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https://www.readbyqxmd.com/read/29031133/nmr-diffusometry-data-sampling-optimization-for-mixture-analysis
#1
Florence Franconi, Laurent Lemaire, Benjamin Siegler, Jean-Christophe Gimel, Patrick Saulnier
NMR diffusometry is a powerful but challenging method to analyze complex mixture. Each component diffuses differently, from the faster small species to the slower large species, corresponding to different signal attenuation. However, the method is highly sensitive to the quality of the acquired data and the performance of the processing used to resolve multiexponential signals influences. Adapting the signal decay sampling to the mixture composition is one way to improve the precision of the measure. In this work, we propose a prediction tool, based on the calculation of the Cramér-Rao lower bound to minimize the variance of diffusion coefficient estimation in order to determine the optimal number of diffusion gradient steps, the best diffusion gradient sampling (among linear, exponential, quadratic and sigmoidal ones) and the optimal maximum diffusion factor...
October 2, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/29029198/different-genomic-changes-underlie-adaptive-evolution-in-populations-of-contrasting-history
#2
S G Seabra, I Fragata, M A Antunes, G S Faria, M A Santos, V C Sousa, P Simões, M Matos
Experimental evolution is a powerful tool to understand the adaptive potential of populations under environmental change. Here, we study the importance of the historical genetic background in the outcome of evolution at the genome-wide level. Using the natural clinal variation of Drosophila subobscura, we sampled populations from two contrasting latitudes (Adraga, Portugal and Groningen, Netherlands) and introduced them in a new common environment in the laboratory. We characterized the genome-wide temporal changes underlying the evolutionary dynamics of these populations, which had previously shown fast convergence at the phenotypic level, but not at chromosomal inversion frequencies...
September 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29029060/metagenomics-novel-enzymes-from-nonculturable-microbes
#3
Francesca Berini, Carmine Casciello, Giorgia Letizia Marcone, Flavia Marinelli
In the transition to the post-petroleum economy, there is a growing demand for novel enzymes with high process performances to replace traditional chemistry with a more 'green' approach. To date, microorganisms encompass the richest source of industrial biocatalysts, but the Earth-living microbiota remains largely untapped by using traditional isolation and cultivation methods. Metagenomics, which is culture-independent, represents a powerful tool for discovering novel enzymes from unculturable microorganisms...
October 4, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29028988/quasar-mpra-accurate-allele-specific-analysis-for-massively-parallel-reporter-assays
#4
Cynthia A Kalita, Gregory A Moyerbrailean, Christopher Brown, Xiaoquan Wen, Francesca Luca, Roger Pique-Regi
Motivation: The majority of the human genome is composed of non-coding regions containing regulatory elements such as enhancers, which are crucial for controlling gene expression. Many variants associated with complex traits are in these regions, and may disrupt gene regulatory sequences. Consequently, it is important to not only identify true enhancers but also to test if a variant within an enhancer affects gene regulation. Recently, allele-specific analysis in high-throughput reporter assays, such as massively parallel reporter assays (MPRA), have been used to functionally validate non-coding variants...
September 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028915/point-of-care-paediatric-gastric-sonography-can-antral-cut-off-values-be-used-to-diagnose-an-empty-stomach
#5
J J Moser, A M Walker, A O Spencer
Background: Gastric sonography is emerging as a valuable clinical point-of-care tool to assess aspiration risk. A recent study proposed that a single cut-off cross-sectional area (CSA) in the supine position could diagnose an empty stomach in the parturient. This study establishes the sensitivity and specificity of a single CSA cut-off measurement in both supine and right lateral decubitus (RLD) positions in the diagnosis of an empty antrum in paediatric patients. Methods: Following induction of anaesthesia, antral sonography was performed in supine and RLD positions in 100 fasted paediatric patients prior to upper endoscopic evaluation...
