Showing papers by "University of California, Davis published in 2015"

Estimating the reproducibility of psychological science

Abstract: Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. Replication effects were half the magnitude of original effects, representing a substantial decline. Ninety-seven percent of original studies had statistically significant results. Thirty-six percent of replications had statistically significant results; 47% of original effect sizes were in the 95% confidence interval of the replication effect size; 39% of effects were subjectively rated to have replicated the original result; and if no bias in original results is assumed, combining original and replication results left 68% with statistically significant effects. Correlational tests suggest that replication success was better predicted by the strength of original evidence than by characteristics of the original and replication teams.

Clinical Features and Outcomes of Takotsubo (Stress) Cardiomyopathy

Abstract: BackgroundThe natural history, management, and outcome of takotsubo (stress) cardiomyopathy are incompletely understood. MethodsThe International Takotsubo Registry, a consortium of 26 centers in Europe and the United States, was established to investigate clinical features, prognostic predictors, and outcome of takotsubo cardiomyopathy. Patients were compared with age- and sex-matched patients who had an acute coronary syndrome. ResultsOf 1750 patients with takotsubo cardiomyopathy, 89.8% were women (mean age, 66.8 years). Emotional triggers were not as common as physical triggers (27.7% vs. 36.0%), and 28.5% of patients had no evident trigger. Among patients with takotsubo cardiomyopathy, as compared with an acute coronary syndrome, rates of neurologic or psychiatric disorders were higher (55.8% vs. 25.7%) and the mean left ventricular ejection fraction was markedly lower (40.7±11.2% vs. 51.5±12.3%) (P<0.001 for both comparisons). Rates of severe in-hospital complications including shock and death were ...

Structure, variation, and assembly of the root-associated microbiomes of rice.

Abstract: Plants depend upon beneficial interactions between roots and microbes for nutrient availability, growth promotion, and disease suppression. High-throughput sequencing approaches have provided recent insights into root microbiomes, but our current understanding is still limited relative to animal microbiomes. Here we present a detailed characterization of the root-associated microbiomes of the crop plant rice by deep sequencing, using plants grown under controlled conditions as well as field cultivation at multiple sites. The spatial resolution of the study distinguished three root-associated compartments, the endosphere (root interior), rhizoplane (root surface), and rhizosphere (soil close to the root surface), each of which was found to harbor a distinct microbiome. Under controlled greenhouse conditions, microbiome composition varied with soil source and genotype. In field conditions, geographical location and cultivation practice, namely organic vs. conventional, were factors contributing to microbiome variation. Rice cultivation is a major source of global methane emissions, and methanogenic archaea could be detected in all spatial compartments of field-grown rice. The depth and scale of this study were used to build coabundance networks that revealed potential microbial consortia, some of which were involved in methane cycling. Dynamic changes observed during microbiome acquisition, as well as steady-state compositions of spatial compartments, support a multistep model for root microbiome assembly from soil wherein the rhizoplane plays a selective gating role. Similarities in the distribution of phyla in the root microbiomes of rice and other plants suggest that conclusions derived from this study might be generally applicable to land plants.

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis.

Abstract: Data-independent acquisition (DIA) in liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS) provides comprehensive untargeted acquisition of molecular data. We provide an open-source software pipeline, which we call MS-DIAL, for DIA-based identification and quantification of small molecules by mass spectral deconvolution. For a reversed-phase LC-MS/MS analysis of nine algal strains, MS-DIAL using an enriched LipidBlast library identified 1,023 lipid compounds, highlighting the chemotaxonomic relationships between the algal strains.

Combined Measurement of the Higgs Boson Mass in pp Collisions at √s=7 and 8 TeV with the ATLAS and CMS Experiments

Abstract: A measurement of the Higgs boson mass is presented based on the combined data samples of the ATLAS and CMS experiments at the CERN LHC in the H→γγ and H→ZZ→4l decay channels. The results are obtained from a simultaneous fit to the reconstructed invariant mass peaks in the two channels and for the two experiments. The measured masses from the individual channels and the two experiments are found to be consistent among themselves. The combined measured mass of the Higgs boson is mH=125.09±0.21 (stat)±0.11 (syst) GeV.

