Miracle-dz/UniFAR-FTUs huggingface dataset:
Potential Anti-Inflammatory Effects of the Hydrophilic Fraction of Pomegranate (Punica granatum L.) Seed Oil on Breast Cancer Cell Lines

In this work, we characterized conjugated linolenic acids (e.g., punicic acid) as the major components of the hydrophilic fraction (80% aqueous methanol extract) from pomegranate (Punica granatum L.) seed oil (PSO) and evaluated their anti-inflammatory potential on some human colon (HT29 and HCT116), liver (HepG2 and Huh7), breast (MCF-7 and MDA-MB-231) and prostate (DU145) cancer lines. Our results demonstrated that punicic acid and its congeners induce a significant decrease of cell viability for two breast cell lines with a related increase of the cell cycle G0/G1 phase respect to untreated cells. Moreover, the evaluation of a great panel of cytokines expressed by MCF-7 and MDA-MB-231 cells showed that the levels of VEGF and nine pro-inflammatory cytokines (IL-2, IL-6, IL-12, IL-17, IP-10, MIP-1α, MIP-1β, MCP-1 and TNF-α) decreased in a dose dependent way with increasing amounts of the hydrophilic extracts of PSO, supporting the evidence of an anti-inflammatory effect. Taken together, the data herein suggest a potential synergistic cytotoxic, anti-inflammatory and anti-oxidant role of the polar compounds from PSO.
Flexible experimentation in the modeling and simulation framework JAMES II - implications for computational systems biology

Dry-lab experimentation is being increasingly used to complement wet-lab experimentation. However, conducting dry-lab experiments is a challenging endeavor that requires the combination of diverse techniques. JAMES II, a plug-in-based open source modeling and simulation framework, facilitates the exploitation and configuration of these techniques. The different aspects that form an experiment are made explicit to facilitate repeatability and reuse. Each of those influences the performance and the quality of the simulation experiment. Common experimentation pitfalls and current challenges are discussed along the way.
A model for fibre washout during high injection pressure resin transfer moulding

High injection pressure resin transfer moulding is a variant of resin transfer moulding in which the preform is compressed in a tool and resin is injected into the mould under very high pressure. The high injection pressure (>20 bar) introduces possible fibre washout that translates into manufacturing defects or causes inconsistencies in processing and leads to scatter in mechanical properties of composite parts. A model is presented which quantifies and provides insight into the influence of process variables such as clamping force and injection pressure on fibre washout distance (the one-dimensional model assumes a rigid preform). A generalised one-dimensional stress model for fibre washout is presented for regions that are impregnated with the resin and the regions that are dry. The model shows fibre washout to be significant at the beginning of the injection process. The model allows one to further refine the injection strategy by adjusting injection pressure to account for washout in high injection pressure resin transfer moulding.
Have a Little Patience: Let Planners Play Cards

As every card player knows, most existing card games share a large number of actions and situations. This is the case, for instance, for stacking cards in columns according to some allowed sequence or taking cards from a deal. This is true for both multi-player and solitaire patience games. Although they have such strong similarities, every game also has some peculiarity making it different, and affecting its complexity and –at the end of the day– its enjoyability. Interestingly, from an AI planning perspective, most of the differences emerge from the problem description: domain models tend to be very similar because of the similar actions that can be
Enhanced Target Driven Smoke Morphing

Target driven smoke morphings are processes, based on the simulation of smoke dynamics, which are so flexible that we are induced to believe that they can produce a continuous transformation of any 2D object into any other. Here they are considered with respect to the ability of reproducing targets of more complex geometry or topology, assuming that the process starts at a generic 2D object. Alternatives for several limitations are proposed to make it possible to cope with fine dents, cavities or holes and to obtain the same brightness in all components of a non-connected target object. The original approach uses a diffusion process to define a field that pulls smoke towards the target. Here that field is replaced by one, depending on a distance transform, which is computationally simpler and helps to deal with peculiarities of the objects. The finalization of the morphing process is also focused with the objective of eliminating oscillations and flickering.
Novel techniques in the scanning electron microscope for characterising polymer-based photovoltaic materials

