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https://www.readbyqxmd.com/read/28454331/centrosome-amplification-in-chondrosarcomas-a-primary-cell-culture-and-cryopreserved-tumor-sample-study
#1
Carla Aparecida Pinheiro, Iberê Cauduro Soares, Valter Penna, Jeremy Squire, Rui Manuel Vieira Reis, Sandra Regina Morini da Silva, Isabela de Carvalho, Marjori Leiva Camparoto, Maicon Fernando Zanon da Silva, Adhemar Longatto Longatto Filho
The genetics background underlying the aggressiveness of chondrosarcoma (CS) is poorly understood. One possible cause of malignant transformation is chromosomal instability, which involves an error in mitotic segregation due to numerical and/or functional abnormalities of centrosomes. The present study aimed to evaluate centrosome amplification in cryopreserved samples of tumor tissue from patients with CS. An analysis was performed on 3 primary cultures of tumors from patients who underwent surgery between January 2012 and December 2012 at the Department of Orthopedics at the Barretos Cancer Hospital (Barretos, Brazil)...
March 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454176/phaseless-incoherent-optical-frequency-domain-spectroscopy
#2
Ziv Glasser, Gidon Zaychik, Rita Abramov, Daniel Gotliv, Shmuel Sternklar
We describe a new technique for incoherent optical frequency domain spectroscopy (I-OFDS) that does not require measurements of the RF phase spectrum in order to reconstruct the optical spectrum. It is based on the addition of either an optical or electronic reference line to the I-OFDS system. Compared to the spectrum acquired by a regular I-OFDS system, high accuracy (error<1%) is predicted and achieved.
May 1, 2017: Optics Letters
https://www.readbyqxmd.com/read/28454174/pilot-tone-based-self-homodyne-detection-using-optical-nonlinear-wave-mixing
#3
Yinwen Cao, Morteza Ziyadi, Ahmed Almaiman, Amirhossein Mohajerin-Ariaei, Peicheng Liao, Changjing Bao, Fatemeh Alishahi, Ahmad Fallahpour, Bishara Shamee, Asher J Willner, Youichi Akasaka, Tadashi Ikeuchi, Steven Wilkinson, Carsten Langrock, Martin M Fejer, Joseph Touch, Moshe Tur, Alan E Willner
An all-optical pilot-tone-based self-homodyne detection scheme using nonlinear wave mixing is experimentally demonstrated. Two scenarios are investigated using (1) multiple wavelength-division-multiplexed channels with sufficient power of the pilot tones and (2) a single channel with a low-power pilot tone. The eye diagram and bit error rate of the system are studied by tuning various parameters such as pump power, relative phase, and pilot-to-signal ratio.
May 1, 2017: Optics Letters
https://www.readbyqxmd.com/read/28454134/self-stabilization-of-an-optical-frequency-comb-using-a-short-path-length-interferometer
#4
James P Cahill, Weimin Zhou, Curtis R Menyuk
We stabilized the repetition rate of an optical frequency comb using a self-referenced phase-locked loop. The phase-locked loop generated its error signal with a fiber-optic delay-line interferometer that had a path-length difference of 8 m. We used the stabilized repetition rate to generate a 10 GHz signal with a single-sideband phase noise that was limited by environmental noise to -120  dBc/Hz at an offset frequency of 1 kHz. Modeling results indicate that thermoconductive noise sets a fundamental phase noise limit for an 8 m interferometer of -152  dBc/Hz at a 1 kHz offset frequency...
May 1, 2017: Optics Letters
https://www.readbyqxmd.com/read/28454130/directly-modulated-green-light-diode-pumped-solid-state-laser-for-underwater-wireless-optical-communication
#5
Jing Xu, Meiwei Kong, Aobo Lin, Yuhang Song, Jun Han, Zhiwei Xu, Bo Wu, Shiming Gao, Ning Deng
It is widely known that a diode-pumped solid-state laser (DPSSL) has very limited modulation bandwidth. Recently, we directed our attention toward the opportunities for directly modulating a DPSSL to generate high-speed green-light signals, with high power and superior beam quality, which are highly desirable in underwater wireless optical communication. The constraint imposed by the limited modulation bandwidth of a DPSSL is circumvented with the strategy of orthogonal frequency-division multiplexing and power loading...