The global distribution of the arbovirus vectors Aedes aegypti and Ae. Albopictus

Abstract: Dengue and chikungunya are increasing global public health concerns due to their rapid geographical spread and increasing disease burden. Knowledge of the contemporary distribution of their shared vectors, Aedes aegypti and Aedes albopictus remains incomplete and is complicated by an ongoing range expansion fuelled by increased global trade and travel. Mapping the global distribution of these vectors and the geographical determinants of their ranges is essential for public health planning. Here we compile the largest contemporary database for both species and pair it with relevant environmental variables predicting their global distribution. We show Aedes distributions to be the widest ever recorded; now extensive in all continents, including North America and Europe. These maps will help define the spatial limits of current autochthonous transmission of dengue and chikungunya viruses. It is only with this kind of rigorous entomological baseline that we can hope to project future health impacts of these viruses.

Crystallization by particle attachment in synthetic, biogenic, and geologic environments

Abstract: Field and laboratory observations show that crystals commonly form by the addition and attachment of particles that range from multi-ion complexes to fully formed nanoparticles. The particles involved in these nonclassical pathways to crystallization are diverse, in contrast to classical models that consider only the addition of monomeric chemical species. We review progress toward understanding crystal growth by particle-attachment processes and show that multiple pathways result from the interplay of free-energy landscapes and reaction dynamics. Much remains unknown about the fundamental aspects, particularly the relationships between solution structure, interfacial forces, and particle motion. Developing a predictive description that connects molecular details to ensemble behavior will require revisiting long-standing interpretations of crystal formation in synthetic systems, biominerals, and patterns of mineralization in natural environments.

Capital in the 21st Century

Abstract: On 19 December 2014, the Centre for Economic Policy Research and the Bank of England hosted a discussion forum based around Thomas Piketty’s book, Capital in the twenty-first century, with a number of economists from academia, public sector bodies and private sector institutions. Four speakers presented research on various issues relating to inequality, including: access to education; wealth and taxation policy; and the role of governance and institutions. This article presents each speaker’s key arguments, and includes a summary of the open-floor debate that followed.

Activity and safety of nivolumab, an anti-PD-1 immune checkpoint inhibitor, for patients with advanced, refractory squamous non-small-cell lung cancer (CheckMate 063): a phase 2, single-arm trial

Abstract: Summary Background Patients with squamous non-small-cell lung cancer that is refractory to multiple treatments have poor outcomes. We assessed the activity of nivolumab, a fully human IgG4 PD-1 immune checkpoint inhibitor antibody, for patients with advanced, refractory, squamous non-small-cell lung cancer. Methods We did this phase 2, single-arm trial at 27 sites (academic, hospital, and private cancer centres) in France, Germany, Italy, and USA. Patients who had received two or more previous treatments received intravenous nivolumab (3 mg/kg) every 2 weeks until progression or unacceptable toxic effects. The primary endpoint was the proportion of patients with a confirmed objective response as assessed by an independent radiology review committee. We included all treated patients in the analyses. This study is registered with ClinicalTrials.gov, number NCT01721759. Findings Between Nov 16, 2012, and July 22, 2013, we enrolled and treated 117 patients. 17 (14·5%, 95% CI 8·7–22·2) of 117 patients had an objective response as assessed by an independent radiology review committee. Median time to response was 3·3 months (IQR 2·2–4·8), and median duration of response was not reached (95% CI 8·31–not applicable); 13 (77%) of 17 of responses were ongoing at the time of analysis. 30 (26%) of 117 patients had stable disease (median duration 6·0 months, 95% CI 4·7–10·9). 20 (17%) of 117 patients reported grade 3–4 treatment-related adverse events, including: fatigue (five [4%] of 117 patients), pneumonitis (four [3%]), and diarrhoea (three [3%]). There were two treatment-associated deaths caused by pneumonia and ischaemic stroke that occurred in patients with multiple comorbidities in the setting of progressive disease. Interpretation Nivolumab has clinically meaningful activity and a manageable safety profile in previously treated patients with advanced, refractory, squamous non-small cell lung cancer. These data support the assessment of nivolumab in randomised, controlled, phase 3 studies of first-line and second-line treatment. Funding Bristol-Myers Squibb.

