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https://www.readbyqxmd.com/read/29769044/visualizing-histopathologic-deep-learning-classification-and-anomaly-detection-using-nonlinear-feature-space-dimensionality-reduction
#1
Kevin Faust, Quin Xie, Dominick Han, Kartikay Goyle, Zoya Volynskaya, Ugljesa Djuric, Phedias Diamandis
BACKGROUND: There is growing interest in utilizing artificial intelligence, and particularly deep learning, for computer vision in histopathology. While accumulating studies highlight expert-level performance of convolutional neural networks (CNNs) on focused classification tasks, most studies rely on probability distribution scores with empirically defined cutoff values based on post-hoc analysis. More generalizable tools that allow humans to visualize histology-based deep learning inferences and decision making are scarce...
May 16, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29768245/exploring-the-potential-of-mucin-13-muc13-as-a-biomarker-for-carcinomas-and-other-diseases
#2
Panagiota S Filippou, Annie H Ren, Dimitrios Korbakis, Lampros Dimitrakopoulos, Antoninus Soosaipillai, Vivian Barak, Shahar Frenkel, Jacob Pe'er, Michal Lotem, Sharon Merims, Rafael Molina, Ivan Blasutig, Dimitrios P Bogdanos, Eleftherios P Diamandis
BACKGROUND: Mucin 13 (MUC13) is a cell surface glycoprotein aberrantly expressed in a variety of epithelial carcinomas. Thus far, the role of MUC13 in various diseases remains elusive. To the best of our knowledge, this is the first study to examine the potential of MUC13 as a serum biomarker in a variety of carcinomas and other conditions. METHODS: We developed a recombinant MUC13 protein, mouse monoclonal antibodies and enzyme immunoassay (ELISA) for MUC13. We used this assay to measure MUC13 levels in the supernatants of cancer cell lines and a large cohort of serum samples from healthy and diseased individuals...
May 16, 2018: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/29750644/the-meteoric-rise-and-dramatic-fall-of-theranos-lessons-learned-for-the-diagnostic-industry
#3
Clare Fiala, Eleftherios P Diamandis
In this piece we discuss and reflect on the conclusion of the Theranos saga in the light of its fraud conviction. Theranos (founded in 2003 by Elizabeth Holmes) was supposed to disrupt the diagnostic testing industry by developing technology which could perform dozens of tests using a tiny amount of blood from a finger-prick. As a result, Ms. Holmes rose to fame, becoming the world's youngest female self-made billionaire and was plastered across magazine covers. However, in 2014, Theranos began to fall apart following increasingly damaging revelations regarding its lack of expertise, technology, framework, extreme secrecy and inaccurate test results...
May 11, 2018: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/29721309/unraveling-endometriosis-associated-ovarian-carcinomas-using-integrative-proteomics
#4
Felix Leung, Marcus Q Bernardini, Kun Liang, Ihor Batruch, Marjan Rouzbahman, Eleftherios P Diamandis, Vathany Kulasingam
Background: To elucidate potential markers of endometriosis and endometriosis-associated endometrioid and clear cell ovarian carcinomas using mass spectrometry-based proteomics. Methods: A total of 21 fresh, frozen tissues from patients diagnosed with clear cell carcinoma, endometrioid carcinoma, endometriosis and benign endometrium were subjected to an in-depth liquid chromatography-tandem mass spectrometry analysis on the Q-Exactive Plus. Protein identification and quantification were performed using MaxQuant, while downstream analyses were performed using Perseus and various bioinformatics databases...
2018: F1000Research
https://www.readbyqxmd.com/read/29708756/targeted-mass-spectrometry-based-assays-for-relative-quantification-of-thirty-brain-related-proteins-and-their-clinical-applications
#5
Ilijana Begcevic, Davor Brinc, Lora Dukic, Ana-Maria Simundic, Iris Zavoreo, Vanja Basic Kes, Eduardo Martínez-Morillo, Ihor Batruch, Andrei P Drabovich, Eleftherios P Diamandis
Cerebrospinal fluid (CSF) is a promising clinical sample for identification of novel biomarkers for various neurological disorders. Considering its direct contact with brain tissue, CSF represents a valuable source of brain-related and brain-specific proteins. Multiple sclerosis is an inflammatory, demyelinating neurological disease affecting the central nervous system and so far there are no diagnostic or prognostic disease specific biomarkers available in the clinic. The primary aim of the present study was to develop a targeted mass spectrometry assay for simultaneous quantification of 30 brain-related proteins in CSF and subsequently to demonstrate assay feasibility in neurological samples derived from multiple sclerosis patients...
