Johns Hopkins Research Data Repository
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Data and code associated with the publication: In vivo fundus imaging and computational refocusing with a diffuser-based fundus camera
No full textThis dataset contains the point spread functions (PSFs) used in the manuscript “In vivo fundus imaging and computational refocusing with a diffuser-based fundus camera.” It also contains relevant MATLAB code for image reconstruction with the diffuser-based fundus camera. The version of code used in the paper is included (as of Jan. 14, 2025) also be available and may be updated in an online repository
PMA (2019-2024) Client Exit Interview Master Codebook
No full textPMA (2019-2024) Client Exit Interview Master Codebook contains Client Exit Interviews conducted between 2019 and 2024 as part of the PMA grant
Data and code associated with the publication: Disassembly of unstable RNA structures by an E. coli DEAD-box chaperone accelerates ribosome assembly
No full textThis dataset is related to a submitted manuscript describing how a general DEAD-box RNA chaperone facilitates the assembly of nascent rRNA into stable RNA-protein complexes, using single molecule total internal reflection fluorescence microscopy.
Ribosome synthesis in bacteria is coupled with transcription of the pre-rRNA that must fold and assemble with 20 or more ribosomal proteins. In vitro, variable folding of the E. coli pre-16S rRNA during transcription delays stable addition of ribosomal protein uS4 that nucleates assembly of the 16S 5’ domain. Using single molecule fluorescence microscopy, we show that general unfolding by the DEAD-box protein CsdA (DeaD) strongly accelerates uS4 binding to nascent rRNA. Stable RNA structures resist unwinding by CsdA, which becomes less efficient as more ribosomal proteins join the complex. Monitoring single RNAs shows that dissociation of unstable complexes is followed by uS4 rebinding. Our results suggest that disassembly of nascent RNA-protein complexes by general chaperones drives cycles of reassembly, fueling the search for native-like complexes that resist unfolding and progress to mature ribosomes
Data associated with the publication: Dissociation of SYNGAP1 enzymatic and structural roles: Intrinsic excitability and seizure susceptibility
No full textSYNGAP1 is a key Ras-GAP protein enriched at excitatory synapses, with mutations causing intellectual disability and epilepsy in humans. Recent studies have revealed that in addition to its role as a negative regulator of G-protein signaling through its GAP enzymatic activity, SYNGAP1 plays an important structural role through its interaction with post-synaptic density proteins. Here, we reveal that intrinsic excitability deficits and seizure phenotypes in heterozygous Syngap1 knockout (KO) mice are differentially dependent on Syngap1 GAP activity. Cortical excitatory neurons in heterozygous KO mice displayed reduced intrinsic excitability, including lower input resistance, and increased rheobase, a phenotype recapitulated in GAP-deficient Syngap1 mutants. However, seizure severity and susceptibility to pentylenetetrazol (PTZ)-induced seizures were significantly elevated in heterozygous KO mice but unaffected in GAP-deficient mutants, implicating the structural rather than enzymatic role of Syngap1 in seizure regulation. These findings highlight the complex interplay between SYNGAP1 structural and catalytic functions in neuronal physiology and disease.
Here we deposit files including Axon binary files (abf), and Excel spreadsheets (xlsx) to supplement the published analysis.</p
Data and code associated with the publication: Increased vulnerability to noise exposure of low spontaneous rate type 1C spiral ganglion neuron synapses with inner hair cells
No full textDataset contains extracted ABR waveform data (Threshold, wave amplitudes and latencies).
Dataset contains raw confocal images, Imaris (Bitplane) analysis and extracted counts of structures of interest.
Dataset contains analysis code in R software
The Economist Intelligence Unit (EIU) CityData
No full textEIU’s CityData contains pricing information on over 160 products and services in 140 cities worldwide, gathered from the EIU Worldwide Cost of Living Survey. More than 50,000 individual prices are collected by field correspondents in each survey. Prices are given for various stores: supermarkets, mid-priced stores, and higher-priced specialty outlets. Prices cover: National economic indicators; Food and drink; Household supplies; Personal care; Tobacco; Clothing; Utilities; Domestic help; Recreation; Transport; Office and residential rents; Schools, health and sports; Business trip costs; Salaries and disposable incomes. Prices correspond to the price the customer is charged, not recommended retail prices or manufacturers’ costs.
Use CityData to support your market entry strategy, assess international pricing for a specific product(s), analyze historical pricing patterns for goods and services since 1990, compare the cost of doing business worldwide, and perform city-to-city pricing comparisons.
EIU CityData provides the most complete picture of global price levels. More information is available at EIU CityData Information
Data associated with the publication: Nanoparticle retention enables non-invasive detection of metastases by magnetic particle imaging
No full textBackground: Early detection of metastatic disease improves cancer survival, yet existing modalities are limited in their detection capabilities. We propose that magnetic particle imaging (MPI), an emerging technology, can be used for early detection of primary tumors and metastases. MPI detects minute quantities of magnetic particles that act as “cold tracers” which accumulate in areas of high immune
activity.
Methods: Pegylated Synomag® nanoparticles were intravenously injected into mouse models of breast cancer bearing primary tumors that spontaneously arise lung metastases. After 72hrs, mice were subjected to three-dimensional MPI followed by structural imaging for co-registration. Non-tumor bearing mice served as controls for background signal correction and toxicity analysis. Animals were then sacrificed to collect tumors and organs of interest for two-dimensional MPI scans before fixing them for histopathological evaluation by hematoxylin and Eosin (H&E), Prussian blue, and immunohistochemistry staining. To further substantiate our findings towards clinical translation, tumor phantoms with nanoparticles were evaluated in a newly-built human scale MPI.
Results: Pegylated Synomag® nanoparticles showed strong signal in both in vitro and in vivo models. Multiple macro and micro metastatic sites were identified by MPI and later confirmed by histology. Ex vivo quantitative analysis showed MPI can detect metastasis with high specificity and sensitivity, with positive correlations between tumor burden and macrophage population in the tumor microenvironment. Towards clinical translation, we also demonstrate nanoparticle detection in tumor phantoms using a human-scale MPI.
Conclusion: MPI using Pegylated Synomag® nanoparticles can successfully detect primary tumors and micrometastases away from large organs of reticuloendothelial system. Nanoparticles were found in the tumor microenvironment, which is associated with stromal and immune cells, with an especially strong correlation with macrophages. This provides evidence to use MPI for noninvasive detection of highly inflammatory tumors and metastasis, as well as exploring their potential for other inflammatory diseases.</p
Data associated with the publication: Multi-contrast laser endoscopy for in vivo gastrointestinal imaging
No full textThis repository contains data and code for replicating the data analysis presented in Multi-contrast laser endoscopy for in vivo gastrointestinal imaging. In this project, we introduce a Multi-contrast Laser Endoscopy (MLE) system with rapidly tunable spectral, coherent, and directional illumination. We demonstrate three capabilities of MLE: enhancing tissue chromophore contrast with multispectral diffuse reflectance, quantifying blood flow using laser speckle contrast imaging, and characterizing mucosal topography using photometric stereo. We validate MLE with benchtop models, then demonstrate MLE in vivo during clinical colonoscopies. The data collection is split into code and data subdirectories. Due to the larger file sizes, the dataset cannot be downloaded as a single combined .zip file, and so should be downloaded individually. Please refer to the README for instructions for reassembling the file directly organization for proper file path access by the code
Data associated with the publication: EyePose: Pose-guided saccadic eye movement video generation for deep learning-based neurologic disease phenotyping
No full textThe synthetic dataset comprises 3,000 labeled saccadic eye movement videos evenly distributed across three classes: normal, hypometria, and hypermetria. Each video simulates horizontal saccades with realistic amplitude and velocity patterns, and is annotated based on saccadic accuracy. The videos are sampled at 25 Hz with a resolution of 256×256 pixels, and span approximately 5 seconds, capturing a sequence of multiple saccadic events per clip. For each video, a corresponding waveform is provided
Data associated with the publication: General approach to achieving electrochemical aptamer-based sensor sensitivity of buffer in blood plasma
No full textElectrochemical aptamer-based (E-AB) sensors enable the accurate measurement of target concentrations in complex matrices such as plasma or serum. However, to function effectively in these environments, the aptamers must resist nonspecific binding to proteins and other interferants. Many research literature and commercially available ("off-the-shelf") aptamers, originally selected without consideration for biofluid compatibility, are prone to such nonspecific interactions, which diminish sensor output and compromise sensitivity. To address this challenge and expand the utility of existing aptamer sequences, we present a tunable, generalizable method to restore the EC50 of E-AB sensors in plasma to levels comparable to those in buffer. We validate this approach using three therapeutically relevant small molecules: the antiretroviral emtricitabine (FTC), the antibiotic tobramycin, and the antimalarial hydroxyquinoline. Applying our method, we recovered EC50 values of 11 ± 3 µM for FTC (buffer: 10.4 ± 0.6 µM), 281 ± 91 µM for tobramycin (buffer: 190 ± 16 µM), and 1.1 ± 0.6 µM for hydroxyquinoline (buffer: 900 ± 95 µM). This strategy should enable the broader application of published small-molecule-binding aptamers for biofluid measurements, regardless of their original selection conditions