Showing papers by "University of California, Davis published in 2010"
TL;DR: This observation shows that quantum confinement in layered d-electron materials like MoS(2), a prototypical metal dichalcogenide, provides new opportunities for engineering the electronic structure of matter at the nanoscale.
Abstract: Novel physical phenomena can emerge in low-dimensional nanomaterials. Bulk MoS2, a prototypical metal dichalcogenide, is an indirect bandgap semiconductor with negligible photoluminescence. When the MoS2 crystal is thinned to monolayer, however, a strong photoluminescence emerges, indicating an indirect to direct bandgap transition in this d-electron system. This observation shows that quantum confinement in layered d-electron materials like MoS2 provides new opportunities for engineering the electronic structure of matter at the nanoscale.
7,886 citations
University of California, Los Angeles1, Jet Propulsion Laboratory2, California Institute of Technology3, University of Arizona4, University of Virginia5, Lawrence Livermore National Laboratory6, University of California, Davis7, Monterey Institute for Research in Astronomy8, Goddard Space Flight Center9, National Radio Astronomy Observatory10, University of California, Berkeley11, Wilmington University12, Advanced Technology Center13
TL;DR: The Wide-field Infrared Survey Explorer (WISE) is mapping the whole sky following its launch on 14 December 2009 and completed its first full coverage of the sky on July 17 as discussed by the authors.
Abstract: The all sky surveys done by the Palomar Observatory Schmidt, the European Southern Observatory Schmidt, and the United Kingdom Schmidt, the InfraRed Astronomical Satellite and the 2 Micron All Sky Survey have proven to be extremely useful tools for astronomy with value that lasts for decades. The Wide-field Infrared Survey Explorer is mapping the whole sky following its launch on 14 December 2009. WISE began surveying the sky on 14 Jan 2010 and completed its first full coverage of the sky on July 17. The survey will continue to cover the sky a second time until the cryogen is exhausted (anticipated in November 2010). WISE is achieving 5 sigma point source sensitivities better than 0.08, 0.11, 1 and 6 mJy in unconfused regions on the ecliptic in bands centered at wavelengths of 3.4, 4.6, 12 and 22 micrometers. Sensitivity improves toward the ecliptic poles due to denser coverage and lower zodiacal background. The angular resolution is 6.1", 6.4", 6.5" and 12.0" at 3.4, 4.6, 12 and 22 micrometers, and the astrometric precision for high SNR sources is better than 0.15".
7,182 citations
TL;DR: This guideline updates recommendations regarding epidemiology, diagnosis, treatment, and infection control and environmental management of Clostridium difficile.
Abstract: Since publication of the Society for Healthcare Epidemiology of America position paper on Clostridium difficile infection in 1995, significant changes have occurred in the epidemiology and treatment of this infection. C. difficile remains the most important cause of healthcareassociated diarrhea and is increasingly important as a community pathogen. A more virulent strain of C. difficile has been identified and has been responsible for more-severe cases of disease worldwide. Data reporting the decreased effectiveness of metronidazole in the treatment of severe disease have been published. Despite the increasing quantity of data available, areas of controversy still exist. This guideline updates recommendations regarding epidemiology, diagnosis, treatment, and infection control and environmental management.
2,872 citations
TL;DR: In this article, a biennial review summarizes much of particle physics using data from previous editions, plus 2158 new measurements from 551 papers, they list, evaluate and average measured properties of gauge bosons, leptons, quarks, mesons, and baryons.
Abstract: This biennial Review summarizes much of particle physics. Using data from previous editions, plus 2158 new measurements from 551 papers, we list, evaluate, and average measured properties of gauge bosons, leptons, quarks, mesons, and baryons. We also summarize searches for hypothetical particles such as Higgs bosons, heavy neutrinos, and supersymmetric particles. All the particle properties and search limits are listed in Summary Tables. We also give numerous tables, figures, formulae, and reviews of topics such as the Standard Model, particle detectors, probability, and statistics. Among the 108 reviews are many that are new or heavily revised including those on neutrino mass, mixing, and oscillations, QCD, top quark, CKM quark-mixing matrix, V-ud & V-us, V-cb & V-ub, fragmentation functions, particle detectors for accelerator and non-accelerator physics, magnetic monopoles, cosmological parameters, and big bang cosmology.
