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"Dinesh, A"
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Empowering artificial intelligence through machine learning : new advances and applications
\"This new volume, Empowering Artificial Intelligence Through Machine Learning: New Advances and Applications, discusses various new applications of machine learning, a subset of the field of artificial intelligence. Artificial intelligence is considered to be the next big-game changer in research and technology. The volume looks at how computing has enabled machines to learn, making machines and tools become smarter in many sectors, including science and engineering, healthcare, finance, education, gaming, security, and even agriculture, plus many more areas. Topics include techniques and methods in artificial intelligence for making machines intelligent, machine learning in healthcare, using machine learning for credit card fraud detection, using artificial intelligence in education using gaming and automatization with courses and outcomes mapping, and much more. The book will be valuable for professionals, faculty, and students in electronics and communication engineering, telecommunication engineering, network engineering, computer science and information technology\"-- Provided by publisher.
Book
Genome-Wide Transcriptional Profiles during Temperature and Oxidative Stress Reveal Coordinated Expression Patterns and Overlapping Regulons in Rice
Genome wide transcriptional changes by cold stress, heat stress and oxidative stress in rice seedlings were analyzed. Heat stress resulted in predominant changes in transcripts of heat shock protein and heat shock transcription factor genes, as well as genes associated with synthesis of scavengers of reactive oxygen species and genes that control the level of sugars, metabolites and auxins. Cold stress treatment caused differential expression of transcripts of various transcription factors including desiccation response element binding proteins and different kinases. Transcripts of genes that are part of calcium signaling, reactive oxygen scavenging and diverse metabolic reactions were differentially expressed during cold stress. Oxidative stress induced by hydrogen peroxide treatment, resulted in significant up-regulation in transcript levels of genes related to redox homeostasis and down-regulation of transporter proteins. ROS homeostasis appeared to play central role in response to temperature extremes. The key transcription factors that may underlie the concerted transcriptional changes of specific components in various signal transduction networks involved are highlighted. Co-ordinated expression pattern and promoter architectures based analysis (promoter models and overrepresented transcription factor binding sites) suggested potential regulons involved in stress responses. A considerable overlap was noted at the level of transcription as well as in regulatory modules of differentially expressed genes.
Journal Article
A WRKY transcription factor from Withania somnifera regulates triterpenoid withanolide accumulation and biotic stress tolerance through modulation of phytosterol and defense pathways
Withania somnifera produces pharmacologically important triterpenoid withanolides that are derived via phytosterol pathway; however, their biosynthesis and regulation remain to be elucidated.
A jasmonate- and salicin-inducible WRKY transcription factor from W. somnifera (WsWRKY1) exhibiting correlation with withaferin A accumulation was functionally characterized employing virus-induced gene silencing and overexpression studies combined with transcript and metabolite analyses, and chromatin immunoprecipitation assay.
WsWRKY1 silencing resulted in stunted plant growth, reduced transcripts of phytosterol pathway genes with corresponding reduction in phytosterols and withanolides in W. somnifera. Its overexpression elevated the biosynthesis of triterpenoids in W. somnifera (phytosterols and withanolides), as well as tobacco and tomato (phytosterols). Moreover, WsWRKY1 binds to W-box sequences in promoters of W. somnifera genes encoding squalene synthase and squalene epoxidase, indicating its direct regulation of triterpenoid pathway. Furthermore, while WsWRKY1 silencing in W. somnifera compromised the tolerance to bacterial growth, fungal infection, and insect feeding, its overexpression in tobacco led to improved biotic stress tolerance.
Together these findings demonstrate that WsWRKY1 has a positive regulatory role on phytosterol and withanolides biosynthesis, and defense against biotic stress, highlighting its importance as a metabolic engineering tool for simultaneous improvement of triterpenoid biosynthesis and plant defense.
