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Article ; Online: Bayes optimal informer sets for early‐stage drug discovery

Yu, Peng / Ericksen, Spencer / Gitter, Anthony / Newton, Michael A.

Biometrics. 2023 June, v. 79, no. 2 p.642-654

2023

Abstract: An important experimental design problem in early‐stage drug discovery is how to prioritize available compounds for testing when very little is known about the target protein. Informer‐based ranking (IBR) methods address the prioritization problem when ... ...

Abstract	An important experimental design problem in early‐stage drug discovery is how to prioritize available compounds for testing when very little is known about the target protein. Informer‐based ranking (IBR) methods address the prioritization problem when the compounds have provided bioactivity data on other potentially relevant targets. An IBR method selects an informer set of compounds, and then prioritizes the remaining compounds on the basis of new bioactivity experiments performed with the informer set on the target. We formalize the problem as a two‐stage decision problem and introduce the Bayes Optimal Informer SEt (BOISE) method for its solution. BOISE leverages a flexible model of the initial bioactivity data, a relevant loss function, and effective computational schemes to resolve the two‐step design problem. We evaluate BOISE and compare it to other IBR strategies in two retrospective studies, one on protein‐kinase inhibition and the other on anticancer drug sensitivity. In both empirical settings BOISE exhibits better predictive performance than available methods. It also behaves well with missing data, where methods that use matrix completion show worse predictive performance.
Keywords	antineoplastic agents ; bioactive properties ; experimental design ; models ; prioritization ; protein kinases
Language	English
Dates of publication	2023-06
Size	p. 642-654.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	213543-7
ISSN	0099-4987 ; 0006-341X
ISSN	0099-4987 ; 0006-341X
DOI	10.1111/biom.13637
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Natural History of Colorectal Polyps Undergoing Longitudinal in Vivo CT Colonography Surveillance.

Pooler, B Dustin / Kim, David H / Matkowskyj, Kristina A / Newton, Michael A / Halberg, Richard B / Grady, William M / Hassan, Cesare / Pickhardt, Perry J

Radiology

2024 Volume 310, Issue 1, Page(s) e232078

Abstract: Background The natural history of colorectal polyps is not well characterized due to clinical standards of care and other practical constraints limiting in vivo longitudinal surveillance. Established CT colonography (CTC) clinical screening protocols ... ...

Abstract	Background The natural history of colorectal polyps is not well characterized due to clinical standards of care and other practical constraints limiting in vivo longitudinal surveillance. Established CT colonography (CTC) clinical screening protocols allow surveillance of small (6-9 mm) polyps. Purpose To assess the natural history of colorectal polyps followed with CTC in a clinical screening program, with histopathologic correlation for resected polyps. Materials and Methods In this retrospective study, CTC was used to longitudinally monitor small colorectal polyps in asymptomatic adult patients from April 1, 2004, to August 31, 2020. All patients underwent at least two CTC examinations. Polyp growth patterns across multiple time points were analyzed, with histopathologic context for resected polyps. Regression analysis was performed to evaluate predictors of advanced histopathology. Results In this study of 475 asymptomatic adult patients (mean age, 56.9 years ± 6.7 [SD]; 263 men), 639 unique polyps (mean initial diameter, 6.3 mm; volume, 50.2 mm
MeSH term(s)	Adult ; Male ; Humans ; Middle Aged ; Colonic Polyps/diagnostic imaging ; Colonography, Computed Tomographic ; Retrospective Studies ; Adenocarcinoma ; Physical Examination
Language	English
Publishing date	2024-01-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	80324-8
ISSN	1527-1315 ; 0033-8419
ISSN (online)	1527-1315
ISSN	0033-8419
DOI	10.1148/radiol.232078
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Article ; Online: A Revised Markov Model Evaluating Oophorectomy at the Time of Hysterectomy for Benign Indication: Age 65 Years Revisited.

Rush, Shannon K / Ma, Xiuyu / Newton, Michael A / Rose, Stephen L

Obstetrics and gynecology

2022 Volume 139, Issue 5, Page(s) 735–744

Abstract: Objective: To perform an updated Markov modeling to assess the optimal age for bilateral salpingo-oophorectomy (BSO) at the time of hysterectomy for benign indication.: Methods: We performed a literature review that assessed hazard ratios (HRs) for ... ...