2,788 citations
TL;DR: This is the first randomized, controlled trial to demonstrate the efficacy of a comprehensive developmental behavioral intervention for toddlers with ASD for improving cognitive and adaptive behavior and reducing severity of ASD diagnosis.
Abstract: OBJECTIVE: To conduct a randomized, controlled trial to evaluate the efficacy of the Early Start Denver Model (ESDM), a comprehensive developmental behavioral intervention, for improving outcomes of toddlers diagnosed with autism spectrum disorder (ASD). METHODS: Forty-eight children diagnosed with ASD between 18 and 30 months of age were randomly assigned to 1 of 2 groups: (1) ESDM intervention, which is based on developmental and applied behavioral analytic principles and delivered by trained therapists and parents for 2 years; or (2) referral to community providers for intervention commonly available in the community. RESULTS: Compared with children who received community-intervention, children who received ESDM showed significant improvements in IQ, adaptive behavior, and autism diagnosis. Two years after entering intervention, the ESDM group on average improved 17.6 standard score points (1 SD: 15 points) compared with 7.0 points in the comparison group relative to baseline scores. The ESDM group maintained its rate of growth in adaptive behavior compared with a normative sample of typically developing children. In contrast, over the 2-year span, the comparison group showed greater delays in adaptive behavior. Children who received ESDM also were more likely to experience a change in diagnosis from autism to pervasive developmental disorder, not otherwise specified, than the comparison group. CONCLUSIONS: This is the first randomized, controlled trial to demonstrate the efficacy of a comprehensive developmental behavioral intervention for toddlers with ASD for improving cognitive and adaptive behavior and reducing severity of ASD diagnosis. Results of this study underscore the importance of early detection of and intervention in autism.
1,990 citations
TL;DR: It is suggested that depletion, soil barriers, and low-P parent material often cause ultimate limitation because they control the ecosystem mass balance of P and cause it to be an ultimate limiting nutrient.
Abstract: Nutrient limitation to primary productivity and other biological processes is widespread in terrestrial ecosystems, and nitrogen (N) and phosphorus (P) are the most common limiting elements, both individually and in combination. Mechanisms that drive P limitation, and their interactions with the N cycle, have received less attention than mechanisms causing N limitation. We identify and discuss six mechanisms that could drive P limitation in terrestrial ecosystems. The best known of these is depletion-driven limitation, in which accumulated P losses during long-term soil and ecosystem development contribute to what Walker and Syers termed a "terminal steady state" of profound P depletion and limitation. The other mechanisms are soil barriers that prevent access to P; transactional limitation, in which weathering of P-containing minerals does not keep pace with the supply of other resources; low-P parent materials; P sinks; and anthropogenic changes that increase the supply of other resources (often N) relative to P. We distinguish proximate nutrient limitation (which occurs where additions of a nutrient stimulate biological processes, especially productivity) from ultimate nutrient limitation (where additions of a nutrient can transform ecosystems). Of the mechanisms that drive P limitation, we suggest that depletion, soil barriers, and low-P parent material often cause ultimate limitation because they control the ecosystem mass balance of P. Similarly, demand-independent losses and constraints to N fixation can control the ecosystem-level mass balance of N and cause it to be an ultimate limiting nutrient.
1,922 citations
Harvard University1, Boston University2, University of California, Davis3, Pompeu Fabra University4, Stony Brook University5, World Health Organization6, Katholieke Universiteit Leuven7, St George's Hospital8, University of Ibadan9, University of Tokyo10, The Chinese University of Hong Kong11, University of Paris12, University of Groningen13, All India Institute of Medical Sciences14, New Bulgarian University15, University of São Paulo16
TL;DR: In this paper, the authors examined joint associations of 12 childhood adversities with first onset of 20 DSM-IV disorders in World Mental Health Surveys in 21 countries and found strong associations with all classes of disorders at all life-course stages.
Abstract: Background
Although significant associations of childhood adversities with adult mental disorders are widely documented, most studies focus on single childhood adversities predicting single disorders.
Aims
To examine joint associations of 12 childhood adversities with first onset of 20 DSM–IV disorders in World Mental Health (WMH) Surveys in 21 countries.
Method
Nationally or regionally representative surveys of 51 945 adults assessed childhood adversities and lifetime DSM–IV disorders with the WHO Composite International Diagnostic Interview (CIDI).
Results
Childhood adversities were highly prevalent and interrelated. Childhood adversities associated with maladaptive family functioning (e.g. parental mental illness, child abuse, neglect) were the strongest predictors of disorders. Co-occurring childhood adversities associated with maladaptive family functioning had significant subadditive predictive associations and little specificity across disorders. Childhood adversities account for 29.8% of all disorders across countries.
Conclusions
Childhood adversities have strong associations with all classes of disorders at all life-course stages in all groups of WMH countries. Long-term associations imply the existence of as-yet undetermined mediators.
1,837 citations
Harvard University1, University of Washington2, University of California, San Francisco3, University of California, San Diego4, Baylor College of Medicine5, Broad Institute6, University of British Columbia7, Salk Institute for Biological Studies8, University of California, Davis9, University of Wisconsin-Madison10
TL;DR: The NIH Roadmap Epigenomics Mapping Consortium aims to produce a public resource of epigenomic maps for stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease.
Abstract: The NIH Roadmap Epigenomics Mapping Consortium aims to produce a public resource of epigenomic maps for stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease.
1,724 citations
Newcastle University1, Children's Hospital of Philadelphia2, Case Western Reserve University3, Duke University4, Veterans Health Administration5, Cincinnati Children's Hospital Medical Center6, University of California, Davis7, University of Rochester8, Baylor College of Medicine9, Boston Children's Hospital10, Centers for Disease Control and Prevention11
TL;DR: These recommendations provide a framework for recognising the multisystem primary manifestations and secondary complications of DMD and for providing coordinated multidisciplinary care.
Abstract: Duchenne muscular dystrophy (DMD) is a severe, progressive disease that aff ects 1 in 3600–6000 live male births. Although guidelines are available for various aspects of DMD, comprehensive clinical care recommendations do not exist. The US Centers for Disease Control and Prevention selected 84 clinicians to develop care recommendations using the RAND Corporation–University of California Los Angeles Appropriateness Method. The DMD Care Considerations Working Group evaluated assessments and interventions used in the management of diagnostics, gastroenterology and nutrition, rehabilitation, and neuromuscular, psychosocial, cardiovascular, respiratory, orthopaedic, and surgical aspects of DMD. These recommendations, presented in two parts, are intended for the wide range of practitioners who care for individuals with DMD. They provide a framework for recognising the multisystem primary manifestations and secondary complications of DMD and for providing coordinated multidisciplinary care. In part 1 of this Review, we describe the methods used to generate the recommendations, and the overall perspective on care, pharmacological treatment, and psychosocial management.
1,664 citations
Agricultural Research Service1, Oregon State University2, University of California, Berkeley3, John Innes Centre4, United States Department of Energy5, United States Department of Agriculture6, University of California, Davis7, University of Silesia in Katowice8, China Agricultural University9, Iowa State University10, Washington State University11, University of Florida12, University of Massachusetts Amherst13, University of Wisconsin-Madison14, Technische Universität München15, Cornell University16, University of Zurich17, University of Helsinki18, Universidade Federal de Pelotas19, Purdue University20, University of Texas at Arlington21, National Center for Genome Resources22, University of Delaware23, Joint BioEnergy Institute24, University of Copenhagen25, Kyung Hee University26, Ghent University27, Centre national de la recherche scientifique28, Oak Ridge National Laboratory29, Ohio State University30, Institut national de la recherche agronomique31, University of Picardie Jules Verne32, Illinois State University33, Sabancı University34, Donald Danforth Plant Science Center35
TL;DR: The high-quality genome sequence will help Brachypodium reach its potential as an important model system for developing new energy and food crops and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat.
Abstract: Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.
1,603 citations
TL;DR: Evidence is provided for an interactionist model of the relationship between SES and family life, which incorporates assumptions from both the social causation and social selection perspectives, and recommendations for future research are made.
