Computer-aided diagnosis of keratoconus through VAE-augmented images using deep learning

Detecting clinical keratoconus (KCN) poses a challenging and time-consuming task. During the diagnostic process, ophthalmologists are required to review demographic and clinical ophthalmic examinations in order to make an accurate diagnosis. This study aims to develop and evaluate the accuracy of deep convolutional neural network (CNN) models for the detection of keratoconus (KCN) using corneal topographic maps. We retrospectively collected 1758 corneal images (978 normal and 780 keratoconus) from 1010 subjects of the KCN group with clinically evident keratoconus and the normal group with regular astigmatism. To expand the dataset, we developed a model using Variational Auto Encoder (VAE) to generate and augment images, resulting in a dataset of 4000 samples. Four deep learning models were used to extract and identify deep corneal features of original and synthesized images. We demonstrated that the utilization of synthesized images during training process increased classification performance. The overall average accuracy of the deep learning models ranged from 99% for VGG16 to 95% for EfficientNet-B0. All CNN models exhibited sensitivity and specificity above 0.94, with the VGG16 model achieving an AUC of 0.99. The customized CNN model achieved satisfactory results with an accuracy and AUC of 0.97 at a much faster processing speed compared to other models. In conclusion, the DL models showed high accuracy in screening for keratoconus based on corneal topography images. This is a development toward the potential clinical implementation of a more enhanced computer-aided diagnosis (CAD) system for KCN detection, which would aid ophthalmologists in validating the clinical decision and carrying out prompt and precise KCN treatment.

Spectroscopic and molecular docking investigation of polynucleotides and DNA binding affinity to Nile blue dye

We used UV-vis absorption spectroscopy, fluorescence spectrophotometry and molecular docking calculations to investigate intermolecular interaction between the cationic dye, Nile blue (NB), and synthetic polynucleotides, poly(A-T), poly(G-C) and calf thymus DNA (Ct-DNA) at physiological pH. Strong hypsochromic absorbance and fluorescence quenching were observed that showed strong binding of NB to these polynucleotides and DNA. The binding affinity values derived from maximum absorption of the spectra of NB bound to various polynucleotides and Ct-DNA concentrations suggests that NB exhibits greater binding affinity to poly(G-C) than to poly(A-T). The thermodynamic parameters suggested that hydrogen bonds and van der Waals forces might play a major role in the binding of NB to DNA. The molecular docking results suggested that NB was an intercalator of the stacked base pairs of Ct-DNA.

Molecular detection of Chlamydophila abortus, Coxiella burnetii, and Mycoplasma agalactiae in small ruminants' aborted fetuses in southern Iran

Abortion in sheep and goats has become increasingly important worldwide because of the significant economic losses and potential zoonotic implication of commonly involved pathogens. Therefore, this cross-sectional study was conducted in southern Iran to detect the Chlamydophila abortus and Coxiella burnetii, as zoonotic pathogens, and Mycoplasma agalactiae, as a neglected abortifacient agent in small ruminants' aborted fetuses, by using polymerase chain reaction (PCR). From a total of 300 aborted fetuses (183 sheep and 117 goats), 46 samples (15.5%) were positive by PCR, 11% for C. abortus, 2% for C. burnetii, and 3% for M. agalactiae. Also, the association of suggested risk factors with abortion due to these bacterial agents was investigated using univariable and multivariable logistic regression. Results of the statistical analysis showed significant association of C. abortus with flock size (OR = 2.82, P = 0.014), season (P < 0.05), and the number of pregnancy in the aborted dam (OR = 2.5, P = 0.05). Our results indicated that C. abortus has a relatively substantial role in small ruminant abortions, and C. burnetii and M. agalactiae are likely important abortifacient agents in our region, too. Regarding veterinary and/or public health importance of these bacterial agents, more attention from veterinary and/or human health services and, maybe, a surveillance system for control and prevention of them are recommended.

DNA fingerprinting approaches to trace Escherichia coli sharing between dogs and owners

AIMS

To determine the prevalence of cross-species sharing of Escherichia coli between healthy dogs and humans living in the same household.

