Miracle-dz/UniFAR-FTUs huggingface dataset:
Position Statement the Authors Our Research on Semantic Integration

where he was involved in the Advanced Knowledge Technologies project, a multi-million pound, six-year collaboration between internationally recognised research groups at five UK universities. Schorlemmer is mainly interested in applying mathematical techniques from theoretical computer science to challenging engineering problems faced by software and knowledge engineers today. In particular, he has been using techniques from category theory and information-flow theory to automate the semantic mapping of ontologies. He has also published over 20 papers in journals and international workshop and conference proceedings in the fields of Formal Specification & Automated is focusing on ontologies, in particular ontology-based services in a variety of application areas. He has researched extensively the intersection of software and knowledge engineering with emphasis on intelligent support for the early stages of software design when working with knowledge models. He has published over 30 papers on this and similar subjects and recently his focus is on ontology mapping and merging technologies. He is an active member of the EU funded OntoWeb & KnowledgeWeb thematic networks of excellence where he is working on industry-strength ontology tools and environments. Our approach draws heavily on proven theoretical work but our work goes further in providing a systematic approach for ontology mapping with precise methodological steps. In particular, our method, Information-Flow based Ontology Mapping (IF-Map) [2], draws on the proven theoretical ground of Information Flow and channel theory [1], and provides a systematic and mechanised way for deploying the approach in a distributed environment to perform ontology mapping among a variety of different ontologies. The IF-Map system formalises mappings of ontology constructs in terms of logic infomorphisms, the fundamental ingredient of Information Flow. These are well suited for representing the bi-directional relation of types and tokens, which corresponds to concepts and instances in the ontology realm. IF-Map is focusing on instances and how these are classified against ontology concepts. This reveals the operational semantics that the ontology's community has chosen by virtue of how it uses its instances. The IF-Map algorithm makes use of this information in order to map onto related concepts from another ontology with which its concepts classify the same instances. We have used IF-Map with success in a variety of ontology mapping scenarios within and outside AKT such as mapping of computer science departments' ontologies from AKT participating universities [3]; mapping of e-government ontologies from a case study using UK and US governments ministries [6]. We have …
Mapping problem-space to solution-space features: a feature interaction approach

Mapping problem-space features into solution-space features is a fundamental configuration problem in software product line engineering. A configuration problem is defined as generating the most optimal combination of software features given a requirements specification and given a set of configuration rules. Current approaches however provide little support for expressing complex configuration rules between problem and solution space that support incomplete requirements specifications. In this paper, we propose an approach to model complex configuration rules based on a generalization of the concept of problem-solution feature interactions. These are interactions between solution-space features that only arise in specific problem contexts. The use of an existing tool to support our approach is also discussed: we use the DLV answer set solver to express a particular configuration problem as a logic program whose answer set corresponds to the optimal combinations of solution-space features. We motivate and illustrate our approach with a case study in the field of managing dynamic adaptations in distributed software, where the goal is to generate an optimal protocol for accommodating a given adaptation.
Effects of Na(+) and K(+) channel blockade on vulnerability to and termination of fibrillation in simulated normal cardiac tissue.

Na(+) and K(+) channel-blocking drugs have anti- and proarrhythmic effects. Their effects during fibrillation, however, remain poorly understood. We used computer simulation of a two-dimensional (2-D) structurally normal tissue model with phase I of the Luo-Rudy action potential model to study the effects of Na(+) and K(+) channel blockade on vulnerability to and termination of reentry in simulated multiple-wavelet and mother rotor fibrillation. Our main findings are as follows: 1) Na(+) channel blockade decreased, whereas K(+) channel blockade increased, the vulnerable window of reentry in heterogeneous 2-D tissue because of opposing effects on dynamical wave instability. 2) Na(+) channel blockade increased the cycle length of reentry more than it increased refractoriness. In multiple-wavelet fibrillation, Na(+) channel blockade first increased and then decreased the average duration or transient time () of fibrillation. In mother rotor fibrillation, Na(+) channel blockade caused peripheral fibrillatory conduction block to resolve and the mother rotor to drift, leading to self-termination or sustained tachycardia. 3) K(+) channel blockade increased dynamical instability by steepening action potential duration restitution. In multiple-wavelet fibrillation, this effect shortened because of enhanced wave instability. In mother rotor fibrillation, this effect converted mother rotor fibrillation to multiple-wavelet fibrillation, which then could self-terminate. Our findings help illuminate, from a theoretical perspective, the possible underlying mechanisms of termination of different types of fibrillation by antiarrhythmic drugs.
MOSFET dosimetry for radiotherapy interface measurements

