Find research datasets worth reusing

opencc-by-4.0Dec 2018View details →

Fig. 2 in Qualitative and quantitative methods for estimating Spirorchiidiasis burden in sea turtles

Fig. 2. Scatter plot with trend line showing the correlation between eggs counts using the two quantitative methods (MH and CH) in the spleen.

opencc-by-4.0Dec 2018View details →

Fig. 1 in Qualitative and quantitative methods for estimating Spirorchiidiasis burden in sea turtles

Fig. 1. Eggs of H. mistroides in the McMaster chamber for quantification of splenic egg burden (Scale bar: 200 μm).

Figure 11 in A quantitative method for collecting water mites in lotic, riffle-run habitats for water quality biomonitoring

Figure 11 An example of how water mites appear under a stereoscope. a – water mites of mixed taxa in a single sample ready to be sorted through and identified; b – water mites belonging to the genusTestudacarus and their easily observable characteristic dorsal plates; c – water mites belonging to the genusKongsbergia and their easily distinguishable posterior body shape.

Figure 6 in A quantitative method for collecting water mites in lotic, riffle-run habitats for water quality biomonitoring

Figure 6 The sieving process proposed in this manuscript. a – collector fills the composited sample container with water and shakes the container for approximately 10 seconds; b – immediately after shaking the collector removes the lid and pours the water through the 3mm and 250 μm sieves; c and d – the 3mm will be placed on top of the 250 μm sieve so it can filter out larger sized substrate and debris. This process is repeated 10x.

Figure 5 in A quantitative method for collecting water mites in lotic, riffle-run habitats for water quality biomonitoring

Figure 5 An example of the collector emptying the net contents from the first of four site collections into sample container; the next three site

Figure 2 in A quantitative method for collecting water mites in lotic, riffle-run habitats for water quality biomonitoring

Figure 2 Collection nets discussed in this manuscript. a – a standard, commercially available, truncated D-frame net with 500 μm mesh; b – our custom made, non-truncated D-frame net with 250 μm mesh.

Figure 1 in A quantitative method for collecting water mites in lotic, riffle-run habitats for water quality biomonitoring

Figure 1 Examples of impaired and attaining riffle-run stream habitats in central Pennsylvania. a – Warriors Mark Run, impaired stream; b – Muddy Run, impaired stream; c – Spruce Run, attaining stream; d – Laurel Run, attaining stream.

Figure 3 What a in A quantitative method for collecting water mites in lotic, riffle-run habitats for water quality biomonitoring

Figure 3 What a single collection site should look like after the proposed three-minute collection effort. The blue arrows indicate stacked rocks that were stacked upstream of the net to better direct flow into the net. Large rocks were moved before digging into the substrate, while medium-sized and smaller rocks were placed as the substrate was dug up.

Figure 10 A in A quantitative method for collecting water mites in lotic, riffle-run habitats for water quality biomonitoring

Figure 10 A final, picked water mite sample preserved in 80% ethanol ready for identification and enumeration.

Figure 7 After sieving, the collector removes the contents from the 250 in A quantitative method for collecting water mites in lotic, riffle-run habitats for water quality biomonitoring

Figure 7 After sieving, the collector removes the contents from the 250 μm sieve and places them into the final sample jar. a – fine sediment

Figure 4 in A quantitative method for collecting water mites in lotic, riffle-run habitats for water quality biomonitoring

Figure 4 An example of the collection process proposed in this manuscript. a – the collector stands upstream of the net and disturbs the substrate; b – a typical collection setup that includes one person shoveling and another holding the net; c – water mites become suspended in the water column and flow downstream into the net.

Figure 9 in A quantitative method for collecting water mites in lotic, riffle-run habitats for water quality biomonitoring

Figure 9 The picking process proposed in this manuscript. a – the picker empties the contents of the sample container into the white photographic

opencc-zeroJul 2020View details →

dryad36/100

UPLC-MS/MS Method for quantitation of the recently FDA approved combination of vaborbactam and meropenem in human plasma

A parenteral medical combination containing vaborbactam (VBR) and meropenem (MRP) is used mainly to treat complicated urinary tract infections. A novel ultra-performance liquid chromatography (UPLC)- tandem mass spectrometric (MS/MS) method was developed for the sensitive determination of both compounds in human plasma. Sample preparation was performed by precipitation technique. The chromatographic separation was accomplished using the Acquity C18-BEH column, 0.01 M ammonium formate: acetonitrile (47:53, v/v) as a mobile phase with a flow rate of 0.2 mL/min. Analytes were monitored by applying multiple reaction monitoring (MRM). The bioanalytical validation criteria were conducted following the FDA recommendations. The method was linear within range 0.5 to 50 µg/mL, for both drugs. The intra-day and inter-day precision, as coefficient variation (%CV) and the accuracy, as % bias not exceed than 15% for both drugs. The percentage recovery of targeted analytes was not less than 77 %, calculated at three QC levels. The proposed method showed a suitable LLOQ value of 0.5 µg/mL for both analytes, which is far lower than the expected Cmax, which permits the use of this method for pharmacokinetic studies. The proposed method proved to be useful for the evaluation of this combination in both human plasma and pharmaceutical formulation.

