Showing papers by "San Diego State University published in 2016"

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Abstract: The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Hearing impairment and cognitive energy: the Framework for Understanding Effortful Listening (FUEL)

Abstract: The Fifth Eriksholm Workshop on “Hearing Impairment and Cognitive Energy” was convened to develop a consensus among interdisciplinary experts about what is known on the topic, gaps in knowledge, the use of terminology, priorities for future research, and implications for practice. The general term cognitive energy was chosen to facilitate the broadest possible discussion of the topic. It goes back to Titchener (1908) who described the effects of attention on perception; he used the term psychic energy for the notion that limited mental resources can be flexibly allocated among perceptual and mental activities. The workshop focused on three main areas: (1) theories, models, concepts, definitions, and frameworks; (2) methods and measures; and (3) knowledge translation. We defined effort as the deliberate allocation of mental resources to overcome obstacles in goal pursuit when carrying out a task, with listening effort applying more specifically when tasks involve listening. We adapted Kahneman’s seminal (1973) Capacity Model of Attention to listening and proposed a heuristically useful Framework for Understanding Effortful Listening (FUEL). Our FUEL incorporates the well-known relationship between cognitive demand and the supply of cognitive capacity that is the foundation of cognitive theories of attention. Our FUEL also incorporates a motivation dimension based on complementary theories of motivational intensity, adaptive gain control, and optimal performance, fatigue, and pleasure. Using a three-dimensional illustration, we highlight how listening effort depends not only on hearing difficulties and task demands but also on the listener’s motivation to expend mental effort in the challenging situations of everyday life.

Compensation Topologies of High-Power Wireless Power Transfer Systems

Abstract: Wireless power transfer (WPT) is an emerging technology that can realize electric power transmission over certain distances without physical contact, offering significant benefits to modern automation systems, medical applications, consumer electronics, etc. This paper provides a comprehensive review of existing compensation topologies for the loosely coupled transformer. Compensation topologies are reviewed and evaluated based on their basic and advanced functions. Individual passive resonant networks used to achieve constant (load-independent) voltage or current output are analyzed and summarized. Popular WPT compensation topologies are given as application examples, which can be regarded as the combination of multiple blocks of resonant networks. Analyses of the input zero phase angle and soft switching are conducted as well. This paper also discusses the compensation requirements for achieving the maximum efficiency according to different WPT application areas.

Modern Advances in Wireless Power Transfer Systems for Roadway Powered Electric Vehicles

Abstract: Wireless power transfer system (WPTS)-based wireless electric vehicles, classified into roadway-powered electric vehicles (RPEVs) and stationary charging electric vehicles (SCEVs), are in the spotlight as future mainstream transportations. RPEVs are free from serious battery problems such as large, heavy, and expensive battery packs and long charging time because they get power directly from the road while moving. The power transfer capacity, efficiency, lateral tolerance, electromagnetic field, air-gap, size, weight, and cost of the WPTSs have been improved by virtues of innovative semiconductor switches, better coil designs, roadway construction techniques, and higher operating frequency. Recent advances in WPTSs for RPEVs are summarized in this review paper. The fifth- and sixth-generation online electric vehicles, which reduce infrastructure cost for commercialization, and the interoperability between RPEVs and SCEVs are addressed in detail in this paper. Major milestones of the developments of other RPEVs are also summarized. The rest of this paper deals with a few important technical issues such as coil structures, power supply schemes, and segmentation switching techniques of a lumped inductive power transfer system for RPEVs.

Challenges in microbial ecology: building predictive understanding of community function and dynamics

Abstract: The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth’s soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development with mathematical model building. We discuss specific examples where model–experiment integration has already resulted in important insights into MC function and structure. We also highlight key research questions that still demand better integration of experiments and models. We argue that such integration is needed to achieve significant progress in our understanding of MC dynamics and function, and we make specific practical suggestions as to how this could be achieved.

