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Article ; Online: Identification and characterization of intact glycopeptides in human urine.

Garcia-Marques, Fernando / Fuller, Keely / Bermudez, Abel / Shamsher, Nikhiya / Zhao, Hongjuan / Brooks, James D / Flory, Mark R / Pitteri, Sharon J

Scientific reports

2024 Volume 14, Issue 1, Page(s) 3716

Abstract: Glycoproteins in urine have the potential to provide a rich class of informative molecules for studying human health and disease. Despite this promise, the urine glycoproteome has been largely uncharacterized. Here, we present the analysis of ... ...

Abstract	Glycoproteins in urine have the potential to provide a rich class of informative molecules for studying human health and disease. Despite this promise, the urine glycoproteome has been largely uncharacterized. Here, we present the analysis of glycoproteins in human urine using LC-MS/MS-based intact glycopeptide analysis, providing both the identification of protein glycosites and characterization of the glycan composition at specific glycosites. Gene enrichment analysis reveals differences in biological processes, cellular components, and molecular functions in the urine glycoproteome versus the urine proteome, as well as differences based on the major glycan class observed on proteins. Meta-heterogeneity of glycosylation is examined on proteins to determine the variation in glycosylation across multiple sites of a given protein with specific examples of individual sites differing from the glycosylation trends in the overall protein. Taken together, this dataset represents a potentially valuable resource as a baseline characterization of glycoproteins in human urine for future urine glycoproteomics studies.
MeSH term(s)	Humans ; Glycopeptides/chemistry ; Chromatography, Liquid ; Tandem Mass Spectrometry ; Glycoproteins/metabolism ; Proteome/chemistry ; Polysaccharides/chemistry
Chemical Substances	Glycopeptides ; Glycoproteins ; Proteome ; Polysaccharides
Language	English
Publishing date	2024-02-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-53299-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Guanylate-binding protein 1 modulates proteasomal machinery in ovarian cancer.

Tailor, Dhanir / Garcia-Marques, Fernando Jose / Bermudez, Abel / Pitteri, Sharon J / Malhotra, Sanjay V

iScience

2023 Volume 26, Issue 11, Page(s) 108292

Abstract: Guanylate-binding protein 1 (GBP1) is known as an interferon-γ-induced GTPase. Here, we used genetically modified ovarian cancer (OC) cells to study the role of GBP1. The data generated show that GBP1 inhibition constrains the clonogenic potential of ... ...

Abstract	Guanylate-binding protein 1 (GBP1) is known as an interferon-γ-induced GTPase. Here, we used genetically modified ovarian cancer (OC) cells to study the role of GBP1. The data generated show that GBP1 inhibition constrains the clonogenic potential of cancer cells.
Language	English
Publishing date	2023-10-24
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.108292
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Article ; Online: Inhibition of protein translational machinery in triple-negative breast cancer as a promising therapeutic strategy.

Dheeraj, Arpit / Garcia Marques, Fernando Jose / Tailor, Dhanir / Bermudez, Abel / Resendez, Angel / Pandrala, Mallesh / Grau, Benedikt / Kumar, Praveen / Haley, Carrsyn B / Honkala, Alexander / Kujur, Praveen / Jeffrey, Stefanie S / Pitteri, Sharon / Malhotra, Sanjay V

Cell reports. Medicine

2024 , Page(s) 101552

Abstract: Y-box binding protein-1 (YB-1) is a proto-oncogenic protein associated with protein translation regulation. It plays a crucial role in the development and progression of triple-negative breast cancer (TNBC). In this study, we describe a promising ... ...

Abstract	Y-box binding protein-1 (YB-1) is a proto-oncogenic protein associated with protein translation regulation. It plays a crucial role in the development and progression of triple-negative breast cancer (TNBC). In this study, we describe a promising approach to inhibit YB-1 using SU056, a small-molecule inhibitor. SU056 physically interacts with YB-1 and reduces its expression, which helps to restrain the progression of TNBC. Proteome profiling analysis indicates that the inhibition of YB-1 by SU056 can alter the proteins that regulate protein translation, an essential process for cancer cell growth. Preclinical studies on human cells, mice, and patient-derived xenograft tumor models show the effectiveness of SU056. Moreover, toxicological studies have shown that SU056 treatment and dosing are well tolerated without any adverse effects. Overall, our study provides a strong foundation for the further development of SU056 as a potential treatment option for patients with TNBC by targeting YB-1.
Language	English
Publishing date	2024-05-02
Publishing country	United States
Document type	Journal Article
ISSN	2666-3791
ISSN (online)	2666-3791
DOI	10.1016/j.xcrm.2024.101552
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Article: Proteomics analysis of urine and catheter-associated biofilms in spinal cord injury patients.

