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  1. Article ; Online: A simulated comparison of lung tumor target verification using stereoscopic tomosynthesis or radiography.

    Hsieh, Scott S / Ng, Lydia W / Cao, Minsong / Lee, Percy

    Medical physics

    2022  Volume 49, Issue 5, Page(s) 3041–3052

    Abstract: Purpose: Mobile lung tumors are increasingly being treated with ablative radiotherapy, for which precise motion management is essential. In-room stereoscopic radiography systems are able to guide ablative radiotherapy for stationary cranial lesions but ... ...

    Abstract Purpose: Mobile lung tumors are increasingly being treated with ablative radiotherapy, for which precise motion management is essential. In-room stereoscopic radiography systems are able to guide ablative radiotherapy for stationary cranial lesions but not optimally for lung tumors unless fiducial markers are inserted. We propose augmenting stereoscopic radiographic systems with multiple small x-ray sources to provide the capability of imaging with stereoscopic, single frame tomosynthesis.
    Methods: In single frame tomosynthesis, nine x-ray sources are placed in a 3 × 3 configuration and energized simultaneously. The beams from these sources are collimated so that they converge on the tumor and then diverge to illuminate nine non-overlapping sectors on the detector. These nine sector images are averaged together and filtered to create the tomosynthesis effect. Single frame tomosynthesis is intended to be an alternative imaging mode for existing stereoscopic systems with a field of view that is three times smaller and a temporal resolution equal to the frame rate of the detector. We simulated stereoscopic tomosynthesis and radiography using Monte Carlo techniques on 60 patients with early-stage lung cancer from the NSCLC-Radiomics dataset. Two board-certified radiation oncologists reviewed these simulated images and rated them on a 4-point scale (1: tumor not visible; 2: tumor visible but inadequate for motion management; 3: tumor visible and adequate for motion management; 4: tumor visibility excellent). Each tumor was independently presented four times (two viewing angles from radiography and two viewing angles from tomosynthesis) in a blinded fashion over two reading sessions.
    Results: The fraction of tumors that were rated as adequate or excellent for motion management (scores 3 or 4) from at least one viewing angle was 53% using radiography and 90% using tomosynthesis. From both viewing angles, the corresponding fractions were 7% for radiography and 48% for tomosynthesis. Readers agreed exactly on 62% of images and within 1 point on 98% of images. The acquisition technique was estimated to be 75 mAs at 120 kVp per treatment fraction assuming one verification image per breath, approximately one order of magnitude less than a standard dose cone beam CT.
    Conclusions: Stereoscopic tomosynthesis may provide a noninvasive, low dose, intrafraction motion verification technique for lung tumors treated by ablative radiotherapy. The system architecture is compatible with real-time video capture at 30 frames per second. Simulations suggest that most, but not all, lung tumors can be adequately visualized from at least one viewing angle.
    MeSH term(s) Cone-Beam Computed Tomography/methods ; Fiducial Markers ; Humans ; Lung Neoplasms/diagnostic imaging ; Lung Neoplasms/pathology ; Lung Neoplasms/radiotherapy ; Motion ; Radiography
    Language English
    Publishing date 2022-03-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 188780-4
    ISSN 2473-4209 ; 0094-2405
    ISSN (online) 2473-4209
    ISSN 0094-2405
    DOI 10.1002/mp.15634
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: NUT Expression Is of Diagnostic Utility in the Distinction of Digital Papillary Carcinoma From Poroid Hidradenoma.

    Iacobelli, Jean / Harvey, Nathan T / Ardakani, Nima Mesbah / Ng, Lydia / Preston, Henry / Wood, Benjamin A

    The American Journal of dermatopathology

    2023  Volume 46, Issue 2, Page(s) 98–100

    Abstract: Abstract: The distinction between digital papillary adenocarcinoma (DPAC) and benign cutaneous adnexal tumors is clinically important and can be challenging. Poroid hidradenoma frequently occurs at acral sites and can show a number of histological ... ...

