Genus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose ...an approach to demarcate genera that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type- and non-type species. More than 3,500 genomes representing type strains of species from >850 genera of either bacterial or archaeal lineages were tested. Over 140 genera were analyzed in detail within the taxonomic context of order/family. Significant genomic differences between members of a genus and type species of other genera in the same order/family were conserved in 94% of the cases. Nearly 90% (92% if polyphyletic genera are excluded) of the type strains were classified in agreement with current taxonomy. The 448 type strains that need reclassification directly impact 33% of the genera analyzed in detail. The results provide a first line of evidence that the combination of genomic indices provides added resolution to effectively demarcate genera within the taxonomic framework that is currently based on the 16S rRNA gene. We also identify the emergence of natural breakpoints at the genome level that can further help in the circumscription of taxa, increasing the proportion of directly impacted genera to at least 43% and pointing at inaccuracies on the use of the 16S rRNA gene as a taxonomic marker, despite its precision. Altogether, these results suggest that genomic coherence is an emergent property of genera in
and
In recent decades, the taxonomy of
and
, and therefore genus designation, has been largely based on the use of a single ribosomal gene, the 16S rRNA gene, as a taxonomic marker. We propose an approach to delineate genera that excludes the direct use of the 16S rRNA gene and focuses on a standard genome relatedness index, the average nucleotide identity. Our findings are of importance to the microbiology community because the emergent properties of
and
that are identified in this study will help assign genera with higher taxonomic resolution.
Abstract
Nuclear charge radii globally scale with atomic mass number
A
as
A
1∕3
, and isotopes with an odd number of neutrons are usually slightly smaller in size than their even-neutron neighbours. ...This odd–even staggering, ubiquitous throughout the nuclear landscape
1
, varies with the number of protons and neutrons, and poses a substantial challenge for nuclear theory
2–4
. Here, we report measurements of the charge radii of short-lived copper isotopes up to the very exotic
78
Cu (with proton number
Z
= 29 and neutron number
N
= 49), produced at only 20 ions s
–1
, using the collinear resonance ionization spectroscopy method at the Isotope Mass Separator On-Line Device facility (ISOLDE) at CERN. We observe an unexpected reduction in the odd–even staggering for isotopes approaching the
N
= 50 shell gap. To describe the data, we applied models based on nuclear density functional theory
5,6
and
A
-body valence-space in-medium similarity renormalization group theory
7,8
. Through these comparisons, we demonstrate a relation between the global behaviour of charge radii and the saturation density of nuclear matter, and show that the local charge radii variations, which reflect the many-body polarization effects, naturally emerge from
A
-body calculations fitted to properties of
A
≤ 4 nuclei.
Defining mechanisms that generate intratumour heterogeneity and branched evolution may inspire novel therapeutic approaches to limit tumour diversity and adaptation. SETD2 (Su(var), Enhancer of ...zeste, Trithorax-domain containing 2) trimethylates histone-3 lysine-36 (H3K36me3) at sites of active transcription and is mutated in diverse tumour types, including clear cell renal carcinomas (ccRCCs). Distinct SETD2 mutations have been identified in spatially separated regions in ccRCC, indicative of intratumour heterogeneity. In this study, we have addressed the consequences of SETD2 loss-of-function through an integrated bioinformatics and functional genomics approach. We find that bi-allelic SETD2 aberrations are not associated with microsatellite instability in ccRCC. SETD2 depletion in ccRCC cells revealed aberrant and reduced nucleosome compaction and chromatin association of the key replication proteins minichromosome maintenance complex component (MCM7) and DNA polymerase δ hindering replication fork progression, and failure to load lens epithelium-derived growth factor and the Rad51 homologous recombination repair factor at DNA breaks. Consistent with these data, we observe chromosomal breakpoint locations are biased away from H3K36me3 sites in SETD2 wild-type ccRCCs relative to tumours with bi-allelic SETD2 aberrations and that H3K36me3-negative ccRCCs display elevated DNA damage in vivo. These data suggest a role for SETD2 in maintaining genome integrity through nucleosome stabilization, suppression of replication stress and the coordination of DNA repair.