Garcia-Marques, Fernando J / Zakrasek, Elissa / Bermudez, Abel / Polasko, Alexandra L / Liu, Shiqin / Stoyanova, Tanya / Brooks, James D / Lavelle, John / Pitteri, Sharon J

American journal of clinical and experimental urology

2023 Volume 11, Issue 3, Page(s) 206–219

Abstract: After spinal cord injury (SCI), use chronic urinary catheters for bladder management is common, making these patients especially vulnerable to catheter-associated complications. Chronic catheterization is associated with bacterial colonization and ... ...

Abstract	After spinal cord injury (SCI), use chronic urinary catheters for bladder management is common, making these patients especially vulnerable to catheter-associated complications. Chronic catheterization is associated with bacterial colonization and frequent catheter-associated urinary tract infections (CAUTI). One determinant of infection success and treatment resistance is production of catheter-associated biofilms, composed of microorganisms and host- and microbial-derived components. To better understand the biofilm microenvironment, we performed proteomics analysis of catheter-associated biofilms and paired urine samples from four people with SCI with chronic indwelling urinary catheters. We developed a novel method for the removal of adhered cellular components on catheters that contained both human and microbial homologous proteins. Proteins from seven microbial species were identified including:
Language	English
Publishing date	2023-06-15
Publishing country	United States
Document type	Journal Article
ISSN	2330-1910
ISSN	2330-1910
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Article ; Online: The role of GCNT1 mediated O-glycosylation in aggressive prostate cancer.

Hodgson, Kirsty / Orozco-Moreno, Margarita / Scott, Emma / Garnham, Rebecca / Livermore, Karen / Thomas, Huw / Zhou, Yuhan / He, Jiepei / Bermudez, Abel / Garcia Marques, Fernando Jose / Bastian, Kayla / Hysenaj, Gerald / Archer Goode, Emily / Heer, Rakesh / Pitteri, Sharon / Wang, Ning / Elliott, David J / Munkley, Jennifer

Scientific reports

2023 Volume 13, Issue 1, Page(s) 17031

Abstract: Prostate cancer is the most common cancer in men and a major cause of cancer related deaths worldwide. Nearly all affected men develop resistance to current therapies and there is an urgent need to develop new treatments for advanced disease. Aberrant ... ...

Abstract	Prostate cancer is the most common cancer in men and a major cause of cancer related deaths worldwide. Nearly all affected men develop resistance to current therapies and there is an urgent need to develop new treatments for advanced disease. Aberrant glycosylation is a common feature of cancer cells implicated in all of the hallmarks of cancer. A major driver of aberrant glycosylation in cancer is the altered expression of glycosylation enzymes. Here, we show that GCNT1, an enzyme that plays an essential role in the formation of core 2 branched O-glycans and is crucial to the final definition of O-glycan structure, is upregulated in aggressive prostate cancer. Using in vitro and in vivo models, we show GCNT1 promotes the growth of prostate tumours and can modify the glycome of prostate cancer cells, including upregulation of core 2 O-glycans and modifying the O-glycosylation of secreted glycoproteins. Furthermore, using RNA sequencing, we find upregulation of GCNT1 in prostate cancer cells can alter oncogenic gene expression pathways important in tumour growth and metastasis. Our study highlights the important role of aberrant O-glycosylation in prostate cancer progression and provides novel insights regarding the mechanisms involved.
MeSH term(s)	Humans ; Male ; Glycosylation ; Polysaccharides/metabolism ; Prostate/pathology ; Prostatic Neoplasms/pathology
Chemical Substances	Polysaccharides ; beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-acetylglucosaminyl transferase (EC 2.4.1.102)
Language	English
Publishing date	2023-10-09
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/s41598-023-43019-8
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Article ; Online: Interplay between the Chd4/NuRD Complex and the Transcription Factor Znf219 Controls Cardiac Cell Identity.

El Abdellaoui-Soussi, Fadoua / Yunes-Leites, Paula S / López-Maderuelo, Dolores / García-Marqués, Fernando / Vázquez, Jesús / Redondo, Juan Miguel / Gómez-Del Arco, Pablo

International journal of molecular sciences

2022 Volume 23, Issue 17

Abstract: The sarcomere regulates striated muscle contraction. This structure is composed of several myofibril proteins, isoforms of which are encoded by genes specific to either the heart or skeletal muscle. The chromatin remodeler complex Chd4/NuRD regulates the ...

