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  1. Article ; Online: Recommendations for the Equitable and Widespread Implementation of Liquid Biopsy for Cancer Care.

    Febbo, Phillip G / Allo, Mina / Alme, Emma B / Cuyun Carter, Gebra / Dumanois, Robert / Essig, Alessia / Kiernan, Estevan / Kubler, Caitlin B / Martin, Nikki / Popescu, Medeea C / Leiman, Lauren C

    JCO precision oncology

    2024  Volume 8, Page(s) e2300382

    Abstract: Liquid biopsies-tests that detect circulating tumor cellular components in the bloodstream-have the potential to transform cancer by reducing health inequities in screening, diagnostics, and monitoring. Today, liquid biopsies are being used to guide ... ...

    Abstract Liquid biopsies-tests that detect circulating tumor cellular components in the bloodstream-have the potential to transform cancer by reducing health inequities in screening, diagnostics, and monitoring. Today, liquid biopsies are being used to guide treatment choices for patients and monitor for cancer recurrence, and promising work in multi-cancer early detection is ongoing. However, without awareness of the barriers to adoption of this new technology and a willingness to build mitigation efforts into the implementation of widespread liquid biopsy testing, the communities that could most benefit may be the last to access and use them. In this work, we review the challenges likely to affect the accessibility of liquid biopsies in both the general population and underserved populations, and recommend specific actions to facilitate equitable access for all patients.
    MeSH term(s) Humans ; Liquid Biopsy ; Neoplastic Cells, Circulating
    Language English
    Publishing date 2024-01-24
    Publishing country United States
    Document type Review ; Journal Article
    ISSN 2473-4284
    ISSN (online) 2473-4284
    DOI 10.1200/PO.23.00382
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Epigenetic events highlight the challenge of validating prognostic biomarkers during the clinical and biologic evolution of prostate cancer.

    Febbo, Phillip G

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

    2009  Volume 27, Issue 19, Page(s) 3088–3090

    MeSH term(s) Animals ; Biomarkers, Tumor/genetics ; Epigenesis, Genetic ; Humans ; Male ; Mice ; Prognosis ; Prostatic Neoplasms/genetics
    Chemical Substances Biomarkers, Tumor
    Language English
    Publishing date 2009-07-01
    Publishing country United States
    Document type Editorial ; Review
    ZDB-ID 604914-x
    ISSN 1527-7755 ; 0732-183X
    ISSN (online) 1527-7755
    ISSN 0732-183X
    DOI 10.1200/JCO.2008.20.9783
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  3. Article: Genomic approaches to outcome prediction in prostate cancer.

    Febbo, Phillip G

    Cancer

    2009  Volume 115, Issue 13 Suppl, Page(s) 3046–3057

    Abstract: Prostate cancer remains a common cause of cancer death in men. Applications of emerging genomic technologies to high-quality prostate cancer models and patient samples in multiple contexts have made significant contributions to our molecular ... ...

    Abstract Prostate cancer remains a common cause of cancer death in men. Applications of emerging genomic technologies to high-quality prostate cancer models and patient samples in multiple contexts have made significant contributions to our molecular understanding of the development and progression of prostate cancer. Genomic analysis of DNA, RNA, and protein alterations allows for the global assessment of this disease and provides the molecular framework to improve risk classification, outcome prediction, and development of targeted therapies. In this review, the author focused on highlighting recent work in genomics and its role in evaluating molecular modifiers of prostate cancer risk and behavior and the development of predictive models that anticipate the risk of developing prostate cancer, prostate cancer progression, and the response of prostate cancer to therapy. This framework has the exciting potential to be predictive and to provide personalized and individual treatment to the large number of men diagnosed with prostate cancer each year. Cancer 2009;115(13 suppl):3046-57. (c) 2009 American Cancer Society.
    MeSH term(s) Epigenesis, Genetic ; Forecasting ; Gene Expression Profiling ; Genomics ; Humans ; Male ; Polymorphism, Genetic ; Prostatic Neoplasms/genetics ; Prostatic Neoplasms/therapy ; Risk Factors ; Treatment Outcome
    Language English
    Publishing date 2009-07-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 1429-1
    ISSN 1097-0142 ; 0008-543X ; 1934-662X
    ISSN (online) 1097-0142
    ISSN 0008-543X ; 1934-662X
    DOI 10.1002/cncr.24350
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  4. Article: Balancing Confounding and Generalizability Using Observational, Real-world Data: 17-gene Genomic Prostate Score Assay Effect on Active Surveillance.

