E2E Refined Dataset

Although the well-known MR-to-text E2E dataset has been used by many researchers, its MR-text pairs include many deletion/insertion/substitution errors. Since such errors affect the quality of MR-to-text systems, they must be fixed as much as possible. Therefore, we developed a refined dataset and some python programs that convert the original E2E dataset into a refined dataset.Comment: 4 page

Automatic Piano Transcription with Hierarchical Frequency-Time Transformer

Taking long-term spectral and temporal dependencies into account is essential for automatic piano transcription. This is especially helpful when determining the precise onset and offset for each note in the polyphonic piano content. In this case, we may rely on the capability of self-attention mechanism in Transformers to capture these long-term dependencies in the frequency and time axes. In this work, we propose hFT-Transformer, which is an automatic music transcription method that uses a two-level hierarchical frequency-time Transformer architecture. The first hierarchy includes a convolutional block in the time axis, a Transformer encoder in the frequency axis, and a Transformer decoder that converts the dimension in the frequency axis. The output is then fed into the second hierarchy which consists of another Transformer encoder in the time axis. We evaluated our method with the widely used MAPS and MAESTRO v3.0.0 datasets, and it demonstrated state-of-the-art performance on all the F1-scores of the metrics among Frame, Note, Note with Offset, and Note with Offset and Velocity estimations.Comment: 8 pages, 6 figures, to be published in ISMIR202

Metastatic Patterns of Myxoid/Round Cell Liposarcoma: A Review of a 25-Year Experience

Myxoid/round cell liposarcoma (MRCL), unlike other soft tissue sarcomas, has been associated with unusual pattern of metastasis to extrapulmonary sites. In an attempt to elucidate the clinical features of MRCL with metastatic lesions, 58 cases, from the medical database of Keio University Hospital were used for the evaluation. 47 patients (81%) had no metastases, whereas 11 patients (11%) had metastases during their clinical course. Among the 11 patients with metastatic lesions, 8 patients (73%) had extrapulmonary metastases and 3 patients (27%) had pulmonary metastases. Patients were further divided into three groups; without metastasis, with extrapulmonary metastasis, and with pulmonary metastasis. When the metastatic patterns were stratified according to tumor size, there was statistical significance between the three groups (P = 0.028). The 8 cases with extrapulmonary metastases were all larger than 10 cm. Similarly, histological grading had a significant impact on metastatic patterns (P = 0.027). 3 cases with pulmonary metastatic lesions were all diagnosed as high grade. In conclusion, large size and low histological grade were significantly associated with extrapulmonary metastasis

Reactive oxygen species induce chondrocyte hypertrophy in endochondral ossification

Chondrocyte hypertrophy during endochondral ossification is a well-controlled process in which proliferating chondrocytes stop proliferating and differentiate into hypertrophic chondrocytes, which then undergo apoptosis. Chondrocyte hypertrophy induces angiogenesis and mineralization. This step is crucial for the longitudinal growth and development of long bones, but what triggers the process is unknown. Reactive oxygen species (ROS) have been implicated in cellular damage; however, the physiological role of ROS in chondrogenesis is not well characterized. We demonstrate that increasing ROS levels induce chondrocyte hypertrophy. Elevated ROS levels are detected in hypertrophic chondrocytes. In vivo and in vitro treatment with N-acetyl cysteine, which enhances endogenous antioxidant levels and protects cells from oxidative stress, inhibits chondrocyte hypertrophy. In ataxia telangiectasia mutated (Atm)–deficient (Atm−/−) mice, ROS levels were elevated in chondrocytes of growth plates, accompanied by a proliferation defect and stimulation of chondrocyte hypertrophy. Decreased proliferation and excessive hypertrophy in Atm−/− mice were also rescued by antioxidant treatment. These findings indicate that ROS levels regulate inhibition of proliferation and modulate initiation of the hypertrophic changes in chondrocytes

Implications of a Multi-Step Trigger of Retinal Regeneration in the Adult Newt

The newt is an amazing four-limbed vertebrate that can regenerate various body parts including the retina. In this animal, when the neural retina (NR) is removed from the eye by surgery (retinectomy), both the NR and the retinal pigment epithelium (RPE) eventually regenerate through the process of reprogramming and proliferation of RPE cells. Thus far, we have pursued the onset mechanism of adult newt retinal regeneration. In this study, using an in vitro system, we found that both mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) kinase (MEK)-ERK and β-catenin were involved in cell cycle re-entry of RPE cells. MEK-ERK signaling activity in RPE cells was strengthened by retinectomy, and nuclear translocation of β-catenin in RPE cells was induced by attenuation of cell–cell contact, which was promoted by incision of the RPE or its treatment with ethylene glycol tetraacetic acid (EGTA). EGTA is a Ca2+ chelator that disrupts cadherin-mediated cell–cell adhesion. Reinforcement of MEK-ERK signaling activity was a prerequisite for nuclear translocation of β-catenin. These results suggest that retinectomy followed by attenuation of cell–cell contact may trigger cell cycle re-entry of RPE cells. This study, together with our previous findings concerning the proliferation and multipotency of adult newt RPE cells, provides insight into the mechanism of the multi-step trigger in which the onset of retinal regeneration in the adult newt is rigorously controlled