An n-channel Metal Oxide Semiconductor Field Effect Transistor (MOSFET) was used to investigate the dose distribution near interfaces. The MOSFETs were irradiated in 5x5cm and 10x1 Ocm radiation field from 6MV x-rays and 12MeV electron beams from a Varian 2100c linear accelerator. The dosimeters were operated in an active mode, biased gate, during irradiation. Two different air cavity geometries were modelled using solid water sheets. An Attix chamber and sheets of Gafchromic films were used to measure the dose near and at the interfaces. Results from obtained by these detectors were used as benchmarks for data comparison. Additionally the results from an ADAC-Pinnacle dose planning system and EGS4 Monte Carlo simulation of the dose build up and build down effects for tissue-air-tissue and tissue-lung interfaces have been simulated. Dose measurements for tissue-lung interface were carried out using an anthropomorphic phantom made from plastic water and inserts of lung phantom material. Depth increments of as small as 100pm enabled the detailed measurement of dose at the interfaces by utilising the MOSFET dosimeter. In all cases, the effects of the loss of electronic equilibrium and the reduced backscatter due to the existence of inhomogeneities were shown. Interface dose distributions obtained by the MOSFET dosimeters were within 5% to 6% of the results of the Attix chamber measurements and Monte CarloEGS4 simulation results. Comparison with the dose distributions near interfaces generated by the ADAC-Pinnacle planning computer system and those experimentally measured showed that it overestimates the dose near the interface (<2mm from interface) by around 7% for small cavity sizes (2x2x30cm) irradiated with 5x5cm~ field size and about 12% for a larger cavity sizes (2x20x30cm') using the same field size. Present inhomogeneity correction algorithms have been found to predict dose distributions where tissue-lung interface is involved to a reasonable accuracy (3%) compared with experimental results. The good agreement between the data obtained by the MOSFET with that of Attix chamber, Radiochromic film and Monte-Carlo EGS4 simulated data indicated the viability of its use as a clinical dosimeter for interface dose measurements. CHAPTER
Sorting out typicality with the inverse moment matrix SOS polynomial

We study a surprising phenomenon related to the representation of a cloud of data points using polynomials. We start with the previously unnoticed empirical observation that, given a collection (a cloud) of data points, the sublevel sets of a certain distinguished polynomial capture the shape of the cloud very accurately. This distinguished polynomial is a sum-of-squares (SOS) derived in a simple manner from the inverse of the empirical moment matrix. In fact, this SOS polynomial is directly related to orthogonal polynomials and the Christoffel function. This allows to generalize and interpret extremality properties of orthogonal polynomials and to provide a mathematical rationale for the observed phenomenon. Among diverse potential applications, we illustrate the relevance of our results on a network intrusion detection task for which we obtain performances similar to existing dedicated methods reported in the literature.
On the Capacity of Point-to-Point and Multiple-Access Molecular Communications With Ligand-Receptors

