Facilitating transparency in spinal cord injury studies using data standards and ontologies

Progress in developing robust therapies for spinal cord injury （SCI）, trau- matic brain injury （TBI） and peripheral nerve injury has been slow. A great deal has been learned over the past 30 years regarding both the intrinsic factors and the environmental factors that regulate axon growth, but this large body of information has not yet resulted in clinically available thera- peutics. This therapeutic bottleneck has many root causes, but a consensus is emerging that one contributing factor is a lack of standards for experi- mental design and reporting. The absence of reporting standards, and even of commonly accepted definitions of key words, also make data mining and bioinformatics analysis of neural plasticity and regeneration difficult, if not impossible. This short review will consider relevant background and poten- tial solutions to this problem in the axon regeneration domain.

Commentary on:“Facilitating transparency in spinal cord injury studies using data standards and ontologies”

Commentary Most would agree that providing comprehensive detail in scientific reporting is critical for the development of mean- ingful therapies and treatments for diseases. Such stellar practices 1） allow for reproduction of experiments to con- firm results, 2） promote thorough analyses of data, and 3） foster the incremental advancement of valid approaches. Unfortunately, most would also agree we have far to go to reach this vital goal （Hackam and Redelmeier, 2006; Prinz et al., 2011; Baker et al., 2014）.

XML-based Data Processing in Network Supported Collaborative Design

In the course of network supported collaborative design, the data processing plays a very vital role. Much effort has been spent in this area, and many kinds of approaches have been proposed. Based on the correlative materials, this paper presents extensible markup language （XML） based strategy for several important problems of data processing in network supported collaborative design, such as the representation of standard for the exchange of product model data （STEP） with XML in the product information expression and the management of XML documents using relational database. The paper gives a detailed exposition on how to clarify the mapping between XML structure and the relationship database structure and how XML-QL queries can be translated into structured query language （SQL） queries. Finally, the structure of data processing system based on XML is presented.

Inorganic Crystal Structure Data to be Presented in a Form More Useful for Further Studies

To make inorganic structure data more useful for further studies a five-point list of simple procedures to be followed by authors of crystal structure papers is proposed. 1. A crystal structure should be described with the space group corresponding to its true symmetry. 2. A new structure proposal should be tested, if it is realistic in principle. 3. A structure should be described with a space group in a setting given in the International Tables. 4. For a comparison with other structures the structure data should be standardized with the program STRUCTURE TIDY. 5. 揘ew?structure data should be checked in the databases, Chemical Abstracts or on-line internet resources, if they are really new. The list is supplemented with many explanations, commentaries, examples and references.

一种用于建立指标体系的柔性数据标准化方法

Data standardization is an important part of data preprocessing,which directly affects the feasibility and distinction of the indicator system.This study proposes a data standardization framework to achieve flexible data standardization through data feature identification,cluster analysis,and weighted data transformation.The proposed method could handle locally inflated distribution with long tails.The results of this study enrich the method library of data standardization,allowing researchers to have more targeted data differentiation capabilities in the establishment of indicator systems.

Establishment of the Secure Channel between Broker Nodes in Pub/Sub System

The paper mainly discusses the integrity of the forwarded subscription message guaranteed by secure channel which encrypted in data communication by using data encryption standard （DES） algorithm and chaos code algorithm between broker nodes in the routing process of the contentbased publish/subscribe system. It analyzes the security of the secure channel encrypted with data communication by DES algorithm and chaos code algorithm, and finds out the secure channel can be easily attacked by known plain text. Therefore, the paper proposes the improved algorithm of message encryption and authentication, combining encryption and the generation of the message authentication code together to finish scanning at one time, which enhances both the secure degree and running efficiency. This secure channel system has a certain reference value to the pub/sub system requiring highly communication security.

