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Analysis matrix data collection

Delfo D'Alessandro, Giuseppe Perale, Mario Milazzo, Stefania Moscato, Cesare Stefanini, Gianni Pertici, Serena Danti
The ideal scaffold for bone regeneration is required to be highly porous, non-immunogenic, biostable until the new tissue formation, bioresorbable and osteoconductive. This study aimed at investigating the process of new bone formation in patients treated with granular SmartBone(®) for sinus augmentation, providing an extensive histologic analysis. Five biopsies were collected at 4-9 months post SmartBone(®) implantation and processed for histochemistry and immunohistochemistry. Histomorphometric analysis was performed...
October 18, 2016: International Journal of Pharmaceutics
Ashton A Connor, Robert E Denroche, Gun Ho Jang, Lee Timms, Sangeetha N Kalimuthu, Iris Selander, Treasa McPherson, Gavin W Wilson, Michelle A Chan-Seng-Yue, Ivan Borozan, Vincent Ferretti, Robert C Grant, Ilinca M Lungu, Eithne Costello, William Greenhalf, Daniel Palmer, Paula Ghaneh, John P Neoptolemos, Markus Buchler, Gloria Petersen, Sarah Thayer, Michael A Hollingsworth, Alana Sherker, Daniel Durocher, Neesha Dhani, David Hedley, Stefano Serra, Aaron Pollett, Michael H A Roehrl, Prashant Bavi, John M S Bartlett, Sean Cleary, Julie M Wilson, Ludmil B Alexandrov, Malcolm Moore, Bradly G Wouters, John D McPherson, Faiyaz Notta, Lincoln D Stein, Steven Gallinger
Importance: Outcomes for patients with pancreatic ductal adenocarcinoma (PDAC) remain poor. Advances in next-generation sequencing provide a route to therapeutic approaches, and integrating DNA and RNA analysis with clinicopathologic data may be a crucial step toward personalized treatment strategies for this disease. Objective: To classify PDAC according to distinct mutational processes, and explore their clinical significance. Design, Setting, and Participants: We performed a retrospective cohort study of resected PDAC, using cases collected between 2008 and 2015 as part of the International Cancer Genome Consortium...
October 20, 2016: JAMA Oncology
Darren Rodenhizer, Dan Cojocari, Bradly G Wouters, Alison P McGuigan
The tumour microenvironment is heterogeneous and consists of multiple cell types, variable extracellular matrix (ECM) composition, and contains cell-defined gradients of small molecules, oxygen, nutrients and waste. Emerging in vitro cell culture systems that attempt to replicate these features often fail to incorporate design strategies to facilitate efficient data collection and stratification. The tissue roll for analysis of cellular environment and response (TRACER) is a novel strategy to assemble layered, three-dimensional tumours with cell-defined, graded heterogeneous microenvironments that also facilitates cellular separation and stratification of data from different cell populations from specific microenvironments...
October 18, 2016: Biofabrication
Jun Hwa Lee, Byong Chul Yoo, Yun Hwan Kim, Sun-A Ahn, Seung-Gu Yeo, Jae Youl Cho, Kyung-Hee Kim, Seung Cheol Kim
BACKGROUND: A low-mass-ion discriminant equation (LOME) was constructed to investigate whether systematic low-mass-ion (LMI) profiling could be applied to ovarian cancer (OVC) screening. RESULTS: Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry was performed to obtain mass spectral data on metabolites detected as LMIs up to a mass-to-charge ratio (m/z) of 2500 for 1184 serum samples collected from healthy individuals and patients with OVC, other types of cancer, or several types of benign tumor...
2016: BioData Mining
Gabriel Ogaya-Pinies, Yash Kadakia, Hariharan Palayapalayam-Ganapathi, Tracey Woodlief, Cathy Jenson, Vipul Patel
BACKGROUND: One of the key factors contributing to morbidity associated with salvage radical prostatectomy is a significant vesicourethral anastomosis (VUA) disruption or postoperative tissue dehiscence in the region of the distal bladder neck that causes a large prolonged urinary leak, perineal pain, and delayed catheter removal. OBJECTIVE: To describe our surgical technique using a urinary bladder extracellular matrix (UB-ECM) scaffold incorporated into the base of the VUA and the distal bladder neck during salvage robot-assisted radical prostatectomy (sRARP) and to assess outcomes and safety...
October 14, 2016: European Urology
Shaoyu Yang, Xueqin Chen, Yuelong Pan, Jiekai Yu, Xin Li, Shenglin Ma
The present study aimed to identify potential serum biomarkers for predicting the clinical outcomes of patients with advanced non-small cell lung cancer (NSCLC) treated with epidermal growth factor receptor tyrosine kinase inhibitors (EGFR‑TKIs). A total of 61 samples were collected and analyzed using the integrated approach of magnetic bead‑based weak cation exchange chromatography and matrix‑assisted laser desorption/ionization‑time of flight‑mass spectrometry. The Zhejiang University Protein Chip Data Analysis system was used to identify the protein spectra of patients that are resistant and sensitive to EGFR‑TKIs...
