Sugar additives for MALDI matrices improve signal allowing the smallest nucleotide change (A:T) in a DNA sequence to be resolved

Sample preparation for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) of DNA is critical for obtaining high quality mass spectra. Sample impurity, solvent content, substrate surface and environmental conditions (temperature and humidity) all affect the rate of matrix–analyte co-crystallization. As a result, laser fluence threshold for desorption/ionization varies from spot to spot. When using 3-hydroxypicolinic acid (3-HPA) as the matrix, laser fluence higher than the threshold value reduces mass resolution in time-of-flight (TOF) MS as the excess energy transferred to DNA causes metastable decay. This can be overcome by either searching for ‘hot’ spots or adjusting the laser fluence. However, both solutions may require a significant amount of operator manipulation and are not ideal for automatic measurements. We have added various sugars for crystallization with the matrix to minimize the transfer of excess laser energy to DNA molecules. Fructose and fucose were found to be the most effective matrix additives. Using these additives, mass resolution for DNA molecules does not show noticeable deterioration as laser energy increases. Improved sample preparation is important for the detection of single nucleotide polymorphisms (SNPs) using primer extension with a single nucleotide. During automatic data acquisition it is difficult to routinely detect heterozygous A/T mutations, which requires resolving a mass difference of 9 Da, unless a sugar is added during crystallization

Dissipation enhanced vibrational sensing in an olfactory molecular switch

Motivated by a proposed olfactory mechanism based on a vibrationally-activated molecular switch, we study electron transport within a donor-acceptor pair that is coupled to a vibrational mode and embedded in a surrounding environment. We derive a polaron master equation with which we study the dynamics of both the electronic and vibrational degrees of freedom beyond previously employed semiclassical (Marcus-Jortner) rate analyses. We show: (i) that in the absence of explicit dissipation of the vibrational mode, the semiclassical approach is generally unable to capture the dynamics predicted by our master equation due to both its assumption of one-way (exponential) electron transfer from donor to acceptor and its neglect of the spectral details of the environment; (ii) that by additionally allowing strong dissipation to act on the odorant vibrational mode we can recover exponential electron transfer, though typically at a rate that differs from that given by the Marcus-Jortner expression; (iii) that the ability of the molecular switch to discriminate between the presence and absence of the odorant, and its sensitivity to the odorant vibrational frequency, are enhanced significantly in this strong dissipation regime, when compared to the case without mode dissipation; and (iv) that details of the environment absent from previous Marcus-Jortner analyses can also dramatically alter the sensitivity of the molecular switch, in particular allowing its frequency resolution to be improved. Our results thus demonstrate the constructive role dissipation can play in facilitating sensitive and selective operation in molecular switch devices, as well as the inadequacy of semiclassical rate equations in analysing such behaviour over a wide range of parameters.Comment: 12 pages, 6 figures, close to published version, comments welcom

Effects of softwood biochar on the status of nitrogen species and elements of potential toxicity in soils

The effects of softwood-derived biochar materials on the chemical behaviour of environmental contaminants in soils were examined in two microcosm scenarios. Addition of the biochar materials into an alkaline sandy soil significantly reduced NH3 volatilization and made it available for conversion into NO3- via nitrification. This process could be enhanced by an increased application rate of biochar produced at a higher pyrolysis temperature. Under the alkaline conditions encountered in the experiment, the biochar surfaces tended to be negatively charged which disfavours the adsorption of NO3-. Therefore, in a fully open system, the addition of biochar materials was likely to contribute to nitrate leaching from the fertilized alkaline sandy soil. The effects of the biochar materials on the immobilization of Fe2+ generated via anaerobic iron reduction in the inundated contaminated soil were not observed, except for the treatment with a higher dose of biochar material produced under pyrolysis temperature at 700°C after the 240th h of incubation. Arsenic showed similar behaviour to Fe. Zn tended to have a higher affinity to the biochar, as compared to Mn. Immobilization of Pb occurred regardless of whether or not the biochar is present

Teleportation of a quantum state of a spatial mode with a single massive particle

Mode entanglement exists naturally between regions of space in ultra-cold atomic gases. It has, however, been debated whether this type of entanglement is useful for quantum protocols. This is due to a particle number superselection rule that restricts the operations that can be performed on the modes. In this paper, we show how to exploit the mode entanglement of just a single particle for the teleportation of an unknown quantum state of a spatial mode. We detail how to overcome the superselection rule to create any initial quantum state and how to perform Bell state analysis on two of the modes. We show that two of the four Bell states can always be reliably distinguished, while the other two have to be grouped together due to an unsatisfied phase matching condition. The teleportation of an unknown state of a quantum mode thus only succeeds half of the time.Comment: 12 pages, 1 figure, this paper was presented at TQC 2010 and extends the work of Phys. Rev. Lett. 103, 200502 (2009

Residual Tumor Confers a 10-Fold Increased Risk of Regrowth in Clinically Nonfunctioning Pituitary Tumors.

