Self-similarity of complex networks and hidden metric spaces

We demonstrate that the self-similarity of some scale-free networks with respect to a simple degree-thresholding renormalization scheme finds a natural interpretation in the assumption that network nodes exist in hidden metric spaces. Clustering, i.e., cycles of length three, plays a crucial role in this framework as a topological reflection of the triangle inequality in the hidden geometry. We prove that a class of hidden variable models with underlying metric spaces are able to accurately reproduce the self-similarity properties that we measured in the real networks. Our findings indicate that hidden geometries underlying these real networks are a plausible explanation for their observed topologies and, in particular, for their self-similarity with respect to the degree-based renormalization.

Decision making techniques with similarity measures and OWA operators

We analyse the use of the ordered weighted average (OWA) in decision-making giving special attention to business and economic decision-making problems. We present several aggregation techniques that are very useful for decision-making such as the Hamming distance, the adequacy coefficient and the index of maximum and minimum level. We suggest a new approach by using immediate weights, that is, by using the weighted average and the OWA operator in the same formulation. We further generalize them by using generalized and quasi-arithmetic means. We also analyse the applicability of the OWA operator in business and economics and we see that we can use it instead of the weighted average. We end the paper with an application in a business multi-person decision-making problem regarding production management

Sequence similarity between the viral cp gene and the transgene in transgenic papayas

The Papaya ringspot virus (PRSV) coat protein transgene present in 'Rainbow' and 'SunUp' papayas disclose high sequence similarity (>89%) to the cp gene from PRSV BR and TH. Despite this, both isolates are able to break down the resistance in 'Rainbow', while only the latter is able to do so in 'SunUp'. The objective of this work was to evaluate the degree of sequence similarity between the cp gene in the challenge isolate and the cp transgene in transgenic papayas resistant to PRSV. The production of a hybrid virus containing the genome backbone of PRSV HA up to the Apa I site in the NIb gene, and downstream from there, the sequence of PRSV TH was undertaken. This hybrid virus, PRSV HA/TH, was obtained and used to challenge 'Rainbow', 'SunUp', and an R2 population derived from line 63-1, all resistant to PRSV HA. PRSV HA/TH broke down the resistance in both papaya varieties and in the 63-1 population, demonstrating that sequence similarity is a major factor in the mechanism of resistance used by transgenic papayas expressing the cp gene. A comparative analysis of the cp gene present in line 55-1 and 63-1-derived transgenic plants and in PRSV HA, BR, and TH was also performed.

Parent-offspring similarity for childhood behaviorial inhibition and associations between inhibition and parental care

