2,133 research outputs found
Species richness, but not phylogenetic diversity, influences community biomass production and temporal stability in a re‐examination of 16 grassland biodiversity studies
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111813/1/fec12432.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111813/2/fec12432-sup-0002-Suppinfo.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111813/3/fec12432-sup-0001-LaySummary.pd
Diel Temperature and pH Variability Scale With Depth Across Diverse Coral Reef Habitats
Coral reefs are facing intensifying stressors, largely due to global increases in seawater temperature and decreases in pH. However, there is extensive environmental variability within coral reef ecosystems, which can impact how organisms respond to global trends. We deployed spatial arrays of autonomous sensors across distinct shallow coral reef habitats to determine patterns of spatiotemporal variability in seawater physicochemical parameters. Temperature and pH were positively correlated over the course of a day due to solar heating and light‐driven metabolism. The mean temporal and spatial ranges of temperature and pH were positively correlated across all sites, with different regimes of variability observed in different reef types. Ultimately, depth was a reliable predictor of the average diel ranges in both seawater temperature and pH. These results demonstrate that there is widespread environmental variability on diel timescales within coral reefs related to water column depth, which needs to be included in assessments of how global change will locally affect reef ecosystems
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alters the connectivity of olfactory neurons in the absence of amyloid plaques in vivo
The amyloid beta peptide aggregates into amyloid plaques at presymptomatic stages of Alzheimer's disease, but the temporal relationship between plaque formation and neuronal dysfunction is poorly understood. Here we demonstrate that the connectivity of the peripheral olfactory neural circuit is perturbed in mice overexpressing human APPsw (Swedish mutation) before the onset of plaques. Expression of human APPsw exclusively in olfactory sensory neurons also perturbs connectivity with associated reductions in odour-evoked gene expression and olfactory acuity. By contrast, olfactory sensory neuron axons project correctly in mice overexpressing wild-type human amyloid precursor protein throughout the brain and in mice overexpressing M671V human APP, a missense mutation that reduces amyloid beta production, exclusively in olfactory sensory neurons. Furthermore, expression of Aβ40 or Aβ42 solely in the olfactory epithelium disrupts the olfactory sensory neuron axon targeting. Our data indicate that altering the structural connectivity and function of highly plastic neural circuits is one of the pleiotropic actions of soluble human amyloid beta
The Bolocam Galactic Plane Survey: Survey Description and Data Reduction
We present the Bolocam Galactic Plane Survey (BGPS), a 1.1 mm continuum
survey at 33" effective resolution of 170 square degrees of the Galactic Plane
visible from the northern hemisphere. The survey is contiguous over the range
-10.5 < l < 90.5, |b| < 0.5 and encompasses 133 square degrees, including some
extended regions |b| < 1.5. In addition to the contiguous region, four targeted
regions in the outer Galaxy were observed: IC1396, a region towards the Perseus
Arm, W3/4/5, and Gem OB1. The BGPS has detected approximately 8400 clumps over
the entire area to a limiting non-uniform 1-sigma noise level in the range 11
to 53 mJy/beam in the inner Galaxy. The BGPS source catalog is presented in a
companion paper (Rosolowsky et al. 2010). This paper details the survey
observations and data reduction methods for the images. We discuss in detail
the determination of astrometric and flux density calibration uncertainties and
compare our results to the literature. Data processing algorithms that separate
astronomical signals from time-variable atmospheric fluctuations in the data
time-stream are presented. These algorithms reproduce the structure of the
astronomical sky over a limited range of angular scales and produce artifacts
in the vicinity of bright sources. Based on simulations, we find that extended
emission on scales larger than about 5.9' is nearly completely attenuated (>
90%) and the linear scale at which the attenuation reaches 50% is 3.8'.
Comparison with other millimeter-wave data sets implies a possible systematic
offset in flux calibration, for which no cause has been discovered. This
presentation serves as a companion and guide to the public data release through
NASA's Infrared Processing and Analysis Center (IPAC) Infrared Science Archive
(IRSA). New data releases will be provided through IPAC IRSA with any future
improvements in the reduction.Comment: Accepted for publication in Astrophysical Journal Supplemen
The Bolocam Galactic Plane Survey IV: 1.1 and 0.35 mm Dust Continuum Emission in the Galactic Center Region
The Bolocam Galactic Plane Survey (BGPS) data for a six square degree region
of the Galactic plane containing the Galactic center is analyzed and compared
to infrared and radio continuum data. The BGPS 1.1 mm emission consists of
clumps interconnected by a network of fainter filaments surrounding cavities, a
few of which are filled with diffuse near-IR emission indicating the presence
of warm dust or with radio continuum characteristic of HII regions or supernova
remnants. New 350 {\mu}m images of the environments of the two brightest
regions, Sgr A and B, are presented. Sgr B2 is the brightest mm-emitting clump
in the Central Molecular Zone and may be forming the closest analog to a super
star cluster in the Galaxy. The Central Molecular Zone (CMZ) contains the
highest concentration of mm and sub-mm emitting dense clumps in the Galaxy.
Most 1.1 mm features at positive longitudes are seen in silhouette against the
3.6 to 24 {\mu}m background observed by the Spitzer Space Telescope. However,
only a few clumps at negative longitudes are seen in absorption, confirming the
hypothesis that positive longitude clumps in the CMZ tend to be on the
near-side of the Galactic center, consistent with the suspected orientation of
the central bar in our Galaxy. Some 1.1 mm cloud surfaces are seen in emission
at 8 {\mu}m, presumably due to polycyclic aromatic hydrocarbons (PAHs). A
~0.2\degree (~30 pc) diameter cavity and infrared bubble between l \approx
0.0\degree and 0.2\degree surrounds the Arches and Quintuplet clusters and Sgr
A. The bubble contains several clumpy dust filaments that point toward Sgr
A\ast; its potential role in their formation is explored. [abstract truncated]Comment: 76 pages, 22 figures, published in ApJ:
http://iopscience.iop.org/0004-637X/721/1/137
Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context
Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts
Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas
Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing
molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin
Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images
Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images
of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL
maps are derived through computational staining using a convolutional neural network trained to
classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and
correlation with overall survival. TIL map structural patterns were grouped using standard
histopathological parameters. These patterns are enriched in particular T cell subpopulations
derived from molecular measures. TIL densities and spatial structure were differentially enriched
among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial
infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic
patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for
the TCGA image archives with insights into the tumor-immune microenvironment
Integrated Molecular Characterization of Uterine Carcinosarcoma
SummaryWe performed genomic, epigenomic, transcriptomic, and proteomic characterizations of uterine carcinosarcomas (UCSs). Cohort samples had extensive copy-number alterations and highly recurrent somatic mutations. Frequent mutations were found in TP53, PTEN, PIK3CA, PPP2R1A, FBXW7, and KRAS, similar to endometrioid and serous uterine carcinomas. Transcriptome sequencing identified a strong epithelial-to-mesenchymal transition (EMT) gene signature in a subset of cases that was attributable to epigenetic alterations at microRNA promoters. The range of EMT scores in UCS was the largest among all tumor types studied via The Cancer Genome Atlas. UCSs shared proteomic features with gynecologic carcinomas and sarcomas with intermediate EMT features. Multiple somatic mutations and copy-number alterations in genes that are therapeutic targets were identified
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