    Canfield, Steven / Kemeter, Michael J / Febbo, Phillip G / Hornberger, John

    Reviews in urology

    2018  Volume 20, Issue 2, Page(s) 69–76

    Abstract: Randomized, controlled trials can provide high-quality, unbiased evidence for therapeutic interventions but are not always a practical or viable study design for certain healthcare decisions, such as those involving prognostic or predictive testing. ... ...

    Abstract Randomized, controlled trials can provide high-quality, unbiased evidence for therapeutic interventions but are not always a practical or viable study design for certain healthcare decisions, such as those involving prognostic or predictive testing. Studies using large, real-world databases may be more appropriate and more generalizable to the intended target population of physicians and patients to answer these questions but carry potential for hidden bias. We illustrate several emerging methods of analyzing observational studies using propensity score matching (PSM) and coarsened exact matching (CEM). These advanced statistical methods are intended to reveal a "hidden experiment" within an observational database, and so refute or confirm a potential causal effect of assignment to an intervention and study outcome. We applied these methods to the Optum™ Research Database (ORD; Eden Prairie, MN) of electronic health records and administrative claims data to assess the effect of the 17-gene Genomic Prostate Score® (GPS™; Genomic Health, Redwood City, CA) assay on use of active surveillance (AS). In a traditional multivariable logistic regression, the GPS assay increased the use of AS by 29% (95% CI, 24%-33%). Upon applying the matching methods, the effect of the GPS assay on AS use varied between 27% and 80% and the matched data were significant among all algorithms. All matching algorithms performed well in identifying matched data that improved the imbalance in baseline covariates. By using different matching methods to assess causal inference in an observational database, we provide further confidence that the effect of the GPS assay on AS use is statistically significant and unlikely to be a result of confounding due to differences in baseline characteristics of the patients or the settings in which they were seen.
    Language English
    Publishing date 2018-09-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2108895-0
    ISSN 2153-8182 ; 1523-6161
    ISSN (online) 2153-8182
    ISSN 1523-6161
    DOI 10.3909/riu0799
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: The current and future role of sequence-based analysis in prostate cancer treatment.

    Kim, Won / Febbo, Phillip G

    Personalized medicine

    2013  Volume 10, Issue 3, Page(s) 257–273

    Abstract: Prostate cancer is the most commonly diagnosed, nondermatologic malignancy in US men. Localized disease can be managed through active surveillance or curative, locally directed therapies, but 30% of men treated with surgery or radiation will need ... ...

    Abstract Prostate cancer is the most commonly diagnosed, nondermatologic malignancy in US men. Localized disease can be managed through active surveillance or curative, locally directed therapies, but 30% of men treated with surgery or radiation will need additional (often systemic) treatment for relapsed disease. While spectacular advances in medical treatment of advanced prostate cancer have improved the quality and duration of patients' lives, metastatic prostate cancer remains an incurable, lethal disease that requires additional therapies and better treatment strategies. The advent of ultra-high-throughput sequencing technology provides an opportunity to comprehensively assess the constellation of genetic and molecular events underlying each patient's tumor, and promises to enhance our ability to deliver specifically tailored personalized treatment to men with prostate cancer. The known biological and clinical heterogeneity of prostate cancer presents both opportunities and challenges to the application and utilization of sequence-based analysis to guide prostate cancer treatment.
    Language English
    Publishing date 2013-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 2299146-3
    ISSN 1744-828X ; 1741-0541
    ISSN (online) 1744-828X
    ISSN 1741-0541
    DOI 10.2217/pme.13.13
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  6. Article ; Online: Genomic surveillance at scale is required to detect newly emerging strains at an early timepoint

