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Article: Longitudinal analysis on the ecological dynamics of the cervicovaginal microbiome in hrHPV infection.

Molina, Mariano A / Melchers, Willem J G / Andralojc, Karolina M / Leenders, William P J / Huynen, Martijn A

Computational and structural biotechnology journal

2023 Volume 21, Page(s) 4424–4431

Abstract: The cervicovaginal microbiome (CVM) is a dynamic continuous microenvironment that can be clustered in microbial community state types (CSTs) and is associated with women's cervical health. ...

Abstract	The cervicovaginal microbiome (CVM) is a dynamic continuous microenvironment that can be clustered in microbial community state types (CSTs) and is associated with women's cervical health.
Language	English
Publishing date	2023-09-13
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2023.09.011
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Article ; Online: In-depth insights into cervicovaginal microbial communities and hrHPV infections using high-resolution microbiome profiling.

Molina, Mariano A / Andralojc, Karolina M / Huynen, Martijn A / Leenders, William P J / Melchers, Willem J G

NPJ biofilms and microbiomes

2022 Volume 8, Issue 1, Page(s) 75

Abstract: The cervicovaginal microbiome (CVM) correlates with women's cervical health, and variations in its composition are associated with high-risk human papillomavirus (hrHPV) infection outcomes. Cervicovaginal microbes have been grouped into five community ... ...

Abstract	The cervicovaginal microbiome (CVM) correlates with women's cervical health, and variations in its composition are associated with high-risk human papillomavirus (hrHPV) infection outcomes. Cervicovaginal microbes have been grouped into five community state types (CSTs) based on microbial community composition and abundance. However, studying the impact of CSTs in health and disease is challenging because the current sequencing technologies have limited confident discrimination between closely related and yet functionally different bacterial species. Circular probe-based RNA sequencing (ciRNAseq) achieves high-resolution microbiome profiling and therefore provides in-depth and unambiguous knowledge about the composition of the CVM. Based on ciRNAseq profiling of a large cohort of cervical smears (n = 541), we here define subgroups of CSTs I, III, and IV based on intra-CST differences with respect to abundances of Lactobacillus acidophilus (CSTs I-A vs. I-B and CSTs III-A vs. III-B), Lactobacillus iners (CSTs I-A vs. I-B and CSTs III-A vs. III-B), and Megasphaera genomosp type 1 (CSTs IV-A vs. IV-B). Our results further support the existence of subgroups of CST IV-C that are dominant for non-Lactobacillus species and have intermediate microbial diversity. We also show that CST V is associated with uninfected conditions, and CST IV-A associates with hrHPV-induced cervical disease. In conclusion, we characterized new subdivisions of cervicovaginal CSTs, which may further advance our understanding of women's cervical health and hrHPV-related progression to disease.
MeSH term(s)	Female ; Humans ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Vagina/microbiology
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2022-09-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2817021-0
ISSN	2055-5008 ; 2055-5008
ISSN (online)	2055-5008
ISSN	2055-5008
DOI	10.1038/s41522-022-00336-6
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Article: Genotyping and Characterization of HPV Status, Hypoxia, and Radiosensitivity in 22 Head and Neck Cancer Cell Lines.

Göttgens, Eva-Leonne / Ansems, Marleen / Leenders, William P J / Bussink, Johan / Span, Paul N

Cancers

2021 Volume 13, Issue 5

Abstract: To study head and neck squamous cell carcinomas (HNSCC) in vitro, a large variety of HNSCC cell lines have been developed. Here, we characterize a panel of 22 HNSCC cell lines, thereby providing a tool for research into tumor-specific treatment options ... ...

Abstract	To study head and neck squamous cell carcinomas (HNSCC) in vitro, a large variety of HNSCC cell lines have been developed. Here, we characterize a panel of 22 HNSCC cell lines, thereby providing a tool for research into tumor-specific treatment options in HNSCC. Both human papillomavirus (HPV) positive and HPV negative tumor cell lines were collected from commercial and collaborative sources. Short tandem repeat profiling was used to confirm or characterize the identity of the cell lines. Targeted sequencing was performed using a standard pathology single molecule Molecular Inversion Probe panel to detect mutations for 23 tumor suppressors and oncogenes. HPV status, p16 status, radiosensitivity data, and hypoxia data are summarized from all cell lines. We detected HPV transcripts in five cell lines, all of which overexpressed p16. One HPV negative cell line was also p16 positive. We detected mutations in
Language	English
Publishing date	2021-03-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers13051069
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Article ; Online: Assessing the Cervicovaginal Microbiota in the Context of hrHPV Infections: Temporal Dynamics and Therapeutic Strategies.

