Low-background temperature sensors fabricated on parylene substrates

Temperature sensors fabricated from ultra-low radioactivity materials have been developed for low-background experiments searching for neutrinoless double-beta decay and the interactions of WIMP dark matter. The sensors consist of electrical traces photolithographically-patterned onto substrates of vapor-deposited parylene. They are demonstrated to function as expected, to do so reliably and robustly, and to be highly radio-pure. This work is a proof-of-concept study of a technology that can be applied to broad class of electronic circuits used in low-background experiments

ATP-Stimulated, DNA-Mediated Redox Signaling by XPD, a DNA Repair and Transcription Helicase

Using DNA-modified electrodes, we show DNA-mediated signaling by XPD, a helicase that contains a [4Fe-4S] cluster and is critical for nucleotide excision repair and transcription. The DNA-mediated redox signal resembles that of base excision repair proteins, with a DNA-bound redox potential of ~80 mV versus NHE. Significantly, this signal increases with ATP hydrolysis. Moreover, the redox signal is substrate-dependent, reports on the DNA conformational changes associated with enzymatic function, and may reflect a general biological role for DNA charge transport

Deconvolving mutational patterns of poliovirus outbreaks reveals its intrinsic fitness landscape.

Vaccination has essentially eradicated poliovirus. Yet, its mutation rate is higher than that of viruses like HIV, for which no effective vaccine exists. To investigate this, we infer a fitness model for the poliovirus viral protein 1 (vp1), which successfully predicts in vitro fitness measurements. This is achieved by first developing a probabilistic model for the prevalence of vp1 sequences that enables us to isolate and remove data that are subject to strong vaccine-derived biases. The intrinsic fitness constraints derived for vp1, a capsid protein subject to antibody responses, are compared with those of analogous HIV proteins. We find that vp1 evolution is subject to tighter constraints, limiting its ability to evade vaccine-induced immune responses. Our analysis also indicates that circulating poliovirus strains in unimmunized populations serve as a reservoir that can seed outbreaks in spatio-temporally localized sub-optimally immunized populations

A systematic review and economic evaluation of subcutaneous and sublingual allergen immunotherapy in adults and children with seasonal allergic rhinitis

© Queen’s Printer and Controller of HMSO 2013Severe allergic rhinitis uncontrolled by conventional medication can substantially affect quality of life. Immunotherapy involves administering increasing doses of a specific allergen, with the aim of reducing sensitivity and symptomatic reactions. Recent meta-analyses have concluded that both subcutaneous immunotherapy (SCIT) and sublingual immunotherapy (SLIT) are more effective than placebo in reducing symptoms. It is uncertain which route of administration is more effective and whether or not treatment is cost-effective.National Institute for Health Research Health Technology Assessment programm

Search for correlation effects in linear chains of trapped ions

We report a precise search for correlation effects in linear chains of 2 and 3 trapped Ca+ ions. Unexplained correlations in photon emission times within a linear chain of trapped ions have been reported, which, if genuine, cast doubt on the potential of an ion trap to realize quantum information processing. We observe quantum jumps from the metastable 3d 2D_{5/2} level for several hours, searching for correlations between the decay times of the different ions. We find no evidence for correlations: the number of quantum jumps with separations of less than 10 ms is consistent with statistics to within errors of 0.05%; the lifetime of the metastable level derived from the data is consistent with that derived from independent single-ion data at the level of the experimental errors 1%; and no rank correlations between the decay times were found with sensitivity to rank correlation coefficients at the level of |R| = 0.024.Comment: With changes to introduction. 5 pages, including 4 figures. Submitted to Europhys. Let

DNA charge transport as a first step in coordinating the detection of lesions by repair proteins

