4,730 research outputs found

    Some new insights in swelling and swelling pressure of low active clay

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    This paper presents a multidimensional chemo-mechanical model for saturated clay treated as a two-phase deformable and chemically reactive porous medium. The constitutive relation is an extension of the original chemo-mechanical model proposed by Gajo et al. (2002) and Loret et al. (2002), in which a q-p formulation was proposed with a Cam-Clay-like elastic response. A novel hyper-elastic law is proposed in which shear stiffness and bulk stiffness change with stress state and ion concentration in pore solution. The proposed constitutive model and the associated coupled finite element formulation are implemented in a 2D, commercial, finite element code (ABAQUS) in the form of user-defined external subroutines. The proposed framework is used to simulate the oedometer tests performed on a low activity clay extracted from Costa della Gaveta slope. The computed chemo mechanical behaviour of the material prepared with distilled water is compared with the experimental results obtained from reconstituted specimens. Moreover, swelling and swelling pressure are computed for the overconsolidated material reconstituted with 1 M NaCl solution and then exposed to distilled water. The comparison of simulations and experiments shows a good agreement

    A functional-cognitive framework for attitude research

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    In attitude research, behaviours are often used as proxies for attitudes and attitudinal processes. This practice is problematic because it conflates the behaviours that need to be explained (explanandum) with the mental constructs that are used to explain these behaviours (explanans). In the current chapter we propose a meta-theoretical framework that resolves this problem by distinguishing between two levels of analysis. According to the proposed framework, attitude research can be conceptualised as the scientific study of evaluation. Evaluation is defined not in terms of mental constructs but in terms of elements in the environment, more specifically, as the effect of stimuli on evaluative responses. From this perspective, attitude research provides answers to two questions: (1) Which elements in the environment moderate evaluation? (2) What mental processes and representations mediate evaluation? Research on the first question provides explanations of evaluative responses in terms of elements in the environment (functional level of analysis); research on the second question offers explanations of evaluation in terms of mental processes and representations (cognitive level of analysis). These two levels of analysis are mutually supportive, in that better explanations at one level lead to better explanations at the other level. However, their mutually supportive relation requires a clear distinction between the concepts of their explanans and explanandum, which are conflated if behaviours are treated as proxies for mental constructs. The value of this functional-cognitive framework is illustrated by applying it to four central questions of attitude research

    The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

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    Shotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many different approaches for inferring the taxonomic composition and AMR gene content of complex community samples from shotgun metagenomic data, but there has been little work establishing the optimum sequencing depth, data processing and analysis methods for these samples. In this study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to address these issues. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced samples with shotgun metagenomics at high depth (~ 200 million reads per sample). Alongside this, we cultured single-colony isolates of Enterobacteriaceae from the same samples and used hybrid sequencing (short- and long-reads) to create high- quality assemblies for comparison to the metagenomic data. To automate data processing, we developed an open- source software pipeline, ‚ÄėResPipe‚Äô

    Variable stars in the Fornax dSph Galaxy. I. The Globular Cluster Fornax 4

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    Variable stars have been identified for the first time in Fornax 4, the globular cluster located near the center of the Fornax dwarf spheroidal galaxy. By applying the image subtraction technique to B,V time series photometry obtained with the MagIC camera of the 6.5-m Magellan/Clay telescope and with the wide field imager of the 4-m Blanco/CTIO telescope, we detected 27 RR Lyrae stars (22 fundamental mode, 3 first overtone, and 2 double-mode pulsators) in a 2.4'x2.4' area centered on Fornax 4. The average and minimum periods of the ab-type RR Lyrae stars, = 0.594 d and P(ab,min)=0.5191 d, respectively, as well as the revised position of the cluster in the horizontal branch type--metallicity plane, all consistently point to an Oosterhoff-intermediate status for the cluster, unlike what is seen for the vast majority of Galactic globular clusters, but in agreement with previous indications for the other globular clusters in Fornax. The average apparent magnitude of the RR Lyrae stars located within 30 arcsec from the cluster center is =21.43 +/- 0.03 mag (sigma=0.10 mag, average on 12 stars), leading to a true distance modulus of (m-M)o=20.64 +/- 0.09 mag or (m-M)o=20.53 +/- 0.09 mag, depending on whether a low ([Fe/H]=-2.0) or a moderately high ([Fe/H]=-1.5) metallicity is adopted.Comment: Apj, in pres

    No evidence that wild red deer (Cervus elaphus) on the Iberian Peninsula are a reservoir of Mycobacterium avium subspecies paratuberculosis infection

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    The potential role of red deer (Cervus elaphus) as a reservoir of Mycobacterium avium subspecies paratuberculosis (MAP) infection is largely unknown. A total of 332 wild red deer were investigated using post-mortem examination, bacteriology and serology. Only three animals (1.12%) were found to have lesions on histopathological examination and no MAP bacteria were recovered on culture. The results suggest it is unlikely that wild red deer make a significant contribution to the maintenance of MAP infection in the region. The cross-reactivity of the ELISAs used indicates this diagnostic modality is ineffective in the detection of MAP infection in this species. The implications of these results for the control of this important pathogen in both livestock and wildlife are discussed

    The degeneracy between star-formation parameters in dwarf galaxy simulations and the Mstar-Mhalo relation

