79 research outputs found
sj-jpg-3-cll-10.1177_09636897231163232 – Supplemental material for Derivation of Sendai-Virus-Reprogrammed Human iPSCs-Neuronal Precursors: In Vitro and In Vivo Post-grafting Safety Characterization
No full textSupplemental material, sj-jpg-3-cll-10.1177_09636897231163232 for Derivation of Sendai-Virus-Reprogrammed Human iPSCs-Neuronal Precursors: In Vitro and In Vivo Post-grafting Safety Characterization by Michiko Shigyo, Yoshiomi Kobayashi, Oleksandr Platoshyn, Silvia Marsala, Tomohisa Kato Jr, Naoki Takamura, Kenji Yoshida, Akiyoshi Kishino, Mariana Bravo-Hernandez, Stefan Juhas, Jana Juhasova, Hana Studenovska, Vladimir Proks, Joseph D. Ciacci and Martin Marsala in Cell Transplantation</p
sj-jpg-4-cll-10.1177_09636897231163232 – Supplemental material for Derivation of Sendai-Virus-Reprogrammed Human iPSCs-Neuronal Precursors: In Vitro and In Vivo Post-grafting Safety Characterization
No full textSupplemental material, sj-jpg-4-cll-10.1177_09636897231163232 for Derivation of Sendai-Virus-Reprogrammed Human iPSCs-Neuronal Precursors: In Vitro and In Vivo Post-grafting Safety Characterization by Michiko Shigyo, Yoshiomi Kobayashi, Oleksandr Platoshyn, Silvia Marsala, Tomohisa Kato Jr, Naoki Takamura, Kenji Yoshida, Akiyoshi Kishino, Mariana Bravo-Hernandez, Stefan Juhas, Jana Juhasova, Hana Studenovska, Vladimir Proks, Joseph D. Ciacci and Martin Marsala in Cell Transplantation</p
sj-jpg-1-cll-10.1177_09636897231163232 – Supplemental material for Derivation of Sendai-Virus-Reprogrammed Human iPSCs-Neuronal Precursors: In Vitro and In Vivo Post-grafting Safety Characterization
No full textSupplemental material, sj-jpg-1-cll-10.1177_09636897231163232 for Derivation of Sendai-Virus-Reprogrammed Human iPSCs-Neuronal Precursors: In Vitro and In Vivo Post-grafting Safety Characterization by Michiko Shigyo, Yoshiomi Kobayashi, Oleksandr Platoshyn, Silvia Marsala, Tomohisa Kato Jr, Naoki Takamura, Kenji Yoshida, Akiyoshi Kishino, Mariana Bravo-Hernandez, Stefan Juhas, Jana Juhasova, Hana Studenovska, Vladimir Proks, Joseph D. Ciacci and Martin Marsala in Cell Transplantation</p
sj-jpg-2-cll-10.1177_09636897231163232 – Supplemental material for Derivation of Sendai-Virus-Reprogrammed Human iPSCs-Neuronal Precursors: In Vitro and In Vivo Post-grafting Safety Characterization
No full textSupplemental material, sj-jpg-2-cll-10.1177_09636897231163232 for Derivation of Sendai-Virus-Reprogrammed Human iPSCs-Neuronal Precursors: In Vitro and In Vivo Post-grafting Safety Characterization by Michiko Shigyo, Yoshiomi Kobayashi, Oleksandr Platoshyn, Silvia Marsala, Tomohisa Kato Jr, Naoki Takamura, Kenji Yoshida, Akiyoshi Kishino, Mariana Bravo-Hernandez, Stefan Juhas, Jana Juhasova, Hana Studenovska, Vladimir Proks, Joseph D. Ciacci and Martin Marsala in Cell Transplantation</p
Quantification of humeroulnar incongruity in Labrador Retrievers with and without medial coronoid disease
No full textObjective
To quantify humeroulnar incongruity on elbow radiographs in Labrador Retrievers with or without medial coronoid disease (MCD).