Journal Article
Predicting the methylation status of CpG islands from read distribution biases
DNA methylation is an important epigenetic mark that plays a major role in transcriptional regulation, development and genome integrity. There are state-of-the-art methods, such as whole-genome bisulfite sequencing or long-read sequencing, which allow accurate detection of DNA methylation at single-base resolution. However, except for these specialized methods, information about DNA methylation status cannot be obtained directly from ordinary short-read sequencing data. Here we propose an approach to predict the methylation status from mapped read coordinates alone. It relies on previous findings that the DNA fragmentation process during library preparation is not random, but is affected by sequence context. In particular, DNA shearing leads to preferential hydrolysis of the sugar-phosphate backbone at CpG dinucleotides. Notably, methylated CpGs are approximately 30% more susceptible to fragmentation than unmethylated CpGs, likely due to subtle differences in the conformational dynamics. These differences are getting prominent when multiple NGS reads at CpG islands are analyzed. Our trained machine learning model is able to detect these biases and predict whether a CpG island of interest is methylated or not. We provide our methods as a tool, WGS2meth, that predicts CpG island methylation from whole-genome sequencing reads of individual or aggregated samples.
Journal Article
An energy-efficient routing protocol for wireless body area networks using hybrid artificial bee colony optimization and chicken swarm optimization algorithm
Wireless body area networks (WBANs) have evolved into effective options for various sports, military, and healthcare applications. Most of the research proposed looking at effective data collection from individuals and conventional WBANs. Energy consumption is critical in WBANs, particularly in implantable wearable sensors that are challenging to access and replace. Various energy-efficiency data collection methods are employed to send data from body sensors to the server base station (BS). To begin, this work presents an efficient algorithm named “Artificial Bee Colony Optimization (ABC) and Chicken Swarm Optimization (CSO) algorithm” to create hybrid trees for data aggregation in networks. ABC-CSO has three phases: clustering, cluster head (CH) selection, and data transmission. It categorizes the wearable sensors into groups and uses the ABC method to choose the best CH for each group. Each sensor sends data to its corresponding relay node (RN) or CH. The CSO method is used to route the aggregated data to the BS. The proposed scheme considers the biosensor routing data’s distance and residual energy. It reduces grid energy consumption and balances the energy required by various biosensors. Furthermore, the simulation outcomes demonstrate that the proposed method can handle rapidly varying WBAN architectures while maintaining a balanced energy consumption and reliability. The proposed work simulates a variety of scenarios to show the suggested algorithm’s superiority over Ant Colony Optimization (ACO), Particle Swarm Optimization (PSO), ABC, and Grey Wolf Optimization (GWO) protocols. Compared to the ACO, PSO, ABC, and GWO protocols, the proposed protocol, i.e., ABC-CSO, has increased the throughput by 26.68%, 21.87%, 18.41%, and 8.79% respectively.
Journal Article
Effect of Poling Methods on the Functional Properties of Fused Deposition Modeling Printed Polyvinylidene Fluoride for Sensing Application
The demand for high performance piezoelectric sensors fabricated through additive manufacturing (AM) is growing due to a flexibility of designing complex structures in AM. In the present work, polyvinylidene fluoride as a piezoelectric material was fabricated by Material Extrusion process with different number of layers such as single, double, and triple at constant layer thickness for sensing applications. To enhance its functional properties, the fabricated materials were subjected to poling by two different types such as contact poling and corona poling process. The effects of poling on the β-phase formation of polyvinylidene fluoride fabricated by Material Extrusion process were explored to reveal the improvement in piezoelectric characteristics. x-ray Diffraction and Fourier Transform Infrared Spectroscopy characterization of the poled samples confirmed the presence of β-phase. The results of the piezoelectric coefficient (d
33
) measurement show that the Corona poled sample produces higher output value of 34 (pC/N) than the non-poled one 2 (pC/N). To better understand the response of the corona poled sample, the COMSOL-based simulation was conducted, and the results were evaluated using the compressive tests performed on the sample poled by the corona poling process.
Journal Article
Molecular characterization of three CYP450 genes reveals their role in withanolides formation and defense in Withania somnifera, the Indian Ginseng
The medicinal properties of Ashwagandha (
Withania somnifera
) are attributed to triterpenoid steroidal lactones, withanolides, which are proposed to be derived from phytosterol pathway, through the action of cytochrome P450 (CYP450) enzymes. Here, we report the characterization of three transcriptome-mined
CYP450
genes (
WsCYP749B1, WsCYP76
and
WsCYP71B10
), which exhibited induced expression in response to methyl jasmonate treatment indicating their role in secondary metabolism. All three
WsCYP450s
had the highest expression in leaf compared to other tissues.
