Counterfactual reasoning and knowledge of possibilities

Williamson has argued against scepticism concerning our metaphysically modal knowledge, by arguing that standard patterns of suppositional reasoning to counterfactual conclusions provide reliable sources of correct ascriptions of possibility and necessity. The paper argues that, while Williamson’s claims relating to necessity may well be right, he has not provided adequate reasons for thinking that the familiar modes of counterfactual reasoning to which he points generalise to provide a decent route to ascriptions of possibility. The paper also explores another path to ascriptions of possibility that may be extracted from Williamson’s ideas, before briefly considering the general status of counterfactual reasoning in relation to our knowledge of possibilities

Effective field theory and the quark model

We analyze the connections between the quark model (QM) and the description of hadrons in the low-momentum limit of heavy-baryon effective field theory in QCD. By using a three-flavor-index representation for the effective baryon fields, we show that the ``nonrelativistic'' constituent QM for baryon masses and moments is completely equivalent through O(m_s) to a parametrization of the relativistic field theory in a general spin--flavor basis. The flavor and spin variables can be identified with those of effective valence quarks. Conversely, the spin-flavor description clarifies the structure and dynamical interpretation of the chiral expansion in effective field theory, and provides a direct connection between the field theory and the semirelativistic models for hadrons used in successful dynamical calculations. This allows dynamical information to be incorporated directly into the chiral expansion. We find, for example, that the striking success of the additive QM for baryon magnetic moments is a consequence of the relative smallness of the non-additive spin-dependent corrections.Comment: 25 pages, revtex, no figure

The velocity of shear waves in unsaturated soil

The velocities of shear waves Vs in two soils, a loamy sand and a sandy clay loam, were measured at various matric potentials and confining pressures. We used a combination of Haines apparatus, pressure plate apparatus and a Bishop and Wesley tri-axial cell to obtain a range of saturation and consolidation states. We proposed a single effective stress variable based on a modification to Bishop’s equation which could be used in a published empirical model (Santamarina et al., 2001) to relate shear wave velocity to soil physical conditions. Net stress required a nonlinear transformation. Matric potential was converted into suction stress with the function proposed by Khallili and Khabbaz (1998), thus requiring an estimate of the air entry potential. We found it was possible to fit Vs to void ratio, net stress and matric potential with a set of four parameters which were common to all soils at various states of saturation and consolidation. In addition to the data collected for this study we also used previously published data (Whalley et al., 2011). The utility of shear wave measurements to deduce soil physical properties is discussed

The effect of radiation therapy on post-prostatectomy urinary function

AimWe sought to evaluate the effect of radiation therapy on post-prostatectomy urinary quality of life in prostate cancer patients.BackgroundIn some men with non-metastatic prostate cancer, radiation therapy is indicated following prostatectomy. The radiation toxicity and quality of life considerations are unique in the post-prostatectomy setting.Materials and methodsA total of 106 patients receiving post-prostatectomy radiation therapy completed the Expanded Prostate Cancer Index Composite questionnaire before radiation and at 2-year follow-up. The primary outcomes of this study were the urinary domain summary score and subscale scores. Planned analysis was performed based on time interval from prostatectomy to radiation therapy.ResultsAmong the 106 patients analyzed, the mean urinary domain summary score worsened at 2-year follow-up after radiation therapy, lowering from 77.23–72.51 (p = 0.0085). Similar worsening was observed in the subscales of function (p = 0.003), bother (p = 0.0397), and incontinence (p = 0.0003). Urinary incontinence showed the greatest observable change among subscales. While the summary score worsened (p = 0.0031) among patients receiving radiation therapy more than 1 year after prostatectomy, it did not show statistically significant change in those treated 1 year or less after prostatectomy.ConclusionOur results demonstrate that post-prostatectomy radiation therapy is associated with modest declines in reportable urinary quality of life. Patients receiving radiation therapy more than 1 year after prostatectomy showed greater worsening of urinary quality of life, which indicates that there may be no functional advantage to delaying radiation therapy beyond the initial postoperative period

Effect of a 6-month vegan low-carbohydrate (‘Eco-Atkins’) diet on cardiovascular risk factors and body weight in hyperlipidaemic adults: a randomised controlled trial