Joint Analysis of BICEP2/Keck Array and Planck Data

Abstract: We report the results of a joint analysis of data from BICEP2/Keck Array and Planck. BICEP2 and Keck Array have observed the same approximately 400 deg2 patch of sky centered on RA 0h, Dec. −57.5deg. The combined maps reach a depth of 57 nK deg in Stokes Q and U in a band centered at 150 GHz. Planck has observed the full sky in polarization at seven frequencies from 30 to 353 GHz, but much less deeply in any given region (1.2 μK deg in Q and U at 143 GHz). We detect 150×353 cross-correlation in B-modes at high significance. We fit the single- and cross-frequency power spectra at frequencies above 150 GHz to a lensed-ΛCDM model that includes dust and a possible contribution from inflationary gravitational waves (as parameterized by the tensor-to-scalar ratio r). We probe various model variations and extensions, including adding a synchrotron component in combination with lower frequency data, and find that these make little difference to the r constraint. Finally we present an alternative analysis which is similar to a map-based cleaning of the dust contribution, and show that this gives similar constraints. The final result is expressed as a likelihood curve for r, and yields an upper limit r0.05<0.12 at 95% confidence. Marginalizing over dust and r, lensing B-modes are detected at 7.0σ significance.

Visible Light Communication, Networking, and Sensing: A Survey, Potential and Challenges

Abstract: The solid-state lighting is revolutionizing the indoor illumination. Current incandescent and fluorescent lamps are being replaced by the LEDs at a rapid pace. Apart from extremely high energy efficiency, the LEDs have other advantages such as longer lifespan, lower heat generation, and improved color rendering without using harmful chemicals. One additional benefit of LEDs is that they are capable of switching to different light intensity at a very fast rate. This functionality has given rise to a novel communication technology (known as visible light communication—VLC) where LED luminaires can be used for high speed data transfer. This survey provides a technology overview and review of existing literature of visible light communication and sensing. This paper provides a detailed survey of 1) visible light communication system and characteristics of its various components such as transmitter and receiver; 2) physical layer properties of visible light communication channel, modulation methods, and MIMO techniques; 3) medium access techniques; 4) system design and programmable platforms; and 5) visible light sensing and application such as indoor localization, gesture recognition, screen-camera communication, and vehicular networking. We also outline important challenges that need to be addressed in order to design high-speed mobile networks using visible light communication.

Terrestrial animal tracking as an eye on life and planet

Abstract: BACKGROUND The movement of animals makes them fascinating but difficult study subjects. Animal movements underpin many biological phenomena, and understanding them is critical for applications in conservation, health, and food. Traditional approaches to animal tracking used field biologists wielding antennas to record a few dozen locations per animal, revealing only the most general patterns of animal space use. The advent of satellite tracking automated this process, but initially was limited to larger animals and increased the resolution of trajectories to only a few hundred locations per animal. The last few years have shown exponential improvement in tracking technology, leading to smaller tracking devices that can return millions of movement steps for ever-smaller animals. Finally, we have a tool that returns high-resolution data that reveal the detailed facets of animal movement and its many implications for biodiversity, animal ecology, behavior, and ecosystem function. ADVANCES Improved technology has brought animal tracking into the realm of big data, not only through high-resolution movement trajectories, but also through the addition of other on-animal sensors and the integration of remote sensing data about the environment through which these animals are moving. These new data are opening up a breadth of new scientific questions about ecology, evolution, and physiology and enable the use of animals as sensors of the environment. High–temporal resolution movement data also can document brief but important contacts between animals, creating new opportunities to study social networks, as well as interspecific interactions such as competition and predation. With solar panels keeping batteries charged, “lifetime” tracks can now be collected for some species, while broader approaches are aiming for species-wide sampling across multiple populations. Miniaturized tags also help reduce the impact of the devices on the study subjects, improving animal welfare and scientific results. As in other disciplines, the explosion of data volume and variety has created new challenges and opportunities for information management, integration, and analysis. In an exciting interdisciplinary push, biologists, statisticians, and computer scientists have begun to develop new tools that are already leading to new insights and scientific breakthroughs. OUTLOOK We suggest that a golden age of animal tracking science has begun and that the upcoming years will be a time of unprecedented exciting discoveries. Technology continues to improve our ability to track animals, with the promise of smaller tags collecting more data, less invasively, on a greater variety of animals. The big-data tracking studies that are just now being pioneered will become commonplace. If analytical developments can keep pace, the field will be able to develop real-time predictive models that integrate habitat preferences, movement abilities, sensory capacities, and animal memories into movement forecasts. The unique perspective offered by big-data animal tracking enables a new view of animals as naturally evolved sensors of environment, which we think has the potential to help us monitor the planet in completely new ways. A massive multi-individual monitoring program would allow a quorum sensing of our planet, using a variety of species to tap into the diversity of senses that have evolved across animal groups, providing new insight on our world through the sixth sense of the global animal collective. We expect that the field will soon reach a transformational point where these studies do more than inform us about particular species of animals, but allow the animals to teach us about the world.

