Showing papers by "University of Colorado Boulder published in 2009"
University of Colorado Boulder1, Harvard University2, Mayo Clinic3, Boston University4, University of Pennsylvania5, University of Pittsburgh6, University of Siena7, University Health Network8, Institut Gustave Roussy9, Oregon Health & Science University10, University of Texas MD Anderson Cancer Center11, Duke University12, University of Cincinnati13, Memorial Sloan Kettering Cancer Center14, MedStar Washington Hospital Center15
TL;DR: Evidence-based recommendations are developed to inform clinical decision-making in the management of thyroid nodules and differentiated thyroid cancer and represent, in the authors' opinion, contemporary optimal care for patients with these disorders.
Abstract: Background: Thyroid nodules are a common clinical problem, and differentiated thyroid cancer is becoming increasingly prevalent. Since the American Thyroid Association's (ATA's) guidelines for the management of these disorders were revised in 2009, significant scientific advances have occurred in the field. The aim of these guidelines is to inform clinicians, patients, researchers, and health policy makers on published evidence relating to the diagnosis and management of thyroid nodules and differentiated thyroid cancer. Methods: The specific clinical questions addressed in these guidelines were based on prior versions of the guidelines, stakeholder input, and input of task force members. Task force panel members were educated on knowledge synthesis methods, including electronic database searching, review and selection of relevant citations, and critical appraisal of selected studies. Published English language articles on adults were eligible for inclusion. The American College of Physicians Guideline Gr...
10,501 citations
TL;DR: The faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers are characterized to address how host genotype, environmental exposure and host adiposity influence the gut microbiome.
Abstract: The human distal gut harbours a vast ensemble of microbes (the microbiota) that provide important metabolic capabilities, including the ability to extract energy from otherwise indigestible dietary polysaccharides. Studies of a few unrelated, healthy adults have revealed substantial diversity in their gut communities, as measured by sequencing 16S rRNA genes, yet how this diversity relates to function and to the rest of the genes in the collective genomes of the microbiota (the gut microbiome) remains obscure. Studies of lean and obese mice suggest that the gut microbiota affects energy balance by influencing the efficiency of calorie harvest from the diet, and how this harvested energy is used and stored. Here we characterize the faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers, to address how host genotype, environmental exposure and host adiposity influence the gut microbiome. Analysis of 154 individuals yielded 9,920 near full-length and 1,937,461 partial bacterial 16S rRNA sequences, plus 2.14 gigabases from their microbiomes. The results reveal that the human gut microbiome is shared among family members, but that each person's gut microbial community varies in the specific bacterial lineages present, with a comparable degree of co-variation between adult monozygotic and dizygotic twin pairs. However, there was a wide array of shared microbial genes among sampled individuals, comprising an extensive, identifiable 'core microbiome' at the gene, rather than at the organismal lineage, level. Obesity is associated with phylum-level changes in the microbiota, reduced bacterial diversity and altered representation of bacterial genes and metabolic pathways. These results demonstrate that a diversity of organismal assemblages can nonetheless yield a core microbiome at a functional level, and that deviations from this core are associated with different physiological states (obese compared with lean).
6,970 citations
University of Gothenburg1, University College Cork2, Paul Scherrer Institute3, Weizmann Institute of Science4, Norwegian Meteorological Institute5, Chalmers University of Technology6, University of Antwerp7, Carnegie Mellon University8, Centre national de la recherche scientifique9, University of Lyon10, University of California, Berkeley11, University of York12, Leibniz Institute for Neurobiology13, University of Mainz14, University of Florida15, University of Colorado Boulder16, Forschungszentrum Jülich17, Ghent University18, University of Manchester19, Aix-Marseille University20, California Institute of Technology21
TL;DR: In this article, an overview of the atmospheric degradation mechanisms for SOA precursors, gas-particle partitioning theory and analytical techniques used to determine the chemical composition of SOA is presented.
