Maintaining Parameter Invariance in Censored Micro-Level Data

Research Methods/ Statistical Methods,

Methodology capture: discriminating between the "best" and the rest of community practice

<p>Abstract</p> <p>Background</p> <p>The methodologies we use both enable and help define our research. However, as experimental complexity has increased the choice of appropriate methodologies has become an increasingly difficult task. This makes it difficult to keep track of available bioinformatics software, let alone the most suitable protocols in a specific research area. To remedy this we present an approach for capturing methodology from literature in order to identify and, thus, define best practice within a field.</p> <p>Results</p> <p>Our approach is to implement data extraction techniques on the full-text of scientific articles to obtain the set of experimental protocols used by an entire scientific discipline, molecular phylogenetics. Our methodology for identifying methodologies could in principle be applied to any scientific discipline, whether or not computer-based. We find a number of issues related to the nature of best practice, as opposed to community practice. We find that there is much heterogeneity in the use of molecular phylogenetic methods and software, some of which is related to poor specification of protocols. We also find that phylogenetic practice exhibits field-specific tendencies that have increased through time, despite the generic nature of the available software. We used the practice of highly published and widely collaborative researchers ("expert" researchers) to analyse the influence of authority on community practice. We find expert authors exhibit patterns of practice common to their field and therefore act as useful field-specific practice indicators.</p> <p>Conclusion</p> <p>We have identified a structured community of phylogenetic researchers performing analyses that are customary in their own local community and significantly different from those in other areas. Best practice information can help to bridge such subtle differences by increasing communication of protocols to a wider audience. We propose that the practice of expert authors from the field of evolutionary biology is the closest to contemporary best practice in phylogenetic experimental design. Capturing best practice is, however, a complex task and should also acknowledge the differences between fields such as the specific context of the analysis.</p

X-ray Fluorescence Analysis of Feldspars and Silicate Glass: Effects of Melting Time on Fused Bead Consistency and Volatilisation

Reproducible preparation of lithium tetraborate fused beads for XRF analysis of glass and mineral samples is of paramount importance for analytical repeatability. However, as with all glass melting processes, losses due to volatilisation must be taken into account and their effects are not negligible. Here the effects of fused bead melting time have been studied for four Certified Reference Materials (CRM’s: three feldspars, one silicate glass), in terms of their effects on analytical variability and volatilisation losses arising from fused bead preparation. At melting temperatures of 1065 °C, and for feldspar samples, fused bead melting times shorter than approximately 25 min generally gave rise to a greater deviation of the XRF-analysed composition from the certified composition. This variation might be due to incomplete fusion and/or fused bead inhomogeneity but further research is needed. In contrast, the shortest fused bead melting time for the silicate glass CRM gave an XRF-analysed composition closer to the certified values than longer melting times. This may suggest a faster rate of glass-in-glass dissolution and homogenization during fused bead preparation. For all samples, longer melting times gave rise to greater volatilisation losses (including sulphates and halides) during fusion. This was demonstrated by a linear relationship between SO3 mass loss and time1/2, as predicted by a simple diffusion-based model. Iodine volatilisation displays a more complex relationship, suggestive of diffusion plus additional mechanisms. This conclusion may have implications for vitrification of iodine-bearing radioactive wastes. Our research demonstrates that the nature of the sample material impacts on the most appropriate fusion times. For feldspars no less than ~25 min and no more than ~60 min of fusion at 1065 °C, using Li2B4O7 as the fusion medium and in the context of feldspar samples and the automatic fusion equipment used here, strikes an acceptable (albeit non-ideal) balance between the competing factors of fused bead quality, analytical consistency and mitigating volatilisation losses. Conversely, for the silicate glass sample, shorter fusion times of less than ~30 min under the same conditions provided more accurate analyses whilst limiting volatile losses

Key challenges for the surveillance of respiratory viruses: transitioning out of the acute phase of the SARS-CoV-2 pandemic

