1,584 research outputs found
Short Courses: Flexible Learning Opportunities in Informatics
In todayâs fast-paced, data-driven world, researchers need to have a good foundation in informatics to store, organize, process, and analyze growing amounts of data. However, not all degree programs offer such training. Obtaining training in informatics on your own can be a daunting task for both new and established researchers who have little informatics experience. Providing educational opportunities appropriate for various skill levels and that mesh with a full-time schedule can remove barriers and foster a collaborative, informatics-savvy community that is better equipped to push science forward.
To enhance informatics education in bioinformatics, VCUs Wright Center for Clinical and Translational Research of- fers a complementary series of seminars and workshops. These short course offerings introduce attendees to bioinformatics concepts and applications, and provide hands-on experience using online Bioinformatics databases. Bioinformatics 101 (B101) is an 8-week long series of 1-hour seminars focused on introducing topics in bioinformatics related to Next Generation Sequencing (NGS). Lectures are application focused and include overviews of NGS technology, practical bioinformatics pipelines, and examples of how the technology can influence downstream bioinformatics analyses. Bioinformatics 102 (B102) is a 5-day, 2 hours per day workshop developed in collaboration with VCU Libraries that provides attendees with hands-on experience accessing and using public data repositories. Sessions include a brief lecture followed by hands-on exercises. A Certificate of Completion is awarded upon meeting certain criteria for either the 101 or 102 courses.
Bioinformatics 101 has been offered 3 times with a combined total of 246 registrants, and Bioinformatics 102 has been offered twice with a total of 78 registrants (limited to 30 per session per day). From course surveys, 82% (n=108) and 95% (n=47) of respondents gave B101 and B102 a positive rating, respectively. In addition, 89% of B101 respondents indicated their knowledge was improved, with 100% of B102 respondents indicating the same. A total of 84 and 33 certificates have been awarded for B101 and B102, respectively.
The Bioinformatics 101 and 102 courses have become highly anticipated across the university, and have gained the external attention of surrounding businesses and colleges. Registrants have diverse backgrounds including biological, clinical, computational, administrative, librarian, business, and others with a total of 77 departments across VCU and VCU Health represented. Due to this interest, Bioinformatics 101 began offering live online attendance to accommodate those who were unable to travel across campus, or who are attending from outside VCU. This past year, 50% of attendance was online indicating a growing need for flexible education opportunities in informatics.
Increasing researcher knowledge of Bioinformatics along with awareness of university resources for informatics support fosters an informatics-savvy research community that is empowered to take advantage of existing and new data sources in the pursuit of new insights and scientific discoveries for the betterment of human health. Future work will include the development of a more comprehensive educational framework by creating new and flexible learning opportunities that will make informatics education easy and convenient for our dedicated researchers
Providing Hands-on Training with Bioinformatics Databases: A Collaboration Between VCU Libraries & Wright Center for Clinical and Translational Research
BackgroundWith the goal of increasing specialized services for researchers, Virginia Commonwealth University (VCU) Libraries sent its basic science librarians to an intensive training on bioinformatics databases, âA Librarianâs Guide to NCBI.â VCUâs Wright Center for Clinical and Translational Research (Wright CCTR) was expanding the educational component of its bioinformatics support around the same time. This year, the librarians partnered with the Wright CCTR to offer an introductory bioinformatics database workshop introducing researchers to genetic/genomic databases. MethodsFor one week in June, sessions were conducted introducing up to 30 faculty and staff to The Cancer Genome Atlas and NCBIâs Gene, BLAST, Variation Viewer and Gene Expression Omnibus. Librarians taught resources they learned in the NCBI training, and Wright CCTR staff taught resources they use often. Each dayâs 1.5 hour session included presentations, demonstrations, and hands-on assignment time. Certificates were awarded to participants who completed 4 out of 5 assignments. ResultsRegistration for the workshop was full in under a week with a waiting list. All survey respondents (n=27) evaluated the overall quality of the workshop as good or excellent and indicated that they would recommend the workshop to a colleague or student. ConclusionsThis successful partnership between VCU Libraries and the Wright CCTR allowed for a broader range of bioinformatics topics to be covered, in addition to easing the planning and teaching workload for each group. The strong interest in this series across a variety of disciplines from both VCU and VCU Health indicates a need for staff and faculty-oriented bioinformatics training within the university
