931 research outputs found
General behaviour of Bianchi VI_0 solutions with an exponential-potential scalar field
The solutions to the Einstein-Klein-Gordon equations without a cosmological
constant are investigated for an exponential potential in a Bianchi VI_0
metric. There exists a two-parameter family of solutions which have a power-law
inflationary behaviour when the exponent of the potential, k, satisfies k^2<2.
In addition, there exists a two-parameter family of singular solutions for all
k^2 values. A simple anisotropic exact solution is found to be stable when
2<k^2.Comment: 10 pages, no figures. To be published in General Relativity and
Gravitatio
Scanned Probe Microscopy of Electronic Transport in Carbon Nanotubes
We use electrostatic force microscopy and scanned gate microscopy to probe
the conducting properties of carbon nanotubes at room temperature. Multi-walled
carbon nanotubes are shown to be diffusive conductors, while metallic
single-walled carbon nanotubes are ballistic conductors over micron lengths.
Semiconducting single-walled carbon nanotubes are shown to have a series of
large barriers to conduction along their length. These measurements are also
used to probe the contact resistance and locate breaks in carbon nanotube
circuits.Comment: 4 page
The positive effect of plant diversity on soil carbon depends on climate
Little is currently known about how climate modulates the relationship between plant diversity and soil organic carbon and the mechanisms involved. Yet, this knowledge is of crucial importance in times of climate change and biodiversity loss. Here, we show that plant diversity is positively correlated with soil carbon content and soil carbon-to-nitrogen ratio across 84 grasslands on six continents that span wide climate gradients. The relationships between plant diversity and soil carbon as well as plant diversity and soil organic matter quality (carbon-to-nitrogen ratio) are particularly strong in warm and arid climates. While plant biomass is positively correlated with soil carbon, plant biomass is not significantly correlated with plant diversity. Our results indicate that plant diversity influences soil carbon storage not via the quantity of organic matter (plant biomass) inputs to soil, but through the quality of
organic matter. The study implies that ecosystem management that restores plant diversity likely enhances soil carbon sequestration, particularly in warm and arid climates.EEA Santa CruzFil: Spohn, Marie. Swedish University of Agricultural Sciences (SLU). Department of Soil and Environment; SueciaFil: Bagchi, Sumanta. Indian Institute of Science; India.Fil: Biederman, Lori A. Iowa State University. Department of Ecology, Evolution, and Organismal Biology; Estados UnidosFil: Borer, Elizabeth T. University of Minnesota. Department of Ecology, Evolution, and Behavior; Estados UnidosFil: BrĂĄthen, Kari Anne. Arctic University of Norway. Department of Arctic and Marine Biology; NoruegaFil: Bugalho, Miguel N. University of Lisbon. Centre for Applied Ecology “Prof. Baeta Neves” (CEABN-InBIO). School of Agriculture; Portugal.Fil: Caldeira, Maria C. University of Lisbon. Forest Research Centre. Associate Laboratory TERRA. School of Agriculture; Portugal.Fil: Catford, Jane A. King’s College London. Department of Geography; Reino UnidoFil: Catford, Jane A. University of Melbourne. School of Agriculture, Food and Ecosystem Sciences; Australia.Fil: Collins, Scott L. University of New Mexico. Department of Biology; Estados UnidosFil: Eisenhauer, Nico. German Centre for Integrative Biodiversity Research (iDiv). Halle-Jena-Leipzig; AlemaniaFil: Eisenhauer, Nico. Leipzig University. Institute of Biology; AlemaniaFil: Peri, Pablo Luis. Instituto Nacional de TecnologĂa Agropecuaria (INTA). EstaciĂłn Experimental Agropecuaria Santa Cruz; Argentina.Fil: Peri, Pablo Luis. Universidad Nacional de la Patagonia Austral; Argentina.Fil: Peri, Pablo Luis. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas; Argentina.Fil: Yahdjian, Laura. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas (CONICET). Instituto de Investigaciones FisiolĂłgicas y EcolĂłgicas Vinculadas a la Agricultura (IFEVA); Argentina.Fil: Yahdjian, Laura. Universidad de Buenos Aires. Facultad de AgronomĂa; Argentina
Newly Developed and Validated Eosinophilic Esophagitis Histology Scoring System and Evidence that it Outperforms Peak Eosinophil Count for Disease Diagnosis and Monitoring
Eosinophilic esophagitis is diagnosed by symptoms, and at least 15 intraepithelial eosinophils per high power field in an esophageal biopsy. Other pathologic features have not been emphasized. We developed a histology scoring system for esophageal biopsies that evaluates eight features: eosinophil density, basal zone hyperplasia, eosinophil abscesses, eosinophil surface layering, dilated intercellular spaces, surface epithelial alteration, dyskeratotic epithelial cells and lamina propria fibrosis. Severity (grade) and extent (stage) of abnormalities were scored using a 4 point scale (0 normal; 3 maximum change). Reliability was demonstrated by strong to moderate agreement among 3 pathologists who scored biopsies independently (p≤0.008). Several features were often abnormal in 201 biopsies (101 distal, 100 proximal) from 104 subjects (34 untreated, 167 treated). Median grade and stage scores were significantly higher in untreated compared to treated subjects (p≤0.0062). Grade scores for features independent of eosinophil