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rabindra.tharu.np@gmail.com
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Developmental mouse brain common coordinate framework
3D brain atlases are key resources to understand the brain’s spatial organization and promote interoperability across different studies. However, unlike the adult mouse brain, the lack of developing mouse brain 3D reference atlases hinders advancements in understanding brain development. Here, we present a 3D developmental common coordinate framework (DevCCF) spanning embryonic day (E)11.5, E13.5, E15.5,…
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rabindra.tharu.np@gmail.com
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Anticipatory and evoked visual cortical dynamics of voluntary temporal attention
We can often anticipate the precise moment when a stimulus will be relevant for our behavioral goals. Voluntary temporal attention, the prioritization of sensory information at task-relevant time points, enhances visual perception. However, the neural mechanisms of voluntary temporal attention have not been isolated from those of temporal expectation, which reflects timing predictability rather than…
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rabindra.tharu.np@gmail.com
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Universal high-efficiency electrocatalytic olefin epoxidation via a surface-confined radical promotion
Production of epoxides via selective oxidation of olefins affords a fundamental source of key intermediates for the industrial manufacture of diverse chemical stocks and materials. Current oxidation strategy generally works under harsh conditions including high temperature, high pressure, and/or request for potentially hazardous oxidants, leading to substantial challenges in sustainability and energy efficiency. To this…
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rabindra.tharu.np@gmail.com
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Time-reversal symmetry breaking in the chemosensory array reveals a general mechanism for dissipation-enhanced cooperative sensing
The Escherichia coli chemoreceptors form an extensive array that achieves cooperative and adaptive sensing of extracellular signals. The receptors control the activity of histidine kinase CheA, which drives a nonequilibrium phosphorylation-dephosphorylation reaction cycle for response regulator CheY. Cooperativity and dissipation are both important aspects of chemotaxis signaling, yet their consequences have only been studied separately.…
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rabindra.tharu.np@gmail.com
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MATES: a deep learning-based model for locus-specific quantification of transposable elements in single cell
Transposable elements (TEs) are crucial for genetic diversity and gene regulation. Current single-cell quantification methods often align multi-mapping reads to either ‘best-mapped’ or ‘random-mapped’ locations and categorize them at the subfamily levels, overlooking the biological necessity for accurate, locus-specific TE quantification. Moreover, these existing methods are primarily designed for and focused on transcriptomics data, which restricts…
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rabindra.tharu.np@gmail.com
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Protein complex structure modeling by cross-modal alignment between cryo-EM maps and protein sequences
Cryo-electron microscopy (cryo-EM) technique is widely used for protein structure determination. Current automatic cryo-EM protein complex modeling methods mostly rely on prior chain separation. However, chain separation without sequence guidance often suffers from errors caused by cross-chain interaction or noise densities, which would accumulate and mislead the subsequent steps. Here, we present EModelX, a fully…
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rabindra.tharu.np@gmail.com
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Four Core Genotypes mice harbour a 3.2MB X-Y translocation that perturbs Tlr7 dosage
The Four Core Genotypes (FCG) is a mouse model system used to disentangle the function of sex chromosomes and hormones. We report that a copy of a 3.2 MB region of the X chromosome has translocated to the Y chromosome and thus increased the expression of X-linked genes including the single-stranded RNA sensor and autoimmune…
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rabindra.tharu.np@gmail.com
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LRRTM2 controls presynapse nano-organization and AMPA receptor sub-positioning through Neurexin-binding interface
Synapses are organized into nanocolumns that control synaptic transmission efficacy through precise alignment of postsynaptic neurotransmitter receptors and presynaptic release sites. Recent evidence show that Leucine-Rich Repeat Transmembrane protein LRRTM2, highly enriched and confined at synapses, interacts with Neurexins through its C-terminal cap, but the role of this binding interface has not been explored in…
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rabindra.tharu.np@gmail.com
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Zika viruses encode 5′ upstream open reading frames affecting infection of human brain cells
Zika virus (ZIKV), an emerging mosquito-borne flavivirus, is associated with congenital neurological complications. Here, we investigate potential pathological correlates of virus gene expression in representative ZIKV strains through RNA sequencing and ribosome profiling. In addition to the single long polyprotein found in all flaviviruses, we identify the translation of unrecognised upstream open reading frames (uORFs)…
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rabindra.tharu.np@gmail.com
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A sequential binding mechanism for 5′ splice site recognition and modulation for the human U1 snRNP
Splice site recognition is essential for defining the transcriptome. Drugs like risdiplam and branaplam change how human U1 snRNP recognizes particular 5′ splice sites (5’SS) and promote U1 snRNP binding and splicing at these locations. Despite the therapeutic potential of 5’SS modulators, the complexity of their interactions and snRNP substrates have precluded defining a mechanism…
