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https://www.readbyqxmd.com/read/29331819/new-strategy-for-determination-of-anthocyanins-polyphenols-and-antioxidant-capacity-of-brassica-oleracea-liquid-extract-using-infrared-spectroscopies-and-multivariate-regression
#1
Isadora R N de Oliveira, Jussara V Roque, Mariza P Maia, Paulo C Stringheta, Reinaldo F Teófilo
A new method was developed to determine the antioxidant properties of red cabbage extract (Brassica oleracea) by mid (MID) and near (NIR) infrared spectroscopies and partial least squares (PLS) regression. A 70% (v/v) ethanolic extract of red cabbage was concentrated to 9° Brix and further diluted (12 to 100%) in water. The dilutions were used as external standards for the building of PLS models. For the first time, this strategy was applied for building multivariate regression models. Reference analyses and spectral data were obtained from diluted extracts...
January 4, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/29331675/module-analysis-captures-pancancer-genetically-and-epigenetically-deregulated-cancer-driver-genes-for-smoking-and-antiviral-response
#2
Magali Champion, Kevin Brennan, Tom Croonenborghs, Andrew J Gentles, Nathalie Pochet, Olivier Gevaert
The availability of increasing volumes of multi-omics profiles across many cancers promises to improve our understanding of the regulatory mechanisms underlying cancer. The main challenge is to integrate these multiple levels of omics profiles and especially to analyze them across many cancers. Here we present AMARETTO, an algorithm that addresses both challenges in three steps. First, AMARETTO identifies potential cancer driver genes through integration of copy number, DNA methylation and gene expression data...
December 1, 2017: EBioMedicine
https://www.readbyqxmd.com/read/29330205/clinical-utility-of-a-stat3-regulated-microrna-200-family-signature-with-prognostic-potential-in-early-gastric-cancer
#3
Liang Yu, Di Wu, Hugh Gao, Jesse Balic, Anna Tsykin, Tae-Su Han, You Dong Liu, Catherine Lydia Kennedy, Ji-Kun Li, Jie-Qi Mao, Patrick Tan, Masanobu Oshima, Gregory J Goodall, Brendan J Jenkins
PURPOSE: The majority of gastric cancer (GC) patients are diagnosed with late stage disease, for which distinct molecular subtypes have been identified that are potentially amenable to targeted therapies. However, there exists no molecular classification system with prognostic power for early stage GC (EGC) because the molecular events promoting GC initiation remain ill-defined. EXPERIMENTAL DESIGN: miRNA microarrays were performed on gastric tissue from the gp130F/F preclinical EGC mouse model, prior to tumor initiation...
January 12, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29328180/modulation-transfer-function-of-a-fish-eye-lens-based-on-the-sixth-order-wave-aberration-theory
#4
Han Jia, Lijun Lu, Yiqing Cao
A calculation program of the modulation transfer function (MTF) of a fish-eye lens is developed with the autocorrelation method, in which the sixth-order wave aberration theory of ultra-wide-angle optical systems is used to simulate the wave aberration distribution at the exit pupil of the optical systems. The autocorrelation integral is processed with the Gauss-Legendre integral, and the magnification chromatic aberration is discussed to calculate polychromatic MTF. The MTF calculation results of a given example are then compared with those previously obtained based on the fourth-order wave aberration theory of plane-symmetrical optical systems and with those from the Zemax program...
January 10, 2018: Applied Optics
https://www.readbyqxmd.com/read/29328166/comprehensive-three-dimensional-ray-tracing-model-for-three-mirror-cavity-enhanced-spectroscopy
#5
Faisal Nadeem, Berber R Postma, Geert Postma, Simona M Cristescu, Julien Mandon, Frans J M Harren
A 3D ray tracing model is used to simulate optical reinjection in a nonresonant optical cavity, for off-axis integrated cavity output spectroscopy. The optical cavities are optimized for maximum intensity enhancement factors via a grid search and a genetic algorithm. Intensity enhancement factors up to 1400 are found for short cavities (3 cm) and up to 101 for long cavities (50 cm). The model predicts that short absorption cells can be used, having a long effective path length and a high throughput power...
