ß-D-glucuronidase activity triggered monitoring of fecal contamination using microbial and chemical source tracking markers at drinking water intakes.

Intense rainfall and snowmelt events may affect the safety of drinking water, as large quantities of fecal material can be discharged from storm or sewage overflows or washed from the catchment into drinking water sources. This study used ß-d-glucuronidase activity (GLUC) with microbial source tracking (MST) markers: human, bovine, porcine mitochondrial DNA markers (mtDNA) and human-associated Bacteroidales HF183 and chemical source tracking (CST) markers including caffeine, carbamazepine, theophylline and acetaminophen, pathogens (Giardia, Cryptosporidium, adenovirus, rotavirus and enterovirus), water quality indicators (Escherichia coli, turbidity) and hydrometeorological data (flowrate, precipitation) to assess the vulnerability of 3 drinking water intakes (DWIs) and identify sources of fecal contamination. Water samples were collected under baseline, snow and rain events conditions in urban and agricultural catchments (Québec, Canada). Dynamics of E. coli, HF183 and WWMPs were similar during contamination events, and concentrations generally varied over 1 order of magnitude during each event. Elevated human-associated marker levels during events demonstrated that urban DWIs were impacted by recent contamination from an upstream municipal water resource recovery facility (WRRF). In the agricultural catchment, mixed fecal pollution was observed with the occurrences and increases of enteric viruses, human bovine and porcine mtDNA during peak contaminating events. Bovine mtDNA qPCR concentrations were indicative of runoff of cattle-derived fecal pollutants to the DWI from diffuse sources following rain events. This study demonstrated that the suitability of a given MST or CST indicator depend on river and catchment characteristics. The sampling strategy using continuous online GLUC activity coupled with MST and CST markers analysis was a more reliable source indicator than turbidity to identify peak events at drinking water intakes.

"It's Not Literally True, But You Get the Gist:" How nuanced understandings of truth encourage people to condone and spread misinformation.

People have a more-nuanced view of misinformation than the binary distinction between "fake news" and "real news" implies. We distinguish between the truth of a statement's verbatim details (i.e., the specific, literal information) and its gist (i.e., the general, overarching meaning), and suggest that people tolerate and intentionally spread misinformation in part because they believe its gist. That is, even when they recognize a claim as literally false, they may judge it as morally acceptable to spread because they believe it is true "in spirit." Prior knowledge, partisanship, and imagination increase belief in the gist. We argue that partisan conflict about the morality of spreading misinformation hinges on disagreements not only about facts but also about gists.

Performance of Portfolios Based on the Expected Utility-Entropy Fund Rating Approach.

Yang and Qiu proposed and reframed an expected utility-entropy (EU-E) based decision model. Later on, a similar numerical representation for a risky choice was axiomatically developed by Luce et al. under the condition of segregation. Recently, we established a fund rating approach based on the EU-E decision model and Morningstar ratings. In this paper, we apply the approach to US mutual funds and construct portfolios using the best rating funds. Furthermore, we evaluate the performance of the fund ratings based on the EU-E decision model against Morningstar ratings by examining the performance of the three models in portfolio selection. The conclusions show that portfolios constructed using the ratings based on the EU-E models with moderate tradeoff coefficients perform better than those constructed using Morningstar. The conclusion is robust to different rebalancing intervals.

The predictive ability of the expected utility-entropy based fund rating approach: A comparison investigation with Morningstar ratings in US.

In this paper, we propose an alternative fund rating approach based on the Expected Utility-Entropy (EU-E) decision model, in which the measure of risk for a risky action was axiomatically developed by Luce et al. We examine the ability of this approach as an alternative fund rating approach for its ability to potentially mitigate the drawbacks of the risk measure used in Morningstar ratings, and investigate the ability of the EU-E model based and Morningstar ratings to predict mutual fund performance. Overall, we find that the risk measure used in both models plays a defining role in their ability to predict future fund performance, and that the EU-E model can effectively consider the behavioral decisions of an investor.

Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets.