Abstract	Objective: To perform an updated Markov modeling to assess the optimal age for bilateral salpingo-oophorectomy (BSO) at the time of hysterectomy for benign indication. Methods: We performed a literature review that assessed hazard ratios (HRs) for mortality by disease, age, hysterectomy with or without BSO, and estrogen therapy use. Base mortality rates were derived from national vital statistics data. A Markov model from reported HRs predicted the proportion of the population staying alive to age 80 years by 1-year and 5-year age groups at time of surgery, from age 45 to 55 years. Those younger than age 50 years were modeled as either taking postoperative estrogen or not; those 50 and older were modeled as not receiving estrogen. Computations were performed with R 3.5.1, using Bayesian integration for HR uncertainty. Results: Performing salpingo-oophorectomy before age 50 years for those not taking estrogen yields a lower survival proportion to age 80 years than hysterectomy alone before age 50 years (52.8% [Bayesian CI 40.7-59.7] vs 63.5% [Bayesian CI 62.2-64.9]). At or after age 50 years, there were similar proportions of those living to age 80 years with hysterectomy alone (66.4%, Bayesian CI 65.0-67.6) compared with concurrent salpingo-oophorectomy (66.9%, Bayesian CI 64.4-69.0). Importantly, those taking estrogen when salpingo-oophorectomy was performed before age 50 years had similar proportions of cardiovascular disease, stroke, and people living to age 80 years as those undergoing hysterectomy alone or those undergoing hysterectomy and salpingo-oophorectomy at age 50 years and older. Conclusion: This updated Markov model argues for the consideration of concurrent salpingo-oophorectomy for patients who are undergoing hysterectomy at age 50 and older and suggests that initiating estrogen in those who need salpingo-oophorectomy before age 50 years mitigates increased mortality risk.
MeSH term(s)	Aged ; Aged, 80 and over ; Bayes Theorem ; Estrogens ; Female ; Humans ; Hysterectomy ; Middle Aged ; Ovariectomy ; Salpingo-oophorectomy
Chemical Substances	Estrogens
Language	English
Publishing date	2022-04-05
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	207330-4
ISSN	1873-233X ; 0029-7844
ISSN (online)	1873-233X
ISSN	0029-7844
DOI	10.1097/AOG.0000000000004732
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Article ; Online: Bayes optimal informer sets for early-stage drug discovery.

Yu, Peng / Ericksen, Spencer / Gitter, Anthony / Newton, Michael A

Biometrics

2022 Volume 79, Issue 2, Page(s) 642–654

Abstract: An important experimental design problem in early-stage drug discovery is how to prioritize available compounds for testing when very little is known about the target protein. Informer-based ranking (IBR) methods address the prioritization problem when ... ...

Abstract	An important experimental design problem in early-stage drug discovery is how to prioritize available compounds for testing when very little is known about the target protein. Informer-based ranking (IBR) methods address the prioritization problem when the compounds have provided bioactivity data on other potentially relevant targets. An IBR method selects an informer set of compounds, and then prioritizes the remaining compounds on the basis of new bioactivity experiments performed with the informer set on the target. We formalize the problem as a two-stage decision problem and introduce the Bayes Optimal Informer SEt (BOISE) method for its solution. BOISE leverages a flexible model of the initial bioactivity data, a relevant loss function, and effective computational schemes to resolve the two-step design problem. We evaluate BOISE and compare it to other IBR strategies in two retrospective studies, one on protein-kinase inhibition and the other on anticancer drug sensitivity. In both empirical settings BOISE exhibits better predictive performance than available methods. It also behaves well with missing data, where methods that use matrix completion show worse predictive performance.
MeSH term(s)	Bayes Theorem ; Retrospective Studies ; Drug Discovery/methods ; Proteins
Chemical Substances	Proteins
Language	English
Publishing date	2022-03-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	213543-7
ISSN	1541-0420 ; 0099-4987 ; 0006-341X
ISSN (online)	1541-0420
ISSN	0099-4987 ; 0006-341X
DOI	10.1111/biom.13637
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: SURROGATE SELECTION OVERSAMPLES EXPANDED T CELL CLONOTYPES.

