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1970 2024
8 results
  • Barcode counts for heterozygous yeast for genes related to the chaperone system
    Haploinsufficiency Chemical Genomic Profiling (HIP) approach is based on the premise that yeast containing a gene expressed in heterozygosis will become hypersensitive to an inhibitor targeting the product of this gene. Here we treated a pool containing ~6000 heterozygous yeast strains with sublethal doses of violacein or vehicle control for further barcode counts comparisson. The BioProject accession number of the SRA database generated from this work is PRJNA689872. In order to guarantee reproducibility of our results, all the code we used to process the data is available in a public databank (
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  • Sensitivity enhancement and the role of orientation in enzyme immunosorbent assay based on half fragment antibodies
    The free sulfhydryl groups of the hinge region of monovalent antibody fragments (rIgG) allow the orientation of rIgG on functionalized surfaces in immunosensors. To evaluate the contribution of reduction and orientation on signal enhancement we compared the performance of whole antibodies and their rIgG in ELISA performed on polystyrene or maleimide-functionalized microplates. Monoclonal anti-horseradish peroxidase (anti-HRP) and monoclonal anti-fPSA antibodies (1mg/ml) were reduced with 2-mercaptoethylamine (53mM). Using anti-HRP we confirmed the retention of the antigen binding capacity of rIgG. Moreover, we observed a signal enhancement for rIgG even if randomly absorbed on polystyrene [linear regression slope (95%CI): rIgG 0.524 (0.434-0.614), IgG 0.370 (0.430-0.399); P=0.0016] suggesting that chemical reduction might affect the antigen binding capacity of antibodies. ELISA with anti-fPSA rIgG coated on polystyrene confirmed these observations. Oriented anti-fPSA rIgG on a maleimide surface showed comparable signals to the assay performed on polystyrene for each analyzed concentration of antigen, anyway, with a significant improvement of the repeatability.
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  • Data from Neural Network Training in the Obstacle Tower Environment to Investigate Embodied, Weakly Supervised Learning
    This repository presents data collected to investigate the role of embodiment and supervision in learning. This is done inside a simulated 3D maze world with a navigation task using mainly visual input in the form of RGB images. The main contribution of this data repository is to provide a network model trained in this environment with weak supervision and a closed loop between action and perception. Additionally, control networks are provided which were trained with varying degrees of supervision and embodiment. In the corresponding paper [1] the representations of these networks are compared based on sparsity measures and well as content of the encodings and the possibility to extract semantic labels. For the training of the control conditions several new data sets were created which are also included here. They contain a collection of images from the simulated world with corresponding semantic labels (hand labeled). Overall, they provide a good basis for further analysis and a more in-depth investigation of representation learning and the effect of embodiment and supervision on representations.
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  • Data of "Epidemiology of Out-of-Hospital Cardiac Arrests,Knowledge of Cardiovascular disease and Risk Factors in a regional setting in India: The Warangal Area out-of -hospital Cardiac Arrest Registry (WACAR)
    Out-of-Hospital Cardiac Arrest (OHCA) is a global public health problem.While several OHCA registries are developed based on the Utstein template, there is limited data on OHCA from India.The Warangal Area out-of-hospital Cardiac Arrest Registry (WACAR) was designed to gain a better understanding of OHCA in a regional setting in India. The WACAR is a prospective one-year observational study of OHCA in Warangal area in the State of Telangana, India.OHCA cases were obtained from a regional Government Hospital, Mahatma Gandhi Memorial Hospital, a secondary care District Headquarters Hospital. Study subjects included all those above 18 years brought to the hospital with a history of non-traumatic OHCA of presumed cardiac origin from January 1, 2018 - December 31, 2018. A total of 814 individuals were included in the study for data analysis. The data are collected on a standard collection form designed with Utstein variables with additional data on clinical characteristics (modified Utstein template). It includes information on demographics, patient characteristics, risk factors, history of heart disease, comorbidities, prior symptoms, resuscitation characteristics, event timing, utilization of Emergency Medical Services (EMS) and outcomes. Study data were obtained from a review of hospital records. Medical staff involved in the care of OHCA were given data collection forms that were filled out in the emergency room setting. Information not obtained during initial emergency room evaluation was obtained from bystanders (including victim’s relatives and attendants) through telephone interviews. Results: A total of 1106 subjects of OHCA attended MGM Hospital during January 2018 and December 2018. After excluding those due to trauma, hanging, and burns, the sample size of OHCA was sized down to 926 subjects and 814 subjects with Presumed Cardiac etiology were included in the study for analysis. The results are tabulated into demographics, patient characteristics and resuscitation characteristics. Majority of subjects were male, with a median age of 60 years. The majority occurred in residential locations and sustained OHCA within one hour of symptom onset. Individuals with knowledge of CVD risk factors were more likely to report symptoms before OHCA. Data on resuscitation characteristics were inadequate. Conclusions: WACAR gives insight into the epidemiology of OHCA in India.The results of WACAR highlight that OHCA of cardiac etiology is a significant public health problem in India.The study demonstrated barriers involving patient knowledge of CVD ,risk factors, data collection, and access to health care. The study results also convey that the knowledge level of CVD risk factors and personal CVD disease have a significant impact on OHCA outcomes. The information from the WACAR registry, the first registry on OHCA in this setting points to the need for a Indian National OHCA Registry and might help to guide future steps to improve care OHCA in India.
