131 research outputs found
The DEEP Groth Strip Galaxy Redshift Survey. III. Redshift Catalog and Properties of Galaxies
The Deep Extragalactic Evolutionary Probe (DEEP) is a series of spectroscopic
surveys of faint galaxies, targeted at the properties and clustering of
galaxies at redshifts z ~ 1. We present the redshift catalog of the DEEP 1 GSS
pilot phase of this project, a Keck/LRIS survey in the HST/WFPC2 Groth Survey
Strip. The redshift catalog and data, including reduced spectra, are publicly
available through a Web-accessible database. The catalog contains 658 secure
galaxy redshifts with a median z=0.65, and shows large-scale structure walls to
z = 1. We find a bimodal distribution in the galaxy color-magnitude diagram
which persists to z = 1. A similar color division has been seen locally by the
SDSS and to z ~ 1 by COMBO-17. For red galaxies, we find a reddening of only
0.11 mag from z ~ 0.8 to now, about half the color evolution measured by
COMBO-17. We measure structural properties of the galaxies from the HST
imaging, and find that the color division corresponds generally to a structural
division. Most red galaxies, ~ 75%, are centrally concentrated, with a red
bulge or spheroid, while blue galaxies usually have exponential profiles.
However, there are two subclasses of red galaxies that are not bulge-dominated:
edge-on disks and a second category which we term diffuse red galaxies
(DIFRGs). The distant edge-on disks are similar in appearance and frequency to
those at low redshift, but analogs of DIFRGs are rare among local red galaxies.
DIFRGs have significant emission lines, indicating that they are reddened
mainly by dust rather than age. The DIFRGs in our sample are all at z>0.64,
suggesting that DIFRGs are more prevalent at high redshifts; they may be
related to the dusty or irregular extremely red objects (EROs) beyond z>1.2
that have been found in deep K-selected surveys. (abridged)Comment: ApJ in press. 24 pages, 17 figures (12 color). The DEEP public
database is available at http://saci.ucolick.org
The DEEP Groth Strip Survey. I. The Sample
The Deep Extragalactic Exploratory Probe (DEEP) is a multi-phase research
program dedicated to the study of the formation and evolution of galaxies and
of large scale structure in the distant Universe. This paper describes the
first five-year phase, denoted DEEP1. A series of ten DEEP1 papers will discuss
a range of scientific topics (e.g., the study of photometric and spectral
properties of a general distant galaxy survey, the evolution observed in galaxy
populations of varied morphologies). The observational basis for these studies
is the Groth Survey Strip field, a 127 square arcminute region which has been
observed with the Hubble Space Telescope in both broad I-band and V-band
optical filters and with the Low Resolution Imaging Spectrograph on the Keck
Telescopes. Catalogs of photometric and structural parameters have been
constructed for 11,547 galaxies and stars at magnitudes brighter than 29, and
spectroscopy has been conducted for a magnitude-color weighted subsample of 818
objects. We evaluate three independent techniques for constructing an imaging
catalog for the field from the HST data, and discuss the depth and sampling of
the resultant catalogs. The selection of the spectroscopic subsample is
discussed, and we describe the multifaceted approach taken to prioritizing
objects of interest for a variety of scientific subprograms. A series of Monte
Carlo simulations then demonstrates that the spectroscopic subsample can be
adequately modeled as a simple function of magnitude and color cuts in the
imaging catalog.Comment: ApJS accepted, 15 pages, 12 figures. Version with higher-quality
figures available at http://astronomy.nmsu.edu/nicol
APOE4 allele-specific associations between diet, multimodal biomarkers, and cognition among Puerto Rican adults in Massachusetts
BackgroundApolipoprotein E (APOE) is the strongest genetic risk factor for sporadic Alzheimer’s Disease (AD), and the ε4 allele (APOE4) may interact with lifestyle factors that relate to brain structural changes, underlying the increased risk of AD. However, the exact role of APOE4 in mediating interactions between the peripheral circulatory system and the central nervous system, and how it may link to brain and cognitive aging requires further elucidation. In this analysis, we investigated the association between APOE4 carrier status and multimodal biomarkers (diet, blood markers, clinical diagnosis, brain structure, and cognition) in the context of gene–environment interactions.MethodsParticipants were older adults from a longitudinal observational study, the Boston Puerto Rican Health Study (BPRHS), who self-identified as of Puerto Rican descent. Demographics, APOE genotype, diet, blood, and clinical data were collected at baseline and at approximately 12th year, with the addition of multimodal brain magnetic resonance imaging (MRI) (T1-weighted and diffusion) and cognitive testing acquired at 12-year. Measures were compared between APOE4 carriers and non-carriers, and