October 11, 2016: Molecular Medicine Reports
Michael P Heaton, Timothy P L Smith, Jacky K Carnahan, Veronica Basnayake, Jiansheng Qiu, Barry Simpson, Theodore S Kalbfleisch
The availability of whole genome sequence (WGS) data has made it possible to discover protein variants in silico. However, existing bovine WGS databases do not show data in a form conducive to protein variant analysis, and tend to under represent the breadth of genetic diversity in U.S. beef cattle. Thus, our first aim was to use 96 beef sires, sharing minimal pedigree relationships, to create a searchable and publicly viewable set of mapped genomes relevant for 19 popular breeds of U.S. cattle. Our second aim was to identify protein variants encoded by the bovine endothelial PAS domain-containing protein 1 gene ( EPAS1), a gene associated with high-altitude pulmonary hypertension in Angus cattle...
2016: F1000Research
M Mulet, M Gomila, A Ramírez, S Cardew, E R B Moore, J Lalucat, E García-Valdés
Fifty-two Pseudomonas strains that were difficult to identify at the species level in the phenotypic routine characterizations employed by clinical microbiology laboratories were selected for genotypic-based analysis. Species level identifications were done initially by partial sequencing of the DNA dependent RNA polymerase sub-unit D gene (rpoD). Two other gene sequences, for the small sub-unit ribosonal RNA (16S rRNA) and for DNA gyrase sub-unit B (gyrB) were added in a multilocus sequence analysis (MLSA) study to confirm the species identifications...
October 15, 2016: European Journal of Clinical Microbiology & Infectious Diseases
Ian Streeter, Peter W Harrison, Adam Faulconbridge, Paul Flicek, Helen Parkinson, Laura Clarke
The Human Induced Pluripotent Stem Cell Initiative (HipSci) isf establishing a large catalogue of human iPSC lines, arguably the most well characterized collection to date. The HipSci portal enables researchers to choose the right cell line for their experiment, and makes HipSci's rich catalogue of assay data easy to discover and reuse. Each cell line has genomic, transcriptomic, proteomic and cellular phenotyping data. Data are deposited in the appropriate EMBL-EBI archives, including the European Nucleotide Archive (ENA), European Genome-phenome Archive (EGA), ArrayExpress and PRoteomics IDEntifications (PRIDE) databases...
October 12, 2016: Nucleic Acids Research
Natasha Pahuja, Nimisha R Kumar, Rushad Shroff, Rohit Shetty, Rudy M M A Nuijts, Anuprita Ghosh, Abhijit Sinha-Roy, Shyam S Chaurasia, Rajiv R Mohan, Arkasubhra Ghosh
Purpose: In this study, we elucidated the differential expression of a set of local molecular factors in ectatic cone area of the cornea to uncover a functional cause for focal corneal weakening characteristic of the keratoconus (KC) disease. Methods: All human corneal samples were collected after approval of Institutional Ethics Committee and informed consent. Keratoconus patients were classified based on clinical parameters, topographical features, and structural deformity...
October 1, 2016: Investigative Ophthalmology & Visual Science
Arminder Deol, Joanne P Webster, Martin Walker, Maria-Gloria Basáñez, T Déirdre Hollingsworth, Fiona M Fleming, Antonio Montresor, Michael D French
BACKGROUND: Understanding whether schistosomiasis control programmes are on course to control morbidity and potentially switch towards elimination interventions would benefit from user-friendly quantitative tools that facilitate analysis of progress and highlight areas not responding to treatment. This study aimed to develop and evaluate such a tool using large datasets collected during Schistosomiasis Control Initiative-supported control programmes. METHODS: A discrete-time Markov model was developed using transition probability matrices parameterized with control programme longitudinal data on Schistosoma mansoni obtained from Uganda and Mali...
October 12, 2016: Parasites & Vectors
Jennifer M Buchman-Schmitt, Sarah J Brislin, Noah C Venables, Thomas E Joiner, Christopher J Patrick
BACKGROUND: The RDoC matrix framework calls for investigation of mental health problems through analysis of core biobehavioral processes quantified and studied across multiple domains of measurement. Critics have raised concerns about RDoC, including overemphasis on biological concepts/measures and disregard for the principle of multifinality, which holds that identical biological predispositions can give rise to differing behavioral outcomes. The current work illustrates an ontogenetic process approach to addressing these concerns, focusing on biobehavioral traits corresponding to RDoC constructs as predictors, and suicidal behavior as the outcome variable...
