Showing papers by "University of Georgia published in 2016"
TL;DR: In this paper, the authors present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macro-autophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes.
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.
5,187 citations
Icahn School of Medicine at Mount Sinai1, Veterans Health Administration2, University of California, San Francisco3, Group Health Research Institute4, University of Wisconsin-Madison5, Columbia University6, University of Georgia7, Harvard University8, Duke University9, Virginia Commonwealth University10, New York University11, Stanford University12, University of Washington13, Brown University14, University of North Carolina at Chapel Hill15
TL;DR: Screening for depression in the general adult population, including pregnant and postpartum women, should be implemented with adequate systems in place to ensure accurate diagnosis, effective treatment, and appropriate follow-up.
Abstract: Description Update of the 2009 US Preventive Services Task Force (USPSTF) recommendation on screening for depression in adults. Methods The USPSTF reviewed the evidence on the benefits and harms of screening for depression in adult populations, including older adults and pregnant and postpartum women; the accuracy of depression screening instruments; and the benefits and harms of depression treatment in these populations. Population This recommendation applies to adults 18 years and older. Recommendation The USPSTF recommends screening for depression in the general adult population, including pregnant and postpartum women. Screening should be implemented with adequate systems in place to ensure accurate diagnosis, effective treatment, and appropriate follow-up. (B recommendation)
1,040 citations
Pacific Northwest National Laboratory1, Yale University2, National Center for Atmospheric Research3, Marine Biological Laboratory4, Colorado State University5, Wageningen University and Research Centre6, University of California, Irvine7, Kansas State University8, University of Oregon9, Michigan Technological University10, University of Sydney11, University of Minnesota12, Duke University13, University of Tennessee14, University of Copenhagen15, Spanish National Research Council16, University of New Hampshire17, Northeast Normal University18, University of California, Berkeley19, University of Oklahoma20, Hungarian Academy of Sciences21, Swedish University of Agricultural Sciences22, University of Manchester23, Tsinghua University24, National University of Singapore25, Chinese Academy of Sciences26, University of Hohenheim27, University of Georgia28, Hampshire College29, Boston University30, University of Alaska Anchorage31
TL;DR: In this article, the authors present a comprehensive analysis of warming-induced changes in soil carbon stocks by assembling data from 49 field experiments located across North America, Europe and Asia, and provide estimates of soil carbon sensitivity to warming that may help to constrain Earth system model projections.
Abstract: The majority of the Earth's terrestrial carbon is stored in the soil. If anthropogenic warming stimulates the loss of this carbon to the atmosphere, it could drive further planetary warming. Despite evidence that warming enhances carbon fluxes to and from the soil, the net global balance between these responses remains uncertain. Here we present a comprehensive analysis of warming-induced changes in soil carbon stocks by assembling data from 49 field experiments located across North America, Europe and Asia. We find that the effects of warming are contingent on the size of the initial soil carbon stock, with considerable losses occurring in high-latitude areas. By extrapolating this empirical relationship to the global scale, we provide estimates of soil carbon sensitivity to warming that may help to constrain Earth system model projections. Our empirical relationship suggests that global soil carbon stocks in the upper soil horizons will fall by 30 ± 30 petagrams of carbon to 203 ± 161 petagrams of carbon under one degree of warming, depending on the rate at which the effects of warming are realized. Under the conservative assumption that the response of soil carbon to warming occurs within a year, a business-as-usual climate scenario would drive the loss of 55 ± 50 petagrams of carbon from the upper soil horizons by 2050. This value is around 12-17 per cent of the expected anthropogenic emissions over this period. Despite the considerable uncertainty in our estimates, the direction of the global soil carbon response is consistent across all scenarios. This provides strong empirical support for the idea that rising temperatures will stimulate the net loss of soil carbon to the atmosphere, driving a positive land carbon-climate feedback that could accelerate climate change.
787 citations
TL;DR: Considering the evidence-based literature review, the National Osteoporosis Foundation recommends lifestyle choices that promote maximal bone health from childhood through young to late adolescence and outline a research agenda to address current gaps in knowledge.
