Mass Spectrometry Informatics in Systems Biology

Mass spectrometry (MS) became a standard tool for identifying metabolites in biological tissues, and metabolomics is slowly acknowledged as a legitimate research discipline for characterizing biological conditions. The computational analyses of metabolomics, however, lag behind compared with the rapid advances in analytical aspects for two reasons. First is the lack of standardized data repository for mass spectra: each research institution is flooded with gigabytes of mass-spectral data from its own analytical groups and cannot host a world-class repository for mass spectra. The second reason is the lack of informatics experts that are fully experienced with spectral analyses. The two barriers must be overcome to establish a publicly free data server for MS analysis in metabolomics as does GenBank in genomics and UniProt in proteomics. The workshop brought together bioinformaticians working on mass spectral analyses in Finland and Japan with the goal to establish a consortium to freely exchange and publicize mass spectra of metabolites measured on various platforms computational tools to analyze spectra spectral knowledge that are computationally predicted from standardized data. This book contains the abstracts of the presentations given in the workshop. The programme of the workshop consisted of oral presentations from Japan and Finland, invited lectures from Steffen Neumann (Leibniz Institute of Plant Biochemistry), Matej Oresic (VTT), Merja Penttila (VTT) and Nicola Zamboni (ETH Zurich) as well as free form discussion among the participants. The event was funded by Academy of Finland (grants 139203 and 118653), Japan Society for the Promotion of Science (JSPS Japan-Finland Bilateral Semi- nar Program 2010) and Department of Computer Science University of Helsinki. We would like to thank all the people contributing to the technical pro- gramme and the sponsors for making the workshop possible. Helsinki, October 2010 Masanori Arita, Markus Heinonen and Juho Rousu

Cubicity, degeneracy, and crossing number

A $k$-box $B=(R_1,...,R_k)$, where each $R_i$ is a closed interval on the real line, is defined to be the Cartesian product $R_1\times R_2\times ...\times R_k$. If each $R_i$ is a unit length interval, we call $B$ a $k$-cube. Boxicity of a graph $G$, denoted as $\boxi(G)$, is the minimum integer $k$ such that $G$ is an intersection graph of $k$-boxes. Similarly, the cubicity of $G$, denoted as $\cubi(G)$, is the minimum integer $k$ such that $G$ is an intersection graph of $k$-cubes. It was shown in [L. Sunil Chandran, Mathew C. Francis, and Naveen Sivadasan: Representing graphs as the intersection of axis-parallel cubes. MCDES-2008, IISc Centenary Conference, available at CoRR, abs/cs/ 0607092, 2006.] that, for a graph $G$ with maximum degree $\Delta$, $\cubi(G)\leq \lceil 4(\Delta +1)\log n\rceil$. In this paper, we show that, for a $k$-degenerate graph $G$, $\cubi(G) \leq (k+2) \lceil 2e \log n \rceil$. Since $k$ is at most $\Delta$ and can be much lower, this clearly is a stronger result. This bound is tight. We also give an efficient deterministic algorithm that runs in $O(n^2k)$ time to output a $8k(\lceil 2.42 \log n\rceil + 1)$ dimensional cube representation for $G$. An important consequence of the above result is that if the crossing number of a graph $G$ is $t$, then $\boxi(G)$ is $O(t^{1/4}{\lceil\log t\rceil}^{3/4})$ . This bound is tight up to a factor of $O((\log t)^{1/4})$. We also show that, if $G$ has $n$ vertices, then $\cubi(G)$ is $O(\log n + t^{1/4}\log t)$. Using our bound for the cubicity of $k$-degenerate graphs we show that cubicity of almost all graphs in $\mathcal{G}(n,m)$ model is $O(d_{av}\log n)$, where $d_{av}$ denotes the average degree of the graph under consideration. model is O(davlogn).

Rainbow connectivity: hardness and tractability

A path in an edge colored graph is said to be a rainbow path if no two edges on the path have the same color. An edge colored graph is (strongly) rainbow connected if there exists a (geodesic) rainbow path between every pair of vertices. The (strong) rainbow connectivity of a graph G, denoted by (src(G), respectively) rc(G) is the smallest number of colors required to edge color the graph such that G is (strongly) rainbow connected. In this paper we study the rainbow connectivity problem and the strong rainbow connectivity problem from a computational point of view. Our main results can be summarised as below: 1) For every fixed k >= 3, it is NP-Complete to decide whether src(G) <= k even when the graph G is bipartite. 2) For every fixed odd k >= 3, it is NP-Complete to decide whether rc(G) <= k. This resolves one of the open problems posed by Chakraborty et al. (J. Comb. Opt., 2011) where they prove the hardness for the even case. 3) The following problem is fixed parameter tractable: Given a graph G, determine the maximum number of pairs of vertices that can be rainbow connected using two colors. 4) For a directed graph G, it is NP-Complete to decide whether rc(G) <= 2.

