Miracle-dz/UniFAR-FTUs huggingface dataset:
Open Access Research Article Species Specificity, Surface Exposure, Protein Expression, Immunogenicity, and Participation in Biofilm Formation of Porphyromonas Gingivalis Hmuy

Background: Porphyromonas gingivalis is a major etiological agent of chronic periodontitis. The aim of this study was to examine the species specificity, surface exposure, protein expression, immunogenicity, and participation in biofilm formation of the P. gingivalis heme-binding protein HmuY. Results: HmuY is a unique protein of P. gingivalis since only low amino-acid sequence homology has been found to proteins encoded in other species. It is exposed on the cell surface and highly abundant in the outer membrane of the cell, in outer-membrane vesicles, and is released into culture medium in a soluble form. The protein is produced constitutively at low levels in bacteria grown under high-iron/heme conditions and at higher levels in bacteria growing under the low-iron/heme conditions typical of dental plaque. HmuY is immunogenic and elicits high IgG antibody titers in rabbits. It is also engaged in homotypic biofilm formation by P. gingivalis. Anti-HmuY antibodies exhibit inhibitory activity against P. gingivalis growth and biofilm formation. Conclusions: Here it is demonstrated that HmuY may play a significant role not only in heme acquisition, but also in biofilm accumulation on abiotic surfaces. The data also suggest that HmuY, as a surface-exposed protein, would be available for recognition by the immune response during chronic periodontitis and the production of anti-HmuY antibodies may inhibit biofilm formation. Background Periodontitis is a complex process affecting tooth-supporting tissues [1]. The pathogenesis of periodontal diseases is largely attributed to localized inflammation, which results from interaction between host and microbial factors [2]. The most common etiological agent of chronic periodontitis is Porphyromonas gingivalis, a Gram-negative anaerobic black-pigmented bacterium [3]. On tooth surfaces, P. gingivalis is a constituent of the complex multispecies biofilm known as dental plaque, which has properties of other biofilms found in the human body and in the environment. P. gingivalis can also colonize the tissues and cells of the gingival epithe-lium [4]. The bacterium can not only invade, but also
Model-based design and implementation of an adaptive digital predistortion filter

Dataflow models of computation are widely used for modeling signal processing systems. These models have inherent concurrency and the task (actor) execution depends only on the availability of the input data (tokens). This property of dataflow models can be exploited for dynamic power management by automatically switching off the actors with no available input tokens. This idea is applied in this paper for efficient modeling and implementation of an adaptive Digital Predistortion (DPD) filter. The DPD filter is required to operate with different profiles under varying operation scenarios, hence requiring a methodology to manage power dynamically. The paper presents a dataflow model for Adaptive Digital Predistortion based on the Core Functional Dataflow (CFDF) model of computation using the Light Weight Dataflow (LWDF) programming methodology. The paper also provides a methodology for dynamic power management under the dataflow paradigm. To the authors' best knowledge, this work is the first to integrate dataflow-based power management systematically in the context of adaptive DPD implementation.
PLAQUE FORMATION AND ISOLATION OF PURE LINES WITH POLIOMYELITIS VIRUSES

Plaques have been produced with the three types of poliomyelitis viruses on monolayer tissue cultures of monkey kidney and monkey testis. The number of plaques was proportional to the concentration of the virus. Each plaque originates, therefore, from a single virus particle, defined as the virus unit that is unseparable by dilution. The plaques are due to the specific action of the virus since they are suppressed by type-specific antiserum. Pure virus lines were established by isolating the virus population produced in single plaques. These derived virus lines had the same morphological, serological, and pathogenic properties as the parent strain. High titer virus stocks, with titers up to 7 x 108 plaque-forming particles per ml. , were obtained.
A resilience-based model for performance evaluation of information systems: the case of a gas company

