Relevant bibliographies by topics / Tissue microarray

Academic literature on the topic 'Tissue microarray'

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Published: 4 June 2021
Last updated: 11 March 2023

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Journal articles on the topic "Tissue microarray"

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Yang, Jun, Mingjuan Zhang, Baoshan Su, XiaoLi Chen, and AnJing Kang. "A novel tissue microarray instrumentation:The HT-1 tissue microarrayer." Indian Journal of Pathology and Microbiology 55, no. 3 (2012): 314. http://dx.doi.org/10.4103/0377-4929.101736.

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Barrette, Kathleen, Joost J. van den Oord, and Marjan Garmyn. "Tissue Microarray." Journal of Investigative Dermatology 134, no. 9 (September 2014): 1–4. http://dx.doi.org/10.1038/jid.2014.277.

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Roszkowiak, Lukasz, and Carlos Lopez. "PATMA: parser of archival tissue microarray." PeerJ 4 (December 1, 2016): e2741. http://dx.doi.org/10.7717/peerj.2741.

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The tissue microarrays are commonly used in modern pathology for cancer tissue evaluation, as it is a very potent technique. Tissue microarray slides are often scanned to perform computer-aided histopathological analysis of the tissue cores. For processing the image, splitting the whole virtual slide into images of individual cores is required. The only way to distinguish cores corresponding to specimens in the tissue microarray is through their arrangement. Unfortunately, distinguishing the correct order of cores is not a trivial task as they are not labelled directly on the slide. The main aim of this study was to create a procedure capable of automatically finding and extracting cores from archival images of the tissue microarrays. This software supports the work of scientists who want to perform further image processing on single cores. The proposed method is an efficient and fast procedure, working in fully automatic or semi-automatic mode. A total of 89% of punches were correctly extracted with automatic selection. With an addition of manual correction, it is possible to fully prepare the whole slide image for extraction in the mean time of 2 min per tissue microarray. The proposed technique requires minimum skill and time to parse big array of cores from tissue microarray whole slide image into individual core images.
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Kaur, Rashmeet, Nagaraja A, Richa Bansal, Sujata Saxena, and Bhavana Rai. "Tissue microarray- A review." International Journal of Oral Health Dentistry 4, no. 3 (October 15, 2018): 152–55. http://dx.doi.org/10.18231/2395-499x.2018.0035.

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Kim, Woo Ho. "High-Density Tissue Microarray." American Journal of Surgical Pathology 26, no. 9 (September 2002): 1236–37. http://dx.doi.org/10.1097/00000478-200209000-00017.

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Rubin, Mark A., and Rodney L. Dunn. "High-Density Tissue Microarray." American Journal of Surgical Pathology 26, no. 9 (September 2002): 1237–38. http://dx.doi.org/10.1097/00000478-200209000-00018.

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Page, Robert N., Roy King, and Paul B. Googe. "Tissue Microarray in Melanoma." Journal of Histotechnology 26, no. 4 (December 2003): 271–74. http://dx.doi.org/10.1179/his.2003.26.4.271.

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Packeisen, J. "Demystified ... Tissue microarray technology." Molecular Pathology 56, no. 4 (August 1, 2003): 198–204. http://dx.doi.org/10.1136/mp.56.4.198.

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Jiang, Hui-Yong, Xue-Feng Zhang, Li Liu, Hui-Ling Li, and Tong Zhao. "A novel tissue array technique for high-throughput tissue microarray analysis — microarray groups." In Vitro Cellular & Developmental Biology - Animal 43, no. 3-4 (May 21, 2007): 109–12. http://dx.doi.org/10.1007/s11626-007-9019-3.

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Rangel, Catherine Starrs. "The Tissue Microarray: Helpful Hints!" Journal of Histotechnology 25, no. 2 (June 2002): 93–100. http://dx.doi.org/10.1179/his.2002.25.2.93.

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Dissertations / Theses on the topic "Tissue microarray"

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Amaral, Telmo. "Analysis of breast tissue microarray spots." Thesis, University of Dundee, 2010. https://discovery.dundee.ac.uk/en/studentTheses/0a83915d-2f11-4b89-9c24-8dc3c15346f2.

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Tissue microarrays (TMAs) are a high-throughput technique that facilitates the survey of very large numbers of tumours, important both in clinical and research applications. However, the assessment of stained TMA sections is laborious and still needs to be carried manually, constituting a bottleneck in the pathologist?s work-flow. This process is also prone to perceptual errors and observer variability.Thus, there is strong motivation for the development of automated quantitative analysis of TMA image data. The analysis of breast TMA sections subjected to nuclear immunostaining begins with the classification of each spot as to the maintype of tissue that it contains, namely tumour, normal, stroma, or fat. Tumour and normal spots are then assigned a so-called quickscore composed of a pair or integer values, the first reflecting the proportion of epithelial nuclei that are stained, and the second reflecting the strength of staining of those nuclei. In this work, an approach was developed to analyse breast TMA spots subjectedto progesterone receptor immunohistochemistry. Spots were classified into their four main types through a method that combined a bag of features approachand classifiers based on either multi-layer perceptrons or latent Dirichlet allocation models. A classification accuracy of 74.6 % was achieved. Tumour and normal spots were scored via an approach that involved the computation of global features formalising the quickscore values used by pathologists, and the use of Gaussian processes for ordinal regression to predict actual quickscores based on global features. Mean absolute errors of 0.888 and 0.779 were achieved in the prediction of the first and second quickscore values, respectively. By setting thresholds on prediction confidence, it was possible to classify and score fractions of spots with substantially higher accuracies and lower mean absolute errors. Amethod for the segmentation of TMA spots into regions of different types was also investigated, to explore the generative nature of latent Dirichlet allocation models.
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Nguyễn, Hoài Nam. "Méthodes et algorithmes de segmentation et déconvolution d'images pour l'analyse quantitative de Tissue Microarrays." Thesis, Rennes 1, 2017. http://www.theses.fr/2017REN1S104/document.