Pan-Arctic ice-wedge degradation in warming permafrost and its influence on tundra hydrology

Abstract: Ice wedges are common features of the subsurface in permafrost regions. They develop by repeated frost cracking and ice vein growth over hundreds to thousands of years. Ice-wedge formation causes the archetypal polygonal patterns seen in tundra across the Arctic landscape. Here we use field and remote sensing observations to document polygon succession due to ice-wedge degradation and trough development in ten Arctic localities over sub-decadal timescales. Initial thaw drains polygon centres and forms disconnected troughs that hold isolated ponds. Continued ice-wedge melting leads to increased trough connectivity and an overall draining of the landscape. We find that melting at the tops of ice wedges over recent decades and subsequent decimetre-scale ground subsidence is a widespread Arctic phenomenon. Although permafrost temperatures have been increasing gradually, we find that ice-wedge degradation is occurring on sub-decadal timescales. Our hydrological model simulations show that advanced ice-wedge degradation can significantly alter the water balance of lowland tundra by reducing inundation and increasing runoff, in particular due to changes in snow distribution as troughs form. We predict that ice-wedge degradation and the hydrological changes associated with the resulting differential ground subsidence will expand and amplify in rapidly warming permafrost regions. The polygonal patterns in permafrost regions are caused by the formation of ice wedges. Observations of polygon evolution reveal that rapid ice-wedge melting has occurred across the Arctic since 1950, altering tundra hydrology.

Updated Clinical Guidelines for Diagnosing Fetal Alcohol Spectrum Disorders

Abstract: The adverse effects of prenatal alcohol exposure constitute a continuum of disabilities (fetal alcohol spectrum disorders [FASD]). In 1996, the Institute of Medicine established diagnostic categories delineating the spectrum but not specifying clinical criteria by which diagnoses could be assigned. In 2005, the authors published practical guidelines operationalizing the Institute of Medicine categories, allowing for standardization of FASD diagnoses in clinical settings. The purpose of the current report is to present updated diagnostic guidelines based on a thorough review of the literature and the authors’ combined expertise based on the evaluation of >10 000 children for potential FASD in clinical settings and in epidemiologic studies in conjunction with National Institute on Alcohol Abuse and Alcoholism–funded studies, the Collaborative Initiative on Fetal Alcohol Spectrum Disorders, and the Collaboration on FASD Prevalence. The guidelines were formulated through conference calls and meetings held at National Institute on Alcohol Abuse and Alcoholism offices in Rockville, MD. Specific areas addressed include the following: precise definition of documented prenatal alcohol exposure; neurobehavioral criteria for diagnosis of fetal alcohol syndrome, partial fetal alcohol syndrome, and alcohol-related neurodevelopmental disorder; revised diagnostic criteria for alcohol-related birth defects; an updated comprehensive research dysmorphology scoring system; and a new lip/philtrum guide for the white population, incorporating a 45-degree view. The guidelines reflect consensus among a large and experienced cadre of FASD investigators in the fields of dysmorphology, epidemiology, neurology, psychology, developmental/behavioral pediatrics, and educational diagnostics. Their improved clarity and specificity will guide clinicians in accurate diagnosis of infants and children prenatally exposed to alcohol.

Global patterns of kelp forest change over the past half-century

Abstract: Kelp forests (Order Laminariales) form key biogenic habitats in coastal regions of temperate and Arctic seas worldwide, providing ecosystem services valued in the range of billions of dollars annually. Although local evidence suggests that kelp forests are increasingly threatened by a variety of stressors, no comprehensive global analysis of change in kelp abundances currently exists. Here, we build and analyze a global database of kelp time series spanning the past half-century to assess regional and global trends in kelp abundances. We detected a high degree of geographic variation in trends, with regional variability in the direction and magnitude of change far exceeding a small global average decline (instantaneous rate of change = −0.018 y−1). Our analysis identified declines in 38% of ecoregions for which there are data (−0.015 to −0.18 y−1), increases in 27% of ecoregions (0.015 to 0.11 y−1), and no detectable change in 35% of ecoregions. These spatially variable trajectories reflected regional differences in the drivers of change, uncertainty in some regions owing to poor spatial and temporal data coverage, and the dynamic nature of kelp populations. We conclude that although global drivers could be affecting kelp forests at multiple scales, local stressors and regional variation in the effects of these drivers dominate kelp dynamics, in contrast to many other marine and terrestrial foundation species.

