Ultrasound-guided targeted biopsies of CT-based radiomic tumour habitats: technical development and initial experience in metastatic ovarian cancer.

PURPOSE: To develop a precision tissue sampling technique that uses computed tomography (CT)-based radiomic tumour habitats for ultrasound (US)-guided targeted biopsies that can be integrated in the clinical workflow of patients with high-grade serous ovarian cancer (HGSOC). METHODS: Six patients with suspected HGSOC scheduled for US-guided biopsy before starting neoadjuvant chemotherapy were included in this prospective study from September 2019 to February 2020. The tumour segmentation was performed manually on the pre-biopsy contrast-enhanced CT scan. Spatial radiomic maps were used to identify tumour areas with similar or distinct radiomic patterns, and tumour habitats were identified using the Gaussian mixture modelling. CT images with superimposed habitat maps were co-registered with US images by means of a landmark-based rigid registration method for US-guided targeted biopsies. The dice similarity coefficient (DSC) was used to assess the tumour-specific CT/US fusion accuracy. RESULTS: We successfully co-registered CT-based radiomic tumour habitats with US images in all patients. The median time between CT scan and biopsy was 21 days (range 7-30 days). The median DSC for tumour-specific CT/US fusion accuracy was 0.53 (range 0.79 to 0.37). The CT/US fusion accuracy was high for the larger pelvic tumours (DSC: 0.76-0.79) while it was lower for the smaller omental metastases (DSC: 0.37-0.53). CONCLUSION: We developed a precision tissue sampling technique that uses radiomic habitats to guide in vivo biopsies using CT/US fusion and that can be seamlessly integrated in the clinical routine for patients with HGSOC. KEY POINTS: • We developed a prevision tissue sampling technique that co-registers CT-based radiomics-based tumour habitats with US images. • The CT/US fusion accuracy was high for the larger pelvic tumours (DSC: 0.76-0.79) while it was lower for the smaller omental metastases (DSC: 0.37-0.53).

A thiotrophic microbial community in an acidic brine lake in Northern Chile.

The endorheic basins of the Northern Chilean Altiplano contain saline lakes and salt flats. Two of the salt flats, Gorbea and Ignorado, have high acidic brines. The causes of the local acidity have been attributed to the occurrence of volcanic native sulfur, the release of sulfuric acid by oxidation, and the low buffering capacity of the rocks in the area. Understanding the microbial community composition and available energy in this pristine ecosystem is relevant in determining the origin of the acidity and in supporting the rationale of conservation policies. Besides, a comparison between similar systems in Australia highlights key microbial components and specific ones associated with geological settings and environmental conditions. Sediment and water samples from the Salar de Gorbea were collected, physicochemical parameters measured and geochemical and molecular biological analyses performed. A low diversity microbial community was observed in brines and sediments dominated by Actinobacteria, Algae, Firmicutes and Proteobacteria. Most of the constituent genera have been reported to be either sulfur oxidizing microorganisms or ones having the potential for sulfur oxidation given available genomic data and information drawn from the literature on cultured relatives. In addition, a link between sulfur oxidation and carbon fixation was observed. In contrast, to acid mine drainage communities, Gorbea microbial diversity is mainly supported by chemolithoheterotrophic, facultative chemolithoautotrophic and oligotrophic sulfur oxidizing populations indicating that microbial activity should also be considered as a causative agent of local acidity.

Correction to: A thiotrophic microbial community in an acidic brine lake in Northern Chile.

In Table 1 of the original article, the unit mg/L was incorrectly published as ng/L in the aluminum, chloride, sulphate and OM columns.

Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria).

Analysis of marine cyanobacteria and proteobacteria genomes has provided a profound understanding of the life strategies of these organisms and their ecotype differentiation and metabolisms. However, a comparable analysis of the Bacteroidetes, the third major bacterioplankton group, is still lacking. In the present paper, we report on the genome of Polaribacter sp. strain MED152. On the one hand, MED152 contains a substantial number of genes for attachment to surfaces or particles, gliding motility, and polymer degradation. This agrees with the currently assumed life strategy of marine Bacteroidetes. On the other hand, it contains the proteorhodopsin gene, together with a remarkable suite of genes to sense and respond to light, which may provide a survival advantage in the nutrient-poor sun-lit ocean surface when in search of fresh particles to colonize. Furthermore, an increase in CO(2) fixation in the light suggests that the limited central metabolism is complemented by anaplerotic inorganic carbon fixation. This is mediated by a unique combination of membrane transporters and carboxylases. This suggests a dual life strategy that, if confirmed experimentally, would be notably different from what is known of the two other main bacterial groups (the autotrophic cyanobacteria and the heterotrophic proteobacteria) in the surface oceans. The Polaribacter genome provides insights into the physiological capabilities of proteorhodopsin-containing bacteria. The genome will serve as a model to study the cellular and molecular processes in bacteria that express proteorhodopsin, their adaptation to the oceanic environment, and their role in carbon-cycling.

