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Scientific Reports May 2022Herbarium specimens are dried plants mounted onto paper. They are used by a limited number of researchers, such as plant taxonomists, as a source of information on...
Herbarium specimens are dried plants mounted onto paper. They are used by a limited number of researchers, such as plant taxonomists, as a source of information on morphology and distribution. Recently, digitised herbarium specimens have begun to be used in comprehensive research to address broader issues. However, some specimens have been misidentified, and if used, there is a risk of drawing incorrect conclusions. In this study, we successfully developed a system for identifying taxon names with high accuracy using an image recognition system. We developed a system with an accuracy of 96.4% using 500,554 specimen images of 2171 plant taxa (2064 species, 9 subspecies, 88 varieties, and 10 forms in 192 families) that grow in Japan. We clarified where the artificial intelligence is looking to make decisions, and which taxa is being misidentified. As the system can be applied to digitalised images worldwide, it is useful for selecting and correcting misidentified herbarium specimens.
Topics: Artificial Intelligence; Humans; Japan; Plants
PubMed: 35577859
DOI: 10.1038/s41598-022-11450-y -
Influenza and Other Respiratory Viruses Nov 2011Most clinical samples collected for diagnostic influenza testing and monitoring require refrigerated or frozen storage or shipment, which imparts logistic and cost...
BACKGROUND
Most clinical samples collected for diagnostic influenza testing and monitoring require refrigerated or frozen storage or shipment, which imparts logistic and cost burdens. The ability to store and ship dried clinical specimens under ambient conditions for influenza testing would significantly reduce costs and protect samples from improper storage or equipment failure, especially in remote or resource-limited areas.
OBJECTIVES
To evaluate the collection and storage of dried clinical samples on a transport matrix (ViveST™, ST) for influenza RNA testing by real-time reverse-transcription PCR (RT-PCR).
METHODS
Viral transport medium from swab or sputum samples was applied to ST, dried, and stored under ambient conditions from 2 days to 6 months. Additional aliquots of samples were frozen. Testing of frozen and ST-stored samples was performed using the WHO/CDC real-time influenza A (H1N1) RT-PCR protocol and compared to the Luminex xTAG RVP assay.
RESULTS
ST-stored samples yielded slightly higher threshold cycle values (median 2·54 cycles) compared to frozen samples tested in parallel. This difference was consistent regardless of viral input. There was no significant difference in signal recovery between samples stored for 1 week versus samples stored for 3 weeks, or from three samples stored for 6 months. Qualitatively, clinical specimens stored on ST were 100% concordant (36/36) with frozen samples for detecting the presence of influenza A RNA.
CONCLUSION
ST-processed dried specimens produced similar rates of seasonal or novel 2009 HIN1 influenza RNA detection compared to conventional sample processing and thus presents a viable alternative to refrigerated or frozen samples.
Topics: Humans; Influenza A Virus, H1N1 Subtype; Influenza A virus; Influenza, Human; RNA, Viral; Real-Time Polymerase Chain Reaction; Specimen Handling
PubMed: 21668673
DOI: 10.1111/j.1750-2659.2011.00253.x -
Journal of Diabetes Science and... Sep 2018Microsampling techniques are alternative methods to venous sampling for obtaining blood for measurement of circulating biomarkers, offering the convenience of reduced...
BACKGROUND
Microsampling techniques are alternative methods to venous sampling for obtaining blood for measurement of circulating biomarkers, offering the convenience of reduced sample volume and elimination of the need for phlebotomists. Dried blood spot (DBS) microsampling methods have been used for many years while more recently a volumetric absorptive microsampling device (VAMS™) has been introduced. In diabetes mellitus, circulating C-peptide is commonly used as an indicator of endogenous insulin secretion and clinical measurement can aid in diagnosis as well as informing on therapy. This pilot study investigated the effectiveness of microsampling collection of capillary blood for measurement of C-peptide.
METHODS
Capillary blood was collected into capillary tubes and centrifuged for plasma samples. Simultaneous samples were also collected using both microsampling methods (DBS and VAMS). Blood from both microsamplers was extracted prior to assaying for C-peptide alongside the corresponding plasma samples, using specific immunoassays and results obtained from microsampling compared to the reference plasma concentrations. Stability was determined by collecting duplicate DBS and VAMS and assaying both in a single assay after storing one at -20°C immediately and one at room temperature for 48 hours post-collection.
