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| 3. |
- 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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- Demetris, A J, et al.
(författare)
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2016 Comprehensive Update of the Banff Working Group on Liver Allograft Pathology: Introduction of Antibody-Mediated Rejection.
- 2016
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Ingår i: American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons. - : Elsevier BV. - 1600-6143. ; 16:10, s. 2816-2835
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Tidskriftsartikel (refereegranskat)abstract
- The Banff Working Group on Liver Allograft Pathology reviewed and discussed literature evidence regarding antibody-mediated liver allograft rejection at the 11th (Paris, France, June 5-10, 2011), 12th (Comandatuba, Brazil, August 19-23, 2013), and 13th (Vancouver, British Columbia, Canada, October 5-10, 2015) meetings of the Banff Conference on Allograft Pathology. Discussion continued online. The primary goal was to introduce guidelines and consensus criteria for the diagnosis of liver allograft antibody-mediated rejection and provide a comprehensive update of all Banff Schema recommendations. Included are new recommendations for complement component 4d tissue staining and interpretation, staging liver allograft fibrosis, and findings related to immunosuppression minimization. In an effort to create a single reference document, previous unchanged criteria are also included.
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| 7. |
- Góralczyk, Katarzyna, et al.
(författare)
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Perfluorinated chemicals in blood serum of inhabitants in central Poland in relation to gender and age.
- 2015
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 1879-1026 .- 0048-9697. ; 532, s. 548-555
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Tidskriftsartikel (refereegranskat)abstract
- The goal of this paper is to determine concentrations of seven selected perfluoroalkylated substances (PFASs): perfluorooctane sulfonic acid (PFOS), perfluorooctanoic acid (PFOA), perfluorohexane sulfonic acid (PFHxS), perfluorononanoic acid (PFNA), perfluorodecanoic acid (PFDA), perfluoroundecanoic acid (PFUnDA), perfluorododecanoic acid (PFDoDA) in the blood serum of men and women of reproductive age from the central region of Poland. The relation between sex of tested subjects and the levels of compounds in blood serum of humans will also be considered and analysed as an element of the risk assessment. The study was made on the blood serum samples collected from 253 women and 176 men of reproductive age between 20 and 44years from Warsaw and surrounding areas. Higher concentrations of five (PFOS, PFOA, PFNA, PFDA, PFUnDA) from among seven selected PFASs were observed in men in comparison to women from the same populations. Only the concentrations of PFHxS and PFDoDA were slightly higher in women than in men. These differences were statistically significant in all cases, except for PFUnDA. The hypothesis that the concentrations of said compounds increase with age of the test subjects, regardless of gender has not been confirmed.
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| 8. |
- Neubauer, T. A., et al.
(författare)
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Short-term paleogeographic reorganizations and climate events shaped diversification of North American freshwater gastropods over deep time
- 2022
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- What controls species diversity and diversification is one of the major questions in evolutionary biology and paleontology. Previous studies have addressed this issue based on various plant and animal groups, geographic regions, and time intervals. However, as most previous research focused on terrestrial or marine ecosystems, our understanding of the controls on diversification of biota (and particularly invertebrates) in freshwater environments in deep time is still limited. Here, we infer diversification rates of North American freshwater gastropods from the Late Triassic to the Pleistocene and explore potential links between shifts in speciation and extinction and major changes in paleogeography, climate, and biotic interactions. We found that variation in the speciation rate is best explained by changes in continental fragmentation, with rate shifts coinciding with major paleogeographic reorganizations in the Mesozoic, in particular the retreat of the Sundance Sea and subsequent development of the Bighorn wetland and the advance of the Western Interior Seaway. Climatic events in the Cenozoic (Middle Eocene Climate Optimum, Miocene Climate Optimum) variably coincide with shifts in speciation and extinction as well, but no significant long-term association could be detected. Similarly, no influence of diversity dependence was found across the entire time frame of similar to 214 Myr. Our results indicate that short-term climatic events and paleogeographic changes are relevant to the diversification of continental freshwater biota, while long-term trends have limited effect.
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| 10. |
- Góralczyk, Katarzyna, et al.
(författare)
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Is the fact of parenting couples cohabitation affecting the serum levels of persistent organohalogen pollutants?
