adrian / Kammerl, Ilona E / Meiners, Silke / Noessner, Elfriede / Deeg, Cornelia A / Hauck, Stefanie M

Biomolecules

2023 Volume 13, Issue 9

Abstract: The majority of peptides presented by MHC class I result from proteasomal protein turnover. The specialized immunoproteasome, which is induced during inflammation, plays a major role in antigenic peptide generation. However, other cellular proteases can, ...

Abstract	The majority of peptides presented by MHC class I result from proteasomal protein turnover. The specialized immunoproteasome, which is induced during inflammation, plays a major role in antigenic peptide generation. However, other cellular proteases can, either alone or together with the proteasome, contribute peptides to MHC class I loading non-canonically. We used an immunopeptidomics workflow combined with prediction software for proteasomal cleavage probabilities to analyze how inflammatory conditions affect the proteasomal processing of immune epitopes presented by A549 cells. The treatment of A549 cells with IFNγ enhanced the proteasomal cleavage probability of MHC class I ligands for both the constitutive proteasome and the immunoproteasome. Furthermore, IFNγ alters the contribution of the different HLA allotypes to the immunopeptidome. When we calculated the HLA allotype-specific proteasomal cleavage probabilities for MHC class I ligands, the peptides presented by HLA-A30:01 showed characteristics hinting at a reduced C-terminal proteasomal cleavage probability independently of the type of proteasome. This was confirmed by HLA-A30:01 ligands from the immune epitope database, which also showed this effect. Furthermore, two additional HLA allotypes, namely, HLA-A03:01 and HLA-A11:01, presented peptides with a markedly reduced C-terminal proteasomal cleavage probability. The peptides eluted from all three HLA allotypes shared a peptide binding motif with a C-terminal lysine residue, suggesting that this lysine residue impairs proteasome-dependent HLA ligand production and might, in turn, favor peptide generation by other cellular proteases.
MeSH term(s)	Proteasome Endopeptidase Complex ; Lysine ; Ligands ; Endopeptidases ; Epitopes ; Probability ; HLA-A Antigens
Chemical Substances	Proteasome Endopeptidase Complex (EC 3.4.25.1) ; Lysine (K3Z4F929H6) ; Ligands ; Endopeptidases (EC 3.4.-) ; Epitopes ; HLA-A Antigens
Language	English
Publishing date	2023-08-24
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom13091300
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Article: Proteomics of the phase angle: Results from the population-based KORA S4 study

Huemer, Marie-Theres / Petrera, Agnese / Hauck, Stefanie M. / Drey, Michael / Peters, Annette / Thorand, Barbara

Clinical nutrition. 2022 Aug., v. 41, no. 8

2022

Abstract: The phase angle (PhA) measured with bioelectrical impedance analysis is considered to reflect the interrelated components body cell mass and fluid distribution based on technical and physical aspects of the PhA measurement. However, the biomedical ... ...

Abstract	The phase angle (PhA) measured with bioelectrical impedance analysis is considered to reflect the interrelated components body cell mass and fluid distribution based on technical and physical aspects of the PhA measurement. However, the biomedical meaning of the PhA remains vague. Previous studies mainly assessed associations of the PhA with numerous diseases and health outcomes, but few connected protein markers to the PhA. To broaden our understanding of the biomedical background of the PhA, we aimed to explore a proteomics profile associated with the PhA and related biological factors. The study sample encompassed 1484 participants (725 women and 759 men) aged 55–74 years from the population-based Cooperative Health Research in the Region of Augsburg (KORA) S4 study. Proteomics measurements were performed with a proximity extension assay. We employed boosting with stability selection to establish a set of markers that was strongly associated with the PhA from a group of 233 plasma protein markers. We integrated the selected protein markers into a network and enrichment analysis to identify gene ontology (GO) terms significantly overrepresented for the selected PhA protein markers. Boosting with stability selection identified seven protein markers that were strongly and independently associated with the PhA: N-terminal prohormone brain natriuretic peptide (NT-proBNP), insulin-like growth factor-binding protein 2 (IGFBP2), adrenomedullin (ADM), myoglobin (MB), matrix metalloproteinase-9 (MMP9), protein-glutamine gamma-glutamyltransferase 2 (TGM2), and fractalkine (CX3CL1) [beta coefficient per 1 standard deviation increase in normalized protein expression values on a log 2 scale (95% confidence interval): −0.12 (−0.15, −0.08), −0.13 (−0.17, −0.09), −0.14 (−0.18, −0.10), 0.10 (0.07, 0.14), 0.07 (0.04, 0.10), 0.08 (0.05, 0.11), −0.06 (−0.10, −0.03), respectively]. According to the enrichment analysis, this protein profile was significantly overrepresented in the following top five GO terms: positive regulation of cell population proliferation (p-value: 1.32E-04), extracellular space (p-value: 1.34E-04), anatomical structure formation involved in morphogenesis (p-value: 2.92E-04), regulation of multicellular organismal development (p-value: 5.72E-04), and metal ion homeostasis (p-value: 8.86E-04). Implementing a proteomics approach, we identified six new protein markers strongly associated with the PhA and confirmed that NT-proBNP is a key PhA marker. The main biological processes that were related to this PhA's protein profile are involved in regulating the amount and growth of cells, reinforcing, from a biomedical perspective, the current technical-based consensus of the PhA to reflect body cell mass.
Keywords	bioelectrical impedance ; blood proteins ; brain ; chemokine CX3CL1 ; clinical nutrition ; confidence interval ; extracellular space ; gelatinase B ; gene ontology ; homeostasis ; insulin-like growth factor binding proteins ; morphogenesis ; myoglobin ; natriuretic peptides ; protein composition ; protein synthesis ; protein-glutamine gamma-glutamyltransferase ; proteomics ; standard deviation
Language	English
Dates of publication	2022-08
Size	p. 1818-1826.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	604812-2
ISSN	1532-1983 ; 0261-5614
ISSN (online)	1532-1983
ISSN	0261-5614
DOI	10.1016/j.clnu.2022.06.038
Database	NAL-Catalogue (AGRICOLA)