Abstract: Lifestyle choices influence 20–40 % of adult peak bone mass. Therefore, optimization of lifestyle factors known to influence peak bone mass and strength is an important strategy aimed at reducing risk of osteoporosis or low bone mass later in life. The National Osteoporosis Foundation has issued this scientific statement to provide evidence-based guidance and a national implementation strategy for the purpose of helping individuals achieve maximal peak bone mass early in life. In this scientific statement, we (1) report the results of an evidence-based review of the literature since 2000 on factors that influence achieving the full genetic potential for skeletal mass; (2) recommend lifestyle choices that promote maximal bone health throughout the lifespan; (3) outline a research agenda to address current gaps; and (4) identify implementation strategies. We conducted a systematic review of the role of individual nutrients, food patterns, special issues, contraceptives, and physical activity on bone mass and strength development in youth. An evidence grading system was applied to describe the strength of available evidence on these individual modifiable lifestyle factors that may (or may not) influence the development of peak bone mass (Table 1). A summary of the grades for each of these factors is given below. We describe the underpinning biology of these relationships as well as other factors for which a systematic review approach was not possible. Articles published since 2000, all of which followed the report by Heaney et al. [1] published in that year, were considered for this scientific statement. This current review is a systematic update of the previous review conducted by the National Osteoporosis Foundation [1].
Considering the evidence-based literature review, we recommend lifestyle choices that promote maximal bone health from childhood through young to late adolescence and outline a research agenda to address current gaps in knowledge. The best evidence (grade A) is available for positive effects of calcium intake and physical activity, especially during the late childhood and peripubertal years—a critical period for bone accretion. Good evidence is also available for a role of vitamin D and dairy consumption and a detriment of DMPA injections. However, more rigorous trial data on many other lifestyle choices are needed and this need is outlined in our research agenda. Implementation strategies for lifestyle modifications to promote development of peak bone mass and strength within one’s genetic potential require a multisectored (i.e., family, schools, healthcare systems) approach.
759 citations
TL;DR: In 2014, the Association for Multicultural Counseling and Development (AMCD) appointed a committee to revise the Multicultural and Social Justice Counseling Competencies (MSJCC) as discussed by the authors.
Abstract: In 2014, the Association for Multicultural Counseling and Development (AMCD) appointed a committee to revise the Multicultural Counseling Competencies developed by Sue, Arredondo, and McDavis in 1992 and operationalized by Arredondo et al. in 1996. This article reflects the updated competencies, titled the Multicultural and Social Justice Counseling Competencies (MSJCC; Ratts, Singh, Nassar-McMillan, Butler, & McCullough, 2015a), which were endorsed by AMCD on June 29, 2015, and by the American Counseling Association on July 20, 2015. A conceptual framework of the MSJCC visually depicts the relationships among the competencies' key constructs: multicultural and social justice praxis, quadrants, domains, and competencies. Implications are discussed.
En 2014, la Asociacion para la Consejeria y el Desarrollo Multicultural (AMCD, en sus siglas en ingles) formo un comite para revisar las Competencias en Consejeria Multicultural desarrolladas por Sue, Arredondo y McDavis en 1992 y operacionalizadas por Arredondo et al. en 1996. Este articulo refleja las competencias actualizadas, denominadas Competencias en Consejeria Multicultural y de Justicia Social (MSJCC, en sus siglas en ingles; Ratts, Singh, Nassar-McMillan, Butler, & McCullough, 2015a), que fueron avaladas por la AMCD el 29 de junio de 2015 y por la Asociacion Americana de Consejeria el 20 de julio de 2015. Un marco conceptual de las MSJCC muestra visualmente las relaciones entre los constructos principales de las competencias: la praxis multicultural y en justicia social, los cuadrantes, dominios y competencias. Se discuten las implicaciones.
719 citations
University of Georgia1, University of Brasília2, United States Department of Agriculture3, University of California, Davis4, National Center for Genome Resources5, Iowa State University6, Empresa Brasileira de Pesquisa Agropecuária7, Texas A&M University8, Texas Tech University9, International Crops Research Institute for the Semi-Arid Tropics10, International Potato Center11, Crops Research Institute12, North Carolina State University13
TL;DR: The genome sequences of its diploid ancestors are reported to show that these genomes are similar to cultivated peanut's A and B subgenomes and used to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanuts' subgenome.