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Ce travail de thèse a pour objectif de développer les méthodes originales pour l'analyse quantitative des images de Tissue Microarrays (TMAs) acquises en fluorescence par des scanners dédiés. Nous avons proposé des contributions en traitement d'images portant sur la segmentation des objets d'intérêts (i.e. des échantillons de tissus sur la lame de TMA scannée), la correction des artefacts d'acquisition liés aux scanners en question ainsi que l'amélioration de la résolution spatiale des images acquises en tenant compte des modalités d'acquisition (imagerie en fluorescence) et la conception des scanners. Les développements permettent d'envisager une nouvelle plateforme d'analyse de TMAs automatisée, qui représente aujourd'hui une forte demande dans la recherche contre les cancers. Les TMAs (ou “puces à tissus”) sont les lames histologiques sur lesquelles de nombreux échantillons tissulaires venant de différents donneurs sont déposés selon une structure de grille afin de faciliter leur identification. Pour pouvoir établir le lien entre chaque échantillon et ses données cliniques correspondantes, on s'intéresse non seulement à segmenter ces échantillons mais encore à retrouver leur position théorique (les indices de ligne et de colonne) sur la grille TMA car cette dernière est souvent très déformée pendant la fabrication des lames. Au lieu de calculer directement les indices de ligne et de colonne (des échantillons), nous avons reformulé ce problème comme un problème d'estimation de la déformation de la grille de TMA théorique à partir du résultat de segmentation en utilisant l'interpolation par splines ''plaques minces''. Nous avons combiné les ondelettes et un modèle d'ellipses paramétriques pour éliminer les fausses alarmes, donc améliorer les résultats de segmentation. Selon la conception des scanners, les images sont acquises pixel par pixel le long de chaque ligne, avec un change de direction lors du balayage entre les deux lignes. Un problème fréquent est le mauvais positionnement des pixels dû à la mauvaise synchronisation des modules mécaniques et électroniques. Nous avons donc proposé une méthode variationnelle pour la correction de ces artefacts en estimant le décalage entre les pixels sur les lignes consécutives. Cette méthode, inspirée du calcul du flot optique, consiste à estimer un champ de vecteurs en minimisant une fonction d'énergie composée d'un terme d'attache aux données non convexe et d'un terme de régularisation convexe. La relaxation quadratique est ainsi utilisée pour découpler le problème original en deux sous-problèmes plus simples à résoudre. Enfin, pour améliorer la résolution spatiale des images acquises qui dépend de la PSF (point spread function) elle-même variant selon le faisceau laser d'excitation, nous avons introduit une méthode de déconvolution d'images en considérant une famille de régulariseurs convexes. Les régulariseurs considérés sont généralisés du concept de la variation parcimonieuses (Sparse Variation) combinant la norme L1 de l'image et la variation totale (Total Variation) pour rehausser les pixels dont l'intensité et le gradient sont non-nuls. Les expériences montrent que l'utilisation de cette régularisation produit des résultats déconvolution d'images très satisfaisants en comparaison avec d'autres approches telles que la variation totale ou la norme de Schatten de la matrice Hessienne
This thesis aims at developing dedicated methods for quantitative analysis of Tissue Microarray (TMA) images acquired by fluorescence scanners. We addressed there issues in biomedical image processing, including segmentation of objects of interest (i.e. tissue samples), correction of acquisition artifacts during scanning process and improvement of acquired image resolution while taking into account imaging modality and scanner design. The developed algorithms allow to envisage a novel automated platform for TMA analysis, which is highly required in cancer research nowadays. On a TMA slide, multiple tissue samples which are collected from different donors are assembled according to a grid structure to facilitate their identification. In order to establish the link between each sample and its corresponding clinical data, we are not only interested in the localization of these samples but also in the computation of their array (row and column) coordinates according to the design grid because the latter is often very deformed during the manufacturing of TMA slides. However, instead of directly computing array coordinates as existing approach, we proposed to reformulate this problem as the approximation of the deformation of the theoretical TMA grid using “thin plate splines” given the result of tissue sample localization. We combined a wavelet-based detection and a ellipse-based segmentation to eliminate false alarms and thus improving the localization result of tissue samples. According to the scanner design, images are acquired pixel by pixel along each line, with a change of scan direction between two subsequent lines. Such scanning system often suffers from pixel mis-positioning (jitter) due to imperfect synchronization of mechanical and electronic components. To correct these scanning artifacts, we proposed a variational method based on the estimation of pixel displacements on subsequent lines. This method, inspired from optical flow methods, consists in estimating a dense displacement field by minimizing an energy function composed of a nonconvex data fidelity term and a convex regularization term. We used half-quadratic splitting technique to decouple the original problem into two small sub-problems: one is convex and can be solved by standard optimization algorithm, the other is non-convex but can be solved by a complete search. To improve the resolution of acquired fluorescence images, we introduced a method of image deconvolution by considering a family of convex regularizers. The considered regularizers are generalized from the concept of Sparse Variation which combines the L1 norm and Total Variation (TV) to favors the co-localization of high-intensity pixels and high-magnitude gradient. The experiments showed that the proposed regularization approach produces competitive deconvolution results on fluorescence images, compared to those obtained with other approaches such as TV or the Schatten norm of Hessian matrix
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Sievertzon, Maria. "Transcript profiling of small tissue samples using microarray technology." Doctoral thesis, Stockholm Department of Biotechnology, Royal Institute of Technology, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-158.