Damaged bases in DNA are known to lead to errors in replication and transcription, compromising the integrity of the genome. We have proposed a model where repair proteins containing redox-active [4Fe-4S] clusters utilize DNA charge transport (CT) as a first step in finding lesions. In this model, the population of sites to search is reduced by a localization of protein in the vicinity of lesions. Here, we examine this model using single-molecule atomic force microscopy (AFM). XPD, a 5′-3′ helicase involved in nucleotide excision repair, contains a [4Fe-4S] cluster and exhibits a DNA-bound redox potential that is physiologically relevant. In AFM studies, we observe the redistribution of XPD onto kilobase DNA strands containing a single base mismatch, which is not a specific substrate for XPD but, like a lesion, inhibits CT. We further provide evidence for DNA-mediated signaling between XPD and Endonuclease III (EndoIII), a base excision repair glycosylase that also contains a [4Fe-4S] cluster. When XPD and EndoIII are mixed together, they coordinate in relocalizing onto the mismatched strand. However, when a CT-deficient mutant of either repair protein is combined with the CT-proficient repair partner, no relocalization occurs. These data not only indicate a general link between the ability of a repair protein to carry out DNA CT and its ability to redistribute onto DNA strands near lesions but also provide evidence for coordinated DNA CT between different repair proteins in their search for damage in the genome

Moving Mirrors and Thermodynamic Paradoxes

Quantum fields responding to "moving mirrors" have been predicted to give rise to thermodynamic paradoxes. I show that the assumption in such work that the mirror can be treated as an external field is invalid: the exotic energy-transfer effects necessary to the paradoxes are well below the scales at which the model is credible. For a first-quantized point-particle mirror, it appears that exotic energy-transfers are lost in the quantum uncertainty in the mirror's state. An accurate accounting of these energies will require a model which recognizes the mirror's finite reflectivity, and almost certainly a model which allows for the excitation of internal mirror modes, that is, a second-quantized model.Comment: 7 pages, Revtex with Latex2

Plastic-crystalline solid-state electrolytes: Ionic conductivity and orientational dynamics in nitrile mixtures

Many plastic crystals, molecular solids with long-range, center-of-mass crystalline order but dynamic disorder of the molecular orientations, are known to exhibit exceptionally high ionic conductivity. This makes them promising candidates for applications as solid-state electrolytes, e.g., in batteries. Interestingly, it was found that the mixing of two different plastic-crystalline materials can considerably enhance the ionic dc conductivity, an important benchmark quantity for electrochemical applications. An example is the admixture of different nitriles to succinonitrile, the latter being one of the most prominent plastic-crystalline ionic conductors. However, until now only few such mixtures were studied. In the present work, we investigate succinonitrile mixed with malononitrile, adiponitrile, and pimelonitrile, to which 1 mol% of Li ions were added. Using differential scanning calorimetry and dielectric spectroscopy, we examine the phase behavior and the dipolar and ionic dynamics of these systems. We especially address the mixing-induced enhancement of the ionic conductivity and the coupling of the translational ionic mobility to the molecular reorientational dynamics, probably arising via a "revolving-door" mechanism.Comment: 9 pages, 7 figures; revised version as accepted for publication in J. Chem. Phy

Optimal Computation of Avoided Words

The deviation of the observed frequency of a word $w$ from its expected frequency in a given sequence $x$ is used to determine whether or not the word is avoided. This concept is particularly useful in DNA linguistic analysis. The value of the standard deviation of $w$, denoted by $std(w)$, effectively characterises the extent of a word by its edge contrast in the context in which it occurs. A word $w$ of length $k>2$ is a $\rho$-avoided word in $x$ if $std(w) \leq \rho$, for a given threshold $\rho < 0$. Notice that such a word may be completely absent from $x$. Hence computing all such words na\"{\i}vely can be a very time-consuming procedure, in particular for large $k$. In this article, we propose an $O(n)$-time and $O(n)$-space algorithm to compute all $\rho$-avoided words of length $k$ in a given sequence $x$ of length $n$ over a fixed-sized alphabet. We also present a time-optimal $O(\sigma n)$-time and $O(\sigma n)$-space algorithm to compute all $\rho$-avoided words (of any length) in a sequence of length $n$ over an alphabet of size $\sigma$. Furthermore, we provide a tight asymptotic upper bound for the number of $\rho$-avoided words and the expected length of the longest one. We make available an open-source implementation of our algorithm. Experimental results, using both real and synthetic data, show the efficiency of our implementation