Showing papers by "University of Colorado Boulder published in 2011"
TL;DR: An issue concerning the criteria for tic disorders is highlighted, and how this might affect classification of dyskinesias in psychotic spectrum disorders.
Abstract: Given the recent attention to movement abnormalities in psychosis spectrum disorders (e.g., prodromal/high-risk syndromes, schizophrenia) (Mittal et al., 2008; Pappa and Dazzan, 2009), and an ongoing discussion pertaining to revisions of the Diagnostic and Statistical Manuel of Mental Disorders (DSM) for the upcoming 5th edition, we would like to take this opportunity to highlight an issue concerning the criteria for tic disorders, and how this might affect classification of dyskinesias in psychotic spectrum disorders.
Rapid, non-rhythmic, abnormal movements can appear in psychosis spectrum disorders, as well as in a host of commonly co-occurring conditions, including Tourette’s Syndrome and Transient Tic Disorder (Kerbeshian et al., 2009). Confusion can arise when it becomes necessary to determine whether an observed movement (e.g., a sudden head jerk) represents a spontaneous dyskinesia (i.e., spontaneous transient chorea, athetosis, dystonia, ballismus involving muscle groups of the arms, legs, trunk, face, and/or neck) or a tic (i.e., stereotypic or patterned movements defined by the relationship to voluntary movement, acute and chronic time course, and sensory urges). Indeed, dyskinetic movements such as dystonia (i.e., sustained muscle contractions, usually producing twisting and repetitive movements or abnormal postures or positions) closely resemble tics in a patterned appearance, and may only be visually discernable by attending to timing differences (Gilbert, 2006).
When turning to the current DSM-IV TR for clarification, the description reads: “Tic Disorders must be distinguished from other types of abnormal movements that may accompany general medical conditions (e.g., Huntington’s disease, stroke, Lesch-Nyhan syndrome, Wilson’s disease, Sydenham’s chorea, multiple sclerosis, postviral encephalitis, head injury) and from abnormal movements that are due to the direct effects of a substance (e.g., a neuroleptic medication)”. However, as it is written, it is unclear if psychosis falls under one such exclusionary medical disorder. The “direct effects of a substance” criteria, referencing neuroleptic medications, further contributes to the uncertainty around this issue. As a result, ruling-out or differentiating tics in psychosis spectrum disorders is at best, a murky endeavor.
Historically, the advent of antipsychotic medication in the 1950s has contributed to the confusion about movement signs in psychiatric populations. Because neuroleptic medications produce characteristic movement disorder in some patients (i.e. extrapyramidal side effects), drug-induced movement disturbances have been the focus of research attention in psychotic disorders. However, accumulating data have documented that spontaneous dyskinesias, including choreoathetodic movements, can occur in medication naive adults with schizophrenia spectrum disorders (Pappa and Dazzan, 2009), as well as healthy first-degree relatives of chronically ill schizophrenia patients (McCreadie et al., 2003). Taken together, this suggests that movement abnormalities may reflect pathogenic processes underlying some psychotic disorders (Mittal et al., 2008; Pappa and Dazzan, 2009).
More specifically, because spontaneous hyperkinetic movements are believed to reflect abnormal striatal dopamine activity (DeLong and Wichmann, 2007), and dysfunction in this same circuit is also proposed to contribute to psychosis, it is possible that spontaneous dyskinesias serve as an outward manifestation of circuit dysfunction underlying some schizophrenia-spectrum symptoms (Walker, 1994). Further, because these movements precede the clinical onset of psychotic symptoms, sometimes occurring in early childhood (Walker, 1994), and may steadily increase during adolescence among populations at high-risk for schizophrenia (Mittal et al., 2008), observable dyskinesias could reflect a susceptibility that later interacts with environmental and neurodevelopmental factors, in the genesis of psychosis.
In adolescents who meet criteria for a prodromal syndrome (i.e., the period preceding formal onset of psychotic disorders characterized by subtle attenuated positive symptoms coupled with a decline in functioning), there is sometimes a history of childhood conditions which are also characterized by suppressible tics or tic like movements (Niendam et al., 2009). On the other hand, differentiating between tics and dyskinesias has also complicated research on childhood disorders such as Tourette syndrome (Kompoliti and Goetz, 1998; Gilbert, 2006).
We propose consideration of more explicit and operationalized criteria for differentiating tics and dyskinesias, based on empirically derived understanding of neural mechanisms. Further, revisions of the DSM should allow for the possibility that movement abnormalities might reflect neuropathologic processes underlying the etiology of psychosis for a subgroup of patients. Psychotic disorders might also be included among the medical disorders that are considered a rule-out for tics.
