292 research outputs found
Bandlimited approximations to the truncated Gaussian and applications
In this paper we extend the theory of optimal approximations of functions in the -metric by entire functions of prescribed
exponential type (bandlimited functions). We solve this problem for the
truncated and the odd Gaussians using explicit integral representations and
fine properties of truncated theta functions obtained via the maximum principle
for the heat operator. As applications, we recover most of the previously known
examples in the literature and further extend the class of truncated and odd
functions for which this extremal problem can be solved, by integration on the
free parameter and the use of tempered distribution arguments. This is the
counterpart of the work \cite{CLV}, where the case of even functions is
treated.Comment: to appear in Const. Appro
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FunFam protein families improve residue level molecular function prediction
BACKGROUND: The CATH database provides a hierarchical classification of protein domain structures including a sub-classification of superfamilies into functional families (FunFams). We analyzed the similarity of binding site annotations in these FunFams and incorporated FunFams into the prediction of protein binding residues. RESULTS: FunFam members agreed, on average, in 36.9 ± 0.6% of their binding residue annotations. This constituted a 6.7-fold increase over randomly grouped proteins and a 1.2-fold increase (1.1-fold on the same dataset) over proteins with the same enzymatic function (identical Enzyme Commission, EC, number). Mapping de novo binding residue prediction methods (BindPredict-CCS, BindPredict-CC) onto FunFam resulted in consensus predictions for those residues that were aligned and predicted alike (binding/non-binding) within a FunFam. This simple consensus increased the F1-score (for binding) 1.5-fold over the original prediction method. Variation of the threshold for how many proteins in the consensus prediction had to agree provided a convenient control of accuracy/precision and coverage/recall, e.g. reaching a precision as high as 60.8 ± 0.4% for a stringent threshold. CONCLUSIONS: The FunFams outperformed even the carefully curated EC numbers in terms of agreement of binding site residues. Additionally, we assume that our proof-of-principle through the prediction of protein binding residues will be relevant for many other solutions profiting from FunFams to infer functional information at the residue level
The NY-Ålesund TurbulencE Fiber Optic eXperiment (NYTEFOX): investigating the Arctic boundary layer, Svalbard
The NY-Ålesund TurbulencE Fiber Optic eXperiment (NYTEFOX) was a field experiment at the
Ny-Ålesund Arctic site (78.9◦ N, 11.9◦ E) and yielded a unique meteorological data set. These data describe the
distribution of heat, airflows, and exchange in the Arctic boundary layer for a period of 14 d from 26 February
to 10 March 2020. NYTEFOX is the first field experiment to investigate the heterogeneity of airflow and its
transport of temperature, wind, and kinetic energy in the Arctic environment using the fiber-optic distributed
sensing (FODS) technique for horizontal and vertical observations. FODS air temperature and wind speed were
observed at a spatial resolution of 0.127 m and a temporal resolution of 9 s along a 700 m horizontal array at
1 m above ground level (a.g.l.) and along three 7 m vertical profiles. Ancillary data were collected from three
sonic anemometers and an acoustic profiler (minisodar; sodar is an acronym for “sound detection and ranging”)
yielding turbulent flow statistics and vertical profiles in the lowest 300 m a.g.l., respectively. The observations
from this field campaign are publicly available on Zenodo (https://doi.org/10.5281/zenodo.4756836, Huss et al.,
2021) and supplement the meteorological data set operationally collected by the Baseline Surface Radiation
Network (BSRN) at Ny-Ålesund, Svalbard
Purple sulfur bacteria fix N-2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue
Biological N-2 fixation was key to the expansion of life on early Earth. The N-2-fixing microorganisms and the nitrogenase type used in the Proterozoic are unknown, although it has been proposed that the canonical molybdenum-nitrogenase was not used due to low molybdenum availability. We investigate N-2 fixation in Lake Cadagno, an analogue system to the sulfidic Proterozoic continental margins, using a combination of biogeochemical, molecular and single cell techniques. In Lake Cadagno, purple sulfur bacteria (PSB) are responsible for high N-2 fixation rates, to our knowledge providing the first direct evidence for PSB in situ N-2 fixation. Surprisingly, no alternative nitrogenases are detectable, and N-2 fixation is exclusively catalyzed by molybdenum-nitrogenase. Our results show that molybdenum-nitrogenase is functional at low molybdenum conditions in situ and that in contrast to previous beliefs, PSB may have driven N-2 fixation in the Proterozoic ocean. N-2 fixation was key to the expansion of life on Earth, but which organisms fixed N-2 and if Mo-nitrogenase was functional in the low Mo early ocean is unknown. Here, the authors show that purple sulfur bacteria fix N-2 using Mo-nitrogenase in a Proterozoic ocean analogue, despite low Mo conditions
Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean
Nitrification, the oxidation of ammonia via nitrite to nitrate, is a key process in marine nitrogen (N) cycling. Although oceanic ammonia and nitrite oxidation are balanced, ammonia-oxidizing archaea (AOA) vastly outnumber the main nitrite oxidizers, the bacterial Nitrospinae. The ecophysiological reasons for this discrepancy in abundance are unclear. Here, we compare substrate utilization and growth of Nitrospinae to AOA in the Gulf of Mexico. Based on our results, more than half of the Nitrospinae cellular N-demand is met by the organic-N compounds urea and cyanate, while AOA mainly assimilate ammonium. Nitrospinae have, under in situ conditions, around four-times higher biomass yield and five-times higher growth rates than AOA, despite their ten-fold lower abundance. Our combined results indicate that differences in mortality between Nitrospinae and AOA, rather than thermodynamics, biomass yield and cell size, determine the abundances of these main marine nitrifiers. Furthermore, there is no need to invoke yet undiscovered, abundant nitrite oxidizers to explain nitrification rates in the ocean
