Abstract: The present methods are exemplified by a process in which maternal blood containing fetal DNA is diluted to a nominal value of approximately 0.5 genome equivalent of DNA per reaction sample. Digital analysis is then be used to detect aneuploidy, such as the trisomy that causes Down Syndrome. Since aneuploidies do not present a mutational change in sequence, and are merely a change in the number of chromosomes, it has not been possible to detect them in a fetus without resorting to invasive techniques such as amniocentesis or chorionic villi sampling. Digital amplification allows the detection of aneuploidy using massively parallel amplification and detection methods, examining, e.g., 10,000 genome equivalents.

Abstract: Methods of beam angle optimization for intensity modulated radiotherapy (IMRT) treatment include determining beam's eye view (BEV) regions and a BEV region connectivity manifold by evaluating dose response of each region of interest for each vertex in a delivery coordinate space (DCS). The information contained in the BEV regions and the BEV region connectivity manifold is used to guide an optimizer to find optimal field geometries in the IMRT treatment. To improve the visibility of insufficiently exposed voxels of planning target volumes (PTVs), a post-processing step may be performed to enlarge certain BEV regions, which are considered for exposing during treatment trajectory optimization.

Abstract: A method for scarless genome editing is disclosed. In particular, the method provides scarless genome modification by using homology directed repair (HDR) steps to genetically modify cells and remove unwanted sequences. This method can be used for genome editing, including introducing mutations, deletions, or insertions at any position in the genome without leaving silent mutations, selection marker sequences, or other additional undesired sequences in the genome.

Abstract: Processes and materials to detect cancer from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences derived from a neoplasm. Detection of somatic variants occurring in phase can indicate the presence of cancer in a diagnostic scan and a clinical intervention can be performed.

Abstract: Provided herein are compositions comprising a calcineurin inhibitor and a nonsteroidal anti-inflammatory drug (NSAID) and related methods of administering such compositions for preventing post-ERCP pancreatitis (PEP).

Abstract: The present embodiments generally relate to enabling participants in an online gathering with networked audio to use a cancelling auralizer at their respective locations to create a common acoustic space or set of acoustic spaces shared among subgroups of participants. For example, there are a set of network connected nodes, and the nodes can contain speakers and microphones, as well as participants and node mixing-processing blocks. The node mixing-processing blocks generate and manipulate signals for playback over the node loudspeakers and for distribution to and from the network. This processing can include cancellation of loudspeaker signals from the microphone signals and auralization of signals according to control parameters that are developed locally and from the network.

Abstract: Systems and methods for spatial graph convolutions in accordance with embodiments of the invention are illustrated. One embodiment includes a method for predicting characteristics for molecules, wherein the method includes performing a first set of graph convolutions with a spatial graph representation of a set of molecules, wherein the first set of graph convolutions are based on bonds between the set of molecules, performing a second set of graph convolutions with the spatial graph representation, wherein the second set of graph convolutions are based on at least a distance between each atom and other atoms of the set of molecules, performing a graph gather with the spatial graph representation to produce a feature vector, and predicting a set of one or more characteristics for the set of molecules based on the feature vector.

Abstract: Methods are provided for the treatment of cancer by administering a combination of metabolic interventions to differentiate the cancer cells. The effect on the targeted cancer cell is enhanced relative to a regimen in which a single agent is used; and the effect may be synergistic relative to a regimen in which a single agent is used.

Abstract: Provided herein are recombinant circular RNA (circRNA) molecules comprising an internal ribosome entry site (IRES) operably linked to a protein-coding nucleic acid sequence. The IRES includes at least one RNA secondary structure element; and a sequence region that is complementary to an 18S ribosomal RNA (rRNA). Methods of producing a protein in a cell using the recombinant circRNA molecules are also provided.

Abstract: The present disclosure provides a device for carrying out magnetic resonance imaging compatible optogenetics; and methods for using the device.

Abstract: In accordance with the purpose(s) of the present disclosure, as embodied and broadly described herein, embodiments of the present disclosure, in one aspect, relate to methods of making a structure including nanotubes, a structure including nanotubes, methods of delivering a fluid to a cell, methods of removing a fluid to a cell, methods of accessing intracellular space, and the like.

