| 1. |
- 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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| 2. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Benavides-Huerto, Miguel Armando, et al.
(författare)
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Idiopathic granulomatous orchitis : A case study
- 2024
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Ingår i: Urology Case Reports. - : Elsevier. - 2214-4420. ; 54
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Tidskriftsartikel (refereegranskat)abstract
- Idiopathic granulomatous orchitis (IGO) is a rare inflammatory disorder of unknown etiology affecting the testis. Presented here is the case of a young patient who developed IGO, potentially associated with an anti -sperm antibody-mediated autoimmune response.
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| 4. |
- Breitburg, Denise, et al.
(författare)
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Declining oxygen in the global ocean and coastal waters
- 2018
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 359:6371
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Forskningsöversikt (refereegranskat)abstract
- Oxygen is fundamental to life. Not only is it essential for the survival of individual animals, but it regulates global cycles of major nutrients and carbon. The oxygen content of the open ocean and coastal waters has been declining for at least the past half-century, largely because of human activities that have increased global temperatures and nutrients discharged to coastal waters. These changes have accelerated consumption of oxygen by microbial respiration, reduced solubility of oxygen in water, and reduced the rate of oxygen resupply from the atmosphere to the ocean interior, with a wide range of biological and ecological consequences. Further research is needed to understand and predict long-term, global-and regional-scale oxygen changes and their effects on marine and estuarine fisheries and ecosystems.
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| 5. |
- Chávez-Valencia, Venice, et al.
(författare)
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Acute Kidney Injury in COVID-19 Patients : Pathogenesis, Clinical Characteristics, Therapy, and Mortality
- 2022
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Ingår i: Diseases. - : MDPI. - 2079-9721. ; 10:3
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Forskningsöversikt (refereegranskat)abstract
- Coronavirus disease 2019 (COVID-19) is a disease caused by infection with the SARS-CoV-2 virus and has represented one of the greatest challenges humanity has faced in recent years. The virus can infect a large number of organs, including the lungs and upper respiratory tract, brain, liver, kidneys, and intestines, among many others. Although the greatest damage occurs in the lungs, the kidneys are not exempt, and acute kidney injury (AKI) can occur in patients with COVID-19. Indeed, AKI is one of the most frequent and serious organic complications of COVID-19. The incidence of COVID-19 AKI varies widely, and the exact mechanisms of how the virus damages the kidney are still unknown. For this reason, the purpose of this review was to assess current findings on the pathogenesis, clinical features, therapy, and mortality of COVID-19 AKI.
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| 6. |
- Lagunas-Rangel, Francisco Alejandro, et al.
(författare)
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FLT3–ITD and its current role in acute myeloid leukaemia
- 2017
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Ingår i: Medical Oncology. - : Springer Nature. - 1357-0560 .- 1559-131X. ; 34:6
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Forskningsöversikt (refereegranskat)abstract
- FMS-like tyrosine kinase 3 (FLT3) is a proto-oncogene involved in crucial steps of haematopoiesis such as proliferation, differentiation and survival. In recent years, FLT3 has been an important marker in different haematological malignancies, highlighting in acute myeloid leukaemia, where FLT3 mutations have been associated with the clinical prognosis, treatment and survival of patients. The most common form of FLT3 mutation is an internal tandem duplication (ITD) that promotes ligand-independent auto-phosphorylation and constitutive activation of the receptor. FLT3–ITD has been strongly associated with a bad prognosis, leukocytosis, high blast counts, increased risk of relapse and shorter overall survival. In order to improve the clinical condition of FLT3–ITD-positive patients, several FLT3 inhibitors have been developed showing variable results. Currently, the main challenges to be overcome are the different forms of resistance to FLT3 inhibitors. Thus, the purpose of this review is to present, in a general way, the current role that FLT3–ITD mutation plays in patients with AML, with a particular emphasis on the molecular mechanisms associated with clinical prognosis, treatment, and survival of patients.