May 1, 2017: Optics Letters
https://www.readbyqxmd.com/read/28454123/sensitivity-and-specificity-of-the-modified-balance-error-scoring-system-in-concussed-collegiate-student-athletes
#6
Thomas A Buckley, Barry A Munkasy, Brandy P Clouse
OBJECTIVE: To assess the efficacy of the modified Balance Error Scoring System (mBESS) compared with the Balance Error Scoring System (BESS) in an acutely concussed population. DESIGN: Prospective observational study. SETTING: University athletic training room. PATIENTS: Thirty-five collegiate student-athletes (18 Female, 18.9 ± 0.8 year old, height: 1.71 ± 0.12 m, weight: 76.3 ± 24.1 kg) with diagnosed concussions and baseline BESS/mBESS tests...
April 27, 2017: Clinical Journal of Sport Medicine: Official Journal of the Canadian Academy of Sport Medicine
https://www.readbyqxmd.com/read/28453911/validation-of-biomechanical-deformable-image-registration-in-the-abdomen-thorax-and-pelvis-in-a-commercial-radiotherapy-treatment-planning-system
#7
Michael Velec, Joanne L Moseley, Stina Svensson, Björn Hårdemark, David A Jaffray, Kristy K Brock
PURPOSE: The accuracy of deformable image registration tools can vary widely between imaging modalities and specific implementations of the same algorithms. A biomechanical model-based algorithm initially developed in-house at an academic institution was translated into a commercial radiotherapy treatment planning system and validated for multiple imaging modalities and anatomic sites. METHODS: Biomechanical deformable registration (Morfeus) is a geometry driven algorithm based on the finite element method...
April 28, 2017: Medical Physics
https://www.readbyqxmd.com/read/28453829/experimenting-the-hospital-survey-on-patient-safety-culture-in-prevention-facilities-in-italy-psychometric-properties
#8
Carmen Tereanu, Scott A Smith, Giuseppe Sampietro, Francesco Sarnataro, Giuliana Mazzoleni, Bruno Pesenti, Luca C Sala, Roberto Cecchetti, Massimo Arvati, Dania Brioschi, Michela Viscardi, Chiara Prati, Giorgio G Barbaglio
Objective: The Agency for Healthcare Research and Quality Hospital Survey on Patient Safety Culture (HSOPS) was designed to assess staff views on patient safety culture in hospital. This study examines psychometrics of the Italian translation of the HSOPS for use in territorial prevention facilities. Design: After minimal adjustments and pre-test of the Italian version, a qualitative cross-sectional study was carried out. Setting: Departments of Prevention (DPs) of four Local Health Authorities in Northern Italy...
April 1, 2017: International Journal for Quality in Health Care
https://www.readbyqxmd.com/read/28453820/reliability-of-clinical-impact-grading-by-healthcare-professionals-of-common-prescribing-error-and-optimisation-cases-in-critical-care-patients
#9
Richard S Bourne, Rob Shulman, Mark Tomlin, Mark Borthwick, Will Berry, Gary H Mills
Objective: To identify between and within profession-rater reliability of clinical impact grading for common critical care prescribing error and optimisation cases. To identify representative clinical impact grades for each individual case. Design: Electronic questionnaire. Setting: 5 UK NHS Trusts. Participants: 30 Critical care healthcare professionals (doctors, pharmacists and nurses). Intervention: Participants graded severity of clinical impact (5-point categorical scale) of 50 error and 55 optimisation cases...