January 10, 2018: Applied Optics
https://www.readbyqxmd.com/read/29327365/millimeter-spatial-resolution-in-vivo-sodium-mri-of-the-human-eye-at-7-t-using-a-dedicated-radiofrequency-transceiver-array
#6
Daniel Wenz, Andre Kuehne, Till Huelnhagen, Armin M Nagel, Helmar Waiczies, Oliver Weinberger, Celal Oezerdem, Oliver Stachs, Soenke Langner, Erdmann Seeliger, Bert Flemming, Russell Hodge, Thoralf Niendorf
PURPOSE: The aim of this study was to achieve millimeter spatial resolution sodium in vivo MRI of the human eye at 7 T using a dedicated six-channel transceiver array. We present a detailed description of the radiofrequency coil design, along with electromagnetic field and specific absorption ratio simulations, data validation, and in vivo application. METHODS: Electromagnetic field and specific absorption ratio simulations were performed. Transmit field uniformity was optimized by using a multi-objective genetic algorithm...
January 12, 2018: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/29325072/sensitive-and-specific-post-call-filtering-of-genetic-variants-in-xenograft-and-primary-tumors
#7
Brian K Mannakee, Uthra Balaji, Agnieszka K Witkiewicz, Ryan N Gutenkunst, Erik S Knudsen
Motivation: Tumor genome sequencing offers great promise for guiding research and therapy, but spurious variant calls can arise from multiple sources. Mouse contamination can generate many spurious calls when sequencing patient-derived xenografts (PDXs). Paralogous genome sequences can also generate spurious calls when sequencing any tumor. We developed a BLAST-based algorithm, MAPEX, to identify and filter out spurious calls from both these sources. Results: When calling variants from xenografts, MAPEX has similar sensitivity and specificity to more complex algorithms...
January 8, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29324743/an-enhanced-artificial-bee-colony-algorithm-eabc-for-solving-dispatching-of-hydro-thermal-system-dhts-problem
#8
Yi Yu, Yonggang Wu, Binqi Hu, Xinglong Liu
The dispatching of hydro-thermal system is a nonlinear programming problem with multiple constraints and high dimensions and the solution techniques of the model have been a hotspot in research. Based on the advantage of that the artificial bee colony algorithm (ABC) can efficiently solve the high-dimensional problem, an improved artificial bee colony algorithm has been proposed to solve DHTS problem in this paper. The improvements of the proposed algorithm include two aspects. On one hand, local search can be guided in efficiency by the information of the global optimal solution and its gradient in each generation...
2018: PloS One
https://www.readbyqxmd.com/read/29324641/genetic-algorithm-based-motion-estimation-method-using-orientations-and-emgs-for-robot-controls
#9
Jeongsook Chae, Yong Jin, Yunsick Sung, Kyungeun Cho
Demand for interactive wearable devices is rapidly increasing with the development of smart devices. To accurately utilize wearable devices for remote robot controls, limited data should be analyzed and utilized efficiently. For example, the motions by a wearable device, called Myo device, can be estimated by measuring its orientation, and calculating a Bayesian probability based on these orientation data. Given that Myo device can measure various types of data, the accuracy of its motion estimation can be increased by utilizing these additional types of data...
January 11, 2018: Sensors
https://www.readbyqxmd.com/read/29323667/making-new-genetic-diagnoses-with-old-data-iterative-reanalysis-and-reporting-from-genome-wide-data-in-1-133-families-with-developmental-disorders
#10
Caroline F Wright, Jeremy F McRae, Stephen Clayton, Giuseppe Gallone, Stuart Aitken, Tomas W FitzGerald, Philip Jones, Elena Prigmore, Diana Rajan, Jenny Lord, Alejandro Sifrim, Rosemary Kelsell, Michael J Parker, Jeffrey C Barrett, Matthew E Hurles, David R FitzPatrick, Helen V Firth
PurposeGiven the rapid pace of discovery in rare disease genomics, it is likely that improvements in diagnostic yield can be made by systematically reanalyzing previously generated genomic sequence data in light of new knowledge.MethodsWe tested this hypothesis in the United Kingdom-wide Deciphering Developmental Disorders study, where in 2014 we reported a diagnostic yield of 27% through whole-exome sequencing of 1,133 children with severe developmental disorders and their parents. We reanalyzed existing data using improved variant calling methodologies, novel variant detection algorithms, updated variant annotation, evidence-based filtering strategies, and newly discovered disease-associated genes...