Molina, Mariano A / Coenen, Britt A / Leenders, William P J / Andralojc, Karolina M / Huynen, Martijn A / Melchers, Willem J G

mBio

2022 Volume 13, Issue 5, Page(s) e0161922

Abstract: Cervical cancer is the third leading cause of female cancers globally, resulting in more than 300,000 deaths every year. The majority of all cervical cancers are caused by persistent infections with high-risk human papillomaviruses (hrHPV) that can ... ...

Abstract	Cervical cancer is the third leading cause of female cancers globally, resulting in more than 300,000 deaths every year. The majority of all cervical cancers are caused by persistent infections with high-risk human papillomaviruses (hrHPV) that can progress to cancer via a series of premalignant lesions. Most women, however, clear this infection within a year, concomitant with disease regression. Both hrHPV clearance and disease regression have been associated with the composition of the cervicovaginal microenvironment, which is defined by the host immune system and the cervicovaginal microbiome (CVM). A healthy microbiome is generally characterized by a high abundance of
MeSH term(s)	Female ; Humans ; Papillomavirus Infections/complications ; Vagina/microbiology ; Microbiota ; Uterine Cervical Neoplasms ; Lactobacillus ; Papillomaviridae ; Tumor Microenvironment
Language	English
Publishing date	2022-08-18
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.01619-22
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Article ; Online: Light-Responsive Elastin-Like Peptide-Based Targeted Nanoparticles for Enhanced Spheroid Penetration.

Le, Duc H T / Ibrahimova, Vusala / van den Wildenberg, Sebastian A H / Wu, Hanglong / Fonseca, Alba / Torres, Tomas / Garanger, Elisabeth / Leenders, William P J / Brock, Roland / Lecommandoux, Sébastien / van Hest, Jan C M

Angewandte Chemie (International ed. in English)

2023 Volume 62, Issue 24, Page(s) e202300511

Abstract: We describe here a near infrared light-responsive elastin-like peptide (ELP)-based targeted nanoparticle (NP) that can rapidly switch its size from 120 to 25 nm upon photo-irradiation. Interestingly, the targeting function, which is crucial for effective ...

Abstract	We describe here a near infrared light-responsive elastin-like peptide (ELP)-based targeted nanoparticle (NP) that can rapidly switch its size from 120 to 25 nm upon photo-irradiation. Interestingly, the targeting function, which is crucial for effective cargo delivery, is preserved after transformation. The NPs are assembled from (targeted) diblock ELP micelles encapsulating photosensitizer TT1-monoblock ELP conjugates. Methionine residues in this monoblock are photo-oxidized by singlet oxygen generated from TT1, turning the ELPs hydrophilic and thus trigger NP dissociation. Phenylalanine residues from the diblocks then interact with TT1 via π-π stacking, inducing the re-formation of smaller NPs. Due to their small size and targeting function, the NPs penetrate deeper in spheroids and kill cancer cells more efficiently compared to the larger ones. This work could contribute to the design of "smart" nanomedicines with deeper penetration capacity for effective anticancer therapies.
MeSH term(s)	Elastin/chemistry ; Peptides/chemistry ; Nanoparticles/chemistry ; Micelles
Chemical Substances	Elastin (9007-58-3) ; Peptides ; Micelles
Language	English
Publishing date	2023-05-08
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2011836-3
ISSN	1521-3773 ; 1433-7851
ISSN (online)	1521-3773
ISSN	1433-7851
DOI	10.1002/anie.202300511
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Article ; Online: Targeted RNA next generation sequencing analysis of cervical smears can predict the presence of hrHPV-induced cervical lesions.

Andralojc, Karolina M / Elmelik, Duaa / Rasing, Menno / Pater, Bernard / Siebers, Albert G / Bekkers, Ruud / Huynen, Martijn A / Bulten, Johan / Loopik, Diede / Melchers, Willem J G / Leenders, William P J

BMC medicine

2022 Volume 20, Issue 1, Page(s) 206

Abstract: Background: Because most cervical cancers are caused by high-risk human papillomaviruses (hrHPVs), cervical cancer prevention programs increasingly employ hrHPV testing as a primary test. The high sensitivity of HPV tests is accompanied by low ... ...