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| 7. |
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| 8. |
- Lagunas-Rangel, Francisco Alejandro, et al.
(författare)
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Learning of nature : The curious case of the naked mole rat
- 2017
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Ingår i: Mechanisms of Ageing and Development. - : Elsevier BV. - 0047-6374 .- 1872-6216. ; 164, s. 76-81
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Tidskriftsartikel (refereegranskat)abstract
- Naked mole rats (NMRs) are the longest-living rodents known, living up to approximately 30 years and showing sustained good health. Nowadays, NMRs are considered excellent models for aging and, additionally, for cancer research, due to the evidence of a remarkable cancer resistance demonstrated through thousands of necropsies performed with very few cases that describe this pathology, which is believed to be a disease that unavoidably accompanies aging. Since some years ago, several studies have tried to explain the possible mechanisms underlying longevity and cancer resistance in NMRs through different perspectives and directions, creating new knowledge that subsequently could be used for cancer prevention and delaying aging in humans. Thus, the purpose of this review is to summarize the recent knowledge on naked mole rats with a particular emphasis on the molecular mechanisms associated with their longevity and cancer resistance.
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| 9. |
- Lagunas-Rangel, Francisco Alejandro, et al.
(författare)
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What do we know about the antibody responses to SARS-CoV-2?
- 2021
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Ingår i: Immunobiology. - : Elsevier BV. - 0171-2985 .- 1878-3279. ; 226:2
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Forskningsöversikt (refereegranskat)abstract
- Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide causing a pandemic with millions of infected people and deaths. Currently, the scientific community is working hard to develop a specific vaccine or treatment. However, since antibody production is an important part of the adaptive immune response, to develop vaccines and therapies, we must understand the antibody response to SARS-CoV-2 infection. In this work, we summarize the most important findings of antibody-mediated immunity against SARS-CoV-2 and highlight its role in the efficient use of plasma from convalescent patients and the direct application of antibodies as treatment.
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| 10. |
- Richards, Stephen, et al.
(författare)
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Genome Sequence of the Pea Aphid Acyrthosiphon pisum
- 2010
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 8:2, s. e1000313-
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Tidskriftsartikel (refereegranskat)abstract
- Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
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| 11. |
- Sepulveda-Falla, Diego, et al.
(författare)
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A multifactorial model of pathology for age of onset heterogeneity in familial Alzheimer's disease.
- 2021
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Ingår i: Acta neuropathologica. - : Springer Science and Business Media LLC. - 1432-0533 .- 0001-6322. ; 141, s. 217-233
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Tidskriftsartikel (refereegranskat)abstract
- Presenilin-1 (PSEN1) mutations cause familial Alzheimer's disease (FAD) characterized by early age of onset (AoO). Examination of a large kindred harboring the PSEN1-E280A mutation reveals a range of AoO spanning 30years. The pathophysiological drivers and clinical impact of AoO variation in this population are unknown. We examined brains of 23 patients focusing on generation and deposition of beta-amyloid (Aβ) and Tau pathology profile. In 14 patients distributed at the extremes of AoO, we performed whole-exome capture to identify genotype-phenotype correlations. We also studied kinome activity, proteasome activity, and protein polyubiquitination in brain tissue, associating it with Tau phosphorylation profiles. PSEN1-E280A patients showed a bimodal distribution for AoO. Besides AoO, there were no clinical differences between analyzed groups. Despite the effect of mutant PSEN1 on production of Aβ, there were no relevant differences between groups in generation and deposition of Aβ. However, differences were found in hyperphosphorylated Tau (pTau) pathology, where early onset patients showed severe pathology with diffuse aggregation pattern associated with increased activation of stress kinases. In contrast, late-onset patients showed lesser pTau pathology and a distinctive kinase activity. Furthermore, we identified new protective genetic variants affecting ubiquitin-proteasome function in early onset patients, resulting in higher ubiquitin-dependent degradation of differentially phosphorylated Tau. In PSEN1-E280A carriers, altered γ-secretase activity and resulting Aβ accumulation are prerequisites for early AoO. However, Tau hyperphosphorylation pattern, and its degradation by the proteasome, drastically influences disease onset in individuals with otherwise similar Aβ pathology, hinting toward a multifactorial model of disease for FAD. In sporadic AD (SAD), a wide range of heterogeneity, also influenced by Tau pathology, has been identified. Thus, Tau-induced heterogeneity is a common feature in both AD variants, suggesting that a multi-target therapeutic approach should be used to treat AD.
