LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 416

Search options

  1. Article ; Online: Automatic severity grade classification of diabetic retinopathy using deformable ladder Bi attention U-net and deep adaptive CNN.

    Durai, D Binny Jeba / Jaya, T

    Medical & biological engineering & computing

    2023  Volume 61, Issue 8, Page(s) 2091–2113

    Abstract: Long-term exposure to diabetes mellitus leads to the formation of diabetic retinopathy (DR), which can cause vision loss in working-age adults. Early stage diagnosis of DR is highly essential for preventing vision loss and preserving vision in people ... ...

    Abstract Long-term exposure to diabetes mellitus leads to the formation of diabetic retinopathy (DR), which can cause vision loss in working-age adults. Early stage diagnosis of DR is highly essential for preventing vision loss and preserving vision in people with diabetes. The motivation behind the severity grade classification of DR is to develop an automated system that can assist ophthalmologists and healthcare professionals in the diagnosis and management of DR. However, existing methods suffer from variability in image quality, similar structures of the normal and lesion regions, high dimensional features, variability in disease manifestations, small datasets, high training loss, model complexity, and overfitting, which leads to high misclassification errors in the severity grading system. Hence, there is a need to develop an automated system using improved deep learning techniques to provide a reliable and consistent grading of DR severity with high classification accuracy using fundus images. To solve these issues, we proposes a Deformable Ladder Bi attention U-shaped encoder-decoder network and Deep Adaptive Convolutional Neural Network (DLBUnet-DACNN) for accurate severity classification of DR. The DLBUnet performs lesion segmentation that can be divided into three parts: the encoder, the central processing module and the decoder. In the encoder part, deformable convolution is used instead of convolution to learn different shapes of the lesion by understanding the offset location. Afterwards, Ladder Atrous Spatial Pyramidal Pooling (LASPP) using variable dilation rates is introduced in the central processing module. LASPP enhance the tiny lesion features and variable dilation rates avoid gridding effects and can learn better global context information. Then the decoder part uses a bi-attention layer contains spatial and channel attention, which can learn contour and edges of the lesion accurately. Finally, the severity of DR is classified using a DACNN by extracting the discriminative features from the segmentation results. Experiments are conducted on the Messidor-2, Kaggle, and Messidor datasets. Our proposed method DLBUnet-DACNN achieves better results in terms of accuracy of 98.2, recall of 0.987, kappa coefficient of 0.993, precision of 0.98, F1-score of 0.981, Matthews Correlation Coefficient (MCC) of 0.93 and Classification Success Index (CSI) of 0.96 when compared to existing methods.
    MeSH term(s) Adult ; Humans ; Diabetic Retinopathy/diagnostic imaging ; Fundus Oculi ; Diabetes Mellitus
    Language English
    Publishing date 2023-06-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 282327-5
    ISSN 1741-0444 ; 0025-696X ; 0140-0118
    ISSN (online) 1741-0444
    ISSN 0025-696X ; 0140-0118
    DOI 10.1007/s11517-023-02860-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  2. Article ; Online: Where Medical Statistics Meets Artificial Intelligence.

    Sundaramoorthi, Durai / Komen, Helga

    The New England journal of medicine

    2024  Volume 389, Issue 25, Page(s) 2402–2403

    MeSH term(s) Humans ; Artificial Intelligence ; Public Health
    Language English
    Publishing date 2024-01-01
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 207154-x
    ISSN 1533-4406 ; 0028-4793
    ISSN (online) 1533-4406
    ISSN 0028-4793
    DOI 10.1056/NEJMc2312332
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  3. Article ; Online: Cell-free supernatants of probiotic consortia impede hyphal formation and disperse biofilms of vulvovaginal candidiasis causing Candida in an ex-vivo model.

    Kumar, Sudaarsan Aruna Senthil / Krishnan, Dhesiga / Jothipandiyan, Sowndarya / Durai, Ramyadevi / Hari, B Narayanan Vedha / Nithyanand, Paramasivam

    Antonie van Leeuwenhoek

    2024  Volume 117, Issue 1, Page(s) 37

    Abstract: Vulvovaginal candidiasis is the second most common vaginal infection caused by drug-resistant Candida species that affects about 70-75% of reproductive age group women across the globe. As current-day antifungal drugs are ineffective against the biofilms ...