Related to this, the reliability of movement assessment needs to be improved, and this may require more training for mental health professionals in movement symptoms. Although standardized assessment of movement and neurological abnormalities is common in research settings, it has been proposed that an examination of neuromotor signs should figure in the assessment of any patient, and be as much a part of the patient assessment as the mental state examination (Picchioni and Dazzan, 2009).
To this end it is important for researchers and clinicians to be aware of differentiating characteristics for these two classes of abnormal movement. For example, tics tend to be more complex than myoclonic twitches, and less flowing than choreoathetodic movements (Kompoliti and Goetz, 1998). Patients with tics often describe a sensory premonition or urge to perform a tic, and the ability to postpone tics at the cost of rising inner tension (Gilbert, 2006). For example, one study showed that patients with tic disorders could accurately distinguish tics from other movement abnormalities based on the subjective experience of some voluntary control of tics (Lang, 1991). Another differentiating factor derives from the relationship of the movement in question to other voluntary movements. Tics in one body area rarely occur during purposeful and voluntary movements in that same body area whereas dyskinesia are often exacerbated by voluntary movement (Gilbert, 2006). Finally, it is noteworthy that tics wax and wane in frequency and intensity and migrate in location over time, often becoming more complex and peaking between the ages of 9 and 14 years (Gilbert, 2006). In the case of dyskinesias among youth at-risk for psychosis, there is evidence that the movements tend to increase in severity and frequency as the individual approaches the mean age of conversion to schizophrenia spectrum disorders (Mittal et al., 2008).
As revisions to the DSM are currently underway in preparation for the new edition (DSM V), we encourage greater attention to the important, though often subtle, distinctions among subtypes of movement abnormalities and their association with psychiatric syndromes.
67,017 citations
TL;DR: UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences, and in testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus.
Abstract: Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments.
Results: We describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer.
Contact: [email protected]
Availability: Source, binaries and data: http://drive5.com/uchime.
Supplementary information:Supplementary data are available at Bioinformatics online.
11,904 citations
TL;DR: This work sequences a diverse array of 25 environmental samples and three known “mock communities” at a depth averaging 3.1 million reads per sample to demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature.
Abstract: The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known “mock communities” at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.
6,767 citations
TL;DR: Alternative enterotype states are associated with long-term diet, particularly protein and animal fat (Bacteroides) versus carbohydrates (Prevotella) and other enterotypes distinguished primarily by levels of Bacteroide and Prevotella.
Abstract: Diet strongly affects human health, partly by modulating gut microbiome composition. We used diet inventories and 16S rDNA sequencing to characterize fecal samples from 98 individuals. Fecal communities clustered into enterotypes distinguished primarily by levels of Bacteroides and Prevotella. Enterotypes were strongly associated with long-term diets, particularly protein and animal fat (Bacteroides) versus carbohydrates (Prevotella). A controlled-feeding study of 10 subjects showed that microbiome composition changed detectably within 24 hours of initiating a high-fat/low-fiber or low-fat/high-fiber diet, but that enterotype identity remained stable during the 10-day study. Thus, alternative enterotype states are associated with long-term diet.
5,174 citations
TL;DR: This new adenocarcinoma classification is needed to provide uniform terminology and diagnostic criteria, especially for bronchioloalveolar carcinoma (BAC), the overall approach to small nonresection cancer specimens, and for multidisciplinary strategic management of tissue for molecular and immunohistochemical studies.
3,850 citations
Earth System Research Laboratory1, University of Colorado Boulder2, Met Office3, National Oceanic and Atmospheric Administration4, University of Bern5, ETH Zurich6, University of East Anglia7, Rovira i Virgili University8, University Corporation for Atmospheric Research9, South African Weather Service10, British Antarctic Survey11, University of Milan12, Norwegian Meteorological Institute13, University of Lisbon14, Environment Canada15, National Center for Atmospheric Research16
TL;DR: The Twentieth Century Reanalysis (20CR) dataset as discussed by the authors provides the first estimates of global tropospheric variability, and of the dataset's time-varying quality, from 1871 to the present at 6-hourly temporal and 2° spatial resolutions.
Abstract: The Twentieth Century Reanalysis (20CR) project is an international effort to produce a comprehensive global atmospheric circulation dataset spanning the twentieth century, assimilating only surface pressure reports and using observed monthly sea-surface temperature and sea-ice distributions as boundary conditions. It is chiefly motivated by a need to provide an observational dataset with quantified uncertainties for validations of climate model simulations of the twentieth century on all time-scales, with emphasis on the statistics of daily weather. It uses an Ensemble Kalman Filter data assimilation method with background ‘first guess’ fields supplied by an ensemble of forecasts from a global numerical weather prediction model. This directly yields a global analysis every 6 hours as the most likely state of the atmosphere, and also an uncertainty estimate of that analysis.
