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Article ; Online: Metagenomics Data Visualization Using R.

Coleman, Alex / Bose, Anupam / Mitra, Suparna

Methods in molecular biology (Clifton, N.J.)

2023 Volume 2649, Page(s) 359–392

Abstract: ... manipulating using the R programming language this, chapter will explore how to use R to plot data and generate ... high-quality graphics. It will cover plotting using the base R plotting functionality and introduce ... the famous ggplot2 package [2] that is widely used for data visualization in R. After this general ...

Abstract	Communicating key finds is a crucial part of the research process. Data visualization is the field of graphically representing data to help communicate key findings. Building on previous chapters around data manipulating using the R programming language this, chapter will explore how to use R to plot data and generate high-quality graphics. It will cover plotting using the base R plotting functionality and introduce the famous ggplot2 package [2] that is widely used for data visualization in R. After this general introduction to data visualization tools, the chapter will explore more specific data visualization techniques for metagenomics data and their use cases using these basic packages.
MeSH term(s)	Software ; Metagenomics ; Data Visualization ; Programming Languages
Language	English
Publishing date	2023-05-31
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3072-3_19
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Article ; Online: Reply to Z.R. McCaw et al.

Matulonis, Ursula A / Lorusso, Domenica / Oaknin, Ana / Pignata, Sandro / Dean, Andrew / Denys, Hannelore / Colombo, Nicoletta / Van Gorp, Toon / Konner, Jason A / Marin, Margarita Romeo / Harter, Philipp / Murphy, Conleth G / Wang, Jiuzhou / Noble, Elizabeth / Esteves, Brooke / Method, Michael / Coleman, Robert L

Journal of clinical oncology : official journal of the American Society of Clinical Oncology

2023 Volume 41, Issue 29, Page(s) 4705–4706

Language	English
Publishing date	2023-08-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	604914-x
ISSN	1527-7755 ; 0732-183X
ISSN (online)	1527-7755
ISSN	0732-183X
DOI	10.1200/JCO.23.00752
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Article ; Online: Manipulating and Basic Analysis of Tabular Metagenomics Datasets Using R.

Coleman, Alex / Callaghan, Martin

Methods in molecular biology (Clifton, N.J.)

2023 Volume 2649, Page(s) 339–357

Abstract: ... pipeline. The R statistical programming language offers a variety of versatile tools for working ... we outline the basics of the R programming language and showcase a number of tools for data manipulation and ...

Abstract	Handling and manipulating tabular datasets is a critical step in every metagenomics analysis pipeline. The R statistical programming language offers a variety of versatile tools for working with tabular data that allow for the development of computationally efficient and reproducible workflows. Here we outline the basics of the R programming language and showcase a number of tools for data manipulation and basic analysis of metagenomics datasets.
MeSH term(s)	Software ; Metagenomics ; Programming Languages ; Workflow
Language	English
Publishing date	2023-05-31
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3072-3_18
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Article: mxnorm: An R Package to Normalize Multiplexed Imaging Data.

Harris, Coleman / Wrobel, Julia / Vandekar, Simon

Journal of open source software

2022 Volume 7, Issue 71

Abstract: ... including software packages in R and Python like spatialTime, imcRtools, MCMICR0, and Squidpy (Creed et al ... is open-source software built with R and S3 methods that implements, evaluates, and visualizes ... we intend to set a foundation for the evaluation of multiplexed imaging normalization methods in R ...