    Abstract Vulvovaginal candidiasis is the second most common vaginal infection caused by drug-resistant Candida species that affects about 70-75% of reproductive age group women across the globe. As current-day antifungal drugs are ineffective against the biofilms formed by the drug-resistant Candida strains, several natural compounds and antagonistic microbes are being explored as alternative antifungal agents. In the present study, we investigated the anti-biofilm activity of Cell-Free Supernatant (CFS) extracted from the commercially available probiotics VSL-3 against the biofilms of Candida species and also evaluated their efficacy in curbing the yeast-to-hyphal transition. Various methodologies like crystal violet staining and scanning electron microscopy were used to study the effect of CFS against the biofilms formed by the species. The ability of CFS to interfere with yeast to hyphal transition in Candida was studied by colony morphology assay and visually confirmed with phase contrast microscopy. The potential of the CFS of the probiotics was also evaluated using goat buccal tissue, a novel ex-vivo model that mimics the vaginal environment. Moreover, the supernatant extracted from VSL-3 had the ability to down-regulate the expression of virulence genes of Candida from the biofilm formed over the ex-vivo model. These results emphasize the anti-fungal and anti-infective properties of the CFS of VSL-3 against drug-resistant Candida strains causing vulvovaginal candidiasis.
    MeSH term(s) Female ; Humans ; Candidiasis, Vulvovaginal/microbiology ; Candida ; Saccharomyces cerevisiae ; Antifungal Agents/pharmacology ; Biofilms ; Probiotics ; Candida albicans
    Chemical Substances Antifungal Agents
    Language English
    Publishing date 2024-02-17
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 214861-4
    ISSN 1572-9699 ; 0003-6072
    ISSN (online) 1572-9699
    ISSN 0003-6072
    DOI 10.1007/s10482-024-01929-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  4. Article ; Online: M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings.

    Shenoy, Aditi / Kalakoti, Yogesh / Sundar, Durai / Elofsson, Arne

    Bioinformatics (Oxford, England)

    2024  Volume 40, Issue 1

    Abstract: Motivation: Understanding metal-protein interaction can provide structural and functional insights into cellular processes. As the number of protein sequences increases, developing fast yet precise computational approaches to predict and annotate metal- ... ...

    Abstract Motivation: Understanding metal-protein interaction can provide structural and functional insights into cellular processes. As the number of protein sequences increases, developing fast yet precise computational approaches to predict and annotate metal-binding sites becomes imperative. Quick and resource-efficient pre-trained protein language model (pLM) embeddings have successfully predicted binding sites from protein sequences despite not using structural or evolutionary features (multiple sequence alignments). Using residue-level embeddings from the pLMs, we have developed a sequence-based method (M-Ionic) to identify metal-binding proteins and predict residues involved in metal binding.
    Results: On independent validation of recent proteins, M-Ionic reports an area under the curve (AUROC) of 0.83 (recall = 84.6%) in distinguishing metal binding from non-binding proteins compared to AUROC of 0.74 (recall = 61.8%) of the next best method. In addition to comparable performance to the state-of-the-art method for identifying metal-binding residues (Ca2+, Mg2+, Mn2+, Zn2+), M-Ionic provides binding probabilities for six additional ions (i.e. Cu2+, Po43-, So42-, Fe2+, Fe3+, Co2+). We show that the pLM embedding of a single residue contains sufficient information about its neighbours to predict its binding properties.
    Availability and implementation: M-Ionic can be used on your protein of interest using a Google Colab Notebook (https://bit.ly/40FrRbK). The GitHub repository (https://github.com/TeamSundar/m-ionic) contains all code and data.
    MeSH term(s) Proteins/chemistry ; Amino Acid Sequence ; Binding Sites ; Ions ; Protein Domains ; Metals/chemistry ; Metals/metabolism
    Chemical Substances Proteins ; Ions ; Metals
    Language English
    Publishing date 2024-01-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btad782
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  5. Article ; Online: Molecular insights into the binding interactions and energetics of the omicron spike variant with hACE2 and a neutralizing antibody.

    Kumar, Vipul / Shefrin, Seyad / Sundar, Durai

    Journal of structural biology

    2024  Volume 216, Issue 2, Page(s) 108087

    Abstract: The global spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) since 2019 has led to a continuous evolution of viral variants, with the latest concern being the Omicron (B.1.1.529) variant. In this study, classical molecular dynamics ... ...