Abstract: Secondary organic aerosol (SOA) accounts for a significant fraction of ambient tropospheric aerosol and a detailed knowledge of the formation, properties and transformation of SOA is therefore required to evaluate its impact on atmospheric processes, climate and human health. The chemical and physical processes associated with SOA formation are complex and varied, and, despite considerable progress in recent years, a quantitative and predictive understanding of SOA formation does not exist and therefore represents a major research challenge in atmospheric science. This review begins with an update on the current state of knowledge on the global SOA budget and is followed by an overview of the atmospheric degradation mechanisms for SOA precursors, gas-particle partitioning theory and the analytical techniques used to determine the chemical composition of SOA. A survey of recent laboratory, field and modeling studies is also presented. The following topical and emerging issues are highlighted and discussed in detail: molecular characterization of biogenic SOA constituents, condensed phase reactions and oligomerization, the interaction of atmospheric organic components with sulfuric acid, the chemical and photochemical processing of organics in the atmospheric aqueous phase, aerosol formation from real plant emissions, interaction of atmospheric organic components with water, thermodynamics and mixtures in atmospheric models. Finally, the major challenges ahead in laboratory, field and modeling studies of SOA are discussed and recommendations for future research directions are proposed.
3,324 citations
TL;DR: The results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.
Abstract: Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R2 = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.
3,151 citations
University of Colorado Boulder1, Carnegie Mellon University2, Paul Scherrer Institute3, University at Albany, SUNY4, University of California, Berkeley5, Swiss Federal Laboratories for Materials Science and Technology6, State University of New York System7, University of California, Davis8, University of Eastern Finland9, Finnish Meteorological Institute10, University of Helsinki11, Stockholm University12, Texas A&M University13, Max Planck Society14, University of Tokyo15, University of New Hampshire16, National Oceanic and Atmospheric Administration17
TL;DR: A unifying model framework describing the atmospheric evolution of OA that is constrained by high–time-resolution measurements of its composition, volatility, and oxidation state is presented, which can serve as a basis for improving parameterizations in regional and global models.
Abstract: Organic aerosol (OA) particles affect climate forcing and human health, but their sources and evolution remain poorly characterized. We present a unifying model framework describing the atmospheric evolution of OA that is constrained by high-time-resolution measurements of its composition, volatility, and oxidation state. OA and OA precursor gases evolve by becoming increasingly oxidized, less volatile, and more hygroscopic, leading to the formation of oxygenated organic aerosol (OOA), with concentrations comparable to those of sulfate aerosol throughout the Northern Hemisphere. Our model framework captures the dynamic aging behavior observed in both the atmosphere and laboratory: It can serve as a basis for improving parameterizations in regional and global models.
3,104 citations
TL;DR: The results indicate that the microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease.
Abstract: Elucidating the biogeography of bacterial communities on the human body is critical for establishing healthy baselines from which to detect differences associated with diseases. To obtain an integrated view of the spatial and temporal distribution of the human microbiota, we surveyed bacteria from up to 27 sites in seven to nine healthy adults on four occasions. We found that community composition was determined primarily by body habitat. Within habitats, interpersonal variability was high, whereas individuals exhibited minimal temporal variability. Several skin locations harbored more diverse communities than the gut and mouth, and skin locations differed in their community assembly patterns. These results indicate that our microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease.
2,839 citations
TL;DR: A translational medicine pipeline is described where human gut microbial communities and diets are re-created in gnotobiotic mice and the impact on microbe and host is defined using metagenomics, creating a well-defined, representative animal model of the human gut ecosystem.