Supercapacitors performance evaluation

Abstract: The performance of a supercapacitor can be characterized by a series of key parameters, including the cell capacitance, operating voltage, equivalent series resistance, power density, energy density, and time constant. To accurately measure these parameters, a variety of methods have been proposed and are used in academia and industry. As a result, some confusion has been caused due to the inconsistencies between different evaluation methods and practices. Such confusion hinders effective communication of new research findings, and creates a hurdle in transferring novel supercapacitor technologies from research labs to commercial applications. Based on public sources, this article is an attempt to inventory, critique and hopefully streamline the commonly used instruments, key performance metrics, calculation methods, and major affecting factors for supercapacitor performance evaluation. Thereafter the primary sources of inconsistencies are identified and possible solutions are suggested, with emphasis on device performance vs. material properties and the rate dependency of supercapacitors. We hope, by using reliable, intrinsic, and comparable parameters produced, the existing inconsistencies and confusion can be largely eliminated so as to facilitate further progress in the field.

Productivity limits and potentials of the principles of conservation agriculture

Abstract: One of the primary challenges of our time is to feed a growing and more demanding world population with reduced external inputs and minimal environmental impacts, all under more variable and extreme climate conditions in the future. Conservation agriculture represents a set of three crop management principles that has received strong international support to help address this challenge, with recent conservation agriculture efforts focusing on smallholder farming systems in sub-Saharan Africa and South Asia. However, conservation agriculture is highly debated, with respect to both its effects on crop yields and its applicability in different farming contexts. Here we conduct a global meta-analysis using 5,463 paired yield observations from 610 studies to compare no-till, the original and central concept of conservation agriculture, with conventional tillage practices across 48 crops and 63 countries. Overall, our results show that no-till reduces yields, yet this response is variable and under certain conditions no-till can produce equivalent or greater yields than conventional tillage. Importantly, when no-till is combined with the other two conservation agriculture principles of residue retention and crop rotation, its negative impacts are minimized. Moreover, no-till in combination with the other two principles significantly increases rainfed crop productivity in dry climates, suggesting that it may become an important climate-change adaptation strategy for ever-drier regions of the world. However, any expansion of conservation agriculture should be done with caution in these areas, as implementation of the other two principles is often challenging in resource-poor and vulnerable smallholder farming systems, thereby increasing the likelihood of yield losses rather than gains. Although farming systems are multifunctional, and environmental and socio-economic factors need to be considered, our analysis indicates that the potential contribution of no-till to the sustainable intensification of agriculture is more limited than often assumed.

Family income, parental education and brain structure in children and adolescents

Abstract: Socioeconomic disparities are associated with differences in cognitive development. The extent to which this translates to disparities in brain structure is unclear. We investigated relationships between socioeconomic factors and brain morphometry, independently of genetic ancestry, among a cohort of 1,099 typically developing individuals between 3 and 20 years of age. Income was logarithmically associated with brain surface area. Among children from lower income families, small differences in income were associated with relatively large differences in surface area, whereas, among children from higher income families, similar income increments were associated with smaller differences in surface area. These relationships were most prominent in regions supporting language, reading, executive functions and spatial skills; surface area mediated socioeconomic differences in certain neurocognitive abilities. These data imply that income relates most strongly to brain structure among the most disadvantaged children.

