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Commonsense Metaphysics and Lexical Semantics

In the TACITUS project for using commonsense knowledge in the understanding of texts about mechanical devices and their failures, we have been developing various commonsense theories that are needed to mediate between the way we talk about the behavior of such devices and causal models of their operation. Of central importance in this effort is the axiomatization of what might be called commonsense metaphysics. This includes a number of areas that figure in virtually every domain of discourse, such as granularity, scales, time, space, material, physical objects, shape, causality, functionality, and force. Our effort has been to construct core theories of each of these areas, and then to define, or at least characterize, a large number of lexical items in terms provided by the core theories. In this paper we discuss our methodological principles and describe the key ideas in the various domains we are investigating

Prevalence and outcomes of chronic liver disease in patients receiving dialysis: systematic review and meta-analysis

© 2021 The Author(s) . Published by Oxford University Press on behalf of the ERA. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License, https://creativecommons.org/licenses/by-nc/4.0/Background Patients receiving dialysis for end-stage kidney disease (ESKD) commonly co-exhibit risk factors for hepatic impairment. This systematic review and meta-analysis aimed to quantify the co-existence of chronic liver disease (CLD) and characterise risk factors and outcomes. Methods We searched the following databases from inception to May 2021: CINAHL, Cochrane Library, EMBASE, Kings Fund Library, MEDLINE and PubMed. The protocol was pre-registered on PROSPERO (study ID: CRD42020206486). Studies were assessed against three inclusion criteria: (1) adults (>18 years) with ESKD receiving dialysis (2) primary outcome involving CLD prevalence (3) publications in English. Moderator analysis was performed for age, gender, study size, and publication year. Sensitivity analysis was performed where applicable by removing outlier results and studies at high risk of bias. Results Searches yielded 7,195 articles, 15 met the inclusion criteria. 320,777 patients were included. Prevalence of cirrhosis and non-alcoholic fatty liver disease (NAFLD) was 5% and 55%, respectively. Individuals with CLD had two-fold higher mortality than those without (OR 2.19; 95% confidence interval 1.39-3.45). Hepatitis B (OR 13.47;1.37-132.55) and hepatitis C (OR 7.05; 4.00-12.45), but not diabetes, conferred increased cirrhosis risk. All studies examining NAFLD were judged to be at high risk of bias. We found no data on non-alcoholic steatohepatitis (NASH). Deaths from CLD, cancer and infection were greater amongst cirrhotic patients. Conclusions CLD is prevalent in dialysis patients. Hepatitis B and C confer increased risk of CLD. The impact of NAFLD and NASH cirrhosis requires further study. CLD associates with increased mortality risk in this setting.Peer reviewe

Detecting Sorghum Plant and Head Features from Multispectral UAV Imagery

In plant breeding, unmanned aerial vehicles (UAVs) carrying multispectral cameras have demonstrated increasing utility for high-throughput phenotyping (HTP) to aid the interpretation of genotype and environment effects on morphological, biochemical, and physiological traits. A key constraint remains the reduced resolution and quality extracted from “stitched” mosaics generated from UAV missions across large areas. This can be addressed by generating high-quality reflectance data from a single nadir image per plot. In this study, a pipeline was developed to derive reflectance data from raw multispectral UAV images that preserve the original high spatial and spectral resolutions and to use these for phenotyping applications. Sequential steps involved (i) imagery calibration, (ii) spectral band alignment, (iii) backward calculation, (iv) plot segmentation, and (v) application. Each step was designed and optimised to estimate the number of plants and count sorghum heads within each breeding plot. Using a derived nadir image of each plot, the coefficients of determination were 0.90 and 0.86 for estimates of the number of sorghum plants and heads, respectively. Furthermore, the reflectance information acquired from the different spectral bands showed appreciably high discriminative ability for sorghum head colours (i.e., red and white). Deployment of this pipeline allowed accurate segmentation of crop organs at the canopy level across many diverse field plots with minimal training needed from machine learning approaches

Age-based disparities in end-of-life decisions in Belgium: a population-based death certificate survey

<p>Abstract</p> <p>Background</p> <p>A growing body of scientific research is suggesting that end-of-life care and decision making may differ between age groups and that elderly patients may be the most vulnerable to exclusion of due care at the end of life. This study investigates age-related disparities in the rate of end-of-life decisions with a possible or certain life shortening effect (ELDs) and in the preceding decision making process in Flanders, Belgium in 2007, where euthanasia was legalised in 2002. Comparing with data from an identical survey in 1998 we also study the plausibility of the ‘slippery slope’ hypothesis which predicts a rise in the rate of administration of life ending drugs without patient request, especially among elderly patients, in countries where euthanasia is legal.</p> <p>Method</p> <p>We performed a post-mortem survey among physicians certifying a large representative sample (n = 6927) of death certificates in 2007, identical to a 1998 survey. Response rate was 58.4%.</p> <p>Results</p> <p>While the rates of non-treatment decisions (NTD) and administration of life ending drugs without explicit request (LAWER) did not differ between age groups, the use of intensified alleviation of pain and symptoms (APS) and euthanasia/assisted suicide (EAS), as well as the proportion of euthanasia requests granted, was bivariately and negatively associated with patient age. Multivariate analysis showed no significant effects of age on ELD rates. Older patients were less often included in decision making for APS and more often deemed lacking in capacity than were younger patients. Comparison with 1998 showed a decrease in the rate of LAWER in all age groups except in the 80+ age group where the rate was stagnant.</p> <p>Conclusion</p> <p>Age is not a determining factor in the rate of end-of-life decisions, but is in decision making as patient inclusion rates decrease with old age. Our results suggest there is a need to focus advance care planning initiatives on elderly patients. The slippery slope hypothesis cannot be confirmed either in general or among older people, as since the euthanasia law fewer LAWER cases were found.</p