April 30, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29704080/mr-spectroscopic-imaging-of-glial-tumors-in-the-spotlight-of-the-2016-who-classification
#6
Elie Diamandis, Carl Phillip Simon Gabriel, Urs Würtemberger, Konstanze Guggenberger, Horst Urbach, Ori Staszewski, Silke Lassmann, Oliver Schnell, Jürgen Grauvogel, Irina Mader, Dieter Henrik Heiland
BACKGROUND: The purpose of this study is to map spatial metabolite differences across three molecular subgroups of glial tumors, defined by the IDH1/2 mutation and 1p19q-co-deletion, using magnetic resonance spectroscopy. This work reports a new MR spectroscopy based classification algorithm by applying a radiomics analytics pipeline. MATERIALS: 65 patients received anatomical and chemical shift imaging (5 × 5 × 20 mm voxel size). Tumor regions were segmented and registered to corresponding spectroscopic voxels...
April 27, 2018: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/29684683/brain-related-proteins-as-potential-csf-biomarkers-of-alzheimer-s-disease-a-targeted-mass-spectrometry-approach
#7
Ilijana Begcevic, Davor Brinc, Marshall Brown, Eduardo Martinez-Morillo, Oliver Goldhardt, Timo Grimmer, Viktor Magdolen, Ihor Batruch, Eleftherios P Diamandis
Alzheimer's disease (AD) is the most common cause of dementia, characterized by progressive cognitive decline. The main disease hallmarks include amyloid beta aggregates and neurofibrillary tangles. Brain pathology is reflected in cerebrospinal fluid (CSF); the core biomarkers amyloid beta 1-42, total and phosphorylated tau protein levels are changed, relative to cognitively normal elderly. Still, there is a need for additional biomarkers which could identify disease more accurately and at an earlier stage, predict severity and be used in research settings...
April 20, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29608889/benign-and-malignant-scientific-irreproducibility
#8
EDITORIAL
Clare Fiala, Eleftherios P Diamandis
Irreproducibility is a widely recognized problem harming scientific progress. Here, we classify types of scientific irreproducibility based on deleteriousness using a cancer analogy: benign, pre-malignant and malignant. We discuss the difficulties of challenging potentially irreproducible papers, especially in high impact journals and/or by famous authors. We advocate for high impact journals publishing papers with large translation value, to implement mandatory author reflections on the reproducibility, utility and relevance of their work 5 to 10 years after publication...
March 30, 2018: Clinical Biochemistry
https://www.readbyqxmd.com/read/29604203/the-mirna-kallikrein-interaction-a-mosaic-of-epigenetic-regulation-in-cancer
#9
Ashley Di Meo, Cong Wang, Yufeng Cheng, Eleftherios P Diamandis, George M Yousef
The kallikrein-related peptidases (KLKs) constitute a family of 15 highly conserved serine proteases with trypsin- and chymotrypsin-like activities. Dysregulated expression and/or aberrant activation of KLKs have been linked to various pathophysiological processes, including cancer. Many KLKs have been identified as potential cancer biomarkers. microRNAs (miRNAs) are a class of small non-coding RNAs that regulate gene expression by pairing to the 3' untranslated region (UTR) of complimentary mRNA targets. miRNAs are dysregulated in many cancers, including prostate, kidney, and ovarian cancers...
March 1, 2018: Biological Chemistry
https://www.readbyqxmd.com/read/29568494/hubris-and-sciences
#10
Eleftherios P Diamandis, Nick Bouras
There has been an increasing awareness of the importance of leadership and decision making, including scientists and academics, over recent times. By whom and how decisions are made can have serious implications across all levels of society. Several people have been successful in their life and have been inflicted by excessive pride and self-confidence. There are times when the manifestations of such behaviours demonstrate noticeable signs of narcissism and on extreme cases, hubris. Hubris is an old concept originated from the Greek mythology...
