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https://www.readbyqxmd.com/read/28231386/evaluating-the-effectiveness-of-rna-in-situ-hybridization-for-detecting-lung-adenocarcinoma-with-anaplastic-lymphoma-kinase-rearrangement
#1
Naoki Nakajima, Akihiko Yoshizawa, Kyoko Kondo, Mariyo Rokutan-Kurata, Masahiro Hirata, Ayako Furuhata, Shinji Sumiyoshi, Makoto Sonobe, Toshi Menju, Masanobu Momose, Masakazu Fujimoto, Hiroshi Date, Hironori Haga
AIMS: An easy and rapid assay for detecting mRNA in formalin-fixed paraffin-embedded samples (RNA-in situ hybridization; RNA-ISH) has been reported recently. We investigated the diagnostic accuracy of RNA-ISH for detecting lung adenocarcinoma (LA) with anaplastic lymphoma kinase (ALK) gene rearrangement. METHODS AND RESULTS: We tested ALK RNA-ISH on 11 resected LAs for which ALK fusion was confirmed by immunohistochemistry (IHC) and/or fluorescence in situ hybridization (FISH)...
February 23, 2017: Histopathology
https://www.readbyqxmd.com/read/28231382/accurate-measurement-of-transgene-copy-number-in-crop-plants-using-droplet-digital-pcr
#2
Ray Collier, Kasturi Dasgupta, Yan-Ping Xing, Bryan Tarape Hernandez, Min Shao, Dominica Rohozinski, Emma Kovak, Jeanie Lin, Maria Luiza P de Oliveira, Ed Stover, Kent F McCue, Frank G Harmon, Ann Blechl, James G Thomson, Roger Thilmony
Genetic transformation is a powerful means for the improvement of crop plants, but requires labor and resource intensive methods. An efficient method for identifying single copy transgene insertion events from a population of independent transgenic lines is desirable. Currently transgene copy number is estimated by either Southern blot hybridization analyses or quantitative polymerase chain reaction (qPCR) experiments. Southern hybridization is a convincing and reliable method, but it also is expensive, time-consuming and often requires a large amount of genomic DNA and radioactively labeled probes...
February 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28231342/nonlinear-image-registration-with-bidirectional-metric-and-reciprocal-regularization
#3
Shihui Ying, Dan Li, Bin Xiao, Yaxin Peng, Shaoyi Du, Meifeng Xu
Nonlinear registration is an important technique to align two different images and widely applied in medical image analysis. In this paper, we develop a novel nonlinear registration framework based on the diffeomorphic demons, where a reciprocal regularizer is introduced to assume that the deformation between two images is an exact diffeomorphism. In detail, first, we adopt a bidirectional metric to improve the symmetry of the energy functional, whose variables are two reciprocal deformations. Secondly, we slack these two deformations into two independent variables and introduce a reciprocal regularizer to assure the deformations being the exact diffeomorphism...
2017: PloS One
https://www.readbyqxmd.com/read/28231286/lexicon-enhanced-sentiment-analysis-framework-using-rule-based-classification-scheme
#4
Muhammad Zubair Asghar, Aurangzeb Khan, Shakeel Ahmad, Maria Qasim, Imran Ali Khan
With the rapid increase in social networks and blogs, the social media services are increasingly being used by online communities to share their views and experiences about a particular product, policy and event. Due to economic importance of these reviews, there is growing trend of writing user reviews to promote a product. Nowadays, users prefer online blogs and review sites to purchase products. Therefore, user reviews are considered as an important source of information in Sentiment Analysis (SA) applications for decision making...
2017: PloS One
https://www.readbyqxmd.com/read/28231144/effects-of-two-step-transamidation-of-wheat-semolina-on-the-technological-properties-of-gluten
#5
Salvatore Moscaritolo, Lucia Treppiccione, Antonio Ottombrino, Mauro Rossi
Celiac disease (CD) is an immune-mediated disorder caused by the ingestion of wheat gluten. A lifelong, gluten-free diet is required to alleviate symptoms and to normalize the intestinal mucosa. We previously found that transamidation reaction by microbial transglutaminase (mTG) was effective in down-regulating the gliadin-specific immune response in CD patients. In this study, the two-step transamidation protocol was adopted to treat commercial wheat semolina on a pilot scale. The effectiveness of the enzymatic reaction was tested by means of consolidated biochemical and immunological methods on isolated prolamins...
