Clustering approaches and ensembles applied in the delineation of management classes in precision agriculture.

Abstract. This paper describes an experiment performed using different approaches for spatial data clustering, aiming to assist the delineation of management classes in Precision Agriculture (PA). These approaches were established from the partitional clustering algorithm Fuzzy c-Means (FCM), traditionally used in this context, and from the hierarchical clustering algorithm HACCSpatial, especially designed for this PA task. We also performed experiments using traditional ensembles approaches from the literature, evaluating their behavior to achieve consensus solutions from individual clusterings obtained from features splitting or running one of the abovementioned algorithms. Results showed some differences between FCM and HACC-Spatial, mainly for the visualization of management classes in the form of maps. Considering the consensus clusterings provided by ensembles, it became clear the attempt to achieve an agreement result that most closely matches the original clusterings, showing us some details that may go undetected when we analyse only the individual clusterings.Geoinfo 2016

Molecular architecture of human polycomb repressive complex 2.

Polycomb Repressive Complex 2 (PRC2) is essential for gene silencing, establishing transcriptional repression of specific genes by tri-methylating Lysine 27 of histone H3, a process mediated by cofactors such as AEBP2. In spite of its biological importance, little is known about PRC2 architecture and subunit organization. Here, we present the first three-dimensional electron microscopy structure of the human PRC2 complex bound to its cofactor AEBP2. Using a novel internal protein tagging-method, in combination with isotopic chemical cross-linking and mass spectrometry, we have localized all the PRC2 subunits and their functional domains and generated a detailed map of interactions. The position and stabilization effect of AEBP2 suggests an allosteric role of this cofactor in regulating gene silencing. Regions in PRC2 that interact with modified histone tails are localized near the methyltransferase site, suggesting a molecular mechanism for the chromatin-based regulation of PRC2 activity.DOI:http://dx.doi.org/10.7554/eLife.00005.001

Shear-Modulus Investigations of Monohydroxy Alcohols: Evidence for a Short-Chain-Polymer Rheological Response

In addition to the ubiquitous structural relaxation of viscous supercooled liquids, monohydroxy alcohols and several other hydrogen-bonded systems display a strong single-exponential electrical low-frequency absorption. So far, this so-called Debye process could be observed only using dielectric techniques. Exploiting a combination of broad-band and high-resolution rheology experiments for three isomeric octanols, unambiguous mechanical evidence for the Debye process is found. Its spectral signature is similar to the viscoelastic fingerprint of small-chain polymers, enabling us to estimate the effective molecular weight for the supramolecular structure formed by the studied monohydroxy alcohols. This finding opens the venue for the application of further non-dielectric techniques directed at unraveling the microscopic nature of the Debye process and for an understanding of this phenomenon in terms of polymer concepts.Comment: 12 pages, 4 figure

Random, blocky and alternating ordering in supramolecular polymers of chemically bidisperse monomers

As a first step to understanding the role of molecular or chemical polydispersity in self-assembly, we put forward a coarse-grained model that describes the spontaneous formation of quasi-linear polymers in solutions containing two self-assembling species. Our theoretical framework is based on a two-component self-assembled Ising model in which the bidispersity is parameterized in terms of the strengths of the binding free energies that depend on the monomer species involved in the pairing interaction. Depending upon the relative values of the binding free energies involved, different morphologies of assemblies that include both components are formed, exhibiting paramagnetic-, ferromagnetic- or anti ferromagnetic-like order,i.e., random, blocky or alternating ordering of the two components in the assemblies. Analyzing the model for the case of ferromagnetic ordering, which is of most practical interest, we find that the transition from conditions of minimal assembly to those characterized by strong polymerization can be described by a critical concentration that depends on the concentration ratio of the two species. Interestingly, the distribution of monomers in the assemblies is different from that in the original distribution, i.e., the ratio of the concentrations of the two components put into the system. The monomers with a smaller binding free energy are more abundant in short assemblies and monomers with a larger binding affinity are more abundant in longer assemblies. Under certain conditions the two components congregate into separate supramolecular polymeric species and in that sense phase separate. We find strong deviations from the expected growth law for supramolecular polymers even for modest amounts of a second component, provided it is chemically sufficiently distinct from the main one.Comment: Submitted to Macromolecules, 6 figures. arXiv admin note: substantial text overlap with arXiv:1111.176

Structural basis for HCMV Pentamer receptor recognition and antibody neutralization

Human cytomegalovirus (HCMV) represents the viral leading cause of congenital birth defects and uses the gH/ gL/UL128-130-131A complex (Pentamer) to enter different cell types, including epithelial and endothelial cells. Upon infection, Pentamer elicits the most potent neutralizing response against HCMV, representing a key vaccine candidate. Despite its relevance, the structural basis for Pentamer receptor recognition and antibody neutralization is largely unknown. Here, we determine the structures of Pentamer bound to neuropilin 2 (NRP2) and a set of potent neutralizing antibodies against HCMV. Moreover, we identify thrombomodulin (THBD) as a functional HCMV receptor and determine the structures of the Pentamer-THBD complex. Unexpectedly, both NRP2 and THBD also promote dimerization of Pentamer. Our results provide a framework for understanding HCMV receptor engagement, cell entry, antibody neutralization, and outline strategies for antiviral therapies against HCMV

