Hierarchical modelling of patient-reported outcomes data based on the beta-binomial distribution

The beta-binomial distribution does not belong to the exponential family and, hence classical regression techniques cannot be used when dealing with outcomes following the mentioned distribution. In this thesis we propose and develop regression models based on the beta-binomial distribution for the analysis of U, J or inverse J-shaped discrete and bounded outcomes. In fact, although this thesis is focused on the analysis of patient-reported outcomes (PROs), which usually follow the mentioned distributional shapes, proposed models can also be extended to several fields. First of all, we make a review and comparison of existing beta-binomial regression approaches in independent data context, concluding that the marginal approach is the most adequate. However, PRO studies are usually carried out in a longitudinal framework, where patients' responses are measured over time. This leads to a multilevel or correlated data structure and consequently, we extend the marginal beta-binomial regression approach to the inclusion of random effects to accommodate the hierarchical structure of the data. We develop the estimation and inference procedure for the model proposal. Furthermore, we compare the performance of our proposal with similar approaches in the literature, showing that it gets better results in terms of reducing the bias of the estimates. We apply the model to a longitudinal Chronic Obstructive Pulmonary Disease study carried out at Galdakao Hospital, reaching clinically and statistically relevant results about the evolution of the patients over time. PROs are usually obtained using rating scale questionnaires consisting of questions or items, grouped into one or more subscales, often called dimensions or domains. Therefore, we also propose a multivariate regression model based on the beta-binomial distribution for the joint analysis of all the longitudinal dimensions provided by different questionnaires. Finally, it is worth mentioning that we have implemented all the proposed regression models in the PROreg R- package which is freely available at CRAN.Department of Education, Language Policy and Culture of the Basque Government IT-620-13 program, MTM2013-40941-P and MTM2016-74931-

Comparison of beta-binomial regression model approaches to analyze health related quality of life data

Health related quality of life (HRQoL) has become an increasingly important indicator of health status in clinical trials and epidemiological research. Moreover, the study of the relationship of HRQoL with patients' and disease's characteristics has become one of the primary aims of many HRQoL studies. HRQoL scores are usually assumed to be distributed as binomial random variables and often highly skewed. The use of the beta-binomial distribution in the regression context has been proposed to model such data, however, the beta-binomial regression has been performed by means of two di erent approaches in the literature: i) beta-binomial distribution with a logistic link; and ii) hierarchical generalized linear models (HGLMs). None of the existing literature in the analysis of HRQoL survey data has performed a comparison of both approaches in terms of adequacy and regression parameter interpretation context. This paper is motivated by the analysis of a real data application of HRQoL outcomes in patients with Chronic Obstructive Pulmonary Disease (COPD), where the use of both approaches yields to contradictory results in terms of covariate e ects signi cance and consequently the interpretation of the most relevant factors in HRQoL. We present an explanation of the results in both methodologies through a simulation study and address the need to apply the proper approach in the analysis of HRQoL survey data for practitioners, providing an R package.IT-620-13, MTM2013-40941-P, MTM2014-52184-P, MTM2016-74931-P, RD12/0001/0001 - REDISSE

Classification and Biogeography of Panicoideae (Poaceae) in the New World

Panicoideae (Poaceae) in the New World comprise 107 genera (86 native) and 1357 species (1248 native). As circumscribed herein, Panicoideae include eight tribes: Andropogoneae, Arundinelleae, Centotheceae, Gynerieae, Isachneae, Paniceae, Steyermarkochloeae, and Thysanolaeneae. The two major tribes are Andropogoneae with 230 species (16.95% of all New World panicoids), and Paniceae with 1082 species (79.73%). Andropogoneae are divided into nine subtribes (Andropogoninae, Anthistiriinae, Coicinae, Germainiinae, Ischaeminae, Rottboelliinae, Saccharinae, Sorghinae, and Tripsacinae), while Paniceae are divided into seven subtribes (Arthropogoninae, Cenchrinae, Digitariinae, Melinidinae, Panicinae, Paspalinae, and Setariinae). Brazil is the center of diversity of New World panicoids with 741 species (54.6% of all species). The distributions of endemic and restricted taxa were analyzed in terms of biogeographical regions and Kranz syndrome. Amphitropical disjuncts and widespread species are also discussed

Transcriptomic analysis of the hepatic response to stress in the red cusk-eel (Genypterus chilensis): Insights into lipid metabolism, oxidative stress and liver steatosis

