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While conventional MRI sequences cannot visualize tissues from the osteochondral junction (OCJ) due to these tissues' short transverse T /T * relaxations, ultrashort echo time (UTE) sequences can overcome this limitation. A 2D UTE sequence with a dual adiabatic inversion recovery preparation (DIR-UTE) for selective imaging of short T tissues with high contrast has previously been developed, but high sensitivity to eddy currents and aliased out-of-slice excitation make it difficult to image the thin layer of the OCJ in vivo. Here, we combine the DIR scheme with a 3D UTE cones sequence for volumetric imaging of OCJ tissues in vivo, aiming to generate higher OCJ contrast compared with a recently developed single IR-prepared UTE sequence with a fat saturation module (IR-FS-UTE). All sequences were implemented on a 3-T clinical scanner. The DIR-UTE cones sequence combined a 3D UTE cones sequence with two narrow-band adiabatic IR preparation pulses centered on water and fat spectrum frequencies, respectively. The 3D DIR-UTE cones sequence was first applied to a phantom, then to the knees of four healthy volunteers and four patients diagnosed with osteoarthritis and compared with the IR-FS-UTE sequence. In both phantom and volunteer studies, the proposed DIR-UTE cones sequence showed much higher contrast for OCJ imaging than the IR-FS-UTE sequence did. The 3D DIR-UTE cones sequence showed a significantly higher contrast-to-noise ratio between the OCJ and subchondral bone fat (mean, standard deviation [SD]: 25.7 ± 2.3) and between the OCJ and superficial layers of cartilage (mean, SD: 22.2 ± 3.5) compared with the IR-FS-UTE sequence (mean, SD: 10.8 ± 2.5 and 16.3 ± 2.6, respectively). The 3D DIR-UTE cones sequence is feasible for imaging of the OCJ region of the knee in vivo and produces both high resolution and high contrast.
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http://dx.doi.org/10.1002/nbm.4559 | DOI Listing |
Lab Invest
August 2025
Department of Gynaecology, Jena University Hospital, 07747 Jena, Germany.
HPV-DNA integration into the host genome is a frequent event in cervical carcinogenesis and may drive clonal expansion of the affected cells. Based on viral cellular junction (vcj) sequences, highly specific vcj-PCRs can be designed to detect viral integrants in DNA from cervical cell scrapes or tissue samples. In a recent study, such patient specific vcj-PCR assays were employed for the detection of recurrent high-grade squamous intraepithelial lesions (HSIL) during post-operative surveillance.
View Article and Find Full Text PDFGenome Biol
August 2025
Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, OX3 7FZ, UK.
We present direct sequencing methodologies, scTAPS for 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) and scCAPS + specifically for 5hmC, enabling quantitative detection of 5mC and 5hmC at single-base resolution and single-cell level. Achieving approximately 90% mapping efficiency, our plate-based methods accurately recover 5mC and 5hmC profiles in CD8 + T and mouse embryonic stem cells. Notably, scCAPS + reveals a global increase in 5hmC across neuronal and non-neuronal cells in the hippocampus of aging mice.
View Article and Find Full Text PDFElife
August 2025
The Vision Center, Department of Surgery, and Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, United States.
Human cone photoreceptors differ from rods and serve as the retinoblastoma cell-of-origin, yet the developmental basis for their distinct behaviors is poorly understood. Here, we used deep full-length single-cell RNA-sequencing (scRNA-seq) to distinguish post-mitotic cone and rod developmental states and identify cone-specific features related to retinoblastomagenesis. The analyses revealed nascent, immediately post-mitotic cone and rod precursors characterized by higher THRB or NRL regulon activities, immature and maturing cone and rod precursors with concurrent cone- and rod-related gene and regulon expression, and distinct early and late cone and rod maturation states distinguished by maturation-associated declines in RAX regulon activity.
View Article and Find Full Text PDFbioRxiv
July 2025
Department of Biology, The City College of New York, City University of New York, New York, NY 10031, USA.
The retinal development of elasmobranchs--the superclass comprising sharks, skates and rays--is a poorly understood phenomenon. The clade is diverse in retinal phenotypes, with many sharks and rays possessing rods and multiple cone types. In contrast, the little skate () has only a single type of rod photoreceptor, which is reported to have taken on some physiological and anatomical properties of cones.
View Article and Find Full Text PDFExp Eye Res
October 2025
Ophthalmology Department, The Tenth Affliated Hospital, Southern Medical University (Dongguan People's Hospital), 78Wandao Road, Dongguan, 523000, China. Electronic address:
This study delineates the single-cell transcriptomic landscape of pigmented guinea pig retinas-an emerging model for myopia research-through integrated single-cell and bulk RNA sequencing, cross-species comparative analysis, and functional validation using form-deprivation myopia models with intravitreal brimonidine intervention. Our results identified six major retinal cell types (rod cells, cone cells, bipolar cells, Müller glial cells, astrocytes, and retinal pigment epithelial cells) subdivided into 16 distinct subclusters, revealing multilineage pseudo time trajectories and specialized intercellular signaling networks: rod cells via NEGR/CADM, cone cells via MPZ, bipolar cells via SEMA6/PTPRM, and astrocytes via ESAM. Cross-species alignment demonstrated closer phylogenetic alignment with human retinal architecture than murine counterparts in pseudo time trajectories and cellular crosstalk.
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