Mamíferos medianos y grandes de la Cuenca media del río Planas, Colombia

We describe the diversity of medium and large mammals from an area in the Colombian Orinoco River basin. For three years we systematically used camera traps at 72 sampling stations and walked forest and savanna transects to determine the diversity of medium and large mammals. Relative abundance was documented for 29 native and 2 feral mammals from a sampling effort of 1789 camera-days and 469.5 km walked. Thirty-one species of mammals (9 orders, 19 families) were recorded. Threatened species recorded included the giant armadillo (Priodontes maximus), lowland tapir (Tapirus terrestris), white-lipped peccary (Tayassu pecari), and giant anteater (Myrmecophaga tridactyla). The most abundant species were the collared peccary (Pecari tajacu) and the common opossum (Didelphis marsupialis). We recorded rare species, including the bush dog (Speothos venaticus) and the Llano semi-endemic long-nosed armadillo (Dasypus sabanicola). The species documented face diverse pressures, including development, hunting for subsistence, and competition with invasive species and livestock. Our results suggest that the surveyed areas are important for the conservation of mammals in the eastern plains of Colombia.Estudiamos la diversidad de mamíferos medianos y grandes en un área no protegida de la Orinoquia Colombiana durante tres años, empleando cámaras trampa en 72 estaciones de muestreo y haciendo recorridos por bosques y sabanas. Con un esfuerzo de 1789 días-cámara y 469.5 km recorridos se documentaron 31 especies de mamíferos (9 órdenes, 19 familias). Se registraron especies amenazadas como ocarro (Priodontes maximus), danta (Tapirus terrestris), pecarí de labio blanco (Tayassu pecari) y hormiguero gigante (Myrmecophaga tridactyla). Se registraron especies raras, como el perro vinagre (Speothos venaticus) y semiendémicas como el cachicamo sabanero (Dasypus sabanicola). Las especies mejor representadas a través del índice de abundancia relativa fueron el pecarí de collar (Pecari tajacu) y la zarigüeya (Didelphis marsupialis). Las especies registradas se enfrentan a diversas presiones, como cacería para subsistencia, especies invasoras y ganadería. Por lo tanto, los resultados sugieren que las áreas no protegidas son importantes para la conservación de los mamíferos en los Llanos Orientales de Colombia

Melanoma circulating tumor cells: Benefits and challenges required for clinical application

The implementation of novel therapeutic interventions has improved the survival rates of melanoma patients with metastatic disease. Nonetheless, only 33% of treated cases exhibit long term responses. Circulating tumor cell (CTC) measurements are currently of clinical value in breast, prostate and colorectal cancers. However, the clinical utility of melanoma CTCs (MelCTCs) is still unclear due to challenges that appear intrinsic to MelCTCs (i.e. rarity, heterogeneity) and a lack of standardization in their isolation, across research laboratories. Here, we review the latest developments, pinpoint the challenges in MelCTC isolation and address their potential role in melanoma management

Bats (Chiroptera) in the department of Tolima, Colombia: diversity in a humid tropical forest and updated species list for Department

