WAVELET PACKET POWER SPECTRUM OF THE SDSS LYMAN-ALPHA FOREST: A TOOL FOR LARGE-SCALE STRUCTURE DETECTION

One of the goals of astrophysics is to obtain a full understanding how the Universe is organized on large scales and how structure evolved. In this thesis we develop a method of detecting structure on Mpc scales by measuring the one-dimensional power spectrum of the transmitted ux in the Lyman- forest. The method is based on the wavelet packet transform (WPT), which has several advantages over the Fourier transform. This includes reduced noise, resulting in less data manipulation and scrubbing in the early stages of analysis. Another advantage is localization of outliers in the data, which allows the general trend of the power spectrum to be revealed despite potentially problematic data. We apply the method to the set of 54,468 quasar spectra from the third collaboration of the Sloan Digital Sky Survey (SDSS-III) Baryonic Oscillation Spectroscopic Survey (BOSS) data release 9 (DR9) catalog. This is intended to be a proof of concept to determine if the wavelet packet power spectrum is a valid technique to extract the power spectrum in order to detect matter density uctuations. Results are in good agreement with previous studies that used conventional Fourier techniques. The power spectrum vs velocity space plots show increasing power at smaller scales for both our results and earlier studies by [21] and [6]. We conclude that the wavelet packet power spectrum is a tool for detecting structure from transmitted ux in the Lyman- forest. The advantages the wavelet packet power spectrum over the Fourier transform method are it requires less data manipulation and minimizes noise and propagation of errors and outliers in the data. As a next step we propose applying the tool to the larger more recent SDSS IV eBOSS dataset

Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation

<p>Abstract</p> <p>Background</p> <p>Human growth factor receptor bound protein 7 (Grb7) is an adapter protein that mediates the coupling of tyrosine kinases with their downstream signaling pathways. Grb7 is frequently overexpressed in invasive and metastatic human cancers and is implicated in cancer progression via its interaction with the ErbB2 receptor and focal adhesion kinase (FAK) that play critical roles in cell proliferation and migration. It is thus a prime target for the development of novel anti-cancer therapies. Recently, an inhibitory peptide (G7-18NATE) has been developed which binds specifically to the Grb7 SH2 domain and is able to attenuate cancer cell proliferation and migration in various cancer cell lines.</p> <p>Results</p> <p>As a first step towards understanding how Grb7 may be inhibited by G7-18NATE, we solved the crystal structure of the Grb7 SH2 domain to 2.1 Å resolution. We describe the details of the peptide binding site underlying target specificity, as well as the dimer interface of Grb 7 SH2. Dimer formation of Grb7 was determined to be in the μM range using analytical ultracentrifugation for both full-length Grb7 and the SH2 domain alone, suggesting the SH2 domain forms the basis of a physiological dimer. ITC measurements of the interaction of the G7-18NATE peptide with the Grb7 SH2 domain revealed that it binds with a binding affinity of K_d= ~35.7 μM and NMR spectroscopy titration experiments revealed that peptide binding causes perturbations to both the ligand binding surface of the Grb7 SH2 domain as well as to the dimer interface, suggesting that dimerisation of Grb7 is impacted on by peptide binding.</p> <p>Conclusion</p> <p>Together the data allow us to propose a model of the Grb7 SH2 domain/G7-18NATE interaction and to rationalize the basis for the observed binding specificity and affinity. We propose that the current study will assist with the development of second generation Grb7 SH2 domain inhibitors, potentially leading to novel inhibitors of cancer cell migration and invasion.</p

Introductory programming: a systematic literature review

As computing becomes a mainstream discipline embedded in the school curriculum and acts as an enabler for an increasing range of academic disciplines in higher education, the literature on introductory programming is growing. Although there have been several reviews that focus on specific aspects of introductory programming, there has been no broad overview of the literature exploring recent trends across the breadth of introductory programming. This paper is the report of an ITiCSE working group that conducted a systematic review in order to gain an overview of the introductory programming literature. Partitioning the literature into papers addressing the student, teaching, the curriculum, and assessment, we explore trends, highlight advances in knowledge over the past 15 years, and indicate possible directions for future research

Bemestingsproef met stikstof en met kali : resultaten van de derde teelt chrysanten (1973)

<p><b>Copyright information:</b></p><p>Taken from "Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation"</p><p>http://www.biomedcentral.com/1472-6807/7/58</p><p>BMC Structural Biology 2007;7():58-58.</p><p>Published online 25 Sep 2007</p><p>PMCID:PMC2131756.</p><p></p>ture elements present in the Grb7 SH2 structure as determined by WHATIF [71] are shaded from purple at the N-terminus to red at the C-terminus. Secondary structure elements of the canonical SH2 domain as defined by Eck . [41] are shown in green and orange symbols above the sequences. The boundaries of these elements differ slightly from that observed in the Grb7 SH2 domain. Residue number is for the Grb7 SH2 domain (b) Cartoon representation of the Grb7 SH2 domain shaded from purple at the N-terminus to red at the C-terminus. The extended DE loop distinguishes this family of SH2 domains from others. (c) A structural comparison of the Grb7 SH2 domain (green) with the Grb7 SH2 domain bound to an ErbB2 derived phosphopeptide (1MW4; black; [29]). The location of the bound phosphopeptide is indicated

Regulation of Hepatitis C Virion Production via Phosphorylation of the NS5A Protein

