Absolute protein quantification based on calibrated particle counting using electrospray-differential mobility analysis

The traceability of in vitro diagnostics or drug products is based on the accurate quantification of proteins. In this study, we developed an absolute quantification approach for proteins. This method is based on calibrated particle counting using electrospray-differential mobility analysis (ES-DMA) coupled with a condensation particle counter (CPC). The absolute concentration of proteins was quantified with the observed protein particle number measured with ES-DMA-CPC, and the detection efficiency was determined by calibrators. The measurement performance and quantitative level were verified using two certificated reference materials, BSA and NIMCmAb. The linear regression fit for the detection efficiency values of three reference materials and one highly purified protein (myoglobin, BSA, NIMCmAb and fibrinogen) indicated that the detection efficiency and the particle size distribution of these proteins exhibited a linear relationship. Moreover, to explore the suitability of the detection efficiency-particle size curve for protein quantification, the concentrations of three typical proteinaceous particles, including two high molecular weight proteins (NIST reference material 8671 and D-dimer) and one protein complex (glutathione S-transferase dimer), were determined. This work suggests that this calibrated particle counting method is an efficient approach for nondestructive, rapid and accurate quantification of proteins, especially for measuring proteinaceous particles with tremendous size and without reference standards.

Simulation of radon detection efficiency with small pulse ionization chamber based on Geant4

Radon measurement is crucial in assessing the damage to the human body caused by natural radiation. Pulsed ionization chambers are effective for real-time radon measurement and have widespread applications in other radiation techniques. However, due to practical constraints such as limited space and portability concerns, it becomes imperative to consider not only the detection efficiency but also their ease of transportation. This work utilizes the Geant4 Monte Carlo simulation toolkit to characterize the detection models of small cylindrical and flat plate-type pulsed ionization chambers, and carry out a simulation study to analyze the three crucial factors that influence detection efficiency, including the geometry of the chamber, electrode size, and operating temperature. The results indicate that the cylindrical pulse ionization chamber, with a length of 8 cm and radius of 2 cm, has the best detection efficiency and portability in terms of geometric dimensions, achieving a detection efficiency of (58 ± 4)%. Meanwhile, the flat plate pulse ionization chamber, with dimensions of 7 cm in length and 3 cm in width, achieves the best detection efficiency and portability, with a detection efficiency of (54 ± 3)%. In terms of electrode wire size, the cylindrical ionization chamber electrode wire with a length of 7 cm and a radius of 2.5 mm was optimal with a detection efficiency of (59 ± 4)%. In terms of operating temperature, the detection efficiency of the flat-plate pulsed ionization chamber was the highest at 30 °C, which was (58 ± 4)%, and that of the cylindrical pulsed ionization chamber was the highest at 20 °C, which was (63 ± 4)%. By analyzing the influencing factors of the detection efficiency of the pulsed ionization chamber, it has a certain reference value and guiding significance for the research and design of small pulsed ionization chamber detectors for radon measuring instruments.

[Comparison of the efficiency of different etiological assays for detection of Schistosoma japonicum infections in wild mice]

OBJECTIVE

To compare the efficiency of multiple etiological techniques for detection of Schistosoma japonicum infections in wild mice, so as to provide technical supports to assessment of schistosomiasis transmission risk.

METHODS

Wild mice were captured with baited traps at night in Oncomelania hupensis snail-infested settings in schistosomiasis-endemic foci of Anhui Province from October to November, 2022. S. japonicum infections were detected in wild mice using microscopy of mouse liver tissues, microscopy of mouse mesenteric tissues, microscopy of mouse liver tissue homogenates, miracidial hatching test of mouse liver tissue homogenates, Kato-Katz technique and miracidial hatching test of mouse stool samples alone and in combinations. Identification of S. japonicum eggs or miracidia by any of these six assays was defined as an infection. The sensitivity of six assays alone or in combinations was compared for detection of S. japonicum infections in wild mice.

RESULTS

A total of 1 703 wild mice were captured, with 366 wild mice detected positive for S. japonicum (21.49%). There were significant differences in the prevalence of S. japonicum infections in wild mice by six assays (Q = 529.33, P < 0.001) and in the sensitivity of six assays for detection of S. japonicum infections in wild mice (χ2 = 527.78, P < 0.001). In addition, the combination of microscopy of mouse liver tissues and mesenteric tissues, combination of microscopy of mouse liver tissues and liver tissue homogenates and combination of microscopy of mouse liver tissues, microscopy of mesenteric tissues, microscopy of liver tissue homogenates and Kato-Katz technique showed 86.61%, 87.16% and 97.27% sensitivities for detection of S. japonicum infections in wild mice, respectively.

