Event trigger identification for biomedical events extraction using domain knowledge

Motivation: In molecular biology, molecular events describe observable alterations of biomolecules, such as binding of proteins or RNA production. These events might be responsible for drug reactions or development of certain diseases. As such, biomedical event extraction, the process of automatically detecting description of molecular interactions in research articles, attracted substantial research interest recently. Event trigger identification, detecting the words describing the event types, is a crucial and prerequisite step in the pipeline process of biomedical event extraction. Taking the event types as classes, event trigger identification can be viewed as a classification task. For each word in a sentence, a trained classifier predicts whether the word corresponds to an event type and which event type based on the context features. Therefore, a well-designed feature set with a good level of discrimination and generalization is crucial for the performance of event trigger identification. Results: In this article, we propose a novel framework for event trigger identification. In particular, we learn biomedical domain knowledge from a large text corpus built from Medline and embed it into word features using neural language modeling. The embedded features are then combined with the syntactic and semantic context features using the multiple kernel learning method. The combined feature set is used for training the event trigger classifier. Experimental results on the golden standard corpus show that >2.5% improvement on F-score is achieved by the proposed framework when compared with the state-of-the-art approach, demonstrating the effectiveness of the proposed framework. © 2014 The Author 2014. The source code for the proposed framework is freely available and can be downloaded at http://cse.seu.edu.cn/people/zhoudeyu/ETI_Sourcecode.zip.

A "Cross-technology" Software Development Approach

Contemporary web-based software solutions are usually composed of many interoperating applications. Classical approach is the different applications of the solution to be created inside one technology/platform, e.g. Java-technology, .NET-technology, etc. Wide spread technologies/platforms practically discourage (and sometime consciously make impossible) the cooperation with elements of the concurrent technologies/platforms. To make possible the usage of attractive features of one technology/platform in another technology/platform some “cross-technology” approach is necessary. In the paper is discussed the possibility to combine two existing instruments – interoperability protocols and “lifting” of procedures – in order to obtain such cross-technology approach.

Real-time intensity domain characterization of fibre lasers using spatio-temporal dynamics

Fibre lasers are light sources that are synonymous with stability. They can give rise to highly coherent continuous-wave radiation, or a stable train of mode locked pulses with well-defined characteristics. However, they can also exhibit an exceedingly diverse range of nonlinear operational regimes spanning a multi-dimensional parameter space. The complex nature of the dynamics poses significant challenges in the theoretical and experimental studies of such systems. Here, we demonstrate how the real-time experimental methodology of spatio-temporal dynamics can be used to unambiguously identify and discern between such highly complex lasing regimes. This two-dimensional representation of laser intensity allows the identification and tracking of individual features embedded in the radiation as they make round-trip circulations inside the cavity. The salient features of this methodology are highlighted by its application to the case of Raman fibre lasers and a partially mode locked ring fibre laser operating in the normal dispersion regime.

Social and cultural influences in the formation of identity: A cross-national/cultural study

This multi-site, multi-ethnic/cultural study examined the effects of variation between ethnic/cultural groups and the effects of institutional variation within ethnic/cultural groups on identity formation. The participants were 892 late adolescent college students from six sites in 5 countries (Brazil, China, Costa Rica, US, and Sweden) representing different linguistic and ethnic/cultural traditions living in the context of varied social conditions. As hypothesized, there were significant differences in the proportion of identity statuses between sites in the Personal domain, $\chi\sp2$(20, N = 858) = 164.78, $p<.001,$ the Interpersonal domain, $\chi\sp2$(20, N = 858) = 145.69, $p<.001,$ and the World View domain, $\chi\sp2$(20, N = 858) = 120.89, $p<.001,$ but the distribution of the differences was more complex than expected. In addition, there were significant differences in Identity Satisfaction among sites, F(15, 2325) = 12.65, $p<.001.$ Further univariate analyses revealed that differences among sites were found on Identity Satisfaction in the personal, interpersonal and world view domain. The direction of the differences, however, were more complex than hypothesized.^ The second hypothesis was confirmed but only with the world view identity status and not for each of the six sites. Stepwise discriminant analyses showed that Identity status in the world view domain was predicted by Institutional Support in Nebraska, gender and Institutional Change in Brazil, and Institutional Access in China. Lastly and as hypothesized, some Institutional Attributes significantly predicted Overall Identity Satisfaction in all sites as revealed by multivariate regression analyses, except in Sweden, F (5, 79) =.660, p =.65. These findings extend the literature on identity formation not only by having investigated how culture influences the process of identity formation with samples representing different ethnic/cultural and linguistically different populations but also by empirically testing the role that social processes play in identity formation at the cross-cultural level. ^