Abstract	The sarcomere regulates striated muscle contraction. This structure is composed of several myofibril proteins, isoforms of which are encoded by genes specific to either the heart or skeletal muscle. The chromatin remodeler complex Chd4/NuRD regulates the transcriptional expression of these specific sarcomeric programs by repressing genes of the skeletal muscle sarcomere in the heart. Aberrant expression of skeletal muscle genes induced by the loss of Chd4 in the heart leads to sudden death due to defects in cardiomyocyte contraction that progress to arrhythmia and fibrosis. Identifying the transcription factors (TFs) that recruit Chd4/NuRD to repress skeletal muscle genes in the myocardium will provide important information for understanding numerous cardiac pathologies and, ultimately, pinpointing new therapeutic targets for arrhythmias and cardiomyopathies. Here, we sought to find Chd4 interactors and their function in cardiac homeostasis. We therefore describe a physical interaction between Chd4 and the TF Znf219 in cardiac tissue. Znf219 represses the skeletal-muscle sarcomeric program in cardiomyocytes in vitro and in vivo, similarly to Chd4. Aberrant expression of skeletal-muscle sarcomere proteins in mouse hearts with knocked down
MeSH term(s)	Animals ; DNA Helicases/metabolism ; DNA-Binding Proteins/metabolism ; Gene Expression Regulation ; Mi-2 Nucleosome Remodeling and Deacetylase Complex/metabolism ; Mice ; Muscle Proteins/genetics ; Muscle Proteins/metabolism ; Myocytes, Cardiac/cytology ; Myocytes, Cardiac/metabolism ; Nucleosomes ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	DNA-Binding Proteins ; Muscle Proteins ; Nucleosomes ; Transcription Factors ; Mi-2 Nucleosome Remodeling and Deacetylase Complex (EC 3.5.1.98) ; Mi-2beta protein, mouse (EC 3.6.1.3) ; DNA Helicases (EC 3.6.4.-)
Language	English
Publishing date	2022-08-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23179565
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Article ; Online: Integrated transcriptome-proteome analyses of human stem cells reveal source-dependent differences in their regenerative signature.

Ganguly, Abantika / Swaminathan, Ganesh / Garcia-Marques, Fernando / Regmi, Shobha / Yarani, Reza / Primavera, Rosita / Chetty, Shashank / Bermudez, Abel / Pitteri, Sharon J / Thakor, Avnesh S

Stem cell reports

2022 Volume 18, Issue 1, Page(s) 190–204

Abstract: Mesenchymal stem cells (MSCs) are gaining increasing prominence as an effective regenerative cellular therapy. However, ensuring consistent and reliable effects across clinical populations has proved to be challenging. In part, this can be attributed to ... ...

Abstract	Mesenchymal stem cells (MSCs) are gaining increasing prominence as an effective regenerative cellular therapy. However, ensuring consistent and reliable effects across clinical populations has proved to be challenging. In part, this can be attributed to heterogeneity in the intrinsic molecular and regenerative signature of MSCs, which is dependent on their source of origin. The present work uses integrated omics-based profiling, at different functional levels, to compare the anti-inflammatory, immunomodulatory, and angiogenic properties between MSCs from neonatal (umbilical cord MSC [UC-MSC]) and adult (adipose tissue MSC [AD-MSC], and bone marrow MSC [BM-MSC]) sources. Using multi-parametric analyses, we identified that UC-MSCs promote a more robust host innate immune response; in contrast, adult-MSCs appear to facilitate remodeling of the extracellular matrix (ECM) with stronger activation of angiogenic cascades. These data should help facilitate the standardization of source-specific MSCs, such that their regenerative signatures can be confidently used to target specific disease processes.
MeSH term(s)	Infant, Newborn ; Humans ; Proteome ; Transcriptome ; Mesenchymal Stem Cells ; Gene Expression Profiling ; Adult Stem Cells ; Bone Marrow Cells
Chemical Substances	Proteome
Language	English
Publishing date	2022-12-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2720528-9
ISSN	2213-6711 ; 2213-6711
ISSN (online)	2213-6711
ISSN	2213-6711
DOI	10.1016/j.stemcr.2022.11.006
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Article ; Online: Protein signatures to distinguish aggressive from indolent prostate cancer.