CONCLUSIONS

Diverse etiological assays show various efficiencies for detection of S. japonicum infections in wild mice. Combination of microscopy of mouse liver tissues and microscopy of mesenteric tissues, and combination of microscopy of mouse liver tissues and microscopy of liver tissue homogenates are potential approaches for field detection of S. japonicum infections in wild mice.

[Preliminary application of recombinase -aided amplification in detection of Clonorchis sinensis metacercariae in freshwater fish]

OBJECTIVE

To evaluate the performance of recombinase-aided amplification (RAA) assay in detection of Clonorchis sinensis metacercariae in freshwater fish samples, so as to provide insights into standardization and field application of this assay.

METHODS

Wild freshwater fish samples were collected in the rivers of administrative villages where C. sinensis-infected residents lived in Jiangyan District, Xinghua County and Taixing County of Taizhou City, Jiangsu Province from June to September 2022. Genomic DNA was extracted from six freshwater fish specimens (5 g each) containing 0, 1, 2, 4, 8 and 16 C. sinensis metacercariae for fluorescent RAA assay, and the diagnostic sensitivity was evaluated. Fluorescent RAA assay was performed with genomic DNA from C. sinensis, Metorchis orientalis, Haplorchis pumilio and Centrocestus formosanus metacercariae as templates to evaluate its cross-reactions. In addition, the detection of fluorescent RAA assay and direct compression method for C. sinensis metacercariae was compared in field-collected freshwater fish samples.

RESULTS

Positive amplification was found in fresh-water fish specimens containing different numbers of C. sinensis metacercariae, and fluorescent RAA assay was effective to detect one C. sinensis metacercaria in 5 g freshwater fish specimens within 20 min. Fluorescent RAA assay tested negative for DNA from M. orientalis, H. pumilio and C. formosanus metacercariae. Fluorescent RAA assay and direct compression method showed 5.36% (93/1 735) and 2.88% (50/1 735) detection rates for C. sinensis metacercariae in 1 735 field-collected freshwater fish samples, with a statistically significant difference seen (χ2 = 478.150, P < 0.001). There was a significant difference in the detection of C. sinensis metacercariae in different species of freshwater fish by both the direct compression method (χ2 = 11.20, P < 0.05) and fluorescent RAA assay (χ2 = 20.26, P < 0.001), and the detection of C. sinensis metacercariae was higher in Pseudorasbora parva than in other fish species by both the direct compression method and fluorescent RAA assay (both P values < 0.05).

CONCLUSIONS

Fluorescent RAA assay has a high sensitivity for detection of C. sinensis metacercariae in freshwater fish samples, and has no cross-reactions with M. orientalis, H. pumilio or C. formosanus metacercariae. Fluorescent RAA assay shows a higher accuracy for detection of C. sinensis infections in field-collected freshwater fish than the direct compression method.

Urban landscape-level biodiversity assessments of aquatic and terrestrial vertebrates by environmental DNA metabarcoding

Globally, expansive urbanization profoundly alters natural habitats and the associated biota. Monitoring biodiversity in cities can provide essential information for conservation management, but the complexity of urban landscapes poses serious challenges to conventional observational and capture-based surveys. Here we assessed pan-vertebrate biodiversity, including both aquatic and terrestrial taxa, using environmental DNA (eDNA) sampled from 109 water sites across Beijing, China. Using eDNA metabarcoding with a single primer set (Tele02), we detected 126 vertebrate species, including 73 fish, 39 birds, 11 mammals, and 3 reptiles belonging to 91 genera, 46 families, and 22 orders. The probability of detection from eDNA varied substantially among species and was related to their lifestyle, as shown by the greater detectability of fish compared to that of terrestrial and arboreal (birds and mammals) groups, as well as the greater detectability of water birds compared to that of forest birds (Wilcoxon rank-sum test p = 0.007). Furthermore, the eDNA detection probabilities across all vertebrates (Wilcoxon rank-sum test p = 0.009), as well as for birds (p < 0.001), were higher at lentic sites in comparison with lotic sites. Also, the detected biodiversity was positively correlated with lentic waterbody size for fish (Spearman p = 0.012), but not for other groups. Our results demonstrate the capacity of eDNA metabarcoding to efficiently surveil diverse vertebrate communities across an extensive spatial scale in heterogenous urban landscapes. With further methodological development and optimization, the eDNA approach has great potential for non-invasive, efficient, economic, and timely assessments of biodiversity responses to urbanization, thus guiding city ecosystem conservation management.