ABSTRACT Information systems (IS) are strongly influenced by changes in new technology and should react swiftly in response to external conditions. Resilience engineering is a new method that can enable these systems to absorb changes. In this study, a new framework is presented for performance evaluation of IS that includes DeLone and McLean’s factors of success in addition to resilience. Hence, this study is an attempt to evaluate the impact of resilience on IS by the proposed model in Iranian Gas Engineering and Development Company via the data obtained from questionnaires and Fuzzy Data Envelopment Analysis (FDEA) approach. First, FDEA model with α-cut = 0.05 was identified as the most suitable model to this application by performing all Banker, Charnes and Cooper and Charnes, Cooper and Rhodes models of and FDEA and selecting the appropriate model based on maximum mean efficiency. Then, the factors were ranked based on the results of sensitivity analysis, which showed resilience had a significantly higher impact on the proposed model relative to other factors. The results of this study were then verified by conducting the related ANOVA test. This is the first study that examines the impact of resilience on IS by statistical and mathematical approaches.
Production and Processing of siRNA Precursor Transcripts from the Highly Repetitive Maize Genome

Mutations affecting the maintenance of heritable epigenetic states in maize identify multiple RNA–directed DNA methylation (RdDM) factors including RMR1, a novel member of a plant-specific clade of Snf2-related proteins. Here we show that RMR1 is necessary for the accumulation of a majority of 24 nt small RNAs, including those derived from Long-Terminal Repeat (LTR) retrotransposons, the most common repetitive feature in the maize genome. A genetic analysis of DNA transposon repression indicates that RMR1 acts upstream of the RNA–dependent RNA polymerase, RDR2 (MOP1). Surprisingly, we show that non-polyadenylated transcripts from a sampling of LTR retrotransposons are lost in both rmr1 and rdr2 mutants. In contrast, plants deficient for RNA Polymerase IV (Pol IV) function show an increase in polyadenylated LTR RNA transcripts. These findings support a model in which Pol IV functions independently of the small RNA accumulation facilitated by RMR1 and RDR2 and support that a loss of Pol IV leads to RNA Polymerase II–based transcription. Additionally, the lack of changes in general genome homeostasis in rmr1 mutants, despite the global loss of 24 nt small RNAs, challenges the perceived roles of siRNAs in maintaining functional heterochromatin in the genomes of outcrossing grass species.
Improving Design and Analysis of Research: Lessons from Clinical Research

There is a clear need to optimise the use of animals in research and to ensure that the studies that are done make a worthwhile contribution to scientific knowledge. Research that has an inappropriate study design, or is improperly analysed or interpreted, may mislead and is not defensible. Published reviews of the quality of design and analysis in clinical studies are used to see what lessons can be drawn in respect of animal research. The need for clear and full reporting of research is discussed.
HMSNN: Hippocampus inspired Memory Spiking Neural Network

Human beings receive stimulations in primary sensory cortex and transfer them to higher brain regions automatically. What happened in this procedure? In this paper, we will focus on one of these regions (hippocampus) and try to simulate its working procedure by building an HMSNN (Hippocampus inspired Memory Spiking Neural Network) model. Dentate Gyrus (DG) and Cornu Ammonis area 3 (CA3) are the main regions of hippocampus and will be simulated by feed forward Spiking Neural Network (SNN) and recurrent Hopfield-like network respectively. From the structural perspective, the computational unit and the connectivity between neurons in HMSNN are all consistent with the anatomical-experimental results in hippocampus. From the functional perspective, the multi-scale memory formation, memory abstraction and memory retention will be shown in HMSNN model. In addition, the HMSNN is tested on MNIST handwritten digit dataset (with static images) and robot walking dataset (with dynamical images). The experimental result shows that: biological neural circuit inspired HMSNN shows comparable classification performance on both datasets compared to the state-of-art convolutional neural networks (CNNs), and shows significantly better performance compared to CNN when noises are introduced to the original images.
Behaviour oriented design for real-time-strategy games

