detection

This study sought to determine the spatial distribution of heavy metal concentrations in water, soil, and vegetables that were irrigated with industrial wastewater in Ethiopia’s Oromia Special Zone. We aimed to make recommendations for corrective actions that would reduce the negative environmental effects of untreated waste. Five sampling sites were meticulously chosen within the Sululta, Laga Tafo Laga Dadi, Galan, Sabata, and Burayu regions, taking into account the varying stressors across the upper stream, middle stream, and downstream segments of the rivers. These sampling sites were strategically selected to capture a comprehensive understanding of heavy metal aggregation within the area. The sampling encompassed the collection and analysis of 25 water and wastewater samples, 13 soil samples, and 8 vegetable samples. The distribution of sampling efforts was tailored to reflect the availability of irrigation sites within the respective areas, resulting in a harmonized amalgamation of 5, 3, and 1 samples for water and wastewater, soil, and vegetable matrices, respectively. The lettuce in the Gelan area had the greatest quantity of lead, suggesting higher cancer risk. The sites of Gelan and Burayu had significant levels of chromium contamination in their lettuce, followed by their cabbage, according to the WHO/FAO and USEPA. As a result, those who eat vegetables that have high levels of heavy metal contamination may be at risk for developing cancer. The concerned institutions and stakeholders must work to mitigate the high concentration of heavy metals in water, soil, and vegetables by the installation of treatment plant.

One of the factors that is widely scattered in nature and causes contamination of food sources in humans and animals is aflatoxin-producing fungi, which can have dangerous effects on the consumer. It seems that aflatoxins produced by Aspergillus species are very dangerous and toxic and cause severe food contamination and high carcinogenic power. It seems that even a low concentration of aflatoxin has dangerous side effects, so the identification and quantification of this toxin in food and feed can have a high degree of sensitivity. In this field, there are strong methods for identification and quantification, which necessitates the development of aflatoxin research. The existence of appropriate methods for quantifying these poisons, accurate diagnosis and control can ensure the health of consumers and prevent the occurrence of dangers and side effects of poisons. There are various laboratory methods such as chromatography for the detection of aflatoxins. in this study, we will compare the analytical and analytical methods of aflatoxin determination, which can be effective in deciding to choose the right method with the appropriate sensitivity level for the qualitative and quantitative analysis of aflatoxin identification in food.

SARS-CoV-2 as the cause of novel coronavirus disease (COVID-19) is a member of the family Coronaviridea that has generated an emerging global health concern. Controlling and preventing the spread of the disease requires a simple, portable, and rapid diagnostic method. Today, a standard method for detecting SARS-CoV-2 is quantitative real-time reverse transcription PCR, which is time-consuming and needs an advanced device. The aim of this study was to evaluate a faster and more cost-effective field-based testing method at the point of risk. We utilized a one-step RT-LAMP assay and developed, for the first time, a simple and rapid screening detection assay targeting the Envelope (E) gene, using specific primers.

For this, the total RNA was extracted from respiratory samples of COVID-19 infected patients and applied to one-step a RT-LAMP reaction. The LAMP products were visualized using green fluorescence (SYBR Green I). Sensitivity testing was conducted using different concentrations of the designed recombinant plasmid (TA-E) as positive control constructs. Additionally, selectivity testing was performed using the influenza H1N1 genome. Finally, the results were compared using with conventional real time RT-PCR.

It was shown that the RT-LAMP assay has a sensitivity of approximately 15 ng for the E gene of SARS-CoV-2 when using extracted total RNA. Additionally, a sensitivity of 112 pg was achieved when using an artificially prepared TA-E plasmid. Accordingly, for the detection of SARS-CoV-2 infection, the RT-LAMP had high sensitivity and specificity and also could be an alternative method for real-time RT-PCR.

Overall, this method can be used as a portable, rapid, and easy method for detecting SARS-CoV-2 in the field and clinical laboratories.

 E. coli O157:H7-related food poisoning is one of the most well-known causes of bloody diarrhea illness around the world. Therefore, devising a rapid, highly sensitive, and convenient detection technique for this species is crucial. In this work, we optimized a colorimetric Loop-mediated isothermal amplification (LAMP) for detecting the intimin gene from E. coli O157:H7.

