Chandra High Energy Transmission Grating Spectrum of AE Aquarii

(Abridged) The results of a Chandra X-ray Observatory High-Energy Transmission Grating (HETG) observation of the nova-like cataclysmic binary AE Aqr are described. First, the X-ray spectrum is that of an optically thin multi-temperature thermal plasma; the X-ray emission lines are broad, with widths that increase with the line energy, from sigma~1 eV for O VIII to sigma~5.5 eV for Si XIV; the X-ray spectrum is reasonably well fit by a plasma model with a Gaussian emission measure distribution that peaks at log T(K)=7.16, has a width sigma=0.48, an Fe abundance equal to 0.44 times solar, and other metal (primarily Ne, Mg, and Si) abundances equal to 0.76 times solar; and for a distance d=100 pc, the total emission measure EM=8.0E53 cm^-3 and the 0.5-10 keV luminosity L_X=1.1E31 erg/s. Second, based on the f/(i+r) flux ratios of the forbidden (f), intercombination (i), and recombination (r) lines of the He alpha triplets of N VI, O VII, and Ne IX measured by Itoh et al. in the XMM-Newton Reflection Grating Spectrometer spectrum and those of O VII, Ne IX, Mg XI, and Si XIII in the Chandra HETG spectrum, either the electron density of the plasma increases with temperature by over three orders of magnitude, from n_e~6E10 cm^-3 for N VI to n_e~1E14 cm^-3 for SI XIII, and/or the plasma is significantly affected by photoexcitation. Third, the radial velocity of the X-ray emission lines varies on the white dwarf spin phase, with two oscillations per spin cycle and an amplitude K~160 km/s. These results appear to be inconsistent with the recent models of Itoh et al., Ikhsanov, and Venter & Meintjes of an extended, low-density source of X-rays in AE Aqr, but instead support earlier models in which the dominant source of X-rays is of high density and/or in close proximity to the white dwarf.Comment: 13 pages including 1 table and 11 encapsulated postscript figure (3 in color); uses emulateapj.cls and apjfonts.sty; accepted on 2009 October 1 for publication in The Astrophysical Journa

Small Angle Neutron Scattering from D2O–H2O Nanodroplets and Binary Nucleation Rates in A Supersonic Nozzle

Small angle neutron scattering (SANS) experiments were used to characterize binary nanodroplets composed of D2O and H2O. The droplets were formed by expanding dilute mixtures of condensible vapor in a N2 carrier gas through a supersonic nozzle, while maintaining the onset of condensation at a fixed position in the nozzle. It is remarkable, given the small coherent scattering length density of light water, that even the pure H2O aerosol gave a scattering signal above background. The scattering spectra were analyzed assuming a log-normal distribution of droplets. On average, the geometric radius of the nanodroplets rg was rg=13 (±1) nm, the polydispersity ln σr was ln σr=0.19 (±0.07), and the number density N was N=(2±0.2)⋅1011 cm−3. The aerosol volume fractions derived from the SANS measurements are consistent with those derived from the pressure trace experiments, suggesting that the composition of the droplets was close to that of the initial condensible mixture. A quantitative analysis of the scattering spectra as a function of the isotopic composition gave further evidence that the binary droplets exhibit ideal mixing behavior. Because both the stagnation temperature T0 and the location of onset were fixed, the temperature corresponding to the maximum nucleation rate was constant at TJ max=229 (±1) K. Thus, the experiments let us estimate the isothermal peak nucleation rates as a function of the isotopic composition. The nucleation rates were found to be essentially constant with Jmax equal to (3.6±0.5)⋅1016 cm−3 s−1 at a mean supersaturation of 44 (±3)

H2O–D2O Condensation in A Supersonic Nozzle

We examined the condensation of H2O, D2O, and four intermediate mixtures (20, 40, 60, and 80 mol % D2O) in a supersonic nozzle. Because the physical and chemical properties of protonated and deuterated water are so similar, this system is ideal for studying the change in condensation behavior as a function of condensible composition. In our experiments dilute mixtures of condensible vapor in N2 are expanded from three different stagnation temperatures resulting in a broad range of onset temperatures (190–238 K) and pressures (27–787 kPa). For a fixed stagnation temperature, the partial pressure required to maintain the onset of condensation at a given location or temperature in the nozzle is consistently higher for H2O than for D2O. In contrast, the supersaturation at fixed onset temperature is usually higher for D2O than for H2O and this difference increases toward lower temperature. The partial pressure at onset for the intermediate mixtures varied linearly between the values observed for the pure components in this ideal system

