Miracle-dz/UniFAR-FTUs huggingface dataset:
Keyword-based Semantic Retrieval System using Location Information in a Mobile Environment

Many services for mobile devices and wireless network have been studied in a Ubiquitous Environment. Mobile information retrieval is crucial to share the vast information and multimedia content. Mobile information retrieval has three challenges; 1) Mobile devices have a small display area. Thus, users are more interested in precision than in recall. 2) Mobile device portability means users frequently change their interest with location. 3) Though wireless development is progressing; its response rate and mobile device processing ability are still lower than for a wired network and PC. To meet these challenges, we propose keyword-based semantic mobile search system using ontology and location information. Through the experiment, we prove that providing the user’s selection of the semantic result improved precision. Current location information can be used to provide location-based multimedia content using GPS module and map with mashup service. Finally, the response rate of the service was demonstrated to be faster through a java-based Lucene engine for keyword-based retrieval module and dividing the result of retrieval.
Home-Made Cost Effective Preservation Buffer Is a Better Alternative to Commercial Preservation Methods for Microbiome Research

The investigation of wildlife gastrointestinal microbiomes by next-generation sequencing approaches is a growing field in microbial ecology and conservation. Such studies often face difficulties in sample preservation if neither freezing facilities nor liquid nitrogen (LQN) are readily available. Thus, in order to prevent microbial community changes because of bacterial growth after sampling, preservation buffers need to be applied to samples. However, the amount of microbial community variation attributable to the different preservation treatments and potentially affecting biological interpretation is hardly known. Here, we sampled feces of 11 sheep (Ovis aries sp.) by using swabs and analyzed the effect of air-drying, an inexpensive self-made nucleic acid preservation buffer (NAP), DNA/RNA Shield™, and RNAlater®, each together with freezing (for 10 days) or storing at room temperature (for 10 days) prior to 16S rRNA gene high-throughput sequencing to determine bacterial communities. Results revealed that the proportions of operational taxonomic units (OTUs) belonging to a bacterial phylum were affected by the preservation treatments, and that alpha diversities [observed OTUs, Shannon index, and phylogenetic diversity (PD)] were lower in all preservation treatments than in samples taken by forensic swabs and immediately frozen which is considered as the favored preservation treatment in the absence of any logistic constraints. Overall, NAP had better preservation qualities than RNAlater® and DNA/RNA Shield™ making this self-made buffer a valuable solution in wildlife microbiome studies.
Assessment of Clinical Validity of a Breast Cancer Risk Model Combining Genetic and Clinical Information

Background The Gail model is widely used for the assessment of risk of invasive breast cancer based on recognized clinical risk factors. In recent years, a substantial number of single-nucleotide polymorphisms (SNPs) associated with breast cancer risk have been identified. However, it remains unclear how to effectively integrate clinical and genetic risk factors for risk assessment. Methods Seven SNPs associated with breast cancer risk were selected from the literature and genotyped in white non-Hispanic women in a nested case–control cohort of 1664 case patients and 1636 control subjects within the Women’s Health Initiative Clinical Trial. SNP risk scores were computed based on previously published odds ratios assuming a multiplicative model. Combined risk scores were calculated by multiplying Gail risk estimates by the SNP risk scores. The independence of Gail risk and SNP risk was evaluated by logistic regression. Calibration of relative risks was evaluated using the Hosmer–Lemeshow test. The performance of the combined risk scores was evaluated using receiver operating characteristic curves. The net reclassification improvement (NRI) was used to assess improvement in classification of women into low (<1.5%), intermediate (1.5%–2%), and high (>2%) categories of 5-year risk. All tests of statistical significance were two-sided. Results The SNP risk score was nearly independent of Gail risk. There was good agreement between predicted and observed SNP relative risks. In the analysis for receiver operating characteristic curves, the combined risk score was more discriminating, with area under the curve of 0.594 compared with area under the curve of 0.557 for Gail risk alone (P < .001). Classification also improved for 5.6% of case patients and 2.9% of control subjects, showing an NRI value of 0.085 (P = 1.0 × 10−5). Focusing on women with intermediate Gail risk resulted in an improved NRI of 0.195 (P = 8.6 × 10−5). Conclusions Combining validated common genetic risk factors with clinical risk factors resulted in modest improvement in classification of breast cancer risks in white non-Hispanic postmenopausal women. Classification performance was further improved by focusing on women at intermediate risk.
What kind of pronunciation variation is hard for triphones to model?

In order to help understand why gains in pronunciation modeling have proven so elusive, we investigated which kinds of pronunciation variation are well captured by triphone models, and which are not. We do this by examining the change in behavior of a recognizer as it receives further triphone training. We show that many of the kinds of variation which previous pronunciation models attempt to capture, including phone substitution or phone reduction, are in fact already well captured by triphones. Our analysis suggests new areas where future pronunciation models should focus, including syllable deletion.
An Analysis of Particle Swarm Optimization with Data Clustering-Technique for Optimization in Data Mining.

