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Robust estimation of bacterial cell count from optical density

Beal, Jacob ; Farny, Natalie G. ; Haddock-Angelli, Traci ; [et al.]

Springer Science and Business Media LLC ; 2020

In: Communications Biology Vol. 3, No. 1 ( 2020-09-17)

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In: Communications Biology, Springer Science and Business Media LLC, Vol. 3, No. 1 ( 2020-09-17)

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.

Type of Medium: Online Resource

ISSN: 2399-3642

URL: Article

DOI: 10.1038/s42003-020-01127-5

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2020

detail.hit.zdb_id: 2919698-X

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Author Correction: Robust estimation of bacterial cell count from optical density

Beal, Jacob ; Farny, Natalie G. ; Haddock-Angelli, Traci ; [et al.]

Springer Science and Business Media LLC ; 2020

In: Communications Biology Vol. 3, No. 1 ( 2020-10-27)

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In: Communications Biology, Springer Science and Business Media LLC, Vol. 3, No. 1 ( 2020-10-27)

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Type of Medium: Online Resource

ISSN: 2399-3642

URL: Article

DOI: 10.1038/s42003-020-01371-9

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2020

detail.hit.zdb_id: 2919698-X

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Figure 9 from: He X-L, Horak E, Wang D, Li T-H, Peng W-H, Gan B-C (2019) Descriptions of five new species in Entoloma subgenus Claudopus from China, with molecular phylogeny of Entoloma s.l. MycoKeys 61: 1-26. https://doi.org/10.3897/mycokeys.61.46446

He, Xiao-Lan ; Horak, Egon ; Wang, Di ; [et al.]

Pensoft Publishers ; 2019

In: MycoKeys Vol. 61 ( 2019-12-05), p. 1-26

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In: MycoKeys, Pensoft Publishers, Vol. 61 ( 2019-12-05), p. 1-26

Abstract: Entoloma subgenus Claudopus is widely distributed, yet the taxonomy and systematics of its species are still poorly documented. In the present study, more than forty collections of Claudopus were gathered in China and subsequently analysed, based on morphological and molecular data. The results revealed first a high level of species diversity of Claudopus in China and second, there is a wide ecological range regarding the substrates and the habitats ranging from temperate, tropical to subalpine locations. Based on morphological and molecular evidence, five novel species from China are proposed, viz. E. conchatum , E. flabellatum , E. gregarium , E. pleurotoides and E. reductum . Molecular phylogeny of Entoloma s.l. was also reconstructed, based on 187 representatives of Entoloma s.l. by employing the combined ITS, LSU, mtSSU and RPB2 sequences. Ten monophyletic clades ( Claudopus , Leptonia , Nolanea , Cuboid-spored Inocephalus , “ Alboleptonia ”, Cyanula , Pouzarella , Rhodopolia , Prunuloides and Rusticoides ) were recovered, while 13 taxa could not be placed in any defined clades. The results confirmed that Claudopus in a traditional morphological sense is not monophyletic and the Rusticoides -group, previously considered within Claudopus , formed a separate clade; but section Claudopus and relatives of E. undatum belong to a distinctive monophyletic group. Despite some monophyletic groups in Entoloma s.l. being distinctive in both morphology and molecular phylogeny, they were still treated as subgenera of Entoloma s.l. temporarily, because accepting them as genera will make Entoloma s.l. paraphyletic.