First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotán in Northern Chile.

Fusibacter sp. 3D3 (ATCC BAA-2418) is an arsenate-reducing halotolerant strain within the Firmicutes phylum, isolated from the Salar de Ascotán, a hypersaline salt flat in Northern Chile. This high-Andean closed basin is an athalassohaline environment located at the bottom of a tectonic basin surrounded by mountain range, including some active volcanoes. This landscape can be an advantageous system to explore the effect of salinity on microorganisms that mediate biogeochemical reactions. Since 2000, microbial reduction of arsenic has been evidenced in the system, and the phylogenetic analysis of the original community plus the culture enrichments has revealed the predominance of Firmicutes phylum. Here, we describe the first whole draft genome sequence of an arsenic-reducing strain belonging to the Fusibacter genus showing the highest 16S rRNA gene sequence similarity (98%) with Fusibacter sp. strain Vns02. The draft genome consists of 57 contigs with 5,111,250 bp and an average G + C content of 37.6%. Out of 4780 total genes predicted, 4700 genes code for proteins and 80 genes for RNAs. Insights from the genome sequence and some microbiological features of the strain 3D3 are available under Bioproject accession PRJDB4973 and Biosample SAMD00055724. The release of the genome sequence of this strain could contribute to the understanding of the arsenic biogeochemistry in extreme environments.

Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile.

10.1601/nm.2199 CLST is an extremely acidophilic gamma-proteobacteria that was isolated from the Gorbea salt flat, an acidic hypersaline environment in northern Chile. This kind of environment is considered a terrestrial analog of ancient Martian terrains and a source of new material for biotechnological applications. 10.1601/nm.2199 plays a key role in industrial bioleaching; it has the capacity of generating and maintaining acidic conditions by producing sulfuric acid and it can also remove sulfur layers from the surface of minerals, which are detrimental for their dissolution. CLST is a strain of 10.1601/nm.2199 able to tolerate moderate chloride concentrations (up to 15 g L-1 Cl-), a feature that is quite unusual in extreme acidophilic microorganisms. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 3,974,949 bp draft genome is arranged into 40 scaffolds of 389 contigs containing 3866 protein-coding genes and 75 RNAs encoding genes. This is the first draft genome of a halotolerant 10.1601/nm.2199 strain. The release of the genome sequence of this strain improves representation of these extreme acidophilic Gram negative bacteria in public databases and strengthens the framework for further investigation of the physiological diversity and ecological function of 10.1601/nm.2199 populations.

The Ecological Coherence of Temperature and Salinity Tolerance Interaction and Pigmentation in a Non-marine Vibrio Isolated from Salar de Atacama.

The occurrence of microorganisms from the Vibrio genus in saline lakes from northern Chile had been evidenced using Numerical Taxonomy decades before and, more recently, by phylogenetic analyses of environmental samples and isolates. Most of the knowledge about this genus came from marine isolates and showed temperature and salinity to be integral agents in shaping the niche of the Vibrio populations. The stress tolerance phenotypes of Vibrio sp. Teb5a1 isolated from Salar de Atacama was investigated. It was able to grow without NaCl and tolerated up to 100 g/L of the salt. Furthermore, it grew between 17° and 49°C (optimum 30°C) in the absence of NaCl, and the range was expanded into cold temperature (4-49°C) in the presence of the salt. Other additional adaptive strategies were observed in response to the osmotic stress: pigment production, identified as the known antibacterial prodigiosin, swimming and swarming motility and synthesis of a polar flagellum. It is possible to infer that environmental congruence might explain the cellular phenotypes observed in Vibrio sp. considering that coupling between temperature and salinity tolerance, the production of antibacterial agents at higher temperatures, flagellation and motility increase the chance of Vibrio sp. to survive in salty environments with high daily temperature swings and UV radiation.

Draft Genome Sequence of Nitrincola sp. Strain A-D6, an Arsenic-Resistant Gammaproteobacterium Isolated from a Salt Flat.

We report Nitrincola sp. strain A-D6, which was characterized as an arsenic-resistant bacterium isolated from the Ascotán Salt Flat in northern Chile. The size of the genome is 3,795,776 bp, with a G+C content of 49.96%. Genes for the arsenic-resistant Ars system and arsenic oxidation have been encoded.

