126 research outputs found
The Hubble Deep Field North SCUBA Super-map III - Optical and near-infrared properties of submillimetre galaxies
We present a new sub-mm Super-map in the HDF-North region (GOODS-North
field), containing 40 statistically robust sources at 850 microns. This map
contains additional data, and several new sources, including one of the
brightest blank-sky extragalactic sub-mm sources ever detected. We have used
the ACS HST images and ground-based near-IR observations from GOODS to develop
a systematic approach for counterpart identification. 72 per cent of our
sources with optical coverage have a unique optical counterpart using our new
techniques for counterpart identification, and an additional 18 per cent have
more than one possibility that meet our criteria in the ACS images. We have
found a much higher ERO rate than other sub-mm surveys, due to the increased
depth in the optical images. The median photometric redshift (and quartile
range), from optical and near-infrared data, is 1.7 (1.3-2.5) for the
radio-detected sub-mm sources, and rises to 2.3 (1.3-2.7) for the
radio-undetected sub-sample. We find interesting correlations between the 850
micron flux and both the i magnitude and the photometric redshift, from which
there appears to be an absence of high redshift faint counterparts to the lower
flux density SCUBA sources. While the quantitative morphologies span a range of
values, in general the sub-mm galaxies show larger sizes and a higher degree of
asymmetry than other galaxy populations at the same redshifts.Comment: 20 pages, 11 eps figures. Accepted for publication in MNRAS December
17, 200
The HDF-North SCUBA Super-map II: Multi-wavelength properties
We present radio, optical and X-ray detected counterparts to the sub-mm
sources found using SCUBA in the Hubble Deep Field North region (GOODS-N). A
new counterpart identification statistic is developed to identify properties of
galaxies detected at other wavelengths that can be used to aid counterpart
identification. We discriminate between criteria that can be used to pre-select
sub-mm bright objects, and those that identify the counterpart to a known
sub-mm object. Optically faint galaxies detected in the deepest 1.4 GHz radio
continuum maps are the only effective way of pre-selecting SCUBA galaxies, and
radio sources are the best way to identify counterparts to known sub-mm
detections. Looking at radio spectral indices, only the steeper sources
(indicative of star formation) are detected in the sub-mm. Although we find
several X-ray identifications, we show that deep Chandra images do not
contribute to counterpart identifications, since in all cases they are already
detected in the more easily obtained VLA radio maps. We also find find no
evidence for clustering between Chandra and SCUBA sources in this field. For a
known SCUBA position, the reddest source tends to be the correct association,
although we can find no cut on colour, magnitude, or clustering property that
efficiently pre-selects for SCUBA sources. 15 micron ISO sources are
statistically detected by SCUBA, but the limiting mid-IR flux is not low enough
to provide useful constraints. We present postage stamp strips for each SCUBA
detection in separate bands from X-ray to radio, providing direct visual
evidence that approximately half of the sub-mm sources in this field remain
unidentified, despite an abundance of deep multi-wavelength data.Comment: Accepted for publication in MNRAS. High resolution version available
at http://www.submm.caltech.edu/~borys/paper
A process-based model of conifer forest structure and function with special emphasis on leaf lifespan
We describe the University of Sheffield Conifer Model (USCM), a process-based approach for simulating conifer forest carbon, nitrogen, and water fluxes by up-scaling widely applicable relationships between leaf lifespan and function. The USCM is designed to predict and analyze the biogeochemistry and biophysics of conifer forests that dominated the ice-free high-latitude regions under the high pCO2 “greenhouse” world 290–50 Myr ago. It will be of use in future research investigating controls on the contrasting distribution of ancient evergreen and deciduous forests between hemispheres, and their differential feedbacks on polar climate through the exchange of energy and materials with the atmosphere. Emphasis is placed on leaf lifespan because this trait can be determined from the anatomical characteristics of fossil conifer woods and influences a range of ecosystem processes. Extensive testing of simulated net primary production and partitioning, leaf area index, evapotranspiration, nitrogen uptake, and land surface energy partitioning showed close agreement with observations from sites across a wide climatic gradient. This indicates the generic utility of our model, and adequate representation of the key processes involved in forest function using only information on leaf lifespan, climate, and soils
Remembering the City: Changing Conceptions of Community in Urban China
Adopting complimentary integrative research methodologies, this article examines changing conceptions of community amongst urban residents within the city of Suzhou, Jiangsu province, China. Whilst the impact of urban transformation from a macro-perspective, deploying large scale quantitative measures to capture resident perceptions within China’s mega-cities, has been addressed, there is something of a scholarly lacuna that adopts a micro-perspective to explore the