Open HD map service model:an interoperable high-Definition map data model for autonomous driving

With the growth in the vehicle industry,autonomous driving has become a hot topic worldwide and has attracted increasing attention from both industrial and academic sectors.Maps,as pivotal geospatial information carriers,play a vital role in route planning and navigation service.Compared with conventional maps,high-definition(HD)maps possesses higher precision,richer information,and various services and are regarded as critical infrastructure for autonomous driving.However,heterogeneous HD map data standards and models have different characteristics and advantages,and thus they rarely meet all autonomous driving requirements for different driving objectives.This research presents an interoperable map data model,the Open HD Map Service Model(OHDMSM),to provide a reference for HD map development.The designed OHDMSM,which contains three data layers and a set of corresponding interfaces,demonstrates high interoperability for HD map data fusion and application.As a proof of concept,an HD map data system is implemented with all functions following the designed data model and interfaces of OHDMSM.The design and development of OHDMSM data structures,interfaces and systems will benefit data requesting,updating,and interoperation for HD map data worldwide,which can be helpful for developing autonomous driving and intelligent transportation in the Digital Earth.

Implementation of the FAIR Data Principles for Exploratory Biomarker Data from Clinical Trials

The FAIR data guiding principles have been recently developed and widely adopted to improve the Findability,Accessibility,Interoperability,and Reuse of digital assets in the face of an exponential increase of data volume and complexity.The FAIR data principles have been formulated on a general level and the technological implementation of these principles remains up to the industries and organizations working on maximizing the value of their data.Here,we describe the data management and curation methodologies and best practices developed for FAIRification of clinical exploratory biomarker data collected from over 250 clinical studies.We discuss the data curation effort involved,the resulting output,and the business and scientific impact of our work.Finally,we propose prospective planning for FAIR data to optimize data management efforts and maximize data value.

Helping the Consumers and Producers of Standards,Repositories and Policies to Enable FAIR Data

Thousands of community-developed(meta)data guidelines,models,ontologies,schemas and formats have been created and implemented by several thousand data repositories and knowledge-bases,across all disciplines.These resources are necessary to meet government,funder and publisher expectations of greater transparency and access to and preservation of data related to research publications.This obligates researchers to ensure their data is FAIR,share their data using the appropriate standards,store their data in sustainable and community-adopted repositories,and to conform to funder and publisher data policies.FAIR data sharing also plays a key role in enabling researchers to evaluate,re-analyse and reproduce each other’s work.We can map the landscape of relationships between community-adopted standards and repositories,and the journal publisher and funder data policies that recommend their use.In this paper,we show how the work of the GO-FAIR FAIR Standards,Repositories and Policies(StRePo)Implementation Network serves as a central integration and cross-fertilisation point for the reuse of FAIR standards,repositories and data policies in general.Pivotal to this effort,the FAIRsharing,an endorsed flagship resource of the Research Data Alliance that maps the landscape of relationships between community-adopted standards and repositories,and the journal publisher and funder data policies that recommend their use.Lastly,we highlight a number of activities around FAIR tools,services and educational efforts to raise awareness and encourage participation.

Integration of biosafety surveillance through Biosafety Surveillance Conceptual Data Model

The global movement of people and goods has increased the risk of biosecurity threats and their potential to induce large economic,social,and environmental harm.Integration of biosafety monitoring networks has become a top priority for addressing biosafety issues.In order to resolve the data standards and integration problems in the field of biosafety in China,the Biosafety Surveillance Conceptual Data Model(BSCDM),which is an object-oriented,hierarchically designed,flexible and scalable biosafety surveillance concept data model,is proposed in this article.This model is based on the integration of business process management and data resources of disease surveillance,animal disease surveillance and potential invasive biological monitoring.In reference to the Public Health Conceptual Data Model(PHCDM)and Federal Enterprise Architecture(FEA),BSCDM conducts a thorough analysis of biosafety monitoring activities,records basic information requirements of biosafety monitoring and provides data set standards for biosafety-related activities.It is developed with the Unified Modeling Language(UML)and could be applied as an open standard for accelerating data analysis and promoting collaboration.This study attempts to integrate biosafety monitoring data and the presented model has been tested in the detection of dengue fever in China and will be applied to other biosafety fields.