In planta
characterization of
WsCYP450s
through virus induced gene silencing (VIGS) and transient overexpression approaches and subsequent metabolite analysis indicated differential modulation in the accumulation of certain withanolides in
W. somnifera
leaves. While
WsCYP749B1
-vigs significantly enhanced withaferin A (~ 450%) and reduced withanolide A (~ 50%), its overexpression drastically led to enhanced withanolide A (> 250%) and withanolide B (> 200%) levels and reduced 12-deoxywithastramonolide (~ 60%). Whereas
WsCYP76-
vigs led to reduced withanolide A (~ 60%) and its overexpression increased withanolide A (~ 150%) and reduced 12-deoxywithastramonolide (~ 60%). Silencing and overexpression of
WsCYP71B10
resulted in significant reduction of withanolide B (~ 50%) and withanolide A (~ 60%), respectively. Further, while VIGS of
WsCYP450s
negatively affected the expression of pathogenesis-related (
PR
) genes and compromised tolerance to bacteria
P. syringae
DC3000, their overexpression in
W. somnifera
and transgenic tobacco led to improved tolerance to the bacteria. Overall, these results showed that the identified
WsCYP450s
have a role in one or several steps of withanolides biosynthetic pathway and are involved in conferring tolerance to biotic stress.
Journal Article
A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer
Amplification and overexpression of the
SOX2
oncogene represent a hallmark of squamous cancers originating from diverse tissue types. Here, we find that squamous cancers selectively amplify a 3’ noncoding region together with
SOX2
, which harbors squamous cancer-specific chromatin accessible regions. We identify a single enhancer e1 that predominantly drives
SOX2
expression. Repression of e1 in
SOX2
-high cells causes collapse of the surrounding enhancers, remarkable reduction in
SOX2
expression, and a global transcriptional change reminiscent of
SOX2
knockout. The e1 enhancer is driven by a combination of transcription factors including SOX2 itself and the AP-1 complex, which facilitates recruitment of the co-activator BRD4. CRISPR-mediated activation of e1 in
SOX2
-low cells is sufficient to rebuild the e1-
SOX2
loop and activate
SOX2
expression. Our study shows that squamous cancers selectively amplify a predominant enhancer to drive
SOX2
overexpression, uncovering functional links among enhancer activation, chromatin looping, and lineage-specific copy number amplifications of oncogenes.
SOX2 amplification and overexpression represents a hallmark of squamous cancers with distinct distribution of chromatin accessible regions depending on cancer type. Here, the authors identify a single enhancer e1 that predominantly drives SOX2 expression in squamous cancer.
Journal Article
Bio Synthesis of Nickel Oxide Nanoparticles from Annona muricata extract as Efficient Inorganic Hole Transport Material in Tandem Perovskite Solar Cell
We report on the successful green synthesis of NiO nanoparticles using the fruit extract derived from
Annona muricata
. The extract has good potential towards strong reducing, stabilizing and capping agent to reduce the size of the particles into nanosized. XRD and FTIR spectrum followed by FESEM and TEM photograph with EDAX has been taken to analyze the crystallinity, purity and morphology of the NiO nanoparticles. The optical properties of prepared particles are subjected for UV–Visible spectrum and Photoluminescence spectrum for the suitability of the particles as the inorganic hole transport layer for perovskite solar cells. The direct bandgap of 2.8 eV is obtained from Tauc plot, NiO stretching is confirmed at 568.66 cm
–1
from FTIR and the composition of nickel and oxygen is 73.10 and 26.90% from EDAX is determined. The TEM analysis confirmed the particle size in the range between 20 to 30 nm. It is revealed that, the synthesized nanoparticles are desired due to its optimum optical properties for the absorption of solar radiation for perovskite solar cells.
Journal Article