Discovery Interface Research Articles

CUPID: Contextual Understanding of Prompt‐conditioned Image Distributions

AbstractWe present CUPID: a visualization method for the contextual understanding of prompt‐conditioned image distributions. CUPID targets the visual analysis of distributions produced by modern text‐to‐image generative models, wherein a user can specify a scene via natural language, and the model generates a set of images, each intended to satisfy the user's description. CUPID is designed to help understand the resulting distribution, using contextual cues to facilitate analysis: objects mentioned in the prompt, novel, synthesized objects not explicitly mentioned, and their potential relationships. Central to CUPID is a novel method for visualizing high‐dimensional distributions, wherein contextualized embeddings of objects, those found within images, are mapped to a low‐dimensional space via density‐based embeddings. We show how such embeddings allows one to discover salient styles of objects within a distribution, as well as identify anomalous, or rare, object styles. Moreover, we introduce conditional density embeddings, whereby conditioning on a given object allows one to compare object dependencies within the distribution. We employ CUPID for analyzing image distributions produced by large‐scale diffusion models, where our experimental results offer insights on language misunderstanding from such models and biases in object composition, while also providing an interface for discovery of typical, or rare, synthesized scenes.

Efficacy of water extracts of mushrooms on multidrug-resistant bacteria isolated from raw cow milk

The high rate of antibiotic-resistant bacteria observed in food samples has been alarming. The majority of the antibiotics now used in medicine have become ineffective against groups of bacteria. The use of bioactive substances from natural products against antibiotic-resistant bacteria is becoming attractive. Mushrooms are natural reservoirs of potent pharmaceuticals and are now the new interface for drug discovery. Aqueous extracts of five medicinal mushrooms namely Agaricus sp., Pleurotus pulmonarius, Pleurotus oestratus., Lentinus sp. and Ganoderma were prepared. Bacteria were isolated from raw cow milk using standard techniques and antibiotic sensitivity testing was carried out using 6 antibiotics. The efficacy of the mushroom extract was tested on 12 MAR bacteria using the disc diffusion method. It was observed that the aqueous extracts from the two Pleurotus spp were very active in killing the bacteria. Pleurotus oestratus was active against 5 isolates while Pleurotus pulmonarius was active against 3 isolates. Agaricus and Lentinus extracts were active against 4 isolates each while Ganoderma was active against only 3. Bacillus tropicus, Enterobacter hormaechei and Klebsiella pneumoniae isolates were totally resistant to the effects of the extracts. This study shows the effectiveness of mushroom aqueous extracts. This may be used to reduce bacterial load in food especially milk so as to prolong its shelf life in the natural state.

Tale of Two Tools

Consistent delivery of full-text content has been a challenge for libraries since the development of online databases. Library systems have attempted to meet this challenge, but link resolvers and early direct linking tools often fell short of patron expectations. In the last several years, a new generation of direct linking tools has appeared, two of which will be discussed in this article: Third Iron’s LibKey Discovery and Quicklinks by Ex Libris, a Clarivate company. Figure 1 shows the “Download PDF” link added by LibKey. Figure 2 shows the “Get PDF” link provided by Quicklinks. The way we configured our discovery interface, a resource cannot receive both the LibKey and Quicklinks PDF links. These two direct linking tools were chosen because they were both relatively new to the market in April 2021 when this analysis took place and they can both be integrated into Primo VE, the library discovery system of choice at the authors’ home institutions of SUNY College of Optometry and Ferris State University. Through analysis of the frequency of direct links, link success rate, and number of clicks, this study may help determine which product is most likely to meet your patrons’ needs.

Musings on Faceted Search, Metadata, and Library Discovery Interfaces

Faceted search is a powerful tool that enables searchers to easily and intuitively take advantage of controlled vocabularies and structured metadata. Faceted search has been widely implemented in library discovery interfaces and has provided many benefits to library users. The effectiveness of facets in library catalogs depends on a complex interaction between facet vocabularies, metadata quality and structure, and the library discovery interface’s capabilities. This article provides a holistic overview of challenges for optimally implementing facets in library catalogs. This supports a systematic approach to refining and enhancing the capacity of faceted search to improve searching and exploring bibliographic metadata.