Quantitative non-canonical amino acid tagging based proteomics identifies distinct patterns of protein synthesis rapidly induced by hypertrophic agents in cardiomyocytes, revealing new aspects of metabolic remodeling

Cardiomyocytes undergo growth and remodeling in response to specific pathological or physiological conditions. Pathological myocardial growth is a risk factor for cardiac failure to which faster protein synthesis is a major driving element. We aimed to quantify the rapid effects of different pro-hypertrophic stimuli on the synthesis of specific proteins in ARVC and to determine whether such effects are due to alterations on mRNA abundance or the translation of specific mRNAs. Cardiomyocytes have very low rates of protein synthesis, posing a challenging problem in terms of studying changes in the synthesis of specific proteins, which also applies to other non-dividing primary cells. To address this, an optimized QuaNCAT LC/MS method was used to selectively quantify newly synthesized proteins in such cells. The study showed both classical (phenylephrine; PE) and more recent (insulin) pathological cardiac hypertrophic agents increased the synthesis of proteins involved in glycolysis, the Krebs cycle / beta-oxidation, and sarcomeric components. However, insulin increased synthesis of many metabolic enzymes to a greater extent than PE. Using a novel validation method, we confirmed that synthesis of selected candidates is indeed up-regulated by PE and insulin. Synthesis of all proteins studied was upregulated by signaling through mTORC1 without changes in their mRNA levels, showing the key importance of translational control in the rapid effects of hypertrophic stimuli. Expression of PKM2 was upregulated in rat hearts following TAC. This isoform possesses specific regulatory properties that may be involved in metabolic remodeling and as a novel candidate biomarker. Levels of translation factor eEF1 also increased during TAC, likely contributing to faster cell mass accumulation. Interestingly, PKM2 and eEF1 were not up-regulated in pregnancy or exercise induced CH, suggesting them as pathological CH specific markers. The study methods may be of utility to the examination of protein synthesis in primary cells

A study of women\u27s preferences regarding the formulation of over-the-counter vaginal spermicides

There is an urgent need for safe, effective, and acceptable vaginal barrier methods for the prevention of sexually transmitted diseases (STDs), including HIV, and a variety of existing spermicides have the potential to be used for both prevention of STDs and unwanted pregnancy. Unfortunately, very little is known about formulation preferences and the desirable characteristics of vaginal preparations among the diverse populations of women who would potentially use these products. In this study, we explored vaginal spermicidal preparations containing nonoxynol-9 and the characteristics that influence user preferences for three formulations, as well as the risk of vaginal and cervical irritation associated with low-to-moderate use of products containing nonoxynol-9. The report recommends that formulation preferences of women be considered in the development and introduction of vaginal microbicides: the specific characteristics of vaginal products and their effect on sexual pleasure and communication will strongly determine the acceptability—and ultimately the use-effectiveness—of female-controlled STD-prevention methods

Long non-coding RNAs and latent HIV : a search for novel targets for latency reversal

The latent cellular reservoir of HIV is recognized as the major barrier to cure from HIV infection. Long non-coding RNAs (lncRNAs) are more tissue and cell type-specific than protein coding genes, and may represent targets of choice for HIV latency reversal. Using two in vitro primary T-cell models, we identified lncRNAs dysregulated in latency. PVT1 and RP11-347C18.3 were up-regulated in common between the two models, and RP11-539L10.2 was down-regulated. The major component of the latent HIV reservoir, memory CD4+ T-cells, had higher expression of these lncRNAs, compared to naive T-cells. Guilt-by-association analysis demonstrated that lncRNAs dysregulated in latency were associated with several cellular pathways implicated in HIV latency establishment and maintenance: proteasome, spliceosome, p53 signaling, and mammalian target of rapamycin (MTOR). PVT1, RP11-347C18.3, and RP11-539L10.2 were down-regulated by latency reversing agents, suberoylanilide hydroxamic acid and Romidepsin, suggesting that modulation of lncRNAs is a possible secondary mechanism of action of these compounds. These results will facilitate prioritization of lncRNAs for evaluation as targets for HIV latency reversal. Importantly, our study provides insights into regulatory function of lncRNA during latent HIV infection

Enhancing the Biological Relevance of Machine Learning Classifiers for Reverse Vaccinology.