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    We present results based on a set of N-Body/SPH simulations of isolated dwarf galaxies. The simulations take into account star formation, stellar feedback, radiative cooling and metal enrichment. The dark matter halo initially has a cusped profile, but, at least in these simulations, starting from idealised, spherically symmetric initial conditions, a natural conversion to a core is observed due to gas dynamics and stellar feedback. A degeneracy between the efficiency with which the interstellar medium absorbs energy feedback from supernovae and stellar winds on the one hand, and the density threshold for star formation on the other, is found. We performed a parameter survey to determine, with the aid of the observed kinematic and photometric scaling relations, which combinations of these two parameters produce simulated galaxies that are in agreement with the observations. With the implemented physics we are unable to reproduce the relation between the stellar mass and the halo mass as determined by Guo et al. (2010), however we do reproduce the slope of this relation.Comment: Accepted for publication in MNRAS | 12 pages, 8 figure

    An average/deprivation/inequality (ADI) analysis of chronic disease outcomes and risk factors in Argentina

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    <p>Abstract</p> <p>Background</p> <p>Recognition of the global economic and epidemiological burden of chronic non-communicable diseases has increased in recent years. However, much of the research on this issue remains focused on individual-level risk factors and neglects the underlying social patterning of risk factors and disease outcomes.</p> <p>Methods</p> <p>Secondary analysis of Argentina's 2005 <it>Encuesta Nacional de Factores de Riesgo </it>(National Risk Factor Survey, <it>N </it>= 41,392) using a novel analytical strategy first proposed by the United Nations Development Programme (UNDP), which we here refer to as the Average/Deprivation/Inequality (ADI) framework. The analysis focuses on two risk factors (unhealthy diet and obesity) and one related disease outcome (diabetes), a notable health concern in Latin America. Logistic regression is used to examine the interplay between socioeconomic and demographic factors. The ADI analysis then uses the results from the logistic regression to identify the most deprived, the best-off, and the difference between the two ideal types.</p> <p>Results</p> <p>Overall, 19.9% of the sample reported being in poor/fair health, 35.3% reported not eating any fruits or vegetables in five days of the week preceding the interview, 14.7% had a BMI of 30 or greater, and 8.5% indicated that a health professional had told them that they have diabetes or high blood pressure. However, significant variation is hidden by these summary measures. Educational attainment displayed the strongest explanatory power throughout the models, followed by household income, with both factors highlighting the social patterning of risk factors and disease outcomes. As educational attainment and household income increase, the probability of poor health, unhealthy diet, obesity, and diabetes decrease. The analyses also point toward important provincial effects and reinforce the notion that both compositional factors (i.e., characteristics of individuals) and contextual factors (i.e., characteristics of places) are important in understanding the social patterning of chronic diseases.</p> <p>Conclusion</p> <p>The application of the ADI framework enables identification of the regions or groups worst-off for each outcome measure under study. This can be used to highlight the variation embedded within national averages; as such, it encourages a social perspective on population health indicators that is particularly attuned to issues of inequity. The ADI framework is an important tool in the evaluation of policies aiming to prevent or control chronic non-communicable diseases.</p

    Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines

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    Background: Accurately identifying SNPs from bacterial sequencing data is an essential requirement for using genomics to track transmission and predict important phenotypes such as antimicrobial resistance. However, most previous performance evaluations of SNP calling have been restricted to eukaryotic (human) data. Additionally, bacterial SNP calling requires choosing an appropriate reference genome to align reads to, which, together with the bioinformatic pipeline, affects the accuracy and completeness of a set of SNP calls obtained. This study evaluates the performance of 209 SNP calling pipelines using a combination of simulated data from 254 strains of 10 clinically common bacteria and real data from environmentally-sourced and genomically diverse isolates within the genera Citrobacter, Enterobacter, Escherichia and Klebsiella. Results: We evaluated the performance of 209 SNP calling pipelines, aligning reads to genomes of the same or a divergent strain. Irrespective of pipeline, a principal determinant of reliable SNP calling was reference genome selection. Across multiple taxa, there was a strong inverse relationship between pipeline sensitivity and precision, and the Mash distance (a proxy for average nucleotide divergence) between reads and reference genome. The effect was especially pronounced for diverse, recombinogenic, bacteria such as Escherichia coli, but less dominant for clonal species such as Mycobacterium tuberculosis. Conclusions: The accuracy of SNP calling for a given species is compromised by increasing intra-species diversity. When reads were aligned to the same genome from which they were sequenced, among the highest performing pipelines was Novoalign/GATK. By contrast, when reads were aligned to particularly divergent genomes, the highest-performing pipelines often employed the aligners NextGenMap or SMALT, and/or the variant callers LoFreq, mpileup or Strelka

    Hadron beam test of a scintillating fibre tracker system for elastic scattering and luminosity measurement in ATLAS

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    A scintillating fibre tracker is proposed to measure elastic proton scattering at very small angles in the ATLAS experiment at CERN. The tracker will be located in so-called Roman Pot units at a distance of 240 m on each side of the ATLAS interaction point. An initial validation of the design choices was achieved in a beam test at DESY in a relatively low energy electron beam and using slow off-the-shelf electronics. Here we report on the results from a second beam test experiment carried out at CERN, where new detector prototypes were tested in a high energy hadron beam, using the first version of the custom designed front-end electronics. The results show an adequate tracking performance under conditions which are similar to the situation at the LHC. In addition, the alignment method using so-called overlap detectors was studied and shown to have the expected precision.Comment: 12 pages, 8 figures. Submitted to Journal of Instrumentation (JINST
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