Detecting the Minimum Limit on Wheat Stripe Rust in the Latent Period Using Proximal Remote Sensing Coupled with Duplex Real-Time PCR and Machine Learning.

Wheat stripe rust (WSR) is an airborne disease that causes severe damage to wheat. The rapid and early detection of WSR is essential for the prevention and control of this disease. The minimum detection limit (MDL) is one of the most important characteristics of quantitative methods that can be used to determine the scope and applicability of a measurement technique. Three wheat cultivars were inoculated with Puccinia striiformis f.sp. tritici (Pst), and a spectrometer was used to collect the canopy hyperspectral data, and the Pst content was obtained via a duplex real-time polymerase chain reaction (PCR) during the latent period, respectively. The disease index (DI) and molecular disease index (MDI) were calculated. The regression tree algorithm was used to determine the MDL of the Pst based on hyperspectral feature parameters. The logistic, IBK, and random committee algorithms were used to construct the classification model based on the MDL. The results showed that when the MDL was 0.7, IBK had the best recognition accuracy. The optimal model, which used the spectral feature R_2nd.dv ((the second derivative of the original hyperspectral value)) and the modeling ratio 2:1, had an accuracy of 91.67% on the testing set and 90.67% on the 10-fold cross-validation. Thus, during the latent period, the MDL of Pst was determined using hyperspectral technology as 0.7.

Liquid scintillation counting at the limit of detection in biogeosciences.

Liquid scintillation is widely used to quantify the activity of radioisotopes. We present an overview of the technique and its application to biogeosciences, particularly for turnover rate measurements. Microbial communities and their metabolism are notoriously difficult to analyze in low energy environments as biomass is exceedingly sparse and turnover rates low. Highly sensitive methods, such as liquid scintillation counting, are required to investigate low metabolic rates and conclusively differentiate them from the background noise of the respective analyzer. We conducted a series of experiments to explore the effects of luminescence, measurement time and temperature on scintillation measurements. Luminescence, the spontaneous emission of photons, disproportionally affects samples within the first few hours after sample preparation and can be minimized by following simple guidelines. Short measurement times will negatively affect liquid scintillation analysis or if background noise makes up a significant proportion of the detected events. Measurement temperature affected liquid scintillation analysis only when the temperature during the measurement reached approximately 30°C or higher, i.e. the liquid scintillation analyzer was placed in an environment without temperature control, but not in cases where chemicals were stored at elevated temperatures prior to measurement. Basic understanding on the functionality of a liquid scintillation analyzer and simple precautions prior to the measurement can significantly lower the minimum detection limit and therefore allow for determination of low turnover rates previously lost in the background noise.

Neutron Activation Analysis: An Excellent Nondestructive Analytical Technique for Trace Metal Analysis.

For proper functioning of the human body, several metals are required in different concentrations but if their concentration slightly elevates, because of any metal-contaminated environment or of other food sources, which leads to high toxicity and different chronic health issues. Different analytical techniques like atomic absorption spectroscopy, X-ray fluorescence, inductively coupled plasma- mass spectroscopy (ICP-MS) and flame atomic absorption spectroscopy are used for metals analysis present in different samples in different fields but nowadays neutron activation analysis (NAA) is preferred over other analytical techniques because it is an efficient, multi-elemental, nondestructive analytical technique having an ultralow minimum detection limit, therefore it can detect heavy metals (HMs) even if at a very trace level parts per billion (ppb) with a quite simple sample preparation technique. This technique is known as "referee technique" because of its accuracy and trustworthiness. There is a widespread use of this technique in biomedical science like in Alzheimer's disease, cancer, arthritis, metabolism study, brain tumor and in many more conditions where metals are actively present. For its typical sample sizes and due to a multitude of additional benefits, it also helps in mapping of pathophysiology of the disease. Besides all, mainly in biomedical science the biological samples can easily be analyzed irrespective of any form. In recent years NAA is preferred over other analytical techniques in several research fields, so this article focuses on the analytical technique, its general principle and recent applications.

Sputtered silicon solid phase microextraction fibers with a polydimethylsiloxane stationary phase with negligible carry-over and phase bleed.

