The Influence of Visual Provenance Representations on Strategies in a Collaborative Hand-off Data Analysis Scenario.

Conducting data analysis tasks rarely occur in isolation. Especially in intelligence analysis scenarios where different experts contribute knowledge to a shared understanding, members must communicate how insights develop to establish common ground among collaborators. The use of provenance to communicate analytic sensemaking carries promise by describing the interactions and summarizing the steps taken to reach insights. Yet, no universal guidelines exist for communicating provenance in different settings. Our work focuses on the presentation of provenance information and the resulting conclusions reached and strategies used by new analysts. In an open-ended, 30-minute, textual exploration scenario, we qualitatively compare how adding different types of provenance information (specifically data coverage and interaction history) affects analysts' confidence in conclusions developed, propensity to repeat work, filtering of data, identification of relevant information, and typical investigation strategies. We see that data coverage (i.e., what was interacted with) provides provenance information without limiting individual investigation freedom. On the other hand, while interaction history (i.e., when something was interacted with) does not significantly encourage more mimicry, it does take more time to comfortably understand, as represented by less confident conclusions and less relevant information-gathering behaviors. Our results contribute empirical data towards understanding how provenance summarizations can influence analysis behaviors.

Situ: Identifying and Explaining Suspicious Behavior in Networks.

Despite the best efforts of cyber security analysts, networked computing assets are routinely compromised, resulting in the loss of intellectual property, the disclosure of state secrets, and major financial damages. Anomaly detection methods are beneficial for detecting new types of attacks and abnormal network activity, but such algorithms can be difficult to understand and trust. Network operators and cyber analysts need fast and scalable tools to help identify suspicious behavior that bypasses automated security systems, but operators do not want another automated tool with algorithms they do not trust. Experts need tools to augment their own domain expertise and to provide a contextual understanding of suspicious behavior to help them make decisions. In this paper we present Situ, a visual analytics system for discovering suspicious behavior in streaming network data. Situ provides a scalable solution that combines anomaly detection with information visualization. The system's visualizations enable operators to identify and investigate the most anomalous events and IP addresses, and the tool provides context to help operators understand why they are anomalous. Finally, operators need tools that can be integrated into their workflow and with their existing tools. This paper describes the Situ platform and its deployment in an operational network setting. We discuss how operators are currently using the tool in a large organization's security operations center and present the results of expert reviews with professionals.

A comparison of methods for EGFR mutation testing in non-small cell lung cancer.

EGFR mutation testing of tumor samples is routinely performed to predict sensitivity to treatment with tyrosine kinase inhibitors for patients with non-small cell lung cancer. At least 9 different methodologies are employed in UK laboratories, and the aim of this study was to compare the sensitivity of different methods for the detection of EGFR mutations. Participating laboratories were sent coded samples with varying mutation loads (from 0% to 15%) to be tested for the p.Leu858Arg (p.L858R) missense mutation and c.2235_2249del exon 19 deletion. The p.L858R mutation and deletions within exon 19 of the EGFR gene account for ∼90% of mutation-positive cases. The 11 laboratories used their standard testing method(s) and submitted 15 sets of results for the p.L858R samples and 10 for the exon 19 deletion. The p.Leu858Arg (p.L858R) mutation was detected at levels between 1% and 7.5% by Sanger sequencing, pyrosequencing, real-time polymerase chain reaction (PCR), amplification refractory mutation system, and capillary electrophoresis single-strand conformation analysis. The c.2235_2249del mutation was detected at 1% to 5% by fragment size analysis, Sanger sequencing or real-time PCR. A mutation was detected in 24/25 (96%) of the samples tested which contained 5% mutated DNA. The 1% sensitivity claimed for commercial real-time PCR-targeted EGFR tests was achieved and our results show greater sensitivity for the Sanger sequencing and pyrosequencing screening methods compared to the 10% to 20% detection levels cited on clinical diagnostic reports. We conclude that multiple methodologies are suitable for the detection of acquired EGFR mutations.

Beyond the ward and waiting room: a community-based non-clinical placement programme for Australian medical students.

BACKGROUND: Placement programmes are essential to medical education but almost invariably take place in clinical settings, even when community based. Australia's Monash University, however, has included in its core MBBS curriculum a non-clinical placement for second-year students, the Community Based Practice (CBP) programme. This involves partnerships with community organisations that are mostly non-medical. The programme includes a health promotion (HP) component where students respond to a HP or support need nominated by their placement organisation. Though inspired by community-based medical education (CBME) programmes in England and South Australia's Flinders University, its non-clinical focus represents a creative development in Australian medical education. METHODS: This article describes the programme, explores its place within CBME and outlines the results of its analysis of student responses using SPSS and NVivo. RESULTS: The evidence showed development of students' communication skills; increased understanding and appreciation of the mainly non-medical health support infrastructure in local communities; increased understanding of HP and community health support at the local level; and contributions to the placement organisations through small-scale research or health support projects. CONCLUSION: Placement programmes such as this can significantly contribute to medical education, especially in supporting health in local communities and understanding the needs of the marginalised.

Active PI3K pathway causes an invasive phenotype which can be reversed or promoted by blocking the pathway at divergent nodes.