April 1, 2017: International Journal for Quality in Health Care
https://www.readbyqxmd.com/read/28453696/epstein-barr-virus-associated-gastric-cancer-reveals-intratumoral-heterogeneity-of-pik3ca-mutations
#10
C Böger, S Krüger, H M Behrens, S Bock, J Haag, H Kalthoff, C Röcken
Background: Recent whole-genome sequencing identified four molecular subtypes of gastric cancer (GC), of which the subgroup of Epstein-Barr virus-associated GC (EBVaGC) showed a significant enrichment of PIK3CA mutations. We here aimed to validate independently the enrichment of PIK3CA mutations in EBVaGC of a Central European GC cohort, to correlate EBV status with clinico-pathological patient characteristics and to test for a major issue of GC, intratumoral heterogeneity. Patients and methods: In a first step, 484 GCs were screened for EBV and PIK3CA hot spot mutations of exon 9/20 using EBER in situ hybridization and pyrosequencing, respectively...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28453674/ntcard-a-streaming-algorithm-for-cardinality-estimation-in-genomics-data
#11
Hamid Mohamadi, Hamza Khan, Inanc Birol
Motivation: Many bioinformatics algorithms are designed for the analysis of sequences of some uniform length, conventionally referred to as k -mers. These include de Bruijn graph assembly methods and sequence alignment tools. An efficient algorithm to enumerate the number of unique k -mers, or even better, to build a histogram of k -mer frequencies would be desirable for these tools and their downstream analysis pipelines. Among other applications, estimated frequencies can be used to predict genome sizes, measure sequencing error rates, and tune runtime parameters for analysis tools...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453672/primerize-2d-automated-primer-design-for-rna-multidimensional-chemical-mapping
#12
Siqi Tian, Rhiju Das
Summary: Rapid RNA synthesis of comprehensive single mutant libraries and targeted multiple mutant libraries is enabling new multidimensional chemical approaches to solve RNA structures. PCR assembly of DNA templates and in vitro transcription allow synthesis and purification of hundreds of RNA mutants in a cost-effective manner, with sharing of primers across constructs allowing significant reductions in expense. However, these protocols require organization of primer locations across numerous 96 well plates and guidance for pipetting, non-trivial tasks for which informatics and visualization tools can prevent costly errors...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453648/recent-advances-in-sequence-assembly-principles-and-applications
#13
Qingfeng Chen, Chaowang Lan, Liang Zhao, Jianxin Wang, Baoshan Chen, Yi-Ping Phoebe Chen
The application of advanced sequencing technologies and the rapid growth of various sequence data have led to increasing interest in DNA sequence assembly. However, repeats and polymorphism occur frequently in genomes, and each of these has different impacts on assembly. Further, many new applications for sequencing, such as metagenomics regarding multiple species, have emerged in recent years. These not only give rise to higher complexity but also prevent short-read assembly in an efficient way. This article reviews the theoretical foundations that underlie current mapping-based assembly and de novo-based assembly, and highlights the key issues and feasible solutions that need to be considered...
April 26, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28453641/phenotypic-and-genetic-analysis-of-the-leopard-complex-spotting-in-noriker-horses
#14
Thomas Druml, Gertrud Grilz-Seger, Markus Neuditschko, Barbara Neuhauser, Gottfried Brem
Genetic analyses of coat colors are frequently restricted to subjectively categorized phenotype information. The aim of this study was to develop a method to numerically quantify the variability of leopard complex spotting phenotypes introducing tools from image analysis. Generalized Procrustes Analysis eliminates systematic errors due to imaging process. The binarization of normalised images and the application of Principal Component Analysis on the derived pixel matrices, transform pixel information into numerical data space...
April 27, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28453637/automated-identification-of-implausible-values-in-growth-data-from-pediatric-electronic-health-records
#15
Carrie Daymont, Michelle E Ross, A Russell Localio, Alexander G Fiks, Richard C Wasserman, Robert W Grundmeier
Objective: Large electronic health record (EHR) datasets are increasingly used to facilitate research on growth, but measurement and recording errors can lead to biased results. We developed and tested an automated method for identifying implausible values in pediatric EHR growth data. Materials and Methods: Using deidentified data from 46 primary care sites, we developed an algorithm to identify weight and height values that should be excluded from analysis, including implausible values and values that were recorded repeatedly without remeasurement...
