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https://www.readbyqxmd.com/read/28454281/current-status-of-the-prognostic-molecular-biomarkers-in-breast-cancer-a-systematic-review
#1
Goro Kutomi, Toru Mizuguchi, Fukino Satomi, Hideki Maeda, Hiroaki Shima, Yasutoshi Kimura, Koichi Hirata
Biomarkers that facilitate the prediction of breast cancer prognosis can improve the quality of life in patients during the long period of illness and treatment. Particularly in recent years, with the advent of a more exhaustive analysis of genetic information and gene products, the molecular mechanisms at play during breast cancer have gradually become clearer. In the present study, a systematic review of the literature between 2009 and 2014 was conducted by searching for the keywords 'breast cancer', 'biomarkers', 'diagnosis', 'prognosis' and 'drug response' to clarify the present state of knowledge regarding biomarkers...
March 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454169/speckle-based-hyperspectral-imaging-combining-multiple-scattering-and-compressive-sensing-in-nanowire-mats
#2
Rebecca French, Sylvain Gigan, Otto L Muskens
Encoding of spectral information onto monochrome imaging cameras is of interest for wavelength multiplexing and hyperspectral imaging applications. Here, the complex spatiospectral response of a disordered material is used to demonstrate retrieval of a number of discrete wavelengths over a wide spectral range. Strong, diffuse light scattering in a semiconductor nanowire mat is used to achieve a highly compact spectrometer of micrometer thickness, transforming different wavelengths into distinct speckle patterns with nanometer sensitivity...
May 1, 2017: Optics Letters
https://www.readbyqxmd.com/read/28454144/automatic-focusing-for-multisectional-objects-in-digital-holography-using-the-structure-tensor
#3
Zhenbo Ren, Ni Chen, Edmund Y Lam
Determining the axial position of the recorded object in digital holography is a crucial step for image reconstruction. When multiple discrete sections of a three-dimensional object are overlapping each other, this issue becomes more challenging. In this Letter, an autofocusing algorithm using the structure tensor and its eigenvalues is proposed. This method can extract the focal distance of each section for a multi-sectional object irrespective of whether the sections are overlapping or not. We validate the applicability of the proposed technique with synthesized and experimental data using two types of holographic systems...
May 1, 2017: Optics Letters
https://www.readbyqxmd.com/read/28454031/automatic-and-adaptive-paddy-rice-mapping-using-landsat-images-case-study-in-songnen-plain-in-northeast-china
#4
Bingwen Qiu, Difei Lu, Zhenghong Tang, Chongcheng Chen, Fengli Zou
Spatiotemporal explicit information on paddy rice distribution is essential for ensuring food security and sustainable environmental management. Paddy rice mapping algorithm through the Combined Consideration of Vegetation phenology and Surface water variations (CCVS) has been efficiently applied based on the 8day composites time series datasets. However, the great challenge for phenology-based algorithms introduced by unpromising data availability in middle/high spatial resolution imagery, such as frequent cloud cover and coarse temporal resolution, remained unsolved...
April 25, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28454025/review-and-analysis-of-strengths-and-weaknesses-of-agro-ecosystem-models-for-simulating-c-and-n-fluxes
#5
REVIEW
Lorenzo Brilli, Luca Bechini, Marco Bindi, Marco Carozzi, Daniele Cavalli, Richard Conant, Cristopher D Dorich, Luca Doro, Fiona Ehrhardt, Roberta Farina, Roberto Ferrise, Nuala Fitton, Rosa Francaviglia, Peter Grace, Ileana Iocola, Katja Klumpp, Joël Léonard, Raphaël Martin, Raia Silvia Massad, Sylvie Recous, Giovanna Seddaiu, Joanna Sharp, Pete Smith, Ward N Smith, Jean-Francois Soussana, Gianni Bellocchi
Biogeochemical simulation models are important tools for describing and quantifying the contribution of agricultural systems to C sequestration and GHG source/sink status. The abundance of simulation tools developed over recent decades, however, creates a difficulty because predictions from different models show large variability. Discrepancies between the conclusions of different modelling studies are often ascribed to differences in the physical and biogeochemical processes incorporated in equations of C and N cycles and their interactions...
