Maximum likelihood estimation of toric Fano varieties

We study the maximum likelihood estimation problem for several classes of toric Fano models. We start by exploring the maximum likelihood degree for all $2$-dimensional Gorenstein toric Fano varieties. We show that the ML degree is equal to the degree of the surface in every case except for the quintic del Pezzo surface with two ordinary double points and provide explicit expressions that allow one to compute the maximum likelihood estimate in closed form whenever the ML degree is less than 5. We then explore the reasons for the ML degree drop using $A$-discriminants and intersection theory. Finally, we show that toric Fano varieties associated to 3-valent phylogenetic trees have ML degree one and provide a formula for the maximum likelihood estimate. We prove it as a corollary to a more general result about the multiplicativity of ML degrees of codimension zero toric fiber products, and it also follows from a connection to a recent result about staged trees.Comment: 28 pages, 4 figures, 4 tables, this article supersedes arXiv:1602.0830

Hepatitis B virus genotypes and resistance mutations in patients under long term lamivudine therapy: characterization of genotype G in Brazil

Submitted by Sandra Infurna ([email protected]) on 2018-08-02T14:46:32Z No. of bitstreams: 1 kiciamro_etal_IOC_2008.pdf: 506267 bytes, checksum: f7829a89c2411e97f96c3d5a4123f436 (MD5)Approved for entry into archive by Sandra Infurna ([email protected]) on 2018-08-02T14:57:58Z (GMT) No. of bitstreams: 1 kiciamro_etal_IOC_2008.pdf: 506267 bytes, checksum: f7829a89c2411e97f96c3d5a4123f436 (MD5)Made available in DSpace on 2018-08-02T14:57:58Z (GMT). No. of bitstreams: 1 kiciamro_etal_IOC_2008.pdf: 506267 bytes, checksum: f7829a89c2411e97f96c3d5a4123f436 (MD5) Previous issue date: 2008Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Virologia Molecular. Rio de Janeiro, RJ. Brasil.Universidade Federal de Mato Grosso. Faculdade de Ciências Médicas. Núcleo de Estudos de Doenças Infecciosas e Tropicais. Cuiabá, MT, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Virologia Molecular. Rio de Janeiro, RJ. Brasil / Fundação Municipal de Saúde de Petrópolis. Hospital Alcides Carneiro. Petrópolis, RJ. Brasil.Universidade Federal do Estado do Rio de Janeiro. Hospital Universitário Gaffrée e Guinle. Rio de Janeiro, RJ, Brasil.Universidade Federal do Estado do Rio de Janeiro. Hospital Universitário Gaffrée e Guinle. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Virologia Molecular. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Virologia Molecular. Rio de Janeiro, RJ. Brasil.Lamivudine is an oral nucleoside analogue widely used for the treatment of chronic hepatitis B. The main limitation of lamivudine use is the selection of resistant mutations that increases with time of utilization. Hepatitis B virus (HBV) isolates have been classified into eight genotypes (A to H) with distinct geographical distributions. HBV genotypes may also influence pathogenic properties and therapeutic features. Here, we analyzed the HBV genotype distribution and the nature and frequency of lamivudine resistant mutations among 36 patients submitted to lamivudine treatment for 12 to 84 months

Time, intersubjectivity, and musical relationship in Alfred Schutz

In questo lavoro, affronto alcuni aspetti della relazione tra tempo e intersoggettività in Alfred Schutz . Presento una sintesi dell’architettura metodologica del sociologo austriaco, delineando la specificità della relazione tra tempo e coscienza. Prendo in esame la trattazione dell’esperienza musicale come esempio di declinazione peculiare di una serie di dinamiche temporali connesse alla costituzione intersoggettiva dei significati. Infine, espongo alcune tesi di autori che si sono occupati della relazione tra tempo, intersoggettività e musica in Schutz. La relazione musicale è un esempio di contesto dotato di senso, non oggetto di concettualizzazione, che esemplifica la relazione tra senso soggettivo ed esperienza dell’altro. La teoria dell’appresentazione di Schutz è il centro del processo di costituzione dei significati della prensione dell’altro. L’emersione dei significati è legata alle dinamiche dei poli passivi e attivi della coscienza e alla costituzione, nella we-relation, di una dimensione radicalmente intersoggettiva nella quale si supera la distinzione cartesiana tra interno ed esterno.Time, intersubjectivity, and musical relationship in Alfred Schutz Riccardo Venturini In this work I tackle certain aspects of the relationship between time and intersubjectivity in Alfred Schutz. I present a summary of the methodological architecture of the Austrian sociologist, outlining the specificity of the relationship between time and consciousness. I discuss the treatment of the musical experience as an example of the peculiar declination of a series of temporal dynamics connected to the intersubjective creation of meanings. Finally, I set out some thoughts related to the debate on the relationship between time, intersubjectivity and music in Schutz. The musical relationship is a context endowed with meaning, not the object of conceptualization, that allows us to identify in a paradigmatic way the relationship between the subjective sense and experience of the other. The theory of appresentation of Schutz is the center of the process of constitution of meaning of the understanding of the other. The emergence of meaning is related to the dynamics of the passive and active poles of the consciousness and the constitution, in the we-relation, of a radically intersubjective dimension that exceeds the Cartesian distinction between inside and outside

