| 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. |
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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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| 4. |
- Abolfathi, Bela, et al.
(författare)
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The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment
- 2018
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Ingår i: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
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Tidskriftsartikel (refereegranskat)abstract
- The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
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| 5. |
- Ahlgren, Per, et al.
(författare)
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The role of the Chinese Key Labs in the international and national scientific arena revisited
- 2017
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Ingår i: Research Evaluation. - : OXFORD UNIV PRESS. - 0958-2029 .- 1471-5449. ; 26:2, s. 132-143
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Tidskriftsartikel (refereegranskat)abstract
- In this contribution, which builds on and develops a study that was published more than 10 years ago, we address the role of the Chinese Key Labs (KLs) in the international and national scientific arena. We give a short overview of the position of KLs in China, including their budget and manpower. Based on large numbers of Chinese publications obtained from the Web of Science (WoS) and the Chinese Science Citation Database (CSCD), the KLs are compared across publication years to the rest of China (ChRest) with respect to publication output and citation impact. We also look at collaboration in terms of co-publishing between the KLs and the ChRest. As to publications in the WoS, we found that the contribution of KLs compared with the ChRest is slightly and irregularly increasing (using full counting as well as fractional counting), whereas a stronger increasing trend is observed for the corresponding contribution in the CSCD. We observed an increase in the number of collaborations between KLs and Chinese colleagues, regardless of database. For WoS and field normalized citation indicators, we obtained the expected results that researchers at KLs perform considerably better than other Chinese colleagues and, moreover, perform clearly better than database average. As such we may conclude that KLs have lived up to their promise and made real impact on the international arena.
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| 6. |
- Ding, Jielan, et al.
(författare)
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Disciplinary structures in Nature, Science and PNAS : journal and country levels
- 2018
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Ingår i: Scientometrics. - : SPRINGER. - 0138-9130 .- 1588-2861. ; 116:3, s. 1817-1852
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Tidskriftsartikel (refereegranskat)abstract
- This paper analyzes, using Web of Science publications and two time periods (2004-2006 and 2014-2016), the disciplinary structures in the three prestigious journals Nature, Science and PNAS, compared with two baselines: Non-NSP_Multi (multidisciplinary publications that have other source journals than Nature, Science and PNAS), and Non-Multi (publications assigned to other categories than Multidisciplinary). We analyze the profiles at two levels, journal and country. The results for the journal level show that for Nature and Science, the publications are considerably less concentrated to certain disciplines compared to PNAS. Biology is the dominant discipline for all the three journals. Nature and Science have similar publication shares in Medicine, Geosciences, Physics, Space science, and Chemistry. The publications of PNAS are highly concentrated to two disciplines: Biology and Medicine. Compared with Non-NSP_Multi and Non-Multi, the shares of Biology in NSP journals are higher, whereas the share of Medicine is lower. At the country level, 14 countries are included, among them the five BRICS countries. With respect to the NSP journals, the emphasis disciplines (in terms of world share of publications) of most countries other than USA are the disciplines in which USA has its weakest performance. The disciplinary structures of USA and of most of the other studied countries therefore tend to be different. Regarding Non-NSP_Multi and Non-Multi, the shapes of the disciplinary structures of the 14 countries can be roughly grouped into three groups, while there are more types of shapes for the countries in the NSP journals. For all five units of analysis, the discipline structures of most countries generally change only slightly between different time periods. The structures of some BRICS countries, however, change to a relatively large extent.
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| 7. |
- He, Ting, et al.
(författare)
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Poly(vinylidene fluoride) (PVDF) membrane fabrication with an ionic liquid via non-solvent thermally induced phase separation (N-TIPs)
- 2022
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Ingår i: Applied water science. - : Springer. - 2190-5487 .- 2190-5495. ; 12:3
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate was the first time successfully utilized as single solvent in preparing the PVDF membrane with a good performance by N-TIPs method. The effects of quenching temperature and hydrophilic additive content on the morphology, permeability, and strength of the membranes were studied. All the prepared PVDF membranes were proved to be a pure β phase by FTIR and XRD, possessing a narrow pore size distribution. By adjusting quenching temperature and additive content, membranes with a flux of 383.2 L/m2 h and concentrated pore diameter of 26 nm obtained.
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| 8. |
- Huang, Zhen, et al.
(författare)
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Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots
- 2022
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Parrots have undergone substantial karyotype evolution compared to most other birds. Here, Huang et al. analyze chromosome-level genome assemblies for four parrot species and elucidate the complex evolutionary history of parrot chromosomes. The karyotype of most birds has remained considerably stable during more than 100 million years' evolution, except for some groups, such as parrots. The evolutionary processes and underlying genetic mechanism of chromosomal rearrangements in parrots, however, are poorly understood. Here, using chromosome-level assemblies of four parrot genomes, we uncover frequent chromosome fusions and fissions, with most of them occurring independently among lineages. The increased activities of chromosomal rearrangements in parrots are likely associated with parrot-specific loss of two genes, ALC1 and PARP3, that have known functions in the repair of double-strand breaks and maintenance of genome stability. We further find that the fusion of the ZW sex chromosomes and chromosome 11 has created a pair of neo-sex chromosomes in the ancestor of parrots, and the chromosome 25 has been further added to the sex chromosomes in monk parakeet. Together, the combination of our genomic and cytogenetic analyses characterizes the complex evolutionary history of chromosomal rearrangements and sex chromosomes in parrots.
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| 9. |
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| 10. |
- Liu, Yue, et al.
(författare)
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The role of nature reserves in conservation effectiveness of ecosystem services in China
- 2023
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Ingår i: Journal of Environmental Management. - 0301-4797 .- 1095-8630. ; 342
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Tidskriftsartikel (refereegranskat)abstract
- Establishing nature reserves (NRs) is a common method to avoid biodiversity loss and degradation of ecosystem services (ESs). The evaluation of ESs in NRs and the exploration of associated influencing factors are the basis for improving ESs and management. However, the ES effectiveness of NRs over time remains questionable, namely due to the heterogeneity of landscape characteristics inside and outside of NRs. This study (i) quantifies the role of 75 NRs in China in maintaining ESs (i.e., net primary production (NPP), soil conservation, sandstorm pre-vention and water yield) from 2000 to 2020, (ii) reveals the trade-offs/synergies, and (iii) identifies the main influencing factors of the ES effectiveness of NRs. The results show that more than 80% of NRs had positive ES effectiveness, which was greater in older NRs. For different ESs, effectiveness over time increases for NPP (E_NPP), soil conservation (E_SC) and sandstorm prevention (E_SP) but declines for water yield (E_WY). There is a clear synergistic relationship between E_NPP and E_SC. Moreover, the effectiveness of ESs is closely correlated with elevation, precipitation, and perimeter area ratio. Our findings can provide important information to support site selection and management of reserves to improve the delivery of critical ecosystem services.
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