We report the preparation of high performance, sputtered, polydimethylsiloxane (PDMS)-coated solid phase microextraction (SPME) fibers that show negligible carry-over and phase bleed. This process involves sputtering silicon onto silica fibers and functionalizing the resulting porous nanostructures with ultrathin films of vapor-deposited PDMS. Different thicknesses of silicon (0.25, 0.8, and 1.8 µm) and PDMS (8, 16, and 36 nm) were produced and their extraction efficiencies evaluated. The deposition of PDMS was confirmed by time-of-fight secondary ion mass spectrometry (ToF-SIMS), X-ray photoelectron spectroscopy (XPS), spectroscopic ellipsometry (SE), and contact angle goniometry on model, planar silicon substrates. These fibers were investigated using direct immersion SPME coupled with gas chromatography-mass spectrometry (GC-MS) analysis of a series of polycyclic aromatic hydrocarbons (PAHs), which are carcinogenic pollutants. The 1.8 µm thick silicon coating with 16 nm of PDMS (Si (1.8 µm)/PDMS (16 nm)) produced the best response among the combinations tested. Conditions for the extraction of PAHs with this fiber were optimized and its extraction performance was compared to that of a commercial 7 µm PDMS fiber. The linearity (1-110 µgL-1), repeatability (RSD%, n = 3) (17% ave.), and minimum detection limits (0.6-1.5 µgL-1) of the sputtered fibers were determined and found to be superior to the commercial 7 µm PDMS fiber in many respects. Carry-over and phase bleed from commercial PDMS-based SPME fibers are two of their major drawbacks, which decrease their lifetimes and usefulness. Minimal carry-over and phase bleed were observed for our sputtered PDMS-coated fibers. In particular, our fiber only shows 12% of the phase bleed of the comparable commercial fiber. In addition, it shows no carry-over for analytes with retention times greater than pyrene, and only 5% of the carry-over of the other analytes. Our fibers could be used for at least 300 injections without any significant loss of performance.

A Trace C2H2 Sensor Based on an Absorption Spectrum Technique Using a Mid-Infrared Interband Cascade Laser.

In this study, tunable diode laser absorption spectroscopy (TDLAS) combined with wavelength modulation spectroscopy (WMS) was used to develop a trace C2H2 sensor based on the principle of gas absorption spectroscopy. The core of this sensor is an interband cascade laser that releases wavelength locks to the best absorption line of C2H2 at 3305 cm-1 (3026 nm) using a driving current and a working temperature control. As the detected result was influenced by 1/f noise caused by the laser or external environmental factors, the TDLAS-WMS technology was used to suppress the 1/f noise effectively, to obtain a better minimum detection limit (MDL) performance. The experimental results using C2H2 gas with five different concentrations show a good linear relationship between the peak value of the second harmonic signal and the gas concentration, with a linearity of 0.9987 and detection accuracy of 0.4%. In total, 1 ppmv of C2H2 gas sample was used for a 2 h observation experiment. The data show that the MDL is low as 1 ppbv at an integration time of 63 s. In addition, the sensor can be realized by changing the wavelength of the laser to detect a variety of gases, which shows the flexibility and practicability of the proposed sensor.

Performance comparison of two Olympus InnovX handheld x-ray analyzers for feasibility of measuring arsenic in skin in vivo - Alpha and Delta models.

The Figure-Of-Merit (FOM) performance, a combination of detection limit and dose, is compared between two generations of handheld X-Ray Fluorescence (XRF) spectrometers for the feasibility of in vivo XRF measurement of arsenic (As) in skin. The Olympus InnovX Delta model analyzer (40 kVp using either 37 or 17µA) was found to show improvements in Minimum Detection Limit (MDL) using arsenic As-doped skin calibration phantoms with bulk tissue backing, when compared to the first generation InnovX Alpha model (40kVp, 20µA) in 120s measurements. Differences between two different definitions of MDL are discussed. On the Delta system, an MDL of (0.462±0.002) µg/g As was found in phantoms, with a nylon backing behind to mimic bulk tissue behind skin. The equivalent and effective doses were found to be (10±2) mSv and ~7×10-3µSv respectively for the Alpha and (15±4) mSv and ~8×10-3µSv respectively for the Delta system in 120s exposures. Combining MDL and effective dose, a lower (better) FOM was found for the Delta, (1.7±0.4) ppm mSv1/2, compared to (4.4±0.5) ppm mSv1/2 for the Alpha model system. The Delta analyzer demonstrates improved overall system performance for a rapid 2-min measurement in As skin phantoms, such that it can be considered for use in populations exposed to arsenic.