January 11, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29322327/combined-and-sequential-liver-kidney-transplantation-in-children
#11
Ryszard Grenda, Piotr Kaliciński
Combined and sequential liver-kidney transplantation (CLKT and SLKT) is a definitive treatment in children with end-stage organ failure. There are two major indications: - terminal insufficiency of both organs, or - need for transplanting new liver as a source of lacking enzyme or specific regulator of the immune system in a patient with renal failure. A third (uncommon) option is secondary end-stage renal failure in liver transplant recipients. These three clinical settings use distinct qualification algorithms...
January 10, 2018: Pediatric Nephrology: Journal of the International Pediatric Nephrology Association
https://www.readbyqxmd.com/read/29321537/computational-investigation-of-environment-noise-interaction-in-single-cell-organisms-the-merit-of-expression-stochasticity-depends-on-the-quality-of-environmental-fluctuations
#12
Anja Lück, Lukas Klimmasch, Peter Großmann, Sebastian Germerodt, Christoph Kaleta
Organisms need to adapt to changing environments and they do so by using a broad spectrum of strategies. These strategies include finding the right balance between expressing genes before or when they are needed, and adjusting the degree of noise inherent in gene expression. We investigated the interplay between different nutritional environments and the inhabiting organisms' metabolic and genetic adaptations by applying an evolutionary algorithm to an agent-based model of a concise bacterial metabolism. Our results show that constant environments and rapidly fluctuating environments produce similar adaptations in the organisms, making the predictability of the environment a major factor in determining optimal adaptation...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29320496/bayesian-inference-of-phylogenetic-networks-from-bi-allelic-genetic-markers
#13
Jiafan Zhu, Dingqiao Wen, Yun Yu, Heidi M Meudt, Luay Nakhleh
Phylogenetic networks are rooted, directed, acyclic graphs that model reticulate evolutionary histories. Recently, statistical methods were devised for inferring such networks from either gene tree estimates or the sequence alignments of multiple unlinked loci. Bi-allelic markers, most notably single nucleotide polymorphisms (SNPs) and amplified fragment length polymorphisms (AFLPs), provide a powerful source of genome-wide data. In a recent paper, a method called SNAPP was introduced for statistical inference of species trees from unlinked bi-allelic markers...
January 10, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29318393/infrared-spectroscopy-and-multivariate-methods-as-a-tool-for-identification-and-quantification-of-fuels-and-lubricant-oils-in-soil
#14
Maurílio Gustavo Nespeca, Gabriel Baroffaldi Piassalonga, José Eduardo de Oliveira
Environmental contamination caused by leakage of fuels and lubricant oils at gas stations is of great concern due to the presence of carcinogenic compounds in the composition of gasoline, diesel, and mineral lubricant oils. Chromatographic methods or non-selective infrared methods are usually used to assess soil contamination, which makes environmental monitoring costly or not appropriate. In this perspective, the present work proposes a methodology to identify the type of contaminant (gasoline, diesel, or lubricant oil) and, subsequently, to quantify the contaminant concentration using attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy and multivariate methods...
January 9, 2018: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/29318005/precision-medicine-does-ethnicity-information-complement-genotype-based-prescribing-decisions
#15
REVIEW
Rashmi R Shah, Andrea Gaedigk
Inter-ethnic differences in drug response are all too well known. These are underpinned by a number of factors, including pharmacogenetic differences across various ethnic populations. Precision medicine relies on genotype-based prescribing decisions with the aim of maximizing efficacy and mitigating the risks. When there is no access to genotyping tests, ethnicity is frequently regarded as a proxy of the patient's probable genotype on the basis of overall population-based frequency of genetic variations in the ethnic group the patient belongs to, with some variations being ethnicity-specific...
