Evaluating disease severity in idiopathic pulmonary fibrosis.

Accurate assessment of idiopathic pulmonary fibrosis (IPF) disease severity is integral to the care provided to patients with IPF. However, to date, there are no generally accepted or validated staging systems. There is an abundance of data on using information acquired from physiological, radiological and pathological parameters, in isolation or in combination, to assess disease severity in IPF. Recently, there has been interest in using serum biomarkers and computed tomography-derived quantitative lung fibrosis measures to stage disease severity in IPF. This review will focus on the suggested methods for staging IPF, at baseline and on serial assessment, their strengths and limitations, as well as future developments

Relationships between Goat Foraging Behaviour and Pastoral Value in High Bassin Zone of Mandrare Rangeland in Southern of Madagascar

Goats have particular anatomical behaviour for browsing leaves to satisfy their energy requirements. In rangelands, available shrubs, leaves and biomass resources influence ruminant’s activities and rhythms such as foraging, walking, resting, ruminating and drinking. At semi-arid areas, this study aimed to determine how shrubs interact with pasture value to effect goat foraging behaviour

Instabilities in the dissolution of a porous matrix

A reactive fluid dissolving the surrounding rock matrix can trigger an instability in the dissolution front, leading to spontaneous formation of pronounced channels or wormholes. Theoretical investigations of this instability have typically focused on a steadily propagating dissolution front that separates regions of high and low porosity. In this paper we show that this is not the only possible dissolutional instability in porous rocks; there is another instability that operates instantaneously on any initial porosity field, including an entirely uniform one. The relative importance of the two mechanisms depends on the ratio of the porosity increase to the initial porosity. We show that the "inlet" instability is likely to be important in limestone formations where the initial porosity is small and there is the possibility of a large increase in permeability. In quartz-rich sandstones, where the proportion of easily soluble material (e.g. carbonate cements) is small, the instability in the steady-state equations is dominant.Comment: to be published in Geophysical Research Letter

Dissolution in a field

We study the dissolution of a solid by continuous injection of reactive ``acid'' particles at a single point, with the reactive particles undergoing biased diffusion in the dissolved region. When acid encounters the substrate material, both an acid particle and a unit of the material disappear. We find that the lengths of the dissolved cavity parallel and perpendicular to the bias grow as t^{2/(d+1)} and t^{1/(d+1)}, respectively, in d-dimensions, while the number of reactive particles within the cavity grows as t^{2/(d+1)}. We also obtain the exact density profile of the reactive particles and the relation between this profile and the motion of the dissolution boundary. The extension to variable acid strength is also discussed.Comment: 6 pages, 6 figures, 2-column format, for submission to PR

Application of emulsified acids on sandstone formation at elevated temperature conditions: an experimental study

Emulsified acid has attracted considerable attention of the oil and gas industry due to its delayed nature that allows deeper penetration of acid into the formation which essentially facilitate further enhancing the well productivity, and at the same time minimizes the corrosion issues. However, emulsified acid has only been extensively studied and applied on carbonate formations. Considering more than half of the reservoirs worldwide are sandstone reservoirs, studying the effects of emulsified acid on sandstone under high-temperature conditions would unlock the potential of emulsified acid and help generate more value for the oil and gas industry by improving the well productivity from sandstone reservoirs. To ensure the applicability of the emulsified acid on the real sandstone reservoir, which usually has a temperature higher than ambient conditions, the stability of emulsified acids is investigated under 300 °F. Then, the stable emulsified acid samples are developed and their impact on the properties of Berea sandstone core samples, including porosity, pore-size distribution, permeability and wettability, are investigated. The core samples have undergone pre-flush (10% HCl:5% CH3COOH) before the main flush (emulsified acid). The emulsified acids are prepared using hydrofluoric acid, hydrochloric acid, phosphoric acid, cationic surfactant and chelating agent. Fourteen core samples are saturated with different emulsified acids under vacuum conditions for 3 days to ensure maximum saturation. The porosity, permeability and wettability of each core sample are measured before and after the reaction with acid. Nuclear magnetic resonance analysis has been applied to evaluate the change in pore size distribution. This study has demonstrated that the emulsified acids are capable of improving the porosity and permeability of Berea sandstone core sample. The pore size distribution has also been affected by the application of emulsified acid, where more large pores have been evolved to the core samples due to the reaction of acids with the sandstone which ultimately helps in improving the productivity of hydrocarbons. This indicates less precipitation of the secondary reaction products resulting better enhancement in sandstone flow properties. These results demonstrate the potential of emulsified acid during sandstone acidizing as emulsified acid significantly improved the sandstone properties which can essentially enhance the well productivity

Azithromycin alters spatial and temporal dynamics of airway microbiota in idiopathic pulmonary fibrosis

BackgroundHigh bacterial burden in the lung microbiota predicts progression of idiopathic pulmonary fibrosis (IPF). Azithromycin (AZT) is a macrolide antibiotic known to alter the lung microbiota in several chronic pulmonary diseases, and observational studies have shown a positive effect of AZT on mortality and hospitalisation rate in IPF. However, the effect of AZT on the lung microbiota in IPF remains unknown.MethodsWe sought to determine the impact of a 3-month course of AZT on the lung microbiota in IPF. We assessed sputum and oropharyngeal swab specimens from 24 adults with IPF included in a randomised controlled crossover trial of oral AZT 500 mg 3 times per week. 16S rRNA gene amplicon sequencing and quantitative PCR (qPCR) were performed to assess bacterial communities. Antibiotic resistance genes (ARGs) were assessed using real-time qPCR.ResultsAZT significantly decreased community diversity with a stronger and more persistent effect in the lower airways (sputum). AZT treatment altered the temporal kinetics of the upper (oropharyngeal swab) and lower airway microbiota, increasing community similarity between the two sites for 1 month after macrolide cessation. Patients with an increase in ARG carriage had lower bacterial density and enrichment of the genusStreptococcus. In contrast, patients with more stable ARG carriage had higher bacterial density and enrichment inPrevotella.ConclusionsAZT caused sustained changes in the diversity and composition of the upper and lower airway microbiota in IPF, with effects on the temporal and spatial dynamics between the two sites

Wormhole formation in dissolving fractures

We investigate the dissolution of artificial fractures with three-dimensional, pore-scale numerical simulations. The fluid velocity in the fracture space was determined from a lattice-Boltzmann method, and a stochastic solver was used for the transport of dissolved species. Numerical simulations were used to study conditions under which long conduits (wormholes) form in an initially rough but spatially homogeneous fracture. The effects of flow rate, mineral dissolution rate and geometrical properties of the fracture were investigated, and the optimal conditions for wormhole formation determined.Comment: to be published in J. Geophys Re

Defining genetic risk factors for scleroderma-associated interstitial lung disease

Although several genetic associations with scleroderma (SSc) are defined, very little is known on genetic susceptibility to SSc-associated interstitial lung disease (SSc-ILD). A number of common polymorphisms have been associated with SSc-ILD, but most have not been replicated in separate populations. Four SNPs in IRF5, and one in each of STAT4, CD226 and IRAK1, selected as having been previously the most consistently associated with SSc-ILD, were genotyped in 612 SSc patients, of European descent, of whom 394 had ILD. The control population (n = 503) comprised individuals of European descent from the 1000 Genomes Project. After Bonferroni correction, two of the IRF5 SNPs, rs2004640 (OR (95% CI)1.30 (1.10–1.54), p^{corr} = 0.015) and rs10488631 (OR 1.48 (1.14–1.92), p^{corr} = 0.022), and the STAT4 SNP rs7574865 (OR 1.43 (1.18–1.73), p^{corr} = 0.0015) were significantly associated with SSc compared with controls. However, none of the SNPs were significantly different between patients with SSc-ILD and controls. Two SNPs in IRF5, rs10488631 (OR 1.72 (1.24–2.39), p^{corr} = 0.0098), and rs2004640 (OR 1.39 (1.11–1.75), p^{corr} = 0.03), showed a significant difference in allele frequency between controls and patients without ILD, as did STAT4 rs7574865 (OR 1.86 (1.45–2.38), p^{corr} = 6.6 × 10^{-6}). A significant difference between SSc with and without ILD was only observed for STAT4 rs7574865, being less frequent in patients with ILD (OR 0.66 (0.51–0.85), p^{corr} = 0.0084). In conclusion, IRF5 rs2004640 and rs10488631, and STAT4 rs7574865 were significantly associated with SSc as a whole. Only STAT4 rs7574865 showed a significant difference in allele frequency in SSc-ILD, with the T allele being protective against ILD

Optical map guided genome assembly

Background The long reads produced by third generation sequencing technologies have significantly boosted the results of genome assembly but still, genome-wide assemblies solely based on read data cannot be produced. Thus, for example, optical mapping data has been used to further improve genome assemblies but it has mostly been applied in a post-processing stage after contig assembly. Results We proposeOpticalKermitwhich directly integrates genome wide optical maps into contig assembly. We show how genome wide optical maps can be used to localize reads on the genome and then we adapt the Kermit method, which originally incorporated genetic linkage maps to the miniasm assembler, to use this information in contig assembly. Our experimental results show that incorporating genome wide optical maps to the contig assembly of miniasm increases NGA50 while the number of misassemblies decreases or stays the same. Furthermore, when compared to the Canu assembler,OpticalKermitproduces an assembly with almost three times higher NGA50 with a lower number of misassemblies on realA. thalianareads. Conclusions OpticalKermitsuccessfully incorporates optical mapping data directly to contig assembly of eukaryotic genomes. Our results show that this is a promising approach to improve the contiguity of genome assemblies.Peer reviewe