| 1. |
- Hudson, Lawrence N, et al.
(författare)
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The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
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Tidskriftsartikel (refereegranskat)abstract
- The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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| 2. |
- López-Isac, Elena, et al.
(författare)
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Brief Report : IRF4 Newly Identified as a Common Susceptibility Locus for Systemic Sclerosis and Rheumatoid Arthritis in a Cross-Disease Meta-Analysis of Genome-Wide Association Studies
- 2016
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Ingår i: Arthritis & Rheumatology. - : Wiley. - 2326-5191 .- 2326-5205. ; 68:9, s. 2338-2344
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Tidskriftsartikel (refereegranskat)abstract
- Objective: Systemic sclerosis (SSc) and rheumatoid arthritis (RA) are autoimmune diseases that have similar clinical and immunologic characteristics. To date, several shared SSc–RA genetic loci have been identified independently. The aim of the current study was to systematically search for new common SSc–RA loci through an interdisease meta–genome-wide association (meta-GWAS) strategy. Methods: The study was designed as a meta-analysis combining GWAS data sets of patients with SSc and patients with RA, using a strategy that allowed identification of loci with both same-direction and opposite-direction allelic effects. The top single-nucleotide polymorphisms were followed up in independent SSc and RA case–control cohorts. This allowed an increase in the sample size to a total of 8,830 patients with SSc, 16,870 patients with RA, and 43,393 healthy controls. Results: This cross-disease meta-analysis of the GWAS data sets identified several loci with nominal association signals (P < 5 × 10−6) that also showed evidence of association in the disease-specific GWAS scans. These loci included several genomic regions not previously reported as shared loci, as well as several risk factors that were previously found to be associated with both diseases. Follow-up analyses of the putatively new SSc–RA loci identified IRF4 as a shared risk factor for these 2 diseases (Pcombined = 3.29 × 10−12). Analysis of the biologic relevance of the known SSc–RA shared loci identified the type I interferon and interleukin-12 signaling pathways as the main common etiologic factors. Conclusion: This study identified a novel shared locus, IRF4, for the risk of SSc and RA, and highlighted the usefulness of a cross-disease GWAS meta-analysis strategy in the identification of common risk loci.
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| 3. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 4. |
- Fierrez, Julian, et al.
(författare)
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BiosecurID : A Multimodal Biometric Database
- 2010
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Ingår i: Pattern Analysis and Applications. - New York, USA : Springer-Verlag New York. - 1433-7541 .- 1433-755X. ; 13:2, s. 235-246
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Tidskriftsartikel (refereegranskat)abstract
- A new multimodal biometric database, acquired in the framework of the BiosecurID project, is presented together with the description of the acquisition setup and protocol. The database includes eight unimodal biometric traits, namely: speech, iris, face (still images, videos of talking faces), handwritten signature and handwritten text (on-line dynamic signals, off-line scanned images), fingerprints (acquired with two different sensors), hand (palmprint, contour-geometry) and keystroking. The database comprises 400 subjects and presents features such as: realistic acquisition scenario, balanced gender and population distributions, availability of information about particular demographic groups (age, gender, handedness), acquisition of replay attacks for speech and keystroking, skilled forgeries for signatures, and compatibility with other existing databases. All these characteristics make it very useful in research and development of unimodal and multimodal biometric systems. © Springer-Verlag London Limited 2009.
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| 5. |
- Giongo, Adriana, et al.
(författare)
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Discovery of a chemosynthesis-based community in the western South Atlantic Ocean
- 2016
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Ingår i: Deep Sea Research Part I. - : Elsevier. - 0967-0637 .- 1879-0119. ; 112, s. 45-56
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Tidskriftsartikel (refereegranskat)abstract
- Chemosynthetic communities have been described from a variety of deep-sea environments across the world's oceans. They constitute very interesting biological systems in terms of their ecology, evolution and biogeography, and also given their potential as indicators of the presence and abundance of consistent hydrocarbon-based nutritional sources. Up to now such peculiar biotic assemblages have not been reported for the western South Atlantic Ocean, leaving this large region undocumented with respect to the presence, composition and history of such communities. Here we report on the presence of a chemosynthetic community off the coast of southern Brazil, in an area where high-levels of methane and the presence of gas hydrates have been detected. We performed metagenomic analyses of the microbial community present at this site, and also employed molecular approaches to identify components of its benthic fauna. We conducted phylogenetic analyses comparing the components of this assemblage to those found elsewhere in the world, which allowed a historical assessment of the structure and dynamics of these systems. Our results revealed that the microbial community at this site is quite diverse, and contains many components that are very closely related to lineages previously sampled in ecologically similar environments across the globe. Anaerobic methanotrophic (ANME) archaeal groups were found to be very abundant at this site, suggesting that methane is indeed an important source of nutrition for this community. In addition, we document the presence at this site of a vestimentiferan siboglinid polychaete and the bivalve Acharax sp., both of which are typical components of deep-sea chemosynthetic communities. The remarkable similarity in biotic composition between this area and other deep-sea communities across the world supports the interpretation that these assemblages are historically connected across the global oceans, undergoing colonization from distant sites and influenced by local ecological features that select a stereotyped suite of specifically adapted organisms. (C) 2015 Elsevier Ltd. All rights reserved.
