Hardness of MSA with Selective Column Scoring

Multiple Sequence Alignment (MSA for short) is a well known problem in the field of computational biology. In order to evaluate the quality of a solution, many different scoring functions have been introduced, the most widely used being the Sum-of-pairs score (SP-score). It is known that computing the best MSA under the SP-score measure is NP-hard. In this paper, we introduce a variant of the Column score (defined in Thompson et al. 1999), which we refer to as Selective Column score: Given a symbol a ∈ Σ, the score of the i-th column is one if and only if all symbols of the same column are a, and otherwise zero. The acolumn score of an alignment is then the number of columns made of only character a. We show that finding the optimal MSA under the Selective Column Score is NP-hard for all alphabets of size |Σ| ≥ 2 by reducing from MIN-2-SAT

Verbi locativi in italiano come varianti di verbi supporto

In questo articolo discuteremo la nozione di "carrier verbs" (secondo la definizione del linguista americano Zellig Harris) o di "light verbs" (come denominata all'inizio del XX secolo da Otto Jespersen). La nostra cornice teorica è rappresentata dal lessico-grammatica di Maurice Gross, una teoria iniziata negli anni settanta a partire dalla sintassi del francese sulle basi matematiche già individuate per la lingua inglese da Zellig Harris. In particolare, discuteremo di come alcuni verbi locativi dell'italiano possano essere usati come verbi supporto (secondo la definizione data da Gross dei "light verbs" harrisiani) e assumano il ruolo sintattico una volta attribuito dai grammatici greci e latini alla copula esse.En aquest article discutirem la noció de "carrier verbs" (segons la definició del lingüista americà Zellig Harris) o de "light verbs" (segons la denominació que Otto Jespersen n'havia donat a principi del segle XX). El nostre marc teòric de referència és el lèxic-gramàtica de Maurice Gross, una teoria començada els anys setanta a partir de la sintaxi del francès en les bases matemàtiques ja individuades per a la llengua anglesa per Zelling Harris. Concretament, tractarem de com alguns verbs locatius de l'italià es poden emprar com a verbs de suport (tal com Gross va definir els "light verbs" harrisians) i de com assumeixen el paper sintàctic que els gramàtics grecs i llatins atribuïen a la còpula esse.In this article we aim at discussing the notion of carrier verbs (according to the definition provided by the American linguist Zellig Harris) or of light verbs (as defined at the beginning of the twentieth century by Otto Jespersen). Our theoretical framework is represented by Maurice Gross' lexicon-grammar, a theory developed during the seventies on the French syntax and directly inspired by Zellig Harris' mathematical grammar of English. Particularly, we are going to discuss of how some Italian locative verbs can be used as support verbs (according to the definition which Maurice Gross has given of the harrisian light verbs) and can play the syntactic role traditionally given to the copula esse by the Greek and Latin grammarians

Normal, Abby Normal, Prefix Normal

A prefix normal word is a binary word with the property that no substring has more 1s than the prefix of the same length. This class of words is important in the context of binary jumbled pattern matching. In this paper we present results about the number $pnw(n)$ of prefix normal words of length $n$, showing that $pnw(n) =\Omega\left(2^{n - c\sqrt{n\ln n}}\right)$ for some $c$ and $pnw(n) = O \left(\frac{2^n (\ln n)^2}{n}\right)$. We introduce efficient algorithms for testing the prefix normal property and a "mechanical algorithm" for computing prefix normal forms. We also include games which can be played with prefix normal words. In these games Alice wishes to stay normal but Bob wants to drive her "abnormal" -- we discuss which parameter settings allow Alice to succeed.Comment: Accepted at FUN '1

Parameterized Inapproximability of Target Set Selection and Generalizations

In this paper, we consider the Target Set Selection problem: given a graph and a threshold value $thr(v)$ for any vertex $v$ of the graph, find a minimum size vertex-subset to "activate" s.t. all the vertices of the graph are activated at the end of the propagation process. A vertex $v$ is activated during the propagation process if at least $thr(v)$ of its neighbors are activated. This problem models several practical issues like faults in distributed networks or word-to-mouth recommendations in social networks. We show that for any functions $f$ and $\rho$ this problem cannot be approximated within a factor of $\rho(k)$ in $f(k) \cdot n^{O(1)}$ time, unless FPT = W[P], even for restricted thresholds (namely constant and majority thresholds). We also study the cardinality constraint maximization and minimization versions of the problem for which we prove similar hardness results

The emerging role of p53 in stem cells

Among the hundreds of oncogenes and tumor suppressors that have been identified in the past 50 years, p53 is probably the best characterized; nevertheless, new functions are constantly being discovered. As a tumor suppressor, p53 regulates cellular responses to different stress stimuli by inducing reversible cell cycle arrest and DNA repair, or triggering senescence or apoptosis. Recent findings on the regulation of stem cell (SC) division and reprogramming suggest the intriguing possibility that p53 also carries out its tumor suppression function by regulating SC homeostasis. Specifically, p53 activation may counteract SC expansion by several emerging mechanisms including restriction of self-renewing divisions, inhibition of symmetric division and block of reprogramming of somatic/progenitor cells into SCs

Negative-Pressure Ventilation in Neuromuscular Diseases in the Acute Setting

Mechanical ventilation started with negative-pressure ventilation (NPV) during the 1950s to assist patients with respiratory failure, secondary to poliomyelitis. Over the years, technological evolution has allowed for the development of more comfortable devices, leading to an increased interest in NPV. The patients affected by neuromuscular diseases (NMD) with chronic and acute respiratory failure (ARF) may benefit from NPV. The knowledge of the available respiratory-support techniques, indications, contraindications, and adverse effects is necessary to offer the patient a personalized treatment that considers the pathology's complexity

Heating cancer stem cells to reduce tumor relapse

Tumour relapse is believed to be caused by rare cancer-cells with stem-cell properties (cancer stem cells) that are intrinsically resistant to available treatments. The identification of novel strategies to increase their sensitivity has major clinical implications. Latest clinical trials have shown a positive antitumoral effect of hyperthermia in combination with chemotherapy or radiotherapy. In a recent paper, the combination of increased temperature at the tumour site, generated by laser treatment of intravenously-injected gold nanoshells, and ionizing radiations enhances radiosensitivity of cancer stem cells and tumor response. At the root of the success of hyperthermia in enhancing radio-sensitization of cancer stem cells is the inhibition of their capacity to repair DNA damage, affecting the survival rate of these cells

Algorithms for Jumbled Pattern Matching in Strings

The Parikh vector p(s) of a string s is defined as the vector of multiplicities of the characters. Parikh vector q occurs in s if s has a substring t with p(t)=q. We present two novel algorithms for searching for a query q in a text s. One solves the decision problem over a binary text in constant time, using a linear size index of the text. The second algorithm, for a general finite alphabet, finds all occurrences of a given Parikh vector q and has sub-linear expected time complexity; we present two variants, which both use a linear size index of the text.Comment: 18 pages, 9 figures; article accepted for publication in the International Journal of Foundations of Computer Scienc