Abstract: Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ∼2.7 Gb. This makes the assembly of chromosomal pseudomolecules very challenging. As a foundation to understanding the genome of cultivated peanut, we report the genome sequences of its diploid ancestors (Arachis duranensis and Arachis ipaensis). We show that these genomes are similar to cultivated peanut's A and B subgenomes and use them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut's subgenomes. On the basis of remarkably high DNA identity of the A. ipaensis genome and the B subgenome of cultivated peanut and biogeographic evidence, we conclude that A. ipaensis may be a direct descendant of the same population that contributed the B subgenome to cultivated peanut.
643 citations
Posted Content•
TL;DR: iTracker, a convolutional neural network for eye tracking, is trained, which achieves a significant reduction in error over previous approaches while running in real time (10-15fps) on a modern mobile device.
Abstract: From scientific research to commercial applications, eye tracking is an important tool across many domains. Despite its range of applications, eye tracking has yet to become a pervasive technology. We believe that we can put the power of eye tracking in everyone's palm by building eye tracking software that works on commodity hardware such as mobile phones and tablets, without the need for additional sensors or devices. We tackle this problem by introducing GazeCapture, the first large-scale dataset for eye tracking, containing data from over 1450 people consisting of almost 2.5M frames. Using GazeCapture, we train iTracker, a convolutional neural network for eye tracking, which achieves a significant reduction in error over previous approaches while running in real time (10-15fps) on a modern mobile device. Our model achieves a prediction error of 1.71cm and 2.53cm without calibration on mobile phones and tablets respectively. With calibration, this is reduced to 1.34cm and 2.12cm. Further, we demonstrate that the features learned by iTracker generalize well to other datasets, achieving state-of-the-art results. The code, data, and models are available at this http URL.
535 citations
TL;DR: Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules in the 1001 Genomes collection of Arabidopsis thaliana.
534 citations
TL;DR: In this paper, the authors take another look at the well-known Carroll's Pyramid of Corporate Social Responsibility (CSR) and present a summary of the four-part definitional framework upon which the pyramid was created.
Abstract: In this review article, the author takes another look at the well-known Carroll's Pyramid of Corporate Social Responsibility (CSR). In this article, he comments on the framework's popular useage and then presents a summary of the four-part definitional framework upon which the pyramid was created. He then comments on several characteristics of the model that were not emphasized when initially published: ethics permeates the pyramid; tensions and tradeoffs inherent; its' integrated, unified whole; its' sustainable stakeholder framework, and; its' global applicability and use in different contexts. The article concludes by looking to the future.
531 citations
TL;DR: These data illustrate how multiple pathways may lead to clinically similar psychosis manifestations, and they provide explanations for the marked heterogeneity observed across laboratories on the same biomarker variables when DSM diagnoses are used as the gold standard.
Abstract: Objective:Clinical phenomenology remains the primary means for classifying psychoses despite considerable evidence that this method incompletely captures biologically meaningful differentiations. Rather than relying on clinical diagnoses as the gold standard, this project drew on neurobiological heterogeneity among psychosis cases to delineate subgroups independent of their phenomenological manifestations.Method:A large biomarker panel (neuropsychological, stop signal, saccadic control, and auditory stimulation paradigms) characterizing diverse aspects of brain function was collected on individuals with schizophrenia, schizoaffective disorder, and bipolar disorder with psychosis (N=711), their first-degree relatives (N=883), and demographically comparable healthy subjects (N=278). Biomarker variance across paradigms was exploited to create nine integrated variables that were used to capture neurobiological variance among the psychosis cases. Data on external validating measures (social functioning, struct...
505 citations
TL;DR: This review addresses the process of adipogenic differentiation, key transcription factors and proteins involved, adipogenic regulators and potential anti-adipogenic bioactive molecules, which are vital to develop therapeutic agents capable of curbing the increasing incidence of obesity.