Type of Medium: Online Resource

ISSN: 1314-4049 , 1314-4057

URL: Article

DOI: 10.3897/mycokeys.61.46446

DOI: 10.3897/mycokeys.61.46446.figure1

DOI: 10.3897/mycokeys.61.46446.figure2

DOI: 10.3897/mycokeys.61.46446.figure3

DOI: 10.3897/mycokeys.61.46446.figure4

DOI: 10.3897/mycokeys.61.46446.figure5

DOI: 10.3897/mycokeys.61.46446.figure6

DOI: 10.3897/mycokeys.61.46446.figure7

DOI: 10.3897/mycokeys.61.46446.figure8

DOI: 10.3897/mycokeys.61.46446.figure9

Language: Unknown

Publisher: Pensoft Publishers

Publication Date: 2019

detail.hit.zdb_id: 2630648-7

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Supplementary material 1 from: Xie D-F, Cheng R-Y, Price M, Chen J-P, Lei J-Q, Zhang Y-Y, He X-J (2022) Allium heterophyllum (Amaryllidaceae), a new species from Henan, China. PhytoKeys 190: 53-67. https://doi.org/10.3897/phytokeys.190.77449

Xie, Deng-Feng ; Cheng, Rui-Yu ; Price, Megan ; [et al.]

Pensoft Publishers ; 2022

In: PhytoKeys Vol. 190 ( 2022-02-18), p. 53-67

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In: PhytoKeys, Pensoft Publishers, Vol. 190 ( 2022-02-18), p. 53-67

Abstract: Allium heterophyllum D.F.Xie & amp; X.J.He, sp. nov. (Amaryllidaceae), is a new species from Henan, China and is described based on morphological and molecular evidence. It is morphologically most similar to A. dumebuchum in the rhomboid scape in cross-section. However, distinctive differences were detected in perianth color, leaf shape and cross-section, flowers’ density as well as flowering season. Similarly, the karyotype of A. heterophyllum is 2 n = 2 x = 16 and in A. dumebuchum is 2 n = 4 x = 32. Phylogenetic analysis based on nuclear ribosomal Internal Transcribed Spacers (ITS) and three cpDNA regions strongly supports that A. heterophyllum is a member of Allium section Rhizirideum and sister to the other species of this section (e.g. A. senescens , A. spirale , and A. prostratum ). Currently, only one population and approximately 120 individuals were discovered; the development of scenic spots in this region may affect its growth and threaten this population. Therefore, this new species is preliminarily considered as Near Threatened (NT) according to criteria of the IUCN Red List.

Type of Medium: Online Resource

ISSN: 1314-2003 , 1314-2011

URL: Article

DOI: 10.3897/phytokeys.190.77449

DOI: 10.3897/phytokeys.190.77449.figure1

DOI: 10.3897/phytokeys.190.77449.figure2

DOI: 10.3897/phytokeys.190.77449.figure3

DOI: 10.3897/phytokeys.190.77449.figure4

DOI: 10.3897/phytokeys.190.77449.figure5

DOI: 10.3897/phytokeys.190.77449.figure6

DOI: 10.3897/phytokeys.190.77449.suppl1

Language: Unknown

Publisher: Pensoft Publishers

Publication Date: 2022

detail.hit.zdb_id: 2579891-1

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Figure 7 from: Wang C-B, He L (2021) Anoplophora huangjianbini sp. n. from Fujian and Guangxi, China (Coleoptera: Cerambycidae: Lamiinae). Biodiversity Data Journal 9: e70936. https://doi.org/10.3897/BDJ.9.e70936

Wang, Cheng-Bin ; He, Li

Pensoft Publishers ; 2021

In: Biodiversity Data Journal Vol. 9 ( 2021-08-12)

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In: Biodiversity Data Journal, Pensoft Publishers, Vol. 9 ( 2021-08-12)

Abstract: The genus Anoplophora Hope, 1839 (Coleoptera: Cerambycidae: Lamiinae: Lamiini) includes 47 species (without subspecies) occurring in East, South and Southeast Asia. Amongst them, 38 species are known from CHINA. Members of this genus are familiar to Chinese people with a widely-used common name: “星天牛 [starry longhorn beetle]”. Anoplophora species have great economic importance, attacking and damaging numerous hardwood trees and some coniferous trees. A new species of starry longhorn beetle, Anoplophora huangjianbini sp. n. (Coleoptera: Cerambycidae: Lamiinae: Lamiini) is described from Fujian and Guangxi, CHINA. Diagnostic characters of the new species are illustrated and comparison with closely-related congeners is provided.

Type of Medium: Online Resource

ISSN: 1314-2828 , 1314-2836

URL: Article

DOI: 10.3897/BDJ.9.e70936

DOI: 10.3897/BDJ.9.e70936.figure1

DOI: 10.3897/BDJ.9.e70936.figure2

DOI: 10.3897/BDJ.9.e70936.figure3

DOI: 10.3897/BDJ.9.e70936.figure4

DOI: 10.3897/BDJ.9.e70936.figure5

DOI: 10.3897/BDJ.9.e70936.figure6

DOI: 10.3897/BDJ.9.e70936.figure7

Language: Unknown

Publisher: Pensoft Publishers

Publication Date: 2021

detail.hit.zdb_id: 2736709-5

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Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Klionsky, Daniel J ; Abdelmohsen, Kotb ; Abe, Akihisa ; [et al.]

Informa UK Limited ; 2016

In: Autophagy Vol. 12, No. 1 ( 2016-01-02), p. 1-222

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In: Autophagy, Informa UK Limited, Vol. 12, No. 1 ( 2016-01-02), p. 1-222

Type of Medium: Online Resource

ISSN: 1554-8627 , 1554-8635

URL: Article

DOI: 10.1080/15548627.2015.1100356

Language: English

Publisher: Informa UK Limited

Publication Date: 2016

detail.hit.zdb_id: 2262043-6

SSG: 12

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Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition) 1

Klionsky, Daniel J. ; Abdel-Aziz, Amal Kamal ; Abdelfatah, Sara ; [et al.]

Informa UK Limited ; 2021

In: Autophagy Vol. 17, No. 1 ( 2021-01-02), p. 1-382

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In: Autophagy, Informa UK Limited, Vol. 17, No. 1 ( 2021-01-02), p. 1-382

Type of Medium: Online Resource

ISSN: 1554-8627 , 1554-8635

URL: Article

DOI: 10.1080/15548627.2020.1797280

Language: English

Publisher: Informa UK Limited

Publication Date: 2021

detail.hit.zdb_id: 2262043-6

SSG: 12

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Figure 6 from: Liu S-L, Ma H-X, He S-H, Dai Y-C (2019) Four new corticioid species in Trechisporales (Basidiomycota) from East Asia and notes on phylogeny of the order. MycoKeys 48: 97-113. https://doi.org/10.3897/mycokeys.48.31956

Liu, Shi-Liang ; Ma, Hai-Xia ; He, Shuang-Hui ; [et al.]

Pensoft Publishers ; 2019

In: MycoKeys Vol. 48 ( 2019-03-08), p. 97-113

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In: MycoKeys, Pensoft Publishers, Vol. 48 ( 2019-03-08), p. 97-113

Abstract: Four new species in Trechisporales from East Asia, Dextrinocystiscalamicola , Subulicystidiumacerosum , S.tropicum and Tubuliciumbambusicola , are described and illustrated, based on morphological and molecular evidence. The phylogeny of Trechisporales was inferred from a combined dataset of ITS-nrLSU sequences. In the phylogenetic tree, Sistotremastrum formed a family-level clade of its own, sister to the Hydnodontaceae clade formed by all other genera. Dextrinocystis , is for the first time, confirmed as a member of Hydnodontaceae. A key to all the accepted genera in Trechisporales is given.

Type of Medium: Online Resource

ISSN: 1314-4049 , 1314-4057

URL: Article

DOI: 10.3897/mycokeys.48.31956

DOI: 10.3897/mycokeys.48.31956.figure1

DOI: 10.3897/mycokeys.48.31956.figure2

DOI: 10.3897/mycokeys.48.31956.figure3

DOI: 10.3897/mycokeys.48.31956.figure4

DOI: 10.3897/mycokeys.48.31956.figure5

DOI: 10.3897/mycokeys.48.31956.figure6

Language: Unknown

Publisher: Pensoft Publishers

Publication Date: 2019

detail.hit.zdb_id: 2630648-7

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Figure 6 from: Liu S-L, Nakasone KK, Wu S-H, He S-H, Dai Y-C (2018) Taxonomy and phylogeny of Lopharia s.s., Dendrodontia, Dentocorticium and Fuscocerrena (Basidiomycota, Polyporales). MycoKeys 32: 25-48. https://doi.org/10.3897/mycokeys.32.23641

Liu, Shi-Liang ; Nakasone, Karen K. ; Wu, Sheng-Hua ; [et al.]

Pensoft Publishers ; 2018

In: MycoKeys Vol. 32 ( 2018-03-15), p. 25-48

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In: MycoKeys, Pensoft Publishers, Vol. 32 ( 2018-03-15), p. 25-48

Abstract: Eleven taxa of Lopharia s.s., Dendrodontia , Dentocorticium and Fuscocerrena in Polyporales are included in the phylogenetic analyses of nuc rDNA ITS1-5.8S-ITS2 (ITS), D1-D2 domains of nuc 28S rDNA (28S) and RNA polymerase II second-largest subunit ( rpb2 ) sequences. New species Lophariaresupinata and L.sinensis are described and illustrated. Lophariaresupinata , from south-eastern China, is closely related to L.ayresii , and L.sinensis , from northern China, is related to L.cinerascens and L.mirabilis . Lophariamirabilis specimens from temperate to tropical areas with varied hymenophore configurations all cluster together in a fully supported clade. Dendrodontia and Fuscocerrena are shown to be synonyms of Dentocorticium , which is phylogenetically related to Lopharia . Four new combinations, Dentocorticiumbicolor , D.hyphopaxillosum , D.portoricense and D.taiwanianum , are proposed. Revised generic descriptions of Lopharia and Dentocorticium are provided with keys to the six accepted species in each genus. A list of all names in Lopharia and Dentocorticium are presented with their current taxonomic status. Type specimens of Dentocorticiumbrasiliense and D.irregulare were examined and determined to be later synonyms of Punctulariasubhepatica and Diplomitoporusdaedaleiformis , respectively. Corticioid fungi, dendrohyphidia, species complex, wood-inhabiting fungi

Type of Medium: Online Resource

ISSN: 1314-4049 , 1314-4057

URL: Article

DOI: 10.3897/mycokeys.32.23641

DOI: 10.3897/mycokeys.32.23641.figure1

DOI: 10.3897/mycokeys.32.23641.figure2

DOI: 10.3897/mycokeys.32.23641.figure3

DOI: 10.3897/mycokeys.32.23641.figure4

DOI: 10.3897/mycokeys.32.23641.figure5

DOI: 10.3897/mycokeys.32.23641.figure6

Language: Unknown

Publisher: Pensoft Publishers

Publication Date: 2018

detail.hit.zdb_id: 2630648-7

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The third Intensive Care Bundle with Blood Pressure Reduction in Acute Cerebral Haemorrhage Trial (INTERACT3): an international, stepped wedge cluster randomised controlled trial

Ma, Lu ; Hu, Xin ; Song, Lili ; [et al.]

Elsevier BV ; 2023

In: The Lancet Vol. 402, No. 10395 ( 2023-07), p. 27-40

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In: The Lancet, Elsevier BV, Vol. 402, No. 10395 ( 2023-07), p. 27-40

Type of Medium: Online Resource

ISSN: 0140-6736

URL: Article

DOI: 10.1016/S0140-6736(23)00806-1

RVK:

XA 10000

Language: English

Publisher: Elsevier BV

Publication Date: 2023

detail.hit.zdb_id: 2067452-1

detail.hit.zdb_id: 3306-6

detail.hit.zdb_id: 1476593-7

SSG: 5,21

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