Word Adjacency Graph Modeling: Separating Signal From Noise in Big Data

There is a need to develop methods to analyze Big Data to inform patient-centered interventions for better health outcomes. The purpose of this study was to develop and test a method to explore Big Data to describe salient health concerns of people with epilepsy. Specifically, we used Word Adjacency Graph modeling to explore a data set containing 1.9 billion anonymous text queries submitted to the ChaCha question and answer service to (a) detect clusters of epilepsy-related topics, and (b) visualize the range of epilepsy-related topics and their mutual proximity to uncover the breadth and depth of particular topics and groups of users. Applied to a large, complex data set, this method successfully identified clusters of epilepsy-related topics while allowing for separation of potentially non-relevant topics. The method can be used to identify patient-driven research questions from large social media data sets and results can inform the development of patient-centered interventions

The delay-reward heuristic: What do people expect in intertemporal choice tasks?

Recent research has shown that risk and reward are positively correlated in many environments, and that people have internalized this association as a "risk-reward heuristic": when making choices based on incomplete information, people infer probabilities from payoffs and vice-versa, and these inferences shape their decisions. We extend this work by examining people's expectations about another fundamental trade-off-that between monetary reward and delay. In 2 experiments (total N = 670), we adapted a paradigm previously used to demonstrate the risk-reward heuristic. We presented participants with intertemporal choice tasks in which either the delayed reward or the length of the delay was obscured. Participants inferred larger rewards for longer stated delays, and longer delays for larger stated rewards; these inferences also predicted people's willingness to take the delayed option. In exploratory analyses, we found that older participants inferred longer delays and smaller rewards than did younger ones. All of these results replicated in 2 large-scale pre-registered studies with participants from a different population (total N = 2138). Our results suggest that people expect intertemporal choice tasks to offer a trade-off between delay and reward, and differ in their expectations about this trade-off. This "delay-reward heuristic" offers a new perspective on existing models of intertemporal choice and provides new insights into unexplained and systematic individual differences in the willingness to delay gratification

Transmission and Transport of Energy in the Western U.S. and Canada: A Law and Policy Road Map

This collection of short essays arose from the inaugural meeting of the Idaho Symposium on Energy in the West, which was held in November, 2014. The topic for this first Symposium was Transmission and Transport of Energy in the Western U.S. and Canada: A Law and Policy Road Map. The essays in this collection provide a notable introduction to the major energy issues facing the West today. Topics include: building a resilient legal architecture for western energy production; natural gas flaring; transmission planning for wind energy; utilities and rooftop solar; special considerations for western states and the Clean Power Plan; the Clean Power Plan\u27s implications for the western grid; siting renewable energy on public lands; and implications of utility reform in New York and Hawaii for the Northwest

Finding the Patient’s Voice Using Big Data: Analysis of Users’ Health-Related Concerns in the ChaCha Question-and-Answer Service (2009–2012)

Background: The development of effective health care and public health interventions requires a comprehensive understanding of the perceptions, concerns, and stated needs of health care consumers and the public at large. Big datasets from social media and question-and-answer services provide insight into the public’s health concerns and priorities without the financial, temporal, and spatial encumbrances of more traditional community-engagement methods and may prove a useful starting point for public-engagement health research (infodemiology). Objective: The objective of our study was to describe user characteristics and health-related queries of the ChaCha question-and-answer platform, and discuss how these data may be used to better understand the perceptions, concerns, and stated needs of health care consumers and the public at large. Methods: We conducted a retrospective automated textual analysis of anonymous user-generated queries submitted to ChaCha between January 2009 and November 2012. A total of 2.004 billion queries were read, of which 3.50% (70,083,796/2,004,243,249) were missing 1 or more data fields, leaving 1.934 billion complete lines of data for these analyses. Results: Males and females submitted roughly equal numbers of health queries, but content differed by sex. Questions from females predominantly focused on pregnancy, menstruation, and vaginal health. Questions from males predominantly focused on body image, drug use, and sexuality. Adolescents aged 12–19 years submitted more queries than any other age group. Their queries were largely centered on sexual and reproductive health, and pregnancy in particular. Conclusions: The private nature of the ChaCha service provided a perfect environment for maximum frankness among users, especially among adolescents posing sensitive health questions. Adolescents’ sexual health queries reveal knowledge gaps with serious, lifelong consequences. The nature of questions to the service provides opportunities for rapid understanding of health concerns and may lead to development of more effective tailored interventions. [J Med Internet Res 2016;18(3):e44

Reorganization of surviving mammal communities after the end-Pleistocene megafaunal extinction

