Showing papers by "Brigham Young University published in 2018"

Analysis of shared heritability in common disorders of the brain

Abstract: Disorders of the brain can exhibit considerable epidemiological comorbidity and often share symptoms, provoking debate about their etiologic overlap. We quantified the genetic sharing of 25 brain disorders from genome-wide association studies of 265,218 patients and 784,643 control participants and assessed their relationship to 17 phenotypes from 1,191,588 individuals. Psychiatric disorders share common variant risk, whereas neurological disorders appear more distinct from one another and from the psychiatric disorders. We also identified significant sharing between disorders and a number of brain phenotypes, including cognitive measures. Further, we conducted simulations to explore how statistical power, diagnostic misclassification, and phenotypic heterogeneity affect genetic correlations. These results highlight the importance of common genetic variation as a risk factor for brain disorders and the value of heritability-based methods in understanding their etiology.

Global estimates of mortality associated with long-term exposure to outdoor fine particulate matter

Abstract: Exposure to ambient fine particulate matter (PM2.5) is a major global health concern. Quantitative estimates of attributable mortality are based on disease-specific hazard ratio models that incorporate risk information from multiple PM2.5 sources (outdoor and indoor air pollution from use of solid fuels and secondhand and active smoking), requiring assumptions about equivalent exposure and toxicity. We relax these contentious assumptions by constructing a PM2.5-mortality hazard ratio function based only on cohort studies of outdoor air pollution that covers the global exposure range. We modeled the shape of the association between PM2.5 and nonaccidental mortality using data from 41 cohorts from 16 countries-the Global Exposure Mortality Model (GEMM). We then constructed GEMMs for five specific causes of death examined by the global burden of disease (GBD). The GEMM predicts 8.9 million [95% confidence interval (CI): 7.5-10.3] deaths in 2015, a figure 30% larger than that predicted by the sum of deaths among the five specific causes (6.9; 95% CI: 4.9-8.5) and 120% larger than the risk function used in the GBD (4.0; 95% CI: 3.3-4.8). Differences between the GEMM and GBD risk functions are larger for a 20% reduction in concentrations, with the GEMM predicting 220% higher excess deaths. These results suggest that PM2.5 exposure may be related to additional causes of death than the five considered by the GBD and that incorporation of risk information from other, nonoutdoor, particle sources leads to underestimation of disease burden, especially at higher concentrations.

Exposure to opposing views on social media can increase political polarization

Abstract: There is mounting concern that social media sites contribute to political polarization by creating “echo chambers” that insulate people from opposing views about current events. We surveyed a large sample of Democrats and Republicans who visit Twitter at least three times each week about a range of social policy issues. One week later, we randomly assigned respondents to a treatment condition in which they were offered financial incentives to follow a Twitter bot for 1 month that exposed them to messages from those with opposing political ideologies (e.g., elected officials, opinion leaders, media organizations, and nonprofit groups). Respondents were resurveyed at the end of the month to measure the effect of this treatment, and at regular intervals throughout the study period to monitor treatment compliance. We find that Republicans who followed a liberal Twitter bot became substantially more conservative posttreatment. Democrats exhibited slight increases in liberal attitudes after following a conservative Twitter bot, although these effects are not statistically significant. Notwithstanding important limitations of our study, these findings have significant implications for the interdisciplinary literature on political polarization and the emerging field of computational social science.

Blended learning: the new normal and emerging technologies

Abstract: This study addressed several outcomes, implications, and possible future directions for blended learning (BL) in higher education in a world where information communication technologies (ICTs) increasingly communicate with each other. In considering effectiveness, the authors contend that BL coalesces around access, success, and students’ perception of their learning environments. Success and withdrawal rates for face-to-face and online courses are compared to those for BL as they interact with minority status. Investigation of student perception about course excellence revealed the existence of robust if-then decision rules for determining how students evaluate their educational experiences. Those rules were independent of course modality, perceived content relevance, and expected grade. The authors conclude that although blended learning preceded modern instructional technologies, its evolution will be inextricably bound to contemporary information communication technologies that are approximating some aspects of human thought processes.