Abstract: Adipogenesis is the process by which precursor stem cells differentiate into lipid laden adipocytes. Adipogenesis is regulated by a complex and highly orchestrated gene expression program. In mammalian cells, the peroxisome proliferator-activated receptor γ (PPARγ), and the CCAAT/enhancer binding proteins (C/EBPs) such as C/EBPα, β and δ are considered the key early regulators of adipogenesis, while fatty acid binding protein 4 (FABP4), adiponectin, and fatty acid synthase (FAS) are responsible for the formation of mature adipocytes. Excess accumulation of lipids in the adipose tissue leads to obesity, which is associated with cardiovascular diseases, type II diabetes and other pathologies. Thus, investigating adipose tissue development and the underlying molecular mechanisms is vital to develop therapeutic agents capable of curbing the increasing incidence of obesity and related pathologies. In this review, we address the process of adipogenic differentiation, key transcription factors and proteins involved, adipogenic regulators and potential anti-adipogenic bioactive molecules.
27 Jun 2016
TL;DR: Gaze Capture as mentioned in this paper is the first large-scale dataset for eye tracking, containing data from over 1450 people consisting of almost 2:5M frames and trained iTracker, a convolutional neural network, which achieves a significant reduction in error over previous approaches while running in real time (10-15fps) on a modern mobile device.
Abstract: From scientific research to commercial applications, eye tracking is an important tool across many domains. Despite its range of applications, eye tracking has yet to become a pervasive technology. We believe that we can put the power of eye tracking in everyone's palm by building eye tracking software that works on commodity hardware such as mobile phones and tablets, without the need for additional sensors or devices. We tackle this problem by introducing GazeCapture, the first large-scale dataset for eye tracking, containing data from over 1450 people consisting of almost 2:5M frames. Using GazeCapture, we train iTracker, a convolutional neural network for eye tracking, which achieves a significant reduction in error over previous approaches while running in real time (10–15fps) on a modern mobile device. Our model achieves a prediction error of 1.71cm and 2.53cm without calibration on mobile phones and tablets respectively. With calibration, this is reduced to 1.34cm and 2.12cm. Further, we demonstrate that the features learned by iTracker generalize well to other datasets, achieving state-of-the-art results. The code, data, and models are available at http://gazecapture.csail.mit.edu.
TL;DR: The authors provided a systematic literature review of 323 publications that examines six key aspects of the literature on public service motivation: the growth of research on the concept, most prominent studies based on a referencing network analysis, the most frequent publication outlets, research designs and methods, lines of inquiry and patterns of empirical findings, and implications for practice drawn from the publications in the study sample.
Abstract: Over the past two decades, research on public service motivation has seen rapid growth. Despite the relatively large number of publications to date, no systematic research overview has been created, leaving the body of literature somewhat unstructured and possibly hampering future research. This article fills this void by providing a systematic literature review of 323 publications that examines six key aspects of the literature on public service motivation: the growth of research on the concept, the most prominent studies based on a referencing network analysis, the most frequent publication outlets, research designs and methods, lines of inquiry and patterns of empirical findings, and implications for practice drawn from the publications in the study sample. Strengths and weaknesses of the existing literature are identified, and future research directions are proposed.
TL;DR: The authors argue that ambiguities surrounding how we conceptualize and therefore operationalize framing have begun to overlap with other media effects models to a point that is dysfunctional, and argue for changes in how communication scholars approach framing as a theoretical construct.
Abstract: Framing has become one of the most popular areas of research for scholars in communication and a wide variety of other disciplines, such as psychology, behavioral economics, political science, and sociology. Particularly in the communication discipline, however, ambiguities surrounding how we conceptualize and therefore operationalize framing have begun to overlap with other media effects models to a point that is dysfunctional. This article provides an in-depth examination of framing and positions the theory in the context of recent evolutions in media effects research. We begin by arguing for changes in how communication scholars approach framing as a theoretical construct. We urge scholars to abandon the general term “framing” altogether and instead distinguish between different types of framing. We also propose that, as a field, we refocus attention on the concept's original theoretical foundations and, more important, the potential empirical contributions that the concept can make to our field and ou...
