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https://www.readbyqxmd.com/read/28214931/subtle-nets-finder-finely-tuned-interaction-networks-in-dna-rna-protein-complexes
#1
Alexander A Kantardjiev
Graphical Abstract Subtle.Nets.Finder is a workflow of algorithms for identification of subtly interacting groups in DNA/RNA/protein complexes. It is founded on detailed and sophisticated evaluation of the self-consistency in the cooperative network of residue interactions via a combination of advanced calculations (fast multipole method and statistical mechanics) supplemented with graph-theoretical procedures.
March 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28213872/capulavirus-and-grablovirus-two-new-genera-in-the-family-geminiviridae
#2
Arvind Varsani, Philippe Roumagnac, Marc Fuchs, Jesús Navas-Castillo, Enrique Moriones, Ali Idris, Rob W Briddon, Rafael Rivera-Bustamante, F Murilo Zerbini, Darren P Martin
Geminiviruses are plant-infecting single-stranded DNA viruses that occur in most parts of the world. Currently, there are seven genera within the family Geminiviridae (Becurtovirus, Begomovirus, Curtovirus, Eragrovirus, Mastrevirus, Topocuvirus and Turncurtovirus). The rate of discovery of new geminiviruses has increased significantly over the last decade as a result of new molecular tools and approaches (rolling-circle amplification and deep sequencing) that allow for high-throughput workflows. Here, we report the establishment of two new genera: Capulavirus, with four new species (Alfalfa leaf curl virus, Euphorbia caput-medusae latent virus, French bean severe leaf curl virus and Plantago lanceolata latent virus), and Grablovirus, with one new species (Grapevine red blotch virus)...
February 17, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28213790/optical-see-through-cancer-vision-goggles-enable-direct-patient-visualization-and-real-time-fluorescence-guided-oncologic-surgery
#3
Suman B Mondal, Shengkui Gao, Nan Zhu, LeMoyne Habimana-Griffin, Walter J Akers, Rongguang Liang, Viktor Gruev, Julie Margenthaler, Samuel Achilefu
BACKGROUND: The inability to visualize the patient and surgical site directly, limits the use of current near infrared fluorescence-guided surgery systems for real-time sentinel lymph node biopsy and tumor margin assessment. METHODS: We evaluated an optical see-through goggle augmented imaging and navigation system (GAINS) for near-infrared, fluorescence-guided surgery. Tumor-bearing mice injected with a near infrared cancer-targeting agent underwent fluorescence-guided, tumor resection...
February 17, 2017: Annals of Surgical Oncology
https://www.readbyqxmd.com/read/28213758/influence-of-a-combined-ct-c-arm-system-on-periprocedural-workflow-and-procedure-times-in-mechanical-thrombectomy
#4
Johannes Pfaff, Silvia Schönenberger, Christian Herweh, Mirko Pham, Simon Nagel, Peter Arthur Ringleb, Sabine Heiland, Martin Bendszus, Markus Alfred Möhlenbruch
OBJECTIVE: To achieve the fastest possible workflow in ischaemic stroke, we developed a CT/C-arm system, which allows imaging and endovascular treatment on the same patient table. METHODS: This prospective, monocentric trial was conducted between October 2014 and August 2016. Patients received stroke imaging and mechanical thrombectomy under general anaesthesia (GA) or conscious sedation (CS) using our combined setup comprising a CT-scanner and a mobile C-arm X-ray device...
February 17, 2017: European Radiology
https://www.readbyqxmd.com/read/28213211/application-of-2d-hplc-coupled-with-principal-component-analysis-to-study-an-industrial-opiate-processing-stream
#5
Paul G Stevenson, Niki K Burns, Stuart D Purcell, Paul S Francis, Neil W Barnett, Fiona Fry, Xavier A Conlan
Principal component analysis (PCA) loading plots were used to elucidate key differences between two-dimensional high performance liquid chromatography (2D-HPLC) fingerprint data from samples collected from stages along the Papaver somniferum industrial process chemistry workflow. Data reduction was completed using a 2D-HPLC peak picking approach as a precursor to chemometric analysis. Using comparisons of the final stages of product extraction as an example, PCA analysis of characteristic 2D-HPLC fingerprints accounted for 84...