Garcia-Marques, Fernando / Liu, Shiqin / Totten, Sarah M / Bermudez, Abel / Tanimoto, Cheylene / Hsu, En-Chi / Nolley, Rosalie / Hembree, Amy / Stoyanova, Tanya / Brooks, James D / Pitteri, Sharon J

The Prostate

2022 Volume 82, Issue 5, Page(s) 605–616

Abstract: Background: Distinguishing men with aggressive from indolent prostate cancer is critical to decisions in the management of clinically localized prostate cancer. Molecular signatures of aggressive disease could help men overcome this major clinical ... ...

Abstract	Background: Distinguishing men with aggressive from indolent prostate cancer is critical to decisions in the management of clinically localized prostate cancer. Molecular signatures of aggressive disease could help men overcome this major clinical challenge by reducing unnecessary treatment and allowing more appropriate treatment of aggressive disease. Methods: We performed a mass spectrometry-based proteomic analysis of normal and malignant prostate tissues from 22 men who underwent surgery for prostate cancer. Prostate cancer samples included Grade Groups (3-5), with 8 patients experiencing recurrence and 14 without evidence of recurrence with a mean of 6.8 years of follow-up. To better understand the biological pathways underlying prostate cancer aggressiveness, we performed a systems biology analysis and gene enrichment analysis. Proteins that distinguished recurrent from nonrecurrent cancer were chosen for validation by immunohistochemical analysis on tissue microarrays containing samples from a larger cohort of patients with recurrent and nonrecurrent prostate cancer. Results: In all, 24,037 unique peptides (false discovery rate < 1%) corresponding to 3,313 distinct proteins were identified with absolute abundance ranges spanning seven orders of magnitude. Of these proteins, 115 showed significantly (p < 0.01) different levels in tissues from recurrent versus nonrecurrent cancers. Analysis of all differentially expressed proteins in recurrent and nonrecurrent cases identified several protein networks, most prominently one in which approximately 24% of the proteins in the network were regulated by the YY1 transcription factor (adjusted p < 0.001). Strong immunohistochemical staining levels of three differentially expressed proteins, POSTN, CALR, and CTSD, on a tissue microarray validated their association with shorter patient survival. Conclusions: The protein signatures identified could improve understanding of the molecular drivers of aggressive prostate cancer and be used as candidate prognostic biomarkers.
MeSH term(s)	Biomarkers, Tumor/metabolism ; Cohort Studies ; Humans ; Male ; Mass Spectrometry ; Prognosis ; Prostate/pathology ; Prostatic Neoplasms/metabolism ; Proteomics
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2022-01-31
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	604707-5
ISSN	1097-0045 ; 0270-4137
ISSN (online)	1097-0045
ISSN	0270-4137
DOI	10.1002/pros.24307
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Article ; Online: Discovery of CASP8 as a potential biomarker for high-risk prostate cancer through a high-multiplex immunoassay.

Liu, Shiqin / Garcia-Marques, Fernando / Zhang, Chiyuan Amy / Lee, Jordan John / Nolley, Rosalie / Shen, Michelle / Hsu, En-Chi / Aslan, Merve / Koul, Kashyap / Pitteri, Sharon J / Brooks, James D / Stoyanova, Tanya

Scientific reports

2021 Volume 11, Issue 1, Page(s) 7612

Abstract: Prostate cancer remains the most common non-cutaneous malignancy among men in the United States. To discover potential serum-based biomarkers for high-risk prostate cancer, we performed a high-multiplex immunoassay utilizing patient-matched pre-operative ...