Self-assembly in solution of a reversible comb-shaped supramolecular polymer

We report a single step synthesis of a polyisobutene with a bis-urea moiety in the middle of the chain. In low polarity solvents, this polymer self-assembles by hydrogen bonding to form a combshaped polymer with a central hydrogen bonded backbone and polyisobutene arms. The comb backbone can be reversibly broken, and consequently, its length can be tuned by changing the solvent, the concentration or the temperature. Moreover, we have proved that the bulkiness of the side-chains have a strong influence on both the self-assembly pattern and the length of the backbone. Finally, the density of arms can be reduced, by simply mixing with a low molar mass bis-urea

A strategy to obtain axenic cultures of Arthrospira spp. cyanobacteria

A strategy to obtain axenic cultures of the cyanobacterium Arthrospira sp. (‘platensis’) Lefevre 1963/M-132-1 strain, consisting of a series of physical and chemical procedures, and the application of an optimized pool of antibiotics, is described in this paper. This strategy, which is an inexpensive and fast way to obtain axenic cultures, can be applied to Arthrospira spp. from culture collections or samples from their natural habitats to eliminate a wide spectrum of contaminants. A high alkaline treatment (pH 12, using KOH) of 72 h is a determinant initial procedure applied to eliminate protozoa and Microcystis sp. Bacteria were eliminated by an optimal antibiotic pool treatment, and Chroococcus sp. residuals were discarded by serial dilution. Optimal concentrations of the antibiotics composing the pool were obtained by a 24 factorial central composite rotatable design (CCRD) and Response Surface Methodology (RSM), resulting in: ampicillin 61.6 μg/ml, penicillin 85.8 μg/ml, cefoxitin 76.9 μg/ml, and meropenem 38.9 μg/ml. The results also indicate that cefoxitin was the most effective antibiotic of this pool. After obtaining the axenic culture, identification of Lefevre 1963/M-132-1 strain was performed using amplification and sequencing of the ITS region (including part of 16S rRNA, tRNA Ile, ITS, tRNA Ala and part of 23S rRNA region) and fatty acid composition data. Data base comparison revealed that Lefevre strain is closely related to A. platensis species (99% identity), while fatty acid composition data suggested A. maxima. These seemingly contradictory results are discussed

Ska3 Ensures Timely Mitotic Progression by Interacting Directly With Microtubules and Ska1 Microtubule Binding Domain

The establishment of physical attachment between the kinetochore and dynamic spindle microtubules, which undergo cycles of polymerization and depolymerization generating straight and curved microtubule structures, is essential for accurate chromosome segregation. The Ndc80 and Ska complexes are the major microtubule-binding factors of the kinetochore responsible for maintaining chromosome-microtubule coupling during chromosome segregation. We previously showed that the Ska1 subunit of the Ska complex binds dynamic microtubules using multiple contact sites in a mode that allows conformation-independent binding. Here, we show that the Ska3 subunit is required to modulate the microtubule binding capability of the Ska complex (i) by directly interacting with tubulin monomers and (ii) indirectly by interacting with tubulin contacting regions of Ska1 suggesting an allosteric regulation. Perturbing either the Ska3-microtubule interaction or the Ska3-Ska1 interactions negatively influences microtubule binding by the Ska complex in vitro and affects the timely onset of anaphase in cells. Thus, Ska3 employs additional modulatory elements within the Ska complex to ensure robust kinetochore-microtubule attachments and timely progression of mitosis

Evaluation of a gelatin-based adhesive for historic paintings that incorporates citronella oil as an eco-friendly biocide

[EN] The presented study focuses on evaluating the efficiency of a gelatin-based product that incorporates a plasticizer (glycerol) and a biocide (citronella oil), proposed as an eco-friendly adhesive for polychrome decoration applied in different parts of the architectural complex of the Longshan Temple in Lukang (eighteenth century, Taiwan). Seven laboratory physico-chemical tests were performed: (a) viscosity measurement; (b) drying curves; (c) moisture content determination; (d) water vapor permeability test; (e) mechanical test; (f) adhesion test; (g) susceptibility to fungi colonization test, which provide information on the workability, water content and water barrier properties, as well as mechanical, adhesion, and the biocide properties of the proposed product. The obtained results indicate that the workability, mechanical and adhesive properties of the new adhesive are adequate. Permeability in polychromies is slightly reduced due to the additional barrier effect of the adhesive incorporated into the paint film. The efficiency of citronella oil for preventing the growth of fungus Aspergillus niger on paintings consolidated with the adhesive was also probed. In parallel to these laboratory trials, the micro-invasive tests carried out, using nanoindentation combined with atomic force microscopy (NI-AFM), provided direct evidence for the improvement in the mechanical properties induced by applying the new adhesive to the original polychromies.This work was supported by the Spanish Ministerio de Economia, Industria y Competitividad (MINECO), the Fondo Europeo de Desarrollo Regional (ERDF), and the Agencia Estatal de Investigacion (AEI).Lee, Y.; Martín Rey, S.; Osete Cortina, L.; Martín-Sánchez, I.; Domenech Carbo, MT.; Bolivar-Galiano, F. (2018). Evaluation of a gelatin-based adhesive for historic paintings that incorporates citronella oil as an eco-friendly biocide. Journal of Adhesion Science and Technology. 32(21):2320-2349. https://doi.org/10.1080/01694243.2018.1477411S23202349322