Geological applications using geospatial standards-an example from OneGeology-Europe and GeoSciML

The Geoscience Markup Language(GeoSciML)has been developed to enable the interchange of geoscience information,principally that portrayed on geological maps as well as boreholes.A GeoSciML testbed was developed both to test the implementation of the data model and its application in web services.The OneGeology-Europe project aims to use the GeoSciML data model,and build on the experience of the GeoSciML testbed,in implementing a geoportal for a harmonised geological map of Europe at 1:1 million scale.This involves the integration of web services from 20 participating organisations.An important objective of OneGeology-Europe is to contribute to Infrastructure for Spatial Information in the European Community(INSPIRE),both through the development of a geological data specification and the use of the INSPIRE technical architecture.GeoSciML and the OneGeology-Europe project are also steps towards incorporating geoscience data into a Digital Earth.Both the development of GeoSciML and the implementation of web services for GeoSciML and OneGeology-Europe,have followed a standards-based metho-dology.The technical architecture comprises a geoportal providing access to a Catalogue Service for the Web for metadata describing both the data and services available.OneGeology-Europe will provide bothWeb Map Services view andWeb Feature Services download services,which aim to be compliant with the INSPIRE implementing rules.

Key Recovery Against 3DES in CPU Smart Card Based on Improved Correlation Power Analysis

The security of CPU smart cards, which are widely used throughout China, is currently being threatened by side-channel analysis. Typical countermeasures to side-channel analysis involve adding noise and filtering the power consumption signal. In this paper, we integrate appropriate preprocessing methods with an improved attack strategy to generate a key recovery solution to the shortcomings of these countermeasures. Our proposed attack strategy improves the attack result by combining information leaked from two adjacent clock cycles. Using our laboratory-based power analysis system, we verified the proposed key recovery solution by performing a successful correlation power analysis on a Triple Data Encryption Standard （3DES） hardware module in a real-life 32-bit CPU smart card. All 112 key bits of the 3DES were recovered with about 80 000 power traces.

Taking FAIR on the ChIN:The Chemistry Implementation Network

The Chemistry Implementation Network(ChIN)is focused on supporting the FAIR Data needs of the research community regarding chemical related data.An Implementation Network is a consortium drawn from a community,in this case the chemistry discipline,committed to defining and constructing standards,materials and software in the spirit of the FAIR data principles and under the structure of the GO FAIR project.Furthermore,as a core science the ChIN has to reach beyond the chemistry community and support the use of chemical information in other disciplines.This will be facilitated through connections in the GO FAIR ecosystem of Implementation Networks.Examples of the FAIR chemical concepts that need to be supported include molecular and materials structures,chemical reactions,nomenclature and other chemical terminology and conventions.The ChIN aims to drive forward the application of the FAIR Data Principles relating to the full range of chemistry concepts that are key to the transparent and efficient communication of chemical information.Realizing the goal of FAIR chemistry data will require a culture change across the discipline.However this is best addressed once a critical mass of tools and approaches has been developed.

STEP-based Feature Recognition System for B-spline Surface Features

The geometrical and topological information of 3D computer aided design （CAD） models should be represented as a neut- ral format file to exchange the data between different CAD systems. Exchange of 3D CAD model data implies that the companies must exchange complete information about their products, all the way from design, manufacturing to inspection and shipping. This informa- tion should be available to each relevant partner over the entire life cycle of the product. This led to the development of an international standard organization （ISO） neutral format file named as standard for the exchange of product model data （STEP）. It has been ob- served from the literature, the feature recognition systems developed were identified as planar, cylindrical, conical and to some extent spherical and toroidal surfaces. The advanced surface features such as B-spline and its subtypes are not identified. Therefore, in this work, a STEP-based feature recognition system is developed to recognize t--spline surface features and its sub-types from the 3D CAD model represented in AP203 neutral file format. The developed feature recognition system is implemented in Java programming language and the product model data represented in STEP AP203 format is interpreted through Java standard data access interface （JSDAI）. The developed system could recognize B-spline surface features such as B-Spline surface with knots, quasi uniform surface, uniform surface, rational surface and Bezier surface. The application of extracted B-spline surface features information is discussed with reference to the toolpath generation for STEP-NC （STEP AP238）.

