| 1. |
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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. |
- Adcox, K, et al.
(författare)
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PHENIX detector overview
- 2003
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Ingår i: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - 0167-5087. ; 499:2-3, s. 469-479
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Tidskriftsartikel (refereegranskat)abstract
- The PHENIX detector is designed to perform a broad study of A-A, p-A, and p-p collisions to investigate nuclear matter under extreme conditions. A wide variety of probes, sensitive to all timescales, are used to study systematic variations with species and energy as well as to measure the spin structure of the nucleon. Designing for the needs of the heavy-ion and polarized-proton programs has produced a detector with unparalleled capabilities. PHENIX measures electron and muon pairs, photons, and hadrons with excellent energy and momentum resolution. The detector consists of a large number of subsystems that are discussed in other papers in this volume. The overall design parameters of the detector are presented. (C) 2002 Elsevier Science B.V. All rights reserved.
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| 4. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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Ingår i: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Forskningsöversikt (refereegranskat)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is 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 verify an autophagic response.
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| 5. |
- Gaziano, Liam, et al.
(författare)
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Actionable druggable genome-wide Mendelian randomization identifies repurposing opportunities for COVID-19
- 2021
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Ingår i: Nature Medicine. - : Springer Nature. - 1078-8956 .- 1546-170X. ; 27:4
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Tidskriftsartikel (refereegranskat)abstract
- Large-scale Mendelian randomization and colocalization analyses using gene expression and soluble protein data for 1,263 actionable druggable genes, which encode protein targets for approved drugs or drugs in clinical development, identify IFNAR2 and ACE2 as the most promising therapeutic targets for early management of COVID-19. Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2, P = 1.6 x 10(-6); IFNAR2, P = 9.8 x 10(-11) and IL-10RB, P = 2.3 x 10(-14)) using cis-expression quantitative trait loci genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared expression quantitative trait loci signal for IL10RB and IFNAR2, we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.
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| 6. |
- Liopyris, Konstantinos, et al.
(författare)
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Expert agreement on the presence and spatial localization of melanocytic features in dermoscopy.
- 2023
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Ingår i: The Journal of investigative dermatology. - 1523-1747. ; 144:3
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Tidskriftsartikel (refereegranskat)abstract
- Dermoscopy aids in melanoma detection; however, agreement on dermoscopic features, including those of high clinical relevance, remains poor. Herein we attempted to evaluate agreement among experts on 'exemplar images' not only for the presence of melanocytic-specific features but also for spatial localization. This was a cross-sectional, multicenter, observational study. Dermoscopy images exhibiting at least one of 31 melanocytic-specific features were submitted by 25 world experts as 'exemplars'. Using a web-based platform that allows for image mark-up of specific contrast-defined regions (superpixels), 20 expert readers annotated 248 dermoscopic images in collections of 62 images. Each collection was reviewed by five independent readers. A total of 4,507 feature observations were performed. Good-to-excellent agreement was found for 14 of 31 features (45.2%), with 8 achieving excellent agreement (Gwet's AC >0.75) and 7 of them being melanoma-specific features. These features were: 'Peppering /Granularity' (0.91); 'Shiny White Streaks' (0.89); 'Typical Pigment network' (0.83); 'Blotch Irregular' (0.82); 'Negative Network' (0.81); 'Irregular Globules' (0.78); 'Dotted Vessels' (0.77) and 'Blue Whitish Veil' (0.76). By utilizing an exemplar dataset, good-to-excellent agreement was found for 14 features that have previously been shown useful in discriminating nevi from melanoma. All images are public (www.isic-archive.com) and can be used for education, scientific communication and machine learning experiments.
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| 7. |
- Alriksson-Schmidt, Ann I., et al.
(författare)
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The natural history of spina bifida in children pilot project : Research protocol
- 2013
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Ingår i: JMIR Research Protocols. - : JMIR Publications Inc.. - 1929-0748. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Population-based empirical information to inform health care professionals working with children with spina bifida currently is lacking. Spina bifida is a highly complex condition that not only affects mobility but many additional aspects of life. We have developed a pilot project that focuses on a broad range of domains: Surgeries, development and learning, nutrition and physical growth, mobility and functioning, general health, and family demographics. Specifically, we will: (1) explore the feasibility of identifying and recruiting participants using different recruitment sources, (2) test a multidisciplinary module to collect the data, (3) determine the utility of different methods of retrieving the data, and (4) summarize descriptive information on living with spina bifida. Objective: The overall objective of the project was to provide information for a future multistate prospective study on the natural history of spina bifida. Methods: Families with a child 3 to 6 years of age with a diagnosis of spina bifida were eligible for enrollment. Eligible families were identified through a US population-based tracking system for birth defects and from a local spina bifida clinic. Results: This is an ongoing project with first results expected in 2013. Conclusions: This project, and the planned multistate follow-up project, will provide information both to health care professionals experienced in providing care to patients with spina bifida, and to those who have yet to work with this population. The long-term purpose of this project is to increase the knowledge about growing up with spina bifida and to guide health care practices by prospectively studying a cohort of children born with this condition.