Characterization of a 4παβ(LS)-γ(HPGe) prototype system for low-background measurements

A ground-level prototype system for low-background measurements was developed and tested. The system consists of a high-purity germanium (HPGe) detector used for detecting γ rays and coupled to a liquid scintillator (LS) used for detecting α and β particles. Both detectors are surrounded by shielding materials and anti-cosmic detectors ("veto") used to suppress background events. The energy and timestamp of detected α, β and γ emissions are recorded event-by-event and analyzed offline. By requiring timing coincidence between the HPGe and LS detectors, background events originating from outside the volume of the measured sample can be effectively rejected. The system performance was evaluated using liquid samples containing known activities of an α emitter (²⁴¹Am) or a β emitter (⁶⁰Co) whose decays are accompanied by γ rays. The LS detector was found to provide a solid angle of almost 4π for α and β particles. Compared to the traditional γ-singles mode, operating the system in coincidence mode (i.e., α-γ or β-γ) reduced the background counts by a factor of ∼100. Consequently, the minimal detectable activity for ²⁴¹Am and ⁶⁰Co was improved by a factor of 9, being 4 mBq and 1 mBq for an 11-d measurement, respectively. Furthermore, by applying a spectrometric cut in the LS spectrum that corresponds to α emission from ²⁴¹Am, a background reduction factor of ∼2400 (compared to γ-singles mode) was achieved. Beyond low-background measurements, this prototype exhibits additional compelling features, such as the ability to focus on certain decay channels and study their properties. This concept for a measurement system may be of interest to laboratories that monitor environmental radioactivity, studies involving environmental measurements and/or trace-level radioactivity.

[Establishment and preliminary evaluation of a fluorescent recombinase-aided amplification/CRISPR-Cas12a system for rapid detection of Plasmodium falciparum]

OBJECTIVE

To establish a fluorescent assay for rapid detection of Plasmodium falciparum based on recombinaseaided amplification (RAA) and CRISPR-Cas12a system,and to preliminarily evaluate the diagnostic efficiency of this system.

METHODS

The 18S ribosomal RNA (rRNA) gene of P. falciparum was selected as the target sequence, and three pairs of RAA primers and CRISPR-derived RNA (crRNA) were designed and synthesized. The optimal combination of RAA primers and crRNA was screened and the reaction conditions of the system were optimized to create a fluorescent RAA/CRISPR-Cas12a system. The plasmid containing 18S rRNA gene of the P. falciparum strain 3D7 was generated, and diluted into concentrations of 1 000, 100, 10, 1 copy/μL for the fluorescent RAA/CRISPR-Cas12a assay, and its sensitivity was evaluated. The genomic DNA from P. vivax, P. malariae, P. ovum, hepatitis B virus, human immunodeficiency virus and Treponema pallidum was employed as templates for the fluorescent RAA/CRISPR-Cas12a assay, and its specificity was evaluated. Fifty malaria clinical samples were subjected to the fluorescent RAA/CRISPR-Cas12a assay and nested PCR assay, and the consistency between two assays was compared. In addition, P. falciparum strain 3D7 was cultured in vitro. Then, the culture was diluted into blood samples with parasite densities of 1 000, 500, 200, 50, 10 parasites/μL with healthy volunteers' O-positive red blood cells for the RAA/CRISPR-Cas12a assay, and the detection efficiency was tested.

RESULTS

The Pf-F3/Pf-R3/crRNA2 combination, 2.5 μL as the addition amount of B buffer, 40 min as the RAA reaction time, 37 °C as the reaction temperature of the CRISPR-Cas12a system were employed to establish the fluorescent RAA/CRISPR-Cas12a system. Such a system was effective to detect the plasmid containing 18S rRNA gene of the P. falciparum strain 3D7 at a concentration of 1 copy/μL, and presented fluorescent signals for detection of P. falciparum, but failed to detect P. ovum, P. malariae, P. vivax, T. pallidum, hepatitis B virus or human immunodeficiency virus. The fluorescent RAA/CRISPR-Cas12a system and nested PCR assay showed completely consistent results for detection of 50 malaria clinical samples (kappa = 1.0, P < 0.001). Following 6-day in vitro culture of the P. falciparum strain 3D7, 10 mL cultures were generated and the fluorescent RAA/CRISPR-Cas12a system showed the minimal detection limit of 50 parasites/μL.

CONCLUSIONS

The fluorescent RAA/CRISPR-Cas12a system is rapid, sensitive and specific for detection of P. falciparum, which shows promising value for rapid detection and risk monitoring of P. falciparum.