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Cheng, Yabin. "Tissue microarray based biomarker study in human cutaneous melanoma." Thesis, University of British Columbia, 2014. http://hdl.handle.net/2429/46655.

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Cancer therapy recently experienced remarkable advances with better understanding of cancer pathogenesis and introduction of new intervention strategies. Biomarkers reflective of the presence of tumor cells, or linked with clinical outcomes, have potential to improve the management of cancers. The purpose of this thesis study is to identify novel biomarkers of human cancers based on tissue microarray (TMA) technology and to determine their value for clinical application in cancer management using melanoma as the model. Melanoma arises from uncontrolled proliferation of melanocytes. Although melanoma accounts for only 4% of all skin cancer, it is responsible for 80% of deaths related to skin malignancies. To discover novel biomarkers of melanoma, we constructed a TMA using biopsies from 707 patients with various stages of melanocytic lesions. Using immunohistochemistry and TMA, multiple biomarker candidates were evaluated, and many were found to have significant prognostic value, including expression loss of Fbw7. To further improve the clinical value of these markers, various combinations of individual markers were evaluated, leading to the identification of KAI1 and p27 that together showed much stronger prognostic value than when used as individual markers. Moreover, since there has been a dearth of reliable prognostic markers to offer prognostic information on specific melanoma stages, we identified the AJCC-stage specific prognostic markers, including BRAF protein expression as a prognostic marker for thin melanomas. In that significant prognostic value was found for Fbw7 protein in melanoma, we performed in vitro experiments on this protein in detail. Our data showed that the alpha isoform of Fbw7, located in the cell nucleus, was the dominant form expressed in melanoma. Knock-down of Fbw7α promoted melanoma cell migration, and the MAPK signaling pathway was required for Fbw7 function in melanoma. These findings indicate loss of Fbw7 to be an independent melanoma prognostic marker, and important for the development of malignant behaviors of melanoma cells. This study has demonstrated that the combination of TMAs of cancers with the corresponding clinical database represents a powerful technological platform for biomarker discovery. TMA/clinical database combination-based investigations should be applicable for the investigation of other types of human cancers as well.
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Xie, Dan, and 謝丹. "Application of high-throughput tissue microarray technology in cancer research." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B30283619.

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Mckenzie, Gavin Medical Sciences Faculty of Medicine UNSW. "The analysis of signalling pathways in sporadic colorectal carcinoma using tissue microarrays." Publisher:University of New South Wales. Medical Sciences, 2008. http://handle.unsw.edu.au/1959.4/43370.

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Colorectal carcinoma arises through sequential genetic changes whereby an adenoma develops from normal colonic epithelium and then becomes a carcinoma. Critical to this process is two forms of mutually exclusive genomic instability ?? chromosomal instability (CIN) and microsatellite instability (MSI). The colorectal tumours that develop from each of these pathways have distinct pathological and molecular differences. Most MSI+ colorectal carcinomas are associated with the CpG island methylator phenotype (CIMP) - an epigenetic phenomenon where a specific and consistent group of genes are silenced through promoter methylation. However, over half of fall CIMP+ colorectal tumours are microsatellite stable (MSS). It is well known that the WNT/β-catenin signalling pathway is instrumental in the initiation and development of CIN type tumours but it is less clear whether this pathway has any significant involvement in MSI+ or methylated tumours. The role of the PI3K1AKT signalling pathway in the development of solid human tumours has only recently been established and the affects of abnormal PI3K/AKT signalling in sporadic colorectal carcinomas is yet to be fully elucidated. The objective of this thesis was to investigate the involvement of the WNT/β-catenin and PI3K/AKT signalling pathways in the CIN, MSI+ and methylated subgroups of sporadic colorectal carcinoma. To achieve this, the expression patterns of β-catenin, p-AKT and PTEN were identified by immunohistochemistry on sections from tissue microarrays consisting of cores from a large group of sporadic colorectal carcinomas. Each of these proteins is an integral part of the constitutive activation of WNT/β-catenin or PI3K/AKT signalling and their expression patterns were correlated with the clinical, pathological and molecular characteristics of the different subgroups of colorectal carcinoma. Increased nuclear β-catenin expression, an indicator of activated WNT signalling, is associated with MSS and the pathological features of CIN type tumours and inversely associated with the pathological and molecular features of MSI+ and CIMP+ tumours. In all forms of sporadic colorectal carcinoma, nuclear β-catenin expression was not an indicator of overall survival. PTEN was not associated with any particular subgroup of sporadic colorectal carcinoma, but decreased cytoplasmic expression was indicative of overall worse outcome, especially in MSS or CIN type tumours. While the identification of nuclear β-catenin in sporadic colorectal carcinomas is not a satisfactory prognostic marker, the immunohistochemical detection of absent PTEN expression may prove useful in identifying poor outcome in individuals with sporadic MSS colorectal carcinoma.
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Jernås, Margareta. "Microarray analysis of gene expression in human adipocytes and adipose tissue /." Göteborg : Institute of Medicine, Dept. of Molecular and Clinical Medicine, Sahlgrenska Academy, Göteborg University, 2008. http://hdl.handle.net/2077/9583.

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PANSINI, P. F. "Potencial Prognóstico da Survivina em Carcinoma Epidermóide da Cavidade Bucal." Universidade Federal do Espírito Santo, 2017. http://repositorio.ufes.br/handle/10/7104.