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  • Co-translational targeting of transcripts to endosomes
    Asymmetric localization and translation of mRNAs is used by single cells to sense their environment and integrate extrinsic cues with the appropriate cellular response. Here we investigate the extent to which endosomes impact subcellular patterning of transcripts and provide a platform for localized translation. Using image-based transcriptomics, indirect immunofluorescence, and RNAseq of isolated organelles, we discover mRNAs that associate with early endosomes in a translation-dependent and -independent manner. We explore this in more detail for the mRNA of a major endosomal tethering factor and fusogen, Early Endosomal Antigen 1, EEA1, which localises to early endosomes in a puromycin-sensitive manner. By reconstituting EEA1 knock-out cells with either the coding sequence or 3’UTR of EEA1, we show that the coding region is sufficient for endosomal localisation of mRNA. Finally, we use quantitative proteomics to discover proteins associated with EEA1 mRNA and identify CSRP1 as a factor that controls EEA1 translational efficiency. Our findings reveal that multiple transcripts associate with early endosomes in a translation-dependent manner and identify mRNA-binding proteins that may participate in controlling endosome-localised translation.
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  • Testing Dataset for Head Segmentation Accuracy for the Algorithms in the ‘BGSLibrary’ v3.0.0 Developed by Andrews Sobral
    This dataset consists of video files that were created to test the accuracy of background segmentation algorithms contained in the C++ wrapper ‘BGSLibrary’ v3.0.0 developed by Andrews Sobral. The comparison is based on segmentation accuracy of the algorithms on a series of indoor color-depth video clips of a single person’s head and upper body, each highlighting a common factor that can influence the accuracy of foreground-background segmentation. The algorithms are run on the color image data, while the ‘ground truth’ is semi-automatically extracted from the depth data. The camera chosen for capturing the videos features paired color-depth image sensors, with the color sensor having specifications typical of mobile devices and webcams, which cover most of the use cases for these algorithms. The factors chosen for testing are derived from a literature review accompanying the dataset as being able to influence the efficacy of background segmentation. The assessment criteria for the results were set based on the requirements of common use cases such as gamecasting and mobile communications to allow the readers to make their own judgements on the merits of each algorithm for their own purposes. A description of the algorithms in the BGSLibrary, the factors tested, and the abbreviations used in labeling the data files and folders can be found in the file 'Mendeley Data Tables.pdf'. The files in GAU10-GAU40 and UNI05-UNI20 have been compressed to save space.
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  • Rainfall, groundwater, and surface water isotope data from extreme tropical cyclones (2016-2019) within the Caribbean Sea and Atlantic Ocean basins
    This data set contains novel surface rainfall isotope compositions (δ18O, δ2H, and d-excess in ‰) of tropical cyclones Otto (Costa Rica, 2016), Nate (Costa Rica, 2017), Irma and María (Cuba and The Bahamas, 2017), and Dorian (The Bahamas, 2019). Unique high frequency tempestology sampling of rainfall enabled δ18O and δ2H isotope analysis. In total, 161 surface rainfall samples were collected in passive devices with event-based and daily frequencies, resulting in the first surface TC isotopic anatomy across the Caribbean Sea and Atlantic Ocean basins to date. Our data also provides spring (N=338) and surface water (N=334) isotope compositions after the impact of Hurricane Otto and Tropical Storm Nate in central Costa Rica. Our data may improve the current understanding of key processes governing rainfall isotope ratios in the Caribbean Sea and Atlantic Ocean basins during continental and maritime TC tracks, with applications to the interpretation of paleo-hydroclimate and groundwater recharge processes across the tropics.
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  • Glia promote synaptogenesis through an IQGAP PES-7 in C. elegans
    Synapses are essential for the function of the nervous system. Glia play an important role in regulating synaptic formation. To address how glia regulate synaptic development, we use cima-1 mutant C. elegans as an in vivo model. In this data set, we provided data that support 1) Rho GTPase CDC-42 and IQGAP PES-7 are required in presynaptic neurons for VCSC glia-induced presynaptic formation; 2) cdc-42 and pes-7 are also required for normal synaptogenesis during postembryonic developmental stages; 3)PES-7 activated by CDC-42 promotes presynaptic formation most likely through regulating F-actin assembly.
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