Large Scale Structure in CHILES

We demonstrate that the Discrete Persistent Source Extractor (DisPerSE) can be used with spectroscopic redshifts to define the cosmic web and its distance to galaxies in small area deepfields. Here we analyze the use of DisPerSE to identify structure in observational data. We apply DisPerSE to the distribution of galaxies in the COSMOS field and find the best parameters to identify filaments. We compile a catalog of 11500 spectroscopic redshifts from the Galaxy and Mass Assembly (GAMA) G10 data release. We analyze two-dimensional slices, extract filaments and calculate the distance for each galaxy to its nearest filament. We find that redder and more massive galaxies are closer to filaments. To study the growth of galaxies across cosmic time, and environment, we are carrying out an HI survey covering redshifts z = 0 - 0.45, the COSMOS HI Large Extragalactic Survey (CHILES). In addition we present the predicted HI mass fraction as a function of distance to filaments for the spectroscopically known galaxies in CHILES. Lastly, we discuss the cold gas morphology of a few individual galaxies and their positions with respect to the cosmic web. The identification of the cosmic web, and the ability of CHILES to study the resolved neutral hydrogen morphologies and kinematics of galaxies, will allow future studies of the properties of neutral hydrogen in different cosmic web environments across the redshift range z = 0.1 - 0.45.Comment: Accepted for publication in the Astronomical Journal; 11 pages ; 8 figure

Oxalate-Induced Damage to Renal Tubular Cells

Our own studies and those of others have shown that the incidence of calcium oxalate stones and plaques is markedly increased by nephrotoxins. The possible role of oxalate as a nephrotoxin has not been fully appreciated. However, recent studies in experimental animals and in cultured cells support this possibility. The results of these studies led us to hypothesize that hyperoxaluria promotes stone formation in several ways: by providing a substrate for the formation of the most common form of renal stones, calcium oxalate stones, and by inducing damage to renal epithelial cells. Damaged cells in turn would produce an environment favorable for crystal retention and provide membranous debris that promotes crystal nucleation, aggregation and adherence. The present report summarizes evidence for oxalate nephrotoxicity and discusses the potential importance of oxalate toxicity in the pathogenesis of stone disease

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

Protein quantification without isotopic labels has been a long-standing interest in the proteomics field. However, accurate and robust proteome-wide quantification with label-free approaches remains a challenge. We developed a new intensity determination and normalization procedure called MaxLFQ that is fully compatible with any peptide or protein separation prior to LC-MS analysis. Protein abundance profiles are assembled using the maximum possible information from MS signals, given that the presence of quantifiable peptides varies from sample to sample. For a benchmark dataset with two proteomes mixed at known ratios, we accurately detected the mixing ratio over the entire protein expression range, with greater precision for abundant proteins. The significance of individual label-free quantifications was obtained via a t test approach. For a second benchmark dataset, we accurately quantify fold changes over several orders of magnitude, a task that is challenging with label-based methods. MaxLFQ is a generic label-free quantification technology that is readily applicable to many biological questions; it is compatible with standard statistical analysis workflows, and it has been validated in many and diverse biological projects. Our algorithms can handle very large experiments of 500+ samples in a manageable computing time. It is implemented in the freely available MaxQuant computational proteomics platform and works completely seamlessly at the click of a button

CHILES: HI morphology and galaxy environment at z=0.12 and z=0.17

We present a study of 16 HI-detected galaxies found in 178 hours of observations from Epoch 1 of the COSMOS HI Large Extragalactic Survey (CHILES). We focus on two redshift ranges between 0.108 <= z <= 0.127 and 0.162 <= z <= 0.183 which are among the worst affected by radio frequency interference (RFI). While this represents only 10% of the total frequency coverage and 18% of the total expected time on source compared to what will be the full CHILES survey, we demonstrate that our data reduction pipeline recovers high quality data even in regions severely impacted by RFI. We report on our in-depth testing of an automated spectral line source finder to produce HI total intensity maps which we present side-by-side with significance maps to evaluate the reliability of the morphology recovered by the source finder. We recommend that this become a common place manner of presenting data from upcoming HI surveys of resolved objects. We use the COSMOS 20k group catalogue, and we extract filamentary structure using the topological DisPerSE algorithm to evaluate the \hi\ morphology in the context of both local and large-scale environments and we discuss the shortcomings of both methods. Many of the detections show disturbed HI morphologies suggesting they have undergone a recent interaction which is not evident from deep optical imaging alone. Overall, the sample showcases the broad range of ways in which galaxies interact with their environment. This is a first look at the population of galaxies and their local and large-scale environments observed in HI by CHILES at redshifts beyond the z=0.1 Universe.Comment: 23 pages, 12 figures, 1 interactive 3D figure, accepted to MNRA

List Of Angiosperm Species In An Atlantic Forest Fragment Reveals Collection Gaps In Espírito Santo State, Brazil

This study presents a list of angiosperm species in an Atlantic Forest fragment in the southern portion of Espírito Santo state, Brazil, a region that represents a collection gap within the Atlantic Forest. The studied site is a relatively small fragment of 144 ha located within a conservation unit, the Mata das Flores State Park. The site belongs to a conservation priority area for the Atlantic Forest in Espírito Santo, and is under strong anthropic pressure. Of the 239 species listed here, 21 are new records for the state, eight are endemic, and 20 figure either in the country’s or the state’s Red Lists of endangered species. Rubiaceae and Piperaceae were the families with the highest number of species. We show that small fragments that were never inventoried before can reveal a relatively large number of threatened species and that collection gaps need to be filled in order to refine our understanding about conservation priorities within the Atlantic Forest Biome. © 2016 Check List and Authors.12111

CHILES VI:HI and H alpha observations for z &lt;0.1 galaxies; probing HI spin alignment with filaments in the cosmic web

We present neutral hydrogen (HI) and ionized hydrogen (H${\alpha}$) observations of ten galaxies out to a redshift of 0.1. The HI observations are from the first epoch (178 hours) of the COSMOS HI Large Extragalactic Survey (CHILES). Our sample is HI biased and consists of ten late-type galaxies with HI masses that range from $1.8\times10^{7}$ M$_{\odot}$ to $1.1\times10^{10}$ M$_{\odot}$. We find that although the majority of galaxies show irregularities in the morphology and kinematics, they generally follow the scaling relations found in larger samples. We find that the HI and H${\alpha}$ velocities reach the flat part of the rotation curve. We identify the large-scale structure in the nearby CHILES volume using DisPerSE with the spectroscopic catalog from SDSS. We explore the gaseous properties of the galaxies as a function of location in the cosmic web. We also compare the angular momentum vector (spin) of the galaxies to the orientation of the nearest cosmic web filament. Our results show that galaxy spins tend to be aligned with cosmic web filaments and show a hint of a transition mass associated with the spin angle alignment.Comment: 24 pages, 25 figures, 6 tables, accepted for publication in MNRA

Sequential decoupling of negative-energy states in Douglas-Kroll-Hess theory

Here, we review the historical development, current status, and prospects of Douglas--Kroll--Hess theory as a quantum chemical relativistic electrons-only theory.Comment: 15 page

Workgroup report: Public health strategies for reducing aflatoxin exposure in developing countries

10.1289/ehp.9302Environmental Health Perspectives114121898-190

Reconstruction of ancient microbial genomes from the human gut

Loss of gut microbial diversity1–6 in industrial populations is associated with chronic diseases7, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces.Ethics Overview of samples Reference-based taxonomic composition De novo genome reconstruction Methanobrevibacter smithii tip dating Functional genomic analysis Discussion Online content Method