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https://www.readbyqxmd.com/read/27914058/osprey-predicts-resistance-mutations-using-positive-and-negative-computational-protein-design
#1
Adegoke Ojewole, Anna Lowegard, Pablo Gainza, Stephanie M Reeve, Ivelin Georgiev, Amy C Anderson, Bruce R Donald
Drug resistance in protein targets is an increasingly common phenomenon that reduces the efficacy of both existing and new antibiotics. However, knowledge of future resistance mutations during pre-clinical phases of drug development would enable the design of novel antibiotics that are robust against not only known resistant mutants, but also against those that have not yet been clinically observed. Computational structure-based protein design (CSPD) is a transformative field that enables the prediction of protein sequences with desired biochemical properties such as binding affinity and specificity to a target...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914055/an-evolution-based-approach-to-de-novo-protein-design
#2
Jeffrey R Brender, David Shultis, Naureen Aslam Khattak, Yang Zhang
EvoDesign is a computational algorithm that allows the rapid creation of new protein sequences that are compatible with specific protein structures. As such, it can be used to optimize protein stability, to resculpt the protein surface to eliminate undesired protein-protein interactions, and to optimize protein-protein binding. A major distinguishing feature of EvoDesign in comparison to other protein design programs is the use of evolutionary information in the design process to guide the sequence search toward native-like sequences known to adopt structurally similar folds as the target...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27911735/computational-protein-design-with-backbone-plasticity
#3
REVIEW
James T MacDonald, Paul S Freemont
The computational algorithms used in the design of artificial proteins have become increasingly sophisticated in recent years, producing a series of remarkable successes. The most dramatic of these is the de novo design of artificial enzymes. The majority of these designs have reused naturally occurring protein structures as 'scaffolds' onto which novel functionality can be grafted without having to redesign the backbone structure. The incorporation of backbone flexibility into protein design is a much more computationally challenging problem due to the greatly increased search space, but promises to remove the limitations of reusing natural protein scaffolds...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27910445/the-advanced-ligo-photon-calibrators
#4
S Karki, D Tuyenbayev, S Kandhasamy, B P Abbott, T D Abbott, E H Anders, J Berliner, J Betzwieser, C Cahillane, L Canete, C Conley, H P Daveloza, N De Lillo, J R Gleason, E Goetz, K Izumi, J S Kissel, G Mendell, V Quetschke, M Rodruck, S Sachdev, T Sadecki, P B Schwinberg, A Sottile, M Wade, A J Weinstein, M West, R L Savage
The two interferometers of the Laser Interferometry Gravitational-wave Observatory (LIGO) recently detected gravitational waves from the mergers of binary black hole systems. Accurate calibration of the output of these detectors was crucial for the observation of these events and the extraction of parameters of the sources. The principal tools used to calibrate the responses of the second-generation (Advanced) LIGO detectors to gravitational waves are systems based on radiation pressure and referred to as photon calibrators...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27903906/eupathdb-the-eukaryotic-pathogen-genomics-database-resource
#5
Cristina Aurrecoechea, Ana Barreto, Evelina Y Basenko, John Brestelli, Brian P Brunk, Shon Cade, Kathryn Crouch, Ryan Doherty, Dave Falke, Steve Fischer, Bindu Gajria, Omar S Harb, Mark Heiges, Christiane Hertz-Fowler, Sufen Hu, John Iodice, Jessica C Kissinger, Cris Lawrence, Wei Li, Deborah F Pinney, Jane A Pulman, David S Roos, Achchuthan Shanmugasundram, Fatima Silva-Franco, Sascha Steinbiss, Christian J Stoeckert, Drew Spruill, Haiming Wang, Susanne Warrenfeltz, Jie Zheng
The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27903527/standardized-flow-cytometry-for-highly-sensitive-mrd-measurements-in-b-cell-acute-lymphoblastic-leukemia
#6
Prisca Theunissen, Ester Mejstrikova, Lukasz Sedek, Alita J van der Sluijs-Gelling, Giuseppe Gaipa, Marius Bartels, Elaine Sobral da Costa, Michaela Kotrova, Michaela Novakova, Edwin Sonneveld, Chiara Buracchi, Paola Bonaccorso, Elen Oliviera, Jeroen G Te Marvelde, Tomasz Szczepanski, Ludovic Lhermitte, Ondrej Hrusak, Quentin Lecrevisse, Georgiana Emilia Grigore, Eva Fronkova, Jan Trka, Monika Brüggemann, Alberto Orfao, Jacques J M van Dongen, Vincent H J van der Velden
A fully-standardized EuroFlow 8-color antibody panel and laboratory procedure was stepwise designed to measure minimal residual disease (MRD) in B-cell precursor (BCP) acute lymphoblastic leukemia (ALL) patients with a sensitivity of ≤10(-5), comparable to real-time quantitative (RQ)-PCR-based MRD detection via antigen-receptor rearrangements. Leukocyte markers and the corresponding antibodies and fluorochromes were selected based on their contribution in separating BCP-ALL cells from normal/regenerating BCP cells in multidimensional principal component analyses...