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| 12. |
- Valente, Andre, et al.
(författare)
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A compilation of global bio-optical in situ data for ocean-colour satellite applications
- 2016
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Ingår i: Earth System Science Data. - : Copernicus GmbH. - 1866-3508 .- 1866-3516. ; 8:1, s. 235-252
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Tidskriftsartikel (refereegranskat)abstract
- A compiled set of in situ data is important to evaluate the quality of ocean-colour satellite-data records. Here we describe the data compiled for the validation of the ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI). The data were acquired from several sources (MOBY, BOUSSOLE, AERONET-OC, SeaBASS, NOMAD, MERMAID, AMT, ICES, HOT, GeP&CO), span between 1997 and 2012, and have a global distribution. Observations of the following variables were compiled: spectral remote-sensing reflectances, concentrations of chlorophyll a, spectral inherent optical properties and spectral diffuse attenuation coefficients. The data were from multi-project archives acquired via the open internet services or from individual projects, acquired directly from data providers. Methodologies were implemented for homogenisation, quality control and merging of all data. No changes were made to the original data, other than averaging of observations that were close in time and space, elimination of some points after quality control and conversion to a standard format. The final result is a merged table designed for validation of satellite-derived ocean-colour products and available in text format. Metadata of each in situ measurement (original source, cruise or experiment, principal investigator) were preserved throughout the work and made available in the final table. Using all the data in a validation exercise increases the number of matchups and enhances the representativeness of different marine regimes. By making available the metadata, it is also possible to analyse each set of data separately. The compiled data are available at doi: 10.1594/PANGAEA.854832 (Valente et al., 2015).
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| 13. |
- Valente, André, et al.
(författare)
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A compilation of global bio-optical in situ data for ocean-colour satellite applications - version two
- 2019
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Ingår i: Earth System Science Data. - : Copernicus GmbH. - 1866-3508 .- 1866-3516. ; 11:3, s. 1037-1068
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Tidskriftsartikel (refereegranskat)abstract
- A global compilation of in situ data is useful to evaluate the quality of ocean-colour satellite data records. Here we describe the data compiled for the validation of the ocean-colour products from the ESA Ocean Colour Climate Change Initiative (OC-CCI). The data were acquired from several sources (including, inter alia, MOBY, BOUSSOLE, AERONET-OC, SeaBASS, NOMAD, MERMAID, AMT, ICES, HOT and GeP&CO) and span the period from 1997 to 2018. Observations of the following variables were compiled: spectral remote-sensing reflectances, concentrations of chlorophyll a, spectral inherent optical properties, spectral diffuse attenuation coefficients and total suspended matter. The data were from multi-project archives acquired via open internet services or from individual projects, acquired directly from data providers. Methodologies were implemented for homogenization, quality control and merging of all data. No changes were made to the original data, other than averaging of observations that were close in time and space, elimination of some points after quality control and conversion to a standard format. The final result is a merged table designed for validation of satellite-derived ocean-colour products and available in text format. Metadata of each in situ measurement (original source, cruise or experiment, principal investigator) was propagated throughout the work and made available in the final table. By making the metadata available, provenance is better documented, and it is also possible to analyse each set of data separately. This paper also describes the changes that were made to the compilation in relation to the previous version (Valente et al., 2016). The compiled data are available at https://doi.org/10.1594/PANGAEA.898188 (Valente et al., 2019).
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