Following birth, the breast-fed infant gastrointestinal tract is rapidly colonized by a microbial consortium often dominated by bifidobacteria. Accordingly, the complete genome sequence of ...Bifidobacterium longum subsp. infantis ATCC15697 reflects a competitive nutrient-utilization strategy targeting milk-borne molecules which lack a nutritive value to the neonate. Several chromosomal loci reflect potential adaptation to the infant host including a 43 kbp cluster encoding catabolic genes, extracellular solute binding proteins and permeases predicted to be active on milk oligosaccharides. An examination of in vivo metabolism has detected the hallmarks of milk oligosaccharide utilization via the central fermentative pathway using metabolomic and proteomic approaches. Finally, conservation of gene clusters in multiple isolates corroborates the genomic mechanism underlying milk utilization for this infant-associated phylotype.
Plant phenology regulates ecosystem services at local and global scales and is a sensitive indicator of global change. Estimates of phenophase transition dates, such as the start of spring or end of ...fall, can be derived from sensor-based time series, but must be interpreted in terms of biologically relevant events. We use the PhenoCam archive of digital repeat photography to implement a consistent protocol for visual assessment of canopy phenology at 13 temperate deciduous forest sites throughout eastern North America, and to perform digital image analysis for time-series-based estimation of phenophase transition dates. We then compare these results to remote sensing metrics of phenophase transition dates derived from the Moderate Resolution Imaging Spectroradiometer (MODIS) and Advanced Very High Resolution Radiometer (AVHRR) sensors. We present a new type of curve fit that uses a generalized sigmoid function to estimate phenology dates, and we quantify the statistical uncertainty of phenophase transition dates estimated using this method. Results show that the generalized sigmoid provides estimates of dates with less statistical uncertainty than other curve-fitting methods. Additionally, we find that dates derived from analysis of high-frequency PhenoCam imagery have smaller uncertainties than satellite remote sensing metrics of phenology, and that dates derived from the remotely sensed enhanced vegetation index (EVI) have smaller uncertainty than those derived from the normalized difference vegetation index (NDVI). Near-surface time-series estimates for the start of spring are found to closely match estimates derived from visual assessment of leaf-out, as well as satellite remote-sensing-derived estimates of the start of spring. However late spring and fall phenology metrics exhibit larger differences between near-surface and remote scales. Differences in late spring phenology between near-surface and remote scales are found to correlate with a landscape metric of deciduous forest cover. These results quantify the effect of landscape heterogeneity when aggregating to the coarser spatial scales of remote sensing, and demonstrate the importance of accurate curve fitting and vegetation index selection when analyzing and interpreting phenology time series.
Rapid rotation is a fundamental characteristic of classical Be stars and a crucial property allowing for the formation of their circumstellar disks. Past evolution in a mass and angular momentum ...transferring binary system offers a plausible solution to how Be stars attained their fast rotation. Although the subdwarf remnants of mass donors in such systems should exist in abundance, only a few have been confirmed due to tight observational constraints. An indirect method of detecting otherwise hidden companions is offered by their effect on the outer parts of Be star disks, which are expected to be disrupted or truncated. In the context of the infrared and radio continuum excess radiation originating in the disk, the disk truncation can be revealed by a turndown in the spectral energy distribution due to reduced radio flux levels. In this work, we search for signs of spectral turndown in a sample of 57 classical Be stars with radio data, which include new data for 23 stars and the longest-wavelength detections so far (λ 10 cm) for two stars. We confidently detect the turndown for all 26 stars with sufficient data coverage (20 of which are not known to have close binary companions). For the remaining 31 stars, the data are inconclusive as to whether the turndown is present or not. The analysis suggests that many if not all Be stars have close companions influencing their outer disks. If confirmed to be subdwarf companions, the mass transfer spin-up scenario might explain the existence of the vast majority of classical Be stars.
Flux data are noisy, and this uncertainty is largely due to random measurement error. Knowledge of uncertainty is essential for the statistical evaluation of modeled and measured fluxes, for ...comparison of parameters derived by fitting models to measured fluxes and in formal data-assimilation efforts. We used the difference between simultaneous measurements from two towers located less than 1 km apart to quantify the distributional characteristics of the measurement error in fluxes of carbon dioxide (CO2) and sensible and latent heat (H and LE, respectively). Flux measurement error more closely follows a double exponential than a normal distribution. The CO2 flux uncertainty is negatively correlated with mean wind speed, whereas uncertainty in H and LE is positively correlated with net radiation flux. Measurements from a single tower made 24 h apart under similar environmental conditions can also be used to characterize flux uncertainty. Uncertainty calculated by this method is somewhat higher than that derived from the two-tower approach. We demonstrate the use of flux uncertainty in maximum likelihood parameter estimates for simple physiological models of daytime net carbon exchange. We show that inferred model parameters are highly correlated, and that hypothesis testing is therefore possible only when the joint distribution of the model parameters is taken into account.
Digital repeat photography is becoming widely used for near-surface remote sensing of vegetation. Canopy greenness, which has been used extensively for phenological applications, can be readily ...quantified from camera images. Important questions remain, however, as to whether the observed changes in canopy greenness are directly related to changes in leaf-level traits, changes in canopy structure, or some combination thereof.
