Sequence searching allowing for non-overlapping adjacent unbalanced translocations

Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in genomic sequence analysis, little attention has been devoted to the problem of matching sequences allowing for this kind of chromosomal alteration. In this paper we investigate the approximate string matching problem when the edit operations are non-overlapping unbalanced translocations of adjacent factors. In particular, we first present a O(nm3)-time and O(m2)-space algorithm based on the dynamic-programming approach. Then we improve our first result by designing a second solution which makes use of the Directed Acyclic Word Graph of the pattern. In particular, we show that under the assumptions of equiprobability and independence of characters, our algorithm has a O(n log2σ m) average time complexity, for an alphabet of size σ, still maintaining the O(nm3)-time and the O(m2)-space complexity in the worst case. To the best of our knowledge this is the first solution in literature for the approximate string matching problem allowing for unbalanced translocations of factors

Effect of Feathers as Nest Insulation on Incubation Behavior and Reproductive Performance of Tree Swallows (\u3cem\u3eTachycineta bicolor\u3c/em\u3e)

Many species of birds line their nests with feathers, presumably because of the insulative qualities of feathers and because feathers may act as a barrier between nest parasites and nestlings. In 1993, we experimentally examined the role of feathers as nest insulation on the incubation behavior, nestling growth, and reproductive performance of Tree Swallows (Tachycineta bicolor) nesting in boxes in western Michigan. There were no significant differences between the incubation rhythms of females with experimental nests (i.e. no feathers) and females with control nests (i.e. with feathers). Nestlings that were reared in control nests had significantly longer right tarsi and right wing chords; their masses were significantly greater than nestlings reared in experimental nests. In addition, nested analyses of variance indicated that both female age class (i.e. second year, after second year, or after hatching year) and the brood within which a nestling was reared had significant effects on nestling growth until nestling day 12. Whether an individual nestling was infected with ectoparasites was independent of whether it was reared in an experimental or control nest. Nest insulation affected reproductive performance: females with experimental nests had significantly longer incubation periods and produced significantly fewer fledglings than did females with control nests. These results suggest that nest insulation may be an important factor influencing incubation behavior, nestling growth, and reproductive performance of Tree Swallows in western Michigan

Jornalismo e crítica da cultura: a urgência da nova identidade

The article discusses the various conceptual issues involving Cultural journalism as a result of the proliferation of virtual spaces of criticism. As a consequence, the system of credibility with which the genus has built its presence in the public sphere seems to be called into question both within the professional activity and in public references. The dilemma, which leverages the difficulties faced by genre historically, suggests a review of theoretical assumptions on which the journalistic practice of critique of culture sits.Key words: cultural journalism, digital technologies, public sphere.O artigo discute as diversas questões conceituais que envolvem o Jornalismo Cultural em consequência da proliferação de espaços virtuais de crítica. Como resultado, o sistema de credibilidade com o qual o gênero construiu sua presença na esfera pública parece estar sendo posto em xeque tanto no interior da atividade profissional quanto nas referências do público. O dilema, que potencializa dificuldades que o gênero enfrenta historicamente, sugere uma revisão de pressupostos teóricos nos quais a prática jornalística da crítica da cultura se assenta.Palavras-chave: jornalismo cultural, tecnologias digitais, esfera pública

Order preserving pattern matching on trees and DAGs

The order preserving pattern matching (OPPM) problem is, given a pattern string $p$ and a text string $t$, find all substrings of $t$ which have the same relative orders as $p$. In this paper, we consider two variants of the OPPM problem where a set of text strings is given as a tree or a DAG. We show that the OPPM problem for a single pattern $p$ of length $m$ and a text tree $T$ of size $N$ can be solved in $O(m+N)$ time if the characters of $p$ are drawn from an integer alphabet of polynomial size. The time complexity becomes $O(m \log m + N)$ if the pattern $p$ is over a general ordered alphabet. We then show that the OPPM problem for a single pattern and a text DAG is NP-complete

Indústrias midiáticas brasileiras: um projeto de História * Doutor em Jornalismo pela ECA/USP, professor do curso de pós-graduação e coordenador dos cursos de graduação da Centro

