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https://www.readbyqxmd.com/read/28821015/extracting-replicable-associations-across-multiple-studies-empirical-bayes-algorithms-for-controlling-the-false-discovery-rate
#1
David Amar, Ron Shamir, Daniel Yekutieli
In almost every field in genomics, large-scale biomedical datasets are used to report associations. Extracting associations that recur across multiple studies while controlling the false discovery rate is a fundamental challenge. Here, we propose a new method to allow joint analysis of multiple studies. Given a set of p-values obtained from each study, the goal is to identify associations that recur in at least k > 1 studies while controlling the false discovery rate. We propose several new algorithms that differ in how the study dependencies are modeled, and compare them and extant methods under various simulated scenarios...
August 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28820986/an-ultrasensitive-sandwich-type-electrochemical-immunosensor-based-on-the-signal-amplification-strategy-of-echinoidea-shaped-au-ag-cu2o-nanoparticles-for-prostate-specific-antigen-detection
#2
Yuying Yang, Qin Yan, Qing Liu, Yongpeng Li, Hui Liu, Ping Wang, Lei Chen, Daopeng Zhang, Yueyun Li, Yunhui Dong
Highly sensitive determination of tumor markers plays an important role in early diagnosis of cancer. Herein, a novel and ultrasensitive sandwich-type electrochemical immunosensor was fabricated for quantitative detection of prostate specific antigen (PSA). In this process, gold nanoparticles functionalized nitrogen-doped graphene quantum dots (Au@N-GQDs) was synthesized through a simple and green hydrothermal procedure to enhance conductivity, specific electrode surface area and quantity of immobilized primary antibodies (Ab1)...
August 10, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28820958/erratum-to-mass-spectrometric-detection-combined-with-bioinformatic-analysis-identified-possible-protein-markers-and-key-pathways-associated-with-bladder-cancer-gene-626c-2017-407-413
#3
Ziyu Wu, Sugui Wang, Fujin Jiang, Qiang Li, Chao Wang, Huanqiang Wang, Wei Zhang, Peng Xue, Shou-Lin Wang
No abstract text is available yet for this article.
August 15, 2017: Gene
https://www.readbyqxmd.com/read/28820953/a-fluorescence-based-high-throughput-assay-for-the-identification-of-anticancer-reagents-targeting-fructose-1-6-bisphosphate-aldolase
#4
Eun Jeong Cho, Ashwini K Devkota, Gabriel Stancu, Ramakrishna Edupunganti, Garth Powis, Kevin N Dalby
A high rate of glycolysis, which supplies energy and materials for anabolism, is observed in a wide range of tumor cells, making it a potential pathway to control cancer growth. ALDOA is a multifunctional enzyme in the glycolytic pathway and also promotes HIF-1α, which is of importance in hypoxic solid tumors. The current method for assaying ALDOA activity involves monitoring the consumption of NADH in vitro using absorbance or intrinsic fluorescence via a coupled enzymatic reaction. Here, we report the development of a homogeneous biochemical assay that can overcome limitations of current methods, in particular for the application of high-throughput drug screening...
August 1, 2017: SLAS Discovery
https://www.readbyqxmd.com/read/28820578/integrated-microfluidic-platform-with-multiple-functions-to-probe-the-tumor-endothelial-cell-interaction
#5
Ling Lin, Xuexia Lin, Luyao Lin, Qiang Feng, Takehiko Kitamori, Jin-Ming Lin, Jiashu Sun
Interaction between tumor and endothelial cells could affect tumor growth and progression, and induce drug resistance during cancer therapy. Investigation on tumor-endothelial cell interaction involves cell co-culture, protein detection, and analysis of drug metabolites, which are complicated and time-consuming. In this work, we present an integrated microfluidic device with three individual components (the cell co-culture component, the protein detection component, and the pre-treatment component for drug metabolites) to probe the interaction between tumor and endothelial cells...
