Cloud-Radiation Interactions and their contributions to Convective Self-Aggregation

<p>Numerical models configured in radiative convective equilibrium (RCE) have shown that convection can self-aggregate, where initially randomly distributed convection becomes clustered despite homogeneous initial conditions and forcing. The degree of self-aggregation within a domain has important consequences for weather and climate, and varies considerably between models. Previous studies have shown that interactions between clouds and radiation are crucial drivers and maintainers of aggregation. This study investigates the direct radiative-convective feedbacks that are important to self-aggregation within elongated channel simulations of the UK Met Office Unified Model (UM) version 11.0. Our simulations are configured using three fixed sea surface temperatures (SSTs) following the radiative-convective equilibrium model intercomparison project (RCEMIP) protocol.</p><p>Our analysis builds on the vertically-integrated frozen moist static energy (FMSE) variance budget framework that assumes that aggregation increases as FMSE variance increases. The budget shows how interactions between FMSE and radiation, surface fluxes and advection contribute to increasing FMSE variance. This variance is highly sensitive to SST, however, by normalising FMSE between theoretical upper and lower limits based on SST, this sensitivity can be eliminated. This allows the variance of normalised FMSE to be a consistent aggregation metric across all SSTs. By deriving a new budget equation for normalised FMSE, we can see which interactions are important for aggregation and how these interactions are sensitive to SST. By defining cloud types based on the vertical distribution of condensed water, we study the importance of radiative interactions with each cloud type to aggregation, and how they change with SST.</p><p>We find that our simulations reach similar degrees of aggregation, despite the contributions of shortwave and longwave interactions decreasing with SST. Surface flux and advective feedbacks with FMSE become less negative with SST, accounting for the decreasing radiative feedback contribution. Longwave interactions with high-topped clouds are the main drivers and maintainers of aggregation, with their influence decreasing with SST as high clouds become less abundant. Longwave interactions in clear regions have significant positive effects in driving aggregation, however their contributions decrease once the convection becomes aggregated. Their longwave contributions to aggregation decrease with SST and can become negative at high SSTs once convection is aggregated. The shortwave interactions with water vapour are one of the key maintainers of aggregation, becoming more important as aggregation increases. Shortwave interactions are more important at cooler SSTs where there is a greater contrast in shortwave heating between moist and dry regions.</p><p>Results presented here are not necessarily representative of real world convection, these are merely results of this model configuration. Applying this technique to other models may highlight key differences in their cloud-radiative feedbacks and may help to explain differences in the degree of aggregation within numerical models.  </p>

Sharing Species Pages in the Atlas of Living Costa Rica using Plinian Core

The Atlas of Living Costa Rica (www.crbio.cr) is a biodiversity data portal based on the Atlas of Living Australia (ALA) and managed by the Biodiversity Informatics Research Center (CRBio) and the National Biodiversity Institute of Costa Rica (INBio). It currently shares nearly eight million occurrence records and more than 5000 species pages about Costa Rican vertebrates, arthropods, molluscs, nematodes, plants, and fungi. These pages contain information elements pertaining to, for instance, morphological descriptions, distribution, habitat, conservation status, management, nomenclature, and multimedia (Vargas et al. 2018). In order to fully integrate species pages into the ALA architecture, CRBio is working in the adoption of the Biodiversity Information Explorer (BIE), an ALA module which manages taxonomic and species contents by integrating global resources like EOL or Wikipedia. This adoption includes the required modifications to use the data model of the Plinian Core (https://github.com/tdwg/PlinianCore), a TDWG draft standard registered as an IPT extension, oriented to share species level information from local and regional sources too (Pando 2018). The advancement of Plinian Core has been lead by INBio, the Spanish Node of GBIF (GBIF Spain), the University of Granada (UG, Spain), the Alexander von Humboldt Institute (IAvH, Colombia), the National Commission for the Knowledge and Use of Biodiversity (Conabio, Mexico) and the University of Sao Paulo (USP, Brazil). This group reviewed the existing data standards to reuse as many elements as possible and avoid redundancy. Besides the aforementioned, Plinian Core is currently used by other institutions like the Chilean Ministry of Environment. Plinian Core was designed to be easy to use, self-contained, able to support data integration from multiple databases, and having the ability to handle different levels of granularity. These requirements are the result of actual needs from content creators that, through an iterative process, have yielded a more complete and flexible exchange standard to aggregate biological and non-biological species information, used by others like IBIN, the Indian Bioresource Information Network (Saran et al. 2018). Plinian Core aims to be a component in producing multiple species catalogues developed under specific constraints to serve specific purposes, instead of focusing on a unified platform while facilitating consistent aggregation and re-utilization of information (GBIF.org 2015). We will present our implementation of the BIE module in the Atlas of Living Costa Rica, following the documented best practices when sharing species level information using Plinian Core. Our demonstration will detail our lessons learned from merging the aforementioned 5000 species pages provided by INBio with several thousand of species pages assembled from the information provided by the World Flora Online through the aggregation of different Flora resources, like Manual de Plantas de Costa Rica (Hammel et al. 2003) that provides 5,000 plants descriptions and 350 vernacular names (http://www.worldfloraonline.org/resource?query=Manual+de+Plantas+de+Costa+Rica).