Large mammals are at high risk of extinction globally. To understand the consequences of their demise for community assembly, we tracked community structure through the end- Pleistocene megafaunal extinction in North America.We decomposed the effects of biotic and abiotic factors by analyzing co-occurrence within the mutual ranges of species pairs. Although shifting climate drove an increase in niche overlap, co-occurrence decreased, signaling shifts in biotic interactions. Furthermore, the effect of abiotic factors on cooccurrence remained constant over time while the effect of biotic factors decreased. Biotic factors apparently played a key role in continental-scale community assembly before the extinctions. Specifically, large mammals likely promoted co-occurrence in the Pleistocene, and their loss contributed to the modern assembly pattern in which co-occurrence frequently falls below random expectations. Includes supplementary materials

Reorganization of surviving mammal communities after the end-Pleistocene megafaunal extinction

Large mammals are at high risk of extinction globally. To understand the consequences of their demise for community assembly, we tracked community structure through the end-Pleistocene megafaunal extinction in North America. We decomposed the effects of biotic and abiotic factors by analyzing co-occurrence within the mutual ranges of species pairs. Although shifting climate drove an increase in niche overlap, co-occurrence decreased, signaling shifts in biotic interactions. Furthermore, the effect of abiotic factors on co-occurrence remained constant over time while the effect of biotic factors decreased. Biotic factors apparently played a key role in continental-scale community assembly before the extinctions. Specifically, large mammals likely promoted co-occurrence in the Pleistocene, and their loss contributed to the modern assembly pattern in which co-occurrence frequently falls below random expectations.Peer reviewe

Investigating Biotic Interactions in Deep Time

Recent renewed interest in using fossil data to understand how biotic interactions have shaped the evolution of life is challenging the widely held assumption that long-term climate changes are the primary drivers of biodiversity change. New approaches go beyond traditional richness and co-occurrence studies to explicitly model biotic interactions using data on fossil and modern biodiversity. Important developments in three primary areas of research include analysis of (i) macroevolutionary rates, (ii) the impacts of and recovery from extinction events, and (iii) how humans (Homo sapiens) affected interactions among non-human species. We present multiple lines of evidence for an important and measurable role of biotic interactions in shaping the evolution of communities and lineages on long timescales.Peer reviewe

Combined approaches, including long-read sequencing, address the diagnostic challenge of HYDIN in primary ciliary dyskinesia

Primary ciliary dyskinesia (PCD), a disorder of the motile cilia, is now recognised as an underdiagnosed cause of bronchiectasis. Accurate PCD diagnosis comprises clinical assessment, analysis of cilia and the identification of biallelic variants in one of 50 known PCD-related genes, including HYDIN. HYDIN-related PCD is underdiagnosed due to the presence of a pseudogene, HYDIN2, with 98% sequence homology to HYDIN. This presents a significant challenge for Short-Read Next Generation Sequencing (SR-NGS) and analysis, and many diagnostic PCD gene panels do not include HYDIN. We have used a combined approach of SR-NGS with bioinformatic masking of HYDIN2, and state-of-the-art long-read Nanopore sequencing (LR_NGS), together with analysis of respiratory cilia including transmission electron microscopy and immunofluorescence to address the underdiagnosis of HYDIN as a cause of PCD. Bioinformatic masking of HYDIN2 after SR-NGS facilitated the detection of biallelic HYDIN variants in 15 of 437 families, but compromised the detection of copy number variants. Supplementing testing with LR-NGS detected HYDIN deletions in 2 families, where SR-NGS had detected a single heterozygous HYDIN variant. LR-NGS was also able to confirm true homozygosity in 2 families when parental testing was not possible. Utilising a combined genomic diagnostic approach, biallelic HYDIN variants were detected in 17 families from 242 genetically confirmed PCD cases, comprising 7% of our PCD cohort. This represents the largest reported HYDIN cohort to date and highlights previous underdiagnosis of HYDIN-associated PCD. Moreover this provides further evidence for the utility of LR-NGS in diagnostic testing, particularly for regions of high genomic complexity.</p

Late quaternary biotic homogenization of North American mammalian faunas

Biotic homogenization-increasing similarity of species composition among ecological communities-has been linked to anthropogenic processes operating over the last century. Fossil evidence, however, suggests that humans have had impacts on ecosystems for millennia. We quantify biotic homogenization of North American mammalian assemblages during the late Pleistocene through Holocene (similar to 30,000 ybp to recent), a timespan encompassing increased evidence of humans on the landscape (similar to 20,000-14,000 ybp). From similar to 10,000 ybp to recent, assemblages became significantly more homogenous (>100% increase in Jaccard similarity), a pattern that cannot be explained by changes in fossil record sampling. Homogenization was most pronounced among mammals larger than 1 kg and occurred in two phases. The first followed the megafaunal extinction at similar to 10,000 ybp. The second, more rapid phase began during human population growth and early agricultural intensification (similar to 2,000-1,000 ybp). We show that North American ecosystems were homogenizing for millennia, extending human impacts back similar to 10,000 years.Peer reviewe