Abstract: Diet and nutritional status are among the most important modifiable determinants of human health. The nutritional value of food is influenced in part by a person's gut microbial community (microbiota) and its component genes (microbiome). Unraveling the interrelations among diet, the structure and operations of the gut microbiota, and nutrient and energy harvest is confounded by variations in human environmental exposures, microbial ecology, and genotype. To help overcome these problems, we created a well-defined, representative animal model of the human gut ecosystem by transplanting fresh or frozen adult human fecal microbial communities into germ-free C57BL/6J mice. Culture-independent metagenomic analysis of the temporal, spatial, and intergenerational patterns of bacterial colonization showed that these humanized mice were stably and heritably colonized and reproduced much of the bacterial diversity of the donor's microbiota. Switching from a low-fat, plant polysaccharide-rich diet to a high-fat, high-sugar "Western" diet shifted the structure of the microbiota within a single day, changed the representation of metabolic pathways in the microbiome, and altered microbiome gene expression. Reciprocal transplants involving various combinations of donor and recipient diets revealed that colonization history influences the initial structure of the microbial community but that these effects can be rapidly altered by diet. Humanized mice fed the Western diet have increased adiposity; this trait is transmissible via microbiota transplantation. Humanized gnotobiotic mice will be useful for conducting proof-of-principle "clinical trials" that test the effects of environmental and genetic factors on the gut microbiota and host physiology. Nearly full-length 16S rRNA gene sequences are deposited in GenBank under the accession numbers GQ491120 to GQ493997.
2,709 citations
TL;DR: The use of both synthetic and natural hydrogels as scaffolds for three-dimensional cell culture as well as synthetic hydrogel hybrids that incorporate sophisticated biochemical and mechanical cues as mimics of the native extracellular matrix are discussed.
Abstract: Methods for culturing mammalian cells ex vivo are increasingly needed to study cell and tissue physiology and to grow replacement tissue for regenerative medicine. Two-dimensional culture has been the paradigm for typical in vitro cell culture; however, it has been demonstrated that cells behave more natively when cultured in three-dimensional environments. Permissive, synthetic hydrogels and promoting, natural hydrogels have become popular as three-dimensional cell culture platforms; yet, both of these systems possess limitations. In this perspective, we discuss the use of both synthetic and natural hydrogels as scaffolds for three-dimensional cell culture as well as synthetic hydrogels that incorporate sophisticated biochemical and mechanical cues as mimics of the native extracellular matrix. Ultimately, advances in synthetic-biologic hydrogel hybrids are needed to provide robust platforms for investigating cell physiology and fabricating tissue outside of the organism.
2,298 citations
Uppsala University1, Iowa State University2, University of Minnesota3, University of Siena4, United States Geological Survey5, Trent University6, University of Regina7, University of North Carolina at Chapel Hill8, Miami University9, Finnish Environment Institute10, Marine Institute of Memorial University of Newfoundland11, University of Oslo12, Université du Québec13, Virginia Commonwealth University14, University of Colorado Boulder15, University of California, Santa Barbara16, University of the Sciences17, Université du Québec à Montréal18, Universidade Federal de Juiz de Fora19, Commonwealth Scientific and Industrial Research Organisation20, University of Alberta21, ETH Zurich22, Hydro-Québec23
TL;DR: The role of lakes in carbon cycling and global climate, examine the mechanisms influencing carbon pools and transformations in lakes, and discuss how the metabolism of carbon in the inland waters is likely to change in response to climate.
Abstract: We explore the role of lakes in carbon cycling and global climate, examine the mechanisms influencing carbon pools and transformations in lakes, and discuss how the metabolism of carbon in the inland waters is likely to change in response to climate. Furthermore, we project changes as global climate change in the abundance and spatial distribution of lakes in the biosphere, and we revise the estimate for the global extent of carbon transformation in inland waters. This synthesis demonstrates that the global annual emissions of carbon dioxide from inland waters to the atmosphere are similar in magnitude to the carbon dioxide uptake by the oceans and that the global burial of organic carbon in inland water sediments exceeds organic carbon sequestration on the ocean floor. The role of inland waters in global carbon cycling and climate forcing may be changed by human activities, including construction of impoundments, which accumulate large amounts of carbon in sediments and emit large amounts of methane to the atmosphere. Methane emissions are also expected from lakes on melting permafrost. The synthesis presented here indicates that (1) inland waters constitute a significant component of the global carbon cycle, (2) their contribution to this cycle has significantly changed as a result of human activities, and (3) they will continue to change in response to future climate change causing decreased as well as increased abundance of lakes as well as increases in the number of aquatic impoundments.
2,140 citations
TL;DR: In this article, the authors present an assessment of 33 deltas chosen to represent the world's Deltas and find that in the past decade, 85% of them experienced severe flooding, resulting in the temporary submergence of 260,000 km2.