Abstract: Methods and materials for preparing DNA complementary to poly(A)-minus RNA are provided. The method includes conducting a template switching reaction by contacting a RNA-cDNA intermediate with a template switching oligonucleotide (TSO), extending the cDNA strand to include sequence complementary to the TSO and degrading the TSO. The method is capable of assaying a broad spectrum of coding and non-coding RNA from a single cell.

Abstract: Methods for labeling and imaging the accessible genome using a transposase are disclosed. In some embodiments, a bifunctional transposase complex or transposome is used to insert adaptors comprising chemical tags selectively at accessible sites in the genome where active regulatory DNA is located. Various chemical tags can be used for labeling DNA at insertion sites, including, for example, fluorescent dyes for fluorescence imaging, metal particles for electron microscopy or magnetic manipulation of DNA, isotopic labels, or biotin or other ligands, haptens, substrates, or inhibitors that are recognized by streptavidin, antibodies, enzymes, or receptors. Labeling DNA in this manner can be used to provide spatial information regarding the positioning of regulatory DNA in the genome and makes possible the imaging and sorting of cells based on the status of their regulatory DNA.

Abstract: A method for magnetic resonance imaging corrects non-stationary off-resonance image artifacts. A magnetic resonance imaging (MRI) apparatus performs an imaging acquisition using non-Cartesian trajectories and processes the imaging acquisitions to produce a final image. The processing includes reconstructing a complex-valued image and using a convolutional neural network (CNN) to correct for non-stationary off-resonance artifacts in the image. The CNN is preferably a residual network with multiple residual layers.

Abstract: Embodiments of the synthesis, radiolabeling and biological applications of an activatable tracer that undergoes intramolecular cyclization and aggregation upon activation by cleavage of a blocking moiety are provided. The probes of the disclosure allow for target-controlled self-assembly of small molecules in living subjects for imaging and drug delivery. The aggregated nanoprobes of the disclosure may be detectable optically, by PET detection, magnetic resonance imaging, and the like depending on the detectable reporter attached to the nanoprobe.

Abstract: Processes and materials to detect cancer from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences derived from a neoplasm. Detection of somatic variants occurring in phase can indicate the presence of cancer in a diagnostic scan and a clinical intervention can be performed.

Abstract: A method for PET image reconstruction acquires PET data by a PET scanner; reconstructs from the acquired PET data a seed PET image; builds a feature space from the seed PET image and anatomical images co-registered with the seed PET image; performs a penalized maximum-likelihood reconstruction of a PET image from the seed PET image and the feature space using a penalty function that is calculated based on the differences between each voxel and its neighbors both on the PET image and in the feature space regardless of their location in the image.

Abstract: Retrospective magnetic resonance imaging (MRI) uses a deep neural network framework [102] to generate from MRI imaging data [100] acquired by an MRI apparatus using a predetermined imaging protocol tissue relaxation parametric maps and magnetic/radiofrequency field maps [104] which are then used to generate using the Bloch equations [106] predicted MRI images [108] corresponding to imaging protocols distinct from the predetermined imaging protocol. This allows obtaining a wide spectrum of tissue contrasts distinct from those of the acquired MRI imaging data.

Abstract: A method for 3D object detection is described. The method includes predicting, using a trained monocular depth network, an estimated monocular input depth map of a monocular image of a video stream and an estimated depth uncertainty map associated with the estimated monocular input depth map. The method also includes feeding back a depth uncertainty regression loss associated with the estimated monocular input depth map during training of the trained monocular depth network to update the estimated monocular input depth map. The method further includes detecting 3D objects from a 3D point cloud computed from the estimated monocular input depth map based on seed positions selected from the 3D point cloud and the estimated depth uncertainty map. The method also includes selecting 3D bounding boxes of the 3D objects detected from the 3D point cloud based on the seed positions and an aggregated depth uncertainty.

Abstract: Described herein are systems for targeting viral genomes. Also described herein are methods for targeting viral genomes utilizing the systems described in the instant disclosure. In some cases, systems and methods disclosed herein can be used to treat viral infections. In preferred embodiments, the systems utilise a CRISPR/Cas13d complex to target the genome of an RNA virus such as coronavirus or influenza virus.