January 2018: Therapeutic Advances in Drug Safety
https://www.readbyqxmd.com/read/29317676/predicting-inhibitory-and-activatory-drug-targets-by-chemically-and-genetically-perturbed-transcriptome-signatures
#16
Ryusuke Sawada, Michio Iwata, Yasuo Tabei, Haruka Yamato, Yoshihiro Yamanishi
Genome-wide identification of all target proteins of drug candidate compounds is a challenging issue in drug discovery. Moreover, emerging phenotypic effects, including therapeutic and adverse effects, are heavily dependent on the inhibition or activation of target proteins. Here we propose a novel computational method for predicting inhibitory and activatory targets of drug candidate compounds. Specifically, we integrated chemically-induced and genetically-perturbed gene expression profiles in human cell lines, which avoided dependence on chemical structures of compounds or proteins...
January 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29317534/linking-secondary-metabolites-to-gene-clusters-through-genome-sequencing-of-six-diverse-aspergillus-species
#17
Inge Kjærbølling, Tammi C Vesth, Jens C Frisvad, Jane L Nybo, Sebastian Theobald, Alan Kuo, Paul Bowyer, Yudai Matsuda, Stephen Mondo, Ellen K Lyhne, Martin E Kogle, Alicia Clum, Anna Lipzen, Asaf Salamov, Chew Yee Ngan, Chris Daum, Jennifer Chiniquy, Kerrie Barry, Kurt LaButti, Sajeet Haridas, Blake A Simmons, Jon K Magnuson, Uffe H Mortensen, Thomas O Larsen, Igor V Grigoriev, Scott E Baker, Mikael R Andersen
The fungal genus of Aspergillus is highly interesting, containing everything from industrial cell factories, model organisms, and human pathogens. In particular, this group has a prolific production of bioactive secondary metabolites (SMs). In this work, four diverse Aspergillus species (A. campestris, A. novofumigatus, A. ochraceoroseus, and A. steynii) have been whole-genome PacBio sequenced to provide genetic references in three Aspergillus sections. A. taichungensis and A. candidus also were sequenced for SM elucidation...
January 9, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29316639/optimization-of-location-routing-problem-for-cold-chain-logistics-considering-carbon-footprint
#18
Songyi Wang, Fengming Tao, Yuhe Shi
In order to solve the optimization problem of logistics distribution system for fresh food, this paper provides a low-carbon and environmental protection point of view, based on the characteristics of perishable products, and combines with the overall optimization idea of cold chain logistics distribution network, where the green and low-carbon location-routing problem (LRP) model in cold chain logistics is developed with the minimum total costs as the objective function, which includes carbon emission costs...
January 6, 2018: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29316045/redescription-of-tintinnopsis-everta-kofoid-campbell-1929-alveolata-ciliophora-tintinnina-based-on-taxonomic-and-genetic-analyses-discovery-of-a-new-complex-ciliary-pattern
#19
Michael S Gruber, Michaela Strüder-Kypke, Sabine Agatha
The about 1,000 species of tintinnid ciliates are identified and classified almost exclusively based on their lorica features, although the shortcomings of this structure are well-known, e.g., causing uncertain species limitations and non-monophyletic taxa. Hence, the present redescription of Tintinnopsis everta Kofoid and Campbell, 1929 considers not only the lorica characteristics, but focuses on cell and genetic features. The species is redescribed from the North Atlantic and adjacent sea areas, namely the east coast of the USA, using live observation, protargol-stained material, scanning electron microscopy, and genetic analyses...
January 5, 2018: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/29313196/tripartite-equilibrium-strategy-for-a-carbon-tax-setting-problem-in-air-passenger-transport
#20
Jiuping Xu, Rui Qiu, Zhimiao Tao, Heping Xie
Carbon emissions in air passenger transport have become increasing serious with the rapidly development of aviation industry. Combined with a tripartite equilibrium strategy, this paper proposes a multi-level multi-objective model for an air passenger transport carbon tax setting problem (CTSP) among an international organization, an airline and passengers with the fuzzy uncertainty. The proposed model is simplified to an equivalent crisp model by a weighted sum procedure and a Karush-Kuhn-Tucker (KKT) transformation method...
January 8, 2018: Environmental Science and Pollution Research International
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