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A short tutorial on Bayesian Nonparametrics
(2016) Jara, Alejandro; Mueller, Peter; Xu, Yanxun
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Los antocerotes tuberosos de Chile Central y sus simbiontes cianobacteriales
(2024) Venegas Inostroza, Nicolás Ignacio; Pérez Trautmann, María Fernanda; Pontificia Universidad Católica de Chile. Facultad de Ciencias Biológicas
Las interacciones mutualistas con microorganismos han sido fundamentales en la historia evolutiva de las plantas terrestres, las que han promovido la diversificación de los grandes linajes de plantas. Estas interacciones han resultado en una diversidad de patrones de especialización. Los briófitos son un grupo de plantas terrestres altamente derivadas, que incluye a los antocerotes, una división que interactúa ubicuamente con simbiontes cianobacteriales (cianobiontes) del género Nostoc, capaces de fijar nitrógeno. Los estudios previos sobre especialización de estas interacciones han abarcado una baja diversidad de antocerotes, ninguno de los cuales transmite verticalmente los cianobiontes. En este trabajo nos centramos en los antocerotes tuberosos de Chile central. Phaeoceros carolinianus y Phaeoceros microsporus forman tubérculos de manera facultativa y se distribuyen ampliamente, mientras que la tercera especie, Paraphymatoceros diadematus, forma tubérculos constitutivamente, aloja cianobiontes al interior de los tubérculos y es endémica de Chile central ¿Existe algún grado de especialización entre P. diadematus y sus cianobiontes? ¿Influye la retención de cianobiontes al interior de los tubérculos en los patrones de diversidad de los cianobiontes? Proponemos que, dado que la especie P. diadematus retiene en los tubérculos cianobiontes con mayor frecuencia que las otras especies de antocerotes tuberosos, la transmisión vertical generará patrones de especialización. Hallamos bajos niveles de especialización por especificidad hacia el subclado 3 de Nostoc, cuya abundancia como cianobionte parece reflejar su abundancia en el suelo. Finalmente exploramos la función ecosistémica de estos antocerotes, la que constituyó una novedosa fuente de fertilidad no considerada previamente en Chile central.
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The Role of Body Mass Index at Diagnosis on Black-White Disparities in Colorectal Cancer Survival: A Density Regression Mediation Approach
(2018) Devick, Katrina L.; Valeri, Linda; Chen, Jarvis; Jara, Alejandro; Bind, Marie-Abèle; Coull, Brent A.
The study of racial/ethnic inequalities in health is important to reduce the uneven burden of disease. In the case of colorectal cancer (CRC), disparities in survival among non-Hispanic Whites and Blacks are well documented, and mechanisms leading to these disparities need to be studied formally. It has also been established that body mass index (BMI) is a risk factor for developing CRC, and recent literature shows BMI at diagnosis of CRC is associated with survival. Since BMI varies by racial/ethnic group, a question that arises is whether disparities in BMI is partially responsible for observed racial/ethnic disparities in CRC survival. This paper presents new methodology to quantify the impact of the hypothetical intervention that matches the BMI distribution in the Black population to a potentially complex distributional form observed in the White population on racial/ethnic disparities in survival. We perform a simulation that shows our proposed Bayesian density regression approach performs as well as or better than current methodology allowing for a shift in the mean of the distribution only, and that standard practice of categorizing BMI leads to large biases. When applied to motivating data from the Cancer Care Outcomes Research and Surveillance (CanCORS) Consortium, our approach suggests the proposed intervention is potentially beneficial for elderly and low income Black patients, yet harmful for young and high income Black populations.
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Genomes of the Orestias pupfish from the Andean Altiplano shed light on their evolutionary history and phylogenetic relationships within Cyprinodontiformes
(2024) Morales, Pamela; Gajardo, Felipe; Valdivieso, Camilo; Valladares, Moisés A.; Di Genova, Alex; Orellana, Ariel; Gutiérrez Ilabaca, Rodrigo Antonio; González, Mauricio; Montecino, Martin; Maass, Alejandro; Méndez, Marco A.; Allende, Miguel L.
To unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon sampling and careful consideration of multiple characters to ensure a complete and accurate reconstruction. The phylogenetic position of the Orestias genus has been estimated partly on unavailable or incomplete information. As a consequence, it was assigned to the family Cyprindontidae, relating this Andean fish to other geographically distant genera distributed in the Mediterranean, Middle East and North and Central America. In this study, using complete genome sequencing, we aim to clarify the phylogenetic position of Orestias within the Cyprinodontiformes order. Results We sequenced the genome of three Orestias species from the Andean Altiplano. Our analysis revealed that the small genome size in this genus (~ 0.7 Gb) was caused by a contraction in transposable element (TE) content, particularly in DNA elements and short interspersed nuclear elements (SINEs). Using predicted gene sequences, we generated a phylogenetic tree of Cyprinodontiformes using 902 orthologs extracted from all 32 available genomes as well as three outgroup species. We complemented this analysis with a phylogenetic reconstruction and time calibration considering 12 molecular markers (eight nuclear and four mitochondrial genes) and a stratified taxon sampling to consider 198 species of nearly all families and genera of this order. Overall, our results show that phylogenetic closeness is directly related to geographical distance. Importantly, we found that Orestias is not part of the Cyprinodontidae family, and that it is more closely related to the South American fish fauna, being the Fluviphylacidae the closest sister group. Conclusions The evolutionary history of the Orestias genus is linked to the South American ichthyofauna and it should no longer be considered a member of the Cyprinodontidae family. Instead, we submit that Orestias belongs to the Orestiidae family, as suggested by Freyhof et al. (2017), and that it is the sister group of the Fluviphylacidae family, distributed in the Amazonian and Orinoco basins. These two groups likely diverged during the Late Eocene concomitant with hydrogeological changes in the South American landscape.
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Nudges as Behavior Change Interventions to Improve Health and Well-Being. Protocol for a scoping review (JMIR Preprint)
(JMIR Publications, 2021) Duarte Anselmi, Giuliano; Ortiz Muñoz, Luis Eugenio; Figueroa, Oriana; Laroze, Denise
Our objective is to map and summarize the evidence on nudges that assess behavior change interventions to improve health and well-being. Design: This is the protocol for a scoping review. Data source: a comprehensive search will be conducted on Cochrane database of systematic reviews (CDSR); Database of Abstracts of Reviews of Effectiveness (DARE); HTA Database; PubMed; LILACS; CINAHL; PsyclNFO; EMBASE; EPPI-Centre Evidence Library; WHO institutional Repository for information Sharing; NICE public health guidelines and systematic reviews; through an advanced search in the Epistemonikos platform. The search will cover the period until the day before this protocol is submitted to a journal. Eligibility criteria for study selection and methods. Only systematic reviews (SR) will be included, which are operationally defined as any secondary research that includes only primary clinical studies, with the above search strategy applied in at least two databases that have assessed the use of nudges related to health, including SR of broader scope. Primary studies, clinical practice guides, abstracts and other evidence summary designs will be excluded. The electronic search results will be added according to the inclusion criteria. This manuscript will follow the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for scoping reviews (PRISMA-ScR).