Abstract: Many of the world's deltas are densely populated and intensively farmed. An assessment of recent publications indicates that the majority of these deltas have been subject to intense flooding over the past decade, and that this threat will grow as global sea-level rises and as the deltas subside. Many of the world's largest deltas are densely populated and heavily farmed. Yet many of their inhabitants are becoming increasingly vulnerable to flooding and conversions of their land to open ocean. The vulnerability is a result of sediment compaction from the removal of oil, gas and water from the delta's underlying sediments, the trapping of sediment in reservoirs upstream and floodplain engineering in combination with rising global sea level. Here we present an assessment of 33 deltas chosen to represent the world's deltas. We find that in the past decade, 85% of the deltas experienced severe flooding, resulting in the temporary submergence of 260,000 km2. We conservatively estimate that the delta surface area vulnerable to flooding could increase by 50% under the current projected values for sea-level rise in the twenty-first century. This figure could increase if the capture of sediment upstream persists and continues to prevent the growth and buffering of the deltas.
1,825 citations
TL;DR: Analysis of longitudinal data from unmanaged old forests in the western United States showed that background (noncatastrophic) mortality rates have increased rapidly in recent decades, with doubling periods ranging from 17 to 29 years among regions.
Abstract: Persistent changes in tree mortality rates can alter forest structure, composition, and ecosystem services such as carbon sequestration. Our analyses of longitudinal data from unmanaged old forests in the western United States showed that background (noncatastrophic) mortality rates have increased rapidly in recent decades, with doubling periods ranging from 17 to 29 years among regions. Increases were also pervasive across elevations, tree sizes, dominant genera, and past fire histories. Forest density and basal area declined slightly, which suggests that increasing mortality was not caused by endogenous increases in competition. Because mortality increased in small trees, the overall increase in mortality rates cannot be attributed solely to aging of large trees. Regional warming and consequent increases in water deficits are likely contributors to the increases in tree mortality rates.
TL;DR: A strategy to create photodegradable poly(ethylene glycol)–based hydrogels through rapid polymerization of cytocompatible macromers for remote manipulation of gel properties in situ is reported.
Abstract: We report a strategy to create photodegradable poly(ethylene glycol)-based hydrogels through rapid polymerization of cytocompatible macromers for remote manipulation of gel properties in situ. Postgelation control of the gel properties was demonstrated to introduce temporal changes, creation of arbitrarily shaped features, and on-demand pendant functionality release. Channels photodegraded within a hydrogel containing encapsulated cells allow cell migration. Temporal variation of the biochemical gel composition was used to influence chondrogenic differentiation of encapsulated stem cells. Photodegradable gels that allow real-time manipulation of material properties or chemistry provide dynamic environments with the scope to answer fundamental questions about material regulation of live cell function and may affect an array of applications from design of drug delivery vehicles to tissue engineering systems.
TL;DR: In this paper, the authors used the phenotype of RELMβ knockout mice to assess the influence of host phenotype, genotype, immune function, and diet on the composition of the human gut microbiome.
TL;DR: The current understanding of the contribution of glia to pathological pain and neuroprotection is reviewed, and how the protective, anti-inflammatory actions ofglia are being harnessed to develop new drug targets for neuropathic pain control is reviewed.
Abstract: Glia have emerged as key contributors to pathological and chronic pain mechanisms. On activation, both astrocytes and microglia respond to and release a number of signalling molecules, which have protective and/or pathological functions. Here we review the current understanding of the contribution of glia to pathological pain and neuroprotection, and how the protective, anti-inflammatory actions of glia are being harnessed to develop new drug targets for neuropathic pain control. Given the prevalence of chronic pain and the partial efficacy of current drugs, which exclusively target neuronal mechanisms, new strategies to manipulate neuron–glia interactions in pain processing hold considerable promise.