Distribution of microbial arsenic reduction, oxidation and extrusion genes along a wide range of environmental arsenic concentrations.

The presence of the arsenic oxidation, reduction, and extrusion genes arsC, arrA, aioA, and acr3 was explored in a range of natural environments in northern Chile, with arsenic concentrations spanning six orders of magnitude. A combination of primers from the literature and newly designed primers were used to explore the presence of the arsC gene, coding for the reduction of As (V) to As (III) in one of the most common detoxification mechanisms. Enterobacterial related arsC genes appeared only in the environments with the lowest As concentration, while Firmicutes-like genes were present throughout the range of As concentrations. The arrA gene, involved in anaerobic respiration using As (V) as electron acceptor, was found in all the systems studied. The As (III) oxidation gene aioA and the As (III) transport gene acr3 were tracked with two primer sets each and they were also found to be spread through the As concentration gradient. Sediment samples had a higher number of arsenic related genes than water samples. Considering the results of the bacterial community composition available for these samples, the higher microbial phylogenetic diversity of microbes inhabiting the sediments may explain the increased number of genetic resources found to cope with arsenic. Overall, the environmental distribution of arsenic related genes suggests that the occurrence of different ArsC families provides different degrees of protection against arsenic as previously described in laboratory strains, and that the glutaredoxin (Grx)-linked arsenate reductases related to Enterobacteria do not confer enough arsenic resistance to live above certain levels of As concentrations.

Novelty and spatio-temporal heterogeneity in the bacterial diversity of hypersaline Lake Tebenquiche (Salar de Atacama).

Lake Tebenquiche is one of the largest saline water bodies in the Salar de Atacama at 2,500 m above sea level in northeastern Chile. Bacteria inhabiting there have to deal with extreme changes in salinity, temperature and UV dose (i.e., high environmental dissimilarity in the physical landscape). We analyzed the bacterioplankton structure of this lake by 16S rRNA gene analyses along a spatio-temporal survey. The bacterial assemblage within the lake was quite heterogeneous both in space and time. Salinity changed both in space and time ranging between 1 and 30% (w/v), and total abundances of planktonic prokaryotes in the different sampling points within the lake ranged between two and nine times 10(6) cells mL(-1). Community composition changed accordingly to the particular salinity of each point as depicted by genetic fingerprinting analyses (denaturing gradient gel electrophoresis), showing a high level of variation in species composition from place to place (beta-diversity). Three selected sites were analyzed in more detail by clone libraries. We observed a predominance of Bacteroidetes (about one third of the clones) and Gammaproteobacteria (another third) with respect to all the other bacterial groups. The diversity of Bacteroidetes sequences was large and showed a remarkable degree of novelty. Bacteroidetes formed at least four clusters with no cultured relatives in databases and rather distantly related to any known 16S rRNA sequence. Within this phylum, a rich and diverse presence of Salinibacter relatives was found in the saltiest part of the lake. Lake Tebenquiche included several novel microorganisms of environmental importance and appeared as a large unexplored reservoir of unknown bacteria.

Factores asociados a consumo de tabaco durante el último año en estudiantes de educación superior / Smoking associated factors in students during their last year of higher education / Fatores associados a consumo do cigarro durante o último ano em estudantes de educação superior

Objetivo. Determinar los factores de riesgo asociados al consumo de tabaco en el último año en una población universitaria chilena. Metodología. Estudio observacional analítico, de corte transversal. Se realizó muestreo aleatorio estratificado según unidad académica y año de carrera, siendo el tamaño muestral de 2045 estudiantes de cuatro Campus de la Universidad Católica de Chile. La toma de la información se hizo con ayuda de un cuestionario autoaplicado. Se realizaron análisis descriptivo, bivariado y de regresión logística. Resultados. El promedio de edad fue 20.4±1,6 años, el 46.6% eran de sexo masculino y el70.3% tenían nivel socioeconómico alto. Un 91.0% había iniciado el consumo después de los 18 años. La prevalencia mensual de consumo de tabaco fue de 40.5%, un 20.0% de los encuestados estaría a riesgo de tener diagnóstico de tabaquismo. Se encontró asociación positiva entre consumo de tabaco durante último año y: la edad (p<0.05), el sexo femenino (p<0.001), el nivel socioeconómico (p<0.05) y la percepción de consumo de droga por parte de padres (p<0.001). Se encontró asociación negativa entre consumo de tabaco y la religiosidad (p<0.001).Conclusión. En el grupo universitario en el que se realizó el estudio se encontró que el problema de tabaquismo merece especial atención por su magnitud, estando asociado a factores de riesgo como la edad, el sexo femenino, el estrato socioeconómico y una baja religiosidad.