Abstract	Multiplexed imaging is an emerging single-cell assay that can be used to understand and analyze complex processes in tissue-based cancers, autoimmune disorders, and more. These imaging technologies, which include co-detection by indexing (CODEX), multiplexed ion beam imaging (MIBI), and multiplexed immunofluorescence imaging (MxIF), provide detailed information about spatial interactions between cells (Angelo et al., 2014; Gerdes et al., 2013; Goltsev et al., 2018). Multiplexed imaging experiments generate data across hundreds of slides and images, often resulting in terabytes of complex data to analyze through imaging analysis pipelines. Methods are rapidly developing to improve particular parts of the pipeline, including software packages in R and Python like spatialTime, imcRtools, MCMICR0, and Squidpy (Creed et al., 2021; Palla et al., 2021; Schapiro et al., 2021; Windhager et al., 2021). An important, but understudied component of this pipeline is the analysis of technical variation within this complex data source - intensity normalization is one way to remove this technical variability. The combination of disparate pre-processing pipelines, imaging variables, optical effects, and within-slide dependencies create batch and slide effects that can be reduced via normalization methods. Current state-of-the-art methods vary heavily across research labs and image acquisition platforms, without one singular method that is uniformly robust - optimal statistical methods seek to improve similarity across images and slides by removing this technical variability while maintaining the underlying biological signal in the data. mxnorm is open-source software built with R and S3 methods that implements, evaluates, and visualizes normalization techniques for multiplexed imaging data. Extending methodology described in Harris et al. (2022), we intend to set a foundation for the evaluation of multiplexed imaging normalization methods in R. This easily allows users to extend normalization methods into the field, and provides a robust evaluation framework to measure both technical variability and the efficacy of various normalization methods. One key component of the R package is the ability to supply user-defined normalization methods and thresholding algorithms to assess normalization in multiplexed imaging data. Core features, usage details, and extensive tutorials are available in the package documentation and vignette on CRAN and the software repository.
Language	English
Publishing date	2022-03-30
Publishing country	United States
Document type	Journal Article
ISSN	2475-9066
ISSN	2475-9066
DOI	10.21105/joss.04180
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Article ; Online: ukbtools: An R package to manage and query UK Biobank data.

Hanscombe, Ken B / Coleman, Jonathan R I / Traylor, Matthew / Lewis, Cathryn M

PloS one

2019 Volume 14, Issue 5, Page(s) e0214311

Abstract: Introduction: The UK Biobank (UKB) is a resource that includes detailed health-related data on about 500,000 individuals and is available to the research community. However, several obstacles limit immediate analysis of the data: data files vary in ... ...

Abstract	Introduction: The UK Biobank (UKB) is a resource that includes detailed health-related data on about 500,000 individuals and is available to the research community. However, several obstacles limit immediate analysis of the data: data files vary in format, may be very large, and have numerical codes for column names. Results: ukbtools removes all the upfront data wrangling required to get a single dataset for statistical analysis. All associated data files are merged into a single dataset with descriptive column names. The package also provides tools to assist in quality control by exploring the primary demographics of subsets of participants; query of disease diagnoses for one or more individuals, and estimating disease frequency relative to a reference variable; and to retrieve genetic metadata. Conclusion: Having a dataset with meaningful variable names, a set of UKB-specific exploratory data analysis tools, disease query functions, and a set of helper functions to explore and write genetic metadata to file, will rapidly enable UKB users to undertake their research.
MeSH term(s)	Data Analysis ; Database Management Systems ; Datasets as Topic ; Disease ; Electronic Health Records ; Humans ; Information Storage and Retrieval ; Metadata ; United Kingdom
Language	English
Publishing date	2019-05-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0214311
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Article ; Online: β-Delayed One and Two Neutron Emission Probabilities Southeast of ^{132}Sn and the Odd-Even Systematics in r-Process Nuclide Abundances.

Phong, V H / Nishimura, S / Lorusso, G / Davinson, T / Estrade, A / Hall, O / Kawano, T / Liu, J / Montes, F / Nishimura, N / Grzywacz, R / Rykaczewski, K P / Agramunt, J / Ahn, D S / Algora, A / Allmond, J M / Baba, H / Bae, S / Brewer, N T /

Bruno, C G / Caballero-Folch, R / Calviño, F / Coleman-Smith, P J / Cortes, G / Dillmann, I / Domingo-Pardo, C / Fijalkowska, A / Fukuda, N / Go, S / Griffin, C J / Ha, J / Harkness-Brennan, L J / Isobe, T / Kahl, D / Khiem, L H / Kiss, G G / Korgul, A / Kubono, S / Labiche, M / Lazarus, I / Liang, J / Liu, Z / Matsui, K / Miernik, K / Moon, B / Morales, A I / Morrall, P / Nepal, N / Page, R D / Piersa-Siłkowska, M / Pucknell, V F E / Rasco, B C / Rubio, B / Sakurai, H / Shimizu, Y / Stracener, D W / Sumikama, T / Suzuki, H / Tain, J L / Takeda, H / Tarifeño-Saldivia, A / Tolosa-Delgado, A / Wolińska-Cichocka, M / Woods, P J / Yokoyama, R

Physical review letters

2022 Volume 129, Issue 17, Page(s) 172701

Abstract: ... emission. The impact of our measurements on r-process nucleosynthesis was studied in a neutron star merger ... of Ba in r-process-enhanced (r-II) stars is also better reproduced using our new data. ...

