Artigos de revistas: "Combinatorial species"

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Faris, W. "Combinatorial Species and Cluster Expansions". Moscow Mathematical Journal 10, n.º 4 (2010): 713–27. http://dx.doi.org/10.17323/1609-4514-2010-10-4-713-727.

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Spivak, Aaron T., e Gary D. Stormo. "Combinatorial Cis-regulation in Saccharomyces Species". G3: Genes|Genomes|Genetics 6, n.º 3 (15 de janeiro de 2016): 653–67. http://dx.doi.org/10.1534/g3.115.024331.

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Schmitt, William R. "Hopf Algebras of Combinatorial Structures". Canadian Journal of Mathematics 45, n.º 2 (1 de abril de 1993): 412–28. http://dx.doi.org/10.4153/cjm-1993-021-5.

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AbstractA generalization of the definition of combinatorial species is given by considering functors whose domains are categories of finite sets, with various classes of relations as moronisms. Two cases in particular correspond to species for which one has notions of restriction and quotient of structures. Coalgebras and/or Hopf algebras can be associated to such species, the duals of which provide an algebraic framework for studying invariants of structures.

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Cho, Bongrae, David C. Taylor, Hugh B. Nicholas e Francis J. Schmidt. "Interacting RNA species identified by combinatorial selection". Bioorganic & Medicinal Chemistry 5, n.º 6 (junho de 1997): 1107–13. http://dx.doi.org/10.1016/s0968-0896(97)00046-1.

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Rajan, Dayanand S. "The equations DkY = Xn in combinatorial species". Discrete Mathematics 118, n.º 1-3 (agosto de 1993): 197–206. http://dx.doi.org/10.1016/0012-365x(93)90061-w.

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Maia, Manuel, e Miguel Méndez. "On the arithmetic product of combinatorial species". Discrete Mathematics 308, n.º 23 (dezembro de 2008): 5407–27. http://dx.doi.org/10.1016/j.disc.2007.09.062.

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Labelle, J., e Y. N. Yeh. "The relation between burnside rings and combinatorial species". Journal of Combinatorial Theory, Series A 50, n.º 2 (março de 1989): 269–84. http://dx.doi.org/10.1016/0097-3165(89)90019-8.

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Balasubramanian, Krishnan. "Symmetry and Combinatorial Concepts for Cyclopolyarenes, Nanotubes and 2D-Sheets: Enumerations, Isomers, Structures Spectra & Properties". Symmetry 14, n.º 1 (28 de dezembro de 2021): 34. http://dx.doi.org/10.3390/sym14010034.

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This review article highlights recent developments in symmetry, combinatorics, topology, entropy, chirality, spectroscopy and thermochemistry pertinent to 2D and 1D nanomaterials such as circumscribed-cyclopolyarenes and their heterocyclic analogs, carbon and heteronanotubes and heteronano wires, as well as tessellations of cyclopolyarenes, for example, kekulenes, septulenes and octulenes. We establish that the generalization of Sheehan’s modification of Pólya’s theorem to all irreducible representations of point groups yields robust generating functions for the enumeration of chiral, achiral, position isomers, NMR, multiple quantum NMR and ESR hyperfine patterns. We also show distance, degree and graph entropy based topological measures combined with techniques for distance degree vector sequences, edge and vertex partitions of nanomaterials yield robust and powerful techniques for thermochemistry, bond energies and spectroscopic computations of these species. We have demonstrated the existence of isentropic tessellations of kekulenes which were further studied using combinatorial, topological and spectral techniques. The combinatorial generating functions obtained not only enumerate the chiral and achiral isomers but also aid in the machine construction of various spectroscopic and ESR hyperfine patterns of the nanomaterials that were considered in this review. Combinatorial and topological tools can become an integral part of robust machine learning techniques for rapid computation of the combinatorial library of isomers and their properties of nanomaterials. Future applications to metal organic frameworks and fullerene polymers are pointed out.

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GAMBETTE, PHILIPPE, VINCENT BERRY e CHRISTOPHE PAUL. "QUARTETS AND UNROOTED PHYLOGENETIC NETWORKS". Journal of Bioinformatics and Computational Biology 10, n.º 04 (23 de julho de 2012): 1250004. http://dx.doi.org/10.1142/s0219720012500047.

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Phylogenetic networks were introduced to describe evolution in the presence of exchanges of genetic material between coexisting species or individuals. Split networks in particular were introduced as a special kind of abstract network to visualize conflicts between phylogenetic trees which may correspond to such exchanges. More recently, methods were designed to reconstruct explicit phylogenetic networks (whose vertices can be interpreted as biological events) from triplet data. In this article, we link abstract and explicit networks through their combinatorial properties, by introducing the unrooted analog of level-k networks. In particular, we give an equivalence theorem between circular split systems and unrooted level-1 networks. We also show how to adapt to quartets some existing results on triplets, in order to reconstruct unrooted level-k phylogenetic networks. These results give an interesting perspective on the combinatorics of phylogenetic networks and also raise algorithmic and combinatorial questions.

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Jansen, Sabine, Tobias Kuna e Dimitrios Tsagkarogiannis. "Lagrange Inversion and Combinatorial Species with Uncountable Color Palette". Annales Henri Poincaré 22, n.º 5 (11 de fevereiro de 2021): 1499–534. http://dx.doi.org/10.1007/s00023-020-01013-0.

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AbstractWe prove a multivariate Lagrange-Good formula for functionals of uncountably many variables and investigate its relation with inversion formulas using trees. We clarify the cancellations that take place between the two aforementioned formulas and draw connections with similar approaches in a range of applications.

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Labelle, Gilbert. "On the generalized iterates of Yeh's combinatorial K-species". Journal of Combinatorial Theory, Series A 50, n.º 2 (março de 1989): 235–58. http://dx.doi.org/10.1016/0097-3165(89)90017-4.

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Scott-Phillips, Thomas C., e Richard A. Blythe. "Why is combinatorial communication rare in the natural world, and why is language an exception to this trend?" Journal of The Royal Society Interface 10, n.º 88 (6 de novembro de 2013): 20130520. http://dx.doi.org/10.1098/rsif.2013.0520.

