Algorithmic and Hardness Results for the Colorful Components Problems

In this paper we investigate the colorful components framework, motivated by applications emerging from comparative genomics. The general goal is to remove a collection of edges from an undirected vertex-colored graph $G$ such that in the resulting graph $G'$ all the connected components are colorful (i.e., any two vertices of the same color belong to different connected components). We want $G'$ to optimize an objective function, the selection of this function being specific to each problem in the framework. We analyze three objective functions, and thus, three different problems, which are believed to be relevant for the biological applications: minimizing the number of singleton vertices, maximizing the number of edges in the transitive closure, and minimizing the number of connected components. Our main result is a polynomial time algorithm for the first problem. This result disproves the conjecture of Zheng et al. that the problem is $NP$-hard (assuming $P \neq NP$). Then, we show that the second problem is $APX$-hard, thus proving and strengthening the conjecture of Zheng et al. that the problem is $NP$-hard. Finally, we show that the third problem does not admit polynomial time approximation within a factor of $|V|^{1/14 - \epsilon}$ for any $\epsilon > 0$, assuming $P \neq NP$ (or within a factor of $|V|^{1/2 - \epsilon}$, assuming $ZPP \neq NP$).Comment: 18 pages, 3 figure

Review of the Laguerre-Gauss mode technology research program at Birmingham

Gravitational wave detectors from the advanced generation onwards are expected to be limited in sensitivity by thermal noise of the optics, making the reduction of this noise a key factor in the success of such detectors. A proposed method for reducing the impact of this noise is to use higher-order Laguerre-Gauss (LG) modes for the readout beam, as opposed to the currently used fundamental mode. We present here a synopsis of the research program undertaken by the University of Birmingham into the suitability of LG mode technology for future gravitational wave detectors. This will cover our previous and current work on this topic, from initial simulations and table-top LG mode experiments up to implementation in a prototype scale suspended cavity and high-power laser bench

Amlexanox Enhances Premature Termination Codon Read-Through in COL7A1 and Expression of Full Length Type VII Collagen: Potential Therapy for Recessive Dystrophic Epidermolysis Bullosa.

Recessive dystrophic epidermolysis bullosa (RDEB) is a rare monogenic blistering disorder caused by the lack of functional type VII collagen, leading to skin fragility and subsequent trauma-induced separation of the epidermis from the underlying dermis. A total of 46% of patients with RDEB harbor at least one premature termination codon (PTC) mutation in COL7A1, and previous studies have shown that aminoglycosides are able to overcome RDEB PTC mutations by inducing read-through and incorporation of an amino acid at the PTC site. However, aminoglycoside toxicity will likely prevent widespread clinical application. Here the FDA-approved drug amlexanox was tested for its ability to read-through PTC mutations in cells derived from patients with RDEB. Eight of 12 different PTC alleles responded to treatment and produced full length protein, in some cases more than 50% relative to normal controls. Read-through type VII collagen was readily detectable in cell culture media and also localized to the dermal-epidermal junction in organotypic skin culture. Amlexanox increased COL7A1 transcript and the phosphorylation of UPF-1, an RNA helicase associated with nonsense-mediated mRNA decay, suggesting that amlexanox inhibits nonsense-mediated mRNA decay in cells from patients with RDEB that respond to read-through treatment. This preclinical study demonstrates the potential of repurposing amlexanox for the treatment of patients with RDEB harboring PTC mutation in COL7A1

Substratos no desenvolvimento inicial de quatro cultivares de pessegueiro e uma nectarineira.

Entre os fatores que contribuem para melhor desenvolvimento inicial das plantas, estão a qualidade da semente e o substrato utilizado.Objetivou-se avaliar o efeito do substrato na formação inicial de pessegueiro e nectarineira. O trabalho foi realizado no Departamento de Fitotecnia, da Universidade Federal de Viçosa, de fevereiro a março de 2004. Foram utilizados quatro cultivares de pessegueiro, 'Alô Doçura', 'Campinas 1', 'Relíquia' e 'Ouromel' e uma cultivar de nectarineira 'Josefina'. Sementes retiradas de frutos maturos, foram estratificadas em câmara fria, com temperatura de 5±1ºC e ausência de luz. Após a germinação, no interior da casa-de-vegetação, procedeu-se à semeadura em recipientes plásticos (3 litros), contendo os substratos: Plantmax®; Plantmax® + Areia (1:1 v/v); Plantmax® + Latossolo Vermelho (1:1 v/v); Plantmax® + Latossolo Vermelho + Areia (1:1:1 v/v). Foi utilizado o delineamento experimental inteiramente casualizado, num fatorial 5 x 4 (cultivar x substrato), com cinco repetições, considerando-se como unidade experimental cada recipiente plástico. Após 38 dias da semeadura foram analisadas: porcentagem de emergência, número de folhas, comprimento total, altura e comprimento de raiz, diâmetro do caule, massa da matéria seca total, da parte aérea e da raiz e o número de brotações primárias. O substrato teve efeito no desenvolvimento inicial de pessegueiro, obtendo-se os melhores resultados com o substrato comercial Plantmax®. O maior acúmulo de massa de matéria seca total e da parte aérea foi obtido com os cultivares 'Campinas 1' e 'Relíquia', sendo que esse último, também proporcionou maior número de brotações primárias

Variabilidade genética em populações naturais de umbuzeiro (Spondias tuberosa Arr. Cam.) com base em dados isoenzimáticos.

