Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities

BACKGROUND: Existing biological databases support a variety of queries such as keyword or definition search. However, they do not provide any measure of relevance for the instances reported, and result sets are usually sorted arbitrarily. RESULTS: We describe a system that builds upon the complex infrastructure of the Biozon database and applies methods similar to those of Google to rank documents that match queries. We explore different prominence models and study the spectral properties of the corresponding data graphs. We evaluate the information content of principal and non-principal eigenspaces, and test various scoring functions which combine contributions from multiple eigenspaces. We also test the effect of similarity data and other variations which are unique to the biological knowledge domain on the quality of the results. Query result sets are assessed using a probabilistic approach that measures the significance of coherence between directly connected nodes in the data graph. This model allows us, for the first time, to compare different prominence models quantitatively and effectively and to observe unique trends. CONCLUSION: Our tests show that the ranked query results outperform unsorted results with respect to our significance measure and the top ranked entities are typically linked to many other biological entities. Our study resulted in a working ranking system of biological entities that was integrated into Biozon at

Another Look at the Urbankte Site (41CV26) in Coryell County, Texas

Perttula (2016) had analyzed ceramic sherds and other material culture remains curated at the Texas Archeological Research Laboratory at The University of Texas at Austin (TARL) from four sites in the Brazos River basin in the Central Texas prairie that had been identified as Prairie Caddo sites by Shafer; one of the sites was the Urbankte site (41CV26). The Urbankte site is on the Leon River in Coryell County, at Belton Reservoir; the Leon River is a southward-flowing tributary to the Brazos River. The term “Prairie Caddo” used by Shafer refers to Caddo groups affiliated with Caddo communities in East Texas, most likely affiliated with the George C. Davis site in the Neches River valley, that occupied portions of the Central Texas prairies in Late Prehistoric times, from ca. A.D. 1000-1300. Each of the four assemblages in the Brazos River basin have sherds that stylistically compare closely to decorated Caddo vessels from East Texas Caddo sites, and the distinctive character of these decorated sherds suggested that the four sites were occupied between ca. A.D. 1000-1200 or to post-ca. A.D. 1200-1300 times in the case of the Urbankte site. Where these ceramic assemblages seemed to differ from East Texas Caddo ceramics, however, was in their manufacture: the grog and bone temper inclusions added to the paste of the ceramic vessel sherds from these sites had numerous, large, and coarse-grained temper inclusions, while East Texas Caddo ceramics tend to have more fine-grained temper inclusions, even in the manufacture of utility ware jars. The Urbankte site ceramics (n=118 sherds) I examined at TARL were heavily bone-tempered (88 percent) and had a considerable proportion of brushed sherds (46 percent of the decorated sherds). Both characteristics were consistent with a post A.D. 1200-1300 Prairie Caddo occupation, as was the fact that eight of the nine arrow points in the TARL collections from the Urbankte site are Perdiz arrow points. The common occurrence of both Perdiz points and brushed ceramic sherds suggested then that this Prairie Caddo occupation at the Urbankte site took place sometime after ca. A.D. 1200-1300. As Dr. Shafer mentions below, the artifacts from the Urbankte site that he had discussed in the Prairie Caddo module were from a different part of the site than the TARL collection I had documented, and were from a different and earlier cultural component. We will return to those artifacts shortly

In Vitro Assessment of Developmental Neurotoxicity: Use of Microelectrode Arrays to Measure Functional Changes in Neuronal Network Ontogeny1

Because the Developmental Neurotoxicity Testing Guidelines require large numbers of animals and is expensive, development of in vitro approaches to screen chemicals for potential developmental neurotoxicity is a high priority. Many proposed approaches for screening are biochemical or morphological, and do not assess function of neuronal networks. In this study, microelectrode arrays (MEAs) were used to determine if chemical-induced changes in function could be detected by assessing the development of spontaneous network activity. MEAs record individual action potential spikes as well as groups of spikes (bursts) in neuronal networks, and activity can be assessed repeatedly over days in vitro (DIV). Primary cultures of rat cortical neurons were prepared on MEAs and spontaneous activity was assessed on DIV 2, 6, 9, 13, and 20 to determine the in vitro developmental profile of spontaneous spiking and bursting in cortical networks. In addition, 5 μM of the protein kinase C inhibitor bisindolylmaleamide-1 (Bis-1) was added to MEAs (n = 9–18) on DIV 5 to determine if changes in spontaneous activity could be detected in response to inhibition of neurite outgrowth. A clear profile of in vitro activity development occurred in control MEAs, with the number of active channels increasing from 0/MEA on DIV 2 to 37 ± 5/MEA by DIV 13; the rate of increase was most rapid between DIV 6 and 9, and activity declined by DIV 20. A similar pattern was observed for the number of bursting channels, as well as the total number of bursts. Bis-1 decreased the number of active channels/MEA and the number of bursting channels/MEA. Burst characteristics, such as burst duration and the number of spikes in a burst, were unchanged by Bis-1. These results demonstrate that MEAs can be used to assess the development of functional neuronal networks in vitro, as well as chemical-induced dysfunction

Evaluating Aspen Responses to Changes in Elk Abundance, Distribution and Behavior Following Wolf Reestablishment in West-Central Yellowstone National Park

