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Article ; Online: Single-cell analysis of psoriasis resolution demonstrates an inflammatory fibroblast state targeted by IL-23 blockade.

Francis, Luc / McCluskey, Daniel / Ganier, Clarisse / Jiang, Treasa / Du-Harpur, Xinyi / Gabriel, Jeyrroy / Dhami, Pawan / Kamra, Yogesh / Visvanathan, Sudha / Barker, Jonathan N / Smith, Catherine H / Capon, Francesca / Mahil, Satveer K

Nature communications

2024 Volume 15, Issue 1, Page(s) 913

Abstract: Biologic therapies targeting the IL-23/IL-17 axis have transformed the treatment of psoriasis. However, the early mechanisms of action of these drugs remain poorly understood. Here, we perform longitudinal single-cell RNA-sequencing in affected ... ...

Abstract	Biologic therapies targeting the IL-23/IL-17 axis have transformed the treatment of psoriasis. However, the early mechanisms of action of these drugs remain poorly understood. Here, we perform longitudinal single-cell RNA-sequencing in affected individuals receiving IL-23 inhibitor therapy. By profiling skin at baseline, day 3 and day 14 of treatment, we demonstrate that IL-23 blockade causes marked gene expression shifts, with fibroblast and myeloid populations displaying the most extensive changes at day 3. We also identify a transient WNT5A+/IL24+ fibroblast state, which is only detectable in lesional skin. In-silico and in-vitro studies indicate that signals stemming from these WNT5A+/IL24+ fibroblasts upregulate multiple inflammatory genes in keratinocytes. Importantly, the abundance of WNT5A+/IL24+ fibroblasts is significantly reduced after treatment. This observation is validated in-silico, by deconvolution of multiple transcriptomic datasets, and experimentally, by RNA in-situ hybridization. These findings demonstrate that the evolution of inflammatory fibroblast states is a key feature of resolving psoriasis skin.
MeSH term(s)	Humans ; Psoriasis/drug therapy ; Psoriasis/genetics ; Psoriasis/metabolism ; Skin/metabolism ; Keratinocytes/metabolism ; Interleukin-23/genetics ; Interleukin-23/metabolism ; RNA/metabolism ; Fibroblasts/metabolism ; Single-Cell Analysis
Chemical Substances	Interleukin-23 ; RNA (63231-63-0)
Language	English
Publishing date	2024-01-30
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-44994-w
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Article ; Online: Comparison and imputation-aided integration of five commercial platforms for targeted DNA methylome analysis.

Tanić, Miljana / Moghul, Ismail / Rodney, Simon / Dhami, Pawan / Vaikkinen, Heli / Ambrose, John / Barrett, James / Feber, Andrew / Beck, Stephan

Nature biotechnology

2022 Volume 40, Issue 10, Page(s) 1478–1487

Abstract: Targeted bisulfite sequencing (TBS) has become the method of choice for the cost-effective, targeted analysis of the human methylome at base-pair resolution. In this study, we benchmarked five commercially available TBS platforms-three hybridization ... ...

Abstract	Targeted bisulfite sequencing (TBS) has become the method of choice for the cost-effective, targeted analysis of the human methylome at base-pair resolution. In this study, we benchmarked five commercially available TBS platforms-three hybridization capture-based (Agilent, Roche and Illumina) and two reduced-representation-based (Diagenode and NuGen)-across 11 samples. Two samples were also compared with whole-genome DNA methylation sequencing with the Illumina and Oxford Nanopore platforms. We assessed workflow complexity, on/off-target performance, coverage, accuracy and reproducibility. Although all platforms produced robust and reproducible data, major differences in the number and identity of the CpG sites covered make it difficult to compare datasets generated on different platforms. To overcome this limitation, we applied imputation and show that it improves interoperability from an average of 10.35% (0.8 million) to 97% (7.6 million) common CpG sites. Our study provides guidance on which TBS platform to use for different methylome features and offers an imputation-based harmonization solution that allows comparative, integrative analysis.
MeSH term(s)	CpG Islands/genetics ; DNA Methylation/genetics ; Epigenome ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Reproducibility of Results ; Sequence Analysis, DNA/methods
Language	English
Publishing date	2022-06-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-022-01336-9
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Article ; Online: Single-cell transcriptomic and spatial landscapes of the developing human pancreas.