In this paper, we consider bacterial point-to-point and multiple-access molecular communications with ligand-receptors. For point-to-point communication, we investigate common signaling methods, namely, the level scenario, in which the information is encoded into multiple concentration levels of a single molecule type, and the type scenario, in which the information bits are encoded in multiple molecule types each with a single concentration level. We investigate the tradeoffs in the two scenarios in terms of the capacity. We derive an upper bound on the capacity using a Binomial channel model and the symmetrized Kullback-Leibler divergence. A lower bound is also derived when the environmental noise is negligible. We also consider the blocking effect of a receptor by a different molecule type. Finally, we study multiple-access communications, for which we investigate three scenarios based on molecule and receptor types: 1) same molecule types with different labeling and the same receptor types; 2) different molecule types with different receptor types; and 3) the same molecule types with the same receptor types. We investigate the tradeoffs in the three scenarios in terms of the total capacity. We derive inner bounds on the capacity region of these scenarios when the environmental noise is negligible.
Examining the Viability of FPGA Supercomputing

For certain applications, custom computational hardware created using field programmable gate arrays (FPGAs) can produce significant performance improvements over processors, leading some in academia and industry to call for the inclusion of FPGAs in supercomputing clusters. This paper presents a comparative analysis of FPGAs and traditional processors, focusing on floating-point performance and procurement costs, revealing economic hurdles in the adoption of FPGAs for general high-performance computing (HPC).
Glutathione Transferases Responses Induced by Microcystin-LR in the Gills and Hepatopancreas of the Clam Venerupis philippinarum

A multi-method approach was employed to compare the responses of Glutatione Transferases (GSTs) in the gills and hepatopancreas of Venerupis philippinarum to microcystins (MCs) toxicity. In this way, using the cytosolic fraction, the enzymatic activity of GSTs, superoxide dismutase (SOD), serine/threonine protein phosphatases (PPP2) along with the gene expression levels of four GST isoforms (pi, mu, sigma1, sigma2) were investigated in both organs of the clams exposed for 24 h to 10, 50 and 100 μg L−1 of MC-LR. Cytosolic GSTs (cGSTs) from both organs of the high dose exposed clams were purified by glutathione-agarose affinity chromatography, characterized kinetically and the changes in the expression of cGSTs of the gills identified using a proteomic approach. MC-LR caused an increase in GST enzyme activity, involved in conjugation reactions, in both gills and hepatopancreas (100 μg L−1 exposure). SOD activity, an indicator of oxidative stress, showed significantly elevated levels in the hepatopancreas only (50 and 100 μg L−1 exposure). No significant changes were found in PPP2 activity, the main target of MCs, for both organs. Transcription responses revealed an up-regulation of sigma2 in the hepatopancreas at the high dose, but no significant changes were detected in the gills. Kinetic analysis evidenced differences between gills of exposed and non-exposed extracts. Using proteomics, qualitative and quantitative differences were found between the basal and inducible cGSTs. Overall, results suggest a distinct role of GST system in counteracting MCs toxicity between the gills and the hepatopancreas of V. philippinarum, revealing different roles between GST isoforms within and among both organs.
Systems Biology: A Brief Overview

To understand biology at the system level, we must examine the structure and dynamics of cellular and organismal function, rather than the characteristics of isolated parts of a cell or organism. Properties of systems, such as robustness, emerge as central issues, and understanding these properties may have an impact on the future of medicine. However, many breakthroughs in experimental devices, advanced software, and analytical methods are required before the achievements of systems biology can live up to their much-touted potential.
Percutaneous nephrolithotomy: is distilled water as safe as saline for irrigation?