The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions

Abstract: We present the molecular landscape of pediatric acute myeloid leukemia (AML) and characterize nearly 1,000 participants in Children's Oncology Group (COG) AML trials. The COG-National Cancer Institute (NCI) TARGET AML initiative assessed cases by whole-genome, targeted DNA, mRNA and microRNA sequencing and CpG methylation profiling. Validated DNA variants corresponded to diverse, infrequent mutations, with fewer than 40 genes mutated in >2% of cases. In contrast, somatic structural variants, including new gene fusions and focal deletions of MBNL1, ZEB2 and ELF1, were disproportionately prevalent in young individuals as compared to adults. Conversely, mutations in DNMT3A and TP53, which were common in adults, were conspicuously absent from virtually all pediatric cases. New mutations in GATA2, FLT3 and CBL and recurrent mutations in MYC-ITD, NRAS, KRAS and WT1 were frequent in pediatric AML. Deletions, mutations and promoter DNA hypermethylation convergently impacted Wnt signaling, Polycomb repression, innate immune cell interactions and a cluster of zinc finger-encoding genes associated with KMT2A rearrangements. These results highlight the need for and facilitate the development of age-tailored targeted therapies for the treatment of pediatric AML.

Many analysts, one dataset: Making transparent how variations in analytical choices affect results

Abstract: Twenty-nine teams involving 61 analysts used the same data set to address the same research question: whether soccer referees are more likely to give red cards to dark-skin-toned players than to light-skin-toned players. Analytic approaches varied widely across the teams, and the estimated effect sizes ranged from 0.89 to 2.93 (Mdn = 1.31) in odds-ratio units. Twenty teams (69%) found a statistically significant positive effect, and 9 teams (31%) did not observe a significant relationship. Overall, the 29 different analyses used 21 unique combinations of covariates. Neither analysts’ prior beliefs about the effect of interest nor their level of expertise readily explained the variation in the outcomes of the analyses. Peer ratings of the quality of the analyses also did not account for the variability. These findings suggest that significant variation in the results of analyses of complex data may be difficult to avoid, even by experts with honest intentions. Crowdsourcing data analysis, a strategy in which numerous research teams are recruited to simultaneously investigate the same research question, makes transparent how defensible, yet subjective, analytic choices influence research results.

Why Social Relationships Are Important for Physical Health: A Systems Approach to Understanding and Modifying Risk and Protection

Abstract: Social relationships are adaptive and crucial for survival This review presents existing evidence indicating that our social connections to others have powerful influences on health and longevity and that lacking social connection qualifies as a risk factor for premature mortality A systems perspective is presented as a framework by which to move social connection into the realm of public health Individuals, and health-relevant biological processes, exist within larger social contexts including the family, neighborhood and community, and society and culture Applying the social ecological model, this review highlights the interrelationships of individuals within groups in terms of understanding both the causal mechanisms by which social connection influences physical health and the ways in which this influence can inform potential intervention strategies A systems approach also helps identify gaps in our current understanding that may guide future research

PLANETARY CANDIDATES OBSERVED BY Kepler. VIII. A FULLY AUTOMATED CATALOG WITH MEASURED COMPLETENESS AND RELIABILITY BASED ON DATA RELEASE 25.

Abstract: We present the Kepler Object of Interest (KOI) catalog of transiting exoplanets based on searching 4 yr of Kepler time series photometry (Data Release 25, Q1–Q17). The catalog contains 8054 KOIs, of which 4034 are planet candidates with periods between 0.25 and 632 days. Of these candidates, 219 are new, including two in multiplanet systems (KOI-82.06 and KOI-2926.05) and 10 high-reliability, terrestrial-size, habitable zone candidates. This catalog was created using a tool called the Robovetter, which automatically vets the DR25 threshold crossing events (TCEs). The Robovetter also vetted simulated data sets and measured how well it was able to separate TCEs caused by noise from those caused by low signal-to-noise transits. We discuss the Robovetter and the metrics it uses to sort TCEs. For orbital periods less than 100 days the Robovetter completeness (the fraction of simulated transits that are determined to be planet candidates) across all observed stars is greater than 85%. For the same period range, the catalog reliability (the fraction of candidates that are not due to instrumental or stellar noise) is greater than 98%. However, for low signal-to-noise candidates between 200 and 500 days around FGK-dwarf stars, the Robovetter is 76.7% complete and the catalog is 50.5% reliable. The KOI catalog, the transit fits, and all of the simulated data used to characterize this catalog are available at the NASA Exoplanet Archive.

