keyword
MENU ▼
Read by QxMD icon Read
search

Dataset

keyword
https://www.readbyqxmd.com/read/28938719/population-wide-sampling-of-retrotransposon-insertion-polymorphisms-using-deep-sequencing-and-efficient-detection
#1
Qichao Yu, Wei Zhang, Xiaolong Zhang, Yongli Zeng, Yeming Wang, Yanhui Wang, Liqin Xu, Xiaoyun Huang, Nannan Li, Xinlan Zhou, Jie Lu, Xiaosen Guo, Guibo Li, Yong Hou, Shiping Liu, Bo Li
Active retrotransposons play important roles during evolution and continue to shape our genomes today, especially in genetic polymorphisms underlying a diverse set of diseases. However, studies of human retrotransposon insertion polymorphisms (RIPs) based on whole-genome deep sequencing at the population level have not been sufficiently undertaken, despite the obvious need for a thorough characterization of RIPs in the general population. Herein, we present a novel and efficient computational tool called Specific Insertions Detector (SID) for the detection of non-reference RIPs...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28938627/prostate-tumor-overexpressed-1-ptov1-promotes-docetaxel-resistance-and-survival-of-castration-resistant-prostate-cancer-cells
#2
Verónica Cánovas, Yolanda Puñal, Valentina Maggio, Enric Redondo, Mercedes Marín, Begoña Mellado, Mireia Olivan, Matilde Lleonart, Jacques Planas, Juan Morote, Rosanna Paciucci
Metastatic prostate cancer is presently incurable. The oncogenic protein PTOV1, first described in prostate cancer, was reported as overexpressed and significantly correlated with poor survival in numerous tumors. Here, we investigated the role of PTOV1 in prostate cancer survival to docetaxel and self-renewal ability. Transduction of PTOV1 in docetaxel-sensitive Du145 and PC3 cells significantly increased cell survival after docetaxel exposure and induced docetaxel-resistance genes expression (ABCB1, CCNG2 and TUBB2B)...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938536/integrating-omics-data-and-protein-interaction-networks-to-prioritize-driver-genes-in-cancer
#3
Tiejun Zhang, Di Zhang
Although numerous approaches have been proposed to discern driver from passenger, identification of driver genes remains a critical challenge in the cancer genomics field. Driver genes with low mutated frequency tend to be filtered in cancer research. In addition, the accumulation of different omics data necessitates the development of algorithmic frameworks for nominating putative driver genes. In this study, we presented a novel framework to identify driver genes through integrating multi-omics data such as somatic mutation, gene expression, and copy number alterations...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938172/artificial-intelligence-for-breast-cancer-screening-opportunity-or-hype
#4
Nehmat Houssami, Christoph I Lee, Diana S M Buist, Dacheng Tao
Interpretation of mammography for breast cancer (BC) screening can confer a mortality benefit through early BC detection, can miss a cancer that is present or fast growing, or can result in false-positives. Efforts to improve screening outcomes have mostly focused on intensifying imaging practices (double instead of single-reading, more frequent screens, or supplemental imaging) that may add substantial resource expenditures and harms associated with population screening. Less attention has been given to making mammography screening practice 'smarter' or more efficient...
September 19, 2017: Breast: Official Journal of the European Society of Mastology
https://www.readbyqxmd.com/read/28938159/lunatic-fringe-and-p53-cooperatively-suppress-mesenchymal-stem-like-breast-cancer
#5
Wen-Cheng Chung, Shubing Zhang, Lavanya Challagundla, Yunyun Zhou, Keli Xu
Claudin-low breast cancer (CLBC) is a poor prognosis molecular subtype showing stemness and mesenchymal features. We previously discovered that deletion of a Notch signaling modulator, Lunatic Fringe (Lfng), in the mouse mammary gland induced a subset of tumors resembling CLBC. Here we report that deletion of one copy of p53 on this background not only accelerated mammary tumor development but also led to a complete penetrance of the mesenchymal stem-like phenotype. All mammary tumors examined in the Lfng/p53 compound mutant mice displayed a mesenchymal/spindloid pathology...