Indexación: Scopus.Teleosts exhibit a broad divergence in their adaptive response to stress, depending on the magnitude, duration, and frequency of stressors and the species receiving the stimulus. We have previously reported that the red cusk-eel (Genypterus chilensis), an important marine farmed fish, shows a physiological response to stress that results in increased skeletal muscle atrophy mediated by over-expression of components of the ubiquitin proteasome and autophagy-lysosomal systems. To better understand the systemic effects of stress on the red cusk-eel metabolism, the present study assessed the transcriptomic hepatic response to repetitive handling-stress. Using high-Throughput RNA-seq, 259 up-regulated transcripts were found, mostly associated with angiogenesis, gluconeogenesis, and triacylglyceride catabolism. Conversely, 293 transcripts were down-regulated, associated to cholesterol biosynthesis, PPARα signaling, fatty acid biosynthesis, and glycolysis. This gene signature was concordant with hepatic metabolite levels and hepatic oxidative damage. Moreover, the increased plasmatic levels of AST (aspartate aminotransferase), ALT (alanine aminotransferase) and AP (alkaline phosphatase), as well as liver histology suggest stress-induced liver steatosis. This study offers an integrative molecular and biochemical analysis of the hepatic response to handling-stress, and reveals unknown aspects of lipid metabolism in a non-model teleost.http://journals.plos.org/plosone/article?id=10.1371/journal.pone.017644

Evolutionary relationships in Panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae)

Background: Panicoideae are the second largest subfamily in Poaceae (grass family), with 212 genera and approximately 3316 species. Previous studies have begun to reveal relationships within the subfamily, but largely lack resolution and/or robust support for certain tribal and subtribal groups. This study aims to resolve these relationships, as well as characterize a putative mitochondrial insert in one linage. Results: 35 newly sequenced Panicoideae plastomes were combined in a phylogenomic study with 37 other species: 15 Panicoideae and 22 from outgroups. A robust Panicoideae topology largely congruent with previous studies was obtained, but with some incongruences with previously reported subtribal relationships. A mitochondrial DNA (mtDNA) to plastid DNA (ptDNA) transfer was discovered in the Paspalum lineage. Conclusions: The phylogenomic analysis returned a topology that largely supports previous studies. Five previously recognized subtribes appear on the topology to be non-monophyletic. Additionally, evidence for mtDNA to ptDNA transfer was identified in both Paspalum fimbriatum and P. dilatatum, and suggests a single rare event that took place in a common progenitor. Finally, the framework from this study can guide larger whole plastome sampling to discern the relationships in Cyperochloeae, Steyermarkochloeae, Gynerieae, and other incertae sedis taxa that are weakly supported or unresolved.Fil: Burke, Sean V.. Northern Illinois University; Estados UnidosFil: Wysocki, William P.. Northern Illinois University; Estados UnidosFil: Zuloaga, Fernando Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Craine, Joseph M.. Jonah Ventures; Estados UnidosFil: Pires, J. Chris. University of Missouri; Estados UnidosFil: Edger, Patrick P.. Michigan State University; Estados UnidosFil: Mayfield Jones, Dustin. Donald Danforth Plant Science Center; Estados UnidosFil: Clark, Lynn G.. Iowa State University; Estados UnidosFil: Kelchner, Scot A.. University of Idaho; Estados UnidosFil: Duvall, Melvin R.. Northern Illinois University; Estados Unido

Macro-Climatic Distribution Limits Show Both Niche Expansion and Niche Specialization among C4 Panicoids

Grasses are ancestrally tropical understory species whose current dominance in warm open habitats is linked to the evolution of C4 photosynthesis. C4 grasses maintain high rates of photosynthesis in warm and water stressed environments, and the syndrome is considered to induce niche shifts into these habitats while adaptation to cold ones may be compromised. Global biogeographic analyses of C4 grasses have, however, concentrated on diversity patterns, while paying little attention to distributional limits. Using phylogenetic contrast analyses, we compared macro-climatic distribution limits among ~1300 grasses from the subfamily Panicoideae, which includes 4/5 of the known photosynthetic transitions in grasses. We explored whether evolution of C4 photosynthesis correlates with niche expansions, niche changes, or stasis at subfamily level and within the two tribes Paniceae and Paspaleae. We compared the climatic extremes of growing season temperatures, aridity, and mean temperatures of the coldest months. We found support for all the known biogeographic distribution patterns of C4 species, these patterns were, however, formed both by niche expansion and niche changes. The only ubiquitous response to a change in the photosynthetic pathway within Panicoideae was a niche expansion of the C4 species into regions with higher growing season temperatures, but without a withdrawal from the inherited climate niche. Other patterns varied among the tribes, as macro-climatic niche evolution in the American tribe Paspaleae differed from the pattern supported in the globally distributed tribe Paniceae and at family level.Fil: Aagesen, Lone. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Biganzoli, Fernando. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Métodos Cuantitativos y Sistemas de Información; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Bena, María Julia. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Godoy Bürki, Ana Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Reinheimer, Renata. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; ArgentinaFil: Zuloaga, Fernando Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; Argentin