November 30, 2016: Blood
https://www.readbyqxmd.com/read/27902532/lean-six-sigma-to-reduce-intensive-care-unit-length-of-stay-and-costs-in-prolonged-mechanical-ventilation
#7
Stephen Trzeciak, Michael Mercincavage, Cory Angelini, William Cogliano, Emily Damuth, Brian W Roberts, Sergio Zanotti, Anthony J Mazzarelli
OBJECTIVE: Patients with prolonged mechanical ventilation (PMV) represent important "outliers" of hospital length of stay (LOS) and costs (∼$26 billion annually in the United States). We tested the hypothesis that a Lean Six Sigma (LSS) approach for process improvement could reduce hospital LOS and the associated costs of care for patients with PMV. DESIGN: Before-and-after cohort study. SETTING: Multidisciplinary intensive care unit (ICU) in an academic medical center...
November 29, 2016: Journal for Healthcare Quality: Official Publication of the National Association for Healthcare Quality
https://www.readbyqxmd.com/read/27900794/fast-and-efficient-free-induction-decay-mr-spectroscopic-imaging-of-the-human-brain-at-9-4-tesla
#8
Grzegorz L Chadzynski, Jonas Bause, Gunamony Shajan, Rolf Pohmann, Klaus Scheffler, Philipp Ehses
PURPOSE: The purpose of this work was to develop a fast and efficient MRSI-FID acquisition scheme and test its performance in vivo. The aim was to find a trade-off between the minimal total acquisition time and signal-to-noise ratio of the acquired spectra. METHODS: Measurements were performed on a 9.4 Tesla system. Sequence optimization included redesign of water suppression, optimization of the sequence gradients, and improvement of the sampling efficiency by minimizing the read-out time...
November 29, 2016: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/27899832/development-and-application-of-a-stepwise-assessment-process-for-rational-redesign-of-sequential-skills-based-courses
#9
Casey E Gallimore, Andrea L Porter, Susanne G Barnett
Objective. To develop and apply a stepwise process to assess achievement of course learning objectives related to advanced pharmacy practice experiences (APPEs) preparedness and inform redesign of sequential skills-based courses. Design. Four steps comprised the assessment and redesign process: (1) identify skills critical for APPE preparedness; (2) utilize focus groups and course evaluations to determine student competence in skill performance; (3) apply course mapping to identify course deficits contributing to suboptimal skill performance; and (4) initiate course redesign to target exposed deficits...