    Vavrek, Darcy / Speroni, Lucia / Curnow, Kirsten J / Oberholzer, Michael / Moeder, Vanessa / Febbo, Phillip G

    medRxiv

    Abstract: Genomic surveillance in the setting of the coronavirus disease 2019 (COVID-19) pandemic has the potential to identify emerging SARS-CoV-2 strains that may be more transmissible, virulent, evade detection by standard diagnostic tests, or vaccine escapes. ... ...

    Abstract Genomic surveillance in the setting of the coronavirus disease 2019 (COVID-19) pandemic has the potential to identify emerging SARS-CoV-2 strains that may be more transmissible, virulent, evade detection by standard diagnostic tests, or vaccine escapes. The rapid spread of the SARS-CoV-2 B.1.1.7 strain from southern England to other parts of the country and globe is a clear example of the impact of such strains. Early discovery of the B.1.1.7 strain was enabled through the proactive COVID-19 Genomics UK (COG-UK) program and the UK9s commitment to genomic surveillance, sequencing about 10% of positive samples. In order to enact more aggressive public health measures to minimize the spread of such strains, genomic surveillance needs to be of sufficient scale to detect early emergence and expansion in the broader virus population. By modeling common performance characteristics of available diagnostic and sequencing tests, we developed a model that assesses the sampling required to detect emerging strains when they are less than 1% of all strains in a population. This model demonstrates that 5% sampling of all positive tests allows the detection of emerging strains when they are a prevalence of 0.1% to 1.0%. While each country will determine their risk tolerance for the emergence of novel strains, as vaccines are distributed and we work to end the pandemic and prevent future SARS-CoV-2 outbreaks, genomic surveillance will be an integral part of success.
    Keywords covid19
    Language English
    Publishing date 2021-01-15
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.01.12.21249613
    Database COVID19

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  7. Article: Active Surveillance Use Among a Low-risk Prostate Cancer Population in a Large US Payer System: 17-Gene Genomic Prostate Score Versus Other Risk Stratification Methods.

    Canfield, Steven / Kemeter, Michael J / Hornberger, John / Febbo, Phillip G

    Reviews in urology

    2017  Volume 19, Issue 4, Page(s) 203–212

    Abstract: Many men with low-risk prostate cancer (PCa) receive definitive treatment despite recommendations that have been informed by two large, randomized trials encouraging active surveillance (AS). We conducted a retrospective cohort study using the Optum™ ... ...

    Abstract Many men with low-risk prostate cancer (PCa) receive definitive treatment despite recommendations that have been informed by two large, randomized trials encouraging active surveillance (AS). We conducted a retrospective cohort study using the Optum™ Research Database (Eden Prairie, MN) of electronic health records and administrative claims data to assess AS use for patients tested with a 17-gene Genomic Prostate Score™ (GPS; Genomic Health, Redwood City, CA) assay and/or prostate magnetic resonance imaging (MRI). De-identified records were extracted on health plan members enrolled from June 2013 to June 2016 who had ≥1 record of PCa (n 5 291,876). Inclusion criteria included age ≥18 years, new diagnosis, American Urological Association low-risk PCa (stage T1-T2a, prostate-specific antigen ≤10 ng/mL, Gleason score 5 6), and clinical activity for at least 12 months before and after diagnosis. Data included baseline characteristics, use of GPS testing and/or MRI, and definitive procedures. GPS or MRI testing was performed in 17% of men (GPS, n 5 375, 4%; MRI, n 5 1174, 13%). AS use varied from a low of 43% for men who only underwent MRI to 89% for GPStested men who did not undergo MRI (
    Language English
    Publishing date 2017-04-25
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2108895-0
    ISSN 2153-8182 ; 1523-6161
    ISSN (online) 2153-8182
    ISSN 1523-6161
    DOI 10.3909/riu0786
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  8. Article ; Online: Cancer gene profiling in prostate cancer.