High resolution single-cell chromatin 3D modeling reveals coherent chromatin aggregation with varied structures in controlling genome function stability

The genome 3D architecture is thought to be related to regulating gene expression levels in cells and can be explained by genome-wide chromatin interactions which have been explored by chromosome conformation capture based techniques, especially Hi-C. Based on single-cell Hi-C data, we developed a new method in constructing experimental consistent 3D intact genome structures for individual cells with a resolution of 10kb or higher. The modeled structures showed marked variations of 3D genome organization across different cells. However, chromosome loci marked by different proteins, such as CTCF and post-translationally modified histones, are consistently non-specifically aggregated in space. Interestingly, similar aggregations between active enhancers and active promoters were observed, especially for those separated by genomic regions of the scale of megabase or larger. Such long-range associations between active enhancers and promoters are strongly correlated with spatial aggregation of chromosome loci marked by different proteins. Through analyzing the 3D structures of intact genome, we proposed that coherent gene activation profiles among individual cells can be achieved by the consistent aggregation of protein marked loci instead of maintaining identical folded conformations.

A mix-and-click method to measure amyloid-β concentration with sub-micromolar sensitivity

Aggregation of amyloid-β (Aβ) protein plays a central role in Alzheimer's disease. Because protein aggregation is a concentration-dependent process, rigorous investigations require accurate concentration measurements. Owing to the high aggregation propensity of Aβ protein, working solutions of Aβ are typically in the low micromolar range. Therefore, an ideal Aβ quantification method requires high sensitivity without sacrificing speed and accuracy. Absorbance at 280 nm is frequently used to measure Aβ concentration, but the sensitivity is low with only one tyrosine and no tryptophan residues in the Aβ sequence. Here we present a fluorescence method for Aβ quantification using fluorescamine, which gives high fluorescence upon reaction with primary amines. We show that, using hen egg white lysozyme as a standard, fluorescence correlates linearly with primary amine concentration across a wide range of fluorescamine concentrations, from 62.5 to 1000 µM. The maximal sensitivity of detection is achieved at a fluorescamine concentration of 250 µM or higher. The fluorescamine method is compatible with the presence of dimethyl sulfoxide, which is commonly used in the preparation of Aβ oligomers, and limits the use of absorbance at 280 nm due to its high background reading. Using aggregation kinetics, we show that the fluorescamine method gives accurate concentration measurements at low micromolar range and leads to highly consistent aggregation data. We recommend the fluorescamine assay to be used for routine and on-the-fly concentration determination in Aβ oligomerization and fibrillization experiments.

Logic-based aggregation methods for ranking student applicants

In this paper, we present logic-based aggregation models used for ranking student applicants and we compare them with a number of existing aggregation methods, each more complex than the previous one. The proposed models aim to include depen- dencies in the data using Logical aggregation (LA). LA is a aggregation method based on interpolative Boolean algebra (IBA), a consistent multi-valued realization of Boolean algebra. This technique is used for a Boolean consistent aggregation of attributes that are logically dependent. The comparison is performed in the case of student applicants for master programs at the University of Belgrade. We have shown that LA has some advantages over other presented aggregation methods. The software realization of all applied aggregation methods is also provided. This paper may be of interest not only for student ranking, but also for similar problems of ranking people e.g. employees, team members, etc.