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Made available in DSpace on 2018-08-01T21:35:01Z (GMT). No. of bitstreams: 1 tese_10831_122ª Ata de Defesa - Paola Fernandes Pansini.PDF: 76 bytes, checksum: e777df9eb60d248d167e2edfa6e23421 (MD5) Previous issue date: 2017-02-15
O carcinoma epidermóide de cabeça e pescoço (CECP) é o sexto tipo de câncer mais comum em todo o mundo. Nos últimos anos, tem sido sugerida a participação da survivina na progressão tumoral em CECP. Este estudo teve como objetivo avaliar a survivina como potencial biomarcador de progressão tumoral em CECB. Foram utilizados no estudo dados clínicos e amostras biológicas de 115 indivíduos com carcinoma epidermóide da cavidade bucal. Lâminas contendo tecidos tumorais coradas pelo método hematoxilina e eosina foram usadas para as análises histopatológicas para avaliar o infiltrado linfocitário tumoral, padrão de invasão tumoral, gradação tumoral, invasão vascular, linfática e perineural. Tissue Microarrays foram construídos para realizar a análise imunohistoquímica da expressão da proteína survivina utilizando o anticorpo primário monoclonal de coelho anti-survivina. Para avaliar as associações entre as variáveis estudadas foram utilizados os testes Qui-Quadrado e o Exato de Fisher. A comparação das médias dos segmentos foi obtida pelo teste T de amostras independentes. As curvas de sobrevida foram calculadas pelo modelo de Kaplan-Meier e confirmadas pelo modelo multivariado de Cox. Nossos resultados mostraram existir correlação entre o infiltrado linfocitário tumoral alto, tamanho do tumor primário T1/T2 (p = 0,001) e estadiamento clínico I e II (p = 0,005). O padrão de invasão tumoral tipo IV foi correlacionado com o tamanho do tumor primário T3/T4 (p = 0,006) e estadiamento clínico avançado (estádio III e IV) (p = 0,028). Invasão perineural foi associada com o tamanho do tumor primário T1/T2 (p = 0,035). A expressão nuclear da survivina na porção mediana do tumor mostrou associação com a metástase em linfonodos regionais (p = 0,004) e o estadiamento clínico (p = 0,041). A análise regressiva multivariada confirmou que as variáveis tamanho do tumor primário (p = 0,004) e acometimento linfonodal (p= 0,06) são fatores prognósticos independentes para sobrevida global, enquanto o etilismo influencia na sobrevida livre de doença (p = 0,048). Com este estudo pode-se concluir que a elevada expressão da survivina está correlacionada com o comportamento tumoral mais agressivo, estadiamento clínico avançado, presença de mestástase linfonodal, podendo ser considerada como indicador de prognóstico em pacientes com CECB. A variável histopatológica padrão de invasão tumoral mostrou que sua correlação com tamanho do tumor primário e estadiamento clínico avançado podendo estar relacionada ao pior prognóstico dos pacientes em CECB.
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Foster, Cheryl June. "Identifying a prognostic test in follicular lymphoma using a tissue microarray and immunohistochemistry." Thesis, Kingston, Ont. : [s.n.], 2008. http://hdl.handle.net/1974/1296.

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Habibi, Golareh. "Y-box binding protein-1 (YB-1) is a bio-marker of aggressiveness in breast cancer and is a potential target for therapeutic intervention." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/911.

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Early detection is one of the most important factors for successful treatment of cancer. Currently, scientists are searching for molecular markers that can help identify and predict outcome and chance of recurrence in patients. In this study, we demonstratet he potential impact of Y-Box binding protein-1 (YB-1) as a marker of aggressiveness and cancer recurrence in breast malignancies by screening one of the largest tissue microarrays in North America. YB-1 is an oncogenic transcription/translation factor, which is over-expressed in the majority of malignancies, including breast cancer. In the cohort of 4049 primary breast tumours, we show that YB-1 is a strong marker of aggressiveness, poor survival and cancer recurrence in all subtypes of human breast cancer with a particularly high frequency of expression in the ER negative basal-like and HER-2 breast cancer subtypes. This suggests that targeting YB-1 may provide a new avenue for therapeutic intervention in these breast cancers that are currently challenging to treat. Cox regression multivariate analysis indicates that YB-1 is second only to nodal status as a strong independent prognostic marker for poor outcome and relapse compared to established clinico-pathological biomarkers, including tumour size, age, grade, ER and HER-2 status. This finding suggests that YB-1 has great potential to be in a priority list of biomarkers for identifying the patients with a higher risk of relapse and poor outcome. Subsequently, we find an association between YB-1 and urokinase Plasminogen Activator (uPA) expression in the basal-like subtype. We then show that YB-1 is involved in the regulation of uPA expression. More importantly, silencing YB-1 or uPA results in a significant reduction in cancer cell invasion. As there are no commercially available YB-linibitors we examine the efficacy of BMS-536924, a small molecule inhibitor for activated IGF-1R/IR on SUM149 cells. We demonstrate that activated IGF-1R is associated with poor survival in primary breast tumours and, that BMS-536924 reduces uPA expression through inhibition YB-1 in SUM149 cells. We therefore conclude that YB-1 is a bio-marker for poor survival and relapse. We also indicate that YB-1 has potential use as a molecular marker in a clinical setting. Inhibiting YB-1 may provide an ideal opportunity for targeted therapy in breast cancer.
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Books on the topic "Tissue microarray"

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-S, Liu Brian C., and Ehrlich Joshua R, eds. Tissue proteomics: Pathways, biomarkers, and drug discovery. Totowa, N.J: Humana Press, 2008.