    Foye, Adam / Febbo, Phillip G

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

    2010  Volume 576, Page(s) 293–326

    Abstract: Gene profiling and expression analysis using microarrays have made a significant impact on our biological understanding of prostate cancer. The procedures for generating high-quality expression data from prostate cancer cell lines and tumors are not ... ...

    Abstract Gene profiling and expression analysis using microarrays have made a significant impact on our biological understanding of prostate cancer. The procedures for generating high-quality expression data from prostate cancer cell lines and tumors are not trivial. However, during the past 9 years, methods by which to process samples for gene profiling have been developed. In this chapter, techniques to process prostate cancer specimens either en bloc (macrodissection) or using laser capture microdissection are presented in detail along with extensive technical notes. Although we focus on prostate cancer and discuss the specific methods utilized in our lab, the processes discussed are generalizable to other tumors and amenable to the substitution of alternative instruments and/or commercially available kits.
    MeSH term(s) Animals ; Biomarkers, Tumor/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Humans ; Lasers ; Male ; Mice ; Microdissection ; Molecular Biology/methods ; Neoplasm Transplantation ; Oligonucleotide Array Sequence Analysis ; Prostatic Neoplasms/genetics ; Prostatic Neoplasms/metabolism ; RNA, Neoplasm/metabolism
    Chemical Substances Biomarkers, Tumor ; RNA, Neoplasm
    Language English
    Publishing date 2010
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-59745-545-9_15
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  9. Article ; Online: Using surrogate biomarkers to predict clinical benefit in men with castration-resistant prostate cancer: an update and review of the literature.

    Armstrong, Andrew J / Febbo, Phillip G

    The oncologist

    2009  Volume 14, Issue 8, Page(s) 816–827

    Abstract: Recurrent prostate cancer has a complex molecular etiology and a prolonged disease course. Although initially responsive to androgen ablation, many men eventually become castration resistant, develop skeletal metastases, and are palliatively treated with ...

    Abstract Recurrent prostate cancer has a complex molecular etiology and a prolonged disease course. Although initially responsive to androgen ablation, many men eventually become castration resistant, develop skeletal metastases, and are palliatively treated with docetaxel-based chemotherapy, radiation therapy, bisphosphonates, and best supportive care. Given the modest success rates of the current standard of care, clinical trial enrollment is encouraged. Castration-resistant prostate cancer (CRPC) is a heterogeneous disease, both in clinical manifestations and outcomes, requiring an individualized approach to both patient care and trial design. Herein, we review surrogate markers of disease progression and treatment efficacy in advanced prostate cancer in light of recently published guidelines that have redefined eligibility, response criteria, and suitable endpoints in prostate cancer drug development. The guidelines have refined outcome measures to potentially better capture clinical benefit and the ability of novel targeted molecular and biologic agents to impact favorably on this disease. We consider prostate-specific antigen changes, circulating tumor cells, bone scan alterations, markers of bone metabolism (urinary N-telopeptide and bone-specific alkaline phosphatase), pain improvements, and progression-free survival. To illustrate the role and challenges of these potential biomarkers and endpoints in drug development, we discuss a class of novel molecularly targeted agents, the src kinase inhibitors. Given that there are currently no validated surrogate markers of overall survival for assessing early clinical benefit from systemic therapy in metastatic CRPC, incorporation of relevant biomarkers into all phases of clinical development is essential to accelerate drug development in this field.
    MeSH term(s) Biomarkers, Tumor/metabolism ; Disease-Free Survival ; Humans ; Male ; Neoplasms, Hormone-Dependent/metabolism ; Neoplasms, Hormone-Dependent/pathology ; Neoplasms, Hormone-Dependent/therapy ; Orchiectomy ; Prostate-Specific Antigen/metabolism ; Prostatic Neoplasms/metabolism ; Prostatic Neoplasms/pathology ; Prostatic Neoplasms/therapy
    Chemical Substances Biomarkers, Tumor ; Prostate-Specific Antigen (EC 3.4.21.77)
    Language English
    Publishing date 2009-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1409038-7
    ISSN 1549-490X ; 1083-7159
    ISSN (online) 1549-490X
    ISSN 1083-7159
    DOI 10.1634/theoncologist.2009-0043
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    Zs.A 4845: Show issues Location:
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    Zs.MO 494: Show issues

