| 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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| 3. |
- Karikari, Thomas, et al.
(författare)
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An extensive plasmid library to prepare tau protein variants and study their functional biochemistry.
- 2020
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Ingår i: ACS chemical neuroscience. - : American Chemical Society (ACS). - 1948-7193. ; 11:19, s. 3117-3129
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Tidskriftsartikel (refereegranskat)abstract
- Tau neurofibrillary tangles are key pathological features of Alzheimer's disease and other tauopathies. Recombinant protein technology is vital for studying the structure and function of tau in physiology and aggregation in pathophysiology. However, open-source and well-characterized plasmids for efficiently expressing and purifying different tau variants are lacking. We generated 44 sequence-verified plasmids including those encoding full length (FL) tau-441, its four-repeat microtubule-binding (K18) fragment, and their respective selected familial pathological variants (N279K, V337M, P301L, C291R and S356T). Moreover, plasmids for expressing single (C291A), double (C291A/C322A) and triple (C291A/C322A/I260C) cysteine-modified variants were generated to study alterations in cysteine content and locations. Furthermore, protocols for producing representative tau forms were developed. We produced and characterized the aggregation behavior of the triple cysteine-modified tau-K18, often used in real-time cell internalization and aggregation studies because it can be fluorescently labeled on a cysteine outside the microtubule-binding core. Similar to the wild type (WT), triple cysteine-modified tau-K18 aggregated by progressive -sheet enrichment, albeit at a slower rate. On prolonged incubation, cysteine-modified K18 formed paired helical filaments similar to those in Alzheimer's disease, sharing morphological phenotypes with WT tau-K18 filaments. Nonetheless, cysteine-modified tau-K18 filaments were significantly shorter (p=0.002) and mostly wider than WT filaments, explainable by their different principal filament elongation pathways: vertical (end-to-end) and lateral growth for WT and cysteine-modified respectively. Cysteine rearrangement may therefore induce filament polymorphism. Together, the plasmid library, the protein production methods, and the new insights into cysteine-dependent aggregation, should facilitate further studies and the design of anti-aggregation agents.
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| 4. |
- Aimo, Alberto, et al.
(författare)
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Cardiac remodelling - Part 2: Clinical, imaging and laboratory findings. A review from the Study Group on Biomarkers of the Heart Failure Association of the European Society of Cardiology
- 2022
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Ingår i: European Journal of Heart Failure. - : WILEY. - 1388-9842 .- 1879-0844. ; 24:6, s. 944-958
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Forskningsöversikt (refereegranskat)abstract
- In patients with heart failure, the beneficial effects of drug and device therapies counteract to some extent ongoing cardiac damage. According to the net balance between these two factors, cardiac geometry and function may improve (reverse remodelling, RR) and even completely normalize (remission), or vice versa progressively deteriorate (adverse remodelling, AR). RR or remission predict a better prognosis, while AR has been associated with worsening clinical status and outcomes. The remodelling process ultimately involves all cardiac chambers, but has been traditionally evaluated in terms of left ventricular volumes and ejection fraction. This is the second part of a review paper by the Study Group on Biomarkers of the Heart Failure Association of the European Society of Cardiology dedicated to ventricular remodelling. This document examines the proposed criteria to diagnose RR and AR, their prevalence and prognostic value, and the variables predicting remodelling in patients managed according to current guidelines. Much attention will be devoted to RR in patients with heart failure with reduced ejection fraction because most studies on cardiac remodelling focused on this setting.
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| 5. |
- Alimena, Juliette, et al.
(författare)
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Searching for long-lived particles beyond the Standard Model at the Large Hadron Collider
- 2020
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Ingår i: Journal of Physics G. - : IOP Publishing. - 0954-3899 .- 1361-6471. ; 47:9
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Tidskriftsartikel (refereegranskat)abstract
- Particles beyond the Standard Model (SM) can generically have lifetimes that are long compared to SM particles at the weak scale. When produced at experiments such as the Large Hadron Collider (LHC) at CERN, these long-lived particles (LLPs) can decay far from the interaction vertex of the primary proton-proton collision. Such LLP signatures are distinct from those of promptly decaying particles that are targeted by the majority of searches for new physics at the LHC, often requiring customized techniques to identify, for example, significantly displaced decay vertices, tracks with atypical properties, and short track segments. Given their non-standard nature, a comprehensive overview of LLP signatures at the LHC is beneficial to ensure that possible avenues of the discovery of new physics are not overlooked. Here we report on the joint work of a community of theorists and experimentalists with the ATLAS, CMS, and LHCb experiments-as well as those working on dedicated experiments such as MoEDAL, milliQan, MATHUSLA, CODEX-b, and FASER-to survey the current state of LLP searches at the LHC, and to chart a path for the development of LLP searches into the future, both in the upcoming Run 3 and at the high-luminosity LHC. The work is organized around the current and future potential capabilities of LHC experiments to generally discover new LLPs, and takes a signature-based approach to surveying classes of models that give rise to LLPs rather than emphasizing any particular theory motivation. We develop a set of simplified models; assess the coverage of current searches; document known, often unexpected backgrounds; explore the capabilities of proposed detector upgrades; provide recommendations for the presentation of search results; and look towards the newest frontiers, namely high-multiplicity 'dark showers', highlighting opportunities for expanding the LHC reach for these signals.
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| 7. |
- Gonzalez, Arantxa, et al.