counts were significantly higher in biopsies from untreated compared to treated subjects (basal zone hyperplasia p≤0.024 and dilated intercellular spaces p≤0.005), and were strongly correlated (r-square\u3e0.67). Principal components analysis identified 3 principal components that explained 78.2% of the variation in the features. In logistic regression models, 2 principal components more closely associated with treatment status than log distal peak eosinophil count (r-square 17, area under the curve 77.8 vs r-square 9, area under the curve 69.8). In summary, the eosinophilic esophagitis histology scoring system provides a method to objectively assess histologic changes in the esophagus beyond eosinophil number. Importantly, it discriminates treated from untreated patients, uses features commonly found in such biopsies, and is utilizable by pathologists after minimal training. These data provide rationales and a method to evaluate esophageal biopsies for features in addition to peak eosinophil count
Understanding the errors of SHAPE-directed RNA structure modeling
Single-nucleotide-resolution chemical mapping for structured RNA is being
rapidly advanced by new chemistries, faster readouts, and coupling to
computational algorithms. Recent tests have shown that selective 2'-hydroxyl
acylation by primer extension (SHAPE) can give near-zero error rates (0-2%) in
modeling the helices of RNA secondary structure. Here, we benchmark the method
using six molecules for which crystallographic data are available: tRNA(phe)
and 5S rRNA from Escherichia coli, the P4-P6 domain of the Tetrahymena group I
ribozyme, and ligand-bound domains from riboswitches for adenine, cyclic
di-GMP, and glycine. SHAPE-directed modeling of these highly structured RNAs
gave an overall false negative rate (FNR) of 17% and a false discovery rate
(FDR) of 21%, with at least one helix prediction error in five of the six
cases. Extensive variations of data processing, normalization, and modeling
parameters did not significantly mitigate modeling errors. Only one varation,
filtering out data collected with deoxyinosine triphosphate during primer
extension, gave a modest improvement (FNR = 12%, and FDR = 14%). The residual
structure modeling errors are explained by the insufficient information content
of these RNAs' SHAPE data, as evaluated by a nonparametric bootstrapping
analysis. Beyond these benchmark cases, bootstrapping suggests a low level of
confidence (<50%) in the majority of helices in a previously proposed
SHAPE-directed model for the HIV-1 RNA genome. Thus, SHAPE-directed RNA
modeling is not always unambiguous, and helix-by-helix confidence estimates, as
described herein, may be critical for interpreting results from this powerful
methodology.Comment: Biochemistry, Article ASAP (Aug. 15, 2011
Different methodological approaches to the assessment of in vivo efficacy of three artemisinin-based combination antimalarial treatments for the treatment of uncomplicated falciparum malaria in African children.
BACKGROUND: Use of different methods for assessing the efficacy of artemisinin-based combination antimalarial treatments (ACTs) will result in different estimates being reported, with implications for changes in treatment policy. METHODS: Data from different in vivo studies of ACT treatment of uncomplicated falciparum malaria were combined in a single database. Efficacy at day 28 corrected by PCR genotyping was estimated using four methods. In the first two methods, failure rates were calculated as proportions with either (1a) reinfections excluded from the analysis (standard WHO per-protocol analysis) or (1b) reinfections considered as treatment successes. In the second two methods, failure rates were estimated using the Kaplan-Meier product limit formula using either (2a) WHO (2001) definitions of failure, or (2b) failure defined using parasitological criteria only. RESULTS: Data analysed represented 2926 patients from 17 studies in nine African countries. Three ACTs were studied: artesunate-amodiaquine (AS+AQ, N = 1702), artesunate-sulphadoxine-pyrimethamine (AS+SP, N = 706) and artemether-lumefantrine (AL, N = 518).Using method (1a), the day 28 failure rates ranged from 0% to 39.3% for AS+AQ treatment, from 1.0% to 33.3% for AS+SP treatment and from 0% to 3.3% for AL treatment. The median [range] difference in point estimates between method 1a (reference) and the others were: (i) method 1b = 1.3% [0 to 24.8], (ii) method 2a = 1.1% [0 to 21.5], and (iii) method 2b = 0% [-38 to 19.3].The standard per-protocol method (1a) tended to overestimate the risk of failure when compared to alternative methods using the same endpoint definitions (methods 1b and 2a). It either overestimated or underestimated the risk when endpoints based on parasitological rather than clinical criteria were applied. The standard method was also associated with a 34% reduction in the number of patients evaluated compared to the number of patients enrolled. Only 2% of the sample size was lost when failures were classified on the first day of parasite recurrence and survival analytical methods were used. CONCLUSION: The primary purpose of an in vivo study should be to provide a precise estimate of the risk of antimalarial treatment failure due to drug resistance. Use of survival analysis is the most appropriate way to estimate failure rates with parasitological recurrence classified as treatment failure on the day it occurs