Abstract: Research during the past decade shows that social class or socioeconomic status (SES) is related to satisfaction and stability in romantic unions, the quality of parent-child relationships, and a range of developmental outcomes for adults and children. This review focuses on evidence regarding potential mechanisms proposed to account for these associations. Research findings reported during the past decade demonstrate support for an interactionist model of the relationship between SES and family life, which incorporates assumptions from both the social causation and social selection perspectives. The review concludes with recommendations for future research on SES, family processes and individual development in terms of important theoretical and methodological issues yet to be addressed.
Stony Brook University1, University of California, Berkeley2, Macquarie University3, University of California, Davis4, University of North Carolina at Chapel Hill5, University of Wisconsin-Madison6, University of California, Santa Barbara7, McGill University8, University of Bergen9, University of California, Irvine10, University of Florida11, University of Colorado Boulder12, University of Georgia13
TL;DR: The mounting evidence for the importance of niche conservatism to major topics in ecology and conservation and other areas where it may be important but has generally been overlooked is described.
Abstract: The diversity of life is ultimately generated by evolution, and much attention has focused on the rapid evolution of ecological traits. Yet, the tendency for many ecological traits to instead remain similar over time [niche conservatism (NC)] has many consequences for the fundamental patterns and processes studied in ecology and conservation biology. Here, we describe the mounting evidence for the importance of NC to major topics in ecology (e.g. species richness, ecosystem function) and conservation (e.g. climate change, invasive species). We also review other areas where it may be important but has generally been overlooked, in both ecology (e.g. food webs, disease ecology, mutualistic interactions) and conservation (e.g. habitat modification). We summarize methods for testing for NC, and suggest that a commonly used and advocated method (involving a test for phylogenetic signal) is potentially problematic, and describe alternative approaches. We suggest that considering NC: (1) focuses attention on the within-species processes that cause traits to be conserved over time, (2) emphasizes connections between questions and research areas that are not obviously related (e.g. invasives, global warming, tropical richness), and (3) suggests new areas for research (e.g. why are some clades largely nocturnal? why do related species share diseases?).
TL;DR: The Alzheimer's Disease Neuroimaging Initiative has successfully recruited cohorts of cognitively normal subjects, subjects with mild cognitive impairment (MCI), and subjects with Alzheimer disease with anticipated baseline characteristics and the CSF measures heralded progression of clinical measures over 12 months.
Abstract: Background: Neuroimaging measures and chemical biomarkers may be important indices of clinical progression in normal aging and mild cognitive impairment (MCI) and need to be evaluated longitudinally. Objective: To characterize cross-sectionally and longitudinally clinical measures in normal controls, subjects with MCI, and subjects with mild Alzheimer disease (AD) to enable the assessment of the utility of neuroimaging and chemical biomarker measures. Methods: A total of 819 subjects (229 cognitively normal, 398 with MCI, and 192 with AD) were enrolled at baseline and followed for 12 months using standard cognitive and functional measures typical of clinical trials. Results: The subjects with MCI were more memory impaired than the cognitively normal subjects but not as impaired as the subjects with AD. Nonmemory cognitive measures were only minimally impaired in the subjects with MCI. The subjects with MCI progressed to dementia in 12 months at a rate of 16.5% per year. Approximately 50% of the subjects with MCI were on antidementia therapies. There was minimal movement on the Alzheimer’s Disease Assessment Scale–Cognitive Subscale for the normal control subjects, slight movement for the subjects with MCI of 1.1, and a modest change for the subjects with AD of 4.3. Baseline CSF measures of A-42 separated the 3 groups as expected and successfully predicted the 12-month change in cognitive measures. Conclusion: The Alzheimer’s Disease Neuroimaging Initiative has successfully recruited cohorts of cognitively normal subjects, subjects with mild cognitive impairment (MCI), and subjects with Alzheimer disease with anticipated baseline characteristics. The 12-month progression rate of MCI was as predicted, and the CSF measures heralded progression of clinical measures over 12 months. Neurology ® 2010;74:201–209
TL;DR: A population genomic survey has revealed a functionally important locus in genetic adaptation to high altitude, and the strongest signal of natural selection came from endothelial Per-Arnt-Sim domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia.