Lytic to temperate switching of viral communities

Abstract: Microbial viruses can control host abundances via density-dependent lytic predator-prey dynamics. Less clear is how temperate viruses, which coexist and replicate with their host, influence microbial communities. Here we show that virus-like particles are relatively less abundant at high host densities. This suggests suppressed lysis where established models predict lytic dynamics are favoured. Meta-analysis of published viral and microbial densities showed that this trend was widespread in diverse ecosystems ranging from soil to freshwater to human lungs. Experimental manipulations showed viral densities more consistent with temperate than lytic life cycles at increasing microbial abundance. An analysis of 24 coral reef viromes showed a relative increase in the abundance of hallmark genes encoded by temperate viruses with increased microbial abundance. Based on these four lines of evidence, we propose the Piggyback-the-Winner model wherein temperate dynamics become increasingly important in ecosystems with high microbial densities; thus 'more microbes, fewer viruses'.

Kepler eclipsing binary stars. vii. the catalog of eclipsing binaries found in the entire kepler data set

Abstract: The primary Kepler Mission provided nearly continuous monitoring of ~200,000 objects with unprecedented photometric precision. We present the final catalog of eclipsing binary systems within the 105 deg^2 Kepler field of view. This release incorporates the full extent of the data from the primary mission (Q0-Q17 Data Release). As a result, new systems have been added, additional false positives have been removed, ephemerides and principal parameters have been recomputed, classifications have been revised to rely on analytical models, and eclipse timing variations have been computed for each system. We identify several classes of systems including those that exhibit tertiary eclipse events, systems that show clear evidence of additional bodies, heartbeat systems, systems with changing eclipse depths, and systems exhibiting only one eclipse event over the duration of the mission. We have updated the period and galactic latitude distribution diagrams and included a catalog completeness evaluation. The total number of identified eclipsing and ellipsoidal binary systems in the Kepler field of view has increased to 2878, 1.3% of all observed Kepler targets. An online version of this catalog with downloadable content and visualization tools is maintained athttp://keplerEBs.villanova.edu.

Computational approaches to predict bacteriophage–host relationships

Abstract: Metagenomics has changed the face of virus discovery by enabling the accurate identification of viral genome sequences without requiring isolation of the viruses. As a result, metagenomic virus discovery leaves the first and most fundamental question about any novel virus unanswered: What host does the virus infect? The diversity of the global virosphere and the volumes of data obtained in metagenomic sequencing projects demand computational tools for virus-host prediction. We focus on bacteriophages (phages, viruses that infect bacteria), the most abundant and diverse group of viruses found in environmental metagenomes. By analyzing 820 phages with annotated hosts, we review and assess the predictive power of in silico phage-host signals. Sequence homology approaches are the most effective at identifying known phage-host pairs. Compositional and abundance-based methods contain significant signal for phage-host classification, providing opportunities for analyzing the unknowns in viral metagenomes. Together, these computational approaches further our knowledge of the interactions between phages and their hosts. Importantly, we find that all reviewed signals significantly link phages to their hosts, illustrating how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage-host relationships, with potential relevance for medical and industrial applications.