The reintroduction of wolves to Yellowstone National Park created a unique “natural experiment” to study trophic interactions in a large-scale terrestrial system among wolves, elk, and aspen. This study utilized data from a long-term elk demography study that was established prior to wolf reintroduction. Significant changes in the abundance and distribution of the Madison headwaters elk herd were observed following wolf reestablishment. The spatial arrangement of these changes made it possible to directly test for the occurrence of a density-mediated trophic cascade. The objectives of this study were to answer the following questions: 1) was there a marked decrease in browsing pressure on aspen where elk densities declined, and 2) was there a corresponding plant-growth response indicating that aspen were released from browsing pressure? Historical browsing conditions and aspen height were observed for 31 aspen stands to assess the occurrence of a density-mediated trophic cascade following wolf reintroduction. Browse conditions and aspen morphology in stands where elk densities declined dramatically following wolf reintroduction were compared to stands that experienced persistent heavy browsing throughout this period. A major decline in browsing pressure along with a modest increase in aspen height and leader longevity was detected, supporting the hypothesis of a density-mediated trophic cascade. However, the magnitude of the growth response was weak, suggesting that browsing was not the dominant limiting factor to aspen growth in the study area and that aspen may be more strongly limited by bottom-up regulation

Integrating Data Science into a General Education Information Technology Course: An Approach to Developing Data Savvy Undergraduates

The National Academies recommend academic institutions foster a basic understanding of data science in all undergraduates. However, data science education is not currently a graduation requirement at most colleges and universities. As a result, many graduates lack even basic knowledge of data science. To address the shortfall, academic institutions should incorporate introductory data science into general education courses. A general education IT course provides a unique opportunity to integrate data science education. Modules covering databases, spreadsheets, and presentation software, already present in many survey IT courses, teach concepts and skills needed for data science. As a result, a survey IT course can provide comprehensive introductory data science education by adding a data science module focused on modeling and evaluation, two key steps in the data science process. The module should use data science software for application, avoiding the complexities of programming and advanced math, while enabling an emphasis on conceptual understanding. We implemented a course built around these ideas and found that the course helps develop data savvy in students

Quit Methods Used by US Adult Cigarette Smokers, 2014–2016

To quantify the prevalence of 10 quit methods commonly used by adult cigarette smokers, we used data from a nationally representative longitudinal (2014-2016) online survey of US adult cigarette smokers (n = 15,943). Overall, 74.7% of adult current cigarette smokers used multiple quit methods during their most recent quit attempt. Giving up cigarettes all at once (65.3%) and reducing the number of cigarettes smoked (62.0%) were the most prevalent methods. Substituting some cigarettes with e-cigarettes was used by a greater percentage of smokers than the nicotine patch, nicotine gum, or other cessation aids approved by the US Food and Drug Administration. Further research into the effectiveness of e-cigarettes as a cessation aid is warranted

Characterization of Early Cortical Neural Network Development in Multiwell Microelectrode Array Plates.

We examined neural network ontogeny using microelectrode array (MEA) recordings made in multiwell MEA (mwMEA) plates over the first 12 days in vitro (DIV). In primary cortical cultures, action potential spiking activity developed rapidly between DIV 5 and 12. Spiking was sporadic and unorganized at early DIV, and became progressively more organized with time, with bursting parameters, synchrony, and network bursting increasing between DIV 5 and 12. We selected 12 features to describe network activity; principal components analysis using these features demonstrated segregation of data by age at both the well and plate levels. Using random forest classifiers and support vector machines, we demonstrated that four features (coefficient of variation [CV] of within-burst interspike interval, CV of interburst interval, network spike rate, and burst rate) could predict the age of each well recording with >65% accuracy. When restricting the classification to a binary decision, accuracy improved to as high as 95%. Further, we present a novel resampling approach to determine the number of wells needed for comparing different treatments. Overall, these results demonstrate that network development on mwMEA plates is similar to development in single-well MEAs. The increased throughput of mwMEAs will facilitate screening drugs, chemicals, or disease states for effects on neurodevelopment.EC was supported by a Wellcome Trust PhD studentship and NIHR Cambridge Biomedical Research Centre studentship. DH was supported by student services contract #EP-13-D-000108 and by a travelling fellowship from the Company of Biologists.This is the final version of the article. It first appeared from SAGE Publications via https://doi.org/10.1177/108705711664052

Resolving IRAS 09111-1007 at 350 microns - a different path to ULIRG formation?

We have resolved the ultraluminous infrared galaxy (ULIRG), IRAS 09111-1007, with the new 350 micron-optimised Second Generation Submillimeter High Angular Resolution Camera (SHARC II) and present the first submillimetre fluxes and images for the system. IRAS 09111-1007 comprises two interacting luminous infrared galaxies (LIRGs) with a projected nuclear separation of 39 kpc. The Western galaxy is roughly four times more luminous in the submillimetre than its Eastern counterpart. It is an extremely bright LIRG with an AGN. The classification of the Eastern source is uncertain: it could be a Seyfert 2 galaxy or a LINER. We highlight IRAS 09111-1007 as a system that necessitates further study: a double AGN ULIRG whose molecular gas content differs from other widely separated pairs and whose ULIRG phase might not be explained by current multiple merger and/or final stage ULIRG scenarios.Comment: 6 pages, 4 figures. Accepted for publication in MNRAS Letter

Adaptive-optics Optical Coherence Tomography Processing Using a Graphics Processing Unit

Graphics processing units are increasingly being used for scientific computing for their powerful parallel processing abilities, and moderate price compared to super computers and computing grids. In this paper we have used a general purpose graphics processing unit to process adaptive-optics optical coherence tomography (AOOCT) images in real time. Increasing the processing speed of AOOCT is an essential step in moving the super high resolution technology closer to clinical viability