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Miguel Álvaro-Benito, Eliot Morrison, Esam T Abualrous, Benno Kuropka, Christian Freund
The major histocompatibility complex of class II (MHCII) immunopeptidome represents the repertoire of antigenic peptides with the potential to activate CD4+ T cells. An understanding of how the relative abundance of specific antigenic epitopes affects the outcome of T cell responses is an important aspect of adaptive immunity and offers a venue to more rationally tailor T cell activation in the context of disease. Recent advances in mass spectrometric instrumentation, computational power, labeling strategies, and software analysis have enabled an increasing number of stratified studies on HLA ligandomes, in the context of both basic and translational research...
2018: Frontiers in Immunology
Yee Sun Tan, Kanokwan Sansanaphongpricha, Yuying Xie, Christopher R Donnelly, Xiaobo Luo, Blake R Heath, Xinyi Zhao, Emily L Bellile, Hongxiang Hu, Hongwei Chen, Peter J Polverini, Qianming Chen, Simon Young, Thomas E Carey, Jacques E Nör, Robert L Ferris, Gregory Wolf, Duxin Sun, Yu L Lei
PURPOSE: The response rates of Head and Neck Squamous Cell Carcinoma (HNSCC) to checkpoint blockade are below 20%. We aim to develop a mechanism-based vaccine to prevent HNSCC immune escape. EXPERIMENTAL DESIGN: We performed RNA-Seq of sensitive and resistant HNSCC cells to discover central pathways promoting resistance to immune killing. Using biochemistry, animal models, HNSCC microarray and immune cell deconvolution, we assessed the role of SOX2 in inhibiting STING-type I interferon (IFN-I) signaling-mediated anti-tumor immunity...
May 16, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Cynthia M Hong, Mariko Morimoto, Eugene A Kapustin, Nicola Alzakhem, Robert G Bergman, Kenneth N Raymond, F Dean Toste
We have demonstrated that the microenvironment of a highly anionic supramolecular catalyst can mimic the active sites of enzymes and impart rate accelerations of a million-fold or more. However, these microenvironments can be challenging to study, especially in the context of understanding which specific features of the catalyst are responsible for its high performance. We report here the development of an experimental mechanistic probe consisting of two isostructural catalysts. When examined in parallel transformations, the behavior of these catalysts provides insight relevant to the importance of anionic host charge on reactivity...
May 16, 2018: Journal of the American Chemical Society
Junhui Lee, Jiwon Park, Ahra Go, Heesung Moon, Sujin Kim, Sohee Jung, Wonjoon Jeong, Heesun Chung
To intoxicated patients in the emergency room, toxicological analysis can be considerably helpful for identifying the involved toxicants. In order to develop a urine multi-drug screening (UmDS) method, gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS-MS) were used to determine targeted and unknown toxicants in urine. A GC-MS method in scan mode was validated for selectivity, limit of detection (LOD) and recovery. An LC-MS-MS multiple reaction monitoring (MRM) method was validated for lower LOD, recovery and matrix effect...
May 14, 2018: Journal of Analytical Toxicology
Dominik Deniffel, Timothé Boutelier, Aissam Labani, Mickael Ohana, Daniela Pfeiffer, Catherine Roy
OBJECTIVES: The aims of this study were to evaluate the agreement of computed tomography (CT)-perfusion parameter values of the normal renal cortex and various renal tumors, which were obtained by different mathematical models, and to evaluate their diagnostic accuracy. MATERIALS AND METHODS: Perfusion imaging was performed prospectively in 35 patients to analyze 144 regions of interest of the normal renal cortex and 144 regions of interest of renal tumors, including 21 clear-cell renal cell carcinomas (RCC), 6 papillary RCCs, 5 oncocytomas, 1 chromophobe RCC, 1 angiomyolipoma with minimal fat, and 1 tubulocystic RCC...
May 14, 2018: Investigative Radiology
Carsten Jaeger, Jan Lisec
Raw data from metabolomics experiments are initially subjected to peak identification and signal deconvolution to generate raw data matrices m × n, where m are samples and n are metabolites. We describe here simple statistical procedures on such multivariate data matrices, all provided as functions in the programming environment R, useful to normalize data, detect biomarkers, and perform sample classification.
2018: Methods in Molecular Biology
Ruilong Ling, Waleed Tahir, Hsing-Ying Lin, Hakho Lee, Lei Tian
We demonstrate a motion-free intensity diffraction tomography technique that enables the direct inversion of 3D phase and absorption from intensity-only measurements for weakly scattering samples. We derive a novel linear forward model featuring slice-wise phase and absorption transfer functions using angled illumination. This new framework facilitates flexible and efficient data acquisition, enabling arbitrary sampling of the illumination angles. The reconstruction algorithm performs 3D synthetic aperture using a robust computation and memory efficient slice-wise deconvolution to achieve resolution up to the incoherent limit...