Whole Genome Sequence Analysis of Burkholderia contaminans FFH2055 Strain Reveals the Presence of Putative β-Lactamases
Burkholderia contaminans is a member of the Burkholderia cepacia complex (Bcc), a pathogen with increasing prevalence among cystic fibrosis (CF) patients and the cause of numerous outbreaks due to the use of contaminated commercial products. The antibiotic resistance determinants, particularly β-lactamases, have been poorly studied in this species. In this work, we explored the whole genome sequence (WGS) of a B. contaminans isolate (FFH 2055) and detected four putative β-lactamase-encoding genes. In general, these genes have more than 93% identity with β-lactamase genes found in other Bcc species. Two β-lactamases, a class A (Pen-like, suggested name PenO) and a class D (OXA-like), were further analyzed and characterized. Amino acid sequence comparison showed that Pen-like has 82% and 67% identity with B. multivorans PenA and B. pseudomallei PenI, respectively, while OXA-like displayed strong homology with class D enzymes within the Bcc, but only 22–44% identity with available structures from the OXA family. PCR reactions designed to study the presence of these two genes revealed a heterogeneous distribution among clinical and industrial B. contaminans isolates. Lastly, bla PenO gene was cloned and expressed into E. coli to investigate the antibiotic resistance profile and confers an extended-spectrum β-lactamase (ESBL) phenotype. These results provide insight into the presence of β-lactamases in B. contaminans, suggesting they play a role in antibiotic resistance of these bacteria.Fil: Degrossi, JosĂ© J.. Universidad de Buenos Aires. Facultad de Farmacia y BioquĂmica; ArgentinaFil: Merino, Cindy. University Fullerton; Estados UnidosFil: Isasmendi, Adela M.. Gobierno de la Ciudad de Buenos Aires. Hospital de PediatrĂa "Juan P. Garrahan"; ArgentinaFil: Ibarra, Lorena M.. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo GutiĂ©rrez"; ArgentinaFil: Collins, Chelsea. University Fullerton; Estados UnidosFil: Bo, Nicolás E.. Universidad de Buenos Aires. Facultad de Farmacia y BioquĂmica; ArgentinaFil: Papalia, Mariana Andrea. Universidad de Buenos Aires. Facultad de Farmacia y BioquĂmica. Departamento de MicrobiologĂa, InmunologĂa y BiotecnologĂa. Cátedra de MicrobiologĂa; Argentina. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Oficina de CoordinaciĂłn Administrativa Houssay; ArgentinaFil: Fernandez, Jennifer S.. University Fullerton; Estados UnidosFil: Hernandez, Claudia M.. Gobierno de la Ciudad de Buenos Aires. Hospital de PediatrĂa "Juan P. Garrahan"; ArgentinaFil: Papp Wallace, Krisztina M.. Case Western Reserve University; Estados UnidosFil: Bonomo, Robert A.. Case Western Reserve University; Estados UnidosFil: Vazquez, Miryam S.. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo GutiĂ©rrez"; ArgentinaFil: Power, Pablo. Universidad de Buenos Aires. Facultad de Farmacia y BioquĂmica. Departamento de MicrobiologĂa, InmunologĂa y BiotecnologĂa. Cátedra de MicrobiologĂa; Argentina. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Oficina de CoordinaciĂłn Administrativa Houssay; ArgentinaFil: Ramirez, MarĂa S.. University Fullerton; Estados Unido
Analysis of Variance in Neuroreceptor Ligand Imaging Studies
Radioligand positron emission tomography (PET) with dual scan paradigms can provide valuable insight into changes in synaptic neurotransmitter concentration due to experimental manipulation. The residual t-test has been utilized to improve the sensitivity of the t-test in PET studies. However, no further development of statistical tests using residuals has been proposed so far to be applied in cases when there are more than two conditions. Here, we propose the residual f-test, a one-way analysis of variance (ANOVA), and examine its feasibility using simulated [11C]raclopride PET data. We also re-visit data from our previously published [11C]raclopride PET study, in which 10 individuals underwent three PET scans under different conditions. We found that the residual f-test is superior in terms of sensitivity than the conventional f-test while still controlling for type 1 error. The test will therefore allow us to reliably test hypotheses in the smaller sample sizes often used in explorative PET studies
The positive effect of plant diversity on soil carbon depends on climate
Little is currently known about how climate modulates the relationship between plant diversity and soil organic carbon and the mechanisms involved. Yet, this knowledge is of crucial importance in times of climate change and biodiversity loss. Here, we show that plant diversity is positively correlated with soil carbon content and soil carbon-to-nitrogen ratio across 84 grasslands on six continents that span wide climate gradients. The relationships between plant diversity and soil carbon as well as plant diversity and soil organic matter quality (carbon-to-nitrogen ratio) are particularly strong in warm and arid climates. While plant biomass is positively correlated with soil carbon, plant biomass is not significantly correlated with plant diversity. Our results indicate that plant diversity influences soil carbon storage not via the quantity of organic matter (plant biomass) inputs to soil, but through the quality of organic matter. The study implies that ecosystem management that restores plant diversity likely enhances soil carbon sequestration, particularly in warm and arid climates
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