Implementation of a Rapid RT-LAMP Saliva-based SARS-CoV-2 Testing Program in the Workplace

Rising SARS-CoV-2 cases, testing delays and the risk of pre-symptomatic and asymptomatic transmission provided the impetus for an in-house rapid testing pro-gram. Employees and their household contacts were encouraged to self-collect saliva samples which were pooled for routine testing using an established colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay. In brief, individual or a maximum of four saliva samples were pooled, heat-inactivated to render microorganisms, especially SARS-CoV-2, non-infectious prior to being added to RT-LAMP assay tubes containing either human sample control gene, RNase P or a region of the SARS-CoV-2 gene, ORF1ab. During the second wave of SARS-CoV-2 infections in November 2020, two samples from an employee and a member of their household tested positive via RT-LAMP within two days of each other. A delayed clinical qRT-PCR test confirmation of both individuals 5 days later underscores the power of routine rapid testing with within-the-hour turnaround times. Workplace rapid testing programs using RT-LAMP are flexible in their design, have a reduced cost compared to qRT-PCR, may involve non-invasive self-saliva collection for increased safety for the testing personnel, and can be performed with minimal training.

Forensic Tools for Species Identification of Skeletal Remains: Metrics, Statistics, and OsteoID

Although nonhuman remains constitute a significant portion of forensic anthropological casework, the potential use of bone metrics to assess the human origin and to classify species of skeletal remains has not been thoroughly investigated. This study aimed to assess the utility of quantitative methods in distinguishing human from nonhuman remains and present additional resources for species identification. Over 50,000 measurements were compiled from humans and 27 nonhuman (mostly North American) species. Decision trees developed from the long bone data can differentiate human from nonhuman remains with over 90% accuracy (>98% accuracy for the human sample), even if all long bones are pooled. Stepwise discriminant function results were slightly lower (>87.4% overall accuracy). The quantitative models can be used to support visual identifications or preliminarily assess forensic significance at scenes. For species classification, bone-specific discriminant functions returned accuracies between 77.7% and 89.1%, but classification results varied highly across species. From the study data, we developed a web tool, OsteoID, for users who can input measurements and be shown photographs of potential bones/species to aid in visual identification. OsteoID also includes supplementary images (e.g., 3D scans), creating an additional resource for forensic anthropologists and others involved in skeletal species identification and comparative osteology.

Comparison of extraction methods for intracellular metabolomics

Measurements of metabolic compounds inside cells or tissues are of high informative potential since they represent the endpoint of biological information flow and a snapshot of the integration of many regulatory processes. However, it requires careful extraction to quantify their abundance. Here we present a comprehensive study using ten extraction protocols on four human sample types (liver tissue, bone marrow, HL60 and HEK cells) targeting 630 metabolites of different chemical classes. We show that the extraction efficiency and stability is highly variable across protocols and tissues by using different quality metrics including the limit of detection and variability between replicates as well as the sum of concentration as a global estimate of extraction stability. The profile of extracted metabolites depends on the used solvents - an observation which has implications for measurements of different sample types and metabolic compounds of interest. To identify the optimal extraction method for future metabolomics studies, the benchmark dataset was implemented in an easy-to-use, interactive and flexible online resource (R/shiny app MetaboExtract).

Toxoplasma gondii Genotypes Circulating in Serbia—Insight into the Population Structure and Diversity of the Species in Southeastern Europe, a Region of Intercontinental Strain Exchange

In Europe, Toxoplasma gondii lineage II is dominant, and ToxoDB#1 the most frequently occurring genotype. The abundance of lineage III genotypes varies geographically and lineage I are rare, yet present in several regions of the continent. Data on the T. gondii population structure in southeastern Europe (SEE) are scarce, yet necessary to appreciate the diversity of the species in Europe. To help fill this gap, we genotyped 67 strains from nine species of intermediate hosts in Serbia by MnPCR-RFLP, determined the population structure, and identified the genotypes using ToxoDB. A neighbor-joining tree was also constructed from the isolates genotyped on nine loci. While 42% of the total genotype population consisted of ToxoDB#1 and ToxoDB#2, variant genotypes of both lineages comprised 46% of the population in wildlife and 28% in domestic animals and humans. One genotype of Africa 4 lineage was detected in a human sample. Interestingly, the findings include one lineage III variant and one II/III recombinant isolate with intercontinental distribution, which appear to be moderately related to South American genotypes. Based on these findings, SEE is a region of underappreciated T. gondii genetic diversity and possible strain exchange between Europe and Africa.