L'article constituant le présent travail de thèse décrit une recherche évaluant les similarités entre l'inhibition comportementale chez des enfants et leurs parents respectifs durant l'enfance, ainsi que l'association éventuelle entre l'inhibition et les attitudes parentales. L'inhibition comportementale - définie comme une prédisposition de l'enfant à réagir avec réticence et angoisse à des situations inhabituelles - est une caractéristique de tempérament qui apparaît tôt dans la vie et est relativement stable dans le temps. L'intérêt qui y est associé repose sur son association avec des conséquences développementales négatives pour l'individu: risque accentué chez les enfants d'inadaptation scolaire, de dysfonctionnement social et de sentiments de détresse; facteur de risque en ce qui concerne le développement ultérieur de troubles psychiatriques de l'adulte, dont les troubles anxieux en particulier. Nous avons dès lors investigué dans cette recherche 1) la présence d'une association entre l'inhibition comportementale actuelle des enfants et celle rétrospective de leurs parents, dans ses deux dimensions spécifiques, soit sociale (« peurs à l'école ») et non-sociale (« peurs générales »), et 2) si ces dimensions d'inhibition étaient associées au niveau de chaleur, d'affectivité et de soutien prodigués par les parents. C'est à partir de la récolte d'auto-questionnaires remplis dans le contexte d'une vaste étude initiée à Lausanne en 1994, que nous avons extrait un échantillon de 453 enfants scolarisés en 6/7ème années et 741 de leurs parents biologiques respectifs. Les analyses ont porté sur les auto-questionnaires évaluant, chez les enfants, leurs degrés d'inhibition comportementale, de symptomatologie psychiatrique actuelle et de perception de chaleur, d'affectivité et de soutien reçu de la part des parents, et, en ce qui concerne les parents, des auto¬questionnaires évaluant rétrospectivement leurs degrés d'inhibition comportementale durant l'enfance et de symptomatologie psychiatrique actuelle. La comparaison des scores des enfants avec ceux de leurs parents sur les échelles de l'inhibition comportementale (CSRCI-Child version of the Self-Report of Child Inhibition - et RSRI - Retrospective Self- Report of Inhibition -), montre la présence d'une similarité significative pour chacune des dimensions spécifiques, suggérant que les enfants de parents ayant présenté une inhibition comportementale dans l'enfance sont plus à risque d'en développer une à leur tour. Nous avons par ailleurs pu établir, au cours d'analyses complémentaires, que cette association se maintenait après l'ajustement des degrés de symptomatologie psychiatrique respectifs des enfants et de leurs parents, ce qui a permis d'écarter ce facteur confondant potentiel. Bien que la nature de cette association ne puisse être élucidée par cette recherche, le fait que la taille de l'effet soit modeste suggère qu'un rôle important dans le développement de l'inhibition soit joué par des facteurs environnementaux non partagés dans une famille. Un de ceux-ci semble suggéré par l'association négative qui apparaît dans cette étude entre le degré d'inhibition dans sa dimension « peurs à l'école » et l'attitude parentale: un bas niveau de chaleur, d'affectivité et de soutien perçu par l'enfant de la part de ses parents aurait ainsi une influence sur le développement de peurs en situations sociales en particulier. Alternativement, cette association négative pourrait suggérer que les peurs de l'enfant aient une influence négative sur le développement d'une attitude parentale de soutien ou, du moins, sur la perception de celle-ci par l'enfant. Il est aussi bien évidemment envisageable que ces processus interagissent dans une boucle de rétroaction. Seules des études longitudinales pourraient nous éclairer sur la nature de cette association. Quoi qu'il en soit, ce résultat présente un intérêt clinique pour orienter des interventions de prévention du développement de troubles psychiatriques chez des enfants inhibés, en proposant d'agir, soit directement sur les attitudes parentales, soit sur les peurs de l'enfant ainsi que sur les caractéristiques perçues par l'enfant de l'attitude parentale. Des études longitudinales sur les ressemblances entre les parents et leurs enfants concernant l'inhibition comportementale, incluant des études de jumeaux, d'enfants adoptés et de familles, sont nécessaires pour mieux comprendre les interactions entre les facteurs génétiques, familiaux et environnementaux dans le développement de l'inhibition comportementale des enfants.

Similarity in food cleaning techniques within matrilines in wild vervet monkeys.

Social learning and the formation of traditions rely on the ability and willingness to copy one another. A central question is under which conditions individuals adapt behaviour to social influences. Here, we demonstrate that similarities in food processing techniques emerge on the level of matrilines (mother-offspring) but not on the group level in an experiment on six groups of wild vervet monkeys that involved grapes covered with sand. Monkeys regularly ate unclean grapes but also used four cleaning techniques more similarly within matrilines: rubbing in hands, rubbing on substrate, open with mouth, and open with hands. Individual cleaning techniques evolved over time as they converged within matrilines, stabilised at the end and remained stable in a follow-up session more than one year later. The similarity within matrilines persisted when we analyzed only foraging events of individuals in the absence of other matriline members and matriline members used more similar methods than adult full sisters. Thus, momentary conversion or purely genetic causation are unlikely explanations, favouring social learning as mechanism for within matriline similarities. The restriction of traditions to matriline membership rather than to the group level may restrict the development of culture in monkeys relative to apes or humans.