The relational view revisited: A dynamic perspective on value creation and value capture

Abstract: Research Summary: This paper extends the relational view to offer a dynamic perspective on the factors that drive value creation and value capture over the alliance life cycle. We argue that access to complementary resources provides an initial rationale for forming alliances, but benefits from complementarity can attenuate over time. Indeed, viewed dynamically, factors that often lead to higher value creation—informal trust, repeated ties, customized assets—may also lead to diminished alliance performance. We highlight interdependence between the complementary resources of partners as the critical factor determining the pattern of alliance value creation, notably how quickly alliances generate value and how quickly they are likely to dissolve. We identify factors, both internal and external to the alliance, that trigger diminished value creation and increased competition for value capture among partners. Managerial Summary: The “relational view” perspective has shown that firms create value in alliances when they identify partners with complementary resources, when they build high levels of informal trust and they share knowledge and make investments that are customized to the partner. The level of resource interdependence in alliances determines how quickly alliances can reach their potential in value creation and how quickly they are likely to dissolve. Viewed dynamically, factors that often lead to higher value creation—like informal trust, repeated ties, customized assets—may also lead to diminished alliance performance. Finally, a number of factors both internal to and external to an alliance may trigger competition between the partners within an alliance to capture the value created by the alliance and also diminish the value created within the alliance.

Ambient PM2.5 Reduces Global and Regional Life Expectancy

Abstract: Exposure to ambient fine particulate matter (PM2.5) air pollution is a major risk for premature death. Here, we systematically quantify the global impact of PM2.5 on life expectancy. Using data from the Global Burden of Disease project and actuarial standard life table methods, we estimate global and national decrements in life expectancy that can be attributed to ambient PM2.5 for 185 countries. In 2016, PM2.5 exposure reduced average global life expectancy at birth by ∼1 year with reductions of ∼1.2–1.9 years in polluted countries of Asia and Africa. If PM2.5 in all countries met the World Health Organization Air Quality Guideline (10 μg m–3), we estimate life expectancy could increase by a population-weighted median of 0.6 year (interquartile range of 0.2–1.0 year), a benefit of a magnitude similar to that of eradicating lung and breast cancer. Because background disease rates modulate the effect of air pollution on life expectancy, high age-specific rates of cardiovascular disease in many polluted low...

Short-term elevation of fine particulate matter air pollution and acute lower respiratory infection

Abstract: Rationale: Nearly 60% of U.S. children live in counties with particulate matter less than or equal to 2.5 μm in aerodynamic diameter (PM2.5) concentrations above air quality standards. Understandin...

Collecting and delivering progress feedback: A meta-analysis of routine outcome monitoring.

Abstract: This systematic review and meta-analysis examines the impact of measuring, monitoring, and feeding back information on client progress to clinicians while they deliver psychotherapy. It considers the effects of the 2 most frequently studied routine outcome monitoring (ROM) practices: The Partners for Change Outcome Management System and the Outcome Questionnaire System. Like other ROM practices, they typify attempts to enhance routine care by assisting psychotherapists in recognizing problematic treatment response and increasing collaboration between therapist and client to overcome poor treatment response. A total of 24 studies were identified and considered suitable for analysis. Two-thirds of the studies found that ROM-assisted psychotherapy was superior to treatment-as-usual offered by the same practitioners. Mean standardized effect sizes indicated that the effects ranged from small to moderate. Feedback practices reduced deterioration rates and nearly doubled clinically significant/reliable change rates in clients who were predicted to have a poor outcome. Clinical examples, diversity considerations, and therapeutic advances are provided. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

The dynamic and stress-adaptive signaling hub of 14-3-3: emerging mechanisms of regulation and context-dependent protein–protein interactions