Yu, Peng / Lian, Yumin / Zuleger, Cindy L / Albertini, Richard J / Albertini, Mark R / Newton, Michael A

bioRxiv : the preprint server for biology

2023

Abstract: Inference from immunological data on cells in the adaptive immune system may benefit from modeling specifications that describe variation in the sizes of various clonal sub-populations. We develop one such specification in order to quantify the effects ... ...

Abstract	Inference from immunological data on cells in the adaptive immune system may benefit from modeling specifications that describe variation in the sizes of various clonal sub-populations. We develop one such specification in order to quantify the effects of surrogate selection assays, which we confirm may lead to an enrichment for amplified, potentially disease-relevant
Language	English
Publishing date	2023-07-15
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.07.13.548950
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: A COMPOSITIONAL MODEL TO ASSESS EXPRESSION CHANGES FROM SINGLE-CELL RNA-SEQ DATA.

Ma, Xiuyu / Korthauer, Keegan / Kendziorski, Christina / Newton, Michael A

The annals of applied statistics

2021 Volume 15, Issue 2, Page(s) 880–901

Abstract: On the problem of scoring genes for evidence of changes in the distribution of single-cell expression, we introduce an empirical Bayesian mixture approach and evaluate its operating characteristics in a range of numerical experiments. The proposed ... ...

Abstract	On the problem of scoring genes for evidence of changes in the distribution of single-cell expression, we introduce an empirical Bayesian mixture approach and evaluate its operating characteristics in a range of numerical experiments. The proposed approach leverages cell-subtype structure revealed in cluster analysis in order to boost gene-level information on expression changes. Cell clustering informs gene-level analysis through a specially-constructed prior distribution over pairs of multinomial probability vectors; this prior meshes with available model-based tools that score patterns of differential expression over multiple subtypes. We derive an explicit formula for the posterior probability that a gene has the same distribution in two cellular conditions, allowing for a gene-specific mixture over subtypes in each condition. Advantage is gained by the compositional structure of the model not only in which a host of gene-specific mixture components are allowed but also in which the mixing proportions are constrained at the whole cell level. This structure leads to a novel form of information sharing through which the cell-clustering results support gene-level scoring of differential distribution. The result, according to our numerical experiments, is improved sensitivity compared to several standard approaches for detecting distributional expression changes.
Language	English
Publishing date	2021-07-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2376910-5
ISSN	1941-7330 ; 1932-6157
ISSN (online)	1941-7330
ISSN	1932-6157
DOI	10.1214/20-aoas1423
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Role of dual specificity phosphatases (DUSPs) in melanoma cellular plasticity and drug resistance.

Singh, Mithalesh K / Altameemi, Sarah / Lares, Marcos / Newton, Michael A / Setaluri, Vijayasaradhi

Scientific reports

2022 Volume 12, Issue 1, Page(s) 14395

Abstract: Melanoma cells exhibit phenotypic plasticity that allows transition from a proliferative and differentiated phenotype to a more invasive and undifferentiated or transdifferentiated phenotype often associated with drug resistance. The mechanisms that ... ...

Abstract	Melanoma cells exhibit phenotypic plasticity that allows transition from a proliferative and differentiated phenotype to a more invasive and undifferentiated or transdifferentiated phenotype often associated with drug resistance. The mechanisms that control melanoma phenotype plasticity and its role in drug resistance are not fully understood. We previously demonstrated that emergence of MAPK inhibitor (MAPKi)-resistance phenotype is associated with decreased expression of stem cell proliferation genes and increased expression of MAPK inactivation genes, including dual specificity phosphatases (DUSPs). Several members of the DUSP family genes, specifically DUSP1, -3, -8 and -9, are expressed in primary and metastatic melanoma cell lines and pre-and post BRAFi treated melanoma cells. Here, we show that knockdown of DUSP1 or DUSP8 or treatment with BCI, a pharmacological inhibitor of DUSP1/6 decrease the survival of MAPKi-resistant cells and sensitizes them to BRAFi and MEKi. Pharmacological inhibition of DUSP1/6 upregulated nestin, a neural crest stem cell marker, in both MAPKi-sensitive cells and cells with acquired MAPKi-resistance. In contrast, treatment with BCI resulted in upregulation of MAP2, a neuronal differentiation marker, only in MAPKi-sensitive cells but caused downregulation of both MAP2 and GFAP, a glial marker, in all MAPKi-resistant cell lines. These data suggest that DUSP proteins are involved in the regulation of cellular plasticity cells and melanoma drug resistance and are potential targets for treatment of MAPKi-resistant melanoma.
MeSH term(s)	Cell Line, Tumor ; Cell Plasticity/genetics ; Drug Resistance, Neoplasm/genetics ; Dual-Specificity Phosphatases/genetics ; Humans ; Melanoma/drug therapy ; Melanoma/genetics ; Melanoma/pathology ; Protein Kinase Inhibitors/pharmacology
Chemical Substances	Protein Kinase Inhibitors ; Dual-Specificity Phosphatases (EC 3.1.3.48)
Language	English
Publishing date	2022-08-23
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-18578-x
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: GM-CSF elicits antibodies to tumor-associated proteins when used as a prostate cancer vaccine adjuvant.

