On Liberalism, Liberty of Conscience, and Toleration: some historical and theoretical reflections

This chapter offers some historical and theoretical reflections on the relationship between liberalism and toleration. It is shown that the terms of that relationship as assumed in the minds of liberal commentators were established quite early, in the eighteenth century, and reproduced down to the present day in multiple versions of a grand narrative in which the liberal tradition originates in conscientious Protestant resistance to Catholic and Catholic-style persecution which, in 1688, would deliver limited government and religious liberty to all. A habitual equation between toleration and liberty of conscience is shown to be operative, legitimated by a reading of Locke which presents him as the intellectual mastermind of 1688, a founder of the liberal tradition, and an exponent of liberty of conscience. It is suggested that hidden within the folds of this reading is an old idea, that progressive thinkers like Locke educate elites who in their turn restrain and re-educate the popular instinct to persecute. History is used to problematize the equation of toleration and liberty of conscience and to give grounds for thinking that the old idea is alive and well in Rawlsian writing about liberalism, its history, and its relation to toleration

Predictive Nomogram for Recurrence following Surgery for Nonmetastatic Renal Cell Cancer with Tumor Thrombus

Purpose Following surgery for nonmetastatic renal cell carcinoma with tumor thrombus the risk of recurrence is significant but variable among patients. The purpose of this study was to develop and validate a predictive nomogram for individual estimation of recurrence risk following surgery for renal cell carcinoma with venous tumor thrombus. Materials and Methods Comprehensive data were collected on patients with nonmetastatic renal cell carcinoma and thrombus treated at a total of 5 institutions from 2000 to 2013. Independent predictors of recurrent renal cell carcinoma from a competing risks analysis were developed into a nomogram. Predictive accuracy was compared between the development and validation cohorts, and between the nomogram and the UISS (UCLA Integrated Staging System, SSIGN (Stage, Size, Grade and Necrosis) and Sorbellini models. Results A total of 636 patients were analyzed, including the development cohort of 465 and the validation cohort of 171. Independent predictors, including tumor diameter, body mass index, preoperative hemoglobin less than the lower limit of normal, thrombus level, perinephric fat invasion and nonclear cell histology, were developed into a nomogram. Estimated 5-year recurrence-free survival was 49% overall. Five-year recurrence-free survival in patients with 0, 1, 2 and more than 2 risk factors was 77%, 53%, 47% and 20%, respectively. Predictive accuracy was similar in the development and validation cohorts (AUC 0.726 and 0.724, respectively). Predictive accuracy of the thrombus nomogram was higher than that of the UISS (AUC 0.726 vs 0.595, p = 0.001), SSIGN (AUC 0.713 vs 0.612, p = 0.04) and Sorbellini models (AUC 0.709 vs 0.638, p = 0.02). Conclusions We present a predictive nomogram for postoperative recurrence in patients with nonmetastatic renal cell carcinoma with venous thrombus. Improving individual postoperative risk assessment may allow for better design and analysis of future adjuvant clinical trials

Chemical data evaluation: General considerations and approaches for IUPAC projects and the chemistry community (IUPAC Technical Report)

The International Union of Pure and Applied Chemistry has a long tradition of supporting the compilation of chemical data and their evaluation through direct projects, nomenclature and terminology work, and partnerships with international scientific bodies, government agencies, and other organizations. The IUPAC Interdivisional Subcommittee on Critical Evaluation of Data has been established to provide guidance on issues related to the evaluation of chemical data. In this first report, we define the general principles of the evaluation of scientific data and describe best practices and approaches to data evaluation in chemistryinfo:eu-repo/semantics/publishedVersio

Diatom ecological response to deposition of the 833-850 CE White River Ash (east lobe) ashfall in a small subarctic Canadian lake