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  10. Article ; Online: Predictive Biomarkers of Overall Survival in Patients with Metastatic Renal Cell Carcinoma Treated with IFNα ± Bevacizumab: Results from CALGB 90206 (Alliance).

    Nixon, Andrew B / Halabi, Susan / Liu, Yingmiao / Starr, Mark D / Brady, John C / Shterev, Ivo / Luo, Bin / Hurwitz, Herbert I / Febbo, Phillip G / Rini, Brian I / Beltran, Himisha / Small, Eric J / Morris, Michael J / George, Daniel J

    Clinical cancer research : an official journal of the American Association for Cancer Research

    2021  Volume 28, Issue 13, Page(s) 2771–2778

    Abstract: Purpose: CALGB 90206 was a phase III trial of 732 patients with metastatic renal cell carcinoma (mRCC) comparing bevacizumab plus IFNα (BEV + IFN) with IFNα alone (IFN). No difference in overall survival (OS) was observed. Baseline samples were analyzed ...

    Abstract Purpose: CALGB 90206 was a phase III trial of 732 patients with metastatic renal cell carcinoma (mRCC) comparing bevacizumab plus IFNα (BEV + IFN) with IFNα alone (IFN). No difference in overall survival (OS) was observed. Baseline samples were analyzed to identify predictive biomarkers for survival benefit.
    Patients and methods: A total of 32 biomarkers were assessed in 498 consenting patients randomly assigned into training (n = 279) and testing (n = 219) sets. The proportional hazards model was used to test for treatment arm and biomarker interactions of OS. The estimated coefficients from the training set were used to compute a risk score for each patient and to classify patients by risk in the testing set. The resulting model was assessed for predictive accuracy using the time-dependent area under the ROC curve (tAUROC).
    Results: A statistically significant three-way interaction between IL6, hepatocyte growth factor (HGF), and bevacizumab treatment was observed in the training set and confirmed in the testing set (P < 0.0001). The model based on IL6, HGF, and bevacizumab treatment was predictive of OS (P < 0.001), with the high- and low-risk groups having a median OS of 10.2 [95% confidence interval (CI), 8.0-13.8] and 34.3 (95% CI, 28.5-40.5) months, respectively. The average tAUROC for the final model of OS based on 100 randomly split testing sets was 0.78 (first, third quartiles = 0.77, 0.79).
    Conclusions: IL6 and HGF are potential predictive biomarkers of OS benefit from BEV + IFN in patients with mRCC. The model based on key biological and clinical factors demonstrated predictive efficacy for OS. These markers warrant further validation in future anti-VEGF and immunotherapy in mRCC trials. See related commentaries by Mishkin and Kohn, p. 2722 and George and Bertagnolli, p. 2725.
    MeSH term(s) Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Bevacizumab/adverse effects ; Biomarkers ; Carcinoma, Renal Cell/drug therapy ; Carcinoma, Renal Cell/mortality ; Disease-Free Survival ; Genotype ; Humans ; Interferon-alpha/administration & dosage ; Interleukin-6 ; Kidney Neoplasms/pathology ; Phenotype
    Chemical Substances Biomarkers ; Interferon-alpha ; Interleukin-6 ; Bevacizumab (2S9ZZM9Q9V)
    Language English
    Publishing date 2021-12-29
    Publishing country United States
    Document type Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Journal Article
    ZDB-ID 1225457-5
    ISSN 1557-3265 ; 1078-0432
    ISSN (online) 1557-3265
    ISSN 1078-0432
    DOI 10.1158/1078-0432.CCR-21-2386
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