Decision making techniques with similarity measures and OWA operators

We analyse the use of the ordered weighted average (OWA) in decision-making giving special attention to business and economic decision-making problems. We present several aggregation techniques that are very useful for decision-making such as the Hamming distance, the adequacy coefficient and the index of maximum and minimum level. We suggest a new approach by using immediate weights, that is, by using the weighted average and the OWA operator in the same formulation. We further generalize them by using generalized and quasi-arithmetic means. We also analyse the applicability of the OWA operator in business and economics and we see that we can use it instead of the weighted average. We end the paper with an application in a business multi-person decision-making problem regarding production management

Chemical similarity among domesticated and wild genotypes of peanut based on n-alkanes profiles

The objective of this work was to analyze the epicuticular n-alkane profile of domesticated and wild peanut genotypes. Foliar epicuticular n-alkanes of four Arachis hypogaea genotypes and two wild species - A. monticola and A. stenosperma - were analyzed by gas chromatography. Chemical relationships between them were evaluated using the Dice coefficient and UPGMA method. Two clusters were formed: one with four A. hypogaea genotypes and the other with the two wild species. There is more similarity between the BR1 and LIGO-PE06 genotypes and between the BRS 151 L-7 and BRS Havana genotypes.

Genetic similarity in a hybrid population of 'Montenegrina' and 'King' mandarins

The objective of this work was to confirm the hybrids obtained in plants originated from the crossing between the mandarins Citrus deliciosa 'Montenegrina' and C. nobilis 'King', and to estimate the genetic similarity among hybrids, and between each hybrid and its parents. Twenty‑three pairs of microsatellite primers were tested. Fourteen of these pairs showed polymorphic bands between parents. Primers CCSM 129 and CCSME 52 were sufficient to identify the 12 nucellar clones observed in the studied population. Genetic similarity analysis of the population (hybrids and parents) showed 0.56 average similarity. Besides the 12 clones of 'Montenegrina' identified, 25 hybrids were found of which D18, C32, D06, C05 and D09 are the more similar to 'Montenegrina'.

Similarity measure based classification

Luokittelujärjestelmää suunniteltaessa tarkoituksena on rakentaa systeemi, joka pystyy ratkaisemaan mahdollisimman tarkasti tutkittavan ongelma-alueen. Hahmontunnistuksessa tunnistusjärjestelmän ydin on luokitin. Luokittelun sovellusaluekenttä on varsin laaja. Luokitinta tarvitaan mm. hahmontunnistusjärjestelmissä, joista kuvankäsittely toimii hyvänä esimerkkinä. Myös lääketieteen parissa tarkkaa luokittelua tarvitaan paljon. Esimerkiksi potilaan oireiden diagnosointiin tarvitaan luokitin, joka pystyy mittaustuloksista päättelemään mahdollisimman tarkasti, onko potilaalla kyseinen oire vai ei. Väitöskirjassa on tehty similaarisuusmittoihin perustuva luokitin ja sen toimintaa on tarkasteltu mm. lääketieteen paristatulevilla data-aineistoilla, joissa luokittelutehtävänä on tunnistaa potilaan oireen laatu. Väitöskirjassa esitetyn luokittimen etuna on sen yksinkertainen rakenne, josta johtuen se on helppo tehdä sekä ymmärtää. Toinen etu on luokittimentarkkuus. Luokitin saadaan luokittelemaan useita eri ongelmia hyvin tarkasti. Tämä on tärkeää varsinkin lääketieteen parissa, missä jo pieni tarkkuuden parannus luokittelutuloksessa on erittäin tärkeää. Väitöskirjassa ontutkittu useita eri mittoja, joilla voidaan mitata samankaltaisuutta. Mitoille löytyy myös useita parametreja, joille voidaan etsiä juuri kyseiseen luokitteluongelmaan sopivat arvot. Tämä parametrien optimointi ongelma-alueeseen sopivaksi voidaan suorittaa mm. evoluutionääri- algoritmeja käyttäen. Kyseisessä työssä tähän on käytetty geneettistä algoritmia ja differentiaali-evoluutioalgoritmia. Luokittimen etuna on sen joustavuus. Ongelma-alueelle on helppo vaihtaa similaarisuusmitta, jos kyseinen mitta ei ole sopiva tutkittavaan ongelma-alueeseen. Myös eri mittojen parametrien optimointi voi parantaa tuloksia huomattavasti. Kun käytetään eri esikäsittelymenetelmiä ennen luokittelua, tuloksia pystytään parantamaan.

