Online Construction of Wavelet Trees

The wavelet tree (WT) is a flexible and efficient data structure for representing character strings in succinct space, while allowing for fast generalised rank, select and access operations. As such, they play an important role in modern text indexing methods. However, despite their popularity, not many algorithms have been published concerning their construction. In particular, while the WT is capable of representing a sequence of length n over an alphabet of size m in nlg m+o(nlg m) bits, much more space is typically used for its construction. Here we propose an O(nlg m)-time online method for the construction of the WT, requiring no prior knowledge about the input alphabet. The proposed algorithm is conceptually simpler than other state-of-the-art methods, while having comparable time performance and being more space-efficient in practice, since it performs just one pass over the input text and uses little extra space other than for the structure itself, as shown both theoretically and empirically

Gravitational Collapse of Self-Similar and Shear-free Fluid with Heat Flow

A class of solutions to Einstein field equations is studied, which represents gravitational collapse of thick spherical shells made of self-similar and shear-free fluid with heat flow. It is shown that such shells satisfy all the energy conditions, and the corresponding collapse always forms naked singularities.Comment: 34 pages, 9 figures, late

On parameters of the Levi-Civita solution

The Levi-Civita (LC) solution is matched to a cylindrical shell of an anisotropic fluid. The fluid satisfies the energy conditions when the mass parameter $\sigma$ is in the range $0 \le \sigma \le 1$. The mass per unit length of the shell is given explicitly in terms of $\sigma$, which has a finite maximum. The relevance of the results to the non-existence of horizons in the LC solution and to gauge cosmic strings is pointed out.Comment: Latex, no figure

Levi-Civita Solutions Coupled with Electromagnetic Fields

The local and global properties of the Levi-Civita (LC) solutions coupled with an electromagnetic field are studied and some limits to the vacuum LC solutions are given. By doing such limits, the physical and geometrical interpretations of the free parameters involved in the solutions are made clear. Sources for both the LC vacuum solutions and the LC solutions coupled with an electromagnetic field are studied, and in particular it is found that all the LC vacuum solutions with $\sigma \ge 0$ can be produced by cylindrically symmetric thin shells that satisfy all the energy conditions, weak, dominant, and strong. When the electromagnetic field is present, the situation changes dramatically. In the case of a purely magnetic field, all the solutions with $\sigma \ge 1/\sqrt{8}$ or $\sigma \le - 1/\sqrt{8}$ can be produced by physically acceptable cylindrical thin shells, while in the case of a purely electric field, no such shells are found for any value of $\sigma$.Comment: Typed in Revtex, including two figure

Exome and Tissue-Associated Microbiota as Predictive Markers of Response to Neoadjuvant Treatment in Locally Advanced Rectal Cancer