Abstract: Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exomes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which represent strong candidates for altitude adaptation, were identified. The strongest signal of natural selection came from endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia. One single-nucleotide polymorphism (SNP) at EPAS1 shows a 78% frequency difference between Tibetan and Han samples, representing the fastest allele frequency change observed at any human gene to date. This SNP's association with erythrocyte abundance supports the role of EPAS1 in adaptation to hypoxia. Thus, a population genomic survey has revealed a functionally important locus in genetic adaptation to high altitude.
TL;DR: Obstructive sleep apnea is associated with an increased risk of incident heart failure in community-dwelling middle-aged and older men; its association with incident coronary heart disease in this sample is equivocal.
Abstract: Background— Clinic-based observational studies in men have reported that obstructive sleep apnea is associated with an increased incidence of coronary heart disease. The objective of this study was to assess the relation of obstructive sleep apnea to incident coronary heart disease and heart failure in a general community sample of adult men and women. Methods and Results— A total of 1927 men and 2495 women ≥40 years of age and free of coronary heart disease and heart failure at the time of baseline polysomnography were followed up for a median of 8.7 years in this prospective longitudinal epidemiological study. After adjustment for multiple risk factors, obstructive sleep apnea was a significant predictor of incident coronary heart disease (myocardial infarction, revascularization procedure, or coronary heart disease death) only in men ≤70 years of age (adjusted hazard ratio 1.10 [95% confidence interval 1.00 to 1.21] per 10-unit increase in apnea-hypopnea index [AHI]) but not in older men or in women of...
Brigham and Women's Hospital1, Harvard University2, Massachusetts Institute of Technology3, National Institutes of Health4, University of Toronto5, University of Manchester6, Celera Corporation7, Leiden University8, Karolinska Institutet9, University of Texas at Austin10, Radboud University Nijmegen Medical Centre11, University of California, San Francisco12, VU University Amsterdam13, University of Leeds14, University of Oxford15, University of Aberdeen16, The Feinstein Institute for Medical Research17, Karolinska University Hospital18, University of Groningen19, University of California, Davis20, King's College21, University of Amsterdam22, University of Sheffield23, Hoffmann-La Roche24, University Health Network25, North Shore-LIJ Health System26, Broad Institute27
TL;DR: Seven new rheumatoid arthritis risk alleles were identified at genome-wide significance (P < 5 × 10−8) in an analysis of all 41,282 samples, and an additional 11 SNPs replicated at P < 0.05, suggesting that most represent genuine rhearatoid arthritisrisk alleles.
Abstract: To identify new genetic risk factors for rheumatoid arthritis, we conducted a genome-wide association study meta-analysis of 5,539 autoantibody-positive individuals with rheumatoid arthritis (cases) and 20,169 controls of European descent, followed by replication in an independent set of 6,768 rheumatoid arthritis cases and 8,806 controls. Of 34 SNPs selected for replication, 7 new rheumatoid arthritis risk alleles were identified at genome-wide significance (P < 5 x 10(-8)) in an analysis of all 41,282 samples. The associated SNPs are near genes of known immune function, including IL6ST, SPRED2, RBPJ, CCR6, IRF5 and PXK. We also refined associations at two established rheumatoid arthritis risk loci (IL2RA and CCL21) and confirmed the association at AFF3. These new associations bring the total number of confirmed rheumatoid arthritis risk loci to 31 among individuals of European ancestry. An additional 11 SNPs replicated at P < 0.05, many of which are validated autoimmune risk alleles, suggesting that most represent genuine rheumatoid arthritis risk alleles.
TL;DR: Most of the evidence examined in this review supports the crucial role of public policy in encouraging bicycling, including infrastructure provision and pro-bicycle programs, supportive land use planning, and restrictions on car use.
TL;DR: This paper aims to review recent in-food applications of EOs and plant-origin natural antimicrobials and recent techniques for screening such compounds.
TL;DR: In this article, the authors present an overview of bio-mediated improvement systems, identifying the primary components and interplay between different disciplines and identifying the geometric compatibility between soil and microbes that restricts the utility of different systems.
TL;DR: The strong adjusted association between ischemic stroke and OAHI in community-dwelling men with mild to moderate sleep apnea suggests that this is an appropriate target for future stroke prevention trials.
Abstract: Rationale: Although obstructive sleep apnea is associated with physiological perturbations that increase risk of hypertension and are proatherogenic, it is uncertain whether sleep apnea is associated with increased stroke risk in the general population.
