Protein-ligand binding region prediction (PLB-SAVE) based on geometric features and CUDA acceleration

[[abstract]]Background Protein-ligand interactions are key processes in triggering and controlling biological functions within cells. Prediction of protein binding regions on the protein surface assists in understanding the mechanisms and principles of molecular recognition. In silico geometrical shape analysis plays a primary step in analyzing the spatial characteristics of protein binding regions and facilitates applications of bioinformatics in drug discovery and design. Here, we describe the novel software, PLB-SAVE, which uses parallel processing technology and is ideally suited to extract the geometrical construct of solid angles from surface atoms. Representative clusters and corresponding anchors were identified from all surface elements and were assigned according to the ranking of their solid angles. In addition, cavity depth indicators were obtained by proportional transformation of solid angles and cavity volumes were calculated by scanning multiple directional vectors within each selected cavity. Both depth and volume characteristics were combined with various weighting coefficients to rank predicted potential binding regions. Results Two test datasets from LigASite, each containing 388 bound and unbound structures, were used to predict binding regions using PLB-SAVE and two well-known prediction systems, SiteHound and MetaPocket2.0 (MPK2). PLB-SAVE outperformed the other programs with accuracy rates of 94.3% for unbound proteins and 95.5% for bound proteins via a tenfold cross-validation process. Additionally, because the parallel processing architecture was designed to enhance the computational efficiency, we obtained an average of 160-fold increase in computational time. Conclusions In silico binding region prediction is considered the initial stage in structure-based drug design. To improve the efficacy of biological experiments for drug development, we developed PLB-SAVE, which uses only geometrical features of proteins and achieves a good overall performance for protein-ligand binding region prediction. Based on the same approach and rationale, this method can also be applied to predict carbohydrate-antibody interactions for further design and development of carbohydrate-based vaccines. PLB-SAVE is available at http://save.cs.ntou.edu.tw.[[booktype]]電子

Penta­aqua­(1H-benzimidazole-5,6-di­carboxyl­ato-κN 3)cobalt(II) penta­hydrate

In the title mononuclear complex, [Co(C9H4N2O4)(H2O)5]·5H2O, the CoII atom exhibits a distorted octa­hedral geometry involving an N atom of a 1H-benzimidazole-5,6-dicarboxyl­ate ligand and five water O atoms. A supra­molecular network is generated through inter­molecular O—H⋯O hydrogen-bonding inter­actions involving the coordinated and uncoordinated water mol­ecules and the carboxyl O atoms of the organic ligand. An inter­molecular N—H⋯O hydrogen bond is also observed

catena-Poly[[diaqua­(1,10-phenanthroline-κ2 N,N′)nickel(II)]-μ-1H-benzimidazole-5,6-dicarboxyl­ato-κ2 N 3:O 6]

In the title complex, [Ni(C9H4N2O4)(C12H8N2)(H2O)2]n, the NiII atom is hexa­coordinated by one N and one O atom from two different 1H-benzimidazole-5,6-dicarboxyl­ate ligands, two N atoms from one 1,10-phenanthroline ligand and two water mol­ecules. The flexible 1H-benzimidazole-5,6-dicarboxyl­ate ligands link the NiII centres, forming an infinite zigzag chain parallel to [001]. The crystal packing is governed by inter­molecular hydrogen-bonding inter­actions of the O—H⋯O, N—H⋯O and C—H⋯O types

Increasing utilization of Internet-based resources following efforts to promote evidence-based medicine: a national study in Taiwan

BACKGROUND: Since the beginning of 2007, the National Health Research Institutes has been promoting the dissemination of evidence-based medicine (EBM). The current study examined longitudinal trends of behaviors in how hospital-based physicians and nurses have searched for medical information during the spread of EBM. METHODS: Cross-sectional postal questionnaire surveys were conducted in nationally representative regional hospitals of Taiwan thrice in 2007, 2009, and 2011. Demographic data were gathered concerning gender, age, working experience, teaching appointment, academic degree, and administrative position. Linear and logistic regression models were used to examine predictors and changes over time. RESULTS: Data from physicians and nurses were collected in 2007 (n = 1156), 2009 (n = 2975), and 2011 (n = 3999). There were significant increases in the use of four Internet-based resources – Web portals, online databases, electronic journals, and electronic books – across the three survey years among physicians and nurses (p < 0.001). Access to textbooks and printed journals, however, did not change over the 4-year study period. In addition, there were significant relationships between the usage of Internet-based resources and users’ characteristics. Age and faculty position were important predictors in relation to the usage among physicians and nurses, while academic degree served as a critical factor among nurses only. CONCLUSIONS: Physicians and nurses used a variety of sources to look for medical information. There was a steady increase in use of Internet-based resources during the diffusion period of EBM. The findings highlight the importance of the Internet as a prominent source of medical information for main healthcare professionals