Abstract	Background: Because most cervical cancers are caused by high-risk human papillomaviruses (hrHPVs), cervical cancer prevention programs increasingly employ hrHPV testing as a primary test. The high sensitivity of HPV tests is accompanied by low specificity, resulting in high rates of overdiagnosis and overtreatment. Targeted circular probe-based RNA next generation sequencing (ciRNAseq) allows for the quantitative detection of RNAs of interest with high sequencing depth. Here, we examined the potential of ciRNAseq-testing on cervical scrapes to identify hrHPV-positive women at risk of having or developing high-grade cervical intraepithelial neoplasia (CIN). Methods: We performed ciRNAseq on 610 cervical scrapes from the Dutch cervical cancer screening program to detect gene expression from 15 hrHPV genotypes and from 429 human genes. Differentially expressed hrHPV- and host genes in scrapes from women with outcome "no CIN" or "CIN2+" were identified and a model was built to distinguish these groups. Results: Apart from increasing percentages of hrHPV oncogene expression from "no CIN" to high-grade cytology/histology, we identified genes involved in cell cycle regulation, tyrosine kinase signaling pathways, immune suppression, and DNA repair being expressed at significantly higher levels in scrapes with high-grade cytology and histology. Machine learning using random forest on all the expression data resulted in a model that detected 'no CIN' versus CIN2+ in an independent data set with sensitivity and specificity of respectively 85 ± 8% and 72 ± 13%. Conclusions: CiRNAseq on exfoliated cells in cervical scrapes measures hrHPV-(onco)gene expression and host gene expression in one single assay and in the process identifies HPV genotype. By combining these data and applying machine learning protocols, the risk of CIN can be calculated. Because ciRNAseq can be performed in high-throughput, making it cost-effective, it can be a promising screening technology to stratify women at risk of CIN2+. Further increasing specificity by model improvement in larger cohorts is warranted.
MeSH term(s)	Early Detection of Cancer/methods ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Papillomaviridae/genetics ; Papillomavirus Infections/complications ; Papillomavirus Infections/diagnosis ; Papillomavirus Infections/genetics ; RNA ; Uterine Cervical Neoplasms/diagnosis ; Uterine Cervical Neoplasms/genetics ; Vaginal Smears
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2022-06-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2131669-7
ISSN	1741-7015 ; 1741-7015
ISSN (online)	1741-7015
ISSN	1741-7015
DOI	10.1186/s12916-022-02386-1
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Article ; Online: Effects of the Green Tea Polyphenol Epigallocatechin-3-Gallate on Glioma: A Critical Evaluation of the Literature.

Le, Chung T / Leenders, William P J / Molenaar, Remco J / van Noorden, Cornelis J F

Nutrition and cancer

2018 Volume 70, Issue 3, Page(s) 317–333

Abstract: The review discusses the effects of Epigallocatechin-3-gallate Gallate (EGCG) on glioma as a basis for future research on clinical application of EGCG. Epidemiological studies on the effects of green tea or EGCG on the risk of glioma is inconclusive due ... ...

Abstract	The review discusses the effects of Epigallocatechin-3-gallate Gallate (EGCG) on glioma as a basis for future research on clinical application of EGCG. Epidemiological studies on the effects of green tea or EGCG on the risk of glioma is inconclusive due to the limited number of studies, the inclusion of all tea types in these studies, and the focus on caffeine rather than EGCG. In vivo experiments using EGCG monotherapy are inconclusive. Nevertheless, EGCG induces cell death, prevents cellular proliferation, and limits invasion in multiple glioma cell lines. Furthermore, EGCG enhances the efficacy of anti-glioma therapies, including irradiation, temozolomide, carmustine, cisplatin, tamoxifen, and TNF-related apoptosis-inducing ligand, but reduces the effect of bortezomib. Pro-drugs, co-treatment, and encapsulation are being investigated to enhance clinical applicability of EGCG. Mechanisms of actions of EGCG have been partly elucidated. EGCG has both anti-oxidant and oxidant properties. EGCG inhibits pro-survival proteins, such as telomerase, survivin, GRP78, PEA15, and P-gp. EGCG inhibits signaling of PDGFR, IGF-1R, and 67LR. EGCG reduces invasiveness of cancer cells by inhibiting the activities of various metalloproteinases, cytokines, and chemokines. Last, EGCG inhibits some NADPH-producing enzymes, thus disturbing redox status and metabolism of glioma cells. In conclusion, EGCG may be a suitable adjuvant to potentiate anti-glioma therapies.
MeSH term(s)	Animals ; Anticarcinogenic Agents/pharmacology ; Antineoplastic Agents, Phytogenic/pharmacokinetics ; Antineoplastic Agents, Phytogenic/pharmacology ; Catechin/analogs & derivatives ; Catechin/pharmacokinetics ; Catechin/pharmacology ; Cell Proliferation/drug effects ; Central Nervous System Neoplasms/drug therapy ; Central Nervous System Neoplasms/pathology ; Central Nervous System Neoplasms/therapy ; Combined Modality Therapy ; Epidemiologic Studies ; Glioma/drug therapy ; Glioma/pathology ; Glioma/therapy ; Humans ; Neoplasms, Experimental/drug therapy ; Signal Transduction/drug effects ; Tea/chemistry
Chemical Substances	Anticarcinogenic Agents ; Antineoplastic Agents, Phytogenic ; Tea ; Catechin (8R1V1STN48) ; epigallocatechin gallate (BQM438CTEL)
Language	English
Publishing date	2018-03-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	424433-3
ISSN	1532-7914 ; 0163-5581
ISSN (online)	1532-7914
ISSN	0163-5581
DOI	10.1080/01635581.2018.1446090
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Article ; Online: Targeted therapies of cancer: angiogenesis inhibition seems not enough.