Dead layer estimation of an HPGe detector using MCNP6 and Geant4

In this study, Monte Carlo simulations were used to calculate the full-energy peak efficiency of a p-type coaxial high-purity germanium (HPGe) detector. The HPGe detector was modeled using MCNP6 and Geant4, and the thickness of the dead layer of germanium crystals was estimated for an accurate simulation. The dead layer was divided into front and side components, where a point source and a Marinelli beaker source were used to estimate each dead layer thickness. The model was validated by comparing the simulated as well as experimental results for the standard sources of cylindrical and Marinelli beakers. The Geant4 results and experimental results matched up to 4% in the 59.54-1836.05 keV energy range, while MCNP6 matched up to 6% when adjusted for coincidence summing effects. HPGe detector modeled in Monte Carlo simulations can be utilized for experimental validation and experimental setup prior to using actual HPGe detectors.

Inconsistent PCR detection of Cacao swollen shoot virus (CSSV) is linked to the occurrence of different variants across the cocoa regions of Ghana

Reliable diagnostic tools capable of detecting latent and asymptomatic infections are critically important to support the management of the cocoa swollen shoot virus disease (CSSVD) and also to complement research activities on screening for resistant cocoa varieties. Development of efficient polymerase chain reaction (PCR) assays sensitive for detection of CSSV infections has thus been a major research focus over the years. Advances in the full genome sequence information have resulted in the design of several Cacao swollen shoot virus (CSSV)-specific and degenerate primers. The objective of the present study was to further assess the detection efficiency of ten (10) of the most utilized and novel CSSV primers on isolates of the virus across Ghana. Results from the PCR assays showed a highly variable and poor efficiency of the primers on the 189 samples of CSSV isolates evaluated. The overall detection potential of the primers ranged from 4 % to 23 % with the four best performing primers in terms of PCR positivity being P4 (23 %), CSSD1 (21 %), JOEL (21 %) CSSD2 (19 %) and BADNA (19 %). The generally poor and inconsistent efficiency of the primers are discussed in the context of the genetic variability and also the occurrence of new variants of the virus in Ghana.

[Development of a fluorescent recombinase-aided isothermal amplification-based nucleic acid assay for detection of Leishmania]

OBJECTIVE

To develop a fluorescent recombinase-aided isothermal amplification (RAA)-based nucleic acid assay for detection of Leshimania.

METHODS

Specific primers and probes were designed targeting Leishmania internal transcribed spacer 1 (ITS1) gene for RAA assay, and a fluorescent RAA assay was developed for detection of Leishmania following screening of primer pairs and optimization of primer and probe concentrations. The sensitivity of RAA assay for detection of Leishmania was evaluated using recombinant plasmid containing Leishmania ITS1 gene sequences at different copies and Leshimania genomic DNA at different concentrations as templates, and the specificity of RAA assay for detection of Leishmania was evaluated using the genomic DNA of transfusion-transmitted parasites, including Babesia microti, Toxoplasma gondii, Plamodium vivax, P. ovale, P. falciparum, P. malariae, L. donovani and L. infantum.

RESULTS

After the optimal primer pair was screened from 9 pairs of primer combinations, the final primer and probe concentrations were optimized as 0.3 μmol/L and 0.08 μmol/L, respectively. Nucleic acid detection of Leishmania was completed by the fluorescent RAA assay at an isothermal temperature of 39 °C within 20 min. Remarkable florescent signals were seen within 5 min following RAA detection of genomic DNA of L. donovani and L. infantum, and no cross-reactions were observed with B. microti, T. gondii, P. vivax, P. ovale, P. falciparum or P. malariae. The lowest limitation of detection of the fluorescent RAA assay was 10 copies/μL recombinant plasmid containing Leishmania ITS1 gene sequences and 1 fg/μL Leishmania genomic DNA.

CONCLUSIONS

A rapid, simple, sensitive and specific fluorescent RAA assay is successfully developed for detection of L. donovani and L. infantum, which is effective for field screening of leishmaniasis.

[Establishment of a fluorescent recombinase-aided isothermal amplification assay for nucleic acid detection of Paraginiumus skrjabini and preliminary evaluation of its detection efficiency]

OBJECTIVE

To establish a nucleic acid assay for detection of Paragonimus skrjabini based on the recombinase-aided isothermal amplification (RAA) technique, and to preliminarily evaluate its detection efficiency.

METHODS

The metacercariae of P. skrjabini, P. westermani and Euparagonimus cenocopiosus were isolated from crabs, and genomic DNA was extracted for molecular characterization. The cytochrome coxidase 1 (cox1) gene sequence of P. skrjabini was selected as the target gene fragment, and the primers and probes were designed, screened and synthesized for RAA assay. The genomic DNA of P. skrjabini metacercariae from Jiyuan City and Yiyang County of Luoyang City, Henan Province were used as templates for verification of the fluorescent RAA assay. The fluorescent RAA assay was performed to detect different concentrations of plasmids containing target gene fragment and P. skrjabini metacercariae genomic DNA to determine the sensitivity. Fluorescent RAA assay was performed with recombinant plasmids containing P. skrjabini cox1 gene sequences at different concentrations and P. skrjabini genomic DNA as templates to evaluate its sensitivity, and the genomic DNA of P. westermani, E. cenocopiosus, Clonorchis sinensis and Schistosoma japonicum was detected with fluorescent RAA assay to evaluate its specificity.