To support the ongoing management of viral respiratory diseases, many countries are moving towards an integrated model of surveillance for SARS-CoV-2, influenza, and other respiratory pathogens. While many surveillance approaches catalysed by the COVID-19 pandemic provide novel epidemiological insight, continuing them as implemented during the pandemic is unlikely to be feasible for non-emergency surveillance, and many have already been scaled back. Furthermore, given anticipated co-circulation of SARS-CoV-2 and influenza, surveillance activities in place prior to the pandemic require review and adjustment to ensure their ongoing value for public health. In this perspective, we highlight key challenges for the development of integrated models of surveillance. We discuss the relative strengths and limitations of different surveillance practices and studies, their contribution to epidemiological assessment, forecasting, and public health decision making

Catalogue of Stone ScuIpture from the Area of Kula Atlagića

U radu se obrađuje problematika atribucije pojedinih kamenih ulomaka s lokaliteta Sv. Petar i Sv. Nikola u Kuli Atlagića. Većina se ulomaka čuva u Muzeju hrvatskih arheoloških spomenika u Splitu, a onamo su dospjeli u nekoliko etapa. Osim činjenice da pripadaju različitim stilskim epohama, postavlja se problem kako odrediti pripadnost ulomaka određenim objektima. U članku je priložen katalog kamenih ulomaka te njihova interpretacija. Rezultati rekognosciranja ponudili su nekoliko mogućih lokacija na kojima bi mogli biti objekti kojima pripadaju ulomci skulpture priloženi u katalogu, no tek sustavna arheološka iskopavanja mogu ponuditi sigurniju atribuciju.The village of Kula Atlagića is located 4km north-west of Benkovac in the direction of the medieval road via Magna which passed through the Zadar hinterland. The name of the village was first mentioned as late as the 17th century, while older documents mention two Croatian villages in that area: TihIići and Bojište (Bojišće). In today\u27s village stand three churches: two Orthodox dedicated to St Nicholas and one Catholic dedicated to St Peter. The two churches are mentioned in the archaeological literature at the beginning of the 20lh century. The church of St Nicholas in the Orthodox graveyard was completed in 1447 as witnessed by the inscription on the transom of the side portal, while the church of St Peter bears early Romanesque features, although it was destroyed several times during its turbulent history. The stone fragments which are presented in the catalogue were gathered over a long period of time. Some were brought to Knin on the prompting of Fra Lujo Marun while most of the sculptures were gathered after the Homeland War from the ruins of the church of St Peter, into which they had been incorporated as building material, and brought to the Museum of Croatian Archaeological Monuments in Split. According to their stylistic characteristics, the sculptures are divided into different groups: ancient, early medieval and early Romanesque. The problem which arose during the work on the sculptures was the attribution of individual groups to a particular object. The ancient sculptures could have belonged to a temple or shrine to the Roman god Liber which was probably located in the area around the church of St Nicholas as evidenced by entries in the diary of Fra Lujo Marun, who on several occasions made notes on both churches and the areas around them. The early medieval sculpture shows different characteristics and we could suppose that the earlier sculptures in this group were replaced by new furniture donated by some worthy benefactor. The question remains open as to where the early medieval church to which this furniture belonged was located. Numerous authors suppose that an early medieval church, which was in the 15\u27h century or earlier replaced by a new one, was situated on the site of today\u27s church of St Nicholas in the Orthodox graveyard. Because the investigations on this site have not been completed, we are left only with suppositions which could be confirmed by archaeological work. The fragments of early Romanesque sculpture are very specific and it is not possible to find close parallel s for them. The sculpture could be connected to the church of St Peter which was founded prior to the 12\u27b century, but investigations carried out in 1997 showed that this building had only one building phase and we cannot therefore talk of the possibility of the existence of an earlier church, at least not in the investigated area inside the church and in its immediate area. Translation: Nicholas Philip Saywel

