| 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. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Block, Keith I., et al.
(författare)
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Designing a broad-spectrum integrative approach for cancer prevention and treatment
- 2015
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Ingår i: Seminars in Cancer Biology. - : Academic Press. - 1044-579X .- 1096-3650. ; 35, s. S276-S304
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Forskningsöversikt (refereegranskat)abstract
- Targeted therapies and the consequent adoption of "personalized" oncology have achieved notable successes in some cancers; however, significant problems remain with this approach. Many targeted therapies are highly toxic, costs are extremely high, and most patients experience relapse after a few disease-free months. Relapses arise from genetic heterogeneity in tumors, which harbor therapy-resistant immortalized cells that have adopted alternate and compensatory pathways (i.e., pathways that are not reliant upon the same mechanisms as those which have been targeted). To address these limitations, an international task force of 180 scientists was assembled to explore the concept of a low-toxicity "broadspectrum" therapeutic approach that could simultaneously target many key pathways and mechanisms. Using cancer hallmark phenotypes and the tumor microenvironment to account for the various aspects of relevant cancer biology, interdisciplinary teams reviewed each hallmark area and nominated a wide range of high-priority targets (74 in total) that could be modified to improve patient outcomes. For these targets, corresponding low-toxicity therapeutic approaches were then suggested, many of which were phytochemicals. Proposed actions on each target and all of the approaches were further reviewed for known effects on other hallmark areas and the tumor microenvironment Potential contrary or procarcinogenic effects were found for 3.9% of the relationships between targets and hallmarks, and mixed evidence of complementary and contrary relationships was found for 7.1%. Approximately 67% of the relationships revealed potentially complementary effects, and the remainder had no known relationship. Among the approaches, 1.1% had contrary, 2.8% had mixed and 62.1% had complementary relationships. These results suggest that a broad-spectrum approach should be feasible from a safety standpoint. This novel approach has potential to be relatively inexpensive, it should help us address stages and types of cancer that lack conventional treatment, and it may reduce relapse risks. A proposed agenda for future research is offered. (C) 2015 The Authors. Published by Elsevier Ltd.
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| 4. |
- Nene, Vishvanath, et al.
(författare)
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Genome sequence of Aedes aegypti, a major arbovirus vector.
- 2007
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Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 316:5832, s. 1718-23
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Tidskriftsartikel (refereegranskat)abstract
- We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae. Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of approximately 4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster. Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of approximately 2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species.
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| 5. |
- Abacan, MaryAnn, et al.
(författare)
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The Global State of the Genetic Counseling Profession
- 2019
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Ingår i: European Journal of Human Genetics. - : NATURE PUBLISHING GROUP. - 1018-4813 .- 1476-5438. ; 27:2, s. 183-197
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Forskningsöversikt (refereegranskat)abstract
- The profession of genetic counseling (also called genetic counselling in many countries) began nearly 50 years ago in the United States, and has grown internationally in the past 30 years. While there have been many papers describing the profession of genetic counseling in individual countries or regions, data remains incomplete and has been published in diverse journals with limited access. As a result of the 2016 Transnational Alliance of Genetic Counseling (TAGC) conference in Barcelona, Spain, and the 2017 World Congress of Genetic Counselling in the UK, we endeavor to describe as fully as possible the global state of genetic counseling as a profession. We estimate that in 2018 there are nearly 7000 genetic counselors with the profession established or developing in no less than 28 countries.
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| 6. |
- Bosch, Jackie, et al.
(författare)
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Effects of blood pressure and lipid lowering on cognition Results from the HOPE-3 study
- 2019
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Ingår i: Neurology. - : LIPPINCOTT WILLIAMS & WILKINS. - 0028-3878 .- 1526-632X. ; 92:13, s. E1435-E1446
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Tidskriftsartikel (refereegranskat)abstract
- Objective: To assess whether long-term treatment with candesartan/hydrochlorothiazide, rosuvastatin, or their combination can slow cognitive decline in older people at intermediate cardiovascular risk.Methods: The Heart Outcomes Prevention Evaluation-3 (HOPE-3) study was a double-blind, randomized, placebo-controlled clinical trial using a 2 x 2 factorial design. Participants without known cardiovascular disease or need for treatment were randomized to candesartan (16 mg) plus hydrochlorothiazide (12.5 mg) or placebo and to rosuvastatin (10 mg) or placebo. Participants who were >= 70 years of age completed the Digit Symbol Substitution Test (DSST), the modified Montreal Cognitive Assessment, and the Trail Making Test Part B at baseline and study end.Results: Cognitive assessments were completed by 2,361 participants from 228 centers in 21 countries. Compared with placebo, candesartan/hydrochlorothiazide reduced systolic blood pressure by 6.0 mm Hg, and rosuvastatin reduced low-density lipoprotein cholesterol by 24.8 mg/dL. Participants were followed up for 5.7 years (median), and 1,626 completed both baseline and study-end assessments. Mean participant age was 74 years (SD +/- 3.5 years); 59% were women; 45% had hypertension; and 24% had >= 12 years of education. The mean difference in change in DSST scores was -0.91 (95% confidence interval [CI] -2.25 to 0.42) for candesartan/hydrochlorothiazide compared with placebo, -0.54 (95% CI -1.88 to 0.80) for rosuvastatin compared with placebo, and -1.43 (95% CI -3.37 to 0.50) for combination therapy vs double placebo. No significant differences were found for other measures.Conclusions: Long-term blood pressure lowering with candesartan plus hydrochlorothiazide, rosuvastatin, or their combination did not significantly affect cognitive decline in older people. ClinicalTrials.gov identifier: NCT00468923. Classification of evidence: This study provides Class II evidence that for older people, candesartan plus hydrochlorothiazide, rosuvastatin, or their combination does not significantly affect cognitive decline.
