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Granulometric analysis of spots in DNA microarray images

Latha B, Venkatesh B

Genomics Proteomics Bioinformatics, 2004 Nov;2(4):222-36.
PMID: 15901251

As the topological properties of each spot in DNA microarray images may vary from one another, we employed granulometries to understand the shape-size content contributed due to a significant intensity value within a spot. Analysis was performed on the microarray image that consisted of 240 spots by using concepts from mathematical morphology. In order to find out indices for each spot and to further classify them, we adopted morphological multiscale openings, which provided microarrays at multiple scales. Successive opened microarrays were subtracted to identify the protrusions that were smaller than the size of structuring element. Spot-wise details, in terms of probability of these observed protrusions, were computed by placing a regularly spaced grid on microarray such that each spot was centered in each grid. Based on the probability of size distribution functions of these protrusions isolated at each level, we estimated the mean size and texture index for each spot. With these characteristics, we classified the spots in a microarray image into bright and dull categories through pattern spectrum and shape-size complexity measures. These segregated spots can be compared with those of hybridization levels.
Fractal characterization of bpn weights evolution

Gunasekaran S, Venkatesh B, Sagar BS

Int J Neural Syst, 2004 Apr;14(2):139-45.
PMID: 15112371

Training methodology of the Back Propagation Network (BPN) is well documented. One aspect of BPN that requires investigation is whether or not the BPN would get trained for a given training data set and architecture. In this paper the behavior of the BPN is analyzed during its training phase considering convergent and divergent training data sets. Evolution of the weights during the training phase was monitored for the purpose of analysis. The evolution of weights was plotted as return map and was characterized by means of fractal dimension. This fractal dimensional analysis of the weight evolution trajectories is used to provide a new insight to understand the behavior of BPN and dynamics in the evolution of weights.
A controller based on Optimal Type-2 Fuzzy Logic: systematic design, optimization and real-time implementation

Fayek HM, Elamvazuthi I, Perumal N, Venkatesh B

ISA Trans, 2014 Sep;53(5):1583-91.
PMID: 24962934 DOI: 10.1016/j.isatra.2014.06.001

A computationally-efficient systematic procedure to design an Optimal Type-2 Fuzzy Logic Controller (OT2FLC) is proposed. The main scheme is to optimize the gains of the controller using Particle Swarm Optimization (PSO), then optimize only two parameters per type-2 membership function using Genetic Algorithm (GA). The proposed OT2FLC was implemented in real-time to control the position of a DC servomotor, which is part of a robotic arm. The performance judgments were carried out based on the Integral Absolute Error (IAE), as well as the computational cost. Various type-2 defuzzification methods were investigated in real-time. A comparative analysis with an Optimal Type-1 Fuzzy Logic Controller (OT1FLC) and a PI controller, demonstrated OT2FLC׳s superiority; which is evident in handling uncertainty and imprecision induced in the system by means of noise and disturbances.
Incidence of Prosthetic Complications associated with Implant-borne Prosthesis in a Sleep Disorder Center

Suneel VB, Kotian S, Jujare RH, Shetty AK, Nidhi S, Grover S

J Contemp Dent Pract, 2017 Sep 01;18(9):821-825.
PMID: 28874648

BACKGROUND: Obstructive sleep apnea (OSA) is one of the common prevalent conditions present worldwide. The process of abnormal habits related to clenching and grinding of teeth is referred to as bruxism and is characterized under the heading of parafunctional activity of the masticatory system. Osseointegrated dental implants represent advancements in the field of odontology. Despite its high success rate, failure and complications are often associated with dental implant treatment due to a number of factors. Hence, we aimed for the present study to assess the incidence of prosthetic complications in patients rehabilitated with implant-borne prosthesis in a sleep disorder unit.
MATERIALS AND METHODS: The present study included the assessment of all the patients who underwent prosthetic rehabilitation by dental implants. An experienced registered prosthodontist was given duty for examination of all the cases from the record file data. Prosthetic complications in the patients were identified using photographs, radiographs, and all other relevant data of the patients obtained from the record files. All types of complications and other factors were recorded separately and analyzed.
RESULTS: While correlating the prosthetic complications in OSA patients grouped based on number of dental implants, nonsignificant results were obtained. Significant correlation was observed while comparing the prosthetic complications divided based on type of prosthesis. Fracture of the porcelain was observed in four and eight cases respectively, of screwed and cemented dental implant cases.
CONCLUSION: Some amount of significant correlation existed between the incidences of prosthetic complications and OSA.
CLINICAL SIGNIFICANCE: Proper history of the patients undergoing dental implant procedures should be taken to avoid failure.
Fulltext The different fates of two Asian horseshoe crab species with different dispersal abilities

Tang Q, Shingate P, Wardiatno Y, John A, Tay BH, Tay YC, et al.

Evol Appl, 2021 Aug;14(8):2124-2133.
PMID: 34429753 DOI: 10.1111/eva.13271

Impending anthropogenic climate change will severely impact coastal organisms at unprecedented speed. Knowledge on organisms' evolutionary responses to past sea-level fluctuations and estimation of their evolutionary potential is therefore indispensable in efforts to mitigate the effects of future climate change. We sampled tens of thousands of genomic markers of ~300 individuals in two of the four extant horseshoe crab species across the complex archipelagic Singapore Straits. Carcinoscorpius rotundicauda Latreille, a less mobile mangrove species, has finer population structure and lower genetic diversity compared with the dispersive deep-sea Tachypleus gigas Müller. Even though the source populations of both species during the last glacial maximum exhibited comparable effective population sizes, the less dispersive C. rotundicauda seems to lose genetic diversity much more quickly because of population fragmentation. Contra previous studies' results, we predict that the more commonly sighted C. rotundicauda faces a more uncertain conservation plight, with a continuing loss in evolutionary potential and higher vulnerability to future climate change. Our study provides important genomic baseline data for the redirection of conservation measures in the face of climate change and can be used as a blueprint for assessment and mitigation of the adverse effects of impending sea-level rise in other systems.
Fulltext Highly efficient Runx1 enhancer eR1-mediated genetic engineering for fetal, child and adult hematopoietic stem cells

Koh CP, Bahirvani AG, Wang CQ, Yokomizo T, Ng CEL, Du L, et al.

Gene, 2023 Jan 30;851:147049.
PMID: 36384171 DOI: 10.1016/j.gene.2022.147049

A cis-regulatory genetic element which targets gene expression to stem cells, termed stem cell enhancer, serves as a molecular handle for stem cell-specific genetic engineering. Here we show the generation and characterization of a tamoxifen-inducible CreERT2 transgenic (Tg) mouse employing previously identified hematopoietic stem cell (HSC) enhancer for Runx1, eR1 (+24 m). Kinetic analysis of labeled cells after tamoxifen injection and transplantation assays revealed that eR1-driven CreERT2 activity marks dormant adult HSCs which slowly but steadily contribute to unperturbed hematopoiesis. Fetal and child HSCs that are uniformly or intermediately active were also efficiently targeted. Notably, a gene ablation at distinct developmental stages, enabled by this system, resulted in different phenotypes. Similarly, an oncogenic Kras induction at distinct ages caused different spectrums of malignant diseases. These results demonstrate that the eR1-CreERT2 Tg mouse serves as a powerful resource for the analyses of both normal and malignant HSCs at all developmental stages.
Fulltext Towards complete and error-free genome assemblies of all vertebrate species

Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, et al.

Nature, 2021 Apr;592(7856):737-746.
PMID: 33911273 DOI: 10.1038/s41586-021-03451-0

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.