Reducing Implicit Racial Preferences: II. Intervention Effectiveness Across Time

Abstract: Implicit preferences are malleable, but does that change last? We tested 9 interventions (8 real and 1 sham) to reduce implicit racial preferences over time. In 2 studies with a total of 6,321 participants, all 9 interventions immediately reduced implicit preferences. However, none were effective after a delay of several hours to several days. We also found that these interventions did not change explicit racial preferences and were not reliably moderated by motivations to respond without prejudice. Short-term malleability in implicit preferences does not necessarily lead to long-term change, raising new questions about the flexibility and stability of implicit preferences. (PsycINFO Database Record

Cold season emissions dominate the Arctic tundra methane budget

Abstract: Arctic terrestrial ecosystems are major global sources of methane (CH4); hence, it is important to understand the seasonal and climatic controls on CH4 emissions from these systems. Here, we report year-round CH4 emissions from Alaskan Arctic tundra eddy flux sites and regional fluxes derived from aircraft data. We find that emissions during the cold season (September to May) account for ≥50% of the annual CH4 flux, with the highest emissions from noninundated upland tundra. A major fraction of cold season emissions occur during the “zero curtain” period, when subsurface soil temperatures are poised near 0 °C. The zero curtain may persist longer than the growing season, and CH4 emissions are enhanced when the duration is extended by a deep thawed layer as can occur with thick snow cover. Regional scale fluxes of CH4 derived from aircraft data demonstrate the large spatial extent of late season CH4 emissions. Scaled to the circumpolar Arctic, cold season fluxes from tundra total 12 ± 5 (95% confidence interval) Tg CH4 y−1, ∼25% of global emissions from extratropical wetlands, or ∼6% of total global wetland methane emissions. The dominance of late-season emissions, sensitivity to soil environmental conditions, and importance of dry tundra are not currently simulated in most global climate models. Because Arctic warming disproportionally impacts the cold season, our results suggest that higher cold-season CH4 emissions will result from observed and predicted increases in snow thickness, active layer depth, and soil temperature, representing important positive feedbacks on climate warming.

Pixilated partnerships, overcoming obstacles in qualitative interviews via Skype: a research note

Abstract: This research note discusses the effectiveness of using video internet technologies, like Skype, for qualitative interviews. Skype may present some challenges for interviewing, including dropped ca...

Reducing Implicit Racial Preferences: II. Intervention Effectiveness Across Time

Abstract: Implicit prejudice is malleable, but does that change last? We tested nine interventions (eight real and one sham) that have been demonstrated to reduce implicit racial prejudice temporarily to determine whether their effects also persisted over time. In two studies with a total of 6,321 participants, all nine interventions immediately reduced implicit prejudice, but none were effective after a delay of several hours to several days. We also found that these interventions did not change explicit racial prejudice and were not reliably moderated by motivations to respond without prejudice. Short-term malleability in implicit prejudice does not necessarily lead to longterm change, raising new questions about the flexibility and stability of implicit attitudes.

A Four-Plate Compact Capacitive Coupler Design and LCL -Compensated Topology for Capacitive Power Transfer in Electric Vehicle Charging Application

Abstract: This paper proposes a four-plate compact capacitive coupler and its circuit model for large air-gap distance capacitive power transfer (CPT). The four plates are arranged vertically, instead of horizontally, to save space in the electric vehicle charging application. The two plates that are on the same side are placed close to each other to maintain a large coupling capacitance, and they are of different sizes to maintain the coupling between the primary and secondary sides. The circuit model of the coupler is presented, considering all six coupling capacitors. The LCL compensation topology is used to resonate with the coupler and provide high voltage on the plates to transfer high power. The circuit model of the coupler is simplified to design the parameters of the compensation circuit. Finite-element analysis is employed to simulate the coupling capacitance and design the dimensions of the coupler. The circuit performance is simulated in LTspice to design the specific parameter values. A prototype of the CPT system was designed and constructed with the proposed vertical plate structure. The prototype achieved an efficiency of 85.87% at 1.88-kW output power with a 150-mm air-gap distance.