Formulations of Some Bit Switching Functions in DES

In the data encryption standard （DES） algorithm, there exist several bit-switching functions, including permutations, expansion, and permuted choices. They are generally presented in the form of matrixes and realized by using table look-up technique in the implementation of the cryptosystem. This paper presents explicit formulas for the initial permutation IP, its inverse IP-1 , the expansion function E, and the permuted choice PC_1. It also gives the program realizations of these functions in C＋＋ applying these formulas. With the advantage of the omission of the storage space for these matrixes and the tedious inputs of tables in the implementations of DES, our experimental results shows that the explicit formulas are useful in some situations, such as wireless sensor networks where the memory capacity is limited, especially when the size of file for encrypting is not too large, preferably smaller than 256KB.

Study on Distributed Knowledge Information System for Product Design

To overcome the limitations of commercial CAD and handbook form of knowledge expression, the Distributed Knowledge Information System (DKIS) for product design is proposed. The structure of DKIS and the key issues in its implementation are introduced; the method of knowledge store and transfer of DKIS is discussed. The mechanism of knowledge representation, acquisition and utilization, based on Internet network, is achieved. Based on the concept of function driven, integrated Artificial Neural Networks and Active Server Pages techniques, transplanting the trained ANN into DKIS system, a new method for retrieving knowledge in DKIS over Internet is achieved. Finally, a prototype of DKIS is developed to demonstrate the feasibility of the structure and constructional method of DKIS. The work pro-vides a scheme for speed knowledge acquisition and shortens the cycle of product development.

Feature Analysis of STEP Application Protocol and its Application

This paper uses semantic data modelling and CAD/CAPP/CAM integration to analyze the features defined in the STEP AP214, its characteristics of definition and distribution, and its influence on the complexity of CAD/CAPP/CAM application integration. A framework is developed for applications of CAD/CAPP/CAM integration based on the STEP to reduce the complexity of integration implementation. Two application program interfaces (API), namely, application protocol API and application API, are developed. The frameworks hierarchy structure and the application program interfaces between the layers make the integration of applications easier.

STEP AP 242 Managed Model-based 3D Engineering:An Application Towards the Automation of Fixture Planning

Fixture design and planning is one of the most important manufacturing activities, playing a pivotal role in deciding the lead time for product development. Fixture design, which affects the part-quality in terms of geometric accuracy and surface finish, can be enhanced by using the product manufacturing information(PMI) stored in the neutral standard for the exchange of product model data(STEP) file, thereby integrating design and manufacturing. The present paper proposes a unique fixture design approach, to extract the geometry information from STEP application protocol(AP) 242 files of computer aided design(CAD) models, for providing automatic suggestions of locator positions and clamping surfaces. Automatic feature extraction software "FiXplan", developed using the programming language C#, is used to extract the part feature, dimension and geometry information. The information from the STEP AP 242 file is deduced using geometric reasoning techniques, which in turn is utilized for fixture planning. The developed software is observed to be adept in identifying the primary, secondary, and tertiary locating faces and locator position configurations of prismatic components. Structural analysis of the prismatic part under different locator positions was performed using commercial finite element method software, ABAQUS, and the optimized locator position was identified on the basis of minimum deformation of the workpiece.The area-ratio(base locator enclosed area(%)/work piece base area(%)) for the ideal locator configuration was observed as 33%. Experiments were conducted on a prismatic workpiece using a specially designed fixture, for different locator configurations. The surface roughness and waviness of the machined surfaces were analysed using an Alicona non-contact optical profilometer. The best surface characteristics were obtained for the surface machined under the ideal locator positions having an area-ratio of 33%, thus validating the predicted numerical results. The efficiency, capability and applicability of the developed software is demonstrated for the finishing operation of a sensor cover – a typical prismatic component having applications in the naval industry, under different locator configurations.The best results were obtained under the proposed ideal locator configuration of area-ratio 33%.