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In a combinatorial communication system, some signals consist of the combinations of other signals. Such systems are more efficient than equivalent, non-combinatorial systems, yet despite this they are rare in nature. Why? Previous explanations have focused on the adaptive limits of combinatorial communication, or on its purported cognitive difficulties, but neither of these explains the full distribution of combinatorial communication in the natural world. Here, we present a nonlinear dynamical model of the emergence of combinatorial communication that, unlike previous models, considers how initially non-communicative behaviour evolves to take on a communicative function. We derive three basic principles about the emergence of combinatorial communication. We hence show that the interdependence of signals and responses places significant constraints on the historical pathways by which combinatorial signals might emerge, to the extent that anything other than the most simple form of combinatorial communication is extremely unlikely. We also argue that these constraints can be bypassed if individuals have the socio-cognitive capacity to engage in ostensive communication. Humans, but probably no other species, have this ability. This may explain why language, which is massively combinatorial, is such an extreme exception to nature's general trend for non-combinatorial communication.

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Du, Meixia, Feng Li e Yanwei Hu. "A Uniform Design Method Can Optimize the Combinatorial Parameters of Antimicrobial Photodynamic Therapy, Including the Concentrations of Methylene Blue and Potassium Iodide, Light Dose, and Methylene Blue’s Incubation Time, to Improve Fungicidal Effects on Candida Species". Microorganisms 11, n.º 10 (13 de outubro de 2023): 2557. http://dx.doi.org/10.3390/microorganisms11102557.

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The optimal combinatorial parameters of antimicrobial photodynamic therapy (aPDT) mediated by methylene blue (MB) with the addition of potassium iodide (KI) against Candida species have never been defined. This study aimed to optimize the combinatorial parameters of aPDT, including the concentrations of MB (X1, 0.1–1.0 mM) and KI (X2, 100–400 mM), light dose (X3, 10–70 J/cm2), and MB’s incubation time (X4, 5–35 min) for three Candida species. The best MB + KI-aPDT fungicidal effects (Y) against Candida albicans ATCC 90028 (YCa), Candida parapsilosis ATCC 22019 (YCp), and Candida glabrata ATCC 2950 (YCg) were investigated using a uniform design method. The regression models deduced using this method were YCa = 7.126 + 1.199X1X3 − 1.742X12 + 0.206X22 − 0.361X32; YCp = 10.724 − 0.867X1 − 1.497X2 + 0.560X3 + 1.298X22; and YCg = 0.892 − 0.956X1 + 2.296X3 + 1.299X42 − 3.316X3X4. The optimal combinatorial parameters inferred from the regression equations were MB 0.1 mM, KI 400 mM, a light dose of 20 J/cm2, and a 5-minute incubation time of MB for Candida albicans; MB 0.1 mM, KI 400 mM, a light dose of 70 J/cm2, and a 5-minute incubation time of MB for Candida parapsilosis; MB 0.1 mM, KI 100 mM, a light dose of 10 J/cm2, and a 35-minute incubation time of MB for Candida glabrata. The uniform design method can optimize the combinatorial parameters of aPDT mediated by MB plus KI to obtain the best aPDT fungicidal effects on Candida species, providing a new method to optimize the combinatorial parameters of aPDT for different pathogens in the future.

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Mander, Luke. "A combinatorial approach to angiosperm pollen morphology". Proceedings of the Royal Society B: Biological Sciences 283, n.º 1843 (30 de novembro de 2016): 20162033. http://dx.doi.org/10.1098/rspb.2016.2033.

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Angiosperms (flowering plants) are strikingly diverse. This is clearly expressed in the morphology of their pollen grains, which are characterized by enormous variety in their shape and patterning. In this paper, I approach angiosperm pollen morphology from the perspective of enumerative combinatorics. This involves generating angiosperm pollen morphotypes by algorithmically combining character states and enumerating the results of these combinations. I use this approach to generate 3 643 200 pollen morphotypes, which I visualize using a parallel-coordinates plot. This represents a raw morphospace. To compare real-world and theoretical morphologies, I map the pollen of 1008 species of Neotropical angiosperms growing on Barro Colorado Island (BCI), Panama, onto this raw morphospace. This highlights that, in addition to their well-documented taxonomic diversity, Neotropical rainforests also represent an enormous reservoir of morphological diversity. Angiosperm pollen morphospace at BCI has been filled mostly by pollen morphotypes that are unique to single plant species. Repetition of pollen morphotypes among higher taxa at BCI reflects both constraint and convergence. This combinatorial approach to morphology addresses the complexity that results from large numbers of discrete character combinations and could be employed in any situation where organismal form can be captured by discrete morphological characters.

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Leger, Daniel W. "First Documentation of Combinatorial Song Syntax in a Suboscine Passerine Species". Condor 107, n.º 4 (1 de novembro de 2005): 765–74. http://dx.doi.org/10.1093/condor/107.4.765.

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AbstractBirds with songs having two or more acoustically distinct elements can arrange them either rigidly (i.e., in the same sequence) or flexibly. Flexible song syntax can be achieved either by varying the number of repetitions of elements or by combining elements in different ways. Combinatorial syntax has been documented only in the songs of oscine passerines and in one nonpasserine, but not in the suboscine passerines. Dawn and day songs of a tyrant flycatcher, the Flammulated Attila (Attila flammulatus), were recorded in Costa Rica. Flexible syntax was noted in both dawn and day song. Attilas not only varied the number of repetitions of their song elements but also combined elements in various ways. This appears to be the first reported case of combinatorial song syntax in a suboscine species.

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Farnia, Farnoush, Jean-Marc Frayret, Luc Lebel e Catherine Beaudry. "Agent-based simulation of multiple-round timber combinatorial auction". Canadian Journal of Forest Research 47, n.º 1 (janeiro de 2017): 1–9. http://dx.doi.org/10.1139/cjfr-2015-0125.

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This paper presents a simulation-based analysis of a multiple-round timber combinatorial auction in the timber industry. Currently, most timber auctions are single-unit auctions (i.e., each forest stand is sold separately). However, other types of auctions could be applied to take advantage of the various needs of the bidders with respect to species, volumes, and quality. This study aims to analyze the use of combinatorial auction to this specific context using a simulation approach. Various number of auctions per year, periodicity, lot size, and number of bidders are considered as parameters to set up the different market configurations. The outcomes of both combinatorial auction and single-unit auction are compared with respect to different setup configurations. This analysis shows that combinatorial auction can bring more profit for both seller and buyer when the market is less competitive.

