| 1. |
- 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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| 2. |
- Huang, Hongyun, et al.
(författare)
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Clinical Cell Therapy Guidelines for Neurorestoration (IANR/CANR 2017)
- 2018
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Ingår i: Cell Transplantation. - : SAGE Publications. - 0963-6897 .- 1555-3892. ; 27:2, s. 310-324
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Forskningsöversikt (refereegranskat)abstract
- Cell therapy has been shown to be a key clinical therapeutic option for central nervous system diseases or damage. Standardization of clinical cell therapy procedures is an important task for professional associations devoted to cell therapy. The Chinese Branch of the International Association of Neurorestoratology (IANR) completed the first set of guidelines governing the clinical application of neurorestoration in 2011. The IANR and the Chinese Association of Neurorestoratology (CANR) collaborated to propose the current version "Clinical Cell Therapy Guidelines for Neurorestoration (IANR/CANR 2017)". The IANR council board members and CANR committee members approved this proposal on September 1, 2016, and recommend it to clinical practitioners of cellular therapy. These guidelines include items of cell type nomenclature, cell quality control, minimal suggested cell doses, patient-informed consent, indications for undergoing cell therapy, contraindications for undergoing cell therapy, documentation of procedure and therapy, safety evaluation, efficacy evaluation, policy of repeated treatments, do not charge patients for unproven therapies, basic principles of cell therapy, and publishing responsibility.
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| 3. |
- Li, Zheng, et al.
(författare)
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A Review of Spatter in Laser Powder Bed Fusion Additive Manufacturing: In Situ Detection, Generation, Effects, and Countermeasures
- 2022
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Ingår i: Micromachines. - : MDPI AG. - 2072-666X. ; 13:8
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Forskningsöversikt (refereegranskat)abstract
- Spatter is an inherent, unpreventable, and undesired phenomenon in laser powder bed fusion (L-PBF) additive manufacturing. Spatter behavior has an intrinsic correlation with the forming quality in L-PBF because it leads to metallurgical defects and the degradation of mechanical properties. This impact becomes more severe in the fabrication of large-sized parts during the multi-laser L-PBF process. Therefore, investigations of spatter generation and countermeasures have become more urgent. Although much research has provided insights into the melt pool, microstructure, and mechanical property, reviews of spatter in L-PBF are still limited. This work reviews the literature on the in situ detection, generation, effects, and countermeasures of spatter in L-PBF. It is expected to pave the way towards a novel generation of highly efficient and intelligent L-PBF systems.
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| 4. |
- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:10, s. 1113-1120
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Forskningsöversikt (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 5. |
- Abazov, V. M., et al.
(författare)
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Evidence for production of single top quarks
- 2008
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Ingår i: Physical Review D. - 1550-7998 .- 1550-2368. ; D:78, s. 012005-
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Forskningsöversikt (refereegranskat)abstract
- We present first evidence for the production of single top quarks in the D0 detector at the Fermilab Tevatron p (p) over bar collider. The standard model predicts that the electroweak interaction can produce a top quark together with an antibottom quark or light quark, without the antiparticle top-quark partner that is always produced from strong-coupling processes. Top quarks were first observed in pair production in 1995, and since then, single top-quark production has been searched for in ever larger data sets. In this analysis, we select events from a 0.9 fb(-1) data set that have an electron or muon and missing transverse energy from the decay of a W boson from the top-quark decay, and two, three, or four jets, with one or two of the jets identified as originating from a b hadron decay. The selected events are mostly backgrounds such as W + jets and t (t) over bar events, which we separate from the expected signals using three multivariate analysis techniques: boosted decision trees, Bayesian neural networks, and matrix-element calculations. A binned likelihood fit of the signal cross section plus background to the data from the combination of the results from the three analysis methods gives a cross section for single top-quark production of sigma(p (p) over bar -> tb + X, tqb + X) = 4.7 +/- 1.3 pb. The probability to measure a cross section at this value or higher in the absence of signal is 0.014%, corresponding to a 3.6 standard deviation significance. The measured cross section value is compatible at the 10% level with the standard model prediction for electroweak top-quark production. We use the cross section measurement to directly determine the Cabibbo-Kobayashi-Maskawa quark mixing matrix element that describes the Wtb coupling and find vertical bar V(tb)f(1)(L)vertical bar = 1.31(-0.21)(+0.25), where f(1)(L) is a generic vector coupling. This model-independent measurement translates into 0.68 <= 1 at the 95% C.L. in the standard model.
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| 6. |
- Jiang, Lan, et al.
(författare)
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Heparin mimetics as potential intervention for COVID-19 and their bio-manufacturing
- 2023
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Ingår i: SYNTHETIC AND SYSTEMS BIOTECHNOLOGY. - : KEAI PUBLISHING LTD. - 2405-805X. ; 8:1, s. 11-19
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Forskningsöversikt (refereegranskat)abstract
- The COVID-19 pandemic has caused severe health problems worldwide and unprecedented decimation of the global economy. Moreover, after more than 2 years, many populations are still under pressure of infection. Thus, a broader perspective in developing antiviral strategies is still of great importance. Inspired by the observed multiple benefits of heparin in the treatment of thrombosis, the potential of low molecular weight heparin (LMWH) for the treatment of COVID-19 have been explored. Clinical applications found that LMWH decreased the level of inflammatory cytokines in COVID-19 patients, accordingly reducing lethality. Furthermore, several in vitro studies have demonstrated the important roles of heparan sulfate in SARS-CoV-2 infection and the inhibitory effects of heparin and heparin mimetics in viral infection. These clinical observations and designed studies argue for the potential to develop heparin mimetics as anti-SARS-CoV-2 drug candidates. In this review, we summarize the properties of heparin as an anticoagulant and the pharmaceutical possibilities for the treatment of virus infection, focusing on the perspectives of developing heparin mimetics via chemical synthesis, chemoenzymatic synthesis, and bioengineered production by microbial cell factories. The ultimate goal is to pave the eminent need for exploring novel compounds to treat coronavirus infection-caused diseases.
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| 7. |
- Joffrin, E., et al.
(författare)
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Overview of the JET preparation for deuterium-tritium operation with the ITER like-wall
- 2019
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 59:11
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Forskningsöversikt (refereegranskat)abstract
- For the past several years, the JET scientific programme (Pamela et al 2007 Fusion Eng. Des. 82 590) has been engaged in a multi-campaign effort, including experiments in D, H and T, leading up to 2020 and the first experiments with 50%/50% D-T mixtures since 1997 and the first ever D-T plasmas with the ITER mix of plasma-facing component materials. For this purpose, a concerted physics and technology programme was launched with a view to prepare the D-T campaign (DTE2). This paper addresses the key elements developed by the JET programme directly contributing to the D-T preparation. This intense preparation includes the review of the physics basis for the D-T operational scenarios, including the fusion power predictions through first principle and integrated modelling, and the impact of isotopes in the operation and physics of D-T plasmas (thermal and particle transport, high confinement mode (H-mode) access, Be and W erosion, fuel recovery, etc). This effort also requires improving several aspects of plasma operation for DTE2, such as real time control schemes, heat load control, disruption avoidance and a mitigation system (including the installation of a new shattered pellet injector), novel ion cyclotron resonance heating schemes (such as the three-ions scheme), new diagnostics (neutron camera and spectrometer, active Alfven eigenmode antennas, neutral gauges, radiation hard imaging systems...) and the calibration of the JET neutron diagnostics at 14 MeV for accurate fusion power measurement. The active preparation of JET for the 2020 D-T campaign provides an incomparable source of information and a basis for the future D-T operation of ITER, and it is also foreseen that a large number of key physics issues will be addressed in support of burning plasmas.
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| 8. |
- Li, Furong, et al.
(författare)
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A Review of Relative Pollen Productivity Estimates From Temperate China for Pollen-Based Quantitative Reconstruction of Past Plant Cover
- 2018
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 9
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Forskningsöversikt (refereegranskat)abstract
- Model-based quantitative reconstruction of past plant cover in Europe has shown great potential for: (i) testing hypotheses related to Holocene vegetation dynamics, biodiversity, and their relationships with climate and land use; (ii) studying long term interactions between climate and land use. Similar model-based quantitative reconstruction of plant cover in China has been restricted due to the lack of standardized datasets of existing estimates of relative pollen productivity (RPP). This study presents the first synthesis of all RPP values available to date for 39 major plant taxa from temperate China and proposes standardized RPP datasets that can be used for model-based quantitative reconstructions of past plant cover using fossil pollen records for the region. We review 11 RPP studies in temperate China based on modern pollen and related vegetation data around the pollen samples. The study areas include meadow, steppe and desert vegetation, various woodland types, and cultural landscapes. We evaluate the strategies of each study in terms of selection of study areas and distribution of study sites; pollen- and vegetation-data collection in field; vegetation-data collection from satellite images and vegetation maps; and data analysis. We compare all available RPP estimates, select values based on precise rules and calculate mean RPP estimates. We propose two standardized RPP datasets for 31 (Alt1) and 29 (Alt2) plant taxa. The ranking of mean RPPs (Alt-2) relative to Poaceae (= 1) for eight major taxa is: Artemisia (21) > Pinus (18.4) > Betula (12.5) > Castanea (11.5) > Elaeagnaceae (8.8) > Juglans (7.5) > Compositae (4.5) > Amaranthaceae/Chenopodiaceae (4). We conclude that although RPPs are comparable between Europe and China for some genera and families, they can differ very significantly, e.g., Artemisia, Compositae, and Amaranthaceae/Chenopodiaceae. For some taxa, we present the first RPP estimates e.g. Castanea, Elaeagnaceae, and Juglans. The proposed standardized RPP datasets are essential for model-based reconstructions of past plant cover using fossil pollen records from temperate China.
