Diallylic and Diallenic Dyotropic Rearrangements

A previously unexamined approach to dyotropic rearrangements involving only atoms from the first row is tested with four substrates. Both migrating groups contain jr orbitals, either allylic or allenic. We have prepared 3,6- dimethyl-1,7-octadiene,1,2-bis(vinyloxy)ethane, ethylene diisocyanate, and ethylene dithiocyanate to test this approach. All four substrates were pyrolyzed in a sealed tube and in a flash system. Products of ene reactions, diradical rearrangements, cycloaddition, and polymerization were observed, but the dyotropic rearrangements did not take place

Identification of single nucleotide polymorphisms from the transcriptome of an organism with a whole genome duplication

BACKGROUND: The common ancestor of salmonid fishes, including rainbow trout (Oncorhynchus mykiss), experienced a whole genome duplication between 20 and 100 million years ago, and many of the duplicated genes have been retained in the trout genome. This retention complicates efforts to detect allelic variation in salmonid fishes. Specifically, single nucleotide polymorphism (SNP) detection is problematic because nucleotide variation can be found between the duplicate copies (paralogs) of a gene as well as between alleles. RESULTS: We present a method of differentiating between allelic and paralogous (gene copy) sequence variants, allowing identification of SNPs in organisms with multiple copies of a gene or set of genes. The basic strategy is to: 1) identify windows of unique cDNA sequences with homology to each other, 2) compare these unique cDNAs if they are not shared between individuals (i.e. the cDNA is homozygous in one individual and homozygous for another cDNA in the other individual), and 3) give a “SNP score” value between zero and one to each candidate sequence variant based on six criteria. Using this strategy we were able to detect about seven thousand potential SNPs from the transcriptomes of several clonal lines of rainbow trout. When directly compared to a pre-validated set of SNPs in polyploid wheat, we were also able to estimate the false-positive rate of this strategy as 0 to 28% depending on parameters used. CONCLUSIONS: This strategy has an advantage over traditional techniques of SNP identification because another dimension of sequencing information is utilized. This method is especially well suited for identifying SNPs in polyploids, both outbred and inbred, but would tend to be conservative for diploid organisms

Dynamic Versus Static Oxidation of Nb/Al-AlOx_x/Nb Trilayer

High quality Nb-based superconductor-insulator-superconductor (SIS) junctions with Al oxide (AlO$_x$) tunnel barriers grown from Al overlayers are widely reported in the literature. However, the thin barriers required for high critical current density (J$_c$) junctions exhibit defects that result in significant subgap leakage current that is detrimental for many applications. High quality, high-J$_c$ junctions can be realized with AlN$_x$ barriers, but control of J$_c$ is more difficult than with AlO$_x$. It is therefore of interest to study the growth of thin AlO$_x$ barriers with the ultimate goal of achieving high quality, high-J$_c$ AlO$_x$ junctions. In this work, 100\%\ O$_2$ and 2\%\ O$_2$ in Ar gas mixtures are used both statically and dynamically to grow AlO$_x$ tunnel barriers over a large range of oxygen exposures. In situ ellipsometry is used for the first time to extensively measure AlO$_x$ tunnel barrier growth in real time, revealing a number of unexpected patterns. Finally, a set of test junction wafers was fabricated that exhibited the well-known dependence of J$_c$ on oxygen exposure (E) in order to further validate the experimental setup

Probing the Space of Toric Quiver Theories

We demonstrate a practical and efficient method for generating toric Calabi-Yau quiver theories, applicable to both D3 and M2 brane world-volume physics. A new analytic method is presented at low order parametres and an algorithm for the general case is developed which has polynomial complexity in the number of edges in the quiver. Using this algorithm, carefully implemented, we classify the quiver diagram and assign possible superpotentials for various small values of the number of edges and nodes. We examine some preliminary statistics on this space of toric quiver theories