Este trabalho teve como objetivo quantificar a variabilidade genética em duas populações naturais de umbuzeiro (fruteira endêmica do semi-árido nordestino) e sua distribuição entre e dentro das populações, de forma a fornecer dados que direcionem a coleta de germoplasma para conservação e melhoramento genético da espécie

Marginal Coral Populations: the Densest Known Aggregation of Pocillopora in the Galápagos Archipelago is of Asexual Origin

Coral populations at distributional margins frequently experience suboptimal and variable conditions. Recurrent El Niño-Southern Oscillation (ENSO) warming events have caused extensive mortality of reef-building corals in the Eastern Pacific, and particularly impacted branching pocilloporid corals in the Galápagos Islands. Pocillopora spp. were previously more common and formed incipient reefs at several locations in the archipelago but now occur as scattered colonies. Here, we report an unusually concentrated aggregation of colonies and evaluate their current genetic diversity. In particular we focus on a large population of 1614 live Pocillopora colonies found in a volcanic lagoon along the southern shore of Isabela Island. Forty seven colonies were sampled, primarily using a spatially explicit sampling design, and all colonies belonged to Pocillopora mitochondrial open reading frame lineage type 3a. Typing of additional Pocillopora samples (n = 40) from three other islands indicated that this stand is the only known representative of type 3a in the Galápagos Islands. The Isabela Pocillopora type 3a colonies harbored Symbiodinium ITS-2 clade C1d. Multilocus genotyping (n = 6 microsatellites) capable of resolving individual clones indicated that this stand is monogenotypic and thus the high density of colonies is a result of asexual reproduction, likely via fragmentation. Colony size distribution, while an imperfect measure, suggested the stand regrew from remnant colonies that survived the 1997/98 ENSO event but may postdate the 1982/83 ENSO. The community of Pocillopora colonies at Isabela is of particular ecological value due to its high density and support of associated organisms such as fish and benthic invertebrates. The Galapagos Pocillopora corals will continue to provide insights into the genetic structure and population dynamics of marginal coral populations

Finding and counting vertex-colored subtrees

The problems studied in this article originate from the Graph Motif problem introduced by Lacroix et al. in the context of biological networks. The problem is to decide if a vertex-colored graph has a connected subgraph whose colors equal a given multiset of colors $M$. It is a graph pattern-matching problem variant, where the structure of the occurrence of the pattern is not of interest but the only requirement is the connectedness. Using an algebraic framework recently introduced by Koutis et al., we obtain new FPT algorithms for Graph Motif and variants, with improved running times. We also obtain results on the counting versions of this problem, proving that the counting problem is FPT if M is a set, but becomes W[1]-hard if M is a multiset with two colors. Finally, we present an experimental evaluation of this approach on real datasets, showing that its performance compares favorably with existing software.Comment: Conference version in International Symposium on Mathematical Foundations of Computer Science (MFCS), Brno : Czech Republic (2010) Journal Version in Algorithmic

Diversidade genética entre progênies de maracujazeiro amarelo baseado em características morfo agronômicas.

O estudo da diversidade genética é básico para subsidiar a escolha de genitores e trabalhos de seleção e melhoramento. Este trabalho foi realizado no Departamento de Fitotecnia da Universidade Federal de Viçosa. Avaliouse a diversidade genética entre 34 famílias de meios-irmãos e 3 cultivares de maracujazeiro amarelo. O delineamento experimental foi em blocos casualizados, com 37 tratamentos, três repetições e quatro plantas por parcela. As características avaliadas foram: altura da planta e diâmetro do caule aos 60 dias após o transplantio, diâmetro do caule no início da produção, vigor, severidade de verrugose e produção por parcela. Os dados foram submetidos à análise de variância e as médias comparadas pelo método de Dunnett. Para o estudo da diversidade genética, foram estimadas as distâncias de Mahalanobis (D2) entre progênies, bem como realizadas análises de agrupamento de Tocher e das Variáveis Canônicas. Por meio da análise de variância, verificou-se efeito dos tratamentos em todas as variáveis, evidenciando a existência de variabilidade genética entre as progênies e cultivares avaliados. Houve concordância na formação dos grupos de similaridade por meio dos diferentes métodos de análise multivariada. Os grupos de tratamentos divergentes entre si e superiores foram: Grupo I - 2, 3, 6 e 15; Grupo II - 14; e Grupo III - 25