Abstract: 14-3-3 proteins are a family of structurally similar phospho-binding proteins that regulate essentially every major cellular function. Decades of research on 14-3-3s have revealed a remarkable network of interacting proteins that demonstrate how 14-3-3s integrate and control multiple signaling pathways. In particular, these interactions place 14-3-3 at the center of the signaling hub that governs critical processes in cancer, including apoptosis, cell cycle progression, autophagy, glucose metabolism, and cell motility. Historically, the majority of 14-3-3 interactions have been identified and studied under nutrient-replete cell culture conditions, which has revealed important nutrient driven interactions. However, this underestimates the reach of 14-3-3s. Indeed, the loss of nutrients, growth factors, or changes in other environmental conditions (e.g., genotoxic stress) will not only lead to the loss of homeostatic 14-3-3 interactions, but also trigger new interactions, many of which are likely stress adaptive. This dynamic nature of the 14-3-3 interactome is beginning to come into focus as advancements in mass spectrometry are helping to probe deeper and identify context-dependent 14-3-3 interactions—providing a window into adaptive phosphorylation-driven cellular mechanisms that orchestrate the tumor cell’s response to a variety of environmental conditions including hypoxia and chemotherapy. In this review, we discuss emerging 14-3-3 regulatory mechanisms with a focus on post-translational regulation of 14-3-3 and dynamic protein–protein interactions that illustrate 14-3-3’s role as a stress-adaptive signaling hub in cancer.

A photophoretic-trap volumetric display

Abstract: Photophoretic optical trapping of cellulose particles and persistence of vision are used to produce real-space volumetric images that can be viewed from all angles, in geometries unachievable by holograms and light-field technologies. Three-dimensional moving images have long been the stuff of science fiction. In reality, the appearance of three dimensions is usually approximated by manipulating light, but such approaches have limitations such as narrow viewing angles and the need for special viewing headwear. Daniel Smalley and colleagues offer a solution in which a three-dimensional object can be represented in real space, viewed from any angle, and even coexist with—and wrap around—solid objects that occupy the same physical volume. A near-invisible light field traps and moves a small particle through a volume of space. As the particle moves, it is illuminated using red, green and blue laser light, producing an arbitrarily coloured point-source that maps out the surface of the object to be imaged. If the particle scanning is fast enough, persistence of vision, which results from the slower 'refresh rate' of the human eye, gives the appearance of a solid three-dimensional surface. At even faster scanning rates, the imaged object can appear to move. Free-space volumetric displays, or displays that create luminous image points in space, are the technology that most closely resembles the three-dimensional displays of popular fiction1. Such displays are capable of producing images in ‘thin air’ that are visible from almost any direction and are not subject to clipping. Clipping restricts the utility of all three-dimensional displays that modulate light at a two-dimensional surface with an edge boundary; these include holographic displays, nanophotonic arrays, plasmonic displays, lenticular or lenslet displays and all technologies in which the light scattering surface and the image point are physically separate. Here we present a free-space volumetric display based on photophoretic optical trapping2 that produces full-colour graphics in free space with ten-micrometre image points using persistence of vision. This display works by first isolating a cellulose particle in a photophoretic trap created by spherical and astigmatic aberrations. The trap and particle are then scanned through a display volume while being illuminated with red, green and blue light. The result is a three-dimensional image in free space with a large colour gamut, fine detail and low apparent speckle. This platform, named the Optical Trap Display, is capable of producing image geometries that are currently unobtainable with holographic and light-field technologies, such as long-throw projections, tall sandtables and ‘wrap-around’ displays1.

Strategic Silence: Withholding Certification Status as a Hypocrisy Avoidance Tactic

Abstract: We examine why organizations that obtain prominent certifications may at times elect not to publicize them. Drawing on the impression management literature, we argue and show that concerns about be...

Rapid transition from continental breakup to igneous oceanic crust in the South China Sea

Abstract: Continental breakup represents the successful process of rifting and thinning of the continental lithosphere, leading to plate rupture and initiation of oceanic crust formation. Magmatism during breakup seems to follow a path of either excessive, transient magmatism (magma-rich margins) or of igneous starvation (magma-poor margins). The latter type is characterized by extreme continental lithospheric extension and mantle exhumation prior to igneous oceanic crust formation. Discovery of magma-poor margins has raised fundamental questions about the onset of ocean-floor type magmatism, and has guided interpretation of seismic data across many rifted margins, including the highly extended northern South China Sea margin. Here we report International Ocean Discovery Program drilling data from the northern South China Sea margin, testing the magma-poor margin model outside the North Atlantic. Contrary to expectations, results show initiation of Mid-Ocean Ridge basalt type magmatism during breakup, with a narrow and rapid transition into igneous oceanic crust. Coring and seismic data suggest that fast lithospheric extension without mantle exhumation generated a margin structure between the two endmembers. Asthenospheric upwelling yielding Mid-Ocean Ridge basalt-type magmatism from normal-temperature mantle during final breakup is interpreted to reflect rapid rifting within thin pre-rift lithosphere.

