The Origin of the 24-micron Excess in Red Galaxies

Observations with the Spitzer Space Telescope have revealed a population of red-sequence galaxies with a significant excess in their 24-micron emission compared to what is expected from an old stellar population. We identify 900 red galaxies with 0.15<z<0.3 from the AGN and Galaxy Evolution Survey (AGES) selected from the NOAO Deep Wide-Field Survey Bootes field. Using Spitzer/MIPS, we classify 89 (~10%) with 24-micron infrared excess (f24>0.3 mJy). We determine the prevalence of AGN and star-formation activity in all the AGES galaxies using optical line diagnostics and mid-IR color-color criteria. Using the IRAC color-color diagram from the IRAC Shallow Survey, we find that 64% of the 24-micron excess red galaxies are likely to have strong PAH emission features in the 8-micron IRAC band. This fraction is significantly larger than the 5% of red galaxies with f24<0.3 mJy that are estimated to have strong PAH emission, suggesting that the infrared emission is largely due to star-formation processes. Only 15% of the 24-micron excess red galaxies have optical line diagnostics characteristic of star-formation (64% are classified as AGN and 21% are unclassifiable). The difference between the optical and infrared results suggest that both AGN and star-formation activity is occurring simultaneously in many of the 24-micron excess red galaxies. These results should serve as a warning to studies that exclusively use optical line diagnostics to determine the dominant emission mechanism in the infrared and other bands. We find that ~40% of the 24-micron excess red galaxies are edge-on spiral galaxies with high optical extinctions. The remaining sources are likely to be red galaxies whose 24-micron emission comes from a combination of obscured AGN and star-formation activity.Comment: ApJ, accepted; 11 pages, 7 figures; corrected reference to IRAC Shallow Survey in abstrac

Mid-IR Luminosities and UV/Optical Star Formation Rates at z<1.4

UV continuum and mid-IR emission constitute two widely used star formation indicators at intermediate and high redshifts. We study 2430 galaxies with z<1.4 in the Extended Groth Strip with MIPS 24 mic observations from FIDEL, spectroscopy from DEEP2, and UV, optical, and near-IR photometry from AEGIS. The data are coupled with stellar population models and Bayesian SED fitting to estimate dust-corrected SFRs. In order to probe the dust heating from stellar populations of various ages, the derived SFRs were averaged over various timescales--from 100 Myr for "current" SFR to 1--3 Gyr for long-timescale SFRs. These SED-based UV/optical SFRs are compared to total infrared luminosities extrapolated from 24 mic observations. We find that for the blue, actively star forming galaxies the correlation between the IR luminosity and the UV/optical SFR shows a decrease in scatter when going from shorter to longer SFR-averaging timescales. We interpret this as the greater role of intermediate age stellar populations in heating the dust than what is typically assumed. This holds over the entire redshift range. Many so-called green valley galaxies are simply dust-obscured actively star-forming galaxies. However, there exist 24 mic-detected galaxies, some with L>10^11 L_sun, yet with little current star formation. For them a reasonable amount of dust absorption of stellar light is sufficient to produce the observed levels of IR. In our sample optical and X-ray AGNs do not contribute on average more than ~50% to the mid-IR luminosity, and we see no evidence for a large population of "IR excess" galaxies (Abridged).Comment: Accepted for publication in ApJ. Content identical to arXiv version 1. No color figure

Hyperpolarized¹³C-Pyruvate Metabolism as a Surrogate for Tumor Grade and Poor Outcome in Renal Cell Carcinoma—A Proof of Principle Study

Differentiating aggressive clear cell renal cell carcinoma (ccRCC) from indolent lesions is challenging using conventional imaging. This work prospectively compared the metabolic imaging phenotype of renal tumors using carbon-13 MRI following injection of hyperpolarized [1-13C]pyruvate (HP-13C-MRI) and validated these findings with histopathology. Nine patients with treatment-naïve renal tumors (6 ccRCCs, 1 liposarcoma, 1 pheochromocytoma, 1 oncocytoma) underwent pre-operative HP-13C-MRI and conventional proton (1H) MRI. Multi-regional tissue samples were collected using patient-specific 3D-printed tumor molds for spatial registration between imaging and molecular analysis. The apparent exchange rate constant (kPL) between 13C-pyruvate and 13C-lactate was calculated. Immunohistochemistry for the pyruvate transporter (MCT1) from 44 multi-regional samples, as well as associations between MCT1 expression and outcome in the TCGA-KIRC dataset, were investigated. Increasing kPL in ccRCC was correlated with increasing overall tumor grade (ρ = 0.92, p = 0.009) and MCT1 expression (r = 0.89, p = 0.016), with similar results acquired from the multi-regional analysis. Conventional 1H-MRI parameters did not discriminate tumor grades. The correlation between MCT1 and ccRCC grade was confirmed within a TCGA dataset (p &lt; 0.001), where MCT1 expression was a predictor of overall and disease-free survival. In conclusion, metabolic imaging using HP-13C-MRI differentiates tumor aggressiveness in ccRCC and correlates with the expression of MCT1, a predictor of survival. HP-13C-MRI may non-invasively characterize metabolic phenotypes within renal cancer.</jats:p

Hyperpolarized 13C-Pyruvate Metabolism as a Surrogate for Tumor Grade and Poor Outcome in Renal Cell Carcinoma-A Proof of Principle Study.