Genotoxicity of Mercury and Its Derivatives Demonstrated In Vitro and In Vivo in Human Populations Studies. Systematic Review

Beside partial coverage in three reviews so far (1994, 2009, 2019), there is no review on genotoxic studies dealing with mercury (Hg) and human exposure using the most usual genotoxic assays: sister chromatid exchanges (SCE), chromosomal aberrations (CA), cytochalasin B blocked micronucleus assay (CBMN), and single-cell gel electrophoresis (SCGE or alkaline comet assay). Fifty years from the first Hg genotoxicity study and with the Minamata Convention in force, the genotoxic potential of Hg and its derivatives is still controversial. Considering these antecedents, we present this first systematic literature overview of genotoxic studies dealing with Hg and human exposure that used the standard genotoxic assays. To date, there is not sufficient evidence for Hg human carcinogen classification, so the new data collections can be of great help. A review was made of the studies available (those published before the end of October 2021 on PubMed or Web of Science in English or Spanish language) in the scientific literature dealing with genotoxic assays and human sample exposure ex vivo, in vivo, and in vitro. Results from a total of 66 articles selected are presented. Organic (o)Hg compounds were more toxic than inorganic and/or elemental ones, without ruling out that all represent a risk. The most studied inorganic (i)Hg compounds in populations exposed accidentally, occupationally, or iatrogenically, and/or in human cells, were Hg chloride and Hg nitrate and of the organic compounds, were methylmercury, thimerosal, methylmercury chloride, phenylmercuric acetate, and methylmercury hydroxide.

Urdu translation and validation of clinically useful anxiety outcome scale in Pakistan: ‘an observational study’

Objective: To translate and evaluate the psychometric properties of the Clinically Useful Anxiety Outcome Scale on Urdu-speaking population. Method: The observational validation study was conducted in Rawalpindi and Islamabad, Pakistan, from January 2018 to December 2019 in two phases. In the first phase, the Clinically Useful Anxiety Outcome Scale was forward and backward translated, while in the second phase, the translated scale was validated on a human sample comprising subjects in clinical and nonclinical settings. Item-to-total correlation, internal consistency and test-retest reliabilities were checked with inter-group comparisons. To find out the level of language equivalence between the original and the translated versions, a separate sample of bilingual participants was raised. Data was analysed using SPSS 22. Continue

Serology for Borrelia spp. in Northwest Italy: A Climate-Matched 10-Year Trend

Ticks are hematophagous parasites that can transmit a variety of human pathogens, and their life cycle is dependent on several climatic factors for development and survival. We conducted a study in Piedmont and Aosta Valley, Italy, between 2009 and 2018. The study matched human sample serologies for Borrelia spp. with publicly available climatic and meteorological data. A total of 12,928 serological immunofluorescence assays (IFA) and Western blot (WB) tests were analysed. The median number of IFA and WB tests per year was 1236 (range 700–1997), with the highest demand in autumn 2018 (N = 289). In the study period, positive WB showed an increasing trend, peaking in 2018 for both IgM (N = 97) and IgG (N = 61). These results were consistent with a regional climatic variation trending towards an increase in both temperature and humidity. Our results suggest that coupling data from epidemiology and the environment, and the use of a “one health” approach, may provide a powerful tool in understanding disease transmission and strengthen collaboration between specialists in the era of climate instability.

Morphological variation of the deciduous second molars in the Baka Pygmies

The Baka Pygmies are known for their short stature resulting from a reduced growth rate during infancy. They are peculiar also for their teeth erupt earlier than in any other African population, and their posterior dentition is larger than in non-Pygmy populations. However, the Baka’s dental morphology, like several other aspects of their biology, is still understudied. Here, we explore the variation of the Baka’s deciduous upper and lower second molars (dm2s) in comparison to a geographically heterogeneous human sample by means of 3D geometric morphometrics and analysis of dental traits. Our results show that the different populations largely overlap based on the shape of their dm2s, especially the lower ones. Their distal region and the height of the dentinal crown differ the most, with the Baka showing the most extreme range of variation. Upper and lower dm2s covary to a great extent (RV = 0.82). The Baka’s and South Americans’ dm2s were confirmed among the largest in our sample. Despite the Baka’s unique growth pattern, long-lasting isolation, and extreme dental variation, it is not possible to distinguish them from other populations based on their dm2s’ morphology only.

Three-step one-way model in terahertz biomedical detection

Terahertz technology has broad application prospects in biomedical detection. However, the mixed characteristics of actual samples make the terahertz spectrum complex and difficult to distinguish, and there is no practical terahertz detection method for clinical medicine. Here, we propose a three-step one-way terahertz model, presenting a detailed flow analysis of terahertz technology in the biomedical detection of renal fibrosis as an example: 1) biomarker determination: screening disease biomarkers and establishing the terahertz spectrum and concentration gradient; 2) mixture interference removal: clearing the interfering signals in the mixture for the biomarker in the animal model and evaluating and retaining the effective characteristic peaks; and 3) individual difference removal: excluding individual interference differences and confirming the final effective terahertz parameters in the human sample. The root mean square error of our model is three orders of magnitude lower than that of the gold standard, with profound implications for the rapid, accurate and early detection of diseases.