Performance tests of a large volume cerium tribromide (CeBr3) scintillation detector.

The response of a large cylindrical 76mm×76mm (height×diameter) cerium tribromide (CeBr3) detector was measured for prompt gamma rays. The total intrinsic activity of the CeBr3 detector, which was measured over 0.33-3.33MeV range, was found to be 0.022±0.001 counts/s/cm(3). The partial intrinsic activity ( due to (227)Ac contamination), was measured over a energy range of 1.22-2.20MeV energy, was found to be 0.007±0.001 counts/s/cm(3). Compared to intrinsic activities of LaBr3:Ce and LaCl3:Ce detectors of equivalent volume, the CeBr3 detector has 7-8 times less total intrinsic activity. The detector response for low energy prompt gamma rays was measured over 0.3-0.6MeVgamma energy range using a portable neutron generator-based Prompt Gamma Neutron Activation Analysis (PGNAA) setup. The experimental yield of boron, cadmium and mercury prompt gamma-rays was measured from water samples contaminated with 0.75-2.5wt% mercury, 0.31-2.50wt% boron, and 0.0625-0.500wt% cadmium, respectively. An excellent agreement has been observed between the calculated and experimental yields of the gamma rays. Also minimum detection limit (MDC) of the CeBr3 detector was measured for boron, cadmium and mercury samples. The CeBr3 detector has 23% smaller value of MDCB and 18% larger value of MDCCd than those of a LaBr3:Ce detector of equivalent size. This study has shown that CeBr3 detector has an excellent response for the low energy prompt gamma-rays with almost an order of magnitude low intrinsic activity as compared to LaCl3:Ce and LaBr3:Ce detectors of equivalent volume.

A phantom-based feasibility study for detection of gadolinium in bone in-vivo using X-ray fluorescence.

Gadolinium (Gd) based contrast agents have been commonly used over the past three decades to improve contrast in magnetic resonance imaging. These complexes, originally thought to be stable and clear from the body shortly after administration, have been shown to dissociate to a small extent and deposit in organs such as bone. A safe and non-invasive method for measuring Gd in bone is necessary for further exploring Gd retention in the body following the administration of a contrast agent. A feasibility study using a K x-ray fluorescence (K-XRF) system to measure Gd in human tibias was investigated. Bone phantoms mimicking human tibia were created with Gd concentrations ranging from 0 to 120ppm. The minimum detection limit (MDL) was calculated from 20-hour and 7-hour phantom measurements with a source activity of 0.11GBq. All MDL values were scaled to a more realistic measurement time of 30-minutes with a stronger source. Scaling arguments were based on activity ratio, measurement time, and system dead time. The MDL for a 1GBq source was estimated to be 3.60-3.64ppm, for an average range of tissue thicknesses overlaying a human tibia. For a stronger source of 5GBq and a four detector cloverleaf system, the MDL was estimated to be 1.49-1.52ppm. Determined and predicted MDLs are within the range of previous in-vitro Gd measurement data. The K-XRF system shows promising results for detecting Gd in bone and should be seriously considered for in-vivo measurements.

Multi-species sensing using multi-mode absorption spectroscopy with mid-infrared interband cascade lasers.

The application of an interband cascade laser, ICL, to multi-mode absorption spectroscopy, MUMAS, in the mid-infrared region is reported. Measurements of individual mode linewidths of the ICL, derived from the pressure dependence of lineshapes in MUMAS signatures of single, isolated, lines in the spectrum of HCl, were found to be in the range 10-80 MHz. Multi-line spectra of methane were recorded using spectrally limited bandwidths, of approximate width 27 cm-1, defined by an interference filter, and consist of approximately 80 modes at spectral locations spanning the 100 cm-1 bandwidth of the ICL output. Calibration of the methane pressures derived from MUMAS data using a capacitance manometer provided measurements with an uncertainty of 1.1 %. Multi-species sensing is demonstrated by the simultaneous detection of methane, acetylene and formaldehyde in a gas mixture. Individual partial pressures of the three gases are derived from best fits of model MUMAS signatures to the data with an experimental error of 10 %. Using an ICL, with an inter-mode interval of ~10 GHz, MUMAS spectra were recorded at pressures in the range 1-10 mbar, and, based on the data, a potential minimum detection limit of the order of 100 ppmv is estimated for MUMAS at atmospheric pressure using an inter-mode interval of 80 GHz.

