Miracle-dz/UniFAR-FTUs huggingface dataset:
Methodology and System for Ontology-Enabled Traceability: Pilot Application to Design and Management of the Washington D.C. Metro System

This report describes a new methodology and system for satisfying requirements, and an architectural framework for linking discipline-specific dependencies through interaction relationships at the meta-model (or ontology) level. In state-of-the-art traceability mechanisms, requirements are connected directly to design objects. Here, in contrast, we ask the question: What design concept (or family of design concepts) should be applied to satisfy this requirement? Solutions to this question establish links between requirements and design concepts. Then, it is the implementation of these concepts that leads to the design itself. These ideas are prototyped through a Washington DC Metro System requirements-to-design model mockup. The proposed methodology offers several benefits not possible with state-of-the-art procedures. First, procedures for design rule checking may be embedded into design concept nodes, thereby creating a pathway for system validation and verification processes that can be executed early in the systems lifecycle where errors are cheapest and easiest to fix. Second, the proposed model provides a much better big-picture view of relevant design concepts and how they fit together, than is possible with linking of domains at the model level. And finally, the proposed procedures are automatically reusable across families of projects where the ontologies are applicable.
The Neuronal Correlate of Bidirectional Synesthesia: A Combined Event-related Potential and Functional Magnetic Resonance Imaging Study

The neuronal correlate of a rare explicit bidirectional synesthesia was investigated with numerical and physical size comparison tasks using both functional magnetic resonance imaging and event-related potentials. Interestingly, although participant I.S. exhibited similar congruity effects for both tasks at the behavioral level, subsequent analyses of the imaging data revealed that different brain areas were recruited for each task, and in different time windows. The results support: (1) the genuineness of bidirectional synesthesia at the neuronal level, (2) the possibility that discrepancy in the neuronal correlates of synesthesia between previous studies might be task-related, and (3) the possibility that synesthesia might not be a unitary phenomenon.
Limitations of interactive music recommendation based on audio content

We present a study on the limitations of an interactive music recommendation service based on automatic computation of audio similarity. Songs which are, according to the audio similarity function, similar to very many other songs and hence appear unwantedly often in recommendation lists keep a significant proportion of the audio collection from being recommended at all. This problem is studied in-depth with a series of computer experiments including analysis of alternative audio similarity functions and comparison with actual download data.
Ed-Join: an efficient algorithm for similarity joins with edit distance constraints

There has been considerable interest in similarity join in the research community recently. Similarity join is a fundamental operation in many application areas, such as data integration and cleaning, bioinformatics, and pattern recognition. We focus on efficient algorithms for similarity join with edit distance constraints. Existing approaches are mainly based on converting the edit distance constraint to a weaker constraint on the number of matching q-grams between pair of strings. In this paper, we propose the novel perspective of investigating mismatching q-grams. Technically, we derive two new edit distance lower bounds by analyzing the locations and contents of mismatching q-grams. A new algorithm, Ed-Join, is proposed that exploits the new mismatch-based filtering methods; it achieves substantial reduction of the candidate sizes and hence saves computation time. We demonstrate experimentally that the new algorithm outperforms alternative methods on large-scale real datasets under a wide range of parameter settings.
Covalent Immobilization of Glycosaminoglycans to Reduce the Inflammatory Effects of Biomaterials

Background The inflammatory responses evoked by artificial organs and implantation of devices like biosensors and guide wires can lead to acute and chronic inflammation, largely limiting the functionality and longevity of the devices with negative effects on patients. Aims The present study aimed to reduce the inflammatory responses to biomaterials by covalent immobilization of glycosaminoglycans (GAGs) on amino-terminated surfaces used as model biomaterials here. Methods and Results Water contact angle (WCA) and zeta potential measurements showed a significant increase in wettability and negative charges on the GAG-modified surfaces, respectively, confirming the successful immobilization of GAGs on the amino-terminated surfaces. THP-1-derived macrophages were used as a model cell type to investigate the efficacy of GAG-modified surfaces in modulating inflammatory responses. It was found that macrophage adhesion, macrophage spreading morphology, foreign body giant cell (FBGC) formation, as well as β1 integrin expression and interleukin-1β (IL-1β) production were all significantly decreased on GAG-modified surfaces compared to the initial amino-terminated surface. Conclusions This study demonstrates the potential of covalent GAG immobilization to reduce the inflammatory potential of biomaterials in different clinical settings.
Cellulose hydrolysis and binding with Trichoderma reesei Cel5A and Cel7A and their core domains in ionic liquid solutions

