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https://www.readbyqxmd.com/read/29031017/how-to-reduce-scientific-irreproducibility-the-5-year-reflection
#1
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
#2
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
#3
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
#4
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
https://www.readbyqxmd.com/read/28815018/serum-complexed-and-free-prostate-specific-antigen-levels-are-lower-in-female-elite-athletes-in-comparison-to-control-women
#5
Emma Eklund, Eleftherios P Diamandis, Carla Muytjens, Sarah Wheeler, Anu Mathew, Martin Stengelin, Eli Glezer, Galina Nikolenko, Marshall D Brown, Yingye Zheng, Angelica Lindén Hirschberg
BACKGROUND: We hypothesize that prostate specific antigen (PSA), a protein that it is under regulation by androgens, may be differentially expressed in female elite athletes in comparison to control women. METHODS: We conducted a cross-sectional study of 106 female athletes and 114 sedentary age-matched controls.  Serum from these women was analyzed for complexed prostate specific antigen (cPSA) and free prostate specific antigen (fPSA), by fifth generation assays with limits of detection of around 6 and 140 fg/mL, respectively...
2017: F1000Research
https://www.readbyqxmd.com/read/28746862/generation-of-monoclonal-antibodies-and-development-of-an-immunofluorometric-assay-for-the-detection-of-cuzd1-in-tissues-and-biological-fluids
#6
Sofia Farkona, Antoninus Soosaipillai, Panagiota Filippou, Dimitrios Korbakis, Stefano Serra, Felix Rückert, Eleftherios P Diamandis, Ivan M Blasutig
BACKGROUND: CUB and zona pellucida-like domain-containing protein 1 (CUZD1) was identified as a pancreas-specific protein and was proposed as a candidate biomarker for pancreatic related disorders. CUZD1 protein levels in tissues and biological fluids have not been extensively examined. The purpose of the present study was to generate specific antibodies targeting CUZD1 to assess CUZD1 expression within tissues and biological fluids. METHODS: Mouse monoclonal antibodies against CUZD1 were generated and used to perform immunohistochemical analyses and to develop a sensitive and specific enzyme-linked immunosorbent assay (ELISA)...
July 23, 2017: Clinical Biochemistry
https://www.readbyqxmd.com/read/28743464/stem-cell-therapy-for-abrogating-stroke-induced-neuroinflammation-and-relevant-secondary-cell-death-mechanisms
#7
REVIEW
Connor Stonesifer, Sydney Corey, Shaila Ghanekar, Zachary Diamandis, Sandra A Acosta, Cesar V Borlongan
Ischemic stroke is a leading cause of death worldwide. A key secondary cell death mechanism mediating neurological damage following the initial episode of ischemic stroke is the upregulation of endogenous neuroinflammatory processes to levels that destroy hypoxic tissue local to the area of insult, induce apoptosis, and initiate a feedback loop of inflammatory cascades that can expand the region of damage. Stem cell therapy has emerged as an experimental treatment for stroke, and accumulating evidence supports the therapeutic efficacy of stem cells to abrogate stroke-induced inflammation...
November 2017: Progress in Neurobiology
https://www.readbyqxmd.com/read/28716573/htra3-stromal-expression-is-correlated-with-tumor-budding-in-stage-ii-colorectal-cancer
#8
Catherine L Forse, Mahdi Rahimi, Eleftherios P Diamandis, Naziheh Assarzadegan, Heather Dawson, Andrea Grin, Erin Kennedy, Brenda O'Connor, David E Messenger, Robert H Riddell, Richard Kirsch, George S Karagiannis
Tumor budding is a well-established adverse prognostic factor in colorectal carcinoma (CRC). It may represent a form of epithelial-to-mesenchymal transition (EMT), although the underlying mechanisms remain unclear. High-temperature requirement A3 (HtrA3) is an inhibitor of the bone morphogenetic protein pathway, the suppression of which has been linked to EMT. Since HtrA3 is highly expressed in the desmoplastic stroma at the CRC invasive front, we sought to evaluate the relationship between tumor budding and HtrA3 expression in 172 stage II CRC resection specimens...