A. Adare1, Serguei Afanasiev2, Christine Angela Aidala3, Christine Angela Aidala4 +601 more•Institutions (57)
Stanford University1, Prescott College2, University of Illinois at Urbana–Champaign3, Cornell University4, National Center for Atmospheric Research5, University of Bristol6, University of São Paulo7, Columbia University8, Michigan State University9, University of Colorado Boulder10, China Agricultural University11
TL;DR: Solutions to the nutrient challenges that face global agriculture can be informed by analyses of trajectories of change within, as well as across, agricultural systems.
Abstract: Nutrient cycles link agricultural systems to their societies and surroundings; inputs of nitrogen and phosphorus in particular are essential for high crop yields, but downstream and downwind losses of these same nutrients diminish environmental quality and human well-being. Agricultural nutrient balances differ substantially with economic development, from inputs that are inadequate to maintain soil fertility in parts of many developing countries, particularly those of sub-Saharan Africa, to excessive and environmentally damaging surpluses in many developed and rapidly growing economies. National and/or regional policies contribute to patterns of nutrient use and their environmental consequences in all of these situations ( 1 ). Solutions to the nutrient challenges that face global agriculture can be informed by analyses of trajectories of change within, as well as across, agricultural systems.
TL;DR: In this paper, positive matrix factorization (PMF) was used to identify and interpret the organic aerosol (OA) data from an Aerodyne Aerosol Mass Spectrometer (Q-AMS) collected at the Pittsburgh Air Quality Study (PAQS) in September 2002.
Abstract: . The organic aerosol (OA) dataset from an Aerodyne Aerosol Mass Spectrometer (Q-AMS) collected at the Pittsburgh Air Quality Study (PAQS) in September 2002 was analyzed with Positive Matrix Factorization (PMF). Three components – hydrocarbon-like organic aerosol OA (HOA), a highly-oxygenated OA (OOA-1) that correlates well with sulfate, and a less-oxygenated, semi-volatile OA (OOA-2) that correlates well with nitrate and chloride – are identified and interpreted as primary combustion emissions, aged SOA, and semivolatile, less aged SOA, respectively. The complexity of interpreting the PMF solutions of unit mass resolution (UMR) AMS data is illustrated by a detailed analysis of the solutions as a function of number of components and rotational forcing. A public web-based database of AMS spectra has been created to aid this type of analysis. Realistic synthetic data is also used to characterize the behavior of PMF for choosing the best number of factors, and evaluating the rotations of non-unique solutions. The ambient and synthetic data indicate that the variation of the PMF quality of fit parameter (Q, a normalized chi-squared metric) vs. number of factors in the solution is useful to identify the minimum number of factors, but more detailed analysis and interpretation are needed to choose the best number of factors. The maximum value of the rotational matrix is not useful for determining the best number of factors. In synthetic datasets, factors are "split" into two or more components when solving for more factors than were used in the input. Elements of the "splitting" behavior are observed in solutions of real datasets with several factors. Significant structure remains in the residual of the real dataset after physically-meaningful factors have been assigned and an unrealistic number of factors would be required to explain the remaining variance. This residual structure appears to be due to variability in the spectra of the components (especially OOA-2 in this case), which is likely to be a key limit of the retrievability of components from AMS datasets using PMF and similar methods that need to assume constant component mass spectra. Methods for characterizing and dealing with this variability are needed. Interpretation of PMF factors must be done carefully. Synthetic data indicate that PMF internal diagnostics and similarity to available source component spectra together are not sufficient for identifying factors. It is critical to use correlations between factor and external measurement time series and other criteria to support factor interpretations. True components with
TL;DR: Age differences in future orientation are examined in a sample of 935 individuals between 10 and 30 years using a delay discounting task as well as a new self-report measure to distinguish between future orientation and impulse control, which may have different neural underpinnings and follow different developmental timetables.
Abstract: Age differences in future orientation are examined in a sample of 935 individuals between 10 and 30 years using a delay discounting task as well as a new self-report measure. Younger adolescents consistently demonstrate a weaker orientation to the future than do individuals aged 16 and older, as reflected in their greater willingness to accept a smaller reward delivered sooner than a larger one that is delayed, and in their characterizations of themselves as less concerned about the future and less likely to anticipate the consequences of their decisions. Planning ahead, in contrast, continues to develop into young adulthood. Future studies should distinguish between future orientation and impulse control, which may have different neural underpinnings and follow different developmental timetables.
