A 2-set-up Routley-Meyer Semantics for the 4-valued Relevant Logic E4

The logic BN4 can be considered as the 4-valued logic of the relevant conditional and the logic E4, as the 4-valued logic of (relevant) entailment. The aim of this paper is to endow E4 with a 2-set-up Routley-Meyer semantics. It is proved that E4 is strongly sound and complete w.r.t. this semantics

Highly variable Vitis microsatellite loci for the identification of Pinot Noir clones

Nineteen new microsatellite loci of Vitis were elaborated by following the procedure of tagging an SSR-enriched library. Primers for these VRG markers were used for genotyping grapevines. Only the markers VRG 1, VRG 2, VRG 4, VRG 7, VRG 9, VRG 10, VRG 15 and VRG 16 show heterozygous alleles and Mendelian segregation. Other VRG loci such as VRG 5, VRG 6, VRG 11, VRG 12 VRG 13 and VRG 17 produce a multiallelic profile and some of them show distorted segregation. Variability of the VRG loci is rather high as compared to other grapevine SSR markers. Stable VRG markers such as VRG 16 can be useful for the identification of cultivars. Highly variable VRG microsatellites could be successfully applied to trace polymorphism within the variety Pinot Noir. Clones of Pinot Noir could be differentiated using these markers. By applying the PhyQuest program, a dendrogramm showing the genetic divergence within Pinot Noir clones was constructed.This project was funded by the Ministry of Agriculture and Forestry in Vienna. J. L. SANTIAGO is funded by a grant from Ministerio de Educación y Ciencia (Spain).Peer reviewe

iMODS: internal coordinates normal mode analysis server

Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends its applicability while implicitly maintaining stereochemistry. Vibrational analysis, motion animationś and morphing trajectories can be easily carried out at different resolution scales almost interactively. The server is versatile; non-specialists can rapidly characterize potential conformational changes, whereas advanced users can customize the model resolution with multiple coarse-grained atomic representations and elastic network potentials. iMODS supports advanced visualization capabilities for illustrating collective motions, including an improved affine-model-based arrow representation of domain dynamics. The generated all-heavy-atoms conformations can be used to introduce flexibility for more advanced modeling or sampling strategies.Human Frontier Science Program—RGP0039/2008, Ministerio de Economía y Competitividad—BFU2013-44306P and Comunidad de Madrid—CAM-S2010/BMD

RCD+: Fast Loop Modeling Server

Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop models are subsequently ranked using a fast distance-orientation dependent energy filter. Top ranked loops are refined with the Rosetta energy function to obtain accurate all-atom predictions that can be interactively inspected in an user-friendly web interface. Using standard benchmarks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 angstrom for 8 and 12 residues loops, respectively, in the challenging modeling scenario in where the side chains of the loop environment are fully remodeled. These results are not only very competitive compared to those obtained with public state of the art methods, but also they are obtained similar to 10-fold faster

Artificial cells for information processing: iris classification

[Abstract]: This paper presents a model in the Artificial Embryogene (AE) framework. The presented system tries to model the main functions of the biological cell model. The main part of this paper describes the Gene Regulatory Network (GRN) model, which has a similar processing information capacity as Boole’s Algebra. This paper also describes how to use it to perform the Iris Classification problem which is a pattern classification problem. The aim of this work is to show that the model can solve this kind of problemsInstituto de Salud Carlos III; RD07/0067/0005Instituto de Salud Carlos III; PIO52048Xunta de Galicia;PGIDIT05SIN10501PRXunta de Galicia;PGDIT 07TMT011CTThis work was partially supported by the Spanish Ministry of Education and Culture (Ref TIN2006-13274) and the European Regional Development Funds (ERDF), grant (Ref. PIO52048 and RD07/0067/0005) funded by the Carlos III Health Institute, grant (Ref. PGIDIT 05 SIN 10501PR) and (Ref. PGDIT 07TMT011CT) from the General Directorate of Research of the Xunta de Galicia and grant (File 2006/60, 2007/127 and 2007/144) from the General Directorate of Scientific and Technologic Promotion of the Galician University System of the Xunta de Galicia. Thanks to the Galician Supercomputation Center (CESGA) which has execute a great part of the tests

Thirty years of the international journal of intelligent systems: a bibliometric review

The International Journal of Intelligent Systems was created in 1986. Today, the journal is 30 years old. To celebrate this anniversary, this study develops a bibliometric review of all of the papers published in the journal between 1986 and 2015. The results are largely based on the Web of Science Core Collection, which classifies leading bibliographic material by using several indicators including total number of publications and citations, the h-index, cites per paper, and citing articles. Thework also uses theVOS viewer software for visualizing the main results through bibliographic coupling and co-citation. The results show a general overview of leading trends that have influenced the journal in terms of highly cited papers, authors, journals, universities and countries. C 2016 Wiley Periodicals, Inc

Current status of using beaks to identify cephalopods: III International Workshop and training course on Cephalopod beaks, Faial island, Azores, April 2007

The identification of cephalopods using their beaks is still a difficult technique. To increase our knowledge of this technique and stimulate a new generation of beak experts, the III International beak workshop and training course was organized in Faial, Azores Islands in 2007. We briefly review the activities of the workshop, including the identification procedure of lower beaks of cephalopods from predators with emphasis on cetaceans, seals, fish and seabirds; provision of basic knowledge to young researchers interested in the study area; identification of recent developments in beak research; and discussion of the main problematic issues. The families that need particular attention are Brachioteuthidae, Chiroteuthidae, Cranchiidae, Cycloteuthidae, Mastigoteuthidae, Octopoteuthidae, Promachoteuthidae, Onychoteuthidae (particularly the genus Walvisteuthis), Mastigoteuthidae and Cirroteuthidae. The stable isotopic signature of beaks is capable of revealing new trophic relationships and migrations. Future work should focus on: a) obtaining more cephalopod material from research cruises; b) promoting a close and continuous collaboration between beak experts and cephalopod taxonomists and; c) developing new, and updated, beak guides

Relational semantics for the 4-valued relevant logics BN4 and E4

The logic BN4 was defined by R.T. Brady in 1982. It can be considered as the 4-valued logic of the relevant conditional. E4 is a variant of BN4 that can be considered as the 4-valued logic of (relevant) entailment. The aim of this paper is to define reduced general Routley-Meyer semantics for BN4 and E4. It is proved that BN4 and E4 are strongly sound and complete w.r.t. their respective semantics

Triazolo[1,5-a]pyridyl phosphines reflecting the influence of phosphorus lone pair orientation on spectroscopic properties

A series of new triazolopyridine-based phosphines has been prepared. These compounds revealed unexpected spectroscopic patterns. In particular, the NMR spectra are highly dependent on the relative conformational preference of the phosphine substituent at C7. Here, we report on their complete NMR analysis, X-ray structures and DFT calculations that confirm the particular arrangement of the phosphorus lone pair orbital related to the substituent pattern of the chosen phosphine. © 2011 The Royal Society of Chemistry.Peer Reviewe