Abstract: Despite recent industry attention, questions remain about how native advertising is perceived and processed by consumers. Two experiments examined effects of language and positioning in native advertising disclosures on recognition of the content as advertising, effects of recognition on brand and publisher evaluations, and whether disclosure position affects visual attention. Findings show that middle or bottom positioning and wording using “advertising” or “sponsored” increased advertising recognition compared to other conditions, and ad recognition generally led to more negative evaluations. Visual attention mediated the relationship between disclosure position and advertising recognition. Theoretical, practical, and regulatory implications for disclosures in native advertising are discussed.
TL;DR: The extent of variation in DNA methylation in angiosperms is revealed and patterns are shown to be broadly a reflection of the evolutionary and life histories of plant species.
Abstract: DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species. By analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species. These results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.
TL;DR: This essay offers empirical evidence that demonstrates that scientists who have less positive attitudes toward the social sciences are more likely to adhere to the knowledge deficit model of science communication, and proposes some ways to uproot the deficit model and move toward more effective science communication efforts.
Abstract: Science communication has been historically predicated on the knowledge deficit model. Yet, empirical research has shown that public communication of science is more complex than what the knowledge deficit model suggests. In this essay, we pose four lines of reasoning and present empirical data for why we believe the deficit model still persists in public communication of science. First, we posit that scientists’ training results in the belief that public audiences can and do process information in a rational manner. Second, the persistence of this model may be a product of current institutional structures. Many graduate education programs in science, technology, engineering, and math (STEM) fields generally lack formal training in public communication. We offer empirical evidence that demonstrates that scientists who have less positive attitudes toward the social sciences are more likely to adhere to the knowledge deficit model of science communication. Third, we present empirical evidence of how scienti...
TL;DR: This article provides an overview of generative learning theory, grounded in Wittrock’s (1974) generative model of comprehension and reflected in more recent frameworks of active learning, such as Mayer's (2014) select-organize-integrate (SOI) framework.
Abstract: Generative learning involves actively making sense of to-be-learned information by mentally reorganizing and integrating it with one’s prior knowledge, thereby enabling learners to apply what they have learned to new situations. In this article, we present eight learning strategies intended to promote generative learning: summarizing, mapping, drawing, imagining, self-testing, self-explaining, teaching, and enacting. First, we provide an overview of generative learning theory, grounded in Wittrock’s (1974) generative model of comprehension and reflected in more recent frameworks of active learning, such as Mayer’s (2014) select-organize-integrate (SOI) framework. Next, for each of the eight generative learning strategies, we provide a description, review exemplary research studies, discuss potential boundary conditions, and provide practical recommendations for implementation. Finally, we discuss the implications of generative learning for the science of learning, and we suggest directions for further research.
TL;DR: Workaholism is related to achievement-oriented personality traits (i.e., perfectionism, Type A personality), but is generally unrelated to many other dispositional (e.g., conscientiousness, self-esteem, positive affect) and demographic variables.
University of Bologna1, University of Cambridge2, Estonian Biocentre3, University of Bristol4, Harvard University5, King Abdullah University of Science and Technology6, University of Tartu7, University of Montpellier8, Massey University9, University of Auckland10, Pennsylvania State University11, University of California, San Francisco12, Biodesign Institute13, Arizona State University14, University of Southampton15, University of Montana16, National Academy of Sciences of Belarus17, Wellcome Trust Sanger Institute18, Kuban State Medical University19, University of Georgia20, University of Copenhagen21, Griffith University22, Academy of Sciences of Uzbekistan23, L.N.Gumilyov Eurasian National University24, University of Dhaka25, University of Pennsylvania26, Georgia Institute of Technology27, Russian Academy of Sciences28, Academy of Medical Sciences, United Kingdom29, Royal Free Hospital30, University of Kharkiv31, Centre national de la recherche scientifique32, Eijkman Institute for Molecular Biology33, North-Eastern Federal University34, Josip Juraj Strossmayer University of Osijek35, Armenian National Academy of Sciences36, University of Winchester37, University Hospital Heidelberg38, Novosibirsk State University39, Bashkir State University40, International Burch University41, Russian Academy42, University College London43, James Cook University44, University of Papua New Guinea45, Max Planck Society46, University of California, Berkeley47, Estonian Academy of Sciences48
TL;DR: A genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa earlier than 75,000 years ago is found.