Fluorescence-enhanced optical imaging on three-dimensional phantoms using a hand-held probe based frequency-domain intensified charge coupled device (ICCD) optical imager

Fluorescence-enhanced optical imaging is an emerging non-invasive and non-ionizing modality towards breast cancer diagnosis. Various optical imaging systems are currently available, although most of them are limited by bulky instrumentation, or their inability to flexibly image different tissue volumes and shapes. Hand-held based optical imaging systems are a recent development for its improved portability, but are currently limited only to surface mapping. Herein, a novel optical imager, consisting primarily of a hand-held probe and a gain-modulated intensified charge coupled device (ICCD) detector, is developed towards both surface and tomographic breast imaging. The unique features of this hand-held probe based optical imager are its ability to; (i) image large tissue areas (5×10 sq. cm) in a single scan, (ii) reduce overall imaging time using a unique measurement geometry, and (iii) perform tomographic imaging for tumor three-dimensional (3-D) localization. Frequency-domain based experimental phantom studies have been performed on slab geometries (650 ml) under different target depths (1-2.5 cm), target volumes (0.45, 0.23 and 0.10 cc), fluorescence absorption contrast ratios (1:0, 1000:1 to 5:1), and number of targets (up to 3), using Indocyanine Green (ICG) as fluorescence contrast agents. An approximate extended Kalman filter based inverse algorithm has been adapted towards 3-D tomographic reconstructions. Single fluorescence target(s) was reconstructed when located: (i) up to 2.5 cm deep (at 1:0 contrast ratio) and 1.5 cm deep (up to 10:1 contrast ratio) for 0.45 cc-target; and (ii) 1.5 cm deep for target as small as 0.10 cc at 1:0 contrast ratio. In the case of multiple targets, two targets as close as 0.7 cm were tomographically resolved when located 1.5 cm deep. It was observed that performing multi-projection (here dual) based tomographic imaging using a priori target information from surface images, improved the target depth recovery over using single projection based imaging. From a total of 98 experimental phantom studies, the sensitivity and specificity of the imager was estimated as 81-86% and 43-50%, respectively. With 3-D tomographic imaging successfully demonstrated for the first time using a hand-held based optical imager, the clinical translation of this technology is promising upon further experimental validation from in-vitro and in-vivo studies.

Social and cultural influences in the formation of identity: a cross-national/cultural study.

This multi-site, multi-ethnic/cultural study examined the effects of variation between ethnic/cultural groups and the effects of institutional variation within ethnic/cultural groups on identity formation. The participants were 892 late adolescent college students from six sites in 5 countries (Brazil, China, Costa Rica, US, and Sweden) representing different linguistic and ethnic/cultural traditions living in the context of varied social conditions. As hypothesized, there were significant differences in the proportion of identity statuses between sites in the Personal domain, X2(20, N=858)= 164.78, p2(20, N=858)= 145.69, p2(20, N=858)= 120.89, p

A Cross-Generational Analysis of Spanish-to-English Lexico-Semantic Phenomena in Emerging Miami English

Sociolinguists have documented the substrate influence of various languages on the formation of dialects in numerous ethnic-regional setting throughout the United States. This literature shows that while phonological and grammatical influences from other languages may be instantiated as durable dialect features, lexical phenomena often fade over time as ethnolinguistic communities assimilate with contiguous dialect groups. In preliminary investigations of emerging Miami Latino English, we have observed that lexical forms based on Spanish lexical forms are not only ubiquitous among the speech of the first generation Cuban Americans but also of the second. Examples, observed in field work, casual observation, and studied formally in an experimental context include the following: “get down from the car,” which derives from the Spanish equivalent, bajar del carro instead of “get out of the car”. The translation task administered to thirty-one participants showed a variety lexical phenomena are still maintained at equal or higher frequencies.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Development of a high-frequency surface-wave radar cross section model for icebergs