Design is an essential part of all games and narratives, yet designing and implementing believable game strategies can be time consuming and error-prone. This motivates the development and application of systems AI methodologies. Here we demonstrate for the first time the iterative development of agent behaviour for a real-time strategy game (here StarCraft) utilising Behaviour Oriented Design (BOD). BOD provides focus on the robust creation and easy adjustment of modular and hierarchical cognitive agents. We demonstrate BOD’s usage in creating an AI capable of playing the StarCraft character the Zerg hive mind, and document its performance against a variety of opponent AI systems. In describing our tool-driven development process, we also describe the new Abode IDE, provide a brief literature review situating BOD in the AI game literature, and propose possible future work.
Finding similar experts

The task of finding people who are experts on a topic has recently received increased attention. We introduce a different expert finding task for which a small number of example experts is given (instead of a natural language query), and the system's task is to return similar experts. We define, compare, and evaluate a number of ways of representing experts, and investigate how the size of theinitial example set affects performance. We show that morefine-grained representations of candidates result in higher performance, and larger sample sets as input lead to improved precision.
COPD phenotypes on computed tomography and its correlation with selected lung function variables in severe patients

Background Computed tomography (CT) phenotypic characterization helps in understanding the clinical diversity of chronic obstructive pulmonary disease (COPD) patients, but its clinical relevance and its relationship with functional features are not clarified. Volumetric capnography (VC) uses the principle of gas washout and analyzes the pattern of CO2 elimination as a function of expired volume. The main variables analyzed were end-tidal concentration of carbon dioxide (ETCO2), Slope of phase 2 (Slp2), and Slope of phase 3 (Slp3) of capnogram, the curve which represents the total amount of CO2 eliminated by the lungs during each breath. Objective To investigate, in a group of patients with severe COPD, if the phenotypic analysis by CT could identify different subsets of patients, and if there was an association of CT findings and functional variables. Subjects and methods Sixty-five patients with COPD Gold III–IV were admitted for clinical evaluation, high-resolution CT, and functional evaluation (spirometry, 6-minute walk test [6MWT], and VC). The presence and profusion of tomography findings were evaluated, and later, the patients were identified as having emphysema (EMP) or airway disease (AWD) phenotype. EMP and AWD groups were compared; tomography findings scores were evaluated versus spirometric, 6MWT, and VC variables. Results Bronchiectasis was found in 33.8% and peribronchial thickening in 69.2% of the 65 patients. Structural findings of airways had no significant correlation with spirometric variables. Air trapping and EMP were strongly correlated with VC variables, but in opposite directions. There was some overlap between the EMP and AWD groups, but EMP patients had signicantly lower body mass index, worse obstruction, and shorter walked distance on 6MWT. Concerning VC, EMP patients had signicantly lower ETCO2, Slp2 and Slp3. Increases in Slp3 characterize heterogeneous involvement of the distal air spaces, as in AWD. Conclusion Visual assessment and phenotyping of CT in COPD patients is feasible and may help identify functional and clinically different subsets of patients. VC may provide useful information about the heterogeneous involvement of lung structures in COPD.
In vivo two-photon imaging reveals monocyte-dependent neutrophil extravasation during pulmonary inflammation

Immune-mediated pulmonary diseases are a significant public health concern. Analysis of leukocyte behavior in the lung is essential for understanding cellular mechanisms that contribute to normal and diseased states. Here, we used two-photon imaging to study neutrophil extravasation from pulmonary vessels and subsequent interstitial migration. We found that the lungs contained a significant pool of tissue-resident neutrophils in the steady state. In response to inflammation produced by bacterial challenge or transplant-mediated, ischemia-reperfusion injury, neutrophils were rapidly recruited from the circulation and patrolled the interstitium and airspaces of the lung. Motile neutrophils often aggregated in dynamic clusters that formed and dispersed over tens of minutes. These clusters were associated with CD115+ F4/80+ Ly6C+ cells that had recently entered the lung. The depletion of blood monocytes with clodronate liposomes reduced neutrophil clustering in the lung, but acted by inhibiting neutrophil transendothelial migration upstream of interstitial migration. Our results suggest that a subset of monocytes serve as key regulators of neutrophil extravasation in the lung and may be an attractive target for the treatment of inflammatory pulmonary diseases.
New Techniques for Generation and Analysis of Evolutionary Trees