Abstract: High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.
TL;DR: The study found that the number of articles reporting QDAS is increasing each year, and that the majority of studies using ATLAS are for data management and analysis, with fewer using it for data collection/creation or to visually display their methods and findings.
Abstract: Qualitative data analysis software QDAS programs are well-established research tools, but little is known about how researchers use them. This article reports the results of a content analysis of 763 empirical articles, published in the Scopus database between 1994 and 2013, which explored how researchers use the ATLAS.ti? and NVivo? QDAS programs.* The analysis specifically investigated who is using these tools in terms of subject discipline and author country of origin, and how they are being used to support research in terms of type of data, type of study, and phase of the research process that QDAS were used to support. The study found that the number of articles reporting QDAS is increasing each year, and that the majority of studies using ATLAS.ti? and NVivo? were published in health sciences journals by authors from the United Kingdom, United States, Netherlands, Canada, and Australia. Researchers used QDAS to support a variety of research designs and most commonly used the programs to support analyses of data gathered through interviews, focus groups, documents, field notes, and open-ended survey questions. Although QDAS can support multiple phases of the research process, the study found the vast majority of researchers are using it for data management and analysis, with fewer using it for data collection/creation or to visually display their methods and findings. This article concludes with some discussion of the extent to which QDAS users appear to have leveraged the potential of these programs to support new approaches to research.
University of Queensland1, University of Western Australia2, University of Warwick3, Michigan State University4, Korea Research Institute of Bioscience and Biotechnology5, Cold Spring Harbor Laboratory6, University of Georgia7, University of Missouri8, National Research Council9, Fujian Agriculture and Forestry University10, J. Craig Venter Institute11
TL;DR: Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis.
Abstract: There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait diversity. Here we show by analysis of the Brassica oleracea pangenome that nearly 20% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis.
TL;DR: Ongoing population growth could greatly exacerbate the human impact of sea-level rise in coastal areas of the continental US this century, with the potential to induce mass population movements unless protective measures are taken as discussed by the authors.
Abstract: Ongoing population growth could greatly exacerbate the human impact of sea-level rise in coastal areas of the continental US this century, with the potential to induce mass population movements unless protective measures are taken.
TL;DR: Many of S&G's criticisms of MSC models are invalidated when concatenation is appropriately viewed as a special case of the MSC, which in turn is aSpecial case of emerging network models in phylogenomics.
TL;DR: Functionality and applicability of food-related nanotechnology are highlighted in order to provide a comprehensive view on the development and safety assessment of nanotechnology in the food industry.
TL;DR: It is shown that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes, and that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements.
Abstract: We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2) that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements; and (3) that various classes of small RNAs help shape genomic architecture and function. We illustrate ways in which understanding these organism-level and molecular genetic processes can be used for crop plant improvement.
TL;DR: The zoonotic potential of host species from the top six most species-rich mammal groups are discussed, and the literature is reviewed to identify analytical and conceptual gaps that must be addressed to improve the ability to generate testable predictions aboutZoonotic diseases originating from wild mammals.
TL;DR: These findings support the hypothesis that diverse measures of impulsivity can broadly be organized into three categories that are largely distinct from one another and warrant investigation among individuals with clinical levels of addictive behavior.