METHODS AND RESULTS

Two faecal E. coli isolates from 25 healthy dog-owner pairs and 16 healthy control humans were tested using three fingerprinting methods. The prevalence of within-household sharing of E. coli was 4, 8 and 8% using pulsed-field gel electrophoresis, randomly amplified polymorphic DNA and enterobacterial repetitive intergenic consensus-PCR analyses respectively. Within-household bacterial sharing was more prevalent than across-household sharing (P < 0·05). According to questionnaire analyses avoiding the dog-owner behaviours such as allowing a dog to kiss or lick the owner's face, sharing people food with dog and feeding it raw meat may decrease the chance of cross-species E. coli sharing.

CONCLUSIONS

Direct contact between humans and dogs and environmental reservoirs may be important routes for cross-species sharing of bacteria. Good personal hygiene and appropriate veterinary care for pets can minimize this risk.

SIGNIFICANCE AND IMPACT OF THE STUDY

Due to the importance of canine pathogenic E. coli reservoir hypothesis, close contacts between humans and dogs raises public health concerns. Determining the rate of cross-species bacterial sharing and confirm its accuracy by different fingerprinting techniques will help to find ways for reducing the economic impact of E. coli infections. This study support claims that public health concerns regarding the cross-species sharing of E. coli are warranted but this risk is minimal.

Distribution of virulence genes and multiple drug-resistant patterns amongst different phylogenetic groups of uropathogenic Escherichia coli isolated from patients with urinary tract infection

A total of 85 Uropathogenic Escherichia coli (UPEC) isolates were screened against ceftiofur, oxacillin, nitrofurantoin and lincospectin using Kirby-Bauer disc diffusion method, following CLSI guidelines. Prevalence of virulent factor genes amongst the isolates was determined by PCR, using gene-specific primers against the different virulent factors. Statistical analysis of the data was performed using SPSS software. The prevalence of traT, ompT, Iss, malX and ibeA genes was 47.1%, 38.8%, 20%, 16.5% and 9.4%, respectively. The most prevalent gene in group A and D was traT, whilst in group B2 was Iss. The highest resistance has been shown against oxacillin (98.8%), followed by ceftiofur (77.6%), whilst resistance to lincospectin (2.4%) and nitrofurantoin (12.9%) had the lowest frequencies. Multidrug resistance was shown in 82.35% of the isolates, whilst this study recommend lincospectin and nitrofurantoin as choice drugs for treatment, but more investigation of the bacterial pathogenicity associated with urinary tract infection (UTI) may contribute to a better medical intervention.

Human endogenous retrovirus protein activates innate immunity and promotes experimental allergic encephalomyelitis in mice

Multiple sclerosis (MS) is a complex multifactorial disease of the central nervous system (CNS) for which animal models have mainly addressed downstream immunopathology but not potential inducers of autoimmunity. In the absence of a pathogen known to cause neuroinflammation in MS, Mycobacterial lysate is commonly used in the form of complete Freund's adjuvant to induce autoimmunity to myelin proteins in Experimental Allergic Encephalomyelitis (EAE), an animal model for MS. The present study demonstrates that a protein from the human endogenous retrovirus HERV-W family (MSRV-Env) can be used instead of mycobacterial lysate to induce autoimmunity and EAE in mice injected with MOG, with typical anti-myelin response and CNS lesions normally seen in this model. MSRV-Env was shown to induce proinflammatory response in human macrophage cells through TLR4 activation pathway. The present results demonstrate a similar activation of murine dendritic cells and show the ability of MSRV-Env to trigger EAE in mice. In previous studies, MSRV-Env protein was reproducibly detected in MS brain lesions within microglia and perivascular macrophages. The present results are therefore likely to provide a model for MS, in which the upstream adjuvant triggering neuroinflammation is the one detected in MS active lesions. This model now allows pre-clinical studies with therapeutic agents targeting this endogenous retroviral protein in MS.