  In this study, eae (intimin), one of the virulence factors of E. coli O157:H7, was selected as the target gene, and specific primers were designed for the sequence of this gene using the Primer Explorer V5 software. The LAMP reaction was optimized with three variable factors of MgSO4 concentration, temperature, and incubation time, in a traditional (separate) way and by Taguchi experimental design. Finally, the LAMP products were visualized by 2% agarose gel electrophoresis stained with ethidium bromide or green fluorescence (SYBR green I) and the pink fluorescence (KBC power load), which can be observed using the naked eye. 

 The LAMP reaction was optimized at 63°C and 8 mM MgSO4 for 40 min. Also, the naked eye can readily visualize the LAMP products within 40 minutes and have a detection limit of 3.2×104 CFU/mL according to 0.38 fg from the genome. Designed primers based on the gene sequence proved their specificity by testing 4 species of other common foodborne pathogenic microorganisms. 

 The rapid, sensitive, one-step-visually developed LAMP assay could be of interest for screening functions in food analytical laboratories without special equipment or trained personnel.

Food is the most unavoidable substance for contamination. It can be contaminated naturally and unintentionally by toxins. Some of these food contaminants contain nephrotoxins. For this purpose, a narrative review study was performed to identify the types of nephrotoxin found in food. This study was performed with the keywords; nephrotoxin, contamination, pollution, and food. The nephrotoxic toxins consist mainly of three categories of toxins; mycotoxins, heavy metals, and Aristolochic acids. About 70% of the selected studies investigated ochratoxin A (OTA). Evaluation of OTA contamination in baby food and infant formula should be considered. We can mention nickel, lead, and cadmium from the category of nephrotoxic heavy metals in food. Also, from compounds with radionucleotide activity, contamination with uranium was observed. Onions and carrots can be good biomarkers for contaminating an area with Aristolochic acids. Some of the nephrotoxins occurred more than permissible levels. Given that the kidneys are a vital organ of the body, human biomonitoring of nephrotoxins is recommended in countries where food is over the permissible level.

We detected a novel strain of picornavirus from dead backyard ducks from Gilan province, In Iran. This new isolated was demonstrated a genome like picornavirus design, specifically Aalivirus (Avihepatovirus/Avisivirus-like virus). Usually, Aalivirus were observed in domestic ducks, turkey and chickens. Ten pooled feces samples were collected from samples. We implemented partial genome sequencing of VP1 gene. We nominated the new strain as duck Aalivirus isolate UT-Ebrahimi. Based on our investigation with phylogenetic tree, we considered this strain is a member of the Aalivirus genus of picornavirus. In this study, we demonstrated that the UT-Ebrahimi is 96.23 % similar to Pacific_black_duck_megrivirus_(MK204391.1).

 Rapid antigen and antibody, serological tests, and RT ‑ PCR-based molecular methods are widely used to detect microorganisms worldwide. This study aimed to detect the covid-19 using Isothermal nucleic acid amplification techniques.

 In this study, we collected 200 samples of nasopharynx and oropharynx from Jamaran Heart Hospital in Tehran. Covid -19 was examined by LAMP-RT PCR and Real-Time RT- PCR techniques. The nasopharynx and oropharynx nucleic acids were extracted both by pishtaz RNA extraction kit. LAMP-RT-PCR was performed on direct samples, while Real-Time RT-PCR samples were tested only using RNA extraction samples. The probe-primer mixture of this kit was designed using a dual-target gene method that simultaneously targets the genomic sequences of the spike region and N nucleocapsid. Fluorescence was measured using Real-Time RT-PCR and LAMP-RT PCR.

Clinical specimens (56%) were positive using Real-Time RT-PCR technique, with mean Ct values less than 30. Clinical samples (52%) were positive for Covid-19 in the RT-LAMP technique of RNA extraction samples. RT-LAMP technique indicated a sensitivity of 92.8%. Also in the RT-LAMP method without RNA extraction, the sensitivity of the technique was 85.7%.