    Abstract Abstract: The distinction between digital papillary adenocarcinoma (DPAC) and benign cutaneous adnexal tumors is clinically important and can be challenging. Poroid hidradenoma frequently occurs at acral sites and can show a number of histological features, which overlap with digital papillary adenocarcinoma. Recent work has shown that YAP1-NUTM1 fusions are frequent in poroid hidradenoma and are associated with nuclear protein in testis (NUT) expression by immunohistochemistry. We evaluated the expression of NUT-1 by immunohistochemistry in 4 cases of DPAC and 4 cases of poroid hidradenoma. Three of 4 cases of poroid hidradenoma showed strong NUT-1 expression, with no staining in any of the cases of DPAC. These results suggest that NUT-1 immunohistochemistry may be a useful additional tool in evaluating this differential diagnosis.
    MeSH term(s) Male ; Humans ; Carcinoma, Papillary ; Acrospiroma/pathology ; Sweat Gland Neoplasms/diagnosis ; Sweat Gland Neoplasms/genetics ; Sweat Gland Neoplasms/metabolism ; Adenocarcinoma, Papillary ; Poroma
    Language English
    Publishing date 2023-11-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 448469-1
    ISSN 1533-0311 ; 0193-1091
    ISSN (online) 1533-0311
    ISSN 0193-1091
    DOI 10.1097/DAD.0000000000002596
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Online conversion of reconstructed neural morphologies into standardized SWC format.

    Mehta, Ketan / Ljungquist, Bengt / Ogden, James / Nanda, Sumit / Ascoli, Ruben G / Ng, Lydia / Ascoli, Giorgio A

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 7429

    Abstract: Digital reconstructions provide an accurate and reliable way to store, share, model, quantify, and analyze neural morphology. Continuous advances in cellular labeling, tissue processing, microscopic imaging, and automated tracing catalyzed a ... ...

    Abstract Digital reconstructions provide an accurate and reliable way to store, share, model, quantify, and analyze neural morphology. Continuous advances in cellular labeling, tissue processing, microscopic imaging, and automated tracing catalyzed a proliferation of software applications to reconstruct neural morphology. These computer programs typically encode the data in custom file formats. The resulting format heterogeneity severely hampers the interoperability and reusability of these valuable data. Among these many alternatives, the SWC file format has emerged as a popular community choice, coalescing a rich ecosystem of related neuroinformatics resources for tracing, visualization, analysis, and simulation. This report presents a standardized specification of the SWC file format. In addition, we introduce xyz2swc, a free online service that converts all 26 reconstruction formats (and 72 variations) described in the scientific literature into the SWC standard. The xyz2swc service is available open source through a user-friendly browser interface ( https://neuromorpho.org/xyz2swc/ui/ ) and an Application Programming Interface (API).
    MeSH term(s) Ecosystem ; Software ; Computer Simulation ; Neurons ; Publications
    Language English
    Publishing date 2023-11-16
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-42931-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Real-time tomosynthesis for radiation therapy guidance.

    Hsieh, Scott S / Ng, Lydia W

    Medical physics

    2017  Volume 44, Issue 11, Page(s) 5584–5595

    Abstract: Purpose: Fluoroscopy has been a tool of choice for monitoring treatments or interventions because of its extremely fast imaging times. However, the contrast obtained in fluoroscopy may be insufficient for certain clinical applications. In stereotactic ... ...

    Abstract Purpose: Fluoroscopy has been a tool of choice for monitoring treatments or interventions because of its extremely fast imaging times. However, the contrast obtained in fluoroscopy may be insufficient for certain clinical applications. In stereotactic ablative radiation therapy of the lung, fluoroscopy often lacks sufficient contrast for gating treatment. The purpose of this work is to describe and assess a real-time tomosynthesis design that can produce sufficient contrast for guidance of lung tumor treatment within a small field of view.
    Methods: Previous tomosynthesis designs in radiation oncology have temporal resolution on the order of seconds. The proposed system design uses parallel acquisition of multiple frames by simultaneously illuminating the field of view with multiple sources, enabling a temporal resolution of up to 30 frames per second. For a small field of view, a single flat-panel detector could be used if different sectors of the detector are assigned to specific sources. Simulated images were generated by forward projection of existing clinical datasets. The authors varied the number of tubes and the power of each tube in order to determine the impact on tumor visualization.
    Results: Visualization of the tumor was much clearer in tomosynthesis than in fluoroscopy. Contrast generally improved with the number of sources used, and a minimum of four sources should be used. The high contrast of the lung allows very low system power, and in most cases, less than 1 mA was needed. More power is required in the lateral direction than the AP direction.
    Conclusions: The proposed system produces images adequate for real-time guidance of radiation therapy. The additional hardware requirements are modest, and the system is capable of imaging at high frame rates and low dose. Further development, including a prototype system and a dosimetry study, is needed to further evaluate the feasibility of this device for radiation therapy guidance.
    MeSH term(s) Humans ; Imaging, Three-Dimensional ; Lung Neoplasms/diagnostic imaging ; Lung Neoplasms/physiopathology ; Lung Neoplasms/radiotherapy ; Movement ; Radiation Dosage ; Radiotherapy, Image-Guided/methods ; Time Factors ; Tomography
    Language English
    Publishing date 2017-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 188780-4
    ISSN 2473-4209 ; 0094-2405
    ISSN (online) 2473-4209
    ISSN 0094-2405
    DOI 10.1002/mp.12530
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Cross-modality mapping using image varifolds to align tissue-scale atlases to molecular-scale measures with application to 2D brain sections.