The PTEN/PI3K pathway is commonly mutated in cancer and therefore represents an attractive target for therapeutic intervention. To investigate the primary phenotypes mediated by increased pathway signaling in a clean, patient-relevant context, an activating PIK3CA mutation (H1047R) was knocked-in to an endogenous allele of the MCF10A non-tumorigenic human breast epithelial cell line. Introduction of an endogenously mutated PIK3CA allele resulted in a marked epithelial-mesenchymal transition (EMT) and invasive phenotype, compared to isogenic wild-type cells. The invasive phenotype was linked to enhanced PIP(3) production via a S6K-IRS positive feedback mechanism. Moreover, potent and selective inhibitors of PI3K were highly effective in reversing this phenotype, which is optimally revealed in 3-dimensional cell culture. In contrast, inhibition of Akt or mTOR exacerbated the invasive phenotype. Our results suggest that invasion is a core phenotype mediated by increased PTEN/PI3K pathway activity and that therapeutic agents targeting different nodes of the PI3K pathway may have dramatic differences in their ability to reverse or promote cancer metastasis.

TNFR1-induced sphingomyelinase activation modulates TCR signaling by impairing store-operated Ca2+ influx.

Tumor necrosis factor alpha (TNF-alpha) is a potent, pleiotrophic cytokine, which is proinflammatory but can also suppress T lymphocyte function. In chronic inflammatory disease such as rheumatoid arthritis, exposure of T cells to TNF-alpha alters their ability to mount a response by modulating the T cell receptor (TCR) signaling pathway, but the mechanisms involved remain obscure. Here, we investigated the specific role of TNF receptor 1 (TNFR1) signaling in the modulation of the TCR signaling pathway. We observed a down-regulation of the intracellular calcium ([Ca(2+)](i)) signal in Jurkat T cells after just 30 min exposure to TNF-alpha, and maximum suppression was reached after 3 h. This effect was transient, and signals returned to normal after 12 h. This depression of [Ca(2+)](i) was also observed in human CD4+ T lymphocytes. The change in Ca(2+) signal was related to a decrease in the plasma membrane Ca(2+) influx, which was apparent even when the TCR signal was bypassed using thapsigargin to induce a Ca(2+) influx. The role of TNF-alpha-induced activation of the sphingolipid cascade in this pathway was examined. The engagement of TNFR1 by TNF-alpha led to a time-dependent increase in acid sphingomyelinase (SMase; ASM) activity, corresponding with a decrease in cellular sphingomyelin. In parallel, there was an increase in cellular ceramide, which correlated directly with the decrease in the magnitude of the Ca(2+) response to phytohemagglutinin. Exogenous addition of SMase or ceramide mimicked the effects of TNFR1 signals on Ca(2+) responses in Jurkat T cells. Direct evidence for the activation of ASM in this pathway was provided by complete abrogation of the TNF-alpha-induced inhibition of the Ca(2+) influx in an ASM-deficient murine T cell line (OT-II(+/+)ASM(-/-)). This potent ability of TNF-alpha to rapidly modulate the TCR Ca(2+) signal via TNFR1-induced ASM activation can explain its suppressive effect on T cell function. This TNFR1 signaling pathway may play a role as an important regulator of T cell responses.

Persistent TNF-alpha exposure impairs store operated calcium influx in CD4+ T lymphocytes.

Persistent tumour necrosis factor alpha (TNF-alpha) exposure uncouples proximal T-cell receptor (TCR)-signalling events. Here, we demonstrate that chronic TNF-alpha exposure also attenuates signalling distal to the TCR, by specifically inhibiting Ca2+ influx evoked by thapsigargin in CD4+ T-cells. Mitogen-induced Ca2+ responses were impaired in a dose dependent manner, and TCR-induced Ca2+ responses were also significantly reduced. The impairment of Ca2+ influx strongly correlated with poor function as proliferative responses to both mitogen and anti-CD3/CD28 stimulation were suppressed. Our findings show that persistent TNF-alpha exposure of T-cells specifically inhibits store operated Ca2+ influx. This may affect gene activation and contribute to the poor T-cell function in chronic inflammatory disease.

GENETIC STRUCTURE AND EVOLUTION OF SPECIES IN THE MANGROVE GENUS AVICENNIA (AVICENNIACEAE) IN THE INDO-WEST PACIFIC.

Allozyme variation in species of the mangrove genus Avicennia was screened in 25 populations collected from 22 locations in the Indo-West Pacific and eastern North America using 11 loci. Several fixed gene differences supported the specific status of Avicennia alba, A. integra, A. marina, and A. rumphiana from the Indo-West Pacific, and A. germinans from the Atlantic-East Pacific. The three varieties of A. marina, var. marina, var. eucalyptifolia, and van australasica, had higher genetic similarities (Nei's I) and no fixed gene differences, confirming their conspecific status. Strong genetic structuring was observed in A. marina, with sharp changes in gene frequencies at the geographical margins of varietal distributions. The occurrence of alleles found otherwise in only one variety, in only immediately adjacent populations of another variety, provided evidence of introgession between varieties. The varieties appear to have diverged recently in the Pleistocene and are apparently not of ancient Cretaceous origin, as suggested earlier. Despite evidence of high degrees of outcrossing, gene flow among populations was relatively low (Ne m < 1-2), except where populations were geographically continuous, questioning assumptions that these widespread mangrove species achieve high levels of long-distance dispersal.