Anthropogenic debris in seafood: Plastic debris and fibers from textiles in fish and bivalves sold for human consumption

Abstract: The ubiquity of anthropogenic debris in hundreds of species of wildlife and the toxicity of chemicals associated with it has begun to raise concerns regarding the presence of anthropogenic debris in seafood. We assessed the presence of anthropogenic debris in fishes and shellfish on sale for human consumption. We sampled from markets in Makassar, Indonesia, and from California, USA. All fish and shellfish were identified to species where possible. Anthropogenic debris was extracted from the digestive tracts of fish and whole shellfish using a 10% KOH solution and quantified under a dissecting microscope. In Indonesia, anthropogenic debris was found in 28% of individual fish and in 55% of all species. Similarly, in the USA, anthropogenic debris was found in 25% of individual fish and in 67% of all species. Anthropogenic debris was also found in 33% of individual shellfish sampled. All of the anthropogenic debris recovered from fish in Indonesia was plastic, whereas anthropogenic debris recovered from fish in the USA was primarily fibers. Variations in debris types likely reflect different sources and waste management strategies between countries. We report some of the first findings of plastic debris in fishes directly sold for human consumption raising concerns regarding human health.

Repair and tissue engineering techniques for articular cartilage

Abstract: Chondral and osteochondral lesions due to injury or other pathology commonly result in the development of osteoarthritis, eventually leading to progressive total joint destruction. Although current progress suggests that biologic agents can delay the advancement of deterioration, such drugs are incapable of promoting tissue restoration. The limited ability of articular cartilage to regenerate renders joint arthroplasty an unavoidable surgical intervention. This Review describes current, widely used clinical repair techniques for resurfacing articular cartilage defects; short-term and long-term clinical outcomes of these techniques are discussed. Also reviewed is a developmental pipeline of acellular and cellular regenerative products and techniques that could revolutionize joint care over the next decade by promoting the development of functional articular cartilage. Acellular products typically consist of collagen or hyaluronic-acid-based materials, whereas cellular techniques use either primary cells or stem cells, with or without scaffolds. Central to these efforts is the prominent role that tissue engineering has in translating biological technology into clinical products; therefore, concomitant regulatory processes are also discussed.

Rapid and highly variable warming of lake surface waters around the globe

Abstract: In this first worldwide synthesis of in situ and satellite-derived lake data, we find that lake summer surface water temperatures rose rapidly (global mean = 0.34°C decade−1) between 1985 and 2009. Our analyses show that surface water warming rates are dependent on combinations of climate and local characteristics, rather than just lake location, leading to the counterintuitive result that regional consistency in lake warming is the exception, rather than the rule. The most rapidly warming lakes are widely geographically distributed, and their warming is associated with interactions among different climatic factors—from seasonally ice-covered lakes in areas where temperature and solar radiation are increasing while cloud cover is diminishing (0.72°C decade−1) to ice-free lakes experiencing increases in air temperature and solar radiation (0.53°C decade−1). The pervasive and rapid warming observed here signals the urgent need to incorporate climate impacts into vulnerability assessments and adaptation efforts for lakes.

A standardised static in vitro digestion method suitable for food – an international consensus