Mitophagy is required for mitochondrial biogenesis and myogenic differentiation of C2C12 myoblasts

Abstract: Myogenesis is a crucial process governing skeletal muscle development and homeostasis. Differentiation of primitive myoblasts into mature myotubes requires a metabolic switch to support the increased energetic demand of contractile muscle. Skeletal myoblasts specifically shift from a highly glycolytic state to relying predominantly on oxidative phosphorylation (OXPHOS) upon differentiation. We have found that this phenomenon requires dramatic remodeling of the mitochondrial network involving both mitochondrial clearance and biogenesis. During early myogenic differentiation, autophagy is robustly upregulated and this coincides with DNM1L/DRP1 (dynamin 1-like)-mediated fragmentation and subsequent removal of mitochondria via SQSTM1 (sequestosome 1)-mediated mitophagy. Mitochondria are then repopulated via PPARGC1A/PGC-1α (peroxisome proliferator-activated receptor gamma, coactivator 1 alpha)-mediated biogenesis. Mitochondrial fusion protein OPA1 (optic atrophy 1 [autosomal dominant]) is then briskly upregulated, resulting in the reformation of mitochondrial networks. The final product is a myotube replete with new mitochondria. Respirometry reveals that the constituents of these newly established mitochondrial networks are better primed for OXPHOS and are more tightly coupled than those in myoblasts. Additionally, we have found that suppressing autophagy with various inhibitors during differentiation interferes with myogenic differentiation. Together these data highlight the integral role of autophagy and mitophagy in myogenic differentiation.

Spider phylogenomics: untangling the Spider Tree of Life

Abstract: Spiders (Order Araneae) are massively abundant generalist arthropod predators that are found in nearly every ecosystem on the planet and have persisted for over 380 million years. Spiders have long served as evolutionary models for studying complex mating and web spinning behaviors, key innovation and adaptive radiation hypotheses, and have been inspiration for important theories like sexual selection by female choice. Unfortunately, past major attempts to reconstruct spider phylogeny typically employing the "usual suspect" genes have been unable to produce a well-supported phylogenetic framework for the entire order. To further resolve spider evolutionary relationships we have assembled a transcriptome-based data set comprising 70 ingroup spider taxa. Using maximum likelihood and shortcut coalescence-based approaches, we analyze eight data sets, the largest of which contains 3,398 gene regions and 696,652 amino acid sites forming the largest phylogenomic analysis of spider relationships produced to date. Contrary to long held beliefs that the orb web is the crowning achievement of spider evolution, ancestral state reconstructions of web type support a phylogenetically ancient origin of the orb web, and diversification analyses show that the mostly ground-dwelling, web-less RTA clade diversified faster than orb weavers. Consistent with molecular dating estimates we report herein, this may reflect a major increase in biomass of non-flying insects during the Cretaceous Terrestrial Revolution 125-90 million years ago favoring diversification of spiders that feed on cursorial rather than flying prey. Our results also have major implications for our understanding of spider systematics. Phylogenomic analyses corroborate several well-accepted high level groupings: Opisthothele, Mygalomorphae, Atypoidina, Avicularoidea, Theraphosoidina, Araneomorphae, Entelegynae, Araneoidea, the RTA clade, Dionycha and the Lycosoidea. Alternatively, our results challenge the monophyly of Eresoidea, Orbiculariae, and Deinopoidea. The composition of the major paleocribellate and neocribellate clades, the basal divisions of Araneomorphae, appear to be falsified. Traditional Haplogynae is in need of revision, as our findings appear to support the newly conceived concept of Synspermiata. The sister pairing of filistatids with hypochilids implies that some peculiar features of each family may in fact be synapomorphic for the pair. Leptonetids now are seen as a possible sister group to the Entelegynae, illustrating possible intermediates in the evolution of the more complex entelegyne genitalic condition, spinning organs and respiratory organs.

Community‐Academic Partnerships: A Systematic Review of the State of the Literature and Recommendations for Future Research

Abstract: Policy Points: Communities, funding agencies, and institutions are increasingly involving community stakeholders as partners in research, to provide firsthand knowledge and insight. Based on our systematic review of major literature databases, we recommend using a single term, community‐academic partnership (CAP), and a conceptual definition to unite multiple research disciplines and strengthen the field. Interpersonal and operational factors that facilitate or hinder the collaborative process have been consistently identified, including “trust among partners” and “respect among partners” (facilitating interpersonal factors) and “excessive time commitment” (hindering operational factor). Once CAP processes and characteristics are better understood, the effectiveness of collaborative partner involvement can be tested.

