Gene Ontology enrichment analysis provides an effective way to extract meaningful information from complex biological datasets. By identifying terms that are significantly overrepresented in a gene ...set, researchers can uncover biological features shared by genes. In addition to extracting enriched terms, it is also important to visualize the results in a way that is conducive to biological interpretation.
Here we present FunSet, a new web server to perform and visualize enrichment analysis. The web server identifies Gene Ontology terms that are statistically overrepresented in a target set with respect to a background set. The enriched terms are displayed in a 2D plot that captures the semantic similarity between terms, with the option to cluster terms via spectral clustering and identify a representative term for each cluster. FunSet can be used interactively or programmatically, and allows users to download the enrichment results both in tabular form and in graphical form as SVG files or in data format as JSON or csv. To enhance reproducibility of the analyses, users have access to historical data for the ontology and the annotations. The source code for the standalone program and the web server are made available with an open-source license.
Human-computer interaction and computer-mediated behavioral psychology research studies often rely on capturing user interaction data to characterize online behaviors. IRB considerations, site ...policies, and/or security and privacy concerns may force researchers to use screenshots or offline copies of pages of interest, instead of live websites, in their study designs. These interaction modalities reduce the fidelity and contextual realism of web content and often affect interface aesthetic quality - due to broken links, missing images, and/or malfunctioning scripts. StudySandboxx is a tool that allows websites to be saved exactly as they appear online. The tool sandboxes websites in a way that removes dangerous scripts that threaten privacy and security. Saved websites are encapsulated into a single portable file that contains all related website resources. Finally, the tool also supports certain types of permutations commonly used in research - such as changing links in a page. The project is housed within a GitHub repository at Keywords: Interactive content, human computer interaction, sandboxing, fidelity, behavioral studies, interaction studies, offline, web
Outcomes of Emotional Content from Agile Team Forum Posts Marshall, Allen; Gamble, Rose F.; Hale, Matthew L.
2016 IEEE/ACM 1st International Workshop on Emotional Awareness in Software Engineering (SEmotion)
Conference Proceeding
Social media and discussion centric collaborative tools have become an integral part of software development team communication. Accessible by mobile apps and alongside development tools, these tools ...provide a medium for conversation and enable teams to share project artifacts including commits, documents, and models. As with other forms of human communication, team members naturally emote during software development, resulting in affective post content expressing emotions such as urgency, frustration, and commendation. The effects of affective interaction on team performance, while studied in the literature, are still not well understood, particularly for student teams. This paper adds to the exploration of affect, by examining the effect of emotional post content on project performance metrics among teams of students in a software engineering course. The data set consists of over thirteen hundred forum posts produced by five teams across three Scrum Sprints in two different classes, each of which was taught by a different instructor. Using manual sentiment analysis techniques, we found that individuals with less emotive posts performed better than those that emoted more and that less affective individuals were evaluated more positively by their peers. From a pedagogical and management perspective, these results indicate that intervention may be needed when posts become emotionally charged in software development team communication.
Chronic kidney disease (CKD) is often under-recognized and poorly documented via diagnoses, but the extent of under-recognition is not well understood among Medicare beneficiaries. The current study ...used claims-based diagnosis and lab data to examine patient factors associated with clinically recognized CKD and CKD stage concordance between claims- and lab-based sources in a cohort of Medicare beneficiaries.
In a cohort of fee-for-service (FFS) beneficiaries with CKD based on 2011 labs, we examined the proportion with clinically recognized CKD via diagnoses and factors associated with clinical recognition in logistic regression. In the subset of beneficiaries with CKD stage identified from both labs and diagnoses, we examined concordance in CKD stage from both sources, and factors independently associated with CKD stage concordance in logistic regression.
Among the subset of 206,036 beneficiaries with lab-based CKD, only 11.8% (n = 24,286) had clinically recognized CKD via diagnoses. Clinical recognition was more likely for beneficiaries who had higher CKD stages, were non-elderly, were Hispanic or non-Hispanic Black, lived in core metropolitan areas, had multiple chronic conditions or outpatient visits in 2010, or saw a nephrologist. In the subset of 18,749 beneficiaries with CKD stage identified from both labs and diagnoses, 70.0% had concordant CKD stage, which was more likely if beneficiaries were older adults, male, lived in micropolitan areas instead of non-core areas, or saw a nephrologist.
There is significant under-diagnosis of CKD in Medicare FFS beneficiaries, which can be addressed with the availability of lab results.
Companies and government organizations are increasingly compelled, if not required by law, to ensure that their information systems will comply with various federal and industry regulatory standards, ...such as the NIST Special Publication on Security Controls for Federal Information Systems (NIST SP-800-53), or the Common Criteria (ISO 15408-2). Such organizations operate business or mission critical systems where a lack of or lapse in security protections translates to serious confidentiality, integrity, and availability risks that, if exploited, could result in information disclosure, loss of money, or, at worst, loss of life. To mitigate these risks and ensure that their information systems meet regulatory standards, organizations must be able to (a) contextualize regulatory documents in a way that extracts the relevant technical implications for their systems, (b) formally represent their systems and demonstrate that they meet the extracted requirements following an accreditation process, and (c) ensure that all third-party systems, which may exist outside of the information system enclave as web or cloud services also implement appropriate security measures consistent with organizational expectations. This paper introduces a step-wise process, based on
semantic hierarchies
, that systematically extracts relevant security requirements from control standards to build a certification baseline for organizations to use in conjunction with formal methods and service agreements for accreditation. The approach is demonstrated following a case study of all audit-related controls in the SP-800-53, ISO 15408-2, and related documents. Accuracy, applicability, consistency, and efficacy of the approach were evaluated using controlled qualitative and quantitative methods in two separate studies.