opencc-by-4.0Dec 2020View details →

A quantitative method to calibrate the SWAN wave model - pre-processed model outputs

The pre-processed MAT files for the paper 'A quantitative method to calibrate the SWAN wave model'

opencc-zeroJun 2016View details →

Retinal status analysis method based on feature extraction and quantitative grading in OCT images

The raw database includes 200 retinal OCT images judged as normal by ophthalmologists and 100 images with various abnormalities. The software includes the main steps for retinal status analysis. The software was carried out in Matlab.

dryad36/100

Induced pluripotent stem cell-derived cardiomyocyte in vitro models: tissue fabrication protocols, assessment methods, and quantitative maturation metrics for benchmarking progress

The advent of human induced pluripotent stem cells (hiPSCs) and techniques to differentiate cardiomyocytes from them has opened a viable path to creating in vitro models of normal and diseased hearts, accelerating more predictive drug screening and therapeutic strategies for cardiac pathologies. Currently, hiPSC-derived cardiomyocytes (hiPSC-CMs) are more similar to fetal than adult cardiomyocytes, leading many in the field to explore approaches to enhance cell and tissue maturation. There are over 2,000 studies utilizing hiPSC-CMs in models composed of various combinations of cell and extracellular matrix components, using a plethora of differentiation protocols, culture formats, and methods for quantifying cardiomyocyte function. To assess the current state of this rapidly growing area, we systematically analyzed 300 studies using hiPSC-CM models for their selection of hiPSC lines, hiPSC-CM differentiation protocols, types of in vitro models, maturation techniques, and metrics used to assess cardiomyocyte functionality and maturity. Here, we provide the data compiled from our analysis of these papers so others in the field can utilize it to inform their research. Based on this analysis, we highlight the diversity of, and current trends in, in vitro model designs and highlight the most common and promising practices for functional assessments. We further analyzed outputs spanning structural maturity, contractile function, electrophysiology, and gene expression and note field-wide improvements over time. Finally, we observe that a persistent lack of coordination amongst investigators is limiting the field's ability to benchmark and advance hiPSC-CM function against previous studies. We discuss opportunities to collectively pursue the common goal of hiPSC-CM model development, maturation, and assessment that we believe are critical to drive the entire community forward in engineering mature cardiac tissue.

opencc-zeroJan 2024View details →

opencc-by-4.0Jul 2022View details →

Data from: A Method for Measuring B0 Field Inhomogeneity using Quantitative DESS (qDESS)

Purpose: To develop and validate a method for B0 mapping for knee imaging using the quantitative Double-Echo in Steady-State (qDESS) exploiting the phase difference (∆θ) between the two echoes acquired. Contrary to a standard two-gradient echo (2-GRE) method, the phase accumulation in qDESS depends only on the first echo time. Methods: Bloch simulations were applied to investigate the robustness to noise of the proposed methodology and all imaging studies were validated with phantoms and in vivo simultaneous bilateral knee acquisitions. Two phantoms and 5 healthy subjects were scanned using qDESS, water saturation shift referencing (WASSR), and multi GRE sequences. ∆B0 maps were calculated with the qDESS and the 2-GRE methods and compared against those obtained with WASSR. The comparison was quantitatively assessed by exploiting pixel-wise difference maps, Bland-Altman (BA) analysis, and Lin’s concordance coefficient (ρc). For in-vivo subjects, the comparison was assessed in cartilage using average values in 6 sub-regions. Results: The proposed method for measuring B0 inhomogeneities in phantom and in-vivo scans from a qDESS acquisition provided ∆B0 maps that were in good agreement with those obtained using WASSR. ∆B0 Lin’s coefficients were greater than or equal to 0.98 and 0.90 in phantoms and in vivo, respectively. The agreement between qDESS and WASSR was comparable to that of a standard 2-GRE method. Conclusion: The proposed method may allow B0 correction for qDESS T2 mapping using an inherently co-registered ∆B0 map without requiring an additional B0 measurement sequence. More generally, the method may help shorten knee imaging protocols that require an auxiliary ∆B0 map by exploiting a qDESS acquisition that also provides T2 measurements and high-quality morphological imaging. Conclusion: The proposed method may allow B0 correction for qDESS T2 mapping using an inherently co-registered ∆B0 map without requiring an additional B0 measurement sequence. More generally, the method may help shorten knee imaging protocols that require an auxiliary ∆B0 map by exploiting a qDESS acquisition that also provides T2 measurements and high-quality morphological imaging. This repository contains the data for reproducing the results reported in the paper. For the in-vivo data, python scripts are provided to perform the data analysis described in the paper. The data are provided in NIFTI format.  Please cite the original paper (10.1002/mrm.29465) and this repository if you use any of the data or code contained here.

Figure 8 in A quantitative method for collecting water mites in lotic, riffle-run habitats for water quality biomonitoring

Figure 8 The final composite, sieved water mite sample ready for the picking process.