The clinical and pathological responses to multimodal neoadjuvant therapy in locally advanced rectal cancers (LARCs) remain unpredictable, and robust biomarkers are still lacking. Recent studies have shown that tumors present somatic molecular alterations related to better treatment response, and it is also clear that tumor-associated bacteria are modulators of chemotherapy and immunotherapy efficacy, therefore having implications for long-term survivorship and a good potential as the biomarkers of outcome. Here, we performed whole exome sequencing and 16S ribosomal RNA (rRNA) amplicon sequencing from 44 pre-treatment LARC biopsies from Argentinian and Brazilian patients, treated with neoadjuvant chemoradiotherapy or total neoadjuvant treatment, searching for predictive biomarkers of response (responders, n = 17; non-responders, n = 27). In general, the somatic landscape of LARC was not capable to predict a response; however, a significant enrichment in mutational signature SBS5 was observed in non-responders (p = 0.0021), as well as the co-occurrence of APC and FAT4 mutations (p < 0.05). Microbiota studies revealed a similar alpha and beta diversity of bacteria between response groups. Yet, the linear discriminant analysis (LDA) of effect size indicated an enrichment of Hungatella, Flavonifractor, and Methanosphaera (LDA score ≥3) in the pre-treatment biopsies of responders, while non-responders had a higher abundance of Enhydrobacter, Paraprevotella (LDA score ≥3) and Finegoldia (LDA score ≥4). Altogether, the evaluation of these biomarkers in pre-treatment biopsies could eventually predict a neoadjuvant treatment response, while in post-treatment samples, it could help in guiding non-operative treatment strategies.Fil: Takenaka, Isabella Kuniko T. M.. No especifíca;Fil: Bartelli, Thais F.. No especifíca;Fil: Defelicibus, Alexandre. No especifíca;Fil: Sendoya, Juan Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Golubicki, Mariano. Gobierno de la Ciudad de Buenos Aires. Hospital de Gastroenterología "Dr. Carlos B. Udaondo"; ArgentinaFil: Robbio, Juan. No especifíca;Fil: Serpa, Marianna S.. No especifíca;Fil: Branco, Gabriela P.. No especifíca;Fil: Santos, Luana B. C.. No especifíca;Fil: Claro, Laura C. L.. No especifíca;Fil: Oliveira dos Santos, Gabriel. No especifíca;Fil: Kupper, Bruna E. C.. No especifíca;Fil: da Silva, Israel T.. No especifíca;Fil: Llera, Andrea Sabina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: de Mello, Celso A. L.. No especifíca;Fil: Riechelmann, Rachel P.. No especifíca;Fil: Dias Neto, Emmanuel. Universidade de Sao Paulo; BrasilFil: Iseas, Soledad. Gobierno de la Ciudad de Buenos Aires. Hospital de Gastroenterología "Dr. Carlos B. Udaondo"; ArgentinaFil: Aguiar, Samuel. No especifíca;Fil: Nunes, Diana Noronha. No especifíca

Modelling the spectral energy distribution of galaxies. V. The dust and PAH emission SEDs of disk galaxies

We present a self-consistent model of the spectral energy distributions (SEDs) of spiral galaxies from the ultraviolet (UV) to the mid-infrared (MIR)/far-infrared (FIR)/submillimeter (submm) based on a full radiative transfer calculation of the propagation of starlight in galaxy disks. This model predicts not only the total integrated energy absorbed in the UV/optical and re-emitted in the infrared/submm, but also the colours of the dust emission based on an explicit calculation of the strength and colour of the UV/optical radiation fields heating the dust, and incorporating a full calculation of the stochastic heating of small dust grains and PAH molecules. The geometry of the translucent components of the model is empirically constrained using the results from the radiation transfer analysis of Xilouris et al. on spirals in the middle range of the Hubble sequence, while the geometry of the optically thick components is constrained from physical considerations with a posteriori checks of the model predictions with observational data. These geometrical constraints enable the dust emission to be predicted in terms of a minimum set of free parameters: the central face-on dust opacity in the B-band tau^f_B, a clumpiness factor F for the star-forming regions, the star-formation rate SFR, the normalised luminosity of the old stellar population old and the bulge-to-disk ratio B/D. We show that these parameters are almost orthogonal in their predicted effect on the colours of the dust/PAH emission. The results of the calculations are made available in the form of a large library of simulated dust emission SEDs spanning the whole parameter space of our model, together with the corresponding library of dust attenuation calculated using the same model. (see full abstract in the paper)Comment: 39 pages; accepted for publication in Astronomy & Astrophysics; For a higher resolution version of Fig.1 and Fig.20 see http://www.star.uclan.ac.uk/~ccp/index.shtm

A canine leishmaniasis pilot survey in an emerging focus of visceral leishmaniasis: Posadas (Misiones, Argentina)