Roodink, Ilse / Leenders, William P J

Cancer letters

2010 Volume 299, Issue 1, Page(s) 1–10

Abstract: The therapeutic potential of targeting tumor endothelium to induce tumor regression is now widely recognized. Tumors obtain their blood supply by the formation of new vasculature and the incorporation of pre-existent vessels. Since anti-angiogenic ... ...

Abstract	The therapeutic potential of targeting tumor endothelium to induce tumor regression is now widely recognized. Tumors obtain their blood supply by the formation of new vasculature and the incorporation of pre-existent vessels. Since anti-angiogenic therapy prevents formation of neovasculature, vessels in more matured stages are not affected by such therapies. Therefore, additional vascular targeting therapy, which aim at regression of existent tumor vasculature, seems an attractive approach to effectively deprive tumors from blood supply. In this review we present an overview of different strategies to target tumor endothelium. In addition, we discuss the pitfalls of anti-angiogenic therapies in clinical settings.
MeSH term(s)	Angiogenesis Inhibitors/therapeutic use ; Animals ; Endothelial Cells/drug effects ; Humans ; Neoplasms/blood supply ; Neoplasms/drug therapy ; Receptor, Notch1/antagonists & inhibitors ; Receptor, Platelet-Derived Growth Factor beta/antagonists & inhibitors ; Receptor, TIE-2/antagonists & inhibitors ; Vascular Endothelial Growth Factor A/antagonists & inhibitors ; Vascular Endothelial Growth Factor Receptor-2/antagonists & inhibitors
Chemical Substances	Angiogenesis Inhibitors ; Receptor, Notch1 ; Vascular Endothelial Growth Factor A ; Receptor, Platelet-Derived Growth Factor beta (EC 2.7.10.1) ; Receptor, TIE-2 (EC 2.7.10.1) ; Vascular Endothelial Growth Factor Receptor-2 (EC 2.7.10.1)
Language	English
Publishing date	2010-12-18
Publishing country	Ireland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	195674-7
ISSN	1872-7980 ; 0304-3835
ISSN (online)	1872-7980
ISSN	0304-3835
DOI	10.1016/j.canlet.2010.09.004
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Article ; Online: In silico gene expression analysis reveals glycolysis and acetate anaplerosis in IDH1 wild-type glioma and lactate and glutamate anaplerosis in IDH1-mutated glioma.

Khurshed, Mohammed / Molenaar, Remco J / Lenting, Krissie / Leenders, William P / van Noorden, Cornelis J F

Oncotarget

2017 Volume 8, Issue 30, Page(s) 49165–49177

Abstract: Hotspot mutations in isocitrate dehydrogenase 1 (IDH1) initiate low-grade glioma and secondary glioblastoma and induce a neomorphic activity that converts α-ketoglutarate (α-KG) to the oncometabolite D-2-hydroxyglutarate (D-2-HG). It causes metabolic ... ...