Objectives: To quantify the incidence of ischemic stroke with sleep apnea in a community-based sample of men and women across a wide range of sleep apnea.
Methods: Baseline polysomnography was performed between 1995 and 1998 in a longitudinal cohort study. The primary exposure was the obstructive apnea–hypopnea index (OAHI) and outcome was incident ischemic stroke.
Measurements and Main Results: A total of 5,422 participants without a history of stroke at the baseline examination and untreated for sleep apnea were followed for a median of 8.7 years. One hundred ninety-three ischemic strokes were observed. In covariate-adjusted Cox proportional hazard models, a significant positive association between ischemic stroke and OAHI was observed in men (P value for linear trend: P = 0.016). Men in the highest OAHI quartile (>19) had an adjusted hazard ratio of 2.86 (95% confidence interval, 1.1–7.4). In the mild to moderate range (OAHI, 5–25), each one-unit increase in OAHI in men was estimated to increase stroke risk by 6% (95% confidence interval, 2–10%). In women, stroke was not significantly associated with OAHI quartiles, but increased risk was observed at an OAHI greater than 25.
Conclusions: The strong adjusted association between ischemic stroke and OAHI in community-dwelling men with mild to moderate sleep apnea suggests that this is an appropriate target for future stroke prevention trials.
TL;DR: The last quarter of the twentieth century and the beginning decade of the twenty-first witnessed spectacular discoveries in the chemistry of the heavier main-group elements, which led to new structural and bonding insights as well as a gradually increasing realization that the science more resembles that of transition-metal complexes than that of their lighter main- group congeners.
Abstract: The chemistry of heavier main-group elements such as aluminium, silicon and phosphorus is very different from that of the lighter ones such as boron, carbon and nitrogen, yet discussions of this topic have been dominated by comparisons with the light elements. Philip Power's review focuses on advances in chemistry of the heavier main-group elements that reveal them as having more in common with the transition metals than the lighter members of the main groups. The concept of heavier main-group elements as 'transition metals' is supported by recent work showing that many of the new compounds react with small molecules such as H2, NH3, C2H4 and CO under mild conditions and display potential as catalysts. The last quarter of the twentieth century and the beginning decade of the twenty-first witnessed spectacular discoveries in the chemistry of the heavier main-group elements. The new compounds that were synthesized highlighted the fundamental differences between their electronic properties and those of the lighter elements to a degree that was not previously apparent. This has led to new structural and bonding insights as well as a gradually increasing realization that the chemistry of the heavier main-group elements more resembles that of transition-metal complexes than that of their lighter main-group congeners. The similarity is underlined by recent work, which has shown that many of the new compounds react with small molecules such as H2, NH3, C2H4 or CO under mild conditions and display potential for applications in catalysis.
TL;DR: The data ascribe a new homeostatic role to α-defensins in regulating the makeup of the commensal microbiota in mice expressing a human and a mouse lacking an enzyme required for the processing of mouse α- defensins.
Abstract: Antimicrobial peptides are important effectors of innate immunity throughout the plant and animal kingdoms. In the mammalian small intestine, Paneth cell alpha-defensins are antimicrobial peptides that contribute to host defense against enteric pathogens. To determine if alpha-defensins also govern intestinal microbial ecology, we analyzed the intestinal microbiota of mice expressing a human alpha-defensin gene (DEFA5) and in mice lacking an enzyme required for the processing of mouse alpha-defensins. In these complementary models, we detected significant alpha-defensin-dependent changes in microbiota composition, but not in total bacterial numbers. Furthermore, DEFA5-expressing mice had striking losses of segmented filamentous bacteria and fewer interleukin 17 (IL-17)-producing lamina propria T cells. Our data ascribe a new homeostatic role to alpha-defensins in regulating the makeup of the commensal microbiota.
TL;DR: It is shown that reactive oxygen species generated during inflammation react with endogenous, luminal sulphur compounds (thiosulphate) to form a new respiratory electron acceptor, tetrathionate, that allows the pathogen to use respiration to compete with fermenting gut microbes.