(författare)
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Cardiac remodelling - Part 1: From cells and tissues to circulating biomarkers. A review from the Study Group on Biomarkers of the Heart Failure Association of the European Society of Cardiology
- 2022
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Ingår i: European Journal of Heart Failure. - : WILEY. - 1388-9842 .- 1879-0844. ; 24:6, s. 927-943
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Forskningsöversikt (refereegranskat)abstract
- Cardiac remodelling refers to changes in left ventricular structure and function over time, with a progressive deterioration that may lead to heart failure (HF) development (adverse remodelling) or vice versa a recovery (reverse remodelling) in response to HF treatment. Adverse remodelling predicts a worse outcome, whilst reverse remodelling predicts a better prognosis. The geometry, systolic and diastolic function and electric activity of the left ventricle are affected, as well as the left atrium and on the long term even right heart chambers. At a cellular and molecular level, remodelling involves all components of cardiac tissue: cardiomyocytes, fibroblasts, endothelial cells and leucocytes. The molecular, cellular and histological signatures of remodelling may differ according to the cause and severity of cardiac damage, and clearly to the global trend toward worsening or recovery. These processes cannot be routinely evaluated through endomyocardial biopsies, but may be reflected by circulating levels of several biomarkers. Different classes of biomarkers (e.g. proteins, non-coding RNAs, metabolites and/or epigenetic modifications) and several biomarkers of each class might inform on some aspects on HF development, progression and long-term outcomes, but most have failed to enter clinical practice. This may be due to the biological complexity of remodelling, so that no single biomarker could provide great insight on remodelling when assessed alone. Another possible reason is a still incomplete understanding of the role of biomarkers in the pathophysiology of cardiac remodelling. Such role will be investigated in the first part of this review paper on biomarkers of cardiac remodelling.
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| 9. |
- Hill, Mattias, et al.
(författare)
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Coronary and Carotid Imaging of Atherosclerosis and Contributing Factors in Middle-aged People with Long-term Cervical and Upper Thoracic Spinal Cord Injuries
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Ingår i: PM and R. - 1934-1563.
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Tidskriftsartikel (refereegranskat)abstract
- INTRODUCTION: Cardiovascular disease (CVD) is a major cause of death in people aging with spinal cord injury (SCI), and is predominantly caused by atherosclerosis, however, knowledge of atherosclerosis in people with SCI is scarce.OBJECTIVE: To describe coronary and carotid atherosclerosis in middle-aged people with long-term cervical and upper thoracic SCI using coronary computed tomography angiography, carotid ultrasound, and CVD risk factors, and to compare with the general population.DESIGN: Cross-sectional study with matched controls.SETTING: Outpatient SCI unit in southern Sweden.PARTICIPANTS: Participants (n=25) in the Swedish SPinal Cord Injury Study on Cardiopulmonary and Autonomic Impairment (SPICA) (20% women, mean age 58 years, mean time since injury 28 years, injury levels C2-T6, American Spinal Injury Association Impairment Scale A-C). Non-SCI controls (n=125; ratio 5:1) from the Swedish CArdioPulmonary bioImage Study (SCAPIS).INTERVENTIONS: Not applicable MAIN OUTCOME MEASURES: Presence of coronary atherosclerosis, coronary artery calcium score (CACS), carotid plaques, carotid intima media thickness, blood pressure, lipids, Systematic Coronary Risk Evaluation (SCORE) and anthropometry.RESULTS: Coronary and carotid atherosclerotic plaques occurred in 44% of the participants, 67% of the controls exhibited coronary and 59% carotid plaques; odds ratios (OR; 95% CI): 0.38 (0.13-1.17) and 0.54 (0.22-1.32), respectively. Mean number of segments with coronary atherosclerosis were 1.0 in participants and 2.1 in controls (OR: 0.74 [0.52-1.06]). CACS >100 occurred in 4 (18%) of the participants and 23 (21%) of the controls. The participants had significantly lower levels of total and non-high density lipoprotein cholesterol and SCORE than the controls.CONCLUSIONS: This is the first comprehensive assessment of atherosclerosis in people with SCI using advanced imaging techniques. The atherosclerotic burden in middle-aged people with long-term cervical and upper thoracic SCI was not increased, whereas SCORE was lower due to lower cholesterol levels. Imaging techniques may be valuable tools for assessment of atherosclerosis in SCI. This article is protected by copyright. All rights reserved.
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| 10. |
- Hill, Mattias, et al.
(författare)
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Functional and structural impairments of the pulmonary system in middle-aged people with cervical and upper thoracic spinal cord injuries
- 2023
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Ingår i: Journal of Spinal Cord Medicine. - : Informa UK Limited. - 2045-7723 .- 1079-0268. ; 46:5, s. 732-741
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: To describe functional and structural impairments of the pulmonary system in middle-aged people with cervical and upper thoracic spinal cord injuries (SCI), and compare findings to the general population. To determine if the neurological level of injury (NLI) is related to functional and structural impairments, and if age is related to structural impairments.DESIGN: Cross-sectional study with matched controls. Data from the Swedish SPinal Cord Injury Study on Cardiopulmonary and Autonomic Impairment (SPICA). Matched control data were obtained from the Swedish CArdioPulmonary bioImage Study (SCAPIS).SETTING: Outpatient SCI unit in southern Sweden.PARTICIPANTS: 25 people (20% women, mean age 58 years, mean time since injury 28 years, NLIs C2-T6, American Spinal Injury Association Impairment Scale A-C).INTERVENTIONS: Not applicable.OUTCOME MEASURES: Lung function was assessed with spirometry, diffusing capacity and impulse oscillometry. Structural assessments were performed with computed tomography.RESULTS: Pulmonary function was generally worse compared to the controls. Structural impairments were common (75% of the participants and 65% of the controls; P = 0.36, NS). NLI was significantly related to some of the functional and structural impairments.CONCLUSIONS: Middle-aged people with long-term cervical and upper thoracic SCI can have substantial pulmonary functional impairments, whereas structural impairments do not differ considerably from the general population. Further larger and longitudinal studies should focus on the clinical impact of these impairments over time.
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