Ionic liquids (ILs) dissolve lignocellulosic biomass and have a high potential as pretreatment prior to total enzymatic hydrolysis. ILs are, however, known to inactivate cellulases. In this article, enzymatic hydrolysis of microcrystalline cellulose (MCC) and enzyme binding onto the cellulosic substrate were studied in the presence of cellulose‐dissolving ILs. Two different ILs, 1,3‐dimethylimidazolium dimethylphosphate ([DMIM]DMP) and 1‐ethyl‐3‐methylimidazolium acetate ([EMIM]AcO), and two monocomponent cellulases, Trichoderma reesei cellobiohydrolase Cel7A and endoglucanase Cel5A, were used in the study. The role and IL sensitivity of the carbohydrate‐binding module (CBM) were studied by performing hydrolysis and binding experiments with both the intact cellulases, and their respective core domains (CDs). Based on hydrolysis yields and substrate binding experiments for the intact enzymes and their CDs in the presence of ILs, the function of the CBM appeared to be very IL sensitive. Binding data suggested that the CBM was more important for the substrate binding of endoglucanase Cel5A than for the binding of cellobiohydrolase Cel7A. The CD of Cel7A was able to bind well to cellulose even without a CBM, whereas Cel5A CD had very low binding affinity. Hydrolysis also occurred with Cel5A CD even if this protein had very low binding affinity in all the studied matrices. Binding and hydrolysis were less affected by the studied ILs for Cel7A than for Cel5A. To our knowledge, this is the first systematic study of IL effects on cellulase substrate binding. Biotechnol. Bioeng. 2014;111: 726–733. © 2013 Wiley Periodicals, Inc.
Bcl-2/Bax protein ratio predicts 5-fluorouracil sensitivity independently of p53 status

p53 tumour-suppressor gene is involved in cell growth control, arrest and apoptosis. Nevertheless cell cycle arrest and apoptosis induction can be observed in p53-defective cells after exposure to DNA-damaging agents such as 5-fluorouracil (5-FU) suggesting the importance of alternative pathways via p53-independent mechanisms. In order to establish relationship between p53 status, cell cycle arrest, Bcl-2/Bax regulation and 5-FU sensitivity, we examined p53 mRNA and protein expression and p53 protein functionality in wild-type (wt) and mutant (mt) p53 cell lines. p53 mRNA and p53 protein expression were determined before and after exposure to equitoxic 5-FU concentration in six human carcinoma cell lines differing in p53 status and displaying marked differences in 5-FU sensitivity, with IC50values ranging from 0.2–22.6 mM. 5-FU induced a rise in p53 mRNA expression in mt p53 cell lines and in human papilloma virus positive wt p53 cell line, whereas significant decrease in p53 mRNA expression was found in wt p53 cell line. Whatever p53 status, 5-FU altered p53 transcriptional and translational regulation leading to up-regulation of p53 protein. In relation with p53 functionality, but independently of p53 mutational status, after exposure to 5-FU equitoxic concentration, all cell lines were able to arrest in G1. No relationship was evidenced between G1 accumulation ability and 5-FU sensitivity. Moreover, after 5-FU exposure, Bax and Bcl-2 proteins regulation was under p53 protein control and a statistically significant relationship (r= 0.880,P= 0.0097) was observed between Bcl-2/Bax ratio and 5-FU sensitivity. In conclusion, whatever p53 status, Bcl-2 or Bax induction and Bcl-2/Bax protein ratio were correlated to 5-FU sensitivity. © 2000 Cancer Research Campaign
Relative Pose Calibration Between Visual and Inertial Sensors

