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- de Vries, Claire E. E., et al.
(författare)
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Outcomes of the first global multidisciplinary consensus meeting including persons living with obesity to standardize patient-reported outcome measurement in obesity treatment research
- 2022
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Ingår i: Obesity Reviews. - : John Wiley & Sons. - 1467-7881 .- 1467-789X. ; 23:8
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Tidskriftsartikel (refereegranskat)abstract
- Quality of life is a key outcome that is not rigorously measured in obesity treatment research due to the lack of standardization of patient-reported outcomes (PROs) and PRO measures (PROMs). The S.Q.O.T. initiative was founded to Standardize Quality of life measurement in Obesity Treatment. A first face-to-face, international, multidisciplinary consensus meeting was conducted to identify the key PROs and preferred PROMs for obesity treatment research. It comprised of 35 people living with obesity (PLWO) and healthcare providers (HCPs). Formal presentations, nominal group techniques, and modified Delphi exercises were used to develop consensus-based recommendations. The following eight PROs were considered important: self-esteem, physical health/functioning, mental/psychological health, social health, eating, stigma, body image, and excess skin. Self-esteem was considered the most important PRO, particularly for PLWO, while physical health was perceived to be the most important among HCPs. For each PRO, one or more PROMs were selected, except for stigma. This consensus meeting was a first step toward standardizing PROs (what to measure) and PROMs (how to measure) in obesity treatment research. It provides an overview of the key PROs and a first selection of the PROMs that can be used to evaluate these PROs.
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- Gorgolewski, Krzysztof J., et al.
(författare)
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BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods
- 2017
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Ingår i: PloS Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 13:3
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Tidskriftsartikel (refereegranskat)abstract
- The rate of progress in human neurosciences is limited by the inability to easily apply a wide range of analysis methods to the plethora of different datasets acquired in labs around the world. In this work, we introduce a framework for creating, testing, versioning and archiving portable applications for analyzing neuroimaging data organized and described in compliance with the Brain Imaging Data Structure (BIDS). The portability of these applications (BIDS Apps) is achieved by using container technologies that encapsulate all binary and other dependencies in one convenient package. BIDS Apps run on all three major operating systems with no need for complex setup and configuration and thanks to the comprehensiveness of the BIDS standard they require little manual user input. Previous containerized data processing solutions were limited to single user environments and not compatible with most multi-tenant High Performance Computing systems. BIDS Apps overcome this limitation by taking advantage of the Singularity container technology. As a proof of concept, this work is accompanied by 22 ready to use BIDS Apps, packaging a diverse set of commonly used neuroimaging algorithms.
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- Adediran, Gbotemi A., et al.
(författare)
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Microbial Biosynthesis of Thiol Compounds : Implications for Speciation, Cellular Uptake, and Methylation of Hg(II)
- 2019
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 53:14, s. 8187-8196
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Tidskriftsartikel (refereegranskat)abstract
- Cellular uptake of inorganic divalent mercury (Hg(II)) is a key step in microbial formation of neurotoxic methylmercury (MeHg), but the mechanisms remain largely unidentified. We show that the iron reducing bacterium Geobacter sulfurreducens produces and exports appreciable amounts of low molecular mass thiol (LMM-RSH) compounds reaching concentrations of about 100 nM in the assay medium. These compounds largely control the chemical speciation and bioavailability of Hg(II) by the formation of Hg(LMM-RS)2 complexes (primarily with cysteine) in assays without added thiols. By characterizing these effects, we show that the thermodynamic stability of Hg(II)-complexes is a principal controlling factor for Hg(II) methylation by this bacterium such that less stable complexes with mixed ligation involving LMM-RSH, OH-, and Cl- are methylated at higher rates than the more stable Hg(LMM-RS)2 complexes. The Hg(II) methylation rate across different Hg(LMM-RS)2 compounds is also influenced by the chemical structure of the complexes. In contrast to the current perception of microbial uptake of Hg, our results adhere to generalized theories for metal biouptake based on metal complexation with cell surface ligands and refine the mechanistic understanding of Hg(II) availability for microbial methylation.
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- Liem-Nguyen, Van, et al.
(författare)
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Determination of picomolar levels of methylmercury complexes with low molecular mass thiols by liquid chromatography tandem mass spectrometry and online preconcentration
- 2020
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Ingår i: Analytical and Bioanalytical Chemistry. - : Springer Berlin/Heidelberg. - 1618-2642 .- 1618-2650. ; 412:7, s. 1619-1628
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Tidskriftsartikel (refereegranskat)abstract
- Methylmercury (MeHg) is one of the most potent neurotoxins. It is produced in nature through the methylation of inorganic divalent mercury (HgII) by phylogenetically diverse anaerobic microbes. The mechanistic understanding of the processes that govern the extent of bacterial export of MeHg, its bioaccumulation, and bio-toxicity depends on accurate quantification of its species, especially its complexation with low molecular mass thiols; organometallic complexes that are difficult to detect and measure in natural conditions. Here, we report the development of a novel analytical method based on liquid chromatography tandem mass spectrometry (LC-MS/MS) to determine 13 MeHg complexes with important thiol compounds which have been observed in the environment and in biological systems. By using online preconcentration via solid phase extraction (SPE), the method offers picomolar (12–530 pM) detection limits, the lowest reported so far for the determination of MeHg compounds. Among three different SPE materials, a weak cation exchange phase showed the best efficiency at a low pH of 2.5. We further report the presence of MeHg-cysteine, MeHg-cysteamine, MeHg-penicillamine, MeHg-cysteinylglycine, and MeHg-glutamylcysteine as the predominant MeHg–thiol complexes in the extracellular milieu of an important HgII methylating bacterium, Geobacter sulfurreducens PCA, exposed to 100 nM of HgII.