May 1, 2017: Talanta
https://www.readbyqxmd.com/read/28212969/lessons-learned-when-introducing-pharmacogenomic-panel-testing-into-clinical-practice
#6
Marc B Rosenman, Brian Decker, Kenneth D Levy, Ann M Holmes, Victoria M Pratt, Michael T Eadon
OBJECTIVES: Implementing new programs to support precision medicine in clinical settings is a complex endeavor. We describe challenges and potential solutions based on the Indiana GENomics Implementation: an Opportunity for the Underserved (INGenious) program at Eskenazi Health-one of six sites supported by the Implementing GeNomics In pracTicE network grant of the National Institutes of Health/National Human Genome Research Institute. INGenious is an implementation of a panel of genomic tests...
January 2017: Value in Health: the Journal of the International Society for Pharmacoeconomics and Outcomes Research
https://www.readbyqxmd.com/read/28212875/genotyping-by-sequencing-provides-the-first-well-resolved-phylogeny-for-coffee-coffea-and-insights-into-the-evolution-of-caffeine-content-in-its-species-gbs-coffee-phylogeny-and-the-evolution-of-caffeine-content
#7
Perla Hamon, Corrinne E Grover, Aaron P Davis, Jean-Jacques Rakotomalala, Nathalie E Raharimalala, Victor A Albert, Hosahalli L Sreenath, Piet Stoffelen, Sharon E Mitchell, Emmanuel Couturon, Serge Hamon, Alexandre de Kochko, Dominique Crouzillat, Michel Rigoreau, Ucu Sumirat, Sélastique Akaffou, Romain Guyot
A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples...
February 14, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28212080/improving-registration-robustness-for-image-guided-liver-surgery-in-a-novel-human-to-phantom-data-framework
#8
Jarrod Collins, Jared Weis, Jon Heiselman, Logan Clements, Amber Simpson, Willam Jarnagin, Michael Miga
In open image-guided liver surgery (IGLS), a sparse representation of the intraoperative organ surface can be acquired to drive image-to-physical registration. We hypothesize that uncharacterized error induced by variation in the collection patterns of organ surface data limits the accuracy and robustness of IGLS registration. Clinical validation of such registration methods is challenged due to the difficulty in obtaining data representative of the true state of organ deformation. We propose a novel human-to-phantom validation framework that transforms surface collection patterns from in vivo IGLS procedures (n=13) onto a well-characterized hepatic deformation phantom for the purpose of validating surface-driven, volumetric nonrigid registration methods...
February 13, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28211501/high-resolution-3d-imaging-of-whole-organ-after-clearing-taking-a-new-look-at-the-zebrafish-testis
#9
Maxence Frétaud, Laurie Rivière, Élodie De Job, Stéphanie Gay, Jean-Jacques Lareyre, Jean-Stéphane Joly, Pierre Affaticati, Violette Thermes
Zebrafish testis has become a powerful model for reproductive biology of teleostean fishes and other vertebrates and encompasses multiple applications in applied and basic research. Many studies have focused on 2D images, which is time consuming and implies extrapolation of results. Three-dimensional imaging of whole organs recently became an important challenge to better understand their architecture and allow cell enumeration. Several protocols have thus been developed to enhance sample transparency, a limiting step for imaging large biological samples...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211456/learning-from-data-to-design-functional-materials-without-inversion-symmetry
#10
Prasanna V Balachandran, Joshua Young, Turab Lookman, James M Rondinelli
Accelerating the search for functional materials is a challenging problem. Here we develop an informatics-guided ab initio approach to accelerate the design and discovery of noncentrosymmetric materials. The workflow integrates group theory, informatics and density-functional theory to uncover design guidelines for predicting noncentrosymmetric compounds, which we apply to layered Ruddlesden-Popper oxides. Group theory identifies how configurations of oxygen octahedral rotation patterns, ordered cation arrangements and their interplay break inversion symmetry, while informatics tools learn from available data to select candidate compositions that fulfil the group-theoretical postulates...
