Explaining Evolution via Constrained Persistent Perfect Phylogeny

BACKGROUND: The perfect phylogeny is an often used model in phylogenetics since it provides an efficient basic procedure for representing the evolution of genomic binary characters in several frameworks, such as for example in haplotype inference. The model, which is conceptually the simplest, is based on the infinite sites assumption, that is no character can mutate more than once in the whole tree. A main open problem regarding the model is finding generalizations that retain the computational tractability of the original model but are more flexible in modeling biological data when the infinite site assumption is violated because of e.g. back mutations. A special case of back mutations that has been considered in the study of the evolution of protein domains (where a domain is acquired and then lost) is persistency, that is the fact that a character is allowed to return back to the ancestral state. In this model characters can be gained and lost at most once. In this paper we consider the computational problem of explaining binary data by the Persistent Perfect Phylogeny model (referred as PPP) and for this purpose we investigate the problem of reconstructing an evolution where some constraints are imposed on the paths of the tree. RESULTS: We define a natural generalization of the PPP problem obtained by requiring that for some pairs (character, species), neither the species nor any of its ancestors can have the character. In other words, some characters cannot be persistent for some species. This new problem is called Constrained PPP (CPPP). Based on a graph formulation of the CPPP problem, we are able to provide a polynomial time solution for the CPPP problem for matrices whose conflict graph has no edges. Using this result, we develop a parameterized algorithm for solving the CPPP problem where the parameter is the number of characters. CONCLUSIONS: A preliminary experimental analysis shows that the constrained persistent perfect phylogeny model allows to explain efficiently data that do not conform with the classical perfect phylogeny model

Approximating Clustering of Fingerprint Vectors with Missing Values

The problem of clustering fingerprint vectors is an interesting problem in Computational Biology that has been proposed in (Figureroa et al. 2004). In this paper we show some improvements in closing the gaps between the known lower bounds and upper bounds on the approximability of some variants of the biological problem. Namely we are able to prove that the problem is APX-hard even when each fingerprint contains only two unknown position. Moreover we have studied some variants of the orginal problem, and we give two 2-approximation algorithm for the IECMV and OECMV problems when the number of unknown entries for each vector is at most a constant.Comment: 13 pages, 4 figure

Parameterized Complexity of the k-anonymity Problem

The problem of publishing personal data without giving up privacy is becoming increasingly important. An interesting formalization that has been recently proposed is the $k$-anonymity. This approach requires that the rows of a table are partitioned in clusters of size at least $k$ and that all the rows in a cluster become the same tuple, after the suppression of some entries. The natural optimization problem, where the goal is to minimize the number of suppressed entries, is known to be APX-hard even when the records values are over a binary alphabet and $k=3$, and when the records have length at most 8 and $k=4$ . In this paper we study how the complexity of the problem is influenced by different parameters. In this paper we follow this direction of research, first showing that the problem is W[1]-hard when parameterized by the size of the solution (and the value $k$). Then we exhibit a fixed parameter algorithm, when the problem is parameterized by the size of the alphabet and the number of columns. Finally, we investigate the computational (and approximation) complexity of the $k$-anonymity problem, when restricting the instance to records having length bounded by 3 and $k=3$. We show that such a restriction is APX-hard.Comment: 22 pages, 2 figure

Review of dohan eherenfest et al. (2009) on “classification of platelet concentrates: from pure platelet-rich plasma (p-prp) to leucocyte- and platelet-rich fibrin (l-prf)”

This classic discusses the original publication of Dohan Eherenfest et al. on "Classification of platelet concentrates: from pure platelet-rich plasma (P-PRP) to leucocyte- and platelet-rich fibrin (L-PRF)", in which the authors propose four categories of platelet concentrates depending on their leukocyte and fibrin content (P-PRP, leucocyte- and platelet-rich plasma (L-PRP), pure platelet-rich fibrin (P-PRF), and L-PRF) to group a "jungle" of products in which the term platelet-rich plasma (PRP) was used indistinctly. They were able to identify common factors such as: (1) the use of anticoagulant and immediate centrifugation of the blood after its collection, (2) most preparation techniques allowed platelet concentrate preparation within an hour, (3) the centrifugation aimed to separate the blood in layers that would allow the extraction of specific fractions, and (4) the product was activated with thrombin or calcium chloride. The reviewed manuscript has been listed among the most cited PRP articles in regenerative medicine, with more than 800 citations, driving the current scientific research and clinical practice by categorizing L-PRP and P-PRP (now, leukocyte-poor PRP). The classification has also opened the door to understanding intrinsic biological mechanisms between the platelets, leukocytes, fibrin, and growth factors, later considered for studying the proliferation and differentiation of cells in different tissues affected by PRP. Since the initial classification of platelet concentrates, several other classification systems have been proposed and published in the current literature, such as the PAW, Mishra, PLRA, DEPA, MARSPILL, etc. These classifications have identified important aspects of PRP that affect the biological composition and, ultimately, the indications and outcomes. To date, there is still a lack of standardization in sample preparation, cohort heterogeneity, and incomplete reporting of sample preparation utilized, leading to a lack of clarity and challenging researchers and clinicians