Olaniru, Oladapo Edward / Kadolsky, Ulrich / Kannambath, Shichina / Vaikkinen, Heli / Fung, Kathy / Dhami, Pawan / Persaud, Shanta J

Cell metabolism

2022 Volume 35, Issue 1, Page(s) 184–199.e5

Abstract: Current differentiation protocols have not been successful in reproducibly generating fully functional human beta cells in vitro, partly due to incomplete understanding of human pancreas development. Here, we present detailed transcriptomic analysis of ... ...

Abstract	Current differentiation protocols have not been successful in reproducibly generating fully functional human beta cells in vitro, partly due to incomplete understanding of human pancreas development. Here, we present detailed transcriptomic analysis of the various cell types of the developing human pancreas, including their spatial gene patterns. We integrated single-cell RNA sequencing with spatial transcriptomics at multiple developmental time points and revealed distinct temporal-spatial gene cascades. Cell trajectory inference identified endocrine progenitor populations and branch-specific genes as the progenitors differentiate toward alpha or beta cells. Spatial differentiation trajectories indicated that Schwann cells are spatially co-located with endocrine progenitors, and cell-cell connectivity analysis predicted that they may interact via L1CAM-EPHB2 signaling. Our integrated approach enabled us to identify heterogeneity and multiple lineage dynamics within the mesenchyme, showing that it contributed to the exocrine acinar cell state. Finally, we have generated an interactive web resource for investigating human pancreas development for the research community.
MeSH term(s)	Humans ; Transcriptome/genetics ; Pancreas/metabolism ; Gene Expression Profiling ; Cell Differentiation/genetics ; Pancreas, Exocrine ; Single-Cell Analysis ; Gene Expression Regulation, Developmental
Language	English
Publishing date	2022-12-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2176834-1
ISSN	1932-7420 ; 1550-4131
ISSN (online)	1932-7420
ISSN	1550-4131
DOI	10.1016/j.cmet.2022.11.009
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Article: Donor whole blood DNA methylation is not a strong predictor of acute graft

Webster, Amy P / Ecker, Simone / Moghul, Ismail / Liu, Xiaohong / Dhami, Pawan / Marzi, Sarah / Paul, Dirk S / Kuxhausen, Michelle / Lee, Stephanie J / Spellman, Stephen R / Wang, Tao / Feber, Andrew / Rakyan, Vardhman / Peggs, Karl S / Beck, Stephan

Frontiers in genetics

2024 Volume 15, Page(s) 1242636

Abstract: Allogeneic hematopoietic cell transplantation (HCT) is used to treat many blood-based disorders and malignancies, however it can also result in serious adverse events, such as the development of acute graft-versus-host disease (aGVHD). This study aimed ... ...

Abstract	Allogeneic hematopoietic cell transplantation (HCT) is used to treat many blood-based disorders and malignancies, however it can also result in serious adverse events, such as the development of acute graft-versus-host disease (aGVHD). This study aimed to develop a donor-specific epigenetic classifier to reduce incidence of aGVHD by improving donor selection. Genome-wide DNA methylation was assessed in a discovery cohort of 288 HCT donors selected based on recipient aGVHD outcome; this cohort consisted of 144 cases with aGVHD grades III-IV and 144 controls with no aGVHD. We applied a machine learning algorithm to identify CpG sites predictive of aGVHD. Receiver operating characteristic (ROC) curve analysis of these sites resulted in a classifier with an encouraging area under the ROC curve (AUC) of 0.91. To test this classifier, we used an independent validation cohort (n = 288) selected using the same criteria as the discovery cohort. Attempts to validate the classifier failed with the AUC falling to 0.51. These results indicate that donor DNA methylation may not be a suitable predictor of aGVHD in an HCT setting involving unrelated donors, despite the initial promising results in the discovery cohort. Our work highlights the importance of independent validation of machine learning classifiers, particularly when developing classifiers intended for clinical use.
Language	English
Publishing date	2024-04-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2024.1242636
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Article ; Online: Double-negative B cells and DNASE1L3 colocalise with microbiota in gut-associated lymphoid tissue.