February 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28208263/visualization-quantification-and-alignment-of-spectral-drift-in-population-scale-untargeted-metabolomics-data
#11
Jeramie D Watrous, Mir Henglin, Brian Claggett, Kim A Lehmann, Martin G Larson, Susan Cheng, Mohit Jain
Untargeted liquid-chromatography-mass spectrometry (LC-MS)-based metabolomics analysis of human biospecimens has become among the most promising strategies for probing the underpinnings of human health and disease. Analysis of spectral data across population scale cohorts, however, is precluded by day-to-day nonlinear signal drifts in LC retention time or batch effects that complicate comparison of thousands of untargeted peaks. To date, there exists no efficient means of visualization and quantitative assessment of signal drift, correction of drift when present, and automated filtering of unstable spectral features, particularly across thousands of data files in population scale experiments...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28208251/rapid-method-development-in-hydrophilic-interaction-liquid-chromatography-for-pharmaceutical-analysis-using-a-combination-of-quantitative-structure-retention-relationships-and-design-of-experiments
#12
Maryam Taraji, Paul R Haddad, Ruth I J Amos, Mohammad Talebi, Roman Szucs, John W Dolan, Chris A Pohl
A design-of-experiment (DoE) model was developed, able to describe the retention times of a mixture of pharmaceutical compounds in hydrophilic interaction liquid chromatography (HILIC) under all possible combinations of acetonitrile content, salt concentration, and mobile-phase pH with R(2) > 0.95. Further, a quantitative structure-retention relationship (QSRR) model was developed to predict retention times for new analytes, based only on their chemical structures, with a root-mean-square error of prediction (RMSEP) as low as 0...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28206676/thoracic-ct-mri-co-registration-for-regional-pulmonary-structure-function-measurements-of-obstructive-lung-disease
#13
Fumin Guo, Sarah Svenningsen, Miranda Kirby, Dante P I Capaldi, Khadija Sheikh, Aaron Fenster, Grace Parraga
PURPOSE: Recent pulmonary imaging research has revealed that in patients with chronic obstructive pulmonary disease (COPD) and asthma, structural and functional abnormalities are spatially heterogeneous. This novel information may help optimize treatment in individual patients, monitor interventional efficacy and develop new treatments. Moreover, by automating the measurement of regional biomarkers for the 19 different anatomical lung segments, there is an opportunity to embed imaging biomarkers into clinically-acceptable clinical workflows and improve lung disease clinical care...
February 16, 2017: Medical Physics
https://www.readbyqxmd.com/read/28205533/a-data-driven-approach-for-evaluating-multi-modal-therapy-in-traumatic-brain-injury
#14
Jenny Haefeli, Adam R Ferguson, Deborah Bingham, Adrienne Orr, Seok Joon Won, Tina I Lam, Jian Shi, Sarah Hawley, Jialing Liu, Raymond A Swanson, Stephen M Massa
Combination therapies targeting multiple recovery mechanisms have the potential for additive or synergistic effects, but experimental design and analyses of multimodal therapeutic trials are challenging. To address this problem, we developed a data-driven approach to integrate and analyze raw source data from separate pre-clinical studies and evaluated interactions between four treatments following traumatic brain injury. Histologic and behavioral outcomes were measured in 202 rats treated with combinations of an anti-inflammatory agent (minocycline), a neurotrophic agent (LM11A-31), and physical therapy consisting of assisted exercise with or without botulinum toxin-induced limb constraint...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28204986/validation-workflow-for-a-clinical-bayesian-network-model-in-multidisciplinary-decision-making-in-head-and-neck-oncology-treatment
#15
Mario A Cypko, Matthaeus Stoehr, Marcin Kozniewski, Marek J Druzdzel, Andreas Dietz, Leonard Berliner, Heinz U Lemke
PURPOSE: Oncological treatment is being increasingly complex, and therefore, decision making in multidisciplinary teams is becoming the key activity in the clinical pathways. The increased complexity is related to the number and variability of possible treatment decisions that may be relevant to a patient. In this paper, we describe validation of a multidisciplinary cancer treatment decision in the clinical domain of head and neck oncology. METHOD: Probabilistic graphical models and corresponding inference algorithms, in the form of Bayesian networks, can support complex decision-making processes by providing a mathematically reproducible and transparent advice...