Potluri, Hemanth K / Ng, Tun L / Newton, Michael A / McNeel, Douglas G

Cancer immunology, immunotherapy : CII

2022 Volume 71, Issue 9, Page(s) 2267–2275

Abstract: Antibody responses to off-target cancer-associated proteins have been detected following immunotherapies for cancer, suggesting these may be the result of antigen spread. We have previously reported that serum antibodies to prostate cancer-associated ... ...

Abstract	Antibody responses to off-target cancer-associated proteins have been detected following immunotherapies for cancer, suggesting these may be the result of antigen spread. We have previously reported that serum antibodies to prostate cancer-associated proteins were detectable using a high-throughput peptide array. We hypothesized that the breadth of antibody responses elicited by a vaccine could serve as a measure of the magnitude of its induced antigen spread. Consequently, sera from patients with prostate cancer, treated prior to or after vaccination in one of four separate clinical trials, were evaluated for antibody responses to an array of 177,604 peptides derived from over 1600 prostate cancer-associated gene products. Antibody responses to the same group of 5680 peptides previously reported were identified following vaccinations in which patients were administered GM-CSF as an adjuvant, but not with vaccine in the absence of GM-CSF. Hence, antibody responses to off-target proteins following vaccination may not necessarily serve as evidence of antigen spread and must be interpreted with particular caution following vaccine strategies that use GM-CSF, as GM-CSF appears to have direct effects on the production of antibodies. The evaluation of T cell responses to non-target antigens is likely a preferred approach for detection of immune-mediated antigen spread.
MeSH term(s)	Adjuvants, Immunologic ; Adjuvants, Vaccine ; Antibodies ; Cancer Vaccines ; Granulocyte-Macrophage Colony-Stimulating Factor/pharmacology ; Humans ; Male ; Neoplasm Proteins ; Prostatic Neoplasms ; Vaccines
Chemical Substances	Adjuvants, Immunologic ; Adjuvants, Vaccine ; Antibodies ; Cancer Vaccines ; Neoplasm Proteins ; Vaccines ; Granulocyte-Macrophage Colony-Stimulating Factor (83869-56-1)
Language	English
Publishing date	2022-02-08
Publishing country	Germany
Document type	Journal Article
ZDB-ID	195342-4
ISSN	1432-0851 ; 0340-7004
ISSN (online)	1432-0851
ISSN	0340-7004
DOI	10.1007/s00262-022-03150-3
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Article: Notch Signaling Suppresses Melanoma Tumor Development in BRAF/Pten Mice.

Mikheil, Dareen / Prabhakar, Kirthana / Ng, Tun Lee / Teertam, Sireesh / Longley, B Jack / Newton, Michael A / Setaluri, Vijayasaradhi

Cancers

2023 Volume 15, Issue 2

Abstract: Both oncogenic and tumor suppressor roles have been assigned to Notch signaling in melanoma. In clinical trials, Notch inhibitors proved to be ineffective for melanoma treatment. Notch signaling has also been implicated in melanoma transdifferentiation, ... ...