RESULTS

P. skrjabini, P. westermani and E. cenocopiosus metacercariae were isolated from crabs, respectively. Molecular characterization and phylogenetic analysis confirmed their homology with the genes sequences of standard Paragonimus strains in GenBank. A fluorescent RAA assay was successfully established for nucleic acid detection of P. skrjabini, and the genomic DNA of P. skrjabini metacercariae from Jiyuan City and Yiyang County of Luoyang City, Henan Province was amplified using the fluorescent RAA assay within 5 min, while the negative control was not amplified. If the recombinant plasmid containing P. skrjabini cox1 gene sequences was used as templates, the fluorescent RAA assay showed the lowest detection limit of 10 copies/μL, and positive amplification was observed within 5 min. If genomic DNA was used as templates, the fluorescent RAA assay showed the lowest detection limit of 10 pg/μL, and all positive amplifications were found within 5 to 10 min. In addition, the fluorescent RAA assay was tested negative for P. westermani, E. cenocopiosus, C. sinensis and S. japonicum.

CONCLUSIONS

A rapid, sensitive and specific fluorescent RAA assay is successfully established for nucleic acid detection of P. skrjabini, which has potential values in rapid field detection and species identification in freshwater crabs in areas endemic for P. skrjabini.

Development of a compensation system for thermal neutron measurements based on Cd(Cu)-covered NaI(Tl) detectors

A compensation system based on NaI (Tl) detectors and cadmium sheet was proposed for thermal neutron detection in the neutron/gamma field. The system consisted of two identical NaI (Tl) detectors covered with copper and cadmium sheets, respectively. The Cd-covered NaI (Tl) recorded the prompt gamma rays produced by the ¹¹³Cd (n, γ)¹¹⁴Cd reaction, while the Cu-covered structure "rejected" the background gamma rays. The moderated thermal neutron fluxes at different distances from an Am-Be neutron source, calibrated by the activation foil method, were investigated using the compensation system. The thermal neutron detection efficiency of this compensation system was compared to those obtained by the CdZnTe detector and He-3 proportional counter. The feasibility of the compensation system used as a thermal neutron counter was demonstrated by the obtained results.

[Performance of a recombinase - aided amplification assay for detection of Schistosoma japonicum infections in Oncomelania hupensis]

OBJECTIVE

To evaluate the efficiency of a recombinase-aided amplification (RAA) assay for the detection of Schistosoma japonicum infections in Oncomelania hupensis snails.

METHODS

A group test was employed. Fifty Oncomelania snails were collected as a detection sample. The detection samples without infected snails were designated as negative specimens, while the detection samples that contained different numbers of infected snails were designated as positive specimens. A total of 10 negative specimens, 10 positive specimens containing 1 infected snail, 20 positive specimens containing 2 infected snails and 10 positive specimens containing 3 infected snails were assigned. Following random grouping, 40 specimens were subject to the florescent RAA assay using a blind method. The miradium shedding method served as a gold standard, and the sensitivity, specificity, Youden's index and coincidence rate of the florescent RAA assay were estimated. In addition, 20 samples consisted of 5 negative specimens and 15 positive specimens with 1, 2 and 3 infected snails respectively were grouped randomly. The same specimens were detected using the crushing method and fluorescent RAA assay with the blind method in a paired-design manner. Then, the test results were compared and analyzed.

RESULTS

Florescent RAA assay detected 29 positives in the 30 specimens containing different numbers of infected snails, with a sensitivity of 96.67%, and 8 negatives in the 10 detection specimens without infected snails, with a specificity of 80.00%, showing a Youden's index of 0.77. The coincidence rate was 100% among 10 repeated assays for a detection specimen. In addition, there was no significant difference in the detection of infected snails between the florescent RAA assay and the crushing method (χ² = 0, P > 0.05), and the actual coincidence rates of the florescent RAA assay and crushing method were 95.00% (19/20) and 90.00% (18/20) with the real results, respectively.

CONCLUSION

Fluorescent RAA assay has a favorable efficiency for the detection of S. japonicum infections in Oncomelania snails, which shows a potential in screening of S. japonicum-infected Oncomelania snails.