Los murciélagos (Chiroptera) representan el orden de mamíferos con mayor número de especies en Colombia, sin embargo, aún son escasos los estudios sobre la diversidad de este grupo taxonómico en algunas regiones del país. Objetivo. Describir la diversidad taxonómica de murciélagos en un bosque húmedo tropical (Reserva Agroecológica Santa Librada: RASL) en el departamento del Tolima, Colombia, y actualizar la lista de especies de los murciélagos en el departamento. Metodología. Se realizaron muestreos sistemáticos utilizando cinco redes de niebla y capturas manuales entre el 2016 y 2018 en la RASL, así como una revisión exhaustiva de registros sobre murciélagos del Tolima, a partir de fuentes literarias y especímenes en museos. Resultados. Para la RASL se registraron 19 especies pertenecientes a 13 géneros y 4 familias. Phyllostomidae fue la familia más representativa con 191 registros. Para el departamento se confirma la presencia de 99 especies de murciélagos. Conclusiones. La diversidad de murciélagos en el departamento del Tolima es mayor de lo que se ha considerado. Se adicionan 18 registros a la lista departamental y se identifican algunos vacíos de información y errores que pueden ser fuente de malas interpretaciones sobre la diversidad de murciélagos del Tolima reportada en la literatura. Finalmente, se reconoce la importancia de los parches de bosque húmedo tropical al norte del Tolima como sitios que albergan una alta diversidad de murciélagos, en su mayoría inexplorada.Bats (Chiroptera) represent the mammalian order with the highest number of species in Colombia, however, the studies on the diversity of this taxonomic group in some regions of the country are scarce. Objectives. The aim of this work is to describe the taxonomic diversity of bats in a humid tropical forest, (Santa Librada Agroecological Reserve, SLAR), in the department of Tolima, Colombia, and to update the bat species checklist and the state of knowledge of bats in the Department of Tolima. Methods. We performed field work sampling using 5 mist-nets and manual captures between 2016 and 2018 in SLAR, as well as, an exhaustive review of bat records of Tolima, from different sources and specimens in museums. Results. For the SLAR, we registered 19 species belonging to 13 genera and 4 families. Phyllostomidae was the most representative family with 191 records. Conclusions. Bats diversity at the Department of Tolima is greater than the previously reported. We included 18 additional species to the Department checklist and identified some information gaps and errors in the literature that might be a source of misunderstandings about the diversity of bats of Tolima. Finally, the patches of tropical humid forest at the north Tolima are recognized as important areas that host a high diversity of bats, mostly unexplored

Immunomagnetic-enriched subpopulations of melanoma circulating tumour cells (CTCs) exhibit distinct transcriptome profiles

Cutaneous melanoma circulating tumour cells (CTCs) are phenotypically and molecularly heterogeneous. We profiled the gene expression of CTC subpopulations immunomagnetic-captured by targeting either the melanoma-associated marker, MCSP, or the melanoma-initiating marker, ABCB5. Firstly, the expression of a subset of melanoma genes was investigated by RT-PCR in MCSP-enriched and ABCB5-enriched CTCs isolated from a total of 59 blood draws from 39 melanoma cases. Of these, 6 MCSP-and 6 ABCB5-enriched CTC fractions were further analysed using a genome-wide gene expression microarray. The transcriptional programs of both CTC subtypes included cell survival maintenance, cell proliferation, and migration pathways. ABCB5-enriched CTCs were specifically characterised by up-regulation of genes involved in epithelial to mesenchymal transition (EMT), suggesting an invasive phenotype. These findings underscore the presence of at least two distinct melanoma CTC subpopulations with distinct transcriptional programs, which may have distinct roles in disease progression and response to therapy. © 2019 by the authors. Licensee MDPI, Basel, Switzerland

Client applications and Server Side docker for management of RNASeq and/or VariantSeq workflows and pipelines of the GPRO Suite

The GPRO suite is an in-progress bioinformatic project for -omic data analyses. As part of the continued growth of this project, we introduce a client side & server side solution for comparative transcriptomics and analysis of variants. The client side consists of two Java applications called "RNASeq" and "VariantSeq" to manage workflows for RNA-seq and Variant-seq analysis, respectively, based on the most common command line interface tools for each topic. Both applications are coupled with a Linux server infrastructure (named GPRO Server Side) that hosts all dependencies of each application (scripts, databases, and command line interface tools). Implementation of the server side requires a Linux operating system, PHP, SQL, Python, bash scripting, and third-party software. The GPRO Server Side can be deployed via a Docker container that can be installed in the user's PC using any operating system or on remote servers as a cloud solution. The two applications are available as desktop and cloud applications and provide two execution modes: a Step-by-Step mode enables each step of a workflow to be executed independently and a Pipeline mode allows all steps to be run sequentially. The two applications also feature an experimental support system called GENIE that consists of a virtual chatbot/assistant and a pipeline jobs panel coupled with an expert system. The chatbot can troubleshoot issues with the usage of each tool, the pipeline job panel provides information about the status of each task executed in the GPRO Server Side, and the expert provides the user with a potential recommendation to identify or fix failed analyses. The two applications and the GPRO Server Side combine the user-friendliness and security of client software with the efficiency of front-end & back-end solutions to manage command line interface software for RNA-seq and variant-seq analysis via interface environments