A <5 mm thick volcanic ashfall layer associated with the White River Ash (east lobe [WRAe]) originating from the eruption of Mount Churchill, Alaska (833-850 CE; 1,117–1,100 cal BP) was observed in two freeze cores obtained from Pocket Lake (62.5090°N, −114.3719°W), a small subarctic lake located within the city limits of Yellowknife, Northwest Territories, Canada. Here we analyze changes in diatom assemblages to assess impact of tephra deposition on the aquatic biota of a subarctic lake. In a well-dated core constrained by 8 radiocarbon dates, diatom counts were carried out at 1-mm intervals through an interval spanning  1 cm above and below the tephra layer with each 1 mm sub-sample represented about 2 years of deposition. Non-metric Multidimensional Scaling (NMDS) and Stratigraphically Constrained Incremental Sum of Squares (CONISS) analyses were carried out and three distinct diatom assemblages were identified throughout the interval. The lowermost “Pre-WRAe Assemblage (Pre-WRAeA)” was indicative of slightly acidic and eutrophic lacustrine conditions. Winter deposition of the tephra layer drove a subsequent diatom flora shift to the “WRAe Assemblage (WRAeA)” the following spring. The WRAeA contained elevated abundances of taxa associated with oligotrophic, nutrient depleted and slightly more alkaline lake waters. These changes were only apparent in samples within the WRAe containing interval indicating that they were short lived and only sustained for a single year of deposition. Immediately above the WRAe horizon, a third, “Post-WRAe Assemblage (Post-WRAeA)” was observed. This assemblage was initially similar to that of the Pre-WRAeA but gradually became more distinct upwards, likely due to climatic patterns independent of the WRAe event. These results suggest that lacustrine environments are sensitive to perturbations such as deposition of ash fall, but that ecological communities in subarctic systems can also have high resilience and can recover rapidly. If subsampling of the freeze cores was carried out at a more standard resolution (0.5–1 cm) these subtle diatom ecological responses to perturbation associated with the WRAe depositional event would not have been observed. This research illustrates the importance of high-resolution subsampling when studying the environmental impact of geologically “near instantaneous” events such as episodic deposition of ashfalls

Redshift measurement and spectral classification for eBOSS galaxies with the redmonster software

We describe the redmonster automated redshift measurement and spectral classification software designed for the extended Baryon Oscillation Spectroscopic Survey (eBOSS) of the Sloan Digital Sky Survey IV (SDSS-IV). We describe the algorithms, the template standard and requirements, and the newly developed galaxy templates to be used on eBOSS spectra. We present results from testing on early data from eBOSS, where we have found a 90.5% automated redshift and spectral classification success rate for the luminous red galaxy sample (redshifts 0.6 ≲ z ≲ 1.0). The redmonster performance meets the eBOSS cosmology requirements for redshift classification and catastrophic failures and represents a significant improvement over the previous pipeline. We describe the empirical processes used to determine the optimum number of additive polynomial terms in our models and an acceptable ΔXr2 threshold for declaring statistical confidence. Statistical errors on redshift measurement due to photon shot noise are assessed, and we find typical values of a few tens of km s-1. An investigation of redshift differences in repeat observations scaled by error estimates yields a distribution with a Gaussian mean and standard deviation of μ ∼ 0.01 and σ ∼ 0.65, respectively, suggesting the reported statistical redshift uncertainties are over-estimated by ∼54%. We assess the effects of object magnitude, signal-to-noise ratio, fiber number, and fiber head location on the pipeline's redshift success rate. Finally, we describe directions of ongoing development.Publisher PDFPeer reviewe

Variants in interferon-alpha pathway genes and response to pegylated interferon-Alpha2a plus ribavirin for treatment of chronic hepatitis C virus infection in the hepatitis C antiviral long-term treatment against cirrhosis trial

Combination treatment with pegylated-interferon-alpha (PEG IFN-Α) and ribavirin, the current recommended therapy for chronic hepatitis C virus (HCV) infection, results in a sustained virological response (SVR) in only about half of patients. Because genes involved in the interferon-alpha pathway may affect antiviral responses, we analyzed the relationship between variants in these genes and SVR among participants in the Hepatitis C Antiviral Long-Term treatment Against Cirrhosis (HALT-C) trial. Patients had advanced chronic hepatitis C that had previously failed to respond to interferon-based treatment. Participants were treated with peginterferon-Α2a and ribavirin during the trial. Subjects with undetectable HCV RNA at week 72 were considered to have had an SVR. Subjects with detectable HCV RNA at week 20 were considered nonresponders. We used TaqMan assays to genotype 56 polymorphisms found in 13 genes in the interferon-alpha pathway. This analysis compares genotypes for participants with an SVR to nonresponders. The primary analysis was restricted to European American participants because a priori statistical power was low among the small number (n = 131) of African American patients. We used logistic regression to control the effect of other variables that are associated with treatment response. Among 581 European American patients, SVR was associated with IFNAR1 IVS1-22G (adjusted odds ratio, 0.57; P = 0.02); IFNAR2 Ex2-33C (adjusted odds ratio, 2.09; P = 0.02); JAK1 IVS22+112T (adjusted odds ratio, 1.66; P = 0.04); and ADAR Ex9+14A (adjusted odds ratio, 1.67; P = 0.03). For the TYK2 -2256A promoter region variant, a borderline association was present among European American participants (OR, 1.51; P = 0.05) and a strong relationship among African American patients; all 10 with SVR who were genotyped for TYK2 -2256 carried the A variant compared with 68 of 120 (57%) nonresponders ( P = 0.006). Conclusion: Genetic polymorphisms in the interferon-Α pathway may affect responses to antiviral therapy of chronic hepatitis C. (H EPATOLOGY 2009.)Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/63061/1/22877_ftp.pd

