Searching for Ground Truth: a stepping stone in automating genre classification

This paper examines genre classification of documents and its role in enabling the effective automated management of digital documents by digital libraries and other repositories. We have previously presented genre classification as a valuable step toward achieving automated extraction of descriptive metadata for digital material. Here, we present results from experiments using human labellers, conducted to assist in genre characterisation and the prediction of obstacles which need to be overcome by an automated system, and to contribute to the process of creating a solid testbed corpus for extending automated genre classification and testing metadata extraction tools across genres. We also describe the performance of two classifiers based on image and stylistic modeling features in labelling the data resulting from the agreement of three human labellers across fifteen genre classes.

Alpha Decay Hindrance Factors: A Probe of Mean Field Wave Functions

A simple model to calculate alpha-decay Hindrance Factors is presented. Using deformation values obtained from PES calculations as the only input, Hindrance Factors for the alpha-decay of Rn- and Po-isotopes are calculated. It is found that the intrinsic structure around the Fermi surface determined by the deformed mean field plays an important role in determining the hindrance of alpha-decay. The fair agreement between experimental and theoretical Hindrance Factors suggest that the wave function obtained from the energy minima of the PES calculations contains an important part of the correlations that play a role for the alpha-decay. The calculated HF that emerges from these calculations render a different interpretation than the commonly assumed n-particle n-hole picture.Comment: 7 pages, 9 figure

Three-dimensional visualisation of authentic cases in anatomy learning – An educational design study

Many studies have investigated the value of three-dimensional (3D) images in learning anatomy. However, there is a lack of knowledge about students learning processes using technology and 3D images. To understand how to facilitate and support the learning of anatomy, there is a need to know more about the student perspectives on how they can use and benefit from 3D images

An intelligent energy management system for educational buildings

There is a wide variation in the energy consumption between different educational institutions due to the adoption of different management strategies and different levels of occupants’ environmental understanding. The presence of large amounts of information and communication technology (ICT) equipment and heating, ventilation, and air conditioning (HVAC) system causes a major consumption of energy in higher education institution (HEI) buildings. The main objective of this research is to investigate the use of ICT to optimize the energy consumption in HEI buildings and reduce carbon dioxide (CO 2 ) emission. The first phase of the system has been implemented at King Saud University to measure energy consumption through sensors that read energy consumption of electrical appliances and devices every 10 seconds. The analysis of collected data allows us to develop and employ energy saving strategies that lead to a reduction in total energy consumption. Our preliminary results show that up to 17% of energy consumption can be reduced by simply dealing with standby energy loss of labs’ computers. The novelty of this research comes from the use of a functional database approach to deal with high volume of data and query performance and the incorporation of a timetabling system in energy management system

Virtual patients designed for training against medical error: Exploring the impact of decision-making on learner motivation.

OBJECTIVES: Medical error is a significant cause of patient harms in clinical practice, but education and training are recognised as having a key role in minimising their incidence. The use of virtual patient (VP) activities targeting training in medical error allows learners to practice patient management in a safe environment. The inclusion of branched decision-making elements in the activities has the potential to drive additional generative cognitive processing and improved learning outcomes, but the increased cognitive load on learning risks negatively affecting learner motivation. The aim of this study is to better understand the impact that the inclusion of decision-making and inducing errors within the VP activities has on learner motivation. METHODS: Using a repeated study design, over a period of six weeks we provided undergraduate medical students at six institutions in three countries with a series of six VPs written around errors in paediatric practice. Participants were divided into two groups and received either linearly structured VPs or ones that incorporated branched decision-making elements. Having completed all the VPs, each participant was asked to complete a survey designed to assess their motivation and learning strategies. RESULTS: Our analysis showed that in general, there was no significant difference in learner motivation between those receiving the linear VPs and those who received branched decision-making VPs. The same results were generally reflected across all six institutions. CONCLUSIONS: The findings demonstrated that the inclusion of decision-making elements did not make a significant difference to undergraduate medical students' motivation, perceived self-efficacy or adopted learning strategies. The length of the intervention was sufficient for learners to overcome any increased cognitive load associated with branched decision-making elements being included in VPs. Further work is required to establish any immediate impact within periods shorter than the length of our study or upon achieved learning outcomes

False friends in the Fanfanyu

In the present article, a remarkable phenomenon is brought to the attention of those interested in early Chinese translations of Buddhist texts: false friends in the Fanfanyu (T54n2130). Baochang's Sanskrit-Chinese lexicon that was compiled as early as 517 AD reveals some curious examples of faux amis. In the present contribution, this case will be illustrated with references from the Shanjian lü piposha (T24n1462), a fifth century Chinese translation of the Samantapāsādikā, Buddhaghosa's commentary on the Pāli Vinaya. The fact that Baochang did not realise that this text was not translated from Sanskrit, inadvertently gave rise to some interesting jeux de mots