Detection of p190BCR-ABL and p210BCR-ABL Fusion Transcripts in Patients with Chronic Myeloid Leukemia (CML) Using Qualitative RT-PCR

RESUMEN: Introducción: la leucemia mieloide crónica (LMC) se caracteriza por la presencia del cromosoma Filadelfia (Ph) que resulta de la translocación recíproca balanceada t(9;22)(q34;q11); este marcador cromosómico se encuentra con menor frecuencia en pacientes con leucemia linfoide aguda (LLA). Objetivo: determinar la frecuencia de las fusiones génicas BCR-ABL, que codifican para transcriptos p210BCR-ABL y p190 BCR-ABL en pacientes colombianos con diagnóstico de LMC, en diferentes fases de la enfermedad o de su tratamiento. Materiales y métodos: estudio descriptivo de corte transversal de 31 pacientes con LMC (15-78 años). El análisis se hizo a partir de muestras de sangre periférica con la técnica PCR anidada cualitativa para las isoformas P210 BCR-ABL (b3a2 e b2a2) y P190 BCR-ABL (e1a2). Resultados: se detectó el transcripto p210BCR-ABL en 29 de los 31 casos (93,6%). En ellos se identificaron las fusiones génicas b2a2 (16/29; 55,2%), b3a2 (10/29; 34,5%) y la coexpresión b3a2 y b2a2 (3/29; 10,3%). Conclusión: la fusión génica b2a2 fue la más frecuente en esta población con LMCSUMMARY: Introduction: Chronic myelogenous leukemia (CML) is characterized by the presence of the Philadelphia chromosome (Ph), resulting from the balanced reciprocal translocation t(9;22)(q34;q11). This marker chromosome is found less frequently in patients suffering from acute lymphoblastic leukemia. Objective: To determine the frequency of BCR-ABL gene fusions encoding the p210BCR-ABL y p190 BCR-ABL transcripts in Colombian patients diagnosed with CML in different stages of the disease and/or its treatment. Materials and methods: Cross sectional, descriptive study of thirty one CML patients (aged 15-78). Analysis was carried out through qualitative nested PCR for the isoforms P210 BCR-ABL (b3a2 e b2a2) and P190 BCR-ABL (e1a2), and based on peripheral blood samples. Results: In 29 of the 31 patients (93.6%) transcript p210BCR-ABL was detected; b2a2 and b3a2 gene fusions and the coexpression b3a2 and b2a2 were identified in 55.2% (16/29), 34.5% (10/29) and 10.3% (3/29) of the cases, respectively. Conclusion: b2a2 gene fusion was the most frequent in this CML populatio

Isolation and detection of circulating tumour cells from metastatic melanoma patients using a slanted spiral microfluidic device

Circulating Tumour Cells (CTCs) are promising cancer biomarkers. Several methods have been developed to isolate CTCs from blood samples. However, the isolation of melanoma CTCs is very challenging as a result of their extraordinary heterogeneity, which has hindered their biological and clinical study. Thus, methods that isolate CTCs based on their physical properties, rather than surface marker expression, such as microfluidic devices, are greatly needed in melanoma. Here, we assessed the ability of the slanted spiral microfluidic device to isolate melanoma CTCs via label-free enrichment. We demonstrated that this device yields recovery rates of spiked melanoma cells of over 80% and 55%, after one or two rounds of enrichment, respectively. Concurrently, a two to three log reduction of white blood cells was achieved with one or two rounds of enrichment, respectively. We characterised the isolated CTCs using multimarker flow cytometry, immunocytochemistry and gene expression. The results demonstrated that CTCs from metastatic melanoma patients were highly heterogeneous and commonly expressed stem-like markers such as PAX3 and ABCB5. The implementation of the slanted microfluidic device for melanoma CTC isolation enables further understanding of the biology of melanoma metastasis for biomarker development and to inform future treatment approaches

