SWING: A system for visualizing web graphs

A Web graph refers to the graph that is used to represent relationships between Web pages in cyberspace, where a node represents a URL and an edge indicates a link between two URLs. A Web graph is a very huge graph as growing with cyberspace. This paper presents a pipeline for extracting web information from cyberspace to a web graph and layout techniques for making the web graph more readable. As the size of computer screen is limited, only a small part of the Web graph can be displayed. Several layout techniques should be adapted and combined effectively for web graph visualization. The visualization process incorporates graph drawing algorithms, layout adjustment methods, as well as filtering and clustering methods in order to decide which part of the Web graph should be displayed and how to display it based on the user's focus in navigation

miRPlant : an integrated tool for identification of plant miRNA from RNA sequencing data

Background Small RNA sequencing is commonly used to identify novel miRNAs and to determine their expression levels in plants. There are several miRNA identification tools for animals such as miRDeep, miRDeep2 and miRDeep*. miRDeep-P was developed to identify plant miRNA using miRDeep’s probabilistic model of miRNA biogenesis, but it depends on several third party tools and lacks a user-friendly interface. The objective of our miRPlant program is to predict novel plant miRNA, while providing a user-friendly interface with improved accuracy of prediction. Result We have developed a user-friendly plant miRNA prediction tool called miRPlant. We show using 16 plant miRNA datasets from four different plant species that miRPlant has at least a 10% improvement in accuracy compared to miRDeep-P, which is the most popular plant miRNA prediction tool. Furthermore, miRPlant uses a Graphical User Interface for data input and output, and identified miRNA are shown with all RNAseq reads in a hairpin diagram. Conclusions We have developed miRPlant which extends miRDeep* to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants. miRPlant does not require any third party tools such as mapping or RNA secondary structure prediction tools. miRPlant is also the first plant miRNA prediction tool that dynamically plots miRNA hairpin structure with small reads for identified novel miRNAs. This feature will enable biologists to visualize novel pre-miRNA structure and the location of small RNA reads relative to the hairpin. Moreover, miRPlant can be easily used by biologists with limited bioinformatics skills

How did the discussion go: Discourse act classification in social media conversations

We propose a novel attention based hierarchical LSTM model to classify discourse act sequences in social media conversations, aimed at mining data from online discussion using textual meanings beyond sentence level. The very uniqueness of the task is the complete categorization of possible pragmatic roles in informal textual discussions, contrary to extraction of question-answers, stance detection or sarcasm identification which are very much role specific tasks. Early attempt was made on a Reddit discussion dataset. We train our model on the same data, and present test results on two different datasets, one from Reddit and one from Facebook. Our proposed model outperformed the previous one in terms of domain independence; without using platform-dependent structural features, our hierarchical LSTM with word relevance attention mechanism achieved F1-scores of 71\% and 66\% respectively to predict discourse roles of comments in Reddit and Facebook discussions. Efficiency of recurrent and convolutional architectures in order to learn discursive representation on the same task has been presented and analyzed, with different word and comment embedding schemes. Our attention mechanism enables us to inquire into relevance ordering of text segments according to their roles in discourse. We present a human annotator experiment to unveil important observations about modeling and data annotation. Equipped with our text-based discourse identification model, we inquire into how heterogeneous non-textual features like location, time, leaning of information etc. play their roles in charaterizing online discussions on Facebook

Mobile devices in PBL

Session: Digital Tsunami / Evidence and Theory - Oral Presentations & 45 Minute Workshop: no. 54INTRODUCTION/ BACKGROUND: Problem-based learning is a dynamic process through which students not only learn content knowledge but also skills important to their medical career, such as problem solving skills and communication skills. Technology can potentially contribute to this process, such as the use of mobile devices (defined in this study to include laptop or notebook computers, smartphones, and tablets) for search of information during PBL. But it presents both opportunities and challenges to the …postprin

Cobalt chloride pretreatment promotes cardiac differentiation of human embryonic stem cells under atmospheric oxygen level

Our previous study demonstrated the direct involvement of the HIF-1α subunit in the promotion of cardiac differentiation of murine embryonic stem cells (ESCs). We report the use of cobalt chloride to induce HIF-1α stabilization in human ESCs to promote cardiac differentiation. Treatment of undifferentiated hES2 human ESCs with 50μM cobalt chloride markedly increased protein levels of the HIF-1α subunit, and was associated with increased expression of early cardiac specific transcription factors and cardiotrophic factors including NK2.5, vascular endothelial growth factor, and cardiotrophin-1. When pretreated cells were subjected to cardiac differentiation, a notable increase in the occurrence of beating embryoid bodies and sarcomeric actinin-positive cells was observed, along with increased expression of the cardiac-specific markers, MHC-A, MHC-B, and MLC2V. Electrophysiological study revealed increased atrial-and nodal-like cells in the cobalt chloride-pretreated group. Confocal calcium imaging analysis indicated that the maximum upstroke and decay velocities were significantly increased in both noncaffeine and caffeine-induced calcium transient in cardiomyocytes derived from the cobalt chloride-pretreated cells, suggesting these cells were functionally more mature. In conclusion, our study demonstrated that cobalt chloride pretreatment of hES2 human ESCs promotes cardiac differentiation and the maturation of calcium homeostasis of cardiomyocytes derived from ESCs. © 2011 Mary Ann Liebert, Inc.published_or_final_versio

Do the omeprazole family compounds exert a protective effect against influenza-like illness?