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Simon, Ronald, ed. Tissue Microarrays. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-806-5.

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Tissue microarrays: Methods and protocols. New York, N.Y: Humana Press, 2010.

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Ehrlich, Joshua R., and Brian Liu. Tissue Proteomics: Pathways, Biomarkers, and Drug Discovery. Humana Press, 2010.

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Tissue proteomics: Pathways, biomarkers, and drug discovery. Totowa, N.J: Humana Press, 2008.

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Tissue Proteomics: Pathways, Biomarkers, and Drug Discovery (Methods in Molecular Biology). Humana Press, 2008.

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Simon, Ronald. Tissue Microarrays: Methods and Protocols. Humana Press, 2016.

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Hewitt, Stephen M. Tissue Microarrays: Methods and Applications (Methods in Molecular Biology). Humana Press, 2007.

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Zrazhevskiy, P., and X. Gao. Bioconjugated quantum dots for tumor molecular imaging and profiling. Edited by A. V. Narlikar and Y. Y. Fu. Oxford University Press, 2017. http://dx.doi.org/10.1093/oxfordhb/9780199533060.013.17.

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This article discusses the use of bioconjugated quantum dots (QDs) for tumor molecular imaging and profiling. The need for personalized diagnostics and therapy is becoming apparent in all areas of medicine, and especially urgent and sought after in treating cancer. Mechanisms of cancerogenesis and cancer response to therapy remain poorly understood, thus precluding accurate cancer diagnosis, prognosis, and effective treatment. Accurate molecular profiling of individual tumors is one key to effective treatment. This article first considers the photophysical properties of QDs before reviewing the most common methods for engineering QD-based probes for biomedical applications, including water solubilization and bioconjugation approaches. It also describes a number of techniques for molecular imagingand profiling of tumors, ranging from QD-based multicolor flow cytometry and applications of QDs in high-resolution correlated fluorescence/electron microscopy, QD bioprobes for molecular profiling of tumor-tissue sections and microarrays, and QD-oligonucleotide bioconjugates for in-situ hybridization.
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Book chapters on the topic "Tissue microarray"

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Wilkerson, Myra L., and Stephen M. Hewitt. "Tissue Microarray." In Handbook of Practical Immunohistochemistry, 105–17. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-1578-1_10.

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Wilkerson, Myra L., and Stephen Hewitt. "Tissue Microarray." In Handbook of Practical Immunohistochemistry, 161–72. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-83328-2_11.

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Wilkerson, Myra, and Erin Powell. "Tissue Microarray." In Handbook of Practical Immunohistochemistry, 45–54. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4419-8062-5_6.

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Faoro, Valentina, and Anna Sapino. "Tissue Microarray (TMA)." In Guidelines for Molecular Analysis in Archive Tissues, 23–26. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-17890-0_5.

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Koo, Matthew, Jill M. Squires, Daphne Ying, and Jiaoti Huang. "Making a Tissue Microarray." In Methods in Molecular Biology, 313–23. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8935-5_27.

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Korenberg, Michael J., Pedro Farinha, and Randy D. Gascoyne. "Predicting Survival in Follicular Lymphoma Using Tissue Microarrays." In Microarray Data Analysis, 255–68. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-390-5_16.

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Simon, Ronald. "Applications of Tissue Microarray Technology." In Methods in Molecular Biology, 1–16. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-806-5_1.

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Gaudreau, Pierre-Olivier, Isabelle Cousineau, and John Stagg. "Optimal CCN4 Immunofluorescence for Tissue Microarray." In Methods in Molecular Biology, 13–21. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2744-0_2.

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Saremi, Nassim, and Alfred K. Lam. "Application of Tissue Microarray in Esophageal Adenocarcinoma." In Methods in Molecular Biology, 105–18. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7734-5_10.

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Hu, Zhongting, Elbert Chang, and Melissa Hodeib. "An Alternative Technology to Prepare Tissue Microarray Using Frozen Tissue Samples." In Methods in Molecular Biology, 81–91. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-806-5_9.

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Conference papers on the topic "Tissue microarray"

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Can, Ali, Musodiq O. Bello, and Michael J. Gerdes. "Quantification of Subcellular Molecules in Tissue Microarray." In 2010 20th International Conference on Pattern Recognition (ICPR). IEEE, 2010. http://dx.doi.org/10.1109/icpr.2010.624.

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Wu, Jiahua, Junyu Dong, and Huiyu Zhou. "Image quantification of high-throughput tissue microarray." In Medical Imaging, edited by Armando Manduca and Amir A. Amini. SPIE, 2006. http://dx.doi.org/10.1117/12.653564.

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Amaral, T., S. McKenna, K. Robertson, and A. Thompson. "Automated classification of breast tissue microarray spots." In CTRC-AACR San Antonio Breast Cancer Symposium: 2008 Abstracts. American Association for Cancer Research, 2009. http://dx.doi.org/10.1158/0008-5472.sabcs-4010.

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Xing, Fuyong, Baiyang Liu, Xin Qi, David J. Foran, and Lin Yang. "Digitized tissue microarray classification using sparse reconstruction." In SPIE Medical Imaging, edited by David R. Haynor and Sébastien Ourselin. SPIE, 2012. http://dx.doi.org/10.1117/12.911900.

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Cline, Harvey E., Ali Can, and Dirk Padfield. "Segmentation of prostate cancer tissue microarray images." In Biomedical Optics 2006, edited by Daniel L. Farkas, Dan V. Nicolau, and Robert C. Leif. SPIE, 2006. http://dx.doi.org/10.1117/12.643180.