Paspalum stellatum Humb. & Bonpl. ex Flüggé

ResistenciapublishedVersio

Refractive-index sensing with ultra-thin plasmonic nanotubes

We study the refractive-index sensing properties of plasmonic nanotubes with a dielectric core and ultra-thin metal shell. The few-nm thin metal shell is described by both the usual Drude model and the nonlocal hydrodynamic model to investigate the effects of nonlocality. We derive an analytical expression for the extinction cross section and show how sensing of the refractive index of the surrounding medium and the figure-of-merit are affected by the shape and size of the nanotubes. Comparison with other localized surface plasmon resonance sensors reveals that the nanotube exhibits superior sensitivity and comparable figure-of-merit

Comparison of conventional and dispersive solid phase extraction clean-up approaches for the simultaneous analysis of tetracyclines and sulfonamides in a variety of fresh vegetables

he extensive use of antibiotics in agriculture has led to the occurrence of residual drugs in different vegetables frequently consumed by humans. This could pose a potential threat to human health, not only because of the possible effects after ingestion but also because the transmission of antibiotic-resistant genes could occur. In this work, two accurate sample preparation procedures were developed and validated for the simultaneous analysis of sulfonamides (SAs) and tetracyclines (TCs) in four of the most widely consumed vegetables (lettuce, onion, tomato, and carrot) in Europe. The evaluated protocols were based on QuECHERS for extraction and subsequent clean-up by SPE (solid phase extraction) or dispersive SPE. Parameters affecting both extraction and clean-up were carefully evaluated and selected for accuracy of results and minimal matrix effect. Overall, apparent recoveries were above 70% for most of the target analytes with both analytical procedures, and adequate precision (RSD<30%) was obtained for all the matrices. The procedural limits of quantification (LOQPRO) values for SPE clean-up remained below 4.4 μg kg−1 for TCs in all vegetables except for chlortetracycline (CTC) in lettuce (11.3 μg kg−1) and 3.0 μg kg−1 for SAs, with the exception of sulfadiazine (SDZ) in onion (3.9 μg kg−1) and sulfathiazole (STZ) in carrot (5.0 μg kg−1). Lower LOQPRO values (0.1–3.7 μg kg−1) were obtained, in general, when dSPE clean-up was employed. Both methods were applied to twenty-five market vegetable samples from ecological and conventional agriculture and only sulfamethazine (SMZ) and sulfapyridine (SPD) were detected in lettuce at 1.2 μg kg−1 and 0.5 μg kg−1, respectively.Authors acknowledge financial support from the Elkartek project entitled “Emergencia y diseminación de resistencia a los antibióticos: vínculos entre salud humana, ganadería, alimentación y medioambiente (elkartek 20/88)”, the projects “Evaluación del riesgo de aparición y diseminación de resistencias a antibióticos en productos vegetales frescos y suelos de cultivo de la comunidad autónoma del País Vasco (PA21/05 and PA22/05)” inside the “Research projects targeted to agriculture 2020 program” of the Basque Government (Basque Country, Spain); and the Basque Government through the financial support as consolidated group of the Basque Research System (IT1446-22). I. Vergara-Luis and B. Gonzalez-Gaya are grateful to the University of the Basque Country (UPV/EHU) for their pre-doctoral and post-doctoral fellowships. I. Baciero thanks to the Basque Government for her pre-doctoral fellowship

Quantum Statistics of Surface Plasmon Polaritons in Metallic Stripe Waveguides

Single surface plasmon polaritons are excited using photons generated via spontaneous parametric down-conversion. The mean excitation rates, intensity correlations and Fock state populations are studied. The observed dependence of the second order coherence in our experiment is consistent with a linear uncorrelated Markovian environment in the quantum regime. Our results provide important information about the effect of loss for assessing the potential of plasmonic waveguides for future nanophotonic circuitry in the quantum regime.Comment: 21 pages, 6 figures, published in Nano Letters, publication date (web): March 27 (2012