BACKGROUND: Infections by influenza viruses place a heavy burden on public health and economies worldwide. Although vaccines are the best weapons against influenza, antiviral drugs could offer an opportunity to alleviate the burden of influenza. Since omeprazole family compounds block the “proton pump”, we hypothesized that they could interfere with the mechanism of fusion of the virus envelope and endosomal membrane, thereby hindering the M2 proton pump mechanism of influenza viruses. METHODS: A matched case-control study was performed in 2010-2011 in Italy. Cases were subjects aged over 18 years with a diagnosis of Influenza-like Illness (ILI); 254 case-control pairs were recruited. A multivariable conditional logistic regression analysis was used to assess the association between the prevention of ILI and the administration of omeprazole family compounds. The interaction between omeprazole family compounds and influenza vaccination was also examined. RESULTS: After control for potential confounders, subjects treated with omeprazole family compounds displayed a lower risk of catching ILI (OR(adj) = 0.29, 95% CI: 0.15-0.52). The risk of ILI in unvaccinated non-OFC users was about six times than that in vaccinated OFC users. CONCLUSIONS: Although confirmation is necessary, these results suggest that omeprazole family compounds could be profitably used in the prevention of ILI

Investigation of the cerebral hemodynamic response function in single blood vessels by functional photoacoustic microscopy

The specificity of the hemodynamic response function (HRF) is determined spatially by the vascular architecture and temporally by the evolution of hemodynamic changes. Here, we used functional photoacoustic microscopy (fPAM) to investigate single cerebral blood vessels of rats after left forepaw stimulation. In this system, we analyzed the spatiotemporal evolution of the HRFs of the total hemoglobin concentration (HbT), cerebral blood volume (CBV), and hemoglobin oxygen saturation (SO2). Changes in specific cerebral vessels corresponding to various electrical stimulation intensities and durations were bilaterally imaged with 36 × 65-μm2 spatial resolution. Stimulation intensities of 1, 2, 6, and 10 mA were applied for periods of 5 or 15 s. Our results show that the relative functional changes in HbT, CBV, and SO2 are highly dependent not only on the intensity of the stimulation, but also on its duration. Additionally, the duration of the stimulation has a strong influence on the spatiotemporal characteristics of the HRF as shorter stimuli elicit responses only in the local vasculature (smaller arterioles), whereas longer stimuli lead to greater vascular supply and drainage. This study suggests that the current fPAM system is reliable for studying relative cerebral hemodynamic changes, as well as for offering new insights into the dynamics of functional cerebral hemodynamic changes in small animals. © 2012 Society of Photo-Optical Instrumentation Engineers (SPIE)

Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'

We combined large-scale mRNA expression analysis and gene mapping to identify genes and loci that control hematopoietic stem cell (HSC) function. We measured mRNA expression levels in purified HSCs isolated from a panel of densely genotyped recombinant inbred mouse strains. We mapped quantitative trait loci (QTLs) associated with variation in expression of thousands of transcripts. By comparing the physical transcript position with the location of the controlling QTL, we identified polymorphic cis-acting stem cell genes. We also identified multiple trans-acting control loci that modify expression of large numbers of genes. These groups of coregulated transcripts identify pathways that specify variation in stem cells. We illustrate this concept with the identification of candidate genes involved with HSC turnover. We compared expression QTLs in HSCs and brain from the same mice and identified both shared and tissue-specific QTLs. Our data are accessible through WebQTL, a web-based interface that allows custom genetic linkage analysis and identification of coregulated transcripts.

Size-Dependent Photon Emission from Organometal Halide Perovskite Nanocrystals Embedded in an Organic Matrix

10.1021/jz502615eJournal of Physical Chemistry Letters63446-45

Protein interactions in Xenopus germ plasm RNP particles

Hermes is an RNA-binding protein that we have previously reported to be found in the ribonucleoprotein (RNP) particles of Xenopus germ plasm, where it is associated with various RNAs, including that encoding the germ line determinant Nanos1. To further define the composition of these RNPs, we performed a screen for Hermes-binding partners using the yeast two-hybrid system. We have identified and validated four proteins that interact with Hermes in germ plasm: two isoforms of Xvelo1 (a homologue of zebrafish Bucky ball) and Rbm24b and Rbm42b, both RNA-binding proteins containing the RRM motif. GFP-Xvelo fusion proteins and their endogenous counterparts, identified with antisera, were found to localize with Hermes in the germ plasm particles of large oocytes and eggs. Only the larger Xvelo isoform was naturally found in the Balbiani body of previtellogenic oocytes. Bimolecular fluorescence complementation (BiFC) experiments confirmed that Hermes and the Xvelo variants interact in germ plasm, as do Rbm24b and 42b. Depletion of the shorter Xvelo variant with antisense oligonucleotides caused a decrease in the size of germ plasm aggregates and loosening of associated mitochondria from these structures. This suggests that the short Xvelo variant, or less likely its RNA, has a role in organizing and maintaining the integrity of germ plasm in Xenopus oocytes. While GFP fusion proteins for Rbm24b and 42b did not localize into germ plasm as specifically as Hermes or Xvelo, BiFC analysis indicated that both interact with Hermes in germ plasm RNPs. They are very stable in the face of RNA depletion, but additive effects of combinations of antisense oligos suggest they may have a role in germ plasm structure and may influence the ability of Hermes protein to effectively enter RNP particles