Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs

We present kleuren, a novel assembly-free method to reconstruct phylogenetic trees using the Colored de Bruijn Graph. kleuren works by constructing the Colored de Bruijn Graph and then traversing it, finding bubble structures in the graph that provide phylogenetic signal. The bubbles are then aligned and concatenated to form a supermatrix, from which a phylogenetic tree is inferred. We introduce the algorithms that kleuren uses to accomplish this task, and show its performance on reconstructing the phylogenetic tree of 12 Drosophila species. kleuren reconstructed the established phylogenetic tree accurately, and is a viable tool for phylogenetic tree reconstruction using whole genome sequences. Software package available at: https://github.com/Colelyman/kleurenComment: 6 pages, 3 figures, accepted at BIBE 2017. Minor modifications to the text due to reviewer feedback and fixed typo

Costs associated with febrile neutropenia in solid tumor and lymphoma patients - an observational study in Singapore.

BackgroundThe primary objective was to describe the total direct inpatient costs among solid tumor and lymphoma patients with chemotherapy-induced febrile neutropenia (FN) and the factors that were associated with higher direct cost. The secondary objective was to describe the out-of-pocket patient payments and the factors that were associated with higher out-of-pocket patient payments.MethodsThis was a single-center observational study conducted at the largest cancer center in Singapore. All of the adult cancer patients hospitalized due to FN from 2009 to 2012 were studied. The primary outcomes were the total hospital cost and the out-of-pocket patient payments (adjusted by government subsidy) per FN episode. Univariate analysis and multiple linear regression were conducted to identify the factors associated with higher FN costs.ResultsThree hundred and sixty seven adult cancer patients were documented with FN-related hospitalizations. The mean total hospital cost was US$4,193 (95$3,779-4,607) and the mean out-of-pocket patient payment was US$2,230 (95$1,976-2,484), per FN episode. The factors associated with a higher total hospital cost were longer length of stay, severe sepsis, and lymphoma as underlying cancer. The out-of-pocket patient payment was positively associated with longer length of stay, severe sepsis, lymphoma diagnosed as underlying cancer, the therapeutic use of granulocyte colony-stimulating factor (GCSF), the private ward class, and younger patients.ConclusionsThe total hospital cost and out-of-pocket patient payments of FN management in lymphoma cases were substantial compared with other solid tumors. Factors associated with a higher FN management cost may be useful for developing appropriate strategies to reduce the cost of FN for cancer patients

Release of mercury halides from KCl denuders in the presence of ozone

KCl-coated denuders have become a standard method for measurement of gaseous oxidized mercury, but their performance has not been exhaustively evaluated, especially in field conditions. In this study, KCl-coated and uncoated quartz denuders loaded with HgCl<sub>2</sub> and HgBr<sub>2</sub> lost 29–55% of these compounds, apparently as elemental mercury, when exposed to ozone (range of 6–100 ppb tested). This effect was also observed for denuders loaded with gaseous oxidized mercury at a field site in Nevada (3–37% of oxidized mercury lost). In addition, collection efficiency decreased by 12–30% for denuders exposed to 50 ppb ozone during collection of HgCl<sub>2</sub>. While data presented were obtained from laboratory tests and as such do not exactly simulate field sampling conditions, these results indicate that the KCl denuder oxidized mercury collection method may not be as robust as previously thought. This work highlights needs for further testing of this method, clear identification of gaseous oxidized mercury compounds in the atmosphere, and development of field calibration methods for these compounds