Data clustering is a popular approach for automatically finding classes, concepts, or groups of patterns. Clustering aims at representing large datasets by a fewer number of prototypes or clusters. It brings simplicity in modeling data and thus plays a central role in the process of knowledge discovery and data mining. Data mining tasks require fast and accurate partitioning of huge datasets, which may come with a variety of attributes or features. This imposes severe computational requirements on the relevant clustering techniques. A family of bio-inspired algorithms, well-known as Swarm Intelligence (SI) has recently emerged that meets these requirements and has successfully been applied to a number of real world clustering problems. This paper looks into the use of Particle Swarm Optimization for cluster analysis. The effectiveness of Fuzzy C-means clustering provides enhanced performance and maintains more diversity in the swarm and also allows the particles to be robust to trace the changing environment. KeywordsParticle Swarm Optimization (PSO), Fuzzy C-Means Clustering (FCM), Data Mining, Data Clustering .
Auxin biosynthesis: spatial regulation and adaptation to stress.

The plant hormone auxin is essential for plant growth and development, controlling both organ development and overall plant architecture. Auxin homeostasis is regulated by coordination of biosynthesis, transport, conjugation, sequestration/storage, and catabolism to optimize concentration-dependent growth responses and adaptive responses to temperature, water stress, herbivory and pathogens. At present, the best defined pathway of auxin biosynthesis is the TAA/YUC route, in which the tryptophan aminotransferases TAA and TAR and YUCCA flavin-dependent monooxygenases produce the auxin indole-3-acetic acid from tryptophan. This review highlights recent advances in our knowledge of TAA/YUC-dependent auxin biosynthesis focussing on membrane localisation of auxin biosynthetic enzymes, differential regulation in root and shoot tissue, and auxin biosynthesis during abiotic stress.
On-line compression of high precision printer images by evolvable hardware

This paper describes an image compression system based on evolvable hardware (EHW) for high precision printers (HPP). These printers are especially flexible for book publishing, but require large disk space for images, in particular those of higher resolution. To increase the printing speed and reduce the disk space, the images should be compressed. The system for this compression must be (1) adaptive, so that it changes depending on image characteristics and (2) on-line, which means implemented in hardware. The standard compression methods have a simple template change strategy which is not efficient for the images of HPP. We used an EHW system for compressing HPP images in real time. The EHW is a type of adaptive hardware which allows evolutionary algorithms to change the hardware configuration in real time. It works as fast as other compression systems (like the JBIG standard), but changes the image modeling to reflect the changes in the image characteristics. Simulation results show more than a 50% increase in compression ratio compared to JBIG for the printer system.
RNA secondary structure diagrams for very large molecules: RNAfdl

SUMMARY There are many programs that can read the secondary structure of an RNA molecule and draw a diagram, but hardly any that can cope with 10(3) bases. RNAfdl is slow but capable of producing intersection-free diagrams for ribosome-sized structures, has a graphical user interface for adjustments and produces output in common formats. AVAILABILITY AND IMPLEMENTATION Source code is available under the GNU General Public License v3.0 at http://sourceforge.net/projects/rnafdl for Linux and similar systems or Windows using MinGW. RNAfdl is implemented in C, uses the Cairo 2D graphics library and offers both command line and graphical user interfaces. CONTACT hecker@rth.dk
Motor-gearbox selection for energy efficiency

Energy consumption of robotic systems is getting more and more attention. Previous work suggests that energy losses in the actuators of robots are a significant source of high energy consumption. A possible reason is that, so far, motor-gearbox selection methods have not focussed on energy efficiency. In this work, we present a model-based motor-gearbox selection procedure with the focus on key mechanisms of energy dissipation. Using an example, we evaluate the possible efficiency gains when selecting a motor-gearbox combination for energy efficiency. In this example, the losses are reduced by 56% to 40%. We conclude that selecting a motor-gearbox combination for energy efficiency can provide a significant improvement in the efficiency. However, the energy losses in the motor-gearbox combination remain significant.
7.6 Modeling Measles Outbreaks