Space telescope and optical reverberation mapping project. III. Optical continuum emission and broadband time delays in NGC 5548

Abstract: The LBT is an international collaboration among institutions in the United States, Italy and Germany. LBT Corporation partners are: The Ohio State University, and The Research Corporation, on behalf of The University of Notre Dame, University of Minnesota and University of Virginia; The University of Arizona on behalf of the Arizona university system; Istituto Nazionale di Astrofisica, Italy; LBT Beteiligungsgesellschaft, Germany, representing the Max-Planck Society, the Astrophysical Institute Potsdam, and Heidelberg University. This paper used data obtained with the MODS spectrographs built with funding from National Science Foundation (NSF) grant AST-9987045 and the NSF Telescope System Instrumentation Program (TSIP), with additional funds from the Ohio Board of Regents and the Ohio State University Office of Research. This paper made use of the modsIDL spectral data reduction pipeline developed in part with funds provided by NSF Grant AST - 1108693. The Liverpool Telescope is operated on the island of La Palma by Liverpool John Moores University in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias with financial support from the UK Science and Technology Facilities Council. KAIT and its ongoing operation were made possible by donations from Sun Microsystems, Inc., the Hewlett-Packard Company, AutoScope Corporation, Lick Observatory, the NSF, the University of California, the Sylvia and Jim Katzman Foundation, and the TABASGO Foundation. Research at Lick Observatory is partially supported by a generous gift from Google. Support for HST program number GO-13330 was provided by NASA through a grant from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555. M.M.F., G.D.R., B.M.P., C.J.G., and R.W.P. are grateful for the support of the NSF through grant AST- 1008882 to The Ohio State University. A.J.B. and L.P. have been supported by NSF grant AST-1412693. A.V.F. and W.- K.Z. are grateful for financial assistance from NSF grant AST- 1211916, the TABASGO Foundation, and the Christopher R. Redlich Fund. M.C. Bentz gratefully acknowledges support through NSF CAREER grant AST-1253702 to Georgia State University. M.C. Bottorff acknowledges HHMI for support through an undergraduate science education grant to Southwestern University. K.D.D. is supported by an NSF Fellowship awarded under grant AST-1302093. R.E. gratefully acknowledges support from NASA under awards NNX13AC26G, NNX13AC63G, and NNX13AE99G. J.M.G. gratefully acknowledges support from NASA under award NNH13CH61C. P.B.H. is supported by NSERC. M.I. acknowledges support from the Creative Initiative program, No. 2008-0060544, of the National Research Foundation of Korea (NRFK) funded by the Korean government (MSIP). M.D.J. acknowledges NSF grant AST-0618209 used for obtaining the 0.91 m telescope at WMO. SRON is financially supported by NWO, the Netherlands Organization for Scientific Research. B.C.K. is partially supported by the UC Center for Galaxy Evolution. C.S.K. acknowledges the support of NSF grant AST-1009756. D.C.L. acknowledges support from NSF grants AST-1009571 and AST-1210311, under which part of this research (photometric observations collected at MLO) was carried out. We thank Nhieu Duong, Harish Khandrika, Richard Mellinger, J. Chuck Horst, Steven Armen, and Eddie Garcia for assistance with the MLO observations. P.L. acknowledges support from Fondecyt grant #1120328. A.P. acknowledges support from a NSF graduate fellowship, a UCSB Dean’s Fellowship, and a NASA Einstein Fellowship. J.S.S. acknowledges CNPq, National Council for Scientific and Technological Development (Brazil) for partial support and The Ohio State University for warm hospitality. T.T. has been supported by NSF grant AST-1412315. T.T. and B.C.K. acknowledge support from the Packard Foundation in the form of a Packard Research Fellowship to T.T.; also, T.T. thanks the American Academy in Rome and the Observatory of Monteporzio Catone for kind hospitality. The Dark Cosmology Centre is funded by the Danish National Research Foundation. M.V. gratefully acknowledges support from the Danish Council for Independent Research via grant no. DFF–4002-00275. J.-H.W. acknowledges support by the National Research Foundation of Korea (NRF) grant funded by the Korean government (No. 2010-0027910). E.D.B. is supported by Padua University through grants 60A02-5857/13, 60A02-5833/14, 60A02-4434/15, and CPDA133894. K.H. acknowledges support from STFC grant ST/M001296/1. S.A.K. thanks Dr. I. A. Rakhimov, the Director of Svetloe Observatory, for his support and hospitality. This research has made use of the NASA/IPAC Extragalactic Database (NED), which is operated by the Jet Propulsion Laboratory, California Institute of Technology, under contract with NASA.