    Stouffer, Kaitlin M / Trouvé, Alain / Younes, Laurent / Kunst, Michael / Ng, Lydia / Zeng, Hongkui / Anant, Manjari / Fan, Jean / Kim, Yongsoo / Chen, Xiaoyin / Rue, Mara / Miller, Michael I

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 3530

    Abstract: This paper explicates a solution to building correspondences between molecular-scale transcriptomics and tissue-scale atlases. This problem arises in atlas construction and cross-specimen/technology alignment where specimens per emerging technology ... ...

    Abstract This paper explicates a solution to building correspondences between molecular-scale transcriptomics and tissue-scale atlases. This problem arises in atlas construction and cross-specimen/technology alignment where specimens per emerging technology remain sparse and conventional image representations cannot efficiently model the high dimensions from subcellular detection of thousands of genes. We address these challenges by representing spatial transcriptomics data as generalized functions encoding position and high-dimensional feature (gene, cell type) identity. We map onto low-dimensional atlas ontologies by modeling regions as homogeneous random fields with unknown transcriptomic feature distribution. We solve simultaneously for the minimizing geodesic diffeomorphism of coordinates through LDDMM and for these latent feature densities. We map tissue-scale mouse brain atlases to gene-based and cell-based transcriptomics data from MERFISH and BARseq technologies and to histopathology and cross-species atlases to illustrate integration of diverse molecular and cellular datasets into a single coordinate system as a means of comparison and further atlas construction.
    MeSH term(s) Animals ; Brain/metabolism ; Mice ; Transcriptome/genetics ; Atlases as Topic ; Image Processing, Computer-Assisted/methods ; Gene Expression Profiling/methods ; Humans
    Language English
    Publishing date 2024-04-25
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-47883-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Traumatic dental injuries presenting to a paediatric emergency department in a tertiary children's hospital, Adelaide, Australia.

    Ng, Lydia / Malandris, Michael / Cheung, Wendy / Rossi-Fedele, Giampiero

    Dental traumatology : official publication of International Association for Dental Traumatology

    2020  Volume 36, Issue 4, Page(s) 360–370

    Abstract: Background/aim: There is a scarcity of data regarding paediatric traumatic dental injuries (TDI) in tertiary teaching hospitals. Therefore, the aim of this study was to review the TDI presenting to the Women's and Children's Hospital in Adelaide ( ... ...

