Reproducibility of the bronchoconstrictive response to eucapnic voluntary hyperpnoea

Background: Eucapnic voluntary hyperpnoea (EVH) is considered an effective bronchoprovocation challenge for identifying exercise-induced bronchoconstriction (EIB). However, the reproducibility of the hyperpnoea-induced bronchoconstriction (HIB) response elicited by EVH remains unknown and was therefore the focus of this study. Methods: Two cohorts of 16 physically active males (each cohort comprised 8 controls and 8 with physician diagnosis of asthma) participated in two studies of the short- and long-term reproducibility of the bronchoconstrictive response to an EVH test with dry air. EVH was performed on days 0, 7, 14, and 21 (short-term study), and 0, 35, and 70 (long-term study). HIB was diagnosed by a ≥10% fall in forced expiratory volume in 1 s (FEV1) after EVH. Results: On day 0 of the short-term study, FEV1 fell by 2 ± 1% (P < 0.05) and 27 ± 18% (P < 0.01) from pre-to post-EVH in control and HIB-positive groups respectively. The post-EVH fall in FEV1 did not differ across the short-term study test days. In the HIB-positive group, the day-to-day coefficient of variation, reproducibility, and smallest meaningful change for the fall in FEV1 were 12%, 328 mL, and 164 mL, respectively. On day 0 of the long-term study, FEV1 fell by 2 ± 2% and 25 ± 18% (P < 0.01) after EVH in control and HIB-positive groups respectively. The post-EVH fall in FEV1 did not differ across the long-term study test days. In the HIB-positive group, the day-to-day coefficient of variation, reproducibility, and smallest meaningful change for the fall in FEV1 were 10%, 196 mL, and 98 mL respectively. Conclusion: The EVH test elicits a reproducible bronchoconstrictive response in physically active males with physician diagnosed asthma. These data thus support the clinical utility of the EVH test for EIB screening and monitoring

Towards Large-scale Inconsistency Measurement

We investigate the problem of inconsistency measurement on large knowledge bases by considering stream-based inconsistency measurement, i.e., we investigate inconsistency measures that cannot consider a knowledge base as a whole but process it within a stream. For that, we present, first, a novel inconsistency measure that is apt to be applied to the streaming case and, second, stream-based approximations for the new and some existing inconsistency measures. We conduct an extensive empirical analysis on the behavior of these inconsistency measures on large knowledge bases, in terms of runtime, accuracy, and scalability. We conclude that for two of these measures, the approximation of the new inconsistency measure and an approximation of the contension inconsistency measure, large-scale inconsistency measurement is feasible.Comment: International Workshop on Reactive Concepts in Knowledge Representation (ReactKnow 2014), co-located with the 21st European Conference on Artificial Intelligence (ECAI 2014). Proceedings of the International Workshop on Reactive Concepts in Knowledge Representation (ReactKnow 2014), pages 63-70, technical report, ISSN 1430-3701, Leipzig University, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-15056

Scatteract: Automated extraction of data from scatter plots

Charts are an excellent way to convey patterns and trends in data, but they do not facilitate further modeling of the data or close inspection of individual data points. We present a fully automated system for extracting the numerical values of data points from images of scatter plots. We use deep learning techniques to identify the key components of the chart, and optical character recognition together with robust regression to map from pixels to the coordinate system of the chart. We focus on scatter plots with linear scales, which already have several interesting challenges. Previous work has done fully automatic extraction for other types of charts, but to our knowledge this is the first approach that is fully automatic for scatter plots. Our method performs well, achieving successful data extraction on 89% of the plots in our test set.Comment: Submitted to ECML PKDD 2017 proceedings, 16 page

The effects of peer influence on adolescent pedestrian road-crossing decisions

Objective: Adolescence is a high-risk period for pedestrian injury. It is also a time of heightened susceptibility to peer influence. The aim of this research was to examine the effects of peer influence on the pedestrian road-crossing decisions of adolescents. Methods: Using 10 videos of road-crossing sites, 80 16- to 18-year-olds were asked to make pedestrian road-crossing decisions. Participants were assigned to one of 4 experimental conditions: negative peer (influencing unsafe decisions), positive peer (influencing cautious decisions), silent peer (who observed but did not comment), and no peer (the participant completed the task alone). Peers from the adolescent’s own friendship group were recruited to influence either an unsafe or a cautious decision. Results: Statistically significant differences were found between peer conditions. Participants least often identified safe road-crossing sites when accompanied by a negative peer and more frequently identified dangerous road-crossing sites when accompanied by a positive peer. Both cautious and unsafe comments from a peer influenced adolescent pedestrians’ decisions. Conclusions: These findings showed that road-crossing decisions of adolescents were influenced by both unsafe and cautious comments from their peers. The discussion highlighted the role that peers can play in both increasing and reducing adolescent risk-taking