nation-state’s smaller developing cities. Thus, through local residents’ past memories, ‘everyday’ experiences of (former) urban communities, and reflections on a particular way of life, we focus upon the subjective/affective meanings and memories attached to processes of urban change. We place emphasis on the manner in which residents make sense of socio-spatial transformations in relation to the (re)making of community, local social interaction, and a sense of belonging. Discussion centres on the affective and embodied notions of a particular way of life in (older) communities; sensory performances that were deemed difficult to replicate within modern development zones and the broader field of contemporary Chinese society
The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli
Background: Escherichia coli is a model prokaryote, an important pathogen, and a key organism for industrial biotechnology. E. coli W (ATCC 9637), one of four strains designated as safe for laboratory purposes, has not been sequenced. E. coli W is a fast-growing strain and is the only safe strain that can utilize sucrose as a carbon source. Lifecycle analysis has demonstrated that sucrose from sugarcane is a preferred carbon source for industrial bioprocesses
Sarilumab in patients admitted to hospital with severe or critical COVID-19: a randomised, double-blind, placebo-controlled, phase 3 trial
Background: Elevated proinflammatory cytokines are associated with greater COVID-19 severity. We aimed to assess safety and efficacy of sarilumab, an interleukin-6 receptor inhibitor, in patients with severe (requiring supplemental oxygen by nasal cannula or face mask) or critical (requiring greater supplemental oxygen, mechanical ventilation, or extracorporeal support) COVID-19. Methods: We did a 60-day, randomised, double-blind, placebo-controlled, multinational phase 3 trial at 45 hospitals in Argentina, Brazil, Canada, Chile, France, Germany, Israel, Italy, Japan, Russia, and Spain. We included adults (≥18 years) admitted to hospital with laboratory-confirmed SARS-CoV-2 infection and pneumonia, who required oxygen supplementation or intensive care. Patients were randomly assigned (2:2:1 with permuted blocks of five) to receive intravenous sarilumab 400 mg, sarilumab 200 mg, or placebo. Patients, care providers, outcome assessors, and investigators remained masked to assigned intervention throughout the course of the study. The primary endpoint was time to clinical improvement of two or more points (seven point scale ranging from 1 [death] to 7 [discharged from hospital]) in the modified intention-to-treat population. The key secondary endpoint was proportion of patients alive at day 29. Safety outcomes included adverse events and laboratory assessments. This study is registered with ClinicalTrials.gov, NCT04327388; EudraCT, 2020-001162-12; and WHO, U1111-1249-6021. Findings: Between March 28 and July 3, 2020, of 431 patients who were screened, 420 patients were randomly assigned and 416 received placebo (n=84 [20%]), sarilumab 200 mg (n=159 [38%]), or sarilumab 400 mg (n=173 [42%]). At day 29, no significant differences were seen in median time to an improvement of two or more points between placebo (12·0 days [95% CI 9·0 to 15·0]) and sarilumab 200 mg (10·0 days [9·0 to 12·0]; hazard ratio [HR] 1·03 [95% CI 0·75 to 1·40]; log-rank p=0·96) or sarilumab 400 mg (10·0 days [9·0 to 13·0]; HR 1·14 [95% CI 0·84 to 1·54]; log-rank p=0·34), or in proportions of patients alive (77 [92%] of 84 patients in the placebo group; 143 [90%] of 159 patients in the sarilumab 200 mg group; difference −1·7 [−9·3 to 5·8]; p=0·63 vs placebo; and 159 [92%] of 173 patients in the sarilumab 400 mg group; difference 0·2 [−6·9 to 7·4]; p=0·85 vs placebo). At day 29, there were numerical, non-significant survival differences between sarilumab 400 mg (88%) and placebo (79%; difference +8·9% [95% CI −7·7 to 25·5]; p=0·25) for patients who had critical disease. No unexpected safety signals were seen. The rates of treatment-emergent adverse events were 65% (55 of 84) in the placebo group, 65% (103 of 159) in the sarilumab 200 mg group, and 70% (121 of 173) in the sarilumab 400 mg group, and of those leading to death 11% (nine of 84) were in the placebo group, 11% (17 of 159) were in the sarilumab 200 mg group, and 10% (18 of 173) were in the sarilumab 400 mg group. Interpretation: This trial did not show efficacy of sarilumab in patients admitted to hospital with COVID-19 and receiving supplemental oxygen. Adequately powered trials of targeted immunomodulatory therapies assessing survival as a primary endpoint are suggested in patients with critical COVID-19. Funding: Sanofi and Regeneron Pharmaceuticals
TRY plant trait database – enhanced coverage and open access
Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives
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
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New paradigms for understanding and step changes in treating active and chronic, persistent apicomplexan infections
Toxoplasma gondii, the most common parasitic infection of human brain and eye, persists across lifetimes, can progressively damage sight, and is currently incurable. New, curative medicines are needed urgently. Herein, we develop novel models to facilitate drug development: EGS strain T. gondii forms cysts in vitro that induce oocysts in cats, the gold standard criterion for cysts. These cysts highly express cytochrome b. Using these models, we envisioned, and then created, novel 4-(1H)-quinolone scaffolds that target the cytochrome bc₁ complex Qi site, of which, a substituted 5,6,7,8-tetrahydroquinolin-4-one inhibits active infection (IC₅₀, 30 nM) and cysts (IC₅₀, 4 μM) in vitro, and in vivo (25 mg/kg), and drug resistant Plasmodium falciparum (IC₅₀, <30 nM), with clinically relevant synergy. Mutant yeast and co-crystallographic studies demonstrate binding to the bc₁ complex Q[subscript]i site. Our results have direct impact on improving outcomes for those with toxoplasmosis, malaria, and ~2 billion persons chronically infected with encysted bradyzoites
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