August 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28687556/spatiotemporal-proteomic-profiling-of-human-cerebral-development
#9
Ugljesa Djuric, Deivid C Rodrigues, Ihor Batruch, James Ellis, Patrick Shannon, Phedias Diamandis
Mass spectrometry (MS) analysis of human post-mortem central nervous system (CNS) tissue and induced pluripotent stem cell (iPSC)-based directed differentiations offer complementary avenues to define protein signatures of neurodevelopment. Methodological improvements of formalin-fixed, paraffin-embedded (FFPE) protein isolation now enable widespread proteomic analysis of well-annotated archival tissue samples in the context of development and disease. Here, we utilize a shotgun label-free quantification (LFQ) MS method to profile magnetically enriched human cortical neurons and neural progenitor cells (NPCs) derived from iPSCs...
September 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28672746/study-of-kallikrein-related-peptidase-6-klk6-and-its-complex-with-%C3%AE-1-antitrypsin-in-biological-fluids
#10
Dimitrios Korbakis, Antoninus Soosaipillai, Eleftherios P Diamandis
BACKGROUND: Human kallikrein-related peptidase 6 (KLK6) is a member of the kallikrein family of serine proteases. KLK6 is synthesized as a preproenzyme, mainly in tissues of the central nervous system (CNS), and secreted as an inactive precursor. Serum KLK6 is a biomarker of unfavorable prognosis for ovarian cancer, but its sensitivity for early detection is relatively low. Differential glycosylation of KLK6 has been identified in ascites fluid obtained from ovarian cancer patients, suggesting the presence of unique KLK6 isoforms in biological samples...
August 28, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28640696/insights-from-molecular-profiling-of-adult-glioma
#11
REVIEW
Phedias Diamandis, Kenneth D Aldape
The comprehensive molecular profiling of cancer has resulted in new insights into the biology and classification of numerous tumor types. In the case of primary brain tumors that commonly affect adults, an emerging set of disease-defining biomarker sets is reshaping existing diagnostic entities that had previously been defined on the basis of their microscopic appearance. Substantial progress has been made in this regard for common primary brain tumors in adults, especially diffuse gliomas, where large-scale profiling efforts have led to the incorporation of highly prevalent molecular alterations that promote a biologically based classification as an adjunct to the traditional histopathologic approach...
July 20, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28636767/aberrant-expression-of-kallikrein-related-peptidase-7-is-correlated-with-human-melanoma-aggressiveness-by-stimulating-cell-migration-and-invasion
#12
Tiphaine Delaunay, Lydia Deschamps, Meriem Haddada, Francine Walker, Antoninus Soosaipillai, Feryel Soualmia, Chahrazade El Amri, Eleftherios P Diamandis, Maria Brattsand, Viktor Magdolen, Dalila Darmoul
Members of the tissue kallikrein-related peptidase (KLK) family not only regulate several important physiological functions, but aberrant expression has also been associated with various malignancies. Clinically, KLKs have been suggested as promising biomarkers for diagnosis and prognosis in many types of cancer. As of yet, expression of KLKs and their role in skin cancers are, however, poorly addressed. Malignant melanoma is an aggressive disease associated with poor prognosis. Hence, diagnostic biomarkers to monitor melanoma progression are needed...
October 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28634222/the-role-of-procalcitonin-in-diagnosis-of-sepsis-and-antibiotic-stewardship-opportunities-and-challenges
#13
Angela W S Fung, Daniel Beriault, Eleftherios P Diamandis, Carey-Ann D Burnham, Todd Dorman, Mark Downing, Joshua Hayden, Bradley J Langford
No abstract text is available yet for this article.
September 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28593880/how-i-first-met-dr-morton-k-schwartz
#14
EDITORIAL
Eleftherios P Diamandis
No abstract text is available yet for this article.