This paper proposes an approach to calibrate off-the-shelf cameras and inertial sensors to have a useful integrated system to be used in static and dynamic situations. When both sensors are integrated in a system their relative pose needs to be determined. The rotation between the camera and the inertial sensor can be estimated, concurrently with camera calibration, by having both sensors observe the vertical direction in several poses. The camera relies on a vertical chequered planar target and the inertial sensor on gravity to obtain a vertical reference. Depending on the setup and system motion, the translation between the two sensors can also be important. Using a simple passive turntable and static images, the translation can be estimated. The system needs to be placed in several poses and adjusted to turn about the inertial sensor centre, so that the lever arm to the camera can be determined. Simulation and real data results are presented to show the validity and simple requirements of the proposed methods.
Acute Effects of Low-Load/High-Repetition Single-Limb Resistance Training in COPD.

Exercising small muscle groups at a time allows higher muscle specific workloads compared with whole body aerobic exercises in people with chronic obstructive pulmonary disease (COPD). Whether similar effects also occur with partitioning exercise during low load/high-repetition resistance exercises is uncertain. PURPOSE To investigate the acute effects of partitioning exercise on exercise workload, exertional symptoms and quadriceps muscle fatigue during low load/high-repetition resistance exercises in people with COPD and healthy controls. METHODS We compared the acute physiological effects of single-limb (SL) versus two-limb (TL) execution of isokinetic knee extension and of six low load/high-repetition elastic resistance exercises in 20 people with COPD (forced expiratory volume in 1 s = 38% predicted) and 15 healthy controls. RESULTS Among people with COPD, SL exercises resulted in higher exercise workloads during isokinetic knee extension (17% ± 31%, P < 0.05) and elastic exercises (rowing, 17% ± 23%; leg curl, 23% ± 21%; elbow flexion, 19% ± 26%; chest press, 14% ± 15%; shoulder flexion, 33% ± 24%; and knee extension, 24% ± 18%, all P < 0.05). Muscle fatigue ratings were similar during SL compared with TL exercises, whereas dyspnea ratings were similar between conditions during isokinetic exercises and lower during SL compared with TL elastic exercises (P < 0.05). In COPD, SL knee extension resulted in greater quadriceps fatigue than TL knee extension as evidenced by a greater fall in quadriceps potentiated twitch force after the former exercise (-24% ± 10% vs -16% ± 8%, P = 0.025). In healthy controls, partitioning exercise with SL exercise did not modify workload, quadriceps fatigue nor dyspnea achieved during the various exercises. CONCLUSIONS Partitioning exercise by exercising using an SL allowed higher muscle localized exercise workloads, larger amount of quadriceps muscle fatigue with lower, or similar level of exertional symptoms during low load/high-repetition resistance exercises in people with advanced COPD.
Study protocolStudy protocol : national research partnership to improve primary health care performance and outcomes for Indigenous peoples

Background: Strengthening primary health care is critical to reducing health inequity between Indigenous and nonIndigenous Australians. The Audit and Best practice for Chronic Disease Extension (ABCDE) project has facilitated the implementation of modern Continuous Quality Improvement (CQI) approaches in Indigenous community health care centres across Australia. The project demonstrated improvements in health centre systems, delivery of primary care services and in patient intermediate outcomes. It has also highlighted substantial variation in quality of care. Through a partnership between academic researchers, service providers and policy makers, we are now implementing a study which aims to 1) explore the factors associated with variation in clinical performance; 2) examine specific strategies that have been effective in improving primary care clinical performance; and 3) work with health service staff, management and policy makers to enhance the effective implementation of successful strategies. Methods/Design: The study will be conducted in Indigenous community health centres from at least six States/ Territories (Northern Territory, Western Australia, New South Wales, South Australia, Queensland and Victoria) over a five year period. A research hub will be established in each region to support collection and reporting of quantitative and qualitative clinical and health centre system performance data, to investigate factors affecting variation in quality of care and to facilitate effective translation of research evidence into policy and practice. The project is supported by a web-based information system, providing automated analysis and reporting of clinical care performance to health centre staff and management. Discussion: By linking researchers directly to users of research (service providers, managers and policy makers), the partnership is well placed to generate new knowledge on effective strategies for improving the quality of primary health care and fostering effective and efficient exchange and use of data and information among service providers and policy makers to achieve evidence-based resource allocation, service planning, system development, and improvements of service delivery and Indigenous health outcomes.
HPV/E7 induces chemotherapy‐mediated tumor suppression by ceramide‐dependent mitophagy