Abstract	The β-delayed one- and two-neutron emission probabilities (P_{1n} and P_{2n}) of 20 neutron-rich nuclei with N≥82 have been measured at the RIBF facility of the RIKEN Nishina Center. P_{1n} of ^{130,131}Ag, ^{133,134}Cd, ^{135,136}In, and ^{138,139}Sn were determined for the first time, and stringent upper limits were placed on P_{2n} for nearly all cases. β-delayed two-neutron emission (β2n) was unambiguously identified in ^{133}Cd and ^{135,136}In, and their P_{2n} were measured. Weak β2n was also detected from ^{137,138}Sn. Our results highlight the effect of the N=82 and Z=50 shell closures on β-delayed neutron emission probability and provide stringent benchmarks for newly developed macroscopic-microscopic and self-consistent global models with the inclusion of a statistical treatment of neutron and γ emission. The impact of our measurements on r-process nucleosynthesis was studied in a neutron star merger scenario. Our P_{1n} and P_{2n} have a direct impact on the odd-even staggering of the final abundance, improving the agreement between calculated and observed Solar System abundances. The odd isotope fraction of Ba in r-process-enhanced (r-II) stars is also better reproduced using our new data.
Language	English
Publishing date	2022-10-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.129.172701
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Article ; Online: GnRH-R-Targeted Lytic Peptide Sensitizes

Ma, Shaolin / Pradeep, Sunila / Villar-Prados, Alejandro / Wen, Yunfei / Bayraktar, Emine / Mangala, Lingegowda S / Kim, Mark Seungwook / Wu, Sherry Y / Hu, Wei / Rodriguez-Aguayo, Cristian / Leuschner, Carola / Liang, Xiaoyan / Ram, Prahlad T / Schlacher, Katharina / Coleman, Robert L / Sood, Anil K

Molecular cancer therapeutics

2019 Volume 18, Issue 5, Page(s) 969–979

Abstract: EP-100 is a synthetic lytic peptide that specifically targets the gonadotropin-releasing hormone receptor on cancer cells. To extend the utility of EP-100, we aimed to identify effective combination therapies with EP-100 for ovarian cancer and explore ... ...

Abstract	EP-100 is a synthetic lytic peptide that specifically targets the gonadotropin-releasing hormone receptor on cancer cells. To extend the utility of EP-100, we aimed to identify effective combination therapies with EP-100 for ovarian cancer and explore potential mechanisms of this combination. A series of
MeSH term(s)	Animals ; BRCA1 Protein/genetics ; Cell Proliferation/drug effects ; Cisplatin/pharmacology ; DNA Damage/drug effects ; Doxorubicin/pharmacology ; Drug Resistance, Neoplasm/genetics ; Female ; Gene Expression Regulation, Neoplastic/drug effects ; Humans ; Mice ; Ovarian Neoplasms/drug therapy ; Ovarian Neoplasms/genetics ; Ovarian Neoplasms/pathology ; Paclitaxel/pharmacology ; Peptides/chemical synthesis ; Peptides/pharmacology ; Phthalazines/pharmacology ; Piperazines/pharmacology ; Poly(ADP-ribose) Polymerase Inhibitors/pharmacology ; Receptors, LHRH/antagonists & inhibitors ; Receptors, LHRH/genetics ; Xenograft Model Antitumor Assays
Chemical Substances	BRCA1 Protein ; Peptides ; Phthalazines ; Piperazines ; Poly(ADP-ribose) Polymerase Inhibitors ; Receptors, LHRH ; Doxorubicin (80168379AG) ; Paclitaxel (P88XT4IS4D) ; Cisplatin (Q20Q21Q62J) ; olaparib (WOH1JD9AR8)
Language	English
Publishing date	2019-03-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2063563-1
ISSN	1538-8514 ; 1535-7163
ISSN (online)	1538-8514
ISSN	1535-7163
DOI	10.1158/1535-7163.MCT-18-0770
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Article ; Online: Enhanced Immunotherapy with LHRH-R Targeted Lytic Peptide in Ovarian Cancer.