August 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28820390/small-molecule-inhibitors-of-dna-pk-for-tumor-sensitization-to-anticancer-therapy
#6
M Pospisilova, M Seifrtova, M Rezacova
The most sensitive cell structure - a DNA molecule, is the common target of cancer therapy. DNA damage response (controlled by enzymes from the phosphatidylinositol 3-kinase-related kinases family - PIKK) presents many encouraging targets for improving both conventional cytotoxic anticancer therapy and individualized monotherapy. DNA-dependent protein kinase (DNA-PK) is a member of the PIKK superfamily and plays an important role in the detection and repair of DNA double-strand breaks via the non-homologous end-joining pathway...
June 2017: Journal of Physiology and Pharmacology: An Official Journal of the Polish Physiological Society
https://www.readbyqxmd.com/read/28820329/sources-to-variability-in-circulating-human-mirna-signatures
#7
Andreas Keller, Trine Rounge, Christina Backes, Nicole Ludwig, Randi Gislefoss, Petra Leidinger, Hilde Langseth, Eckart Meese
An increasing number of studies propose circulating microRNAs (miRNAs) as biomarkers for a large number of human diseases including cancer, cardiovascular diseases, neurological pathologies and others. To further validate miRNA as biomarkers it is indispensable to understand the variability of circulating miRNAs in healthy individuals. We determined the longitudinal miRNomes of 90 serum samples from the Janus Serum Bank in Norway, which have been stored between 23 and 40 years at -25 degrees Celsius. We profiled three serum samples with microarrays for 30 individuals, each...
August 18, 2017: RNA Biology
https://www.readbyqxmd.com/read/28820223/a-dual-modal-silver-bumpy-nanoprobe-for-photoacoustic-imaging-and-sers-multiplexed-identification-of-in-vivo-lymph-nodes
#8
Myeong Geun Cha, Seunghyun Lee, Sungjo Park, Homan Kang, Sung Gun Lee, Cheolhwan Jeong, Yoon-Sik Lee, Chulhong Kim, Dae Hong Jeong
Multimodal imaging can provide complementary biomedical information which has huge potential in pre-clinical and clinical imaging and sensing. In this study, we introduce dual modal NIR silver bumpy nanoprobes for in vivo imaging and multiplexed detection of biomolecules by both photoacoustic imaging (PAI) and surface-enhanced Raman scattering (SERS) techniques. For this study, we used silica-coated silver bumpy nanoshell probes (AgNS@SiO2). AgNS@SiO2 have strong NIR-absorption and scattering properties compared with other nanostructures, and therefore, can be a good candidate for photoacoustic (PA) and SERS multimodal imaging...
August 18, 2017: Nanoscale
https://www.readbyqxmd.com/read/28819937/the-presence-of-a5935g-g5949a-g6081a-g6267a-t9540c-mutations-in-mt-co1-and-mt-co3-genes-and-other-variants-of-mt-co1-and-mt-co3-gene-fragments-in-the-study-population-diagnosed-with-endometrial-cancer
#9
Kinga Księżakowska-Łakoma, Dominika Kulczycka-Wojdala, Andrzej Kulig, Marcin Baum, Jacek Radosław Wilczyński
OBJECTIVES: The specific purpose of this study was the assessment of A5935G, G5949A, G6081A, G6267A mutations in MT-CO1 and T9540C in MT-CO3, and alterations detected during the analysis of MT-CO gene fragments in subject and control groups. A secondary aim was to assess the relationship between MT-CO1 and MT-CO3 gene alterations and endometrial cancer incidence and evaluation of the prognostic value of MT-CO1 and MT-CO3 gene alterations. MATERIAL AND METHODS: In this study, we investigated A5935G, G5949A, G6081A, G6267A mutations in MT-CO1 and T9540C in MT-CO3, and alterations detected during the analysis of MT-CO gene fragments in formalin-fixed, paraffin-embedded endometrial and benign endometrial hyperplasia of a cohort of 125 subjects...