Mock galaxy redshift catalogues from simulations: implications for Pan-STARRS1

We describe a method for constructing mock galaxy catalogues which are well suited for use in conjunction with large photometric surveys. We use the semi-analytic galaxy formation model of Bower et al. implemented in the Millennium simulation. We apply our method to the specific case of the surveys soon to commence with PS1, the first of 4 telescopes planned for the Pan-STARRS system. PS1 has 5 photometric bands (grizy), and will carry out an all-sky 3pi survey and a medium deep survey (MDS) over 84 sq.deg. We calculate the expected magnitude limits for extended sources in the two surveys. We find that, after 3 years, the 3pi survey will have detected over 10^8 galaxies in all 5 bands, 10 million of which will lie at redshift z>0.9, while the MDS will have detected over 10^7 galaxies with 0.5 million lying at z>2. These numbers at least double if detection in the shallowest band, y is not required. We then evaluate the accuracy of photometric redshifts estimated using an off-the-shelf photo-z code. With the grizy bands alone it is possible to achieve an accuracy in the 3pi survey of Delta z/(1+z)~0.06 for 0.25<z<0.8, which could be reduced by about 15% using near infrared photometry from the UKIDDS survey, but would increase by about 25% for the deeper sample without the y band photometry. For the MDS an accuracy of Delta z/(1+z)~0.05 is achievable for 0.02<z<1.5 using grizy. A dramatic improvement in accuracy is possible by selecting only red galaxies. In this case, Delta z/(1+z)~0.02-0.04 is achievable for ~100 million galaxies at 0.4<z<1.1 in the 3pi survey and for 30 million galaxies in the MDS at 0.4<z<2. We investigate the effect of using photo-z in the estimate of the baryonic acoustic oscillation scale. We find that PS1 will achieve a similar accuracy in this estimate as a spectroscopic survey of 20 million galaxies.Comment: 23 pages, 18 figures, accepted by MNRA

Measuring large-scale structure with quasars in narrow-band filter surveys

We show that a large-area imaging survey using narrow-band filters could detect quasars in sufficiently high number densities, and with more than sufficient accuracy in their photometric redshifts, to turn them into suitable tracers of large-scale structure. If a narrow-band optical survey can detect objects as faint as i=23, it could reach volumetric number densities as high as 10^{-4} h^3 Mpc^{-3} (comoving) at z~1.5 . Such a catalog would lead to precision measurements of the power spectrum up to z~3-4. We also show that it is possible to employ quasars to measure baryon acoustic oscillations at high redshifts, where the uncertainties from redshift distortions and nonlinearities are much smaller than at z<1. As a concrete example we study the future impact of J-PAS, which is a narrow-band imaging survey in the optical over 1/5 of the unobscured sky with 42 filters of ~100 A full-width at half-maximum. We show that J-PAS will be able to take advantage of the broad emission lines of quasars to deliver excellent photometric redshifts, \sigma_{z}~0.002(1+z), for millions of objects.Comment: Matches version published in MNRAS (2012