September 19, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28938131/characterization-of-the-changes-in-eicosanoid-profiles-of-activated-macrophages-treated-with-20-s-ginsenoside-rg3
#6
Jae Won Lee, Yu Ri Choi, Hyuck Jun Mok, Hyun-A Seong, Dae Young Lee, Geum-Soog Kim, Ji Hye Yoon, Kwang Pyo Kim, Hyung Don Kim
In this study, we used ultra-performance liquid chromatography coupled with tandem mass spectrometry to assess the levels of eicosanoids from RAW264.7 macrophages treated with lipopolysaccharides (LPS) and 20(S)-ginsenoside Rg3 (Rg3). The production of nitric oxide (NO) and the secretion of tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) were increased in inflammatory macrophages treated with LPS. Rg3 treatment, however, decreased the levels of NO, TNF-α, and IL-6 in activated macrophages. Eicosanoids, known as major metabolites correlated with inflammation, have pro- or anti-inflammatory activities...
September 5, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28938087/emerging-opportunities-for-target-discovery-in-rare-cancers
#7
REVIEW
Tanaz Sharifnia, Andrew L Hong, Corrie A Painter, Jesse S Boehm
Rare cancers pose unique challenges to research due to their low incidence. Barriers include a scarcity of tissue and experimental models to enable basic research and insufficient patient accrual for clinical studies. Consequently, an understanding of the genetic and cellular features of many rare cancer types and their associated vulnerabilities has been lacking. However, new opportunities are emerging to facilitate discovery of therapeutic targets in rare cancers. Online platforms are allowing patients with rare cancers to organize on an unprecedented scale, tumor genome sequencing is now routinely performed in research and clinical settings, and the efficiency of patient-derived model generation has improved...
September 21, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28938012/f-map-a-bayesian-approach-to-infer-the-gene-regulatory-network-using-external-hints
#8
Maryam Shahdoust, Hamid Pezeshk, Hossein Mahjub, Mehdi Sadeghi
The Common topological features of related species gene regulatory networks suggest reconstruction of the network of one species by using the further information from gene expressions profile of related species. We present an algorithm to reconstruct the gene regulatory network named; F-MAP, which applies the knowledge about gene interactions from related species. Our algorithm sets a Bayesian framework to estimate the precision matrix of one species microarray gene expressions dataset to infer the Gaussian Graphical model of the network...
2017: PloS One
https://www.readbyqxmd.com/read/28937987/combination-of-minimum-enclosing-balls-classifier-with-svm-in-coal-rock-recognition
#9
QingJun Song, HaiYan Jiang, Qinghui Song, XieGuang Zhao, Xiaoxuan Wu
Top-coal caving technology is a productive and efficient method in modern mechanized coal mining, the study of coal-rock recognition is key to realizing automation in comprehensive mechanized coal mining. In this paper we propose a new discriminant analysis framework for coal-rock recognition. In the framework, a data acquisition model with vibration and acoustic signals is designed and the caving dataset with 10 feature variables and three classes is got. And the perfect combination of feature variables can be automatically decided by using the multi-class F-score (MF-Score) feature selection...
2017: PloS One
https://www.readbyqxmd.com/read/28937576/chronic-pain-in-families-a-cross-sectional-study-of-shared-social-behavioural-and-environmental-influences
#10
Paul Campbell, Kelvin P Jordan, Blair H Smith, Kate M Dunn
Chronic pain is common and creates significant burden to the individual and society. Emerging research has shown the influence of the family environment on pain outcomes. However it is not clear what shared factors between family members associate with chronic pain. This study aimed to investigate the family level contribution to an individual's chronic pain status. This was a cross sectional study using the Generation Scotland: Scottish Family Health Study dataset. This study focused on a nested cohort of dyads (only 2 relatives per family, n = 2714)...