Combination of high spatial resolution and low minimum detection limit using thinned specimens in cutting-edge electron probe microanalysis.

The effect of sample thickness on the spatial resolution and minimum detection limit (MDL) has been investigated for field-emission electron probe microanalysis with wavelength dispersive X-ray spectroscopy (FE-EPMA-WDX). Indium gallium phosphide samples thinned to thicknesses of about 100, 130, 210, 310, and 430 nm provided effective thin-sample FE-EPMA-WDX in the resolution range of 40-350 nm and MDL range of 13,000-600 ppm (mass). A comparison of the FE-EPMA results for thin and bulk samples demonstrated that thin-sample FE-EPMA can achieve both higher sensitivity and better spatial resolution than is possible using bulk samples. Most of the X-rays that determine the MDL are generated in a surface region of the sample with a depth of approximately 300 nm. The spatial resolution and MDL can be tuned by the sample thickness. Furthermore, analysis of small amounts of Cl in SiO2 indicated that thin-sample FE-EPMA can realize a spatial resolution and MDL of 41 nm and 446 ppm at Iprob=50 nA, respectively, whereas bulk-sample FE-EPMA offers a resolution of only 348 nm and MDL of 426 ppm.

Determinação do limite mínimo de detecção da técnica de Nested-PCR para os poliomavírus JC e BK / Assessment of minimum detection limit of Nested-PCR for JC and BK polyomaviruses

Introduction: Polyomaviruses (BKV and JCV) cause infection mainly in immunocompromised adults. A sensitive and specific diagnosis tool is fundamental to demonstrate the BKV and JCV infections. Nowadays many laboratories are using a PCR technique for detecting polyomaviruses genome in clinical samples. In this context, the purpose of this study is to determine the threshold of detection of the nested-PCR for polyomaviruses JC and BK. Methods: Serial dilutions of the samples of BKV and JCV of known concentration (100 copies/mL, 50 copies/mL, 25 copies/mL, 10 copies/mL, 5 copies/mL, and 1 copy/ml) were subjected to the technique of nested-PCR. All dilutions were tested 11 times to determine the minimum detection limit. Results: The minimum detection limit of the nested-PCR for JC and BK viruses was 25 copies/mL. This dilution (25 copies/mL) showed 100% PCR positive reaction. Furthermore, we found that weak positive results were obtained at dilutions of 1,5 and 10 copies/mL in some repetitions. Dilutions of 25, 50, and 100 copies/mL always had very positive results. Conclusions: These values are similar to those reported in other studies, contributing to the indication of this PCR for potential diagnostic purposes.

Introdução: Os poliomavírus (JCV e BKV) causam infecções principalmente em adultos imunocomprometidos. Um diagnóstico sensível e específico é de fundamental importância para os pacientes portadores de JCV e BKV. Atualmente alguns laboratórios têm utilizado a técnica de PCR para a detecção do material genético destes vírus em amostras clínicas. Assim, o objetivo deste estudo é determinar o limite mínimo de detecção da técnica de nested-PCR para os poliomavírus JC e BK. Métodos: Diluições seriadas (100 cópias/mL; 50 cópias/mL; 25 cópias/mL; 10 cópias/mL; 5 cópias/mL e 1 cópia/mL) de controles positivos comerciais de JCV e BKV com concentrações conhecidas foram submetidas à técnica de nested-PCR semi-duplex. Todas as diluições foram testadas 11 vezes para determinação do limite mínimo de detecção. Resultados: O limite mínimo de detecção da reação de nested-PCR para os vírus JC e BK foi de 25 cópias/mL para ambos, com 100% de positividade das diluições testadas na reação de PCR. Ainda, pudemos observar que resultados positivos fracos foram obtidos nas diluições de 1, 5 e 10 cópias/mL em algumas das repetições realizadas. As diluições de 25, 50 e 100 cópias/mL sempre obtiveram resultado rancamente positivo. Conclusões: Estes valores são semelhantes aos relatados em outros estudos, contribuindo para a indicação desta reação de PCR para potenciais fins diagnósticos.

