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https://www.readbyqxmd.com/read/27914059/evolution-inspired-computational-design-of-symmetric-proteins
#1
Arnout R D Voet, David Simoncini, Jeremy R H Tame, Kam Y J Zhang
Monomeric proteins with a number of identical repeats creating symmetrical structures are potentially very valuable building blocks with a variety of bionanotechnological applications. As such proteins do not occur naturally, the emerging field of computational protein design serves as an excellent tool to create them from nonsymmetrical templates. Existing pseudo-symmetrical proteins are believed to have evolved from oligomeric precursors by duplication and fusion of identical repeats. Here we describe a computational workflow to reverse-engineer this evolutionary process in order to create stable proteins consisting of identical sequence repeats...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913729/qsea-modelling-of-genome-wide-dna-methylation-from-sequencing-enrichment-experiments
#2
Matthias Lienhard, Sabrina Grasse, Jana Rolff, Steffen Frese, Uwe Schirmer, Michael Becker, Stefan Börno, Bernd Timmermann, Lukas Chavez, Holger Sültmann, Gunda Leschber, Iduna Fichtner, Michal R Schweiger, Ralf Herwig
Genome-wide enrichment of methylated DNA followed by sequencing (MeDIP-seq) offers a reasonable compromise between experimental costs and genomic coverage. However, the computational analysis of these experiments is complex, and quantification of the enrichment signals in terms of absolute levels of methylation requires specific transformation. In this work, we present QSEA, Quantitative Sequence Enrichment Analysis, a comprehensive workflow for the modelling and subsequent quantification of MeDIP-seq data...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913183/nmr-strategies-to-support-medicinal-chemistry-workflows-for-primary-structure-determination
#3
Paul Oguadinma, Francois Bilodeau, Steven R LaPlante
Central to drug discovery is the correct characterization of the primary structures of compounds. In general, medicinal chemists make great synthetic and characterization efforts to deliver the intended compounds. However, there are occasions which incorrect compounds are presented, such as those reported for Bosutinib and TIC10. This may be due to a variety of reasons such as uncontrolled reaction schemes, reliance on limited characterization techniques (LC-MS and/or 1D 1H NMR spectra), or even the lack of availability or knowledge of characterization strategies...
November 24, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27909575/a-step-by-step-workflow-for-low-level-analysis-of-single-cell-rna-seq-data
#4
Aaron T L Lun, Davis J McCarthy, John C Marioni
Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of individual cells. This provides biological resolution that cannot be matched by bulk RNA sequencing, at the cost of increased technical noise and data complexity. The differences between scRNA-seq and bulk RNA-seq data mean that the analysis of the former cannot be performed by recycling bioinformatics pipelines for the latter. Rather, dedicated single-cell methods are required at various steps to exploit the cellular resolution while accounting for technical noise...
2016: F1000Research
https://www.readbyqxmd.com/read/27908978/potential-of-laboratory-execution-systems-less-to-simplify-the-application-of-business-process-management-systems-bpmss-in-laboratory-automation
#5
Sebastian Neubert, Bernd Göde, Xiangyu Gu, Norbert Stoll, Kerstin Thurow
Modern business process management (BPM) is increasingly interesting for laboratory automation. End-to-end workflow automation and improved top-level systems integration for information technology (IT) and automation systems are especially prominent objectives. With the ISO Standard Business Process Model and Notation (BPMN) 2.X, a system-independent and interdisciplinary accepted graphical process control notation is provided, allowing process analysis, while also being executable. The transfer of BPM solutions to structured laboratory automation places novel demands, for example, concerning the real-time-critical process and systems integration...
December 1, 2016: Journal of Laboratory Automation
https://www.readbyqxmd.com/read/27908162/an-efficient-method-to-determine-double-gaussian-fluence-parameters-in-the-eclipse%C3%A2-proton-pencil-beam-model
#6
Jiajian Shen, Wei Liu, Joshua Stoker, Xiaoning Ding, Aman Anand, Yanle Hu, Michael G Herman, Martin Bues
PURPOSE: To find an efficient method to configure the proton fluence for a commercial proton pencil beam scanning (PBS) treatment planning system (TPS). METHODS: An in-water dose kernel was developed to mimic the dose kernel of the pencil beam convolution superposition algorithm, which is part of the commercial proton beam therapy planning software, eclipse™ (Varian Medical Systems, Palo Alto, CA). The field size factor (FSF) was calculated based on the spot profile reconstructed by the in-house dose kernel...
