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Article ; Online: Introduction to the special issue on status epilepticus: neuronal injury, plasticity, and therapies; Celebrating the legacy of Dr. Claude G. Wasterlain.

Engel, Jerome / Moshé, Solomon L / Nehlig, Astrid / Fujikawa, Denson G / Sankar, Raman / Naylor, David E / Mazarati, Andrey M / Wasterlain, Claude G

Epilepsia open

2023 Volume 8 Suppl 1, Page(s) S7–S17

MeSH term(s)	Humans ; Neurons ; Status Epilepticus/therapy
Language	English
Publishing date	2023-04-20
Publishing country	United States
Document type	Journal Article
ISSN	2470-9239
ISSN (online)	2470-9239
DOI	10.1002/epi4.12724
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Article ; Online: G4mismatch: Deep neural networks to predict G-quadruplex propensity based on G4-seq data.

Barshai, Mira / Engel, Barak / Haim, Idan / Orenstein, Yaron

PLoS computational biology

2023 Volume 19, Issue 3, Page(s) e1010948

Abstract: G-quadruplexes are non-B-DNA structures that form in the genome facilitated by Hoogsteen bonds ... between guanines in single or multiple strands of DNA. The functions of G-quadruplexes are linked ... to various molecular and disease phenotypes, and thus researchers are interested in measuring G-quadruplex ...

Abstract	G-quadruplexes are non-B-DNA structures that form in the genome facilitated by Hoogsteen bonds between guanines in single or multiple strands of DNA. The functions of G-quadruplexes are linked to various molecular and disease phenotypes, and thus researchers are interested in measuring G-quadruplex formation genome-wide. Experimentally measuring G-quadruplexes is a long and laborious process. Computational prediction of G-quadruplex propensity from a given DNA sequence is thus a long-standing challenge. Unfortunately, despite the availability of high-throughput datasets measuring G-quadruplex propensity in the form of mismatch scores, extant methods to predict G-quadruplex formation either rely on small datasets or are based on domain-knowledge rules. We developed G4mismatch, a novel algorithm to accurately and efficiently predict G-quadruplex propensity for any genomic sequence. G4mismatch is based on a convolutional neural network trained on almost 400 millions human genomic loci measured in a single G4-seq experiment. When tested on sequences from a held-out chromosome, G4mismatch, the first method to predict mismatch scores genome-wide, achieved a Pearson correlation of over 0.8. When benchmarked on independent datasets derived from various animal species, G4mismatch trained on human data predicted G-quadruplex propensity genome-wide with high accuracy (Pearson correlations greater than 0.7). Moreover, when tested in detecting G-quadruplexes genome-wide using the predicted mismatch scores, G4mismatch achieved superior performance compared to extant methods. Last, we demonstrate the ability to deduce the mechanism behind G-quadruplex formation by unique visualization of the principles learned by the model.
MeSH term(s)	Animals ; Humans ; G-Quadruplexes ; DNA/genetics ; DNA/chemistry ; Genome, Human ; Genomics ; Neural Networks, Computer
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2023-03-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1010948
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Article ; Online: A Bayesian approach to the g-formula.

Keil, Alexander P / Daza, Eric J / Engel, Stephanie M / Buckley, Jessie P / Edwards, Jessie K

Statistical methods in medical research

2017 Volume 27, Issue 10, Page(s) 3183–3204

Abstract: ... that the parametric g-formula is easily amenable to a Bayesian approach. We show that the frequentist properties ... of the Bayesian g-formula suggest it improves the accuracy of estimates of causal effects in small samples or ...

Abstract	Epidemiologists often wish to estimate quantities that are easy to communicate and correspond to the results of realistic public health interventions. Methods from causal inference can answer these questions. We adopt the language of potential outcomes under Rubin's original Bayesian framework and show that the parametric g-formula is easily amenable to a Bayesian approach. We show that the frequentist properties of the Bayesian g-formula suggest it improves the accuracy of estimates of causal effects in small samples or when data are sparse. We demonstrate an approach to estimate the effect of environmental tobacco smoke on body mass index among children aged 4-9 years who were enrolled in a longitudinal birth cohort in New York, USA. We provide an algorithm and supply SAS and Stan code that can be adopted to implement this computational approach more generally.
MeSH term(s)	Algorithms ; Bayes Theorem ; Body Mass Index ; Child ; Child, Preschool ; Humans ; Longitudinal Studies ; Models, Statistical ; New York ; Observational Studies as Topic ; Public Health ; Tobacco Smoke Pollution/adverse effects
Chemical Substances	Tobacco Smoke Pollution
Language	English
Publishing date	2017-03-02
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1136948-6
ISSN	1477-0334 ; 0962-2802
ISSN (online)	1477-0334
ISSN	0962-2802
DOI	10.1177/0962280217694665
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Zs.A 3564: Show issues