`NMR Crystallization': in-situ NMR techniques for time-resolved monitoring of crystallization processes
Solid-state NMR spectroscopy is a well-established and versatile technique for studying structural and dynamic properties of solids, and there is considerable potential to exploit the power and versatility of solid-state NMR for in-situ studies of chemical processes. However, a number of technical challenges are associated with adapting this technique for in-situ studies, depending on the process of interest. Recently, an in-situ solid-state NMR strategy for monitoring the evolution of crystallization processes has been developed and has proven to be a promising approach for identifying the sequence of distinct solid forms present as a function of time during crystallization from solution, and for the discovery of new polymorphs. The latest development of this technique, called âCLASSICâ NMR, allows simultaneous measurement of both liquid-state and solid-state NMR spectra as a function of time, thus yielding complementary information on the evolution of both the liquid phase and the solid phase during crystallization from solution. This article gives an overview of the range of NMR strategies that are currently available for in-situ studies of crystallization processes, with examples of applications that highlight the potential of these strategies to deepen our understanding of crystallization phenomena
X-ray Birefringence Imaging and other fundamental aspects of solid organic inclusion compounds
This thesis presents new experimental techniques and utilizes these strategies in the analysis of solid organic inclusion compounds. This thesis also reports the production of a new series of co-crystals and examines their crystal structures.
Chapter 1 acts as an introduction to the materials studied in this research. It explains the properties of inclusion compounds and lists the chemical materials used for these experiments.
Chapter 2 explains the experimental techniques used in this research. Specifically it explains X-ray diffraction, X-ray birefringence and in-situ solid-state NMR.
Chapter 3 presents a new technique for spatially resolved mapping of specific bond orientations in anisotropic solid materials using wide beam linearly polarized X-rays and an area detector. Earlier work with a focussed beam and a point detector showed the sensitivity of X-ray Birefringence to the orientation of specific energy-matching bonds inside a material, but these experiments only probed a small section of the crystal. Our wide beam imaging technique (X-ray Birefringence Imaging) shows similar sensitivity but allows us to investigate the full crystal simultaneously, which allows us to identify different domains within a single crystal. We apply this technique to a model material (1 bromocyclohexane/thiourea) which undergoes a low temperature phase transition and serves to demonstrate the usefulness of imaging techniques - in the high temperature phase the relevant CâBr bonds are isotropically disordered and no birefringence is observed, in the low temperature phase the relevant CâBr bonds are ordered but there are three possible orientations for the bromocyclohexane molecule so different regions of the crystal exhibit different birefringent signal. This behaviour is very clear on an imaging technique, but can appear highly confusing when using point-detector techniques.
Chapter 4 utilizes X-ray Birefringence Imaging to investigate the dynamic rotational properties of guest molecules in a different set of solid organic inclusion compounds. By studying the known structures of 1,10-dibromodecane/urea and 1,8-dibromooctance/urea we have determined that XBI is a time-averaged and space-averaged technique. Additionally this chapter utilizes a Ge(555) analyzer instead of the Si(555) analyzer, which results in better spatial resolution and a different beam shape on the final images.
Chapter 5 utilizes solid-state in-situ NMR to monitor crystallization processes as they occur and gain insight on competitive uptake of different guest molecules within the inclusion compound. These experiments use alkane and α,Ï-dibromoalkane guest molecules inside urea inclusion compounds where the urea host structure (created in-situ) acts like a one-dimensional tunnel confining the guest. Every position within the urea tunnel is equivalent (a property of the incommensurate structure) which serves to simply the solid-state NMR spectra and means that for a given atom at the end of an alkane chain the only difference in NMR site comes from the neighbour molecule along the tunnel. This means in the solid phase we can observe peak splitting on certain atoms based on neighbour environment (e.g. the -CH3 in undecane will give a slightly different chemical shift if the neighbouring guest molecule is another undecane compared to if the neighbouring guest molecule is 1,8-dibromooctane) which in turn allows us to extract some information about the ordering within the inclusion compound. In these experiments we can also clearly distinguish between the same molecules in different phases, so as crystallization occurs we observe the loss of solution signal alongside the gain of solid signal. Additionally these experiments show no evidence of any intermediate structures or transition states.