February 15, 2017: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/28204885/de-bugging-and-maximizing-plant-cytochrome-p450-production-in-escherichia-coli-with-c-terminal-gfp-fusions
#16
Ulla Christensen, Dario Vazquez-Albacete, Karina M Søgaard, Tonja Hobel, Morten T Nielsen, Scott James Harrison, Anders Holmgaard Hansen, Birger Lindberg Møller, Susanna Seppälä, Morten H H Nørholm
Cytochromes P450 (CYP) are attractive enzyme targets in biotechnology as they catalyze stereospecific C-hydroxylations of complex core skeletons at positions that typically are difficult to access by chemical synthesis. Membrane bound CYPs are involved in nearly all plant pathways leading to the formation of high-value compounds. In the present study, we systematically maximize the heterologous expression of six different plant-derived CYP genes in Escherichia coli, using a workflow based on C-terminal fusions to the green fluorescent protein...
February 15, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28202595/image-based-modelling-of-skeletal-muscle-oxygenation
#17
REVIEW
B Zeller-Plumhoff, T Roose, G F Clough, P Schneider
The supply of oxygen in sufficient quantity is vital for the correct functioning of all organs in the human body, in particular for skeletal muscle during exercise. Disease is often associated with both an inhibition of the microvascular supply capability and is thought to relate to changes in the structure of blood vessel networks. Different methods exist to investigate the influence of the microvascular structure on tissue oxygenation, varying over a range of application areas, i.e. biological in vivo and in vitro experiments, imaging and mathematical modelling...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28202219/virtual-reconstruction-of-midface-defects-using-statistical-shape-models
#18
Wiebke Semper-Hogg, Marc Anton Fuessinger, Stefan Schlager, Edward Ellis, Carl-Peter Cornelius, Florian Probst, Marc Christian Metzger, Steffen Schwarz
PURPOSE: This study evaluates the accuracy of a statistical shape model (SSM) for virtual fracture reconstruction of the lateral midface. MATERIALS AND METHODS: A uniform bony defect of the right zygoma was created. A virtual reconstruction was performed by using the standard procedure of mirroring the unaffected to the affected side (Group I) and by using the statistical model based on 178 pathologically unaffected CT scans (Group II). The accuracy of the statistical shape model was evaluated in comparison to the present mirroring protocol...
December 24, 2016: Journal of Cranio-maxillo-facial Surgery
https://www.readbyqxmd.com/read/28201984/improvement-of-peptide-identification-with-considering-the-abundance-of-mrna-and-peptide
#19
Chunwei Ma, Shaohang Xu, Geng Liu, Xin Liu, Xun Xu, Bo Wen, Siqi Liu
BACKGROUND: Tandem mass spectrometry (MS/MS) followed by database search is a main approach to identify peptides/proteins in proteomic studies. A lot of effort has been devoted to improve the identification accuracy and sensitivity for peptides/proteins, such as developing advanced algorithms and expanding protein databases. RESULTS: Herein, we described a new strategy for enhancing the sensitivity of protein/peptide identification through combination of mRNA and peptide abundance in Percolator...
February 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28199054/optimization-by-infusion-of-multiple-reaction-monitoring-transitions-for-sensitive-peptides-lc-ms-quantification
#20
Bandar Alghanem, Frédéric Nikitin, Thomas Stricker, Eva Duchoslav, Jeremy Luban, Caterina Strambio-De-Castillia, Markus Muller, Frédérique Lisacek, Emmanuel Varesio, Gérard Hopfgartner
RATIONALE: In LC-MS peptide quantification, the optimization of multiple reaction monitoring (MRM) parameters is essential for sensitive detection. We have compared different approaches to build MRM assays, based either on flow injection analysis (FIA) of isotopically labelled peptides, or on the knowledge and the prediction of the best settings for MRM transitions and collision energies (CE). In this context, we introduce MRMOptimizer, an open source software tool that processes spectra and assists the user in selecting transitions in the FIA workflow...
February 15, 2017: Rapid Communications in Mass Spectrometry: RCM
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