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| 8. |
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Avian Behavioral and Physiological Responses to Challenging Thermal Environments and Extreme Weather Events
- 2022
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Samlingsverk (redaktörskap) (refereegranskat)abstract
- Birds occupy habitats ranging from Antarctic ice shelves and Arctic tundra to low-latitude deserts and lowland rainforests, and so are exposed to the full range of climates present on Earth. Cold, hot, or variable (on a variety of temporal scales) thermal conditions can present significant thermoregulatory challenges to birds, which typically must maintain body temperatures within narrow physiological tolerance limits. Such challenges may occur in all stages of the annual cycle and in all life stages of birds, so the ability to adjust to these conditions is required to maintain stable populations through time. For this Research Topic, we broadly define a challenging thermal environment as one necessitating behavioral or physiological adjustments to maintain body temperatures at levels appropriate for continued physiological function.Avian abilities to respond to extreme cold and heat are defined by thermoregulatory capacities for heat production or dissipation, respectively. Behavioral responses to temperature challenges can reduce the necessity for and magnitude of physiological adjustments, so together, physiological capacities and behavioral responses determine the probability of survival in thermally challenging situations. Moreover, thermal conditions experienced during reproduction can affect parental investment in the nesting effort and, independently, alter the course of nestling development, with potentially long-term consequences. Behavioral responses to these conditions as well as physiological responses at multiple levels of organization, from organisms to molecules, allow birds to tolerate thermal challenges. Our knowledge of the mechanisms by which birds respond, the time course for such responses, and the impacts on fitness, however, remain incompletely understood. Studies examining behavioral and physiological responses of birds to extreme and/or seasonally variable climates have been a research focus for decades, but recent advances in methods of measurement and analyses of physiological and behavioral traits have led to novel findings regarding the patterns and mechanisms by which birds adjust to challenging thermal environments.This Research Topic examines how thermal conditions in the environment pose challenges to birds and the physiological and behavioral adjustments that birds employ to meet them. Articles for this Research Topic may be original research papers, reviews, or perspectives. Specific themes that we believe are suitable for this Research Topic include, but are not limited to:• Integrative mechanisms underlying bird thermoregulatory capacities contributing to a tolerance of challenging thermal environments and their links to fitness• Influence of thermal conditions during reproduction on parental investment or nestling development• Behavioral responses to challenging thermal conditions and their mechanistic underpinnings• Time courses for physiological adjustments to environmental temperature variation• Physiological and behavioral flexibility associated with daily or seasonal temperature variation• Physiological and behavioral responses and tolerance limits during extreme weather events• Body temperature regulation under challenging thermal conditions and energy or water restrictions, including real-time field measurements and thermal imaging• Body temperature regulation and environmental or ecological drivers of hypometabolic strategies• Physiological consequences of exceeding thermoregulatory capacities
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| 9. |
- Bennett, Deborah, et al.
(författare)
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Project TENDR : Targeting Environmental Neuro-Developmental Risks. The TENDR Consensus Statement
- 2016
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Ingår i: Journal of Environmental Health Perspectives. - : National Institute of Environmental Health Science. - 0091-6765 .- 1552-9924. ; 124:7, s. A118-A122
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Tidskriftsartikel (refereegranskat)abstract
- Children in America today are at an unacceptably high risk of developing neurodevelopmental disorders that affect the brain and nervous system including autism, attention deficit hyperactivity disorder, intellectual disabilities, and other learning and behavioral disabilities. These are complex disorders with multiple causes-genetic, social, and environmental. The contribution of toxic chemicals to these disorders can be prevented. Approach: Leading scientific and medical experts, along with children's health advocates, came together in 2015 under the auspices of Project TENDR: Targeting Environmental Neuro-Developmental Risks to issue a call to action to reduce widespread exposures to chemicals that interfere with fetal and children's brain development. Based on the available scientific evidence, the TENDR authors have identified prime examples of toxic chemicals and pollutants that increase children's risks for neurodevelopmental disorders. These include chemicals that are used extensively in consumer products and that have become widespread in the environment. Some are chemicals to which children and pregnant women are regularly exposed, and they are detected in the bodies of virtually all Americans in national surveys conducted by the U.S. Centers for Disease Control and Prevention. The vast majority of chemicals in industrial and consumer products undergo almost no testing for developmental neurotoxicity or other health effects. Conclusion: Based on these findings, we assert that the current system in the United States for evaluating scientific evidence and making health-based decisions about environmental chemicals is fundamentally broken. To help reduce the unacceptably high prevalence of neurodevelopmental disorders in our children, we must eliminate or significantly reduce exposures to chemicals that contribute to these conditions. We must adopt a new framework for assessing chemicals that have the potential to disrupt brain development and prevent the use of those that may pose a risk. This consensus statement lays the foundation for developing recommendations to monitor, assess, and reduce exposures to neurotoxic chemicals. These measures are urgently needed if we are to protect healthy brain development so that current and future generations can reach their fullest potential.
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| 10. |
- Evans, David A.D., et al.
(författare)
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An expanding list of reliable paleomagnetic poles for Precambrian tectonic reconstructions
- 2021
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Ingår i: Ancient Supercontinents and the Paleogeography of Earth. - : Elsevier. ; , s. 605-639
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Bokkapitel (refereegranskat)abstract
- We present a compilation of reliable Precambrian paleomagnetic poles from three successive international workshops (in years 2009, 2014, 2017), comprising paleomagnetists specializing in Precambrian tectonic reconstructions. The working groups compiled lists of two global classes of poles, published through the end of 2017. “Grade-A” results are judged to provide essential constraints on tectonic reconstructions; “Grade-B” poles are judged to be suggestive of high-quality, but not yet demonstrated to be primary, or perhaps lacking precise geochronologic or other constraints. Our catalog documents a resurgence of high-quality data acquisition in recent years, and highlights specific cratons and time intervals that are most lacking in the data needed to reconstruct those blocks through supercontinental cycles.
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| 11. |
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