The 20CR dataset provides the first estimates of global tropospheric variability, and of the dataset's time-varying quality, from 1871 to the present at 6-hourly temporal and 2° spatial resolutions. Intercomparisons with independent radiosonde data indicate that the reanalyses are generally of high quality. The quality in the extratropical Northern Hemisphere throughout the century is similar to that of current three-day operational NWP forecasts. Intercomparisons over the second half-century of these surface-based reanalyses with other reanalyses that also make use of upper-air and satellite data are equally encouraging.
It is anticipated that the 20CR dataset will be a valuable resource to the climate research community for both model validations and diagnostic studies. Some surprising results are already evident. For instance, the long-term trends of indices representing the North Atlantic Oscillation, the tropical Pacific Walker Circulation, and the Pacific–North American pattern are weak or non-existent over the full period of record. The long-term trends of zonally averaged precipitation minus evaporation also differ in character from those in climate model simulations of the twentieth century. Copyright © 2011 Royal Meteorological Society and Crown Copyright.
3,043 citations
TL;DR: An automated brain-mapping framework that uses text-mining, meta-analysis and machine-learning techniques to generate a large database of mappings between neural and cognitive states is described and validated.
Abstract: The rapid growth of the literature on neuroimaging in humans has led to major advances in our understanding of human brain function but has also made it increasingly difficult to aggregate and synthesize neuroimaging findings. Here we describe and validate an automated brain-mapping framework that uses text-mining, meta-analysis and machine-learning techniques to generate a large database of mappings between neural and cognitive states. We show that our approach can be used to automatically conduct large-scale, high-quality neuroimaging meta-analyses, address long-standing inferential problems in the neuroimaging literature and support accurate 'decoding' of broad cognitive states from brain activity in both entire studies and individual human subjects. Collectively, our results have validated a powerful and generative framework for synthesizing human neuroimaging data on an unprecedented scale.
2,853 citations
TL;DR: Ischemia and reperfusion-elicited tissue injury contributes to morbidity and mortality in a wide range of pathologies, including myocardial infarction, ischemic stroke, acute kidney injury, trauma, circulatory arrest, sickle cell disease and sleep apnea as discussed by the authors.
Abstract: Ischemia and reperfusion-elicited tissue injury contributes to morbidity and mortality in a wide range of pathologies, including myocardial infarction, ischemic stroke, acute kidney injury, trauma, circulatory arrest, sickle cell disease and sleep apnea. Ischemia-reperfusion injury is also a major challenge during organ transplantation and cardiothoracic, vascular and general surgery. An imbalance in metabolic supply and demand within the ischemic organ results in profound tissue hypoxia and microvascular dysfunction. Subsequent reperfusion further enhances the activation of innate and adaptive immune responses and cell death programs. Recent advances in understanding the molecular and immunological consequences of ischemia and reperfusion may lead to innovative therapeutic strategies for treating patients with ischemia and reperfusion-associated tissue inflammation and organ dysfunction.
2,368 citations
Daniel J. Eisenstein1, Daniel J. Eisenstein2, David H. Weinberg3, Eric Agol4 +260 more•Institutions (62)
TL;DR: SDSS-III as mentioned in this paper is a program of four spectroscopic surveys on three scientific themes: dark energy and cosmological parameters, the history and structure of the Milky Way, and the population of giant planets around other stars.
Abstract: Building on the legacy of the Sloan Digital Sky Survey (SDSS-I and II), SDSS-III is a program of four spectroscopic surveys on three scientific themes: dark energy and cosmological parameters, the history and structure of the Milky Way, and the population of giant planets around other stars. In keeping with SDSS tradition, SDSS-III will provide regular public releases of all its data, beginning with SDSS DR8 (which occurred in Jan 2011). This paper presents an overview of the four SDSS-III surveys. BOSS will measure redshifts of 1.5 million massive galaxies and Lya forest spectra of 150,000 quasars, using the BAO feature of large scale structure to obtain percent-level determinations of the distance scale and Hubble expansion rate at z 100 per resolution element), H-band (1.51-1.70 micron) spectra of 10^5 evolved, late-type stars, measuring separate abundances for ~15 elements per star and creating the first high-precision spectroscopic survey of all Galactic stellar populations (bulge, bar, disks, halo) with a uniform set of stellar tracers and spectral diagnostics. MARVELS will monitor radial velocities of more than 8000 FGK stars with the sensitivity and cadence (10-40 m/s, ~24 visits per star) needed to detect giant planets with periods up to two years, providing an unprecedented data set for understanding the formation and dynamical evolution of giant planet systems. (Abridged)
2,265 citations
TL;DR: This study revealed that seemingly chaotic shifts in the microbiome are associated with life events; however, additional experiments ought to be conducted to assess how different infants respond to similar life events.