TL;DR: The findings suggest that Twitter messages sent during these types of events contain more displays of information broadcasting and brokerage, and that general Twitter use seems to have evolved over time to offer more of an information-sharing purpose.
Abstract: This paper offers a descriptive account of Twitter (a microblogging service) across four high-profile, mass convergence events - two emergency and two national security. We statistically examine how Twitter is being used surrounding these events, and compare and contrast how that behaviour is different from more general Twitter use. Our findings suggest that Twitter messages sent during these types of events contain more displays of information broadcasting and brokerage, and we observe that general Twitter use seems to have evolved over time to offer more of an information-sharing purpose. We also provide preliminary evidence that Twitter users who join during and in apparent relation to a mass convergence or emergency event are more likely to become long-term adopters of the technology.
TL;DR: Acidobacteria communities were more phylogenetically clustered as soil pH departed from neutrality, suggesting that pH is an effective habitat filter, restricting community membership to progressively more narrowly defined lineages as pH deviates from neutrality.
Abstract: Acidobacteria are ubiquitous and abundant members of soil bacterial communities. However, an ecological understanding of this important phylum has remained elusive because its members have been difficult to culture and few molecular investigations have focused exclusively on this group. We generated an unprecedented number of acidobacterial DNA sequence data using pyrosequencing and clone libraries (39 707 and 1787 sequences, respectively) to characterize the relative abundance, diversity and composition of acidobacterial communities across a range of soil types. To gain insight into the ecological characteristics of acidobacterial taxa, we investigated the largescale biogeographic patterns exhibited by acidobacterial communities, and related soil and site characteristics to acidobacterial community assemblage patterns. The 87 soils analyzed by pyrosequencing contained more than 8600 unique acidobacterial phylotypes (at the 97% sequence similarity level). One phylotype belonging to Acidobacteria subgroup 1, but not closely related to any cultured representatives, was particularly abundant, accounting for 7.4% of bacterial sequences and 17.6% of acidobacterial sequences, on average, across the soils. The abundance of Acidobacteria relative to other bacterial taxa was highly variable across the soils examined, but correlated strongly with soil pH (R ¼� 0.80, Po0.001). Soil pH was also the best predictor of acidobacterial community composition, regardless of how the communities were characterized, and the relative abundances of the dominant Acidobacteria subgroups were readily predictable. Acidobacterial communities were more phylogenetically clustered as soil pH departed from neutrality, suggesting that pH is an effective habitat filter, restricting community membership to progressively more narrowly defined lineages as pH deviates from neutrality.
TL;DR: A water soluble lithium acylphosphinate salt is evaluated for its ability to polymerize diacrylated poly(ethylene glycol) (PEGDA) monomers rapidly into hydrogels, while maintaining high viability during direct encapsulation of cells.
TL;DR: A meta-analysis of published data identifies robust patterns in the structure of belowground microbial and faunal communities at broad scales which may be explained by universal mechanisms that regulate belowground biota across biomes.
Abstract: Although belowground ecosystems have been studied extensively and soil biota play integral roles in biogeochemical processes, surprisingly we have a limited understanding of global patterns in belowground biomass and community structure. To address this critical gap, we conducted a meta-analysis of published data (> 1300 datapoints) to compare belowground plant, microbial and faunal biomass across seven of the major biomes on Earth. We also assembled data to assess biome-level patterns in belowground microbial community composition. Our analysis suggests that variation in microbial biomass is predictable across biomes, with microbial biomass carbon representing 0.6-1.1% of soil organic carbon (r(2) = 0.91) and 1-20% of total plant biomass carbon (r(2) = 0.42). Approximately 50% of total animal biomass can be found belowground and soil faunal biomass represents < 4% of microbial biomass across all biomes. The structure of belowground microbial communities is also predictable: bacterial community composition and fungal : bacterial gene ratios can be predicted reasonably well from soil pH and soil C : N ratios respectively. Together these results identify robust patterns in the structure of belowground microbial and faunal communities at broad scales which may be explained by universal mechanisms that regulate belowground biota across biomes.