PURPOSE To compare dilutional effect of distilled water with saline solution as an irrigation fluid in percutaneous nephrolithotomy (PCNL). MATERIALS AND METHODS Three hundred twenty eight adult patients (191 men, 137 women) who were candidates for PCNL were randomly assigned into two groups (distilled water, n = 158, group 1; saline solution, n = 162, group 2). Stone size, operation time, irrigation fluid volume, blood hemoglobin level, urea nitrogen, creatinine, sodium and potassium levels were checked before and at 6 and 12 hours after operation. RESULTS The mean age of the patients was 37.8 years, and the mean stone diameter was 31.5 mm. There was no clinical case of transurethral resection (TUR) syndrome. Serum sodium depletion was significantly more in group 1 than group 2 (P < .0001). Group 1 had significant decreased post-operative serum sodium levels (P < .0003). Similarly in group 2, postoperative serum sodium levels were significantly lower than the preoperative concentration (P < .01), but it was not the same 6 hours after the operation (P = .23). Serum sodium concentrations remained within normal limits in all cases, without causing clinical signs and symptoms of hyponatremia. CONCLUSION We found that distilled water is safe irrigation fluid for PCNL in adults. In addition, it is more available and cost effective.
Detection of novel tandem duplication with next-generation sequencing

Detection of structural variations is an important problem. With the next generation sequencing technology, it is relatively easier to obtain a set of paired-end short reads from an individual (the donor). By aligning these reads onto a reference genome (the reference), we are able to detect some of the structural variations that exist between the donor and the reference. A number of tools were developed in this direction. However, these tools are not able to detect all types of variations. In particular, they do not perform well for the detection of tandem duplications which are found to be associated with some diseases. In this paper, we try to solve this problem and developed algorithm to identify novel tandem duplications that exist in donor and vice versa. Experimental results on both simulated and real datasets showed that our solutions are effective.
Data De-duplication for Primary Storage System

Data De-duplication has being used comprehensively within Disk-based Backups, Archives and Disaster Recovery. This technology's high data reduction ratio and satisfied performance in secondary data storage system has aroused huge interests in other fields. The primary storage system is indeed a field being long for data reduction. Data de-duplication maybe a chance to alleviate data redundancy problem within that field. Actually, there are still lots of problems and technology challenges in resolving the contradiction between strict performance requirements in the primary storage system and the resources consuming character of the data de-duplication. This article will give an introduction about those technology challenges and propose a new data storage framework trying to improve those problems.
Transsulfuration, protein synthesis rate and follicle mRNA in the skin of young Merino lambs in response to infusions of methionine and serine

Methionine (Met) is usually the first limiting amino acid for sheep and supplements of Met may increase production of wool and meat. The wool response may be due to an increased supply of cysteine (Cys) from transsulfuration (TS) of Met. Met is catabolized through homocysteine to form Cys when the S from Met is transferred to serine (Ser). We hypothesized that providing additional Met would create a deficiency of Ser and that by simultaneously providing Met and Ser, TS and wool growth could be increased more than by providing Met alone. The effects of i.v. infusions of Met and Ser to young Merino lambs on TS, fractional synthesis rate (FSR) of protein in skin, follicle mRNA and wool growth were examined. Following 4 d of constant i.v. infusion of 3 g Met/d, or 10 g Ser/d or both, the isotope tracers: L-[3-13C]CYS, l-[ring-d5]phenylalanine (Phe) and l-[2,3,3-d3]Ser were infused over 8 h to allow for measurements of irreversible loss rate (ILR), and TS in whole body and skin. Skin biopsies were taken for measurement of FSR. Wool growth rate was measured using autoradiography. An infusion of Met significantly (P < 0·05) improved wool growth rate and increased skin FSR, Cys supply from TS and enhanced levels of follicle mRNA (from the K2.10 intermediate filament gene and three gene families encoding keratin associated proteins KAP1, KAP4 and KAP12). The extra Met lowered Ser ILR. The infusion of Ser doubled Ser ILR in the body and increased skin FSR calculated using the Cys tracer in plasma (P < 0·05). However, there were no significant (P > 0·05) changes in TS, skin FSR calculated using the Phe and Ser tracers, follicle mRNA or wool growth rate as a result of Ser infusion. While there were trends towards increased TS and FSR with Ser infusion, the overall lack of significant changes indicates a high capacity for the de novo synthesis of Ser.
α‐Synuclein abnormalities in mouse models of peroxisome biogenesis disorders