RESULTS
Good agreement was observed between C-peptide concentrations in plasma and equivalent DBS and VAMS samples ( R = .929 and .9231, DBS and VAMS, respectively), with mean differences of 75.7 and 8.4 pmol/L observed for DBS and VAMS. Small decreases in C-peptide of 11.6% and 0.1% were observed after 48 hours storage for DBS and VAMS, respectively.
CONCLUSIONS
C-peptide collected using DBS and VAMS showed good agreement with reference plasma concentrations, suggesting both would be an effective microsampling method for collection and measurement of C-peptide.
Topics: Blood Specimen Collection; C-Peptide; Diabetes Mellitus; Dried Blood Spot Testing; Healthy Volunteers; Humans; Pilot Projects
PubMed: 29521111
DOI: 10.1177/1932296818763464 -
International Journal of Neonatal... Jun 2020Monitoring of patients with inherited metabolic disorders (IMDs) using dried blood spot (DBS) specimens has been routinely used since the inception of newborn screening... (Review)
Review
Monitoring of patients with inherited metabolic disorders (IMDs) using dried blood spot (DBS) specimens has been routinely used since the inception of newborn screening (NBS) for phenylketonuria in the 1960s. The introduction of flow injection analysis tandem mass spectrometry (FIA-MS/MS) in the 1990s facilitated the expansion of NBS for IMDs. This has led to increased identification of patients who require biochemical monitoring. Monitoring of IMD patients using DBS specimens is widely favoured due to the convenience of collecting blood from a finger prick onto filter paper devices in the patient's home, which can then be mailed directly to the laboratory. Ideally, analytical methodologies with a short analysis time and high sample throughput are required to enable results to be communicated to patients in a timely manner, allowing prompt therapy adjustment. The development of ultra-performance liquid chromatography (UPLC-MS/MS), means that metabolic laboratories now have the capability to routinely analyse DBS specimens with superior specificity and sensitivity. This advancement in analytical technology has led to the development of numerous assays to detect analytes at low concentrations (pmol/L) in DBS specimens that can be used to monitor IMD patients. In this review, we discuss the pre-analytical, analytical and post-analytical variables that may affect the final test result obtained using DBS specimens used for monitoring of patients with an IMD.
PubMed: 33073023
DOI: 10.3390/ijns6020026 -
Frontiers in Plant Science 2019The world's herbaria collectively house millions of diverse plant specimens, including endangered or extinct species and type specimens. Unlocking genetic data from the...
The world's herbaria collectively house millions of diverse plant specimens, including endangered or extinct species and type specimens. Unlocking genetic data from the typically highly degraded DNA obtained from herbarium specimens was difficult until the arrival of high-throughput sequencing approaches, which can be applied to low quantities of severely fragmented DNA. Target enrichment involves using short molecular probes that hybridise and capture genomic regions of interest for high-throughput sequencing. In this study on herbariomics, we used this targeted sequencing approach and the Angiosperms353 universal probe set to recover up to 351 nuclear genes from 435 herbarium specimens that are up to 204 years old and span the breadth of angiosperm diversity. We show that on average 207 genes were successfully retrieved from herbarium specimens, although the mean number of genes retrieved and target enrichment efficiency is significantly higher for silica gel-dried specimens. Forty-seven target nuclear genes were recovered from a herbarium specimen of the critically endangered St Helena boxwood, , collected in 1815. Herbarium specimens yield significantly less high-molecular-weight DNA than silica gel-dried specimens, and genomic DNA quality declines with sample age, which is negatively correlated with target enrichment efficiency. Climate, taxon-specific traits, and collection strategies additionally impact target sequence recovery. We also detected taxonomic bias in targeted sequencing outcomes for the 10 most numerous angiosperm families that were investigated in depth. We recommend that (1) for species distributed in wet tropical climates, silica gel-dried specimens should be used preferentially; (2) for species distributed in seasonally dry tropical climates, herbarium and silica gel-dried specimens yield similar results, and either collection can be used; (3) taxon-specific traits should be explored and established for effective optimisation of taxon-specific studies using herbarium specimens; (4) all herbarium sheets should, in future, be annotated with details of the preservation method used; (5) long-term storage of herbarium specimens should be in stable, low-humidity, and low-temperature environments; and (6) targeted sequencing with universal probes, such as Angiosperms353, should be investigated closely as a new approach for DNA barcoding that will ensure better exploitation of herbarium specimens than traditional Sanger sequencing approaches.
