A Novel Optical Tissue Clearing Protocol for Mouse Skeletal Muscle to Visualize Endplates in Their Tissue Context

Neuromuscular junctions (NMJs) mediate skeletal muscle contractions and play an important role in several neuromuscular disorders when their morphology and function are compromised. However, due to their small size and sparse distribution throughout the comparatively large, inherently opaque muscle tissue the analysis of NMJ morphology has been limited to teased fiber preparations, longitudinal muscle sections, and flat muscles. Consequently, whole mount analyses of NMJ morphology, numbers, their distribution, and assignment to a given muscle fiber have also been impossible to determine in muscle types that are frequently used in experimental paradigms. This impossibility is exacerbated by the lack of optical tissue clearing techniques that are compatible with clear and persistent NMJ stains. Here, we present MYOCLEAR, a novel and highly reproducible muscle tissue clearing protocol. Based on hydrogel-based tissue clearing methods, this protocol permits the labeling and detection of all NMJs in adult hindleg extensor digitorum longus muscles from wildtype and diseased mice. The method is also applicable to adult mouse diaphragm muscles and can be used for different staining agents, including toxins, lectins, antibodies, and nuclear dyes. It will be useful in understanding the distribution, morphological features, and muscle tissue context of NMJs in hindleg muscle whole mounts for biomedical and basic research.</p

A Novel Optical Tissue Clearing Protocol for Mouse Skeletal Muscle to Visualize Endplates in Their Tissue Context

Neuromuscular junctions (NMJs) mediate skeletal muscle contractions and play an important role in several neuromuscular disorders when their morphology and function are compromised. However, due to their small size and sparse distribution throughout the comparatively large, inherently opaque muscle tissue the analysis of NMJ morphology has been limited to teased fiber preparations, longitudinal muscle sections, and flat muscles. Consequently, whole mount analyses of NMJ morphology, numbers, their distribution, and assignment to a given muscle fiber have also been impossible to determine in muscle types that are frequently used in experimental paradigms. This impossibility is exacerbated by the lack of optical tissue clearing techniques that are compatible with clear and persistent NMJ stains. Here, we present MYOCLEAR, a novel and highly reproducible muscle tissue clearing protocol. Based on hydrogel-based tissue clearing methods, this protocol permits the labeling and detection of all NMJs in adult hindleg extensor digitorum longus muscles from wildtype and diseased mice. The method is also applicable to adult mouse diaphragm muscles and can be used for different staining agents, including toxins, lectins, antibodies, and nuclear dyes. It will be useful in understanding the distribution, morphological features, and muscle tissue context of NMJs in hindleg muscle whole mounts for biomedical and basic research

A randomized comparison of right ventricular function after on-pump versus off-pump coronary artery bypass graft surgery

Right ventricular dysfunction occurs very soon after conventional coronary bypass surgery with cardiopulmonary bypass and might not recover within 1 year after the operation. It has been postulated that performing coronary surgery without cardiopulmonary bypass might preserve right ventricular function. We hypothesized that right ventricular global and overall systolic functions are better preserved 3 months after off-pump surgery than after conventional coronary bypass surgery

Coreference in Universal Dependencies 1.0 (CorefUD 1.0)

CorefUD is a collection of previously existing datasets annotated with coreference, which we converted into a common annotation scheme. In total, CorefUD in its current version 1.0 consists of 17 datasets for 11 languages. The datasets are enriched with automatic morphological and syntactic annotations that are fully compliant with the standards of the Universal Dependencies project. All the datasets are stored in the CoNLL-U format, with coreference- and bridging-specific information captured by attribute-value pairs located in the MISC column. The collection is divided into a public edition and a non-public (ÚFAL-internal) edition. The publicly available edition is distributed via LINDAT-CLARIAH-CZ and contains 13 datasets for 10 languages (1 dataset for Catalan, 2 for Czech, 2 for English, 1 for French, 2 for German, 1 for Hungarian, 1 for Lithuanian, 1 for Polish, 1 for Russian, and 1 for Spanish), excluding the test data. The non-public edition is available internally to ÚFAL members and contains additional 4 datasets for 2 languages (1 dataset for Dutch, and 3 for English), which we are not allowed to distribute due to their original license limitations. It also contains the test data portions for all datasets. When using any of the harmonized datasets, please get acquainted with its license (placed in the same directory as the data) and cite the original data resource too. Version 1.0 consists of the same corpora and languages as the previous version 0.2; however, the English GUM dataset has been updated to a newer and larger version, and in the Czech/English PCEDT dataset, the train-dev-test split has been changed to be compatible with OntoNotes. Nevertheless, the main change is in the file format (the MISC attributes have new form and interpretation)

CorefUD 1.0

CorefUD is a collection of previously existing datasets annotated with coreference, which we converted into a common annotation scheme. In total, CorefUD in its current version 0.2 consists of 17 datasets for 11 languages, and compared to the version 0.2, the file format has been reworked and a number of annotation errors have been fixed

Coreference in Universal Dependencies 1.1 (CorefUD 1.1)

CorefUD is a collection of previously existing datasets annotated with coreference, which we converted into a common annotation scheme. In total, CorefUD in its current version 1.1 consists of 21 datasets for 13 languages. The datasets are enriched with automatic morphological and syntactic annotations that are fully compliant with the standards of the Universal Dependencies project. All the datasets are stored in the CoNLL-U format, with coreference- and bridging-specific information captured by attribute-value pairs located in the MISC column. The collection is divided into a public edition and a non-public (ÚFAL-internal) edition. The publicly available edition is distributed via LINDAT-CLARIAH-CZ and contains 17 datasets for 12 languages (1 dataset for Catalan, 2 for Czech, 2 for English, 1 for French, 2 for German, 2 for Hungarian, 1 for Lithuanian, 2 for Norwegian, 1 for Polish, 1 for Russian, 1 for Spanish, and 1 for Turkish), excluding the test data. The non-public edition is available internally to ÚFAL members and contains additional 4 datasets for 2 languages (1 dataset for Dutch, and 3 for English), which we are not allowed to distribute due to their original license limitations. It also contains the test data portions for all datasets. When using any of the harmonized datasets, please get acquainted with its license (placed in the same directory as the data) and cite the original data resource too. Compared to the previous version 1.0, the version 1.1 comprises new languages and corpora, namely Hungarian-KorKor, Norwegian-BokmaalNARC, Norwegian-NynorskNARC, and Turkish-ITCC. In addition, the English GUM dataset has been updated to a newer and larger version, and the conversion pipelines for most datasets have been refined (a list of all changes in each dataset can be found in the corresponding README file)