In this thesis, a range of new techniques are developed in the scanning electron microscope (SEM) for investigating and imaging the nanoscale morphology of polymer:fullerene blends with organic photovoltaic (OPV) applications. The primary focus of these techniques is energy-selective detection of secondary electrons (SE) emitted in the SEM, applied both to measure the energy spectrum of a sample’s SE emissions, and for high-resolution energy-filtered SEM (EFSEM) imaging with improved material contrast. The SE energy-filtering performance of a FEI Sirion SEM is evaluated, and the SE spectrum of P3HT, a popular polymer for OPV, is measured and found to demonstrate a range of spectral features. These features are believed to reflect molecular ordering in the polymer. It is also found that degradation of the P3HT film under air and light alters the SE spectrum of the sample. Based upon SE spectroscopy methods, energy-filtered SE images are then applied to image the phase-separated morphology of a P3HT:PC60BM film with increased material contrast. EFSEM images of the blend film surface are found capable of mapping the blend morphology with a lateral resolution of (0.8 ± 0.1) nm, and demonstrate approximately double the material contrast in conventional SEM images. This improved contrast allows for the direct identification of mixed phase material in the image data, a first for this particular blend system. In P3HT:PC60BM films processed for optimal performance, (25 ± 5) % of the imaged phase area is classified as mixed phase by the technique. A further imaging technique is developed using low-energy backscattered electrons (BSE) in the SEM to probe the 3-dimensional morphology of the polymer:fullerene film as well as the surface. The technique is used to compare reference P3HT:PC60BM blends with a modern, high-performance PffBT4T-2OD:PC70BM blend film. At the surface, correlation between the phase size of fullerene domains in both blend systems is found, with both films showing a most probable domain radius of 6 nm. Further, by carefully tuning the primary beam energy, BSE images are used to probe for ‘columnlike’ phases that penetrate a large fraction of the film’s thickness; a characteristic feature of optimised OPV blend morphologies. The subsurface characterisation of the two blend systems reveals the highly optimised morphology of the modern, high-performance system.
Token+constraint systems for tangible interaction with digital information

We identify and present a major interaction approach for tangible user interfaces based upon systems of tokens and constraints. In these interfaces, tokens are discrete physical objects which represent digital information. Constraints are confining regions that are mapped to digital operations. These are frequently embodied as structures that mechanically channel how tokens can be manipulated, often limiting their movement to a single degree of freedom. Placing and manipulating tokens within systems of constraints can be used to invoke and control a variety of computational interpretations.We discuss the properties of the token+constraint approach; consider strengths that distinguish them from other interface approaches; and illustrate the concept with eleven past and recent supporting systems. We present some of the conceptual background supporting these interfaces, and consider them in terms of Bellotti et al.'s [2002] five questions for sensing-based interaction. We believe this discussion supports token+constraint systems as a powerful and promising approach for sensing-based interaction.
Audio watermarking based on amplitude modulation and modulation masking

An audio watermarking system based on amplitude modulation (AM) is tested under the evaluation criteria proposed by the Information Hiding Criteria committee. Sinusoidal AMs at relatively low modulation frequencies, applied in opposite phase to neighboring subband signals, are used as the carrier of embedded information. The embedded information is encoded in the form of the relative phase differences between the AMs applied to several groups of subband signals. Results of computer simulation to test robustness and objective sound quality of stego audio showed that the quality degradation caused by the watermarking was tolerable and the detectability of the watermark under mandatory attack tests (DA/AD conversion and MP3 coding) and optional attack tests (bandpass filtering, tandem MP3 coding, MPEG4AAC coding) was sufficiently maintained.
Touring protein fold space with Dali/FSSP

The FSSP database and its new supplement, the Dali Domain Dictionary, present a continuously updated classification of all known 3D protein structures. The classification is derived using an automatic structure alignment program (Dali) for the all-against-all comparison of structures in the Protein Data Bank. From the resulting enumeration of structural neighbours (which form a surprisingly continuous distribution in fold space) we derive a discrete fold classification in three steps: (i) sequence-related families are covered by a representative set of protein chains; (ii) protein chains are decomposed into structural domains based on the recurrence of structural motifs; (iii) folds are defined as tight clusters of domains in fold space. The fold classification, domain definitions and test sets for sequence-structure alignment (threading) are accessible on the web at www.embl-ebi.ac. uk/dali . The web interface provides a rich network of links between neighbours in fold space, between domains and proteins, and between structures and sequences leading, for example, to a database of explicit multiple alignments of protein families in the twilight zone of sequence similarity. The Dali/FSSP organization of protein structures provides a map of the currently known regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination.
Shared-port register file architecture for low-energy VLIW processors

We propose a reduced-port Register File (RF) architecture for reducing RF energy in a VLIW processor. With port reduction, RF ports need to be shared among Function Units (FUs), which may lead to access conflicts, and thus, reduced performance. Our solution includes (i) a carefully designed RF-FU interconnection network that permits port sharing with minimum conflicts and without any delay/energy overheads, and (ii) a novel scheduling and binding algorithm that reduces the performance penalty. With our solution, we observed as much as 83% RF energy savings with no more than a 10% loss in performance for a set of Mediabench and Mibench benchmarks.
Dynamic performance analysis of 3-level integrated buck converters

A systematic analysis of 3-level integrated buck converters is conducted in this paper. Detailed derivations of the working principles, voltage conversion ratio and output voltage ripple are given. In particular, the system loop gain of 3-level buck converters is analyzed, which provides guidance on designing fast and robust 3-level converters. The derived loop gain is verified with time-domain small signal injection analysis. The results show a good match between analytical and simulation results.
Walking-in-Place for VR Navigation Independent of Gaze Direction Using a Waist-Worn Inertial Measurement Unit

Many techniques have been proposed for navigation using head-mounted-displays (HMDs) in virtual reality (VR). A walking-in-place (WIP) interface for virtual locomotion provides a high presence and an immersive experience in a virtual environment (VE). However, most of the WIP techniques can only navigate users in the direction of their gaze. Other WIP methods considering virtual locomotion direction have complex configurations or are only feasible when the tracking spaces are not limited. This paper proposes a WIP interface independent of gaze direction based on the data analysis of waist-mounted inertial sensors. Our method can navigate in the locomotion direction by calculating the orientation of the pelvis. We experimentally compared two WIP methods using a navigation task that required participants to periodically observe the surrounding VE: (1) Conventional WIP (gaze-based direction) (2) Proposed WIP (pelvis-based direction). While there was no difference in learnability or cybersickness between the two methods, the proposed method had shorter task time and higher efficiency.
Seed Scheduling for Peer-to-Peer Networks

The initial phase in a content distribution (filesharing) scenario is delicate due to the lack of global knowledge and the dynamics of the overlay. An unwise distribution of the pieces in this phase can cause delays in reaching steady state, thus increasing file download times. We devise a scheduling algorithm at the seed (source peer with full content), based on a proportional fair approach, and we implement it on a real file sharing client. In dynamic overlays, our solution improves by up to 25% the average downloading time of a standard protocol ala BitTorrent.
Assessing the Fecal Microbiota: An Optimized Ion Torrent 16S rRNA Gene-Based Analysis Protocol

Assessing the distribution of 16S rRNA gene sequences within a biological sample represents the current state-of-the-art for determination of human gut microbiota composition. Advances in dissecting the microbial biodiversity of this ecosystem have very much been dependent on the development of novel high-throughput DNA sequencing technologies, like the Ion Torrent. However, the precise representation of this bacterial community may be affected by the protocols used for DNA extraction as well as by the PCR primers employed in the amplification reaction. Here, we describe an optimized protocol for 16S rRNA gene-based profiling of the fecal microbiota.
What Do Kernel Density Estimators Optimize

Some linkages between kernel and penalty methods of density estimation are explored. It is recalled that classical Gaussian kernel density estimation can be viewed as the solution of the heat equation with initial condition given by data. We then observe that there is a direct relationship between the kernel method and a particular penalty method of density estimation. For this penalty method, solutions can be characterized as a weighted average of Gaussian kernel density estimates, the average taken with respect to the bandwidth parameter. A Laplace transform argument shows that this weighted average of Gaussian kernel estimates is equivalent to a fixed bandwidth kernel estimate using a Laplace kernel. Extensions to higher order kernels are considered and some connections to penalized likelihood density estimators are made in the concluding sections.
Scalability of findability: decentralized search and retrieval in large information networks

Amid the rapid growth of information today is the increasing challenge for people to survive and navigate its magnitude. Dynamics and heterogeneity of large information spaces such as the Web challenge information retrieval in these environments. Collection of information in advance and centralization of IR operations are hardly possible because systems are dynamic and information is distributed. While monolithic search systems continue to struggle with scalability problems of today, the future of search likely requires a decentralized architecture where many information systems can participate. As individual systems interconnect to form a global structure, finding relevant information in distributed environments transforms into a problem concerning not only information retrieval but also complex networks. Understanding network connectivity will provide guidance on how decentralized search and retrieval methods can function in these information spaces. The dissertation studies one aspect of scalability challenges facing classic information retrieval models and presents a decentralized, organic view of information systems pertaining to search in large scale networks. It focuses on the impact of network structure on search performance and investigates a phenomenon we refer to as the Clustering Paradox, in which the topology of interconnected systems imposes a scalability limit. Experiments involving large scale benchmark collections provide evidence on the Clustering Paradox in the IR context. In an increasingly large, distributed environment, decentralized searches for relevant information can continue to function well only when systems interconnect in certain ways. Relying on partial indexes of distributed systems, some level of network clustering enables very efficient and effective discovery of relevant information in large scale networks. Increasing or reducing network clustering degrades search performances. Given this specific level of network clustering, search time is well explained by a poly-logarithmic relation to network size, indicating a high scalability potential for searching in a continuously growing information space.
Emerging patterns in the comparative analysis of phylogenetic community structure

