Improving Compound–Protein Interaction Prediction by Self-Training with Augmenting Negative Samples

Identifying compound-protein interactions (CPIs) is crucial for drug discovery. Since experimentally validating CPIs is often time-consuming and costly, computational approaches are expected to facilitate the process. Rapid growths of available CPI databases have accelerated the development of many machine-learning methods for CPI predictions. However, their performance, particularly their generalizability against external data, often suffers from a data imbalance attributed to the lack of experimentally validated inactive (negative) samples. In this study, we developed a self-training method for augmenting both credible and informative negative samples to improve the performance of models impaired by data imbalances. The constructed model demonstrated higher performance than those constructed with other conventional methods for solving data imbalances, and the improvement was prominent for external datasets. Moreover, examination of the prediction score thresholds for pseudo-labeling during self-training revealed that augmenting the samples with ambiguous prediction scores is beneficial for constructing a model with high generalizability. The present study provides guidelines for improving CPI predictions on real-world data, thus facilitating drug discovery

Suzaku Observation Adjacent to the South End of the Radio Arc

Suzaku observed the Galactic center region near the Radio Arc at ~20' southeast of Sagittarius A*.In the 18'x18' field of view, we found four distinct X-ray sources: a bright star and a diffuse source associated with the star clusters in the soft band (0.5-2.0 keV), a small clump in a higher energy band (4-6 keV), and a peculiar clump in the 6.4 keV line band.The latter two clumps are located at the south end of the Radio Arc. This paper reports on the results, and discusses the origin of these X-ray sources, with a particular emphasis on small clumps.Comment: 16 pages, 9figures, accepted for publication in PASJ (Vol.61 No.3

Two-Dimensional Band Dispersion of Ultra-Flat Hexagonal Bismuthene Grown on Ag(111) Bulk and Quantum-Well Films

Two-dimensional band dispersion of (2$\times$2) superstructure with Bi grown on Ag(111), which has been urged as an ultraflat hexagonal bismuthene, is investigated using angle-resolved photoemission spectroscopy (ARPES). The (2$\times$2)-Bi superstructure can be grown on the Ag(111) surface at low temperatures; it transforms into a surface alloy with a ($\sqrt{3}\times\sqrt{3}$) superstructure at 300 K. ARPES measurements reveal the consistency with the band structure of ultraflat bismuthene in previous reports. The band structure of (2$\times$2)-Bi surface remains unchanged with decreasing Ag layer thickness, indicating the limited penetration of Bi p-orbitals into the Ag layer.Comment: 6 pages, 4 figure

An X-Ray Face-on View of the Sgr B Molecular Clouds Observed with Suzaku

We present a new methodology to derive the positions of the Sgr B molecular clouds (MCs) along the line of sight, as an application study of the Galactic center diffuse X-rays (GCDX). The GCDX is composed of hot plasma emission of about 7 keV and 1 keV temperatures, and non-thermal continuum emission including the 6.4 keV line from neutral irons. The former, the Galactic center plasma emission (GCPE), is uniformly distributed over 1 degree in longitude, while the latter is clumpy emission produced by Thomson scattering and fluorescence from MCs irradiated by external X-rays (the X-ray reflection nebula emission: XRNE). We examined the Suzaku X-ray spectra of the GCPE and XRNE near to the Sgr B MC complex, and found that the spectra suffer from two different absorptions of N_H (Abs1) >10^23 H cm^-2 and N_H (Abs2) ~6 x 10^22 H cm^-2. Abs1 is proportional to the 6.4 keV-line flux, and hence is due to the MCs, while Abs2 is typical of interstellar absorption toward the Galactic center. Assuming that the GCPE plasma is spherically-extended around Sgr A* with a uniform density and the same angular distribution of the two temperature components, we quantitatively estimated the line-of-sight positions of the MCs from the flux ratio the GCPE spectrum suffered by Abs1 and that with no Abs1. The results suggest that the Sgr B MCs are located at the near side of Sgr A* in the GCPE.Comment: 11 pages, 8 figures, accepted for publication in PASJ (Publications of the Astronomical Society of Japan

Novel Treatment Criteria for Persistent Ductus Arteriosus in Neonates

BackgroundThe indications for ductus arteriosus ligation in very-low-birth-weight infants (VLBWIs) with persistent ductus arteriosus (PDA) are unclear. Increased left ventricular end-diastolic dimension (LVDd) is commonly found in patients with PDA. Here, the enlargement of LVDd in term and preterm neonates without congenital heart disease was estimated by two-dimensional echocardiography.MethodsThe value of the measured LVDd was divided by the normal LVDd as an index (LVDd ratio) to compare 30 patients who underwent PDA ligation with 30 patients treated with indomethacin and 30 patients who did not undergo radical therapy.ResultsAn LVDd ratio between 122% and 197% (mean, 142%) was considered to be an indication for the ligation procedure. The proportion of patients exceeding 130% in the LVDd ratio was 87% (26/30) in those patients who underwent ligation. Catecholamines and/or vasodilators were required in 83% patients for the treatment of low ejection fraction or hypertension after operations, suggesting that patients had been in preload and/or afterload remodeling failure during the operation. The percentage of patients with less than 115% in the LVDd ratio was 90% in the non-radical-therapy patients. The LVDd ratios of 130% and 115% were regarded as cut-off values for surgical ligation and indomethacin treatment.ConclusionThe LVDd ratio is a useful measure to determine the treatment of VLBWIs with PDA

Long-Term Follow-Up of 12 Patients Treated with Bilateral Pallidal Stimulation for Tardive Dystonia

Tardive dystonia (TD) is a side effect of prolonged dopamine receptor antagonist intake. TD can be a chronic disabling movement disorder despite medical treatment. We previously demonstrated successful outcomes in six patients with TD using deep brain stimulation (DBS); however, more patients are needed to better understand the efficacy of DBS for treating TD. We assessed the outcomes of 12 patients with TD who underwent globus pallidus internus (GPi) DBS by extending the follow-up period of previously reported patients and enrolling six additional patients. All patients were refractory to pharmacotherapy and were referred for surgical intervention by movement disorder neurologists. In all patients, DBS electrodes were implanted bilaterally within the GPi under general anesthesia. The mean ages at TD onset and surgery were 39.2 ± 12.3 years and 44.6 ± 12.3 years, respectively. The Burke–Fahn–Marsden Dystonia Rating Scale (BFMDRS) performed the preoperative and postoperative evaluations. The average BFMDRS improvement rate at 1 month postoperatively was 75.6 ± 27.6% (p < 0.001). Ten patients were assessed in the long term (78.0 ± 50.4 months after surgery), and the long-term BFMDRS improvement was 78.0 ± 20.4%. Two patients responded poorly to DBS. Both had a longer duration from TD onset to surgery and older age at surgery. A cognitive and psychiatric decline was observed in the oldest patients, while no such decline ware observed in the younger patients. In most patients with TD, GPi-DBS could be a beneficial therapeutic option for long-term relief of TD

Five case of tardive dystonia treatment with pallidal deep brain stimulation

We assessed the efficiency of pallidal deep brain stimulation for tardive dystonia. This search was carried out in Electronic chart of Tokushima University Hospital. ５ patients with tardive dystonia were enrolled. GPi（internal segment of globus pallidus）was the target in all patients. The motor part of Burke-Fahn-Marsden Dystonia Rating Scale（BFMDRS）was improved by ７８．４％ on average when compared to preoperative BFMDRS scores. The performed analysis indicates that GPi-DBS is an effective and safe treatment for tardive dystonia