Genetic Diversity and Association Studies in US Hispanic/Latino Populations: Applications in the Hispanic Community Health Study/Study of Latinos

Abstract: US Hispanic/Latino individuals are diverse in genetic ancestry, culture, and environmental exposures. Here, we characterized and controlled for this diversity in genome-wide association studies (GWASs) for the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). We simultaneously estimated population-structure principal components (PCs) robust to familial relatedness and pairwise kinship coefficients (KCs) robust to population structure, admixture, and Hardy-Weinberg departures. The PCs revealed substantial genetic differentiation within and among six self-identified background groups (Cuban, Dominican, Puerto Rican, Mexican, and Central and South American). To control for variation among groups, we developed a multi-dimensional clustering method to define a "genetic-analysis group" variable that retains many properties of self-identified background while achieving substantially greater genetic homogeneity within groups and including participants with non-specific self-identification. In GWASs of 22 biomedical traits, we used a linear mixed model (LMM) including pairwise empirical KCs to account for familial relatedness, PCs for ancestry, and genetic-analysis groups for additional group-associated effects. Including the genetic-analysis group as a covariate accounted for significant trait variation in 8 of 22 traits, even after we fit 20 PCs. Additionally, genetic-analysis groups had significant heterogeneity of residual variance for 20 of 22 traits, and modeling this heteroscedasticity within the LMM reduced genomic inflation for 19 traits. Furthermore, fitting an LMM that utilized a genetic-analysis group rather than a self-identified background group achieved higher power to detect previously reported associations. We expect that the methods applied here will be useful in other studies with multiple ethnic groups, admixture, and relatedness.

197 candidates and 104 validated planets in K2's first five fields

Abstract: We present 197 planet candidates discovered using data from the first year of the NASA K2 mission (Campaigns 0-4), along with the results of an intensive program of photometric analyses, stellar spectroscopy, high-resolution imaging, and statistical validation. We distill these candidates into sets of 104 validated planets (57 in multi-planet systems), false positives, and 63 remaining candidates. Our validated systems span a range of properties, with median values of RP= 2.3 R⊕, P = 8.6 days, Teff = 5300 K, and Kp = 12.7mag. Stellar spectroscopy provides precise stellar and planetary parameters for most of these systems. We show that K2 has increased by 30% the number of small planets known to orbit moderately bright stars (1-4 R R⊕, Kp = 9-13 mag). Of particular interest are planets smaller than 2 R⊕, orbiting stars brighter than Kp = 11.5 mag, 5 receiving Earth-like irradiation levels, and several multi-planet systems - including 4 planets orbiting the M dwarf K2-72 near mean-motion resonances. By quantifying the likelihood that each candidate is a planet we demonstrate that our candidate sample has an overall false positive rate of 15%-30%, with rates substantially lower for small candidates ( 8 R⊕ and/or with P<3 days. Extrapolation of the current planetary yield suggests that K2 will discover between 500 and 1000 planets in its planned four-year mission, assuming sufficient follow-up resources are available. Efficient observing and analysis, together with an organized and coherent follow-up strategy, are essential for maximizing the efficacy of planet-validation efforts for K2, TESS, and future large-scale surveys.