Epidemiology is one of the areas in biology to which mathematical modeling has been applied most successfully. It was through the mathematical concept of basic reproductive number that Ronald Ross gained the insight that malaria could be controlled if the mosquito population was sufficiently suppressed (Heesterbeek 2002). Later, similar concepts were applied to the eradication of smallpox and the control of many viral diseases through vaccination campaigns (Anderson and May 1991). To date, mathematical models remain an important tool. Epidemiology studies the distribution of a disease within a host population. Most models used for infectious diseases are based on partitioning the host population into different classes that correspond to the different stages of the infectious process (e.g., susceptible, infectious, and recovered) and the transitions between these classes. Such models work particularly well for diseases caused by micropar-asites, a class of pathogens that comprises viruses and bacteria and that are characterized by an infection normally accomplished with a single dose that consists of a relatively small number of infective particles (Anderson and May 1991). Mathematical epidemiology has concentrated on cases for which the disease is endemic or in which large epidemics occur. In this context the reproductive number is an important parameter. It is defined as the average number of secondary infections caused by an infected host over the lifetime of the infection. In a completely susceptible population, this number is known as the basic reproductive number, R 0. If the reproductive number is larger than one, a single infection can lead to a chain reaction of infections and, eventually, to an epidemic or an endemic state. If the reproductive number is smaller than one, large epidemics do not occur and the pathogen is bound to disappear from the population. If the basic reproductive number is less than one, the numbers of infected individuals hardly ever become truly large and stochastic effects prevail. If this is the case the disease manifests itself in the form of outbreaks that follow the introduction of the disease into the population. The size and duration of an outbreak can vary enormously through chance events. To capture these dynamics a stochas-tic formalism is needed. In this section we illustrate how the theory of branching processes can be used to describe the epidemiology of pathogens with a reproductive number smaller than one, using the epidemiology of measles as an example. We use this to explain the distribution …
Does eating family meals and having the television on during dinner correlate with overweight? A sub-study of the PRO GREENS project, looking at children from nine European countries

Abstract Objective Family meals have been negatively associated with overweight in children, while television (TV) viewing during meals has been associated with a poorer diet. The aim of the present study was to assess the association of eating family breakfast and dinner, and having a TV on during dinner, with overweight in nine European countries and whether these associations differed between Northern and Southern & Eastern Europe. Design Cross-sectional data. Schoolchildren reported family meals and TV viewing. BMI was based on parental reports on height and weight of their children. Cut-off points for overweight by the International Obesity Task Force were used. Logistic regressions were performed adjusted by age, gender and parental education. Setting Schools in Northern European (Sweden, the Netherlands, Iceland, Germany and Finland) and Southern & Eastern European (Portugal, Greece, Bulgaria and Slovenia) countries, participating in the PRO GREENS project. Subjects Children aged 10–12 years in (n 6316). Results In the sample, 21 % of the children were overweight, from 35 % in Greece to 10 % in the Netherlands. Only a few associations were found between family meals and TV viewing during dinner with overweight in the nine countries. Northern European children, compared with other regions, were significantly more likely to be overweight if they had fewer family breakfasts and more often viewed TV during dinner. Conclusions The associations between family meals and TV viewing during dinner with overweight were few and showed significance only in Northern Europe. Differences in foods consumed during family meals and in health-related lifestyles between Northern and Southern & Eastern Europe may explain these discrepancies.
Algebraic realization of supersymmetric quantum mechanics for cyclic shape invariant potentials

We study in detail the spectrum of the bosonic oscillator Hamiltonian associated with the C 3-extended oscillator algebra A α0α1 (3), where C 3 denotes a cyclic group of order three, and classify the various types of spectra in terms of the algebra parameters α 0, α 1. In such a classification, we identify those spectra having an infinite number of periodically spaced levels, similar to those of cyclic shape invariant potentials of period three. We prove that the hierarchy of supersymmetric Hamiltonians and supercharges, corresponding to the latter, can be realized in terms of some appropriately chosen A α0α1 (3) algebras, and of Pauli spin matrices. Extension to period-λ spectra in terms of C λ-extcnded oscillator algebras is outlined. © Birkhauser Verlag, 1999.
High-Precision Five-Axis Machine for High-Speed Material Processing Using Linear Motors and Parallel-Serial Kinematics

The paper describes some details of the mechanical and kinematics design of a five-axis mechanism. The design has been utilized to physically realize an industrial-scale five-axis milling machine that can carry a three KW spindle. However, the mechanism could be utilized in other material processing and factory automation applications. The mechanism has five rectilinear joints/axes. Two of these axes are arranged traditionally, i.e. in series, and the other three axes utilize the concept of parallel kinematics. This combination results in a design that allows three translational and two rotational two-mode degrees of freedom (DOFs). The design provides speed, accuracy and cost advantages over traditional five-axis machines. All axes are actuated using linear motors.
Direct Cell Adhesion to the Angiopoietins Mediated by Integrins*

Genetic ablation of angiopoietin-1 (Ang-1) or of its cognate receptor, Tie2, disrupts angiogenesis in mouse embryos. The endothelial cells in growing blood vessels of Ang-1 knockout mice have a rounded appearance and are poorly associated with one another and their underlying basement membranes (Dumont, D. J., Gradwohl, G., Fong, G. H., Puri, M. C., Gertsenstein, M., Auerbach, A., and Breitman, M. L. (1994) Genes Dev. 8, 1897–1909; Sato, T. N. , Tozawa, Y. , Deutsch, U. , Wolburg-Buchholz, K. , Fujiwara, Y. , Gendron-Maguire, M. , Gridley, T. , Wolburg, H. , Risau, W. , and Qin, Y. (1995) Nature 376, 70–74; Suri, C. , Jones, P. F. , Patan, S. , Bartunkova, S. , Maisonpierre, P. C. , Davis, S. , Sato, T. N. , and Yancopoulos, G. D. (1996) Cell 87, 1171–1180). It is therefore possible that Ang-1 regulates endothelial cell adhesion. In this study we asked whether Ang-1 might act as a direct substrate for cell adhesion. Human umbilical vein endothelial cells (HUVECs) plated for a brief period on different substrates were found to adhere and spread well on Ang-1. Similar results were seen on angiopoietin-2 (Ang-2)-coated surfaces, although cells did not spread well on Ang-2. Ang-1, but not Ang-2, supported HUVEC migration, and this was independent of growth factor activity. When the same experiments were done with fibroblasts that either lacked, or stably expressed, Tie2, results similar to those with HUVECs were seen, suggesting that adhesion to the angiopoietins was independent of Tie2 and not limited to endothelial cells. Interestingly, when integrin-blocking agents were included in these assays, adhesion to either angiopoietin was significantly reduced. Moreover, Chinese hamster ovary-B2 cells lacking the α5 integrin subunit did not adhere to Ang-1, but they did adhere to Ang-2. Stable expression of the human α5 integrin subunit in these cells rescued adhesion to Ang-1 and promoted an increase in adhesion to Ang-2. We also found that Ang-1 and Ang-2 bind rather selectively to vitronectin. These results suggest that, beyond their role in modulating Tie2 signaling, Ang-1 and Ang-2 can directly support cell adhesion mediated by integrins.
Melanocytes—A Novel Tool to Study Mitochondrial Dysfunction in Duchenne Muscular Dystrophy

Dystrophin is a subsarcolemmal protein that, by linking the actin cytoskeleton to the extracellular matrix via dystroglycans, is critical for the integrity of muscle fibers. Here, we report that epidermal melanocytes, obtained from conventional skin biopsy, express dystrophin with a restricted localization to the plasma membrane facing the dermal–epidermal junction. In addition the full‐length muscle isoform mDp427 was clearly detectable in melanocyte cultures as assessed by immunohistochemistry, RNA, and Western blot analysis. Melanocytes of Duchenne muscular dystrophy (DMD) patients did not express dystrophin, and the ultrastructural analysis revealed typical mitochondrial alterations similar to those occurring in myoblasts from the same patients. Mitochondria of melanocytes from DMD patients readily accumulated tetramethylrhodamine methyl ester, indicating that they are energized irrespective of the presence of dystrophin but, at variance from mitochondria of control donors, depolarized upon the addition of oligomycin, suggesting that they are affected by a latent dysfunction unmasked by inhibition of the ATP synthase. Pure melanocyte cultures can be readily obtained by conventional skin biopsies and may be a feasible and reliable tool alternative to muscle biopsy for functional studies in dystrophinopathies. The mitochondrial dysfunction occurring in DMD melanocytes could represent a promising cellular biomarker for monitoring dystrophinopathies also in response to pharmacological treatments. J. Cell. Physiol. 228: 1323–1331, 2013. © 2012 Wiley Periodicals, Inc.
RAAS: a reliable analyzer and archiver for snort intrusion detection system

One of the primary challenges in IDS alerts analysis is controlling and archiving the huge amount of alerts that have been triggered mainly in attack periods. We have developed a self-adaptive controlling mechanism which archives the Snort generated alerts in a well-formed abstracted format. An appropriate hashing technique along with a full-automated time-based hierarchical archiving approach has been used to reach this end. The developed system prevents the Snort database size to grow uncontrollably and unexpectedly. Results obtained from experiments and test cases show that especially in critical attack situations the system responds to queries well in a reasonable amount of time. The developed analyzer with new archiving approach is also able to compress the generated alerts effectively and generate statistical reports fast. The developed system is platform independent and can be deployed on mid-range servers and workstations. Also employing it does not require much degree of security expertise.
Euler spring collision protection for flying robots

This paper addresses the problem of adequately protecting flying robots from damage resulting from collisions that may occur when exploring constrained and cluttered environments. A method for designing protective structures to meet the specific constraints of flying systems is presented and applied to the protection of a small coaxial hovering platform. Protective structures in the form of Euler springs in a tetrahedral configuration are designed and optimised to elastically absorb the energy of an impact while simultaneously minimizing the forces acting on the robot's stiff inner frame. These protective structures are integrated into a 282 g hovering platform and shown to consistently withstand dozens of collisions undamaged.