December 2016: Medical Physics
https://www.readbyqxmd.com/read/27907243/an-optimized-centrifugal-method-for-separation-of-semen-from-superabsorbent-polymers-for-forensic-analysis
#7
Lucy R Camarena, Bailey K Glasscock, Demi Daniels, Nicolle Ackley, Marybeth Sciarretta, Sarah J Seashols-Williams
Connection of a perpetrator to a sexual assault is best performed through the confirmed presence of semen, thereby proving sexual contact. Evidentiary items can include sanitary napkins or diapers containing superabsorbent polymers (SAPs), complicating spermatozoa visualization and DNA analysis. In this report, we evaluated the impact of SAPS on the current forensic DNA workflow, developing an efficient centrifugal protocol for separating spermatozoa from SAP material. The optimized filtration method was compared to common practices of excising the top layer only, resulting in significantly higher sperm yields when a core sample of the substrate was taken...
December 1, 2016: Journal of Forensic Sciences
https://www.readbyqxmd.com/read/27906451/proximity-dependent-biotinylation-for-identification-of-interacting-proteins
#8
Valerie Le Sage, Alessandro Cinti, Andrew J Mouland
Complex interaction networks orchestrate key cellular processes including but not limited to transcription, translation, metabolism, and cell signaling. Delineating these interactions will aid in deciphering the regulation and function of these pathways and potential for manipulation. Proximity-dependent biotin identification (BioID) is quickly gaining popularity as a powerful tool for identifying novel protein-protein and proximity-based interactions in live cells. This technique relies on a promiscuous biotin ligase, which is fused to a protein of interest and, upon expression in the desired cell, will biotinylate proximal endogenous proteins...
December 1, 2016: Current Protocols in Cell Biology
https://www.readbyqxmd.com/read/27906192/thematic-analysis-of-barriers-and-facilitators-to-implementation-of-neonatal-resuscitation-guideline-changes
#9
H C Lee, V Arora, T Brown, A Lyndon
OBJECTIVE: To evaluate experiences regarding implementation of Neonatal Resuscitation Program (NRP) guideline changes in the context of a collaborative quality improvement (QI) project. STUDY DESIGN: Focus groups were conducted with local QI leaders and providers from nine sites that participated in a QI collaborative. Thematic analysis identified facilitators and barriers to implementation of NRP guideline changes and QI in general. RESULTS: Facilitators for QI included comparative process measurement and data tracking...
December 1, 2016: Journal of Perinatology: Official Journal of the California Perinatal Association
https://www.readbyqxmd.com/read/27906039/peering-below-the-diffraction-limit-robust-and-specific-sorting-of-viruses-with-flow-cytometry
#10
Shea T Lance, David J Sukovich, Kenneth M Stedman, Adam R Abate
BACKGROUND: Viruses are incredibly diverse organisms and impact all forms of life on Earth; however, individual virions are challenging to study due to their small size and mass, precluding almost all direct imaging or molecular analysis. Moreover, like microbes, the overwhelming majority of viruses cannot be cultured, impeding isolation, replication, and study of interesting new species. Here, we introduce PCR-activated virus sorting, a method to isolate specific viruses from a heterogeneous population...
December 1, 2016: Virology Journal
https://www.readbyqxmd.com/read/27904975/rayplus-a-web-based-platform-for-medical-image-processing
#11
Rong Yuan, Ming Luo, Zhi Sun, Shuyue Shi, Peng Xiao, Qingguo Xie
Medical image can provide valuable information for preclinical research, clinical diagnosis, and treatment. As the widespread use of digital medical imaging, many researchers are currently developing medical image processing algorithms and systems in order to accommodate a better result to clinical community, including accurate clinical parameters or processed images from the original images. In this paper, we propose a web-based platform to present and process medical images. By using Internet and novel database technologies, authorized users can easily access to medical images and facilitate their workflows of processing with server-side powerful computing performance without any installation...
November 30, 2016: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
https://www.readbyqxmd.com/read/27904452/virtual-modelling-of-novel-applicator-prototypes-for-cervical-cancer-brachytherapy
#12
Primoz Petric, Robert Hudej, Noora Al-Hammadi, Barbara Segedin
BACKGROUND: Standard applicators for cervical cancer Brachytherapy (BT) do not always achieve acceptable balance between target volume and normal tissue irradiation. We aimed to develop an innovative method of Target-volume Density Mapping (TDM) for modelling of novel applicator prototypes with optimal coverage characteristics. Patients and methods. Development of Contour-Analysis Tool 2 (CAT-2) software for TDM generation was the core priority of our task group. Main requests regarding software functionalities were formulated and guided the coding process...
December 1, 2016: Radiology and Oncology
https://www.readbyqxmd.com/read/27903906/eupathdb-the-eukaryotic-pathogen-genomics-database-resource
#13
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/27902553/perspectives-and-uses-of-the-electronic-health-record-among-us-pediatricians-a-national-survey
#14
Julie W Doberne, Travis Redd, Daniel Lattin, Thomas R Yackel, Carl O Eriksson, Vishnu Mohan, Jeffrey A Gold, Joan S Ash, Michael F Chiang
Little is known about how existing electronic health records (EHRs) influence the practice of pediatric medicine. A total of 808 pediatricians participated in a survey about workflows using the EHR. The EHR was the most commonly used source of initial patient information. Seventy-two percent reported requiring between 2 and 10 minutes to complete an initial review of the EHR. Several moderately severe information barriers were reported regarding the display of information in the EHR. Pediatricians acquire information about new patients from EHRs more often than any other source...
