Using compression to identify acronyms in text

Text mining is about looking for patterns in natural language text, and may be defined as the process of analyzing text to extract information from it for particular purposes. In previous work, we claimed that compression is a key technology for text mining, and backed this up with a study that showed how particular kinds of lexical tokens---names, dates, locations, etc.---can be identified and located in running text, using compression models to provide the leverage necessary to distinguish different token types (Witten et al., 1999)Comment: 10 pages. A short form published in DCC200

Studies of the surface and bulk reactivity of calcium hydroxide

This thesis was submitted for the degree of Doctor of Philosophy and was awarded by Brunel University.The physical characteristics and reactivity of a number of commercially available samples of calcium oxide and hydroxide were investigated. 'Fresh' and 'aged' (Le. exposed to the atmosphere) samples were characterised by Fourier Transform Infra-Red Spectroscopy, Thermo-Gravimetric Analysis, Nitrogen Adsorption, Water Adsorption, Scanning Electron Microscopy and Microprobe Analysis. From this slight differences in the 'fresh' samples were found to be due to various degrees of atmospheric ageing. The main process involved in the ageing process was confirmed to be carbonatation (or carbonation). This ageing process was then followed by analysing a sample of calcium hydroxide over a long time period (350 days) and by looking at variations in the process by exposure of the sample to various gases and vapours, i.e. water, dried carbon dioxide, deuterium oxide, ethanol and methanol. These experiments showed that the reaction probably proceeded by a direct reaction between the carbon dioxide gas and the solid and confirmed that water was important when considering the rate of the carbonatation reaction. This was thought to be due to its influence in disrupting the calcium hydroxide structure, thus allowing new surface to become available for reaction and allowing the formation of a bulk calcium carbonate structure. Water adsorption isotherms carried out on the calcium hydroxide at elevated temperatures (250°C and above) showed that outgassing at such temperatures caused a partial decomposition to calcium oxide but that the original calcium hydroxide structure remained intact. These isotherms also had negative hysteresis which was thought to be due to the take up of water in an expanded skeletal calcium hydroxide structure which was expelled from the structure when it fully reconstituted at higher relative pressures to reform calcium hydroxide.Exxon Chemical Lt

Can whole-drawer images measure up? A reply to Johnson et al. (2013)?

Johnson et al. (2013) found that morphometric measurements of dragonfly wings taken from actual specimens and measurements taken from whole-drawer images of those specimens were equally accurate. We do not believe that their conclusions are justified by their data and analysis. Our reasons are, first, that their study was constrained in ways that restrict the generalisability of their results, but second, and of far greater significance, their statistical approach was entirely unsuited to their data and their results misled them to erroneous conclusions. We offer an alternative analysis of their data as published. Our reanalysis demonstrates, contra Johnson et al., that measurements from scanned images are not a reliable substitute for direct measurement

Drivers of inter-year variability of plant production and decomposers across contrasting island ecosystems

Despite the likely importance of inter-year dynamics of plant production and consumer biota for driving community- and ecosystem-level processes, very few studies have explored how and why these dynamics vary across contrasting ecosystems. We utilized a well characterized system of 30 lake islands in the boreal forest zone of northern Sweden across which soil fertility and productivity vary considerably, with larger islands being more fertile and productive than smaller ones. In this system we assessed the inter-year dynamics of several measures of plant production and the soil microbial community (primary consumers in the decomposer food web) for each of 9 years, and soil microfaunal groups (secondary and tertiary consumers) for each of 6 of those years. We found that for measures of plant production and each of the three consumer trophic levels, inter-year dynamics were strongly affected by island size. Further, many variables were strongly affected by island size (and thus bottom-up regulation by soil fertility and resources) for some years but none in others, most likely due to inter-year variation in climatic conditions. For each of the plant and microbial variables for which we had 9 years of data, we also determined the inter-year coefficient of variation (CV), an inverse measure of stability. We found that CVs of some measures of plant productivity were greater on large islands while those of other measures were greater on smaller islands; CVs of microbial variables were unresponsive to island7 size. We also found that the effects of island size on the temporal dynamics of some variables were related to inter-year variability of macroclimatic variables. As such, our results show that the inter year dynamics of both plant productivity and decomposer biota across each of three trophic levels, as well as the inter-year stability of plant productivity, differs greatly across contrasting ecosystems, with potentially important but largely overlooked implications for community and ecosystem processes

The cladistics and classification of the Bombyliidae (Diptera: Asiloidea). Bulletin of the AMNH ; no. 219

