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Author (up) Allende, C.; Sohn, E.; Little, C.
Title Treelink: data integration, clustering and visualization of phylogenetic trees Type
Year 2015 Publication Bmc Bioinformatics Abbreviated Journal BMC Bioinformatics
Volume 16 Issue Pages 6 pp
Keywords Phylogenetic tree; Data integration; Clustering; Visualization
Abstract Background: Phylogenetic trees are central to a wide range of biological studies. In many of these studies, tree nodes need to be associated with a variety of attributes. For example, in studies concerned with viral relationships, tree nodes are associated with epidemiological information, such as location, age and subtype. Gene trees used in comparative genomics are usually linked with taxonomic information, such as functional annotations and events. A wide variety of tree visualization and annotation tools have been developed in the past, however none of them are intended for an integrative and comparative analysis. Results: Treelink is a platform-independent software for linking datasets and sequence files to phylogenetic trees. The application allows an automated integration of datasets to trees for operations such as classifying a tree based on a field or showing the distribution of selected data attributes in branches and leafs. Genomic and proteonomic sequences can also be linked to the tree and extracted from internal and external nodes. A novel clustering algorithm to simplify trees and display the most divergent clades was also developed, where validation can be achieved using the data integration and classification function. Integrated geographical information allows ancestral character reconstruction for phylogeographic plotting based on parsimony and likelihood algorithms. Conclusion: Our software can successfully integrate phylogenetic trees with different data sources, and perform operations to differentiate and visualize those differences within a tree. File support includes the most popular formats such as newick and csv. Exporting visualizations as images, cluster outputs and genomic sequences is supported. Treelink is available as a web and desktop application at http://www. treelinkapp. com.
Address [Allende, Christian; Sohn, Erik; Little, Cedric] Univ Adolfo Ibanez, Fac Sci & Engn, Santiago 7941169, Chile, Email: christian.allende.cid@gmail.com
Corporate Author Thesis
Publisher Biomed Central Ltd Place of Publication Editor
Language English Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1471-2105 ISBN Medium
Area Expedition Conference
Notes WOS:000367229200001 Approved
Call Number UAI @ eduardo.moreno @ Serial 559
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Author (up) Little, C.; Felzensztein, C.; Gimmon, E.; Munoz, P.
Title The business management of the Chilean salmon farming industry Type
Year 2015 Publication Marine Policy Abbreviated Journal Mar. Pol.
Volume 54 Issue Pages 108-117
Keywords Environmentally responsible management; Restorative justice; Moral reengagement; International competitiveness; Natural resources-based clusters; Salmon farming
Abstract This study reviews and explores the salmon farming industry management in an emerging economy context, in the light of environmental responsibility, restorative justice and moral reengagement. Strategic information were gathered, performing in-depth interviews with CEOs and other key senior executives, to analyze the managerial behavior regarding environmental care and moral engagement to industry production standards. The results reveal issues related to firms and government roles on setting industry standards and enforcing them. Firms required to be perceived as renewed in order to receive help from the government and convince the market on their IPOs. Government lack of technical strength and capacity to reestablish order forced the industry firms association to propose a new regulatory standard. But this new order seems not to be satisfactory and this industry will continue to be on the verge of a crisis. (C) 2015 Elsevier Ltd. All rights reserved.
Address [Little, Cedric] Pontificia Univ Catolica Chile, Dept Chem Engn & Bioproc, Santiago, Chile, Email: cedric.little@uai.cl;
Corporate Author Thesis
Publisher Elsevier Sci Ltd Place of Publication Editor
Language English Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0308-597x ISBN Medium
Area Expedition Conference
Notes WOS:000351647500013 Approved
Call Number UAI @ eduardo.moreno @ Serial 477
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Author (up) Mancilla, R.A.; Little, C.; Amoroso, A.
Title Efficient Bioconversion of High Concentration Phytosterol Microdispersion to 4-Androstene-3,17-Dione (AD) by Mycobacterium sp B3805 Type
Year 2018 Publication Applied Biochemistry And Biotechnology Abbreviated Journal Appl. Biochem. Biotechnol.
