Continuation methods for approximate large scale object sequencing

Machine Learning - We propose a set of highly scalable algorithms for the combinatorial data analysis problem of seriating similarity matrices. Seriation consists of finding a permutation of data...     

7,8-Dihydro-8-oxoguanosine Lesions Inhibit the Theophylline Aptamer or Change Its Selectivity

Aptamers are attractive constructs due to their high affinity/selectivity towards a target. Here 7,8-dihydro-8-oxoguanosine (8-oxoG) has been used, due in part to its unique H-bonding capabilities (Watson–Crick or Hoogsteen), to expand the “RNA alphabet”. Its impact on the theophylline RNA aptamer was explored by modifying its binding pocket at positions G11, G25, or G26. Structural probing, with RNases A and T₁, showed that modification at G11 leads to a drastic structural change, whereas the G25-/G26-modified analogues exhibited cleavage patterns similar to that of the canonical construct. The recognition properties towards three xanthine derivatives were then explored through thermophoresis. Modifying the aptamer at position G11 led to binding inhibition. Modification at G25, however, changed the selectivity towards theobromine (K_d≈160 μm ), with a poor affinity for theophylline (K_d>1.5 mm ) being observed. Overall, 8-oxoG can have an impact on the structures of aptamers in a position-dependent manner, leading to altered target selectivity.     

Metastatic renal cell carcinoma presenting as an aural polyp

Renal cell carcinoma may metastasize to the head and neck region at different stages of its evolution. We present a case of an undiagnosed renal cell carcinoma presenting as an ear polyp, and discuss the difficulties of the diagnosis and the management of these tumours.     

Use of weibull statistics to quantify property variability in TiAl alloys

Tensile experiments have been performed on specimens of four different investment-cast TiAl-based alloys with variations in casting conditions. The average ductilities obtained in these experiments vary between approximately 0.8 to 2.0 pct plastic strain to failure in tension. By using the three-parameter form of the Weibull relation, with the 0.2 pct offset yield strength as the minimum failure strength, the resulting variability in the data can be quantified and is found to be similar for those alloys with similar microstructural scale (grain size). Large variations in lamellar volume fraction, segregation, and phase distribution have a minor influence on property variability, compared to changes in the scale of the grain structure caused by either variations in cooling rate during casting or the addition of grain refiners.     

Thermodynamic properties and defect structure of semiconducting compound phases: Tin telluride

Defect equilibria for binary semiconducting compound phases which exhibit ionized native donor and acceptor defects were considered, and equations describing the pressure-temperature-composition relationships for these compound phases were derived. These equations were used to analyze experimental data from the literature for tin telluride. Excellent agreement was obtained between calculated thermodynamic and phase boundary values and experimental data. The approach presented is readily extended to obtain equations for the thermodynamic properties of ternary and higher order semiconducting compound phases.     

Ganglioside content of human platelets--differences in resting and activated platelets

Gangliosides may play functional roles in platelet physiology, therefore this study has been designed to evaluate whether changes in ganglioside composition may occur as a consequence of platelet activation. The results obtained indicate that lactosylceramide and GM3 are the major glycosphingolipids of human platelets. The lipid-bound sialic acid (LBSA) content was 1.27 +/- 0.04 micrograms/mg of protein. Resting platelets did not express GD3; GD3 was synthesized upon platelet activation (24 +/- 8 ng/mg of protein). The stimulation of platelets with adenosine diphosphate showed the appearance of GD3 even in the absence of degranulation. Finally, incorporation of pyrene-labeled GM3 into platelet membranes, followed by stimulation with adenosine diphosphate, resulted in the appearance of a fluorescent band comigrating with GD3. The present studies indicate that sialytransferase activation may occur as an early event following platelet stimulation, leading to GD3 synthesis mainly from the GM3 pool.     

Dependence on the motif YIPP for the physical association of Jak2 kinase with the intracellular carboxyl tail of the angiotensin II AT1 receptor

Angiotensin II is the effector molecule of the renin-angiotensin system. Virtually all of its biochemical actions are mediated through a single class of cell-surface receptors called AT1. These receptors contain the structural features of the seven-transmembrane, G-protein-coupled receptor superfamily. Angiotensin II, acting through the AT1 receptor, also stimulates the Jak/STAT pathway by inducing ligand-dependent Jak2 tyrosine phosphorylation and activation. Here, we show that a glutathione S-transferase fusion protein containing the carboxyl-terminal 54 amino acids of the rat AT1A receptor physically binds to Jak2 in an angiotensin II-dependent manner. Deletional analysis, using both in vitro protocols and cell transfection analysis, showed that this association is dependent on the AT1A receptor motif YIPP (amino acids 319-322). The wild-type AT1A receptor can induce Jak2 tyrosine phosphorylation. In contrast, an AT1A receptor lacking the YIPP motif is unable to induce ligand-dependent phosphorylation of Jak2. Competition experiments with synthetic peptides suggest that each of the YIPP amino acids, including tyrosine 319, is important in Jak2 binding to the AT1A receptor. The binding of the AT1A receptor to the intracellular tyrosine kinase Jak2 supports the concept that the seven-transmembrane superfamily of receptors can physically associate with enzymatically active intracellular proteins, creating a signaling complex mechanistically similar to that observed with growth factor and cytokine receptors.     

Planning for CAD systems

A basic problem in buying a CAD system arises from the fact that, if you do not know where you are going, any road will take you there. The solution is to plan where you want to go, and the rest more-or-less follows. The author shows how there are several ways in which you can acquire the expertise so that you can define your destination (i.e. your total CAD requirement) and hence plan your route (the justification and selection of the system)