Montorsi, Lucia / Pitcher, Michael J / Zhao, Yuan / Dionisi, Chiara / Demonti, Alicia / Tull, Thomas J / Dhami, Pawan / Ellis, Richard J / Bishop, Cynthia / Sanderson, Jeremy D / Jain, Sahil / D'Cruz, David / Gibbons, Deena L / Winkler, Thomas H / Bemark, Mats / Ciccarelli, Francesca D / Spencer, Jo

Nature communications

2024 Volume 15, Issue 1, Page(s) 4051

Abstract: Intestinal homeostasis is maintained by the response of gut-associated lymphoid tissue to bacteria transported across the follicle associated epithelium into the subepithelial dome. The initial response to antigens and how bacteria are handled is ... ...

Abstract	Intestinal homeostasis is maintained by the response of gut-associated lymphoid tissue to bacteria transported across the follicle associated epithelium into the subepithelial dome. The initial response to antigens and how bacteria are handled is incompletely understood. By iterative application of spatial transcriptomics and multiplexed single-cell technologies, we identify that the double negative 2 subset of B cells, previously associated with autoimmune diseases, is present in the subepithelial dome in health. We show that in this location double negative 2 B cells interact with dendritic cells co-expressing the lupus autoantigens DNASE1L3 and C1q and microbicides. We observe that in humans, but not in mice, dendritic cells expressing DNASE1L3 are associated with sampled bacteria but not DNA derived from apoptotic cells. We propose that fundamental features of autoimmune diseases are microbiota-associated, interacting components of normal intestinal immunity.
MeSH term(s)	Animals ; Humans ; Mice ; B-Lymphocytes/immunology ; B-Lymphocytes/metabolism ; Gastrointestinal Microbiome/immunology ; Endodeoxyribonucleases/metabolism ; Endodeoxyribonucleases/genetics ; Dendritic Cells/immunology ; Dendritic Cells/metabolism ; Lymphoid Tissue/immunology ; Lymphoid Tissue/metabolism ; Female ; Mice, Inbred C57BL ; Intestinal Mucosa/immunology ; Intestinal Mucosa/microbiology ; Intestinal Mucosa/metabolism ; Male
Language	English
Publishing date	2024-05-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-48267-4
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Article ; Online: Spatially resolved transcriptomics reveals pro-inflammatory fibroblast involved in lymphocyte recruitment through CXCL8 and CXCL10.

Caetano, Ana J / Redhead, Yushi / Karim, Farah / Dhami, Pawan / Kannambath, Shichina / Nuamah, Rosamond / Volponi, Ana A / Nibali, Luigi / Booth, Veronica / D'Agostino, Eleanor M / Sharpe, Paul T

eLife

2023 Volume 12

Abstract: The interplay among different cells in a tissue is essential for maintaining homeostasis. Although disease states have been traditionally attributed to individual cell types, increasing evidence and new therapeutic options have demonstrated the primary ... ...

Abstract	The interplay among different cells in a tissue is essential for maintaining homeostasis. Although disease states have been traditionally attributed to individual cell types, increasing evidence and new therapeutic options have demonstrated the primary role of multicellular functions to understand health and disease, opening new avenues to understand pathogenesis and develop new treatment strategies. We recently described the cellular composition and dynamics of the human oral mucosa; however, the spatial arrangement of cells is needed to better understand a morphologically complex tissue. Here, we link single-cell RNA sequencing, spatial transcriptomics, and high-resolution multiplex fluorescence
MeSH term(s)	Humans ; Chemokine CXCL10/genetics ; Fibroblasts ; Gene Expression Profiling ; Lymphocytes ; Transcriptome ; Interleukin-8/metabolism
Chemical Substances	Chemokine CXCL10 ; CXCL10 protein, human ; Interleukin-8 ; CXCL8 protein, human
Language	English
Publishing date	2023-01-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.81525
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Article ; Online: Psoriatic and rheumatoid arthritis joints differ in the composition of CD8+ tissue-resident memory T cell subsets.

Povoleri, Giovanni A M / Durham, Lucy E / Gray, Elizabeth H / Lalnunhlimi, Sylvine / Kannambath, Shichina / Pitcher, Michael J / Dhami, Pawan / Leeuw, Thomas / Ryan, Sarah E / Steel, Kathryn J A / Kirkham, Bruce W / Taams, Leonie S

Cell reports

2023 Volume 42, Issue 5, Page(s) 112514

Abstract: CD69+CD103+ tissue-resident memory T ( ... ...