Abstract: The colonization process of the infant gut microbiome has been called chaotic, but this view could reflect insufficient documentation of the factors affecting the microbiome. We performed a 2.5-y case study of the assembly of the human infant gut microbiome, to relate life events to microbiome composition and function. Sixty fecal samples were collected from a healthy infant along with a diary of diet and health status. Analysis of >300,000 16S rRNA genes indicated that the phylogenetic diversity of the microbiome increased gradually over time and that changes in community composition conformed to a smooth temporal gradient. In contrast, major taxonomic groups showed abrupt shifts in abundance corresponding to changes in diet or health. Community assembly was nonrandom: we observed discrete steps of bacterial succession punctuated by life events. Furthermore, analysis of ≈500,000 DNA metagenomic reads from 12 fecal samples revealed that the earliest microbiome was enriched in genes facilitating lactate utilization, and that functional genes involved in plant polysaccharide metabolism were present before the introduction of solid food, priming the infant gut for an adult diet. However, ingestion of table foods caused a sustained increase in the abundance of Bacteroidetes, elevated fecal short chain fatty acid levels, enrichment of genes associated with carbohydrate utilization, vitamin biosynthesis, and xenobiotic degradation, and a more stable community composition, all of which are characteristic of the adult microbiome. This study revealed that seemingly chaotic shifts in the microbiome are associated with life events; however, additional experiments ought to be conducted to assess how different infants respond to similar life events.
2,038 citations
TL;DR: It is confirmed with actual sequence data that UniFrac values can be influenced by the number of sequences/sample, and sequence jackknifing is recommended to avoid this issue.
Abstract: UniFrac is a β-diversity measure that uses phylogenetic information to compare environmental samples. UniFrac, coupled with standard multivariate statistical techniques including principal coordinates analysis (PCoA), identifies factors explaining differences among microbial communities. A recent simulation study concluded that UniFrac is unsuitable as a distance metric and should not be used for multivariate analysis (Schloss, 2008). We counter this argument by reassessing the data that led to this conclusion and by providing a mathematical proof showing that UniFrac is a distance metric. However, we confirm with actual sequence data that UniFrac values can be influenced by the number of sequences/sample, and recommend sequence jackknifing (that is, determining how often the cluster results are recovered using random subsets of the data) to avoid this issue.
Massey University1, Miami University2, Washington University in St. Louis3, University of British Columbia4, Florida State University5, Temple University6, University of Tennessee7, University of California, Davis8, University of California, Santa Barbara9, University of Colorado Boulder10, University of North Carolina at Chapel Hill11, Michigan State University12
TL;DR: A roadmap of the most widely used and ecologically relevant approaches for analysis through a series of mission statements is provided, distinguishing two types of β diversity: directional turnover along a gradient vs. non-directional variation.
Abstract: A recent increase in studies of β diversity has yielded a confusing array of concepts, measures and methods. Here, we provide a roadmap of the most widely used and ecologically relevant approaches for analysis through a series of mission statements. We distinguish two types of β diversity: directional turnover along a gradient vs. non-directional variation. Different measures emphasize different properties of ecological data. Such properties include the degree of emphasis on presence/absence vs. relative abundance information and the inclusion vs. exclusion of joint absences. Judicious use of multiple measures in concert can uncover the underlying nature of patterns in β diversity for a given dataset. A case study of Indonesian coral assemblages shows the utility of a multi-faceted approach. We advocate careful consideration of relevant questions, matched by appropriate analyses. The rigorous application of null models will also help to reveal potential processes driving observed patterns in β diversity.
TL;DR: This review summarizes acute and chronic inflammatory diseases that are treated by reducing IL-1β activity and proposes that disease severity is affected by the anti-inflammatory members of the IL- 1 family of ligands and receptors.
TL;DR: Sideband cooling of an approximately 10-MHz micromechanical oscillator to the quantum ground state is demonstrated and the device exhibits strong coupling, allowing coherent exchange of microwave photons and mechanical phonons.