•A Conditional Generative Adversarial Network was trained to fill in missing fruit surface data.•The deep learning algorithm was trained using a large synthesised dataset.•The model predicted weight ...to within 5%.•The missing parts of kiwifruit surfaces were realistically reconstructed.
Non-destructive crop yield estimation is a major ambition for the development of digital horticulture systems, where the goal is to have a machine that can look at fruit on the vine/tree and estimate key performance metrics such as fruit weight, size and shape. The on-orchard partial occlusion problem is a major obstacle for the creation of such systems, where it is not possible for a single camera/scanner to capture the complete fruit surface due to its limited field of view. In this work, a deep learning approach was taken to solve this problem. Framing the issue as an image-to-image translation problem, a Conditional Generative Adversarial Network was trained to realistically reconstruct the enclosed and complete surface of kiwifruit when supplied with incomplete surface data, where the surface data was missing due to occlusion. Rather than training the deep learning algorithm with empirically collected data, an alternative approach was taken: the model was trained using a synthesised dataset, a large collection of kiwifruit shapes generated computationally via a Monte-Carlo routine. This was an attempt to generalise the approach to be applicable to other crops and other domains, and to provide substantial savings in time, labour and material costs. The trained model was later applied to a smaller population of kiwifruit empirically scanned using an infrared scanner and could predict fruit weight with a mean absolute percentage error of less than 5% and was successful in realistically reconstructing the whole enclosed surface over a range of sizes, shapes and orientations.
•Mechanistic model describing three phases of kiwifruit softening was developed.•Chilling injury evolution during cool storage was modelled.•Starch solubilisation was modelled.•The link between ...starch solubilisation, chilling injury, and softening was modelled.
Flesh softening and chilling injury related storage breakdown disorder (SBD) are the most important quality issues in the kiwifruit industry. This study was aimed at developing a mathematical model that could describe and predict evolution of storage breakdown disorder and firmness. A mechanistic modelling approach was adopted, with different concepts used to model the three phases of softening often observed in kiwifruit. The initial rapid softening phase was modelled as a function of starch breakdown, the slow softening phase was modelled as function of pectin degradation, while the final softening phase often characterised by tissue collapse, was modelled as a function of chilling injury related storage breakdown disorder. The model was calibrated using data collected from three seasons, across multiple maturity areas and subjected to different cooling and storage temperature regimes. 93 % of the total variance in the firmness data could be explained by the model. A mean absolute error of 0.2–2.2 % was obtained for SBD predictions. The developed model could be used by growers and postharvest managers to predict kiwifruit softening under different supply chain conditions.
A shape equation for Hayward Kiwifruit Olatunji, J. R.; Love, R. J.; Shim, Y. M. ...
International journal of food properties,
01/01/2019, 2019-01-00, 20190101, 2019-01-01, Letnik:
22, Številka:
1
Journal Article
Recenzirano
Odprti dostop
In this paper, a new shape equation for Hayward kiwifruit is developed. Being simple and generic, it required only the major measurable dimensions of a kiwifruit as inputs (length, major-diameter, ...and minor-diameter). The equation was validated against empirical shape data with a maximum 3.09% error. The new shape equation can estimate important metrics, such as volume, mass and surface area. Equation development was generalized, so shape equations for other crops could be produced using the same methodology. The simplicity and speed of this new method allow realistic populations of Hayward kiwifruit to be rapidly generated in a modeling environment.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
•Delays in cooling of blueberries resulted in impacting weight loss increases only.•Low O2, high CO2 atmospheres resulted in the least decay.•Low O2, high CO2 atmospheres also tended to cause reduced ...firming.•Cultivar specific optimising of O2 atmosphere to combine with high CO2 is required.•Minimising temperature variability during transport will improve delivered quality.