We investigated relationships between canopy greenness and various metrics of canopy structure and function, using five years (2008-2012) of automated digital imagery, ground observations of phenological transitions, leaf area index (LAI) measurements, and eddy covariance estimates of gross ecosystem photosynthesis from the Harvard Forest, a temperate deciduous forest in the northeastern United States. Additionally, we sampled canopy sunlit leaves on a weekly basis throughout the growing season of 2011. We measured physiological and morphological traits including leaf size, mass (wet/dry), nitrogen content, chlorophyll fluorescence, and spectral reflectance and characterized individual leaf color with flatbed scanner imagery.
Our results show that observed spring and autumn phenological transition dates are well captured by information extracted from digital repeat photography. However, spring development of both LAI and the measured physiological and morphological traits are shown to lag behind spring increases in canopy greenness, which rises very quickly to its maximum value before leaves are even half their final size. Based on the hypothesis that changes in canopy greenness represent the aggregate effect of changes in both leaf-level properties (specifically, leaf color) and changes in canopy structure (specifically, LAI), we developed a two end-member mixing model. With just a single free parameter, the model was able to reproduce the observed seasonal trajectory of canopy greenness. This analysis shows that canopy greenness is relatively insensitive to changes in LAI at high LAI levels, which we further demonstrate by assessing the impact of an ice storm on both LAI and canopy greenness.
Our study provides new insights into the mechanisms driving seasonal changes in canopy greenness retrieved from digital camera imagery. The nonlinear relationship between canopy greenness and canopy LAI has important implications both for phenological research applications and for assessing responses of vegetation to disturbances.
Premature wind turbine gearbox bearing failures in the form of white structure flaking (WSF) can occur in as little as 6–24 months of operation. WSF is not fully understood but is thought to be due ...to hydrogen release and diffusion into the bearing steel and/or transient operating conditions not fully understood. The initiation mechanisms of white etching cracks (WECs) are contested, where amongst others mechanisms, subsurface initiation at non-metallic inclusions (perhaps associated with extension of butterfly cracks) and surface crack initiation are cited. For the first time this study applies serial sectioning to map WEC networks in wind turbine gearbox bearings to elucidate WEC initiation mechanisms. A comparison is made between WEC data for inner rings of an industrial transient test gearbox bearing and a planet bearing that spalled in service. It is proposed that one mechanism of WEC formation in wind turbine gearbox bearings is due to subsurface WEC initiation from inclusions, either in a butterfly manner or non-butterfly manner; where these small WECs link together to form larger WEC networks, these eventually propagating to the surface resulting in WSF. Small size/length inclusions were found to be likely WEC initiators, therefore the data suggests that steel cleanliness standards analysing inclusion density (as opposed to maximum inclusion lengths) are more relevant in understanding butterfly/WEC initiation in wind turbine gearbox bearings. However standards used should be able to differentiate pure sulfides from sulfides+oxide encapsulations and record inclusions that are only a couple of mircometer’s in length/diameter.
Aim: The complex palaeogeography of the Malesian archipelago, characterized by the evolution of an ever-changing mosaic of terrestrial and marine areas throughout the Cenozoic, provides the ...geographic backdrop for the remarkable diversification of Malesian Begonia (> 450 species). This study aimed to investigate the origin of Malesian Begonia, the directionality of dispersal events within the Malesian archipelago and the impact of ancient water gaps on colonization patterns, and to identify drivers of diversification. Location: Asia, Southeast Asia, Malesia. Methods: Plastid DNA sequence data of representatives of all families of the Cucurbitales and Fagales (matK, rbcL, trnL intron, trnL-F spacer, 4076 aligned positions, 92 taxa) and a sample of all major Asian Begonia sections (ndhA intron, ndhF -rpl32 spacer, rpl32-trnL spacer, 4059 aligned positions, 112 taxa) were analysed under an uncorrelated-rates relaxed molecular clock model to estimate the age of the Begonia crown group divergence and divergence ages within Asian Begonia. Ancestral areas were reconstructed using a likelihood approach implementing a dispersal-extinction-cladogenesis model, and with a Bayesian approach to dispersal-vicariance analysis. Results: The results indicated an initial diversification of Asian Begonia in continental Asia in the Miocene, and subsequent colonization of Malesia by multiple lineages. There was support for at least six independent dispersal events from continental Asia and western Malesia to Wallacea dating from the late Miocene to the Pleistocene. Begonia section Petermannia (> 270 species) originated in Western Malesia, and subsequently dispersed to Wallacea, New Guinea and the Philippines. Lineages within this section diversified rapidly since the Pliocene, coinciding with rapid orogenesis on Sulawesi and New Guinea. Main conclusions: The predominant trend of Begonia dispersals between continental Asia and Malesia, and also within Malesia, has been from west to east. The water bodies separating the Sunda Shelf region from Wallacea have been porous barriers to dispersal in Begonia following the emergence of substantial land in eastern Malesia from the late Miocene onwards. We hypothesize two major drivers of the diversification of Malesian Begonia: (1) the formation of topographical heterogeneity and the promotion of microallopatry by orogenesis in the Pliocene and Pleistocene; and (2) cyclic vicariance by frequent habitat fragmentations and amalgamations due to climate and sea-level fluctuations during the Pleistocene.