associations between multimodal variables were examined using correlation and multivariate network analyses within each group.ResultsA total of 156 BPRHS participants (mean age at imaging = 68 years, 77% female, mean follow-up 12.7 years) with complete multimodal data were included in the current analysis. APOE4 carriers (n = 43) showed reduced medial temporal lobe (MTL) white matter (WM) microstructural integrity and lower mini-mental state examination (MMSE) score than non-carriers (n = 113). This pattern was consistent with an independent sample from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) of n = 283 non-Hispanic White adults without dementia (mean age = 75, 40% female). Within BPRHS, carriers showed distinct connectivity patterns between multimodal biomarkers, characterized by stronger direct network connections between baseline diet/blood markers with 12-year blood/clinical measures, and between blood markers (especially lipids and cytokines) and WM. Cardiovascular burden (i.e., hypertension and diabetes status) was associated with WM integrity for both carriers and non-carriers.ConclusionAPOE4 carrier status affects interactions between dietary factors, multimodal blood biomarkers, and MTL WM integrity across ~12 years of follow-up, which may reflect increased peripheral-central systems crosstalk following blood–brain barrier breakdown in carriers
COVID-19 y su impacto en la odontología
COVID-19 is a recent disease, this virus has shown in various studies to have an approximate incubation time of five days. The health areas, including the area of dentistry, have been seen in a panorama of high vulnerability and exposure, this has allowed modifying the role of the dental surgeon during this pandemic, adopting new biosafety guidelines to keep the health of healthcare personnel and patients. Thus, the protocols for the use of PPE, oral cavity antisepsis and disinfection have become pillars of emergency and emergency treatment care. The objective of this literature review is to highlight the information collected during the health crisis and the updating of protocols adopted by dental surgeons and healthcare personnel to provide adequate care during the pandemic.El COVID-19 es una nueva enfermedad, este virus ha demostrado en diversos estudios tener un tiempo de incubación aproximado de cinco días. Las áreas sanitarias, incluyendo el área odontológica, se han visto en un panorama de alta vulnerabilidad y exposición, ello ha permitido modificar el rol del cirujano dentista durante esta pandemia, adoptando nuevos lineamientos de bioseguridad para preservar la salud del personal asistencial y pacientes. Es así que los protocolos en el uso de EPP, antisepsia de la cavidad bucal y desinfección se han convertido en pilares de la atención de tratamientos de urgencia y emergencia. El objetivo de la presente revisión de literatura es evidenciar la información recolectada durante la crisis sanitaria y la actualización de protocolos adoptados por los cirujanos dentistas y personal asistencial para dar una atención adecuada durante la pandemia
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
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
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
Assessing the barriers to image‐guided drug delivery
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102084/1/wnan1247.pd
NOD2, RIP2 and IRF5 Play a Critical Role in the Type I Interferon Response to Mycobacterium tuberculosis
While the recognition of microbial infection often occurs at the cell surface via Toll-like receptors, the cytosol of the cell is also under surveillance for microbial products that breach the cell membrane. An important outcome of cytosolic recognition is the induction of IFNα and IFNβ, which are critical mediators of immunity against both bacteria and viruses. Like many intracellular pathogens, a significant fraction of the transcriptional response to Mycobacterium tuberculosis infection depends on these type I interferons, but the recognition pathways responsible remain elusive. In this work, we demonstrate that intraphagosomal M. tuberculosis stimulates the cytosolic Nod2 pathway that responds to bacterial peptidoglycan, and this event requires membrane damage that is actively inflicted by the bacterium. Unexpectedly, this recognition triggers the expression of type I interferons in a Tbk1- and Irf5-dependent manner. This response is only partially impaired by the loss of Irf3 and therefore, differs fundamentally from those stimulated by bacterial DNA, which depend entirely on this transcription factor. This difference appears to result from the unusual peptidoglycan produced by mycobacteria, which we show is a uniquely potent agonist of the Nod2/Rip2/Irf5 pathway. Thus, the Nod2 system is specialized to recognize bacteria that actively perturb host membranes and is remarkably sensitive to mycobacteria, perhaps reflecting the strong evolutionary pressure exerted by these pathogens on the mammalian immune system
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