Release of mercury halides from KCl denuders in the presence of ozone

KCl-coated denuders have become a standard method for measurement of gaseous oxidized mercury, but their performance has not been exhaustively evaluated, especially in field conditions. In this study, KCl-coated and uncoated quartz denuders loaded with HgCl<sub>2</sub> and HgBr<sub>2</sub> lost 29–55% of these compounds, apparently as elemental mercury, when exposed to ozone (range of 6–100 ppb tested). This effect was also observed for denuders loaded with gaseous oxidized mercury at a field site in Nevada (3–37% of oxidized mercury lost). In addition, collection efficiency decreased by 12–30% for denuders exposed to 50 ppb ozone during collection of HgCl<sub>2</sub>. While data presented were obtained from laboratory tests and as such do not exactly simulate field sampling conditions, these results indicate that the KCl denuder oxidized mercury collection method may not be as robust as previously thought. This work highlights needs for further testing of this method, clear identification of gaseous oxidized mercury compounds in the atmosphere, and development of field calibration methods for these compounds

Galactic emission at 19 GHz

We cross-correlate a 19 GHz full sky Cosmic Microwave Background (CMB) survey with other maps to quantify the foreground contribution. Correlations are detected with the Diffuse Infrared Background Experiment (DIRBE) 240, 140 and 100 micron maps at high latitudes (|b|>30degrees), and marginal correlations are detected with the Haslam 408 MHz and the Reich & Reich 1420 MHz synchrotron maps. The former agree well with extrapolations from higher frequencies probed by the COBE DMR and Saskatoon experiments and are consistent with both free-free and rotating dust grain emission.Comment: 4 pages, with 4 figures included. Accepted for publication in ApJL. Color figure and links at http://www.sns.ias.edu/~angelica/foreground.html#19 or from [email protected]

Galactic microwave emission at degree angular scales

We cross-correlate the Saskatoon Ka and Q-Band Cosmic Microwave Background (CMB) data with different maps to quantify possible foreground contamination. We detect a marginal correlation (2 sigma) with the Diffuse Infrared Background Experiment (DIRBE) 240, 140 and 100 microm maps, but we find no significant correlation with point sources, with the Haslam 408 MHz map or with the Reich and Reich 1420 MHz map. The rms amplitude of the component correlated with DIRBE is about 20% of the CMB signal. Interpreting this component as free-free emission, this normalization agrees with that of Kogut et al. (1996a; 1996b) and supports the hypothesis that the spatial correlation between dust and warm ionized gas observed on large angular scales persists to smaller angular scales. Subtracting this contribution from the CMB data reduces the normalization of the Saskatoon power spectrum by only a few percent.Comment: Minor revisions to match published version. 14 pages, with 2 figures included. Color figure and links at http://www.sns.ias.edu/~angelica/foreground.htm

Mapping the CMB II: the second flight of the QMAP experiment

We report the results from the second flight of QMAP, an experiment to map the cosmic microwave background near the North Celestial Pole. We present maps of the sky at 31 and 42 GHz as well as a measurement of the angular power spectrum covering the l-range 40-200. Anisotropy is detected at about 20 sigma and is in agreement with previous results at these angular scales. We also report details of the data reduction and analysis techniques which were used for both flights of QMAP.Comment: 4 pages, with 5 figures included. Submitted to ApJL. Window functions and color figures are available at http://pupgg.princeton.edu/~cmb/welcome.htm

Learning the Language of Genes: Representing Global Codon Bias with Deep Language Models

Codon bias, the usage patterns of synonymous codons for encoding a protein sequence as nucleotides, is a biological phenomenon that is not well understood. Current methods that measure and model the codon bias of an organism exist for usage in codon optimization. In synthetic biology, codon optimization is a task the involves selecting the appropriate codons to reverse translate a protein sequence into a nucleotide sequence to maximize expression in a vector. These features include codon adaptation index (CAI) [1], individual codon usage (ICU), hidden stop codons (HSC) [2] and codon context (CC) [3]. While explicitly modeling these features has helped us to engineer high synthesis yield proteins, it is unclear what other biological features should be taken into account during codon selection for protein synthesis maximization. In this article, we present a method for modeling global codon bias through deep language models that is more robust than current methods by providing more contextual information and long-range dependencies to be considered during codon selection