191 p. : ill. (some col.) ; 26 cm.Includes bibliographical references (p. 165-172)."Previous classifications and phylogenetic trees of the Asiloidea and the Bombyliidae are reviewed. Data from male genital musculature presented by Ovchinnikova (1989) and female genitalia by Muhlenberg (1971b) are reanalyzed within a numerical cladistic framework. A cladogram of the Bombyliidae and their relatives is constructed based on a data matrix containing 87 taxa and 154 characters. This study includes 24 non-Bombyliidae taxa used as outgroups, from the families Rhagionidae, Nemestrinidae, Acroceridae, Asilidae, Therevidae, Apioceridae, Mydidae, Scenopinidae, Hilarimorphidae, and Apsilocephalidae. I chose 63 ingroup species representing all the currently accepted subfamilies and tribes except the Xenoprosopinae and Villoestrini. 147 of the characters used were derived from adult morphology and 7 were from larval morphology. The data set was analyzed using the parsimony program Hennig86 which identified 8 most parsimonious trees, each with a length of 716 steps, consistency index of 0.25, and retention index of 0.71. All characters are described and almost all are illustrated using line drawings, photographs, and scanning electron micrographs. Previously used characters are reanalyzed and new character systems are introduced, especially features of the postcranium and cibarium. The Acroceridae and Nemestrinidae do not form a monophyletic group and each should be recognized at superfamily level. The Asiloidea is also weakly monophyletic, based largely on larval features. The Apioceridae is found not to be monophyletic, some included genera being more closely related to the Mydidae. The Hilarimorphidae, including the proratine Apystomyia Melander, form the sister-group to the Bombyliidae. The remaining Proratinae form a clade with the Scenopinidae, confirming recent work on the subfamily. Bombyliidae, as here defined to exclude genera traditionally placed in the Proratinae, is found to be monophyletic, however the evidence for its monophyly is weak. The subfamily Heterotropinae was found to be nested within the Bombyliidae, thus the free-living, predatory habits of Heterotropus Loew larvae are interpreted as reversals from a parasitoid lifestyle rather than a primary plesiomorphic condition. In a reclassification of the Bombyliidae, 15 subfamilies are recognized: the Mythicomyiinae, Oligodraninae, Usiinae, Toxophorinae, Lordotinae new subfamily, Heterotropinae, Bombyliinae, Crocidiinae new statues, Mariobezziinae, Oniromyiinae, Cythereinae, Lomatiinae, Anthracinae, Tomomyzinae, and Antoniinae. The position of Sericosoma Macquart requires further research; it exhibits closest affinity with the Mariobezziinae. The proposed classification is conservative and reflects much of the structure of previous classifications. Chief differences include the recognition of the Gerontini and Systropodini as tribes of the Toxophorinae rather than separate subfamilies and the synonomy of the Cylleniinae within the Cythereinae. Crocidiinae is recognized as a subfamily, rather than a tribe of the Bombyliinae. Lordotinae is the only new family-level taxon proposed, characterized by the highly modified, telescoping female genitalia which are adapted for inserting the eggs into the substrate. Tribal divisions within the Bombyliinae, Lomatiinae, and Anthracinae are discussed. A key to the subfamilies of Bombyliidae is presented, and all subfamilies are diagnosed, synapomorphies listed, and their taxonomic scope, distribution, and biogeography briefly discussed. The fossil history of the Bombyliidae is discussed in relation to the cladogram. Bombyliidae probably originated in the Jurassic and had undergone much diversification at subfamily level by the end of the Cretaceous. The evolution of the bombyliid postcranium and female sand chamber is discussed in light of the cladogram. The evolution of the acanthophorites within the Bombyliidae is discussed in relation to the occurrence of this feature in other families of Asiloidea"--P. 5

Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression

<p>Abstract</p> <p>Background</p> <p>Many of the functional units in cells are multi-protein complexes such as RNA polymerase, the ribosome, and the proteasome. For such units to work together, one might expect a high level of regulation to enable co-appearance or repression of sets of complexes at the required time. However, this type of coordinated regulation between whole complexes is difficult to detect by existing methods for analyzing mRNA co-expression. We propose a new methodology that is able to detect such higher order relationships.</p> <p>Results</p> <p>We detect coordinated regulation of multiple protein complexes using <it>logic analysis </it>of gene expression data. Specifically, we identify gene triplets composed of genes whose expression profiles are found to be related by various types of logic functions. In order to focus on complexes, we associate the members of a gene triplet with the distinct protein complexes to which they belong. In this way, we identify complexes related by specific kinds of regulatory relationships. For example, we may find that the transcription of complex C is increased only if the transcription of both complex A AND complex B is repressed. We identify hundreds of examples of coordinated regulation among complexes under various stress conditions. Many of these examples involve the ribosome. Some of our examples have been previously identified in the literature, while others are novel. One notable example is the relationship between the transcription of the ribosome, RNA polymerase and mannosyltransferase II, which is involved in N-linked glycan processing in the Golgi.</p> <p>Conclusions</p> <p>The analysis proposed here focuses on relationships among triplets of genes that are not evident when genes are examined in a pairwise fashion as in typical clustering methods. By grouping gene triplets, we are able to decipher coordinated regulation among sets of three complexes. Moreover, using all triplets that involve coordinated regulation with the ribosome, we derive a large network involving this essential cellular complex. In this network we find that all multi-protein complexes that belong to the same functional class are regulated in the same direction as a group (either induced or repressed).</p