A practical approach to determining soil-sample detection efficiency in field gamma-ray spectroscopy

Field measurements of radionuclide activities in soil samples via gamma spectroscopy measurements are conducted for many applications. One example application space is on-site inspection for the Comprehensive Nuclear-Test-Ban Treaty. To extract isotopic activities from observed peak counting rates, it is necessary to understand the absolute efficiency of the detector system for a sample. In principle, this efficiency is a function of many parameters, such as sample geometry, soil elemental composition, and soil density. The demands of field measurements within the context of on-site inspections, however, places a premium on an easy-to-implement approach at the possible expense of accuracy given the need to process many samples in a short period of time. This paper presents a semi-empirical approach, using a calibrated standard and a correction that depends only on the relative differences in density of the sample and the standard. Field measurements were conducted to demonstrate the validity of the approach.

[Establishment of a recombinase-aided isothermal amplification assay for nucleic acid detection of Angiostrongylus cantonensis]

OBJECTIVE

To establish a recombinase-aided isothermal amplification (RAA) assay for the nucleic acid detection of Angiostrongylus cantonensis.

METHODS

The internal transcribed spacer-1 (ITS1) gene sequence of A. cantonensis was used as the detection target sequence, and the specific primers and probes were designed and synthesized, followed by screening of the primers and probes with the highest specificity, to establish the basic and fluorescent RAA assay for nucleic acid detection of A. cantonensis. The sensitivity of the fluorescent RAA assay was evaluated by using the target gene fragment sequence-contained recombinant plasmids at various copy numbers and the genomic DNA from A. cantonensis as the template DNA samples, and the specificity of the fluorescent RAA assay was evaluated by using the genomic DNA from A. cantonensis, Schistosoma mansoni, Ascaris lumbricoides, Clonorchis sinensis, Echinococcus granulosus and Ancylostoma duodenale, as well as Pomacea canaliculata and Biomphalaria straminea snail tissues as the template DNA samples.

RESULTS

A fluorescent RAA assay was successfully established for nucleic acid detection of A. cantonensis, which achieved real-time amplification of the specific DNA fragment of A. cantonensis within 20 min at 37 ℃. By using the target gene fragment sequence-contained recombinant plasmids at various copy numbers and the genomic DNA from A. cantonensis as the DNA templates, the lowest detection limits of the fluorescent RAA assay were 10 copies/μL of recombinant plasmids and 100 pg/μL of genomic DNA, respectively. The fluorescent RAA assay was negative for detection of the genomic DNA from A. cantonensis, S. mansoni, A. lumbricoides, C. sinensis, E. granulosus, A. duodenale, and P. canaliculata and B. straminea snail tissues.

CONCLUSIONS

A simple, rapid fluorescent RAA assay has been successfully established, which has a high sensitivity and specificity for the nucleic acid detection of A. cantonensis.

[Establishment and preliminary evaluation of recombinase aided isothermal amplification (RAA) assay for specific nucleic acid detection of Clonorchis sinensis]

OBJECTIVE

To establish a recombinase aided isothermal amplification (RAA) assay for detection of Clonorchis sinensis.

METHODS

The 18S ribosomal RNA (18S rRNA) sequence of C. sinensis was used as the target sequence, and specific primers and probes were designed, synthesized and screened to establish a rapid fluorescent RAA assay for the detection of C. sinensis. Then, the sensitivity of the fluorescent RAA assay was evaluated using the recombinant plasmids containing various copy numbers of DNA fragments and C. sinensis genomic DNA at various concentrations, and the specificity of the fluorescent RAA as say was evaluated using the genomic DNA of Ascaris lumbricoides, Echinococcus granulosus, Schistosoma japonicum, Ancylostoma duodenale and S. mansoni as templates. DNA samples were extracted from the feces containing C. sinensis eggs and freshwater fish containing metacercaria for the fluorescent RAA assay, and the performance for detection of C. sinensis-infected samples was preliminarily assessed in the field.

RESULTS

A fluorescent RAA assay for detection of C. sinensis was successfully established, which was feasible for specific amplification of C. sinensis genomic DNA at 39 °C within 20 min. The lowest detection limit was 10 copies/μL if the recombinant plasmid containing various copy numbers of DNA fragments was used as a template, and the lowest detection limit was 3 pg/μL if the C. sinensis genomic DNA at various concentrations served as a template. All detections were negative if the genomic DNA of A. lumbricoides, E. granulosus, S. japonicum, A. duodenale, and S. mansoni was used as templates. In addition, the fluorescent RAA assay showed a high performance for the detection of C. sinensis-infected samples in the field, which successfully detected C. sinensis-infected human and rat fecal samples and Pseudorasbora parva samples.

CONCLUSIONS

A fluorescent RAA assay is successfully established, which is simple, rapid, sensitivity and specific for detection of C. sinensis.