The WiggleZ Dark Energy Survey: the transition to large-scale cosmic homogeneity

We have made the largest-volume measurement to date of the transition to large-scale homogeneity in the distribution of galaxies. We use the WiggleZ survey, a spectroscopic survey of over 200,000 blue galaxies in a cosmic volume of ~1 (Gpc/h)^3. A new method of defining the 'homogeneity scale' is presented, which is more robust than methods previously used in the literature, and which can be easily compared between different surveys. Due to the large cosmic depth of WiggleZ (up to z=1) we are able to make the first measurement of the transition to homogeneity over a range of cosmic epochs. The mean number of galaxies N(<r) in spheres of comoving radius r is proportional to r^3 within 1%, or equivalently the fractal dimension of the sample is within 1% of D_2=3, at radii larger than 71 \pm 8 Mpc/h at z~0.2, 70 \pm 5 Mpc/h at z~0.4, 81 \pm 5 Mpc/h at z~0.6, and 75 \pm 4 Mpc/h at z~0.8. We demonstrate the robustness of our results against selection function effects, using a LCDM N-body simulation and a suite of inhomogeneous fractal distributions. The results are in excellent agreement with both the LCDM N-body simulation and an analytical LCDM prediction. We can exclude a fractal distribution with fractal dimension below D_2=2.97 on scales from ~80 Mpc/h up to the largest scales probed by our measurement, ~300 Mpc/h, at 99.99% confidence.Comment: 21 pages, 16 figures, accepted for publication in MNRA

False Vacuum Inflation with Einstein Gravity

We investigate chaotic inflation models with two scalar fields, such that one field (the inflaton) rolls while the other is trapped in a false vacuum state. The false vacuum becomes unstable when the inflaton field falls below some critical value, and a first or second order transition to the true vacuum ensues. Particular attention is paid to Linde's second-order `Hybrid Inflation'; with the false vacuum dominating, inflation differs from the usual true vacuum case both in its cosmology and in its relation to particle physics. The spectral index of the adiabatic density perturbation can be very close to 1, or it can be around ten percent higher. The energy scale at the end of inflation can be anywhere between $10^{16}$\,GeV and $10^{11}$\,GeV, though reheating is prompt so the reheat temperature can't be far below $10^{11}\,$GeV. Topological defects are almost inevitably produced at the end of inflation, and if the inflationary energy scale is near its upper limit they can have significant effects. Because false vacuum inflation occurs with the inflaton field far below the Planck scale, it is easier to implement in the context of supergravity than standard chaotic inflation. That the inflaton mass is small compared with the inflationary Hubble parameter is still a problem for generic supergravity theories, but remarkably this can be avoided in a natural way for a class of supergravity models which follow from orbifold compactification of superstrings. This opens up the prospect of a truly realistic, superstringComment: 37 pages, LaTeX (3 figures available as hard copies only), SUSSEX-AST 94/1-

High rate of depression in patients with chronic hepatitis C / Taxa elevada de depressão em pacientes com hepatite C crônica

Objectives: To describe the frequency of depression in patients with hepatitis C (HCV) and relate to the biological variables and liver function. Methods: Cross-sectional, descriptive study with a quantitative approach, which assessed depression using the criteria of the Diagnostic and Statistical Manual of Mental Disorders (DSM-V) and the association with biological and liver function variables in 85 patients HCV chronically infected indicated for direct-acting antiviral therapy (DAA) between May 2018 and May 2019. Results: Depression was detected in 47.1% of patients, predominantly mild depression (95%). However, depression occurred independently of biological characteristics, such as gender, age, education, associated comorbidities and liver function, such as degree of fibrosis and viral genotype. Conclusions: The frequency of depression was high in patients with HCV and had no statistical relationship with biological characteristics and liver function, suggesting that active search for depression could be a valuable strategy in managing these patients.Objetivos: Describir la frecuencia de depresión en pacientes con hepatitis C (VHC) y relacionarla con variables biológicas y función hepática. Métodos: Estudio descriptivo transversal con abordaje cuantitativo, que evaluó la depresión utilizando los criterios del Manual Diagnóstico y Estadístico de los Trastornos Mentales (DSM-V) y la asociación con variables biológicas y de función hepática en 85 pacientes con VHC crónico indicados para tratamento com terapia antiviral de acción directo (AAD) entre mayo de 2018 y 2019. Resultados: Se detectó depresión en el 47,1% de los pacientes, predominantemente depresión leve (95%). Sin embargo, la depresión se produjo independientemente de las características biológicas, como el sexo, la edad, la educación, las comorbilidades asociadas y la función hepática, como el grado de fibrosis y el genotipo viral. Conclusiones: La frecuencia de depresión fue alta en pacientes con VHC y no tuvo relación estadística con características biológicas y función hepática, sugiriendo la búsqueda activa de depresión como estrategia en el manejo de estos pacientes.Objetivos: descrever a frequência de depressão em pacientes com hepatite C (HCV) e relacionar com as variáveis biológicas e função hepática. Métodos: estudo transversal, descritivo, de abordagem quantitativa, que avaliou a depressão utilizando os critérios do Manual de diagnóstico e estatístico de transtornos mentais (DSM-V) e a associação com as variáveis biológicas e de função hepática em 85 pacientes com HCV crônica indicados para a terapia antiviral de ação direta (DAA) entre maio de 2018 e 2019. Resultados: detectou-se depressão em 47,1% dos pacientes, predominantemente depressão leve (95%). Entretanto a depressão ocorreu de forma independente das características biológicas, como sexo, idade, escolaridade, comorbidades associadas e da função hepática, como grau de fibrose e genótipo viral. Conclusões: a frequência de depressão foi alta em pacientes com HCV e não teve relação estatística com as características biológicas e função hepática, sugerindo a busca ativa da depressão como estratégia na condução destes pacientes.