Effects of essential oils of oregano and nutmeg on growth and survival of Yersinia enterocolitica and Listeria monocytogenes in barbecued chicken

The in vitro effects of plant essential oils (EOs) against pathogenic bacteria are well known, yet few studies have addressed the effects of these compounds against pathogens associated with ready-to-cook foods. Experiments were conducted to determine the effectiveness of oregano and nutmeg EOs on the growth and survival of Yersinia enterocolitica and Listeria monocytogenes in broth culture and in Iranian barbecued chicken. Ready-to-cook Iranian barbecued chicken was prepared according to the common practice with 1, 2, and 3 microl/g of oregano and nutmeg EOs. The test and control (without EOs) samples were inoculated with Y. enterocolitica and L. monocytogenes to a final concentration of 6 to 7 log CFU/g and stored at 3, 8, and 20 degrees C. Microorganisms were counted just before and at 24, 48, and 72 h after storage based on growth on Yersinia selective agar supplemented with cefsulodine, igrasan, and novobiocin and on Listeria selective agar supplemented with nalidixic acid and acriflavin. In the broth culture system, the nutmeg EO had a greater effect on L. monocytogenes (MIC = 0.20 nicrol/ml) than did the oregano EO (MIC = 0.26 microl/ml). However, the oregano EO had a greater effect on Y. enterocolitica (MIC = 0.16 microl/ml) than did the nutmeg EO (MIC = 0.25 microl/ml). In ready-to-cook Iranian barbecued chicken, the log CFU per gram of both bacteria after up to 72 h of incubation was not decreased significantly by various combinations of oregano and nutmeg EOs (1, 2, and 3 microl/g) and storage temperatures (3, 8, and 20 degrees C) when compared with control samples (without EOs). Although examination of spices in culture media can yield accurate microbiological data, without complementary tests in foods these data are of limited value for assessing food safety.

Multiple sclerosis-associated retrovirus particles cause T lymphocyte-dependent death with brain hemorrhage in humanized SCID mice model

A retroviral element (multiple sclerosis-associated retrovirus, MSRV) defining a family of genetically inherited endogenous retroviruses (human endogenous retrovirus type W, HERV-W) has been characterized in cell cultures from patients with multiple sclerosis. Recently, MSRV retroviral particles or the envelope recombinant protein were shown to display superantigen activity in vitro, but no animal model has yet been set up for studying the pathogenicity of this retrovirus. In the present study, the pathogenicity of different sources of MSRV retroviral particles has been evaluated in a hybrid animal model: severe combined immunodeficiency (SCID) mice grafted with human lymphocytes and injected intraperitoneally with MSRV virion or mock controls. MSRV-injected mice presented with acute neurological symptoms and died within 5 to 10 days post injection. Necropsy revealed disseminated and major brain hemorrhages, whereas control animals did not show abnormalities (P <.001). In ill animals, reverse transcriptase-polymerase chain reaction (RT-PCR) analyses showed circulating MSRV RNA in serum, whereas overexpression of proinflammatory cytokines such as tumor necrosis factor (TNF)-alpha and interferon (IFN)-gamma was evidenced in spleen RNA. Neuropathological examination confirmed that hemorrhages occurred prior to death in multifocal areas of brain parenchyma and meninges. Further series addressed the question of immune-mediated pathogenicity, by inoculating virion to SCID mice grafted with total and T lymphocyte-depleted cells in parallel: dramatic and statistically significant reduction in the number of affected mice was observed in T-depleted series (P <.001). This in vivo study suggests that MSRV retroviral particles from MS cultures have potent immunopathogenic properties mediated by T cells compatible with the previously reported superantigen activity in vitro, which appear to be mediated by an overexpression of proinflammatory cytokines.

Gene transfer of anti-gp41 antibody and CD4 immunoadhesin strongly reduces the HIV-1 load in humanized severe combined immunodeficient mice

OBJECTIVE

To study the anti-HIV-1 effects of the delivery of anti-gp41 monoclonal antibody (mAb) and soluble CD4 (sCD4) immunoadhesin by genetically modified cells in HIV-1-infected, humanized severe combined immunodeficient (SCID) mice.