September 27, 2017: British Journal of Anaesthesia
https://www.readbyqxmd.com/read/29028901/a-collaborative-filtering-based-approach-to-biomedical-knowledge-discovery
#6
Jake Lever, Sitanshu Gakkhar, Michael Gottlieb, Tahereh Rashnavadi, Santina Lin, Celia Siu, Maia Smith, Martin Jones, Martin Krzywinski, Steven J Jones
Motivation: The increase in publication rates makes it challenging for an individual researcher to stay abreast of all relevant research in order to find novel research hypotheses. Literature-based discovery methods make use of knowledge graphs built using text mining and can infer future associations between biomedical concepts that will likely occur in new publications. These predictions are a valuable resource for researchers to explore a research topic. Current methods for prediction are based on the local structure of the knowledge graph...
September 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028892/nephele-a-cloud-platform-for-simplified-standardized-and-reproducible-microbiome-data-analysis
#7
Nick Weber, David Liou, Jennifer Dommer, Philip MacMenamin, Mariam Quiñones, Ian Misner, Andrew Oler, Joe Wan, Lewis Kim, Meghan Coakley McCarthy, Samuel Ezeji, Karlynn Noble, Darrell E Hurt
Motivation: Widespread interest in the study of the microbiome has resulted in data proliferation and the development of powerful computational tools. However, many scientific researchers lack the time, training, or infrastructure to work with large datasets or to install and use command line tools. Results: The National Institute of Allergy and Infectious Diseases (NIAID) has created Nephele, a cloud-based microbiome data analysis platform with standardized pipelines and a simple web interface for transforming raw data into biological insights...
September 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028392/application-of-selected-reaction-monitoring-and-parallel-reaction-monitoring-for-investigation-of-hl-60-cell-line-differentiation
#8
Svetlana E Novikova, Olga V Tikhonova, Leonid K Kurbatov, Tatiana E Farafonova, Igor V Vakhrushev, Victor G Zgoda
Targeted mass spectrometry represents a powerful tool for investigation of biological processes. The convenient approach of selected reaction monitoring using stable isotope-labeled peptide standard (SIS) is widely applied for protein quantification. Along with this method, high-resolution parallel reaction monitoring has been increasingly used for protein targeted analysis. Here we applied two targeted approaches (selected reaction monitoring with SIS and label-free parallel reaction monitoring) to investigate expression of 11 proteins during all-trans retinoic acid-induced differentiation of HL-60 cells...
August 2017: European Journal of Mass Spectrometry
https://www.readbyqxmd.com/read/29028381/dependence-of-matrix-effect-on-ionization-polarity-during-lc-esi-ms-analysis-of-derivatized-amino-acids-in-some-natural-samples
#9
Maarja-Liisa Oldekop, Riin Rebane, Koit Herodes
Matrix effect, the influence of co-eluting components on the ionization efficiency of the analyte, affects the trueness and precision of the LC-ESI-MS analysis. Derivatization can reduce or eliminate matrix effect, for example, diethyl ethoxymethylenemalonate (DEEMM) derivatives have shown less matrix effect compared to other derivatives. Moreover, the use of negative ion mode can further reduce matrix effect. In order to investigate the combination of derivatization and different ionization modes, an LC-ESI-MS/MS method using alternating positive/negative ion mode was developed and validated...
October 2017: European Journal of Mass Spectrometry
https://www.readbyqxmd.com/read/29028305/fast-image-guided-stratification-using-anti-programmed-death-ligand-1-gold-nanoparticles-for-cancer-immunotherapy
#10
Rinat Meir, Katerina Shamalov, Tamar Sadan, Menachem Motiei, Gur Yaari, Cyrille J Cohen, Rachela Popovtzer
Cancer immunotherapy has made enormous progress in offering safer and more effective treatments for the disease. Specifically, programmed death-ligand 1 antibody (αPDL1), designed to perform immune checkpoint blockade (ICB), is now considered a pillar in cancer immunotherapy. However, due to the complexity and heterogeneity of tumors, as well as the diversity in patient response, ICB therapy has only a 30 percent success rate, at most; moreover, the efficacy of ICB can be evaluated only two months after start of treatment...