Abstract: It has been a long-standing goal in the field of cavity optomechanics to cool down a mechanical resonator to its motional quantum ground state by using light. Teufel et al. have now achieved just that with a recently developed system in which a drum-like flexible aluminium membrane is incorporated in a superconducting circuit. Ground-state cooling of a mechanical resonator was demonstrated for the first time last year in a different type of device, but the quantum states in this new device should be much longer lived, allowing direct tests of fundamental principles of quantum mechanics. As a first step, the authors perform a quantum-limited position measurement that is only a factor of about five away from the Heisenberg limit. The advent of laser cooling techniques revolutionized the study of many atomic-scale systems, fuelling progress towards quantum computing with trapped ions1 and generating new states of matter with Bose–Einstein condensates2. Analogous cooling techniques3,4 can provide a general and flexible method of preparing macroscopic objects in their motional ground state. Cavity optomechanical or electromechanical systems achieve sideband cooling through the strong interaction between light and motion5,6,7,8,9,10,11,12,13,14,15. However, entering the quantum regime—in which a system has less than a single quantum of motion—has been difficult because sideband cooling has not sufficiently overwhelmed the coupling of low-frequency mechanical systems to their hot environments. Here we demonstrate sideband cooling of an approximately 10-MHz micromechanical oscillator to the quantum ground state. This achievement required a large electromechanical interaction, which was obtained by embedding a micromechanical membrane into a superconducting microwave resonant circuit. To verify the cooling of the membrane motion to a phonon occupation of 0.34 ± 0.05 phonons, we perform a near-Heisenberg-limited position measurement3 within (5.1 ± 0.4)h/2π, where h is Planck’s constant. Furthermore, our device exhibits strong coupling, allowing coherent exchange of microwave photons and mechanical phonons16. Simultaneously achieving strong coupling, ground state preparation and efficient measurement sets the stage for rapid advances in the control and detection of non-classical states of motion17,18, possibly even testing quantum theory itself in the unexplored region of larger size and mass19. Because mechanical oscillators can couple to light of any frequency, they could also serve as a unique intermediary for transferring quantum information between microwave and optical domains20.
Stephan Ripke1, Alan R. Sanders2, Kenneth S. Kendler3, Douglas F. Levinson4 +207 more•Institutions (71)
TL;DR: The authors examined the role of common genetic variation in schizophrenia in a genome-wide association study of substantial size: a stage 1 discovery sample of 21,856 individuals of European ancestry and a stage 2 replication sample of 29,839 independent subjects.
Abstract: We examined the role of common genetic variation in schizophrenia in a genome-wide association study of substantial size: a stage 1 discovery sample of 21,856 individuals of European ancestry and a stage 2 replication sample of 29,839 independent subjects. The combined stage 1 and 2 analysis yielded genome-wide significant associations with schizophrenia for seven loci, five of which are new (1p21.3, 2q32.3, 8p23.2, 8q21.3 and 10q24.32-q24.33) and two of which have been previously implicated (6p21.32-p22.1 and 18q21.2). The strongest new finding (P = 1.6 x 10(-11)) was with rs1625579 within an intron of a putative primary transcript for MIR137 (microRNA 137), a known regulator of neuronal development. Four other schizophrenia loci achieving genome-wide significance contain predicted targets of MIR137, suggesting MIR137-mediated dysregulation as a previously unknown etiologic mechanism in schizophrenia. In a joint analysis with a bipolar disorder sample (16,374 affected individuals and 14,044 controls), three loci reached genome-wide significance: CACNA1C (rs4765905, P = 7.0 x 10(-9)), ANK3 (rs10994359, P = 2.5 x 10(-8)) and the ITIH3-ITIH4 region (rs2239547, P = 7.8 x 10(-9)).
TL;DR: It was found that mitochondrial division occurred at positions where ER tubules contacted mitochondria and mediated constriction before Drp1 recruitment, suggesting that ERtubules may play an active role in defining the position of mitochondrial division sites.
Abstract: Mitochondrial structure and distribution are regulated by division and fusion events. Mitochondrial division is regulated by Dnm1/Drp1, a dynamin-related protein that forms helices around mitochondria to mediate fission. Little is known about what determines sites of mitochondrial fission within the mitochondrial network. The endoplasmic reticulum (ER) and mitochondria exhibit tightly coupled dynamics and have extensive contacts. We tested whether ER plays a role in mitochondrial division. We found that mitochondrial division occurred at positions where ER tubules contacted mitochondria and mediated constriction before Drp1 recruitment. Thus, ER tubules may play an active role in defining the position of mitochondrial division sites.
TL;DR: The value of characterizing vertebrate gut microbiomes to understand host evolutionary histories at a supraorganismal level is illustrated by shotgun sequencing of microbial community DNA and targeted sequencing of bacterial 16S ribosomal RNA genes.