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Leger, Daniel W. "FIRST DOCUMENTATION OF COMBINATORIAL SONG SYNTAX IN A SUBOSCINE PASSERINE SPECIES". Condor 107, n.º 4 (2005): 765. http://dx.doi.org/10.1650/7851.1.

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Steglich-Petersen, Asbjørn, e Mattias Skipper. "An Instrumentalist Account of How to Weigh Epistemic and Practical Reasons for Belief". Mind 129, n.º 516 (1 de outubro de 2019): 1071–94. http://dx.doi.org/10.1093/mind/fzz062.

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Abstract When one has both epistemic and practical reasons for or against some belief, how do these reasons combine into an all-things-considered reason for or against that belief? The question might seem to presuppose the existence of practical reasons for belief. But we can rid the question of this presupposition. Once we do, a highly general ‘Combinatorial Problem’ emerges. The problem has been thought to be intractable due to certain differences in the combinatorial properties of epistemic and practical reasons. Here we bring good news: if we accept an independently motivated version of epistemic instrumentalism—the view that epistemic reasons are a species of instrumental reasons—we can reduce The Combinatorial Problem to the relatively benign problem of how to weigh different instrumental reasons against each other. As an added benefit, the instrumentalist account can explain the apparent intractability of The Combinatorial Problem in terms of a common tendency to think and talk about epistemic reasons in an elliptical manner.

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Bolshoy, Alexander, e Tatiana Tatarinova. "Methods of Combinatorial Optimization to Reveal Factors Affecting Gene Length". Bioinformatics and Biology Insights 6 (janeiro de 2012): BBI.S10525. http://dx.doi.org/10.4137/bbi.s10525.

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In this paper we present a novel method for genome ranking according to gene lengths. The main outcomes described in this paper are the following: the formulation of the genome ranking problem, presentation of relevant approaches to solve it, and the demonstration of preliminary results from prokaryotic genomes ordering. Using a subset of prokaryotic genomes, we attempted to uncover factors affecting gene length. We have demonstrated that hyperthermophilic species have shorter genes as compared with mesophilic organisms, which probably means that environmental factors affect gene length. Moreover, these preliminary results show that environmental factors group together in ranking evolutionary distant species.

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Jaillard, Benoît, Philippe Deleporte, Michel Loreau e Cyrille Violle. "A combinatorial analysis using observational data identifies species that govern ecosystem functioning". PLOS ONE 13, n.º 8 (1 de agosto de 2018): e0201135. http://dx.doi.org/10.1371/journal.pone.0201135.

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Caves, Eleanor M., Tanmay Dixit, John F. R. Colebrook-Robjent, Lazaro Hamusikili, Martin Stevens, Rose Thorogood e Claire N. Spottiswoode. "Hosts elevate either within-clutch consistency or between-clutch distinctiveness of egg phenotypes in defence against brood parasites". Proceedings of the Royal Society B: Biological Sciences 288, n.º 1953 (23 de junho de 2021): 20210326. http://dx.doi.org/10.1098/rspb.2021.0326.

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In host–parasite arms races, hosts can evolve signatures of identity to enhance the detection of parasite mimics. In theory, signatures are most effective when within-individual variation is low (‘consistency’), and between-individual variation is high (‘distinctiveness’). However, empirical support for positive covariation in signature consistency and distinctiveness across species is mixed. Here, we attempt to resolve this puzzle by partitioning distinctiveness according to how it is achieved: (i) greater variation within each trait, contributing to elevated ‘ absolute distinctiveness’ or (ii) combining phenotypic traits in unpredictable combinations (‘ combinatorial distinctiveness’). We tested how consistency covaries with each type of distinctiveness by measuring variation in egg colour and pattern in two African bird families (Cisticolidae and Ploceidae) that experience mimetic brood parasitism. Contrary to predictions, parasitized species, but not unparasitized species, exhibited a negative relationship between consistency and combinatorial distinctiveness. Moreover, regardless of parasitism status, consistency was negatively correlated with absolute distinctiveness across species. Together, these results suggest that (i) selection from parasites acts on how traits combine rather than absolute variation in traits, (ii) consistency and distinctiveness are alternative rather than complementary elements of signatures and (iii) mechanistic constraints may explain the negative relationship between consistency and absolute distinctiveness across species.

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Veggiani, Gianluca, Jessica Zuin, Luca Beneduce, Andrea Gallotta, Paolo Pengo e Giorgio Fassina. "Combinatorial Semisynthesis of Biomarker-IgM Complexes". Journal of Biomolecular Screening 15, n.º 10 (11 de outubro de 2010): 1274–80. http://dx.doi.org/10.1177/1087057110378623.

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Circulating immune complexes formed by tumor antigens and immunoglobulin M (IgM) represent a novel class of biomarkers with diagnostic value for early cancer detection. The quantitative analysis of these immune complexes is achieved by enzyme-linked immunosorbent assay (ELISA) methods using a purified calibrator from samples of patients with cancer. These complexes obtained from samples of human origin are not suitable for cost-effective production processes with high safety standards. Given the ill-defined biomarker/IgM ratio in these complexes, semisynthesis with retention of functional properties is difficult to achieve and may vary widely according to the batch-to-batch heterogeneity of starting biological preparations. Here the authors describe the development of a combinatorial method for defining the optimal reaction conditions for the reproducible semisynthesis of biomarker-IgM complexes by exploiting the biotin-avidin technology. The method relies on screening by ELISA the 3D composition space defined by the combinatorial variation of biotinylated-biomarker, biotinylated-IgM, and avidin concentrations aiming to select those conditions leading to biomarker-IgM complexes with the highest immunoreactivity. The method allows the reproducible synthesis of species with immunoreactivity comparable to that of natural immune complexes and endowed with sufficient stability to be used as calibrators in ELISA.

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Vasilyeva, L. N. "The hierarchy and combinatorial space of characters in evolutionary systematics". Species and speciation. Analysis of new views and trends 313, Supplement 1 (25 de julho de 2009): 235–49. http://dx.doi.org/10.31610/trudyzin/2009.supl.1.235.