October 25, 2016: American Journal of Pharmaceutical Education
https://www.readbyqxmd.com/read/27899675/jet2-viewer-a-database-of-predicted-multiple-possibly-overlapping-protein-protein-interaction-sites-for-pdb-structures
#10
Hughes Ripoche, Elodie Laine, Nicoletta Ceres, Alessandra Carbone
The database JET2 Viewer, openly accessible at http://www.jet2viewer.upmc.fr/, reports putative protein binding sites for all three-dimensional (3D) structures available in the Protein Data Bank (PDB). This knowledge base was generated by applying the computational method JET(2) at large-scale on more than 20 000 chains. JET(2) strategy yields very precise predictions of interacting surfaces and unravels their evolutionary process and complexity. JET2 Viewer provides an online intelligent display, including interactive 3D visualization of the binding sites mapped onto PDB structures and suitable files recording JET(2) analyses...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899670/the-new-nhgri-ebi-catalog-of-published-genome-wide-association-studies-gwas-catalog
#11
Jacqueline MacArthur, Emily Bowler, Maria Cerezo, Laurent Gil, Peggy Hall, Emma Hastings, Heather Junkins, Aoife McMahon, Annalisa Milano, Joannella Morales, Zoe May Pendlington, Danielle Welter, Tony Burdett, Lucia Hindorff, Paul Flicek, Fiona Cunningham, Helen Parkinson
The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality and an improved curation interface. These developments have improved the data release frequency by increasing automation of curation and providing scaling improvements. The range of available Catalog data has also been extended with structured ancestry and recruitment information added for all studies...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899667/rice-snp-seek-database-update-new-snps-indels-and-queries
#12
Locedie Mansueto, Roven Rommel Fuentes, Frances Nikki Borja, Jeffery Detras, Juan Miguel Abriol-Santos, Dmytro Chebotarov, Millicent Sanciangco, Kevin Palis, Dario Copetti, Alexandre Poliakov, Inna Dubchak, Victor Solovyev, Rod A Wing, Ruaraidh Sackville Hamilton, Ramil Mauleon, Kenneth L McNally, Nickolai Alexandrov
We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899627/improvements-to-patric-the-all-bacterial-bioinformatics-database-and-analysis-resource-center
#13
Alice R Wattam, James J Davis, Rida Assaf, Sébastien Boisvert, Thomas Brettin, Christopher Bun, Neal Conrad, Emily M Dietrich, Terry Disz, Joseph L Gabbard, Svetlana Gerdes, Christopher S Henry, Ronald W Kenyon, Dustin Machi, Chunhong Mao, Eric K Nordberg, Gary J Olsen, Daniel E Murphy-Olson, Robert Olson, Ross Overbeek, Bruce Parrello, Gordon D Pusch, Maulik Shukla, Veronika Vonstein, Andrew Warren, Fangfang Xia, Hyunseung Yoo, Rick L Stevens
The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user-created genome-groups, with detailed summaries and views of the data that researchers have selected...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899599/pubchem-bioassay-2017-update
#14
Yanli Wang, Stephen H Bryant, Tiejun Cheng, Jiyao Wang, Asta Gindulyte, Benjamin A Shoemaker, Paul A Thiessen, Siqian He, Jian Zhang
PubChem's BioAssay database (https://pubchem.ncbi.nlm.nih.gov) has served as a public repository for small-molecule and RNAi screening data since 2004 providing open access of its data content to the community. PubChem accepts data submission from worldwide researchers at academia, industry and government agencies. PubChem also collaborates with other chemical biology database stakeholders with data exchange. With over a decade's development effort, it becomes an important information resource supporting drug discovery and chemical biology research...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899584/cath-an-expanded-resource-to-predict-protein-function-through-structure-and-sequence
#15
Natalie L Dawson, Tony E Lewis, Sayoni Das, Jonathan G Lees, David Lee, Paul Ashford, Christine A Orengo, Ian Sillitoe
The latest version of the CATH-Gene3D protein structure classification database has recently been released (version 4.1, http://www.cathdb.info). The resource comprises over 300 000 domain structures and over 53 million protein domains classified into 2737 homologous superfamilies, doubling the number of predicted protein domains in the previous version. The daily-updated CATH-B, which contains our very latest domain assignment data, provides putative classifications for over 100 000 additional protein domains...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27889192/evolving-concepts-in-the-treatment-of-relapsing-multiple-sclerosis
#16
REVIEW
Giancarlo Comi, Marta Radaelli, Per Soelberg Sørensen
In the past 20 years the treatment scenario of multiple sclerosis has radically changed. The increasing availability of effective disease-modifying therapies has shifted the aim of therapeutic interventions from a reduction in relapses and disability accrual, to the absence of any sign of clinical or MRI activity. The choice for therapy is increasingly complex and should be driven by an appropriate knowledge of the mechanisms of action of the different drugs and of their risk-benefit profile. Because the relapsing phase of the disease is characterised by inflammation, treatment should be started as early as possible and aim to re-establish the normal complex interactions in the immune system...
