Oxygen deficiency in oxide films grown by PLD

The incorporation of oxygen atoms in oxide films grown by pulsed laser deposition depends upon the oxygen pressure and laser power density. By carefully controlling these two parameters it is possible to control the oxygen deficiency in the samples, and thus to change their physical properties from insulating and transparent to absorbing and conducting. By using X-ray diffraction, Rutherford backscattering spectroscopy and resistivity measurements, we show that depending upon the oxide materials oxygen deficiency in the films can induce either the growth of stable sub-oxide phases or the formation of nanocomposite films by phase separation. The first case corresponds to oxides with a mixed valency cation like Ti, which leads to the formation of stable, crystalline and highly conductive TiO_x sub-oxide phases. The second case is well described by the indium tin oxides (ITO) in which a large oxygen deficiency leads to metallic clusters embedded into a stoichiometric matrix, i.e. nanocomposite films. This phenomenon is due to the fact that sub-oxides of these compounds are not stable and thus the oxygen deficiency induced a phase separation.     

Specificity of human thymine DNA glycosylase depends on N-glycosidic bond stability

Initiating the DNA base excision repair pathway, DNA glycosylases find and hydrolytically excise damaged bases from DNA. While some DNA glycosylases exhibit narrow specificity, others remove multiple forms of damage. Human thymine DNA glycosylase (hTDG) cleaves thymine from mutagenic G.T mispairs, recognizes many additional lesions, and has a strong preference for nucleobases paired with guanine rather than adenine. Yet, hTDG avoids cytosine, despite the million-fold excess of normal G.C pairs over G.T mispairs. The mechanism of this remarkable and essential specificity has remained obscure. Here, we examine the possibility that hTDG specificity depends on the stability of the scissile base-sugar bond by determining the maximal activity (k(max)) against a series of nucleobases with varying leaving-group ability. We find that hTDG removes 5-fluorouracil 78-fold faster than uracil, and 5-chlorouracil, 572-fold faster than thymine, differences that can be attributed predominantly to leaving-group ability. Moreover, hTDG readily excises cytosine analogues with improved leaving ability, including 5-fluorocytosine, 5-bromocytosine, and 5-hydroxycytosine, indicating that cytosine has access to the active site. A plot of log(k(max)) versus leaving-group pK(a) reveals a Br?nsted-type linear free energy relationship with a large negative slope of beta(lg) = -1.6 +/- 0.2, consistent with a highly dissociative reaction mechanism. Further, we find that the hydrophobic active site of hTDG contributes to its specificity by enhancing the inherent differences in substrate reactivity. Thus, hTDG specificity depends on N-glycosidic bond stability, and the discrimination against cytosine is due largely to its very poor leaving ability rather than its exclusion from the active site.     

Active localization of virtual sounds

A simple virtual sound display built around a microcomputer and analog hardware is described. The display implements most of the primary cues for sound localization in the ear-level plane. Judging both from informal observations by users and from objective data obtained in an experiment on homing to virtual and real sounds, it is concluded that simple displays like the one described are effective in creating the impression of external sounds to which observers can locomote with ease; in particular, this means that simulation of the direction-dependent spectral shaping effects of the pinnae is not a necessary requirement for extracranial sound localization.     

Sixty Years of Network Reliability

The study of network reliability started in 1956 with a groundbreaking paper by E.F. Moore and C.E. Shannon. They introduced a probabilistic model of network reliability, where the nodes of the network were considered to be perfectly reliable, and the links or edges could fail independently with a certain probability. The problem is to determine the probability that the network remains connected under these conditions. If all the edges have the same probability of failing, this leads to the so-called reliability polynomial of the network. Sixty years later, a lot of research has accumulated on this topic, and many variants of the original problem have been investigated. We review the basic concepts and results, as well as some recent developments in this area, and we outline some important research directions.     

