Project description:Introduction:Trypanosoma cruzi (Tc) infection is usually acquired in childhood in endemic areas, leading to Chagas disease, which progresses to Chagas cardiomyopathy in 20-30% of infected individuals over decades. The pathogenesis of Chagas cardiomyopathy involves the host inflammatory response to T. cruzi, in which upstream caspase-1 activation prompts the cascade of inflammatory chemokines/cytokines, cardiac remodeling, and myocardial dysfunction. The aim of the present study was to examine the association of two caspase-1 single nucleotide polymorphisms (SNPs) with cardiomyopathy.Methods:We recruited infected (Tc+, n = 149) and uninfected (Tc-, n = 87) participants in a hospital in Santa Cruz, Bolivia. Cardiac status was classified (I, II, III, IV) based on Chagas cardiomyopathy-associated electrocardiogram findings and ejection fractions on echocardiogram. Genotypes were determined using Taqman probes via reverse transcription-polymerase chain reaction of peripheral blood DNA. Genotype frequencies were analyzed according to three inheritance patterns (dominant, recessive, additive) using logistic regression adjusted for age and sex.Results:The AA allele for the caspase-1 SNP rs501192 was more frequent in Tc+ cardiomyopathy (classes II, III, IV) patients compared to those with a normal cardiac status (class I) [odds ratio (OR) = -2.18, p = 0.117]. This trend approached statistical significant considering only Tc+ patients in class I and II (OR = -2.64, p = 0.064).Conclusions:Caspase-1 polymorphisms may play a role in Chagas cardiomyopathy development and could serve as markers to identify individuals at higher risk for priority treatment.
Project description:We describe a case of chronic meningoencephalitis with hydrocephalus caused by Cryptococcus bacillisporus (VGIII) in an immunocompetent patient from Santa Cruz, Bolivia. This first report of a member of the Cryptococcus gattii species complex from Bolivia suggests that C. bacillisporus (VGIII) is present in this tropical region of the country and complements our epidemiological and clinical knowledge of this group of emerging fungal pathogens in South America.
Project description:Relative crustal motions along active faults generate earthquakes, and repeated earthquake cycles build mountain ranges over millions of years. However, the long-term summation of elastic, earthquake-related deformation cannot produce the deformation recorded within the rock record. Here, we provide an explanation for this discrepancy by showing that increases in strain facilitated by plastic deformation of Earth's crust during the earthquake cycle, in conjunction with isostatic deflection and erosion, transform relative fault motions that produce individual earthquakes to geologic deformations. We focus our study on the data-rich Santa Cruz Mountains, CA, USA and compare predicted and observed quantities for rock uplift, apatite (U-Th)/He thermochronology, topographic relief, 10Be-based erosion rates, and interseismic surface velocities. This approach reconciles these disparate records of mountain-building processes, allowing us to explicitly bridge decadal measures of deformation with that produced by millions of years of plate motion.
Project description:BackgroundAcute respiratory infections represent a serious public health issue worldwide but virological aetiologies of Influenza Like Illnesses (ILIs) remain largely unknown in developing countries. This study represents the first attempt to characterise viral aetiologies of ILIs in Bolivia.MethodsIt was performed in Santa Cruz city from January 2010 to September 2012, based on 564 naso-pharyngeal swabs collected in a National Reference Laboratory and real-time PCR techniques, viral cultures and phylogenetic analyses.Results50.2% of samples were positive for at least one virus with influenza viruses (Flu A: ~15%; Flu B: ~9%), rhinoviruses (~8%), coronaviruses (~5%) and hRSV (~4%) being the most frequently identified. The pattern of viral infections varied according to age groups. The elucidation rate was the highest (>60%) amongst patients under 10 yo and the lowest (<40%) amongst patients ≥60 yo. Nearly 3% of samples showed dual viral infections. Epidemiological peaks were associated with a predominant virus but generally included 30-50% of infections by different viruses. Unexpectedly, the frequency of influenza in the 0-4 yo population was very low and a complete hRSV eclipse occurred in 2011. Genetic analyses indicated that distinct evolutionary lineages of Flu A(H1N1)pdm2009, Flu A/H3N2 and Flu B have co-circulated in Bolivia in the study period, originating from Central and North America, Europe, Asia and Australia.ConclusionOur results emphasise the requirement for a reinforced epidemiological and genetic follow-up of influenza and other ILIs in Bolivia to further inform the preparation of vaccines used in the region, guide vaccination campaigns and improve the medical management of patients.
Project description:BackgroundIn the context of a rapid increase of dengue cases in the Americas, a monitoring system based on systematic serological control (IgM) of patients consulting for suspected dengue was developed in Bolivia at the end of the 1990s. In the most affected city of Santa Cruz, this system was complemented by an entomological surveillance program based on periodical search for immature stages of Aedes aegypti in dwelling water-holding containers. Here, we analyze these data and describe dengue patterns over 6 years (2002-2008), highlighting the spatial distribution of patients and vectors.Methodology /principal findingsData mining concerned six annual epidemic cycles (2002-2008), with continuous serological and clinical results and entomological data from 16 surveys, examined at the scales of 36 urban areas and four concentric areas covering the entire city. Annual incidence varied from 0.28‰ to 0.95‰; overall incidence was higher in women and adults, and dengue dynamics followed successive periods of high (January-June) and low (July-December) transmission. Lower numbers of cases from the city center to the periphery were observed, poorly related to the more homogeneous and permanent distribution of A. aegypti. "Plant pots" were a major vector source in the city center, and "Tires" and "Odds and ends" beyond the second ring of the city.Conclusions/significanceOver the years, the increasing trend of dengue cases has been highlighted as well as its widespread distribution over the entire city, but an underestimation of the number of cases is strongly suspected. Contrary to popular belief, the city center appears more affected than the periphery, and dengue is not particularly related to waste. Interestingly, the clinical diagnosis of dengue by physicians improved over the years, whatever the gender, age and residential area of suspected cases.