June 29, 2016: Foods (Basel, Switzerland)
https://www.readbyqxmd.com/read/28231069/the-potential-of-transcranial-photobiomodulation-therapy-for-treatment-of-major-depressive-disorder
#6
Farzad Salehpour, Seyed Hossein Rasta
Major depressive disorder is a common debilitating mood disorder that affects quality of life. Prefrontal cortex abnormalities, an imbalance in neurotransmitters, neuroinflammation, and mitochondrial dysfunction are the major factors in the etiology of major depressive disorder. Despite the efficacy of pharmacotherapy in the treatment of major depressive disorder, 30%-40% of patients do not respond to antidepressants. Given this, exploring the alternative therapies for treatment or prevention of major depressive disorder has aroused interest among scientists...
February 23, 2017: Reviews in the Neurosciences
https://www.readbyqxmd.com/read/28230979/simple-expendable-3d-printed-microfluidic-systems-for-sample-preparation-of-petroleum
#7
Erica Megumi Kataoka, Rui Cesar Murer, Jandyson Machado Santos, Rogerio Mesquita de Carvalho, Marcos Nogueira Eberlin, Fabio Augusto, Ronei Jesus Poppi, Angelo Luiz Gobbi, Leandro Wang Hantao
In this study, we introduce a simple protocol to manufacture disposable, 3D-printed microfluidic systems for sample preparation of petroleum. Such platform is produced with a consumer-grade 3D-printer, using fused deposition modeling. Successful incorporation of solid-phase extraction (SPE) to microchip was ensured by facile 3D element integration using proposed approach. This 3D-printed μSPE device was applied to challenging matrices in oil & gas industry, such as crude oil and oil-brine emulsions. Case studies investigated important limitations of non-silicon and non-glass microchips, namely, resistance to nonpolar solvents and conservation of sample integrity...
February 23, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28230906/evaluation-of-skin-surface-as-an-alternative-source-of-reference-dna-samples-a-pilot-study
#8
Mohammed H Albujja, Abdul Aziz Bin Dukhyil, Abdul Rauf Chaudhary, Ahmed Ch Kassab, Ahmed M Refaat, Saranya Ramesh Babu, Mohammad K Okla, Sachil Kumar
An acceptable area for collecting DNA reference sample is a part of the forensic DNA analysis development. The aim of this study was to evaluate skin surface cells (SSC) as an alternate source of reference DNA sample. From each volunteer (n = 10), six samples from skin surface areas (forearm and fingertips) and two traditional samples (blood and buccal cells) were collected. Genomic DNA was extracted and quantified then genotyped using standard techniques. The highest DNA concentration of SSC samples was collected using the tape/forearm method of collection (2...
February 23, 2017: Journal of Forensic Sciences
https://www.readbyqxmd.com/read/28230805/preparation-of-photoirradiation-molecular-imprinting-polymer-for-selective-separation-of-branched-cyclodextrins
#9
Haoran Fan, Jinpeng Wang, Qingran Meng, Xueming Xu, Tianming Fan, Zhengyu Jin
In the present study, photoirradiation molecularly imprinted polymer (MIP) with azobenzene was used as a functional monomer for the selective separation of the branched cyclodextrins. The functional monomer 4-methacryloyloxy azobenzene (MAA) and the molecular template 6-O-α-d-maltosyl-β-cyclodextrin (G2-β-CD) were implemented for the molecular imprinting. The core-shell structure of photoirradiation MIP was visualized by the transmission electron microscopy (TEM). With Fourier transform infrared spectroscopy (FTIR) and thermogravimetric analysis (TGA), we identified that G2-β-CD was imprinted into the polymer and removed from the MIP...