Abstract: Salmonella enterica serotype Typhimurium (S. Typhimurium) causes acute gut inflammation by using its virulence factors to invade the intestinal epithelium and survive in mucosal macrophages. The inflammatory response enhances the transmission success of S. Typhimurium by promoting its outgrowth in the gut lumen through unknown mechanisms. Here we show that reactive oxygen species generated during inflammation react with endogenous, luminal sulphur compounds (thiosulphate) to form a new respiratory electron acceptor, tetrathionate. The genes conferring the ability to use tetrathionate as an electron acceptor produce a growth advantage for S. Typhimurium over the competing microbiota in the lumen of the inflamed gut. We conclude that S. Typhimurium virulence factors induce host-driven production of a new electron acceptor that allows the pathogen to use respiration to compete with fermenting gut microbes. Thus the ability to trigger intestinal inflammation is crucial for the biology of this diarrhoeal pathogen.
TL;DR: In this paper, the authors use fluorescence spectroscopy to provide a novel approach to understand the dynamics and biogeochemical role of dissolved organic matter (DOM) in aquatic ecosystems.
Abstract: The biochemical composition of dissolved organic matter (DOM) strongly influences its biogeochemical role in freshwater ecosystems, yet DOM composition measurements are not routinely incorporated into ecological studies. To date, the majority of studies of freshwater ecosystems have relied on bulk analyses of dissolved organic carbon and nitrogen to obtain information about DOM cycling. The problem with this approach is that the biogeochemical significance of DOM can only partially be elucidated using bulk analyses alone because bulk measures cannot detect most carbon and nitrogen transformations. Advances in fluorescence spectroscopy provide an alternative to traditional approaches for characterizing aquatic DOM, and allow for the rapid and precise characterization of DOM necessary to more comprehensively trace DOM dynamics. It is within this context that we discuss the use of fluorescence spectroscopy to provide a novel approach to tackling a longstanding problem: understanding the dynamics and biogeochemical role of DOM. We highlight the utility of fluorescence characterization of DOM and provide examples of the potential range of applications for incorporating DOM fluorescence into ecological studies in the hope that this rapidly evolving technique will further our understanding of the biogeochemical role of DOM in freshwater ecosystems.
TL;DR: Recordings of extracellular activity from 1177 cells in human medial frontal and temporal cortices while patients executed or observed hand grasping actions and facial emotional expressions suggest that multiple systems in humans may be endowed with neural mechanisms of mirroring for both the integration and differentiation of perceptual and motor aspects of actions performed by self and others.
Newcastle University1, Children's Hospital of Philadelphia2, Case Western Reserve University3, Duke University4, Veterans Health Administration5, Cincinnati Children's Hospital Medical Center6, University of California, Davis7, University of Rochester8, Baylor College of Medicine9, Boston Children's Hospital10, Centers for Disease Control and Prevention11
TL;DR: A comprehensive set of DMD care recommendations for management of rehabilitation, orthopaedic, respiratory, cardiovascular, gastroenterology/nutrition, and pain issues, as well as general surgical and emergency-room precautions are presented.
Abstract: Optimum management of Duchenne muscular dystrophy (DMD) requires a multidisciplinary approach that focuses on anticipatory and preventive measures as well as active interventions to address the primary and secondary aspects of the disorder. Implementing comprehensive management strategies can favourably alter the natural history of the disease and improve function, quality of life, and longevity. Standardised care can also facilitate planning for multicentre trials and help with the identification of areas in which care can be improved. Here, we present a comprehensive set of DMD care recommendations for management of rehabilitation, orthopaedic, respiratory, cardiovascular, gastroenterology/nutrition, and pain issues, as well as general surgical and emergency-room precautions. Together with part 1 of this Review, which focuses on diagnosis, pharmacological treatment, and psychosocial care, these recommendations allow diagnosis and management to occur in a coordinated multidisciplinary fashion.
TL;DR: Mechanistic studies show that SR1 acts by antagonizing the aryl hydrocarbon receptor (AHR) and AHR modulation as a means to induce ex vivo HSC expansion should facilitate the clinical use of HSC therapy.