Reverse vaccinology (RV) is a bioinformatics approach that can predict antigens with protective potential from the protein coding genomes of bacterial pathogens for subunit vaccine design. RV has become firmly established following the development of the BEXSERO® vaccine against Neisseria meningitidis serogroup B. RV studies have begun to incorporate machine learning (ML) techniques to distinguish bacterial protective antigens (BPAs) from non-BPAs. This research contributes significantly to the RV field by using permutation analysis to demonstrate that a signal for protective antigens can be curated from published data. Furthermore, the effects of the following on an ML approach to RV were also assessed: nested cross-validation, balancing selection of non-BPAs for subcellular localization, increasing the training data, and incorporating greater numbers of protein annotation tools for feature generation. These enhancements yielded a support vector machine (SVM) classifier that could discriminate BPAs (n = 200) from non-BPAs (n = 200) with an area under the curve (AUC) of 0.787. In addition, hierarchical clustering of BPAs revealed that intracellular BPAs clustered separately from extracellular BPAs. However, no immediate benefit was derived when training SVM classifiers on data sets exclusively containing intra- or extracellular BPAs. In conclusion, this work demonstrates that ML classifiers have great utility in RV approaches and will lead to new subunit vaccines in the future

Upregulated Glucose Metabolism Correlates Inversely with CD8(+) T-cell Infiltration and Survival in Squamous Cell Carcinoma

Antibodies that block T-cell–regulatory checkpoints have recently emerged as a transformative approach to cancer treatment. However, the clinical efficacy of checkpoint blockade depends upon inherent tumor immunogenicity, with variation in infiltrating T cells contributing to differences in objective response rates. Here, we sought to understand the molecular correlates of tumor-infiltrating T lymphocytes (TIL) in squamous cell carcinoma (SCC), using a systems biologic approach to integrate publicly available omics datasets with histopathologic features. We provide evidence that links TIL abundance and therapeutic outcome to the regulation of tumor glycolysis by EGFR and HIF, both of which are attractive molecular targets for use in combination with immunotherapeutics

Dose-responsive gene expression in suberoylanilide hydroxamic acid-treated resting CD4+ T cells

Persistent latently infected CD4+ T cells represent a major obstacle to HIV eradication. Histone deacetylase inhibitors (HDACis) are a proposed activation therapy. However, off-target effects on expression in host immune cells are poorly understood. We hypothesized that HDACi-modulated genes would be best identified with dose-response analysis

HPV, tumour metabolism and novel target identification in head and neck squamous cell carcinoma

Background Metabolic changes in tumour cells are used in clinical imaging and may provide potential therapeutic targets. Human papillomavirus (HPV) status is important in classifying head and neck cancers (HNSCC), identifying a distinct clinical phenotype; metabolic differences between these HNSCC subtypes remain poorly understood. Methods We used RNA sequencing to classify the metabolic expression profiles of HPV+ve and HPV−ve HNSCC, performed a meta-analysis on FDG-PET imaging characteristics and correlated results with in vitro extracellular flux analysis of HPV−ve and HPV+ve HNSCC cell lines. The monocarboxylic acid transporter-1 (MCT1) was identified as a potential metabolic target and tested in functional assays. Results Specific metabolic profiles were associated with HPV status, not limited to carbohydrate metabolism. There was dominance of all energy pathways in HPV-negative disease, with elevated expression of genes associated with glycolysis and oxidative phosphorylation. In vitro analysis confirmed comparative increased rates of oxidative phosphorylation and glycolysis in HPV-negative cell lines. PET SUV(max) scores however were unable to reliably differentiate between HPV-positive and HPV-negative tumours. MCT1 expression was significantly increased in HPV-negative tumours, and inhibition suppressed tumour cell invasion, colony formation and promoted radiosensitivity. Conclusion HPV-positive and negative HNSCC have different metabolic profiles which may have potential therapeutic applications