We introduce new distance measures for the construction and analysis of phylogenies, focusing on thioredoxin-fold proteins. Our distance measures for tree construction are based on several criteria, including pairwise alignment of only the thioredoxin fold region of each sequence, Hausdorff distance between sequences represented by sets of real vectors derived from per-residue features of the sequences, and properties of each sequence such as protein function and organism type. We also analyze and compare our trees in several ways. To corroborate the trees, we first compute the distance between the evolutionary trees, and then evaluate the trees based on conditional entropy. We also analyze the trees by finding common subtrees within and between our trees. Fina lly, biological analysis shows that trees based on our measures yield new information on proteins within the thioredoxin superfamily. Index Terms thioredoxin-fold proteins, evolutionary tree, Hausdorff distance, most common sub-tree.
Tight convex relaxations for vector-valued labeling problems

The multi-label problem is of fundamental importance to computer vision, yet finding global minima of the associated energies is very hard and usually impossible in practice. Recently, progress has been made using continuous formulations of the multi-label problem and solving a convex relaxation globally, thereby getting a solution with optimality bounds. In this work, we develop a novel framework for continuous convex relaxations, where the label space is a continuous product space. In this setting, we can combine the memory efficient product relaxation of [9] with the much tighter relaxation of [5], which leads to solutions closer to the global optimum. Furthermore, the new setting allows us to formulate more general continuous regularizers, which can be freely combined in the different label dimensions. We also improve upon the relaxation of the products in the data term of [9], which removes the need for artificial smoothing and allows the use of exact solvers.
Barnacle settlement and the adhesion of protein and diatom microfouling to xerogel films with varying surface energy and water wettability

Previous work has shown that organosilica-based xerogels have the potential to control biofouling. In this study, modifications of chemistry were investigated with respect to their resistance to marine slimes and to settlement of barnacle cyprids. Adhesion force measurements of bovine serum albumin (BSA)-coated atomic force microscopy (AFM) tips to xerogel surfaces prepared from aminopropylsilyl-, fluorocarbonsilyl-, and hydrocarbonsilyl-containing precursors, indicated that adhesion was significantly less on the xerogel surfaces in comparison to a poly(dimethylsiloxane) elastomer (PDMSE) standard. The strength of adhesion of BSA on the xerogels was highest on surfaces with the highest and the lowest critical surface tensions, γC and surface energies, γS, and duplicated the ‘Baier curve’. The attachment to and removal of cells of the diatom Navicula perminuta from a similar series of xerogel surfaces were examined. Initial attachment of cells was comparable on all of the xerogel surfaces, but the percentage removal of attached cells by hydrodynamic shear stress increased with γC and increased wettability as measured by the static water contact angle, θWs, of the xerogel surfaces. The percentage removal of cells of Navicula was linearly correlated with both properties (R 2 = 0.74 for percentage removal as a function of θWs and R 2 = 0.69 for percentage removal as a function of γC). Several of the aminopropylsilyl-containing xerogels showed significantly greater removal of Navicula compared to a PDMSE standard. Cypris larvae of the barnacle B. amphitrite showed preferred settlement on hydrophilic/higher energy surfaces. Settlement was linearly correlated with θWs (R 2 = 0.84) and γC (R 2 = 0.84). Hydrophilic xerogels should prove useful as coatings for boats in regions where fouling is dominated by microfouling (protein and diatom slimes).
Comparative transcriptomic analysis of male and female flowers of monoecious Quercus suber