Objective. To determine the risk factors associated to smokingin the last year of school in a Chilean university population. Methodology. Analytical, observational, transversal cut study. Stratified randomized sampling was conducted according to academic unit and year of career; the size of the sample was of 2045 students from four campuses of the catholic university of Chile. The information was collected with a self-applied questionnaire. A descriptive, bivariate and logistic regression analysis was made. Results. The average age was 20.4±1.6,46% were males and 70.3% had a high socioeconomic status. 91% had started cigarette consumption before the age of 18. The smoking monthly prevalence was of 40.5%, 20% of the surveyed would be atrisk of having diagnosis of smoking. A positive association was found between smoking during the last year of university and: age (p<0.05), female sex (p<0.001), socioeconomic status (p<0.05) and parents drugconsumption perception (p<0.001). A negative association was found between smoking and religiosity(p<0.001). Conclusion. In the studied university group it was found that the smoking problem requires special attention due to its magnitude and association to risk factors as age, female gender, socioeconomic status and a low religiosity.

Objetivo. Determinar os fatores de risco associados ao consumo do cigarro no último ano numa população universitária chilena. Metodologia. Estudo observacional analítico, de corte transversal. Realizou-se amostra gemaleatória estratificado segundo unidade acadêmica e ano de carreira, sendo o tamanho da mostra de2 045 estudantes de quatro Campus da Universidade Católica de Chile. A tomada da informação se fez comajuda de um questionário auto-aplicado. Realizaram-se análise descritiva, bivariado e de regressão logística. Resultados. A média de idade foi 20.4±1,6 anos, o 46.6% eram de sexo masculino e o 70.3% tinham nível socioeconômico alto. Um 91% tinha iniciado o consumo depois dos 18 anos. A prevalência mensal de consumo do cigarro foi de 40.5%, um 20% dos interrogados estaria a risco de ter diagnóstico de tabagismo. Encontrou-se associação positiva entre consumo de fumo durante último ano e: a idade (p<0.05), o sexo feminino (p<0.001), o nível socioeconômico (p<0.05) e a percepção de consumo de droga por parte de pais (p<0.001). Encontrou-se associação negativa entre consumo de fumo e a religiosidade (p<0.001). Conclusão. No grupo universitário no que se realizou o estudo se encontrou que o problema de tabagismo merece especial atendimento por sua magnitude, estando sócio a fatores de risco como a idade, o sexo feminino,o estrato socioeconômico e uma baixa religiosidade.

[Design and implementation of an epidemiological surveillance system for mental health]. / Diseño y puesta en marcha de un sistema de vigilancia epidemiológica en salud mental.

OBJECTIVE: To design and test a surveillance system to detect and rank the most significant mental health problems in a community and to establish their association with the living conditions in that community. METHODS: The system was designed and tested at a primary health care center in the community of La Florida, which is in the metropolitan region of Santiago, the capital of Chile. The health problems that were under surveillance, with monthly monitoring, were: addiction (to alcohol, tobacco, and benzodiazepines or other drugs), violence (domestic violence and sexual abuse, real or suspected), and disorders in children (attention deficit and behavioral disorders). By means of a computerized geographical information system (GIS), those surveillance data were combined with other data. These other data included sociodemographic information on the persons who went to the health center for care as well as data on local risk factors and protective factors for health problems, some of which are indicators of the local residents' living conditions. RESULTS: The proposed epidemiological surveillance system, which takes into account local living conditions and environmental variables, is a good tool for health action. The proposed system also complements the incomplete perspective of monitoring systems, which do not include variables describing the local context and that focus only on health problems. The information synthesized in the GIS maps makes it possible to simultaneously display different layers of information on factors related to the health problems studied, linked to a specific area and all its environmental variables, in an easy-to-read, self-explanatory format. CONCLUSIONS: These results and the concurring opinions of the participating physicians show that the experimental system effectively met the basic requirements of an epidemiological surveillance system of this kind.

Distribution of prokaryotic genetic diversity in athalassohaline lakes of the Atacama Desert, Northern Chile.

