Performance and error analysis of three part of speech taggers on health texts

Increasingly, natural language processing (NLP) techniques are being developed and utilized in a variety of biomedical domains. Part of speech tagging is a critical step in many NLP applications. Currently, we are developing a NLP tool for text simplification. As part of this effort, we set off to evaluate several part of speech (POS) taggers. We selected 120 sentences (2375 tokens) from a corpus of six types of diabetes-related health texts and asked human reviewers to tag each word in these sentences to create a "Gold Standard." We then tested each of the three POS taggers against the "Gold Standard." One tagger (dTagger) had been trained on health texts and the other two (MaxEnt and Curran & Clark) were trained on general news articles. We analyzed the errors and placed them into five categories: systematic, close, subtle, difficult source, and other. The three taggers have relatively similar rates of success: dTagger, MaxEnt, and Curran & Clark had 87%, 89% and 90% agreement with the gold standard, respectively. These rates of success are lower than published rates for these taggers. This is probably due to our testing them on a corpus that differs significantly from their training corpora. The taggers made different errors: the dTagger, which had been trained on a set of medical texts (MedPost), made fewer errors on medical terms than MaxEnt and Curran & Clark. The latter two taggers performed better on non-medical terms and we found the difference between their performance and that of dTagger was statistically significant. Our findings suggest that the three POS taggers have similar correct tagging rates, though they differ in the types of errors they make. For the task of text simplification, we are inclined to perform additional training of the Curran & Clark tagger with the Medpost corpus because both the fine grained tagging provided by this tool and the correct recognition of medical terms are equally important

System Support for Bandwidth Management and Content Adaptation in Internet Applications

This paper describes the implementation and evaluation of an operating system module, the Congestion Manager (CM), which provides integrated network flow management and exports a convenient programming interface that allows applications to be notified of, and adapt to, changing network conditions. We describe the API by which applications interface with the CM, and the architectural considerations that factored into the design. To evaluate the architecture and API, we describe our implementations of TCP; a streaming layered audio/video application; and an interactive audio application using the CM, and show that they achieve adaptive behavior without incurring much end-system overhead. All flows including TCP benefit from the sharing of congestion information, and applications are able to incorporate new functionality such as congestion control and adaptive behavior.Comment: 14 pages, appeared in OSDI 200

Evaluating follow- up and complexity in cancer clinical trials (EFACCT): an eDelphi study of research professionals’ perspectives.

Objectives: To evaluate patient follow-up and complexity in cancer clinical trial delivery, using consensus methods to: (1) identify research professionals’ priorities, (2) understand localised challenges, (3) define study complexity and workloads supporting the development of a trial rating and complexity assessment tool (TRACAT). Design: A classic eDelphi completed in three rounds, conducted as the launch study to a multiphase national project (evaluating follow-up and complexity in cancer clinical trials). Setting: Multicentre online survey involving professionals at National Health Service secondary care hospital sites in Scotland and England varied in scale, geographical location and patient populations. Participants: Principal investigators at 13 hospitals across nine clinical research networks recruited 33 participants using pre-defined eligibility criteria to form a multidisciplinary panel. Main outcome measures: Statements achieving a consensus level of 70% on a 7-point Likert-type scale and ranked trial rating indicators (TRIs) developed by research professionals. Results: The panel developed 75 consensus statements illustrating factors contributing to complexity, follow-up intensity and operational performance in trial delivery, and specified 14 ranked TRIs. Seven open questions in the first qualitative round generated 531 individual statements. Iterative survey rounds returned rates of 82%, 82% and 93%. Conclusions: Clinical trials operate within a dynamic, complex healthcare and innovation system where rapid scientific advances present opportunities and challenges for delivery organisations and professionals. Panellists highlighted cultural and organisational factors limiting the profession’s potential to support growing trial complexity and patient follow-up. Enhanced communication, interoperability, funding and capacity have emerged as key priorities. Future operational models should test dialectic Singerian-based approaches respecting open dialogue and shared values. Research capacity building should prioritise innovative, collaborative approaches embedding validated review and evaluation models to understand changing operational needs and challenges. TRACAT provides a mechanism for continual knowledge assimilation to improve decision-making

Organic Indoor Location Discovery

We describe an indoor, room-level location discovery method based on spatial variations in "wifi signatures," i.e., MAC addresses and signal strengths of existing wireless access points. The principal novelty of our system is its organic nature; it builds signal strength maps from the natural mobility and lightweight contributions of ordinary users, rather than dedicated effort by a team of site surveyors. Whenever a user's personal device observes an unrecognized signature, a GUI solicits the user's location. The resulting location-tagged signature or "bind" is then shared with other clients through a common database, enabling devices subsequently arriving there to discover location with no further user contribution. Realizing a working system deployment required three novel elements: (1) a human-computer interface for indicating location over intervals of varying duration; (2) a client-server protocol for pre-fetching signature data for use in localization; and (3) a location-estimation algorithm incorporating highly variable signature data. We describe an experimental deployment of our method in a nine-story building with more than 1,400 distinct spaces served by more than 200 wireless access points. At the conclusion of the deployment, users could correctly localize to within 10 meters 92 percent of the time

Menstrual fluctuation in the symptoms of panic anxiety

Ten women with DSM-III-defined panic attacks (five with and five without agoraphobia) had symptom severity rated daily, weekly, and retrospectively through one full menstrual cycle. Substantial fluctuations in retrospective ratings of severity were observed, with the premenstrual week being rated as most severe. Daily and weekly ratings showed much smaller fluctuations in the predicted direction. Possible reasons for this outcome are considered.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/27149/1/0000143.pd

Muses

Utah State University\u27s music therapy students present a concert on Muses.https://digitalcommons.usu.edu/music_programs/1138/thumbnail.jp

Muses

Utah State University\u27s music therapy students present a concert on Muses.https://digitalcommons.usu.edu/music_programs/1138/thumbnail.jp

American Gut: an Open Platform for Citizen Science Microbiome Research

McDonald D, Hyde E, Debelius JW, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018;3(3):e00031-18

An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers

Introduction: Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers. Methods: We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals. Results: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk. Conclusions: This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.Peer reviewe

Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7×10-8, HR = 1.14, 95% CI: 1.09-1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4×10-8, HR = 1.27, 95% CI: 1.17-1.38) and 4q32.3 (rs4691139, P = 3.4×10-8, HR = 1.20, 95% CI: 1.17-1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific associat