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Article ; Online: Yeast-based directed-evolution for high-throughput structural stabilization of G protein-coupled receptors (GPCRs).

Meltzer, M / Zvagelsky, T / Hadad, U / Papo, Niv / Engel, Stanislav

Scientific reports

2022 Volume 12, Issue 1, Page(s) 8657

Abstract: The immense potential of G protein-coupled receptors (GPCRs) as targets for drug discovery is not ...

Abstract	The immense potential of G protein-coupled receptors (GPCRs) as targets for drug discovery is not fully realized due to the enormous difficulties associated with structure elucidation of these profoundly unstable membrane proteins. The existing methods of GPCR stability-engineering are cumbersome and low-throughput; in addition, the scope of GPCRs that could benefit from these techniques is limited. Here, we present a yeast-based screening platform for a single-step isolation of GRCR variants stable in the presence of short-chain detergents, a feature essential for their successful crystallization using vapor diffusion method. The yeast detergent-resistant cell wall presents a unique opportunity for compartmentalization, to physically link the receptor's phenotype to its encoding DNA, and thus enable discovery of stable GPCR variants with unprecedent efficiency. The scope of mutations identified by the method reveals a surprising amenability of the GPCR scaffold to stabilization, and suggests an intriguing possibility of amending the stability properties of GPCR by varying the structural status of the C-terminus.
MeSH term(s)	Drug Discovery ; Membrane Proteins/metabolism ; Receptors, G-Protein-Coupled/genetics ; Receptors, G-Protein-Coupled/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism
Chemical Substances	Membrane Proteins ; Receptors, G-Protein-Coupled
Language	English
Publishing date	2022-05-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-12731-2
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Article ; Online: Quantification of polyreactive immunoglobulin G facilitates the diagnosis of autoimmune hepatitis.

Taubert, Richard / Engel, Bastian / Diestelhorst, Jana / Hupa-Breier, Katharina L / Behrendt, Patrick / Baerlecken, Niklas T / Sühs, Kurt-Wolfram / Janik, Maciej K / Zachou, Kalliopi / Sebode, Marcial / Schramm, Christoph / Londoño, María-Carlota / Habes, Sarah / Oo, Ye H / Lalanne, Claudine / Pape, Simon / Schubert, Maren / Hust, Michael / Dübel, Stefan /

Thevis, Mario / Jonigk, Danny / Beimdiek, Julia / Buettner, Falk F R / Drenth, Joost P H / Muratori, Luigi / Adams, David H / Dyson, Jessica K / Renand, Amédée / Graupera, Isabel / Lohse, Ansgar W / Dalekos, George N / Milkiewicz, Piotr / Stangel, Martin / Maasoumy, Benjamin / Witte, Torsten / Wedemeyer, Heiner / Manns, Michael P / Jaeckel, Elmar

Hepatology (Baltimore, Md.)

2021 Volume 75, Issue 1, Page(s) 13–27

Abstract: Background and aims: Detection of autoantibodies is a mainstay of diagnosing autoimmune hepatitis (AIH). However, conventional autoantibodies for the workup of AIH lack either sensitivity or specificity, leading to substantial diagnostic uncertainty. We ...