PubMed: 31620145
DOI: 10.3389/fpls.2019.01102 -
Data in Brief Jun 2024This dataset presents a comprehensive collection of images representing both dried and live samples from eight distinct Thai cannabis classes. The dataset includes a...
This dataset presents a comprehensive collection of images representing both dried and live samples from eight distinct Thai cannabis classes. The dataset includes a total of 14,094 images, with images depicting dried and healthy specimens. These images serve as a valuable resource for researchers engaged in botanical exploration, machine learning, and computer vision studies. Additionally, the dataset facilitates investigations into the medicinal properties of Thai cannabis. Interdisciplinary collaboration is encouraged, providing opportunities for innovative insights spanning biology, horticulture, and data science. Beyond fundamental research, this dataset holds practical implications for agriculture, technology development, and disease prevention, offering insights into both dried and live states of Thai cannabis plants across various strains.
PubMed: 38516281
DOI: 10.1016/j.dib.2024.110292 -
International Journal of Legal Medicine Jul 2013Ethyl glucuronide (EtG) and ethyl sulfate (EtS) are non-oxidative minor metabolites of ethanol. They are detectable in various body fluids shortly after initial...
BACKGROUND
Ethyl glucuronide (EtG) and ethyl sulfate (EtS) are non-oxidative minor metabolites of ethanol. They are detectable in various body fluids shortly after initial consumption of ethanol and have a longer detection time frame than the parent compound. They are regarded highly sensitive and specific markers of recent alcohol uptake. This study evaluates the determination of EtG and EtS from dried blood spots (DBS), a simple and cost-effective sampling method that would shorten the time gap between offense and blood sampling and lead to a better reflectance of the actual impairment.
METHODS
For method validation, EtG and EtS standard and quality control samples were prepared in fresh human heparinized blood and spotted on DBS cards, then extracted and measured by an LC-ESI-MS/MS method. Additionally, 76 heparinized blood samples from traffic offense cases were analyzed for EtG and EtS as whole blood and as DBS specimens. The results from these measurements were then compared by calculating the respective mean values, by a matched-paired t test, by a Wilcoxon test, and by Bland-Altman and Mountain plots.
RESULTS AND DISCUSSION
Calibrations for EtG and EtS in DBS were linear over the studied calibration range. The precision and accuracy of the method met the requirements of the validation guidelines that were employed in the study. The stability of the biomarkers stored as DBS was demonstrated under different storage conditions. The t test showed no significant difference between whole blood and DBS in the determination of EtG and EtS. In addition, the Bland-Altman analysis and Mountain plot confirmed that the concentration differences that were measured in DBS specimens were not relevant.
Topics: Alcohol Drinking; Biomarkers; Blood Chemical Analysis; Blood Stains; Chromatography, Liquid; Forensic Toxicology; Glucuronates; Humans; Mass Spectrometry; Specimen Handling; Sulfuric Acid Esters
PubMed: 23283405
DOI: 10.1007/s00414-012-0815-2 -
MSphere Aug 2021Fingerprick blood spotted onto filter paper offers an alternative to venous blood for use in population-based surveillance because it is comparatively inexpensive,... (Comparative Study)
Comparative Study
Fingerprick blood spotted onto filter paper offers an alternative to venous blood for use in population-based surveillance because it is comparatively inexpensive, acceptable, and easy to manage in the field. Prior studies have shown excellent agreement for immunoglobulin G (IgG) antibody detection from dried blood spots (DBS) and venous blood samples. However, much of this evidence is from high-income settings or laboratories where the samples were unlikely to be exposed to extreme temperatures and humidity, factors known to degrade DBS. We report the diagnostic accuracy of DBS collected using HemaSpot HF devices against venous sera in measuring measles- and rubella-specific IgG antibodies in a household serosurvey conducted in two districts in India. Paired serum and DBS samples collected by fingerprick were collected from women aged 15 to 50 years enrolled in a serosurvey in Palghar District of Maharashtra and Kanpur Nagar District of Uttar Pradesh in India. Specimen quality and volume were assessed in the laboratory. Samples were tested for antimeasles and antirubella IgG antibodies by an enzyme-linked immunosorbent assay (ELISA) (Euroimmun). Sensitivity of antibody detection by DBS was greater than 98%, and specificity was 90% and 98%, for measles and rubella IgG, respectively. Antibody concentrations were strongly correlated between paired specimens with adequate volume (measles = 0.94; rubella = 0.89). Although correlation was poor if DBS specimens had lower volumes, impact on qualitative results was minimal. This study showed DBS collected with HemaSpot HF devices can generate highly accurate results of measles- and rubella-specific IgG compared to sera in community-based surveys when protocols are optimized for DBS specimens. Dried blood spot (DBS) collection provides an easy, practical, and acceptable alternative to venous blood collection, especially for community-based studies, provided that results from DBS are accurate. We demonstrated high sensitivity and specificity for measles- and rubella-specific immunoglobulin G (IgG) with DBS collected via HemaSpot HF devices compared to serum samples. This is one of the largest community-based diagnostic accuracy studies of measles and rubella antibody testing with DBS and the first application we are aware of using HemaSpot HF device for measles and rubella serology. Results support the use of DBS in community-based serosurveillance.
