MIPS: analysis and annotation of proteins from whole genomes in 2005

The Munich Information Center for Protein Sequences (MIPS at the GSF), Neuherberg, Germany, provides resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of >400 genomes automatically annotated with the PEDANT system are maintained. The main goal of our current work on creating and maintaining genome databases is to extend gene centered information to information on interactions within a generic comprehensive framework. We have concentrated our efforts along three lines (i) the development of suitable comprehensive data structures and database technology, communication and query tools to include a wide range of different types of information enabling the representation of complex information such as functional modules or networks Genome Research Environment System, (ii) the development of databases covering computable information such as the basic evolutionary relations among all genes, namely SIMAP, the sequence similarity matrix and the CABiNet network analysis framework and (iii) the compilation and manual annotation of information related to interactions such as protein–protein interactions or other types of relations (e.g. MPCDB, MPPI, CYGD). All databases described and the detailed descriptions of our projects can be accessed through the MIPS WWW server ()

An Overview of Ontology Application for Policy-Based Management using POPPET

The use of ontology to describe the key concepts and their interrelationships within a particular area has become a widely recognised and advantageous means of sharing information about the structure of knowledge within a domain. Ontologies provide a way of integrating structured data within an application. This report provides an overview of how the ACCENT policy-based management system [1] was significantly re-engineered to utilise an ontology in place of previously hard-coded, domain-specific information within its user interface. In order to successfully integrate the ontology with the policy system, a new framework named POPPET was developed, responsible for parsing and querying ontological data. Although a substantial alteration in technical structure, the process vastly generalises the policy system, enabling adaptation for policy management within any custom domain. An introduction to the concepts and motivation for ontology creation using OWL is presented, together with general background to the ACCENT policy system. A technical overview is then given covering the developed ontologies, the POPPET system design, and the policy system re-engineering process. Finally, a comparison is made between the new and old policy system structures, and the impact on system performance is evaluated

DEXTER: An end-to-end system to extract table contents from electronic medical health documents

In this paper, we propose DEXTER, an end to end system to extract information from tables present in medical health documents, such as electronic health records (EHR) and explanation of benefits (EOB). DEXTER consists of four sub-system stages: i) table detection ii) table type classification iii) cell detection; and iv) cell content extraction. We propose a two-stage transfer learning-based approach using CDeC-Net architecture along with Non-Maximal suppression for table detection. We design a conventional computer vision-based approach for table type classification and cell detection using parameterized kernels based on image size for detecting rows and columns. Finally, we extract the text from the detected cells using pre-existing OCR engine Tessaract. To evaluate our system, we manually annotated a sample of the real-world medical dataset (referred to as Meddata) consisting of wide variations of documents (in terms of appearance) covering different table structures, such as bordered, partially bordered, borderless, or coloured tables. We experimentally show that DEXTER outperforms the commercially available Amazon Textract and Microsoft Azure Form Recognizer systems on the annotated real-world medical datase

KOSTASystem, a multipurpose coastal videometry system

This contribution presents the KOSTASystem technology, a multipurpose coastal videometry system. It is implemented in 20 operational stations distributed along the Basque Coast (Spain), covering urban and natural beaches, port protection structures and natural coastal stretches. The purpose of this technology is to provide basic quantitative and qualitative data for coastal management applications. The most representative advances are related to the hardware, with the development of autonomous photovoltaic stations, and to the software, developing several tools for the calibration and restitution of the images and for the extraction of the information used in the different applications. In the longterm, within a climate change context, the most essential results have been obtained in the monitoring of beach morphology. In the short-term, the camera network works under extreme wave conditions, monitoring wave overtopping and flooding. Apart from this, it is also used for the daily management of the beaches in the summer season, improving the safety by detecting and predicting rip currents and providing information about beach user density (BUD). Finally, the constant improvement of this technology and its applications help to grow and collaborate within the European framework of the coastal observation network.Peer Reviewe

Mapping atmospheric waves and unveiling phase coherent structures in a global surface air temperature reanalysis dataset