Study Design
Retrospective study of 92 elbows.
Sample Population
Radiographic projections of elbow joints from Labrador Retrievers with MCD (n = 42 elbows; 26 dogs) and without MCD (n = 50 elbows; 25 dogs).
Procedure
The congruity of the humeroulnar joint was measured using an index of subluxation (SI) for each elbow. SI was defined as the distance between the centers of 2 circles drawn along the margins of the incisura trochlearis and the trochlea of humerus on mediolateral digital radiographic projections, normalized by the radius of the circle circumscribing the humeral trochlea. SI was compared between right and left elbows with and without pathology using a Wilcoxon test for paired data, and between normal and abnormal groups with a Wilcoxon test for unpaired data. Mismatch between ulnar curvature and curvature of humeral trochlea and radioulnar incongruency were also noted (Wilcoxon test). The intraobserver repeatability, correlation between SI and radioulnar incongruency, and between SI and mismatch elbow curvature were estimated with a Pearson's correlation coefficient.
Results
Intraobserver repeatability of SI measurement was high (r = 0.97). Mean ± SD humeroulnar incongruity (SI) was greater in elbows with MCD (18.5 ± 6.6) than in the normal elbows (1.7 ± 2.0, P < 0.001). The difference between the diameters of the curvatures of the ulnar and humeral trochlea was greater in elbows with MCD (12.5 ± 4.4) than in the normal group (10.7 ± 4.1, P < 0.05). A moderate correlation was found between the degree of humeroulnar incongruity and a radioulnar step (r = 0.63); however, no correlation was identified between SI and the difference between the diameters of the curvatures of the ulnar and humeral trochleae (r = 0.14).
Conclusion
We propose a radiographic index to measure humeroulnar incongruity on mediolateral digital radiographic projections. This index (SI) supports the presence of humeroulnar incongruity in Labrador Retrievers with MCD. Further evaluation of its reproducibility and clinical importance are warranted. Although there is a moderate correlation between humeroulnar incongruity and radioulnar incongruency, causation has not been established
nf-core/marsseq:systematic preprocessing pipeline for MARS-seq experiments
No full textMotivation: Single sequencing technology (scRNA-seq) enables the study of gene regulation at a single cell level. Although many sc-RNA-seq protocols have been established, they have varied in technical complexity, sequencing depth and multimodal capabilities leading to shared limitations in data interpretation due to a lack of standardized preprocessing and consistent data reproducibility. While plate based techniques such as Massively Parallel RNA Single cell Sequencing (MARS-seq2.0) provide reference data on the cells that will be sequenced, the data format limits the possible analysis. Here, we focus on the standardization of MARS-seq analysis and its applicability to RNA velocity. Results: We have taken the original MARS-seq2.0 pipeline and revised it to enable implementation using the nf-core framework. By doing so, we have simplified pipeline execution, enabling a streamlined application with increased transparency and scalability. We have incorporated additional checkpoints to verify experimental metadata and improved the pipeline by implementing a custom workflow for RNA velocity estimation. The pipeline is part of the nf-core bioinformatics community and is freely available at https://github.com/nfcore/marsseq with data analysis at https://github.com/brickmanlab/proks-et-al-2023.</p
matq007/fusion-report: fusion-report:2.1.4
No full textFixed
Using header columns to extract values from the fusion output
matq007/fusion-report: fusion-report:2.1.0
No full textAdded
sync option for downloading all databases
Changed
all databases except COSMIC are now versioned in fusion-report-db
Fixed
Issues with downloading too many stuff (#28
matq007/fusion-report: fusion-report:2.0.1
No full textQuick FIX of version 2.0. FusionGDB database was not loading correctly.
FIX
Fixed missing Mitelman database fil
matq007/fusion-report: fusion-report:2.0.2
No full textChanged
moved from Travis to Github Actions
FIX
tool_cutoff was not casted to int (#25)
csv export missing data (#26)
better exception handling for downloading database
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