Ontology-based Extraction of Transcription Regulation Events

I present an on-going work on extraction of transcription regulation events from text by using an ontology which plays a central role in integrating information from different sources. The events of transcription regulation are expressed in the literature with a high degree of compositeness. They have elements such as event types, participants, and attributes. These elements are associated with different keywords, which should be merged into a shared structure. I use the Gene Regulation Ontology (GRO) for the integration purpose. It contains not only biological concepts related to transcription regulation, but also inference rules for deduction of specific event types and attributes from semantics of sentences. It is also used to represent the semantics of linguistic patterns that are used to identify the semantics of sentences. The ontology provides the formality which is required for the extraction of specific and well-defined events as those of transcription regulation

Spatial map for thermal image processing at Wendelstein 7-X

Wendelstein 7-X is a Stellator fusion reactor prototype. Many experiments are currently being performed obtaining data from cameras located at different points of the reactor. In this project, image processing is applied to treat these data in order to analyze the behavior of the plasma and the temperature at each instant. Using the captured images, we study the physical reactor surface covered by every pixel so as to achieve which elements are overheating or to detect anomalies.Wendelstein 7-X es un prototipo de reactor de fusión Stellator. Actualmente se realizan experimentos en los que se obtienen datos a partir de cámaras situadas en diferentes puntos del reactor. En este proyecto se tratan estos datos aplicando conocimientos de procesamiento de imagen para obtener características que sirvan para analizar el comportamiento del plasma y la temperatura en cada instante. Utilizando las imágenes capturadas, se estudia cuál es la superfície física del reactor cubierta por el campo visual de cada pixel. De esta manera se puede saber qué elementos se están tratando para en un futuro saber si se están sobrecalentando o poder estudiar otro tipo de comportamientos.Wendelstein 7-X és un prototip de reactor de fusió Stellator. Actualment es realitzen experiments en els quals s'obtenen moltes dades a partir de càmeres situades a diferents punts del reactor. En aquest projecte es tracten aquestes dades aplicant coneixements de processament d'imatge per tal d'obtenir característiques que serveixin per analitzar el comportament del plasma i la temperatura en cada instant. D'aquesta manera, utilitzant les imatges capturades, es calcula quina superfície física del reactor és visualitzada pel camp visual de cada píxel i així poder saber quins elements del reactor s'estan tractant per veure en el futur si s'estan sobreescalfant o poder estudiar altres tipus de comportament

Exact multi-parameter persistent homology of time-series data: one-dimensional reduction of multi-parameter persistence theory

In various applications of data classification and clustering problems, multi-parameter analysis is effective and crucial because data are usually defined in multi-parametric space. Multi-parameter persistent homology, an extension of persistent homology of one-parameter data analysis, has been developed for topological data analysis (TDA). Although it is conceptually attractive, multi-parameter persistent homology still has challenges in theory and practical applications. In this study, we consider time-series data and its classification and clustering problems using multi-parameter persistent homology. We develop a multi-parameter filtration method based on Fourier decomposition and provide an exact formula and its interpretation of one-dimensional reduction of multi-parameter persistent homology. The exact formula implies that the one-dimensional reduction of multi-parameter persistent homology of the given time-series data is equivalent to choosing diagonal ray (standard ray) in the multi-parameter filtration space. For this, we first consider the continuousization of time-series data based on Fourier decomposition towards the construction of the exact persistent barcode formula for the Vietoris-Rips complex of the point cloud generated by sliding window embedding. The proposed method is highly efficient even if the sliding window embedding dimension and the length of time-series data are large because the method precomputes the exact barcode and the computational complexity is as low as the fast Fourier transformation of $O(N \log N)$. Further the proposed method provides a way of finding different topological inferences by trying different rays in the filtration space in no time.Comment: 29 page

Synchronous double primary malignant tumor of the gallbladder and liver: a case report

We report a case of synchronous double primary tumor of gallbladder and liver. A 63-year-old male was admitted to the hospital complaining of abdominal discomfort. Enhanced computed tomography of the abdomen showed acute cholecystitis with tiny gallbladder stones and a 2.2 cm size enhanced nodule in the left lobe of the liver. Under the impression of acute cholecystitis with gall bladder stones and hepatocellular carcinoma of the left Liver, the patient underwent a laparotomy. At laparotomy, a mass was palpated on the surface of the neck portion of the gall bladder. Intraoperative frozen diagnosis revealed adenocarcinoma of the gall bladder. The patient was diagnosed as having gall bladder cancer and hepatocellular carcinoma, so extended cholecystectomy with dissection of regional lymph nodes and left hemihepatectomy were performed. Histological examination revealed moderated differentiated adenocarcinoma of gallbladder and hepatocellular carcinoma of liver. To our knowledge, the simultaneous occurrence of primary malignant tumor of the gallbladder and liver has never been published before. The patient is doing well with no evidence of recurrence 17 months after surgery

