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publicDec 2022View details →

Supplemental files to: Probe-based quantitative PCR and RPA-Cas12a molecular diagnostics for detection of the tomato pest Phthorimaea absoluta (Lepidoptera: Gelechiidae)

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publicSep 2022View details →

Data from: Assessment of coyote-wolf-dog admixture using ancestry-informative diagnostic SNPs

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publicMar 2025View details →

Reducing Hepatitis C diagnostic disparities with a point of care assay for HCV antigen detection

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publicNov 2024View details →

Lanes, clusters, lines of Sight: Modelling diagnostic eyecare clinics to improve patient flow

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opencc-bySep 2019View details →

Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics

Datasets for manuscript "Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics" Metadata.zip <ol> <li>phenotypes.txt: tabular file containing binary resistance phenotypes based on CLSI guidelines, where the rows are the isolates and the columns correspond to different drugs. Resistance : 1, susceptibility: 0, missing: intermediate resistant</li> </ol> Features_gpa_exp_snps.zip   We provide the processed molecular data as Numpy compressed files (npz.). You can use the Numpy load method to read in these tables https://docs.scipy.org/doc/numpy/reference/generated/numpy.load.htm. The row (strains_list) and column labels (feature_lists) are stored separately. <ol> <li>genexp: gene expression table directory <ul> <li>genexp_feature_vect.npz: The feature matrix in the numpy format</li> <li>genexp_feature_list.txt: The columns of the feature matrix (features)</li> <li>genexp_strains_list.txt: The rows of the feature matrix (isolates)</li> </ul> </li> <li>gpa: gene presence/absence table directory <ul> <li>gpa_feature_vect.npz: The feature matrix in the numpy format</li> <li>gpa_feature_list.txt: The columns of the feature matrix (features)</li> <li>gpa_strains_list.txt: The rows of the feature matrix (isolates)</li> </ul> </li> <li>snps: SNPs table directory <ul> <li>snps_feature_vect.npz: The feature matrix in the numpy format</li> <li>snps_feature_list.txt: The columns of the feature matrix (features)</li> <li>snps_strains_list.txt: The rows of the feature matrix (isolates)</li> </ul> </li> </ol>

opencc-zeroAug 2020View details →

Hybrid nanoplasmonic porous biomaterial scaffold for liquid biopsy diagnostics using extracellular vesicles: data and media

Raw datasets and media accompanying the manuscript: Hybrid nanoplasmonic porous biomaterial scaffold for liquid biopsy diagnostics using extracellular vesicles, published in ACS Sensors

opencc-zeroDec 2019View details →

Bayesian diagnostic meta-analysis dataset of pelvic examination in pelvic inflammatory disease

Pelvic inflammatory disease (PID) is not merely a transient sexually transmitted disease. It can lead to chronic pain, ectopic pregnancy, and infertility. Although the Centers for Disease Control and Prevention have established minimum diagnostic criteria, including pelvic examination, the diagnostic value of pelvic tenderness has recently garnered controversy. Our meta-analysis aimed to confirm whether pelvic examination can help diagnose PID among at-risk women. Design A Bayesian meta-analysis of studies reporting diagnostic data of patients at risk for PID. Setting We searched MEDLINE, EMBASE, CENTRAL, CINAHL, Google, and Google Scholar for eligible articles. Participants Female patients at risk for PID. Main results The literature search produced 5,395 articles. After quality assessment, 16 studies and their 4,083 participants were eligible for synthesis on pelvic tenderness.

opencc-zeroSep 2020View details →

Association between susceptibility of Thrips palmi to spinetoram and frequency of G275E mutation provides basis for molecular diagnostics of field-evolved resistance

Background: Spinosyn resistance is an increasing problem in field control of targeted pests. While putative mechanisms underlying spinosyn resistance have been identified in controlled studies on many species, mechanisms underlying field-evolved resistance and the development of a molecular diagnostic method for monitoring field resistance have lagged behind. Here, we examined levels of resistance of melon thrips, Thrips palmi, to spinetoram as well as target site mutations in field populations across China to identify potential mechanisms and useful molecular markers for diagnostic purposes. Results: LC50 of 16 field-collected populations to the spinetoram varied from 0.12 to 759.34 mg L-1. In resistant populations, we identified the G275E mutation, which has previously been linked to spinosyns resistance, as well as another nonsynonymous mutation, F314V, both located in the α6 subunit of the nicotinic acetylcholine receptor. There was a strong correlation between levels of spinetoram resistance and allele frequency of G275E mutation in field-collected populations (r2 = 0.84) and those reared under laboratory conditions for two to five generations (r2 = 0.91). LC50 ranged from 0.12 to 0.66 mg L-1 in populations without G275E mutation, while it ranged from 33.12 to 39.91 mg L-1 in most populations with a G275E mutation frequency > 90%, with the exception of one field-collected population which had an G275E frequency of 92% and a very high LC50 value of 759.34 mg L-1, suggesting additional mechanisms. Conclusions: Our results indicate that field-evolved resistance of T. palmi to spinetoram in China is mainly conferred by the G275E mutation, with other mechanisms contributing to a higher level of resistance. The frequency of the G275E mutation provides a useful diagnostic for quantifying resistance levels in field populations of T. palmi.

opencc-zeroDec 2020View details →

Identifying diagnostic genetic markers for a cryptic invasive agricultural pest: a test case using the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae)

Insect pests destroy ~15% of all USA crops, resulting in losses of $15 billion annually. Thus, developing cheap, quick and reliable methods for detecting harmful species is critical to curtail insect damage and lessen economic impact. The apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae), is a major invasive pest threatening the multibillion-dollar apple industry in the Pacific Northwest USA. The fly is also sympatric with a benign but morphologically similar and genetically closely related species, R. zephyria, which attacks non-commercial snowberry. Unambiguous species identification is essential due to a zero-infestation policy of apple maggot for fruit export. Mistaking R. zephyria for R. pomonella triggers unnecessary and costly quarantines, diverting valuable control resources. Here we develop and apply a relatively simple and cost-effective diagnostic approach using Illumina sequencing of double digest restriction-site associated DNA markers. We identified five informative single nucleotide polymorphisms (SNPs) and designed a diagnostic test based on agarose gel electrophoresis of restriction enzyme digested polymerase chain reaction amplification products (RFLPs) to distinguish fly species. We demonstrated the utility of this approach for immediate, one day species identification by scoring apple- and snowberry-infesting flies of known host plant identity, reared directly from 11 sites throughout Washington. However, if immediate diagnosis is not required, or hundreds to thousands of specimens must be assessed, then a direct Illumina-based sequencing strategy, similar to that used here for diagnostic SNP identification can be powerful and cost-effective. The genomic strategy we present is effective for R. pomonella and also transferable to many cryptic pests.

opencc-zeroFeb 2020View details →

Critical PO2 as a diagnostic biomarker for the effects of low-oxygen modified and controlled atmospheres on phytosanitary irradiation treatments in the Cabbage Looper Trichoplusia ni (Hübner)

BACKGROUND: Phytosanitary irradiation is a sustainable alternative to chemical fumigants for disinfesting fresh commodities from insect pests. However, irradiating insects in modified atmospheres with very low oxygen (<1 kPa O2) has repeatedly been shown to increase radioprotective response. Thus, there is a concern that modified atmosphere packaging could reduce the efficacy of phytosanitary irradiation. One hurdle slowing the widespread application of phytosanitary irradiation is a lack of knowledge about how moderate levels of hypoxia relevant to modified atmosphere packaging of most fresh commodities (3-10 kPa O2) may affect phytosanitary irradiation treatments. Therefore, we hypothesize that critical PO2 (Pcrit), the level of oxygen at which an insect's metabolism becomes impaired, can be used as a diagnostic biomarker to predict the induction of a radioprotective response. RESULTS: Using the cabbage looper Trichoplusia ni (Hübner), we show that there is a substantial increase in radiation resistance when larvae are irradiated in atmospheres more hypoxic than their Pcrit (3.3 kPa O2). These data are consistent with our hypothesis that Pcrit could be used as a diagnostic biomarker for what levels of hypoxia may induce radioprotective effects that could impact phytosanitary irradiation treatments. CONCLUSION: We propose that the relationship between Pcrit and radioprotective effects could allow us to build a framework for predicting the effects of low-oxygen atmospheres on the efficacy of phytosanitary irradiation. However, more widespread studies across pest species are still needed to test the generality of this idea.

opencc-by-4.0Jan 2023View details →

1/8˚ resolution MOM6-COBALT physical and biogeochemical diagnostics for the Gulf of Mexico, monthly means between 2008-2018

The files in this dataset contain monthly mean chlorophyll (µg/kg), pH, nitrate (mol/kg), dissolved oxygen (mol/kg), potential temperature (˚C) and salinity model outputs for 2008-2018 for the region between 18-31˚N, 98-80˚W. Data was extracted from a global grid run with coupled ocean-ice model configured using the Modular Ocean Model 6 (MOM6, https://github.com/NOAA-GFDL/MOM6 ) and Sea Ice Simulator (SIS2) developed at the NOAA Geophysical Fluid Dynamics Laboratory (Adcroft et al., 2019). The horizontal resolution of the grid is 1/8˚, which is considered eddying and no eddy parameterization was included. Vertically, the model uses 75 hybrid vertical-sigma2 layer coordinates that is remapped onto 35 World Ocean Atlas/Coupled Model Intercomparison Project standard depth levels. The atmospheric forcing was derived from the Japanese 55-year Reanalysis version 1.5 (JRA55 1.5, https://jra.kishou.go.jp/JRA-55/index_en.html#jra-55). The model is driven by river freshwater runoff from a monthly climatology derived from Dai and Trenberth (2002) and Dai et al. (2009), which can be assessed at https://rda.ucar.edu/datasets/ds551.0/. A remapping scheme was used to add freshwater into the appropriate coastal grid cells near the river mouths. The biogeochemical model used was the Carbon, Ocean Biogeochemistry and Lower Trophics (COBALTv2, Stock et al., 2020), which uses 33 tracers for representation of coupled elemental cycles of carbon, nitrogen, phosphorus, iron, silicon, alkalinity, oxygen and lithogenic matter and associated plankton food web dynamics. More details about the model setup are described in Liu et al. (2019) and Liu et al. (2021). References: Adcroft, A., Anderson, W., Blanton, C., Bushuk, M., Dufour, C.O., Dunne, J.P., Griffies, S.M. et al. (2019). The GFDL Global Ocean and Sea Ice Model OM4.0: Model description and simulation features. Journal of Advances in Modeling Earth System, doi: 10.1029/2019MS001726 Dai, A., T. Qian, K. E. Trenberth, and J. D Milliman, 2009: Changes in continental freshwater discharge from 1948-2004. J. Climate, 22, 2773-2791 Dai, A., and K. E. Trenberth, 2002: Estimates of freshwater discharge from continents: Latitudinal and seasonal variations. J. Hydrometeorol., 3, 660-687 Liu, X., Dunne, J.P., Stock, C. A., Harrison, M.J., Adcroft, A., Resplandy, L. (2019). Simulating Water Residence Time in the Coastal Ocean: A Global Perspective. Geophysical Research Letters, 46, 22, 13910-13919. Doi:10.1029/2019GL085097 Liu, X., Stock, C.A., Dunne, J.P., Lee, M., Shevliakova, E., Malyshev, S., Milly, P.C.D (2021). Simulated Global Coastal Ecosystem Responses to a Half-Century Increase in River Nitrogen Loads. Stock, C. A., Dunne, J. P., Fan, S., Ginoux, P., John, J., Krasting, J. P., et al. (2020). Ocean biogeochemistry in GFDL's Earth System Model 4.1 and its response to increasing atmospheric CO2. Journal of Advances in Modeling Earth Systems, 12, e2019MS002043. https://doi.org/10.1029/2019MS002043

opencc-by-4.0Apr 2023View details →

Fig. 3 in First Japanese Records of the Indo-Pacific Scorpionfish (Scorpaenidae) Scorpaenodes corallinus, with a Re-evaluation of Coronal Spines as a Diagnostic Character

Fig. 3. Holotype of Scorpaenodes corallinus (SAIAB 301, 64.4 mm SL, Pinda Island, Mozambique).

opencc-by-4.0Mar 2024View details →

Diagnostic and prediction value of synthetic magnetic resonance imaging in acute ischemic stroke patients

This is the supplementary tables for the above paper, mainly including original statistical analysis data.

opencc-by-4.0Mar 2024View details →

Datasets for the article "Evaporative controls on Antarctic precipitation: an ECHAM6 model study using innovative water tracer diagnostics"

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opencc-by-4.0Nov 2024View details →

Model Data and Diagnostics used for the Age of Air Diagnostic Paper

Model data and derived diagnostics used in the Age of Air paper, from Unified Model output. © Crown Copyright, Met Office

opencc-by-2.0Nov 2021View details →

TG 36: The Revision of Dose Coefficients in Diagnostic Nuclear Medicine

The ICRP Task Group 36 "Radiation Dose to Patients in Diagnostic Nuclear Medicine" is currently working on the revision of ICRP Publication 128 (2015) by updating the dose coefficients using the new ICRP adult and paediatric reference voxel phantoms from ICRP Publications 110 (2009) and 143 (2020), nuclear decay data from Publication 107 (2008) and the dosimetry methodology of ICRP described in Publication 103 (2007). Also the biokinetic information on the radiopharmaceuticals is being updated based on the most recent literature data and will be presented in form of compartmental structures, similarly to what already done by ICRP for workers and members of the public. To assess more realistically the dose to the urinary bladder wall, which is in most cases one of the most exposed tissues, a dynamic bladder model will also be introduced. Although the quantity effective dose, calculated for a (hypothetical) reference person, is useful (and used) in comparing exposures, and consequently risks, from different radiopharmaceuticals and/or different alternative diagnostic procedures, its application in medicine is controversial and also goes beyond its originally intended purpose. For the specific work of Task Group 36 in diagnostic nuclear medicine it is indeed planned to provide estimates of whole body dose quantities that account for the fact that some investigations are performed on patients of only one sex (e.g., differential diagnosis of prostate cancer with 18F-choline) or in patient groups with anatomical or physiological characteristics differing from the reference persons (for instance, patients with abnormal liver or spleen masses due to diffuse parenchymal disease, or with unilateral kidney blockage). It is therefore appreciated that the ICRP, in its mission to keep the recommendations fit for purpose, is seeking to revise the concept of the radiation detriment to account for age- and sex-dependence of radiation sensitivity, and to recommend tissue weighting factors which are differentiated accordingly. The idea of no longer referring the effective dose for a hypothetical reference person only, but separately for different subgroups in the population (depending on age, sex, health condition or other characteristics) would actually be very practicable in all medical dosimetric application, including nuclear medicine. Presented by Augusto Giussani on behalf of the whole Task Group.

opencc-by-4.0Nov 2021View details →

Seasonal cycles of the 234Th profiles and each term of the 234Th diagnostic equation from a realistic simulation at SEATS

This dataset provides the diagnostic results of the 234Th equation from a physical-biogeochemical-234Th model simulation at SEATS. It includes two files: (file1)seasonal_mean_of_vertical_profiles.mat and (file2) each term of the 234Th diagnostic equation.mat. In file1, seasonal cycle of tracers (e.g., temperature, salinity, particulate 234Th and total 234Th)  at SEATS were saved. File 2 provides the diagnostic results of the 234Th equation at SEATS, including the rate of 234Th over time, the deficit of 238U-234Th term, the particle sinking term, the vertical advection and diffusion term.

opencc-by-4.0Jan 2022View details →

data set regarding to project Optimal assessment of nutritional status in older subjects with the chronic obstructive pulmonary disease – a comparison of three screening tools used in the GLIM diagnostic algorithm

data set regarding to project Optimal assessment of nutritional status in older subjects with the chronic obstructive pulmonary disease – a comparison of three screening tools used in the GLIM diagnostic algorithm

opencc-by-4.0Jan 2022View details →

A Diagnostic Classifier for Gene Expression-Based Identification of Early Lyme Disease

This data repository contains the source code and pertinent training and test data sets used in the manuscript, A Diagnostic Classifier for Gene Expression-Based Identification of Early Lyme Disease.