Hepatitis C virus (HCV) is a significant pathogen, infecting some 170 million people worldwide. Persistent virus infection often leads to cirrhosis and liver cancer. In the infected cell many RNA directed processes must occur to maintain and spread infection. Viral genomic RNA is constantly replicating, serving as template for translation, and being packaged into new virus particles; processes that cannot occur simultaneously. Little is known about the regulation of these events. The viral NS5A phosphoprotein has been proposed as a regulator of events in the HCV life cycle for years, but the details have remained enigmatic. NS5A is a three-domain protein and the requirement of domains I and II for RNA replication is well documented. NS5A domain III is not required for RNA replication, and the function of this region in the HCV lifecycle is unknown. We have identified a small deletion in domain III that disrupts the production of infectious virus particles without altering the efficiency of HCV RNA replication. This deletion disrupts virus production at an early stage of assembly, as no intracellular virus is generated and no viral RNA and nucleocapsid protein are released from cells. Genetic mapping has indicated a single serine residue within the deletion is responsible for the observed phenotype. This serine residue lies within a casein kinase II consensus motif, and mutations that mimic phosphorylation suggest that phosphorylation at this position regulates the production of infectious virus. We have shown by genetic silencing and chemical inhibition experiments that NS5A requires casein kinase II phosphorylation at this position for virion production. A mutation that mimics phosphorylation at this position is insensitive to these manipulations of casein kinase II activity. These data provide the first evidence for a function of the domain III of NS5A and implicate NS5A as an important regulator of the RNA replication and virion assembly of HCV. The ability to uncouple virus production from RNA replication, as described herein, may be useful in understanding HCV assembly and may be therapeutically important

Design and development of the 2002 michigan tech FutureTruck, a parallel hybrid electric vehicle

In this paper, the conversion of a production sport utility vehicle (SUV) to a hybrid electric vehicle utilizing a through-the-road parallel hybrid configuration is presented. The uniqueness of this design comes from its ability to decouple the front and rear drivetrain to simplify the packaging of underbody components. The Hybrid Theory utilizes a 2.0L, 4-cylinder engine that supplies 101kW (135hp) to the front wheels and a DC motor that supplies an additional 53kW (70hp) to the rear wheels to achieve the competition goals of a 25% improvement in fuel economy, a reduction in Green House Gas (GHG) emissions, as well as maintaining stock performance. The effects on drivability, manufacturing, fuel economy, emissions, and performance are presented along with the design, selection, and implementation of all of the vehicle conversion components. The result is a simple, low-cost option that increases the environmental friendliness that customers expect without compromising the performance they demand

Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation-1

<p><b>Copyright information:</b></p><p>Taken from "Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation"</p><p>http://www.biomedcentral.com/1472-6807/7/58</p><p>BMC Structural Biology 2007;7():58-58.</p><p>Published online 25 Sep 2007</p><p>PMCID:PMC2131756.</p><p></p>l is coloured blue and negatively charged electrostatic potential is coloured red. The positions of the phosphate binding pocket is indicated. (b) A 2F- Felectron density map depicting the phosphate binding pocket of Grb7 SH2. A sulphate ion co-crystallised in this pocket in all four molecules in the asymmetric unit. The map is contoured at 1 σ. R438, R458, Q461 and S460 form direct contacts with the sulphate ion and are labeled. The side-chain of R462 lacks well defined density and is probably fairly mobile in the crystal

Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation-3

<p><b>Copyright information:</b></p><p>Taken from "Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation"</p><p>http://www.biomedcentral.com/1472-6807/7/58</p><p>BMC Structural Biology 2007;7():58-58.</p><p>Published online 25 Sep 2007</p><p>PMCID:PMC2131756.</p><p></p>ion of 36 μM. The data collected at 14,000 rpm (), 16,600 rpm (), 24,300 rpm () and 28,800 rpm () were fitted simultaneously using the nonlinear regression program [48]. (b) Absorbance at 280 nm verses radius data at sedimentation equilibrium for Grb7 at an initial loading concentrations of 12 μM. The data collected at 10,000 rpm () and 11,800 rpm () were fitted simultaneously using the nonlinear regression program NONLIN [77]. The represents the calculated fit to a monomer-dimer model. The residuals of the fit are shown in the . Samples were in 50 mM MES pH 6.6, 100 mM NaCl and 1 mM DTT. The experiments were conducted at 20°C

Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation-0

<p><b>Copyright information:</b></p><p>Taken from "Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation"</p><p>http://www.biomedcentral.com/1472-6807/7/58</p><p>BMC Structural Biology 2007;7():58-58.</p><p>Published online 25 Sep 2007</p><p>PMCID:PMC2131756.</p><p></p>ture elements present in the Grb7 SH2 structure as determined by WHATIF [71] are shaded from purple at the N-terminus to red at the C-terminus. Secondary structure elements of the canonical SH2 domain as defined by Eck . [41] are shown in green and orange symbols above the sequences. The boundaries of these elements differ slightly from that observed in the Grb7 SH2 domain. Residue number is for the Grb7 SH2 domain (b) Cartoon representation of the Grb7 SH2 domain shaded from purple at the N-terminus to red at the C-terminus. The extended DE loop distinguishes this family of SH2 domains from others. (c) A structural comparison of the Grb7 SH2 domain (green) with the Grb7 SH2 domain bound to an ErbB2 derived phosphopeptide (1MW4; black; [29]). The location of the bound phosphopeptide is indicated