Learning to distinguish hypernyms and co-hyponyms

This work is concerned with distinguishing different semantic relations which exist between distributionally similar words. We compare a novel approach based on training a linear Support Vector Machine on pairs of feature vectors with state-of-the-art methods based on distributional similarity. We show that the new supervised approach does better even when there is minimal information about the target words in the training data, giving a 15% reduction in error rate over unsupervised approaches

Preservation Appraisal and Selection How We Determine What Actually Needs to be Preserved

presentationPresentation given at the ALCTS Digital Preservation Interest Group meeting at the American Library Association Annual Conference, Chicago, IL

PREMIS of our not so SIMP-le story: Implementing preservation metadata using homegrown and vendor solutions

presentationPresentation given at the ALCTS Preservation Metadata Interest Group, American Library Association Annual Conference, Orlando, FL

The distribution of Dishevelled in convergently extending mesoderm

Convergent extension (CE) is a conserved morphogenetic movement that drives axial lengthening of the primary body axis and depends on the planar cell polarity (PCP) pathway. In Drosophila epithelia, a polarised subcellular accumulation of PCP core components, such as Dishevelled (Dvl) protein, is associated with PCP function. Dvl has long been thought to accumulate in the mediolateral protrusions in Xenopus chordamesoderm cells undergoing CE. Here we present a quantitative analysis of Dvl intracellular localisation in Xenopus chordamesoderm cells. We find that, surprisingly, accumulations previously observed at mediolateral protrusions of chordamesodermal cells are not protrusion-specific but reflect yolk-free cytoplasm and are quantitatively matched by the distribution of the cytoplasm-filling lineage marker dextran. However, separating cell cortex-associated from bulk Dvl signal reveals a statistical enrichment of Dvl in notochord–somite boundary-(NSB)-directed protrusions, which is dependent upon NSB proximity. Dvl puncta were also observed, but only upon elevated overexpression. These puncta showed no statistically significant spatial bias, in contrast to the strongly posteriorly-enriched GFP-Dvl puncta previously reported in zebrafish. We propose that Dvl distribution is more subtle and dynamic than previously appreciated and that in vertebrate mesoderm it reflects processes other than protrusion as such

Long-term monitoring reveals forest tree community change driven by atmospheric sulphate pollution and contemporary climate change

Diversity and Distributions published by John Wiley & Sons Ltd Aim: Montane environments are sentinels of global change, providing unique opportunities to assess impacts on species diversity. Multiple anthropogenic stressors such as climate change and atmospheric pollution may act concurrently or synergistically in restructuring communities. Thus, a major challenge for conservation is untangling the relative importance of different stressors. Here, we combine long-term monitoring with multivariate community modelling to estimate the anthropogenic drivers shaping forest tree diversity along an elevational gradient. Location: Camels Hump Mountain, Vermont, USA. Methods: We used Generalized Dissimilarity Modelling (GDM) to model spatial and temporal turnover in beta diversity along an elevational gradient over a 50-year period and tested for spatiotemporal shifts in density and elevational distribution of individual species. GDMs were used to predict community turnover as nonlinear functions of changes in elevation, climate and atmospheric pollution. Results: We observed significant shifts in elevational range and density of individual species, which contributed to an overall reduction in the elevational gradient in beta diversity through time. GDMs showed the combined effects of sulphate deposition and temperature as drivers of this temporal reduction in beta diversity. Spatiotemporal changes differed among species, with shifts observed both up- and downslope. For example, in a reversal of a previous upslope range contraction, red spruce (Picea rubens Sarg.) increased in density and shifted downslope since the 1990s, occupying warmer, drier climates. Main conclusion: Our results demonstrate that global change is impacting the stratification of forest tree diversity along elevational gradients, but the responses of individual species are complex and variable in direction. We suggest abiotic drivers may directly impact individual species while also indirectly altering species interactions along elevational gradients. Our approach modelling the drivers of compositional turnover quantifies the rate and amount of change in beta diversity along environmental gradients and serves as a powerful complement to studying species-specific responses

Evaluation of a web-based asthma self-management system: a randomised controlled pilot trial