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| 23. |
- Lindskog, Cecilia, et al.
(författare)
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The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling
- 2015
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 16
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Tidskriftsartikel (refereegranskat)abstract
- Background: To understand cardiac and skeletal muscle function, it is important to define and explore their molecular constituents and also to identify similarities and differences in the gene expression in these two different striated muscle tissues. Here, we have investigated the genes and proteins with elevated expression in cardiac and skeletal muscle in relation to all other major human tissues and organs using a global transcriptomics analysis complemented with antibody-based profiling to localize the corresponding proteins on a single cell level. Results: Our study identified a comprehensive list of genes expressed in cardiac and skeletal muscle. The genes with elevated expression were further stratified according to their global expression pattern across the human body as well as their precise localization in the muscle tissues. The functions of the proteins encoded by the elevated genes are well in line with the physiological functions of cardiac and skeletal muscle, such as contraction, ion transport, regulation of membrane potential and actomyosin structure organization. A large fraction of the transcripts in both cardiac and skeletal muscle correspond to mitochondrial proteins involved in energy metabolism, which demonstrates the extreme specialization of these muscle tissues to provide energy for contraction. Conclusions: Our results provide a comprehensive list of genes and proteins elevated in striated muscles. A number of proteins not previously characterized in cardiac and skeletal muscle were identified and localized to specific cellular subcompartments. These proteins represent an interesting starting point for further functional analysis of their role in muscle biology and disease.
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- Nguyen, Viet-Tien, et al.
(författare)
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GIS Based Novel Hybrid Computational Intelligence Models for Mapping Landslide Susceptibility : A Case Study at Da Lat City, Vietnam
- 2019
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Ingår i: Sustainability. - Switzerland : MDPI. - 2071-1050. ; 11:24
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Tidskriftsartikel (refereegranskat)abstract
- Landslides affect properties and the lives of a large number of people in many hilly parts of Vietnam and in the world. Damages caused by landslides can be reduced by understanding distribution, nature, mechanisms and causes of landslides with the help of model studies for better planning and risk management of the area. Development of landslide susceptibility maps is one of the main steps in landslide management. In this study, the main objective is to develop GIS based hybrid computational intelligence models to generate landslide susceptibility maps of the Da Lat province, which is one of the landslide prone regions of Vietnam. Novel hybrid models of alternating decision trees (ADT) with various ensemble methods, namely bagging, dagging, MultiBoostAB, and RealAdaBoost, were developed namely B-ADT, D-ADT, MBAB-ADT, RAB-ADT, respectively. Data of 72 past landslide events was used in conjunction with 11 landslide conditioning factors (curvature, distance from geological boundaries, elevation, land use, Normalized Difference Vegetation Index (NDVI), relief amplitude, stream density, slope, lithology, weathering crust and soil) in the development and validation of the models. Area under the receiver operating characteristic (ROC) curve (AUC), and several statistical measures were applied to validate these models. Results indicated that performance of all the models was good (AUC value greater than 0.8) but B-ADT model performed the best (AUC= 0.856). Landslide susceptibility maps generated using the proposed models would be helpful to decision makers in the risk management for land use planning and infrastructure development.
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| 27. |
- Soerensen, Anne L., et al.
(författare)
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Deciphering the Role of Water Column Redoxclines on Methylmercury Cycling Using Speciation Modeling and Observations From the Baltic Sea
- 2018
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Ingår i: Global Biogeochemical Cycles. - : American Geophysical Union (AGU). - 0886-6236 .- 1944-9224. ; 32:10, s. 1498-1513
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Tidskriftsartikel (refereegranskat)abstract
- Oxygen-depleted areas are spreading in coastal and offshore waters worldwide, but the implication for production and bioaccumulation of neurotoxic methylmercury (MeHg) is uncertain. We combined observations from six cruises in the Baltic Sea with speciation modeling and incubation experiments to gain insights into mercury (Hg) dynamics in oxygen depleted systems. We then developed a conceptual model describing the main drivers of Hg speciation, fluxes, and transformations in water columns with steep redox gradients. MeHg concentrations were 2-6 and 30-55 times higher in hypoxic and anoxic than in normoxic water, respectively, while only 1-3 and 1-2 times higher for total Hg (THg). We systematically detected divalent inorganic Hg (Hg-II) methylation in anoxic water but rarely in other waters. In anoxic water, high concentrations of dissolved sulfide cause formation of dissolved species of Hg-II: HgS2H(aq)- and Hg (SH)(2)(0)((aq)). This prolongs the lifetime and increases the reservoir of Hg-II readily available for methylation, driving the high MeHg concentrations in anoxic zones. In the hypoxic zone and at the hypoxic-anoxic interface, Hg concentrations, partitioning, and speciation are all highly dynamic due to processes linked to the iron and sulfur cycles. This causes a large variability in bioavailability of Hg, and thereby MeHg concentrations, in these zones. We find that zooplankton in the summertime are exposed to 2-6 times higher MeHg concentrations in hypoxic than in normoxic water. The current spread of hypoxic zones in coastal systems worldwide could thus cause an increase in the MeHg exposure of food webs.