Host genetics and viral load in primary HIV-1 infection: clear evidence for gene by sex interactions

© 2014, The Author(s).Research in the past two decades has generated unequivocal evidence that host genetic variations substantially account for the heterogeneous outcomes following human immunodeficiency virus type 1 (HIV-1) infection. In particular, genes encoding human leukocyte antigens (HLA) have various alleles, haplotypes, or specific motifs that can dictate the set-point (a relatively steady state) of plasma viral load (VL), although rapid viral evolution driven by innate and acquired immune responses can obscure the long-term relationships between HLA genotypes and HIV-1-related outcomes. In our analyses of VL data from 521 recent HIV-1 seroconverters enrolled from eastern and southern Africa, HLA-A*03:01 was strongly and persistently associated with low VL in women (frequency = 11.3 %, P  0.50). In a reduced multivariable model, age, sex, geography (clinical sites), previously identified HLA factors (HLA-B*18, B*45, B*53, and B*57), and the interaction term for female sex and HLA-A*03:01 collectively explained 17.0 % of the overall variance in geometric mean VL over a 3-year follow-up period (P < 0.0001). Multiple sensitivity analyses of longitudinal and cross-sectional VL data yielded consistent results. These findings can serve as a proof of principle that the gap of “missing heritability” in quantitative genetics can be partially bridged by a systematic evaluation of sex-specific associations

A fixed-target platform for serial femtosecond crystallography in a hydrated environment.

For serial femtosecond crystallography at X-ray free-electron lasers, which entails collection of single-pulse diffraction patterns from a constantly refreshed supply of microcrystalline sample, delivery of the sample into the X-ray beam path while maintaining low background remains a technical challenge for some experiments, especially where this methodology is applied to relatively low-ordered samples or those difficult to purify and crystallize in large quantities. This work demonstrates a scheme to encapsulate biological samples using polymer thin films and graphene to maintain sample hydration in vacuum conditions. The encapsulated sample is delivered into the X-ray beam on fixed targets for rapid scanning using the Roadrunner fixed-target system towards a long-term goal of low-background measurements on weakly diffracting samples. As a proof of principle, we used microcrystals of the 24 kDa rapid encystment protein (REP24) to provide a benchmark for polymer/graphene sandwich performance. The REP24 microcrystal unit cell obtained from our sandwiched in-vacuum sample was consistent with previously established unit-cell parameters and with those measured by us without encapsulation in humidified helium, indicating that the platform is robust against evaporative losses. While significant scattering from water was observed because of the sample-deposition method, the polymer/graphene sandwich itself was shown to contribute minimally to background scattering

Building Interprofessional Global Health Infrastructure at a University and Health System: Navigating Challenges and Scaling Successes

Mission: Global Jefferson will create sustainable programs of global distinction through collaboration that position Jefferson as a local and international destination and resource for education, research, and clinical activities. Global Jefferson is supported by the Associate Provost for Global Affairs, part of the Office of the Provost. Global activity at Jefferson includes: Global Health Initiatives Committee (GHIC) Service Learning Global Research & Exchange between institutions Pre-clinical, translational, clinical, and applied research Poster presented at: 8th Annual Global Health Conference of the Consortium of Universities for Global Health (CUGH)https://jdc.jefferson.edu/globalhealthposters/1000/thumbnail.jp

Privacy-preserving collaborative machine learning on genomic data using TensorFlow

Machine learning (ML) methods have been widely used in genomic studies. However, genomic data are often held by different stakeholders (e.g. hospitals, universities, and healthcare companies) who consider the data as sensitive information, even though they desire to collaborate. To address this issue, recent works have proposed solutions using Secure Multi-party Computation (MPC), which train on the decentralized data in a way that the participants could learn nothing from each other beyond the final trained model. We design and implement several MPC-friendly ML primitives, including class weight adjustment and parallelizable approximation of activation function. In addition, we develop the solution as an extension to TF Encrypted~\citep{dahl2018private}, enabling us to quickly experiment with enhancements of both machine learning techniques and cryptographic protocols while leveraging the advantages of TensorFlow's optimizations. Our implementation compares favorably with state-of-the-art methods, winning first place in Track IV of the iDASH2019 secure genome analysis competition.Comment: Description of the winning solution at Track IV of iDASH competition 2019, to be presented at the Trustworthy ML workshop co-located with ICLR202