February 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28230746/oxidation-of-5-chloromethylfurfural-cmf-to-2-5-diformylfuran-dff
#10
Ana I Vicente, Jaime A S Coelho, Svilen P Simeonov, Hristina I Lazarova, Margarita D Popova, Carlos A M Afonso
2,5-Diformylfuran (DFF) is an important biorenewable building block, namely for the manufacture of new polymers that may replace existing materials derived from limited fossil fuel resources. The current reported methods for the preparation of DFF are mainly derived from the oxidation of 5-hydroxymethylfurfural (HMF) and, to a lesser extent, directly from fructose. 5-Chloromethylfurfural (CMF) has been considered an alternative to HMF as an intermediate building block due to its advantages regarding stability, polarity, and availability from glucose and cellulose...
February 20, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28230584/microsurgical-replantation-of-total-avulsed-scalp-extending-the-limits
#11
Yunbo Jin, Chen Hua, Xiaojie Hu, Hui Chen, Gang Ma, Yun Zou, Bin Chen, Dongze Lyu, Mathias Tremp, Xiaoxi Lin
BACKGROUND: Avulsion of the scalp is a rare but severe trauma and challenging to the reconstructive surgeon. It poses not only physical concussion but also significant persisting psychological distress to the patients. METHODS: Medical records from 5 patients who suffered scalp avulsion were reviewed retrospectively. The following data and methods were assessed: age, number of vessels repaired, method of replantation, vein grafts required, blood transfusion, ischemia time, total operating time, and percentage of scalp survival...
February 22, 2017: Journal of Craniofacial Surgery
https://www.readbyqxmd.com/read/28230532/optimization-of-volumetric-breast-density-estimation-in-digital-mammograms
#12
Katharina Holland, Albert Gubern-Merida, Ritse Mann, Nico Karssemeijer
Fibroglandular tissue volume and percent density can be estimated in unprocessed mammograms using a physics-based method, which relies on an internal reference value representing the projection of fat only. However, pixels representing fat only may not be present in dense breasts, causing an underestimation of density measurements. In this work, we investigate alternative approaches for obtaining a tissue reference value to improve density estimations, particularly in dense breasts. Two of three investigated reference values (F1, F2) are percentiles of the pixel value distribution in the breast interior (the contact area of breast and compression paddle)...
February 23, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28230271/consumer-acceptance-and-aroma-characterization-of-navy-bean-phaseolus-vulgaris-powders-prepared-by-extrusion-and-conventional-processing-methods
#13
Edward Szczygiel, Janice B Harte, Gale M Strasburg, Sungeun Cho
BACKGROUND: Food products produced with bean ingredients are gaining in popularity among consumers due to the reported health benefits. Navy bean (Phaseolus vulgaris) powder produced through extrusion can be considered as a resource-efficient alternative to conventional methods, which often involve high water inputs. Therefore, navy bean powders produced with extrusion and conventional methods were assessed for the impact of processing on consumer liking in end-use products and odor-active compounds...
February 23, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28230179/crowdsourcing-scoring-of-immunohistochemistry-images-evaluating-performance-of-the-crowd-and-an-automated-computational-method
#14
Humayun Irshad, Eun-Yeong Oh, Daniel Schmolze, Liza M Quintana, Laura Collins, Rulla M Tamimi, Andrew H Beck
The assessment of protein expression in immunohistochemistry (IHC) images provides important diagnostic, prognostic and predictive information for guiding cancer diagnosis and therapy. Manual scoring of IHC images represents a logistical challenge, as the process is labor intensive and time consuming. Since the last decade, computational methods have been developed to enable the application of quantitative methods for the analysis and interpretation of protein expression in IHC images. These methods have not yet replaced manual scoring for the assessment of IHC in the majority of diagnostic laboratories and in many large-scale research studies...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28230006/evaluation-of-the-safety-and-efficacy-of-percutaneous-radiofrequency-ablation-for-treating-multiple-breast-fibroadenoma
#15
Ping Li, Tang Xiao-Yin, Dan Cui, Jia-Chang Chi, Zhi Wang, Tao Wang, Xing-Xing Qi, Bo Zhai
BACKGROUND: This study was conducted to evaluate the safety and efficacy of ultrasound (US)-guided percutaneous radiofrequency ablation (RFA) for multiple breast fibroadenoma as an alternative to surgical resection. PATIENTS AND METHODS: Sixty-five patients with multiple breast fibroadenoma accepted general anesthesia and US-guided percutaneous RFA in our hospital from September 2014 to January 2016. Contrast-enhanced US (CEUS) was used immediately after operation to determine whether the tumor was ablated completely...