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Galizia, Antonella, Federica Viti, Alessandro Orro, Daniele D'Agostino, Ivan Merelli, Luciano Milanesi, and Andrea Clematis. "TMAinspect, an EGEE Framework for Tissue MicroArray Image Handling." In 2008 8th IEEE International Symposium on Cluster Computing and the Grid (CCGrid). IEEE, 2008. http://dx.doi.org/10.1109/ccgrid.2008.100.

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"SCORING OF BREAST TISSUE MICROARRAY SPOTS THROUGH ORDINAL REGRESSION." In International Conference on Computer Vision Theory and Applications. SciTePress - Science and and Technology Publications, 2009. http://dx.doi.org/10.5220/0001808202430248.

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Zhou, A., Z. Zhou, and P. Chen. "Microarray Analysis of Noncoding RNA in Lung Tissue of COPD Patients." In American Thoracic Society 2019 International Conference, May 17-22, 2019 - Dallas, TX. American Thoracic Society, 2019. http://dx.doi.org/10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a5381.

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Nguyen, Hoai-Nam, Charles Kervrann, Cyril Cauchois, and Vincent Paveau. "Automatic core segmentation and registration for fast tissue microarray de-arraying." In 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI 2015). IEEE, 2015. http://dx.doi.org/10.1109/isbi.2015.7164147.

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Amaral, Telmo, Stephen McKenna, Katherine Robertson, and Alastair Thompson. "Classification of breast-tissue microarray spots using colour and local invariants." In 2008 5th IEEE International Symposium on Biomedical Imaging (ISBI 2008). IEEE, 2008. http://dx.doi.org/10.1109/isbi.2008.4541167.

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Reports on the topic "Tissue microarray"

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Dolled-Filhart, Marisa. Tissue Microarray Based Investigation of Stat3 Signaling Pathway in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, May 2004. http://dx.doi.org/10.21236/ada425703.

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Mehra, Rohit. Tissue Microarray Assessment of Novel Prostate Cancer Biomarkers AMACR and EZH2 and Immunologic Response to Them in African-American and Caucasian Men. Fort Belvoir, VA: Defense Technical Information Center, April 2007. http://dx.doi.org/10.21236/ada470995.

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Meir, Shimon, Michael S. Reid, Cai-Zhong Jiang, Amnon Lers, and Sonia Philosoph-Hadas. Molecular Studies of Postharvest Leaf and Flower Senescence. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7592657.bard.

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Original objectives: To understand the regulation of abscission by exploring the nature of changes of auxin-related gene expression in tomato (Lycopersicon esculatumMill) abscission zones (AZs) following organ removal, and by analyzing the function of these genes. Our specific goals were: 1) To complete the microarray analyses in tomato flower and leaf AZs, for identifying genes whose expression changes early in response to auxin depletion; 2) To examine, using virus-induced gene silencing (VIGS), the effect of silencing target genes on ethylene sensitivity and abscission competence of the leaf and flower AZs; 3) To isolate and characterize promoters from AZ-specific genes to be used in functional analysis; 4) To generate stable transgenic tomato plants with selected genes silenced with RNAi, under the control of an AZ-specific promoter, for further characterization of their abscission phenotypes. Background: Abscission, the separation of organs from the parent plant, results in postharvest quality loss in many ornamentals and other fresh produce. The process is initiated by changes in the auxin gradient across the AZ, and is triggered by ethylene. Although changes in gene expression have been correlated with the ethylene-mediated execution of abscission, there is almost no information on the initiation of the abscission process, as the AZ becomes sensitized to ethylene. The present project was focused on elucidating these early molecular regulatory events, in order to gain a better control of the abscission process for agricultural manipulations. Major conclusions, solutions, achievements: Microarray analyses, using the Affymetrix Tomato GeneChip®, revealed changes in expression, occurring early in abscission, of many genes with possible regulatory functions. These included a range of auxin- and ethylene-related transcription factors (TFs), other TFs that are transiently induced just after flower removal, and a set of novel AZ-specific genes. We also identified four different defense-related genes, including: Cysteine-type endopeptidase, α- DOX1, WIN2, and SDF2, that are newly-associated with the late stage of the abscission process. This supports the activation of different defense responses and strategies at the late abscission stages, which may enable efficient protection of the exposed tissue toward different environmental stresses. To facilitate functional studies we implemented an efficient VIGS system in tomato, and isolated two abscission-specific promoters (pTAPG1 and pTAPG4) for gene silencing in stable transformation. Using the VIGS system we could demonstrate the importance of TAPGs in abscission of tomato leaf petioles, and evaluated the importance of more than 45 genes in abscission. Among them we identified few critical genes involved in leaf and flower abscission. These included: PTRP-F1, PRP, TKN4, KNOTTED-like homeobox TF, KD1, and KNOX-like homeodomain protein genes, the silencing of which caused a striking retardation of pedicel abscission, and ERF1, ERF4, Clavata-like3 protein, Sucrose transporter protein, and IAA10 genes, the silencing of which delayed petiole abscission. The importance of PRPand KD1 genes in abscission was confirmed also by antisense–silencing using pTAPG4. Experiments testing the effects of RNAi silencing of few other genes are still in progress, The analysis of the microarray results of flower and leaf AZs allowed us to establish a clear sequence of events occurring during acquisition of tissue sensitivity to ethylene, and to confirm our hypothesis that acquisition of ethylene sensitivity in the AZ is associated with altered expression of auxin-regulated genes in both AZs. Implication, both scientific and agricultural: Our studies had provided new insights into the regulation of the abscission process, and shaded light on the molecular mechanisms that drive the acquisition of abscission competence in the AZ. We pointed out some critical genes involved in regulation of abscission, and further expanded our knowledge of auxin-ethylene cross talk during the abscission process. This permits the development of novel techniques for manipulating abscission, and thereby improving the postharvest performance of ornamentals and other crops.
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Rimm, David L. Spectral Analysis of Breast Cancer on Tissue Microarrays: Seeing Beyond Morphology. Fort Belvoir, VA: Defense Technical Information Center, May 2003. http://dx.doi.org/10.21236/ada417663.