October 1, 2016: Journal of Affective Disorders
Mohammad Mahdi Moein, Aziza El Beqqali, Mohamed Abdel-Rehim
Bioanalysis is an essential part in drug discovery and development. Bioanalysis is related to the analysis of analytes (drugs, metabolites, biomarkers) in biological samples and it involves several steps from sample collection to sample analysis and data reporting. The first step is sample collection from clinical or preclinical studies; then sending the samples to laboratory for analysis. Second step is sample clean-up (sample preparation) and it is very important step in bioanalysis. In order to reach reliable results, a robust and stable sample preparation method should be applied...
September 20, 2016: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
P Gonzalez-Navarro, M Moghadamfalahi, M Akcakaya, D Erdogmus
Multichannel electroencephalography (EEG) is widely used in non-invasive brain computer interfaces (BCIs) for user intent inference. EEG can be assumed to be a Gaussian process with unknown mean and autocovariance, and the estimation of parameters is required for BCI inference. However, the relatively high dimensionality of the EEG feature vectors with respect to the number of labeled observations lead to rank deficient covariance matrix estimates. In this manuscript, to overcome ill-conditioned covariance estimation, we propose a structure for the covariance matrices of the multichannel EEG signals...
February 2017: Signal Processing
Chengjun Huang, Xiang Chen, Shuai Cao, Xu Zhang
OBJECTIVE: Some skeletal muscles can be subdivided into smaller segments called muscle-tendon units (MTUs). The purpose of this paper is to propose a framework to locate the active region of the corresponding MTUs within a single skeletal muscle and to analyze the activation level varieties of different MTUs during a dynamic motion task. APPROACH: Biceps brachii and gastrocnemius were selected as targeted muscles and three dynamic motion tasks were designed and studied...
October 5, 2016: Journal of Neural Engineering
David R Espeso, Esteban Martínez-García, Víctor de Lorenzo, Ángel Goñi-Moreno
The often striking macroscopic patterns developed by motile bacterial populations on agar plates are a consequence of the environmental conditions where the cells grow and spread. Parameters such as medium stiffness and nutrient concentration have been reported to alter cell swimming behavior, while mutual interactions among populations shape collective patterns. One commonly observed occurrence is the mutual inhibition of clonal bacteria when moving toward each other, which results in a distinct halt at a finite distance on the agar matrix before having direct contact...
2016: Frontiers in Microbiology
Stavros-Konstantinos Stavrakos, Saeema Ahmed-Kristensen
BACKGROUND: Past research on anthropometry, especially in the industry of external ear worn products, stresses that positive comfort is enhanced when there is sufficient knowledge of human factors; however, most anthropometric studies focus only on the acquirement and presentation of data. OBJECTIVE: The aim of this paper is to provide with different methods to support design applications of 3-dimensional head and ear data with a focus on external ear products. METHODS: Two hundred persons representing the Danish population were scanned...
October 17, 2016: Work: a Journal of Prevention, Assessment, and Rehabilitation
Kh Rezaee, E Azizi, J Haddadnia
BACKGROUND: Epilepsy is a severe disorder of the central nervous system that predisposes the person to recurrent seizures. Fifty million people worldwide suffer from epilepsy; after Alzheimer's and stroke, it is the third widespread nervous disorder. OBJECTIVE: In this paper, an algorithm to detect the onset of epileptic seizures based on the analysis of brain electrical signals (EEG) has been proposed. 844 hours of EEG were recorded form 23 pediatric patients consecutively with 163 occurrences of seizures...
June 2016: Journal of Biomedical Physics & Engineering
Dawn Magnusson, Monica Roe, Jeff Hartman
PURPOSE: To examine community perspectives regarding the strengths, weaknesses, opportunities, and threats of a community-based rehabilitation (CBR) program in Toledo District, Belize. METHOD: A participatory approach was implemented using the CBR Matrix as a conceptual framework. Semi-structured interviews were conducted with CBR community partners and program participants living in Toledo District. Respondents were recruited until thematic saturation was achieved (i...
September 27, 2016: Disability and Rehabilitation
Zihe Wang, Chuanhao Tang, Yi Liu, Bin Xu, Haifeng Qin, Yangyang Lei, Hongjun Gao, Kun He, Xiaoqing Liu
BACKGROUND: This study aimed at using matrix-assisted laser desorption ionization - time of flight mass spectrometer (matrix-assisted laser desorption ionization time-of-flight mass spectrometry, MALDI-TOF-MS) screening the difference serum peptides during epidermal growth factor tyrosine kinase inhibitors (EGFR-TKIs) treatment and exploring their significance of advanced NSCLC patients. METHODS: Collect 102 serum samples from 34 advanced NSCLC patients, which are before TKI treatment, best effect of treatment and after progession...
September 20, 2016: Zhongguo Fei Ai za Zhi, Chinese Journal of Lung Cancer
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