Abstract	CD69+CD103+ tissue-resident memory T (T
MeSH term(s)	Humans ; Arthritis, Psoriatic/metabolism ; Memory T Cells ; T-Lymphocyte Subsets/metabolism ; CD8-Positive T-Lymphocytes/metabolism ; Arthritis, Rheumatoid/metabolism ; Immunologic Memory
Language	English
Publishing date	2023-05-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2023.112514
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Article ; Online: Loss of the crumbs cell polarity complex disrupts epigenetic transcriptional control and cell cycle progression in the developing retina.

Owen, Nicholas / Toms, Maria / Tian, Yuan / Toualbi, Lyes / Richardson, Rose / Young, Rodrigo / Tracey-White, Dhani / Dhami, Pawan / Beck, Stephan / Moosajee, Mariya

The Journal of pathology

2023 Volume 259, Issue 4, Page(s) 441–454

Abstract: The crumbs cell polarity complex plays a crucial role in apical-basal epithelial polarity, cellular adhesion, and morphogenesis. Homozygous variants in human CRB1 result in autosomal recessive Leber congenital amaurosis (LCA) and retinitis pigmentosa (RP) ...

Abstract	The crumbs cell polarity complex plays a crucial role in apical-basal epithelial polarity, cellular adhesion, and morphogenesis. Homozygous variants in human CRB1 result in autosomal recessive Leber congenital amaurosis (LCA) and retinitis pigmentosa (RP), with no established genotype-phenotype correlation. The associated protein complexes have key functions in developmental pathways; however, the underlying disease mechanism remains unclear. Using the oko meduzy
MeSH term(s)	Animals ; Humans ; Zebrafish/genetics ; Cell Polarity/genetics ; Retina/metabolism ; Cell Cycle ; Epigenesis, Genetic ; Eye Proteins/genetics ; Eye Proteins/metabolism ; Membrane Proteins/metabolism ; Nerve Tissue Proteins/metabolism ; Zebrafish Proteins/genetics ; Zebrafish Proteins/metabolism
Chemical Substances	CRB1 protein, human ; Eye Proteins ; Membrane Proteins ; Nerve Tissue Proteins ; Crb1 protein, zebrafish ; Zebrafish Proteins
Language	English
Publishing date	2023-02-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3119-7
ISSN	1096-9896 ; 0022-3417
ISSN (online)	1096-9896
ISSN	0022-3417
DOI	10.1002/path.6056
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Article ; Online: Repurposing Metformin for periodontal disease management as a form of oral-systemic preventive medicine.

Neves, Vitor C M / Satie Okajima, Luciana / Elbahtety, Eyad / Joseph, Susan / Daly, James / Menon, Athul / Fan, Di / Volkyte, Ayste / Mainas, Giuseppe / Fung, Kathy / Dhami, Pawan / Pelegrine, Andre A / Sharpe, Paul / Nibali, Luigi / Ide, Mark

Journal of translational medicine

2023 Volume 21, Issue 1, Page(s) 655

Abstract: Background: Despite the improvements in treatment over the last decades, periodontal disease (PD) affects millions of people around the world and the only treatment available is based on controlling microbial load. Diabetes is known to increase the risk ...