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In this paper, the Linnaean hierarchy is discussed as the taxonomic model for the evolutionary differentiation of the earth’s biota. This model allows us to understand why a number of ideas and arguments in the evolutionary theory are unfortunate. Among these is the idea of a linear ladder of nature («scala natura»). The arguments about species constancy versus species variability, natural species versus «artificial» higher taxa, a single type of animals versus multiple types, as well as about the connection versus disconnection of microevolution and macroevolution are meaningless. Two kinds of phylogeny are considered. The first reflects the appearance of new characters in the course of evolution, and their sequence provides the nesting hierarchy of groups. The second reflects the appearance of new character states and provides a basis for the diversity of taxa at each hierarchical level. The taxonomic hierarchy is an embodiment of the first kind of phylogeny and does not require the tracing of ancestors and descendants along the lines of character development. Character ranking and the improvement of a tentative taxonomic hierarchy with the help of a posteriori weighting of differences are discussed. The method of character weighting leads to the construction of prognostic combinatorial arrangements that can predict the existence of organisms with certain character state combinations at each hierarchical level. The drawbacks of cladistic methodology, especially the «synapomorphy principle», the «dichotomy principle», and the monophyly «definition» through the internal composition of groups, are noted. It is pointed out that these principles only lead to the creation of heterogeneous groups and wrong character ranking.

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Demongeot, Jacques, Jules Waku e and Olivier Cohen. "Combinatorial and frequency properties of the ribosome ancestors". Mathematical Biosciences and Engineering 21, n.º 1 (2023): 884–902. http://dx.doi.org/10.3934/mbe.2024037.

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<abstract> <sec><title>Background</title> The current ribosome has evolved from the primitive stages of life on Earth. Its function is to build proteins and on the basis of this role, we are looking for a universal common ancestor to the ribosome which could: i) present optimal combinatorial properties, and ii) have left vestiges in the current molecules composing the ribosome (rRNA or r-proteins) or helping in its construction and functioning. </sec> <sec><title>Methods</title> Genomic public databases are used for finding the nucleotide sequences of rRNAs and mRNA of r-proteins and statistical calculations are performed on the occurrence in these genes of some pentamers belonging to the RNA proposed as optimal ribosome ancestor. </sec> <sec><title>Results</title> After having exhibited a possible solution to the problem of an RNA capable of catalyzing peptide genesis, traces of this RNA are found in many rRNAs and mRNA of r-proteins, as well as in factors contributing to the construction of the current ribosome. </sec> <sec><title>Conclusions</title> The existence of an optimal primordial RNA whose function is to facilitate the creation of peptide bonds between amino acids may have contributed to accelerate the emergence of the first vital processes. Its traces should be found in many living species inside structures structurally and functionally close to the ribosome, which is already the case in the species studied in this article.</sec> </abstract>

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Wilson, Benjamin, e Christopher I. Petkov. "From evolutionarily conserved frontal regions for sequence processing to human innovations for syntax". Interaction Studies 19, n.º 1-2 (17 de setembro de 2018): 318–35. http://dx.doi.org/10.1075/is.17038.wil.

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Abstract Empirical advances have been made in understanding how human language, in its combinatorial complexity and unbounded expressivity, may have evolved from the communication systems present in our evolutionary ancestors. However, a number of cognitive processes and neurobiological mechanisms that support language may not have evolved specifically for communication, but rather from abilities that support perception and cognition more generally. We review recent evidence from comparative behavioural and neurobiological studies on structured sequence learning in human and nonhuman primates. These studies support the notion that certain sequence learning abilities are evolutionarily conserved and engage corresponding inferior frontal brain regions across the species, regions also involved in processing language in humans. Alongside the cross-species similarities is evidence for human specialisations, illuminating the likely evolutionary pathways towards language in modern humans. We argue that cognitive abilities that were in place for animals to learn combinatorial relationships in the sensory world were available and co-opted for language in humans.

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Singh, Roshan Kumar, Sandeep Satapathy, Chanchal Kumar e Kirti. "The Complex Triad of Combinatorial Anticancer Therapy: Curcumin, p53, and Reactive Oxygen Species". Clinical Medicine Insights: Therapeutics 7 (janeiro de 2015): CMT.S33407. http://dx.doi.org/10.4137/cmt.s33407.

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Cancer therapies based on single target molecules have proved to be ineffective both in terms of their desired action and associated undesired side effects. Combinatorial cancer therapies involve selection of different components with targeted effects, which can lead to a synergistic effect for anticancer therapy. Curcumin induces the expression of p53 and downregulates that of Mdm2, ultimately resulting in induction of apoptosis. Subsequently, there is an elevated expression of p53-induced genes, which activate reactive oxygen species (ROS) thereby establishing cellular communication and disposition of any aberrant cell by growth arrest or apoptotic cell death. As a whole, the triad of curcumin, p53, and ROS presents a unique and promising solution to the designing of modern and patient-specific cancer therapeutics.

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Springer, Stevan A., Gary W. Moy, Daniel S. Friend, Willie J. Swanson e Victor D. Vacquier. "Oyster sperm bindin is a combinatorial fucose lectin with remarkable intra-species diversity". International Journal of Developmental Biology 52, n.º 5-6 (2008): 759–68. http://dx.doi.org/10.1387/ijdb.082581ss.

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Jaillard, Benoît, Philippe Deleporte, Michel Loreau e Cyrille Violle. "Correction: A combinatorial analysis using observational data identifies species that govern ecosystem functioning". PLOS ONE 13, n.º 9 (5 de setembro de 2018): e0203681. http://dx.doi.org/10.1371/journal.pone.0203681.

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Gutman, Ivan, Izudin Redžepović e Veerabhadrappa R. Kulli. "KG-Sombor index of Kragujevac trees". Open Journal of Discrete Applied Mathematics 5, n.º 2 (30 de agosto de 2022): 19–25. http://dx.doi.org/10.30538/psrp-odam2022.0075.

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The paper is concerned with the KG-Sombor index (\(KG\)), a recently introduced vertex-and-edge-degree-based version of the Sombor index, applied to Kragujevac trees (\(Kg\)). A general combinatorial expression for \(KG(Kg)\) is established. The species with minimum and maximum \(KG(Kg)\)-values are determined.

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Gutman, Ivan, Veerabhadrappa Kulli e Izudin Redžepović. "Sombor index of Kragujevac trees". Scientific Publications of the State University of Novi Pazar Series A: Applied Mathematics, Informatics and mechanics 13, n.º 2 (2021): 61–70. http://dx.doi.org/10.5937/spsunp2102061g.