Emotion-aware music tower blocks (EmoMTB ): an intelligent audiovisual interface for music discovery and recommendation

Music listening has experienced a sharp increase during the last decade thanks to music streaming and recommendation services. While they offer text-based search functionality and provide recommendation lists of remarkable utility, their typical mode of interaction is unidimensional, i.e., they provide lists of consecutive tracks, which are commonly inspected in sequential order by the user. The user experience with such systems is heavily affected by cognition biases (e.g., position bias, human tendency to pay more attention to first positions of ordered lists) as well as algorithmic biases (e.g., popularity bias, the tendency of recommender systems to overrepresent popular items). This may cause dissatisfaction among the users by disabling them to find novel music to enjoy. In light of such systems and biases, we propose an intelligent audiovisual music exploration system named EmoMTB . It allows the user to browse the entirety of a given collection in a free nonlinear fashion. The navigation is assisted by a set of personalized emotion-aware recommendations, which serve as starting points for the exploration experience. EmoMTB adopts the metaphor of a city, in which each track (visualized as a colored cube) represents one floor of a building. Highly similar tracks are located in the same building; moderately similar ones form neighborhoods that mostly correspond to genres. Tracks situated between distinct neighborhoods create a gradual transition between genres. Users can navigate this music city using their smartphones as control devices. They can explore districts of well-known music or decide to leave their comfort zone. In addition, EmoMTB integrates an emotion-aware music recommendation system that re-ranks the list of suggested starting points for exploration according to the user’s self-identified emotion or the collective emotion expressed in EmoMTB ’s Twitter channel. Evaluation of EmoMTB has been carried out in a threefold way: by quantifying the homogeneity of the clustering underlying the construction of the city, by measuring the accuracy of the emotion predictor, and by carrying out a web-based survey composed of open questions to obtain qualitative feedback from users.

Orbis Cascade Alliance’s Migration of Faceted Vocabularies to Primo VE

There has been a continued effort among cataloging communities to implement new fields and subfields in MARC 21 to support more structured data that benefit end users. In the current article, we describe how the Orbis Cascade Alliance integrated fields and subfields of this type into Primo VE, in order to provide faceted vocabularies and other facets within the discovery interface that were otherwise unavailable from the vendor. We discuss challenges in migrating the normalization rules behind the facets, the extent to which they are being utilized by member institutions, and possible next steps for promoting their use more extensively.

Serendipity in Library Retrieval: Reinforcing Discovery through Visualization of Bibliographic Relationships

This work starts with a background study of serendipity, its meaning in the context of information discovery, its interrelation with bibliographic relationships, and the technical possibilities for practical implementation of a relationships based visual navigation in a library discovery interface to achieve serendipitous resource discovery. The methodology for developing the prototype consists of two components – theoretical base and practical steps. The theoretical framework includes an indepth study of the concept of bibliographic relationships as proposed by experts, as reflected in bibliographic data models and as included in bibliographic formats and metadata schemas. The practical sides deal with the application of the theoretical framework in designing a prototype that, in addition to other typical retrieval features, supports visual navigational facility driven by bibliographic relationships. The components, tools and standards of the entire software architecture are all open source and open standards.

Enabling modern data discovery for atmospheric measurements

The Atmospheric Radiation Measurement (ARM) user facility is a US Department of Energy Office of Science user facility that is managed and operated through a collaborative effort led by nine US Department of Energy national laboratories. The ARM Data Center, located at Oak Ridge National Laboratory, is responsible for the timely collection, processing, and delivery of data products to the scientific community. The ARM Data Center holds more than 11,000 data products, including metadata collected from field campaigns, instruments, value-added products, and principal investigator–contributed data. These data sets are checked for successful transfer (for most data, this transfer is carried out automatically via the network; however, some of the largest data sets and some of the most remote sites require manual shipping of hard disks) and both the data and metadata are processed to a standard format, which is an ARM-standardized structure, via the Network Common Data Form. The Network Common Data Form is a self-describing binary format with many compatible software tools. Once processed, the data are cataloged, stored in the ARM Data Archive, and made discoverable through association with an array of metadata-characterizing information, such as location and measurement classification. These metadata enable powerful search capabilities through the ARM Data Center Data Discovery interface. This paper discusses the workflow of how the new discovery system has been redesigned from user requirements and how the data are distributed to the scientific community.