Use of light scattering in characterizing reactively ion etched profiles

Currently, profile control in plasma etching of submicron structures requires inspection of cleaved samples by scanning electron microscopy. This is time consuming, destructive, and limited to a small subset of processed wafers. We show that light scattering can be used to rapidly characterize submicron differences in reactively ion etched, periodic Si structures. A similar approach has been used previously to monitor etching rates and undercutting using specular and first order diffraction peaks. Here, we measure all orders scattered over 180° as a function of incident angle and polarization and focus on the use of this technique coupled with statistical methodology to distinguish subtle changes in line profile. Although scatter from grating test patterns is examined here, this method should also be applicable to complex, submicron device structures

Phases of planar 5-dimensional supersymmetric Chern-Simons theory

In this paper we investigate the large-$N$ behavior of 5-dimensional $\mathcal{N}=1$ super Yang-Mills with a level $k$ Chern-Simons term and an adjoint hypermultiplet. As in three-dimensional Chern-Simons theories, one must choose an integration contour to completely define the theory. Using localization, we reduce the path integral to a matrix model with a cubic action and compute its free energy in various scenarios. In the limit of infinite Yang-Mills coupling and for particular choices of the contours, we find that the free-energy scales as $N^{5/2}$ for $U(N)$ gauge groups with large values of the Chern-Simons 't\,Hooft coupling, $\tilde\lambda\equiv N/k$. If we also set the hypermultiplet mass to zero, then this limit is a superconformal fixed point and the $N^{5/2}$ behavior parallels other fixed points which have known supergravity duals. We also demonstrate that $SU(N)$ gauge groups cannot have this $N^{5/2}$ scaling for their free-energy. At finite Yang-Mills coupling we establish the existence of a third order phase transition where the theory crosses over from the Yang-Mills phase to the Chern-Simons phase. The phase transition exists for any value of $\tilde\lambda$, although the details differ between small and large values of $\tilde\lambda$. For pure Chern-Simons theories we present evidence for a chain of phase transitions as $\tilde\lambda$ is increased. We also find the expectation values for supersymmetric circular Wilson loops in these various scenarios and show that the Chern-Simons term leads to different physical properties for fundamental and anti-fundamental Wilson loops. Different choices of the integration contours also lead to different properties for the loops.Comment: 40 pages, 17 figures, Minor corrections, Published versio

Validation and characterisation of a novel peptide that binds monomeric and aggregated beta-amyloid and inhibits the formation of neurotoxic oligomers

Although the formation of β-amyloid (Aβ) deposits in the brain is a hallmark of Alzheimer disease (AD), the soluble oligomers rather than the mature amyloid fibrils most likely contribute to Aβ toxicity and neurodegeneration. Thus, the discovery of agents targeting soluble Aβ oligomers is highly desirable for early diagnosis prior to the manifestation of a clinical AD phenotype and also more effective therapies. We have previously reported that a novel 15-amino acid peptide (15-mer), isolated via phage display screening, targeted Aβ and attenuated its neurotoxicity (Taddei, K., Laws, S. M., Verdile, G., Munns, S., D'Costa, K., Harvey, A. R., Martins, I. J., Hill, F., Levy, E., Shaw, J. E., and Martins, R. N. (2010) Neurobiol. Aging 31, 203–214). The aim of the current study was to generate and biochemically characterize analogues of this peptide with improved stability and therapeutic potential. We demonstrated that a stable analogue of the 15-amino acid peptide (15M S.A.) retained the activity and potency of the parent peptide and demonstrated improved proteolytic resistance in vitro (stable to t = 300 min, c.f. t = 30 min for the parent peptide). This candidate reduced the formation of soluble Aβ42 oligomers, with the concurrent generation of non-toxic, insoluble aggregates measuring up to 25–30 nm diameter as determined by atomic force microscopy. The 15M S.A. candidate directly interacted with oligomeric Aβ42, as shown by coimmunoprecipitation and surface plasmon resonance/Biacore analysis, with an affinity in the low micromolar range. Furthermore, this peptide bound fibrillar Aβ42 and also stained plaques ex vivo in brain tissue from AD model mice. Given its multifaceted ability to target monomeric and aggregated Aβ42 species, this candidate holds promise for novel preclinical AD imaging and therapeutic strategies