Lower export production during glacial periods in the equatorial Pacific derived from (231Pa/230Th)xs,0 measurements in deep-sea sediments

Author Posting. © American Geophysical Union, 2004. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Paleoceanography 19 (2004): PA4023, doi:10.1029/2003PA000994.The (231Pa/230Th)xs,0 records obtained from two cores from the western (MD97-2138; 1°25′S, 146°24′E, 1900 m) and eastern (Ocean Drilling Program Leg 138 Site 849, 0°11.59′N, 110°31.18′W, 3851 m) equatorial Pacific display similar variability over the last 85,000 years, i.e., from isotopic stages 1 to 5a, with systematically higher values during the Holocene, isotopic stage 3, and isotopic stage 5a, and lower values, approaching the production rate ratio of the two isotopes (0.093), during the colder periods corresponding to isotopic stages 2 and 4. We have also measured the 230Th-normalized biogenic preserved and terrigenous fluxes, as well as major and trace elements concentrations, in both cores. The (231Pa/230Th)xs,0 results combined with the changes in preserved carbonate and opal fluxes at the eastern site indicate lower productivity in the eastern equatorial Pacific during glacial periods. The (231Pa/230Th)xs,0 variations in the western equatorial Pacific also seem to be controlled by productivity (carbonate and/or opal). The generally high (231Pa/230Th)xs,0 ratios (>0.093) of the profile could be due to opal and/or MnO2 in the sinking particles. The profiles of (231Pa/230Th)xs,0 and 230Th-normalized fluxes indicate a decrease in exported carbonate, and possibly opal, during isotopic stages 2 and 4 in MD97-2138. Using 230Th-normalized flux, we also show that sediments from the two cores were strongly affected by sediment redistribution by bottom currents suggesting a control of mass accumulation rates by sediment focusing variability.SP funding for this research was provided by grants from the French Minister of Research and a EURODOC grant of the Re´gion Rhoˆne-Alpes (SAFIR-980065327). SP also gratefully acknowledges the financial support of the WHOI Geology and Geophysics Dept. This work was also supported by a CNRS-NSF grant (SP and KWWS). The contribution of JFM to this study was supported in part by the US NSF and by WHOI OCCI and Mellon awards

Pathways between Primary Production and Fisheries Yields of Large Marine Ecosystems

The shift in marine resource management from a compartmentalized approach of dealing with resources on a species basis to an approach based on management of spatially defined ecosystems requires an accurate accounting of energy flow. The flow of energy from primary production through the food web will ultimately limit upper trophic-level fishery yields. In this work, we examine the relationship between yield and several metrics including net primary production, chlorophyll concentration, particle-export ratio, and the ratio of secondary to primary production. We also evaluate the relationship between yield and two additional rate measures that describe the export of energy from the pelagic food web, particle export flux and mesozooplankton productivity. We found primary production is a poor predictor of global fishery yields for a sample of 52 large marine ecosystems. However, chlorophyll concentration, particle-export ratio, and the ratio of secondary to primary production were positively associated with yields. The latter two measures provide greater mechanistic insight into factors controlling fishery production than chlorophyll concentration alone. Particle export flux and mesozooplankton productivity were also significantly related to yield on a global basis. Collectively, our analyses suggest that factors related to the export of energy from pelagic food webs are critical to defining patterns of fishery yields. Such trophic patterns are associated with temperature and latitude and hence greater yields are associated with colder, high latitude ecosystems

The astrobiology primer: An outline of general knowledge - Version 1, 2006

Peer reviewe

Arginine Metabolism by Macrophages Promotes Cardiac and Muscle Fibrosis in mdx Muscular Dystrophy

Duchenne muscular dystrophy (DMD) is the most common, lethal disease of childhood. One of 3500 new-born males suffers from this universally-lethal disease. Other than the use of corticosteroids, little is available to affect the relentless progress of the disease, leading many families to use dietary supplements in hopes of reducing the progression or severity of muscle wasting. Arginine is commonly used as a dietary supplement and its use has been reported to have beneficial effects following short-term administration to mdx mice, a genetic model of DMD. However, the long-term effects of arginine supplementation are unknown. This lack of knowledge about the long-term effects of increased arginine metabolism is important because elevated arginine metabolism can increase tissue fibrosis, and increased fibrosis of skeletal muscles and the heart is an important and potentially life-threatening feature of DMD.We use both genetic and nutritional manipulations to test whether changes in arginase metabolism promote fibrosis and increase pathology in mdx mice. Our findings show that fibrotic lesions in mdx muscle are enriched with arginase-2-expressing macrophages and that muscle macrophages stimulated with cytokines that activate the M2 phenotype show elevated arginase activity and expression. We generated a line of arginase-2-null mutant mdx mice and found that the mutation reduced fibrosis in muscles of 18-month-old mdx mice, and reduced kyphosis that is attributable to muscle fibrosis. We also observed that dietary supplementation with arginine for 17-months increased mdx muscle fibrosis. In contrast, arginine-2 mutation did not reduce cardiac fibrosis or affect cardiac function assessed by echocardiography, although 17-months of dietary supplementation with arginine increased cardiac fibrosis. Long-term arginine treatments did not decrease matrix metalloproteinase-2 or -9 or increase the expression of utrophin, which have been reported as beneficial effects of short-term treatments.Our findings demonstrate that arginine metabolism by arginase promotes fibrosis of muscle in muscular dystrophy and contributes to kyphosis. Our findings also show that long-term, dietary supplementation with arginine exacerbates fibrosis of dystrophic heart and muscles. Thus, commonly-practiced dietary supplementation with arginine by DMD patients has potential risk for increasing pathology when performed for long periods, despite reports of benefits acquired with short-term supplementation