Objective: Low-carbohydrate diets may be useful for weight loss. Diets high in vegetable proteins and oils may reduce the risk of coronary heart disease. The main objective was to determine the longer term effect of a diet that was both low-carbohydrate and plant-based on weight loss and low-density lipoprotein cholesterol (LDL-C). Design, setting, participants A parallel design study of 39 overweight hyperlipidaemic men and postmenopausal women conducted at a Canadian university-affiliated hospital nutrition research centre from April 2005 to November 2006. Intervention Participants were advised to consume either a low-carbohydrate vegan diet or a high-carbohydrate lacto-ovo vegetarian diet for 6 months after completing 1-month metabolic (all foods provided) versions of these diets. The prescribed macronutrient intakes for the low-carbohydrate and high-carbohydrate diets were: 26% and 58% of energy from carbohydrate, 31% and 16% from protein and 43% and 25% from fat, respectively. Primary outcome Change in body weight. Results: 23 participants (50% test, 68% control) completed the 6-month ad libitum study. The approximate 4 kg weight loss on the metabolic study was increased to −6.9 kg on low-carbohydrate and −5.8 kg on high-carbohydrate 6-month ad libitum treatments (treatment difference (95% CI) −1.1 kg (−2.1 to 0.0), p=0.047). The relative LDL-C and triglyceride reductions were also greater on the low-carbohydrate treatment (treatment difference (95% CI) −0.49 mmol/L (−0.70 to −0.28), p<0.001 and −0.34 mmol/L (−0.57 to −0.11), p=0.005, respectively), as were the total cholesterol:HDL-C and apolipoprotein B:A1 ratios (−0.57 (−0.83, −0.32), p<0.001 and −0.05 (−0.09, −0.02), p=0.003, respectively). Conclusions: A self-selected low-carbohydrate vegan diet, containing increased protein and fat from gluten and soy products, nuts and vegetable oils, had lipid lowering advantages over a high-carbohydrate, low-fat weight loss diet, thus improving heart disease risk factors. Trial Registration clinicaltrials.gov (http://www.clinicaltrials.gov/), #NCT00256516

Genome landscapes and bacteriophage codon usage

Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonmous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes the patterns of codon usage in prokaryotes and simple eukaryotes. Here we analyze patterns of codon usage across 74 diverse bacteriophages that infect E. coli, P. aeruginosa and L. lactis as their primary host. We introduce the concept of a `genome landscape,' which helps reveal non-trivial, long-range patterns in codon usage across a genome. We develop a series of randomization tests that allow us to interrogate the significance of one aspect of codon usage, such a GC content, while controlling for another aspect, such as adaptation to host-preferred codons. We find that 33 phage genomes exhibit highly non-random patterns in their GC3-content, use of host-preferred codons, or both. We show that the head and tail proteins of these phages exhibit significant bias towards host-preferred codons, relative to the non-structural phage proteins. Our results support the hypothesis of translational selection on viral genes for host-preferred codons, over a broad range of bacteriophages.Comment: 9 Color Figures, 5 Tables, 53 Reference

Leptomeningeal disease in oligodendroglial tumors: a population-based study

In this population-based study, we determined the frequency and clinical characteristics of leptomeningeal disease (LMD) developing in the context of oligodendroglial tumors (oligodendrogliomas and oligoastrocytomas). LMD occurred in only 3.9% (8/204) of oligodendroglial tumors and in patients with more recurrences [mean 2.88 vs. 1.27 in LMD and non-LMD, respectively (p = 0.001)]. In contrast to LMD from systemic solid tumors, the median survival following the diagnosis of LMD in oligodendroglial tumors was surprisingly long at 22 months (95% CI 11–33 months). Treatment with oral chemotherapy seemed as effective as more aggressive treatments (e.g. repeat RT or intrathecal chemotherapy) in these patients

Evaluation of regression models in metabolic physiology: predicting fluxes from isotopic data without knowledge of the pathway

This study explores the ability of regression models, with no knowledge of the underlying physiology, to estimate physiological parameters relevant for metabolism and endocrinology. Four regression models were compared: multiple linear regression (MLR), principal component regression (PCR), partial least-squares regression (PLS) and regression using artificial neural networks (ANN). The pathway of mammalian gluconeogenesis was analyzed using [U−(13)C]glucose as tracer. A set of data was simulated by randomly selecting physiologically appropriate metabolic fluxes for the 9 steps of this pathway as independent variables. The isotope labeling patterns of key intermediates in the pathway were then calculated for each set of fluxes, yielding 29 dependent variables. Two thousand sets were created, allowing independent training and test data. Regression models were asked to predict the nine fluxes, given only the 29 isotopomers. For large training sets (>50) the artificial neural network model was superior, capturing 95% of the variability in the gluconeogenic flux, whereas the three linear models captured only 75%. This reflects the ability of neural networks to capture the inherent non-linearities of the metabolic system. The effect of error in the variables and the addition of random variables to the data set was considered. Model sensitivities were used to find the isotopomers that most influenced the predicted flux values. These studies provide the first test of multivariate regression models for the analysis of isotopomer flux data. They provide insight for metabolomics and the future of isotopic tracers in metabolic research where the underlying physiology is complex or unknown

Kepler eclipsing binary stars. VII. the catalogue of eclipsing binaries found in the entire Kepler data set

The primary Kepler Mission provided nearly continuous monitoring of ~200,000 objects with unprecedented photometric precision. We present the final catalog of eclipsing binary systems within the 105 deg2 Kepler field of view. This release incorporates the full extent of the data from the primary mission (Q0-Q17 Data Release). As a result, new systems have been added, additional false positives have been removed, ephemerides and principal parameters have been recomputed, classifications have been revised to rely on analytical models, and eclipse timing variations have been computed for each system. We identify several classes of systems including those that exhibit tertiary eclipse events, systems that show clear evidence of additional bodies, heartbeat systems, systems with changing eclipse depths, and systems exhibiting only one eclipse event over the duration of the mission. We have updated the period and galactic latitude distribution diagrams and included a catalog completeness evaluation. The total number of identified eclipsing and ellipsoidal binary systems in the Kepler field of view has increased to 2878, 1.3% of all observed Kepler targets