Technical Efficiency in the Iron and Steel Industry: A Stochastic Frontier Approach

In this paper we examine the technical efficiency of firms in the iron and steel industry and try to identify the factors contributing to the industry's efficiency growth, using a time-varying stochastic frontier model. Based on our findings, which pertain to 52 iron and steel firms over the period of 1978-1997, POSCO and Nippon Steel were the most efficient firms, with their production, on average, exceeding 95 percent of their potential output. Our findings also shed light on possible sources of efficiency growth in the industry. If a firm is government-owned, its privatization is likely to improve its technical efficiency to a great extent. A firm's technical efficiency also tends to be positively related to its production level as measured by a share of the total world production of crude steel. Another important source of efficiency growth identified by our empirical findings is adoption of new technologies and equipment. Our findings clearly indicate that continued efforts to update technologies and equipment are critical in pursuit of efficiency in the iron and steel industry.

Improving the extraction of complex regulatory events from scientific text by using ontology-based inference

<p>Abstract</p> <p>Background</p> <p>The extraction of complex events from biomedical text is a challenging task and requires in-depth semantic analysis. Previous approaches associate lexical and syntactic resources with ontologies for the semantic analysis, but fall short in testing the benefits from the use of domain knowledge.</p> <p>Results</p> <p>We developed a system that deduces implicit events from explicitly expressed events by using inference rules that encode domain knowledge. We evaluated the system with the inference module on three tasks: First, when tested against a corpus with manually annotated events, the inference module of our system contributes 53.2% of correct extractions, but does not cause any incorrect results. Second, the system overall reproduces 33.1% of the transcription regulatory events contained in RegulonDB (up to 85.0% precision) and the inference module is required for 93.8% of the reproduced events. Third, we applied the system with minimum adaptations to the identification of cell activity regulation events, confirming that the inference improves the performance of the system also on this task.</p> <p>Conclusions</p> <p>Our research shows that the inference based on domain knowledge plays a significant role in extracting complex events from text. This approach has great potential in recognizing the complex concepts of such biomedical ontologies as Gene Ontology in the literature.</p

Galatheoid squat lobsters (Crustacea: Decapoda: Anomura) from Korean waters

Abstract Ten species of Galatheoidea (squat lobsters), belonging to two families, were collected in the Korean exclusive economic zone: Galathea balssi Miyake and Baba, 1964, Galathea orientalis Stimpson, 1858, Galathea pubescens Stimpson, 1858, and Galathea rubromaculata Miyake and Baba, 1967 belonging to Galatheidae; Bathymunida brevirostris Yokoya, 1933, Cervimunida princeps Benedict, 1902, Munida caesura Macpherson and Baba, 1993, Munida japonica Stimpson, 1858, Munida pherusa Macpherson and Baba, 1993, and Paramunida scabra (Henderson, 1885) belonging to Munididae. The present study comprises the morphological description of these ten species, including drawings and color photographs, a brief review of their regional records, and a key for their identification. Although all species are common in Japanese waters, G. balssi, G. rubromaculata, B. brevirostris, C. princeps, M. caesura, and M. pherusa are new to Korean marine fauna

Investigating the Role of Network Exteranlities and Perceived Value in User Loyalty Toward a SNS Site: Integrating Network Externalities and VTSL Model

As the number of SNSs increases, it is challenging for SNS providers to obtain and retain user loyalty toward a SNS site. By integrating both network externalities theory and VTSL (Value-Trust-Satisfaction-Loyalty) model, we propose a research model to investigate how perceived value derived from network externalities affects trust in SNS site and user satisfaction, which further lead to user loyalty. Data analysis was conducted using a total of 267 responses. The results show that perceived network size and perceived complementarity exert significant effect on functional, emotional, and social value. It is also shown that functional and social value influence positively on trust in SNS site, but emotional value is not related to trust. Functional and emotional value are found to be significant determinants of user satisfaction, however social value is not related to user satisfaction. User satisfaction is found to be a strong determinant of user loyalty. Given the findings, SNS providers need to increase network size and accommodate complementary services, applications, and supporting tools to obtain and retain user loyalty