Differentiating aggressive clear cell renal cell carcinoma (ccRCC) from indolent lesions is challenging using conventional imaging. This work prospectively compared the metabolic imaging phenotype of renal tumors using carbon-13 MRI following injection of hyperpolarized [1-13C]pyruvate (HP-13C-MRI) and validated these findings with histopathology. Nine patients with treatment-naïve renal tumors (6 ccRCCs, 1 liposarcoma, 1 pheochromocytoma, 1 oncocytoma) underwent pre-operative HP-13C-MRI and conventional proton (1H) MRI. Multi-regional tissue samples were collected using patient-specific 3D-printed tumor molds for spatial registration between imaging and molecular analysis. The apparent exchange rate constant (kPL) between 13C-pyruvate and 13C-lactate was calculated. Immunohistochemistry for the pyruvate transporter (MCT1) from 44 multi-regional samples, as well as associations between MCT1 expression and outcome in the TCGA-KIRC dataset, were investigated. Increasing kPL in ccRCC was correlated with increasing overall tumor grade (ρ = 0.92, p = 0.009) and MCT1 expression (r = 0.89, p = 0.016), with similar results acquired from the multi-regional analysis. Conventional 1H-MRI parameters did not discriminate tumor grades. The correlation between MCT1 and ccRCC grade was confirmed within a TCGA dataset (p < 0.001), where MCT1 expression was a predictor of overall and disease-free survival. In conclusion, metabolic imaging using HP-13C-MRI differentiates tumor aggressiveness in ccRCC and correlates with the expression of MCT1, a predictor of survival. HP-13C-MRI may non-invasively characterize metabolic phenotypes within renal cancer

Ascites induces modulation of α6β1 integrin and urokinase plasminogen activator receptor expression and associated functions in ovarian carcinoma

Interactions between cancer cells and the surrounding medium are not fully understood. In this study, we demonstrate that ascites induces selective changes in the expression of integrins and urokinase plasminogen activator/urokinase plasminogen activator receptor (uPA/uPAR) in ovarian cancer cells. We hypothesise that this change of integrin and uPA/uPAR expression triggers signalling pathways responsible for modulating phenotype-dependent functional changes in ovarian cancer cells. Human ovarian surface epithelial (HOSE) cell lines and epithelial ovarian cancer cell lines were treated with ascites for 48 h. Ascites induced upregulation of α6 integrin, without any change in the expression of αv, β1 and β4 integrin subunits. Out of the four ovarian cancer cell lines studied, ascites induced enhancement in the expression of uPA/uPAR in the more invasive OVCA 433 and HEY cell lines without any change in the noninvasive OVHS1 and moderately invasive PEO.36 cell lines. On the other hand, no change in the expression of α6 integrin or uPAR, in response to ascites, was observed in HOSE cells. In response to ascites, enhancement in proliferation and in adhesion was observed in all four ovarian cancer cell lines studied. In contrast, no significant increase in proliferation or adhesion by ascites was observed in HOSE cells. Ascites-induced expression of uPA/uPAR correlated with the increased invasiveness of HEY and OVCA 433 cell lines but was not seen in OVHS1, PEO.36 and HOSE cell lines. Upregulation of α6 integrin and uPA/uPAR correlated with the activation of Ras and downstream Erk pathways. Ascites-induced activation of Ras and downstream Erk can be inhibited by using inhibitory antibodies against α6 and β1 integrin and uPAR, consistent with the inhibition of proliferation, adhesion and invasive functions of ovarian cancer cell lines. Based on these findings, we conclude that ascites can induce selective upregulation of integrin and uPA/uPAR in ovarian cancer cells and these changes may modulate the functions of ovarian carcinomas

Star-forming cores embedded in a massive cold clump: Fragmentation, collapse and energetic outflows

The fate of massive cold clumps, their internal structure and collapse need to be characterised to understand the initial conditions for the formation of high-mass stars, stellar systems, and the origin of associations and clusters. We explore the onset of star formation in the 75 M_sun SMM1 clump in the region ISOSS J18364-0221 using infrared and (sub-)millimetre observations including interferometry. This contracting clump has fragmented into two compact cores SMM1 North and South of 0.05 pc radius, having masses of 15 and 10 M_sun, and luminosities of 20 and 180 L_sun. SMM1 South harbours a source traced at 24 and 70um, drives an energetic molecular outflow, and appears supersonically turbulent at the core centre. SMM1 North has no infrared counterparts and shows lower levels of turbulence, but also drives an outflow. Both outflows appear collimated and parsec-scale near-infrared features probably trace the outflow-powering jets. We derived mass outflow rates of at least 4E-5 M_sun/yr and outflow timescales of less than 1E4 yr. Our HCN(1-0) modelling for SMM1 South yielded an infall velocity of 0.14 km/s and an estimated mass infall rate of 3E-5 M_sun/yr. Both cores may harbour seeds of intermediate- or high-mass stars. We compare the derived core properties with recent simulations of massive core collapse. They are consistent with the very early stages dominated by accretion luminosity.Comment: Accepted for publication in ApJ, 14 pages, 7 figure

International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways.

Primary biliary cirrhosis (PBC) is a classical autoimmune liver disease for which effective immunomodulatory therapy is lacking. Here we perform meta-analyses of discovery data sets from genome-wide association studies of European subjects (n=2,764 cases and 10,475 controls) followed by validation genotyping in an independent cohort (n=3,716 cases and 4,261 controls). We discover and validate six previously unknown risk loci for PBC (Pcombined<5 × 10(-8)) and used pathway analysis to identify JAK-STAT/IL12/IL27 signalling and cytokine-cytokine pathways, for which relevant therapies exist

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead