Antimicrobial resistance in community and nosocomial Escherichia coli urinary tract isolates, London 2005 – 2006

<p>Abstract</p> <p>Background</p> <p><it>Escherichia coli </it>is the commonest cause of community and nosocomial urinary tract infection (UTI). Antibiotic treatment is usually empirical relying on susceptibility data from local surveillance studies. We therefore set out to determine levels of resistance to 8 commonly used antimicrobial agents amongst all urinary isolates obtained over a 12 month period.</p> <p>Methods</p> <p>Antimicrobial susceptibility to ampicillin, amoxicillin/clavulanate, cefalexin, ciprofloxacin, gentamicin, nitrofurantoin, trimethoprim and cefpodoxime was determined for 11,865 <it>E. coli </it>urinary isolates obtained from community and hospitalised patients in East London.</p> <p>Results</p> <p>Nitrofurantoin was the most active agent (94% susceptible), followed by gentamicin and cefpodoxime. High rates of resistance to ampicillin (55%) and trimethoprim (40%), often in combination were observed in both sets of isolates. Although isolates exhibiting resistance to multiple drug classes were rare, resistance to cefpodoxime, indicative of Extended spectrum β-lactamase production, was observed in 5.7% of community and 21.6% of nosocomial isolates.</p> <p>Conclusion</p> <p>With the exception of nitrofurantoin, resistance to agents commonly used as empirical oral treatments for UTI was extremely high. Levels of resistance to trimethoprim and ampicillin render them unsuitable for empirical use. Continued surveillance and investigation of other oral agents for treatment of UTI in the community is required.</p

Installation instructions for GLiMR version 1.pdf

Here, we describe and demonstrate a geographic information systems-based lithic morphometric research (GLiMR) software approach. GLiMR accurately and rapidly handles a sequence of ArcGIS procedures to extract geometric morphometric data from 2D and 3D scan files of lithic artifacts. GLiMR generates three main types of geometric properties: shape data, topographic data and domain aggregate data. These data can be extracted in ways that support other analyses of artifact form, including Generalized Procrustes Analysis, Principal Components Analysis and Cluster Analyses. We illustrate the use of GLiMR by presenting a basic case study that compares the geometric morphometry of Western Stemmed Tradition projectile points found in two cache features at Idaho’s Cooper’s Ferry site and from other sites in the Columbia River Plateau region of the Pacific Northwest. This collection also includes the XYZ scan files for artifacts used for case study analysis

Background Oriented Schlieren (BOS) of a Supersonic Aircraft In Flight

This article describes the development and use of Background Oriented Schlieren on a full-scale supersonic jet in flight. A series of flight tests was performed in October, 2014 and February 2015 using the flora of the desert floor in the Supersonic Flight Corridor on the Edwards Air Force Base as a background. Flight planning was designed based on the camera resolution, the mean size and color of the predominant plants, and the navigation and coordination of two aircraft. Software used to process the image data was improved with additional utilities. The planning proved to be effective and the vast majority of the passes of the target aircraft were successfully recorded. Results were obtained that are the most detailed schlieren imagery of an aircraft in flight to date

Vegetation response to invasive Tamarix control in southwestern U.S. rivers: a collaborative study including 416 sites

Most studies assessing vegetation response following control of invasive Tamarix trees along southwestern U.S. rivers have been small in scale (e.g., river reach), or at a regional scale but with poor spatial-temporal replication, and most have not included testing the effects of a now widely used biological control. We monitored plant composition following Tamarix control along hydrologic, soil, and climatic gradients in 244 treated and 172 reference sites across six U.S. states. This represents the largest comprehensive assessment to date on the vegetation response to the four most common Tamarix control treatments. Biocontrol by a defoliating beetle (treatment 1) reduced the abundance of Tamarix less than active removal by mechanically using hand and chain-saws (2), heavy machinery (3) or burning (4). Tamarix abundance also decreased with lower temperatures, higher precipitation, and follow-up treatments for Tamarix resprouting. Native cover generally increased over time in active Tamarix removal sites, however, the increases observed were small and was not consistently increased by active revegetation. Overall, native cover was correlated to permanent stream flow, lower grazing pressure, lower soil salinity and temperatures, and higher precipitation. Species diversity also increased where Tamarix was removed. However, Tamarix treatments, especially those generating the highest disturbance (burning and heavy machinery), also often promoted secondary invasions of exotic forbs. The abundance of hydrophytic species was much lower in treated than in reference sites, suggesting that management of southwestern U.S. rivers has focused too much on weed control, overlooking restoration of fluvial processes that provide habitat for hydrophytic and floodplain vegetation. These results can help inform future management of Tamarix-infested rivers to restore hydrogeomorphic processes, increase native biodiversity and reduce abundance of noxious species

The Detectability of Rocky Planet Surface and Atmosphere Composition with JWST: The Case of LHS 3844b

The spectroscopic characterization of terrestrial exoplanets will be made possible for the first time with JWST. One challenge to characterizing such planets is that it is not known a priori whether they possess optically thick atmospheres or even any atmospheres altogether. But this challenge also presents an opportunity - the potential to detect the surface of an extrasolar world. This study explores the feasibility of characterizing the atmosphere and surface of a terrestrial exoplanet with JWST, taking LHS 3844b as a test case because it is the highest signal-to-noise rocky thermal emission target among planets that are cool enough to have non-molten surfaces. We model the planetary emission, including the spectral signal of both atmosphere and surface, and we explore all scenarios that are consistent with the existing Spitzer 4.5 $\mu$m measurement of LHS 3844b from Kreidberg et al. (2019). In summary, we find a range of plausible surfaces and atmospheres that are within 3 $\sigma$ of the observation - less reflective metal-rich, iron oxidized and basaltic compositions are allowed, and atmospheres are restricted to a maximum thickness of 1 bar, if near-infrared absorbers at $\gtrsim$ 100 ppm are included. We further make predictions on the observability of surfaces and atmospheres, perform a Bayesian retrieval analysis on simulated JWST data and find that a small number, ~3, of eclipse observations should suffice to differentiate between surface and atmospheric features. However, the surface signal may make it harder to place precise constraints on the abundance of atmospheric species and may even falsely induce a weak H$_2$O detection.Comment: 33 pages, 20 figure

6-thioguanine treatment in inflammatory bowel disease: A critical appraisal by a European 6-TG working party

Recently, the suggestion to use 6-thioguanine (6-TG) as an alternative thiopurine in patients with inflammatory bowel disease (IBD) has been discarded due to reports about possible (hepato) toxicity. During meetings arranged in Vienna and Prague in 2004, European experts applying 6-TG further on in IBD patients presented data on safety and efficacy of 6-TG. After thorough evaluation of its risk-benefit ratio, the group consented that 6-TG may still be considered as a rescue drug in stringently defined indications in IBD, albeit restricted to a clinical research setting. As a potential indication for administering 6-TG, we delineated the requirement for maintenance therapy as well as intolerance and/or resistance to aminosalicylates, azathioprine, 6-mercaptopurine, methotrexate and infliximab. Furthermore, indications are preferred in which surgery is thought to be inappropriate. The standard 6-TG dosage should not exceed 25 mg daily. Routine laboratory controls are mandatory in short intervals. Liver biopsies should be performed after 6-12 months, three years and then three-yearly accompanied by gastroduodenoscopy, to monitor for potential hepatotoxicity, including nodular regenerative hyperplasia (NRH) and veno-occlusive disease (VOD). Treatment with 6-TG must be discontinued in case of overt or histologically proven hepatotoxicity. Copyright (c) 2006 S. Karger AG, Basel

Gastrointestinal microbiota composition predicts peripheral inflammatory state during treatment of human tuberculosis

The composition of the gastrointestinal microbiota influences systemic immune responses, but how this affects infectious disease pathogenesis and antibiotic therapy outcome is poorly understood. This question is rarely examined in humans due to the difficulty in dissociating the immunologic effects of antibiotic-induced pathogen clearance and microbiome alteration. Here, we analyze data from two longitudinal studies of tuberculosis (TB) therapy (35 and 20 individuals) and a cross sectional study from 55 healthy controls, in which we collected fecal samples (for microbiome analysis), sputum (for determination of Mycobacterium tuberculosis (Mtb) bacterial load), and peripheral blood (for transcriptomic analysis). We decouple microbiome effects from pathogen sterilization by comparing standard TB therapy with an experimental TB treatment that did not reduce Mtb bacterial load. Random forest regression to the microbiome-transcriptome-sputum data from the two longitudinal datasets reveals that renormalization of the TB inflammatory state is associated with Mtb pathogen clearance, increased abundance of Clusters IV and XIVa Clostridia, and decreased abundance of Bacilli and Proteobacteria. We find similar associations when applying machine learning to peripheral gene expression and microbiota profiling in the independent cohort of healthy individuals. Our findings indicate that antibiotic-induced reduction in pathogen burden and changes in the microbiome are independently associated with treatment-induced changes of the inflammatory response of active TB, and the response to antibiotic therapy may be a combined effect of pathogen killing and microbiome driven immunomodulation