    Abstract Background/aim: There is a scarcity of data regarding paediatric traumatic dental injuries (TDI) in tertiary teaching hospitals. Therefore, the aim of this study was to review the TDI presenting to the Women's and Children's Hospital in Adelaide (Australia) on an emergency basis and to identify the characteristics of the presenting patient cohort, their accident, injuries and management.
    Methods: Medical health records of 337 paediatric patients attending the Paediatric Emergency Department (PED) for the management of TDI over 18 months were prospectively reviewed.
    Results: TDI were more frequent in children under 5 years of age (56.1%) with a predominance of injuries sustained by males (63.8%). The accident characteristics included weekend occurrence (35.6%), the most common aetiology was falls (64.4%) and many incidents occurred at home (48.5%). Overall, 654 teeth were injured with the majority affecting deciduous teeth (58.4%) and the maxillary central incisors (69.9%). The most frequent injury was lateral luxation (27.5%). The majority of patients were referred to the Paediatric Dentistry Department (60.8%). However, almost half of presenting patients did not require further management locally and were subsequently discharged to their dental practitioners (39.2%). Most patients receiving treatment were managed under general anaesthetic (36.9%), and there was often a delay of 3-12 hours before treatment commenced (49.1%). Similarly, more severe injuries in the permanent dentition (avulsion, extrusion, root fracture, intrusion, alveolar fracture) were more frequently managed between 3 and 12 hours following the accident.
    Conclusion: The patient, accident, injury and management characteristics are comparable to what has previously been reported in other studies in paediatric populations. Injuries affecting the permanent dentition are more likely to be managed within 3 and 12 hours in an outpatient setting, whereas injuries affecting the deciduous dentition had a delay in management between 12 and 24 hours under general anaesthetic.
    MeSH term(s) Australia ; Child ; Child, Preschool ; Dentists ; Emergency Service, Hospital ; Female ; Humans ; Male ; Professional Role ; Retrospective Studies ; Tooth Avulsion ; Tooth Fractures ; Tooth Injuries
    Language English
    Publishing date 2020-02-18
    Publishing country Denmark
    Document type Journal Article
    ZDB-ID 2030722-6
    ISSN 1600-9657 ; 1600-4469
    ISSN (online) 1600-9657
    ISSN 1600-4469
    DOI 10.1111/edt.12548
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: epDevAtlas: Mapping GABAergic cells and microglia in postnatal mouse brains.

    Liwang, Josephine K / Kronman, Fae A / Minteer, Jennifer A / Wu, Yuan-Ting / Vanselow, Daniel J / Ben-Simon, Yoav / Taormina, Michael / Parmaksiz, Deniz / Way, Sharon W / Zeng, Hongkui / Tasic, Bosiljka / Ng, Lydia / Kim, Yongsoo

    bioRxiv : the preprint server for biology

    2023  

    Abstract: During development, brain regions follow encoded growth trajectories. Compared to classical brain growth charts, high-definition growth charts could quantify regional volumetric growth and constituent cell types, improving our understanding of typical ... ...

    Abstract During development, brain regions follow encoded growth trajectories. Compared to classical brain growth charts, high-definition growth charts could quantify regional volumetric growth and constituent cell types, improving our understanding of typical and pathological brain development. Here, we create high-resolution 3D atlases of the early postnatal mouse brain, using Allen CCFv3 anatomical labels, at postnatal days (P) 4, 6, 8, 10, 12, and 14, and determine the volumetric growth of different brain regions. We utilize 11 different cell type-specific transgenic animals to validate and refine anatomical labels. Moreover, we reveal region-specific density changes in γ-aminobutyric acid-producing (GABAergic), cortical layer-specific cell types, and microglia as key players in shaping early postnatal brain development. We find contrasting changes in GABAergic neuronal densities between cortical and striatal areas, stabilizing at P12. Moreover, somatostatin-expressing cortical interneurons undergo regionally distinct density reductions, while vasoactive intestinal peptide-expressing interneurons show no significant changes. Remarkably, microglia transition from high density in white matter tracks to gray matter at P10, and show selective density increases in sensory processing areas that correlate with the emergence of individual sensory modalities. Lastly, we create an open-access web-visualization (https://kimlab.io/brain-map/epDevAtlas) for cell-type growth charts and developmental atlases for all postnatal time points.
    Language English
    Publishing date 2023-11-25
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.11.24.568585
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: A Universal Method for Crossing Molecular and Atlas Modalities using Simplex-Based Image Varifolds and Quadratic Programming.

    Stouffer, Kaitlin M / Trouv, Alain / Younes, Laurent / Kunst, Michael / Ng, Lydia / Zeng, Hongkui / Anant, Manjari / Fan, Jean / Kim, Yongsoo / Miller, Michael I

    bioRxiv : the preprint server for biology

    2023  

    Abstract: This paper explicates a solution to the problem of building correspondences between molecular-scale transcriptomics and tissue-scale atlases. The central model represents spatial transcriptomics as generalized functions encoding molecular position and ... ...