Background Asthma is the most common chronic condition of childhood and disproportionately affects inner-city minority children. Low rates of asthma preventer medication adherence is a major contributor to poor asthma control in these patients. Web-based methods have potential to improve patient knowledge and medication adherence by providing interactive patient education, monitoring of symptoms and medication use, and by facilitation of communication and teamwork among patients and health care providers. Few studies have evaluated web-based asthma support environments using all of these potentially beneficial interventions. The multidimensional website created for this study, BostonBreathes, was designed to intervene on multiple levels, and was evaluated in a pilot trial. Methods An interactive, engaging website for children with asthma was developed to promote adherence to asthma medications, provide a platform for teamwork between caregivers and patients, and to provide primary care providers with up-to-date symptom information and data on medication use. Fifty-eight (58) children primarily from inner city Boston with persistent-level asthma were randomised to either usual care or use of BostonBreathes. Subjects completed asthma education activities, and reported their symptoms and medication use. Primary care providers used a separate interface to monitor their patients’ website use, their reported symptoms and medication use, and were able to communicate online via a discussion board with their patients and with an asthma specialist. Results After 6-months, reported wheezing improved significantly in both intervention and control groups, and there were significant improvements in the intervention group only in night-time awakening and parental loss of sleep, but there were no significant differences between intervention and control groups in these measures. Emergency room or acute visits to a physician for asthma did not significantly change in either group. Among the subgroup of subjects with low controller medication adherence at baseline, adherence improved significantly only in the intervention group. Knowledge of the purpose of controller medicine increased significantly in the intervention group, a statistically significant improvement over the control group. Conclusions This pilot study suggests that a multidimensional web-based educational, monitoring, and communication platform may have positive influences on pediatric patients’ asthma-related knowledge and use of asthma preventer medications

miRSwitch: detecting microRNA arm shift and switch events

Arm selection, the preferential expression of a 3′ or 5′ mature microRNA (miRNA), is a highly dynamic and tissue-specific process. Time-dependent expression shifts or switches between the arms are also relevant for human diseases. We present miRSwitch, a web server to facilitate the analysis and interpretation of arm selection events. Our species-independent tool evaluates pre-processed small non-coding RNA sequencing (sncRNA-seq) data, i.e. expression matrices or output files from miRNA quantification tools (miRDeep2, miRMaster, sRNAbench). miRSwitch highlights potential changes in the distribution of mature miRNAs from the same precursor. Group comparisons from one or several user-provided annotations (e.g. disease states) are possible. Results can be dynamically adjusted by choosing from a continuous range of highly specific to very sensitive parameters. Users can compare potential arm shifts in the provided data to a human reference map of pre-computed arm shift frequencies. We created this map from 46 tissues and 30 521 samples. As case studies we present novel arm shift information in a Alzheimer’s disease biomarker data set and from a comparison of tissues in Homo sapiens and Mus musculus. In summary, miRSwitch offers a broad range of customized arm switch analyses along with comprehensive visualizations, and is freely available at: https://www.ccb.uni-saarland.de/mirswitch/

Genomic Mining for Aspergillus Natural Products

SummaryThe genus Aspergillus is renowned for its ability to produce a myriad of bioactive secondary metabolites. Although the propensity of biosynthetic genes to form contiguous clusters greatly facilitates assignment of putative secondary metabolite genes in the completed Aspergillus genomes, such analysis cannot predict gene expression and, ultimately, product formation. To circumvent this deficiency, we have examined Aspergillus nidulans microarrays for expressed secondary metabolite gene clusters by using the transcriptional regulator LaeA. Deletion or overexpression of laeA clearly identified numerous secondary metabolite clusters. A gene deletion in one of the clusters eliminated the production of the antitumor compound terrequinone A, a metabolite not described, from A. nidulans. In this paper, we highlight that LaeA-based genome mining helps decipher the secondary metabolome of Aspergilli and provides an unparalleled view to assess secondary metabolism gene regulation

The Lantern Vol. 18, No. 2, Winter 1950

• To Pledge Allegiance • The Back Porch • Love Story • Symphony Finale • Bruised Hands • Defeat • Concerning Utility • Triplet • I Echo the Common Sentiment • Heads in Pen and Inkhttps://digitalcommons.ursinus.edu/lantern/1050/thumbnail.jp