Extended X-ray Emission From a Quasar-Driven Superbubble

We present observations of extended, 20-kpc scale soft X-ray gas around a luminous obscured quasar hosted by an ultra-luminous infrared galaxy caught in the midst of a major merger. The extended X-ray emission is well fit as a thermal gas with a temperature of kT ~ 280 eV and a luminosity of L_X ~ 10^42 erg/s and is spatially coincident with a known ionized gas outflow. Based on the X-ray luminosity, a factor of ~10 fainter than the [OIII] emission, we conclude that the X-ray emission is either dominated by photoionization, or by shocked emission from cloud surfaces in a hot quasar-driven wind.Comment: Accepted for publication in ApJ, 6 pages, 2 figure

Brain-Blood Partition Coefficient and Cerebral Blood Flow in Canines Using Calibrated Short TR Recovery (CaSTRR) Correction Method.

The brain-blood partition coefficient (BBPC) is necessary for quantifying cerebral blood flow (CBF) when using tracer based techniques like arterial spin labeling (ASL). A recent improvement to traditional MRI measurements of BBPC, called calibrated short TR recovery (CaSTRR), has demonstrated a significant reduction in acquisition time for BBPC maps in mice. In this study CaSTRR is applied to a cohort of healthy canines (n = 17, age = 5.0 - 8.0 years) using a protocol suited for application in humans at 3T. The imaging protocol included CaSTRR for BBPC maps, pseudo-continuous ASL for CBF maps, and high resolution anatomical images. The standard CaSTRR method of normalizing BBPC to gadolinium-doped deuterium oxide phantoms was also compared to normalization using hematocrit (Hct) as a proxy value for blood water content. The results show that CaSTRR is able to produce high quality BBPC maps with a 4 min acquisition time. The BBPC maps demonstrate significantly higher BBPC in gray matter (0.83 ± 0.05 mL/g) than in white matter (0.78 ± 0.04 mL/g, p = 0.006). Maps of CBF acquired with pCASL demonstrate a negative correlation between gray matter perfusion and age (p = 0.003). Voxel-wise correction for BBPC is also shown to improve contrast to noise ratio between gray and white matter in CBF maps. A novel aspect of the study was to show that that BBPC measurements can be calculated based on the known Hct of the blood sample placed in scanner. We found a strong correlation (R 2 = 0.81 in gray matter, R 2 = 0.59 in white matter) established between BBPC maps normalized to the doped phantoms and BBPC maps normalized using Hct. This obviates the need for doped water phantoms which simplifies both the acquisition protocol and the post-processing methods. Together this suggests that CaSTRR represents a feasible, rapid method to account for BBPC variability when quantifying CBF. As canines have been used widely for aging and Alzheimer's disease studies, the CaSTRR method established in the animals may further improve CBF measurements and advance our understanding of cerebrovascular changes in aging and neurodegeneration

Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base

<p>Abstract</p> <p>Background</p> <p>The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO).</p> <p>Results</p> <p>We define the Saliva Ontology (SALO; <url>http://www.skb.ucla.edu/SALO/</url>) as a consensus-based controlled vocabulary of terms and relations dedicated to the salivaomics domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies) Foundry.</p> <p>Conclusions</p> <p>The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging') of a representative corpus of salivaomics research literature that is to be incorporated into the SKB.</p

B-Cell Gene Therapy for Tolerance Induction: Host but Not Donor B-Cell Derived IL-10 is Necessary for Tolerance

Genetically modified B cells are excellent tolerogenic antigen-presenting cells (APCs) in multiple models of autoimmunity. However, the mechanisms of action are still not completely understood. In our models, we generate antigen-specific tolerogenic B cells by transducing naïve or primed B cells with an antigen–immunoglobulin G (peptide–IgG) construct. In order to be transduced, B cells require activation with mitogens such as LPS. We and others have found that LPS stimulation of B cells upregulates the production of IL-10, a key cytokine for maintaining immune tolerance. In the current study, we defined the role of B-cell produced IL-10 in tolerance induction by using IL-10 deficient B cells as donor APCs. We found that peptide–IgG transduced IL-10 KO B cells have the same effects as wt B cells in tolerance induction in an experimental autoimmune encephalomyelitis model. Moreover, we demonstrated that the tolerogenic effect of peptide–IgG B cells was completely abrogated in anti-IL-10 receptor antibody treated recipients. Taken together, our results suggest that tolerance induced by peptide–IgG B-cell gene therapy requires IL-10 from the host but not donor B cells. These data shed important insights into the mechanisms of tolerance induction mediated by B-cell gene therapy

Gold(I)-Catalysed Direct Thioetherifications Using Allylic Alcohols: an Experimental and Computational Study