The liquid-crystal dimer 1'',7''-bis(4-cyanobiphenyl-4'-yl)heptane (CB7CB) exhibits two liquid-crystalline mesophases on cooling from the isotropic phase. The high-temperature phase is nematic; the ...identification and characterization of the other liquid-crystal phase is reported in this paper. It is concluded that the low-temperature mesophase of CB7CB is a new type of uniaxial nematic phase having a nonuniform director distribution composed of twist-bend deformations. The techniques of small-angle x-ray scattering, modulated differential scanning calorimetry, and dielectric spectroscopy have been applied to establish the nature of the nematic-nematic phase transition and the structural features of the twist-bend nematic phase. In addition, magnetic resonance studies (electron-spin resonance and (2)H nuclear magnetic resonance) have been used to investigate the orientational order and director distribution in the liquid-crystalline phases of CB7CB. The synthesis of a specifically deuterated sample of CB7CB is reported, and measurements showed a bifurcation of the quadrupolar splitting on entering the low-temperature mesophase from the high-temperature nematic phase. This splitting could be interpreted in terms of the chirality of the twist-bend structure of the director. Calculations using an atomistic model and the surface interaction potential with Monte Carlo sampling have been carried out to determine the conformational distribution and predict dielectric and elastic properties in the nematic phase. The former are in agreement with experimental measurements, while the latter are consistent with the formation of a twist-bend nematic phase.
Abstract Background Analyses of phase III trials showed that denosumab was superior to zoledronic acid (ZA) in preventing skeletal-related events (SREs) irrespective of age, history of SREs, or ...baseline pain status. This analysis assessed the risk of SREs across additional baseline characteristics. Patients and Methods Patients (N = 5543) from three phase III trials who had breast cancer, prostate cancer, or other solid tumours and one or more bone metastasis were included. Superiority of denosumab versus ZA in reducing risk of first SRE and first and subsequent SREs was assessed in subgroups defined by the Eastern Cooperative Oncology Group performance status (ECOG PS), bone metastasis location, bone metastasis number, visceral metastasis presence/absence, and urinary N-telopeptide (uNTx) level using Cox proportional hazards and Anderson–Gill models. Subgroups except bone metastasis location were also assessed for each solid tumour type. Results Compared with ZA, denosumab significantly reduced the risk of first SRE across all subgroups (hazard ratio HR ranges: ECOG PS, 0.79–0.84; bone metastasis location, 0.78–0.83; bone metastasis number, 0.78–0.84; visceral metastasis presence/absence, 0.80–0.82; uNTx level, 0.73–0.86) and reduced the risk of first and subsequent SREs in all subgroups (HR ranges: ECOG PS, 0.76–0.83; bone metastasis location, 0.78–0.84; bone metastasis number, 0.79–0.81; visceral metastasis presence/absence, 0.79–0.81; uNTx level, 0.74–0.83). Similar results were observed in subgroups across tumour types. Conclusion Denosumab was superior to ZA in preventing SREs in patients with bone metastases from advanced cancer, regardless of ECOG PS, bone metastasis number, baseline visceral metastasis presence/absence, and uNTx level.
Gross primary productivity (GPP) is the largest and most variable component of the global terrestrial carbon cycle. Repeatable and accurate monitoring of terrestrial GPP is therefore critical for ...quantifying dynamics in regional-to-global carbon budgets. Remote sensing provides high frequency observations of terrestrial ecosystems and is widely used to monitor and model spatiotemporal variability in ecosystem properties and processes that affect terrestrial GPP. We used data from the Moderate Resolution Imaging Spectroradiometer (MODIS) and FLUXNET to assess how well four metrics derived from remotely sensed vegetation indices (hereafter referred to as proxies) and six remote sensing-based models capture spatial and temporal variations in annual GPP. Specifically, we used the FLUXNET La Thuile data set, which includes several times more sites (144) and site years (422) than previous studies have used. Our results show that remotely sensed proxies and modeled GPP are able to capture significant spatial variation in mean annual GPP in every biome except croplands, but that the percentage of explained variance differed substantially across biomes (10-80%). The ability of remotely sensed proxies and models to explain interannual variability in GPP was even more limited. Remotely sensed proxies explained 40-60% of interannual variance in annual GPP in moisture-limited biomes, including grasslands and shrublands. However, none of the models or remotely sensed proxies explained statistically significant amounts of interannual variation in GPP in croplands, evergreen needleleaf forests, or deciduous broadleaf forests. Robust and repeatable characterization of spatiotemporal variability in carbon budgets is critically important and the carbon cycle science community is increasingly relying on remotely sensing data. Our analyses highlight the power of remote sensing-based models, but also provide bounds on the uncertainties associated with these models. Uncertainty in flux tower GPP, and difference between the footprints of MODIS pixels and flux tower measurements are acknowledged as unresolved challenges.
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