ObjectiveWe evaluated tumor recurrence and regrowth rates following endoscopic transnasal transsphenoidal (TNTS) surgical removal in a consecutive series of clinically nonfunctioning pituitary adenomas (CNFTs).DesignRetrospective chart review of clinical, biochemical, and sellar MRI findings in all TNTS surgeries in patients with CNFT, performed by a single surgeon, between 2008 and 2015 (n = 280).PatientsNinety-three patients met eligibility criteria, with complete clinical, biochemical, and imaging follow-up for a 3-year minimum.ResultsOf 85 patients who were not irradiated, 3-month postsurgical MRI demonstrated no residual tumor in 58 of 85 (68.2%), equivocal findings in 12 of 85 (14.1%), and definite residual tumor in 15 of 85 (17.6%) patients. Six of 85 (7.1%) demonstrated tumor regrowth by 3 years, and 2 further patients demonstrated true tumor recurrence at 3 and 6 years after surgery, respectively, for a total recurrence rate of 9.4% (8 of 85). Eight of the 93 patients were irradiated between 3 months and 4 years after pituitary surgery. In 3 patients with tumor regrowth, 2 exhibited residual tumor and 1 had no residual findings at the 3-month postoperative imaging. Overall, Ki-67 labeling index or Knosp grading did not predict recurrence.ConclusionTumor recurrence at 3 years was low (1 of 58; 1.7%) if the 3-month postoperative MRI showed no residual tumor. The findings support a less frequent imaging schedule for this group. Patients with definite residual tumor visible at 3 months harbor the greatest risk for tumor growth, but regrowth does not occur in all patients (6 of 15; 40%)

Free energy and configurational entropy of liquid silica: fragile-to-strong crossover and polyamorphism

Recent molecular dynamics (MD) simulations of liquid silica, using the ``BKS'' model [Van Beest, Kramer and van Santen, Phys. Rev. Lett. {\bf 64}, 1955 (1990)], have demonstrated that the liquid undergoes a dynamical crossover from super-Arrhenius, or ``fragile'' behavior, to Arrhenius, or ``strong'' behavior, as temperature $T$ is decreased. From extensive MD simulations, we show that this fragile-to-strong crossover (FSC) can be connected to changes in the properties of the potential energy landscape, or surface (PES), of the liquid. To achieve this, we use thermodynamic integration to evaluate the absolute free energy of the liquid over a wide range of density and $T$. We use this free energy data, along with the concept of ``inherent structures'' of the PES, to evaluate the absolute configurational entropy $S_c$ of the liquid. We find that the temperature dependence of the diffusion coefficient and of $S_c$ are consistent with the prediction of Adam and Gibbs, including in the region where we observe the FSC to occur. We find that the FSC is related to a change in the properties of the PES explored by the liquid, specifically an inflection in the $T$ dependence of the average inherent structure energy. In addition, we find that the high $T$ behavior of $S_c$ suggests that the liquid entropy might approach zero at finite $T$, behavior associated with the so-called Kauzmann paradox. However, we find that the change in the PES that underlies the FSC is associated with a change in the $T$ dependence of $S_c$ that elucidates how the Kauzmann paradox is avoided in this system. Finally, we also explore the relation of the observed PES changes to the recently discussed possibility that BKS silica exhibits a liquid-liquid phase transition, a behavior that has been proposed to underlie the observed polyamorphism of amorphous solid silica.Comment: 14 pages, 18 figure

Modulation of interleukin 2 high affinity binding to human T cells by a pyrimidodiazepine insect metabolite

AbstractAn insect metabolite containing the little known pyrimido[4,5-b][l,4]diazepine ring system has been found to act as an effective mimic of tetrahydrobiopterin in its ability to modulate the affinity of interleukin 2 (IL-2) for its receptors on human T cells. Semi-empirical molecular orbital calculations reveal that while tetrahydrobiopterin has considerable flexibility, the pyrimidodiazepine has rather few conformational options and offers a useful model for exploring the nature of the pterin binding site

Causality in Political Networks

As the study of political networks becomes more common in political science, greater attention to questions of causality is warranted. This essay explores competing visions of causality in political networks. Independent essays address issues of statistical model specification, identification of multi-step personal influence, measurement error, causality in historical perspective, and the insights of field experiments. These essays do not agree entirely on the nature of causality in political networks, though they commonly take seriously concerns regarding homophily, time- consistency, and the uniqueness of political network data. Serious consideration of these methodological issues promises to enhance the value-added of network analysis in the study of politics

"Remember Everything": things past in Station Island

Book synopsis: Seamus Heaney: Poet, Critic, Translator explores the range of Heaney's writing, emphasizing significant intersections in his work - meeting places; spaces between; tradition meeting the contemporary context as life meets death; liminal poetic representations and political divisions; town and woods, absence and presence; inner reality facing external reality; the timely and the transcendent; region and wider world; Irish tradition encountering Polish tradition; the space between modern English and ancient Greek; the meeting of personal and formal in the translation of Beowulf; different times and perceptions meeting problematic memory; Heaney's Leavisite stance in the face of contemporary critical currents; and Heaney's imagination approaching the imaginations of other poets