Exploring Archives Space an Open Source Solution for Digital Archiving

The advent of digital and networking technologies has begun to embrace the genesis of the next-generation digital archive. The inclusion of cross-domain objects like manuscript documents, audio and video recordings, photographs, paintings, sculptures and other digitised cultural heritage materials increases the complexity of digital archiving in terms of preservation, collection, and discovery of these resources. Introducing a high definition information retrieval system to exhibit the library and museum’s digital resources to a maximum number of users in an open-access environment can satisfy the S. R. Ranganathan’s fourth law – save the time of reader as well as the staffs. Nevertheless, from the perspective of acquiring an advanced OPAC view (web-scale discovery interface) with index-based searching, metadata harvesting, and accessing the physical as well as digital holdings is always a better option for Archival Collections Management System (ACMS). This paper illustrates the fundamental notions and applications of ArchivesSpace, a useful open-source digital archiving toolkit of the contemporary world and analyses its relevance in digital language archiving.

An Overview of the Relevance Ranking Based Open Source Resource Discovery Interface (VuFind) for Library and Information Services

An Overview of the Relevance Ranking Based Open Source Resource Discovery Interface (VuFind) for Library and Information Services

Epithelial Modelling Platform: A Tool for Investigating Hypothesis through Discovery and Assembly of Computational Models of Epithelial Transport

Scientists often leverage computational models of biological systems to investigate hypotheses which are difficult or prohibitively expensive to achieve experimentally. Such investigations are best achieved by utilizing suitable computational models, reusing existing validated models where possible and creating novel models consistently as needed. This requires tools which enable the discovery and exploration of existing models matched with assistance in constructing and testing new models. Enabling scientists or clinicians to use such a tool by describing their requirements in a manner familiar to themselves greatly improves the accessibility of the tool. We have developed a web-based tool, the Epithelial Modelling Platform, for scientists and clinicians to discover relevant models and then assemble these into a novel model customized for investigating their hypotheses. While our tool specifically focuses on epithelial transport, by utilizing relevant community standards and publicly accessible knowledge repositories, it is extensible to other areas of application. The platform abstracts underlying mathematics of the computational models and provides a visual environment which mimics biological phenomena of an epithelial cell. Beyond the mathematical models, we have implemented a feature to discover existing simulation experiments which match the features of the novel models users create. By executing these simulation experiments with the novel models and comparing to previous model predictions and/or experimental or clinical observations we are able to provide the user with some measure of verification that their model matches, or doesn't match, existing knowledge captured in the various repositories utilized. Support or Funding Information Supported by the Medical Technologies Center of Research Excellence (MedTech CoRE), the Aotearoa Foundation, and the Auckland Bioengineering Institute Model discovery interface to search for models in the Physiome Model Repository (PMR) which are relevant to the query “flux of sodium”. By querying the biological knowledge stored in PMR the Epithelial Modelling Paltform retrieves components from the weinstein, mackenzie, and chang fujita models. Illustrating a similarity between weinstein and mackenzie model. In this case both models have similar compartment labeled with a unique color. An instance of the Epithelial Modelling Platform. It consists of five compartments and three membranes. Biological processes have been represented with various shapes: fluxes with circles; channels with polygons; and diffusive fluxes with a text, a line, and an arrow. On the right, check boxes have been generated for the visualized shapes on the membranes to allow the user to drag and drop. Concentration of the biological description of CellML variables float in the respective compartments. A suggestion window based on the biological description in the Physiome Model Repository when a circle, represented as flux of Na+ in the weinstein model, is moved from apical to basolateral membrane. A model verification instance for testing components of an assembled epithelial model reproduce the same simulation experiment. A model verification instance for testing components of an assembled epithelial model reproduce the same simulation experiment. A spider chart to find similarity of models with respect to an assembled epithelial model. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Improved Resource Directory Based on DNS Name Self-Registration for Device Transparent Access in Heterogeneous IoT Networks

