| 1. |
- Jönsson, K. Ingemar, 1959-, et al.
(author)
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Sexual patterns of prebreeding energy reserves in the common frog Rana temporaria along a latitudinal gradient
- 2009
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In: Ecography. - : Wiley-Blackwell. - 0906-7590 .- 1600-0587. ; 32:5, s. 831-839
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Journal article (peer-reviewed)abstract
- The ability to store energy is an important life history trait for organisms facing long periods without energy income, and in particular for capital breeders such as temperate zone amphibians, which rely on stored energy during reproduction. However, large scale comparative studies of energy stores in populations with different environmental constraints on energy allocation are scarce. We investigated energy storage patterns in spring (after hibernation and before reproduction) in eight common frog (Rana temporaria) populations exposed to different environmental conditions along a 1600 km latitudinal gradient across Scandinavia (range of annual activity period 3-7 months). Analyses of lean body weight (eviscerated body mass), weight of fat bodies, liver weight, and liver fat content, showed that (i) post-hibernation/pre-breeding energy stores increased with increasing latitude in both sexes, (ii) males generally had larger energy reserves than females and (iii) the difference in energy stores between sexes decreased towards the north. Larger energy reserves towards the north can serve as a buffer against less predictable and/or less benign weather conditions during the short activity period, and may also represent a risk-averse tactic connected with a more pronounced iteroparous life history. In females, the continuous and overlapping vitellogenic activity in the north may also demand more reserves in early spring. The general sexual difference could be a consequence of the fact that, at the time of our sampling, females had already invested their energy into reproduction in the given year (i.e. their eggs were already ovulated), while the males' main reproductive activities (e.g. calling, mate searching, sexual competition) occurred later in the season.
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| 2. |
- Bengtsson-Palme, Johan, 1985, et al.
(author)
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Strategies to improve usability and preserve accuracy in biological sequence databases
- 2016
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In: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 16:18, s. 2454-2460
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Journal article (peer-reviewed)abstract
- Biology is increasingly dependent on large-scale analysis, such as proteomics, creating a requirement for efficient bioinformatics. Bioinformatic predictions of biological functions rely upon correctly annotated database sequences, and the presence of inaccurately annotated or otherwise poorly described sequences introduces noise and bias to biological analyses. Accurate annotations are, for example, pivotal for correct identifications of polypeptide fragments. However, standards for how sequence databases are organized and presented are currently insufficient. Here, we propose five strategies to address fundamental issues in the annotation of sequence databases: (i) to clearly separate experimentally verified and unverified sequence entries; (ii) to enable a system for tracing the origins of annotations; (iii) to separate entries with high-quality, informative annotation from less useful ones; (iv) to integrate automated quality-control software whenever such tools exist; and (v) to facilitate post-submission editing of annotations and metadata associated with sequences. We believe that implementation of these strategies, for example as requirements for publication of database papers, would enable biology to better take advantage of large-scale data.
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| 3. |
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| 4. |
- Glimelius, Bengt, et al.
(author)
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U-CAN : a prospective longitudinal collection of biomaterials and clinical information from adult cancer patients in Sweden.
- 2018
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In: Acta Oncologica. - : Taylor & Francis. - 0284-186X .- 1651-226X. ; 57:2, s. 187-194
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Journal article (peer-reviewed)abstract
- Background: Progress in cancer biomarker discovery is dependent on access to high-quality biological materials and high-resolution clinical data from the same cases. To overcome current limitations, a systematic prospective longitudinal sampling of multidisciplinary clinical data, blood and tissue from cancer patients was therefore initiated in 2010 by Uppsala and Umeå Universities and involving their corresponding University Hospitals, which are referral centers for one third of the Swedish population.Material and Methods: Patients with cancer of selected types who are treated at one of the participating hospitals are eligible for inclusion. The healthcare-integrated sampling scheme encompasses clinical data, questionnaires, blood, fresh frozen and formalin-fixed paraffin-embedded tissue specimens, diagnostic slides and radiology bioimaging data.Results: In this ongoing effort, 12,265 patients with brain tumors, breast cancers, colorectal cancers, gynecological cancers, hematological malignancies, lung cancers, neuroendocrine tumors or prostate cancers have been included until the end of 2016. From the 6914 patients included during the first five years, 98% were sampled for blood at diagnosis, 83% had paraffin-embedded and 58% had fresh frozen tissues collected. For Uppsala County, 55% of all cancer patients were included in the cohort.Conclusions: Close collaboration between participating hospitals and universities enabled prospective, longitudinal biobanking of blood and tissues and collection of multidisciplinary clinical data from cancer patients in the U-CAN cohort. Here, we summarize the first five years of operations, present U-CAN as a highly valuable cohort that will contribute to enhanced cancer research and describe the procedures to access samples and data.