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The paper is concerned with the Sombor index (SO) of Kragujevac trees (Kg). A slightly more general definition of Kg is offered. SO is a recently introduced degree-based topological index. A general combinatorial expression for SO(Kg) is established. The species with minimum and maximum SO(Kg)-values are determined.

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Jiang, Yang, Zhaoxue Zhang, Jie Zhang, Shi Wang e Xiuguo Zhang. "Morphological and Phylogenetic Analyses Reveal Three New Species of Phyllosticta (Botryosphaeriales, Phyllostictaceae) in China". Journal of Fungi 10, n.º 1 (22 de dezembro de 2023): 7. http://dx.doi.org/10.3390/jof10010007.

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The genus Phyllosticta has been reported worldwide and contains many pathogenic and endophytic species isolated from a wide range of plant hosts. A multipoint phylogeny based on gene coding combinatorial data sets for the internal transcribed spacer (ITS), large subunit of ribosomal RNA (LSU rDNA), translation elongation factor 1α (TEF1α), actin (ACT), and glycerol-3-phosphate dehydrogenase (GPDH), combined with morphological characteristics, was performed. We describe three new species, P. fujianensis sp. nov., P. saprophytica sp. nov., and P. turpiniae sp. nov., and annotate and discusse their similarities and differences in morphological relationships and phylogenetic phases with closely related species.

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Amin, Kadji. "Taxonomically Queer?" GLQ: A Journal of Lesbian and Gay Studies 29, n.º 1 (1 de janeiro de 2023): 91–107. http://dx.doi.org/10.1215/10642684-10144435.

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Can taxonomy—a scientific method critiqued for its utility within Western imperial projects of racial and species classification—be queered? This article mines the tensions between the hostility to taxonomy within critical theory and the taxonomical renaissance within contemporary queer, trans, and asexual vernacular systems of classification. Contemporary queer uses of taxonomy express a shared utopian vision of combinatorial queerness, in which sexual, gender, and relational liberation occur through a multiplying menu of increasingly fine-grained identity options. The article examines the untimely echoes between contemporary queer classification systems and German sexologist Magnus Hirschfeld's 1910 taxonomy of “sexual intermediaries,” which forwards a combinatorially lush kaleidoscope of sexual and gendered possibilities that outflanks even contemporary developments. The goal is to simultaneously challenge the notion that sexology is contrary to queer projects and to consider the consequences of acknowledging sexology as a living inheritance of contemporary queer and trans culture. The conclusion asks how Native and racialized queers might resist the universalizing logics of taxonomy from within.

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Keuter, Philipp, Soheil Karimi Aghda, Denis Music, Pauline Kümmerl e Jochen M. Schneider. "Synthesis of Intermetallic (Mg1−x,Alx)2Ca by Combinatorial Sputtering". Materials 12, n.º 18 (18 de setembro de 2019): 3026. http://dx.doi.org/10.3390/ma12183026.

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The synthesis–composition–structure relationship in the Mg–Ca–Al system is studied using combinatorial magnetron sputtering. With increasing deposition temperature, a drastic decrease in Mg concentration is obtained. This behavior can be understood based on density functional theory calculations yielding a desorption energy of 1.9 eV/atom for Mg from a hexagonal Mg nanocluster which is far below the desorption energy of Mg from a Mg2Ca nanocluster (3.4 eV/atom) implying desorption of excess Mg during thin film growth at elevated temperatures. Correlative structural and chemical analysis of binary Mg–Ca thin films suggests the formation of hexagonal Mg2Ca (C14 Laves phase) in a wide Mg/Ca range from 1.7 to 2.2, expanding the to date reported stoichiometry range. Pronounced thermally-induced desorption of Mg is utilized to synthesize stoichiometric (Mg1−x,Alx)2Ca thin films by additional co-sputtering of elemental Al, exhibiting a higher desorption energy (6.7 eV/atom) compared to Mg (3.4 eV/atom) from Mg2Ca, which governs its preferred incorporation during synthesis. X-ray diffraction investigations along the chemical gradient suggest the formation of intermetallic C14 (Mg1–x,Alx)2Ca with a critical aluminum concentration of up to 23 at.%. The introduced synthesis strategy, based on the thermally-induced desorption of weakly bonded species, and the preferential incorporation of strongly bonded species, may also be useful for solubility studies of other phases within this ternary system as well as for other intermetallics with weakly bonded alloying constituents.

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von Reuss, Stephan H., e Frank C. Schroeder. "Combinatorial chemistry in nematodes: modular assembly of primary metabolism-derived building blocks". Natural Product Reports 32, n.º 7 (2015): 994–1006. http://dx.doi.org/10.1039/c5np00042d.

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Nematodes are amazingly skilled chemists: using simple building blocks from conserved primary metabolism and a strategy of modular assembly, C. elegans and other nematode species create complex molecular architectures to regulate their development and behaviour.

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Pardo, Michael A., Joyce H. Poole, Angela S. Stoeger, Peter H. Wrege, Caitlin E. O’Connell-Rodwell, Udaha Kapugedara Padmalal e Shermin de Silva. "Differences in combinatorial calls among the 3 elephant species cannot be explained by phylogeny". Behavioral Ecology 30, n.º 3 (23 de fevereiro de 2019): 809–20. http://dx.doi.org/10.1093/beheco/arz018.

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Desjonquères, Camille, Rebecca R. Holt, Bretta Speck e Rafael L. Rodríguez. "The relationship between a combinatorial processing rule and a continuous mate preference function in an insect". Proceedings of the Royal Society B: Biological Sciences 287, n.º 1935 (16 de setembro de 2020): 20201278. http://dx.doi.org/10.1098/rspb.2020.1278.

