Cross-genera amplification and identification of Colpodella sp. with Cryptosporidium primers in fecal samples of zoo felids from northeast China

The protozoans include many intracellular human pathogens. Accurate detection of these pathogens is necessary to treat the diseases. In clinical epidemiology, molecular identification of protozoan is considered a more reliable and rapid method for identification than microscopy. Among these protozoans, Cryptosporidium considered being one of the important water-borne zoonotic pathogens and a major cause of a diarrheal disease named cryptosporidiosis in humans, domestic animals, and wild animals. This study was aimed to identify Cryptosporidium in zoo felids (N= 56) belonging to different zoo of China, but accidentlly Colpodella was encountered in the zoo felids sample and phylogenetic data confirmed this unexpected amplification from fecal samples using two-step nested-PCR. Phylogenetic analysis revealed the fact about the specific primers used previously by many researchers and cross-genera amplification. We came to know that genetically sequenced amplicon gives more accurate identification of species. This study suggests more investigation on Colpodella which has been neglected previously but gains the attention of researchers after identified from humans and animals and has been known to correlate with neurological symptoms in patients.

On the Performance of Energy Criterion Method in Wi-Fi Transient Signal Detection

In the development of radiofrequency fingerprinting (RFF), one of the major challenges is to extract subtle and robust features from transmitted signals of wireless devices to be used in accurate identification of possible threats to the wireless network. To overcome this challenge, the use of the transient region of the transmitted signals could be one of the best options. For an efficient transient-based RFF, it is also necessary to accurately and precisely estimate the transient region of the signal. Here, the most important difficulty can be attributed to the detection of the transient starting point. Thus, several methods have been developed to detect transient start in the literature. Among them, the energy criterion method based on the instantaneous amplitude characteristics (EC-a) was shown to be superior in a recent study. The study reported the performance of the EC-a method for a set of Wi-Fi signals captured from a particular Wi-Fi device brand. However, since the transient pattern varies according to the type of wireless device, the device diversity needs to be increased to achieve more reliable results. Therefore, this study is aimed at assessing the efficiency of the EC-a method across a large set of Wi-Fi signals captured from various Wi-Fi devices for the first time. To this end, Wi-Fi signals are first captured from smartphones of five brands, for a wide range of signal-to-noise ratio (SNR) values defined as low (−3 to 5 dB), medium (5 to 15 dB), and high (15 to 30 dB). Then, the performance of the EC-a method and well-known methods was comparatively assessed, and the efficiency of the EC-a method was verified in terms of detection accuracy.

A New Approach for Accurate Identification of Allele State Based on Real-Time PCR for Biomedical Tasks

Genotyping of single nucleotide polymorphisms (SNPs) is an important task in medicine, veterinary medicine and biology. Precise differentiation of SNPs can be challenging. Methods based onTaqman can lead to false positive results due to nonspecific annealing of the probe. The aim of this research was to develop a new approach for the accurate differentiation of SNPs based on real-time PCR with Taqmanprobes and their rivals.The rivals competed with the Taqmanprobes for annealing to the site. The rivals blocked the nonspecific allele so that the Taqmanprobe could not anneal to it. Thus,the Taqmanprobe only detected specific alleles.This approach madeit possible to fine-tune the diagnostic system by selecting the ratio of Taqmanprobes and rivals (in non-equimolar amounts too).The new approach was tested on several diagonally significant SNPs in veterinary medicine.Using Taqman probes and rival probes showed a significantly greater specificity and efficiency in the determination of both homozygotes and heterozygotes than when conventional systems based only on Taqmanwere used. Keywords: SNP, allele identification, real-time PCR, fluorescent dye

The contribution of reduced COVID-19 test time in controlling the spread of the disease: A simulation-based approach

The novel coronavirus COVID-19 has known a large spread over the globe threatening human health. Recommendations from WHO and specialists insist on testing on a mass scale. However, health systems do not have enough resources. The current process requires the isolation of testees in the hospitals’ isolation rooms for several hours until the test results are revealed, limiting hospitals’ capacities to test large numbers of cases. The aim of this paper was to estimate the impact of reducing the COVID-19 test time on controlling the pandemic spread, through increasing hospitals’ capacities to test on a mass scale. First, a discrete-event simulation was used to model and simulate the COVID-19 testing process in Morocco. Second, a mathematical model was developed to demonstrate the effect of accurate identification of infected cases on controlling the disease’s spread. Simulation results showed that hospitals’ testing capacities could be increased six times if the test duration fell from 10 hours to 10 minutes. The reduction of test time would increase testing capacities, which help to identify all the infected cases. In contrast, the simulation results indicated that if the infected population is not accurately identified and no precautionary measures are taken, the virus will continue to spread until it reaches the total population. Reducing test time is a vital component of the response to the COVID-19 pandemic. It is essential for the effective implementation of policies to contain the virus.

