Biology subjects

Velmurugan, R.

Publications and source records attributed to Velmurugan, R..

4 recordsLinked to original sources

bioRxiv2025

High-precision Biomedical Text Corpora for Multi-Entity Recognition: A CoDiet study

We present here five biomedical, multi-entity corpora that can be used as benchmarks for named-entity recognition (NER), targeted to literature on metabolic syndrome. The CoDiet-Gold corpus contains annotations for 500 full-text publications and 348,406 annotations. It is divided into CoDiet-Gold-public (450 documents) and CoDiet-Gold-private (50 documents). Each document was independently annotated by two human experts, with disagreements fully adjudicated by a third expert. The CoDiet-Electrum corpus (2,998,273 annotations) contains 4,423 publications that were annotated using case-insensitive matching of the surface forms with punctuation ignored, found in CoDiet-Gold-public. Finally, for the same 4,423 documents, two fully machine annotated corpora CoDiet-Bronze (2,938,738 annotations) and CoDiet-Silver (2,298,988 annotations), were created by utilising existing NER algorithms to annotate these. These corpora contain categories (organisms, disease, genes, proteins, metabolites) that add depth to existing corpora, as well as new categories that do not appear in other corpora (food, dietary methods, sample types, computational methods, study methodology, population characteristics, data types, and microbiome).

bioinformatics↗

bioRxiv2019

Nanoparticle Mediated NADPH Regeneration for Enhanced Ethanol Production by Engineered Synechocystis sp. PCC 6803

The ethanol synthesis pathway engineered Synechocystis sp. PCC 6803 was used to investigate the influence of metal oxide mediated NADPH regeneration on ethanol synthesis. Among the metal oxides, Fe2O3 and MgO showed considerable improvement in growth, chlorophyll a content and ethanol synthesis. The in-vitro studies proved that the selected metal oxides have the potential to regenerate the NADPH under light illumination. The results clearly indicate that the light energy is the key factor for activation of metal oxides and to a less extent light itself has the possibility for direct regeneration of NADPH. Under optimized light intensity and NADP addition, the maximum MgO mediated ethanol production of 5100mg/L, about a 2-fold increase compared to the control, was obtained after 20 days cultivation at 5L level. This study indicates that the efficient NADPH regeneration aided by metal oxide is crucial to improve ethanol productivity in Synechocystis sp. PCC 6803. IMPORTANCECyanobacteria are efficient ethanol producing organisms from atmospheric CO2 upon engineering of pathway. In cyanobacterial ethanol synthesis pathway, NADPH plays an important role acetaldehyde to ethanol conversion. Here we elucidated the NADPH regeneration through extracellular addition of metal oxides. The metal oxide mediated NADPH regeneration study allows us to dissect the importance of metal oxides in enhancing ethanol production through NADPH regeneration while also providing insight into the regulatory functions of metal oxides in growth, photosynthetic apparatus and various carbon metabolisms.

bioengineering↗

bioRxiv2018

Super-resolution fight club: A broad assessment of 2D & 3D single-molecule localization microscopy software

With the widespread uptake of 2D and 3D single molecule localization microscopy, a large set of different data analysis packages have been developed to generate super-resolution images. To guide researchers on the optimal analytical software for their experiments, we have designed, in a large community effort, a competition to extensively characterise and rank these options. We generated realistic simulated datasets for popular imaging modalities - 2D, astigmatic 3D, biplane 3D, and double helix 3D - and evaluated 36 participant packages against these data. This provides the first broad assessment of 3D single molecule localization microscopy software, provides a holistic view of how the latest 2D and 3D single molecule localization software perform in realistic conditions, and ultimately provides insight into the current limits of the field.

biophysics↗

bioRxiv2016

Intensity-based axial localization approaches for multifocal plane microscopy

Multifocal plane microscopy (MUM) can be used to visualize biological samples in three dimensions over large axial depths and provides for the high axial localization accuracy that is needed in applications such as the three-dimensional tracking of single particles and superresolution microscopy. This report analyzes the performance of intensity-based axial localization approaches as applied to MUM data using Fisher information calculations. In addition, a new non-parametric intensity-based axial location estimation method, Multi-Intensity Lookup Algorithm (MILA), is introduced that, unlike typical intensity-based methods that make use of a single intensity value per data image, utilizes multiple intensity values per data image in determining the axial location of a point source. MILA is shown to be robust against potential bias induced by differences in the sub-pixel location of the imaged point source. The method's effectiveness on experimental data is also evaluated.

biophysics↗