Risk of venous thromboembolism in people admitted to hospital with selected immune-mediated diseases: record-linkage study

BACKGROUND: Venous thromboembolism (VTE) is a common complication during and after a hospital admission. Although it is mainly considered a complication of surgery, it often occurs in people who have not undergone surgery, with recent evidence suggesting that immune-mediated diseases may play a role in VTE risk. We, therefore, decided to study the risk of deep vein thrombosis (DVT) and pulmonary embolism (PE) in people admitted to hospital with a range of immune-mediated diseases. METHODS: We analysed databases of linked statistical records of hospital admissions and death certificates for the Oxford Record Linkage Study area (ORLS1:1968 to 1998 and ORLS2:1999 to 2008) and the whole of England (1999 to 2008). Rate ratios for VTE were determined, comparing immune-mediated disease cohorts with comparison cohorts. RESULTS: Significantly elevated risks of VTE were found, in all three populations studied, in people with a hospital record of admission for autoimmune haemolytic anaemia, chronic active hepatitis, dermatomyositis/polymyositis, type 1 diabetes mellitus, multiple sclerosis, myasthenia gravis, myxoedema, pemphigus/pemphigoid, polyarteritis nodosa, psoriasis, rheumatoid arthritis, Sjogren's syndrome, and systemic lupus erythematosus. Rate ratios were considerably higher for some of these diseases than others: for example, for systemic lupus erythematosus the rate ratios were 3.61 (2.36 to 5.31) in the ORLS1 population, 4.60 (3.19 to 6.43) in ORLS2 and 3.71 (3.43 to 4.02) in the England dataset. CONCLUSIONS: People admitted to hospital with immune-mediated diseases may be at an increased risk of subsequent VTE. Our findings need independent confirmation or refutation; but, if confirmed, there may be a role for thromboprophylaxis in some patients with these diseases

A practice-related risk score (PRS): a DOPPS-derived aggregate quality index for haemodialysis facilities

Background. The Dialysis Outcomes and Practice Patterns Study (DOPPS) database was used to develop and validate a practice-related risk score (PRS) based on modifiable practices to help facilities assess potential areas for improving patient care. Methods. Relative risks (RRs) from a multivariable Cox mortality model, based on observational haemodialysis (HD) patient data from DOPPS I (1996-2001, seven countries), were used. The four practices were the percent of patients with Kt/V >= 1.2, haemoglobin >= 11 g/dl (110 g/l), albumin >= 4.0 g/dl (40g/l) and catheter use, and were significantly related to mortality when modelled together. DOPPS II data (2002-2004, 12 countries) were used to evaluate the relationship between PRS and mortality risk using Cox regression. Results. For facilities in DOPPS I and II, changes in PRS over time were significantly correlated with changes in the standardized mortality ratio (SMR). The PRS ranged from 1.0 to 2.1. Overall, the adjusted RR of death was 1.05 per 0.1 points higher PRS (P < 0.0001). For facilities in both DOPPS I and II (N = 119), a 0.2 decrease in PRS was associated with a 0.19 decrease in SMR (P = 0.005). On average, facilities that improved PRS practices showed significantly reduced mortality over the same time frame. Conclusions. The PRS assesses modifiable HD practices that are linked to improved patient survival. Further refinements might lead to improvements in the PRS and will address regional variations in the PRS/mortality relationship

Two new genera of Apsilocephalidae from mid-Cretaceous Burmese amber

Apsilocephalidae is an enigmatic dipteran family erected by Nagatomi et al. (1991), including three extant genera and three additional extinct genera from the Eocene Baltic amber, Eocene Florissant, and mid-Cretaceous Burmese amber. We describe herein two new taxa, Myanmarpsilocephala grimaldii gen. et sp. nov. and Irwinimyia spinosa gen. et sp. nov., from mid-Cretaceous Burmese amber. The female genitalia of Myanmarpsilocephala gen. nov. and male genitalia of Irwinimyia gen. nov. are described and illustrated. The distribution of all Apsilocephalidae species and a key to all genera of Apsilocephalidae is provided. The described diversity of Apsilocephalidae in Burmese amber strongly suggests that apsilocephalid flies diversified at least by the mid-Cretaceous.This research was supported by the National Natural Science Foundation of China (41572010, 41622201, 41688103), the Chinese Academy of Sciences (XDPB05), and Youth Innovation Promotion Association of CAS (No. 2011224)