Regulation of Pacing Strategy during Athletic Competition

Background: Athletic competition has been a source of interest to the scientific community for many years, as a surrogate of the limits of human ambulatory ability. One of the remarkable things about athletic competition is the observation that some athletes suddenly reduce their pace in the mid-portion of the race and drop back from their competitors. Alternatively, other athletes will perform great accelerations in mid-race (surges) or during the closing stages of the race (the endspurt). This observation fits well with recent evidence that muscular power output is regulated in an anticipatory way, designed to prevent unreasonably large homeostatic disturbances. Principal Findings: Here we demonstrate that a simple index, the product of the momentary Rating of Perceived Exertion (RPE) and the fraction of race distance remaining, the Hazard Score, defines the likelihood that athletes will change their velocity during simulated competitions; and may effectively represent the language used to allow anticipatory regulation of muscle power output. Conclusions: These data support the concept that the muscular power output during high intensity exercise performance is actively regulated in an anticipatory manner that accounts for both the momentary sensations the athlete is experiencing as well as the relative amount of a competition to be completed

Polycyclic Aromatic Hydrocarbons in Maternal and Umbilical Cord Blood from Pregnant Hispanic Women Living in Brownsville, Texas

Venous blood was drawn from 35 pregnant Hispanic women living in Brownsville, Texas, and matched cord blood was collected at birth. Gas chromatography/mass spectrometry was used to measure concentrations of 55 individual PAHs or groups of PAHs. Results indicate that these women and their fetuses were regularly exposed to multiple PAHs at comparatively low concentrations, with levels in cord blood generally exceeding levels in paired maternal blood. While the possibility of related adverse effects on the fetus is uncertain, these exposures in combination with socioeconomically-disadvantaged and environmentally-challenging living conditions raise legitimate public health concerns

Prevalence and Prognostic Features of ECG Abnormalities in Acute Stroke: Findings From the SIREN Study Among Africans

Background Africa has a growing burden of stroke with associated high morbidity and a 3-year fatality rate of 84%. Cardiac disease contributes to stroke occurrence and outcomes, but the precise relationship of abnormalities as noted on a cheap and widely available test, the electrocardiogram (ECG), and acute stroke outcomes have not been previously characterized in Africans. Objectives The study assessed the prevalence and prognoses of various ECG abnormalities among African acute stroke patients encountered in a multisite, cross-national epidemiologic study. Methods We included 890 patients from Nigeria and Ghana with acute stroke who had 12-lead ECG recording within first 24 h of admission and stroke classified based on brain computed tomography scan or magnetic resonance imaging. Stroke severity at baseline was assessed using the Stroke Levity Scale (SLS), whereas 1-month outcome was assessed using the modified Rankin Scale (mRS). Results Patients\u27 mean age was 58.4 ± 13.4 years, 490 were men (55%) and 400 were women (45%), 65.5% had ischemic stroke, and 85.4% had at least 1 ECG abnormality. Women were significantly more likely to have atrial fibrillation, or left ventricular hypertrophy with or without strain pattern. Compared to ischemic stroke patients, hemorrhagic stroke patients were less likely to have atrial fibrillation (1.0% vs. 6.7%; p = 0.002), but more likely to have left ventricular hypertrophy (64.4% vs. 51.4%; p = 0.004). Odds of severe disability or death at 1 month were higher with severe stroke (AOR: 2.25; 95% confidence interval: 1.44 to 3.50), or atrial enlargement (AOR: 1.45; 95% confidence interval: 1.04 to 2.02). Conclusions About 4 in 5 acute stroke patients in this African cohort had evidence of a baseline ECG abnormality, but presence of any atrial enlargement was the only independent ECG predictor of death or disability