Field test of a practical secure communication network with decoy-state quantum cryptography

We present a secure network communication system that operated with decoy-state quantum cryptography in a real-world application scenario. The full key exchange and application protocols were performed in real time among three nodes, in which two adjacent nodes were connected by approximate 20 km of commercial telecom optical fiber. The generated quantum keys were immediately employed and demonstrated for communication applications, including unbreakable real-time voice telephone between any two of the three communication nodes, or a broadcast from one node to the other two nodes by using one-time pad encryption.Comment: 10 pages, 2 figures, 2 tables, typos correcte

A Real-Time Pothole Detection Approach for Intelligent Transportation System

In recent years, fast economic growth and rapid technology advance have led to significant impact on the quality of traditional transport system. Intelligent transportation system (ITS), which aims to improve the transport system, has become more and more popular. Furthermore, improving the safety of traffic is an important issue of ITS, and the pothole on the road causes serious harm to drivers’ safety. Therefore, drivers’ safety may be improved with the establishment of real-time pothole detection system for sharing the pothole information. Moreover, using the mobile device to detect potholes has been more popular in recent years. This approach can detect potholes with lower cost in a comprehensive environment. This study proposes a pothole detection method based on the mobile sensing. The accelerometer data is normalized by Euler angle computation and is adopted in the pothole detection algorithm to obtain the pothole information. Moreover, the spatial interpolation method is used to reduce the location errors from global positioning system (GPS) data. In experiments, the results show that the proposed approach can precisely detect potholes without false-positives, and the higher accuracy is performed by the proposed approach. Therefore, the proposed real-time pothole detection approach can be used to improve the safety of traffic for ITS

Synthesizing Speech Test Cases with Text-to-Speech? An Empirical Study on the False Alarms in Automated Speech Recognition Testing

Recent studies have proposed the use of Text-To-Speech (TTS) systems to automatically synthesise speech test cases on a scale and uncover a large number of failures in ASR systems. However, the failures uncovered by synthetic test cases may not reflect the actual performance of an ASR system when it transcribes human audio, which we refer to as false alarms. Given a failed test case synthesised from TTS systems, which consists of TTS-generated audio and the corresponding ground truth text, we feed the human audio stating the same text to an ASR system. If human audio can be correctly transcribed, an instance of a false alarm is detected. In this study, we investigate false alarm occurrences in five popular ASR systems using synthetic audio generated from four TTS systems and human audio obtained from two commonly used datasets. Our results show that the least number of false alarms is identified when testing Deepspeech, and the number of false alarms is the highest when testing Wav2vec2. On average, false alarm rates range from 21% to 34% in all five ASR systems. Among the TTS systems used, Google TTS produces the least number of false alarms (17%), and Espeak TTS produces the highest number of false alarms (32%) among the four TTS systems. Additionally, we build a false alarm estimator that flags potential false alarms, which achieves promising results: a precision of 98.3%, a recall of 96.4%, an accuracy of 98.5%, and an F1 score of 97.3%. Our study provides insight into the appropriate selection of TTS systems to generate high-quality speech to test ASR systems. Additionally, a false alarm estimator can be a way to minimise the impact of false alarms and help developers choose suitable test inputs when evaluating ASR systems. The source code used in this paper is publicly available on GitHub at https://github.com/julianyonghao/FAinASRtest.Comment: 12 pages, Accepted at ISSTA202

ACVR1, a Therapeutic Target of Fibrodysplasia Ossificans Progressiva, Is Negatively Regulated by miR-148a

Fibrodysplasia ossificans progressiva (FOP) is a rare congenital disorder of skeletal malformations and progressive extraskeletal ossification. There is still no effective treatment for FOP. All FOP individuals harbor conserved point mutations in ACVR1 gene that are thought to cause ACVR1 constitutive activation and activate BMP signal pathway. The constitutively active ACVR1 is also found to be able to cause endothelial-to-mesenchymal transition (EndMT) in endothelial cells, which may cause the formation of FOP lesions. MicroRNAs (miRNAs) play an essential role in regulating cell differentiation. Here, we verified that miR-148a directly targeted the 3′ UTR of ACVR1 mRNA by reporter gene assays and mutational analysis at the miRNA binding sites, and inhibited ACVR1 both at the protein level and mRNA level. Further, we verified that miR-148a could inhibit the mRNA expression of the Inhibitor of DNA binding (Id) gene family thereby suppressing the BMP signaling pathway. This study suggests miR-148a is an important mediator of ACVR1, thus offering a new potential target for the development of therapeutic agents against FOP