Scalable In Situ Hybridization on Tissue Arrays for Validation of Novel Cancer and Tissue-Specific Biomarkers

Tissue localization of gene expression is increasingly important for accurate interpretation of large scale datasets from expression and mutational analyses. To this end, we have (1) developed a robust and scalable procedure for generation of mRNA hybridization probes, providing >95% first-pass success rate in probe generation to any human target gene and (2) adopted an automated staining procedure for analyses of formalin-fixed paraffin-embedded tissues and tissue microarrays. The in situ mRNA and protein expression patterns for genes with known as well as unknown tissue expression patterns were analyzed in normal and malignant tissues to assess procedure specificity and whether in situ hybridization can be used for validating novel antibodies. We demonstrate concordance between in situ transcript and protein expression patterns of the well-known pathology biomarkers KRT17, CHGA, MKI67, PECAM1 and VIL1, and provide independent validation for novel antibodies to the biomarkers BRD1, EZH2, JUP and SATB2. The present study provides a foundation for comprehensive in situ gene set or transcriptome analyses of human normal and tumor tissues

Classification of Inhibitors of Hepatic Organic Anion Transporting Polypeptides (OATPs): Influence of Protein Expression on Drug–Drug Interactions

ABSTRACT: The hepatic organic anion transporting poly-peptides (OATPs) influence the pharmacokinetics of several drug classes and are involved in many clinical drug−drug interactions. Predicting potential interactions with OATPs is, therefore, of value. Here, we developed in vitro and in silico models for identification and prediction of specific and general inhibitors of OATP1B1, OATP1B3, and OATP2B1. The maximal transport activity (MTA) of each OATP in human liver was predicted from transport kinetics and protein quantification. We then used MTA to predict the effects of a subset of inhibitors on atorvastatin uptake in vivo. Using a data set of 225 drug-like compounds, 91 OATP inhibitors were identified. In silico models indicated that lipophilicity and polar surface area are key molecular features of OATP inhibition. MTA predictions identified OATP1B1 and OATP1B3 as major determinants of atorvastatin uptake in vivo. The relative contributions to overall hepatic uptake varied with isoform specificities of the inhibitors

Identification and developmental expression of the full complement of Cytochrome P450 genes in Zebrafish

© The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 11 (2010): 643, doi:10.1186/1471-2164-11-643.Increasing use of zebrafish in drug discovery and mechanistic toxicology demands knowledge of cytochrome P450 (CYP) gene regulation and function. CYP enzymes catalyze oxidative transformation leading to activation or inactivation of many endogenous and exogenous chemicals, with consequences for normal physiology and disease processes. Many CYPs potentially have roles in developmental specification, and many chemicals that cause developmental abnormalities are substrates for CYPs. Here we identify and annotate the full suite of CYP genes in zebrafish, compare these to the human CYP gene complement, and determine the expression of CYP genes during normal development. Zebrafish have a total of 94 CYP genes, distributed among 18 gene families found also in mammals. There are 32 genes in CYP families 5 to 51, most of which are direct orthologs of human CYPs that are involved in endogenous functions including synthesis or inactivation of regulatory molecules. The high degree of sequence similarity suggests conservation of enzyme activities for these CYPs, confirmed in reports for some steroidogenic enzymes (e.g. CYP19, aromatase; CYP11A, P450scc; CYP17, steroid 17a-hydroxylase), and the CYP26 retinoic acid hydroxylases. Complexity is much greater in gene families 1, 2, and 3, which include CYPs prominent in metabolism of drugs and pollutants, as well as of endogenous substrates. There are orthologous relationships for some CYP1 s and some CYP3 s between zebrafish and human. In contrast, zebrafish have 47 CYP2 genes, compared to 16 in human, with only two (CYP2R1 and CYP2U1) recognized as orthologous based on sequence. Analysis of shared synteny identified CYP2 gene clusters evolutionarily related to mammalian CYP2 s, as well as unique clusters. Transcript profiling by microarray and quantitative PCR revealed that the majority of zebrafish CYP genes are expressed in embryos, with waves of expression of different sets of genes over the course of development. Transcripts of some CYP occur also in oocytes. The results provide a foundation for the use of zebrafish as a model in toxicological, pharmacological and chemical disease research.This work was supported by NIH grants R01ES015912 and P42ES007381 (Superfund Basic Research Program at Boston University) (to JJS). MEJ was a Guest Investigator at the Woods Hole Oceanographic Institution (WHOI) and was supported by grants from the Swedish research council Formas and Carl Trygger's foundation. AK was a Post-doctoral Fellow at WHOI, and was supported by a fellowship from the Japanese Society for Promotion of Science (JSPS). JZ and TP were Guest Students at the WHOI and were supported by a CAPES Ph.D. Fellowship and CNPq Ph.D. Sandwich Fellowship (JZ), and by a CNPq Ph.D. Fellowship (TP), from Brazil