Chapter 6 describes a new set of organic co-crystals formed by reacting thiourea with α,Ï-diiodoalkane chains and examines the crystal structures of these materials.
Chapter 7 details further work and potential applications of this research.
Digital data includes animated videos of the X-ray birefringence imaging data obtained in Chapter 3 and CIF files of the structures determined in Chapter 6
Phenotypic indicators to identify methionine rich European grain legumes and the correlation of grain methionine contents with the sulphur supply
Home grown legumes are a valuable protein source for pure on-farm diets for livestock in organic farming. Whereas protein of Glycine max naturally has higher contents of methionine nand also lysine typical European grain legumes (Pisum sativum L., Vicia faba L., Lupinus angustifolius L.) used in organic farms as component of animal food are relatively low in those amino acids
Limits on the Dipole Moments of the -Lepton via the Process $e^{+}e^{-}\to \tau^+ \tau^- \gamma in a Left-Right Symmetric Model
Limits on the anomalous magnetic moment and the electric dipole moment of the
lepton are calculated through the reaction at the -pole and in the framework of a left-right symmetric model.
The results are based on the recent data reported by the L3 Collaboration at
CERN LEP. Due to the stringent limit of the model mixing angle , the
effect of this angle on the dipole moments is quite small.Comment: 15 pages, 3 figure
Recommended from our members
The role of EGFR double minutes in modulating the response of malignant gliomas to radiotherapy.
EGFR amplification in cells having double minute chromosomes (DM) is commonly found in glioblastoma multiforme (GBM); however, how much it contributes to the current failure to treat GBM successfully is unknown. We studied two syngeneic primary cultures derived from a GBM with and without cells carrying DM, for their differential molecular and metabolic profiles, in vivo growth patterns, and responses to irradiation (IR). Each cell line has a distinct molecular profile consistent with an invasive "go" (with DM) or angiogenic "grow" phenotype (without DM) demonstrated in vitro and in intracranial xenograft models. Cells with DM were relatively radio-resistant and used higher glycolytic respiration and lower oxidative phosphorylation in comparison to cells without them. The DM-containing cell was able to restore tumor heterogeneity by mis-segregation of the DM-chromosomes, giving rise to cell subpopulations without them. As a response to IR, DM-containing cells switched their respiration from glycolic metabolism to oxidative phosphorylation and shifted molecular profiles towards that of cells without DM. Irradiated cells with DM showed the capacity to alter their extracellular microenvironment to not only promote invasiveness of the surrounding cells, regardless of DM status, but also to create a pro-angiogenic tumor microenvironment. IR of cells without DM was found primarily to increase extracellular MMP2 activity. Overall, our data suggest that the DM-containing cells of GBM are responsible for tumor recurrence due to their high invasiveness and radio-resistance and the mis-segregation of their DM chromosomes, to give rise to fast-growing cells lacking DM chromosomes
Templeting of Thin Films Induced by Dewetting on Patterned Surfaces
The instability, dynamics and morphological transitions of patterns in thin
liquid films on periodic striped surfaces (consisting of alternating less and
more wettable stripes) are investigated based on 3-D nonlinear simulations that
account for the inter-site hydrodynamic and surface-energetic interactions. The
film breakup is suppressed on some potentially destabilizing nonwettable sites
when their spacing is below a characteristic lengthscale of the instability,
the upper bound for which is close to the spinodal lengthscale. The thin film
pattern replicates the substrate surface energy pattern closely only when, (a)
the periodicity of substrate pattern matches closely with the characteristic
lengthscale, and (b) the stripe-width is within a range bounded by a lower
critical length, below which no heterogeneous rupture occurs, and an upper
transition length above which complex morphological features bearing little
resemblance to the substrate pattern are formed.Comment: 5 pages TeX (REVTeX 4), other comments: submitted to Phys. Rev.Let
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