Genetic similarity of citrus fresh fruit market cultivars

The objective of this work was to assess the genetic similarity of the following citrus fresh fruit market seedless cultivars: Lane Late, Navelate, Navelina and Salustiana sweet oranges (Citrus sinensis (L.) Osbeck), Clemenules and Marisol mandarins (C. reticulata Blanco) and Okitsu satsuma mandarin (C. unshiu Marcovitch), and the hybrids Nova [C. clementina x (C. paradisi x C. tangerina)] and Ortanique (tangor probably derived from C. sinensis (L.) Osbeck x C. reticulata Blanco), utilizing isoenzymatic markers. Electrophoresis analysis of proteins extracted from leaf tissues was utilized to detect polymorphisms at ten isoenzymatic systems. Out of 30 alleles, 16 were polymorphic. The Jaccard coefficient was utilized to estimate the genetic similarity between the cultivars and the unweigthed pair-group method using an arithmetic average (UPGMA) was used to obtain the phenogram (NTSYS 1.7). The cultivars showed high genetic similarity (>72.5%), and were classified in five main groups: sweet oranges, 'Clemenules' and 'Marisol' mandarins, 'Nova', 'Ortanique', and 'Okitsu' satsuma mandarin.

Adding similarity-based reasoning capabilities to a Horn fragment of possibilistic logic with fuzzy constants

PLFC is a first-order possibilistic logic dealing with fuzzy constants and fuzzily restricted quantifiers. The refutation proof method in PLFC is mainly based on a generalized resolution rule which allows an implicit graded unification among fuzzy constants. However, unification for precise object constants is classical. In order to use PLFC for similarity-based reasoning, in this paper we extend a Horn-rule sublogic of PLFC with similarity-based unification of object constants. The Horn-rule sublogic of PLFC we consider deals only with disjunctive fuzzy constants and it is equipped with a simple and efficient version of PLFC proof method. At the semantic level, it is extended by equipping each sort with a fuzzy similarity relation, and at the syntactic level, by fuzzily “enlarging” each non-fuzzy object constant in the antecedent of a Horn-rule by means of a fuzzy similarity relation.

Extending the roughness of the data via transitive closures of similarity indexes

One main assumption in the theory of rough sets applied to information tables is that the elements that exhibit the same information are indiscernible (similar) and form blocks that can be understood as elementary granules of knowledge about the universe. We propose a variant of this concept defining a measure of similarity between the elements of the universe in order to consider that two objects can be indiscernible even though they do not share all the attribute values because the knowledge is partial or uncertain. The set of similarities define a matrix of a fuzzy relation satisfying reflexivity and symmetry but transitivity thus a partition of the universe is not attained. This problem can be solved calculating its transitive closure what ensure a partition for each level belonging to the unit interval [0,1]. This procedure allows generalizing the theory of rough sets depending on the minimum level of similarity accepted. This new point of view increases the rough character of the data because increases the set of indiscernible objects. Finally, we apply our results to a not real application to be capable to remark the differences and the improvements between this methodology and the classical one

Structural aspects and floristic similarity among tropical dry forest fragments with different management histories in northern Minas Gerais, Brazil

In order to produce useful knowledge to the initiatives of protection and management of forest fragments, more specifically for tropical dry forests which suffer with frequent anthropic activities, and due to the lack of specific studies, this article aimed describe the structure and the floristic similarity among three areas of dry forest with different management histories. The study was developed in Capitão Enéas municipality, Northern Minas Gerais, Brazil, where three fragments were evaluated, being one in regeneration for 30 years, another submitted to occasional fire and the third with selective cut in small scale. The sampling was developed through the point quarter method considering all the alive phanerophyte individuals with circumference at breast height (CBH) > 15 cm. In the three fragments, 512 individuals, distributed in 60 species, 47 genera, and 23 families were sampled. The most representative families were Fabaceae (26), Anacardiaceae (4), Bignoniaceae (3) and Combretaceae (3). However, fourteen families were represented by only one species. Only eight species were common to all fragments - Myracrodruon urundeuva standed out with 26.9% of all sampled individuals - while a great number of species were exclusive of each fragment. The floristic and structural differences between the fragments are possibly related to the history and intensity of management in each area besides the topography variations and the presence or absence of limestone outcrops. These results show the importance of each fragment, indicating that the loss of anyone would cause negative impacts on the regional flora and consequently to the associated biodiversity.