Abstract	Background: Despite the improvements in treatment over the last decades, periodontal disease (PD) affects millions of people around the world and the only treatment available is based on controlling microbial load. Diabetes is known to increase the risk of PD establishment and progression, and recently, glucose metabolism modulation by pharmaceutical or dietarian means has been emphasised as a significant modulator of non-communicable disease development. Methods: The impact of pharmaceutically controlling glucose metabolism in non-diabetic animals and humans (REBEC, UTN code: U1111-1276-1942) was investigated by repurposing Metformin, as a mean to manage periodontal disease and its associated systemic risk factors. Results: We found that glucose metabolism control via use of Metformin aimed at PD management resulted in significant prevention of bone loss during induced periodontal disease and age-related bone loss in vivo. Metformin also influenced the bacterial species present in the oral environment and impacted the metabolic epithelial and stromal responses to bacterial dysbiosis at a single cell level. Systemically, Metformin controlled blood glucose levels and age-related weight gain when used long-term. Translationally, our pilot randomized control trial indicated that systemic Metformin was safe to use in non-diabetic patients and affected the periodontal tissues. During the medication window, patients showed stable levels of systemic blood glucose, lower circulating hsCRP and lower insulin levels after periodontal treatment when compared to placebo. Finally, patients treated with Metformin had improved periodontal parameters when compared to placebo treated patients. Conclusion: This is the first study to demonstrate that systemic interventions using Metformin in non-diabetic individuals aimed at PD prevention have oral-systemic effects constituting a possible novel form of preventive medicine for oral-systemic disease management.
MeSH term(s)	Animals ; Humans ; Metformin/pharmacology ; Metformin/therapeutic use ; Hypoglycemic Agents/pharmacology ; Hypoglycemic Agents/therapeutic use ; Diabetes Mellitus, Type 2 ; Blood Glucose ; Periodontal Diseases/drug therapy ; Disease Management
Chemical Substances	Metformin (9100L32L2N) ; Hypoglycemic Agents ; Blood Glucose
Language	English
Publishing date	2023-10-10
Publishing country	England
Document type	Randomized Controlled Trial ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2118570-0
ISSN	1479-5876 ; 1479-5876
ISSN (online)	1479-5876
ISSN	1479-5876
DOI	10.1186/s12967-023-04456-1
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Article ; Online: Molecular, clinical and therapeutic determinants of outcome in NPM1 mutated AML.

Othman, Jad / Potter, Nicola / Ivey, Adam / Tazi, Yanis / Papaemmanuil, Elli / Jovanovic, Jelena / Freeman, Sylvie D / Gilkes, Amanda Frances / Gale, Rosemary E / Rapoz-D'Silva, Tanya / Runglall, Manohursingh / Kleeman, Michelle / Dhami, Pawan / Thomas, Ian / Johnson, Sean / Canham, Joanna / Cavenagh, James Durrell / Kottaridis, Panagiotis / Arnold, Claire /

Ommen, Hans Beier / Overgaard, Ulrik Malthe / Dennis, Mike / Burnett, Alan Kenneth / Wilhelm-Benartzi, Charlotte S / Huntly, Brian Jp / Russell, Nigel H / Dillon, Richard James

Blood

2024

Abstract: Although NPM1-mutated acute myeloid leukemia (AML) carries a generally favorable prognosis, many patients still relapse and die. Previous studies identified several molecular and clinical features associated with poor outcome, however only FLT3-ITD ... ...

Abstract	Although NPM1-mutated acute myeloid leukemia (AML) carries a generally favorable prognosis, many patients still relapse and die. Previous studies identified several molecular and clinical features associated with poor outcome, however only FLT3-ITD mutation and adverse karyotype are currently used for risk stratification due to inconsistent results and uncertainty around how other factors should influence treatment, particularly given the strong prognostic impact of post-induction measurable residual disease (MRD). Here we analyzed a large group of patients with NPM1mut AML enrolled in prospective trials (NCRI AML17 and AML19, n=1357) to delineate the impact of baseline molecular and clinical features, post induction MRD status and treatment intensity on outcome. FLT3-ITD (HR 1.28, 95%CI 1.01-1.63), DNMT3A (HR 1.65, 95%CI 1.32-2.05), WT1 (HR 1.74, 95%CI 1272-2.38) and non-ABD NPM1 mutations (HR 1.64, 95%CI 1.22-2.21) were independently associated with poorer overall survival (OS). These factors were also strongly associated with MRD positivity. For patients achieving MRD negativity, these mutations (except FLT3-ITD) were associated with an increased cumulative incidence of relapse (CIR) and poorer OS. However, apart from the few patients with adverse cytogenetics, we could not identify any group of MRD negative patients with a CIR >40% or with benefit from allograft in first remission. Intensified chemotherapy with the FLAG-Ida regimen was associated with improved outcomes in all subgroups, with greater benefits observed in the highest risk molecular subgroups.
Language	English
Publishing date	2024-05-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	80069-7
ISSN	1528-0020 ; 0006-4971
ISSN (online)	1528-0020
ISSN	0006-4971
DOI	10.1182/blood.2024024310
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