Integrated genetic and clinical prognostic factors for aggressive adult T-cell leukemia/lymphoma

成人T細胞白血病リンパ腫（ATL）におけるゲノム情報と臨床情報を統合したリスクモデルを確立 --ATLの個別化医療を推進--. 京都大学プレスリリース. 2023-04-10.The prognosis of aggressive adult T-cell leukemia/lymphoma (ATL) is poor, and allogeneic hematopoietic stem-cell transplantation (allo-HSCT) is a curative treatment. To identify favorable prognostic patients after intensive chemotherapy, and who therefore might not require upfront allo-HSCT, we aimed to improve risk stratification of aggressive ATL patients aged <70 years. The clinical risk factors and genetic mutations were incorporated into risk modeling for overall survival (OS). We generated the m7-ATLPI, a clinicogenetic risk model for OS, that included the ATL prognostic index (PI) (ATL-PI) risk category, and non-silent mutations in seven genes, namely TP53, IRF4, RHOA, PRKCB, CARD11, CCR7, and GATA3. In the training cohort of 99 patients, the m7-ATLPI identified a low-, intermediate-, and high-risk group with 2-year OS of 100%, 43%, and 19%, respectively (hazard ratio [HR] 5.46, p < 0.0001). The m7-ATLPI achieved superior risk stratification compared to the current ATL-PI (C-index 0.92 vs. 0.85, respectively). In the validation cohort of 84 patients, the m7-ATLPI defined low-, intermediate-, and high-risk groups with a 2-year OS of 81%, 30%, and 0%, respectively (HR 2.33, p = 0.0094), and the model again outperformed the ATL-PI (C-index 0.72 vs. 0.70, respectively). The simplified m7-ATLPI, which is easier to use in clinical practice, achieved superior risk stratification compared to the ATL-PI, as did the original m7-ATLPI; the simplified version was calculated by summing the following: high-risk ATL-PI category (+10), low-risk ATL-PI category (−4), and non-silent mutations in TP53 (+4), IRF4 (+3), RHOA (+1), PRKCB (+1), CARD11 (+0.5), CCR7 (−2), and GATA3 (−3)

Live imaging of apoptosis in a novel transgenic mouse highlights its role in neural tube closure

Imaging of caspase activation in living mouse embryos during development suggests that caspase-mediated cell removal facilitates neural tube closure in a temporally regulated manner

A model for longitudinal data sets relating wind-damage probability to biotic and abiotic factors: a Bayesian approach

Aim of study: To develop a statistical model framework to analyze longitudinal wind-damage records while accounting for autocorrelation, and to demonstrate the usefulness of the model in understanding the regeneration process of a natural forest.Area of study: University of Tokyo Chiba Forest (UTCBF), southern Boso peninsula, Japan.Material and methods: We used the proposed model framework with wind-damage records from UTCBF and wind metrics (speed, direction, season, and mean stand volume) from 1905–1985 to develop a model predicting wind-damage probability for the study area. Using the resultant model, we calculated past wind-damage probabilities for UTCBF. We then compared these past probabilities with the regeneration history of major species, estimated from ring records, in an old-growth fir–hemlock forest at UTCBF.Main results: Wind-damage probability was influenced by wind speed, direction, and mean stand volume. The temporal pattern in the expected number of wind-damage events was similar to that of evergreen broad-leaf regeneration in the old-growth fir–hemlock forest, indicating that these species regenerated after major wind disturbances.Research highlights: The model framework presented in this study can accommodate data with temporal interdependencies, and the resultant model can predict past and future patterns in wind disturbances. Thus, we have provided a basic model framework that allows for better understanding of past forest dynamics and appropriate future management planning.Keywords: dendrochronology; tree regeneration; wind-damage probability model; wind disturbance.Abbreviations used: intrinsic CAR model (intrinsic conditional autoregressive model); MCMC (Markov chain Monte Carlo); 16 compass points = N, NNE, NE, ENE, E, ESE, SE, SSE, S, SSW, SW, WSW, W, WNW, NW, NNW (north, north-northeast, northeast, east-northeast, east, east-southeast, southeast, south-southeast, south, south-southwest, southwest, west-southwest, west, west-northwest, northwest, north-northwest, respectively); UTCBF (the University of Tokyo Chiba Forest)