Multi-omics analysis identifies potential microbial and metabolite diagnostic biomarkers of bacterial vaginosis

BACKGROUND

Bacterial vaginosis (BV) is a common clinical manifestation of a perturbed vaginal ecology associated with adverse sexual and reproductive health outcomes if left untreated. The existing diagnostic modalities are either cumbersome or require skilled expertise, warranting alternate tests. Application of machine-learning tools to heterogeneous and high-dimensional multi-omics datasets finds promising potential in data integration and may aid biomarker discovery.

OBJECTIVES

The present study aimed to evaluate the potential of the microbiome and metabolome-derived biomarkers in BV diagnosis. Interpretable machine-learning algorithms were used to evaluate the utility of an integrated-omics-derived classification model.

METHODS

Vaginal samples obtained from reproductive-age group women with (n = 40) and without BV (n = 40) were subjected to 16S rRNA amplicon sequencing and LC-MS-based metabolomics. The vaginal microbiome and metabolome were characterized, and machine-learning analysis was performed to build a classification model using biomarkers with the highest diagnostic accuracy.

RESULTS

Microbiome-based diagnostic model exhibited a ROC-AUC (10-fold CV) of 0.84 ± 0.21 and accuracy of 0.79 ± 0.18, and important features were Aerococcus spp., Mycoplasma hominis, Sneathia spp., Lactobacillus spp., Prevotella spp., Gardnerella spp. and Fannyhessea vaginae. The metabolome-derived model displayed superior performance with a ROC-AUC of 0.97 ± 0.07 and an accuracy of 0.92 ± 0.08. Beta-leucine, methylimidazole acetaldehyde, dimethylethanolamine, L-arginine and beta cortol were among key predictive metabolites for BV. A predictive model combining both microbial and metabolite features exhibited a high ROC-AUC of 0.97 ± 0.07 and accuracy of 0.94 ± 0.08 with diagnostic performance only slightly superior to the metabolite-based model.

CONCLUSION

Application of machine-learning tools to multi-omics datasets aid biomarker discovery with high predictive performance. Metabolome-derived classification models were observed to have superior diagnostic performance in predicting BV than microbiome-based biomarkers.

Assessing the effects of common topical exposures on skin bacteria associated with atopic dermatitis

Background

While patients and families struggling with atopic dermatitis (AD) have documented concerns for a contributory role of skin care products in AD pathology, nearly all the skin microbiome studies to date have asked participants to avoid topical products (such as soaps or select medications) for the preceding days to weeks prior to sample collection. Thus, given the established role of the microbiome in AD, the interactions between topical exposures, dysbiosis and AD remains underrepresented in the academic literature.

Objectives

To address this knowledge gap, we expanded our previous evaluations to test the toxicological effects of a broader range of common chemicals, AD treatment lotions, creams and ointments using both health- and AD-associated strains of Roseomonas mucosa and Staphylococcus spp.

Methods

Use of in vitro culture techniques and mouse models were deployed to identify chemicals with dysbiotic or pre-biotic potential. A proof-of-concept study was subsequently performed in healthy volunteers to assess global microbiome shifts after exposure to select chemicals using dermatologic patch testing.

Results

Numerous chemicals possessed antibiotic properties, including many not marketed as anti-microbials. Through targeted combination of potentially beneficial chemicals, we identified combinations which promoted the growth of health-associated isolates over disease-associated strains in bacterial culture and enhanced microbe-specific outcomes in an established mouse model of AD; the most promising of which was the combination of citral and colophonium (often sold as lemon myrtle oil and pine tar). Additional studies would likely further optimize the combination of ingredients use. Similar results were seen in the proof-of-concept human studies.

Conclusions

Our results could offer a systematic, multiplex approach to identify which products carry dysbiotic potential and thus may guide formulation of new topicals to benefit patients with AD.

Comparative Assessment of Revascularization Versus Drug Management in Coronary Artery Disease (CAD) Associated with Left Ventricular Dysfunction (EF < 40%) - A 12 Month Study with FDG PET and SPECT MPI Analyses

AIM OF THE STUDY

Left Ventricular (LV) function and myocardial viability is the key predictor of prognosis after myocardial infarction. Management of ischemic cardiomyopathy (revascularization and or drugs alone) is the objective of this study.

METHODOLOGY

72 patients were assigned to revascularization and medical management group based on the inclusion criteria Follow up was done upto 12 months with advanced imaging techniques (FDG PET and SPECT MPI analyses).

RESULTS

Subjects with significant viable myocardium, revascularization resulted in significant improvement in heart failure symptoms. The mean NYHA functional class improved from 2.9 ± 0.3 to 2.3 ± 0.5(mean ± SD) after 6 months of revascularization (p < 0.01). This improvement in functional class was maintained after 12 months of revascularization (2.0 ± 0.4 (mean ± SD). Subjects on medical management with a baseline NYHA functional class 2.7 ± 0.5, at 6 months of follow, there was no significant change in functional class (2.8 ± 0.3) (p<0.24). However at 12 months follow up functional class had dropped to 3.0 + 0.3, which was significant as compared to baseline (p <0.03).

CONCLUSION

coronary revascularization has a protective effect on patients with ischemic coronary who have viable myocardium and reversible myocardial ischemia as assessed by 18F-FDG PET and SPECT MPI Imaging.

Overview of the rules of the microbial engagement in the gut microbiome: a step towards microbiome therapeutics

Human gut microbiome is a diversified, resilient, immuno-stabilized, metabolically active and physiologically essential component of the human body. Scientific explorations have been made to seek in-depth information about human gut microbiome establishment, microbiome functioning, microbiome succession, factors influencing microbial community dynamics and the role of gut microbiome in health and diseases. Extensive investigations have proposed the microbiome therapeutics as a futuristic medicine for various physiological and metabolic disorders. A comprehensive outlook of microbial colonization, host-microbe interactions, microbial adaptation, commensal selection and immuno-survivability is still required to catalogue the essential genetic and physiological features for the commensal engagement. Evolution of a structured human gut microbiome relies on the microbial flexibility towards genetic, immunological and physiological adaptation in the human gut. Key features for commensalism could be utilized in developing tailor-made microbiome-based therapy to overcome various physiological and metabolic disorders. This review describes the key genetics and physiological traits required for host-microbe interaction and successful commensalism to institute a human gut microbiome.

Analysis on novel coronavirus (COVID-19) using machine learning methods

In this paper, we are working on a pandemic of novel coronavirus (COVID-19). COVID-19 is an infectious disease, it creates severe damage in the lungs. COVID-19 causes illness in humans and has killed many people in the entire world. However, this virus is reported as a pandemic by the World Health Organization (WHO) and all countries are trying to control and lockdown all places. The main objective of this work is to solve the five different tasks such as I) Predicting the spread of coronavirus across regions. II) Analyzing the growth rates and the types of mitigation across countries. III) Predicting how the epidemic will end. IV) Analyzing the transmission rate of the virus. V) Correlating the coronavirus and weather conditions. The advantage of doing these tasks to minimize the virus spread by various mitigation, how well the mitigations are working, how many cases have been prevented by this mitigations, an idea about the number of patients that will recover from the infection with old medication, understand how much time will it take to for this pandemic to end, we will be able to understand and analyze how fast or slow the virus is spreading among regions and the infected patient to reduce the spread based clear understanding of the correlation between the spread and weather conditions. In this paper, we propose a novel Support Vector Regression method to analysis five different tasks related to novel coronavirus. In this work, instead of simple regression line we use the supported vectors also to get better classification accuracy. Our approach is evaluated and compared with other well-known regression models on standard available datasets. The promising results demonstrate its superiority in both efficiency and accuracy.

Late onset systemic sclerosis with seronegativity: a rare presentation of an uncommon disease

Systemic sclerosis (SSc) is an uncommon connective tissue disorder characterized by multisystem involvement with fibrosis of skin and internal organs. Antibody formation is one of the hallmarks of SSc. Antinuclear antibodies (ANA) are positive in 97% of patients with SSc. We report a rare case where the patient was negative for ANA, Anti-topoisomerase I, Anti-centromere and Anti-RNA polymerase III antibodies.

Osteopontin regulates dentin and alveolar bone development and mineralization

The periodontal complex is essential for tooth attachment and function and includes the mineralized tissues, cementum and alveolar bone, separated by the unmineralized periodontal ligament (PDL). To gain insights into factors regulating cementum-PDL and bone-PDL borders and protecting against ectopic calcification within the PDL, we employed a proteomic approach to analyze PDL tissue from progressive ankylosis knock-out (Ank^-/-) mice, featuring reduced PP_i, rapid cementogenesis, and excessive acellular cementum. Using this approach, we identified the matrix protein osteopontin (Spp1/OPN) as an elevated factor of interest in Ank^-/- mouse molar PDL. We studied the role of OPN in dental and periodontal development and function. During tooth development in wild-type (WT) mice, Spp1 mRNA was transiently expressed by cementoblasts and strongly by alveolar bone osteoblasts. Developmental analysis from 14 to 240days postnatal (dpn) indicated normal histological structures in Spp1^-/- comparable to WT control mice. Microcomputed tomography (micro-CT) analysis at 30 and 90dpn revealed significantly increased volumes and tissue mineral densities of Spp1^-/- mouse dentin and alveolar bone, while pulp and PDL volumes were decreased and tissue densities were increased. However, acellular cementum growth was unaltered in Spp1^-/- mice. Quantitative PCR of periodontal-derived mRNA failed to identify potential local compensators influencing cementum in Spp1^-/- vs. WT mice at 26dpn. We genetically deleted Spp1 on the Ank^-/- mouse background to determine whether increased Spp1/OPN was regulating periodontal tissues when the PDL space is challenged by hypercementosis in Ank^-/- mice. Ank^-/-; Spp1^-/- double deficient mice did not exhibit greater hypercementosis than that in Ank^-/- mice. Based on these data, we conclude that OPN has a non-redundant role regulating formation and mineralization of dentin and bone, influences tissue properties of PDL and pulp, but does not control acellular cementum apposition. These findings may inform therapies targeted at controlling soft tissue calcification.

Humoral and T cell-mediated immune response against trichomoniasis

Trichomonas vaginalis (T. vaginalis) infection leads to the synthesis of specific antibodies in the serum and local secretions. The profile of T. vaginalis-specific antibodies and T cell-mediated immune responses may influence the outcome of infection, towards parasite elimination, persistence or pathological reactions. Studies have indicated that Th1-, Th17- and Th22 cell-related cytokines may be protective or pathogenic, whereas Th2- and Treg cell-related cytokines can exert anti-inflammatory effects during T. vaginalis infection. A number of T. vaginalis-related components such as lipophosphoglycan (TvLPG), α-actinin, migration inhibitory factor (TvMIF), pyruvate:ferredoxin oxidoreductase (PFO), legumain-1 (TvLEGU-1), adhesins and cysteine proteases lead to the induction of specific antibodies. T. vaginalis has acquired several strategies to evade the humoral immune responses such as degradation of immunoglobulins by cysteine proteases, antigenic variation and killing of antibody-producing B cells. The characterization of the T. vaginalis-specific antibodies to significant immunogenic molecules and formulation of strategies to promote their induction in vaginal mucosa may reveal their potential protective effects against trichomoniasis. In this review, we discuss the current understanding of antibody and T cell-mediated immune responses to T. vaginalis and highlight novel insights into the possible role of immune responses in protection against parasite.

MINIMAL INVASIVE SURGICAL APPROACH IN THEMANAGEMENT OF COMMINUTED CROWN-ROOT FRACTURE- A CASE REPORT

Comminuted root fractures have a questionable prognosis and present with limited treatment options. In the following case, a comminuted crown root fracture in relation to maxillary left central incisor was managed with a minimally invasive surgical approach. The procedure involved repairing the multiple fracture lines in the root with Biodentine following the endodontic therapy and root resection. The patient was found to be asymptomatic at the end of a follow up period of ten months.

MARGINAL MICROLEAKAGE PROPERTIES OF ACTIVA BIOACTIVE RESTORATIVE AND NANOHYBRID COMPOSITE RESIN USING TWO DIFFERENT ADHESIVES IN NON CARIOUS CERVICAL LESIONS - AN IN VITRO STUDY

BACKGROUND

In clinical practice, the restoration of non-carious cervical lesions is a challenge, because most of the time the cervical margin is located in cementum or dentin. This characteristic makes the cervical margin more susceptible to microleakage, causing cavosurface stains, postoperative sensitivity and also favours the incidence of carious lesions.

AIM

To compare and evaluate the microleakage in class V lesions restored with Activa Bioactive restorative and nanohybrid composite resin using two different bonding agents.

METHODOLOGY

In this study, 50 class V cavities were prepared in freshly extracted teeth. The samples were randomly divided into 5 groups (n=10), depending on the type of restorative material and bonding agent: Group 1 - Activa Bioactive (Pulpdent, USA) + No bonding, Group 2 - Activa Bioactive + Tetric N Bond (Ivoclar Vivadent, Colombia),Group 3 - Activa Bioactive + G Bond (GC Corp., Tokyo, Japan), Group 4 - Nanohybrid Composite (Ivoclar Vivadent, Colombia) + Tetric N Bond, Group 5 - Nanohybrid Composite + G Bond. The samples were restored with their respective material based on the group. After curing all the specimens were subjected to thermocycling and cyclic loading. Specimens were stained with 2% rhodamin b dye and evaluated for dye penetration.

RESULTS

Results were obtained based on Kruskal Wallis and Mann Whitney U- test.

CONCLUSION

Within the limitations of this study, none of the materials were free from microleakage. All the materials showed more microleakage at gingival margins compared to occlusal margins. Among all the groups Activa Bioactive restorative when used in combination with Tetric N Bond showed the least microleakage.

Kallman Syndrome

Kallman syndrome (KS) is a rare genetic disorder characterized clinically by failure to attain puberty or failure to fully complete it along with an absent or impaired sense of smell with absence of bilateral olfactory bulbi and sulci alongwith absent olfactory tracts. Only very few cases of Kallman syndrome have been reported in females in Indian population.

Escherichia vulneris: an unusual cause of complicated diarrhoea and sepsis in an infant. A case report and review of literature

Escherichia vulneris is an opportunistic human pathogen. It has been primarily reported in adult patients and invasive infections have been observed in immune-suppressed individuals. This is the first report of E. vulneris causing complicated diarrhoea and sepsis in an infant.

Two month old sick infant, born full-term, was admitted to the paediatrics department with loose motions and refusal to feed for four days. E. vulneris was isolated from blood in pure culture. The isolate was characterized for diarrhoeal virulence markers: heat labile and heat stable toxins (LT, ST) and hemolysin (hlyA) by PCR. The presence of LT enterotoxin and hemolysin provides strong evidence of the diarrhoeagenic potential of E. vulneris, further leading to the invasive infection triggering sepsis.

As E. vulneris can lead to serious complications, an attempt should be made in clinical laboratories to identify and further characterize this new Escherichia species.

Role of PHOSPHO1 in Periodontal Development and Function

The tooth root and periodontal apparatus, including the acellular and cellular cementum, periodontal ligament (PDL), and alveolar bone, are critical for tooth function. Cementum and bone mineralization is regulated by factors including enzymes and extracellular matrix proteins that promote or inhibit hydroxyapatite crystal growth. Orphan Phosphatase 1 (Phospho1, PHOSPHO1) is a phosphatase expressed by chondrocytes, osteoblasts, and odontoblasts that functions in skeletal and dentin mineralization by initiating deposition of hydroxyapatite inside membrane-limited matrix vesicles. The role of PHOSPHO1 in periodontal formation remains unknown and we aimed to determine its functional importance in these tissues. We hypothesized that the enzyme would regulate proper mineralization of the periodontal apparatus. Spatiotemporal expression of PHOSPHO1 was mapped during periodontal development, and Phospho1(-/-) mice were analyzed using histology, immunohistochemistry, in situ hybridization, radiography, and micro-computed tomography. The Phospho1 gene and PHOSPHO1 protein were expressed by active alveolar bone osteoblasts and cementoblasts during cellular cementum formation. In Phospho1(-/-) mice, acellular cementum formation and mineralization were unaffected, whereas cellular cementum deposition increased although it displayed delayed mineralization and cementoid. Phospho1(-/-) mice featured disturbances in alveolar bone mineralization, shown by accumulation of unmineralized osteoid matrix and interglobular patterns of protein deposition. Parallel to other skeletal sites, deposition of mineral-regulating protein osteopontin (OPN) was increased in alveolar bone in Phospho1(-/-) mice. In contrast to the skeleton, genetic ablation of Spp1, the gene encoding OPN, did not ameliorate dentoalveolar defects in Phospho1(-/-) mice. Despite alveolar bone mineralization defects, periodontal attachment and function appeared undisturbed in Phospho1(-/-) mice, with normal PDL architecture and no evidence of bone loss over time. This study highlights the role of PHOSPHO1 in mineralization of alveolar bone and cellular cementum, further revealing that acellular cementum formation is not substantially regulated by PHOSPHO1 and likely does not rely on matrix vesicle-mediated initiation of mineralization.

Carbohydrate compounds as green corrosion inhibitors: electrochemical, XPS, DFT and molecular dynamics simulation studies

Corrosion inhibition effect of 5,6-bis(2-(1H-benzo[d]imidazol-2-yl)hydrazono)hexane-1,2,3,4-tetraol (BIHT) and 5,6-bis(2-(1-methyl-1H-imidazol-2-yl)hydrazono)hexane-1,2,3,4-tetraol (MIHT) on N80 steel in 15% HCl was measured by electrochemical method.

Families of Pseudohypoparathyroidism presenting as Seizure

Pseudohypoparathyroidism (PHP) is a heterogeneous group of disorders characterized by variable insensitivity to parathyroid hormone. We describe two cases of 22 year male and 24 year female who have typical clinical features of Albright's hereditary osteodystrophy (AHO). Laboratory investigation revealed evidence of pseudohypoparathyroidism and skeletal survey showed shortening of the metacarpals and metatarsals.

Targeting leukemia stem cells in vivo with antagomiR-126 nanoparticles in acute myeloid leukemia

Current treatments for acute myeloid leukemia (AML) are designed to target rapidly dividing blast populations with limited success in eradicating the functionally distinct leukemia stem cell (LSC) population, which is postulated to be responsible for disease resistance and relapse. We have previously reported high miR-126 expression levels to be associated with a LSC-gene expression profile. Therefore, we hypothesized that miR-126 contributes to “stemness” and is a viable target for eliminating the LSC in AML. Here we first validate the clinical relevance of miR-126 expression in AML by showing that higher expression of this microRNA (miR) is associated with worse outcome in a large cohort of older (≥60 years) cytogenetically normal AML patients treated with conventional chemotherapy. We then show that miR-126 overexpression characterizes AML LSC-enriched cell subpopulations and contributes to LSC long-term maintenance and self-renewal. Finally, we demonstrate the feasibility of therapeutic targeting of miR-126 in LSCs with novel targeting nanoparticles (NP) containing antagomiR-126 resulting in in vivo reduction of LSCs likely by depletion of the quiescent cell subpopulation. Our findings suggest that by targeting a single miR, i.e., miR-126, it is possible to interfere with LSC activity, thereby opening potentially novel therapeutic approaches to treat AML patients.

Faecal Escherichia coli isolates show potential to cause endogenous infection in patients admitted to the ICU in a tertiary care hospital

Nosocomial infections are acquired during hospital treatment or in a hospital environment. One such infecting agent, Escherichia coli, harbours many virulence genes that enable it to become pathogenic, causing damage to the host. The mechanism of the E. coli virulence factors provenance to cause infection in host environments is not clearly elucidated. We investigated the virulence and pathogenicity of E. coli affected by the host environment. For this, blood (n = 78) and faecal (n = 83) E. coli isolates were collected from patients with and without sepsis, respectively, who had been admitted to the intensive care unit. The E. coli genomic DNA was isolated; the phylogenetic grouping was conducted by triplex PCR. The occurrence of nine virulence genes among the all the isolates was confirmed by gene-specific PCR. The prevalence of E. coli in blood isolates was more in phylogenetic groups B2 and D compared to groups A and B1. However, in faecal isolates, there was no significant difference. The prevalence of adhesin and toxin (papG, sfa, afa, cnf1, hlyA) genes was higher in blood compared to faecal E. coli isolates. However, the prevalence of aer, traT and PAI was similar as well as higher among both of these groups. These observations indicate a role of external environment (hospital setting) on host susceptibility (development of infection) in the faecal E. coli isolates, thereby making the patient prone to a sepsis condition.

tcpC as a prospective new virulence marker in blood Escherichia coli isolates from sepsis patients admitted to the intensive care unit

The prevalence of the tcpC in the blood Escherichia coli isolates collected from the sepsis patients admitted to the intensive care unit was investigated for the first time. The blood and faecal samples were collected from sepsis and nonsepsis patients, respectively. The prevalence of the tcpC and phylogroups was confirmed by gene-specific PCR. The occurrence of the tcpC in the blood E. coli isolates from sepsis patients was significantly higher than the faecal isolates. The higher prevalence of blood E. coli isolates among the pathogenic groups (B2, D) compared to the commensal groups (A, B1) suggests tcpC as a prospective new virulence marker for sepsis.

Dental exarticulation

Tooth exarticulation or avulsion refers to the complete displacement of the tooth out of its socket. It is a complex injury, requiring immediate intervention for optimal results. Literature indicates that prolonged dry time and improper handling may be associated with increased risk of failure. Immediate replantation of the tooth allows for immediate restoration of esthetics and phonetics. This case report presents the management of an avulsed mature tooth in a young boy, with a two-year follow-up, which had been preserved in milk after around 15-20 minutes of injury and transplanted after two hours at a dental hospital. Timely modified endodontic therapy prevented subsequent inflammatory root resorption.

Corrosion inhibition effect of spiropyrimidinethiones on mild steel in 15% HCl solution: insight from electrochemical and quantum studies

The effect of synthesized spiropyrimidinethiones on the corrosion of mild steel in 15% HCl solution was investigated by using weight loss and electrochemical methods.

Immunity in urogenital protozoa

Innate and adaptive immunity play a significant role in urogenital infections. Innate immunity is provided by the epithelial cells and mucus lining along with acidic pH, which forms a strong physical barrier against the pathogens in female reproductive tract. Cells of innate immune system, antimicrobial peptides, cytokines, chemokines and adaptive immunity in the reproductive tract are evolved during infection, and a pro-inflammatory response is generated to fight against the invading pathogen Trichomonas vaginalis, a primary urogenital protozoa, the etiological agent of human trichomoniasis, a curable sexually transmitted infection. The involvement of the urogenital tract by other protozoal infections such as P. falciparum, Trypanosoma, Leishmania, Toxoplasma, Entamoeba histolytica and Acanthamoeba infection is rarely reported. Trichomonas induce pro-inflammatory and immunosuppressive responses in infected subjects. Multifactorial pathogenic mechanisms including parasite adherence, cysteine proteases, lipophosphoglycan, free radical, cytokine generation and Toll-like receptors appear to interplay with the induction of local and systemic immune responses that ultimately determine the outcome of the infection. However, the involvement of urogenital pathogen-specific immune mechanisms and effect of normal local resident flora on the outcome (symptomatic vs. asymptomatic) of infection are poorly understood. Moreover, immune interactions in trichomoniasis subjects co-infected with bacterial and viral pathogens need to be elucidated.