Nikita Vladimirov
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View article: Precise, predictable genome integrations by deep-learning-assisted design of microhomology-based templates
Precise, predictable genome integrations by deep-learning-assisted design of microhomology-based templates Open
Precise CRISPR-based DNA integration and editing remain challenging, largely because of insufficient control of the repair process. We find that repair at the genome–cargo interface is predictable by deep learning models and adheres to seq…
View article: aDISCO: A Broadly Applicable Method for 3D Microscopy of Archival Paraffin-Embedded Human Tissues
aDISCO: A Broadly Applicable Method for 3D Microscopy of Archival Paraffin-Embedded Human Tissues Open
During human surgeries and autopsies, specimens are regularly sampled and stored as formalin-fixed paraffin-embedded (FFPE) tissue blocks. Diagnoses are rendered by microscopical examination of two-dimensional sections. Good clinical pract…
View article: Optimization of pulsed saturation transfer MR fingerprinting (ST MRF) acquisition using the Cramér-Rao bound and sequential quadratic programming
Optimization of pulsed saturation transfer MR fingerprinting (ST MRF) acquisition using the Cramér-Rao bound and sequential quadratic programming Open
Purpose: To develop a method for optimizing pulsed saturation transfer MR fingerprinting (ST MRF) acquisition. Methods: The Cramér-Rao bound (CRB) for variance assessment was employed on Bloch-McConnell-based simulated signals, followed by…
View article: Nuclear recoil detection with color centers in bulk lithium fluoride
Nuclear recoil detection with color centers in bulk lithium fluoride Open
We present initial results on nuclear recoil detection based on the fluorescence of color centers created by nuclear recoils in lithium fluoride. We use gamma rays, fast and thermal neutrons, and study the difference in responses they indu…
View article: Multi-Parameter Molecular MRI Quantification using Physics-Informed Self-Supervised Learning
Multi-Parameter Molecular MRI Quantification using Physics-Informed Self-Supervised Learning Open
Biophysical model fitting plays a key role in obtaining quantitative parameters from physiological signals and images. However, the model complexity for molecular magnetic resonance imaging (MRI) often translates into excessive computation…
View article: Shared and unique consequences of Joubert Syndrome gene dysfunction on the zebrafish central nervous system
Shared and unique consequences of Joubert Syndrome gene dysfunction on the zebrafish central nervous system Open
Joubert Syndrome (JBTS) is a neurodevelopmental ciliopathy defined by a highly specific midbrain–hindbrain malformation, variably associated with additional neurological features. JBTS displays prominent genetic heterogeneity with >40 c…
View article: Pythia: Non-random DNA repair allows predictable CRISPR/Cas9 integration and gene editing
Pythia: Non-random DNA repair allows predictable CRISPR/Cas9 integration and gene editing Open
Summary CRISPR-based genome engineering holds enormous promise for basic science and therapeutic applications. Integrating and editing DNA sequences is still challenging in many cellular contexts, largely due to insufficient control of the…
View article: Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for cleared samples
Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for cleared samples Open
View article: Shared and unique consequences of Joubert Syndrome gene dysfunction on the zebrafish central nervous system
Shared and unique consequences of Joubert Syndrome gene dysfunction on the zebrafish central nervous system Open
Joubert Syndrome (JBTS) is a neurodevelopmental ciliopathy defined by a highly specific midbrain-hindbrain malformation, variably associated with additional neurological features. JBTS displays prominent genetic heterogeneity with >40 caus…
View article: Dynamic and rapid deep synthesis of chemical exchange saturation transfer and semisolid magnetization transfer MRI signals
Dynamic and rapid deep synthesis of chemical exchange saturation transfer and semisolid magnetization transfer MRI signals Open
View article: The Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for large cleared samples
The Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for large cleared samples Open
In 2015, we launched the mesoSPIM initiative ( www.mesospim.org ), an open-source project for making light-sheet microscopy of large cleared tissues more accessible. Meanwhile, the demand for imaging larger samples at higher speed and reso…
View article: Prox2 and Runx3 vagal sensory neurons regulate esophageal motility
Prox2 and Runx3 vagal sensory neurons regulate esophageal motility Open
View article: Mineral detection of neutrinos and dark matter. A whitepaper
Mineral detection of neutrinos and dark matter. A whitepaper Open
View article: Mineral Detection of Neutrinos and Dark Matter. A Whitepaper
Mineral Detection of Neutrinos and Dark Matter. A Whitepaper Open