Project description:Successful invasive species can overcome or circumvent the potential genetic loss caused by an introduction bottleneck through a rapid population expansion and admixture from multiple introductions. We explore the genetic makeup and the timing of a species introduction to Santa Cruz Island in the Galápagos archipelago. We investigate the presence of processes that can maintain genetic diversity in populations of the broad-nosed weevil Galapaganus howdenae howdenae. Analyses of combined genotypes for 8 microsatellite loci showed evidence of past population size reductions through moment and likelihood-based estimators. No evidence of admixture through multiple introductions was found, but substantial current population sizes (N0 298, 95% credible limits 50-2300), genetic diversity comparable with long-established endemics (Mean number of alleles = 3.875), and lack of genetic structure across the introduced range (F ST = 0.01359) could suggest that foundations are in place for populations to rapidly recover any loss of genetic variability. The time estimates for the introduction into Santa Cruz support an accidental transfer during the colonization period (1832-1959) predating the spurt in human population growth. Our evaluation of the genetic status of G. h. howdenae suggests potential for population growth in addition to our field observations of a concurrent expansion in range and feeding preferences towards protected areas and endemic host plants.
Project description:The free-living marine nematodes of San Julián Bay dataset is based on sediment samples collected in January 2009 during the project PICT AGENCIA-FONCYT 2/33345-2005. A total of 36 samples have been taken at three locations in the San Julián Bay, Santa Cruz Province, Argentina on the coastal littoral at three tidal levels. This presents a unique and important collection for the nematode benthic biodiversity assessment as this area remains one of the least known regions in Patagonia. In total 10,030 specimens of free-living marine nematodes belonging to 2 classes, 9 orders, 35 families, 78 genera and 125 species were collected. The San Julián city site presented a very high species richness.
Project description:We examine patterns of reported crime in Santa Monica, California before and after the passage of Proposition 47, a 2014 initiative that reclassified some non-violent felonies as misdemeanors. We also investigate impacts of the opening of four new light rail stations in 2016 and of increased community-based policing starting in late 2018. Our statistical analyses of reclassified crimes-larceny, fraud, possession of narcotics, forgery, receiving/possessing stolen property-and non-reclassified ones are based on publicly available reported crime data from 2006 to 2019. These analyses examine reported crime at various levels: city-wide, within eight neighborhoods, and within a 450-meter radius of the new transit stations. Monthly reported reclassified crimes increased city-wide by approximately 15% after enactment of Proposition 47, with a significant drop observed in late 2018. Downtown exhibited the largest overall surge. Reported non-reclassified crimes fell overall by approximately 9%. Areas surrounding two new train stations, including Downtown, saw significant increases in reported crime after train service began. While reported reclassified crimes increased after passage of Proposition 47, non-reclassified crimes, for the most part, decreased or stayed constant, suggesting that Proposition 47 may have impacted reported crime in Santa Monica. Reported crimes decreased in late 2018 concurrent with the adoption of new community-based policing measures. Follow-up studies needed to confirm long-term trends may be challenging due to the COVID-19 pandemic that drastically changed societal conditions. While our research detects changes in reported crime, it does not provide causative explanations. Our work, along with other considerations relevant to public utility, respect for human rights, and existence of socioeconomic disparities, may be useful to law enforcement and policymakers to assess the overall effect of Proposition 47.
Project description:To facilitate efficient selection and the prioritization of candidate complex disease susceptibility genes for association analysis, increasingly comprehensive annotation tools are essential to integrate, visualize and analyze vast quantities of disparate data generated by genomic screens, public human genome sequence annotation and ancillary biological databases. We have developed a plug-in package for Ensembl called "Statistical Viewer" that facilitates the analysis of genomic features and annotation in the regions of interest defined by linkage analysis.Statistical Viewer is an add-on package to the open-source Ensembl Genome Browser and Annotation System that displays disease study-specific linkage and/or association data as 2 dimensional plots in new panels in the context of Ensembl's Contig View and Cyto View pages. An enhanced upload server facilitates the upload of statistical data, as well as additional feature annotation to be displayed in DAS tracts, in the form of Excel Files. The Statistical View panel, drawn directly under the ideogram, illustrates lod score values for markers from a study of interest that are plotted against their position in base pairs. A module called "Get Map" easily converts the genetic locations of markers to genomic coordinates. The graph is placed under the corresponding ideogram features a synchronized vertical sliding selection box that is seamlessly integrated into Ensembl's Contig- and Cyto- View pages to choose the region to be displayed in Ensembl's "Overview" and "Detailed View" panels. To resolve Association and Fine mapping data plots, a "Detailed Statistic View" plot corresponding to the "Detailed View" may be displayed underneath.Features mapping to regions of linkage are accentuated when Statistic View is used in conjunction with the Distributed Annotation System (DAS) to display supplemental laboratory information such as differentially expressed disease genes in private data tracks. Statistic View is a novel and powerful visual feature that enhances Ensembl's utility as valuable resource for integrative genomic-based approaches to the identification of candidate disease susceptibility genes. At present there are no other tools that provide for the visualization of 2-dimensional plots of quantitative data scores against genomic coordinates in the context of a primary public genome annotation browser.