BACKGROUND AND OBJECTIVES
Opioid use and misuse are prevalent and remain a national crisis. This study identified beneficiary characteristics associated with filling opioid prescriptions, variation ...in opioid dosing, and opioid use with average daily doses (ADDs) equal to 120 morphine milligram equivalents (MMEs) or more in the 100% Medicare fee‐for‐service (FFS) population.
DESIGN, SETTING, PARTICIPANTS, AND MEASUREMENTS
In a cohort of FFS beneficiaries with 12 months of Medicare Part D coverage in 2016, we examined patient factors associated with filling an opioid prescription (n = 20,880,490) and variation in ADDs (n = 7,325,031) in a two‐part model. Among those filling opioids, we also examined the probability of ADD equal to 120 MMEs or more via logistic regression.
RESULTS
About 35% of FFS beneficiaries had one or more opioid prescription fills in 2016 and 1.5% had ADDs equal to 120 MMEs or more. Disability‐eligible beneficiaries and beneficiaries with multiple chronic conditions were more likely to fill opioids, to have higher ADDs or were more likely to have ADD equal to 120 MMEs or more. Beneficiaries with chronic obstructive pulmonary disease (COPD) were more likely to fill opioids (odds ratio (OR) = 1.47, 95% confidence interval (CI) = 1.46–1.47), have higher ADDs (rate ratio = 1.06, 95% CI = 1.06–1.06) when filled and were more likely to have ADD equal to 120 MMEs or more (OR = 1.23, 95% CI = 1.21–1.24). Finally, black and Hispanic beneficiaries were less likely to fill opioids, had lower overall doses and were less likely to have ADDs equal to 120 MMEs or more compared to white beneficiaries.
CONCLUSION
Several beneficiary subgroups have underappreciated risk of adverse events associated with ADD equal to 120 MMEs or more that may benefit from opioid optimization interventions that balance pain management and adverse event risk, especially beneficiaries with COPD who are at risk for respiratory depression.
Operating in a body area network around a smartphone user, wearables serve a variety of commercial, medical and personal uses. Depending on a certain smartphone application, a wearable can capture ...sensitive data about the user and provide critical, possibly life-or-death, functionality. When using wearables, security problems might occur on hardware/software of wearables, connected phone apps or web services devices, or Bluetooth channels used for communication. This paper develops an open source platform called SecuWear for identifying vulnerabilities in these areas and facilitating wearable security research to mitigate them. SecuWear supports the creation, evaluation, and analysis of security vulnerability tests on actual hardwares. Extending earlier results, this paper includes an empirical evaluation that demonstrates proof of concept attacks on commercial wearable devices and shows how SecuWear captures the information necessary for identifying such attacks. Also included is a process for releasing attack and mitigation information to the security community. Keywords: Bluetooth LE, Internet of things, Man-in-the-middle attacks, Security, Vulnerability discovery, Wearables
Phishing attacks sap billions of dollars annually from unsuspecting individuals while compromising individual privacy. Companies and privacy advocates seek ways to better educate the populace against ...such attacks. Current approaches examining phishing include test-based techniques that ask subjects to classify content as phishing or not and inthe- wild techniques that directly observe subject behavior through distribution of faked phishing attacks. Both approaches have issues. Test-based techniques produce less reliable data since subjects may adjust their behavior with the expectation of seeing phishing stimuli, while in-the-wild studies can put subjects at risk through lack of consent or exposure of data. This paper examines a third approach that seeks to incorporate game-based learning techniques to combine the realism of in-thewild approaches with the training features of testing approaches. We propose a three phase experiment to test our approach on our CyberPhishing simulation platform, and present the results of phase one.
During HAZMAT emergencies, first responders are the first to reach the incident site. Over the years, there has been an increase in the number of first responder deaths and heat related illness. ...Heat-related illnesses are most often studied in outdoor workers and wild land firefighters but occur in a variety of workers across the US. Surveillance programs reported approximately 28,000 HRI hospitalizations between 2001 and 2010. The progression from heat exhaustion to heat stroke can occur rapidly so first responders need warning systems to alert them to the impending health hazards of heat stress. This study works with HAZMAT first responders in Nebraska to explore and assess the status of responder safety in the state and begins with the first responder focus group requirements gathering process. A consensus building process was used for the focus group sessions and yielded thematic areas of health and safety concern. Responder safety was named the most common area of concern and solutions to individual risks were proposed by focus group participants from a local HAZMAT response team. The results of this focus group serve to inform researchers of priorities to consider in the development of responder health monitoring systems and to continue with research in wearable technology for real time health monitoring. Early intervention when monitored responders demonstrate signs of distress ultimately saves lives.
Although the Internet has been touted as a means to improve democratic governance, there has been little systematic analysis of its use. The authors analyze the diffusion of municipal Web sites that ...include information concerning a specific locality. The analysis is based on demographic and fiscal data from 454 California cities and two surveys of Web site adoption. The authors’ theoretical framework draws from the political economy and technology diffusion literatures. City size, government resources, concentration of social-economic elites, and voter registration levels are the most significant predictors of adoption. In contrast to previous adoption studies, the authors find that liberal political ideology and experience with advanced communication technologies do not appreciably increase the probability of adoption.
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