Words Volume 1 2007-2009

https://openspace.dmacc.edu/words/1000/thumbnail.jp

Role of genetic testing for inherited prostate cancer risk: Philadelphia prostate cancer consensus conference 2017

Purpose: Guidelines are limited for genetic testing for prostate cancer (PCA). The goal of this conference was to develop an expert consensus-dri

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

Intercomparison of airborne and surface-based measurements during the CLARIFY, ORACLES and LASIC field experiments

This is the final version. Available on open access from the European Geosciences Union via the DOI in this recordCode availability: Processing code for the FAAM core measurements suite is available from GitHub (Sproson et al., 2020).Data availability Airborne data for the CLARIFY campaign are available from the Centre for Environmental Data Analysis (Facility for Airborne Atmospheric Measurements et al., 2017) and for the ORACLES campaign from NASA Earth Science Project Office (ORACLES Science Team, 2020). The LASIC ground-based data sets are publicly available from the Atmospheric Radiation Measurement Climate Research Facility (Zuidema et al., 2017) with specialist data sets available for the following: SP2 – https://iop.archive.arm.gov/arm-iop/2016/ (last access: 25 October 2022, Sedlacek, 2017), CO – https://doi.org/10.5439/1046183 (Springston, 2018b), CAPS PMSSA – https://adc.arm.gov/discovery/#/results/s::caps-ssa (Onasch et al., 2015), ACSM – https://doi.org/10.5439/1763029 (Zawadowicz and Howie, 2021).Data are presented from intercomparisons between two research aircraft, the FAAM BAe-146 and the NASA Lockheed P3, and between the BAe-146 and the surface-based DOE (Department of Energy) ARM (Atmospheric Radiation Measurement) Mobile Facility at Ascension Island (8∘ S, 14.5∘ W; a remote island in the mid-Atlantic). These took place from 17 August to 5 September 2017, during the African biomass burning (BB) season. The primary motivation was to give confidence in the use of data from multiple platforms with which to evaluate numerical climate models. The three platforms were involved in the CLouds–Aerosol–Radiation Interaction and Forcing for Year 2017 (CLARIFY-2017), ObseRvations of Aerosols above CLouds and their intEractionS (ORACLES), and Layered Atlantic Smoke and Interactions with Clouds (LASIC) field experiments. Comparisons from flight segments on 6 d where the BAe-146 flew alongside the ARM facility on Ascension Island are presented, along with comparisons from the wing-tip-to-wing-tip flight of the P3 and BAe-146 on 18 August 2017. The intercomparison flight sampled a relatively clean atmosphere overlying a moderately polluted boundary layer, while the six fly-bys of the ARM site sampled both clean and polluted conditions 2–4 km upwind. We compare and validate characterisations of aerosol physical, chemical and optical properties as well as atmospheric radiation and cloud microphysics between platforms. We assess the performance of measurement instrumentation in the field, under conditions where sampling conditions are not as tightly controlled as in laboratory measurements where calibrations are performed. Solar radiation measurements compared well enough to permit radiative closure studies. Optical absorption coefficient measurements from all three platforms were within uncertainty limits, although absolute magnitudes were too low (<10 Mm−1) to fully support a comparison of the absorption Ångström exponents. Aerosol optical absorption measurements from airborne platforms were more comparable than aircraft-to-ground observations. Scattering coefficient observations compared adequately between airborne platforms, but agreement with ground-based measurements was worse, potentially caused by small differences in sampling conditions or actual aerosol population differences over land. Chemical composition measurements followed a similar pattern, with better comparisons between the airborne platforms. Thermodynamics, aerosol and cloud microphysical properties generally agreed given uncertainties.Natural Environment Research Council (NERC)NERC/Met Office Industrial Case studentshipResearch Council of NorwayUS Department of Energy, Office of ScienceNASAUS Department of Energy Atmospheric Systems Research (ASR) programm

The Youth Anxiety Measure for DSM-5 (YAM-5):Development and First Psychometric Evidence of a New Scale for Assessing Anxiety Disorders Symptoms of Children and Adolescents

The Youth Anxiety Measure for DSM-5 (YAM-5) is a new self- and parent-report questionnaire to assess anxiety disorder symptoms in children and adolescents in terms of the contemporary classification system. International panels of childhood anxiety researchers and clinicians were used to construct a scale consisting of two parts: part one consists of 28 items and measures the major anxiety disorders including separation anxiety disorder, selective mutism, social anxiety disorder, panic disorder, and generalized anxiety disorder, whereas part two contains 22 items that focus on specific phobias and (given its overlap with situational phobias) agoraphobia. In general, the face validity of the new scale was good; most of its items were successfully linked to the intended anxiety disorders. Notable exceptions were the selective mutism items, which were frequently considered as symptoms of social anxiety disorder, and some specific phobia items especially of the natural environment, situational and other type, that were regularly assigned to an incorrect category. A preliminary investigation of the YAM-5 in non-clinical (N = 132) and clinically referred (N = 64) children and adolescents indicated that the measure was easy to complete by youngsters. In addition, support was found for the psychometric qualities of the measure: that is, the internal consistency was good for both parts, as well as for most of the subscales, the parent-child agreement appeared satisfactory, and there was also evidence for the validity of the scale. The YAM-5 holds promise as a tool for assessing anxiety disorder symptoms in children and adolescents

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe