The presence of fungi in the indoor environment is associated with allergies and other respiratory symptoms. The aim of this study was to use sequencing and molecular methods, including next-generation sequencing (NGS) approaches, to explore the bacterial and fungal communities and their abundance in the indoor environment of houses (n = 20) with visible \"moldy\" (HVM) and nonvisible \"non-moldy\" (HNM) in Memphis, TN, USA. Dust samples were collected from air vents and ground surfaces, and the total DNA was analyzed for bacteria and fungi by amplifying 16S rRNA and ITS genes on the Illumina Miseq. Results indicated that Leptosphaerulina was the most abundant fungal genus present in the air vent and ground samples from HNM and HVM. At the same time, the most abundant bacterial genera in the air vent and ground samples were Propionibacterium and Streptococcus. The fungi community diversity was significantly different in the air vent samples. The abundance of fungal species known to be associated with respiratory diseases in indoor dust samples was similar, regardless of the visibility of fungi in the houses. The existence of fungi associated with respiratory symptoms was compared with several parameters like dust particulate matter (PM), CO2 level, temperature, and humidity. Most of these parameters are either positively or negatively correlated with the existence of fungi associated with respiratory diseases; however, none of these correlations were significant at p = 0.05. Our results indicate that implementing molecular methods for detecting indoor fungi may strengthen common exposure and risk assessment practices.

BACKGROUND: Monocyte-macrophage lineage cells are committed towards osteoclast differentiation in vitro by the downregulation of microphthalmia-induced transcription factor (MITF) by miRNA-155. Therefore, we aimed to evaluate miRNA-155 expression and explore the regulation of MITF by miRNA-155 during osteoclastogenesis in periodontitis.
METHODS: Ninety-eight subjects were recruited and categorized into the following: group I (cases)-systemically healthy with localized stage III/IV periodontitis (N = 49) and group II (controls)-systemically and periodontally healthy (N = 49). Gingival tissue samples were procured and qRT-PCR analysis was carried out for relative gene expression.
RESULTS: The mean ΔCT of miRNA-155 expression was -1.04 ± 2.26 and -0.01 ± 1.4 respectively for groups I and II. There was a statistically significant difference in the miRNA-155 expression (P ≤ 0.01) between the groups. The mean ΔCT of MITF expression for groups I and II was 4.15± 2.16 and 3.51± 1.57 respectively with no significant difference (P > 0.01) between the groups. In the periodontitis group, miRNA-155 expression increased by fivefolds (P ≤ 0.01) whereas MITF expression showed no significant difference in the fold change between the groups (P > 0.01). The site-specific clinical parameters showed a statistically significant strong negative and positive correlation with the ΔCT and fold change values of miRNA-155 respectively in the total 98 samples (P < 0.01). miRNA-155 was able to discriminate between periodontal health and disease with a diagnostic accuracy of 96.9% (95%CI: 91.38-98.95) and the AUC was 0.98 (95%CI: 0.97-1.0, SE = 0.008, P < 0.001) in ROC analysis with a sensitivity of 93.8% (95%CI: 83.48-97.9) and specificity of 100% (95%CI: 92.73-100).
CONCLUSIONS: miRNA-155 was dysregulated and upregulated by fivefolds in periodontal disease. It can be used as a potential biomarker to discriminate between periodontal health and disease. No difference in the MITF gene expression was demonstrated between periodontal health and disease. The result suggested that miRNA-155 does not affect the expression of MITF gene in the process of osteoclastogenesis in localized stage III/IV periodontitis within this study design and limitations.

BACKGROUND: Highly Active Antiretroviral Therapy (HAART) is composed of several drugs in the antiretroviral class to better treat human immunodeficiency virus type 1 (HIV-1) patients. The estimation of CD4+ T cell counts and HIV-1 viral load in plasma is required to evaluate the treatment success of a specific HAART.
METHODS: The study included the effects of NRTIs (nucleoside reverse transcriptase inhibitors) and novel protease inhibitors (HAART) on normal control subjects and HIV-1 positive subjects from SGPGIMS, Lucknow, with different age groups and genders. Furthermore, the study was conducted by the estimation of HIV through ELISA, measurement of absolute CD4+ cell count, and the measurement of viral load through qRT-PCR. Furthermore, NRTIs (Retrovir and Epivir) were administered orally one tablet daily in the morning followed by newly FDA-approved protease inhibitors (fosamprenavir and darunavir) orally in the evening at the same dose. Furthermore, CD4+T cell counts and HIV-1 viral load were investigated and correlated in patients with different genders and age groups.
RESULTS: Administration of NRTIs and novel protease inhibitors (HAART) in HIV patients had a significant effect on the CD4+ cell count in various age intervals among males and females. The mean comparison of viral load distribution based on gender in CD4 +ve patients in the case group exhibited a viral load higher in females compared to males, indicating a statistically significant difference between males and females (p<0.05). A notable association between virological and immunological parameters was observed with a reciprocal relationship between viral load and CD4 cell count in CD4 +ve patients, demonstrating multiple correlation coefficients with an R-value of 0.853.
CONCLUSIONS: The administration of specific HAART (NRTIs and novel protease inhibitors) in HIV patients had a notable improvement in the CD4+ cell count and viral load with significant age and gender disparity.