September 11, 2017: Pain
https://www.readbyqxmd.com/read/28937505/measuring-outcomes-in-cataract-surgery
#11
Vivian L Qin, Felipe F Conti, Rishi P Singh
PURPOSE OF REVIEW: The article presents a review of recently published studies reporting postcataract surgery outcomes and the use of electronic systems to track them. RECENT FINDINGS: Current publications report several parameters to measure cataract outcomes such as visual acuity, patient-reported visual function, contrast sensitivity, reading speed, residual refractive errors and complications (intraoperative and postoperative). SUMMARY: Cataracts currently afflict an estimated 94 million people worldwide, and surgical removal is the only effective therapy known...
September 20, 2017: Current Opinion in Ophthalmology
https://www.readbyqxmd.com/read/28937491/improved-calcium-scoring-at-dual-energy-computed-tomography-angiography-using-a-high-z-contrast-element-and-novel-material-separation-technique
#12
Jack W Lambert, Yuxin Sun, Karen G Ordovas, Robert G Gould, Sizhe Wang, Benjamin M Yeh
OBJECTIVES: The aim of this study was to compare the accuracy of existing dual-energy computed tomography (CT) angiography coronary artery calcium scoring methods to those obtained using an experimental tungsten-based contrast material and a recently described contrast material extraction process (CMEP). METHODS: Phantom coronary arteries of varied diameters, with different densities and arcs of simulated calcified plaque, were sequentially filled with water, iodine, and tungsten contrast materials and scanned within a thorax phantom at rapid-kVp-switching dual-energy CT...
September 20, 2017: Journal of Computer Assisted Tomography
https://www.readbyqxmd.com/read/28937443/reducing-disability-durations-and-medical-costs-for-patients-with-a-carpal-tunnel-release-surgery-through-the-use-of-opioid-prescribing-guidelines
#13
Fraser W Gaspar, Roman Kownacki, Catherine S Zaidel, Craig F Conlon, Kurt T Hegmann
OBJECTIVE: The impacts of compliance with opioid prescribing guidelines on disability durations and medical costs for carpal tunnel release (CTR) were examined. METHODS: Using a dataset of insured US employees, opioid prescriptions for 7840 short-term disability cases with a CTR procedure were identified. Opioids prescriptions were compared with the American College of Occupational and Environmental Medicine (ACOEM)'s opioid prescribing guidelines for postoperative, acute pain, which recommends no more than a 5-day supply, a maximum morphine equivalent dose of 50 mg/day, and only short-acting opioids...
September 20, 2017: Journal of Occupational and Environmental Medicine
https://www.readbyqxmd.com/read/28937298/probing-the-toxicity-of-nanoparticles-a-unified-in-silico-machine-learning-model-based-on-perturbation-theory
#14
Riccardo Concu, Valeria V Kleandrova, Alejandro Speck-Planche, M Natália D S Cordeiro
Nanoparticles (NPs) are part of our daily life, having a wide range of applications in engineering, physics, chemistry, and biomedicine. However, there are serious concerns regarding the harmful effects that NPs can cause to the different biological systems and their ecosystems. Toxicity testing is an essential step for assessing the potential risks of the NPs, but the experimental assays are often very expensive and usually too slow to flag the number of NPs that may cause adverse effects. In silico models centered on quantitative structure-activity/toxicity relationships (QSAR/QSTR) are alternative tools that have become valuable supports to risk assessment, rationalizing the search for safer NPs...
September 22, 2017: Nanotoxicology
https://www.readbyqxmd.com/read/28937156/carsite-identifying-carbonylated-sites-of-human-proteins-based-on-a-one-sided-selection-resampling-method
#15
Yun Zuo, Cang-Zhi Jia
Protein carbonylation is one of the most important biomarkers of oxidative protein damage and such protein damage is linked to various diseases and aging. It is thus vital that carbonylation sites are identified accurately. In this study, CarSite, a novel bioinformatics tool, was established to identify carbonylation sites in human proteins. The one-sided selection (OSS) resampling method was used to establish balanced training datasets and this resampling method is demonstrated to perform better than a Monte Carlo resampling method via 10-fold cross-validation tests on the Jia dataset...
