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.     

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.     

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)     

The role of tyrosine-114 in the enzymatic activity of the Shiga-like toxin I A-chain

Shiga-like toxin I (SLT-I), the potent cytotoxin produced by certain pathogenic strains of Escherichia coli, is a member of a burgeoning family of ribosome-in-activating proteins (RIPs), which share common structural and mechanistic features. The prototype of the group is the plant toxin ricin. Recently we proposed a structural model for the Slt-IA active site, based in part on the known geometry of the enzymatic subunit of the ricin toxin. The model places three aromatic residues within the putative Slt-IA active site cleft: tyrosine 77, tyrosine 114, and tryptophan 203. Here we present biochemical and biophysical data regarding, the phenotypes of conservative point mutants of Slt-IA in which tyrosine 114 is altered. We used oligonucleotide-directed mutagenesis to replace tyrosine 114 with either phenylalanine (Y114F) or serine (Y114S). Periplasmic extracts of E. coli containing wild-type or mutant Slt-IA were tested for their ability to inhibit protein synthesis in vitro. Relative to wild-type, the activity of mutant Y114F was attenuated about 30-fold, while the mutant Y114S was attenuated about 500 to 1000-fold. In order to address the possibility that differential activation of the mutants rather than local effects at the active site might account for their diminished activity, we engineered the same mutations into a truncated slt-IA cassette that directs expression of a product corresponding to the activated A1 form of Slt-IA (wild-type-delta). The same general relationships held: relative to wild type-delta, Y114F-delta was attenuated about 7-fold, and Y114S-delta about 300-fold.(ABSTRACT TRUNCATED AT 250 WORDS)     

Scanning the controls: genomics and nanotechnology

We outline some of the possible applications of nanotechnology to modern molecular biology and discuss several technologies that can be used to make nanoscale confining environments (channels or post arrays) for long polymers such as DNA. A particular emphasis is placed on making large arrays using non-electron beam lithography methods. We then discuss how focused ion beam (FIB) milling can be used to construct nearfield slits for examining molecules     

Personality and the predisposition to engage in risky or problem behaviors during adolescence.

Longitudinal data from a representative sample of 1,978 Black and White adolescents were used to examine the role of personality in multiple risk or problem behaviors. Results indicate that covariation among diverse behaviors (educational underachievement, delinquent behavior, substance use, sexual behavior) can be adequately modeled by a single higher order factor, and that impulsivity and avoidance coping serve as generalized risk factors for involvement in these behaviors. Whereas none of the personality variables examined explained change in problem behaviors once established, avoidance coping prospectively predicted involvement among a subgroup of adolescents with little or no prior involvement. Results suggest that dysfunctional styles of regulating emotions and emotionally driven behaviors are core features of risky or problem behaviors during adolescence. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Fuzzy relations and fuzzy relational databases

This paper deals with the connections existing between fuzzy set theory and fuzzy relational databases. Our new result dealing with fuzzy relations is how to calculate the greatest lower bound (glb) of two similarity relations. Our main contributions in fuzzy relational databases are establishing from fuzzy set theory what a fuzzy relational database should be (the result is both surprising and elegant), and making fuzzy relational databases even more robust.Our work in fuzzy relations and in fuzzy databases had led us into other interesting problems—two of which we mention in this paper. The first is primarily mathematical, and the second provides yet another connection between fuzzy set theory and artificial intelligence. In understanding similarity relations in terms of other fuzzy relations and in making fuzzy databases more robust, we work with closure and interior operators; we present some important properties of these operators. In establishing the connection between fuzzy set theory and artificial intelligence, we show that an abstraction on a set is in fact a partition on the set; that is, an abstraction defines an equivalence relation on the underlying set.