Volume 185 Issue 2 Pages 494-506
Keywords Bioconversion; Phytosterols; Microdispersion; AD; Steroids
Abstract Low solubility of sterols in aqueous media limits efficient steroid production mediated by biocatalytic microorganisms such as Mycobacterium. Sterol emulsion technologies have been developed with low success rates, largely due to the complexity of generating stable and bioavailable particles. In this study, several aqueous dispersions of sterols in-water of different particle sizes were bioconverted to 4-androstene-3,17-dione (AD) in a solvent-free environment, using a classic microorganism Mycobacterium sp. B3805 as a model system. According to our results, the high concentration (20 g/L) phytosterol dispersions with the smallest particle size tested (370 nm) achieved up to 54% (7.4 g/L) AD production yield in 11 days. Moreover, the use of 0.1 biomass/sterols ratio in a complex bioconversion media containing yeast extract, and a 1:1 glucose/microdispersion ratio in the presence of the surfactant DK-Ester P-160 (HLB16), allowed homogenization and increased microdispersion stability, thus achieving the best results using emulsion technologies to date.
Address [Mancilla, Rodrigo A.] Pontificia Univ Catolica Valparaiso, Fac Biochem Engn, Valparaiso 2340000, Chile, Email: rodrigo.mancilla.v@mail.pucv.cl
Corporate Author Thesis
Publisher Humana Press Inc Place of Publication Editor
Language English Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0273-2289 ISBN Medium
Area Expedition Conference
Notes WOS:000431503400011 Approved
Call Number UAI @ eduardo.moreno @ Serial 849
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Author (up) Perez-Pantoja, D.; Leiva-Novoa, P.; Donoso, R.A.; Little, C.; Godoy, M.; Pieper, D.H.; Gonzalez, B.
Title Hierarchy of Carbon Source Utilization in Soil Bacteria: Hegemonic Preference for Benzoate in Complex Aromatic Compound Mixtures Degraded by Cupriavidus pinatubonensis Strain JMP134 Type
Year 2015 Publication Applied And Environmental Microbiology Abbreviated Journal Appl. Environ. Microbiol.
Volume 81 Issue 12 Pages 3914-3924
Keywords
Abstract Cupriavidus pinatubonensis JMP134, like many other environmental bacteria, uses a range of aromatic compounds as carbon sources. Previous reports have shown a preference for benzoate when this bacterium grows on binary mixtures composed of this aromatic compound and 4-hydroxybenzoate or phenol. However, this observation has not been extended to other aromatic mixtures resembling a more archetypal context. We carried out a systematic study on the substrate preference of C. pinatubonensis JMP134 growing on representative aromatic compounds channeled through different catabolic pathways described in aerobic bacteria. Growth tests of nearly the entire set of binary combinations and in mixtures composed of 5 or 6 aromatic components showed that benzoate and phenol were always the preferred and deferred growth substrates, respectively. This pattern was supported by kinetic analyses that showed shorter times to initiate consumption of benzoate in aromatic compound mixtures. Gene expression analysis by real-time reverse transcription-PCR (RT-PCR) showed that, in all mixtures, the repression by benzoate over other catabolic pathways was exerted mainly at the transcriptional level. Additionally, inhibition of benzoate catabolism suggests that its multiple repressive actions are not mediated by a sole mechanism, as suggested by dissimilar requirements of benzoate degradation for effective repression in different aromatic compound mixtures. The hegemonic preference for benzoate over multiple aromatic carbon sources is not explained on the basis of growth rate and/or biomass yield on each single substrate or by obvious chemical or metabolic properties of these aromatic compounds.
Address [Leiva-Novoa, Pablo; Donoso, Raul A.; Little, Cedric; Gonzalez, Bernardo] Univ Adolfo Ibanez, Ctr Appl Ecol & Sustainabil, Fac Ingn & Ciencias, Santiago, Chile, Email: bernardo.gonzalez@uai.cl
Corporate Author Thesis
Publisher Amer Soc Microbiology Place of Publication Editor
Language English Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0099-2240 ISBN Medium
Area Expedition Conference
Notes WOS:000354864000002 Approved
Call Number UAI @ eduardo.moreno @ Serial 491
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Author (up) Rubilar, P.; Hirmas, M.; Matute, I.; Browne, J.; Little, C.; Ruz, G.A.; Aguilera, X.; Avila, C.; Vial, P.; Mackenzie, T.G.
Title Seroprevalence and estimation of the impact of SARS-CoV-2 infection in older adults residing in Long-term Care Facilities in Chile Type
Year 2022 Publication Medwave Abbreviated Journal Medwave
Volume 22 Issue 3 Pages 002553
Keywords COVID-19 Serological Testing; Long-Term Careaged; SARS-CoV-2
Abstract Introduction