The effects of concentration and salinity on polymer adsorption isotherm at sandstone rock surface
Adsorption of hydrolyzed polyacrylamide (HPAM) polymers on sandstone rock surface was studied by static adsorption experiments. Total of 10 Runs of static experiments were conducted in test tubes by mixing the desired solution with crushed rock sample, at temperature of 25 °C, and salinity range from 0-4 wt%. The results are in conformity with Langmuir's isotherm. Ten different isotherms were generated at each Run. The initial polymer concentration was varied from 0.3-2.1 g/l. The effects of salinity have been studied by observation on Langmuir adsorption coefficients (Y and K). The results show that the adsorption coefficient (Y) was found to have linear relationship with salinity. The adsorption coefficient (K) was found to be related to salinity by a quadratic relationship
Antimicrobial Footprints, Fairness, and Collective Harm
This chapter explores the question of whether or not individual agents
are under a moral obligation to reduce their ‘antimicrobial footprint’. An agent’s
antimicrobial footprint measures the extent to which her actions are causally linked
to the use of antibiotics. As such, it is not necessarily a measure of her contribution
to antimicrobial resistance. Talking about people’s antimicrobial footprint in a way
we talk about our carbon footprint may be helpful for drawing attention to the global
effects of individual behaviour and for highlighting that our choices can collectively
make a real difference. But can we be morally obligated to make a contribution to
resolving a collective action problem when our individual contributions by themselves
make no discernible difference? I will focus on two lines of argument in
favour of such obligations: whether a failure to reduce one’s antimicrobial footprint
is unfair and whether it constitutes wrongdoing because it is harmful. I conclude by
suggesting that the argument from collective harm is ultimately more successful
Exploring the evidence base for national and regional policy interventions to combat resistance
The effectiveness of existing policies to control antimicrobial resistance is not yet fully understood. A strengthened evidence base is needed to inform effective policy interventions across countries with different income levels and the human health and animal sectors. We examine three policy domains—responsible use, surveillance, and infection prevention and control—and consider which will be the most effective at national and regional levels. Many complexities exist in the implementation of such policies across sectors and in varying political and regulatory environments. Therefore, we make recommendations for policy action, calling for comprehensive policy assessments, using standardised frameworks, of cost-effectiveness and generalisability. Such assessments are especially important in low-income and middle-income countries, and in the animal and environmental sectors. We also advocate a One Health approach that will enable the development of sensitive policies, accommodating the needs of each sector involved, and addressing concerns of specific countries and regions
Extent of non-publication in cohorts of studies approved by research ethics committees or included in trial registries
Background: The synthesis of published research in systematic reviews is essential when providing evidence to inform clinical and health policy decisionmaking. However, the validity of systematic reviews is threatened if journal publications represent a biased selection of all studies that have been conducted (dissemination bias). To investigate the extent of dissemination bias we conducted a systematic review that determined the proportion of studies published as peerreviewed journal articles and investigated factors associated with full publication in cohorts of studies (i) approved by research ethics committees (RECs) or (ii) included in trial registries. Copyright:Methods and Findings: Four bibliographic databases were searched for methodological research projects (MRPs) without limitations for publication year, language or study location. The searches were supplemented by handsearching the references of included MRPs. We estimated the proportion of studies published using prediction intervals (PI) and a random effects meta-analysis. Pooled odds ratios (OR) were used to express associations between study characteristics and journal publication. Seventeen MRPs (23 publications) evaluated cohorts of studies approved by RECs; the proportion of published studies had a PI between 22% and 72% and the weighted pooled proportion when combining estimates would be 46.2% (95% CI 40.2%-52.4%, I2594.4%). Twenty-two MRPs (22 publications) evaluated cohorts of studies included in trial registries; the PI of the proportion published ranged from 13% to 90% and the weighted pooled proportion would be 54.2% (95% CI 42.0%-65.9%, I2598.9%). REC-approved studies with statistically significant results (compared with those without statistically significant results) were more likely to be published (pooled OR 2.8; 95% CI 2.2-3.5). Phase-III trials were also more likely to be published than phase II trials (pooled OR 2.0; 95% CI 1.6- 2.5). The probability of publication within two years after study completion ranged from 7% to 30%.Conclusions: A substantial part of the studies approved by RECs or included in trial registries remains unpublished. Due to the large heterogeneity a prediction of the publication probability for a future study is very uncertain. Non-publication of research is not a random process, e.g., it is associated with the direction of study findings. Our findings suggest that the dissemination of research findings is biased
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