Abstract	Prostate cancer remains the most common non-cutaneous malignancy among men in the United States. To discover potential serum-based biomarkers for high-risk prostate cancer, we performed a high-multiplex immunoassay utilizing patient-matched pre-operative and post-operative serum samples from ten men with high-grade and high-volume prostate cancer. Our study identified six (CASP8, MSLN, FGFBP1, ICOSLG, TIE2 and S100A4) out of 174 proteins that were significantly decreased after radical prostatectomy. High levels of CASP8 were detected in pre-operative serum samples when compared to post-operative serum samples and serum samples from patients with benign prostate hyperplasia (BPH). By immunohistochemistry, CASP8 protein was expressed at higher levels in prostate cancer tissues compared to non-cancerous and BPH tissues. Likewise, CASP8 mRNA expression was significantly upregulated in prostate cancer when compared to benign prostate tissues in four independent clinical datasets. In addition, mRNA levels of CASP8 were higher in patients with recurrent prostate cancer when compared to patients with non-recurrent prostate cancer and high expression of CASP8 was associated with worse disease-free survival and overall survival in renal cancer. Together, our results suggest that CASP8 may potentially serve as a biomarker for high-risk prostate cancer and possibly renal cancer.
MeSH term(s)	Aged ; Biomarkers, Tumor/blood ; Caspase 8/genetics ; Caspase 8/metabolism ; Disease-Free Survival ; Humans ; Immunoassay/methods ; Immunohistochemistry/methods ; Immunologic Tests/methods ; Male ; Middle Aged ; Neoplasm Recurrence, Local/genetics ; Neoplasm Recurrence, Local/metabolism ; Prostate/pathology ; Prostate-Specific Antigen/blood ; Prostatectomy ; Prostatic Hyperplasia/metabolism ; Prostatic Neoplasms/genetics ; Prostatic Neoplasms/metabolism ; Risk Factors
Chemical Substances	Biomarkers, Tumor ; Prostate-Specific Antigen (EC 3.4.21.77) ; CASP8 protein, human (EC 3.4.22.-) ; Caspase 8 (EC 3.4.22.-)
Language	English
Publishing date	2021-04-07
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; 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/s41598-021-87155-5
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Article ; Online: MCM2-7 complex is a novel druggable target for neuroendocrine prostate cancer.

Hsu, En-Chi / Shen, Michelle / Aslan, Merve / Liu, Shiqin / Kumar, Manoj / Garcia-Marques, Fernando / Nguyen, Holly M / Nolley, Rosalie / Pitteri, Sharon J / Corey, Eva / Brooks, James D / Stoyanova, Tanya

Scientific reports

2021 Volume 11, Issue 1, Page(s) 13305

Abstract: Neuroendocrine prostate cancer (NEPC) is a lethal subtype of prostate cancer that rarely develops de novo in primary tumors and is commonly acquired during the development of treatment resistance. NEPC is characterized by gain of neuroendocrine markers ... ...

Abstract	Neuroendocrine prostate cancer (NEPC) is a lethal subtype of prostate cancer that rarely develops de novo in primary tumors and is commonly acquired during the development of treatment resistance. NEPC is characterized by gain of neuroendocrine markers and loss of androgen receptor (AR), making it resistant to current therapeutic strategies targeting the AR signaling axis. Here, we report that MCM2, MCM3, MCM4, and MCM6 (MCM2/3/4/6) are elevated in human NEPC and high levels of MCM2/3/4/6 are associated with liver metastasis and poor survival in prostate cancer patients. MCM2/3/4/6 are four out of six proteins that form a core DNA helicase (MCM2-7) responsible for unwinding DNA forks during DNA replication. Inhibition of MCM2-7 by treatment with ciprofloxacin inhibits NEPC cell proliferation and migration in vitro, significantly delays NEPC tumor xenograft growth, and partially reverses the neuroendocrine phenotype in vivo. Our study reveals the clinical relevance of MCM2/3/4/6 proteins in NEPC and suggests that inhibition of MCM2-7 may represent a new therapeutic strategy for NEPC.
MeSH term(s)	Animals ; Carcinoma, Neuroendocrine/metabolism ; Cell Line, Tumor ; Gene Expression Regulation, Neoplastic/physiology ; Humans ; Male ; Mice ; Mice, Inbred NOD ; Mice, SCID ; Minichromosome Maintenance Complex Component 2/metabolism ; Minichromosome Maintenance Complex Component 7/metabolism ; Minichromosome Maintenance Proteins/metabolism ; Neuroendocrine Tumors/metabolism ; PC-3 Cells ; Prostate/metabolism ; Prostatic Neoplasms/metabolism ; Receptors, Androgen/metabolism ; Signal Transduction/physiology ; Up-Regulation/physiology ; Xenograft Model Antitumor Assays/methods
Chemical Substances	Receptors, Androgen ; MCM2 protein, human (EC 3.6.4.12) ; MCM7 protein, human (EC 3.6.4.12) ; Minichromosome Maintenance Complex Component 2 (EC 3.6.4.12) ; Minichromosome Maintenance Complex Component 7 (EC 3.6.4.12) ; Minichromosome Maintenance Proteins (EC 3.6.4.12)
Language	English
Publishing date	2021-06-25
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; 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/s41598-021-92552-x
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