Abstract: Coevolution of mammals and their gut microbiota has profoundly affected their radiation into myriad habitats. We used shotgun sequencing of microbial community DNA and targeted sequencing of bacterial 16S ribosomal RNA genes to gain an understanding of how microbial communities adapt to extremes of diet. We sampled fecal DNA from 33 mammalian species and 18 humans who kept detailed diet records, and we found that the adaptation of the microbiota to diet is similar across different mammalian lineages. Functional repertoires of microbiome genes, such as those encoding carbohydrate-active enzymes and proteases, can be predicted from bacterial species assemblages. These results illustrate the value of characterizing vertebrate gut microbiomes to understand host evolutionary histories at a supraorganismal level.
Hiroaki Aihara1, Carlos Allende Prieto2, Carlos Allende Prieto3, Deokkeun An4 +191 more•Institutions (58)
TL;DR: The first data release of SDSS-III is described in this article, which includes five-band imaging of roughly 5200 deg2 in the southern Galactic cap, bringing the total footprint of the Sloan Digital Sky Survey imaging to 14,555 deg2, or over a third of the Celestial Sphere.
Abstract: The Sloan Digital Sky Survey (SDSS) started a new phase in 2008 August, with new instrumentation and new surveys focused on Galactic structure and chemical evolution, measurements of the baryon oscillation feature in the clustering of galaxies and the quasar Lyα forest, and a radial velocity search for planets around ~8000 stars. This paper describes the first data release of SDSS-III (and the eighth counting from the beginning of the SDSS). The release includes five-band imaging of roughly 5200 deg2 in the southern Galactic cap, bringing the total footprint of the SDSS imaging to 14,555 deg2, or over a third of the Celestial Sphere. All the imaging data have been reprocessed with an improved sky-subtraction algorithm and a final, self-consistent photometric recalibration and flat-field determination. This release also includes all data from the second phase of the Sloan Extension for Galactic Understanding and Exploration (SEGUE-2), consisting of spectroscopy of approximately 118,000 stars at both high and low Galactic latitudes. All the more than half a million stellar spectra obtained with the SDSS spectrograph have been reprocessed through an improved stellar parameter pipeline, which has better determination of metallicity for high-metallicity stars.
TL;DR: It is demonstrated that MEG charge carriers can be collected in suitably designed QD solar cells, providing ample incentive to better understand MEG within isolated and coupled QDs as a research path to enhancing the efficiency of solar light harvesting technologies.
Abstract: Multiple exciton generation (MEG) is a process that can occur in semiconductor nanocrystals, or quantum dots (QDs), whereby absorption of a photon bearing at least twice the bandgap energy produces two or more electron-hole pairs. Here, we report on photocurrent enhancement arising from MEG in lead selenide (PbSe) QD-based solar cells, as manifested by an external quantum efficiency (the spectrally resolved ratio of collected charge carriers to incident photons) that peaked at 114 ± 1% in the best device measured. The associated internal quantum efficiency (corrected for reflection and absorption losses) was 130%. We compare our results with transient absorption measurements of MEG in isolated PbSe QDs and find reasonable agreement. Our findings demonstrate that MEG charge carriers can be collected in suitably designed QD solar cells, providing ample incentive to better understand MEG within isolated and coupled QDs as a research path to enhancing the efficiency of solar light harvesting technologies.
Washington University in St. Louis1, Argonne National Laboratory2, Polytechnic University of Turin3, Imperial College London4, Yale University5, Lawrence Berkeley National Laboratory6, University of California, Berkeley7, National Renewable Energy Laboratory8, City University of New York9, University of Osnabrück10, Michigan State University11, Arizona State University12, University of Pennsylvania13, Massachusetts Institute of Technology14, University of Colorado Boulder15, University of Illinois at Urbana–Champaign16, University of Washington17, ExxonMobil18, Donald Danforth Plant Science Center19
TL;DR: Natural photosynthesis is compared with present technologies for photovoltaic-driven electrolysis of water to produce hydrogen and opportunities in which the frontiers of synthetic biology might be used to enhance natural photosynthesis for improved solar energy conversion efficiency are considered.
Abstract: Comparing photosynthetic and photovoltaic efficiencies is not a simple issue. Although both processes harvest the energy in sunlight, they operate in distinctly different ways and produce different types of products: biomass or chemical fuels in the case of natural photosynthesis and nonstored electrical current in the case of photovoltaics. In order to find common ground for evaluating energy-conversion efficiency, we compare natural photosynthesis with present technologies for photovoltaic-driven electrolysis of water to produce hydrogen. Photovoltaic-driven electrolysis is the more efficient process when measured on an annual basis, yet short-term yields for photosynthetic conversion under optimal conditions come within a factor of 2 or 3 of the photovoltaic benchmark. We consider opportunities in which the frontiers of synthetic biology might be used to enhance natural photosynthesis for improved solar energy conversion efficiency.