April 24, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28454015/air-pollution-characteristics-and-health-risks-in-henan-province-china
#6
Fuzhen Shen, Xinlei Ge, Jianlin Hu, Dongyang Nie, Li Tian, Mindong Chen
Events of severe air pollution occurred frequently in China recently, thus understanding of the air pollution characteristics and its health risks is very important. In this work, we analyzed a two-year dataset (March 2014 - February 2016) including daily concentrations of six criteria pollutants (PM2.5, PM10, CO, SO2, NO2, and O3) from 18 cities in Henan province. Results reveal the serious air pollution status in Henan province, especially the northern part, and Zhengzhou is the city with the worst air quality...
April 25, 2017: Environmental Research
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/28453708/towards-a-global-cancer-knowledge-network-dissecting-the-current-international-cancer-genomic-sequencing-landscape
#8
D J Vis, J Lewin, R G Liao, M Mao, F Andre, R L Ward, F Calvo, B T Teh, A A Camargo, B M Knoppers, C L Sawyers, L F A Wessels, M Lawler, L L Siu, E Voest
Background: While next generation sequencing has enhanced our understanding of the biological basis of malignancy, current knowledge on global practices for sequencing cancer samples is limited. To address this deficiency, we developed a survey to provide a snapshot of current sequencing activities globally, identify barriers to data sharing and use this information to develop sustainable solutions for the cancer research community. Methods: A multi-item survey was conducted assessing demographics, clinical data collection, genomic platforms, privacy/ethics concerns, funding sources and data sharing barriers for sequencing initiatives globally...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28453705/optimal-sequencing-of-ibrutinib-idelalisib-and-venetoclax-in-chronic-lymphocytic-leukemia-results-from-a-multicenter-study-of-683-patients
#9
A R Mato, B T Hill, N Lamanna, P M Barr, C S Ujjani, D M Brander, C Howlett, A P Skarbnik, B D Cheson, C S Zent, J J Pu, P Kiselev, K Foon, J Lenhart, S Henick Bachow, A M Winter, A-L Cruz, D F Claxton, A Goy, C Daniel, K Isaac, K H Kennard, C Timlin, M Fanning, L Gashonia, M Yacur, J Svoboda, S J Schuster, C Nabhan
Background: Ibrutinib, idelalisib, and venetoclax are approved for treating CLL patients in the United States. However, there is no guidance as to their optimal sequence. Patients and methods: We conducted a multicenter, retrospective analysis of CLL patients treated with kinase inhibitors (KIs) or venetoclax. We examined demographics, discontinuation reasons, overall response rates (ORR), survival, and post-KI salvage strategies. Primary endpoint was progression-free survival (PFS)...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28453685/phenocurve-capturing-dynamic-phenotype-environment-relationships-using-phenomics-data
#10
Yifan Yang, Lei Xu, Zheyun Feng, Jeffrey A Cruz, Linda J Savage, David M Kramer, Jin Chen
Motivation: Phenomics is essential for understanding the mechanisms that regulate or influence growth, fitness, and development. Techniques have been developed to conduct high-throughput large-scale phenotyping on animals, plants and humans, aiming to bridge the gap between genomics, gene functions and traits. Although new developments in phenotyping techniques are exciting, we are limited by the tools to analyze fully the massive phenotype data, especially the dynamic relationships between phenotypes and environments...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453681/sphinx-merging-knowledge-based-and-ab-initio-approaches-to-improve-protein-loop-prediction
#11
Claire Marks, Jaroslaw Nowak, Stefan Klostermann, Guy Georges, James Dunbar, Jiye Shi, Sebastian Kelm, Charlotte M Deane
Motivation: Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453674/ntcard-a-streaming-algorithm-for-cardinality-estimation-in-genomics-data
#12
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/28453668/a-mass-graph-based-approach-for-the-identification-of-modified-proteoforms-using-top-down-tandem-mass-spectra
#13
Qiang Kou, Si Wu, Nikola Tolic, Ljiljana Paša-Tolic, Yunlong Liu, Xiaowen Liu
Motivation: Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453648/recent-advances-in-sequence-assembly-principles-and-applications
#14
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/28453640/pioneering-topological-methods-for-network-based-drug-target-prediction-by-exploiting-a-brain-network-self-organization-theory
#15
Claudio Durán, Simone Daminelli, Josephine M Thomas, V Joachim Haupt, Michael Schroeder, Carlo Vittorio Cannistraci
The bipartite network representation of the drug-target interactions (DTIs) in a biosystem enhances understanding of the drugs' multifaceted action modes, suggests therapeutic switching for approved drugs and unveils possible side effects. As experimental testing of DTIs is costly and time-consuming, computational predictors are of great aid. Here, for the first time, state-of-the-art DTI supervised predictors custom-made in network biology were compared-using standard and innovative validation frameworks-with unsupervised pure topological-based models designed for general-purpose link prediction in bipartite networks...