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Rimm, David L. Outcome Based Screening for Prognostic Phospho-RTK (Receptor Tyrosine Kinase) Antibodies Using Tissue Microarrays. Fort Belvoir, VA: Defense Technical Information Center, August 2002. http://dx.doi.org/10.21236/ada410085.

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Rimm, David. Outcome Based Screening for Prognostic Phospho-RTK (Receptor Tyrosine Kinase) Antibodies Using Tissue Microarrays). Fort Belvoir, VA: Defense Technical Information Center, August 2004. http://dx.doi.org/10.21236/ada430123.

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Rimm, David L. Outcome Based Screening for Prognostic Phospho-RTK (Receptor Tyrosine Kinase) Antibodies Using Tissue Microarrays. Fort Belvoir, VA: Defense Technical Information Center, August 2003. http://dx.doi.org/10.21236/ada420064.

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Ginzberg, Idit, and Walter De Jong. Molecular genetic and anatomical characterization of potato tuber skin appearance. United States Department of Agriculture, September 2008. http://dx.doi.org/10.32747/2008.7587733.bard.

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Potato (Solanum tuberosum L.) skin is composed of suberized phellem cells, the outer component of the tuber periderm. The focus of the proposed research was to apply genomic approaches to identify genes that control tuber skin appearance - smooth and shiny skin is highly preferred by the customers while russeted/netted skin potatoes are rejected. The breeding program (at Cornell University) seeks to develop smooth-skin varieties but has encountered frequent difficulties as inheritance of russeting involves complementary action by independently segregating genes, where a dominant allele at each locus is required for any degree of skin russeting. On the other hand, smooth-skin varieties frequently develop unsightly russeting in response to stress conditions, mainly high soil temperatures. Breeding programs in Israel aimed towards the improvement of heat tolerant varieties include skin quality as one of the desired characteristics. At the initiation of the present project it was unclear whether heat induced russeting and genetically inherited russeting share the same genes and biosynthesis pathways. Nevertheless, it has been suggested that russeting might result from increased periderm thickness, from strong cohesion between peridermal cells that prevents the outer layers from sloughing off, or from altered suberization processes in the skin. Hence, the original objectives were to conduct anatomical study of russet skin development, to isolate skin and russeting specific genes, to map the loci that determine the russet trait, and to compare with map locations the candidate russet specific genes, as well as to identify marker alleles that associated with russet loci. Anatomical studies suggested that russet may evolve from cracking at the outer layers of the skin, probably when skin development doesn’t meet the tuber expansion rate. Twodimensional gel electrophoresis and transcript profiling (cDNA chip, potato functional genomic project) indicated that in comparison to the parenchyma tissue, the skin is enriched with proteins/genes that are involved in the plant's responses to biotic and abiotic stresses and further expand the concept of the skin as a protective tissue containing an array of plantdefense components. The proteomes of skin from heat stressed tubers and native skin didn’t differ significantly, while transcript profiling indicated heat-related increase in three major functional groups: transcription factors, stress response and protein degradation. Exceptional was ACC synthase isogene with 4.6 fold increased level in the heat stressed skin. Russeting was mapped to two loci: rusB on chromosome 4 and rusC on chromosome 11; both required for russeting. No evidence was found for a third locus rusA that was previously proposed to be required for russeting. In an effort to find a link between the russeting character and the heat-induced russeting an attempt was made to map five genes that were found in the microarray experiment to be highly induced in the skin under heat stress in the segregating russet population. Only one gene was polymorphic; however it was localized to chromosome 2, so cannot correspond to rusB or rusC. Evaluation of AFLP markers tightly linked to rusB and rusC showed that these specific alleles are not associated with russeting in unrelated germplasm, and thus are not useful for MAS per se. To develop markers useful in applied breeding, it will be necessary to screen alleles of additional tightly linked loci, as well as to identify additional russet (heat-induced and/or native) related genes.
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Droby, Samir, Michael Wisniewski, Ron Porat, and Dumitru Macarisin. Role of Reactive Oxygen Species (ROS) in Tritrophic Interactions in Postharvest Biocontrol Systems. United States Department of Agriculture, December 2012. http://dx.doi.org/10.32747/2012.7594390.bard.