Southern hemisphere blueberry producers often export their products through extended supply chains to Northern hemisphere consumers. During extended storage, small variations in temperature or atmosphere concentrations may generate significant differences in final product quality. In addition, relatively short delays in establishing cool storage temperatures may contribute to quality loss. In these experiments a full factorial analysis was done of the effects of three cooling delays (0, 12 or 24h at 10°C), three atmosphere concentrations (air, 10% CO2+2.5% O2 and 10% CO2+20% O2) and two storage temperatures (0°C and 4°C) which were assessed for their impact on final quality, measured as weight loss, firmness and rot incidence. Two blueberry cultivars were studied: ‘Brigitta’, a highbush cultivar, and ‘Maru’, a rabbiteye. Delays in cooling had a small effect on final product weight, whereas variation in storage temperature and atmosphere during simulated transport influenced both firmness and rot incidence. Atmospheres with 10% CO2 reduced decay incidence, particularly at low oxygen concentration (2.5% O2), although the latter conditions tended to soften fruit. In order to achieve optimal postharvest storage for blueberries, minimising temperature variability in the supply chain is important, as is finding the potentially cultivar-specific optimal combination of high CO2 and low O2 concentration that results in simultaneously minimising rot incidence and induced softening.
In September 2006, the 7-valent pneumococcal conjugate vaccine (PCV7) was added to the UK immunization programme. We aimed to evaluate the impact of PCV7 on the incidence of all-cause ...community-acquired pneumonia (CAP) in children. A prospective survey was undertaken in 2008–2009 at 11 hospitals in North East England of children aged 0–16 years with radiologically confirmed pneumonia. Data were compared to those from a similar survey undertaken in the same hospitals in 2001–2002. A total of 542 children were enrolled, of which 74% were aged <5 years. PCV7 uptake was 90·7%. The incidence of pneumonia was 11·8/10 000 95% confidence interval (CI) 10·9–12·9, and the hospitalization rate was 9·9/10 000 (95% CI 9·0–10·9). Compared to 2001, there was a 19% (95% CI 8–29) reduction in the rate of CAP in those aged <5 years, and in those <2 years a 33·1% (95% CI 20–45) reduction in the incidence of CAP and 38·1% (95% CI 24–50) reduction in hospitalization rates. However, for those unvaccinated aged ⩾5 years, there was no difference in the incidence of CAP and hospitalization rate between both surveys. Since 2001, the overall reduction in incidence was 17·7% (95% CI 8–26) and for hospitalization 18·5% (95% CI 8–28). For the <5 years age group there was a lower incidence of CAP in PCV7-vaccinated children (25·2/10 000, 95% CI 22·6–28·2) than in those that were not vaccinated (37·4/10 000, 95% CI 29·2–47·1). In conclusion, PCV7 has reduced both incidence and rate of hospitalization of pneumonia in children, particularly in the <2 years age group.
.
The properties of the two-quasiparticle-like soft
E
1-modes and Pygmy Dipole Resonances (PDR) have been and are systematically studied with the help of inelastic and electromagnetic experiments ...which essentially probe the particle-hole components of these vibrations. It is shown that further insight in their characterisation can be achieved with the help of two-nucleon transfer reactions, in particular concerning the particle-particle components of the modes, in terms of absolute differential cross sections which take properly into account successive and simultaneous transfer mechanisms corrected for non-orthogonality, able to reproduce the experimental findings at the 10% level. The process
9
Li(
t
,
p
)
11
Li(1
-
) is discussed, and absolute cross sections predicted.
Agent-based models (ABMs) are well suited to representing the spatiotemporal spread and control of disease in a population. The explicit modelling of individuals in a large population, however, can ...be computationally intensive, especially when models are stochastic and/or spatially-explicit. Large-scale ABMs often require a highly parallel platform such as a high-performance computing cluster, which tends to confine their utility to university, defence and scientific research environments. This poses a challenge for those interested in modelling the spread of disease on a large scale with access only to modest hardware platforms.
The Australian Animal DISease (AADIS) model is a spatiotemporal ABM of livestock disease spread and control. The AADIS ABM is able to complete complex national-scale simulations of disease spread and control on a personal computer. Computational efficiency is achieved through a hybrid model architecture that embeds equation-based models inside herd agents, an asynchronous software architecture, and a grid-based spatial indexing scheme.
•A hybrid model architecture that combines equation-based and agent-based modelling.•Asynchronous software architecture featuring lightweight agents in an active concurrent environment.•Uniform grid-based spatial indexing in lieu of R-Tree-over-GiST spatial indexing.
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