The strength model of self-regulation: Conclusions from the second decade of willpower research

Abstract: The strength model of self-regulation uses a muscle analogy to explain patterns of ego depletion, conservation of willpower, and improved performance after frequent exercise. Our 2007 overview of the literature has been well cited, presumably because of the phenomenon's importance to theories of selfhood and a wide assortment of applied contexts, including problem behaviors. Some researchers have put forward rival theoretical accounts, and others have questioned the existence of the phenomenon. The weight of evidence continues to support the usefulness of the strength model, albeit amid continuing updates and revisions.

Genomic architecture and introgression shape a butterfly radiation

Abstract: We here pioneer a low-cost assembly strategy for 20 Heliconiini genomes to characterize the evolutionary history of the rapidly radiating genus Heliconius. A bifurcating tree provides a poor fit to the data, and we therefore explore a reticulate phylogeny for Heliconius. We probe the genomic architecture of gene flow, and develop a new method to distinguish incomplete lineage sorting from introgression. We find that most loci with non-canonical histories arose through introgression, and are strongly underrepresented in regions of low recombination and low gene density. This is expected if introgressed alleles are more likely to be purged in such regions due to tighter linkage with incompatibility loci. Finally, we identify a hitherto unrecognized inversion, and show it is a convergent structural rearrangement that captures a known color pattern switch locus within the genus. Our multi-genome assembly approach enables an improved understanding of adaptive radiation.

Cooperating with machines.

Abstract: Since Alan Turing envisioned artificial intelligence, technical progress has often been measured by the ability to defeat humans in zero-sum encounters (e.g., Chess, Poker, or Go). Less attention has been given to scenarios in which human–machine cooperation is beneficial but non-trivial, such as scenarios in which human and machine preferences are neither fully aligned nor fully in conflict. Cooperation does not require sheer computational power, but instead is facilitated by intuition, cultural norms, emotions, signals, and pre-evolved dispositions. Here, we develop an algorithm that combines a state-of-the-art reinforcement-learning algorithm with mechanisms for signaling. We show that this algorithm can cooperate with people and other algorithms at levels that rival human cooperation in a variety of two-player repeated stochastic games. These results indicate that general human–machine cooperation is achievable using a non-trivial, but ultimately simple, set of algorithmic mechanisms.

Defining OER-Enabled Pedagogy

Abstract: The term “open pedagogy” has been used in a variety of different ways over the past several decades. In recent years, its use has also become associated with Open Educational Resources (OER). The wide range of competing definitions of open pedagogy, together with its semantic overlap with another underspecified term, open educational practices, makes it difficult to conduct research on the topic of open pedagogy. In making this claim we do not mean to cast doubt on the potential effectiveness of the many pedagogical approaches labeled open. In this article, rather than attempting to argue for a canonical definition of open pedagogy, we propose a new term, “OER-enabled pedagogy,” defined as the set of teaching and learning practices that are only possible or practical in the context of the 5R permissions that are characteristic of OER. We propose criteria used to evaluate whether a form of teaching constitutes OER-enabled pedagogy and analyze several examples of OER-enabled pedagogy with these criteria.

Organic phosphorus in the terrestrial environment: a perspective on the state of the art and future priorities

Abstract: Background: The dynamics of phosphorus (P) in the environment is important for regulating nutrient cycles in natural and managed ecosystems and an integral part in assessing biological resilience against environmental change. Organic P (Po) compounds play key roles in biological and ecosystems function in the terrestrial environment being critical to cell function, growth and reproduction. Scope: We asked a group of experts to consider the global issues associated with Po in the terrestrial environment, methodological strengths and weaknesses, benefits to be gained from understanding the Po cycle, and to set priorities for Po research. Conclusions: We identified seven key opportunities for Po research including: the need for integrated, quality controlled and functionally based methodologies; assessment of stoichiometry with other elements in organic matter; understanding the dynamics of Po in natural and managed systems; the role of microorganisms in controlling Po cycles; the implications of nanoparticles in the environment and the need for better modelling and communication of the research. Each priority is discussed and a statement of intent for the Po research community is made that highlights there are key contributions to be made toward understanding biogeochemical cycles, dynamics and function of natural ecosystems and the management of agricultural systems.

