Overview of the INEX 2009 Interactive Track

In the paper we present the organization of the INEX 2009 interactive track. For the 2009 experiments the iTrack has gathered data on user search behavior in a collection consisting of book metadata taken from the online bookstore Amazon and the social cataloguing application LibraryThing. Thus the data are more structured than in previous years’ experiments, consisting of traditional bibliographic metadata, user-generated tags and reviews and promotional texts and reviews from publishers and professional reviewers. Through monitoring searches based on three different task types the experiment aims at studying how users interact with highly structured data. We describe the methods used for data collection and the tasks performed by the participants. Some preliminary results of the interaction analysis are reported

First results from Faint Infrared Grism Survey (FIGS): first simultaneous detection of Lyman-alpha emission and Lyman break from a galaxy at z=7.51

Galaxies at high redshifts provide a valuable tool to study cosmic dawn, and therefore it is crucial to reliably identify these galaxies. Here, we present an unambiguous and first simultaneous detection of both the Lyman-alpha emission and the Lyman break from a z = 7.512+/- 0.004 galaxy, observed in the Faint Infrared Grism Survey (FIGS). These spectra, taken with G102 grism on Hubble Space Telescope (HST), show a significant emission line detection (6 sigma) in multiple observational position angles (PA), with total integrated Ly{\alpha} line flux of 1.06+/- 0.12 e10-17erg s-1cm-2. The line flux is nearly a factor of four higher than the previous MOSFIRE spectroscopic observations of faint Ly{\alpha} emission at {\lambda} = 1.0347{\mu}m, yielding z = 7.5078+/- 0.0004. This is consistent with other recent observations implying that ground-based near-infrared spectroscopy underestimates total emission line fluxes, and if confirmed, can have strong implications for reionization studies that are based on ground-based Lyman-{\alpha} measurements. A 4-{\sigma} detection of the NV line in one PA also suggests a weak Active Galactic Nucleus (AGN), potentially making this source the highest-redshift AGN yet found. Thus, this observation from the Hubble Space Telescope clearly demonstrates the sensitivity of the FIGS survey, and the capability of grism spectroscopy to study the epoch of reionization.Comment: Published in ApJL; matches published versio

Onset of Cosmic Reionization: Evidence of An Ionized Bubble Merely 680 Myrs after the Big Bang

While most of the inter-galactic medium (IGM) today is permeated by ionized hydrogen, it was largely filled with neutral hydrogen for the first 700 million years after the Big Bang. The process that ionized the IGM (cosmic reionization) is expected to be spatially inhomogeneous, with fainter galaxies playing a significant role. However, we still have only a few direct constraints on the reionization process. Here we report the first spectroscopic confirmation of two galaxies and very likely a third galaxy in a group (hereafter EGS77) at redshift z = 7.7, merely 680 Myrs after the Big Bang. The physical separation among the three members is < 0.7 Mpc. We estimate the radius of ionized bubble of the brightest galaxy to be about 1.02 Mpc, and show that the individual ionized bubbles formed by all three galaxies likely overlap significantly, forming a large yet localized ionized region, which leads to the spatial inhomogeneity in the reionization process. It is striking that two of three galaxies in EGS77 are quite faint in the continuum, thanks to our selection of reionizing sources using their Lyman-alpha line emission. Indeed, one is the faintest spectroscopically confirmed galaxy yet discovered at such high redshifts. Our observations provide direct constraints in the process of cosmic reionization, and allow us to investigate the properties of sources responsible for reionizing the universe.Comment: Submitted after addressing referee's comment

Early and accurate detection of cholangiocarcinoma in patients with primary sclerosing cholangitis by methylation markers in bile

Background and Aims Primary sclerosing cholangitis (PSC) is associated with increased risk of cholangiocarcinoma (CCA). Early and accurate CCA detection represents an unmet clinical need as the majority of patients with PSC are diagnosed at an advanced stage of malignancy. In the present study, we aimed at establishing robust DNA methylation biomarkers in bile for early and accurate diagnosis of CCA in PSC. Approach and Results Droplet digital PCR (ddPCR) was used to analyze 344 bile samples from 273 patients with sporadic and PSC-associated CCA, PSC, and other nonmalignant liver diseases for promoter methylation of cysteine dioxygenase type 1, cannabinoid receptor interacting protein 1, septin 9, and vimentin. Receiver operating characteristic (ROC) curve analyses revealed high AUCs for all four markers (0.77-0.87) for CCA detection among patients with PSC. Including only samples from patients with PSC diagnosed with CCA 36 months) as controls, and remained high (83%) when only including patients with PSC and dysplasia as controls (n = 23). Importantly, the bile samples from the CCA-PSCPeer reviewe

Control of CD1d-restricted antigen presentation and inflammation by sphingomyelin.

Invariant natural killer T (iNKT) cells recognize activating self and microbial lipids presented by CD1d. CD1d can also bind non-activating lipids, such as sphingomyelin. We hypothesized that these serve as endogenous regulators and investigated humans and mice deficient in acid sphingomyelinase (ASM), an enzyme that degrades sphingomyelin. We show that ASM absence in mice leads to diminished CD1d-restricted antigen presentation and iNKT cell selection in the thymus, resulting in decreased iNKT cell levels and resistance to iNKT cell-mediated inflammatory conditions. Defective antigen presentation and decreased iNKT cells are also observed in ASM-deficient humans with Niemann-Pick disease, and ASM activity in healthy humans correlates with iNKT cell phenotype. Pharmacological ASM administration facilitates antigen presentation and restores the levels of iNKT cells in ASM-deficient mice. Together, these results demonstrate that control of non-agonistic CD1d-associated lipids is critical for iNKT cell development and function in vivo and represents a tight link between cellular sphingolipid metabolism and immunity

FIGS-Faint Infrared Grism Survey: Description and Data Reduction

The Faint Infrared Grism Survey (FIGS) is a deep Hubble Space Telescope (HST) WFC3/IR (Wide Field Camera 3 Infrared) slitless spectroscopic survey of four deep fields. Two fields are located in the Great Observatories Origins Deep Survey-North (GOODS-N) area and two fields are located in the Great Observatories Origins Deep Survey-South (GOODS-S) area. One of the southern fields selected is the Hubble Ultra Deep Field. Each of these four fields were observed using the WFC3/G102 grism (0.8 μm–1.15 μm continuous coverage) with a total exposure time of 40 orbits (≈100 kilo-seconds) per field. This reaches a $3\sigma$ continuum depth of $\approx 26$ AB magnitudes and probes emission lines to $\sim {10}^{-17}\,\mathrm{erg}\,{{\rm{s}}}^{-1}\,{\mathrm{cm}}^{-2}$. This paper details the four FIGS fields and the overall observational strategy of the project. A detailed description of the Simulation Based Extraction (SBE) method used to extract and combine over 10,000 spectra of over 2000 distinct sources brighter than ${m}_{F105W}=26.5$ mag is provided. High fidelity simulations of the observations is shown to significantly improve the background subtraction process, the spectral contamination estimates, and the final flux calibration. This allows for the combination of multiple spectra to produce a final high quality, deep, 1D spectra for each object in the survey

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

BACKGROUND: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution