1,721,231 research outputs found
A master regulator orchestrates bacterial stress response genes in space and time
No full textThis material relates to the article ‘A master regulator orchestrates bacterial stress response genes in space and time’' by Choudhary et al. The quantitative microscopy data collected from the microfluidics imaging experiments were processed using BACMMAN software (Ollion et al. Nat Protoc. 2019, 3144-3161. doi: 10.1038/s41596-019-0216-9.) and then processed using custom Python code detailed in Choudhary et al. Cell Rep. 2023 (doi: 10.1016/j.celrep.2023.112168) and Choudhary et al. Curr. Bio. 2023 (doi: 10.1016/j.cub.2023.11.002). This folder contains:
(A) Experiment_List: Excel file listing the experiments, including Experiment_ID (enumaerated 1 to 80), Promoter analysed, strain (WT: wild type, or Katg-), H2O2 concentration, Treatment type (step or gradual), treatment time, Start_ROI (Positions greater than this are analysed), and Stop_ROI (Positions smaller than this are analysed).
(B) The output files obtained from BACMMAN for all experiments described in the article by Choudhary et al.
Details of the data collection and analysis procedures can be found in the accompanying article. The folders are named as E1 to E80, corresponding to the experiments listed in Excel file (A) .
Default experiment protocol refers to wild-type E. coli bacteria growing in 1.2 um trenches that were fully loaded and provided with a step treatment of H2O2 and imaged with a time-lag between frames of 3 minutes.
Each of the folders contains subfolders pertaining to different experiments performed in the given conditions. Each subfolder contains BACMMAN output files named as 'SubFolderName'_'0 or 1 or 2 or 3'. Here, 0 relates to measurements of growth channels tracked over time to correct for any drifts while imaging. 1 relates to measurements of the cell mask from the mKate2 cell segmentation marker signal. 2 relates to measurements of CFP or GFP fluorescence inside the segmented cell masks. 3 relates to measurements of YFP fluorescence inside the segmented cell masks (For dual reporter strains). The folder also contains the BACMMAN config file used for each experiment
Phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactions
Full text linkThis material relates to the article 'Phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactions' by Choudhary et al. The quantitative microscopy data collected from the microfluidics imaging experiments were processed using BACMMAN software (Ollion et al. Nat Protoc. 2019, 3144-3161. doi: 10.1038/s41596-019-0216-9.) and then processed using custom Python code. This folder contains:
(A) The output files obtained from BACMMAN for all experiments described in the article by Choudhary et al.
(B) Python codes that were used to generate the data plots in the article by Choudhary et al .
Details of the data collection and analysis procedures can be found in the accompanying article.The folders are named as 'Concentration of H2O2 used'_'Promoter'_'Any changes to default experiment protocol'.
Default experiment protocol refers to wild-type E. coli bacteria growing in 1.2 um trenches that were fully loaded and provided with a step treatment of H2O2 and imaged with a time-lag between frames of 3 minutes.
These folders are :
(1)100uM_Pahpc_default
(2)100uM_PgrxA_1p4
(3)100uM_PgrxA_1p4,lowload
(4)100uM_PgrxA_45secResolution
(5)100uM_PgrxA_default
(6)100uM_PgrxA_DoxyRandWTmix
(7)100uM_PgrxA_InactiveWTmix
(8)100uM_PgrxA_Lowloading
(9)100um_PgrxA_oxyRMutant
(10)100uM_PgrxA_Pulses
(11)100uM_Pkatg_default
(12)500uM_PgrxA_grad
(13)500uM_PgrxA_PIStain
(14)500uM_PgrxA_step
Each of the folders contains subfolders pertaining to different experiments performed in the given conditions. Each subfolder contains BACMMAN output files named as 'SubFolderName'_'0 or 1 or 2 or 3'. Here, 0 relates to measurements of growth channels tracked over time to correct for any drifts while imaging. 1 relates to measurements of the cell mask from the mKate2 cell segmentation marker signal. 2 relates to measurements of CFP fluorescence inside the segmented cell masks. 3 relates to MutL-mYPet foci detection in the segmented cell masks. The folder also contains the BACMMAN config file used for each experiment.
The other folders:
(15) ExperimentsForCalibration: contains the BACMMAN output files of the experiments that were used for calibration experiments performed at different H2O2 concentrations.
(16) ExperimentsForMachineLearningAnalysis: contains BACMMAN output files of experiments for Machine Learning Analysis.
(17) Experiment_details.CSV contains details of each experiment, such as the time of H2O2 treatment and the ROIs used in analysis (annotated as ‘Position’ in the data files).
(18) Figures_codes : contains Python codes for generating the figures in accompanying article.
The subheading in each code file correspond to different panels within the same figures
FIGURES 27–38 in Vulgarogamasus sphecophilus (Cooreman) comb. nov. (Acari: Mesostigmata: Parasitidae): a redescription and new hymenopteran association
No full textFIGURES 27–38. Vulgarogamasus sphecophilus comb. nov., deutonymph, male unless stated otherwise (27–29, 31, 36–38, newly recorded British specimens; 30, 32–33, slide M71; 34–35, M69). 27, idiosoma, dorsal view; 28, idiosoma, ventral view; 29, sternal shield showing shape variation; 30, sternal shield; 31, female, posterior part of sternal shield; 32, podosomal and opisthonotal shields; 33, anal shield; 34, chelicera, antiaxial view; 35–38, gnathotectum (36–37, female). Scale bars in micrometres.Published as part of Baker, Anne S. & Foster, Kevin R., 2009, Vulgarogamasus sphecophilus (Cooreman) comb. nov. (Acari: Mesostigmata: Parasitidae): a redescription and new hymenopteran association, pp. 51-64 in Zootaxa 2088 on page 60, DOI: 10.5281/zenodo.18743
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
FIGURES 8–16 in Vulgarogamasus sphecophilus (Cooreman) comb. nov. (Acari: Mesostigmata: Parasitidae): a redescription and new hymenopteran association
No full textFIGURES 8–16. Vulgarogamasus sphecophilus comb. nov., adult female (8, 10 and 15, slide M66; 9, M83; 16, M81; 11, Poecilochirus britannicus holotype; 12, P. britannicus paratype; 13–14, newly recorded British specimens). 8, hypostome, basis gnathosomatica and palp trochanter–genu; 9–14, gnathotectum; 15, chelicera, antiaxial view; 16, tarsus II, dorsal view. ant.hyp.s. = anterior hypostomatic seta, d.l. = dorsal lyrifissure, d.s. = dorsal cheliceral seta, ext.post.hyp.s. = external posterior hypostomatic seta, h.d. = hypognathal denticles, int.post.hyp.s. = internal posterior hypostomatic seta, l.l. = lateral lyrifissure, pcx.s. = palpcoxal seta, p.d. = pilus dentilis. Scale bars in micrometres.Published as part of Baker, Anne S. & Foster, Kevin R., 2009, Vulgarogamasus sphecophilus (Cooreman) comb. nov. (Acari: Mesostigmata: Parasitidae): a redescription and new hymenopteran association, pp. 51-64 in Zootaxa 2088 on page 56, DOI: 10.5281/zenodo.18743
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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