Katsir: A Framework for Harvesting Digital Libraries on the Web

The information era has brought with it the wellknown problem of \u27Information Explosion\u27. There are many and varied search engines on the Internet but it is still hard to locate and concentrate only on materials relevant to a specific task. Digital libraries, on the other hand, provide better services for focused discovery of relevant Web resources. However, digital libraries have been much less researched and implemented than search engines. The \u27Katsir/Harvest\u27 project laid the ground for our understanding that a new paradigm should to be developed - the Harvested Digital Library (HDL). The contribution of this article is in presenting a new framework and harvesting model for constructing HDLs. The open harvesting architecture proposed here uses advanced information retrieval tools and provides a set of integrated DL services to its users. This model and architecture are discussed throughout the article, including description of the implemented Katsir system and discussion of future research directions. The future DLs will be knowledge rich in the sense that each DL contains relevant meta-information on its domain and employs advanced knowledge management techniques

The Use Of Bioacoustics In Anuran Taxonomy: Theory, Terminology, Methods And Recommendations For Best Practice

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Vocalizations of anuran amphibians have received much attention in studies of behavioral ecology and physiology, but also provide informative characters for identifying and delimiting species. We here review the terminology and variation of frog calls from a perspective of integrative taxonomy, and provide hands-on protocols for recording, analyzing, comparing, interpreting and describing these sounds. Our focus is on advertisement calls, which serve as premating isolation mechanisms and, therefore, convey important taxonomic information. We provide recommendations for terminology of frog vocalizations, with call, note and pulse being the fundamental subunits to be used in descriptions and comparisons. However, due to the complexity and diversity of these signals, an unequivocal application of the terms call and note can be challenging. We therefore provide two coherent concepts that either follow a note-centered approach (defining uninterrupted units of sound as notes, and their entirety as call) or a call-centered approach (defining uninterrupted units as call whenever they are separated by long silent intervals) in terminology. Based on surveys of literature, we show that numerous call traits can be highly variable within and between individuals of one species. Despite idiosyncrasies of species and higher taxa, the duration of calls or notes, pulse rate within notes, and number of pulses per note appear to be more static within individuals and somewhat less affected by temperature. Therefore, these variables might often be preferable as taxonomic characters over call rate or note rate, which are heavily influenced by various factors. Dominant frequency is also comparatively static and only weakly affected by temperature, but depends strongly on body size. As with other taxonomic characters, strong call divergence is typically indicative of species-level differences, whereas call similarities of two populations are no evidence for them being conspecific. Taxonomic conclusions can especially be drawn when the general advertisement call structure of two candidate species is radically different and qualitative call differences are thus observed. On the other hand, quantitative differences in call traits might substantially vary within and among conspecific populations, and require careful evaluation and analysis. We provide guidelines for the taxonomic interpretation of advertisement call differences in sympatric and allopatric situations, and emphasize the need for an integrative use of multiple datasets (bio-acoustics, morphology, genetics), particularly for allopatric scenarios. We show that small-sized frogs often emit calls with frequency components in the ultrasound spectrum, although it is unlikely that these high frequencies are of biological relevance for the majority of them, and we illustrate that detection of upper harmonics depends also on recording distance because higher frequencies are attenuated more strongly. Bioacoustics remains a prime approach in integrative taxonomy of anurans if uncertainty due to possible intraspecific variation and technical artifacts is adequately considered and acknowledged.425111124Alexander von Humboldt fellowshipFonds voor Wetenschappelijk Onderzoek Vlaanderen [FWO12A7614N/12A7617N]National Council of Technological and Scientific Development (CNPq)Sao Paulo Research Foundation (FAPESP) [302589/2013-9, 2011/52070-7, 2013/50741-7, 2014/23388-7, 2014/50342-8]CAPESConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

Quantitative analysis of numerical estimates for the permeability of porous media from lattice-Boltzmann simulations

During the last decade, lattice-Boltzmann (LB) simulations have been improved to become an efficient tool for determining the permeability of porous media samples. However, well known improvements of the original algorithm are often not implemented. These include for example multirelaxation time schemes or improved boundary conditions, as well as different possibilities to impose a pressure gradient. This paper shows that a significant difference of the calculated permeabilities can be found unless one uses a carefully selected setup. We present a detailed discussion of possible simulation setups and quantitative studies of the influence of simulation parameters. We illustrate our results by applying the algorithm to a Fontainebleau sandstone and by comparing our benchmark studies to other numerical permeability measurements in the literature.Comment: 14 pages, 11 figure