Abstract	Background and aims: Detection of autoantibodies is a mainstay of diagnosing autoimmune hepatitis (AIH). However, conventional autoantibodies for the workup of AIH lack either sensitivity or specificity, leading to substantial diagnostic uncertainty. We aimed to identify more accurate serological markers of AIH with a protein macroarray. Approach and results: During the search for more-precise autoantibodies to distinguish AIH from non-AIH liver diseases (non-AIH-LD), IgG antibodies with binding capacities to many human and foreign proteins were identified with a protein macroarray and confirmed with solid-phase ELISAs in AIH patients. Subsequently, polyreactive IgG (pIgG) was exemplarily quantified by reactivity against human huntingtin-interacting protein 1-related protein in bovine serum albumin blocked ELISA (HIP1R/BSA). The diagnostic fidelity of HIP1R/BSA binding pIgG to diagnose AIH was assessed in a retrospective training, a retrospective multicenter validation, and a prospective validation cohort in cryoconserved samples from 1,568 adults from 10 centers from eight countries. Reactivity against HIP1R/BSA had a 25% and 14% higher specificity to diagnose AIH than conventional antinuclear and antismooth muscle antibodies, a significantly higher sensitivity than liver kidney microsomal antibodies and antisoluble liver antigen/liver pancreas antigen, and a 12%-20% higher accuracy than conventional autoantibodies. Importantly, HIP1R/BSA reactivity was present in up to 88% of patients with seronegative AIH and in up to 71% of AIH patients with normal IgG levels. Under therapy, pIgG returns to background levels of non-AIH-LD. Conclusions: pIgG could be used as a promising marker to improve the diagnostic workup of liver diseases with a higher specificity for AIH compared to conventional autoantibodies and a utility in autoantibody-negative AIH. Likewise, pIgG could be a major source of assay interference in untreated AIH.
MeSH term(s)	Adolescent ; Adult ; Aged ; Aged, 80 and over ; Autoantibodies/blood ; Biomarkers/blood ; Diagnosis, Differential ; Female ; Hepatitis, Autoimmune/blood ; Hepatitis, Autoimmune/diagnosis ; Hepatitis, Autoimmune/immunology ; Humans ; Immunoglobulin G/blood ; Male ; Middle Aged ; Retrospective Studies ; Young Adult
Chemical Substances	Autoantibodies ; Biomarkers ; Immunoglobulin G
Language	English
Publishing date	2021-12-05
Publishing country	United States
Document type	Journal Article ; Multicenter Study ; Research Support, Non-U.S. Gov't
ZDB-ID	604603-4
ISSN	1527-3350 ; 0270-9139
ISSN (online)	1527-3350
ISSN	0270-9139
DOI	10.1002/hep.32134
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Zs.A 1660: Show issues

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Article ; Online: The expanding functional roles and signaling mechanisms of adhesion G protein-coupled receptors.

Morgan, Rory K / Anderson, Garret R / Araç, Demet / Aust, Gabriela / Balenga, Nariman / Boucard, Antony / Bridges, James P / Engel, Felix B / Formstone, Caroline J / Glitsch, Maike D / Gray, Ryan S / Hall, Randy A / Hsiao, Cheng-Chih / Kim, Hee-Yong / Knierim, Alexander B / Kusuluri, Deva Krupakar / Leon, Katherine / Liebscher, Ines / Piao, Xianhua /

Prömel, Simone / Scholz, Nicole / Srivastava, Swati / Thor, Doreen / Tolias, Kimberley F / Ushkaryov, Yuri A / Vallon, Mario / Van Meir, Erwin G / Vanhollebeke, Benoit / Wolfrum, Uwe / Wright, Kevin M / Monk, Kelly R / Mogha, Amit

Annals of the New York Academy of Sciences

2019 Volume 1456, Issue 1, Page(s) 5–25

Abstract: The adhesion class of G protein-coupled receptors (GPCRs) is the second largest family of GPCRs (33 ... while the CTFs are involved in classical G protein signaling, as well as other intracellular signaling ...

Abstract	The adhesion class of G protein-coupled receptors (GPCRs) is the second largest family of GPCRs (33 members in humans). Adhesion GPCRs (aGPCRs) are defined by a large extracellular N-terminal region that is linked to a C-terminal seven transmembrane (7TM) domain via a GPCR-autoproteolysis inducing (GAIN) domain containing a GPCR proteolytic site (GPS). Most aGPCRs undergo autoproteolysis at the GPS motif, but the cleaved fragments stay closely associated, with the N-terminal fragment (NTF) bound to the 7TM of the C-terminal fragment (CTF). The NTFs of most aGPCRs contain domains known to be involved in cell-cell adhesion, while the CTFs are involved in classical G protein signaling, as well as other intracellular signaling. In this workshop report, we review the most recent findings on the biology, signaling mechanisms, and physiological functions of aGPCRs.
MeSH term(s)	Animals ; Humans ; Receptors, G-Protein-Coupled/chemistry ; Receptors, G-Protein-Coupled/metabolism ; Signal Transduction
Chemical Substances	Receptors, G-Protein-Coupled
Language	English
Publishing date	2019-06-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	211003-9
ISSN	1749-6632 ; 0077-8923
ISSN (online)	1749-6632
ISSN	0077-8923
DOI	10.1111/nyas.14094
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Article ; Online: The orphan G protein-coupled receptor, GPR139, is expressed in the hypothalamus and is involved in the regulation of body mass, blood glucose, and insulin.

Nogueira, Pedro A S / Moura-Assis, Alexandre / Zanesco, Ariane M / Bombassaro, Bruna / Gallo-Ferraz, Ana L / Simões, Marcela R / Engel, Daiane F / Razolli, Daniela S / Gaspar, Joana M / Junior, Jose Donato / Velloso, Licio A

Neuroscience letters

2022 Volume 792, Page(s) 136955

Abstract: GPR139 is an orphan G-protein-coupled receptor that is expressed in restricted areas ...

Abstract	GPR139 is an orphan G-protein-coupled receptor that is expressed in restricted areas of the nervous system, including the hypothalamus. In this study, we hypothesized that GPR139 could be involved in the regulation of energy balance and metabolism. In the first part of the study, we confirmed that GPR139 is expressed in the hypothalamus and particularly in proopiomelanocortin and agouti-related peptide neurons of the mediobasal hypothalamus. Using a lentivirus with a short-hairpin RNA, we inhibited the expression of GPR139 bilaterally in the mediobasal hypothalamus of mice. The intervention promoted a 40% reduction in the hypothalamic expression of GPR139, which was accompanied by an increase in body mass, a reduction in fasting blood glucose levels, and an increase in insulin levels. In the hypothalamus, inhibition of GPR139 was accompanied by a reduction in the expression of orexin. As previous studies using a pharmacological antagonist of orexin showed a beneficial impact on type 2 diabetes and glucose metabolism, we propose that the inhibition of hypothalamic GPR139 could be acting indirectly through the orexin system to control systemic glucose and insulin. In conclusion, this study advances the characterization of GPR139 in the hypothalamus, demonstrating its involvement in the regulation of body mass, blood insulin, and glycemia.
MeSH term(s)	Mice ; Animals ; Orexins/metabolism ; Insulin/metabolism ; Blood Glucose/metabolism ; Diabetes Mellitus, Type 2/metabolism ; Hypothalamus/metabolism ; Receptors, G-Protein-Coupled/metabolism ; Nerve Tissue Proteins/metabolism
Chemical Substances	Orexins ; Insulin ; Blood Glucose ; Receptors, G-Protein-Coupled ; Gpr139 protein, mouse ; Nerve Tissue Proteins
Language	English
Publishing date	2022-11-05
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	194929-9
ISSN	1872-7972 ; 0304-3940
ISSN (online)	1872-7972
ISSN	0304-3940
DOI	10.1016/j.neulet.2022.136955
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Article ; Online: Yeast-based directed-evolution for high-throughput structural stabilization of G protein-coupled receptors (GPCRs)

M. Meltzer / T. Zvagelsky / U. Hadad / Niv Papo / Stanislav Engel

Scientific Reports, Vol 12, Iss 1, Pp 1-

2022 Volume 14

Abstract: Abstract The immense potential of G protein-coupled receptors (GPCRs) as targets for drug discovery ...