Abstract: Simulated gastro-intestinal digestion is widely employed in many fields of food and nutritional sciences, as conducting human trials are often costly, resource intensive, and ethically disputable. As a consequence, in vitro alternatives that determine endpoints such as the bioaccessibility of nutrients and non-nutrients or the digestibility of macronutrients (e.g. lipids, proteins and carbohydrates) are used for screening and building new hypotheses. Various digestion models have been proposed, often impeding the possibility to compare results across research teams. For example, a large variety of enzymes from different sources such as of porcine, rabbit or human origin have been used, differing in their activity and characterization. Differences in pH, mineral type, ionic strength and digestion time, which alter enzyme activity and other phenomena, may also considerably alter results. Other parameters such as the presence of phospholipids, individual enzymes such as gastric lipase and digestive emulsifiers vs. their mixtures (e.g. pancreatin and bile salts), and the ratio of food bolus to digestive fluids, have also been discussed at length. In the present consensus paper, within the COST Infogest network, we propose a general standardised and practical static digestion method based on physiologically relevant conditions that can be applied for various endpoints, which may be amended to accommodate further specific requirements. A frameset of parameters including the oral, gastric and small intestinal digestion are outlined and their relevance discussed in relation to available in vivo data and enzymes. This consensus paper will give a detailed protocol and a line-by-line, guidance, recommendations and justifications but also limitation of the proposed model. This harmonised static, in vitro digestion method for food should aid the production of more comparable data in the future.

Naturalistic Developmental Behavioral Interventions: Empirically Validated Treatments for Autism Spectrum Disorder

Abstract: Earlier autism diagnosis, the importance of early intervention, and development of specific interventions for young children have contributed to the emergence of similar, empirically supported, autism interventions that represent the merging of applied behavioral and developmental sciences. “Naturalistic Developmental Behavioral Interventions (NDBI)” are implemented in natural settings, involve shared control between child and therapist, utilize natural contingencies, and use a variety of behavioral strategies to teach developmentally appropriate and prerequisite skills. We describe the development of NDBIs, their theoretical bases, empirical support, requisite characteristics, common features, and suggest future research needs. We wish to bring parsimony to a field that includes interventions with different names but common features thus improving understanding and choice-making among families, service providers and referring agencies.

Symbol Nomenclature for Graphical Representations of Glycans.

Abstract: Author(s): Varki, Ajit; Cummings, Richard D; Aebi, Markus; Packer, Nicole H; Seeberger, Peter H; Esko, Jeffrey D; Stanley, Pamela; Hart, Gerald; Darvill, Alan; Kinoshita, Taroh; Prestegard, James J; Schnaar, Ronald L; Freeze, Hudson H; Marth, Jamey D; Bertozzi, Carolyn R; Etzler, Marilynn E; Frank, Martin; Vliegenthart, Johannes Fg; Lutteke, Thomas; Perez, Serge; Bolton, Evan; Rudd, Pauline; Paulson, James; Kanehisa, Minoru; Toukach, Philip; Aoki-Kinoshita, Kiyoko F; Dell, Anne; Narimatsu, Hisashi; York, William; Taniguchi, Naoyuki; Kornfeld, Stuart

Delivery of crop pollination services is an insufficient argument for wild pollinator conservation

Abstract: There is compelling evidence that more diverse ecosystems deliver greater benefits to people, and these ecosystem services have become a key argument for biodiversity conservation. However, it is unclear how much biodiversity is needed to deliver ecosystem services in a cost-effective way. Here we show that, while the contribution of wild bees to crop production is significant, service delivery is restricted to a limited subset of all known bee species. Across crops, years and biogeographical regions, crop-visiting wild bee communities are dominated by a small number of common species, and threatened species are rarely observed on crops. Dominant crop pollinators persist under agricultural expansion and many are easily enhanced by simple conservation measures, suggesting that cost-effective management strategies to promote crop pollination should target a different set of species than management strategies to promote threatened bees. Conserving the biological diversity of bees therefore requires more than just ecosystem-service-based arguments.

OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

Abstract: Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that is useful for genome wide comparisons and visualization of orthologous clusters. OrthoVenn provides coverage of vertebrates, metazoa, protists, fungi, plants and bacteria for the comparison of orthologous clusters and also supports uploading of customized protein sequences from user-defined species. An interactive Venn diagram, summary counts, and functional summaries of the disjunction and intersection of clusters shared between species are displayed as part of the OrthoVenn result. OrthoVenn also includes in-depth views of the clusters using various sequence analysis tools. Furthermore, OrthoVenn identifies orthologous clusters of single copy genes and allows for a customized search of clusters of specific genes through key words or BLAST. OrthoVenn is an efficient and user-friendly web server freely accessible at http://probes.pw.usda.gov/OrthoVenn or http://aegilops.wheat.ucdavis.edu/OrthoVenn.