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| 9. |
- Li, Furong, et al.
(författare)
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Towards quantification of Holocene anthropogenic land-cover change in temperate China : A review in the light of pollen-based REVEALS reconstructions of regional plant cover
- 2020
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Ingår i: Earth-Science Reviews. - : Elsevier. - 0012-8252 .- 1872-6828. ; 203, s. 1-25
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Forskningsöversikt (refereegranskat)abstract
- In an attempt to quantify Holocene anthropogenic land-cover change in temperate China, we 1) applied the REVEALS model to estimate plant-cover change using 94 pollen records and relative pollen productivity for 27 plant taxa, 2) reviewed earlier interpretation of pollen studies in terms of climate- and human-induced vegetation change, and 3) reviewed information on past land use from archaeological studies. REVEALS achieved a more realistic reconstruction of plant-cover change than pollen percentages in terms of openland versus woodland. The study suggests successive human-induced changes in vegetation cover. The first signs of human-induced land-cover change (crop cultivation, otherwise specified) are found c. 7 ka BP in the temperate deciduous forest, and S and NE Tibetan Plateau (mainly grazing, possibly crop cultivation), 6.5-6 ka BP in the temperate steppe and temperate desert (grazing, uncertain), and 5.5-5 ka BP in the coniferous-deciduous mixed forest, NE subtropical region, and NW Tibetan Plateau (grazing). Further intensification of anthropogenic land-cover change is indicated 5-4.5 ka BP in the E temperate steppe, and S and NE Tibetan Plateau (grazing, cultivation uncertain), 3.5-3 ka BP in S and NE Tibetan Plateau, W temperate steppe, temperate desert (grazing), and NW Tibetan Plateau (probably grazing), and 2.5-2 ka BP in the temperate deciduous forest, N subtropical region, and temperate desert (grazing). These changes generally agree with increased human activity as documented by archaeological studies. REVEALS reconstructions have a stronger potential than biomization to evaluate scenarios of anthropogenic land-cover change such as HYDE, given they are combined with information from archaeological studies.
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| 10. |
- Li, Junrui, et al.
(författare)
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Joint analysis of demography and selection in population genetics : where do we stand and where could we go?
- 2012
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 21:1, s. 28-44
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Forskningsöversikt (refereegranskat)abstract
- Teasing apart the effects of selection and demography on genetic polymorphism remains one of the major challenges in the analysis of population genomic data. The traditional approach has been to assume that demography would leave a genome-wide signature, whereas the effect of selection would be local. In the light of recent genomic surveys of sequence polymorphism, several authors have argued that this approach is questionable based on the evidence of the pervasive role of positive selection and that new approaches are needed. In the first part of this review, we give a few empirical and theoretical examples illustrating the difficulty in teasing apart the effects of selection and demography on genomic polymorphism patterns. In the second part, we review recent efforts to detect recent positive selection. Most available methods still rely on an a priori classification of sites in the genome but there are many promising new approaches. These new methods make use of the latest developments in statistics, explore aspects of the data that had been neglected hitherto or take advantage of the emerging population genomic data. A current and promising approach is based on first estimating demographic and genetic parameters, using, e.g., a likelihood or approximate Bayesian computation framework, focusing on extreme outlier regions, and then using an independent method to confirm these. Finally, especially for species where evidence of natural selection has been limited, more experimental and versatile approaches that contrast populations under varied environmental constraints might be more successful compared with species-wide genome scans in search of specific signatures.
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