Abstract	Hotspot mutations in isocitrate dehydrogenase 1 (IDH1) initiate low-grade glioma and secondary glioblastoma and induce a neomorphic activity that converts α-ketoglutarate (α-KG) to the oncometabolite D-2-hydroxyglutarate (D-2-HG). It causes metabolic rewiring that is not fully understood. We investigated the effects of IDH1 mutations (IDH1MUT) on expression of genes that encode for metabolic enzymes by data mining The Cancer Genome Atlas. We analyzed 112 IDH1 wild-type (IDH1WT) versus 399 IDH1MUT low-grade glioma and 157 IDH1WT versus 9 IDH1MUT glioblastoma samples. In both glioma types, IDH1WT was associated with high expression levels of genes encoding enzymes that are involved in glycolysis and acetate anaplerosis, whereas IDH1MUT glioma overexpress genes encoding enzymes that are involved in the oxidative tricarboxylic acid (TCA) cycle. In vitro, we observed that IDH1MUT cancer cells have a higher basal respiration compared to IDH1WT cancer cells and inhibition of the IDH1MUT shifts the metabolism by decreasing oxygen consumption and increasing glycolysis. Our findings indicate that IDH1WT glioma have a typical Warburg phenotype whereas in IDH1MUT glioma the TCA cycle, rather than glycolytic lactate production, is the predominant metabolic pathway. Our data further suggest that the TCA in IDH1MUT glioma is driven by lactate and glutamate anaplerosis to facilitate production of α-KG, and ultimately D-2-HG. This metabolic rewiring may be a basis for novel therapies for IDH1MUT and IDH1WT glioma.
Language	English
Publishing date	2017-07-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	2560162-3
ISSN	1949-2553 ; 1949-2553
ISSN (online)	1949-2553
ISSN	1949-2553
DOI	10.18632/oncotarget.17106
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Article ; Online: Self-Assembling VHH-Elastin-Like Peptides for Photodynamic Nanomedicine.

Pille, Jan / van Lith, Sanne A M / van Hest, Jan C M / Leenders, William P J

Biomacromolecules

2017 Volume 18, Issue 4, Page(s) 1302–1310

Abstract: Recombinant llama heavy-chain antibody fragments (VHHs) are promising tools in the field of targeted nanomedicine. 7D12, a VHH against the epidermal growth factor receptor (EGFR) that is overexpressed in various cancers, has been evaluated as an ... ...

Abstract	Recombinant llama heavy-chain antibody fragments (VHHs) are promising tools in the field of targeted nanomedicine. 7D12, a VHH against the epidermal growth factor receptor (EGFR) that is overexpressed in various cancers, has been evaluated as an effective cancer-targeting VHH in multiple studies. The small size of VHHs (15-20 kDa) results in a low circulation half-life, which can be disadvantageous for certain applications. A solution to this problem is to attach VHHs to the surface of nanoparticles to increase the hydrodynamic radius of the conjugate. This approach simultaneously allows the incorporation of different VHHs and other targeting moieties and therapeutic components into one structure, creating multispecificity and versatility for therapy and diagnosis. Here, we present the construction of highly defined 7D12-containing nanoparticles by utilizing thermoresponsive diblock elastin-like peptides that reversibly self-assemble into micellar structures. The resulting particles have a hydrodynamic radius of 24.3 ± 0.9 nm and retain full EGFR-binding capacity. We present proof of concept of the usability of such particles by controlled incorporation of a photosensitizer and show that the resulting nanoparticles induce EGFR-specific light-induced cell killing. This approach is easily extended to the controlled incorporation of various functional modules, improving therapy and diagnosis with targeted nanomedicine.
MeSH term(s)	Animals ; Camelids, New World ; Cell Line, Tumor ; Cell Survival/drug effects ; Cell Survival/radiation effects ; Drug Stability ; Elastin/chemistry ; Escherichia coli/genetics ; Humans ; Light ; Nanomedicine ; Nanoparticles/chemistry ; Peptides/chemistry ; Photochemotherapy ; Photosensitizing Agents/chemistry ; Receptor, Epidermal Growth Factor/antagonists & inhibitors ; Receptor, Epidermal Growth Factor/genetics ; Recombinant Fusion Proteins/blood ; Recombinant Fusion Proteins/chemistry ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/pharmacology ; Single-Domain Antibodies/chemistry
Chemical Substances	Peptides ; Photosensitizing Agents ; Recombinant Fusion Proteins ; Single-Domain Antibodies ; Elastin (9007-58-3) ; Receptor, Epidermal Growth Factor (EC 2.7.10.1)
Language	English
Publishing date	2017-04-10
Publishing country	United States
Document type	Journal Article
ISSN	1526-4602
ISSN (online)	1526-4602
DOI	10.1021/acs.biomac.7b00064
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