Abstract	Both oncogenic and tumor suppressor roles have been assigned to Notch signaling in melanoma. In clinical trials, Notch inhibitors proved to be ineffective for melanoma treatment. Notch signaling has also been implicated in melanoma transdifferentiation, a prognostic feature in primary melanoma. In this study, we investigated the role of Notch signaling in melanoma tumor development and growth using the genetic model of mouse melanoma by crossing BRAFCA/+/Pten+/+/Tyr-CreER+ (B) and BRAFCA/+/Pten-/-/Tyr-CreER + (BP) mice with Notch1 or Notch2 floxed allele mice. The topical application of tamoxifen induced tumors in BP mice but not in B mice with or without the deletion of either Notch1 or Notch2. These data show that the loss of either Notch1 nor Notch2 can substitute the tumor suppressor function of Pten in BRAFV600E-induced melanomagenesis. However, in Pten-null background, the loss of either Notch1 or Notch2 appeared to accelerate BRAFV600E-induced tumor development, suggesting a tumor suppressor role for Notch1 and Notch2 in BRAFV600E/Pten-null driven melanomagenesis. Quantitative immunochemical analysis of a human cutaneous melanoma tissue microarray that consists of >100 primary tumors with complete clinical history showed a weak to moderate correlation between NOTCH protein levels and clinical and pathological parameters. Our data show that Notch signaling is involved during melanomagenesis and suggest that the identification of genes and signaling pathways downstream of Notch could help devise strategies for melanoma prevention.
Language	English
Publishing date	2023-01-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers15020519
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Article: Novel autoantibodies help diagnose anti-SSA antibody negative Sjögren's disease and predict abnormal labial salivary gland pathology.

Parker, Maxwell / Zheng, Zihao / Lasarev, Michael / Alexandridis, Roxana A / Newton, Michael A / Shelef, Miriam A / McCoy, Sara S

medRxiv : the preprint server for health sciences

2023

Abstract: Objectives: Sj□gren's disease (SjD) diagnosis requires either positive anti-SSA antibodies or a labial salivary gland biopsy with a positive focus score (FS). One-third of SjD patients lack anti-SSA antibodies (SSA-), requiring a positive FS for ... ...

Abstract	Objectives: Sj□gren's disease (SjD) diagnosis requires either positive anti-SSA antibodies or a labial salivary gland biopsy with a positive focus score (FS). One-third of SjD patients lack anti-SSA antibodies (SSA-), requiring a positive FS for diagnosis. Our objective was to identify novel autoantibodies to diagnose 'seronegative' SjD. Methods: IgG binding to a high density whole human peptidome array was quantified using sera from SSA- SjD cases and matched non-autoimmune controls. We identified the highest bound peptides using empirical Bayesian statistical filters, which we confirmed in an independent cohort comprising SSA- SjD (n=76), sicca controls without autoimmunity (n=75), and autoimmune controls (SjD features but not meeting SjD criteria; n=41). In this external validation, we used non-parametric methods for peptide abundance and controlled false discovery rate in group comparisons. For predictive modeling, we used logistic regression, model selection methods, and cross-validation to identify clinical and peptide variables that predict SSA- SjD and FS positivity. Results: IgG against a peptide from D-aminoacyl-tRNA deacylase (DTD2) was bound more in SSA- SjD than sicca controls (p=.004) and more than combined controls (sicca and autoimmune controls combined; p=0.003). IgG against peptides from retroelement silencing factor-1 (RESF1) and DTD2, were bound more in FS-positive than FS-negative participants (p=.010; p=0.012). A predictive model incorporating clinical variables showed good discrimination between SjD versus control (AUC 74%) and between FS-positive versus FS-negative (AUC 72%). Conclusion: We present novel autoantibodies in SSA- SjD that have good predictive value for SSA- SjD and FS-positivity. Key messages: What is already known on this topic - Seronegative (anti-SSA antibody negative [SSA-]) Sjögren's disease (SjD) requires a labial salivary gland biopsy for diagnosis, which is challenging to obtain and interpret. What this study adds - We identified novel autoantibodies in SSA- SjD that, when combined with readily available clinical variables, provide good predictive ability to discriminate 1) SSA- SjD from control participants and 2) abnormal salivary gland biopsies from normal salivary gland biopsies. How this study might affect research, practice or policy - This study provides novel diagnostic antibodies addressing the critical need for improvement of SSA- SjD diagnostic tools.
Language	English
Publishing date	2023-08-29
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.08.29.23294775
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