Kim, Mark Seungwook / Ma, Shaolin / Chelariu-Raicu, Anca / Leuschner, Carola / Alila, Hector W / Lee, Sanghoon / Coleman, Robert L / Sood, Anil K

Molecular cancer therapeutics

2020 Volume 19, Issue 11, Page(s) 2396–2406

Abstract: ... to a lytic peptide], improving the efficacy of immune checkpoint blockade. LHRH-R-positive murine ... micromolar levels through LHRH-R. EP-100 increased PD-L1 levels on murine ovarian cancer cells. ...

Abstract	Here, we examined the role of EP-100 [luteinizing hormone-releasing hormone (LHRH) ligand joined to a lytic peptide], improving the efficacy of immune checkpoint blockade. LHRH-R-positive murine ovarian cancer cells (ID8, IG10, IF5, and 2C12) were sensitive to EP-100 and were specifically killed at low micromolar levels through LHRH-R. EP-100 increased PD-L1 levels on murine ovarian cancer cells.
MeSH term(s)	Animals ; Antineoplastic Agents/pharmacology ; Apoptosis/drug effects ; Cell Line, Tumor ; Cell Survival/drug effects ; Cytokines/genetics ; Cytokines/metabolism ; Disease Models, Animal ; Female ; Gene Expression ; Humans ; Mice ; Molecular Targeted Therapy/methods ; Peptide Fragments/pharmacology ; Receptors, LHRH/antagonists & inhibitors ; Recombinant Fusion Proteins/pharmacology ; T-Lymphocyte Subsets/drug effects ; T-Lymphocyte Subsets/immunology ; T-Lymphocyte Subsets/metabolism ; Xenograft Model Antitumor Assays
Chemical Substances	Antineoplastic Agents ; Cytokines ; EP-100 membrane-disrupting peptide ; Peptide Fragments ; Receptors, LHRH ; Recombinant Fusion Proteins
Language	English
Publishing date	2020-09-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2063563-1
ISSN	1538-8514 ; 1535-7163
ISSN (online)	1538-8514
ISSN	1535-7163
DOI	10.1158/1535-7163.MCT-20-0030
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Article ; Online: Long-term follow-up of R-CHOP with bevacizumab as initial therapy for mantle cell lymphoma: clinical and correlative results.

Ruan, Jia / Gregory, Stephanie A / Christos, Paul / Martin, Peter / Furman, Richard R / Coleman, Morton / Leonard, John P

Clinical lymphoma, myeloma & leukemia

2014 Volume 14, Issue 2, Page(s) 107–113

Abstract: ... within the tumor microenvironment. We initiated a phase II trial to determine if the addition of bevacizumab to the standard R-CHOP ... Results: Beyond the standard R-CHOP safety profile, Grade 3 left ventricular dysfunction developed in 2 ... vascular endothelial growth factor (VEGF) throughout treatment.: Conclusion: The addition of bevacizumab to the standard R-CHOP ...