In this thesis, the first-order radar cross section (RCS) of an iceberg is derived and simulated. This analysis takes place in the context of a monostatic high frequency surface wave radar with a vertical dipole source that is driven by a pulsed waveform. The starting point of this work is a general electric field equation derived previ- ously for an arbitrarily shaped iceberg region surrounded by an ocean surface. The condition of monostatic backscatter is applied to this general field equation and the resulting expression is inverse Fourier transformed. In the time domain the excitation current of the transmit antenna is specified to be a pulsed sinusoid signal. The result- ing electric field equation is simplified and its physical significance is assessed. The field equation is then further simplified by restricting the iceberg's size to fit within a single radar patch width. The power received by the radar is calculated using this electric field equation. Comparing the received power with the radar range equation gives a general expression for the iceberg RCS. The iceberg RCS equation is found to depend on several parameters including the geometry of the iceberg, the radar frequency, and the electrical parameters of both the iceberg and the ocean surface. The RCS is rewritten in a form suitable for simulations and simulations are carried out for rectangularly shaped icebergs. Simulation results are discussed and are found to be consistent with existing research.

Prognostic value of the diagnostic criteria distinguishing endometrial stromal sarcoma, low grade from undifferentiated endometrial sarcoma, 2 entities within the invasive endometrial stromal neoplasia family

The World Health Organization (WHO 2003) recognizes 3 endometrial stromal neoplasms: noninvasive endometrial stromal nodule and the 2 invasive neoplasms, endometrial stromal sarcoma (ESS), low grade and undifferentiated endometrial sarcoma (UES). It is important to note that the WHO 2003 does not define moderate atypia (an important differentiating diagnostic criterion for ESS, low grade and UES), nor does it discuss its significance. Moreover, studies on reproducibility and additional prognostic value of other diagnostic features in large are lacking. Using strict definitions, we analyzed the agreement between routine and expert-review necrosis and nuclear atypia in 91 invasive endometrial stromal neoplasias (IESN). The overall 5-year and 10-year recurrence-free survival rate estimates of the 91 IESN patients were 82% and 75%, respectively. Necrosis was well reproducible, and nuclear atypia was reasonably well reproducible. The 10-year recurrence-free survival rates for necrosis absent/inconspicuous versus prominent were 89% and 45% (P<0.001) and those for review-confirmed none/mild, moderate, severe atypia were 90%, 30%, and <20% (P<0.00001). Therefore, cases with moderate/severe atypia should be grouped together. Nuclear atypia and necrosis had independent prognostic values (Cox regression). Once these features were taken into account, no other feature had an independent additional prognostic value, including mitotic count. Using "none/mild atypia, necrosis absent/inconspicuous" as ESS, low grade versus "moderate/severe atypia present or necrosis present" as UES resulted in 68 ESS, low grade and 23 UES cases with disease-specific overall mortality-free survival of 99% versus 48% (P<0.00001, hazard ratio=45.4). When strictly defined microscopic criteria are used, the WHO 2003 diagnoses of ESS, low grade and UES are well reproducible and prognostically strong. © 2012 International Society of Gynecological Pathologists.

The association between parental attitudes and alcohol consumption and adolescent alcohol consumption in Southern Ireland: a cross-sectional study

Background: Alcohol plays a complex role in society. A recent study showed that over half of Irish adults drink hazardously. Adolescents report increased levels of alcohol consumption. Previous research has inferred the influence of the parent on their adolescent. Thus, the aim of the current study was to investigate the association between adolescent alcohol consumption and their parent’s consumption pattern and attitude toward alcohol use in Southern Ireland. Methods: A cross-sectional survey was undertaken in November 2014. This involved distributing a survey to adolescents (n = 982) in their final two years of second level education and at least one of their parents from a local electorate area in Southern Ireland. This survey included: alcohol use, self- reported height and weight, smoking status, mental health and well-being along with attitudinal questions. Chi-square tests and multivariate logistic regression were utilised. Results: A 37 % response rate was achieved. Over one-third (34.2 %) of adolescents and 47 % of parents surveyed reported hazardous drinking. Over 90 % of parents disagreed with allowing their adolescent to get drunk and rejected the idea that getting drunk is part of having fun as an adolescent. The majority (79.5 %) of parents surveyed believed that their alcohol consumption pattern set a good example for their adolescent. Multivariate logistic regression highlights the association between adolescent hazardous alcohol consumption and hazardous drinking by the father. Furthermore either parent permitting their adolescent to drink alcohol on special occasions was associated with hazardous alcohol consumption in the adolescent. Conclusion: The findings of this research notes a liberal attitude to alcohol and increased levels of consumption by the parent are linked to hazardous adolescent drinking behaviour. Future action plans aimed at combatting adolescent hazardous alcohol consumption should also be aimed at tackling parents’ attitudes towards and consumption of alcohol.