Topics: Adolescent; Adult; Antibodies, Viral; Blood Specimen Collection; Dried Blood Spot Testing; Enzyme-Linked Immunosorbent Assay; Female; Humans; Immunoglobulin G; Immunoglobulin M; India; Measles; Middle Aged; Reproducibility of Results; Rubella; Seroepidemiologic Studies; Young Adult
PubMed: 34259557
DOI: 10.1128/mSphere.01330-20 -
Scientific Reports Mar 2020Although hepatitis B (HBV) and C (HCV) virus infections are still global health issues, measuring sero-markers by standard venipuncture is challenging in areas limited...
Although hepatitis B (HBV) and C (HCV) virus infections are still global health issues, measuring sero-markers by standard venipuncture is challenging in areas limited with the adequate human resources and basic infrastructure. This study aimed to inform the usefulness of dried blood spot (DBS) sampling technique for epidemiological study of HBV and HCV in the resources limited areas. We compared specimen recovery rate expressed as analytical sensitivity ratio of HBsAg, HBcAb and anti-HCV between serum specimens and DBS samples (HemaSpot vs Whatman903). Sensitivity ratio was calculated as the ratio of the measured value from DBS to the measured value from serum. Then both the qualitative and quantitative comparisons of HBsAg detection by DBS were done using Cambodian samples. HBsAg, HBcAb and anti-HCV sensitivity ratios for the highest sample dilution (8-fold) were 31.2:1, 38.9:1 and 32.0:1 for Whatman903 card and 17.6:1, 23.5:1 and 26.3:1 for HemaSpot respectively. Detection efficacy of HemaSpot (80%) was not inferior to Whatman903 (60%) after 1 month storage, and no significant difference in any hepatitis virus sero-markers was observed in HemaSpot-spotted patient samples stored for 2 weeks at -25 °C and 29 °C. All reference HemaSpot -spotted 400 HBsAg sero-negative samples showed negative. Sensitivity and specificity of HBsAg in HemaSpot were 92.3% and 100%. The recovery expressed as analytical sensitivity ratio of HBsAg, HBcAb and anti-HCV of HemaSpot specimen were not inferior to Whatman903. Therefore, DBS with its usefulness proved as an acceptable tool for large epidemiological study of HBV and HCV in resources limited remote area.
Topics: Aged; Aged, 80 and over; Biomarkers; Dried Blood Spot Testing; Female; Hepatitis B; Hepatitis B Core Antigens; Hepatitis B Surface Antigens; Hepatitis C; Hepatitis C Antibodies; Humans; Male; Middle Aged
PubMed: 32123234
DOI: 10.1038/s41598-020-60703-1 -
Epigenetics Aug 2013Epigenome-wide association studies (EWAS) are being extensively performed to identify epigenetic variants associated to complex diseases. However, EWAS may identify... (Review)
Review
Epigenome-wide association studies (EWAS) are being extensively performed to identify epigenetic variants associated to complex diseases. However, EWAS may identify variants that are disease-induced rather than disease-causal. Recent studies have highlighted the use of Guthrie cards to profile the methylome at birth, permitting researchers to find epigenetic variants present in patients before they are diagnosed with clinical disease, with the implicit suggestion that these variants are more likely to be disease causal. The use of Guthrie cards for research purposes throws up a number of ethical issues. We review here the promises and pitfalls of Guthrie cards for disease research.
Topics: Blood Specimen Collection; DNA Methylation; Dried Blood Spot Testing; Epigenesis, Genetic; Humans; Infant, Newborn
PubMed: 23880534
DOI: 10.4161/epi.25357