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Mate choice involves processing signals that can reach high levels of complexity and feature multiple components, even in small animals with tiny brains. This raises the question of whether and how such organisms deal with this complexity. One solution involves combinatorial processing, whereby different signal elements are processed as single units. Combinatorial processing has been described in several mammals and birds, and recently in a vibrationally signalling insect, Enchenopa treehoppers. Here, we ask about the relationship between combinatorial rules and mate preferences for continuously varying signal features. Enchenopa male advertisement signals are composed of two elements: a ‘whine’ followed by a set of pulses. The dominant frequency of the whine and element combination both matter to females. We presented synthetic signals varying in element order (natural [whine-pulses], reverse [pulses-whine]) and in frequency to Enchenopa females and recorded their responses. The reverse combination resulted in a decrease in attractiveness of the signals, and also slightly changed the shape of the preference for frequency. We found that females could be classified into three ‘types’: females with both a strong preference and a strong combinatorial rule, females with both a weak preference and weak rule, and females with a strong preference but a weak rule. Our results suggest that in Enchenopa signal processing, the mate preference for a continuous signal feature ‘takes precedence’ over, but also interacts with, the combinatorial rule. The relationship between the preference and the rule could evolve to take different forms according to selection on mate choice decisions. We suggest that exploring the relationship between such preferences and rules in species with more complex signals will bring insight into the evolution of the multi-component communication systems.

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Dombrovskaya, Y. V., e A. S. Opaev. "Organization of song of the Yellow-rumped flycatcher (Ficedula zanthopygia, Muscicapidae, Aves)". Povolzhskiy Journal of Ecology, n.º 2 (24 de junho de 2023): 131–47. http://dx.doi.org/10.35885/1684-7318-2023-2-131-147.

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Birdsong consists of stereotypical song types or syllables which follow each other according to certain rules. Based on these rules, linear and combinatorial syntaxes are identified. The former one implies a fixed sequence of song types repeated cyclically. In the combinatorial syntax, there are clusters of song types, within which song types may be performed in a varying sequence. The structure and organization of birdsong have been described for many species, but still remain unexplored for most of them. We studied for the first time the song structure and organization, as well as song sharing for the Yellow-rumped flycatcher Ficedula zanthopygia (Hay, 1845). First of all, we determined the repertoire of song types in each male. Then, the organization of singing was analyzed using methods of information theory and network analysis. To analyze the patterns of song sharing, we compared all song types of all males. Individual repertoires consisted from 8–31 song types. While singing, male flycatchers avoid repeating the same song type two or more times in a row (continuous variety). At the same time, different song types alternate with a much degree of freedom: we did not reveal any patterns which could indicate the presence of either linear or combinatorial syntax. Males generally shared few song types, and the similarity of the repertoires of any two males was small. Besides, males did not preferably use shared or individual (i.e., found in the only one male) song types. Song sharing was not related to the distance between males. The results were compared to what is known about the song structure and organization of the other three Ficedula species studied to date.

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Guadalupi, Chiara, Luca Braglia, Floriana Gavazzi, Laura Morello e Diego Breviario. "A Combinatorial Q-Locus and Tubulin-Based Polymorphism (TBP) Approach Helps in Discriminating Triticum Species". Genes 13, n.º 4 (1 de abril de 2022): 633. http://dx.doi.org/10.3390/genes13040633.

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The simple and straightforward recognition of Triticum species is not an easy task due to their complex genetic origins. To provide a recommendation, we have compared the performance of different PCR-based methods relying on the discrimination ability of the Q- and γ-gliadin (GAG56D) genes, as well as TBP (Tubulin-Based Polymorphism), a method based on the multiple amplification of genes of the β-tubulin family. Among these approaches, the PCR-RFLP (Restriction Fragment Length Polymorphism) assay based on a single-nucleotide polymorphism (SNP) present in the Q gene is the only one capable of fully discerning hexaploid spelt and common wheat species, while both γ-gliadin and TBP fail with similar error frequencies. The Q-locus assay results in the attainment of either a single fragment or a doublet, depending on the presence of a suitable restriction site, which is affected by the mutation. This dual pattern of resolution limits both the diagnostic effectiveness, when additional Triticum species are assayed and compared to each other, and its usefulness, when commercially available flours are analyzed. These limitations are overtaken by flanking the Q-locus assay with the TBP analysis. In this way, almost all of the Triticum species can be accurately identified.

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Kini, Deepthi, Harish Kumar e Manjunath Ghate. "Microwave Assisted Liquid Phase Synthesis of Benzimidazolo Benzothiophenes for Antimicrobial Activity". E-Journal of Chemistry 6, s1 (2009): S25—S32. http://dx.doi.org/10.1155/2009/934706.

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Benzimidazolo benzothiophene derivatives were prepared by liquid phase combinatorial synthesis using soluble polymer support PEG 5000 and 4-fluoro-3-nitrobenzoic acid as starting materials with substituted primary amines. All these synthesized compounds were established by the spectral data and tested for antimicrobial activity against gram positive bacteria,i.e. S. aureus, B. subtilisand gram negative bacteria,E.coliandP.aeruginosaand anti fungal activity againstC. albicans. Ampicillin and ciprofloxacin were used as standard for antibacterial activity and cotrimoxazole for anti fungal activity. Compared with standards compounds(1a-h)showed significant activity against bacterial species and1gshowed significant activity against fungal species.

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Adamyk, K. L. M., E. Holmes, G. R. Mayfield, D. J. Moritz, M. Scheepers, B. E. Tenner e H. C. Wauck. "Sorting permutations: Games, genomes, and cycles". Discrete Mathematics, Algorithms and Applications 09, n.º 05 (outubro de 2017): 1750063. http://dx.doi.org/10.1142/s179383091750063x.

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Permutation sorting, one of the fundamental steps in pre-processing data for the efficient application of other algorithms, has a long history in mathematical research literature and has numerous applications. Two special-purpose sorting operations are considered in this paper: context directed swap, (cds) and context directed reversal, (cdr). These are special cases of sorting operations that were studied in prior work on permutation sorting. Moreover, cds and cdr have been postulated to model molecular sorting events that occur in the genome maintenance program of certain species of single-celled organisms called ciliates. This paper investigates mathematical aspects of these two sorting operations. The main result of this paper is a generalization of previously discovered characterizations of cds-sortability of a permutation. The combinatorial structure underlying this generalization suggests natural combinatorial two-player games. These games are the main mathematical innovation of this paper.

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He, Qiye, Anaïs F. Bardet, Brianne Patton, Jennifer Purvis, Jeff Johnston, Ariel Paulson, Madelaine Gogol, Alexander Stark e Julia Zeitlinger. "High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species". Nature Genetics 43, n.º 5 (10 de abril de 2011): 414–20. http://dx.doi.org/10.1038/ng.808.