TL;DR: In this paper, a novel definition for the hydrogen bond is proposed, which takes into account the theoretical and experimental knowledge acquired over the past century, and six criteria are listed that could be used as evidence for the presence of a hydrogen bond.
Abstract: A novel definition for the hydrogen bond is recommended here. It takes into account the theoretical and experimental knowledge acquired over the past century. This def- inition insists on some evidence. Six criteria are listed that could be used as evidence for the presence of a hydrogen bond.
TL;DR: The T2K experiment observes indications of ν (μ) → ν(e) appearance in data accumulated with 1.43×10(20) protons on target, and under this hypothesis, the probability to observe six or more candidate events is 7×10(-3), equivalent to 2.5σ significance.
Abstract: The T2K experiment observes indications of nu(mu) -> nu(mu) e appearance in data accumulated with 1.43 x 10(20) protons on target. Six events pass all selection criteria at the far detector. In a three-flavor neutrino oscillation scenario with |Delta m(23)(2)| = 2.4 x 10(-3) eV(2), sin(2)2 theta(23) = 1 and sin(2)2 theta(13) = 0, the expected number of such events is 1.5 +/- 0.3(syst). Under this hypothesis, the probability to observe six or more candidate events is 7 x 10(-3), equivalent to 2.5 sigma significance. At 90% C.L., the data are consistent with 0.03(0.04) < sin(2)2 theta(13) < 0.28(0.34) for delta(CP) = 0 and a normal (inverted) hierarchy.
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TL;DR: A theory that answers the question “what is the self?,” where this question is understood in a scientific sense that includes both natural science and systematic fundamental metaphysics is sketched.
Abstract: In this paper I briefly sketch a theory that answers the question "what is the self?," where this question is understood in a scientific sense that includes both natural science and systematic fundamental metaphysics. As selves, we are essentially rational human minded animals or real persons in a fully natural and desperately non-ideal world-animals with meaningful lives, for better or worse.
Journal Article•
TL;DR: The epidemiological distinction between the generic term "physical activity" and the specific category of "exercise", which implies activity for a specific purpose such as improvement of physical condition or competition is recognised.
Abstract: An ever-growing volume of peer-reviewed publications speaks to the recent and rapid growth in both scope and understanding of exercise immunology. Indeed, more than 95% of all peer-reviewed publications in exercise immunology (currently >2, 200 publications using search terms "exercise" and "immune") have been published since the formation of the International Society of Exercise and Immunology (ISEI) in 1989 (ISI Web of Knowledge). We recognise the epidemiological distinction between the generic term "physical activity" and the specific category of "exercise", which implies activity for a specific purpose such as improvement of physical condition or competition. Extreme physical activity of any type may have implications for the immune system. However, because of its emotive component, exercise is likely to have a larger effect, and to date the great majority of our knowledge on this subject comes from exercise studies.
TL;DR: Yt, an open source, community-developed astrophysical analysis and visualization toolkit, is presented and its methods for reading, handling, and visualizing data, including projections, multivariate volume rendering, multi-dimensional histograms, halo finding, light cone generation, and topologically connected isocontour identification are reported.
Abstract: The analysis of complex multiphysics astrophysical simulations presents a unique and rapidly growing set of challenges: reproducibility, parallelization, and vast increases in data size and complexity chief among them. In order to meet these challenges, and in order to open up new avenues for collaboration between users of multiple simulation platforms, we present yt (available at http://yt.enzotools.org/) an open source, community-developed astrophysical analysis and visualization toolkit. Analysis and visualization with yt are oriented around physically relevant quantities rather than quantities native to astrophysical simulation codes. While originally designed for handling Enzo's structure adaptive mesh refinement data, yt has been extended to work with several different simulation methods and simulation codes including Orion, RAMSES, and FLASH. We report on its methods for reading, handling, and visualizing data, including projections, multivariate volume rendering, multi-dimensional histograms, halo finding, light cone generation, and topologically connected isocontour identification. Furthermore, we discuss the underlying algorithms yt uses for processing and visualizing data, and its mechanisms for parallelization of analysis tasks.
TL;DR: SourceTracker, a Bayesian approach to estimate the proportion of contaminants in a given community that come from possible source environments, is presented, and microbial surveys from neonatal intensive care units, offices and molecular biology laboratories are applied.