 The LAMP-RT PCR technique is emerging as an appropriate alternative to the Real-Time RT-PCR method. This technique has basic advantages, such as constant temperature amplification, thermal cycle elimination, faster results, and potentially greater detection capacity. Therefore, the RT-LAMP-PCR can be used as a quick and cost-effective technique that can be employed in all areas.

Bacterial food poisoning is considered a global concern in terms of economical and human health. Staphylococcus aureus produces low molecular weight extracellular toxins. These enterotoxins (SEs) are similar in structure and bioactivity. Today, there are several methods to detect SE genes. Nevertheless, culture-based and immunological methods are simple and cheaper than molecular techniques, they are time-consuming, with low sensitivity and specificity. In this field, loop-mediated isothermal amplification (LAMP) is a fast and simple method for gene amplification. The aim of this work was to optimize the LAMP reaction using the Taguchi method. For this, in order to improve and accelerate the LAMP diagnostic process, essential factors for the identification of enterotoxin, including MgSO4 concentration, time, and temperature reaction were optimized separately and using Taguchi experimental design. The results showed that 57 µg/ml of S. aureus genome as template is suitable for the replication, and in optimization of LAMP assay in separate condition the best replication rate was observed at 6 mM MgSO4, 45 min, and 65 °C. Whereas using Taguchi methods, the optimum condition was at 8 mM MgSO4, 60 min and 65 °C. The one-step-visual developed LAMP assay with the optimum conditions could be of interest for screening functions in food analytical laboratories, and a portable detection method could be used to design a suitable identification kit for S. aureus without the need for special equipment or trained personnel.

Diagnosis of musculoskeletal abnormalities is critical because of the large number of people affected by these disorders worldwide. The recent advances in deep learning techniques show that convolutional neural networks can be a useful tool for the computer-aided detection of radiographic abnormalities. This study focuses on diagnosing musculoskeletal abnormalities in the lower extremities using X-Ray images by deep architecture neural networks.

The dataset contains 61,098 musculoskeletal radiographic images, including 42,658 normal and 18,440 abnormal images. Each image belongs to a single type of lower extremity radiography, including the toe, foot, ankle, leg, knee, femur, and hip joints, which were prepared with standard projection without artifacts and with high quality. A novel deep neural network architecture is proposed with two different scenarios that perform the lower extremity lesion diagnosis functions with high accuracy. The foundation of the proposed method is a deep learning framework based on the Mask Regional Convolutional Neural Network (R-CNN) and Convolutional Neural Network (CNN). The model with the best results incorporated the Mask R-CNN algorithm to produce the bounding box, followed by the CNN algorithm to detect the class based on that.

The proposed model can identify different types of lower limb lesions by an Area Under the Curve (AUC) of the Receiver Operating Characteristics (ROC) curve 0.925 with an operating point of 0.859 of sensitivity and a specificity of 0.893.

The results indicated that the consecutive implementation of Mask R-CNN and CNN has a higher efficiency than Mask R-CNN and CNN separately in lesion detection of lower limb X-ray images.

 Broad-spectrum antibiotic resistance genes are one of the most common developing resistance genes worldwide. Accordingly, it is of paramount importance to study the extended-spectrum beta-lactamase genes to report them to physicians to select the most appropriate treatment.

 This study aimed to detect three genes of ESBL such as TEM, AmpC, and KPC simultaneously.

 Primers were designed for ESBL genes such as TEM, AmpC, and KPC with Genscript software. In this study, control-positive genes were used for the PCR set-up. Fifty isolates of Escherichia coli isolated in the Baqiyatallah Hospital were confirmed and checked by Multiplex PCR.

 This study revealed that TEM, AmpC, and KPC primers could detect positive control genes. The sensitivity and specificity of the multiplex PCR technique for these genes were 0.001 ng and 100%, respectively.

 This study revealed that a Multiplex PCR with a sensitivity of 0.001 ng and 100% specificity can detect ESBL genes precisely. Accordingly, the rapid and precise detection of the antibiotic resistance genes and the recommendation of an appropriate treatment pattern can decrease the distribution of antibiotic resistance occurrence and economic cost.