- 2015
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Ingår i: International Journal of Hygiene and Environmental Health. - : Elsevier BV. - 1618-131X .- 1438-4639. ; 218:4, s. 392-400
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Tidskriftsartikel (refereegranskat)abstract
- Organohalogen compounds constitute one of the important groups of persistent organic pollutants (POPs). Among them, due to their long-term health effects, one should pay attention on organochlorine pesticides, polychlorinated biphenyls (PCBs) and perfluoroalkylated substances (PFASs). This paper is an attempt to answer the question about relation between the fact of cohabitation by couples expecting a child and the level of the organohalogen compounds in the blood serum of both parents. The study was done on a population of parent couples from Greenland, Poland and Ukraine, from whom blood samples were collected in order to establish the levels of marker organohalogen compounds. We selected, as the representative of these compounds, the most persistent metabolite of DDT, i.e. p,p'-DDE, the most frequently detected PCB congener - CB-153, and PFOS and PFOA as the representatives of PFASs. The results show that in case of all compounds under study the highest concentrations were present always in men in relation to the levels detected in the blood serum of their female partners, regardless of the country of origin of the couple. A positive correlation was noted between the concentrations of the studied compounds in the blood serum of men and women in parenting couples. In some cases these correlations were statistically significant, e.g. for concentrations of p,p'-DDE in pairs from Greenland and Ukraine, of CB-153 in pairs from Poland and Ukraine, and of PFOS for parents from Greenland and Poland, while for PFOA - only for couples from Greenland. The concentrations of the compounds included in the study were similar to the levels found in general population in other countries. Our results show that the exposure to POPs resulting from cohabitation plays a role in the general exposure to these compounds.
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| 11. |
- Jakubek, Ryan S., et al.
(författare)
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Calibration of Raman Bandwidths on the Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals (SHERLOC) Deep Ultraviolet Raman and Fluorescence Instrument Aboard the Perseverance Rover
- 2023
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Ingår i: Applied Spectroscopy. - : SAGE Publications Inc.. - 0003-7028 .- 1943-3530.
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Tidskriftsartikel (refereegranskat)abstract
- In this work, we derive a simple method for calibrating Raman bandwidths for the Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals (SHERLOC) instrument onboard NASA’s Perseverance rover. Raman bandwidths and shapes reported by an instrument contain contributions from both the intrinsic Raman band (IRB) and instrumental artifacts. To directly correlate bandwidth to sample properties and to compare bandwidths across instruments, the IRB width needs to be separated from instrumental effects. Here, we use the ubiquitous bandwidth calibration method of modeling the observed Raman bands as a convolution of a Lorentzian IRB and a Gaussian instrument slit function. Using calibration target data, we calculate that SHERLOC has a slit function width of 34.1 cm–1. With a measure of the instrument slit function, we can deconvolve the IRB from the observed band, providing the width of the Raman band unobscured by instrumental artifact. We present the correlation between observed Raman bandwidth and intrinsic Raman bandwidth in table form for the quick estimation of SHERLOC Raman intrinsic bandwidths. We discuss the limitations of using this model to calibrate Raman bandwidth and derive a quantitative method for calculating the errors associated with the calibration. We demonstrate the utility of this method of bandwidth calibration by examining the intrinsic bandwidths of SHERLOC sulfate spectra and by modeling the SHERLOC spectrum of olivine.
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| 12. |
- Ludwicki, Jan K, et al.
(författare)
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Hazard quotient profiles used as a risk assessment tool for PFOS and PFOA serum levels in three distinctive European populations.
- 2015
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Ingår i: Environment International. - : Elsevier BV. - 1873-6750 .- 0160-4120. ; 74, s. 112-118
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Tidskriftsartikel (refereegranskat)abstract
- Perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA) blood levels are commonly used as biomarkers of human environmental exposure to these compounds. Many biomonitoring studies indicate 100% detection for PFOS and PFOA thus justifying a concern of possible risk for the most exposed individuals. This study addresses the predictive value of hazard quotients (HQs) calculated on the basis of serum PFOS and PFOA in male and female populations of reproductive age in Greenland, Poland and Ukraine. Overall, 2026 results of PFOS and PFOA serum concentrations (589 males, 1437 females) were obtained from the INUENDO database. HQs were calculated from the actual biomonitoring results and literature-based animal data linking toxicological outcomes and critical PFOS/PFOA serum levels. HQs for serum PFOS were calculated based on Points of Departure (PoD) at 13μgmL(-1) (cynomolgus monkeys, 183days, changes in THS and T3) and for PFOA at 7.1μgmL(-1) serum (male rats, 90days, hepatocellular necrosis, increased liver weight). Uncertainty factors were applied to reflect interspecies differences and human variability. Serum HQs were expressed as a ratio relative to the point of departure for each PFOS and PFOA. Only in the three cases of males in Greenland were there serum PFOS levels showing HQ values exceeding 1, so indicating that such serum levels may be of concern. The mean serum concentration of PFOS was significantly higher in male than in female populations. Despite significant differences between HQ profiles for PFOS and PFOA in donors from Greenland, Poland and Ukraine, the concentrations of these perfluoroalkylated compounds do not indicate a cause for concern, except for the three aforementioned cases from Greenland. This study demonstrates that the HQ approach can help to interpret human biomonitoring data and thus serve as a valuable tool in further risk assessment priority settings and may also be used as a basis for taking decisions in risk management.