Unexpected spatial stability of water chemistry in headwater stream networks.

Abstract: Understanding how water and solutes enter and propagate through freshwater landscapes in the Anthropocene is critical to protecting and restoring aquatic ecosystems and ensuring human water security. However, high hydrochemical variability in headwater streams, where most carbon and nutrients enter river networks, has hindered effective modelling and management. We developed an analytical framework informed by landscape ecology and catchment hydrology to quantify spatiotemporal variability across scales, which we tested in 56 headwater catchments, sampled periodically over 12 years in western France. Unexpectedly, temporal variability in dissolved carbon, nutrients and major ions was preserved moving downstream and spatial patterns of water chemistry were stable on annual to decadal timescales, partly because of synchronous variation in solute concentrations. These findings suggest that while concentration and flux cannot be extrapolated among subcatchments, periodic sampling of headwaters provides valuable information about solute sources and subcatchment resilience to disturbance.

Language learning and study abroad

Abstract: The aim of this review is to synthesize empirical studies on undergraduate language learners’ experience abroad during a time period of a year or less To help provide a framework to this synthesis, we begin our review by tracing the recent evolution of empirical mixed-method research on the learner, identifying problems and characteristics that language learners generally encounter in the study abroad (SA) experience We take a closer look at variables related to individual difference such as anxiety, motivation, and attitudes to more recent views of learner identity in language learning We highlight the shift to language learner agency, a topic that merits more discussion in SA literature We then review how the SA learning environments are treated This review takes a closer look at research informed by socially grounded theories Finally, we review the role that SA plays in undergraduate language curricula, where the objectives of the experience are aligned with at-home (AH) curricula, a topic that has not been fully discussed in SA literature The conclusions offer suggestions for keeping pace with the broader field of applied/educational linguistics

Pairwise Confusion for Fine-Grained Visual Classification

Abstract: Fine-Grained Visual Classification (FGVC) datasets contain small sample sizes, along with significant intra-class variation and inter-class similarity. While prior work has addressed intra-class variation using localization and segmentation techniques, inter-class similarity may also affect feature learning and reduce classification performance. In this work, we address this problem using a novel optimization procedure for the end-to-end neural network training on FGVC tasks. Our procedure, called Pairwise Confusion (PC) reduces overfitting by intentionally introducing confusion in the activations. With PC regularization, we obtain state-of-the-art performance on six of the most widely-used FGVC datasets and demonstrate improved localization ability. PC is easy to implement, does not need excessive hyperparameter tuning during training, and does not add significant overhead during test time.

Reviews and syntheses: Changing ecosystem influences on soil thermal regimes in northern high-latitude permafrost regions

Abstract: . Soils in Arctic and boreal ecosystems store twice as much carbon as the atmosphere, a portion of which may be released as high-latitude soils warm. Some of the uncertainty in the timing and magnitude of the permafrost–climate feedback stems from complex interactions between ecosystem properties and soil thermal dynamics. Terrestrial ecosystems fundamentally regulate the response of permafrost to climate change by influencing surface energy partitioning and the thermal properties of soil itself. Here we review how Arctic and boreal ecosystem processes influence thermal dynamics in permafrost soil and how these linkages may evolve in response to climate change. While many of the ecosystem characteristics and processes affecting soil thermal dynamics have been examined individually (e.g., vegetation, soil moisture, and soil structure), interactions among these processes are less understood. Changes in ecosystem type and vegetation characteristics will alter spatial patterns of interactions between climate and permafrost. In addition to shrub expansion, other vegetation responses to changes in climate and rapidly changing disturbance regimes will affect ecosystem surface energy partitioning in ways that are important for permafrost. Lastly, changes in vegetation and ecosystem distribution will lead to regional and global biophysical and biogeochemical climate feedbacks that may compound or offset local impacts on permafrost soils. Consequently, accurate prediction of the permafrost carbon climate feedback will require detailed understanding of changes in terrestrial ecosystem distribution and function, which depend on the net effects of multiple feedback processes operating across scales in space and time.