May 1, 2018: Biomedical Optics Express
Xinzi He, Zhen Yu, Tianfu Wang, Baiying Lei, Yiyan Shi
BACKGROUND: Dermoscopy imaging has been a routine examination approach for skin lesion diagnosis. Accurate segmentation is the first step for automatic dermoscopy image assessment. OBJECTIVE: The main challenges for skin lesion segmentation are numerous variations in viewpoint and scale of skin lesion region. METHODS: To handle these challenges, we propose a novel skin lesion segmentation network via a very deep dense deconvolution network based on dermoscopic images...
April 24, 2018: Technology and Health Care: Official Journal of the European Society for Engineering and Medicine
Sirajul Salekin, Jianqiu Michelle Zhang, Yufei Huang
Motivation: Transcription factor (TF) binds to the promoter region of a gene to control gene expression. Identifying precise transcription factor binding sites (TFBS) is essential for understanding the detailed mechanisms of TF mediated gene regulation. However, there is a shortage of computational approach that can deliver single base pair (bp) resolution prediction of TFBS. Results: In this paper, we propose DeepSNR, a Deep Learning algorithm for predicting transcription factor binding location at Single Nucleotide Resolution de novo from DNA sequence...
May 10, 2018: Bioinformatics
R Ayana, Shailja Singh, Soumya Pati
Microglial cells form a context-dependent network of brain immunoeffector cells. Despite their indispensable roles, unresolved questions exist around biomarker discovery relevant to their cellular localization, self-renewing potential, and brain developmental dynamics. To resolve the existent gap in the annotation of candidate biomarkers, we conducted a meta-analysis of brain cells using available high-throughput data sets for deciphering microglia-specific expression profiles. We have identified 3,290 significant genes specific to microglia and further selected the top 20 dysregulated genes on the basis of p -value and log2 FC...
2018: Frontiers in Neurology
Zachary R Hinton, Nicolas J Alvarez
HYPOTHESIS: Drop shape analysis (DSA) techniques measure interfacial tension subject to error in image analysis and the optical system. While considerable efforts have been made to minimize image analysis errors, very little work has treated optical errors. There are two main sources of error when considering the optical system: the angle of misalignment and the choice of focal plane. Due to the convoluted nature of these sources, small angles of misalignment can lead to large errors in measured curvature...
April 27, 2018: Journal of Colloid and Interface Science
Dennis Hedderich, Anne Kluge, Thomas Pyka, Claus Zimmer, Jan S Kirschke, Benedikt Wiestler, Christine Preibisch
BACKGROUND AND PURPOSE: Several leakage correction algorithms for dynamic susceptibility contrast (DSC) magnetic resonance imaging (MRI)-based cerebral blood volume (CBV) measurement have been proposed, and combination with a preload of contrast agent is generally recommended. A single bolus application scheme would largely simplify and facilitate standardized clinical applications, while reducing contrast agent (CA) dose. The aim of this study was, therefore, to investigate whether appropriate leakage correction redundantizes prebolus application by comparing normalized DSC-based CBV (nCBV) measures of two consecutive CA boli...
May 10, 2018: Journal of Neuroradiology. Journal de Neuroradiologie
Hari Ram Upadhayay, Hugh G Smith, Marco Griepentrog, Samuel Bodé, Roshan Man Bajracharya, William Blake, Wim Cornelis, Pascal Boeckx
Soil erosion by water is critical for soil, lake and reservoir degradation in the mid-hills of Nepal. Identification of the nature and relative contribution of sediment sources in rivers is important to mitigate water erosion within catchments and siltation problems in lakes and reservoirs. We estimated the relative contribution of land uses (i.e. sources) to suspended and streambed sediments in the Chitlang catchment using stable carbon isotope signature (δ13 C) of long-chain fatty acids as a tracer input for MixSIAR, a Bayesian mixing model used to apportion sediment sources...
May 8, 2018: Science of the Total Environment
John D Biglands, Montasir Ibraheem, Derek R Magee, Aleksandra Radjenovic, Sven Plein, John P Greenwood
OBJECTIVES: This study sought to compare the diagnostic accuracy of visual and quantitative analyses of myocardial perfusion cardiovascular magnetic resonance against a reference standard of quantitative coronary angiography. BACKGROUND: Visual analysis of perfusion cardiovascular magnetic resonance studies for assessing myocardial perfusion has been shown to have high diagnostic accuracy for coronary artery disease. However, only a few small studies have assessed the diagnostic accuracy of quantitative myocardial perfusion...