Abstract: Contamination is a critical issue in high-throughput metagenomic studies, yet progress toward a comprehensive solution has been limited. We present SourceTracker, a Bayesian approach to estimate the proportion of contaminants in a given community that come from possible source environments. We applied SourceTracker to microbial surveys from neonatal intensive care units (NICUs), offices and molecular biology laboratories, and provide a database of known contaminants for future testing.
Journal Article•
TL;DR: In this article, a microwave cavity optomechanical system was realized by coupling the motion of an aluminum membrane to the resonance frequency of a superconducting circuit, and damping and cooling the membrane motion with radiation pressure forces.
Abstract: Accessing the full quantum nature of a macroscopic mechanical oscillator first requires elimination of its classical, thermal motion. The flourishing field of cavity optomechanics provides a nearly ideal architecture for both preparation and detection of mechanical motion at the quantum level. We realize a microwave cavity optomechanical system by coupling the motion of an aluminum membrane to the resonance frequency of a superconducting circuit [1]. By exciting the microwave circuit below its resonance frequency, we damp and cool the membrane motion with radiation pressure forces, analogous to laser cooling of the motion of trapped ions. The microwave excitation serves not only to cool, but also to monitor the displacement of the membrane. A nearly shot-noise limited, Josephson parametric amplifier is used to detect the mechanical sidebands of this microwave excitation and quantify the thermal motion as it is cooled with radiation pressure forces to its quantum ground state [2].
TL;DR: In this paper, the authors used barcoded pyrosequencing to comprehensively survey archaeal and bacterial communities in 146 soils, representing a multitude of soil and ecosystem types from across the globe.
Abstract: Archaea, primarily Crenarchaeota, are common in soil; however, the structure of soil archaeal communities and the factors regulating their diversity and abundance remain poorly understood. Here, we used barcoded pyrosequencing to comprehensively survey archaeal and bacterial communities in 146 soils, representing a multitude of soil and ecosystem types from across the globe. Relative archaeal abundance, the percentage of all 16S rRNA gene sequences recovered that were archaeal, averaged 2% across all soils and ranged from 0% to >10% in individual soils. Soil C:N ratio was the only factor consistently correlated with archaeal relative abundances, being higher in soils with lower C:N ratios. Soil archaea communities were dominated by just two phylotypes from a constrained clade within the Crenarchaeota, which together accounted for >70% of all archaeal sequences obtained in the survey. As one of these phylotypes was closely related to a previously identified putative ammonia oxidizer, we sampled from two long-term nitrogen (N) addition experiments to determine if this taxon responds to experimental manipulations of N availability. Contrary to expectations, the abundance of this dominant taxon, as well as archaea overall, tended to decline with increasing N. This trend was coupled with a concurrent increase in known N-oxidizing bacteria, suggesting competitive interactions between these groups.
TL;DR: The areas of energy, water and food policy have numerous interwoven concerns ranging from ensuring access to services, to environmental impacts to price volatility as mentioned in this paper, and these issues manifest in very di...
TL;DR: In this paper, a review summarizes the current knowledge on aqueous phase organic reactions and combines evidence that points to a significant role of aqSOA formation in the atmosphere.
Abstract: . Progress has been made over the past decade in predicting secondary organic aerosol (SOA) mass in the atmosphere using vapor pressure-driven partitioning, which implies that SOA compounds are formed in the gas phase and then partition to an organic phase (gasSOA). However, discrepancies in predicting organic aerosol oxidation state, size and product (molecular mass) distribution, relative humidity (RH) dependence, color, and vertical profile suggest that additional SOA sources and aging processes may be important. The formation of SOA in cloud and aerosol water (aqSOA) is not considered in these models even though water is an abundant medium for atmospheric chemistry and such chemistry can form dicarboxylic acids and "humic-like substances" (oligomers, high-molecular-weight compounds), i.e. compounds that do not have any gas phase sources but comprise a significant fraction of the total SOA mass. There is direct evidence from field observations and laboratory studies that organic aerosol is formed in cloud and aerosol water, contributing substantial mass to the droplet mode. This review summarizes the current knowledge on aqueous phase organic reactions and combines evidence that points to a significant role of aqSOA formation in the atmosphere. Model studies are discussed that explore the importance of aqSOA formation and suggestions for model improvements are made based on the comprehensive set of laboratory data presented here. A first comparison is made between aqSOA and gasSOA yields and mass predictions for selected conditions. These simulations suggest that aqSOA might contribute almost as much mass as gasSOA to the SOA budget, with highest contributions from biogenic emissions of volatile organic compounds (VOC) in the presence of anthropogenic pollutants (i.e. NOx) at high relative humidity and cloudiness. Gaps in the current understanding of aqSOA processes are discussed and further studies (laboratory, field, model) are outlined to complement current data sets.