TL;DR: Some of the different approaches to community profiling are discussed, highlighting strengths and weaknesses of various experimental approaches, sequencing methodologies, and analytical methods and addressing one key question emerging from various Human Microbiome Projects.
Abstract: High-throughput sequencing studies and new software tools are revolutionizing microbial community analyses, yet the variety of experimental and computational methods can be daunting. In this review, we discuss some of the different approaches to community profiling, highlighting strengths and weaknesses of various experimental approaches, sequencing methodologies, and analytical methods. We also address one key question emerging from various Human Microbiome Projects: Is there a substantial core of abundant organisms or lineages that we all share? It appears that in some human body habitats, such as the hand and the gut, the diversity among individuals is so great that we can rule out the possibility that any species is at high abundance in all individuals: It is possible that the focus should instead be on higher-level taxa or on functional genes instead.
TL;DR: The design criteria that are important in maintaining the availability and stability of the biomolecules as well as the mechanisms for loading of biomolecule within PEG hydrogels will also be discussed.
Abstract: Polyethylene glycol (PEG) hydrogels are widely used in a variety of biomedical applications, including matrices for controlled release of biomolecules and scaffolds for regenerative medicine. The design, fabrication, and characterization of PEG hydrogels rely on the understanding of fundamental gelation kinetics as well as the purpose of the application. This review article will focus on different polymerization mechanisms of PEG-based hydrogels and the importance of these biocompatible hydrogels in regenerative medicine applications. Furthermore, the design criteria that are important in maintaining the availability and stability of the biomolecules as well as the mechanisms for loading of biomolecules within PEG hydrogels will also be discussed. Finally, we overview and provide a perspective on some of the emerging novel design and applications of PEG hydrogel systems, including the spatiotemporal-controlled delivery of biomolecules, hybrid hydrogels, and PEG hydrogels designed for controlled stem cell differentiation.
TL;DR: In this article, the effect of photo-ionization on the cooling rate of heavy ionizing background radiation has been investigated, and it has been shown that photoionization by the background radiation can reduce cooling rates by up to an order of magnitude.
Abstract: A B ST R A C T Radiativecooling iscentralto a widerangeofastrophysicalproblem s.Despiteits im portance,cooling ratesaregenerally com puted using very restrictiveassum ptions, such as collisionalionization equilibrium and solar relative abundances.W e sim ul- taneously relax both assum ptions and investigate the eects ofphoto-ionization of heavy elem entsby them eta-galacticUV/X-ray background and ofvariationsin rela- tiveabundanceson thecoolingratesofopticallythin gasin ionization equilibrium .W e �nd thatphoto-ionization by them eta-galacticbackground radiation reducesthenet cooling ratesby up to an orderofm agnitudeforgasdensitiesand tem peraturestyp- icalofthe shock-heated intergalactic m edium and proto-galaxies(10 4 K< T < 10 6 K, �=hi < 100).In addition,photo-ionization changesthe relative contributionsofdif- ferentelem entstothecoolingrates.W econcludethatphoto-ionization by theionizing background and heavy elem entsboth need to be taken into accountin orderforthe cooling ratesto be correctto orderofm agnitude.M oreover,ifthe ratesneed to be known to better than a factor ofa few,then departures ofthe relative abundances from solar need to be taken into account.W e propose a m ethod to com pute cool- ing rateson an elem ent-by-elem entbasisby interpolating pre-com puted tables that take photo-ionization into account.W e provide such tables for a popular m odelof the evolving UV/X-ray background radiation,com puted using the photo-ionization package cloudy. K ey w ords: atom icprocesses| plasm as| coolingows| galaxies:form ation | intergalacticm edium
TL;DR: It is shown that peer discussion enhances understanding, even when none of the students in a discussion group originally knows the correct answer, when students answer individually and then revote on the same question.