The International Caries Detection and Assessment System (ICDAS) was developed to integrate several criteria systems into one standard system for caries detection and assessment. The aim of this study was to identify Turkish dental practitioners’ perceptions and experience about ICDAS II and assess how they could affect clinical decision-making. A web-based data collection form, including demographic characteristics, experience of caries detection systems, and two different clinical images with caries and treatment options, was given to Turkish dental practitioners. Data were analyzed with the chi-square test and logistic regression using SPSS 22.0 software (IBM, Chicago, IL) at a significance level of P < 0.05. Data collection forms were completed by 382 general dental practitioners. For the first clinical scenario 70.7% of the practitioners decided that no treatment was required. For the second clinical scenario 89.5% of the practitioners decided to perform tooth restoration. Considering the clinical scenario 2 treatment options, while practitioners working in the public hospital marked amalgam restoration at a higher rate, practitioners working in private clinics marked composite resin restoration and root canal treatment at a higher rate (P < 0.05). With regard to effects on treatment choices for clinical scenarios, binary logistic regression analysis found no significant effects of gender, age, or institution (P > 0.05). The visual caries detection system, ICDAS II, was a useful tool in standardizing caries diagnostic skills for practitioners and improving decision-making abilities on caries treatment.

 The high mortality rate of Gastric Cancer (GC) is a consequence of delayed diagnosis. The early diagnosis of GC could increase the five-year survival rate among patients. We aimed to find a panel of microRNAs (miRNA) for the detection of GC in the early stages.

 In this case-control study, we selected consistently upregulated miRNAs from the results of 12 high-throughput miRNA profiling studies in GC. In the profiling phase, the differential expressions of 13 candidate miRNAs were analyzed by quantitative reverse-transcription PCR (qRT-PCR) in two pooled RNA samples prepared from the plasma of eight GC patients and eight matched controls. In the validation phase, significantly upregulated miRNAs from the profiling phase were further evaluated in the plasma samples of 97 patients with stage I-IV gastric adenocarcinoma and 100 healthy controls.

 In the profiling phase, six miRNAs (miR-18a, 21, 25, 92a, 125b and 221) were significantly upregulated in the GC patients compared to the controls (p<0.05). However, in the validation phase, only significant up-regulation of miR-18a, 21 and 125b was confirmed (p<0.05). A panel of miR-18a/21/125b was able to detect GC patients with stage I-IV from the controls (p<0.001; AUC=0.92, sensitivity=86%; specificity=85%). In addition, the panel could distinguish the early-stage GC (I+II) from the control group with an AUC of 0.83, a sensitivity of 83%, and a specificity of 75%.

 A panel of circulating miR18a/21/125b could be suggested as a potential biomarker for the early detection of GC.

Staphylococcus epidermidis (S. epidermidis) is the most frequently isolated pathogen from prostheses infections in the body. Therefore, improving its diagnostic methods, including rapid Nucleic Acid Amplification Tests (NAAT), seems necessary. Since the first step in designing a NAAT is to find a specific sequence and all DNA targets that have been introduced so far are not completely specific, we introduced a new 100% specific DNA target sequence to identify S. epidermidis in this study.

Modified comparative genomic analysis was used to find the best specific target sequence to detect S. epidermidis. A PCR method was designed for the evaluation of this target. To determine the detection limit and analytical specificity, pure genomic DNA of 18 bacteria include 12 standard strains (one S. epidermidis and 11 non-S. epidermidis) and six clinical isolates (five S. epidermidis and one non-S. epidermidis) were used.

The 400 bp sequence of S. epidermidis ATCC 14990 was identified as the most specific sequence (Se400), having a 100% sequence similarity to S. epidermidis genomes but not with other bacteria. The detection limit of Se400-PCR was 10 fg, equal to about 4 copies of S. epidermidis genomic DNA/μl. All pure DNA templates from S. epidermidis generated a detectable amplicon by 264 bp length, but the PCR test was negative for the non-S. epidermidis group.

The Se400 sequence can be considered as a specific target for detecting S. epidermidis, based on our findings.