    Abstract The global spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) since 2019 has led to a continuous evolution of viral variants, with the latest concern being the Omicron (B.1.1.529) variant. In this study, classical molecular dynamics simulations were conducted to elucidate the biophysical aspects of the Omicron spike protein's receptor-binding domain (RBD) in its interaction with human angiotensin-converting enzyme 2 (hACE2) and a neutralizing antibody, comparing it to the wildtype (WT). To model the Omicron variant, 15 in silico mutations were introduced in the RBD region of WT (retrieved from PDB). The simulations of WT spike-hACE2 and Omicron spike-hACE2 complexes revealed comparable binding stability and dynamics. Notably, the Q493R mutation in the Omicron spike increased interactions with hACE2, particularly with ASP38 and ASP355. Additionally, mutations such as N417K, T478K, and Y505H contributed to enhanced structural stability in the Omicron variant. Conversely, when comparing WT with Omicron in complex with a neutralizing antibody, simulation results demonstrated poorer binding dynamics and stability for the Omicron variant. The E484K mutation significantly decreased binding interactions, resulting in an overall decrease in binding energy (∼-57 kcal/mol) compared to WT (∼-84 kcal/mol). This study provides valuable molecular insights into the heightened infectivity of the Omicron variant, shedding light on the specific mutations influencing its interactions with hACE2 and neutralizing antibodies.
    Language English
    Publishing date 2024-03-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1032718-6
    ISSN 1095-8657 ; 1047-8477
    ISSN (online) 1095-8657
    ISSN 1047-8477
    DOI 10.1016/j.jsb.2024.108087
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  6. Article ; Online: DNA shape features improve prediction of CRISPR/Cas9 activity.

    Vora, Dhvani Sandip / Bhandari, Sakshi Manoj / Sundar, Durai

    Methods (San Diego, Calif.)

    2024  Volume 226, Page(s) 120–126

    Abstract: The CRISPR/Cas9 genome editing technology has transformed basic and translational research in biology and medicine. However, the advances are hindered by off-target effects and a paucity in the knowledge of the mechanism of the Cas9 protein. Machine ... ...

    Abstract The CRISPR/Cas9 genome editing technology has transformed basic and translational research in biology and medicine. However, the advances are hindered by off-target effects and a paucity in the knowledge of the mechanism of the Cas9 protein. Machine learning models have been proposed for the prediction of Cas9 activity at unintended sites, yet feature engineering plays a major role in the outcome of the predictors. This study evaluates the improvement in the performance of similar predictors upon inclusion of epigenetic and DNA shape feature groups in the conventionally used sequence-based Cas9 target and off-target datasets. The approach involved the utilization of neural networks trained on a diverse range of parameters, allowing us to systematically assess the performance increase for the meticulously designed datasets- (i) sequence only, (ii) sequence and epigenetic features, and (iii) sequence, epigenetic and DNA shape feature datasets. The addition of DNA shape information significantly improved predictive performance, evaluated by Akaike and Bayesian information criteria. The evaluation of individual feature importance by permutation and LIME-based methods also indicates that not only sequence features like mismatches and nucleotide composition, but also base pairing parameters like opening and stretch, that are indicative of distortion in the DNA-RNA hybrid in the presence of mismatches, influence model outcomes.
    Language English
    Publishing date 2024-04-17
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2024.04.012
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  7. Article ; Online: Clinical value and cost saving of therapeutic drug monitoring of infliximab in adult patients with inflammatory bowel disease.

    Ganesananthan, Sashiananthan / Durai, Dharmaraj

    Clinical medicine (London, England)

    2020  Volume 20, Issue Suppl 2, Page(s) s23–s24

    MeSH term(s) Adult ; Cost Savings ; Drug Monitoring ; Gastrointestinal Agents/therapeutic use ; Humans ; Inflammatory Bowel Diseases/drug therapy ; Infliximab/therapeutic use
    Chemical Substances Gastrointestinal Agents ; Infliximab (B72HH48FLU)
    Language English
    Publishing date 2020-05-13
    Publishing country England
    Document type Journal Article
    ZDB-ID 2048646-7
    ISSN 1473-4893 ; 1470-2118
    ISSN (online) 1473-4893
    ISSN 1470-2118
    DOI 10.7861/clinmed.20-2-s23
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  8. Article ; Online: Analytical insights into the detoxification process and characterization of a traditional metallopharmaceutical formulation.

    K, Malarvizhi / B N, Vedha Hari / P, Rajalakshmi / S, Devaraj / Durai, Ramyadevi

    RSC medicinal chemistry

    2023  Volume 14, Issue 6, Page(s) 1143–1157

    Abstract: Metallopharmaceuticals possess unique medicinal properties and have been used since ancient times. In spite of the inclusion of several metals and minerals, there is an increased interest in metallo-drugs for clinical and research purposes because of ... ...

    Abstract Metallopharmaceuticals possess unique medicinal properties and have been used since ancient times. In spite of the inclusion of several metals and minerals, there is an increased interest in metallo-drugs for clinical and research purposes because of their immense therapeutic efficiency and non-toxic claim, as they are processed in addition to specific poly herbals.
    Language English
    Publishing date 2023-05-01
    Publishing country England
    Document type Journal Article
    ISSN 2632-8682
    ISSN (online) 2632-8682
    DOI 10.1039/d3md00123g
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  9. Article ; Online: Layered KTO/BiOCl nanostructures for the efficient visible light photocatalytic degradation of harmful dyes.