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

COVIDiSTRESS Global Survey dataset on psychological and behavioural consequences of the COVID-19 outbreak

This N = 173,426 social science dataset was collected through the collaborative COVIDiSTRESS Global Survey - an open science effort to improve understanding of the human experiences of the 2020 COVID-19 pandemic between 30th March and 30th May, 2020. The dataset allows a cross-cultural study of psychological and behavioural responses to the Coronavirus pandemic and associated government measures like cancellation of public functions and stay at home orders implemented in many countries. The dataset contains demographic background variables as well as measures of Asian Disease Problem, perceived stress (PSS-10), availability of social provisions (SPS-10), trust in various authorities, trust in governmental measures to contain the virus (OECD trust), personality traits (BFF-15), information behaviours, agreement with the level of government intervention, and compliance with preventive measures, along with a rich pool of exploratory variables and written experiences. A global consortium from 39 countries and regions worked together to build and translate a survey with variables of shared interests, and recruited participants in 47 languages and dialects. Raw plus cleaned data and dynamic visualizations are available.Measurement(s) psychological measurement center dot anxiety-related behavior trait center dot Stress center dot response to center dot Isolation center dot loneliness measurement center dot Emotional Distress Technology Type(s) Survey Factor Type(s) geographic location center dot language center dot age of participant center dot responses to the Coronavirus pandemic Sample Characteristic - Organism Homo sapiens Sample Characteristic - Location global Machine-accessible metadata file describing the reported data:Peer reviewe

Stress and worry in the 2020 coronavirus pandemic: Relationships to trust and compliance with preventive measures across 48 countries in the COVIDiSTRESS global survey

The COVIDiSTRESS global survey collects data on early human responses to the 2020 COVID-19 pandemic from 173 429 respondents in 48 countries. The open science study was co-designed by an international consortium of researchers to investigate how psychological responses differ across countries and cultures, and how this has impacted behaviour, coping and trust in government efforts to slow the spread of the virus. Starting in March 2020, COVIDiSTRESS leveraged the convenience of unpaid online recruitment to generate public data. The objective of the present analysis is to understand relationships between psychological responses in the early months of global coronavirus restrictions and help understand how different government measures succeed or fail in changing public behaviour. There were variations between and within countries. Although Western Europeans registered as more concerned over COVID-19, more stressed, and having slightly more trust in the governments' efforts, there was no clear geographical pattern in compliance with behavioural measures. Detailed plots illustrating between-countries differences are provided. Using both traditional and Bayesian analyses, we found that individuals who worried about getting sick worked harder to protect themselves and others. However, concern about the coronavirus itself did not account for all of the variances in experienced stress during the early months of COVID-19 restrictions. More alarmingly, such stress was associated with less compliance. Further, those most concerned over the coronavirus trusted in government measures primarily where policies were strict. While concern over a disease is a source of mental distress, other factors including strictness of protective measures, social support and personal lockdown conditions must also be taken into consideration to fully appreciate the psychological impact of COVID-19 and to understand why some people fail to follow behavioural guidelines intended to protect themselves and others from infection. The Stage 1 manuscript associated with this submission received in-principle acceptance (IPA) on 18 May 2020. Following IPA, the accepted Stage 1 version of the manuscript was preregistered on the Open Science Framework at https://osf.io/g2t3b. This preregistration was performed prior to data analysis