Use of an electrochemically labeled nucleotide terminator for known point mutation analysis

A novel single nucleotide polymorphism (SNP) assay utilizing an electrochemically tagged chain terminator is described. The system employs the single-base extension (SBE) technique coupled to capillary gel electrophoresis with end-column electrochemical detection. A redox-labeled chain terminator, ferrocene-acycloATP, is used in the SBE reaction. When the mutation site corresponds to the labeled chain terminator, the extension product is rendered electroactive. The reaction mixture is subsequently separated by capillary gel electrophoresis and the extension product detected at the separation anode with sinusoidal voltammetry. This work demonstrates the first known SNP assay utilizing redox-active chain terminators coupled to electrochemical detection. The methodology presented could lead to a fast, simple, and cost-effective SNP scoring system.     

Experimental limit on the cosmic diffuse ultrahigh energy neutrino flux

We report results from 120 h of live time with the Goldstone lunar ultrahigh energy neutrino experiment (GLUE). The experiment searches for < or = 10 ns microwave pulses from the lunar regolith, appearing in coincidence at two large radio telescopes separated by 22 km and linked by optical fiber. Such pulses would arise from subsurface electromagnetic cascades induced by interactions of > or = 100 EeV (1 EeV = 10(18) eV neutrinos in the lunar regolith. No candidates are yet seen, and the implied limits constrain several current models for ultrahigh energy neutrino fluxes.     

Determination of acephate in human urine

Acephate is a commonly used organophosphate insecticide applied on agricultural crops and in residential communities. Because very little acephate is metabolized prior to excretion, the parent pesticide compound can be measured in human urine. The residue method must be sensitive enough to determine human exposure and potential health risk for both agricultural workers and their families who may be exposed by pesticide drift or by inadvertent carry-home residues. A reliable and sensitive method was developed to measure acephate concentrations in human urine. Urine was diluted with water and acetone, adjusted to a neutral pH, and partitioned twice in acetone-methylene chloride (1 + 1, v/v), with NaCl added to aid separation. The solvent-reduced organic phase extracts were clarified by activated charcoal solid-phase extraction and then adjusted to a final volume with the addition of a D-xylose analyte protectant solution to reduce matrix enhancement effects. Acephate concentrations in urine were determined by gas chromatography using pulsed flame photometric detection. The method limit of detection was established at 2 microg/L, with a method limit of quantitation of 10 microg/L. The average recovery from urine fortified with 10-500 microg/L was 102 +/- 12% (n = 32).     

Observations of the Askaryan effect in ice

We report on observations of coherent, impulsive radio Cherenkov radiation from electromagnetic showers in solid ice. This is the first observation of the Askaryan effect in ice. As part of the complete validation process for the ANITA experiment, we performed an experiment at the Stanford Linear Accelerator Center in June 2006 using a 7.5 metric ton ice target. We measure for the first time the large-scale angular dependence of the radiation pattern, a major factor in determining the solid-angle acceptance of ultrahigh-energy neutrino detectors.     

Gender Diversity in a STEM Subfield – Analysis of a Large Scientific Society and Its Annual Conferences

Speaking engagements, serving as session chairs, and receiving awards at national meetings are essential stepping stones towards professional success for scientific researchers. Studies of gender parity in meetings of national scientific societies repeatedly uncover bias in speaker selection, engendering underrepresentation of women among featured presenters. To continue this dialogue, we analyzed membership data and annual conference programs of a large scientific society (>7000 members annually) in a male-rich (~70% males), technology-oriented STEM subfield. We detected a pronounced skew towards males among invited keynote lecturers, plenary speakers, and recipients of the society’s Senior Investigator award (15%, 13%, and 8% females, respectively). However, the proportion of females among Mid-Career and Young Investigator award recipients and oral session chairs resembled the current gender distribution of the general membership. Female members were more likely to present at the conferences and equally likely to apply and be accepted for oral presentations as their male counterparts. The gender of a session chair had no effect on the gender distribution of selected applicants. Interestingly, we identified several research subareas that were naturally enriched (i.e., not influenced by unequal selection of presenters) for either female or male participants, illustrating within a single subfield the gender divide along biology-technology line typical of all STEM disciplines. Two female-enriched topics experienced a rapid growth in popularity within the examined period, more than doubling the number of associated researchers. Collectively, these findings contribute to the contemporary discourse on gender in science and hopefully will propel positive changes within this and other societies.

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