Older adults are at a higher risk of severe illness and death from COVID-19. This vulnerability increases in those who live in long-term care facilities due to overcrowding, greater physical dependence, and contact with health workers. Evidence on the impact of the pandemic on these establishments in low- and middle-income countries has been scant. This study aims to determine the seroprevalence of SARS-CoV-2 in older people residing in long-term care facilities and estimate the impact of infection after the first wave of the pandemic.

Methods

A cross-sectional design with 2099 residents in three regions of Chile was carried out between September and November 2020. Measurement of antibodies was performed with a rapid test. The impact of SARS-CoV-2 infection was estimated with seropositive residents, those who had a history of positive polymerase chain reaction tests, and those who died from COVID-19. Bivariate analysis with the region, sex, age, history of COVID-19, physical dependence, and serological results were performed. In addition, we performed a correlation analysis between the seroprevalence of the centers by the municipality and the rate of confirmed cases.

Results

The seroprevalence of SARS-CoV-2 antibodies in the three regions was 14.7% (95% confidence interval: 13.2 to 16.3%), the infection impact was 46.4%, and the fatality rate was 19.6%. A significant correlation was found between the seroprevalence of older adults residing in long-term care facilities and the cumulative incidence by municipalities.

Conclusions

The seroprevalence of older adults residing in long-term care facilities was higher than the general population. The high impact of infection among this population at the end of the first wave of the COVID-19 pandemic is similar to other countries. The centers' environment is directly related to COVID-19 infection. Morbidity and mortality monitoring systems should be implemented promptly to establish prevention and control measures.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0717-6384 ISBN Medium
Area Expedition Conference
Notes WOS:000800849400003 Approved
Call Number UAI @ alexi.delcanto @ Serial 1586
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Author (up) Tolorza, V.; Poblete-Caballero, D.; Banda, D.; Little, C.; Leal, C.; Galleguillos, M.
Title An operational method for mapping the composition of post-fire litter Type
Year 2022 Publication Remote Sensing Letters Abbreviated Journal Remote Sens. Lett.
Volume 13 Issue 5 Pages 511-521
Keywords SOIL; BIODIVERSITY; WILDFIREI; MPACTS; CHILE
Abstract Recent increase in the frequency and spatial extent of wildfires motivates the quick recognition of the affected soil properties over large areas. Digital Soil Mapping is a valuable approach to map soil attributes based on remote sensing and field observations. We predicted the spatial distribution of post-fire litter composition in a 40,600 ha basin burned on the 2017 wildfire of Chile. Remotely sensed data of topography, vegetation structure and spectral indices (SI) were used as predictors of random forest (RF) models. Litter sampled in 60 hillslopes after the fire provided training and validation data. Predictors selected by the Variable Selection Using Random Forests (VSURF) algorithm resulted in models for litter composition with acceptable accuracy (coefficient of determination, R (2) = 0.51-0.64, Normalized Root Mean Square Error, NRMSE = 16.9-22.1, percentage bias, pbias = -0.35%-0.5%). Modelled litter parameters decrease in concentration respect to the degree of burn severity, and the pre-fire biomass. Because pre-fire vegetation was conditioned by land cover and by a previous (2 years old) wildfire event, our results highlight the cumulative effect of severe wildfires in the depletion of litter composition.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Summary Language Original Title
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2150-704X ISBN Medium
Area Expedition Conference
Notes WOS:000763106200001 Approved
Call Number UAI @ alexi.delcanto @ Serial 1547
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