May 2018: JACC. Cardiovascular Imaging
Alejandro Ruiz-Picazo, Mª Teresa Martinez-Martinez, Sarin Colon-Useche, Ramon Iriarte, Barbara Sanchez-Dengra, Marta Gonzalez-Alvarez, Alfredo Garcia-Arieta, Isabel Gonzalez Alvarez, Marival Bermejo
The main objective of this investigation was to develop an exploratory two-step level A IVIVC for three Telmisartan oral immediate release formulations, the reference product Micardis and two generic formulations (X1 and X2). Correlation was validated with a third test formulation Y1. Experimental solubility and permeability data was obtained to confirm that Telmisartan is a class II compound under the Biopharmaceutic Classification System. BE studies plasma profiles were combined using a previously published reference scaling procedure...
May 10, 2018: Molecular Pharmaceutics
Shu-Hwa Chen, Wen-Yu Kuo, Sheng-Yao Su, Wei-Chun Chung, Jen-Ming Ho, Henry Horng-Shing Lu, Chung-Yen Lin
BACKGROUND: A new emerged cancer treatment utilizes intrinsic immune surveillance mechanism that is silenced by those malicious cells. Hence, studies of tumor infiltrating lymphocyte populations (TILs) are key to the success of advanced treatments. In addition to laboratory methods such as immunohistochemistry and flow cytometry, in silico gene expression deconvolution methods are available for analyses of relative proportions of immune cell types. RESULTS: Herein, we used microarray data from the public domain to profile gene expression pattern of twenty-two immune cell types...
May 8, 2018: BMC Bioinformatics
Yun'er Chen, Chang'an Zhan, Xian Peng, Qiuyang Fu, Tao Wang
The maximum length sequence (m-sequence) has been successfully used to study the linear/nonlinear components of auditory evoked potential (AEP) with rapid stimulation. However, more study is needed to evaluate the effect of the m-sequence order in terms of the noise attenuation performance. This study aimed to address this issue using response-free electroencephalogram (EEG) and EEGs with nonlinear AEPs. We examined the noise attenuation ratios to evaluate the noise variation for the calculations of superimposed averaging and cross-correlation, respectively, which constitutes the main process in the deconvolution method using the dataset of spontaneous EEGs to simulate the cases of different orders (order 5 to 12) of m-sequences...
April 1, 2018: Sheng Wu Yi Xue Gong Cheng Xue za Zhi, Journal of Biomedical Engineering, Shengwu Yixue Gongchengxue Zazhi
Li Guo, Yingjie Mei, Jijing Guan, Xiangliang Tan, Yikai Xu, Wufan Chen, Qianjin Feng, Yanqiu Feng
Quantitative susceptibility mapping (QSM) is a magnetic resonance imaging technique that quantifies the magnetic susceptibility distribution within biological tissues. QSM calculates the underlying magnetic susceptibility by deconvolving the tissue magnetic field map with a unit dipole kernel. However, this deconvolution problem is ill-posed. The morphology enabled dipole inversion (MEDI) introduces total variation (TV) to regularize the susceptibility reconstruction. However, MEDI results still contain artifacts near tissue boundaries because MEDI only imposes TV constraint on voxels inside smooth regions...
2018: PloS One
E Jared Shamwell, William D Nothwang, Donald Perlis
Aimed at improving size, weight, and power (SWaP)-constrained robotic vision-aided state estimation, we describe our unsupervised, deep convolutional-deconvolutional sensor fusion network, Multi-Hypothesis DeepEfference (MHDE). MHDE learns to intelligently combine noisy heterogeneous sensor data to predict several probable hypotheses for the dense, pixel-level correspondence between a source image and an unseen target image. We show how our multi-hypothesis formulation provides increased robustness against dynamic, heteroscedastic sensor and motion noise by computing hypothesis image mappings and predictions at 76⁻357 Hz depending on the number of hypotheses being generated...
May 4, 2018: Sensors
Nicole C Parsley, Christine L Kirkpatrick, Christopher M Crittenden, Javad Ghassemi Rad, David W Hoskin, Jennifer S Brodbelt, Leslie M Hicks
Widespread resistance to antimicrobial and cancer therapeutics is evolving in every country worldwide and has a direct impact on global health, agriculture and the economy. The specificity and selectivity of bioactive peptide natural products present a possible stopgap measure to address the ongoing deficit of new therapeutic compounds. PepSAVI-MS (Statistically-guided bioActive Peptides prioritized VIa Mass Spectrometry) is an adaptable method for the analysis of natural product libraries to rapidly identify bioactive peptides...
May 4, 2018: Phytochemistry
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