Monoecious species provide a comprehensive system to study the developmental programs underlying the establishment of female and male organs in unisexual flowers. However, molecular resources for most monoecious non-model species are limited, hampering our ability to study the molecular mechanisms involved in flower development of these species. The objective of this study was to identify differentially expressed genes during the development of male and female flowers of the monoecious species Quercus suber, an economically important Mediterranean tree. Total RNA was extracted from different developmental stages of Q. suber flowers. Non-normalized cDNA libraries of male and female flowers were generated using 454 pyrosequencing technology producing a total of 962,172 high-quality reads with an average length of 264 nucleotides. The assembly of the reads resulted in 14,488 contigs for female libraries and 10,438 contigs for male libraries. Comparative analysis of the transcriptomes revealed genes differentially expressed in early and late stages of development of female and male flowers, some of which have been shown to be involved in pollen development, in ovule formation and in flower development of other species with a monoecious, dioecious, or hermaphroditic sexual system. Moreover, we found differentially expressed genes that have not yet been characterized and others that have not been previously shown to be implicated in flower development. This transcriptomic analysis constitutes a major step toward the characterization of the molecular mechanisms involved in flower development in a monoecious tree with a potential contribution toward the knowledge of conserved developmental mechanisms in other species.
Tracking Resource Usage Using Heterogeneous Feature Spaces with Local Exceptions

We describe a method for tracking usage of resources in a web environment by representing the resources as a feature space in which usage instances appear as trails, so that common access patterns are shown as similar trails. To improve the analysis of usage data, prior knowledge about usage patterns can be specified by the server administrator as local exceptions to the standard dissimilarity measure, or local dissimilarity measures, which can be combined in non-linear ways. We outline a method to find similar trails under user-defined restrictions within this heterogeneous feature space and an associated similarity space, and to describe progressions of trails representing a web access history. This information can then be used to reassign resources, e.g. by a web site administrator, to address deficiencies or shifting priorities in accessing web-based materials.
Synthesis and Terahertz Applications of Large-Area Monolayer Graphene

[Synthesis and Terahertz Applications of Large-Area Monolayer Graphene] by Minjie Wang Monolayer graphene, successfully isolated in 2004 for the first time, is the first member of the class of materials called two-dimensional (2D) materials. It consists of a 2D honeycomb lattice of sp2-bonded carbon atoms, possessing extraordinary mechanical, chemical, and physical properties. The unique band structure and gate tunability of graphene are expected to result in novel highfrequency (THz) and optical phenomena. In this thesis work, we used two different ways to grow graphene on a copper foil via chemical vapor deposition (CVD). One method synthesized continuous, large-size monolayer graphene, while the other method created signalcrystal graphene with no domain boundaries. We transferred grown graphene from copper foil to SiO2/Si substrates by the wet-etch method with four types of copper etchants that are commonly used by researcher: HNO3, FeCl3, (NH4)2S2O8, and a commercial copper etchant. Further tests and analysis showed that the commercial copper etchant is the best for transfer purposes from the perspective of structural integrity, amount of residues, and doping carrier concentration. We conducted strain-dependent THz transmission measurements of graphene on a polyimide substrate (Kapton) using a strain-controllable mechanicaloptical testing system. Experimental results showed that THz transmittance of graphene changes significantly with strain up to ~30%, but no reversible change of THz transmittance was observed. On the other hand, by using a recently proposed total internal reflection (TIR) geometry, we demonstrated significant enhancement of THz-wave absorption in monolayer graphene. Our scheme allowed the incident THz beam to be reflected by graphene four times at varying incidence angles, both below and above the critical angle for TIR. We observed extremely large THz absorption, especially for spolarized radiation. The experimental results are quantitatively consistent with our calculations, incorporating realistic values of carrier scattering time and Fermi energy.
Structure and Stability of Intermediate (Fe, Cr)7C3 Carbides

The paper presents a systematic approach to calculate the structure and stability of intermediate (Cr, Fe)7C3 carbides in hexagonal and orthorhombic phases within the framework of density functional theory. It was shown, that the formation energy of the system changes non-monotonically with chromium concentration; the fact is consistent with thermodynamics. It was found, that some intermetallic carbides in the system are more stable than binary counterparts.