The evolution of the dust and gas content in galaxies

We use deep Herschel observations taken with both PACS and SPIRE imaging cameras to estimate the dust mass of a sample of galaxies extracted from the GOODS-S, GOODS-N and the COSMOS fields. We divide the redshift–stellar mass (M star )–star formation rate (SFR) parameter space into small bins and investigate average properties over this grid. In the first part of the work we investigate the scaling relations between dust mass, stellar mass and SFR out to z = 2.5. No clear evolution of the dust mass with redshift is observed at a given SFR and stellar mass. We find a tight correlation between the SFR and the dust mass, which, under reasonable assumptions, is likely a consequence of the Schmidt-Kennicutt (S-K) relation. The previously observed correlation between the stellar content and the dust content flattens or sometimes disappears when considering galaxies with the same SFR. Our finding suggests that most of the correlation between dust mass and stellar mass obtained by previous studies is likely a consequence of the correlation between the dust mass and the SFR combined with the main sequence, i.e., the tight relation observed between the stellar mass and the SFR and followed by the majority of star-forming galaxies. We then investigate the gas content as inferred from dust mass measurements. We convert the dust mass into gas mass by assuming that the dust-to-gas ratio scales linearly with the gas metallicity (as supported by many observations). For normal star-forming galaxies (on the main sequence) the inferred relation between the SFR and the gas mass (integrated S-K relation) broadly agrees with the results of previous studies based on CO measurements, despite the completely different approaches. We observe that all galaxies in the sample follow, within uncertainties, the same S-K relation. However, when investigated in redshift intervals, the S-K relation shows a moderate, but significant redshift evolution. The bulk of the galaxy population at z ∼ 2 converts gas into stars with an efficiency (star formation efficiency, SFE = SFR/M gas , equal to the inverse of the depletion time) about 5 times higher than at z ∼ 0. However, it is not clear what fraction of such variation of the SFE is due to an intrinsic redshift evolution and what fraction is simply a consequence of high-z galaxies having, on average, higher SFR, combined with thesuper-linear slope of the S-K relation (whileother studies finda linear slope). We confirm that the gas fraction (f gas = M gas /(M gas + M star )) decreases with stellar mass and increases with the SFR. We observe no evolution with redshift once M star and SFR are fixed. We explain these trends by introducing a universal relation between gas fraction, stellar mass and SFR that does not evolve with redshift, at least out to z ∼ 2.5. Galaxies move across this relation as their gas content evolves across the cosmic epochs. We use the 3D fundamental f gas –M star –SFR relation, along with the evolution of the main sequence with redshift, to estimate the evolution of the gas fraction in the average population of galaxies as a function of redshift and as a function of stellar mass: we find that M star > ∼ 10 11 M ? galaxies show the strongest evolution at z > ∼ 1.3 and a flatter trend at lower redshift, while f gas decreases more regularly over the entire redshift range probed in M star < ∼ 10 11 Mo galaxies, in agreement with a downsizing scenario

SPIRE imaging of M82: cool dust in the wind and tidal streams

M82 is a unique representative of a whole class of galaxies, starbursts with superwinds, in the Very Nearby Galaxy Survey with Herschel. In addition, its interaction with the M81 group has stripped a significant portion of its interstellar medium from its disk. SPIRE maps now afford better characterization of the far-infrared emission from cool dust outside the disk, and sketch a far more complete picture of its mass distribution and energetics than previously possible. They show emission coincident in projection with the starburst wind and in a large halo, much more extended than the PAH band emission seen with Spitzer. Some complex substructures coincide with the brightest PAH filaments, and others with tidal streams seen in atomic hydrogen. We subtract the far-infrared emission of the starburst and underlying disk from the maps, and derive spatially-resolved far-infrared colors for the wind and halo. We interpret the results in terms of dust mass, dust temperature, and global physical conditions. In particular, we examine variations in the dust physical properties as a function of distance from the center and the wind polar axis, and conclude that more than two thirds of the extraplanar dust has been removed by tidal interaction, and not entrained by the starburst wind.Comment: accepted in A&A Herschel special issu

The Herschel Virgo Cluster Survey. IX. Dust-to-gas mass ratio and metallicity gradients in four Virgo spiral galaxies