October 13, 2017: ACS Nano
https://www.readbyqxmd.com/read/29028042/nonlinear-pulse-compression-to-43%C3%A2-%C3%A2-w-gw-class-few-cycle-pulses-at-2%C3%A2-%C3%A2-%C3%AE-m-wavelength
#11
M Gebhardt, C Gaida, T Heuermann, F Stutzki, C Jauregui, J Antonio-Lopez, A Schulzgen, R Amezcua-Correa, J Limpert, A Tünnermann
High-average power laser sources delivering intense few-cycle pulses in wavelength regions beyond the near infrared are promising tools for driving the next generation of high-flux strong-field experiments. In this work, we report on nonlinear pulse compression to 34.4 μJ-, 2.1-cycle pulses with 1.4 GW peak power at a central wavelength of 1.82 μm and an average power of 43 W. This performance level was enabled by the combination of a high-repetition-rate ultrafast thulium-doped fiber laser system and a gas-filled antiresonant hollow-core fiber...
October 15, 2017: Optics Letters
https://www.readbyqxmd.com/read/29028033/flat-top-surface-plasmon-polariton-beams
#12
Lauren Zundel, Rosario Martinez-Herrero, Alejandro Manjavacas
Surface plasmon polaritons (SPPs) have emerged as powerful tools for guiding and manipulating light below the diffraction limit. In this context, the availability of flat top SPP beams displaying a constant transversal profile can allow for uniform excitation and coupling scenarios, thus opening the door to developing novel applications that cannot be achieved using conventional Gaussian SPP beams. Here, we present a rigorous theoretical description of flat top SPP beams propagating along flat metal-dielectric interfaces...
October 15, 2017: Optics Letters
https://www.readbyqxmd.com/read/29027325/ecological-plant-epigenetics-evidence-from-model-and-non-model-species-and-the-way-forward
#13
Christina L Richards, Conchita Alonso, Claude Becker, Oliver Bossdorf, Etienne Bucher, Maria Colomé-Tatché, Walter Durka, Jan Engelhardt, Bence Gaspar, Andreas Gogol-Döring, Ivo Grosse, Thomas P van Gurp, Katrin Heer, Ilkka Kronholm, Christian Lampei, Vít Latzel, Marie Mirouze, Lars Opgenoorth, Ovidiu Paun, Sonja J Prohaska, Stefan A Rensing, Peter F Stadler, Emiliano Trucchi, Kristian Ullrich, Koen J F Verhoeven
Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted to merge ecological experiments with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress responses, adaptation to habitat, and range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation...
October 12, 2017: Ecology Letters
https://www.readbyqxmd.com/read/29027176/analysis-of-chip-seq-data-in-r-bioconductor
#14
Ines de Santiago, Thomas Carroll
The development of novel high-throughput sequencing methods for ChIP (chromatin immunoprecipitation) has provided a very powerful tool to study gene regulation in multiple conditions at unprecedented resolution and scale. Proactive quality-control and appropriate data analysis techniques are of critical importance to extract the most meaningful results from the data. Over the last years, an array of R/Bioconductor tools has been developed allowing researchers to process and analyze ChIP-seq data. This chapter provides an overview of the methods available to analyze ChIP-seq data based primarily on software packages from the open-source Bioconductor project...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29027094/multimodal-functional-neuroimaging-by-simultaneous-bold-fmri-and-fiber-optic-calcium-recordings-and-optogenetic-control
#15
REVIEW
Franziska Albers, Lydia Wachsmuth, Timo Mauritz van Alst, Cornelius Faber
Recent developments of optogenetic tools and fluorescence-based calcium recording techniques enable the manipulation and monitoring of neural circuits on a cellular level. Non-invasive imaging of brain networks, however, requires the application of methods such as blood oxygen level-dependent (BOLD) functional magnetic resonance imaging (fMRI), which is commonly used for functional neuroimaging. While BOLD fMRI provides brain-wide non-invasive reading of the hemodynamic response, it is only an indirect measure of neural activity...