April 26, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28453637/automated-identification-of-implausible-values-in-growth-data-from-pediatric-electronic-health-records
#16
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/28453623/bayesian-inference-of-allele-specific-gene-expression-indicates-abundant-cis-regulatory-variation-in-natural-flycatcher-populations
#17
Mi Wang, Severin Uebbing, Hans Ellegren
Polymorphism in cis-regulatory sequences can lead to different levels of expression for the two alleles of a gene, providing a starting point for the evolution of gene expression. Little is known about the genome-wide abundance of genetic variation in gene regulation in natural populations but analysis of allele-specific expression (ASE) provides a means for investigating such variation. We performed RNA-seq of multiple tissues from population samples of two closely related flycatcher species and developed a Bayesian algorithm that maximises data usage by borrowing information from the whole dataset and combines several SNPs per transcript to detect ASE...
April 26, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28453611/modsara-a-computationally-efficient-r-package-for-cnv-identification
#18
Feifei Xiao, Yue Niu, Ning Hao, Yanxun Xu, Zhilin Jin, Heping Zhang
Summary: Chromosomal copy number variation (CNV) refers to a polymorphism that a DNA segment presents deletion or duplication in the population. The computational algorithms developed to identify this type of variation are usually of high computational complexity. Here we present a user-friendly R package, modSaRa, designed to perform copy number variants identification. The package is developed based on a change-point based method with optimal computational complexity and desirable accuracy...
April 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453546/improved-approximation-of-spatial-light-distribution
#19
David Kaljun, Tina Novak, Janez Žerovnik
The rapid worldwide evolution of LEDs as light sources has brought new challenges, which means that new methods are needed and new algorithms have to be developed. Since the majority of LED luminaries are of the multi-source type, established methods for the design of light engines cannot be used in the design of LED light engines. This is because in the latter case what is involved is not just the design of a good reflector or projector lens, but the design of several lenses which have to work together in order to achieve satisfactory results...
2017: PloS One
https://www.readbyqxmd.com/read/28453515/reliable-reference-genes-for-normalization-of-gene-expression-data-in-tea-plants-camellia-sinensis-exposed-to-metal-stresses
#20
Ming-Le Wang, Qing-Hui Li, Hua-Hong Xin, Xuan Chen, Xu-Jun Zhu, Xing-Hui Li
Tea plants [Camellia sinensis (L.) O. Kuntze] are an important leaf-type crop that are widely used for the production of non-alcoholic beverages in the world. Exposure to excessive amounts of heavy metals adversely affects the quality and yield of tea leaves. To analyze the molecular responses of tea plants to heavy metals, a reliable quantification of gene expression is important and of major importance herein is the normalization of the measured expression levels for the target genes. Ideally, stably expressed reference genes should be evaluated in all experimental systems...
2017: PloS One
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