September 22, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28936795/the-ugly-truth-about-ourselves-and-our-robot-creations-the-problem-of-bias-and-social-inequity
#16
Ayanna Howard, Jason Borenstein
Recently, there has been an upsurge of attention focused on bias and its impact on specialized artificial intelligence (AI) applications. Allegations of racism and sexism have permeated the conversation as stories surface about search engines delivering job postings for well-paying technical jobs to men and not women, or providing arrest mugshots when keywords such as "black teenagers" are entered. Learning algorithms are evolving; they are often created from parsing through large datasets of online information while having truth labels bestowed on them by crowd-sourced masses...
September 21, 2017: Science and Engineering Ethics
https://www.readbyqxmd.com/read/28936667/rna-seq-data-analysis-from-raw-data-quality-control-to-differential-expression-analysis
#17
Weihong Qi, Ralph Schlapbach, Hubert Rehrauer
As a revolutionary technology for life sciences, RNA-seq has many applications and the computation pipeline has also many variations. Here, we describe a protocol to perform RNA-seq data analysis where the aim is to identify differentially expressed genes in comparisons of two conditions. The protocol follows the recently published RNA-seq data analysis best practice and applies quality checkpoints throughout the analysis to ensure reliable data interpretation. It is written to help new RNA-seq users to understand the basic steps necessary to analyze an RNA-seq dataset properly...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28936494/detection-of-intracranial-hypertension-using-deep-learning
#18
Benjamin Quachtran, Robert Hamilton, Fabien Scalzo
Intracranial Hypertension, a disorder characterized by elevated pressure in the brain, is typically monitored in neurointensive care and diagnosed only after elevation has occurred. This reaction-based method of treatment leaves patients at higher risk of additional complications in case of misdetection. The detection of intracranial hypertension has been the subject of many recent studies in an attempt to accurately characterize the causes of hypertension, specifically examining waveform morphology. We investigate the use of Deep Learning, a hierarchical form of machine learning, to model the relationship between hypertension and waveform morphology, giving us the ability to accurately detect presence hypertension...
December 2016: Proceedings of the ... IAPR International Conference on Pattern Recognition
https://www.readbyqxmd.com/read/28936445/principal-components-analysis-in-clinical-studies
#19
EDITORIAL
Zhongheng Zhang, Adela Castelló
In multivariate analysis, independent variables are usually correlated to each other which can introduce multicollinearity in the regression models. One approach to solve this problem is to apply principal components analysis (PCA) over these variables. This method uses orthogonal transformation to represent sets of potentially correlated variables with principal components (PC) that are linearly uncorrelated. PCs are ordered so that the first PC has the largest possible variance and only some components are selected to represent the correlated variables...
September 2017: Annals of Translational Medicine
https://www.readbyqxmd.com/read/28936280/enhancing-diffusion-mri-measures-by-integrating-grey-and-white-matter-morphometry-with-hyperbolic-wasserstein-distance
#20
Wen Zhang, Jie Shi, Jun Yu, Liang Zhan, Paul M Thompson, Yalin Wang
In order to improve the preclinical diagnose of Alzheimer's disease (AD), there is a great deal of interest in analyzing the AD related brain structural changes with magnetic resonance image (MRI) analyses. As the major features, variation of the structural connectivity and the cortical surface morphometry provide different views of structural changes to determine whether AD is present on presymptomatic patients. However, the large scale tensor-valued information and relatively low imaging resolution in diffusion MRI (dMRI) have created huge challenges for analysis...
2017: Proceedings of the IEEE International Symposium on Biomedical Imaging: from Nano to Macro
keyword
keyword
34174
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"