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| 28. |
- Van, den Berg M, et al.
(författare)
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Toxic equivalency factors (TEFs) for PCBs, PCDDs, PCDFs for humans and wildlife
- 1998
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Ingår i: ENVIRONMENTAL HEALTH PERSPECTIVES. - : US DEPT HEALTH HUMAN SERVICES PUBLIC HEALTH SERVICE. ; 106:12, s. 775-792
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Recension (övrigt vetenskapligt/konstnärligt)abstract
- An expert meeting was organized by the World Health Organization (WHO) and held in Stockholm on 15-18 June 1997. The objective of this meeting was to derive consensus toxic equivalency factors (TEFs) for polychlorinated dibenzo-p-dioxins (PCDDs) and diben
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| 30. |
- van der Meer, Rieneke, et al.
(författare)
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Genetic variants associated with weight loss and metabolic outcomes after bariatric surgery : A systematic review
- 2023
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Ingår i: Obesity Reviews. - 1467-7881. ; 24:12
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Forskningsöversikt (refereegranskat)abstract
- The extent to which genetic variations contribute to interindividual differences in weight loss and metabolic outcomes after bariatric surgery is unknown. Identifying genetic variants that impact surgery outcomes may contribute to clinical decision making. This review evaluates current evidence addressing the association of genetic variants with weight loss and changes in metabolic parameters after bariatric surgery. A search was conducted using Medline, Embase, Scopus, Web of Science, and Cochrane Library. Fifty-two eligible studies were identified. Single nucleotide polymorphisms (SNPs) at ADIPOQ (rs226729, rs1501299, rs3774261, and rs17300539) showed a positive association with postoperative change in measures of glucose homeostasis and lipid profiles (n = 4), but not with weight loss after surgery (n = 6). SNPs at FTO (rs11075986, rs16952482, rs8050136, rs9939609, rs9930506, and rs16945088) (n = 10) and MC4R (rs11152213, rs476828, rs2229616, rs9947255, rs17773430, rs5282087, and rs17782313) (n = 9) were inconsistently associated with weight loss and metabolic improvement. Four studies examining the UCP2 SNP rs660339 reported associations with postsurgical weight loss. In summary, there is limited evidence supporting a role for specific genetic variants in surgical outcomes after bariatric surgery. Most studies have adopted a candidate gene approach, limiting the scope for discovery, suggesting that the absence of compelling evidence is not evidence of absence.
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| 31. |
- Zong, N. C., et al.
(författare)
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Integration of cardiac proteome biology and medicine by a specialized knowledgebase
- 2013
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Ingår i: Circulation Research. - 0009-7330 .- 1524-4571. ; 113:9, s. 1043-1053
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Tidskriftsartikel (refereegranskat)abstract
- Rationale: Omics sciences enable a systems-level perspective in characterizing cardiovascular biology. Integration of diverse proteomics data via a computational strategy will catalyze the assembly of contextualized knowledge, foster discoveries through multidisciplinary investigations, and minimize unnecessary redundancy in research efforts. Objective: The goal of this project is to develop a consolidated cardiac proteome knowledgebase with novel bioinformatics pipeline and Web portals, thereby serving as a new resource to advance cardiovascular biology and medicine. Methods and results: We created Cardiac Organellar Protein Atlas Knowledgebase (COPaKB; www.HeartProteome.org), a centralized platform of high-quality cardiac proteomic data, bioinformatics tools, and relevant cardiovascular phenotypes. Currently, COPaKB features 8 organellar modules, comprising 4203 LC-MS/MS experiments from human, mouse, drosophila, and Caenorhabditis elegans, as well as expression images of 10 924 proteins in human myocardium. In addition, the Java-coded bioinformatics tools provided by COPaKB enable cardiovascular investigators in all disciplines to retrieve and analyze pertinent organellar protein properties of interest. Conclusions: COPaKB provides an innovative and interactive resource that connects research interests with the new biological discoveries in protein sciences. With an array of intuitive tools in this unified Web server, nonproteomics investigators can conveniently collaborate with proteomics specialists to dissect the molecular signatures of cardiovascular phenotypes.
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