November 23, 2016: Lancet
https://www.readbyqxmd.com/read/27882613/improvements-of-procedural-results-with-a-new-generation-self-expanding-transfemoral-aortic-valve-prosthesis-in-comparison-to-the-old-generation-device
#17
Bruna Gomes, Nicolas A Geis, Emmanuel Chorianopoulos, Benjamin Meder, Florian Leuschner, Hugo A Katus, Raffi Bekeredjian
OBJECTIVES: In this study, we compare procedural results of our first Evolut R (Medtronic, Minneapolis, MN, USA) implantations with the last CoreValve implantations. Main endpoints include paravalvular regurgitation, major vascular complications, stroke, and pacemaker implantation. BACKGROUND: The evolution of transcatheter aortic valve replacement (TAVR) was possible due to various technical improvements, leading to better periprocedural and long-term outcome. The newly designed Evolut R valve has the potential to further improve TAVR's performance...
November 24, 2016: Journal of Interventional Cardiology
https://www.readbyqxmd.com/read/27871224/insights-into-the-human-mesenchymal-stromal-stem-cell-identity-through-integrative-transcriptomic-profiling
#18
Beatriz Roson-Burgo, Fermin Sanchez-Guijo, Consuelo Del Cañizo, Javier De Las Rivas
BACKGROUND: Mesenchymal Stromal/Stem Cells (MSCs), isolated under the criteria established by the ISCT, still have a poorly characterized phenotype that is difficult to distinguish from similar cell populations. Although the field of transcriptomics and functional genomics has quickly grown in the last decade, a deep comparative analysis of human MSCs expression profiles in a meaningful cellular context has not been yet performed. There is also a need to find a well-defined MSCs gene-signature because many recent biomedical studies show that key cellular interaction processes (i...
November 21, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27870546/integrated-care-organizations-medicare-financing-for-care-at-home
#19
Karen Davis, Amber Willink, Cathy Schoen
OBJECTIVES: As the boomer population ages, there is a growing need for integrated care organizations (ICOs) that can integrate both medical care and long-term services and supports in the home. This paper presents a policy proposal to support the creation of ICOs, redesign care, and provide financing for home- and community-based services (HCBS), with the goal of enhancing financial protection for beneficiaries, coordinating care, and preventing costly hospital and nursing home use. METHODS: This study used the 2012 Medicare Current Beneficiary Survey (MCBS) Cost and Use File, inflated to 2016 figures, to describe the characteristics of Medicare beneficiaries and their healthcare utilization and spending...
November 2016: American Journal of Managed Care
https://www.readbyqxmd.com/read/27869887/-anmco-position-paper-hospital-discharge-planning
#20
Mauro Mennuni, Michele Massimo Gulizia, Gianfranco Alunni, Antonio Francesco Amico, Francesco Maria Bovenzi, Roberto Caporale, Furio Colivicchi, Andrea Di Lenarda, Giuseppe Di Tano, Sabrina Egman, Francesco Fattirolli, Domenico Gabrielli, Giovanna Geraci, Giovanni Gregorio, Gian Francesco Mureddu, Federico Nardi, Donatella Radini, Carmine Riccio, Fausto Rigo, Marco Sicuro, Stefano Urbinati, Guerrino Zuin
Hospital discharge is often poorly standardized and is characterized by discontinuity and fragmentation of care, putting patients at high risk of post-discharge adverse events and early readmission. The present ANMCO position paper reviews the modifiable components of the hospital discharge process related to adverse events or rehospitalizations and suggests the optimal methods for redesign the whole discharge process. The key principles for proper hospital discharge or transfer of care acknowledge that hospital discharge:- is not an isolated event, but a process that has to be planned immediately after admission, ensuring that the patient and the caregiver understand and contribute to the planned decisions as equal partners;- is facilitated by a comprehensive systemic approach that begins with a multidimensional evaluation process;- must be organized by an operator who is responsible for the coordination of all phases of the hospital patient pathway, involving afterwards the physician and transferring to them the information and responsibility;- is the result of an integrated multidisciplinary team approach;- uses appropriately the transitional and intermediate care services;- is carried out in an organized system of care and continuum of services;- programs the passage of information to after-discharge services...
September 2016: Giornale Italiano di Cardiologia
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