2018: F1000Research
https://www.readbyqxmd.com/read/29455189/is-it-time-to-abandon-the-nobel-prize
#11
EDITORIAL
Clare Fiala, Eleftherios P Diamandis
No abstract text is available yet for this article.
February 19, 2018: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/29416756/a-mirna-based-classification-of-renal-cell-carcinoma-subtypes-by-pcr-and-in-situ-hybridization
#12
Ashley Di Meo, Rola Saleeb, Samantha J Wala, Heba W Khella, Qiang Ding, Haiyan Zhai, Kalra Krishan, Adriana Krizova, Manal Gabril, Andrew Evans, Fadi Brimo, Maria D Pasic, Antonio Finelli, Eleftherios P Diamandis, George M Yousef
Renal cell carcinoma (RCC) constitutes an array of morphologically and genetically distinct tumors the most prevalent of which are clear cell, papillary, and chromophobe RCC. Accurate distinction between the typically benign-behaving renal oncocytoma and RCC subtypes is a frequent challenge for pathologists. This is critical for clinical decision making. Subtypes also have different survival outcomes and responses to therapy. We extracted RNA from ninety formalin-fixed paraffin-embedded (FFPE) tissues (27 clear cell, 29 papillary, 19 chromophobe, 4 unclassified RCC and 11 oncocytomas)...
January 5, 2018: Oncotarget
https://www.readbyqxmd.com/read/29416136/proteinases-and-their-receptors-in-inflammatory-arthritis-an-overview
#13
REVIEW
Katerina Oikonomopoulou, Eleftherios P Diamandis, Morley D Hollenberg, Vinod Chandran
Proteinases are enzymes with established roles in physiological and pathological processes such as digestion and the homeostasis, destruction and repair of tissues. Over the past few years, the hormone-like properties of circulating proteinases have become increasingly appreciated. Some proteolytic enzymes trigger cell signalling via proteinase-activated receptors, a family of G protein-coupled receptors that have been implicated in inflammation and pain in inflammatory arthritis. Proteinases can also regulate ion flux owing to the cross-sensitization of transient receptor potential cation channel subfamily V members 1 and 4, which are associated with mechanosensing and pain...
March 2018: Nature Reviews. Rheumatology
https://www.readbyqxmd.com/read/29378650/assessment-of-kallikrein-6-as-a-cross-sectional-and-longitudinal-biomarker-for-alzheimer-s-disease
#14
Kalicharan Patra, Antoninus Soosaipillai, Sigrid Botne Sando, Camilla Lauridsen, Guro Berge, Ina Møller, Gøril Rolfseng Grøntvedt, Geir Bråthen, Ilijana Begcevic, Simon Moussaud, Lennart Minthon, Oskar Hansson, Eleftherios P Diamandis, Linda R White, Henrietta M Nielsen
BACKGROUND: Kallikrein 6 (KLK6) is known to be an age-related protease expressed at high levels in the central nervous system. It was previously shown to be involved in proteolysis of extracellular proteins implicated in neurodegenerative diseases such as Alzheimer's disease (AD), prompting validation of KLK6 as a potential biomarker of disease. However, analyses of both plasma and cerebrospinal fluid (CSF) levels of KLK6 in patients with AD have been inconclusive. We present a detailed analysis of KLK6 in plasma and CSF in two separate cohorts in a cross-sectional and a longitudinal clinical setting...
January 29, 2018: Alzheimer's Research & Therapy
https://www.readbyqxmd.com/read/29202618/synovial-fluid-proteomics-in-the-pursuit-of-arthritis-mediators-an-evolving-field-of-novel-biomarker-discovery
#15
Shalini M Mahendran, Katerina Oikonomopoulou, Eleftherios P Diamandis, Vinod Chandran
Synovial fluid (SF) is a protein-rich fluid produced into the joint cavity by cells of the synovial membrane. Due to its direct contact with articular cartilage, surfaces of the bone, and the synoviocytes of the inner membrane, it provides a promising reflection of the biochemical state of the joint under varying physiological and pathophysiological conditions. This property of SF has been exploited within numerous studies in search of unique biomarkers of joint pathologies with the ultimate goal of developing minimally invasive clinical assays to detect and/or monitor disease states...