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| 7. |
- Carlsson, Ingegerd, et al.
(författare)
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The Creative Personality in a Gender Perspective
- 2005
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Ingår i: Focus on Gender Identity. - 1594542120 ; , s. 81-93
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Two empirical investigations of the creative personality, including a gender perspective, are described. In one of them the participants were school children and in the other the group consisted mainly of university students. Creativity is here conceived within a particular theoretical frame which is particularly focussing on individual differences in the perceptual process. Gender was studied from two angles. The youngsters were investigated for gender differences in a semi-projective test of defense mechanisms, whereas the students filled out a questionnaire.
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| 8. |
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| 9. |
- Della Bruna, Lorenza, et al.
(författare)
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Studying the ISM at ∼10 pc scale in NGC 7793 with MUSEII : Constraints on the oxygen abundance and ionising radiation escape (Corrigendum)
- 2022
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 663
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Tidskriftsartikel (refereegranskat)abstract
- Table 3 in the original paper reports inaccurate values of Q0exp;YSC and Q0obs(and hence of the related quantities Qexp;tot, Qexptot=Qobs, and fesc). The error in Q0exp;YSC results from a mistake in the sampling of the cluster probability distribution functions (PDFs), whereas Q0obswas mistakenly computed from non-dereddened values of L(Hα). In Table 1 we provide a revised version of the original Table 3, and in Figs. 1 and 2 we show revised versions of the original Figs. 10 and 11. The revised values do not change any of the conclusions stated in the original paper. In the following we provide revised text for the affected sections. (Figure Presented).
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| 10. |
- Della Bruna, Lorenza, et al.
(författare)
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Studying the ISM at similar to 10 pc scale in NGC 7793 with MUSE : II. Constraints on the oxygen abundance and ionising radiation escape
- 2021
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 650
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Tidskriftsartikel (refereegranskat)abstract
- Context. Feedback from massive stars a ffects the interstellar medium (ISM) from the immediate surroundings of the stars (parsec scales) to galactic (kiloparsec) scales. High-spatial resolution studies of H ii regions are critical to investigate how this mechanism operates.Aims. We study the ionised ISM in NGC7793 with the MUSE instrument at ESO Very Large Telescope (VLT), over a field of view (FoV) of similar to 2 kpc2 and at a spatial resolution of similar to 10 pc. The aim is to link the physical conditions of the ionised gas (reddening, ionisation status, abundance measurements) within the spatially resolved H ii regions to the properties of the stellar populations producing Lyman continuum photons.Methods. The analysis of the MUSE dataset, which provides a map of the ionised gas and a census of Wolf Rayet stars, is complemented with a sample of young star clusters (YSCs) and O star candidates observed with the Hubble Space Telescope (HST) and of giant molecular clouds traced in CO(2-1) emission with the Atacama Large Millimeter /submillimeter Array (ALMA). We estimated the oxygen abundance using a temperature-independent strong-line method. We determined the observed total amount of ionising photons ( Q(H0)) from the extinction corrected H ff luminosity. This estimate was then compared to the expected Q(H0) obtained by summing the contributions of YSCs and massive stars. The ratio of the two values gives an estimate for the escape fraction ( fesc) of photons in the region of interest. We used the [S ii] /[O iii] ratio as a proxy for the optical depth of the gas and classified H ii regions into ionisation bounded, or as featuring channels of optically thin gas. We compared the resulting ionisation structure with the computed fesc. We also investigated the dependence of fesc on the age spanned by the stellar population in each region.Results. We find a median oxygen abundance of 12 + log (O =H) similar to 8 :37, with a scatter of 0.25 dex, which is in agreement with previous estimates for our target. We furthermore observe that the abundance map of H ii regions is rich in substructures, surrounding clusters and massive stars, although clear degeneracies with photoionisation are also observed. From the population synthesis analysis, we find that YSCs located in H ii regions have a higher probability of being younger and less massive as well as of emitting a higher number of ionising photons than clusters in the rest of the field. Overall, we find fesc;H ii = 0:67+0:08 0:12 for the population of H ii regions. We also conclude that the sources of ionisation observed within the FoV are more than su fficient to explain the amount of di ffuse ionised gas (DIG) observed in this region of the galaxy. We do not observe a systematic trend between the visual appearance of H ii regions and fesc, pointing to the e ffect of 3D geometry in the small sample probed.
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