Abstract	Abstract The immense potential of G protein-coupled receptors (GPCRs) as targets for drug discovery is not fully realized due to the enormous difficulties associated with structure elucidation of these profoundly unstable membrane proteins. The existing methods of GPCR stability-engineering are cumbersome and low-throughput; in addition, the scope of GPCRs that could benefit from these techniques is limited. Here, we present a yeast-based screening platform for a single-step isolation of GRCR variants stable in the presence of short-chain detergents, a feature essential for their successful crystallization using vapor diffusion method. The yeast detergent-resistant cell wall presents a unique opportunity for compartmentalization, to physically link the receptor's phenotype to its encoding DNA, and thus enable discovery of stable GPCR variants with unprecedent efficiency. The scope of mutations identified by the method reveals a surprising amenability of the GPCR scaffold to stabilization, and suggests an intriguing possibility of amending the stability properties of GPCR by varying the structural status of the C-terminus.
Keywords	Medicine ; R ; Science ; Q
Subject code	500
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Preliminary consultation on preferred product characteristics of benzathine penicillin G for secondary prophylaxis of rheumatic fever.

Wyber, Rosemary / Boyd, Ben J / Colquhoun, Samantha / Currie, Bart J / Engel, Mark / Kado, Joseph / Karthikeyan, Ganesan / Sullivan, Mark / Saxena, Anita / Sheel, Meru / Steer, Andrew / Mucumbitsi, Joseph / Zühlke, Liesl / Carapetis, Jonathan

Drug delivery and translational research

2016 Volume 6, Issue 5, Page(s) 572–578

Abstract: ... after the last episode of rheumatic fever. Benzathine penicillin G is the first line antibiotic ... in rheumatic heart disease on the characteristics of benzathine penicillin G formulations which could be changed to improve ... cold chain independence and cost. A sample target product profile for reformulated benzathine penicillin G is ...

Abstract	Rheumatic fever is caused by an abnormal immune reaction to group A streptococcal infection. Secondary prophylaxis with antibiotics is recommended for people after their initial episode of rheumatic fever to prevent recurrent group A streptococcal infections, recurrences of rheumatic fever and progression to rheumatic heart disease. This secondary prophylaxis must be maintained for at least a decade after the last episode of rheumatic fever. Benzathine penicillin G is the first line antibiotic for secondary prophylaxis, delivered intramuscularly every 2 to 4 weeks. However, adherence to recommended secondary prophylaxis regimens is a global challenge. This paper outlines a consultation with global experts in rheumatic heart disease on the characteristics of benzathine penicillin G formulations which could be changed to improve adherence with secondary prophylaxis. Characteristics included dose interval, pain, administration mechanism, cold chain independence and cost. A sample target product profile for reformulated benzathine penicillin G is presented.
Language	English
Publishing date	2016-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	2590155-2
ISSN	2190-3948 ; 2190-393X
ISSN (online)	2190-3948
ISSN	2190-393X
DOI	10.1007/s13346-016-0313-z
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Article ; Online: Computational Investigations on the Binding Mode of Ligands for the Cannabinoid-Activated G Protein-Coupled Receptor GPR18.

Neumann, Alexander / Engel, Viktor / Mahardhika, Andhika B / Schoeder, Clara T / Namasivayam, Vigneshwaran / Kieć-Kononowicz, Katarzyna / Müller, Christa E

Biomolecules

2020 Volume 10, Issue 5

Abstract: GPR18 is an orphan G protein-coupled receptor (GPCR) expressed in cells of the immune system. It is ...

Abstract	GPR18 is an orphan G protein-coupled receptor (GPCR) expressed in cells of the immune system. It is activated by the cannabinoid receptor (CB) agonist ∆
MeSH term(s)	Binding Sites ; Cannabinoid Receptor Agonists/chemistry ; Cannabinoid Receptor Agonists/pharmacology ; Cannabinoid Receptor Antagonists/chemistry ; Cannabinoid Receptor Antagonists/pharmacology ; Dronabinol/chemistry ; Dronabinol/pharmacology ; Humans ; Molecular Docking Simulation ; Protein Binding ; Receptors, G-Protein-Coupled/agonists ; Receptors, G-Protein-Coupled/antagonists & inhibitors ; Receptors, G-Protein-Coupled/chemistry ; Receptors, G-Protein-Coupled/metabolism
Chemical Substances	Cannabinoid Receptor Agonists ; Cannabinoid Receptor Antagonists ; GPR18 protein, mouse ; Receptors, G-Protein-Coupled ; Dronabinol (7J8897W37S)
Language	English
Publishing date	2020-04-29
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/biom10050686
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