Athalassohaline lakes are inland saline aquatic environments with ionic proportions quite different from the dissolved salts in seawater. Prokaryotes inhabiting athalassohaline environments are poorly known and very few of such places have been surveyed for microbial diversity studies around the world. We analyzed the planktonic bacterial and archaeal assemblages inhabiting several of these evaporitic basins in a remote and vast area in northern Chile by PCR-denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rRNA gene fragments. Most systems were springs and athalassohaline ponds in different saltflats of the Atacama Desert region, including Salar de Llamará (in the Central Depression), Salar de Atacama (in the Pre-Andean Depression) and Salar de Ascotán (in the Altiplano). Overall, we analyzed more than 25 samples from 19 different environments with strong gradients of altitude, qualitative ionic compositions and UV influence. Between 4 and 25 well-defined DGGE bands were detected for Bacteria in each sample, whereas Archaea ranged between 1 and 5. Predominant DGGE bands (defined by intensity and frequency of appearance) were excised from the gel and sequenced. Bacterial assemblages were dominated by the Cytophaga-Flavobacterium-Bacteroides (CFB) phylum and a few Proteobacteria. There was a tendency for increasing contribution of CFB with higher salinities and altitude. Thus, CFB accounted for the major fraction of band intensity in the Ascotán samples and for lower percentages in Atacama and Llamará. When the distribution of particular CFB sequences was examined, there were several relatives of Psychroflexus torquis substituting each other as salinity changed in Ascotán. Another set of CFB sequences, very distantly related to Cytophaga marinovorus, was abundant in both Llamará and Atacama at salinities lower than 7%. Archaeal assemblages were dominated by uncultured haloarchaea distantly related to cultured strains mostly obtained from thalassohaline environments. Most of the archaeal sequences did not have a close match with environmental 16S rRNA genes deposited in the database either. Therefore, athalassohaline environments are excellent sources of new microorganisms different from their counterparts in thalassohaline sites and useful tools to relate microbial genetic diversity and environmental characteristics such as changes in salinity (both qualitative and quantitative) and altitude.

Diseño y puesta en marcha de un sistema de vigilancia epidemiológica en salud mental / Design and implementation of an epidemiological surveillance system for mental health

Objetivos. Diseñar y poner a prueba un sistema de vigilancia que permita detectar y jerarquizar los problemas más relevantes de salud mental y establecer su asociación con las condiciones de vida de la comunidad estudiada. Métodos. El sistema se diseñó y puso a prueba en un centro de salud de la comuna La Florida, región metropolitana de Chile. Los problemas de salud que se sometieron a vigilancia con seguimiento mensual fueron: adicción (al alcohol, tabaco, drogas y benzodiazepinas), violencia (violencia o sospecha de violencia intrafamiliar y abuso sexual) y trastornos en niños (déficit de atención y trastornos de conducta). Mediante un sistema computacional de información geográfica se combinaron estos elementos con datos sociodemográficos de las personas que acudieron a consulta y con datos territoriales que pueden considerarse factores protectores o de riesgo de los problemas de salud, y algunos de los cuales constituyen indicadores de las condiciones de vida de las personas. Resultados. Se probó que el sistema de vigilancia epidemiológica propuesto ­que incorpora las condiciones de vida y las variables ambientales­ es una buena herramienta para la acción en salud y complementa la visión parcial de los sistemas de seguimiento, que no incluyen variables de contexto y se centran sólo en los problemas de salud. La información sintetizada en mapas permite visualizar simultáneamente diferentes capas de información sobre los factores relacionados con los problemas de salud estudiados, asociados a un territorio específico, con todas las variables ambientales que implican, en un formato de lectura ágil y evidente por sí mismo. Conclusiones. Estos resultados y la opinión convergente de los médicos participantes y usuarios permiten afirmar que el sistema de vigilancia epidemiológica puesto a prueba en fase experimental logró cumplir los requerimientos básicos de un método de esta naturaleza

Objective. To design and test a surveillance system to detect and rank the most significant mental health problems in a community and to establish their association with the living conditions in that community. Methods. The system was designed and tested at a primary health care center in the community of La Florida, which is in the metropolitan region of Santiago, the capital of Chile. The health problems that were under surveillance, with monthly monitoring, drugs), violence (domestic violence and sexual abuse, real or suspected), and disorders in children (attention deficit and behavioral disorders). By means of a computerized geographical information system (GIS), those surveillance data were combined with other data. These other data included sociodemographic information on the persons who went to the health center for care as well as data on local risk factors and protective factors for health problems, some of which are indicators of the local residents' living conditions. Results. The proposed epidemiological surveillance system, which takes into account local living conditions and environmental variables, is a good tool for health action. The proposed system also complements the incomplete perspective of monitoring systems, which do not include variables describing the local context and that focus only on health problems. The information synthesized in the GIS maps makes it possible to simultaneously display different layers of information on factors related to the health problems studied, linked to a specific area and all its environmental variables, in an easy-to-read, self-explanatory format. Conclusions. These results and the concurring opinions of the participating physicians show that the experimental system effectively met the basic requirements of an epidemiological surveillance system of this kind