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Jo, Yunhui, Eun Kim, Sei Sai, Jin Kim, Jae-Min Cho, Hyeongi Kim, Jeong-Hwa Baek, Jeong-Yub Kim, Sang-Gu Hwang e Myonggeun Yoon. "Functional Biological Activity of Sorafenib as a Tumor-Treating Field Sensitizer for Glioblastoma Therapy". International Journal of Molecular Sciences 19, n.º 11 (21 de novembro de 2018): 3684. http://dx.doi.org/10.3390/ijms19113684.

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Glioblastoma, the most common primary brain tumor in adults, is an incurable malignancy with poor short-term survival and is typically treated with radiotherapy along with temozolomide. While the development of tumor-treating fields (TTFields), electric fields with alternating low and intermediate intensity has facilitated glioblastoma treatment, clinical outcomes of TTFields are reportedly inconsistent. However, combinatorial administration of chemotherapy with TTFields has proven effective for glioblastoma patients. Sorafenib, an anti-proliferative and apoptogenic agent, is used as first-line treatment for glioblastoma. This study aimed to investigate the effect of sorafenib on TTFields-induced anti-tumor and anti-angiogenesis responses in glioblastoma cells in vitro and in vivo. Sorafenib sensitized glioblastoma cells to TTFields, as evident from significantly decreased post-TTFields cell viability (p < 0.05), and combinatorial treatment with sorafenib and TTFields accelerated apoptosis via reactive oxygen species (ROS) generation, as evident from Poly (ADP-ribose) polymerase (PARP) cleavage. Furthermore, use of sorafenib plus TTFields increased autophagy, as evident from LC3 upregulation and autophagic vacuole formation. Cell cycle markers accumulated, and cells underwent a G2/M arrest, with an increased G0/G1 cell ratio. In addition, the combinatorial treatment significantly inhibited tumor cell motility and invasiveness, and angiogenesis. Our results suggest that combination therapy with sorafenib and TTFields is slightly better than each individual therapy and could potentially be used to treat glioblastoma in clinic, which requires further studies.

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de Francesco Albasini, Luisa, e Norma Zagaglia Salvi. "On the Adjacent Cycle Derangements". ISRN Discrete Mathematics 2012 (2 de dezembro de 2012): 1–12. http://dx.doi.org/10.5402/2012/340357.

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A derangement, that is, a permutation without fixed points, of a finite set is said to be an adjacent cycle when all its cycles are formed by a consecutive set of integers. In this paper we determine enumerative properties of these permutations using analytical and bijective proofs. Moreover a combinatorial interpretation in terms of linear species is provided. Finally we define and investigate the case of the adjacent cycle derangements of a multiset.

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Reynaud, C. A., V. Dufour e J. C. Weill. "Generation of diversity in mammalian gut-associated lymphoid tissues: restricted V gene usage does not preclude complex V gene organization." Journal of Immunology 159, n.º 7 (1 de outubro de 1997): 3093–95. http://dx.doi.org/10.4049/jimmunol.159.7.3093.

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Abstract The sheep genome contains 60 to 90 V lambda genes distributed in least 6 different families, whereas 37 V lambda genes and 10 families exist in humans. Comparison with human V lamda sequences indicates that sheep V lambda genes display less overall sequence divergence, but are closer to the genes most frequently used in the human peripheral repertoire. In both species, 2 to 3 genes contribute half of the expressed sequences. Therefore, similar large combinatorial potential and restriction of the expressed repertoire can exist in two species whose strategy of diversification differs widely (ongoing rearrangement throughout life in human bone marrow vs postrearrangement diversification during early development in sheep ileal Peyer's patches).

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Guénard, Guillaume, Peter Carsten von der Ohe, Steven Carlisle Walker, Sovan Lek e Pierre Legendre. "Using phylogenetic information and chemical properties to predict species tolerances to pesticides". Proceedings of the Royal Society B: Biological Sciences 281, n.º 1789 (22 de agosto de 2014): 20133239. http://dx.doi.org/10.1098/rspb.2013.3239.

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Direct estimation of species' tolerance to pesticides and other toxic organic substances is a combinatorial problem, because of the large number of species–substance pairs. We propose a statistical modelling approach to predict tolerances associated with untested species–substance pairs, by using models fitted to tested pairs. This approach is based on the phylogeny of species and physico-chemical descriptors of pesticides, with both kinds of information combined in a bilinear model. This bilinear modelling approach predicts tolerance in untested species–compound pairs based on the facts that closely related species often respond similarly to toxic compounds and that chemically similar compounds often have similar toxic effects. The three tolerance models (median lethal concentration after 96 h) used up to 25 aquatic animal species and up to nine pesticides (organochlorines, organophosphates and carbamates). Phylogeny was estimated using DNA sequences, while the pesticides were described by their mode of toxic action and their octanol–water partition coefficients. The models explained 77–84% of the among-species variation in tolerance (log 10 LC 50 ). In cross-validation, 84–87% of the predicted tolerances for individual species were within a factor of 10 of the observed values. The approach can also be used to model other species response to multivariate stress factors.

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Doan, Phuong, Phung Nguyen, Akshaya Murugesan, Nuno R. Candeias, Olli Yli-Harja e Meenakshisundaram Kandhavelu. "Alkylaminophenol and GPR17 Agonist for Glioblastoma Therapy: A Combinational Approach for Enhanced Cell Death Activity". Cells 10, n.º 8 (3 de agosto de 2021): 1975. http://dx.doi.org/10.3390/cells10081975.