Slow-Speed Supernovae from the Palomar Transient Factory: Two Channels

Since the discovery of the unusual prototype SN 2002cx, the eponymous class of low-velocity, hydrogen-poor supernovae has grown to include at most another two dozen members identified from several heterogeneous surveys, in some cases ambiguously. Here we present the results of a systematic study of 1077 hydrogen-poor supernovae discovered by the Palomar Transient Factory, leading to nine new members of this peculiar class. Moreover we find there are two distinct subclasses based on their spectroscopic, photometric, and host galaxy properties: The "SN 2002cx-like" supernovae tend to be in later-type or more irregular hosts, have more varied and generally dimmer luminosities, have longer rise times, and lack a Ti II trough when compared to the "SN 2002es-like" supernovae. None of our objects show helium, and we counter a previous claim of two such events. We also find that these transients comprise 5.6+17-3.7% (90% confidence) of all SNe Ia, lower compared to earlier estimates. Combining our objects with the literature sample, we propose that these subclasses have two distinct physical origins.Comment: 49 pages, 36 figures, submitted to Ap

Epidemiology, patterns of care, and mortality for patients with acute respiratory distress syndrome in intensive care units in 50 countries

IMPORTANCE: Limited information exists about the epidemiology, recognition, management, and outcomes of patients with the acute respiratory distress syndrome (ARDS). OBJECTIVES: To evaluate intensive care unit (ICU) incidence and outcome of ARDS and to assess clinician recognition, ventilation management, and use of adjuncts-for example prone positioning-in routine clinical practice for patients fulfilling the ARDS Berlin Definition. DESIGN, SETTING, AND PARTICIPANTS:The Large Observational Study to Understand the Global Impact of Severe Acute Respiratory Failure (LUNG SAFE) was an international, multicenter, prospective cohort study of patients undergoing invasive or noninvasive ventilation, conducted during 4 consecutive weeks in the winter of 2014 in a convenience sample of 459 ICUs from 50 countries across 5 continents. EXPOSURES:Acute respiratory distress syndrome. MAIN OUTCOMES AND MEASURES: The primary outcome was ICU incidence of ARDS. Secondary outcomes included assessment of clinician recognition of ARDS, the application of ventilatory management, the use of adjunctive interventions in routine clinical practice, and clinical outcomes from ARDS. RESULTS: Of 29,144 patients admitted to participating ICUs, 3022 (10.4%) fulfilled ARDS criteria. Of these, 2377 patients developed ARDS in the first 48 hours and whose respiratory failure was managed with invasive mechanical ventilation. The period prevalence of mild ARDS was 30.0% (95% CI, 28.2%-31.9%); of moderate ARDS, 46.6% (95% CI, 44.5%-48.6%); and of severe ARDS, 23.4% (95% CI, 21.7%-25.2%). ARDS represented 0.42 cases per ICU bed over 4 weeks and represented 10.4% (95% CI, 10.0%-10.7%) of ICU admissions and 23.4% of patients requiring mechanical ventilation. Clinical recognition of ARDS ranged from 51.3% (95% CI, 47.5%-55.0%) in mild to 78.5% (95% CI, 74.8%-81.8%) in severe ARDS. Less than two-thirds of patients with ARDS received a tidal volume 8 of mL/kg or less of predicted body weight. Plateau pressure was measured in 40.1% (95% CI, 38.2-42.1), whereas 82.6% (95% CI, 81.0%-84.1%) received a positive end-expository pressure (PEEP) of less than 12 cm H2O. Prone positioning was used in 16.3% (95% CI, 13.7%-19.2%) of patients with severe ARDS. Clinician recognition of ARDS was associated with higher PEEP, greater use of neuromuscular blockade, and prone positioning. Hospital mortality was 34.9% (95% CI, 31.4%-38.5%) for those with mild, 40.3% (95% CI, 37.4%-43.3%) for those with moderate, and 46.1% (95% CI, 41.9%-50.4%) for those with severe ARDS. CONCLUSIONS AND RELEVANCE: Among ICUs in 50 countries, the period prevalence of ARDS was 10.4% of ICU admissions. This syndrome appeared to be underrecognized and undertreated and associated with a high mortality rate. These findings indicate the potential for improvement in the management of patients with ARDS

The Science Case for a Return to Enceladus

The plume of Enceladus is unique in the solar system in providing direct access to fresh material from an extraterrestrial subsurface ocean. The Cassini Mission, though not specifically designed for it, was able to take advantage of the plume to conduct the best characterization to date of an extraterrestrial ocean. Evidence gathered from multiple instruments points to a global, subsurface liquid water ocean rich in salts and organic compounds, with water-rock interactions occurring presumably in hydrothermal systems at or below the moon’s sea floor. Meeting the criteria of “extended regions of liquid water, conditions favorable for the assembly of complex organic molecules, and energy source(s) to sustain metabolism,” the ocean of Enceladus can therefore be considered habitable. It is also the only confirmed place beyond the Earth where we can easily sample fresh material from a demonstrably habitable environment without the complications of digging or drilling. The next step is to investigate whether Enceladus’ ocean is actually inhabited. Here, we summarize the evidence for Enceladus’ ocean and its habitability, identify constraints and outstanding questions on the detectability of life within its ocean, and recommend a return to Enceladus with a dedicated search-for-life mission (or missions)

Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function

The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14–15,000 Sanger reads per site) was obtained for five high-temperature (>65°C) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, Fe, O2) control microbial community structure and function in YNP geothermal springs

First-Year Spectroscopy for the SDSS-II Supernova Survey

This paper presents spectroscopy of supernovae discovered in the first season of the Sloan Digital Sky Survey-II Supernova Survey. This program searches for and measures multi-band light curves of supernovae in the redshift range z = 0.05 - 0.4, complementing existing surveys at lower and higher redshifts. Our goal is to better characterize the supernova population, with a particular focus on SNe Ia, improving their utility as cosmological distance indicators and as probes of dark energy. Our supernova spectroscopy program features rapid-response observations using telescopes of a range of apertures, and provides confirmation of the supernova and host-galaxy types as well as precise redshifts. We describe here the target identification and prioritization, data reduction, redshift measurement, and classification of 129 SNe Ia, 16 spectroscopically probable SNe Ia, 7 SNe Ib/c, and 11 SNe II from the first season. We also describe our efforts to measure and remove the substantial host galaxy contamination existing in the majority of our SN spectra.Comment: Accepted for publication in The Astronomical Journal(47pages, 9 figures

ZTF Early Observations of Type Ia Supernovae. III. Early-time Colors As a Test for Explosion Models and Multiple Populations

Colors of Type Ia supernovae (SNe Ia) in the first few days after explosion provide a potential discriminant between different models. In this paper, we present g-r colors of 65 SNe Ia discovered within 5 days from first light by the Zwicky Transient Facility in 2018, a sample that is about three times larger than that in the literature. We find that g-r colors are intrinsically rather homogeneous at early phases, with about half of the dispersion attributable to photometric uncertainties (σnoise ∼ σ int ∼ 0.18 mag). Colors are nearly constant starting from 6 days after first light (g-r ∼-0.15 mag), while the time evolution at earlier epochs is characterized by a continuous range of slopes, from events rapidly transitioning from redder to bluer colors (slope of ∼-0.25 mag day-1) to events with a flatter evolution. The continuum in the slope distribution is in good agreement both with models requiring some amount of 56Ni mixed in the outermost regions of the ejecta and with "double-detonation"models having thin helium layers MHe=0.01 M⊙) and varying carbon-oxygen core masses. At the same time, six events show evidence for a distinctive "red bump"signature predicted by double-detonation models with larger helium masses. We finally identify a significant correlation between the early-time g-r slopes and supernova brightness, with brighter events associated to flatter color evolution (p-value = 0.006). The distribution of slopes, however, is consistent with being drawn from a single population, with no evidence for two components as claimed in the literature based on B-V colors

ZTF Early Observations of Type Ia Supernovae. III. Early-time Colors As a Test for Explosion Models and Multiple Populations

Colors of Type Ia supernovae (SNe Ia) in the first few days after explosion provide a potential discriminant between different models. In this paper, we present g − r colors of 65 SNe Ia discovered within 5 days from first light by the Zwicky Transient Facility in 2018, a sample that is about three times larger than that in the literature. We find that g − r colors are intrinsically rather homogeneous at early phases, with about half of the dispersion attributable to photometric uncertainties (σ_(noise)∼σ_(int) ~ 0.18 mag). Colors are nearly constant starting from 6 days after first light (g − r ~ −0.15 mag), while the time evolution at earlier epochs is characterized by a continuous range of slopes, from events rapidly transitioning from redder to bluer colors (slope of ~−0.25 mag day⁻¹) to events with a flatter evolution. The continuum in the slope distribution is in good agreement both with models requiring some amount of ⁵⁶Ni mixed in the outermost regions of the ejecta and with "double-detonation" models having thin helium layers (M_(He) = 0.01 M_⊙) and varying carbon–oxygen core masses. At the same time, six events show evidence for a distinctive "red bump" signature predicted by double-detonation models with larger helium masses. We finally identify a significant correlation between the early-time g − r slopes and supernova brightness, with brighter events associated to flatter color evolution (p-value = 0.006). The distribution of slopes, however, is consistent with being drawn from a single population, with no evidence for two components as claimed in the literature based on B − V colors