Research on minimum detectable activity (MDA) of underwater gamma spectrometer for radioactivity measurement in the marine environment

To improve the capability of underwater gamma spectrometer to quantify radiation levels slightly above the background radiation in the seawater, the minimum detection activity (MDA) and factors including the background count, detection efficiency and acquisition time were studied using Monte Carlo simulation and field experiments. The simulation results show that the crystal type selected in the spectrometer and its volume, enclosure materials of the spectrometer and its thickness all affect the marine detection efficiency in in-situ measurement, and thus determine MDA of the underwater gamma spectrometer. The acquisition time and the placement depth of the spectrometer in the seawater also affect the MDA in the in-situ measurement. Some research data and suggestions on design and use of underwater gamma spectrometer were presented, which are of guiding significance for the in-situ radioactivity measurement in the marine environment.

Influence of smear matrix types on detection behaviors and efficiencies of polycyclic aromatic hydrocarbons using ion mobility spectrometry

Influence of smear matrix types on detection behaviors and efficiencies of polycyclic aromatic hydrocarbons (PAHs) with different molecular weights in ion mobility spectrometry (IMS) were investigated. Various smear matrices of stainless steel mesh (SM), cellulose paper (CP), and cotton fabric (CF) were employed. Anisole was used as the solvent and IMS analysis was performed without evaporation step of the solvent to apply charge transfer reactions between PAH molecules and the molecular ions of solvent. Shapes of reactant ion peaks (RIPs) were varied according to the smear matrix types. At the beginning of the sample inlet, intensity of RIPs of air and moisture notably decreased due to the lots of solvent vapor. The SM with good gas permeability showed relatively strong RIPs of air and moisture, whereas the CP with no gas permeability showed weak ones. Detection times and efficiencies of PAH ions were varied according to the smear matrix types as well as the kinds of PAHs. PAHs were on the whole detected well in 1-3 s after the sample inlet. Detection limits of PAHs measured using the SM were slightly better than those measured using the CP, while those measured using the CP were much better than those measured using the CF. The experimental results could be explained by structures of the smear matrices and evaporation behaviors of the PAH solutions.

Self-consistent atom probe tomography reconstructions utilizing electron microscopy

Atom probe tomography reconstructions provide valuable information on nanometer-scale compositional variations within materials. As such, the spatial accuracy of the reconstructions is of primary importance for the resulting conclusions to be valid. Here, the use of transmission electron microscopy images before and after atom probe analysis to provide additional information and constraints is examined for a number of different materials. In particular, the consistency between the input reconstruction parameters and the output reconstruction is explored. It is demonstrated that it is possible to generate reconstructions in which the input and known values are completely consistent with the output reconstructions. Yet, it is also found that for all of the datasets examined, a particular power law relationship exists such that, if the image compression factor or detection efficiency is not constrained, a series of similarly spatially accurate reconstructions results. However, if one of these values can be independently assessed, then the other is known as well. Means of incorporating these findings and this general methodology into reconstruction protocols are also discussed.

On the security of semi-device-independent QKD protocols

While fully device-independent security in (BB84-like) prepare-and-measure quantum key distribution (QKD) is impossible, it can be guaranteed against individual attacks in a semi-device-independent (SDI) scenario, wherein no assumptions are made on the characteristics of the hardware used except for an upper bound on the dimension of the communicated system. Studying security under such minimal assumptions is especially relevant in the context of the recent quantum hacking attacks wherein the eavesdroppers can not only construct the devices used by the communicating parties but are also able to remotely alter their behavior. In this work, we study the security of a SDIQKD protocol based on the prepare-and-measure quantum implementation of a well-known cryptographic primitive, the random access code (RAC). We consider imperfect detectors and establish the critical values of the security parameters (the observed success probability of the RAC and the detection efficiency) required for guaranteeing security against eavesdroppers with and without quantum memory. Furthermore, we suggest a minimal characterization of the preparation device in order to lower the requirements for establishing a secure key.

Ultrasound scans and dual energy CT identify tendons as preferred anatomical location of MSU crystal depositions in gouty joints

OBJECTIVE

The present study was performed to localize the articular deposition of monosodium urate (MSU) crystal in joints. We compare the detection efficiencies of dual-energy CT (DECT) and ultrasound scans.