Human papillomavirus (HPV) infection is linked to improved survival in response to chemo‐radiotherapy for patients with oropharynx head and neck squamous cell carcinoma (HNSCC). However, mechanisms involved in increased HNSCC cell death by HPV signaling in response to therapy are largely unknown. Here, using molecular, pharmacologic and genetic tools, we show that HPV early protein 7 (E7) enhances ceramide‐mediated lethal mitophagy in response to chemotherapy‐induced cellular stress in HPV‐positive HNSCC cells by selectively targeting retinoblastoma protein (RB). Inhibition of RB by HPV‐E7 relieves E2F5, which then associates with DRP1, providing a scaffolding platform for Drp1 activation and mitochondrial translocation, leading to mitochondrial fission and increased lethal mitophagy. Ectopic expression of a constitutively active mutant RB, which is not inhibited by HPV‐E7, attenuated ceramide‐dependent mitophagy and cell death in HPV(+) HNSCC cells. Moreover, mutation of E2F5 to prevent Drp1 activation inhibited mitophagy in HPV(+) cells. Activation of Drp1 with E2F5‐mimetic peptide for inducing Drp1 mitochondrial localization enhanced ceramide‐mediated mitophagy and led to tumor suppression in HPV‐negative HNSCC‐derived xenograft tumors in response to cisplatin in SCID mice.
The Financial Crimes Enforcement Network AI System (FAIS) Identifying Potential Money Laundering from Reports of Large Cash Transactions

The Financial Crimes Enforcement Network (FIN-CEN) AI system (FAIS) links and evaluates reports of large cash transactions to identify potential money laundering. The objective of FAIS is to discover previously unknown, potentially high-value leads for possible investigation. FAIS integrates intelligent human and software agents in a cooperative discovery task on a very large data space. It is a complex system incorporating several aspects of AI technology, including rule-based reasoning and a blackboard. FAIS consists of an underlying database (that functions as a black-board), a graphic user interface, and several preprocessing and analysis modules. FAIS has been in operation at FINCEN since March 1993; a dedicated group of analysts process approximately 200,000 transactions a week, during which time over 400 investigative support reports corresponding to over $1 billion in potential laundered funds were developed. FAIS's unique analytic power arises primarily from a change in view of the underlying data from a transaction-oriented perspective to a subject-oriented (that is, person or organization) perspective.
Polyhedral Visual Hulls for Real-Time Rendering

We present new algorithms for creating and rendering visual hulls in real-time. Unlike voxel or sampled approaches, we compute an exact polyhedral representation for the visual hull directly from the silhouettes. This representation has a number of advantages: 1) it is a view-independent representation, 2) it is well-suited to rendering with graphics hardware, and 3) it can be computed very quickly. We render these visual hulls with a view-dependent texturing strategy, which takes into account visibility information that is computed during the creation of the visual hull. We demonstrate these algorithms in a system that asynchronously renders dynamically created visual hulls in real-time. Our system outperforms similar systems of comparable computational power.
Genetics of age at menarche: a systematic review.