A gold(I)-catalysed direct thioetherification reaction between allylic alcohols and thiols is presented. The reaction is generally highly regioselective (S(N)2′). This dehydrative allylation procedure is very mild and atom economical, producing only water as the by-product and avoiding any unnecessary waste/steps associated with installing a leaving or activating group on the substrate. Computational studies are presented to gain insight into the mechanism of the reaction. Calculations indicate that the regioselectivity is under equilibrium control and is ultimately dictated by the thermodynamic stability of the products

New Characterizations in Turnstile Streams with Applications

Recently, [Li, Nguyen, Woodruff, STOC 2014] showed any 1-pass constant probability streaming algorithm for computing a relation f on a vector x in {-m, -(m-1), ..., m}^n presented in the turnstile data stream model can be implemented by maintaining a linear sketch Ax mod q, where A is an r times n integer matrix and q = (q_1, ..., q_r) is a vector of positive integers. The space complexity of maintaining Ax mod q, not including the random bits used for sampling A and q, matches the space of the optimal algorithm. We give multiple strengthenings of this reduction, together with new applications. In particular, we show how to remove the following shortcomings of their reduction: 1. The Box Constraint. Their reduction applies only to algorithms that must be correct even if x_{infinity} = max_{i in [n]} |x_i| is allowed to be much larger than m at intermediate points in the stream, provided that x is in {-m, -(m-1), ..., m}^n at the end of the stream. We give a condition under which the optimal algorithm is a linear sketch even if it works only when promised that x is in {-m, -(m-1), ..., m}^n at all points in the stream. Using this, we show the first super-constant Omega(log m) bits lower bound for the problem of maintaining a counter up to an additive epsilon*m error in a turnstile stream, where epsilon is any constant in (0, 1/2). Previous lower bounds are based on communication complexity and are only for relative error approximation; interestingly, we do not know how to prove our result using communication complexity. More generally, we show the first super-constant Omega(log(m)) lower bound for additive approximation of l_p-norms; this bound is tight for p in [1, 2]. 2. Negative Coordinates. Their reduction allows x_i to be negative while processing the stream. We show an equivalence between 1-pass algorithms and linear sketches Ax mod q in dynamic graph streams, or more generally, the strict turnstile model, in which for all i in [n], x_i is nonnegative at all points in the stream. Combined with [Assadi, Khanna, Li, Yaroslavtsev, SODA 2016], this resolves the 1-pass space complexity of approximating the maximum matching in a dynamic graph stream, answering a question in that work. 3. 1-Pass Restriction. Their reduction only applies to 1-pass data stream algorithms in the turnstile model, while there exist algorithms for heavy hitters and for low rank approximation which provably do better with multiple passes. We extend the reduction to algorithms which make any number of passes, showing the optimal algorithm is to choose a new linear sketch at the beginning of each pass, based on the output of previous passes

Bioinformatics advances in saliva diagnostics

There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva diagnostics made possible by the Saliva Ontology and SDxMart

Novel Calibrated Short TR Recovery (CaSTRR) Method for Brain-Blood Partition Coefficient Correction Enhances Gray-White Matter Contrast in Blood Flow Measurements in Mice

The goal of the study was to develop a novel, rapid Calibrated Short TR Recovery (CaSTRR) method to measure the brain-blood partition coefficient (BBPC) in mice. The BBPC is necessary for quantifying cerebral blood flow (CBF) using tracer-based techniques like arterial spin labeling (ASL), but previous techniques required prohibitively long acquisition times so a constant BBPC equal to 0.9 mL/g is typically used regardless of studied species, condition, or disease. An accelerated method of BBPC correction could improve regional specificity in CBF maps particularly in white matter. Male C57Bl/6N mice (n = 8) were scanned at 7T using CaSTRR to measure BBPC determine regional variability. This technique employs phase-spoiled gradient echo acquisitions with varying repetition times (TRs) to estimate proton density in the brain and a blood sample. Proton density weighted images are then calibrated to a series of phantoms with known concentrations of deuterium to determine BBPC. Pseudo-continuous ASL was also acquired to quantify CBF with and without empirical BBPC correction. Using the CaSTRR technique we demonstrate that, in mice, white matter has a significantly lower BBPC (BBPCwhite = 0.93 ± 0.05 mL/g) than cortical gray matter (BBPCgray = 0.99 ± 0.04 mL/g, p = 0.03), and that when voxel-wise BBPC correction is performed on CBF maps the observed difference in perfusion between gray and white matter is improved by as much as 14%. Our results suggest that BBPC correction is feasible and could be particularly important in future studies of perfusion in white matter pathologies