2017: Ginekologia Polska
https://www.readbyqxmd.com/read/28819909/adjunctive-breast-specific-gamma-imaging-for-detecting-cancer-in-women-with-calcifications-at-mammography
#10
Hyun Woo Chung, Young So, Jung-Hyun Yang, Kyoung Sik Park, Young Bum Yoo, Nami Choi, Mi Young Kim, Jayoun Kim, Eun Jeong Lee
BACKGROUND: Mammography detects calcium deposits sensitively, but the specificity for differentiating malignancy from benign calcifications is low. Thus, we investigated whether adjunctive breast-specific gamma imaging (BSGI) has incremental value for detecting cancer in women with suspicious calcifications detected by mammography, and compared BSGI with adjunctive ultrasonography (US). METHODS: The medical records of women without a personal history of breast cancer who underwent mammography for breast evaluation from 2009 to 2014 were reviewed retrospectively...
August 17, 2017: Annals of Surgical Oncology
https://www.readbyqxmd.com/read/28819868/one-level-step-section-histological-analysis-is-insufficient-to-confirm-complete-pathological-response-after-neoadjuvant-chemoradiation-for-rectal-cancer
#11
M A Pereira, A R Dias, S F Faraj, C S R Nahas, A R Imperiale, C F S Marques, G C Cotti, B C Camargo, S C Nahas, E S de Mello, U Ribeiro
BACKGROUND: Neoadjuvant chemoradiation therapy (nCRT) for rectal cancer may lead to cure. As we currently lack reliable methods to clinically confirm the absence of disease, some patients undergo radical resection and have pathological complete response (pCR) still undergo surgery. Furthermore, it is uncertain if conventional one-level histopathological analysis is accurate enough to determine complete response. Confirming pCR is essential to determine the prognosis and to consider the patient's inclusion in trials of adjuvant therapy...
August 17, 2017: Techniques in Coloproctology
https://www.readbyqxmd.com/read/28819860/circulating-tumor-cells-markers-and-methodologies-for-enrichment-and-detection
#12
M J Alvarez Cubero, J A Lorente, I Robles-Fernandez, A Rodriguez-Martinez, J L Puche, M J Serrano
Cancer is a leading cause of disease worldwide; however, nowadays many points of its initiation processes are unknown. In this chapter, we are focusing on the role of liquid biopsies in cancer detection and progression. CTCs are one of the main components of liquid biopsies, they represent a subset of tumor cells that have acquired the ability to disseminate from the primary tumor and intravasate to the circulatory system. The greatest challenge in the detection of CTCs is their rarity in the blood. Human blood consists of white blood cells (5-10 × 10(6)/mL), red blood cells (5-9 × 10(9)/mL), and platelets (2...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28819859/utilizing-matrigel-transwell-invasion-assay-to-detect-and-enumerate-circulating-tumor-cells
#13
Xingtong Liu, Xiangwei Wu
Metastasis is the cause of 90% of human cancer deaths. Circulating tumor cells (CTCs) in the peripheral blood and/or lymphatic vessels are cells shed from primary tumors and considered to be precursors of metastasis. Study of CTCs allows the serial monitoring of tumor progression and may provide predictive and prognostic biomarkers in clinic. Current CTC isolation and detection technologies encounter several challenges, including: heterogeneity of CTCs, low cell viability and/or high rate of contamination post-isolation, and the inability to distinguish viable/invasive from nonviable/nonfunctional CTCs, all of which can limit in vitro and in vivo characterization of CTCs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28819858/epcam-independent-enrichment-and-detection-of-viable-circulating-tumor-cells-using-the-epispot-assay
#14
Alexandra Soler, Laure Cayrefourcq, Martine Mazel, Catherine Alix-Panabières
Identification and characterization of circulating tumor cells (CTCs) in peripheral blood can provide information on the direction and the efficacy of treatments. Current techniques such as CellSearch(®) are limited in differentiating between apoptotic and viable CTCs. In contrast, the fluorescent EPISPOT assay allows for the identification of viable cells by detecting proteins secreted/released/shed by functional single epithelial cancer cells. In addition, as CTCs are rare events, it is required to combine the EPISPOT assay with an enrichment step...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28819857/a-noninvasive-and-real-time-method-for-circulating-tumor-cell-detection-by-in-vivo-flow-cytometry
#15
Xunbin Wei, Jian Zhou, Xi Zhu, Xinrong Yang, Ping Yang, Qiyan Wang