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| 5. |
- Hagman, Henning, 1981, et al.
(author)
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Plasmon-enhanced four-wave mixing by nanoholes in thin gold films
- 2014
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In: Optics Letters. - : Optical Society of America. - 0146-9592 .- 1539-4794. ; 39:4, s. 1001-1004
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Journal article (peer-reviewed)abstract
- Nonlinear plasmonics opens up for wavelength conversion, reduced interaction/emission volumes, and nonlinear enhancement effects at the nanoscale with many compelling nanophotonic applications foreseen. We investigate nonlinear plasmonic responses of nanoholes in thin gold films by exciting the holes individually with tightly focused laser beams, employing a degenerated pump/probe and Stokes excitation scheme. Excitation of the holes results in efficient generation of both narrowband four-wave mixing (FWM) and broadband multiphoton excited luminescence, blueshifted relative to the excitation beams. Clear enhancements were observed when matching the pump/probe wavelength with the hole plasmon resonance. These observations show that the FWM generation is locally excited by nanoholes and has a resonant behavior primarily governed by the dimensions of the individual holes.
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| 6. |
- Hallor, Karolin H, et al.
(author)
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Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumors.
- 2009
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In: Clinical Cancer Research. - 1078-0432. ; 15:8, s. 2685-2694
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Journal article (peer-reviewed)abstract
- PURPOSE: Histologic grade is currently the best predictor of clinical course in chondrosarcoma patients. Grading suffers, however, from extensive interobserver variability and new objective markers are needed. Hence, we have investigated DNA copy numbers in chondrosarcomas with the purpose of identifying markers useful for prognosis and subclassification. EXPERIMENTAL DESIGN: The overall pattern of genomic imbalances was assessed in a series of 67 chondrosarcomas using array comparative genomic hybridization. Statistical analyses were applied to evaluate the significance of alterations detected in subgroups based on clinical data, morphology, grade, tumor size, and karyotypic features. Also, the global gene expression profiles were obtained in a subset of the tumors. RESULTS: Genomic imbalances, in most tumors affecting large regions of the genome, were found in 90% of the cases. Several apparently distinctive aberrations affecting conventional central and peripheral tumors, respectively, were identified. Although rare, recurrent amplifications were found at 8q24.21-q24.22 and 11q22.1-q22.3, and homozygous deletions of loci previously implicated in chondrosarcoma development affected the CDKN2A, EXT1, and EXT2 genes. The chromosomal imbalances in two distinct groups of predominantly near-haploid and near-triploid tumors, respectively, support the notion that polyploidization of an initially hyperhaploid/hypodiploid cell population is a common mechanism of chondrosarcoma progression. Increasing patient age as well as tumor grade were associated with adverse outcome, but no copy number imbalance affected metastasis development or tumor-associated death. CONCLUSION: Despite similarities in the overall genomic patterns, the present findings suggest that some regions are specifically altered in conventional central and peripheral tumors, respectively.
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| 7. |
- Johansson, LarsErik, et al.