Abstract: Although practiced clinically for more than 40 years, the use of hematopoietic stem cell (HSC) transplants remains limited by the ability to expand these cells ex vivo. An unbiased screen with primary human HSCs identified a purine derivative, StemRegenin 1 (SR1), that promotes the ex vivo expansion of CD34+ cells. Culture of HSCs with SR1 led to a 50-fold increase in cells expressing CD34 and a 17-fold increase in cells that retain the ability to engraft immunodeficient mice. Mechanistic studies show that SR1 acts by antagonizing the aryl hydrocarbon receptor (AHR). The identification of SR1 and AHR modulation as a means to induce ex vivo HSC expansion should facilitate the clinical use of HSC therapy.
TL;DR: The factors and mechanistic stages of recombination that are subject to regulation are reviewed and it is suggested that recombination achieves flexibility and robustness by proceeding through metastable, reversible intermediates.
Abstract: Homologous recombination (HR) is required for accurate chromosome segregation during the first meiotic division and constitutes a key repair and tolerance pathway for complex DNA damage, including DNA double-strand breaks, interstrand crosslinks, and DNA gaps. In addition, recombination and replication are inextricably linked, as recombination recovers stalled and broken replication forks, enabling the evolution of larger genomes/replicons. Defects in recombination lead to genomic instability and elevated cancer predisposition, demonstrating a clear cellular need for recombination. However, recombination can also lead to genome rearrangements. Unrestrained recombination causes undesired endpoints (translocation, deletion, inversion) and the accumulation of toxic recombination intermediates. Evidently, HR must be carefully regulated to match specific cellular needs. Here, we review the factors and mechanistic stages of recombination that are subject to regulation and suggest that recombination achieves fle...
University of California, Berkeley1, Massachusetts Institute of Technology2, Heidelberg University3, Joint Genome Institute4, University of Queensland5, University of California, Santa Barbara6, Salk Institute for Biological Studies7, Rice University8, University of California, Davis9, University of Alberta10, Paris Diderot University11
TL;DR: In this paper, the authors present the draft genome sequence of Amphimedon queenslandica, a demosponge from the Great Barrier Reef, and show that it is remarkably similar to other animal genomes in content, structure and organization.
Abstract: Sponges are an ancient group of animals that diverged from other metazoans over 600 million years ago. Here we present the draft genome sequence of Amphimedon queenslandica, a demosponge from the Great Barrier Reef, and show that it is remarkably similar to other animal genomes in content, structure and organization. Comparative analysis enabled by the sequencing of the sponge genome reveals genomic events linked to the origin and early evolution of animals, including the appearance, expansion and diversification of pan-metazoan transcription factor, signalling pathway and structural genes. This diverse ‘toolkit’ of genes correlates with critical aspects of all metazoan body plans, and comprises cell cycle control and growth, development, somatic- and germ-cell specification, cell adhesion, innate immunity and allorecognition. Notably, many of the genes associated with the emergence of animals are also implicated in cancer, which arises from defects in basic processes associated with metazoan multicellularity.
TL;DR: In this paper, the authors presented new determinations of the cosmic expansion history from red-envelope galaxies using the Keck-LRIS spectrograph of 24 galaxy clusters in the redshift range 0.2 < z < 1.0.
Abstract: We present new determinations of the cosmic expansion history from red-envelope galaxies. We have obtained for this purpose high-quality spectra with the Keck-LRIS spectrograph of red-envelope galaxies in 24 galaxy clusters in the redshift range 0.2 < z < 1.0. We complement these Keck spectra with high-quality, publicly available archival spectra from the SPICES and VVDS surveys. We improve over our previous expansion history measurements in Simon et al. (2005) by providing two new determinations of the expansion history: H(z) = 97±62 km sec^(−1) Mpc^(−1) at z ≃ 0.5 and H(z) = 90±40 km sec^(−1) Mpc^(−1) at z ≃ 0.9. We discuss the uncertainty in the expansion history determination that arises from uncertainties in the synthetic stellar-population models. We then use these new measurements in concert with cosmic-microwave-background (CMB) measurements to constrain cosmological parameters, with a special emphasis on dark-energy parameters and constraints to the curvature. In particular, we demonstrate the usefulness of direct H(z) measurements by constraining the dark-energy equation of state parameterized by w_0 and w_a and allowing for arbitrary curvature. Further, we also constrain, using only CMB and H(z) data, the number of relativistic degrees of freedom to be 4±0.5 and their total mass to be < 0.2 eV, both at 1σ.