Coronavirus disease 2019 spreads worldwide and needs detection systems capable of rapid diagnostic of this virus (SARS-CoV-2). The aim of this study is to design the homemade RT-PCR method for the Detection and phylogenetic analysis of this virus

The genes selected for diagnosis were E and M genes for this virus. PCR product was cloned in pTZ57R/T plasmid for preparation of positive control. In order to determine the sensitivity of this molecular method, the genes mentioned in the clone pTZ57R/T vector and the Limit of detection (LOD) the genes were determined and phylogenetic analysis was performed using partial E and M gene sequences.

PCR product was observed for E and M genes 156 and 547 bp on the Agarose gel. The LOD of the E and M gene was 60 and 82 copies. There was also a positive response to the samples of patients who were positive by other methods.

Since this virus is considered to be the cause of a pandemic in different countries all over the world, the present study is very important as a method of rapid and low-cost molecular diagnosis for monitoring this virus. Phylogenetic analysis is necessary for epidemiological studies for the control and prevention of the disease.

Substance use disorder is one of the most critical social problems in Iran. For this disorder, weneed a proper assessment tool based on our indigenous culture.

This study assesses the factor structure and psychometric properties of 10-item and 20-item Persian versions of Drug Abuse Screening Tests (DAST-10 and DAST-20).

In this cross-sectional study, we randomly selected 200 participants referred to addiction treatment centers in Rasht City, Iran. After translation to Persian and back-translation to English, the face and content validity of DAST-10 and DAST-20 Persian versions were evaluated using the opinions of a panel of expertsand calculatingthe content validity ratio and content validity index. Then, the construct validity was evaluated by Confirmatory Factor Analysis(CFA), the Cronbach α coefficient was used for assessing internal consistency, and the Intraclass Correlation Coefficient (ICC) was used for assessing test-retest reliability.

The Mean±SD age of participants was 39.02±11.67 years. The majority (50%) were in the age range of 30-50 years. Based on the CFA fit indices, the two instruments had a good fit to the data, confirming the theoretical model Root Mean Square Error of Approximation (RMSEA) (RMSEA for DAST-20=0.080; RMSEA for DAST-10=0.055). The Cronbach α values of DAST-20 and DAST-10 were 0.772 and 0.749, respectively, indicating their good and acceptable internal consistency. Their test-retest reliability was reported at 0.997 and 0.995 based on the results of ICC, respectively. There was a strong and significant positive correlation between the scores of Persian DAST-20 and DAST-10 (r=0.851, P=0.001).

The DAST-20 and DAST-10 Persian versions which after correcting the model using confirmatory factor analysis, they were studies in DAST-8 and DAST-16 have good validity and reliability and can be used for screening the possible involvement of drugs in Iranian samples.

Mentha is a genus from the family Lamiaceae, whose essential oils has long been used in different forms. This herbal plant has traditionally been used as an alternative medicine to treat candidiasis. So, it seems crucial to find new antimicrobials that have fewer side effects. In this study, we investigated the antifungal effects of Mentha aquatica L essential oil on pathogenic Candida spp. This descriptive cross-sectional study was performed on 137 Candida spp isolated from vulvovaginal candidiasis. These yeasts were confirmed by Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Mentha aquatica L essential oil was prepared by water distillation and Clevenger apparatus. The antifungal activity of Mentha aquatica L essential oil and fluconazole versus Candida spp was determined by microbroth dilution method using CLSI guidelines. The most common species were identified that Candida albicans (63.5%), Candida glabrata (28.5%) and Candida krusei (8%), respectively. MIC50, MIC90 and geometric mean (GM) of fluconazole were 0.5 µg/ml, 4 µg/ml and 0.573 µg/ml and for Mentha aquatica L essential oil 1 µg/ml, 4 µg/ml and 0.931 µg/ml, respectively. The antifungal effect of fluconazole on Candida spp was higher than that of essential oil of plant. It seems that the inhibitory effect of essential oil of Mentha aquatica L has shown that this plant can be considered as a potential candidate for the development of antifungal drug in the treatment of vulvovaginal candidiasis.