January 2017: Journal of Ambulatory Care Management
https://www.readbyqxmd.com/read/27902548/leveraging-electronic-health-record-implementation-to-facilitate-clinical-and-operational-quality-improvement-in-an-ambulatory-surgical-clinic
#15
Joseph L Bobadilla, Cathy S Roe, Patricia Estes, Jennifer Lackey, Carol L Steltenkamp
The implementation of electronic health records is a challenging, complex process requiring significant resources. The temptation is to convert a paper process into electronic format. This strategy fosters a familiar product to the users but is fraught with pitfalls. We chose to utilize the opportunity of the implementation of an enterprise-wide ambulatory electronic health record to foster an overreaching clinical and operational improvement project in a multispecialty surgical ambulatory clinic practice. We interrogated every aspect of the practice: clinic design, scheduling, physical space, staffing, and clinical and operational workflows...
January 2017: Journal of Ambulatory Care Management
https://www.readbyqxmd.com/read/27901096/image-based-in-vivo-assessment-of-targeting-accuracy-of-stereotactic-brain-surgery-in-experimental-rodent-models
#16
Janaki Raman Rangarajan, Greetje Vande Velde, Friso van Gent, Philippe De Vloo, Tom Dresselaers, Maarten Depypere, Kris van Kuyck, Bart Nuttin, Uwe Himmelreich, Frederik Maes
Stereotactic neurosurgery is used in pre-clinical research of neurological and psychiatric disorders in experimental rat and mouse models to engraft a needle or electrode at a pre-defined location in the brain. However, inaccurate targeting may confound the results of such experiments. In contrast to the clinical practice, inaccurate targeting in rodents remains usually unnoticed until assessed by ex vivo end-point histology. We here propose a workflow for in vivo assessment of stereotactic targeting accuracy in small animal studies based on multi-modal post-operative imaging...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900688/degradation-network-reconstruction-guided-by-metagenomic-data
#17
Rafael Bargiela, Manuel Ferrer
Network reconstruction procedures based on meta-"omics" data are an invaluable tool for inferring total and active set of reactions mediated by different members in a microbial community. Within them, network-based methods for automatic analysis of catabolic capacities in metagenomes are currently limited. Here, we describe the complete workflow, scripts, and commands allowing the automatic reconstruction of biodegradation networks using as an input meta-sequences generated by direct DNA sequencing.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900686/shotgun-metagenomic-sequencing-analysis-of-soft-rot-enterobacteriaceae-in-polymicrobial-communities
#18
James Doonan, Sandra Denman, James E McDonald, Peter N Golyshin
Shotgun metagenomic sequencing of bacterial communities in necrotic plant lesions allows insights of host-pathogen molecular interactions. Soft-rot Enterobacteriaceae are significant crop pathogens with a wide host range. Reconstructed polymicrobial community DNA from soft-rot affected crops provides details of species relative abundance and functional potential, enabling significant insights into their lifestyle. Here, we describe a workflow for DNA recovery, metagenomic shotgun sequencing and in particular, an in silico analysis of bacterial isolates from affected plant tissue...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900504/a-large-scale-chromosome-specific-snp-discovery-guideline
#19
Bala Ani Akpinar, Stuart Lucas, Hikmet Budak
Single-nucleotide polymorphisms (SNPs) are the most prevalent type of variation in genomes that are increasingly being used as molecular markers in diversity analyses, mapping and cloning of genes, and germplasm characterization. However, only a few studies reported large-scale SNP discovery in Aegilops tauschii, restricting their potential use as markers for the low-polymorphic D genome. Here, we report 68,592 SNPs found on the gene-related sequences of the 5D chromosome of Ae. tauschii genotype MvGB589 using genomic and transcriptomic sequences from seven Ae...
November 29, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27900429/highly-selective-sio2-nh2-tio2-hollow-microspheres-for-simultaneous-enrichment-of-phosphopeptides-and-glycopeptides
#20
Dongpo Xu, Guoquan Yan, Mingxia Gao, Chunhui Deng, Xiangmin Zhang
Glycosylation and phosphorylation as the commonest and most important posttranslational modifications of proteins play critical roles in biological processes. Specific and sensitive strategies have been developed to identify the glycosylation and phosphorylation of proteins by mass spectrometry but most of these methods have mainly focused on enriching glycopeptides or phosphopeptides separately, and few of them can enrich both of them. In this work, highly selective SiO2-NH2@TiO2 hollow microspheres were designed and synthesized for the simultaneous selective enrichment of both phosphopeptides and glycopeptides...
November 29, 2016: Analytical and Bioanalytical Chemistry
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