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To elucidate the role of ROS in the tri-trophic interactions in postharvest biocontrol systems a detailed molecular and biochemical investigation was undertaken. The application of the yeast biocontrol agent Metschnikowia fructicola, microarray analysis was performed on grapefruit surface wounds using an Affymetrix Citrus GeneChip. the data indicated that 1007 putative unigenes showed significant expression changes following wounding and yeast application relative to wounded controls. The expression of the genes encoding Respiratory burst oxidase (Rbo), mitogen-activated protein kinase (MAPK) and mitogen-activated protein kinase kinase (MAPKK), G-proteins, chitinase (CHI), phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS) and 4-coumarate-CoA ligase (4CL). In contrast, three genes, peroxidase (POD), superoxide dismutase (SOD) and catalase (CAT), were down-regulated in grapefruit peel tissue treated with yeast cells. The yeast antagonists, Metschnikowia fructicola (strain 277) and Candida oleophila (strain 182) generate relatively high levels of super oxide anion (O2−) following its interaction with wounded fruit surface. Using laser scanning confocal microscopy we observed that the application of M. fructicola and C. oleophila into citrus and apple fruit wounds correlated with an increase in H2O2 accumulation in host tissue. The present data, together with our earlier discovery of the importance of H₂O₂ production in the defense response of citrus flavedo to postharvest pathogens, indicate that the yeast-induced oxidative response in fruit exocarp may be associated with the ability of specific yeast species to serve as biocontrol agents for the management of postharvest diseases. Effect of ROS on yeast cells was also studied. Pretreatment of the yeast, Candida oleophila, with 5 mM H₂O₂ for 30 min (sublethal) increased yeast tolerance to subsequent lethal levels of oxidative stress (50 mM H₂O₂), high temperature (40 °C), and low pH (pH 4). Suppression subtractive hybridization analysis was used to identify genes expressed in yeast in response to sublethal oxidative stress. Transcript levels were confirmed using semi quantitative reverse transcription-PCR. Seven antioxidant genes were up regulated. Pretreatment of the yeast antagonist Candida oleophila with glycine betaine (GB) increases oxidative stress tolerance in the microenvironment of apple wounds. ROS production is greater when yeast antagonists used as biocontrol agents are applied in the wounds. Compared to untreated control yeast cells, GB-treated cells recovered from the oxidative stress environment of apple wounds exhibited less accumulation of ROS and lower levels of oxidative damage to cellular proteins and lipids. Additionally, GB-treated yeast exhibited greater biocontrol activity against Penicillium expansum and Botrytis cinerea, and faster growth in wounds of apple fruits compared to untreated yeast. The expression of major antioxidant genes, including peroxisomal catalase, peroxiredoxin TSA1, and glutathione peroxidase was elevated in the yeast by GB treatment. A mild heat shock (HS) pretreatment (30 min at 40 1C) improved the tolerance of M. fructicola to subsequent high temperature (45 1C, 20–30 min) and oxidative stress (0.4 mol-¹) hydrogen peroxide, 20–60 min). HS-treated yeast cells showed less accumulation of reactive oxygen species (ROS) than non-treated cells in response to both stresses. Additionally, HS-treated yeast exhibited significantly greater (P≥0.0001) biocontrol activity against Penicillium expansum and a significantly faster (Po0.0001) growth rate in wounds of apple fruits stored at 25 1C compared with the performance of untreated yeast cells. Transcription of a trehalose-6-phosphate synthase gene (TPS1) was up regulated in response to HS and trehalose content also increased.
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Heifetz, Yael, and Michael Bender. Success and failure in insect fertilization and reproduction - the role of the female accessory glands. United States Department of Agriculture, December 2006. http://dx.doi.org/10.32747/2006.7695586.bard.

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The research problem. Understanding of insect reproduction has been critical to the design of insect pest control strategies including disruptions of mate-finding, courtship and sperm transfer by male insects. It is well known that males transfer proteins to females during mating that profoundly affect female reproductive physiology, but little is known about the molecular basis of female mating response and no attempts have yet been made to interfere with female post-mating responses that directly bear on the efficacy of fertilization. The female reproductive tract provides a crucial environment for the events of fertilization yet thus far those events and the role of the female tract in influencing them are poorly understood. For this project, we have chosen to focus on the lower reproductive tract because it is the site of two processes critical to reproduction: sperm management (storage, maintenance, and release from storage) and fertilization. E,fforts during this project period centered on the elucidation of mating responses in the female lower reproductive tract The central goals of this project were: 1. To identify mating-responsive genes in the female lower reproductive tract using DNA microarray technology. 2. In parallel, to identify mating-responsive genes in these tissues using proteomic assays (2D gels and LC-MS/MS techniques). 3. To integrate proteomic and genomic analyses of reproductive tract gene expression to identify significant genes for functional analysis. Our main achievements were: 1. Identification of mating-responsive genes in the female lower reproductive tract. We identified 539 mating-responsive genes using genomic and proteomic approaches. This analysis revealed a shift from gene silencing to gene activation soon after mating and a peak in differential gene expression at 6 hours post-mating. In addition, comparison of the two datasets revealed an expression pattern consistent with the model that important reproductive proteins are pre-programmed for synthesis prior to mating. This work was published in Mack et al. (2006). Validation experiments using real-time PCR techniques suggest that microarray assays provide a conservativestimate of the true transcriptional activity in reproductive tissues. 2.lntegration of proteomics and genomics data sets. We compared the expression profiles from DNA microarray data with the proteins identified in our proteomic experiments. Although comparing the two data sets poses analyical challenges, it provides a more complete view of gene expression as well as insights into how specific genes may be regulated. This work was published in Mack et al. (2006). 3. Development of primary reproductive tract cell cultures. We developed primary cell cultures of dispersed reproductive tract cell types and determined conditions for organ culture of the entire reproductive tract. This work will allow us to rapidly screen mating-responsive genes for a variety of reproductive-tract specifi c functions. Scientific and agricultural significance. Together, these studies have defined the genetic response to mating in a part of the female reproductive tract that is critical for successful fertllization and have identified alarge set of mating-responsive genes. This work is the first to combine both genomic and proteomic approaches in determining female mating response in these tissues and has provided important insights into insect reproductive behavior.
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