Abstract: Impulsivity has been strongly linked to addictive behaviors, but can be operationalized in a number of ways that vary considerably in overlap, suggesting multidimensionality. This study tested the hypothesis that the latent structure among multiple measures of impulsivity would reflect the following three broad categories: impulsive choice, reflecting discounting of delayed rewards; impulsive action, reflecting ability to inhibit a prepotent motor response; and impulsive personality traits, reflecting self-reported attributions of self-regulatory capacity. The study used a cross-sectional confirmatory factor analysis of multiple impulsivity assessments. Participants were 1252 young adults (62 % female) with low levels of addictive behavior, who were assessed in individual laboratory rooms at the University of Chicago and the University of Georgia. The battery comprised a Delay (replace hyphen with space) Discounting Task, Monetary Choice Questionnaire, Conners’ Continuous Performance Test, Go/NoGo Task, Stop Signal Task, Barratt Impulsiveness Scale, and the UPPS-P Impulsive Behavior Scale. The hypothesized three-factor model provided the best fit to the data, although sensation seeking was excluded from the final model. The three latent factors were largely unrelated to each other and were variably associated with substance use. These findings support the hypothesis that diverse measures of impulsivity can broadly be organized into three categories that are largely distinct from one another. These findings warrant investigation among individuals with clinical levels of addictive behavior and may be applied to understanding the underlying biological mechanisms of these categories.
University of Florida1, University of Western Ontario2, United States Environmental Protection Agency3, University of Waterloo4, University of Maine5, Indiana University6, North Dakota State University7, University of Georgia8, University of Maryland, College Park9, University of South Florida10, Virginia Tech11, United States Geological Survey12
TL;DR: It is argued that sustaining landscape functions requires conserving the entire continuum of wetland connectivity, including GIWs, which constitute most of the wetlands in many North American landscapes.
Abstract: Geographically isolated wetlands (GIWs), those surrounded by uplands, exchange materials, energy, and organisms with other elements in hydrological and habitat networks, contributing to landscape functions, such as flow generation, nutrient and sediment retention, and biodiversity support. GIWs constitute most of the wetlands in many North American landscapes, provide a disproportionately large fraction of wetland edges where many functions are enhanced, and form complexes with other water bodies to create spatial and temporal heterogeneity in the timing, flow paths, and magnitude of network connectivity. These attributes signal a critical role for GIWs in sustaining a portfolio of landscape functions, but legal protections remain weak despite preferential loss from many landscapes. GIWs lack persistent surface water connections, but this condition does not imply the absence of hydrological, biogeochemical, and biological exchanges with nearby and downstream waters. Although hydrological and biogeochemical connectivity is often episodic or slow (e.g., via groundwater), hydrologic continuity and limited evaporative solute enrichment suggest both flow generation and solute and sediment retention. Similarly, whereas biological connectivity usually requires overland dispersal, numerous organisms, including many rare or threatened species, use both GIWs and downstream waters at different times or life stages, suggesting that GIWs are critical elements of landscape habitat mosaics. Indeed, weaker hydrologic connectivity with downstream waters and constrained biological connectivity with other landscape elements are precisely what enhances some GIW functions and enables others. Based on analysis of wetland geography and synthesis of wetland functions, we argue that sustaining landscape functions requires conserving the entire continuum of wetland connectivity, including GIWs.
Veterans Health Administration1, Icahn School of Medicine at Mount Sinai2, University of California, San Francisco3, Group Health Cooperative4, University of Wisconsin-Madison5, Columbia University6, University of Georgia7, Harvard University8, Duke University9, Virginia Commonwealth University10, New York University11, Stanford University12, United States Department of Veterans Affairs13, University of Washington14, Brown University15, University of North Carolina at Chapel Hill16
TL;DR: The overall magnitude of harms to the fetus is small to moderate and the USPSTF recommends diagnosis and treatment as a grade B definition, and that treatment of pregnant and postpartum women with depression using CBT improves clinical outcomes.
Abstract: Description Update of the 2009 US Preventive Services Task Force (USPSTF) recommendation on screening for depression in adults. Methods The USPSTF reviewed the evidence on the benefits and harms of screening for depression in adult populations, including older adults and pregnant and postpartum women; the accuracy of depression screening instruments; and the benefits and harms of depression treatment in these populations. Population This recommendation applies to adults 18 years and older. Recommendation The USPSTF recommends screening for depression in the general adult population, including pregnant and postpartum women. Screening should be implemented with adequate systems in place to ensure accurate diagnosis, effective treatment, and appropriate follow-up. (B recommendation)