BACKGROUND: Modern pyrosequencing techniques make it possible to study complex bacterial populations, such as 16S rRNA, directly from environmental or clinical samples without the need for laboratory purification. Alignment of sequences across the resultant large data sets (100,000+ sequences) is of particular interest for the purpose of identifying potential gene clusters and families, but such analysis represents a daunting computational task. The aim of this work is the development of an efficient pipeline for the clustering of large sequence read sets. METHODS: Pairwise alignment techniques are used here to calculate genetic distances between sequence pairs. These methods are pleasingly parallel and have been shown to more accurately reflect accurate genetic distances in highly variable regions of rRNA genes than do traditional multiple sequence alignment (MSA) approaches. By utilizing Needleman-Wunsch (NW) pairwise alignment in conjunction with novel implementations of interpolative multidimensional scaling (MDS), we have developed an effective method for visualizing massive biosequence data sets and quickly identifying potential gene clusters. RESULTS: This study demonstrates the use of interpolative MDS to obtain clustering results that are qualitatively similar to those obtained through full MDS, but with substantial cost savings. In particular, the wall clock time required to cluster a set of 100,000 sequences has been reduced from seven hours to less than one hour through the use of interpolative MDS. CONCLUSIONS: Although work remains to be done in selecting the optimal training set size for interpolative MDS, substantial computational cost savings will allow us to cluster much larger sequence sets in the future.

Mining relational paths in integrated biomedical data.

Much life science and biology research requires an understanding of complex relationships between biological entities (genes, compounds, pathways, diseases, and so on). There is a wealth of data on such relationships in publicly available datasets and publications, but these sources are overlapped and distributed so that finding pertinent relational data is increasingly difficult. Whilst most public datasets have associated tools for searching, there is a lack of searching methods that can cross data sources and that in particular search not only based on the biological entities themselves but also on the relationships between them. In this paper, we demonstrate how graph-theoretic algorithms for mining relational paths can be used together with a previous integrative data resource we developed called Chem2Bio2RDF to extract new biological insights about the relationships between such entities. In particular, we use these methods to investigate the genetic basis of side-effects of thiazolinedione drugs, and in particular make a hypothesis for the recently discovered cardiac side-effects of Rosiglitazone (Avandia) and a prediction for Pioglitazone which is backed up by recent clinical studies.

Communication and data-intensive science in the beginning of the 21st century.

The advent of data-intensive science has sharpened our need for better communication within and between the fields of science and technology, to name a few. No one mind can encompass all that is necessary to be successful in controlling and analyzing the data deluge we are experiencing. Therefore, we must bring together diverse fields, communicate clearly, and build crossdisciplinary methods and tools to realize its potential. This article is a summary of the communication issues and challenges as discussed in the Data-Intensive Science (DIS) workshop in Seattle, September 19-20, 2010.

Finding complex biological relationships in recent PubMed articles using Bio-LDA.

The overwhelming amount of available scholarly literature in the life sciences poses significant challenges to scientists wishing to keep up with important developments related to their research, but also provides a useful resource for the discovery of recent information concerning genes, diseases, compounds and the interactions between them. In this paper, we describe an algorithm called Bio-LDA that uses extracted biological terminology to automatically identify latent topics, and provides a variety of measures to uncover putative relations among topics and bio-terms. Relationships identified using those approaches are combined with existing data in life science datasets to provide additional insight. Three case studies demonstrate the utility of the Bio-LDA model, including association predication, association search and connectivity map generation. This combined approach offers new opportunities for knowledge discovery in many areas of biology including target identification, lead hopping and drug repurposing.

Hybrid cloud and cluster computing paradigms for life science applications.

BACKGROUND: Clouds and MapReduce have shown themselves to be a broadly useful approach to scientific computing especially for parallel data intensive applications. However they have limited applicability to some areas such as data mining because MapReduce has poor performance on problems with an iterative structure present in the linear algebra that underlies much data analysis. Such problems can be run efficiently on clusters using MPI leading to a hybrid cloud and cluster environment. This motivates the design and implementation of an open source Iterative MapReduce system Twister. RESULTS: Comparisons of Amazon, Azure, and traditional Linux and Windows environments on common applications have shown encouraging performance and usability comparisons in several important non iterative cases. These are linked to MPI applications for final stages of the data analysis. Further we have released the open source Twister Iterative MapReduce and benchmarked it against basic MapReduce (Hadoop) and MPI in information retrieval and life sciences applications. CONCLUSIONS: The hybrid cloud (MapReduce) and cluster (MPI) approach offers an attractive production environment while Twister promises a uniform programming environment for many Life Sciences applications. METHODS: We used commercial clouds Amazon and Azure and the NSF resource FutureGrid to perform detailed comparisons and evaluations of different approaches to data intensive computing. Several applications were developed in MPI, MapReduce and Twister in these different environments.