June 27, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28586166/novel-serum-biomarkers-differentiate-psoriatic-arthritis-from-psoriasis-without-psoriatic-arthritis
#15
Daniela Cretu, Lisa Gao, Kun Liang, Antoninus Soosaipillai, Eleftherios P Diamandis, Vinod Chandran
OBJECTIVES: There is a high prevalence of undiagnosed psoriatic arthritis (PsA) in psoriasis patients. Identifying soluble biomarkers for PsA will help in screening psoriasis patients for appropriate rheumatology referral. We therefore aimed to investigate whether serum levels of novel markers previously discovered by quantitative mass spectrometric (MS) analysis of synovial fluid and skin biopsies, performs better than CRP in differentiating PsA patients from those with psoriasis without PsA (PsC)...
June 6, 2017: Arthritis Care & Research
https://www.readbyqxmd.com/read/28559305/biochemical-and-functional-characterization-of-the-human-tissue-kallikrein-9
#16
Panagiota S Filippou, Sofia Farkona, Davor Brinc, Yijing Yu, Ioannis Prassas, Eleftherios P Diamandis
Human tissue kallikrein 9 (KLK9) is a member of the kallikrein-related family of proteases. Despite its known expression profile, much less is known about the functional roles of this protease and its implications in normal physiology and disease. We present here the first data on the biochemical characterization of KLK9, investigate parameters that affect its enzymatic activity (such as inhibitors) and provide preliminary insights into its putative substrates. We show that mature KLK9 is a glycosylated chymotrypsin-like enzyme with strong preference for tyrosine over phenylalanine at the P1 cleavage position...
July 6, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28553338/translational-research-in-early-neuroscience-careers-of-high-school-students
#17
EDITORIAL
Zachary M Diamandis, Nicholas S Diaco, Kelsey Duncan, Marci Crowley, M Grant Liska, Cesar V Borlongan
No abstract text is available yet for this article.
April 2017: Neural Regeneration Research
https://www.readbyqxmd.com/read/28434986/the-emerging-landscape-of-scientific-publishing
#18
REVIEW
Clare Fiala, Eleftherios P Diamandis
We present emerging models of publishing which have grown from the phenomenon of open access, the changing role of peer review in the scientific process and the new position of the impact factor. We juxtapose the new models of paid review, eponymous review, no review, post publication review and light review with the classic model which has dominated for a century, detailing advantages, problems and examples of each model to provide a comprehensive overview of the changing landscape of scientific publishing...
August 2017: Clinical Biochemistry
https://www.readbyqxmd.com/read/28432186/wellness-initiatives-benefits-and-limitations
#19
Michelle Li, Eleftherios P Diamandis, Nigel Paneth, Kiang-Teck J Yeo, Henrik Vogt, Stephen R Master
No abstract text is available yet for this article.
April 21, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28427756/human-tissue-kallikreins-blood-levels-and-response-to-radiotherapy-in-intermediate-risk-prostate-cancer
#20
Nicola J Nasser, John Thoms, Antoninus Soosaipillai, Melania Pintilie, Ri Wang, Eleftherios P Diamandis, Robert G Bristow
OBJECTIVES: Kallikreins are serine proteases over expressed in many malignancies. In this study, we measure changes in serum kallikrein (KLKs) levels during intensity-modulated radiotherapy (IMRT) in prostate cancer patients, and find potential correlations between serum kallikrein level and normal tissues toxicity during radiation. METHODS: Forty-nine patients with prostate cancer were recruited as follows: group 1, definitive standard fractionation IMRT (78Gy in 39 fractions, n=15); group 2, definitive hypofractionated IMRT (60Gy in 20 fractions, n=15); and group 3, IMRT postprostatectomy (66Gy in 33 fractions, n=19)...
September 2017: Radiotherapy and Oncology: Journal of the European Society for Therapeutic Radiology and Oncology
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