In the analysis of empirical signals, detecting correlations that capture genuine interactions between the elements of a complex system is a challenging task with applications across disciplines. Here, we analyze a global dataset of surface air temperature (SAT) with daily resolution. Hilbert analysis is used to obtain phase, instantaneous frequency, and amplitude information of SAT seasonal cycles in different geographical zones. The analysis of the phase dynamics reveals large regions with coherent seasonality. The analysis of the instantaneous frequencies uncovers clean wave patterns formed by alternating regions of negative and positive correlations. In contrast, the analysis of the amplitude dynamics uncovers wave patterns with additional large-scale structures. These structures are interpreted as due to the fact that the amplitude dynamics is affected by processes that act in long and short time scales, while the dynamics of the instantaneous frequency is mainly governed by fast processes. Therefore, Hilbert analysis allows us to disentangle climatic processes and to track planetary atmospheric waves. Our results are relevant for the analysis of complex oscillatory signals because they offer a general strategy for uncovering interactions that act at different time scales. In our “big data” times, extracting useful information from complex signals is an important challenge with applications across disciplines. Due to the presence of multiple time scales, climatological signals are particularly challenging to analyze. Here, we present a technique based on the Hilbert transform (HT) that, when applied to time series of surface air temperature (SAT) (with daily resolution, covering the last 30 years), unveils clear wave patterns that are interpreted as due to Rossby waves (these are atmospheric waves that propagate across our planet and have a major influence on weather). We also show that the patterns uncovered by analyzing anomaly times series include additional structures which likely appear due to climatic phenomena that have long time scales.Postprint (published version

Building the hybrid organisation through ERP and enterprise social software

This research traces the implementation of an information system in the form of ERP modules covering tenant and contract management in a Chinese service company. Misalignments between the ERP system specification and user needs led to the adoption of informal processes within the organisation. These processes are facilitated within an informal organisational structure and are based on human interactions undertaken within the formal organisation. Rather than to attempt to suppress the emergence of the informal organisation the company decided to channel the energies of staff involved in informal processes towards organisational goals. The company achieved this by harnessing the capabilities of what we term a hybrid ERP system, combining the functionality of a traditional (formal) ERP installation with the capabilities of Enterprise Social Software (ESS). However the company recognised that the successful operation of the hybrid ERP system would require a number of changes in organisational design in areas such as reporting structures and communication channels. A narrative provided by interviews with company personnel is thematised around the formal and informal characteristics of the organisation as defined in the literature. This leads to a definition of the characteristics of the hybrid organisation and strategies for enabling a hybrid organisation, facilitated by a hybrid ERP system, which directs formal and informal behaviour towards organisational goals and provides a template for future hybrid implementations

Graph-based View Motion Planning for Fruit Detection

Crop monitoring is crucial for maximizing agricultural productivity and efficiency. However, monitoring large and complex structures such as sweet pepper plants presents significant challenges, especially due to frequent occlusions of the fruits. Traditional next-best view planning can lead to unstructured and inefficient coverage of the crops. To address this, we propose a novel view motion planner that builds a graph network of viable view poses and trajectories between nearby poses, thereby considering robot motion constraints. The planner searches the graphs for view sequences with the highest accumulated information gain, allowing for efficient pepper plant monitoring while minimizing occlusions. The generated view poses aim at both sufficiently covering already detected and discovering new fruits. The graph and the corresponding best view pose sequence are computed with a limited horizon and are adaptively updated in fixed time intervals as the system gathers new information. We demonstrate the effectiveness of our approach through simulated and real-world experiments using a robotic arm equipped with an RGB-D camera and mounted on a trolley. As the experimental results show, our planner produces view pose sequences to systematically cover the crops and leads to increased fruit coverage when given a limited time in comparison to a state-of-the-art single next-best view planner.Comment: 7 pages, 10 figures, accepted at IROS 202

UNIVERSITY AS A VALUABLE UNIT OF SELF- KNOWLEDGE

This article discusses the trend of successful university activity as an integral unit of the educational system with its proper management. Successful activities of the university are realized in the formation and maintenance of the internal atmosphere of the university itself. A manifestation of such activity is the open character of university management (transparency in making important decisions, the elective nature of governing bodies and staff appointments), as well as the tendency to provide a centralized information environment for staff (creating an extensive internal electronic information network covering all structures). This activity is essential for maintaining the cohesion of labor collectives in higher education. Elements of competitive relations are among the university staff in the field of higher education. The purpose of competition is to attract quantitative and qualitative applicants, as well as gaining public recognition. Most teachers are proud of the prestige of the university.This article analyzes socially significant and personal values. The student’s personal and professional growth is a qualitative change in his position and role in society. The source of personal and professional development are the contradictions between the achieved level of student development and the requirements that the university community makes to him. Self-educational activity is the main condition necessary for the development of professional competence among students of engineering universities at the present stage. Given the variety of definitions of self-education, we can highlight some of its essential features, such as: an independent search for additional information, the acquisition of knowledge and on-going development. Further, the article expresses the opinion that self-education can exist only on the basis of deep perspective internal motives. Individual cases of searching for answers to questions of interest to a person under the influence of any motives cannot be considered self-education.In this paper, self-education is considered as purposeful, systematic, cognitive activity managed by students themselves, necessary for improving education.This article discusses the trend of successful university activity as an integral unit of the educational system with its proper management. Successful activities of the university are realized in the formation and maintenance of the internal atmosphere of the university itself. A manifestation of such activity is the open character of university management (transparency in making important decisions, the elective nature of governing bodies and staff appointments), as well as the tendency to provide a centralized information environment for staff (creating an extensive internal electronic information network covering all structures). This activity is essential for maintaining the cohesion of labor collectives in higher education. Elements of competitive relations are among the university staff in the field of higher education. The purpose of competition is to attract quantitative and qualitative applicants, as well as gaining public recognition. Most teachers are proud of the prestige of the university.This article analyzes socially significant and personal values. The student’s personal and professional growth is a qualitative change in his position and role in society. The source of personal and professional development are the contradictions between the achieved level of student development and the requirements that the university community makes to him. Self-educational activity is the main condition necessary for the development of professional competence among students of engineering universities at the present stage. Given the variety of definitions of self-education, we can highlight some of its essential features, such as: an independent search for additional information, the acquisition of knowledge and on-going development. Further, the article expresses the opinion that self-education can exist only on the basis of deep perspective internal motives. Individual cases of searching for answers to questions of interest to a person under the influence of any motives cannot be considered self-education.In this paper, self-education is considered as purposeful, systematic, cognitive activity managed by students themselves, necessary for improving education