A suite of global, cross-scale topographic variables for environmental and biodiversity modeling, links to files in GeoTIFF format

Topographic variation, the spatial variation in elevation and terrain features, underpins a myriad of patterns and processes in geography and ecology and is key to understanding the variation of life on the planet. The characterization of this variation is scale-dependent, i.e. it varies with the distance over which features are assessed and with the spatial grain (grid cell resolution) of analysis. A fully standardized and global multivariate product of different terrain features has the potential to support many large-scale basic research and analytical applications, however to date, such technique is unavailable. Here we used the digital elevation model products of global 250 m GMTED and near-global 90 m SRTM to derive a suite of topographic variables: elevation, slope, aspect, eastness, northness, roughness, terrain roughness index, topographic position index, vector ruggedness measure, profile and tangential curvature, and 10 geomorphological landform classes. We aggregated each variable to 1, 5, 10, 50 and 100 km spatial grains using several aggregation approaches (median, average, minimum, maximum, standard deviation, percent cover, count, majority, Shannon Index, entropy, uniformity). While a global cross-correlation underlines the high similarity of many variables, a more detailed view in four mountain regions reveals local differences, as well as scale variations in the aggregated variables at different spatial grains. All newly-developed variables are available for download at http://www.earthenv.org and can serve as a basis for standardized hydrological, environmental and biodiversity modeling at a global extent.

Comprehensive Transcriptome Analysis of Sex-Biased Expressed Genes Reveals Discrete Biological and Physiological Features of Male and Female Schistosoma japonicum

Schistosomiasis is a chronic and debilitating disease caused by blood flukes (digenetic trematodes) of the genus Schistosoma. Schistosomes are sexually dimorphic and exhibit dramatic morphological changes during a complex lifecycle which requires subtle gene regulatory mechanisms to fulfil these complex biological processes. In the current study, a 41,982 features custom DNA microarray, which represents the most comprehensive probe coverage for any schistosome transcriptome study, was designed based on public domain and local databases to explore differential gene expression in S. japonicum. We found that approximately 1/10 of the total annotated genes in the S. japonicum genome are differentially expressed between adult males and females. In general, genes associated with the cytoskeleton, and motor and neuronal activities were readily expressed in male adult worms, whereas genes involved in amino acid metabolism, nucleotide biosynthesis, gluconeogenesis, glycosylation, cell cycle processes, DNA synthesis and genome fidelity and stability were enriched in females. Further, miRNAs target sites within these gene sets were predicted, which provides a scenario whereby the miRNAs potentially regulate these sex-biased expressed genes. The study significantly expands the expressional and regulatory characteristics of gender-biased expressed genes in schistosomes with high accuracy. The data provide a better appreciation of the biological and physiological features of male and female schistosome parasites, which may lead to novel vaccine targets and the development of new therapeutic interventions.

A Bias Compensated Cross-Relation approach to Thermocouple Characterisation

The measurement of fast changing temperature fluctuations is a challenging problem due to the inherent limited bandwidth of temperature sensors. This results in a measured signal that is a lagged and attenuated version of the input. Compensation can be performed provided an accurate, parameterised sensor model is available. However, to account for the in influence of the measurement environment and changing conditions such as gas velocity, the model must be estimated in-situ. The cross-relation method of blind deconvolution is one approach for in-situ characterisation of sensors. However, a drawback with the method is that it becomes positively biased and unstable at high noise levels. In this paper, the cross-relation method is cast in the discrete-time domain and a bias compensation approach is developed. It is shown that the proposed compensation scheme is robust and yields unbiased estimates with lower estimation variance than the uncompensated version. All results are verified using Monte-Carlo simulations.

A Bias Compensated Cross-Relation approach to Thermocouple Characterisation

The measurement of fast changing temperature fluctuations is a challenging problem due to the inherent limited bandwidth of temperature sensors. This results in a measured signal that is a lagged and attenuated version of the input. Compensation can be performed provided an accurate, parameterised sensor model is available. However, to account for the influence of the measurement environment and changing conditions such as gas velocity, the model must be estimated in-situ. The cross-relation method of blind deconvolution is one approach for in-situ characterisation of sensors. However, a drawback with the method is that it becomes positively biased and unstable at high noise levels. In this paper, the cross-relation method is cast in the discrete-time domain and a bias compensation approach is developed. It is shown that the proposed compensation scheme is robust and yields unbiased estimates with lower estimation variance than the uncompensated version. All results are verified using Monte-Carlo simulations.