Targeting rehabilitation to improve outcomes after total knee arthroplasty in patients at risk of poor outcomes: randomised controlled trial

Objective: To evaluate whether a progressive course of outpatient physiotherapy offers superior outcomes to a single physiotherapy review and home exercise based intervention when targeted at patients with a predicted poor outcome after total knee arthroplasty.Design: Parallel group randomised controlled trial.Setting: 13 secondary and tertiary care centres in the UK providing postoperative physiotherapy.Participants: 334 participants with knee osteoarthritis who were defined as at risk of a poor outcome after total knee arthroplasty, based on the Oxford knee score, at six weeks postoperatively. 163 were allocated to therapist led outpatient rehabilitation and 171 to a home exercise based protocol.Interventions: All participants were reviewed by a physiotherapist and commenced 18 sessions of rehabilitation over six weeks, either as therapist led outpatient rehabilitation (progressive goal oriented functional rehabilitation protocol, modified weekly in one-one contact sessions) or as physiotherapy review followed by a home exercise based regimen (without progressive input from a physiotherapist).Main outcome measures: Primary outcome was Oxford knee score at 52 weeks, with a 4 point difference between groups considered to be clinically meaningful. Secondary outcomes included additional patient reported outcome measures of pain and function at 14, 26, and 52 weeks post-surgery.Results: 334 patients were randomised. Eight were lost to follow-up. Intervention compliance was more than 85%. The between group difference in Oxford knee score at 52 weeks was 1.91 (95% confidence interval ?0.18 to 3.99) points, favouring the outpatient rehabilitation arm (P=0.07). When all time point data were analysed, the between group difference in Oxford knee score was a non-clinically meaningful 2.25 points (0.61 to 3.90, P=0.01). No between group differences were found for secondary outcomes of average pain (0.25 points, ?0.78 to 0.28, P=0.36) or worst pain (0.22 points, ?0.71 to 0.41, P=0.50) at 52 weeks or earlier time points, or of satisfaction with outcome (odds ratio 1.07, 95% confidence interval 0.71 to 1.62, P=0.75) or post-intervention function (4.64 seconds, 95% confidence interval ?14.25 to 4.96, P=0.34).Conclusions: Outpatient therapist led rehabilitation was not superior to a single physiotherapist review and home exercise based regimen in patients at risk of poor outcomes after total knee arthroplasty. No clinically relevant differences were observed across primary or secondary outcome measures.Trials registration: Current Controlled Trials ISRCTN23357609 and ClinicalTrials.gov NCT01849445

Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain

A key aspect of nearly all single-cell sequencing experiments is dissociation of intact tissues into single-cell suspensions. While many protocols have been optimized for optimal cell yield, they have often overlooked the effects that dissociation can have on ex vivo gene expression. Here, we demonstrate that use of enzymatic dissociation on brain tissue induces an aberrant ex vivo gene expression signature, most prominently in microglia, which is prevalent in published literature and can substantially confound downstream analyses. To address this issue, we present a rigorously validated protocol that preserves both in vivo transcriptional profiles and cell-type diversity and yield across tissue types and species. We also identify a similar signature in postmortem human brain single-nucleus RNA-sequencing datasets, and show that this signature is induced in freshly isolated human tissue by exposure to elevated temperatures ex vivo. Together, our results provide a methodological solution for preventing artifactual gene expression changes during fresh tissue digestion and a reference for future deeper analysis of the potential confounding states present in postmortem human samples

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected