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opencc-by-4.0Oct 2020View details →

Illuminating the planktonic stages of salmon lice: a unique fluorescence signal for rapid identification of a rare copepod in zooplankton assemblages.

The Excitation Emission Matrix (EEM) measurements were taken with Shimadzu's proprietary software ‘LabSolutions RF’. All files are in the exported csv format with columns representing the excitation wavelengths and rows the emission wavelengths. Wavelengths range from 200-600 nm with a 2 nm increment. Fluorescence intensity was influenced by the fluctuating number of animals in the path of the excitation beam during the 5 minute measurement. We compensated for this artefact by repeating measurements of each sample five times, calculating the mean, and applying a smoothing function which found the median value within 10 nm. The fluorescence intensity was further normalized on a 0 to 1 scale by dividing intensity by the maximum fluorescence within each EEM measurement. Supplemental Table 1. The metadata of EEM measurements. The measurements were used for the spectrum section analysis and correspond to those depicted in Figures 2, 3, 4, & 5. See sections 3.1, 3.1.1, & 3.1.2. The Sample column indicates which lab culture cohort the sea lice came from (BGO*), which wild caught fish sample they came from (WC*), or the sampling date of non-target copepods (DDMMYY). The filename of each mean measurement is listed and indicates the first of 5 repeated measurements. Corresponding files can be found in the deposited.csv files at Zendo. In those files, data columns represent the excitation wavelengths, 200nm to 600nm increasing in 2 nm increments. Likewise, the rows represent the emission wavelengths. NaN’s are present where scattering layers were removed. All fluorescence intensity values are normalized to the maximum within each EEM.

opencc-by-4.0Sep 2021View details →

Rapid identification of MRSA using mass spectrometry and machine learning from over 20000 clinical isolates

Rapidly identifying methicillin-resistant Staphylococcus aureus (MRSA) with high integration in the current workflow is critical in clinical practices. We proposed a MALDI-TOF MS based machine learning model for rapidly MRSA prediction, the model was evaluated on a prospective test and four external clinical sites. On the dataset comprising 20359 clinical isolates, the area under the receiver operating curve of the classification model was 0.78–0.88. Our MALDI–TOF MS-based ML model for the rapid MRSA identification can be easily integrated into the current clinical workflows and can further support physicians prescribe proper antibiotic treatments.

opencc-by-4.0Nov 2022View details →

The rapid and highly parallel identification of antibodies with defined biological activities by SLISY

This is the sequencing data that accompanies the manuscript published in Nature Communications titled "The rapid and highly parallel identification of antibodies with defined biological activities by SLISY".

opencc-by-4.0May 2023View details →

Onco-mNGS Facilitates Rapid and Precise Identification of The Etiology of Fever of Unknown Origin: A Single-centre Prospective Study in North China

Supplemental Files and Data. Raw data for the copy numbers of chromosome were shown in fd.txt format. The picture of genomic of each sample was shown in png format.

opencc-by-4.0Feb 2020View details →

Rapid and real-time identification of fungi up to the species level with long amplicon Nanopore sequencing from clinical samples

Samples collected from fungal cultures, skin of dogs and ZymoBIOMICSTM mock community (which includes Saccharomyces cerevisiae and Cryptococcus neoformans). The amplicons length of the fungal cultures and ZymoBIOMICSTM mock community is 3,5 Kb and 6 Kb, while the Malassezia spp samples used as control is 3,5 Kb. The amplicons length of the four samples from the skin is 3,5 Kb.

opencc-by-4.0Mar 2024View details →

Rapid and Accurate Identification of Stem Cell Differentiation Stages via SERS and Convolutional Neural Networks

<a name="OLE_LINK2"></a>Monitoring the transition of cell states during induced pluripotent stem cell (iPSC) differentiation is crucial for clinical medicine and basic research. However, both identification category and prediction accuracy need further improvement. Here, we propose a method combining Surface-Enhanced Raman spectroscopy (SERS) with convolutional neural networks (CNN) to precisely identify and distinguish cell states during stem cell differentiation. First, mitochondria-targeted probes were synthesized by combining AuNRs and mitochondrial localization signal (MLS) peptides to obtain effective and stable SERS spectra signals at various stages of cell differentiation. Then, the SERS spectra served as input datasets, and their distinctive features were learned and distinguished by CNN. As a result, rapid and accurate identification of six different cell states, including the embryoid body (EB) stage, was successfully achieved throughout the stem cell differentiation process with an impressive prediction accuracy of 98.5%. Furthermore, the impact of different spectral feature peaks on the identification results was investigated, which provides a valuable reference for selecting appropriate spectral bands to identify cell states. This is also beneficial for shortening the spectral acquisition region to enhance spectral acquisition speed. These results suggest the potential for SERS-CNN models in quality monitoring of stem cells, advancing the practical applications of stem cells.

opencc-by-4.0Aug 2022View details →

Rapid pathogen identification in aqueous humor samples by combining Fc-MBL@Fe3O4 enrichment and MALDI-TOF MS profiling

Prompt clinical diagnosis and antimicrobial therapy are key to managing infective endophthalmitis. The small volume of aqueous humor, low bacterial counts, and empirical medication by physicians make existing diagnostic methods time-consuming and imprecise. Here, we investigated the feasibility of combining Fc-MBL@Fe3O4 enrichment with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling to identify pathogens in aqueous humor. Aqueous humor aspirated from freshly enucleated porcine eyes was inoculated with different inocula of Staphylococcus aureus (S. aureus), Staphylococcus epidermidis (S. epidermidis), and Klebsiella pneumoniae (K. pneumoniae). We performed identification directly in aqueous humor samples and after short-term culture of micro-LB broth. Aqueous humor endophthalmitis samples were enriched with Fc-MBL@Fe3O4 and analyzed with MALDI-TOF MS. The identification time and minimum bacterial concentration required for identification were determined. The enrichment efficiency of Fc-MBL@Fe3O4 for different bacteria was > (87.5±5.0)%. The objects of direct identification include live bacteria and bacteria treated with antibiotics, which can be completed within 1.5 hours. The minimum number of bacteria needed for positive identification was 2.20×106 CFU. For micro-LB broth culture, the identification of bacteria can be completed within 6.5-9.5 h for aqueous humor samples with an initial bacterial count of tens to hundreds.

opencc-by-4.0Jul 2024View details →

ZymoSoups: A high-throughput forward genetics method for rapid identification of virulence genes in Zymoseptoria tritici

These data were used to generate figures and summarise the number of mutations in 18 re-sequenced genomes of Zymoseptoria tritici. The isolates genotyped in this VCF file are all UV-mutegenized strains of the reference isolate IPO323. Abstract Septoria tritici blotch is caused by the fungus Zymoseptoria tritici and poses a major threat to wheat productivity. There are over twenty mapped loci in wheat that confer strong (gene-for-gene) resistance against this pathogen, however the corresponding genes in Z. tritici that confer virulence against distinct R genes remain largely unknown. In this study, we developed a rapid forward genetics methodology to identify genes that enable Z. tritici to gain virulence on previously resistant wheat varieties. We used the known gene-for-gene interaction between Stb6 and AvrStb6 as a proof of concept that this method could quickly recover single candidate virulence genes. We subjected the avirulent Z. tritici strain IPO323, which carries the recognized AvrStb6 allele, to UV mutagenesis and generated a library of over 66,000 surviving spores. We screened these survivors on leaves of the resistant wheat variety Cadenza, in mixtures (soups) ranging from 100-500 survivors per soup. We identified five soups with a gain-of-virulence (GoV) phenotype relative to the IPO323 parental strain and re-sequenced 18 individual isolates, including four control isolates and two isolates lacking virulence, when screened individually. Of the 12 confirmed GoV isolates, one had a single nucleotide polymorphism (SNP) in the AvrStb6 coding region. The other 11 GoV isolates exhibited large (~70Kb) deletions at the end of chromosome 5, including the AvrStb6 locus. Our findings demonstrate the efficiency of this forward genetic approach in elucidating the genetic basis of qualitative resistance to Z. tritici and the potential to rapidly identify other, currently unknown, Avr genes in this pathogen.  Analysis pipeline The pipeline used to generate this filtered vcf file and tab delimited file is publicly available at https://github.com/megancamilla/GATK4_Zymoseptoria Isolate Data Accessibility The individual fastq files for each isolate included in this study have been uploaded to NCBI's Short Read Archive (SRA), project number PRJNA1017776. This project contains 18 re-sequenced samples (SAMN37407989-SAMN37407972), which are UV mutagenized IPO323. Short Read Archive (SRA) accession numbers are SRR26072101-SRR26072118.

opencc-by-4.0Sep 2019View details →

NGS data produced in 'Rapid selection and identification of functional CD8+ T-cell epitopes from large peptide-coding libraries'; Nature Communications (2019)

Sharma, G et al. Rapid selection and identification of functional CD8+ T-cell epitopes from large peptide-coding libraries. Nature Communications. Accepted (August 2019) Abstract: Cytotoxic CD8+ T-cells recognize and eliminate infected or malignant cells that present, at their cell surfaces, short peptide epitopes derived from intracellularly processed antigens. However, broadly searching for specific major histocompatibility complex (MHC)-bound peptide epitopes that are naturally processed and capable of eliciting a functional T-cell response has been challenging. Here, we report a method for deep and unbiased T-cell epitope profiling, which is done by using in vitro co-culture of CD8+ T-cells and target cells transduced with high-complexity epitope-encoding minigene libraries. Target cells that are subject to cytotoxic attack from T-cells in co-culture are isolated, before they are lost to apoptosis, by fluorescence-activated cell sorting and characterized by sequencing the minigenes encoded within. In the present study, we validate this highly parallelized method using known murine T-cell receptor/peptide-MHC pairs and diverse minigene-encoded epitope libraries to identify naturally processed and MHC-presented peptide epitopes unambiguously and with high sensitivity.

opencc-by-4.0Aug 2024View details →

Rapid Identification of Bacterial isolates Using Microfluidic Adaptive Channels and Multiplexed Fluorescence Microscopy

Dataset for: Rapid Identification of Bacterial isolates Using Microfluidic Adaptive Channels and Multiplexed Fluorescence Microscopy doi: <a title="Link to landing page via DOI" href="https://doi.org/10.1039/D4LC00325J">10.1039/D4LC00325J</a>

ClinicalTrials.gov36/100

Rapid Identification and Susceptibility Testing of Pathogens From Blood Cultures

ClinicalTrials.gov study NCT01898208. IPD Sharing: NO. Countries: 1. Publications: 1.

closedIPD-NOFeb 2026View details →

ClinicalTrials.gov36/100

Rapid Blood Culture Identification Panel in Pediatric Patients in Guatemala

ClinicalTrials.gov study NCT05314816. IPD Sharing: Not stated. Countries: 1. Publications: 1.

restrictedIPD-UNDECIDEDFeb 2026View details →

ClinicalTrials.gov36/100

Rapid Identification and Phenotypic Susceptibility Testing for Gram-Negative Bacteremia

ClinicalTrials.gov study NCT03218397. IPD Sharing: NO. Countries: 1. Publications: 1.

closedIPD-NOFeb 2026View details →

dryad32/100

Rapid and accurate species identification for ecological studies and monitoring using CRISPR-based SHERLOCK

One of the most foundational aspects of ecological studies and monitoring is accurate species identification, but cryptic speciation and observer error can confound phenotype-based identification. The CRISPR-Cas toolkit has facilitated remarkable advances in many scientific disciplines, but the fields of ecology and conservation biology have yet to fully embrace this powerful technology. The recently developed CRISPR-Cas13a platform SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) enables highly accurate taxonomic identification and has all the characteristics needed to transition to ecological and environmental disciplines. Here we conducted a series of proof of principle experiments to characterize SHERLOCK's ability to accurately, sensitively, and rapidly distinguished three fish species (two with protected status and one non-native) co-occurring in the San Francisco Estuary which are easily misidentified in the field. We improved SHERLOCK's ease of field deployment by combining its rapid isothermal amplification and CRISPR genetic identification with a minimally invasive and extraction-free DNA collection protocol as well as the option of instrument-free lateral flow detection. This approach opens the door for redefining how, where and by whom genetic identifications occur in the future.

opencc-zeroApr 2020View details →

opennotspecifiedMar 2018View details →

FIGURE 1 in A simple molecular method for rapid identification of commercially used Amblyseius and Neoseiulus species (Acari: Phytoseiidae)

FIGURE 1. Products of endonuclease digestion of the PCR products (ITS1/ITS4 primers): 1, AccB1I; 2, AspLEI; 3, SspI.

opennotspecifiedMay 2020View details →

FIG. 3 in Morphological Change during Rapid Population Expansion Confounds Leopard Frog Identifications in the Southwestern United States

FIG. 3. Distribution of morphometric characters for Rana berlandieri (Rb), uncertain individuals, and Rana yavapaiensis (Ry). Trait values are log transformed. Different letters indicate significant differences between groups based on Tukey multiple comparison tests (ANOVA, P, 0.05). Abbreviations as in Table 2.

opennotspecifiedMay 2020View details →

FIG. 4. Character states for the left and right dorsolateral folds for R in Morphological Change during Rapid Population Expansion Confounds Leopard Frog Identifications in the Southwestern United States

FIG. 4. Character states for the left and right dorsolateral folds for R. berlandieri, uncertain individuals, and R. yavapaiensis. Points along the dark line indicate individuals with the same character state for the left and right dorsolateral folds. See text for description of character states. We have applied a small amount of random noise to the points to enhance visibility.