(author)
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Determination of conductivity of bacteria by using cross-flow filtration
- 2006
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In: Biotechnology letters. - : Springer Science and Business Media LLC. - 0141-5492 .- 1573-6776. ; 28:8, s. 601-603
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Journal article (peer-reviewed)abstract
- An important property of the bacterial surface is its conductivity. To obtain reliable conductivity values, it is essential to handle the cells as gently as possible during the measurement procedure. We have developed a method where a standard conductivity meter is used in combination with cross-flow filtration, thus avoiding repeated centrifugation and resuspension. With this method, the conductivity of Bacillus subtilis was determined to be 7000 mu S/cm, which is a deviation from previously published data by almost an order of a magnitude.
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| 8. |
- Jonsson, Anna, et al.
(author)
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Comparison of creatinine-based methods for estimating glomerular filtration rate in patients with heart failure
- 2020
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In: ESC Heart Failure. - : John Wiley & Sons. - 2055-5822. ; 7:3, s. 1150-1160
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Journal article (peer-reviewed)abstract
- Aims: Glomerular filtration rate is an important factor in management of heart failure (HF). Our objective was to validate eight creatinine-based equations for estimating glomerular filtration rate (eGFR) in an HF population against measured glomerular filtration rate.Methods and results: One hundred forty-six HF patients (mean age 68 +/- 13 years, mean left ventricular ejection fraction 45% +/- 15) within a single-centre hospital that underwent Cr-51-EDTA clearance between 2010 and 2018 were included in this retrospective study. eGFR was estimated by means of Cockcroft-Gault ideal and actual weight, the Modification of Diet in Renal Disease Study (MDRD), simplified MDRD with isotope dilution mass spectroscopy traceable calibration, the Chronic Kidney Disease Epidemiology Collaboration, revised Lund-Malmo, full age spectrum, and the Berlin Initiative Study 1. Mean measured glomerular filtration rate was 42 mL/min/1.73 m(2). Pearson's correlation coefficient (r) had the highest precision for MDRD (r = 0.9), followed by revised Lund-Malmo (r = 0.88). All equations except MDRD (mean difference -4.8%) resulted in an overestimation of the renal function. The accuracy was below 75% for all equations except MDRD.Conclusions: None of the exclusively creatinine-based methods was accurate in predicting eGFR in HF patients. Our findings suggest that more accurate methods are needed for determining eGFR in patients with HF.
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| 9. |
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| 10. |
- Jonsson, Fredrik, et al.
(author)
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The application of a Bayesian approach to the analysis of a complex, mechanistically based model
- 2007
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In: Journal of Biopharmaceutical Statistics. - : Informa UK Limited. - 1054-3406 .- 1520-5711. ; 17:1, s. 65-92
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Journal article (peer-reviewed)abstract
- The Bayesian approach has been suggested as a suitable method in the context of mechanistic pharmacokinetic-pharmacodynamic (PK-PD) modeling, as it allows for efficient use of both data and prior knowledge regarding the drug or disease state. However, to this day, published examples of its application to real PK-PD problems have been scarce. We present an example of a fully Bayesian re-analysis of a previously published mechanistic model describing the time course of circulating neutrophils in stroke patients and healthy individuals. While priors could be established for all population parameters in the model, not all variability terms were known with any degree of precision. A sensitivity analysis around the assigned priors used was performed by testing three different sets of prior values for the population variance terms for which no data were available in the literature: “informative”, “semi-informative”, and “noninformative”, respectively. For all variability terms, inverse gamma distributions were used. It was possible to fit the model to the data using the “informative” priors. However, when the “semi-informative” and “noninformative” priors were used, it was impossible to accomplish convergence due to severe correlations between parameters. In addition, due to the complexity of the model, the process of defining priors and running the Markov chains was very time-consuming. We conclude that the present analysis represents a first example of the fully transparent application of Bayesian methods to a complex, mechanistic PK-PD problem with real data. The approach is time-consuming, but enables us to make use of all available information from data and scientific evidence. Thereby, it shows potential both for detection of data gaps and for more reliable predictions of various outcomes and “what if” scenarios.
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