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Drug resistance and tumor heterogeneity limits the therapeutic efficacy in treating glioblastoma, an aggressive infiltrative type of brain tumor. GBM cells develops resistance against chemotherapeutic agent, temozolomide (TMZ), which leads to the failure in treatment strategies. This enduring challenge of GBM drug resistance could be rational by combinatorial targeted therapy. Here, we evaluated the combinatorial effect of phenolic compound (2-(3,4-dihydroquinolin-1(2H)-yl)(p-tolyl)methyl)phenol (THTMP), GPR17 agonist 2-({5-[3-(Morpholine-4-sulfonyl)phenyl]-4-[4-(trifluoromethoxy)phenyl]-4H-1,2,4-triazol-3-yl}sulfanyl)-N-[4-(propan-2-yl)phenyl]acetamide (T0510.3657 or T0) with the frontline drug, TMZ, on the inhibition of GBM cells. Mesenchymal cell lines derived from patients’ tumors, MMK1 and JK2 were treated with the combination of THTMP + T0, THTMP + TMZ and T0 + TMZ. Cellular migration, invasion and clonogenicity assays were performed to check the migratory behavior and the ability to form colony of GBM cells. Mitochondrial membrane permeability (MMP) assay and intracellular calcium, [Ca2+]i, assay was done to comprehend the mechanism of apoptosis. Role of apoptosis-related signaling molecules was analyzed in the induction of programmed cell death. In vivo validation in the xenograft models further validates the preclinical efficacy of the combinatorial drug. GBM cells exert better synergistic effect when exposed to the cytotoxic concentration of THTMP + T0, than other combinations. It also inhibited tumor cell proliferation, migration, invasion, colony-forming ability and cell cycle progression in S phase, better than the other combinations. Moreover, the combination of THTMP + T0 profoundly increased the [Ca2+]i, reactive oxygen species in a time-dependent manner, thus affecting MMP and leading to apoptosis. The activation of intrinsic apoptotic pathway was regulated by the expression of Bcl-2, cleaved caspases-3, cytochrome c, HSP27, cIAP-1, cIAP-2, p53, and XIAP. The combinatorial drug showed promising anti-tumor efficacy in GBM xenograft model by reducing the tumor volume, suggesting it as an alternative drug to TMZ. Our findings indicate the coordinated administration of THTMP + T0 as an efficient therapy for inhibiting GBM cell proliferation.

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Rasib, Khalid, e Hina Ashraf. "Combinatorial Potential of bait matrix against subterranean termites under lab and field conditions". Sociobiology 63, n.º 2 (20 de julho de 2016): 831. http://dx.doi.org/10.13102/sociobiology.v63i2.894.

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Bait matrix of different treatments were evaluated against two termite species i.e. Odontotermes obesus and Coptotermes heimi both under laboratory and field conditions. Mean wood consumption in laboratory bioassays were investigated for 2, 4 and 6 weeks with maximum consumption was noted after 4 weeks. While, field experiment was conducted for 24 there was greater consumption of the loosely bound bait matrix compared to the tightly bound matrix. However, feeding was comparatively high in combinations with attractants. Overall, treated colonies experienced a 90-95% decrease in population size after 24 weeks of baiting. The queen in the royal chamber of the mound was found dead.

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Varfolomeyev, Sergey, Elena Efremenko, Irina P. Beletskaya, Ivano Bertini, G. Michael Blackburn, Alexey Bogdanov, Raimond Cunin et al. "Postgenomic chemistry (IUPAC Technical Report)". Pure and Applied Chemistry 77, n.º 9 (1 de janeiro de 2005): 1641–54. http://dx.doi.org/10.1351/pac200577091641.

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Numerous areas of chemistry can benefit from the ongoing genomic revolution. Here, we discuss and highlight trends in chemistry in the postgenomic era. The areas of interest include combinatorial approaches in organic chemistry; design and analysis of proteins containing unnatural amino acids; trace element-containing proteins; design and characterization of new enzyme types; applications of postgenomic chemistry in drug design; identification of lipid networks and global characterization of lipid molecular species; development of recombinant and self-proliferating polymers; and applications in food chemistry and bioanalytical chemistry based on new nanoanalytical systems and novel recognition elements.

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Bjorck, Johan, Qinru Shi, Carrie Brown-Lima, Jennifer Dean, Angela Fuller e Carla Gomes. "Learning Augmented Methods for Matching: Improving Invasive Species Management and Urban Mobility". Proceedings of the AAAI Conference on Artificial Intelligence 35, n.º 17 (18 de maio de 2021): 14702–10. http://dx.doi.org/10.1609/aaai.v35i17.17727.

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With the success of machine learning, integrating learned models into real-world systems has become a critical challenge. Naively applying predictions to combinatorial optimization problems can incur high costs, which has motivated researchers to consider learning augmented algorithms that can make use of faulty or incomplete predictions. Inspired by two matching problems in computational sustainability where data is abundant, we consider the learning augmented min weight matching problem where some nodes are revealed online while others are known a priori, e.g., by being predicted by machine learning. We develop an algorithm that is able to make use of this extra information and provably improves upon pessimistic online algorithms. We evaluate our algorithm on two settings from computational sustainability -- the coordination of unreliable citizen scientists for invasive species management, and the matching between taxis and riders under uncertain trip duration predictions. In both cases, we perform extensive experiments on real-world datasets and find that our method outperforms baselines, showing how learning augmented algorithms can reliably improve solutions for problems in computational sustainability.

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Jaleel, Zaroug, Shun Zhou, Zaira Martín-Moldes, Lauren M. Baugh, Jonathan Yeh, Nina Dinjaski, Laura T. Brown, Jessica E. Garb e David L. Kaplan. "Expanding Canonical Spider Silk Properties through a DNA Combinatorial Approach". Materials 13, n.º 16 (14 de agosto de 2020): 3596. http://dx.doi.org/10.3390/ma13163596.

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The properties of native spider silk vary within and across species due to the presence of different genes containing conserved repetitive core domains encoding a variety of silk proteins. Previous studies seeking to understand the function and material properties of these domains focused primarily on the analysis of dragline silk proteins, MaSp1 and MaSp2. Our work seeks to broaden the mechanical properties of silk-based biomaterials by establishing two libraries containing genes from the repetitive core region of the native Latrodectus hesperus silk genome (Library A: genes masp1, masp2, tusp1, acsp1; Library B: genes acsp1, pysp1, misp1, flag). The expressed and purified proteins were analyzed through Fourier Transform Infrared Spectrometry (FTIR). Some of these new proteins revealed a higher portion of β-sheet content in recombinant proteins produced from gene constructs containing a combination of masp1/masp2 and acsp1/tusp1 genes than recombinant proteins which consisted solely of dragline silk genes (Library A). A higher portion of β-turn and random coil content was identified in recombinant proteins from pysp1 and flag genes (Library B). Mechanical characterization of selected proteins purified from Library A and Library B formed into films was assessed by Atomic Force Microscopy (AFM) and suggested Library A recombinant proteins had higher elastic moduli when compared to Library B recombinant proteins. Both libraries had higher elastic moduli when compared to native spider silk proteins. The preliminary approach demonstrated here suggests that repetitive core regions of the aforementioned genes can be used as building blocks for new silk-based biomaterials with varying mechanical properties.

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