With the rapid development of Internet of Things (IoT) technologies in various domains including smart homes, smart cities, smart factories and smart buildings where Internet-connected devices are deployed to provide IoT services based on heterogeneous frameworks and platforms. Many standard protocols, frameworks, libraries and specifications have been proposed for developing IoT applications. Therefore, providing a consistent scheme is important for supporting the interoperability in heterogeneous IoT devices to interact in the same domain and cross-domain. Moreover, supporting the device transparent access for clients to consume IoT service from the different environment that can provide user-friendly service scenarios although the user consumes services in different IoT networks. In this paper, we propose an improved Resource Directory (RD) based on a Domain Name System (DNS) Name Self-Registration (DNSNSR) for the device transparent access in heterogeneous IoT networks. For supporting proposed DNSNSR, an IoT RD is presented based on the Open Connectivity Foundation (OCF) standard specification to provide device registration and discovery service. Through the registration interface, the IoT RD configures the DNS names using Bind 9 to provide the DNS service in an IoT network based on the published device information. Using the discovery interface of RD and name resolution of DNS, the IoT Client gets devices information including (Identifier) ID and Internet Protocol (IP) to access IoT Devices without considering underlying protocols through the interworking proxy of proposed RD in heterogeneous IoT networks. Therefore, the proposed RD based on DNSNSR enables the IoT devices to be discovered by IoT clients in the various environment through the RD and DNS functions. Furthermore, using the OCF-direct and proxy-based access mechanism, the proposed RD based on DNSNSR supports IoT devices to be accessed by clients in various IoT environment.

Trapping of the transport-segment DNA by the ATPase domains of a type II topoisomerase

Type II topoisomerases alter DNA topology to control DNA supercoiling and chromosome segregation and are targets of clinically important anti-infective and anticancer therapeutics. They act as ATP-operated clamps to trap a DNA helix and transport it through a transient break in a second DNA. Here, we present the first X-ray crystal structure solved at 2.83 Å of a closed clamp complete with trapped T-segment DNA obtained by co-crystallizing the ATPase domain of S. pneumoniae topoisomerase IV with a nonhydrolyzable ATP analogue and 14-mer duplex DNA. The ATPase dimer forms a 22 Å protein hole occupied by the kinked DNA bound asymmetrically through positively charged residues lining the hole, and whose mutagenesis impacts the DNA decatenation, DNA relaxation and DNA-dependent ATPase activities of topo IV. These results and a side-bound DNA-ParE structure help explain how the T-segment DNA is captured and transported by a type II topoisomerase, and reveal a new enzyme–DNA interface for drug discovery.

Development of Virtual Resource Based IoT Proxy for Bridging Heterogeneous Web Services in IoT Networks.

The Internet of Things is comprised of heterogeneous devices, applications, and platforms using multiple communication technologies to connect the Internet for providing seamless services ubiquitously. With the requirement of developing Internet of Things products, many protocols, program libraries, frameworks, and standard specifications have been proposed. Therefore, providing a consistent interface to access services from those environments is difficult. Moreover, bridging the existing web services to sensor and actuator networks is also important for providing Internet of Things services in various industry domains. In this paper, an Internet of Things proxy is proposed that is based on virtual resources to bridge heterogeneous web services from the Internet to the Internet of Things network. The proxy enables clients to have transparent access to Internet of Things devices and web services in the network. The proxy is comprised of server and client to forward messages for different communication environments using the virtual resources which include the server for the message sender and the client for the message receiver. We design the proxy for the Open Connectivity Foundation network where the virtual resources are discovered by the clients as Open Connectivity Foundation resources. The virtual resources represent the resources which expose services in the Internet by web service providers. Although the services are provided by web service providers from the Internet, the client can access services using the consistent communication protocol in the Open Connectivity Foundation network. For discovering the resources to access services, the client also uses the consistent discovery interface to discover the Open Connectivity Foundation devices and virtual resources.

GrammarViz 3.0

The problems of recurrent and anomalous pattern discovery in time series, e.g., motifs and discords, respectively, have received a lot of attention from researchers in the past decade. However, since the pattern search space is usually intractable, most existing detection algorithms require that the patterns have discriminative characteristics and have its length known in advance and provided as input, which is an unreasonable requirement for many real-world problems. In addition, patterns of similar structure, but of different lengths may co-exist in a time series. Addressing these issues, we have developed algorithms for variable-length time series pattern discovery that are based on symbolic discretization and grammar inference—two techniques whose combination enables the structured reduction of the search space and discovery of the candidate patterns in linear time. In this work, we present GrammarViz 3.0—a software package that provides implementations of proposed algorithms and graphical user interface for interactive variable-length time series pattern discovery. The current version of the software provides an alternative grammar inference algorithm that improves the time series motif discovery workflow, and introduces an experimental procedure for automated discretization parameter selection that builds upon the minimum cardinality maximum cover principle and aids the time series recurrent and anomalous pattern discovery.

Edge-Centric Distributed Discovery and Access in the Internet of Things

Massive diffusion of constrained devices communicating through low-power wireless technologies in the future Internet of Things (IoT) will require in many scenarios the deployment of IoT gateways to allow applications to discover and access IoT resources. In this context, Fog/Edge computing will represent an opportunity to deploy IoT gateways in proximity of IoT domains, meeting the requirements of applications needing low-latency interactions with devices. In this paper, we present an edge-centric distributed architecture to provide resource discovery and access services to IoT applications. The proposed approach leverages the CoRE Resource Directory interface and the Constrained Application Protocol (CoAP) to expose a standard interface for global discovery and access. Multiple IoT gateways are federated through a peer-to-peer overlay implemented by a distributed hash table, which is exploited to share the information on IoT resources available across multiple domains. The proposed solution is validated by means of a small-scale prototype, and extensively evaluated through emulation in large scale deployment in comparison to a centralized Cloud-based approach. Experimental results demonstrated that the proposed approach guarantees lower latencies than a centralized solution and can ensure scalability for small to medium sized deployments.

Suomalaisten yliopistojen avoimet julkaisut vuonna 2016 OKM:n julkaisutiedonkeruun tietojen valossa

The Finnish Open Access monitoring efforts are integrated with the national data collection conducted by CSC – IT Center for Science for the Ministry of Education and Culture. The publication data collected from the CRIS of each participating organization can be browsed at Juuli (www.juuli.fi), a discovery interface developed by the National Library of Finland.
 Starting from 2016, two separate fields have been used for indicating the OA status of each publication. One of the fields indicates whether the publication is OA via a Gold or a Hybrid channel, and the second field is used for indicating whether it has been deposited into a repository. The OA definition used in the data collection has also been updated to make it as clear as possible. According to the current dataset for the year 2016, 28.9 % of all peer-reviewed articles produced within the Finnish universities were reported as being OA. There was a lot of overlap between Gold/Hybrid and Green OA, as about 60 % of the articles deposited into repositories were already OA via Gold or Hybrid OA publication channels.

Measuring Open Access in Finland

In Finland the national Open Access monitoring efforts are integrated with the national data collection conducted by CSC - IT Centre for Science for the Ministry of Education and Culture. The collection of data on research publications encompasses universities, universities of applied sciences, central hospital districts and many of the state research institutes. The publication metadata is collected from the CRIS of each participating organization. A new automated data collection process was launched in 2016, but while some of the organizations update their data daily, many others still upload their data on annual basis. The data is stored in the Virta service built by CSC, and the de-duplicated publication data can be browsed at Juuli ( http://www.juuli.fi ), a VuFind-based discovery interface developed by the National Library of Finland. Starting from 2016, the Ministry has improved the way the OA status information is reported. There are two separate fields for indicating the OA status of each publication. One of the fields indicates whether the publication is OA via a Gold or a Hybrid channel, and the second field is used for indicating whether it has been deposited into a repository (Green OA). The OA definition used in the data collection has been made as clear as possible: The publication should be at least free to read Gold/Hybrid and Green Open Access are all accepted Embargoes are allowed for Green OA but not for Gold or Hybrid Depositing into an institutional or a subject-based repository is OK, but papers available at personal/project websites or at sites like Research Gate or Academia.edu don’t count The OA version must be peer-reviewed to qualify Although the quality of the data has improved, it is still far from perfect. Some of the organizations are putting more effort into the collection and verification of the data than others. At the moment no data is collected on the embargoes, the use of licenses or the APC costs associated with each publication. According to the current dataset for the year 2016, 28.6% of all peer-reviewed articles produced within the Finnish universities were reported as being Open Access. The amount of overlap between Gold/Hybrid and Green Open Access was higher than was expected. Only about 40% of the articles that the universities reported as being openly available via Green route were originally issued in non-OA publication channels. At the moment the share of OA publications is highest within the natural sciences (34%) and lowest in engineering and technology (20%), with medicine and health sciences, agriculture and forestry, humanities and social sciences falling in between them.

Measuring Open Access in Finland

In Finland the national Open Access monitoring efforts are integrated with the national data collection conducted by CSC - IT Centre for Science for the Ministry of Education and Culture. The collection of data on research publications encompasses universities, universities of applied sciences, central hospital districts and many of the state research institutes.The publication metadata is collected from the CRIS of each participating organization. A new automated data collection process was launched in 2016, but while some of the organizations update their data daily, many others still upload their data on annual basis. The data is stored in the Virta service built by CSC, and the de-duplicated publication data can be browsed at Juuli (http://www.juuli.fi), a VuFind-based discovery interface developed by the National Library of Finland.Starting from 2016, the Ministry has improved the way the OA status information is reported. There are two separate fields for indicating the OA status of each publication. One of the fields indicates whether the publication is OA via a Gold or a Hybrid channel, and the second field is used for indicating whether it has been deposited into a repository (Green OA).The OA definition used in the data collection has been made as clear as possible:The publication should be at least free to readGold/Hybrid and Green Open Access are all acceptedEmbargoes are allowed for Green OA but not for Gold or HybridDepositing into an institutional or a subject-based repository is OK, but papers available at personal/project websites or at sites like Research Gate or Academia.edu don’t countThe OA version must be peer-reviewed to qualifyAlthough the quality of the data has improved, it is still far from perfect. Some of the organizations are putting more effort into the collection and verification of the data than others. At the moment no data is collected on the embargoes, the use of licenses or the APC costs associated with each publication.According to the current dataset for the year 2016, 28.6% of all peer-reviewed articles produced within the Finnish universities were reported as being Open Access. The amount of overlap between Gold/Hybrid and Green Open Access was higher than was expected. Only about 40% of the articles that the universities reported as being openly available via Green route were originally issued in non-OA publication channels.At the moment the share of OA publications is highest within the natural sciences (34%) and lowest in engineering and technology (20%), with medicine and health sciences, agriculture and forestry, humanities and social sciences falling in between them.

Mapping the ARIADNE Catalogue Data Model to CIDOC CRM: bridging resource discovery and item-level access

ARIADNE is a European project aiming to integrate existing archaeological research infrastructures, services and distributed datasets, and to develop new technologies and tools to improve archaeological research methodology. The ARIADNE registry contains information about resources available among the various partners of the project and the metadata repository, which contains item level information of these resources. In order to provide an advanced discovery mechanism combining both item level and registry level information we propose a mapping from the ARIADNE Catalog Data Model, the model of the ARIADNE registry, to the CIDOC CRM, the underlying model of the metadata repository. The paper will present the requirements that led to the choice of different models for the registry and the metadata repository, will elaborate on the mapping, and will propose an integrated interface for information discovery and presentation.