November 2017: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/29167737/make-researchers-revisit-past-publications-to-improve-reproducibility
#16
Clare Fiala, Eleftherios P Diamandis
Scientific irreproducibility is a major issue that has recently increased attention from publishers, authors, funders and other players in the scientific arena.  Published literature suggests that 50-80% of all science performed is irreproducible.  While various solutions to this problem have been proposed, none of them are quick and/or cheap.  Here, we propose one way of reducing scientific irreproducibility by asking authors to revisit their previous publications and provide a commentary after five years...
2017: F1000Research
https://www.readbyqxmd.com/read/29031017/how-to-reduce-scientific-irreproducibility-the-5-year-reflection
#17
Clare Fiala, Eleftherios P Diamandis
We discuss in depth six causes of scientific irreproducibility and their ramifications for the clinical sciences: fraud, unfounded papers published by prominent authorities, bias, technical deficiencies, fragmented science and problems with big data. Some proposed methods to combat this problem are briefly described, including an effort to replicate results from some high impact papers and a proposal that authors include detailed preclinical data in papers with supposedly high translational value. We here advocate for a 5-year reflection on papers with seemingly high clinical/translational potential, published alongside the original paper where authors reflect on the quality, reproducibility and impact of their findings...
October 26, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/29025326/onco-proteogenomics-multi-omics-level-data-integration-for-accurate-phenotype-prediction
#18
Lampros Dimitrakopoulos, Ioannis Prassas, Eleftherios P Diamandis, George S Charames
The overall goal of translational oncology is to identify molecular alterations indicative of cancer or of responsiveness to specific therapeutic regimens. While next-generation sequencing has played a pioneering role in this quest, the latest advances in proteomic technologies promise to provide a holistic approach to the further elucidation of tumor biology. Genetic information may be written in DNA and flow from DNA to RNA to protein, according to the central dogma of molecular biology, but the observed phenotype is dictated predominantly by the DNA protein coding region-derived proteotype...
October 12, 2017: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/28974041/brillouin-optical-correlation-domain-analysis-in-composite-material-beams
#19
Yonatan Stern, Yosef London, Eyal Preter, Yair Antman, Hilel Hagai Diamandi, Maayan Silbiger, Gadi Adler, Eyal Levenberg, Doron Shalev, Avi Zadok
Structural health monitoring is a critical requirement in many composites. Numerous monitoring strategies rely on measurements of temperature or strain (or both), however these are often restricted to point-sensing or to the coverage of small areas. Spatially-continuous data can be obtained with optical fiber sensors. In this work, we report high-resolution distributed Brillouin sensing over standard fibers that are embedded in composite structures. A phase-coded, Brillouin optical correlation domain analysis (B-OCDA) protocol was employed, with spatial resolution of 2 cm and sensitivity of 1 °K or 20 micro-strain...
October 2, 2017: Sensors
https://www.readbyqxmd.com/read/28941238/discovery-of-antimicrobial-peptides-in-cervical-vaginal-fluid-from-healthy-nonpregnant-women-via-an-integrated-proteome-and-peptidome-analysis
#20
Carla M J Muytjens, Yijing Yu, Eleftherios P Diamandis
Cervical-vaginal fluid (CVF) covers the lower part of the female reproductive system and functions in the homeostasis and immunity of the surrounding tissues. In contrast to the CVF proteome of both nonpregnant and pregnant women, the CVF peptidome has not been reported to date. In the current study, we identified 1087 proteins in CVF, of which 801 proteins were not previously identified in CVF proteomes. The presence of the tissue-specific proteins oviductal glycoprotein 1 and tubulin polymerization-promoting protein family member 3 strongly suggests that the tissues of the upper female reproductive tract contribute to the protein composition of CVF...
September 23, 2017: Proteomics
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