Entropy-scaling search of massive biological data

Many datasets exhibit a well-defined structure that can be exploited to design faster search tools, but it is not always clear when such acceleration is possible. Here, we introduce a framework for similarity search based on characterizing a dataset's entropy and fractal dimension. We prove that searching scales in time with metric entropy (number of covering hyperspheres), if the fractal dimension of the dataset is low, and scales in space with the sum of metric entropy and information-theoretic entropy (randomness of the data). Using these ideas, we present accelerated versions of standard tools, with no loss in specificity and little loss in sensitivity, for use in three domains---high-throughput drug screening (Ammolite, 150x speedup), metagenomics (MICA, 3.5x speedup of DIAMOND [3,700x BLASTX]), and protein structure search (esFragBag, 10x speedup of FragBag). Our framework can be used to achieve "compressive omics," and the general theory can be readily applied to data science problems outside of biology.Comment: Including supplement: 41 pages, 6 figures, 4 tables, 1 bo

Obiskovanje srednjih šol med mladimi z nizkimi dohodki: pojasnjevanje razlik med srednjimi šolami v Wisconsinu

Bolstering low-income students’ postsecondary participation is important to remediate these students’ disadvantages and to improve society’s overall level of education. Recent research has demonstrated that secondary schools vary considerably in their tendencies to send students to postsecondary education, but existing research has not systematically identified the school characteristics that explain this variation. Identifying these characteristics can help improve low-income students’ postsecondary outcomes. We identify relevant characteristics using population-level data from Wisconsin, a mid-size state in the United States. We first show that Wisconsin’s income-based disparities in postsecondary participation are wide, even net of academic achievement. Next, we show that several geographic characteristics of schools help explain between-secondary school variation in low-income students’ postsecondary outcomes. Finally, we test whether a dense set of school organisational features explain any remaining variation. We find that these features explain virtually no variation in secondary schools’ tendencies to send low-income students to postsecondary education. (DIPF/Orig.

Peer Assessments May Predict Objective Long-Term Academic Performance

Introduction: A common challenge in medical education is to create a curriculum that both teaches the required material but still delivers a personable physician. In this data study, 673 Sidney Kimmel Medical College (SKMC) students were given a required survey to judge their group members on personal attributes ranging from preparedness to affability. These scores were used to aid students and hopefully prevent unfortunate habits from settling. We hypothesize that peer assessments will predict academic performance. Methods: A five-question, Likert scale, peer assessment was given to each first-year medical student at SKMC. The electronic survey was given twice during the dissection portion of the curriculum, when students are assigned to groups with 2-3 other students. As the students finished their time at Jefferson, they were assigned a class ranking based on test and clerkship scores, and took national board exams (Step 1 and 2). These metrics were then compared via multi-variable linear regression to determine any correlation. Results: The study found that the peer assessment of another’s preparation (question 1 of the assessment) showed a strong, positive correlation to class rank, Step 1, and Step 2 scores. Conclusion: This study shows the efficacy of a subjective peer assessment of preparation predicting objective academic performance. Further research will determine other predictive value of peer assessments in empathy and mental health

Disc Golf Locator

Disc golf is a game similar to traditional golf where players throw small plastic discs into chain-link nets. Disc golf courses cover several acres containing lakes, small wooded areas, large bushes, and grassy fields. It is not uncommon to accidentally throw a golf disc into the woods or bushes, so it is the goal of this project to create a device to locate the disc and make suggestions for the player to improve performance. A small device will be attached the disc which will track its location and flight characteristics. The device will contain a GPS receiver, an inertial measurement unit (IMU), data storage device, wireless transfer device, and an audio alarm to locate the disc. The GPS will record the flight path of the disc and the IMU will measure flight characteristics which will be stored locally on the disc during flight. After the disc is thrown and recovered, players will be able to use a smartphone app to retrieve the flight data from the tracking device by wireless communication. The smartphone app will plot the flight path on a map and analyze the inertial data to make suggestions for players to improve their throws

Fake News Perception in Germany: A Representative Study of People’s Attitudes and Approaches to Counteract Disinformation

Fake news has become an important topic in our social and political environment. While research is coming up for the U.S. and European countries, many aspects remain uncovered as long as existing work only marginally investigates people’s attitudes towards fake news. In this work, we present the results of a representative study (N=1023) in Germany asking participants about their attitudes towards fake news and approaches to counteract disinformation. More than 80% of the participants agree that fake news poses a threat. 78% see fake news as harming democracy. Even though about half of the respondents (48%) have noticed fake news, most participants stated to have never liked, shared or commented on fake news. Regarding demographic factors, our findings support the view of younger and relatively educated people being more informed about fake news. Concerning ideological motives, the evaluation suggests left-wing or liberal respondents to be more critical of fake news

SB41-19/20: Resolution Regarding Referendum Language for Article 4 of the ASUM Constitution

SB41-19/20: Resolution Regarding Referendum Language for Article 4 of the ASUM Constitution Passed Unanimously in the December 4, 2019 ASUM Senate Meetin

SB52-19/20: Resolution Regarding Referendum Language for Article 6 of the ASUM Constitution

SB52-19/20: Resolution Regarding Referendum Language for Article 6 of the ASUM Constitution was approved unanimously during the January 29th, 2020 meeting of the Associated Students of the University of Montana

SB52-19/20: Resolution Regarding Referendum Language for Article 6 of the ASUM Constitution

SB52-19/20: Resolution Regarding Referendum Language for Article 6 of the ASUM Constitution. This resolution was passed unanimously during the January 29, 2020 meeting of the Associated Students of the University of Montana (ASUM)

The Yeast Heat Shock Transcription Factor Changes Conformation in Response to Superoxide and Temperature

In vitro DNA-binding assays demonstrate that the heat shock transcription factor (HSF) from the yeast Saccharomyces cerevisiae can adopt an altered conformation when stressed. This conformation, reflected in a change in electrophoretic mobility, requires that two HSF trimers be bound to DNA. Single trimers do not show this change, which appears to represent an alteration in the cooperative interactions between trimers. HSF isolated from stressed cells displays a higher propensity to adopt this altered conformation. Purified HSF can be stimulated in vitro to undergo the conformational change by elevating the temperature or by exposing HSF to superoxide anion. Mutational analysis maps a region critical for this conformational change to the flexible loop between the minimal DNA-binding domain and the flexible linker that joins the DNA-binding domain to the trimerization domain. The significance of these findings is discussed in the context of the induction of the heat shock response by ischemic stroke, hypoxia, and recovery from anoxia, all known to stimulate the production of superoxide