The sequence and structure of snake gourd (Trichosanthes anguina) seed lectin, a three-chain nontoxic homologue of type II RIPs

The sequence and structure of snake gourd seed lectin (SGSL), a nontoxic homologue of type II ribosome-inactivating proteins (RIPs), have been determined by mass spectrometry and X-ray crystallography, respectively. As in type II RIPs, the molecule consists of a lectin chain made up of two beta-trefoil domains. The catalytic chain, which is connected through a disulfide bridge to the lectin chain in type II RIPs, is cleaved into two in SGSL. However, the integrity of the three-dimensional structure of the catalytic component of the molecule is preserved. This is the first time that a three-chain RIP or RIP homologue has been observed. A thorough examination of the sequence and structure of the protein and of its interactions with the bound methyl-alpha-galactose indicate that the nontoxicity of SGSL results from a combination of changes in the catalytic and the carbohydrate-binding sites. Detailed analyses of the sequences of type II RIPs of known structure and their homologues with unknown structure provide valuable insights into the evolution of this class of proteins. They also indicate some variability in carbohydrate-binding sites, which appears to contribute to the different levels of toxicity exhibited by lectins from various sources.

Sapientia, 1946, Vol. I, nº 2 (número completo)

Contenido: El significado histórico de Godofredo G. Leibniz (1646-1946) / La Dirección – La “comprehensión” del estado en Wilhelm Dilthey / Arturo Enrique Sampay – La subalternación de la ética a la psicología / Julio Meinvielle – Mundo del accidente / G. K. E. – Notas -- Bibliografía

La teoría aristotélica de la abstracción y su olvido moderno

Resumen: Este estudio analiza la teoría aristotélica de la abstracción, tratando de rescatar su sentido originario a partir de los textos del autor, así como los aportes de los aristotélicos medievales más relevantes, especialmente Tomás de Aquino. Y luego se pasa a describir algunos hitos fundamentales de la evolución posterior de dicha teoría en la historia de la Filosofía, como son: 1) La contraposición entre abstracción e intuición en Duns Escoto y Guillermo de Ockham. 2) el intuicionismo de Descartes 3) La reinterpretación empirista de la abstracción en J. Locke 4) La ausencia de la abstracción en el Espinoza, Leibniz y Kant, así como su sustitución por la “aufhebung” en Hegel. 5) La peculiar aproximación husserliana a la abstracción a partir de su método fenomenológico y 6) la relación de la teoría de la abstracción con el pensamiento de algunos autores contemporáneos como Zubiri, Polo y, especialmente, Heidegger.

Heróis a contrapelo: lampejos do gênio na escrita dos jovens Goethe e Schiller

O estilo de época Sturm und Drang, o primeiro movimento literário genuinamente alemão, surgido na segunda metade do século XVIII, possibilitou a emancipação literária da Alemanha e introduziu naquele país o conceito de gênio original. A partir da descoberta da obra do gênio inglês Shakespeare (possibilitada pelas traduções de Christoph Martin Wieland), os alemães se depararam com o modelo de revolução literária que necessitavam para instituir as bases da originalidade literária alemã. Pautando-se na estrutura dramática shakespeariana, Johann Wolfgang von Goethe e Friedrich Schiller elaboraram seus dramas de estreia, obras foco da presente pesquisa: Götz von Berlichingen e Os bandoleiros, respectivamente. O presente estudo propõe-se, por conseguinte, a analisar as obras supracitadas à luz da temática do gênio original. Mas, primeiramente, são observados os fatores (como a ascenção do romance inglês) e escritores (como Gothold Ephraim Lessing, Johann Jakob Bodmer, Johann Jakob Breitinger, Friedrich Gottlieb Klopstock, Johann Joachim Winckelmann, Wieland e Johann Gottfried von Herder) que colaboraram para a instituição da era genial na Alemanha

Mündliche Literatur und nationale Identitätskonstruktion bei José de Alencar und Mário de Andrade

O presente trabalho tem por objetivo analisar a construção da identidade nos discursos literários de José de Alencar e Mário de Andrade em que o recurso à literatura oral aparece como elemento central. O foco da análise são os textos críticos e teóricos desses autores, tomando-se especialmente em consideração questões da teoria de Johann Gottfried Herder sobre a poesia popular enquanto poesia natural, que deveria servir de matéria prima para a literatura erudita

Das Bistum Würzburg 7. Die Würzburger Bischöfe von 1617 bis 1684

Winfried Romberg führt mit dem Band Die Würzburger Bischöfe von 1617 bis 1684 die Bischofsreihe fort, die Alfred Wendehorst begonnen hat (Germania Sacra Neue Folge 1/4/13). Damit erscheint ein Band, der in besonderer Weise für den Schwerpunkt der Dritten Folge der Germania Sacra steht: Die Darstellung von Diözesen und Domkapiteln der Kirche des Alten Reiches. Er beleuchtet die Lebensläufe und Amtstätigkeiten neuzeitlicher Würzburger Bischöfe des 17. Jahrhunderts und umfasst die Pontifikate von Johann Gottfried I. von Aschhausen (1617–1622) bis zum Pontifikat von Konrad Wilhelm von Wernau (1683–1684). Die Bischöfe dieser Zeit waren von überregionaler Bedeutung und Wirksamkeit, wie sich beispielhaft in der Person des Bischofs Johann Philipp I. von Schönborn (1642–1673) zeigt, der zugleich Erzbischof von Mainz war. Johann Gottfried I. von Aschhausen, Franz von Hatzfeld und Peter Philipp von Dernbach waren Bischöfe von Würzburg und Bamberg in Personalunion, womit sich der Band auch an die Darstellung der Bamberger Bischofsreihe von 1522 bis 1693 von Dieter J. Weiß (Germania Sacra Neue Folge 38) anschließt. Die Viten, die das Wirken des einzelnen Bischofs in seinem Amt in den Vordergrund stellen, bewegen sich im geschichtsträchtigen Umfeld von Rekatholisierung, Dreißigjährigem Krieg und Frühabsolutismus.