BACKGROUND Menarche is the first menstrual period of a girl at puberty. The timing of menarche is important for health in later life. Age at menarche is a complex trait and has a strong genetic component. This review summarizes the results of the genetic studies of age at menarche conducted to date, highlights existing problems in this area and outlines prospects of future studies on genetic factors for the trait. METHODS PubMed and Google Scholar were searched until May 2011 using the keywords: 'menarche', 'puberty' and 'age at menarche' in combination with the keywords 'polymorphism', 'candidate gene', 'genome-wide association study' and 'linkage'. RESULTS Our search yielded 170 papers, 35 of which were selected for further analysis. Several large-scale genome-wide association studies along with a powerful meta-analysis of their aggregated data identified about 50 candidate genes for the trait. Some genes were replicated in different studies of Caucasians (e.g. LIN28B, TMEM38B) or in different ethnicities (e.g. SPOCK, RANK and RANKL). However, despite the large volume of results obtained, there is a huge gap in relevant data on ethnic groups other than Caucasians. CONCLUSIONS The reviewed studies laid a solid basis for future research on genetics of age at menarche. However, as yet specific genes for this trait have not been identified consistently in all ethnicities and types of studies. We suggest expanding the research to different ethnicities and propose several methodologies to increase the efficiency of studies in this area, including a systems approach, which combines existing high-throughput methods in a single pipeline.
Prior Structure for On-line Learning

On-line learning and adaptation capabilities are important for robot systems which operate in the real world and have to react to changes in the environment and the task requirements. Such learning schemes, however, often suffer from problems of complexity, rendering them intractable for on-line learning in complex domains. To address these problems, the approach presented here introduces prior structure which drastically reduces the size of the state and action spaces. Deriving control from a set of predictable control laws, the system is modeled more abstractly as a discrete event dynamic system which represents all possible system behavior. Use of this framework also permits the automatic incorporation of knowledge in the form of constraints, providing a basis for the explicit representation of safety conditions and “maturational” effects which can be used to further enhance learning performance. To illustrate this structure and to show its applicability, the acquisition of a rotation gait on a four-legged walking platform is demonstrated.
Synthesis and investigation of physico-chemical properties of dicationic ionic liquids

A series of dicationic ionic liquids (ILs) including [C4(MIM)2][PF6]2, [C5(MIM)2][PF6]2, [C6(MIM)2][PF6]2 and [C4(PYR)2][PF6]2 were synthesized. Their thermal stability and melting points were analysed. It was found that dicationic ILs presented important implications in the design of homogeneous and heterogeneous system with water. A homogeneous system of dicationic ILs with water could be formed at a relatively high temperature and then a heterogeneous system was formed when the solution was cooled to a low temperature. The ILs recovered by altering the temperature were obtained in high percentage yields of [C4(MIM)2][PF6]2 (97.6%), [C5(MIM)2][PF6]2 (97.3%), [C6(MIM)2][PF6]2 (98.0%) and [C4(PYR)2][PF6]2 (94.2%). On the other hand, [C4(MIM)2][PF6]2 and [C5(MIM)2][PF6]2 exhibited good solubility in acetonitrile and acetone. A homogeneous system could be achieved with imidazolium-based ILs with a relatively low amount of water and acetonitrile at room temperature. All of the properties of dicationic ILs have a strong correlation with the nature of dications, the linkage chain and the symmetry of dications. Dicationic ILs may provide a new opportunity for some specific applications in order to enable the effective separation and isolation of products.
Discovering Meta-Paths in Large Heterogeneous Information Networks

The Heterogeneous Information Network (HIN) is a graph data model in which nodes and edges are annotated with class and relationship labels. Large and complex datasets, such as Yago or DBLP, can be modeled as HINs. Recent work has studied how to make use of these rich information sources. In particular, meta-paths, which represent sequences of node classes and edge types between two nodes in a HIN, have been proposed for such tasks as information retrieval, decision making, and product recommendation. Current methods assume meta-paths are found by domain experts. However, in a large and complex HIN, retrieving meta-paths manually can be tedious and difficult. We thus study how to discover meta-paths automatically. Specifically, users are asked to provide example pairs of nodes that exhibit high proximity. We then investigate how to generate meta-paths that can best explain the relationship between these node pairs. Since this problem is computationally intractable, we propose a greedy algorithm to select the most relevant meta-paths. We also present a data structure to enable efficient execution of this algorithm. We further incorporate hierarchical relationships among node classes in our solutions. Extensive experiments on real-world HIN show that our approach captures important meta-paths in an efficient and scalable manner.