Acoustic sequences in non-human animals: a tutorial review and prospectus.

Abstract: This review was developed at an investigative workshop, “Analyzing Animal Vocal Communication Sequences” that took place on October 21–23 2013 in Knoxville, Tennessee, sponsored by the National Institute for Mathematical and Biological Synthesis (NIMBioS). NIMBioS is an Institute sponsored by the National Science Foundation, the U.S. Department of Homeland Security, and the U.S. Department of Agriculture through NSF Awards #EF-0832858 and #DBI-1300426, with additional support from The University of Tennessee, Knoxville. In addition to the authors, Vincent Janik participated in the workshop. D.T.B.’s research is currently supported by NSF DEB-1119660. M.A.B.’s research is currently supported by NSF IOS-0842759 and NIH R01DC009582. M.A.R.’s research is supported by ONR N0001411IP20086 and NOPP (ONR/BOEM) N00014-11-1-0697. S.L.DeR.’s research is supported by the U.S. Office of Naval Research. R.F.-i-C.’s research was supported by the grant BASMATI (TIN2011-27479-C04-03) from the Spanish Ministry of Science and Innovation. E.C.G.’s research is currently supported by a National Research Council postdoctoral fellowship. E.E.V.’s research is supported by CONACYT, Mexico, award number I010/214/2012.

Women 1.5 Times More Likely to Leave STEM Pipeline after Calculus Compared to Men: Lack of Mathematical Confidence a Potential Culprit.

Abstract: The substantial gender gap in the science, technology, engineering, and mathematics (STEM) workforce can be traced back to the underrepresentation of women at various milestones in the career pathway. Calculus is a necessary step in this pathway and has been shown to often dissuade people from pursuing STEM fields. We examine the characteristics of students who begin college interested in STEM and either persist or switch out of the calculus sequence after taking Calculus I, and hence either continue to pursue a STEM major or are dissuaded from STEM disciplines. The data come from a unique, national survey focused on mainstream college calculus. Our analyses show that, while controlling for academic preparedness, career intentions, and instruction, the odds of a woman being dissuaded from continuing in calculus is 1.5 times greater than that for a man. Furthermore, women report they do not understand the course material well enough to continue significantly more often than men. When comparing women and men with above-average mathematical abilities and preparedness, we find women start and end the term with significantly lower mathematical confidence than men. This suggests a lack of mathematical confidence, rather than a lack of mathematically ability, may be responsible for the high departure rate of women. While it would be ideal to increase interest and participation of women in STEM at all stages of their careers, our findings indicate that if women persisted in STEM at the same rate as men starting in Calculus I, the number of women entering the STEM workforce would increase by 75%.

Learning Collaborative Sparse Representation for Grayscale-Thermal Tracking

Abstract: Integrating multiple different yet complementary feature representations has been proved to be an effective way for boosting tracking performance. This paper investigates how to perform robust object tracking in challenging scenarios by adaptively incorporating information from grayscale and thermal videos, and proposes a novel collaborative algorithm for online tracking. In particular, an adaptive fusion scheme is proposed based on collaborative sparse representation in Bayesian filtering framework. We jointly optimize sparse codes and the reliable weights of different modalities in an online way. In addition, this paper contributes a comprehensive video benchmark, which includes 50 grayscale-thermal sequences and their ground truth annotations for tracking purpose. The videos are with high diversity and the annotations were finished by one single person to guarantee consistency. Extensive experiments against other state-of-the-art trackers with both grayscale and grayscale-thermal inputs demonstrate the effectiveness of the proposed tracking approach. Through analyzing quantitative results, we also provide basic insights and potential future research directions in grayscale-thermal tracking.

Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Abstract: This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.