Using Herschel data from the Open Time Key Project the Herschel Virgo Cluster Survey (HeViCS), we investigated the relationship between the metallicity gradients expressed by metal abundances in the gas phase as traced by the chemical composition of HII regions, and in the solid phase, as traced by the dust-to-gas mass ratio. We derived the radial gradient of the dust-to-gas mass ratio for all galaxies observed by HeViCS whose metallicity gradients are available in the literature. They are all late type Sbc galaxies, namely NGC4254, NGC4303, NGC4321, and NGC4501. We examined different dependencies on metallicity of the CO-to-H$_2$ conversion factor (\xco), used to transform the $^{12}$CO observations into the amount of molecular hydrogen. We found that in these galaxies the dust-to-gas mass ratio radial profile is extremely sensitive to choice of the \xco\ value, since the molecular gas is the dominant component in the inner parts. We found that for three galaxies of our sample, namely NGC4254, NGC4321, and NGC4501, the slopes of the oxygen and of the dust-to-gas radial gradients agree up to $\sim$0.6-0.7R$_{25}$ using \xco\ values in the range 1/3-1/2 Galactic \xco. For NGC4303 a lower value of \xco$\sim0.1\times$ 10$^{20}$ is necessary. We suggest that such low \xco\ values might be due to a metallicity dependence of \xco (from close to linear for NGC4254, NGC4321, and NGC4501 to superlinear for NGC4303), especially in the radial regions R$_G<$0.6-0.7R$_{25}$ where the molecular gas dominates. On the other hand, the outer regions, where the atomic gas component is dominant, are less affected by the choice of \xco, and thus we cannot put constraints on its value.Comment: 13 pages, 8 figures, A&A accepte

Galaxy and Mass Assembly (GAMA): time-scales for galaxies crossing the green valley

We explore the constraints that can be placed on the evolutionary time-scales for typical low-redshift galaxies evolving from the blue cloud through the green valley and on to the red sequence. We utilize galaxies from the GAMA survey with 0.1 < z < 0.2 and classify them according to the intrinsic (u*-r*) colours of their stellar populations, as determined by fits to their multiwavelength spectral energy distributions. Using these fits to also determine stellar population ages and star formation time-scales, we argue that our results are consistent with a green valley population dominated by galaxies that are simply decreasing their star formation (running out of gas) over a time-scale of 2-4 Gyr which are seen at a specific epoch in their evolution (approximately 1.6 e-folding times after their peak in star formation). If their fitted star formation histories are extrapolated forward, the green galaxies will further redden over time, until they attain the colours of a passive population. In this picture, no specific quenching event which cuts-off their star formation is required, though it remains possible that the decline in star formation in green galaxies may be expedited by internal or external forces. However, there is no evidence that green galaxies have recently changed their star formation time-scales relative to their previous longer term star formation histories

Epigenome-Wide Association Study of Kidney Function Identifies Trans-Ethnic and Ethnic-Specific Loci

BACKGROUND: DNA methylation (DNAm) is associated with gene regulation and estimated glomerular filtration rate (eGFR), a measure of kidney function. Decreased eGFR is more common among US Hispanics and African Americans. The causes for this are poorly understood. We aimed to identify trans-ethnic and ethnic-specific differentially methylated positions (DMPs) associated with eGFR using an agnostic, genome-wide approach. METHODS: The study included up to 5428 participants from multi-ethnic studies for discovery and 8109 participants for replication. We tested the associations between whole blood DNAm and eGFR using beta values from Illumina 450K or EPIC arrays. Ethnicity-stratified analyses were performed using linear mixed models adjusting for age, sex, smoking, and study-specific and technical variables. Summary results were meta-analyzed within and across ethnicities. Findings were assessed using integrative epigenomics methods and pathway analyses. RESULTS: We identified 93 DMPs associated with eGFR at an FDR of 0.05 and replicated 13 and 1 DMPs across independent samples in trans-ethnic and African American meta-analyses, respectively. The study also validated 6 previously published DMPs. Identified DMPs showed significant overlap enrichment with DNase I hypersensitive sites in kidney tissue, sites associated with the expression of proximal genes, and transcription factor motifs and pathways associated with kidney tissue and kidney development. CONCLUSIONS: We uncovered trans-ethnic and ethnic-specific DMPs associated with eGFR, including DMPs enriched in regulatory elements in kidney tissue and pathways related to kidney development. These findings shed light on epigenetic mechanisms associated with kidney function, bridging the gap between population-specific eGFR-associated DNAm and tissue-specific regulatory context