Triplet-based similarity score for fully multilabeled trees with poly-occurring labels

Motivation: The latest advances in cancer sequencing, and the availability of a wide range of methods to infer the evolutionary history of tumors, have made it important to evaluate, reconcile and cluster different tumor phylogenies. Recently, several notions of distance or similarities have been proposed in the literature, but none of them has emerged as the golden standard. Moreover, none of the known similarity measures is able to manage mutations occurring multiple times in the tree, a circumstance often occurring in real cases. Results: To overcome these limitations, in this article, we propose MP3, the first similarity measure for tumor phylogenies able to effectively manage cases where multiple mutations can occur at the same time and mutations can occur multiple times. Moreover, a comparison of MP3 with other measures shows that it is able to classify correctly similar and dissimilar trees, both on simulated and on real data

It’s not just what you eat but when: The impact of eating a meal during simulated shift work on driving performance

Published online: 13 Oct 2016.Shiftworkers have impaired performance when driving at night and they also alter their eating patterns during nightshifts. However, it is unknown whether driving at night is influenced by the timing of eating. This study aims to explore the effects of timing of eating on simulated driving performance across four simulated nightshifts. Healthy, non-shiftworking males aged 18-35 years (n = 10) were allocated to either an eating at night (n = 5) or no eating at night (n = 5) condition. During the simulated nightshifts at 1730, 2030 and 0300 h, participants performed a 40-min driving simulation, 3-min Psychomotor Vigilance Task (PVT-B), and recorded their ratings of sleepiness on a subjective scale. Participants had a 6-h sleep opportunity during the day (1000-1600 h). Total 24-h food intake was consistent across groups; however, those in the eating at night condition ate a large meal (30% of 24-h intake) during the nightshift at 0130 h. It was found that participants in both conditions experienced increased sleepiness and PVT-B impairments at 0300 h compared to 1730 and 2030 h (p < 0.001). Further, at 0300 h, those in the eating condition displayed a significant decrease in time spent in the safe zone (p < 0.05; percentage of time within 10 km/h of the speed limit and 0.8 m of the centre of the lane) and significant increases in speed variability (p < 0.001), subjective sleepiness (p < 0.01) and number of crashes (p < 0.01) compared to those in the no eating condition. Results suggest that, for optimal performance, shiftworkers should consider restricting food intake during the night.Charlotte C. Gupta, Jill Dorrian, Crystal L. Grant, Maja Pajcin, Alison M. Coates, David J. Kennaway, Gary A. Wittert, Leonie K. Heilbronn, Chris B. Della Vedova, and Siobhan Bank