Lesão renal aguda após cirurgias não cardíacas: incidência e impacto das disfunções orgânicas extra-renais nos desfechos

Introdução: A permanência de pacientes em Unidades de Terapia Intensiva (UTI) é frequentemente complicada por Lesão Renal Aguda (LRA), principalmente em casos de sepse, baixo débito cardíaco e pós-operatório de grandes cirurgias. Objetivo: Avaliar a incidência, características, desenvolvimento de outras disfunções orgânicas, e desfechos de pacientes com LRA adquirida na UTI após cirurgias não cardíacas. Métodos: Estudo de coorte, prospectivo. Todos os pacientes internados consecutivamente nas UTIs após cirurgias não cardíacas nos meses de abril e maio de 2017 foram analisados quanto ao desenvolvimento ou não de LRA, de outras disfunções orgânicas e ao balanço hídrico. Resultados: A incidência de LRA foi de 16,2%. Os pacientes que desenvolveram LRA no pós-operatório eram mais graves, e diferiram quanto à necessidade de ventilação mecânica (60% vs. 11%, p < 0,001), uso de drogas vasoativas (82% vs. 44%, p = 0,021); presença de infecção (80% vs. 21%, p < 0,001), sepse ou choque séptico (50% vs. 9%, p < 0,001) e a outras complicações pós-operatórias (91% vs. 58%, p = 0,023). Outras disfunções de órgãos e sistemas foram mais fre-quentes nos pacientes com IRA (2 [2-3] vs. 1 [0-1], p < 0,001), particularmente disfunção gas-trointestinal (73% vs. 19%, p < 0,001) e cardiovascular (73% vs. 33%, p = 0,015). O número de pacientes com duas ou mais disfunções orgânicas aumentou de 21% para 82% em pacientes com LRA (RR 3,89, IC: 2,18 – 6,90, p < 0,001). O tempo de internação (13 ± 9 vs. 5 ± 6 dias, p < 0,001) e a mortalidade hospitalar (54,5% vs. 7%, p = 0,013) foram maiores nos pacientes com LRA. Conclusão: Entre pacientes com cirurgias não cardíacas e necessidade de UTI, a incidência de LRA é elevada e associada a complicações de outros sistemas, incluindo os sistemas neurológico, gastrointestinal, respiratório e cardiovascular; somandose a isso, balanço hídrico acumulado positivo, sepse e choque, maior tempo de internação e maiores taxas de mortalidade também foram encontrados nesses pacientes

Actionable, Pathogenic Incidental Findings in 1,000 Participants’ Exomes

The incorporation of genomics into medicine is stimulating interest on the return of incidental findings (IFs) from exome and genome sequencing. However, no large-scale study has yet estimated the number of expected actionable findings per individual; therefore, we classified actionable pathogenic single-nucleotide variants in 500 European- and 500 African-descent participants randomly selected from the National Heart, Lung, and Blood Institute Exome Sequencing Project. The 1,000 individuals were screened for variants in 114 genes selected by an expert panel for their association with medically actionable genetic conditions possibly undiagnosed in adults. Among the 1,000 participants, 585 instances of 239 unique variants were identified as disease causing in the Human Gene Mutation Database (HGMD). The primary literature supporting the variants’ pathogenicity was reviewed. Of the identified IFs, only 16 unique autosomal-dominant variants in 17 individuals were assessed to be pathogenic or likely pathogenic, and one participant had two pathogenic variants for an autosomal-recessive disease. Furthermore, one pathogenic and four likely pathogenic variants not listed as disease causing in HGMD were identified. These data can provide an estimate of the frequency (∼3.4% for European descent and ∼1.2% for African descent) of the high-penetrance actionable pathogenic or likely pathogenic variants in adults. The 23 participants with pathogenic or likely pathogenic variants were disproportionately of European (17) versus African (6) descent. The process of classifying these variants underscores the need for a more comprehensive and diverse centralized resource to provide curated information on pathogenicity for clinical use to minimize health disparities in genomic medicine