| 1. |
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| 2. |
- 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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| 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. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 5. |
- Xin, Yan-Bo, et al.
(författare)
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Research progress of hydrogen tunneling in two-dimensional materials
- 2017
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Ingår i: Wuli xuebao. - : CHINESE PHYSICAL SOC. - 1000-3290. ; 66:5
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Forskningsöversikt (refereegranskat)abstract
- One-atom-thick material such as graphene, graphene derivatives and graphene-like materials, usually has a dense network lattice structure and therefore dense distribution of electronic clouds in the atomic plane. This unique structure makes it have great significance in both basic research and practical applications. Studies have shown that molecules, atoms and ions are very difficult to permeate through these above-mentioned two-dimensional materials. Theoretical investigations demonstrate that even hydrogen, the smallest in atoms, is expected to take billions of years to penetrate through the dense electronic cloud of graphene. Therefore, it is generally considered that one-atom-thin materialis impermeable for hydrogen. However, recent experimental results have shown that the hydrogen atoms can tunnel through graphene and monolayer hexagonal boron nitride at room temperature. The existence of defects in one-atomthin material can also effectively reduce the barrier height of the hydrogen tunneling through graphene. Controversy exists about whether hydrogen particles such as atoms, ions or hydrogen molecules can tunnel through two-dimensional materials, and it has been one of the popular topics in the fields of two-dimensional materials. In this paper, the recent research progressof hydrogen tunneling through two-dimensional materials is reviewed. The characteristics of hydrogen isotopes tunneling through different two-dimensional materials are introduced. Barrier heights of hydrogen tunneling through different graphene and graphene-like materials are discussed and the difficulties in its transition are compared. Hydrogen cannot tunnel through the monolayer molybdenum disulfide, only a little small number of hydrogen atoms can tunnel hrough graphene and hexagonal boron nitride, while hydrogen is relatively easy to tunnel through silicene and phosphorene. The introduction of atomic defects or some oxygen-containing functional groups into the two-dimensional material is discussed, which can effectively reduce the barrier height of the hydrogen tunneling barrier. By adding the catalyst and adjusting the temperature and humidity of the tunneling environment, the hydrogen tunneling ability can be enhanced and the hydrogen particles tunneling through the two-dimensional material can be realized. Finally, the applications of hydrogen tunneling through two-dimensional materials in ion-separation membranes, fuel cells and hydrogen storage materials are summarized. The potential applications of hydrogen permeable functional thin film materials, lithium ion battery electrode materials and nano-channel ions in low energy transmission are prospected. The exact mechanism of hydrogen tunneling through two-dimensional material is yet to be unravelled. In order to promote these applications and to realize large-scale production and precision machining of these two-dimensional materials, an in-depth understanding of the fundamental questions of the hydrogen tunneling mechanism is needed. Further studies are needed to predict the tunneling process quantitatively and to understand the effects of catalyst and the influences of chemical environments.
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| 6. |
- Wan, Cheng-Liang, et al.
(författare)
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Dynamics of slow electrons transmitting through straight glass capillary and tapered glass capillary
- 2016
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Ingår i: Wuli xuebao. - : Acta Physica Sinica, Chinese Physical Society and Institute of Physics, Chinese Academy of Sciences. - 1000-3290. ; 65:20
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Tidskriftsartikel (refereegranskat)abstract
- It has been found that the transmission rate of the electrons through insulating capillaries as a function of time/incident charge is not the same as that of the ions. The question arises that by using the electrons, if the negative charge patches can be formed to facilitate the transmission of the following electrons, thereby substantiating that the so-called guiding effect works also for electrons. This study aims to observe the time evolutions of the transmission of electrons through a straight glass tube and a tapered glass capillary. This will reveal the details of how and (or) if the negative charge patches can be formed when the electrons transport through them. In this work, a set of MCP/phosphor two-dimensional detection system based on Labview platform is developed to obtain the time evolution of the angular distribution of the transmitted electrons. The pulsed electron beams are obtained to test our detection system. The time evolution of the angular profile of 1.5 keV electrons transmitting through the glass tube/capillary is observed. The transmitted electrons are observed on the detector for a very short time and disappear for a time and then appear again for both the glass tube and tapered glass capillary, leading to an oscillation. The positive charge patches are formed in the insulating glass tube and tapered glass capillary since the secondary electron emission coefficient for the incident energy is larger than 1. It is due to the fact that fast discharge of the deposited charge leads to the increase of the transmission rate, while the fast blocking of the incident electrons due to the deposited positive charge leads to the decrease of the transmission rate. The geometrical configuration of the taper glass capillary tends to make the secondary electrons deposited at the exit part to form the negative patches that facilitate the transmission of electrons. This suggests that if the stable transmission needs to be reached for producing the electron micro-beam by using tapered glass capillaries, the steps must be taken to have the proper grounding and shielding of the glass capillaries and tubes. Our results show a difference in transmission through the insulating capillary between electrons and highly charged ions.
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| 7. |
- 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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| 8. |
- Blanton, Michael R., et al.
(författare)
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Sloan Digital Sky Survey IV : Mapping the Milky Way, Nearby Galaxies, and the Distant Universe
- 2017
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Ingår i: Astronomical Journal. - : IOP Publishing Ltd. - 0004-6256 .- 1538-3881. ; 154:1
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Tidskriftsartikel (refereegranskat)abstract
- We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and. high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median z similar to 0.03). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between z similar to 0.6 and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs. and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the. Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July.
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| 9. |
- Elsik, Christine G., et al.
(författare)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Tidskriftsartikel (refereegranskat)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 10. |
- Han, Xin-Bao, et al.
(författare)
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Ultrasmall Abundant Metal-Based Clusters as Oxygen-Evolving Catalysts
- 2019
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 141:1, s. 232-239
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Tidskriftsartikel (refereegranskat)abstract
- The oxygen evolution reaction is a crucial step in water electrolysis to develop clean and renewable energy. Although noble metal-based catalysts have demonstrated high activity for the oxygen evolution reaction, their application is limited by their high cost and low availability. Here we report the use of a molecule-to-cluster strategy for preparing ultrasmall trimetallic clusters by using the polyoxometalate molecule as a precursor. Ultrafine (0.8 nm) transition-metal clusters with controllable chemical composition are obtained. The transition-metal clusters enable highly efficient oxygen evolution through water electrolysis in alkaline media, manifested by an overpotential of 192 mV at 10 mA cm–2, a low Tafel slope of 36 mV dec–1, and long-term stability for 30 h of electrolysis. We note, however, that besides the excellent performance as an oxygen evolution catalyst, our molecule-to-cluster strategy provides a means to achieve well-defined transition-metal clusters in the subnanometer regime, which potentially can have an impact on several other applications.
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