No conjunto da reconstituição dos processos culturais, elemento essencial paraa compreensão das transformações do final do século, a História da IndústriaMidiática no Brasil recupera o papel dos meios de comunicação comoinstrumento de intervenção do Homem no tempo vivido e, ao mesmo tempo,permite o entendimento dos próprios relatos em torno dos quais a sociedadese estrutura e através dos quais ela olha para si mesma. O desafio de suafeitura, no entanto, situa-se fora do espaço e do tempo específicos do país:percorre o traçado da moderna civilização capitalista (séc. XVI), estende-sepelos vários momentos do séc. XIX e culmina com o painel contemporâneonacional e internacional. O projeto proposto privilegia três objetos de estudo:a imprensa, o rádio e a televisão.Palavras-chaves: História da cultura, história dos meios de comunicação,imprensa, rádio, televisão

Persistent oral and urinary Candida spp. carriagein Italian HIV-seropositive asymptomatic subjects

The aim of the present study was to ascertain frequency and persistence of Candida spp. oral and urinary carriage in asymptomatic, HAART-naive HIV-seropositive subjects who had not undergone therapy with antimycotic drugs, and whose CD4+ lymphocyte count was greater than 200/?l. Oral carriage was the most common Candida spp. carriage (63.0% of the subjects), while candiduria was more rarely observed (6.5%). C. albicans was recovered from the majority of the subjects examined (56.5%), followed by C. krusey (4.3%), C. tropicalis (2.2%) and C. dubliniensis (2.2%). C. albicans was also isolated from two urinary carriers (4.3%) and C. glabrata from another one (2.2%). The same C. albicans clone was repeatedly isolated from 14 out of 15 oral carriers while the same clone of C. dubliniensis was repeatedly isolated from one carrier, as shown by the persistence of RAPD fingerprint of serial isolates during one year of follow-up. Since persistence of Candida spp. carriage may influence the development of clinical candidiasis in immunocompromised hosts, monitoring of the carrier status could be useful for preventing clinical thrush in HIV-seropositive subjects

Duel and sweep algorithm for order-preserving pattern matching

Given a text $T$ and a pattern $P$ over alphabet $\Sigma$, the classic exact matching problem searches for all occurrences of pattern $P$ in text $T$. Unlike exact matching problem, order-preserving pattern matching (OPPM) considers the relative order of elements, rather than their real values. In this paper, we propose an efficient algorithm for OPPM problem using the "duel-and-sweep" paradigm. Our algorithm runs in $O(n + m\log m)$ time in general and $O(n + m)$ time under an assumption that the characters in a string can be sorted in linear time with respect to the string size. We also perform experiments and show that our algorithm is faster that KMP-based algorithm. Last, we introduce the two-dimensional order preserved pattern matching and give a duel and sweep algorithm that runs in $O(n^2)$ time for duel stage and $O(n^2 m)$ time for sweeping time with $O(m^3)$ preprocessing time.Comment: 13 pages, 5 figure

Safety Study of an Antimicrobial Peptide Lactocin 160, Produced by the Vaginal Lactobacillus rhamnosus

Objective. To evaluate the safety of the antimicrobial peptide, lactocin 160. Methods. Lactocin 160, a product of vaginal probiotic Lactobacillus rhamnosus 160 was evaluated for toxicity and irritation. An in vitro human organotypic vaginal-ectocervical tissue model (EpiVaginal) was employed for the safety testing by determining the exposure time to reduce tissue viability to 50% (ET-50). Hemolytic activity of lactocin160 was tested using 8% of human erythrocyte suspension. Susceptibility of lactobacilli to lactocin160 was also studied. Rabbit vaginal irritation (RVI) model was used for an in vivo safety evaluation. Results. The ET-50 value was 17.5 hours for lactocin 160 (4.9 hours for nonoxynol 9, N9). Hemolytic activity of lactocin 160 was 8.2% (N9 caused total hemolysis). Lactobacilli resisted to high concentrations of peptide preparation. The RVI model revealed slight vaginal irritation. An average irritation index grade was evaluated as “none.” Conclusions. Lactocin 160 showed minimal irritation and has a good potential for intravaginal application