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Zs.A 1774: Show issues

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Article ; Online: Adipose microtissue-on-chip: a 3D cell culture platform for differentiation, stimulation, and proteomic analysis of human adipocytes.

Compera, Nina / Atwell, Scott / Wirth, Johannes / von Törne, Christine / Hauck, Stefanie M / Meier, Matthias

Lab on a chip

2022 Volume 22, Issue 17, Page(s) 3172–3186

Abstract: Human fat tissue has evolved to serve as a major energy reserve. An imbalance between energy intake and expenditure leads to an expansion of adipose tissue. Maintenance of this energy imbalance over long periods leads to obesity and metabolic disorders ... ...

Abstract	Human fat tissue has evolved to serve as a major energy reserve. An imbalance between energy intake and expenditure leads to an expansion of adipose tissue. Maintenance of this energy imbalance over long periods leads to obesity and metabolic disorders such as type 2 diabetes, for which a clinical cure is not yet available. In this study, we developed a microfluidic large-scale integration chip platform to automate the formation, long-term culture, and retrieval of 3D adipose microtissues to enable longitudinal studies of adipose tissue
MeSH term(s)	Adipocytes ; Adipose Tissue ; Cell Culture Techniques, Three Dimensional ; Cell Differentiation ; Diabetes Mellitus, Type 2/metabolism ; Glucose/metabolism ; Humans ; Obesity/pathology ; Proteome ; Proteomics
Chemical Substances	Proteome ; Glucose (IY9XDZ35W2)
Language	English
Publishing date	2022-08-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2056646-3
ISSN	1473-0189 ; 1473-0197
ISSN (online)	1473-0189
ISSN	1473-0197
DOI	10.1039/d2lc00245k
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Article ; Online: Pre-Activated Granulocytes from an Autoimmune Uveitis Model Show Divergent Pathway Activation Profiles upon IL8 Stimulation In Vitro.

Hoffmann, Anne L C / Hauck, Stefanie M / Deeg, Cornelia A / Degroote, Roxane L

International journal of molecular sciences

2022 Volume 23, Issue 17

Abstract: In the pathophysiology of autoimmune-mediated uveitis, granulocytes have emerged as possible disease mediators and were shown to be pre-activated in equine recurrent uveitis (ERU), a spontaneous disease model. We therefore used granulocytes from ERU ... ...

Abstract	In the pathophysiology of autoimmune-mediated uveitis, granulocytes have emerged as possible disease mediators and were shown to be pre-activated in equine recurrent uveitis (ERU), a spontaneous disease model. We therefore used granulocytes from ERU horses to identify early molecular mechanisms involved in this dysregulated innate immune response. Primary granulocytes from healthy and ERU horses were stimulated with IL8, and cellular response was analyzed with differential proteomics, which revealed significant differences in protein abundance of 170 proteins in ERU. Subsequent ingenuity pathway analysis identified three activated canonical pathways "PKA signaling", "PTEN signaling" and "leukocyte extravasation". Clustered to the leukocyte extravasation pathway, we found the membrane-type GPI-anchored protease MMP25, which was increased in IL8 stimulated ERU granulocytes. These findings point to MMP25 as a possible regulator of granulocyte extravasation in uveitis and a role of this molecule in the impaired integrity of the blood-retina-barrier. In conclusion, our analyses show a clearly divergent reaction profile of pre-activated granulocytes upon IL8 stimulation and provide basic information for further in-depth studies on early granulocyte activation in non-infectious ocular diseases. This may be of interest for the development of new approaches in uveitis diagnostics and therapy. Raw data are available via ProteomeXchange with identifier PXD013648.
MeSH term(s)	Animals ; Autoimmune Diseases ; Granulocytes/metabolism ; Horse Diseases/metabolism ; Horses ; Interleukin-8 ; Proteomics ; Recurrence ; Uveitis/metabolism
Chemical Substances	Interleukin-8
Language	English
Publishing date	2022-08-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23179555
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