October 12, 2017: Molecular Imaging and Biology: MIB: the Official Publication of the Academy of Molecular Imaging
https://www.readbyqxmd.com/read/29027028/determination-of-avidity-of-igg-against-protein-antigens-from-streptococcus-pneumoniae-assay-development-and-preliminary-application-in-clinical-settings
#16
D C Andrade, I C Borges, N Ekström, T Jartti, T Puhakka, A Barral, H Kayhty, O Ruuskanen, C M Nascimento-Carvalho
The measurement of antibody levels is a common test for the diagnosis of Streptococcus pneumoniae infection in research. However, the quality of antibody response, reflected by avidity, has not been adequately evaluated. We aimed to evaluate the role of avidity of IgG against eight pneumococcal proteins in etiologic diagnosis. Eight pneumococcal proteins (Ply, CbpA, PspA1 and 2, PcpA, PhtD, StkP-C, and PcsB-N) were used to develop a multiplex bead-based avidity immunoassay. The assay was tested for effects of the chaotropic agent, multiplexing, and repeatability...
October 12, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/29026291/psychometric-properties-of-the-farsi-version-of-attitudes-to-aging-questionnaire-in-iranian-older-adults
#17
Nahid Rejeh, Majideh Heravi-Karimooi, Mojtaba Vaismoradi, Pauline Griffiths, Maryam Nikkhah, Tahereh Bahrami
BACKGROUND: Attitudes to the aging process are affected by the individual's sociocultural background. The measurement of this important concept among older people in various societies requires the use of tools that are able to demonstrate both reliability and validity. OBJECTIVE: The objectives of this study were to translate and validate the Attitudes to Aging Questionnaire (AAQ) and investigate its psychometric features among Iranian older people. METHODS: In this methodological study, the Farsi version of the AAQ was validated among 400 Iranian older adults who were members of citizen clubs in an urban area of Iran...
2017: Clinical Interventions in Aging
https://www.readbyqxmd.com/read/29026102/fast-identification-of-the-conduction-type-of-nanomaterials-by-field-emission-technique
#18
Xun Yang, Haibo Gan, Yan Tian, Luxi Peng, Ningsheng Xu, Jun Chen, Huanjun Chen, Shaozhi Deng, Shi-Dong Liang, Fei Liu
There are more or less dopants or defects existing in nanomaterials, so they usually have different conduct-types even for the same substrate. Therefore, fast identification of the conduction-type of nanomaterials is very essential for their practical application in functional nanodevices. Here we use the field emission (FE) technique to research nanomaterials and establish a generalized Schottky-Nordheim (SN) model, in which an important parameter λ (the image potential factor) is first introduced to describe the effective image potential...
October 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29025326/onco-proteogenomics-multi-omics-level-data-integration-for-accurate-phenotype-prediction
#19
Lampros Dimitrakopoulos, Ioannis Prassas, Eleftherios P Diamandis, George S Charames
The overall goal of translational oncology is to identify molecular alterations indicative of cancer or of responsiveness to specific therapeutic regimens. While next-generation sequencing has played a pioneering role in this quest, the latest advances in proteomic technologies promise to provide a holistic approach to the further elucidation of tumor biology. Genetic information may be written in DNA and flow from DNA to RNA to protein, according to the central dogma of molecular biology, but the observed phenotype is dictated predominantly by the DNA protein coding region-derived proteotype...
October 12, 2017: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/29024450/optical-clearing-for-multi-scale-biological-tissues
#20
REVIEW
Tingting Yu, Yisong Qi, Hui Gong, Qingming Luo, Dan Zhu
Three-dimensional reconstruction of tissue structures is essential for biomedical researches. The development of light microscopies and various fluorescent labeling techniques provides powerful tools for this motivation. However, optical imaging depth suffers from strong light scattering due to inherent heterogeneity of biological tissues. The tissue optical clearing technology provides a distinct solution and permits us to image large volume with high resolution. Up to date, various clearing methods have been developed...
October 12, 2017: Journal of Biophotonics
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