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| 6. |
- Miller, Dennis J., et al.
(författare)
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Natural gas hydrates in the Rio Grande Cone (Brazil) : A new province in the western South Atlantic
- 2015
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Ingår i: Marine and Petroleum Geology. - : Elsevier. - 0264-8172 .- 1873-4073. ; 67, s. 187-196
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Tidskriftsartikel (refereegranskat)abstract
- The Rio Grande Cone is a large-scale fanlike feature in the continental slope of the Pelotas Basin, Southern Brazil, where ubiquitous world-class bottom simulating reflectors (BSRs) are readily observed in seismic records. With the purpose of searching for natural gas hydrate deposits in the Cone area, four oceanographic cruises were carried out between May 2011 and July 2013, leading to the discovery of two pockmark fields, active faults and gas hydrates in shallow sediments. Multichannel seismic, multibeam echo sounder, side scan sonar and sub-bottom profiler records were used to map the shallow section and select sites for piston core sampling. Gas hydrates were recovered in several piston cores within muddy sediments collected inside pockmarks displaying high backscatter in the multibeam and side scan sonar data. We present two representative piston cores where numerous levels of gas hydrates occur, along with degassing features, authigenic carbonate and soupy sediments. Gas dissociated from gas hydrate samples is dominantly methane (>99.78%) with minor quantities of ethane. The chemical and isotopic compositions of the gas strongly suggest a biogenic origin for the analyzed samples. These new findings are regarded as strong enough evidence to consider the Rio Grande Cone as a new gas hydrate province. (C) 2015 Elsevier Ltd. All rights reserved.
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| 7. |
- Pádua, Diana, et al.
(författare)
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A SOX2 reporter system identifies gastric cancer stem-like cells sensitive to monensin
- 2020
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Ingår i: Cancers. - : MDPI AG. - 2072-6694. ; 12:2
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Tidskriftsartikel (refereegranskat)abstract
- Gastric cancer remains a serious health burden with few therapeutic options. Therefore, the recognition of cancer stem cells (CSCs) as seeds of the tumorigenic process makes them a prime therapeutic target. Knowing that the transcription factors SOX2 and OCT4 promote stemness, our approach was to isolate stem-like cells in human gastric cancer cell lines using a traceable reporter system based on SOX2/OCT4 activity (SORE6-GFP). Cells transduced with the SORE6-GFP reporter system were sorted into SORE6+ and SORE6– cell populations, and their biological behavior characterized. SORE6+ cells were enriched for SOX2 and exhibited CSC features, including a greater ability to proliferate and form gastrospheres in non-adherent conditions, a larger in vivo tumor initiating capability, and increased resistance to 5-fluorouracil (5-FU) treatment. The overexpression and knockdown of SOX2 revealed a crucial role of SOX2 in cell proliferation and drug resistance. By combining the reporter system with a high-throughput screening of pharmacologically active small molecules we identified monensin, an ionophore antibiotic, displaying selective toxicity to SORE6+ cells. The ability of SORE6-GFP reporter system to recognize cancer stem-like cells facilitates our understanding of gastric CSC biology and serves as a platform for the identification of powerful therapeutics for targeting gastric CSCs.
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| 8. |
- Parmar, Priya, et al.
(författare)
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The Stroke Riskometer (TM) App: Validation of a data collection tool and stroke risk predictor
- 2015
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Ingår i: International Journal of Stroke. - : SAGE Publications. - 1747-4949 .- 1747-4930. ; 10:2, s. 231-244
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundThe greatest potential to reduce the burden of stroke is by primary prevention of first-ever stroke, which constitutes three quarters of all stroke. In addition to population-wide prevention strategies (the mass' approach), the high risk' approach aims to identify individuals at risk of stroke and to modify their risk factors, and risk, accordingly. Current methods of assessing and modifying stroke risk are difficult to access and implement by the general population, amongst whom most future strokes will arise. To help reduce the burden of stroke on individuals and the population a new app, the Stroke Riskometer(TM), has been developed. We aim to explore the validity of the app for predicting the risk of stroke compared with current best methods. Methods752 stroke outcomes from a sample of 9501 individuals across three countries (New Zealand, Russia and the Netherlands) were utilized to investigate the performance of a novel stroke risk prediction tool algorithm (Stroke Riskometer(TM)) compared with two established stroke risk score prediction algorithms (Framingham Stroke Risk Score [FSRS] and QStroke). We calculated the receiver operating characteristics (ROC) curves and area under the ROC curve (AUROC) with 95% confidence intervals, Harrels C-statistic and D-statistics for measure of discrimination, R-2 statistics to indicate level of variability accounted for by each prediction algorithm, the Hosmer-Lemeshow statistic for calibration, and the sensitivity and specificity of each algorithm. ResultsThe Stroke Riskometer(TM) performed well against the FSRS five-year AUROC for both males (FSRS=750% (95% CI 723%-776%), Stroke Riskometer(TM)=740(95% CI 713%-767%) and females [FSRS=703% (95% CI 679%-728%, Stroke Riskometer(TM)=715% (95% CI 690%-739%)], and better than QStroke [males - 597% (95% CI 573%-620%) and comparable to females=711% (95% CI 690%-731%)]. Discriminative ability of all algorithms was low (C-statistic ranging from 051-056, D-statistic ranging from 001-012). Hosmer-Lemeshow illustrated that all of the predicted risk scores were not well calibrated with the observed event data (P<0006). ConclusionsThe Stroke Riskometer(TM) is comparable in performance for stroke prediction with FSRS and QStroke. All three algorithms performed equally poorly in predicting stroke events. The Stroke Riskometer(TM) will be continually developed and validated to address the need to improve the current stroke risk scoring systems to more accurately predict stroke, particularly by identifying robust ethnic/race ethnicity group and country specific risk factors.