    Durai, Mani / Chauhan, Deepak / Durai, Mathivanan / Saravanan, Mathavan / Kumaravel, Sakthivel / Erusappan, Elangovan / Ahn, Young-Ho

    Chemosphere

    2022  Volume 306, Page(s) 135659

    Abstract: Novel KTO/BiOCl nanostructured photocatalysts with various weight proportions were synthesized using a simple hydrothermal process. The as-prepared nanostructured composite catalysts were characterized by powder X-ray diffraction, Fourier transform ... ...

    Abstract Novel KTO/BiOCl nanostructured photocatalysts with various weight proportions were synthesized using a simple hydrothermal process. The as-prepared nanostructured composite catalysts were characterized by powder X-ray diffraction, Fourier transform infrared spectroscopy, UV-vis diffused reflectance spectroscopy, Raman spectroscopy, field emission scanning electron microscopy, transmission electron microscopy with high resolution, X-ray photoelectron spectroscopy, and photoluminescence (PL). The photocatalytic activity of prepared catalysts was examined using Rhodamine B (RhB) and Congo Red (CR) as the aimed pollutants. BiOCl nanoparticles were distributed uniformly on the surface of the K
    MeSH term(s) Catalysis ; Coloring Agents ; Light ; Nanostructures/chemistry ; Photoelectron Spectroscopy
    Chemical Substances Coloring Agents
    Language English
    Publishing date 2022-07-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 120089-6
    ISSN 1879-1298 ; 0045-6535 ; 0366-7111
    ISSN (online) 1879-1298
    ISSN 0045-6535 ; 0366-7111
    DOI 10.1016/j.chemosphere.2022.135659
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  10. Article: Refractive outcomes following silicone oil tamponade in vitreoretinal surgery.

    Natarajan, Ramya / Mohamed, Ashik / Parameswarappa, Deepika C / Rani, Padmaja Kumari / Bagga, Deepak Kumar / Durai, C Vijay Reena

    Oman journal of ophthalmology

    2024  Volume 17, Issue 1, Page(s) 25–31

    Abstract: ... in diopters (D). The mean ± SD refraction with SOT in phakic, pseudophakic, and aphakic was 4.28 ± 2.59 D, 2 ... 94 ± 2.58 D, and 3.98 ± 4.82 D. The mean SER post-SOR in phakic, pseudophakic, and aphakic was -2.72 ... 2.03 D, -1.12 ± 1.41 D, and 8.22 ± 3.70 D. The diagnosis of rhegmatogenous retinal detachment (RRD ...

    Abstract Purpose: To evaluate the factors influencing the refractive outcomes following silicone oil tamponade (SOT) and silicone oil removal (SOR) in different lens statuses post-vitreoretinal surgery.
    Design: Retrospective analysis of three different lens statuses.
    Materials and methods: This was a descriptive study that included 150 eyes of 147 patients who had undergone pars plana vitrectomy with SOT and SOR between January 2017 and June 2021. Demographic profile, spherical equivalent refraction (SER), and its association with clinical features were evaluated with SOT and post-SOR.
    Results: The mean (±standard deviation [SD]) age was 47 ± 17.8 years, including all three groups. SER was represented in diopters (D). The mean ± SD refraction with SOT in phakic, pseudophakic, and aphakic was 4.28 ± 2.59 D, 2.94 ± 2.58 D, and 3.98 ± 4.82 D. The mean SER post-SOR in phakic, pseudophakic, and aphakic was -2.72 ± 2.03 D, -1.12 ± 1.41 D, and 8.22 ± 3.70 D. The diagnosis of rhegmatogenous retinal detachment (RRD) among 96 eyes (64%) is the common indicator to perform vitreoretinal (VR) surgery. A minority of subjects were managed with retinal lasers before VR surgery (14%). The macula was attached in 100 eyes (67.6%), the belt buckle was done in 37 eyes (24.7%), and the silicone oil viscosity with 1000 centistoke was chosen in 129 eyes (86%).
    Conclusion: SOT was used as a tamponade in VR surgeries irrespective of lens status. The significant predictor for post-SOR refraction in phakic and aphakic is post-SOT refraction. In pseudophakic, gender and diagnosis of RRD are the predictors of SOR refraction.
    Language English
    Publishing date 2024-02-21
    Publishing country India
    Document type Journal Article
    ZDB-ID 2484272-2
    ISSN 0974-7842 ; 0974-620X
    ISSN (online) 0974-7842
    ISSN 0974-620X
    DOI 10.4103/ojo.ojo_274_22
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

To top