DESIGN

The complementary DNA of mAb 2F5, an anti-HIV-1 gp41 antibody, and of sCD4-IgG chimeric immunoadhesin were transferred into 3T3 cells using Moloney murine leukaemia virus vectors. The cells were then incorporated into a collagen structure called the neo-organ, which allowed the continuous production of the therapeutic molecules.

METHODS

The antiviral effects in vivo of 2F5 or sCD4-IgG or both compounds were evaluated in neo-organ-implanted SCID mice that were grafted with human CD4 CEM T cells and challenged with HIV-1 Lai or MN.

RESULTS

In SCID mice implanted with 2F5 neo-organs, antibody plasma levels reached 500-2000 ng/ml. Viral loads after HIV-1 challenge were significantly reduced in neo-organ-implanted HIV-infected mice. Although 29 x 10(7) and 13 x 10(8) HIV-1-RNA copies/ml were detected at 12 days in the controls (mice injected with Lai and MN, respectively) less than 16.5 x 10(3) HIV-1-RNA copies/ml were observed in all implanted mice injected with either Lai or MN. The intracellular viral load was also reduced in CD4 cells recovered from the implanted mice. Comparable antiviral effects were obtained with CD4-IgG neo-organs.

CONCLUSION

Our results confirm the anti-HIV properties of 2F5 and sCD4-IgG continuously produced in vivo after ex-vivo gene therapy in SCID mice.

Experimental gene therapy: the transfer of Tat-inducible interferon genes protects human cells against HIV-1 challenge in vitro and in vivo in severe combined immunodeficient mice

OBJECTIVES

To evaluate in vitro and in vivo a strategy for gene therapy for AIDS based on the transfer on interferon (IFN)-alpha, -beta and -gamma genes to human cells.

DESIGN

Human U937 promonocytic cells were stably transfected with Tat-inducible IFN expression vectors conferring an antiviral state against infection with HIV.

METHODS

Transfected cells were either infected by HIV-1 in vitro or transplanted into severe combined immunodeficient (SCID) mice for an HIV challenge in vivo.

RESULTS

U937 cell lines stably carrying IFN transgenes under the positive control of the HIV-1 Tat protein were highly resistant to HIV-1 replication in vitro. This antiviral resistance was associated with a strong induction of IFN synthesis immediately following the viral infection. HIV-1 proteins were found to be specifically trapped within the genetically modified cells. In contrast, all IFN-U937 cells permitted full HIV-2 replication. Transfected cells injected into SCID mice and challenged against HIV-1 were strongly resistant to infection when cells were transduced with IFN-alpha of IFN-beta genes. However, IFN-gamma-transfected cells permitted HIV-1 infection in vivo despite the induction of a high level of IFN-gamma secretion. The quantity of proviral DNA was 10(5)-fold lower in IFN-alpha- or IFN-beta-transfected U937 cells collected from these SCID mice than that in non-transfected cells.

CONCLUSIONS

Our results substantiated the validity of a strategy, bases on the transfer of HIV-1-inducible IFN-alpha or IFN-beta genes, to confer antiviral resistance to human cells.

Cell cultures and associated retroviruses in multiple sclerosis. Collaborative Research Group on MS

Retroviral particles associated with reverse transcriptase (RT) activity in cell-cultures from MS patients have been reported by different groups. Cell-cultures have been used for the study and characterization of the corresponding retroviral genome which we have shown is related to ERV9 in the pol region. Previously unpublished details of a study with monocyte cultures are presented together with observations on leptomeningeal and choroid-plexus cultures. The generation of self-transformed cultures after inhibition of interferon, followed by the loss of retroviral expression and recurrent apoptosis, is analyzed. Retroviral particles with RT-activity are produced in monocyte cultures with an apparent correlation with MS disease activity. However, though leptomeningeal and choroid plexus cells from MS can be passaged for a limited period, their evolution in vitro is not compatible with stable retroviral expression. These culture limitations greatly hampered progress on the elucidation of the retroviral genome sequence.