Abstract: When students answer an in-class conceptual question individually using clickers, discuss it with their neighbors, and then revote on the same question, the percentage of correct answers typically increases. This outcome could result from gains in understanding during discussion, or simply from peer influence of knowledgeable students on their neighbors. To distinguish between these alternatives in an undergraduate genetics course, we followed the above exercise with a second, similar (isomorphic) question on the same concept that students answered individually. Our results indicate that peer discussion enhances understanding, even when none of the students in a discussion group originally knows the correct answer.
TL;DR: A robust synthetic strategy is introduced where macromolecular precursors react via a copper-free click chemistry, allowing for the direct encapsulation of cells within click hydrogels for the first time and enables patterning of biological functionalities within the gel in real-time and with micron-scale resolution.
Abstract: Click chemistry provides extremely selective and orthogonal reactions that proceed with high efficiency and under a variety of mild conditions, the most common example being the copper(I)-catalysed reaction of azides with alkynes. While the versatility of click reactions has been broadly exploited, a major limitation is the intrinsic toxicity of the synthetic schemes and the inability to translate these approaches into biological applications. This manuscript introduces a robust synthetic strategy where macromolecular precursors react through a copper-free click chemistry, allowing for the direct encapsulation of cells within click hydrogels for the first time. Subsequently, an orthogonal thiol-ene photocoupling chemistry is introduced that enables patterning of biological functionalities within the gel in real time and with micrometre-scale resolution. This material system enables us to tailor independently the biophysical and biochemical properties of the cell culture microenvironments in situ. This synthetic approach uniquely allows for the direct fabrication of biologically functionalized gels with ideal structures that can be photopatterned, and all in the presence of cells.
TL;DR: Shuster et al. as discussed by the authors developed and investigated a new kinetic model, the radiation damage accumulation and annealing model (RDAAM), that adopts the effective fission track density as a proxy for accumulated radiation damage.
TL;DR: A brief introduction to the concept of executive function and a short overview of the diverse theoretical viewpoints regarding its psychological and biological underpinnings is also provided in this paper, concluding with a consideration of how a multilevel approach may provide a more integrated account of the executive function than has been previously available.
Abstract: In general, executive function can be thought of as the set of abilities required to effortfully guide behavior toward a goal, especially in nonroutine situations. Psychologists are interested in expanding the understanding of executive function because it is thought to be a key process in intelligent behavior, it is compromised in a variety of psychiatric and neurological disorders, it varies across the life span, and it affects performance in complicated environments, such as the cockpits of advanced aircraft. This article provides a brief introduction to the concept of executive function and discusses how it is assessed and the conditions under which it is compromised. A short overview of the diverse theoretical viewpoints regarding its psychological and biological underpinnings is also provided. The article concludes with a consideration of how a multilevel approach may provide a more integrated account of executive function than has been previously available.
TL;DR: The seroprevalence in children under 21 years of age for all Pys was similar to that of the adult population, suggesting that primary exposure to these viruses likely occurs in childhood.
Abstract: In addition to the previously characterized viruses BK and JC, three new human polyomaviruses (Pys) have been recently identified: KIV, WUV, and Merkel Cell Py (MCV). Using an ELISA employing recombinant VP1 capsid proteins, we have determined the seroprevalence of KIV, WUV, and MCV, along with BKV and JCV, and the monkey viruses SV40 and LPV. Soluble VP1 proteins were used to assess crossreactivity between viruses. We found the seroprevalence (+/- 1%) in healthy adult blood donors (1501) was SV40 (9%), BKV (82%), JCV (39%), LPV (15%), KIV (55%), WUV (69%), MCV strain 350 (25%), and MCV strain 339 (42%). Competition assays detected no sero-crossreactivity between the VP1 proteins of LPV or MCV or between WUV and KIV. There was considerable sero-crossreactivity between SV40 and BKV, and to a lesser extent, between SV40 and JCV VP1 proteins. After correcting for crossreactivity, the SV40 seroprevalence was approximately 2%. The seroprevalence in children under 21 years of age (n = 721) for all Pys was similar to that of the adult population, suggesting that primary exposure to these viruses likely occurs in childhood.