April 26, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28453624/inferring-rates-and-length-distributions-of-indels-using-approximate-bayesian-computation
#16
Eli Levy Karin, Dafna Shkedy, Haim Ashkenazy, Reed A Cartwright, Tal Pupko
The most common evolutionary events at the molecular level are single-base substitutions, and insertions and deletions of short DNA segments (indels). A large body of research has been devoted to develop probabilistic substitution models and to infer their parameters using likelihood and Bayesian approaches. In contrast, relatively little has been done to model indel dynamics, probably due to the difficulty in writing explicit likelihood functions. Here, we contribute to the effort of modeling indel dynamics by presenting SpartaABC, an approximate Bayesian computation (ABC) approach to infer indel parameters from sequence data (either aligned or unaligned)...
April 26, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28453597/-a-modification-of-cronbach%C3%A2-s-alpha-coefficient-by-correlated-errors
#17
Sergio Alexis Dominguez-Lara, César Merino-Soto
No abstract text is available yet for this article.
February 2017: Revista Médica de Chile
https://www.readbyqxmd.com/read/28453559/evaluation-of-the-reproducibility-of-amplicon-sequencing-with-illumina-miseq-platform
#18
Chongqing Wen, Liyou Wu, Yujia Qin, Joy D Van Nostrand, Daliang Ning, Bo Sun, Kai Xue, Feifei Liu, Ye Deng, Yuting Liang, Jizhong Zhou
Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33...
2017: PloS One
https://www.readbyqxmd.com/read/28453544/predicting-herbivore-faecal-nitrogen-using-a-multispecies-near-infrared-reflectance-spectroscopy-calibration
#19
Miriam Villamuelas, Emmanuel Serrano, Johan Espunyes, Néstor Fernández, Jorge R López-Olvera, Mathieu Garel, João Santos, María Ángeles Parra-Aguado, Maurizio Ramanzin, Xavier Fernández-Aguilar, Andreu Colom-Cadena, Ignasi Marco, Santiago Lavín, Jordi Bartolomé, Elena Albanell
Optimal management of free-ranging herbivores requires the accurate assessment of an animal's nutritional status. For this purpose 'near-infrared reflectance spectroscopy' (NIRS) is very useful, especially when nutritional assessment is done through faecal indicators such as faecal nitrogen (FN). In order to perform an NIRS calibration, the default protocol recommends starting by generating an initial equation based on at least 50-75 samples from the given species. Although this protocol optimises prediction accuracy, it limits the use of NIRS with rare or endangered species where sample sizes are often small...
2017: PloS One
https://www.readbyqxmd.com/read/28453537/an-efficient-and-robust-mri-guided-radiotherapy-planning-approach-for-targeting-abdominal-organs-and-tumours-in-the-mouse
#20
Veerle Kersemans, John S Beech, Stuart Gilchrist, Paul Kinchesh, Philip D Allen, James Thompson, Ana L Gomes, Zenobia D'Costa, Luke Bird, Iain D C Tullis, Robert G Newman, Aurelien Corroyer-Dulmont, Nadia Falzone, Abul Azad, Katherine A Vallis, Owen J Sansom, Ruth J Muschel, Borivoj Vojnovic, Mark A Hill, Emmanouil Fokas, Sean C Smart
INTRODUCTION: Preclinical CT-guided radiotherapy platforms are increasingly used but the CT images are characterized by poor soft tissue contrast. The aim of this study was to develop a robust and accurate method of MRI-guided radiotherapy (MR-IGRT) delivery to abdominal targets in the mouse. METHODS: A multimodality cradle was developed for providing subject immobilisation and its performance was evaluated. Whilst CT was still used for dose calculations, target identification was based on MRI...
2017: PloS One
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