The quantification of circulating tumor cells (CTCs) has been considered a potentially powerful tool in cancer diagnosis and prognosis, as CTCs have been shown to appear very early in cancer development. Great efforts have been made to develop methods that were less invasive and more sensitive to detect CTCs earlier. There is growing evidence that CTC clusters have greater metastatic potential than single CTCs. Therefore, the detection of CTC clusters is also important. This chapter is aimed to introduce a noninvasive technique for CTCs detection named in vivo flow cytometry (IVFC), which has been demonstrated to be capable of monitoring CTCs dynamics continuously...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28819856/fiber-optic-array-scanning-technology-fast-for-detection-and-molecular-characterization-of-circulating-tumor-cells
#16
Zheng Ao, Xiaohe Liu
Circulating tumor cell (CTC) as an important component in "liquid biopsy" holds crucial clinical relevance in cancer prognosis, treatment efficiency evaluation, prediction and potentially early detection. Here, we present a Fiber-optic Array Scanning Technology (FAST) that enables antigen-agnostic, size-agnostic detection of CTC. By immunofluorescence staining detection of a combination of a panel of markers, FAST technology can be applied to detect rare CTC in non-small cell lung cancer (NSCLC) setting with high sensitivity and specificity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28819854/flow-cytometric-detection-of-circulating-tumor-cells-using-a-candidate-stem-cell-marker-p75-neurotrophin-receptor-p75ntr
#17
Tomoyuki Okumura, Tetsuji Yamaguchi, Toru Watanabe, Takuya Nagata, Yutaka Shimada
The most widely studied detection for circulating tumor cells (CTCs) in peripheral blood of cancer patients has been based on immunomagnetic enrichment using antibodies against epithelial cell adhesion molecule (EpCAM), which is overexpressed in epithelial cells. A neurotrophin receptor p75 (p75NTR) is expressed in a candidate stem cell fraction in esophageal squamous cell carcinoma (ESCC), which shows significantly higher colony formation, enhanced tumor formation in mice, along with strong expression of epithelial mesenchymal transition-related genes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28819845/automated-microfluidic-filtration-and-immunocytochemistry-detection-system-for-capture-and-enumeration-of-circulating-tumor-cells-and-other-rare-cell-populations-in-blood
#18
Michael Pugia, Mark Jesus M Magbanua, John W Park
Isolation by size using a filter membrane offers an antigen-independent method for capturing rare cells present in blood of cancer patients. Multiple cell types, including circulating tumor cells (CTCs), captured on the filter membrane can be simultaneously identified via immunocytochemistry (ICC) analysis of specific cellular biomarkers. Here, we describe an automated microfluidic filtration method combined with a liquid handling system for sequential ICC assays to detect and enumerate non-hematologic rare cells in blood...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28819839/a-novel-microfluidic-device-for-isolation-of-circulating-tumor-cells-from-pancreatic-cancer-blood-samples
#19
Jose I Varillas, Kangfu Chen, Jinling Zhang, Thomas J George, Z Hugh Fan
Enumeration of circulating tumor cells (CTCs) can provide valuable prognostic information to guide cancer treatment as well as help monitor disease progression. Analysis of these rare malignant cells has the potential to further our understanding of cancer metastasis by gaining insights into CTC characteristics and properties. Microfluidics presents a unique platform to isolate and study CTCs. In this chapter, we describe the detailed procedures for the fabrication and use of a microfluidic device to detect CTCs from the blood of pancreatic cancer patients...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28819833/-lymphocytic-myocarditis-in-a%C3%A2-patient-with-metastatic-clear-cell-renal-cell-carcinoma-treated-with-nivolumab
#20
R Sauer, P Kiewe, M Desole, M Schuler, F Theissig, A Roth, T Mairinger
Immune checkpoint inhibitors against the PD-1 protein offer a new therapy option for many solid cancers. We report a patient with metastatic renal cell cancer treated with Nivolumab. As a rare immune-mediated adverse event, we describe a fatal lymphocytic myocarditis two weeks after starting immune therapy. The cause of death was first diagnosed at autopsy. This case report underlines the importance and need of clinical autopsies as an instrument of quality assurance and detection of rare therapy-induced adverse effects...
August 17, 2017: Der Pathologe
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