Abstract	Background: Emerging evidence indicates that MCL has increased angiogenesis within the tumor microenvironment. We initiated a phase II trial to determine if the addition of bevacizumab to the standard R-CHOP regimen could enhance antitumor effects in patients with previously untreated MCL. Patients and methods: Eleven patients with previously untreated MCL received bevacizumab at 15 mg/kg on day 1, and standard CHOP-21 (CHOP given every 21 days per cycle) with rituximab (375 mg/m(2) per cycle) on day 3 of each cycle for a total of 6 cycles. Planned study end points included safety and efficacy assessment, and exploratory analysis of angiogenic profiles. The study was suspended in August of 2010 based on safety findings in DLBCL (diffuse large B-cell lymphoma) of increased cardiovascular events with the regimen. Results: Beyond the standard R-CHOP safety profile, Grade 3 left ventricular dysfunction developed in 2 patients (18%), Grade 1/2 hypertension, proteinuria, and bleeding each developed in 1 patient (9%). The overall response rate was 82% with 36% complete response (CR)/complete response unconfirmed (CRu). The median progression-free survival (n = 11) was 18 months (95% confidence interval, 3-not reached), and 3-year overall survival rate was 82%. Correlative studies showed increased vascular endothelial growth factor receptor 1 expression in tumor cells at baseline, and elevated levels of plasma vascular endothelial growth factor (VEGF) throughout treatment. Conclusion: The addition of bevacizumab to the standard R-CHOP regimen did not appear to significantly improve efficacy beyond that observed from previous studies using R-CHOP alone. Therapeutic strategies that provide sustained inhibition on VEGF-related and VEGF-independent targets within the tumor microenvironment might further improve antiangiogenic effects and warrant further exploration in MCL.
MeSH term(s)	Adult ; Aged ; Anemia/chemically induced ; Antibodies, Monoclonal, Humanized/administration & dosage ; Antibodies, Monoclonal, Humanized/adverse effects ; Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Bevacizumab ; Cell Line, Tumor ; Cyclophosphamide/administration & dosage ; Cyclophosphamide/adverse effects ; Doxorubicin/administration & dosage ; Doxorubicin/adverse effects ; Fatigue/chemically induced ; Female ; Follow-Up Studies ; Gene Expression Regulation, Neoplastic/drug effects ; Humans ; Kaplan-Meier Estimate ; Lymphoma, Mantle-Cell/drug therapy ; Male ; Middle Aged ; Prednisone/administration & dosage ; Prednisone/adverse effects ; Reverse Transcriptase Polymerase Chain Reaction ; Time Factors ; Treatment Outcome ; Vascular Endothelial Growth Factor A/blood ; Vascular Endothelial Growth Factor Receptor-1/genetics ; Ventricular Dysfunction, Left/chemically induced ; Vincristine/administration & dosage ; Vincristine/adverse effects
Chemical Substances	Antibodies, Monoclonal, Humanized ; Vascular Endothelial Growth Factor A ; Bevacizumab (2S9ZZM9Q9V) ; Vincristine (5J49Q6B70F) ; Doxorubicin (80168379AG) ; Cyclophosphamide (8N3DW7272P) ; Vascular Endothelial Growth Factor Receptor-1 (EC 2.7.10.1) ; Prednisone (VB0R961HZT)
Language	English
Publishing date	2014-04
Publishing country	United States
Document type	Clinical Trial, Phase II ; Journal Article ; Multicenter Study ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2540992-X
ISSN	2152-2669 ; 2152-2650
ISSN (online)	2152-2669
ISSN	2152-2650
DOI	10.1016/j.clml.2013.10.002
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Article: Human-based systems in drug and chemical safety testing--toward replacement, the 'single R'.

Coleman, Robert A

Alternatives to laboratory animals : ATLA

2014 Volume 42, Issue 6, Page(s) 357–366

Abstract: ... we should concentrate on the third R: Replacement. And if this is the best way forward, it is inevitable that this R ... weaknesses and opportunities, and goes on to address the prospect of achieving a single R ...

Abstract	The Three Rs was a concept originally conceived as a means of reducing the suffering of laboratory animals that are used largely in identifying any potential safety issues with chemicals to which humans may be exposed. However, with growing evidence of the shortcomings of laboratory animal testing to reliably predict human responsiveness to such chemicals, questions are now being asked as to whether it is appropriate to use animals as human surrogates at all. This raises the question of whether, of the original Three Rs, two--Reduction and Refinement--are potentially redundant, and whether, instead, we should concentrate on the third R: Replacement. And if this is the best way forward, it is inevitable that this R should be based firmly on human biology. The present review outlines the current state-of-the-art regarding our access to human biology through in vitro, in silico and in vivo technologies, identifying strengths, weaknesses and opportunities, and goes on to address the prospect of achieving a single R, with some suggestions as to how to progress toward this goal.
MeSH term(s)	Biomarkers, Pharmacological ; Computer Simulation ; Humans ; In Vitro Techniques ; Stem Cell Research ; Toxicity Tests
Chemical Substances	Biomarkers, Pharmacological
Language	English
Publishing date	2014-12-08
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	605800-0
ISSN	0261-1929
ISSN	0261-1929
DOI	10.1177/026119291404200605
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