High-spin states and band terminations in v 49

High-spin states in 49 V have been studied through the 28 Si(28 Si, α3p) reaction using the EUROBALL γ-ray detector array. The 49 V level scheme has been extended up to 13.1 MeV including 21 new states. Both negative and positive parity states have been interpreted in the framework of theShell Model. The 27/2− and the 31/2+ band termination states have been observed in agreement with theoretical predictions.Fil: Rodrigues Ferreira Maltez, Dario Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Comisión Nacional de Energía Atómica. Gerencia del Área de Investigación y Aplicaciones No Nucleares. Gerencia Física (Centro Atómico Constituyentes). Proyecto Tandar; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; ArgentinaFil: Hojman, Daniel Leonardo. Comisión Nacional de Energía Atómica. Gerencia del Área de Investigación y Aplicaciones No Nucleares. Gerencia Física (Centro Atómico Constituyentes). Proyecto Tandar; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Lenzi, Silvia M.. Istituto Nazionale Di Fisica Nucleare.; Italia. Università di Padova; ItaliaFil: Cardona, Maria Angelica. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Comisión Nacional de Energía Atómica. Gerencia del Área de Investigación y Aplicaciones No Nucleares. Gerencia Física (Centro Atómico Constituyentes). Proyecto Tandar; Argentina. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; ArgentinaFil: Fernea, Enrico. Università di Padova; Italia. Istituto Nazionale Di Fisica Nucleare.; ItaliaFil: Axiotis, M.. Istituto Nazionale Di Fisica Nucleare.; ItaliaFil: Beck, C.. Université de Strasbourg; Francia. Centre National de la Recherche Scientifique; FranciaFil: Bednarczyk, P.. Polish Academy of Sciences; ArgentinaFil: Bizzetti, P. G.. Università di Padova; Italia. Istituto Nazionale Di Fisica Nucleare.; ItaliaFil: Bizzetti Sona, A. M.. Università di Padova; Italia. Istituto Nazionale Di Fisica Nucleare.; ItaliaFil: Della Vedova, F.. Università di Padova; Italia. Istituto Nazionale Di Fisica Nucleare.; ItaliaFil: Grebosz, J.. Polish Academy of Sciences; ArgentinaFil: Haas, F.. Université de Strasbourg; Francia. Centre National de la Recherche Scientifique; FranciaFil: Kmiecik, M.. Polish Academy of Sciences; ArgentinaFil: Maj, A.. Polish Academy of Sciences; ArgentinaFil: Męczyński, W.. Polish Academy of Sciences; ArgentinaFil: Napoli, D. R.. Istituto Nazionale Di Fisica Nucleare.; ItaliaFil: Nespolo, M.. Università di Padova; Italia. Istituto Nazionale Di Fisica Nucleare.; ItaliaFil: Papka, P.. Université de Strasbourg; Francia. Centre National de la Recherche Scientifique; FranciaFil: Sánchez i Zafra, A.. Université de Strasbourg; Francia. Centre National de la Recherche Scientifique; FranciaFil: Styczen, J.. Polish Academy of Sciences; ArgentinaFil: Thummerer, S.. Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung; AlemaniaFil: Ziębliński, M.. Polish Academy of Sciences; Argentin

The Italian language postpartum specific anxiety scale [PSAS-IT]: translation, psychometric evaluation, and validation.

Introduction: While often positive, the lifecourse transition to motherhood is susceptible to the risk for developing mood disorders. Postpartum anxiety has often been overshadowed by other perinatal-specific mental health disorders, such as postpartum depression, and therefore has not been at the forefront or center of as much empirical study. This has meant there is a lack of effective and reliable tools with which to measure it, despite growing evidence suggesting its detrimental impact on mothers, their babies, wider family and social contacts, and on healthcare systems. This current study aimed to translate and validate the Postpartum Specific Anxiety Scale [PSAS] into the Italian language, and to validate the tool for its use in detecting anxiety specific to motherhood. Methods: The study (N = 457) comprised 4 stages: English-Italian translation and back-translation to obtain the Italian version [PSAS-IT]; a preliminary pilot study to adapt the PSAS to the characteristics of the Italian population; measurement invariance; and internal reliability of subscales. Results: The PSAS-IT demonstrates similar psychometric properties as the original English-language PSAS, with acceptable acceptability, construct and convergent validity, and internal consistency. Confirmatory factor analysis for multiple groups (Italy and United Kingdom) showed that the factor structure of the PSAS was valid for both groups [χ2 (2436) = 4679.481, p < 0.001, TLI = 0.969, CFI =0.972, RMSEA = 0.045, SRMR =0.064]. Discussion: The resulting findings offer a reliable measure of postpartum anxiety in Italian language up to six months after birth

Transition probabilities in the X(5) candidate 122^{122}Ba

To investigate the possible X(5) character of 122Ba, suggested by the ground state band energy pattern, the lifetimes of the lowest yrast states of 122Ba have been measured, via the Recoil Distance Doppler-Shift method. The relevant levels have been populated by using the 108Cd(16O,2n)122Ba and the 112Sn(13C,3n)122Ba reactions. The B(E2) values deduced in the present work are compared to the predictions of the X(5) model and to calculations performed in the framework of the IBA-1 and IBA-2 models