Planning for mental wellbeing in an old age home during the Covid-19 pandemic by homoeopathic institution: Structuring the intervention

Objectives: During the on-going COVID-19 pandemic, the risk to the mental well-being of the elderly living in an old age home (OAH) has increased considerably. Dealing with this issue requires special measures. The current literature has very few examples of such programmes. We aimed to promote emotional balance and an independent living with positive outlook on life among the residents of the OAH facility during the pandemic based on action learning principles. This programme was conducted in an OAH that our institute has been associated with for several years. HelpAge India, a non-governmental organisation working in India to assist disadvantaged senior citizens, provided a programme that covered 12 themes. This article deals with the structuring process of the programme. Materials and Methods: The team comprised homoeopathic consultants and the faculty and students of a postgraduate homoeopathic institute. An extensive literature search and consultation with experts from various fields enabled the team to plan and build the final programme were evolved. Results: Broad themes gave rise to distinct modules and objectives were derived for each of these. Detailed action plans were worked out and a plan of evaluation for each of these modules was worked out. Conclusion: Planning a programme to ensure well-being needs a close and accurate identification of the needs of the residents of a particular OAH. A multidisciplinary approach can help in evolving effective strategies to formulate models for geriatric mental well-being.

Intraoperative hyperspectral imaging (HSI) as a new diagnostic tool for the detection of cartilage degeneration

To investigate, whether hyperspectral imaging (HSI) is able to reliably differentiate between healthy and damaged cartilage tissue. A prospective diagnostic study was performed including 21 patients undergoing open knee surgery. HSI data were acquired during surgery, and the joint surface’s cartilage was assessed according to the ICRS cartilage injury score. The HSI system records light spectra from 500 to 1000 nm and generates several parameters including tissue water index (TWI) and the absorbance at 960 nm and 540 nm. Receiver operating characteristic curves were calculated to assess test parameters for threshold values of HSI. Areas with a cartilage defect ICRS grade ≥ 3 showed a significantly lower TWI (p = 0.026) and higher values for 540 nm (p < 0.001). No difference was seen for 960 nm (p = 0.244). For a threshold of 540 nm > 0.74, a cartilage defect ICRS grade ≥ 3 could be detected with a sensitivity of 0.81 and a specificity of 0.81. TWI was not suitable for cartilage defect detection. HSI can provide reliable parameters to differentiate healthy and damaged cartilage. Our data clearly suggest that the difference in absorbance at 540 nm would be the best parameter to achieve accurate identification of damaged cartilage.

Rapid and Accurate Identification of SARS-CoV-2 Omicron Variants Using Droplet Digital PCR (RT-ddPCR)

Background Mutations in the receptor binding domain of the SARS-CoV-2 Spike protein are associated with increased transmission or substantial reductions in vaccine efficacy, including in the recently described Omicron variant. The changing frequencies of these mutations combined with their differing susceptibility to available therapies have posed significant problems for clinicians and public health professionals. Objective To develop an assay capable of rapidly and accurately identifying variants including Omicron in clinical specimens to enable case tracking and/or selection of appropriate clinical treatment. Study Design Using three duplex RT-ddPCR reactions targeting four amino acids, we tested 419 positive clinical specimens from February to December 2021 during a period of rapidly shifting variant prevalences and compared genotyping results to genome sequences for each sample, determining the sensitivity and specificity of the assay for each variant. Results Mutation determinations for 99.7% of detected samples agree with NGS data for those samples, and are accurate despite wide variation in RNA concentration and potential confounding factors like transport medium, presence of additional respiratory viruses, and additional mutations in primer and probe sequences. The assay accurately identified the first 15 Omicron variants in our laboratory including the first Omicron in Washington State and discriminated against S-gene dropout Delta specimen. Conclusion We describe an accurate, precise, and specific RT-ddPCR assay for variant detection that remains robust despite being designed prior the emergence of Delta and Omicron variants. The assay can quickly identify mutations in current and past SARS-CoV-2 variants, and can be adapted to future mutations.

Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward

DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.

Omics Approaches to Assess Flavor Development in Cheese

Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.