METHODS

Analyses by DECT and ultrasound were performed with 184 bilateral joints of the lower limbs of 54 consecutive gout patients. All joints were categorized into (1) knee, (2) ankle, (3) MTP1, and (4) MTP2, and sorted into those with and those without detectable MSU deposition. The comparison of the positive rate between DECT and ultrasound and the agreement was performed using the McNemar test and the Cohen's κ coefficient, respectively. Next, we listed the MSU crystal deposition as assessed by ultrasound between the DECT-positive and -negative joints according to their interior structure. We included tendons, synovia, cartilage, subcutaneous tissue, etc. RESULTS: Among all joints, the percentages with MSU crystal deposition detected by DECT (99/184, 53.8%) and ultrasound (106/184, 57.6%) were comparable (P = 0.530 > 0.05). For MTP1 (21/34, 61.8%; 12/34, 35.3%; P < 0.05) and MTP2-5 (17/34, 50.0%; 10/34, 29.4%, P < 0.05), ultrasound and DECT were more efficient, respectively. The data concordance in 46 of 50 joints (92.00%; κ = 0.769, P < 0.05) for knee; and 27 of 34 joints (79.41%; κ = 0.588, P < 0.05) for MTP2-5 and suggested that tendons were the most frequent anatomical location of MSU crystal deposition.

CONCLUSIONS

The tendons are the most frequent anatomical location of MSU crystal depositions. The concordance rate of knee joints and MTP2-5 joints shows good agreement between DECT and ultrasound depending on the location.

Modeling the detection efficiency of an HP-Ge detector for use in boron neutron capture therapy

The multi-foil method is commonly used to determine upon an energy spectrum of neutrons in boron neutron capture therapy. The method requires to measure the radioactivation of the foils. This study develops a simple modeling procedure of a high-purity Ge detector, which is used to measure the radioactivation, in order to calculate the detection efficiency with GEANT4. By changing four parameters from their manufacturing specifications of the detector, the simulated detection efficiency is able to reproduce the actual detection efficiency.

Improvement of the detection efficiency calibration and homogeneity measurement of Si-SPAD detectors

Background

Silicon single-photon avalanche diodes (Si-SPADs) are the most used devices for measuring ultra-weak optical radiant fluxes in many quantum technology fields, such as quantum optics, quantum communication, quantum computing, etc. In all these fields, the detection efficiency is the main parameter, which has to be accurately known for achieving reliable measurements. In this paper we present the improvements performed on the setup described in López et al. (J Mod Opt 62:S21–S27, 2015) for determining the detection efficiency of Si-SPAD detectors with a low measurement uncertainty. The improvement arises from the precise alignment of the Si-SPAD detector and the low deviation reached between the total calculated filter transmission and the individual filter transmission measurements (≤0.05%) performed with an integrating sphere with attached Si-photodiode as standard detector.

Results

The relative standard uncertainty of the Si-SPAD detection efficiency measurement achieved is now as low as ~0.16%. Furthermore, the investigation of the detection efficiency homogeneity of two commercial Si-SPAD detectors from different manufacturers and with different sensor diameters is also presented. The obtained homogeneity is ≤2.2% within a region of diameter of 40 μm.

Conclusions

The detailed analysis presented in this paper shows the potential for achieving low measurement uncertainties for Si-SPAD detector calibration even in the low photon flux range. The low uncertainties are only to be realized for reproducible measurement conditions, i.e. in specific for equal beam sizes and beam shapes and well as for an irradiation of equal active areas of the detector. This, however, will be difficult to obtain when measurements are performed at different national metrology institutes.

Determination of HPGe peak efficiency for voluminous gamma-ray sources by using an effective solid angle method

A code called EXVol has been developed to obtain the absolute peak efficiency for an extended or voluminous γ-ray source. The method is based on the concept of effective solid angles. Several efficiency curves that have been determined semi-empirically for voluminous sources are compared with the experimental values based on certified reference volume sources. To study the geometric and matrix effects, standard γ-ray sources of several media, volumes and shapes were measured using HPGe detectors with three different efficiencies. For the n-type detector of 32% relative efficiency, the relative deviations are less than ±10%; this performance is similar to that of existing programs for similar purposes. The EXVol code is able to calculate the detection efficiency within approximately five minutes or less. Systematic errors based on EXVol input parameters, which are mainly due to the inherent uncertainty in the detector's characteristic dimensions provided by the vendor, are studied to obtain more accurate specifications of the detectors.

Characterizations of BC501A and BC537 liquid scintillator detectors

Two 2″×2″ liquid scintillator detectors BC537 and BC501A have been characterized for their responses and efficiencies to γ-ray detection. Light output resolution and response functions were derived by least-squares minimization of a simulated response function, fitted to experimental data. The γ-ray response matrix and detection efficiency were simulated with Monte Carlo (MC) methods and validated. For photon energies below 2.4 MeVee, the resolution, as well as the efficiency, of BC501A is better than BC537 scintillator. The situation is reversed when the energy is higher than 2.4 MeVee. BC537 has higher γ-ray detection efficiency than BC501A if the impinging photon energy is more than 2 MeV due to different ratios of C to H/D atoms.