This short communication describes the reinfection after nearly 18 months of the same patient who was previously infected with coronavirus disease 2019 (COVID-19) and who showed multiple negative real-time quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) results by nasal swabs for severe acute respiratory syndrome coronavirus (SARS-CoV-2) but positive results on a fecal sample. We previously noted how, in the presence of symptoms suggestive of pneumonia, visible on a chest computed tomography (CT) scan and confirmed by fecal molecular testing, it was possible to draw the diagnosis of SARS-CoV-2 infection. One year later, the same patient was again affected by SARS-CoV-2. This time, the first antigenic nasal swab showed readily positive results. However, the patient\'s clinical course appeared to be more attenuated, showing no signs of pulmonary involvement in the radiographic examinations performed. This case shows a novelty in the pulmonary radiological evaluation of new SARS-CoV-2 infection.

COVID-19 is an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus affecting the world population. Early detection has become one of the most successful strategies to alleviate the epidemic and pandemic of this contagious coronavirus. Surveillance testing programs have been initiated in many countries worldwide to prevent the outbreak of COVID-19. In this study, we demonstrated that our previously established clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a-based assay could detect variants of concern during 2021 in Thailand, including Alpha, Beta, and Delta strains as well as Omicron strain in early 2022. In combination with the newly designed saliva collection funnel, we established a safe, simple, economical, and efficient self-collection protocol for the COVID-19 screening process. We successfully utilized the assay in an active case finding with a total number of 578 asymptomatic participants to detect the SARS-CoV-2 in saliva samples. We finally demonstrated that the validation and evaluation in a large-scale setting could provide valuable information and elaborate the practicality of the test in real-world settings. Our optimized protocol yielded effective results with high sensitivity, specificity, and diagnostic accuracy (96.86%). In addition, this study demonstrates COVID-19 active case findings in low-resource settings, which would be feasible and attractive for surveillance and outbreak prevention in the future.

BACKGROUND: Quantitative, reverse transcription PCR (qRT-PCR) is currently the gold-standard for SARS-CoV-2 detection and it is also used for detection of other virus. Manual data analysis of a small number of qRT-PCR plates per day is a relatively simple task, but automated, integrative strategies are needed if a laboratory is dealing with hundreds of plates per day, as is being the case in the COVID-19 pandemic.
RESULTS: Here we present shinyCurves, an online shiny-based, free software to analyze qRT-PCR amplification data from multi-plate and multi-platform formats. Our shiny application does not require any programming experience and is able to call samples Positive, Negative or Undetermined for viral infection according to a number of user-defined settings, apart from providing a complete set of melting and amplification curve plots for the visual inspection of results.
CONCLUSIONS: shinyCurves is a flexible, integrative and user-friendly software that speeds-up the analysis of massive qRT-PCR data from different sources, with the possibility of automatically producing and evaluating melting and amplification curve plots.

We report a rare laboratory-confirmed, clinical case of Echovirus-7 infection in an immuno-competent child with central nervous system and systemic manifestation. Echovirus infection is usually mild, however in this case we identified echovirus-7 infection with 91% homology with the Echovirus-7 strain previously isolated in neighbouring country with severe manifestation.