<p>Abstract</p> <p>Background</p> <p>An increasing number of reports are calling our attention to the worldwide spread of leishmaniasis. The urbanization of zoonotic visceral leishmaniasis (VL) has been observed in different South American countries, due to changes in demographic and ecological factors. In May 2006, VL was detected for the first time in the city of Posadas (Misiones, Argentina). This event encouraged us to conduct a clinical and parasitological pilot survey on domestic dogs from Posadas to identify their potential role as reservoirs for the disease.</p> <p>Methods</p> <p>One hundred and ten dogs from the city of Posadas were included in the study. They were selected based on convenience and availability. All dogs underwent clinical examination. Symptomatology related to canine leishmaniasis was recorded, and peripheral blood and lymph node aspirates were collected. Anti-<it>Leishmania </it>antibodies were detected using rK39-immunocromatographic tests and IFAT. Parasite detection was based on peripheral blood and lymph node aspirate PCR targeting the <it>SSUrRNA </it>gene. Molecular typing was addressed by DNA sequence analysis of the PCR products obtained by <it>SSUrRNA </it>and ITS-1 PCR.</p> <p>Results</p> <p>According to clinical examination, 69.1% (76/110) of the dogs presented symptoms compatible with canine leishmaniasis. Serological analyses were positive for 43.6% (48/110) of the dogs and parasite DNA was detected in 47.3% (52/110). A total of 63 dogs (57.3%) were positive by serology and/or PCR. Molecular typing identified <it>Leishmania infantum </it>(syn. <it>Leishmania chagasi</it>) as the causative agent.</p> <p>Conclusions</p> <p>This work confirms recent findings which revealed the presence of <it>Lutzomyia longipalpis</it>, the vector of <it>L. infantum </it>in this area of South America. This new VL focus could be well established, and further work is needed to ascertain its magnitude and to prevent further human VL cases.</p

Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual

Although patterns of somatic alterations have been reported for tumor genomes, little is known on how they compare with alterations present in non-tumor genomes. A comparison of the two would be crucial to better characterize the genetic alterations driving tumorigenesis. We sequenced the genomes of a lymphoblastoid (HCC1954BL) and a breast tumor (HCC1954) cell line derived from the same patient and compared the somatic alterations present in both. The lymphoblastoid genome presents a comparable number and similar spectrum of nucleotide substitutions to that found in the tumor genome. However, a significant difference in the ratio of non-synonymous to synonymous substitutions was observed between both genomes (P = 0.031). Protein–protein interaction analysis revealed that mutations in the tumor genome preferentially affect hub-genes (P = 0.0017) and are co-selected to present synergistic functions (P < 0.0001). KEGG analysis showed that in the tumor genome most mutated genes were organized into signaling pathways related to tumorigenesis. No such organization or synergy was observed in the lymphoblastoid genome. Our results indicate that endogenous mutagens and replication errors can generate the overall number of mutations required to drive tumorigenesis and that it is the combination rather than the frequency of mutations that is crucial to complete tumorigenic transformation

f(R) theories

Over the past decade, f(R) theories have been extensively studied as one of the simplest modifications to General Relativity. In this article we review various applications of f(R) theories to cosmology and gravity - such as inflation, dark energy, local gravity constraints, cosmological perturbations, and spherically symmetric solutions in weak and strong gravitational backgrounds. We present a number of ways to distinguish those theories from General Relativity observationally and experimentally. We also discuss the extension to other modified gravity theories such as Brans-Dicke theory and Gauss-Bonnet gravity, and address models that can satisfy both cosmological and local gravity constraints.Comment: 156 pages, 14 figures, Invited review article in Living Reviews in Relativity, Published version, Comments are welcom

Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual

Although patterns of somatic alterations have been reported for tumor genomes, little is known on how they compare with alterations present in non-tumor genomes. A comparison of the two would be crucial to better characterize the genetic alterations driving tumorigenesis. We sequenced the genomes of a lymphoblastoid (HCC1954BL) and a breast tumor (HCC1954) cell line derived from the same patient and compared the somatic alterations present in both. The lymphoblastoid genome presents a comparable number and similar spectrum of nucleotide substitutions to that found in the tumor genome. However, a significant difference in the ratio of non-synonymous to synonymous substitutions was observed between both genomes (P = 0.031). Protein–protein interaction analysis revealed that mutations in the tumor genome preferentially affect hub-genes (P = 0.0017) and are co-selected to present synergistic functions (P < 0.0001). KEGG analysis showed that in the tumor genome most mutated genes were organized into signaling pathways related to tumorigenesis. No such organization or synergy was observed in the lymphoblastoid genome. Our results indicate that endogenous mutagens and replication errors can generate the overall number of mutations required to drive tumorigenesis and that it is the combination rather than the frequency of mutations that is crucial to complete tumorigenic transformation