December 2016: Journal of Cancer Research and Therapeutics
https://www.readbyqxmd.com/read/28229948/mixing-and-capping-techniques-for-activated-carbon-based-sediment-remediation-efficiency-and-adverse-effects-for-lumbriculus-variegatus
#16
Sebastian Abel, Inna Nybom, Kimmo Mäenpää, Sarah E Hale, Gerard Cornelissen, Jarkko Akkanen
Activated carbon (AC) has been proven to be highly effective for the in-situ remediation of sediments contaminated with a wide range of hydrophobic organic contaminants (HOCs). However, adverse biological effects, especially to benthic organisms, can accompany this promising remediation potential. In this study, we compare both the remediation potential and the biological effects of several AC materials for two application methods: mixing with sediment (MIX) at doses of 0.1 and 1.0% based on sediment dw and thin layer capping (TLC) with 0...
February 16, 2017: Water Research
https://www.readbyqxmd.com/read/28229483/venous-hemodialysis-catheters-and-cardiac-implantable-electronic-devices-avoiding-a-high-risk-combination
#17
EDITORIAL
Theodore F Saad, Henry L Weiner
End-stage renal disease is frequently accompanied by cardiac comorbidity that warrants treatment with a cardiovascular implantable electronic device (permanent pacemaker or implantable cardioverter-defibrillator). In the United States, chronic hemodialysis (HD) population, cardiac implantable devices are present in up to 10.5% of patients; a venous HD catheter is utilized for blood access in 18% of prevalent patients. The concomitant presence of a venous HD catheter and cardiovascular implantable device creates a high-risk circumstance, with potential for causing symptomatic central venous stenosis, and for developing complicated endovascular infection...
February 23, 2017: Seminars in Dialysis
https://www.readbyqxmd.com/read/28229414/isolation-and-culture-of-satellite-cells-from-mouse-skeletal-muscle
#18
Antonio Musarò, Silvia Carosio
Skeletal muscle tissue is characterized by a population of quiescent mononucleated myoblasts, localized between the basal lamina and sarcolemma of myofibers, known as satellite cells. Satellite cells play a pivotal role in muscle homeostasis and are the major source of myogenic precursors in mammalian muscle regeneration.This chapter describes protocols for isolation and culturing satellite cells isolated from mouse skeletal muscles. The classical procedure, which will be discussed extensively in this chapter, involves the enzymatic dissociation of skeletal muscles, while the alternative method involves isolation of satellite cells from isolated myofibers in which the satellite cells remain in their in situ position underneath the myofiber basal lamina...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28229175/survival-prediction-of-trauma-patients-a-study-on-us-national-trauma-data-bank
#19
I Sefrioui, R Amadini, J Mauro, A El Fallahi, M Gabbrielli
BACKGROUND: Exceptional circumstances like major incidents or natural disasters may cause a huge number of victims that might not be immediately and simultaneously saved. In these cases it is important to define priorities avoiding to waste time and resources for not savable victims. Trauma and Injury Severity Score (TRISS) methodology is the well-known and standard system usually used by practitioners to predict the survival probability of trauma patients. However, practitioners have noted that the accuracy of TRISS predictions is unacceptable especially for severely injured patients...
February 22, 2017: European Journal of Trauma and Emergency Surgery: Official Publication of the European Trauma Society
https://www.readbyqxmd.com/read/28229145/oxidation-potentials-of-phenols-and-anilines-correlation-analysis-of-electrochemical-and-theoretical-values
#20
Ania S Pavitt, Eric J Bylaska, Paul G Tratnyek
Phenols and anilines have been studied extensively as reductants of environmental oxidants (such as manganese dioxide) and as reductates (e.g., model contaminants) that are transformed by environmental oxidants (ozone, triple organic matter, etc.). The thermodynamics and kinetics of these reactions have been interpreted using oxidation potentials for substituted phenols and anilines, often using a legacy experimental dataset that is of uncertain quality. Although there are many alternative oxidation potential data, there has been little systematic analysis of the relevance, reliability, and consistency of the data obtained by different methods...
February 23, 2017: Environmental Science. Processes & Impacts
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