358 research outputs found
Phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactions
No full textThis 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
Chaos in a bacterial stress response
No full textThis material relates to the article 'Chaos in a bacterial stress response' 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 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
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
Merchants of Virtue
No full textMerchants of Virtue explores the question of what it meant to be Hindu in precolonial South Asia. Divya Cherian presents a fine-grained study of everyday life and local politics in the kingdom of Marwar in eighteenth-century western India to uncover how merchants enforced their caste ideals of vegetarianism and bodily austerity as universal markers of Hindu identity. Using legal strategies and alliances with elites, these merchants successfully remade the category of “Hindu,” setting it in contrast to “Untouchable” in a process that reconfigured Hinduism in caste terms. In a history pertinent to understanding India today, Cherian establishes the centrality of caste to the early-modern Hindu self and to its imagination of inadmissible others.
“A refreshingly different perspective on the history of caste and untouchability in India, enlarging the field of scholarship from its focus on the colonial era by telling us how precolonial configurations of power in the locality shaped the everyday experience of caste.” — GOPAL GURU, coauthor of The Cracked Mirror and Experience, Caste, and the Everyday Social
“This provocative and empirically rich study offers a plenitude of fascinating insights into aspects of western Indian history ca. 1800, from kingship and caste hierarchy to abortion and alcohol consumption. Particularly innovative is its focus on the critical role played by merchants in articulating social identities that became widespread in modern times.” — CYNTHIA TALBOT, author of The Last Hindu Emperor
“A pathbreaking book that explodes essentialist views of the construction of Hindu and Muslim identities in precolonial India. Divya Cherian provocatively argues that the category of ‘Hindu’ was the primary locus for a system of radical othering that excluded Untouchables (and Muslims as Untouchables) through mechanisms of state, law, and everyday life.” — CHRISTIAN LEE NOVETZKE, Professor of South Asian and Religious Studies, University of Washingto
Merchants of Virtue
No full textMerchants of Virtue explores the question of what it meant to be Hindu in precolonial South Asia. Divya Cherian presents a fine-grained study of everyday life and local politics in the kingdom of Marwar in eighteenth-century western India to uncover how merchants enforced their caste ideals of vegetarianism and bodily austerity as universal markers of Hindu identity. Using legal strategies and alliances with elites, these merchants successfully remade the category of “Hindu,” setting it in contrast to “Untouchable” in a process that reconfigured Hinduism in caste terms. In a history pertinent to understanding India today, Cherian establishes the centrality of caste to the early-modern Hindu self and to its imagination of inadmissible others.
“A refreshingly different perspective on the history of caste and untouchability in India, enlarging the field of scholarship from its focus on the colonial era by telling us how precolonial configurations of power in the locality shaped the everyday experience of caste.” — GOPAL GURU, coauthor of The Cracked Mirror and Experience, Caste, and the Everyday Social
“This provocative and empirically rich study offers a plenitude of fascinating insights into aspects of western Indian history ca. 1800, from kingship and caste hierarchy to abortion and alcohol consumption. Particularly innovative is its focus on the critical role played by merchants in articulating social identities that became widespread in modern times.” — CYNTHIA TALBOT, author of The Last Hindu Emperor
“A pathbreaking book that explodes essentialist views of the construction of Hindu and Muslim identities in precolonial India. Divya Cherian provocatively argues that the category of ‘Hindu’ was the primary locus for a system of radical othering that excluded Untouchables (and Muslims as Untouchables) through mechanisms of state, law, and everyday life.” — CHRISTIAN LEE NOVETZKE, Professor of South Asian and Religious Studies, University of Washingto
Improved collision detection in StarLogo Nova
No full textThesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2015.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (page 65).StarLogo Nova is blocks-based educational software that allows students to write and play their own 3D games online. It is the online version of StarLogo TNG. This thesis explores the problem of needing more accurate collision detection in StarLogo Nova while maintaining reasonable performance. Three new collision detection systems for StarLogo Nova are developed and evaluated. Compared to the spheres used to perform collision checks in the current system, the first new system, called the TightestFitCollider, introduces a variety of bounding spheres, bounding boxes, and bounding capsules as bounding structures that may fit the models in StarLogo Nova more closely. The second system, called the HierarchicalCollider, uses hierarchies of bounding boxes to perform even more precise collision detection than the TightestFitCollider. Finally, the third system combines the first two systems, so that the advantages of each can be used as appropriate. The three systems are evaluated for their accuracy and performance within the StarLogo Nova framework.by Divya Bajekal.M. Eng
Second Chance
No full text36-39This is December 3020. The Plabsonian Mission conducted by the Government of India has been completed successfully. Under this Mission, Manish, a young scientist, was assigned the task of conducting a research project for studying a newly found planet in a remote corner of the Milky Way galaxy
Antiepileptic drugs for the primary and secondary prevention of seizures after subarachnoid haemorrhage
No full textBackground: subarachnoid haemorrhage may result in seizures both acutely and in the longer term. The use of antiepileptic drugs (AEDs) in the primary and secondary prevention of seizures after subarachnoid haemorrhage is uncertain, and there is currently no consensus on treatment.Objectives: to assess the effects of AEDs for the primary and secondary prevention of seizures after subarachnoid haemorrhage.Search methods: we searched the Cochrane Epilepsy Group Specialised Register, the Cochrane Central Register of Controlled Trials (CENTRAL) (2013, Issue 1) in The Cochrane Library, and MEDLINE (1946 to 12th March 2013). We checked the reference lists of articles retrieved from these searches.Selection criteria: we considered all randomised and quasi-randomised controlled trials in which patients were assigned to a treatment (one or more AEDs) or placebo.Data collection and analysis: two review authors (RM and JK) independently screened and assessed the methodological quality of the studies. If studies were included, one author extracted the data and the other checked it.Main results: no relevant studies were found.Authors' conclusions: there was no evidence to support or refute the use of antiepileptic drugs for the primary or secondary prevention of seizures related to subarachnoid haemorrhage. Well-designed randomised controlled trials are urgently needed to guide clinical practice
Dowling-Degos disease and hidradenitis suppurativa: Co occurrence or association?
No full textA 44 year old female patient presented with multiple, painful, relapsing, nodules, plaques with sinuses discharging pus and scars in apocrine gland bearing region since past 17 years. These lesions were clinically and histopathologically suggestive of hidradenitis suppurativa. Our patient was not aware about the flexural pigmentary lesions, comedones and pitted scars which were also clinically and histopathologically suggestive of Dowling-Degos disease.
We are reporting a rare interesting association of Dowling Degos disease and hidradenitis suppurativa which is not reported in Indian literature till date
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