    Abstract This paper explicates a solution to the problem of building correspondences between molecular-scale transcriptomics and tissue-scale atlases. The central model represents spatial transcriptomics as generalized functions encoding molecular position and high-dimensional transcriptomic-based (gene, cell type) identity. We map onto low-dimensional atlas ontologies by modeling each atlas compartment as a homogeneous random field with unknown transcriptomic feature distribution. The algorithm presented solves simultaneously for the minimizing geodesic diffeomorphism of coordinates and latent atlas transcriptomic feature fractions by alternating LDDMM optimization for coordinate transformations and quadratic programming for the latent transcriptomic variables. We demonstrate the universality of the algorithm in mapping tissue atlases to gene-based and cell-based MERFISH datasets as well as to other tissue scale atlases. The joint estimation of diffeomorphisms and latent feature distributions allows integration of diverse molecular and cellular datasets into a single coordinate system and creates an avenue of comparison amongst atlas ontologies for continued future development.
    Language English
    Publishing date 2023-03-29
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.03.28.534622
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Developmental Mouse Brain Common Coordinate Framework.

    Kronman, Fae A / Liwang, Josephine K / Betty, Rebecca / Vanselow, Daniel J / Wu, Yuan-Ting / Tustison, Nicholas J / Bhandiwad, Ashwin / Manjila, Steffy B / Minteer, Jennifer A / Shin, Donghui / Lee, Choong Heon / Patil, Rohan / Duda, Jeffrey T / Puelles, Luis / Gee, James C / Zhang, Jiangyang / Ng, Lydia / Kim, Yongsoo

    bioRxiv : the preprint server for biology

    2023  

    Abstract: 3D standard reference brains serve as key resources to understand the spatial organization of the brain and promote interoperability across different studies. However, unlike the adult mouse brain, the lack of standard 3D reference atlases for developing ...

    Abstract 3D standard reference brains serve as key resources to understand the spatial organization of the brain and promote interoperability across different studies. However, unlike the adult mouse brain, the lack of standard 3D reference atlases for developing mouse brains has hindered advancement of our understanding of brain development. Here, we present a multimodal 3D developmental common coordinate framework (DevCCF) spanning mouse embryonic day (E) 11.5, E13.5, E15.5, E18.5, and postnatal day (P) 4, P14, and P56 with anatomical segmentations defined by a developmental ontology. At each age, the DevCCF features undistorted morphologically averaged atlas templates created from Magnetic Resonance Imaging and co-registered high-resolution templates from light sheet fluorescence microscopy. Expert-curated 3D anatomical segmentations at each age adhere to an updated prosomeric model and can be explored via an interactive 3D web-visualizer. As a use case, we employed the DevCCF to unveil the emergence of GABAergic neurons in embryonic brains. Moreover, we integrated the Allen CCFv3 into the P56 template with stereotaxic coordinates and mapped spatial transcriptome cell-type data with the developmental ontology. In summary, the DevCCF is an openly accessible resource that can be used for large-scale data integration to gain a comprehensive understanding of brain development.
    Language English
    Publishing date 2023-09-15
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.09.14.557789
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: The Neurodata Without Borders ecosystem for neurophysiological data science.

    Rübel, Oliver / Tritt, Andrew / Ly, Ryan / Dichter, Benjamin K / Ghosh, Satrajit / Niu, Lawrence / Baker, Pamela / Soltesz, Ivan / Ng, Lydia / Svoboda, Karel / Frank, Loren / Bouchard, Kristofer E

    eLife

    2022  Volume 11

    Abstract: The neurophysiology of cells and tissues are monitored electrophysiologically and optically in diverse experiments and species, ranging from flies to humans. Understanding the brain requires integration of data across this diversity, and thus these data ... ...

    Abstract The neurophysiology of cells and tissues are monitored electrophysiologically and optically in diverse experiments and species, ranging from flies to humans. Understanding the brain requires integration of data across this diversity, and thus these data must be findable, accessible, interoperable, and reusable (FAIR). This requires a standard language for data and metadata that can coevolve with neuroscience. We describe design and implementation principles for a language for neurophysiology data. Our open-source software (Neurodata Without Borders, NWB) defines and modularizes the interdependent, yet separable, components of a data language. We demonstrate NWB's impact through unified description of neurophysiology data across diverse modalities and species. NWB exists in an ecosystem, which includes data management, analysis, visualization, and archive tools. Thus, the NWB data language enables reproduction, interchange, and reuse of diverse neurophysiology data. More broadly, the design principles of NWB are generally applicable to enhance discovery across biology through data FAIRness.
    MeSH term(s) Data Science ; Ecosystem ; Humans ; Metadata ; Neurophysiology ; Software
    Language English
    Publishing date 2022-10-04
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.78362
    Database MEDical Literature Analysis and Retrieval System OnLINE

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