A study of fluid structure interactions in hydraulic piping of passive interconnected suspensions

University of Technology, Sydney. Faculty of Engineering and Information Technology.This thesis examines the fluid-induced high-frequency vibrations in the hydraulic pipelines of a recently invented vehicle suspension, namely Hydraulically Interconnected Suspension (HIS), which is applied to overcome the compromise between comfort and handling performance. The basic system of the suspension is a liquid-filled pipe-guided fluidic circuit, inside which the produced pressure changes often lead to vibrations of the whole pipeline and associated structures and hence become a source of noise. The results of this study can be extended to similar piping systems. The modelling approach proposed here is necessarily multidisciplinary, covering vibration theory and fluid dynamics. The one-dimensional wave theory is employed to formulate the equations of motions that govern the dynamics of the fluid-structural system. Piping sections are defined as continuous line elements and discontinuities between the sections as point elements. The Transfer Matrix Method (TMM) is applied to determine the relationships between individual components. The resulting sets of linear, frequency-dependent state-space equations, which govern the coupled dynamics of the system, are derived and then applied in a variety of ways. Key parameters that influence system dynamics are identified and analyses of their effects are presented. The theoretical model is validated by experimental investigations. Two piping systems are assembled and free vibration results acquired through both the systems agree well with those of the proposed linear models. The deviation is reasonable and possible impact factors are described. However, the results from a different system configuration reveal the limitations in terms of the linear modelling to precisely represent curved hoses. The methodology presented is found to be an effective and useful way of modelling liquid-filled pipe-guided piping systems, particularly in the frequency domain. The obtained results suggest possible improvements can be made in relation to decreasing the fluid induced vibration in the piping system and the surrounding structures. However, further investigation is needed. For example, the development of the precise hose bend model or the coupling between the piping system and the connected structures could provide the topic of future studies

Transboundary geophysical mapping of geological elements and salinity distribution critical for the assessment of future sea water intrusion in response to sea level rise

Geophysical techniques are increasingly being used as tools for characterising the subsurface, and they are generally required to develop subsurface models that properly delineate the distribution of aquifers and aquitards, salt/freshwater interfaces, and geological structures that affect groundwater flow. In a study area covering 730 km2 across the border between Germany and Denmark, a combination of an airborne electromagnetic survey (performed with the SkyTEM system), a high-resolution seismic survey and borehole logging has been used in an integrated mapping of important geological, physical and chemical features of the subsurface. The spacing between flight lines is 200–250 m which gives a total of about 3200 line km. About 38 km of seismic lines have been collected. Faults bordering a graben structure, buried tunnel valleys, glaciotectonic thrust complexes, marine clay units, and sand aquifers are all examples of geological structures mapped by the geophysical data that control groundwater flow and to some extent hydrochemistry. Additionally, the data provide an excellent picture of the salinity distribution in the area and thus provide important information on the salt/freshwater boundary and the chemical status of groundwater. Although the westernmost part of the study area along the North Sea coast is saturated with saline water and the TEM data therefore are strongly influenced by the increased electrical conductivity there, buried valleys and other geological elements are still revealed. The mapped salinity distribution indicates preferential flow paths through and along specific geological structures within the area. The effects of a future sea level rise on the groundwater system and groundwater chemistry are discussed with special emphasis on the importance of knowing the existence, distribution and geometry of the mapped geological elements, and their control on the groundwater salinity distribution is assessed