Pharmaceuticals and personal care products found in the Great Lakes above concentrations of environmental concern.

The monitoring of pharmaceuticals and personal care products (PPCPs) has focused on the distribution in rivers and small lakes, but data regarding their occurrence and effects in large lake systems, such as the Great Lakes, are sparse. Wastewater treatment processes have not been optimized to remove influent PPCPs and are a major source of PPCPs in the environment. Furthermore, PPCPs are not currently regulated in wastewater effluent. In this experiment we evaluated the concentration, and corresponding risk, of PPCPs from a wastewater effluent source at varying distances in Lake Michigan. Fifty-four PPCPs and hormones were assessed on six different dates over a two-year period from surface water and sediment samples up to 3.2 km from a wastewater treatment plant and at two sites within a harbor. Thirty-two PPCPs were detected in Lake Michigan and 30 were detected in the sediment, with numerous PPCPs being detected up to 3.2 km away from the shoreline. The most frequently detected PPCPs in Lake Michigan were metformin, caffeine, sulfamethoxazole, and triclosan. To determine the ecological risk, the maximum measured environmental concentrations were compared to the predicted no-effect concentration and 14 PPCPs were found to be of medium or high ecological risk. The environmental risk of PPCPs in large lake systems, such as the Great Lakes, has been questioned due to high dilution; however, the concentrations found in this study, and their corresponding risk quotient, indicate a significant threat by PPCPs to the health of the Great Lakes, particularly near shore organisms.

Determinação do limite mínimo de detecção da técnica de PCR “nested” para o vírus da hepatite B (HBV) / Evaluation of minimum detection limit to hepatitis B virus (HBV) PCR “nested”

Mundialmente, a hepatite pelo vírus B (HBV) é considerada um dos maiores problemas de saúde pública, apesar da vacinação. A Organização Mundial da Saúde (OMS) estima que mais de 2 bilhões de pessoas estejam infectadas pelo HBV. O Brasil é classificado como área de incidência intermediária pela OMS. No entanto, estudos de prevalência detectaram diferenças de índices de infecção nas regiões geográficas: 8% na região Amazônica, 2,5% nas regiões Centro-Oeste e Nordeste, 2% na Sudeste e 1% na região Sul. Um diagnóstico sensível e específico é de fundamental importância para os pacientes portadores do HBV. O objetivo deste estudo foi determinar o limite mínimo de detecção da técnica de PCR “nested” “in house” para o HBV. Diluições seriadas de uma amostra quantificada de HBV (1000 cópias/mL; 750 cópias/mL; 500 cópias/mL; 250 cópias/mL) foram submetidas à técnica de PCR “nested”. O alvo da amplificação por PCR foi a região do core e pré-core do vírus. Para extração dos ácidos nucléicos da amostra foi empregado o kit comercial QIAmp. O limite mínimo de detecção encontrado foi de 500 cópias/mL ou 10 cópias por reação de PCR.

All over the world, the hepatitis B virus (HBV) is considered one of the major problems of public health, despite vaccination. World Health Organization (WHO) estimates that more than 2 billions of persons are infected by HBV. Brazil is classified as an area of intermediary incidence by WHO. However, prevalence studies have detected differences of infection indexes in geographic regions: 8% in the Amazonian region, 2,5% in middle-west and Northeast, 2% in Southeast and 1% in South. A sensitive and specific diagnosis is very important to the HBV carrier patients. The aim of this study was to determine the minimum limit of detection of the nested PCR in house technique for HBV. Serial dilutions of one quantified sample of HBV (1000 copies/mL; 750 copies/mL; 500 copies/mL; 250 copies/mL) were submitted to a nested PCR. The target of PCR was viral core and pre-core region. Commercial kit, QiAmp, was employed to purify nucleic acids from the sample. The minimum detection limit found was 500 copies/mL or 10 copies per PCR reaction.