The analysis of the phylogenetic structure of communities can help reveal contemporary ecological interactions, as well as link community ecology with biogeography and the study of character evolution. The number of studies employing this broad approach has increased to the point where comparison of their results can now be used to highlight successes and deficiencies in the approach, and to detect emerging patterns in community organization. We review studies of the phylogenetic structure of communities of different major taxa and trophic levels, across different spatial and phylogenetic scales, and using different metrics and null models. Twenty‐three of 39 studies (59%) find evidence for phylogenetic clustering in contemporary communities, but terrestrial and/or plant systems are heavily over‐represented among published studies. Experimental investigations, although uncommon at present, hold promise for unravelling mechanisms underlying the phylogenetic community structure patterns observed in community surveys. We discuss the relationship between metrics of phylogenetic clustering and tree balance and explore the various emerging biases in taxonomy and pitfalls of scale. Finally, we look beyond one‐dimensional metrics of phylogenetic structure towards multivariate descriptors that better capture the variety of ecological behaviours likely to be exhibited in communities of species with hundreds of millions of years of independent evolution.
Visceral Leishmania tropica infection of BALB/c mice: cellular analysis of in vitro unresponsiveness to sheep erythrocytes

In mice, infection with Leishmania tropica initially produced a nonspecific enhancement of the immune response to sheep erythrocytes as measured both in vitro and in vivo. Subsequently, the spleen cell responses of susceptible mice (BALB/c) to sheep erythrocytes and T- and B-cell mitogens in vitro decreased dramatically, whereas those of the resistant strain (C57BL/6) returned to normal. Analysis of the spleen cells of infected animals revealed that macrophages (the target cells of Leishmania) were not defective. However, both T- and B-cell-depleted splenocyte populations of infected animals lacked the ability to respond in the presence of their corresponding B- and T-cell-depleted populations of normal spleen cells. It was also observed that the addition of various numbers of Leishmania organisms did not alter the response of normal spleen cells in vitro. The results of cocultures of various ratios of cells from the spleen of infected and normal animals ruled out the possibility of a strong active immunosuppression. The decrease of in vitro response is attributed to the depletion of immunocompetent cells in the spleen of infected mice, which is heavily populated by null cells.
A Statistical Method for Extracting Uninterrupted and Interrupted Collocations from Very Large Corpora

In order to extract rigid expressions with a high frequency of use, new algorithm that can efficiently extract both uninterrupted and interrupted collocations from very large corpora has been proposed.The statistical method recently proposed for calculating N-gram of arbitrary N can be applied to the extraction of uninterrupted collocations. But this method posed problems that so large volumes of fractional and unnecessary expressions are extracted that it was impossible to extract interrupted collocations combining the results. To solve this problem, this paper proposed a new algorithm that restrains extraction of unnecessary substrings. This is followed by the proposal of a method that enable to extract interrupted collocations.The new methods are applied to Japanese newspaper articles involving 8.92 million characters. In the case of uninterrupted collocations with string length of 2 or mere characters and frequency of appearance 2 or more times, there were 4.4 millions types of expressions (total frequency of 31.2 millions times) extracted by the N-gram method. In contrast, the new method has reduced this to 0.97 million types (total frequency of 2.6 million times) revealing a substantial reduction in fractional and unnecessary expressions. In the case of interrupted collocational substring extraction, combining the substring with frequency of 10 times or more extracted by the first method, 6.5 thousand types of pairs of substrings with the total frequency of 21.8 thousands were extracted.
Mutational and acquired carbapenem resistance mechanisms in multidrug resistant Pseudomonas aeruginosa clinical isolates from Recife, Brazil

An investigation was carried out into the genetic mechanisms responsible for multidrug resistance in nine carbapenem-resistant Pseudomonas aeruginosaisolates from different hospitals in Recife, Brazil. Susceptibility to antimicrobial agents was determined by broth microdilution. Polymerase chain reaction (PCR) was employed to detect the presence of genes encoding β-lactamases, aminoglycoside-modifying enzymes (AMEs), 16S rRNA methylases, integron-related genes and OprD. Expression of genes coding for efflux pumps and AmpC cephalosporinase were assessed by quantitative PCR. The outer membrane proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The blaSPM-1, blaKPC-2 and blaGES-1 genes were detected in P. aeruginosaisolates in addition to different AME genes. The loss of OprD in nine isolates was mainly due to frameshift mutations, premature stop codons and point mutations. An association of loss of OprD with the overexpression of MexAB-OprM and MexXY-OprM was observed in most isolates. Hyper-production of AmpC was also observed in three isolates. Clonal relationship of the isolates was determined by repetitive element palindromic-PCR and multilocus sequence typing. Our results show that the loss of OprD along with overexpression of efflux pumps and β-lactamase production were responsible for the multidrug resistance in the isolates analysed.