ABCB1 (MDR1) polymorphisms and ovarian cancer progression and survival: A comprehensive analysis from the Ovarian Cancer Association Consortium and The Cancer Genome Atlas

&lt;b&gt;Objective&lt;/b&gt; &lt;i&gt;ABCB1&lt;/i&gt; encodes the multi-drug efflux pump P-glycoprotein (P-gp) and has been implicated in multi-drug resistance. We comprehensively evaluated this gene and flanking regions for an association with clinical outcome in epithelial ovarian cancer (EOC).&lt;p&gt;&lt;/p&gt; &lt;b&gt;Methods&lt;/b&gt; The best candidates from fine-mapping analysis of 21 &lt;i&gt;ABCB1&lt;/i&gt; SNPs tagging C1236T (rs1128503), G2677T/A (rs2032582), and C3435T (rs1045642) were analysed in 4616 European invasive EOC patients from thirteen Ovarian Cancer Association Consortium (OCAC) studies and The Cancer Genome Atlas (TCGA). Additionally we analysed 1,562 imputed SNPs around ABCB1 in patients receiving cytoreductive surgery and either ‘standard’ first-line paclitaxel–carboplatin chemotherapy (n = 1158) or any first-line chemotherapy regimen (n = 2867). We also evaluated ABCB1 expression in primary tumours from 143 EOC patients.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Result&lt;/b&gt; Fine-mapping revealed that rs1128503, rs2032582, and rs1045642 were the best candidates in optimally debulked patients. However, we observed no significant association between any SNP and either progression-free survival or overall survival in analysis of data from 14 studies. There was a marginal association between rs1128503 and overall survival in patients with nil residual disease (HR 0.88, 95% CI 0.77–1.01; p = 0.07). In contrast, &lt;i&gt;ABCB1&lt;/i&gt; expression in the primary tumour may confer worse prognosis in patients with sub-optimally debulked tumours.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Conclusion&lt;/b&gt; Our study represents the largest analysis of &lt;i&gt;ABCB1&lt;/i&gt; SNPs and EOC progression and survival to date, but has not identified additional signals, or validated reported associations with progression-free survival for rs1128503, rs2032582, and rs1045642. However, we cannot rule out the possibility of a subtle effect of rs1128503, or other SNPs linked to it, on overall survival.&lt;p&gt;&lt;/p&gt

A combined measurement of cosmic growth and expansion from clusters of galaxies, the CMB and galaxy clustering

Combining galaxy cluster data from the ROSAT All-Sky Survey and the Chandra X-ray Observatory, cosmic microwave background data from the Wilkinson Microwave Anisotropy Probe, and galaxy clustering data from the WiggleZ Dark Energy Survey, the 6-degree Field Galaxy Survey and the Sloan Digital Sky Survey III, we test for consistency the cosmic growth of structure predicted by General Relativity (GR) and the cosmic expansion history predicted by the cosmological constant plus cold dark matter paradigm (LCDM). The combination of these three independent, well studied measurements of the evolution of the mean energy density and its fluctuations is able to break strong degeneracies between model parameters. We model the key properties of cosmic growth with the normalization of the matter power spectrum, sigma_8, and the cosmic growth index, gamma, and those of cosmic expansion with the mean matter density, Omega_m, the Hubble constant, H_0, and a kinematical parameter equivalent to that for the dark energy equation of state, w. For a spatially flat geometry, w=-1, and allowing for systematic uncertainties, we obtain sigma_8=0.785+-0.019 and gamma=0.570+0.064-0.063 (at the 68.3 per cent confidence level). Allowing both w and gamma to vary we find w=-0.950+0.069-0.070 and gamma=0.533+-0.080. To further tighten the constraints on the expansion parameters, we also include supernova, Cepheid variable and baryon acoustic oscillation data. For w=-1, we have gamma=0.616+-0.061. For our most general model with a free w, we measure Omega_m=0.278+0.012-0.011, H_0=70.0+-1.3 km s^-1 Mpc^-1 and w=-0.987+0.054-0.053 for the expansion parameters, and sigma_8=0.789+-0.019 and gamma=0.604+-0.078 for the growth parameters. These results are in excellent agreement with GR+LCDM (gamma~0.55; w=-1) and represent the tightest and most robust simultaneous constraint on cosmic growth and expansion to date.Comment: 14 pages, 5 figures, 1 table. Matches the accepted version for MNRAS. New sections 3 and 6 added, containing 2 new figures. Table extended. The results including BAO data have been slightly modified due to an updated BAO analysis. Conclusions unchange