BACKGROUND: Neuroendocrine neoplasms (NENs) are a complex group of tumours that occur in many organs. Routinely used IHC markers for NEN diagnosis include CgA, synaptophysin, Ki67 and CD56. These have limitations including lack of correlation to clinical outcomes and their presence in non-tumour tissue. Identification of additional markers and more quantitative analyses of tumour tissue has the potential to contribute to improved clinical outcomes. We used qRT-PCR to profile the expression levels of a panel of markers in tumour and matched non-tumour tissue from a patient with a G1 pancreatic neuroendocrine tumour. Differences in mRNA levels between tumour and non-tumour tissue were compared with IHC analyses of the same sample.
METHODS: An elderly man presented with lower abdominal pain for 6 months. Histological analysis identified a low grade, well differentiated pancreatic endocrine neoplasm. Twenty-seven tumour markers for neuroendocrine status, proliferation, stem cell phenotype, angiogenesis, epithelial to mesenchymal transition, cell adhesion, differentiation and tumour suppression were selected from previous studies and mRNA levels of these markers were measured in tumour and adjacent non-tumour tissue sample using qRT-PCR. IHC was carried out on the same tissue to detect the corresponding marker proteins. Of the markers analysed, seven showed higher mRNA levels in tumour relative to non-tumour tissue while thirteen had lower expression in tumour relative to non-tumour tissue. Substantial differences in mRNA levels were a gain of CgA, CD56, β-catenin, CK20, PDX1 and p53 and loss of Ki67, PCAD, CK7, CD31, MENA, ECAD, EPCAM, CDX2 and CK6. Comparison of qRT-PCR data with IHC showed correlation between fifteen markers.
CONCLUSIONS: Our study is unique as it included matched controls that provided a comparative assessment for tumour tissue analysis, whereas many previous studies report tumour data only. Additionally, we utilised qRT-PCR, a relatively quantitative diagnostic tool for differential marker profiling, having the advantage of being reproducible, fast, cheap and accurate. qRT-PCR has the potential to improve the defining of tumour phenotypes and, in combination with IHC may have clinical utility towards improving tumour stratification or distinguishing tumour grades. The results need to be validated with different grades of NENs and related to clinical outcomes.

The potential role of environmental M. leprae in the transmission of leprosy remains unknown. We investigated role of environment as a possible source of viable M. leprae responsible for transmission of leprosy. The samples were collected from 10 multi-case leprosy families comprising, slit skin smear (SSS) from 9 multibacillary (MB), 16 paucibacillary cases (PB), 22 household contacts, and 38 environmental soil samples. The quantum of viable M. leprae was estimated by qRT-PCR using 16S rRNA gene from soil and SSS. Genotypes of M. leprae were determined by gene sequencing. We could observe presence of viable M. leprae in 11 (44%) leprosy cases (M. leprae 16S rRNA gene copies range from 1.78 × 102 to 8.782 × 109) and 4 (18%) household contacts (M. leprae 16S rRNA gene copies range from 2.54 × 103 and 7.47 × 104). Remarkably, presence of viable M. leprae was also noted in 10 (53%) soil samples where in M. leprae 16S rRNA gene copies ranged from 4.36 × 102 to 7.68 × 102. M leprae subtype 1D was noted in most of the leprosy cases their household contacts and in the surrounding soil samples indicating source of infection in household contacts could be from environment or patients. M. leprae 16S rRNA copies were approximately similar in both PB cases and soil samples along with presence of SNP type 1 subtype 1D in both samples indicating source of M. leprae from patients to contacts was either from patients or environment or both.

Ghrelin has been found to be expressed in the human endometrium. Emerging evidence links ghrelin and its receptor with the reproductive system. Certain associations between ghrelin and angiogenesis have also been established. The aim of this small case-control study was to quantify and compare the expression of mRNA encoding ghrelin, ghrelin receptor (GHS-R), vascular endothelial growth factor A (VEGF A) and its receptors (VEGFR1-3) in the endometrium of women with recurrent miscarriage compared to parous controls. Correlations between the expression of particular genes were also investigated. Endometrial samples were obtained during the secretory phase of the menstrual cycle from 15 women with a history of recurrent miscarriage (first trimester pregnancy loss without a known cause) and 10 healthy parous controls. Ghrelin, GHS-R, VEGF A and VEGFR1-3 mRNA expression was analyzed by quantitative RT-PCR. The expression of mRNA for ghrelin and VEGF A was significantly higher in the study group than the control group. In the control group, the expression of ghrelin mRNA was positively correlated with the expression of VEGF A and VEGFR1 mRNA. In the study group, no such associations were observed. These results show that the expression of mRNA for ghrelin and VEGF A may be increased in the endometrium of women with recurrent miscarriage thus suggesting that ghrelin may play a role in the pathogenesis of recurrent miscarriage.