α‐Synuclein (αS) is a presynaptic protein implicated in Parkinson's disease (PD). Growing evidence implicates mitochondrial dysfunction, oxidative stress, and αS–lipid interactions in the gradual accumulation of αS in pathogenic forms and its deposition in Lewy bodies, the pathological hallmark of PD and related synucleinopathies. The peroxisomal biogenesis disorders (PBD), with Zellweger syndrome serving as the prototype of this group, are characterized by malformed and functionally impaired peroxisomes. Here we utilized the PBD mouse models Pex2–/–, Pex5–/–, and Pex13–/– to study the potential effects of peroxisomal dysfunction on αS‐related pathogenesis. We found increased αS oligomerization and phosphorylation and its increased deposition in cytoplasmic inclusions in these PBD mouse models. Furthermore, we show that αS abnormalities correlate with the altered lipid metabolism and, specifically, with accumulation of long chain, n‐6 polyunsaturated fatty acids that occurs in the PBD models. © 2009 Wiley‐Liss, Inc.
MPF-FDTD Simulations of Fabrication and Optical Analysis of Ordered Gold Nano-Dots Array

Recently, the authors have proposed a hybrid fabrication method of an ordered gold nano-dots array using a combination of the nano plastic forming and thermal annealing. In this study, in order to investigate morphology and optical properties of the gold nano-dots array fabricated by the proposed method, we develop a coupled three-dimensional simulation model by using the multi-phase-field method and the finite-difference-time-domain method. The simulation results demonstrate that the ordered gold nano-dots array which can be obtained by the proposed method exhibits quite characteristic optical responses due to the localized surface plasmon resonance.
INHALATION EXPOSURE TO CARBON NANOTUBES (CNT) AND CARBON NANOFIBERS (CNF): METHODOLOGY AND DOSIMETRY

Dedicated to Professor Paul Morrow, 1922–2013 In respectful and fond memory of a devoted scientist, inspirational colleague, caring mentor, selfless friend, and in gratitude for his lasting groundbreaking contributions to inhalation toxicology Carbon nanotubes (CNT) and nanofibers (CNF) are used increasingly in a broad array of commercial products. Given current understandings, the most significant life-cycle exposures to CNT/CNF occur from inhalation when they become airborne at different stages of their life cycle, including workplace, use, and disposal. Increasing awareness of the importance of physicochemical properties as determinants of toxicity of CNT/CNF and existing difficulties in interpreting results of mostly acute rodent inhalation studies to date necessitate a reexamination of standardized inhalation testing guidelines. The current literature on pulmonary exposure to CNT/CNF and associated effects is summarized; recommendations and conclusions are provided that address test guideline modifications for rodent inhalation studies that will improve dosimetric extrapolation modeling for hazard and risk characterization based on the analysis of exposure-dose-response relationships. Several physicochemical parameters for CNT/CNF, including shape, state of agglomeration/aggregation, surface properties, impurities, and density, influence toxicity. This requires an evaluation of the correlation between structure and pulmonary responses. Inhalation, using whole-body exposures of rodents, is recommended for acute to chronic pulmonary exposure studies. Dry powder generator methods for producing CNT/CNF aerosols are preferred, and specific instrumentation to measure mass, particle size and number distribution, and morphology in the exposure chambers are identified. Methods are discussed for establishing experimental exposure concentrations that correlate with realistic human exposures, such that unrealistically high experimental concentrations need to be identified that induce effects under mechanisms that are not relevant for workplace exposures. Recommendations for anchoring data to results seen for positive and negative benchmark materials are included, as well as periods for postexposure observation. A minimum data set of specific bronchoalveolar lavage parameters is recommended. Retained lung burden data need to be gathered such that exposure-dose-response correlations may be analyzed and potency comparisons between materials and mammalian species are obtained considering dose metric parameters for interpretation of results. Finally, a list of research needs is presented to fill data gaps for further improving design, analysis, and interpretation and extrapolation of results of rodent inhalation studies to refine meaningful risk assessments for humans.