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| 13. |
- Messori, Gabriele, et al.
(författare)
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On the Spatial and Temporal Variability of Atmospheric Heat Transport in a Hierarchy of Models
- 2017
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Ingår i: Journal of the Atmospheric Sciences. - 0022-4928 .- 1520-0469. ; 74:7, s. 2163-2189
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Tidskriftsartikel (refereegranskat)abstract
- The present study analyzes the spatial and temporal variability of zonally integrated meridional atmospheric heat transport due to transient eddies in a hierarchy of datasets. These include a highly idealized two-layer model seeded with point geostrophic vortices, an intermediate complexity GCM, and the European Centre for Medium-Range Weather Forecasts interim reanalysis (ERA-Interim) data. The domain of interest is the extratropics. Both the two-layer model and the GCMdisplay a pronounced temporal variability in the zonally integrated meridional transport, with the largest values (or pulses) of zonally integrated transport being associated with extended regions of anomalously strong local heat transport. In the two-layer model these largescale coherent transport regions, termed heat transport bands,'' are linked to densely packed baroclinic vortex pairs and can be diagnosed as low-wavenumber streamfunction anomalies. In the GCM they are associated with both the warm and cold sectors of midlatitude weather systems. Both these features are also found in ERA-Interim: the heat transport bands match weather systems and occur primarily in the storm-track regions, which in turn correspond to planetary-scale climatological streamfunction anomalies. The authors hypothesize that the temporal variability of the zonally integrated heat transport is partly linked to oscillatory variations in the stormtrack activity but also contains a background red noise component. The existence of a pronounced variability in the zonally integrated meridional heat transport can have important consequences for the interplay between midlatitude dynamics and the energy balance of the high latitudes.
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| 14. |
- Sun, Vivian Z., et al.
(författare)
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Overview and Results From the Mars 2020 Perseverance Rover's First Science Campaign on the Jezero Crater Floor
- 2023
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Ingår i: Journal of Geophysical Research: Planets. - : John Wiley and Sons Inc. - 2169-9097 .- 2169-9100. ; 128:6
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Tidskriftsartikel (refereegranskat)abstract
- The Mars 2020 Perseverance rover landed in Jezero crater on 18 February 2021. After a 100-sol period of commissioning and the Ingenuity Helicopter technology demonstration, Perseverance began its first science campaign to explore the enigmatic Jezero crater floor, whose igneous or sedimentary origins have been much debated in the scientific community. This paper describes the campaign plan developed to explore the crater floor's Máaz and Séítah formations and summarizes the results of the campaign between sols 100–379. By the end of the campaign, Perseverance had traversed more than 5 km, created seven abrasion patches, and sealed nine samples and a witness tube. Analysis of remote and proximity science observations show that the Máaz and Séítah formations are igneous in origin and composed of five and two geologic members, respectively. The Séítah formation represents the olivine-rich cumulate formed from differentiation of a slowly cooling melt or magma body, and the Máaz formation likely represents a separate series of lava flows emplaced after Séítah. The Máaz and Séítah rocks also preserve evidence of multiple episodes of aqueous alteration in secondary minerals like carbonate, Fe/Mg phyllosilicates, sulfates, and perchlorate, and surficial coatings. Post-emplacement processes tilted the rocks near the Máaz-Séítah contact and substantial erosion modified the crater floor rocks to their present-day expressions. Results from this crater floor campaign, including those obtained upon return of the collected samples, will help to build the geologic history of events that occurred in Jezero crater and provide time constraints on the formation of the Jezero delta.
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