Minerals are solid state nuclear track detectors - nuclear recoils in a mineral leave latent damage to the crystal structure. Depending on the mineral and its temperature, the damage features are retained in the material from minutes (in l…
View article: A brainstem integrator for self-location memory and positional homeostasis in zebrafish
A brainstem integrator for self-location memory and positional homeostasis in zebrafish Open
To track and control self-location, animals integrate their movements through space. Representations of self-location are observed in the mammalian hippocampal formation, but it is unknown if positional representations exist in more ancien…
View article: Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice
Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice Open
Life-long brain function and mental health are critically determined by developmental processes occurring before birth. During mammalian pregnancy, maternal cells are transferred to the fetus. They are referred to as maternal microchimeric…
View article: Prox2+ and Runx3+ neurons regulate esophageal motility
Prox2+ and Runx3+ neurons regulate esophageal motility Open
Summary Sensory neurons of the vagus nerve monitor distention and stretch in the gastrointestinal tract. Major efforts are underway to assign physiological functions to the many distinct subtypes of vagal sensory neurons. Here, we used gen…
View article: Imaging data (part 1) for the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice"
Imaging data (part 1) for the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice" Open
This archive contains part 1 of the raw imaging data of the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice".
View article: Imaging data (part 2) for the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice"
Imaging data (part 2) for the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice" Open
This archive contains part 2 of the raw imaging data of the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice".
View article: Imaging data (part 2) for the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice"
Imaging data (part 2) for the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice" Open
This archive contains part 2 of the raw imaging data of the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice".
View article: Raw data for the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice"
Raw data for the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice" Open
This archive contains the raw data of the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice".
View article: Raw data for the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice"
Raw data for the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice" Open
This archive contains the raw data of the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice".
View article: Imaging data (part 1) for the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice"
Imaging data (part 1) for the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice" Open
This archive contains part 1 of the raw imaging data of the manuscript "Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice".
View article: CNN-based fully automatic wrist cartilage volume quantification in MR Image
CNN-based fully automatic wrist cartilage volume quantification in MR Image Open
Detection of cartilage loss is crucial for the diagnosis of osteo- and rheumatoid arthritis. A large number of automatic segmentation tools have been reported so far for cartilage assessment in magnetic resonance images of large joints. As…
View article: CAD we share? Publishing reproducible microscope hardware
CAD we share? Publishing reproducible microscope hardware Open
View article: A brainstem integrator for self-localization and positional homeostasis
A brainstem integrator for self-localization and positional homeostasis Open
To accurately track self-location, animals need to integrate their movements through space. In amniotes, representations of self-location have been found in regions such as the hippocampus. It is unknown whether more ancient brain regions …
View article: Dual-view light-sheet imaging through a tilted glass interface using a deformable mirror
Dual-view light-sheet imaging through a tilted glass interface using a deformable mirror Open
Light-sheet microscopy has become indispensable for imaging developing organisms, and imaging from multiple directions (views) is essential to improve its spatial resolution. We combine multi-view light-sheet microscopy with microfluidics …
View article: Dual-view light-sheet imaging through tilted glass interface using a deformable mirror
Dual-view light-sheet imaging through tilted glass interface using a deformable mirror Open
Light-sheet microscopy has become one of the primary tools for imaging live developing organisms because of its high speed, low phototoxicity, and optical sectioning capabilities. Detection from multiple sides (multi-view imaging) addition…