Inversion from redundant data

info:eu-repo/semantics/published

Euler y el número π

Uno de los más prolíficos matemáticos, sino el que más, que han existido a lo largo de toda la historia, ha sido el suizo Leonhard Euler (1707-1783). Además de, en nuestro caso, introducir el uso de la letra griega π (inicial de perímetro) para nuestro número, dió numerosas aproximaciones mediante desarrollos en serie de la relación existente entre la circunferencia y su diámetro. El presente articulo trata de explicar el ingenioso procedimiento de dos de dichas series: la serie de Jacques Bernouilli y, la serie de Leibniz.

Vacuum arc remelting time dependent modelling

Vacuum arc remelting (VAR) aims at production of high quality, segregation-free alloys. The quality of the produced ingots depends on the operating conditions which could be monitored and analyzed using numerical modelling. The remelting process uniformity is controlled by critical medium scale time variations of the order 1-100 s, which are physically initiated by the droplet detachment and the large scale arc motion at the top of liquid pool [1,2]. The newly developed numerical modelling tools are addressing the 3-dimensional magnetohydrodynamic and thermal behaviour in the liquid zone and the adjacent ingot, electrode and crucible.

Communicating Answer Set Programs

Answer set programming is a form of declarative programming that has proven very successful in succinctly formulating and solving complex problems. Although mechanisms for representing and reasoning with the combined answer set programs of multiple agents have already been proposed, the actual gain in expressivity when adding communication has not been thoroughly studied. We show that allowing simple programs to talk to each other results in the same expressivity as adding negation-as-failure. Furthermore, we show that the ability to focus on one program in a network of simple programs results in the same expressivity as adding disjunction in the head of the rules.

Evangélicos en América Latina

Considerada tradicionalmente "el continente católico" por excelencia, Latinoamérica siempre ha contado con una presencia minoritaria protestante, y en los últimos treinta años, a pesar de llegar a concentrar en su territorio a la mitad de los católicos del mundo, ha visto una acelerada diversificación del universo religioso, con una proliferación impresionante de denominaciones y grupos, cuya mayorÍa se declara "evangélica". Este proceso, con frecuencia descrito con expresión simplista "invasión de las sectas", se muestra complejo en sus características y articulado en su composición. Frente a tal crecimiento numérico, que en el año 2000 deberÍa involucrar al 20% de la población del continente, la Iglesia Católica parece oscilar entre la crÍtica al papel "alienante" de estos movimientos y la adopción de sus formas culturales celebrativas y espiritualizantes. Además, desde la mitad de los años 80, luego -y acaso como consecuencia- de tal expansión, los evangélicos empezaron a afirmar una inédita presencia polÍtica, culminada en l991 con la obtención en Guatemala del máximo cargo del Estado por parte de Jorge Serrano, primer presidente evangélico elegido en Latinoamérica. Contando con un sólido arraigo popular, los partidos y políticos evangélicos ya están difundidos en todos los paÍses, con un papel que alterna el conservadorismo milenarista, el corporativismo confesional y la concientización liberadora. Con este número especial, SIAL pretende principalmente ofrecer algunos materiales para un mejor conocimiento de este dinámico y complejo fenómeno religioso y social.

A review of dynamic Bayesian network techniques with applications in healthcare risk modelling

Coping with an ageing population is a major concern for healthcare organisations around the world. The average cost of hospital care is higher than social care for older and terminally ill patients. Moreover, the average cost of social care increases with the age of the patient. Therefore, it is important to make efficient and fair capacity planning which also incorporates patient centred outcomes. Predictive models can provide predictions which their accuracy can be understood and quantified. Predictive modelling can help patients and carers to get the appropriate support services, and allow clinical decision-makers to improve care quality and reduce the cost of inappropriate hospital and Accident and Emergency admissions. The aim of this study is to provide a review of modelling techniques and frameworks for predictive risk modelling of patients in hospital, based on routinely collected data such as the Hospital Episode Statistics database. A number of sub-problems can be considered such as Length-of-Stay and End-of-Life predictive modelling. The methodologies in the literature are mainly focused on addressing the problems using regression methods and Markov models, and the majority lack generalisability. In some cases, the robustness, accuracy and re-usability of predictive risk models have been shown to be improved using Machine Learning methods. Dynamic Bayesian Network techniques can represent complex correlations models and include small probabilities into the solution. The main focus of this study is to provide a review of major time-varying Dynamic Bayesian Network techniques with applications in healthcare predictive risk modelling.