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| 9. |
- Perez-Nadales, Elena, et al.
(författare)
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Predictors of mortality in solid organ transplant recipients with bloodstream infections due to carbapenemase-producing Enterobacterales : The impact of cytomegalovirus disease and lymphopenia
- 2020
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Ingår i: American Journal of Transplantation. - : WILEY. - 1600-6135 .- 1600-6143. ; 20:6, s. 1629-1641
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Tidskriftsartikel (refereegranskat)abstract
- Treatment of carbapenemase-producing Enterobacterales bloodstream infections in solid organ transplant recipients is challenging. The objective of this study was to develop a specific score to predict mortality in solid organ transplant recipients with carbapenemase-producing Enterobacterales bloodstream infections. A multinational, retrospective (2004-2016) cohort study (INCREMENT-SOT, ClinicalTrials.gov NCT02852902) was performed. The main outcome variable was 30-day all-cause mortality. The INCREMENT-SOT-CPE score was developed using logistic regression. The global cohort included 216 patients. The final logistic regression model included the following variables: INCREMENT-CPE mortality score >= 8 (8 points), no source control (3 points), inappropriate empirical therapy (2 points), cytomegalovirus disease (7 points), lymphopenia (4 points), and the interaction between INCREMENT-CPE score >= 8 and CMV disease (minus 7 points). This score showed an area under the receiver operating characteristic curve of 0.82 (95% confidence interval [CI] 0.76-0.88) and classified patients into 3 strata: 0-7 (low mortality), 8-11 (high mortality), and 12-17 (very-high mortality). We performed a stratified analysis of the effect of monotherapy vs combination therapy among 165 patients who received appropriate therapy. Monotherapy was associated with higher mortality only in the very-high (adjusted hazard ratio [HR] 2.82, 95% CI 1.13-7.06, P = .03) and high (HR 9.93, 95% CI 2.08-47.40, P = .004) mortality risk strata. A score-based algorithm is provided for therapy guidance.
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| 10. |
- Rodrigues, Luiz Frederico, et al.
(författare)
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The influence of methane fluxes on the sulfate/methane interface in sediments from the Rio Grande Cone Gas Hydrate Province, southern Brazil : A influência dos fluxos de metano na interface sulfato/metano em sedimentos de hidrato de gás do Cone do Rio Grande, Sul do Brasil
- 2017
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Ingår i: Brazilian Journal of Geology. - : FapUNIFESP (SciELO). - 2317-4692 .- 2317-4889. ; 47:3, s. 369-381
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Tidskriftsartikel (refereegranskat)abstract
- Much research has been published regarding the relation between major gas hydrate accumulations and the global carbon cycle. In this context, the determination of the sulfate/methane interface (SMI) depth is of primary importance in order to understand the dynamics of methane flux in the shallow section. This paper identifies the depth of the SMI in sediments based on sulfate and methane concentration profiles in cores recovered in the Rio Grande Cone Gas Hydrate Province, Pelotas Basin, southern Brazil. The shape of methane and sulfate concentration profiles in the sediments can be linked to the local methane flux rate as follows: (i) near linear, high upward-diffusing methane flux coupled with high sulfate diffusion from seawater; (ii) irregular, variable methane flux rates; and (iii) kink-type profile, which is indicative of variable rather than strictly high upward methane flux. The areas in which a high methane flux was identified are spatially associated with gas chimneys in sediments within pockmarks, whereas profiles with low methane flux are present in adjacent areas. These chimneys appear as acoustic blankings in seismic records and can therefore be mapped in subsurface. The wavy-like seismic reflection following the SMI coincides with the occurrence of authigenic carbonate nodules and concretions. In addition, high methane fluxes and the occurrence of concretions and nodules carbonates were correlated by stratigraphic position of the concretions bearing intervals and sulfate profiles
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