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rabindra.tharu.np@gmail.com
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Longitudinal deep neural networks for assessing metastatic brain cancer on a large open benchmark
The detection and tracking of metastatic cancer over the lifetime of a patient remains a major challenge in clinical trials and real-world care. Advances in deep learning combined with massive datasets may enable the development of tools that can address this challenge. We present NYUMets-Brain, the world’s largest, longitudinal, real-world dataset of cancer consisting of…
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rabindra.tharu.np@gmail.com
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Sustainable-use marine protected areas to improve human nutrition
Coral reef fisheries are a vital source of nutrients for thousands of nutritionally vulnerable coastal communities around the world. Marine protected areas are regions of the ocean designed to preserve or rehabilitate marine ecosystems and thereby increase reef fish biomass. Here, we evaluate the potential effects of expanding a subset of marine protected areas that…
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rabindra.tharu.np@gmail.com
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Regional patterns of human cortex development correlate with underlying neurobiology
Human brain morphology undergoes complex changes over the lifespan. Despite recent progress in tracking brain development via normative models, current knowledge of underlying biological mechanisms is highly limited. We demonstrate that human cortical thickness development and aging trajectories unfold along patterns of molecular and cellular brain organization, traceable from population-level to individual developmental trajectories. During…
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rabindra.tharu.np@gmail.com
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Low-dose cryo-electron ptychography of proteins at sub-nanometer resolution
Cryo-transmission electron microscopy (cryo-EM) of frozen hydrated specimens is an efficient method for the structural analysis of purified biological molecules. However, cryo-EM and cryo-electron tomography are limited by the low signal-to-noise ratio (SNR) of recorded images, making detection of smaller particles challenging. For dose-resilient samples often studied in the physical sciences, electron ptychography – a…
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rabindra.tharu.np@gmail.com
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Impact and characterization of serial structural variations across humans and great apes
Modern sequencing technology enables the systematic detection of complex structural variation (SV) across genomes. However, extensive DNA rearrangements arising through a series of mutations, a phenomenon we refer to as serial SV (sSV), remain underexplored, posing a challenge for SV discovery. Here, we present NAHRwhals ( https://github.com/WHops/NAHRwhals ), a method to infer repeat-mediated series of…
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rabindra.tharu.np@gmail.com
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Histones and histone variant families in prokaryotes
Histones are important chromatin-organizing proteins in eukaryotes and archaea. They form superhelical structures around which DNA is wrapped. Recent studies have shown that some archaea and bacteria contain alternative histones that exhibit different DNA binding properties, in addition to highly divergent sequences. However, the vast majority of these histones are identified in metagenomes and thus…
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rabindra.tharu.np@gmail.com
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Aging is associated with functional and molecular changes in distinct hematopoietic stem cell subsets
Age is a risk factor for hematologic malignancies. Attributes of the aging hematopoietic system include increased myelopoiesis, impaired adaptive immunity, and a functional decline of the hematopoietic stem cells (HSCs) that maintain hematopoiesis. Changes in the composition of diverse HSC subsets have been suggested to be responsible for age-related alterations, however, the underlying regulatory mechanisms…
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rabindra.tharu.np@gmail.com
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Fixational eye movements enhance the precision of visual information transmitted by the primate retina
Fixational eye movements alter the number and timing of spikes transmitted from the retina to the brain, but whether these changes enhance or degrade the retinal signal is unclear. To quantify this, we developed a Bayesian method for reconstructing natural images from the recorded spikes of hundreds of retinal ganglion cells (RGCs) in the macaque…
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rabindra.tharu.np@gmail.com
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Sub-threshold neuronal activity and the dynamical regime of cerebral cortex
Cortical neurons exhibit temporally irregular spiking patterns and heterogeneous firing rates. These features arise in model circuits operating in a ‘fluctuation-driven regime’, in which fluctuations in membrane potentials emerge from the network dynamics. However, it is still debated whether the cortex operates in such a regime. We evaluated the fluctuation-driven hypothesis by analyzing spiking and…
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rabindra.tharu.np@gmail.com
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Omicron COVID-19 immune correlates analysis of a third dose of mRNA-1273 in the COVE trial
In the phase 3 Coronavirus Efficacy (COVE) trial (NCT04470427), post-dose two Ancestral Spike-specific binding (bAb) and neutralizing (nAb) antibodies were shown to be correlates of risk (CoR) and of protection against Ancestral-lineage COVID-19 in SARS-CoV-2 naive participants. In the SARS-CoV-2 Omicron era, Omicron subvariants with varying degrees of immune escape now dominate, seropositivity rates are…
