Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Expression of Lytic Endopeptidases AlpA and AlpB from Lysobacter sp. XL1 in Pseudomonads

Development of an efficient expression system for (especially secreted) bacterial lytic enzymes is a complicated task due to the specificity of their action. The substrate for such enzymes is peptidoglycan, the main structural component of bacterial cell walls. For this reason, expression of recombinant lytic proteins is often accompanied with lysis of the producing bacterium. This paper presents data on the construction of an inducible system for expression of the lytic peptidases AlpA and AlpB from Lysobacter sp. XL1 in Pseudomonas fluorescens Q2-87, which provides for the successful secretion of these proteins into the culture liquid. In this system, the endopeptidase gene under control of the T7lac promoter was integrated into the bacterial chromosome, as well as the Escherichia coli lactose operon repressor protein gene. The T7 pol gene under lac promoter control, which encodes the phage T7 RNA polymerase, is maintained in Pseudomonas cells on the plasmids. Media and cultivation conditions for the recombinant strains were selected to enable the production of AlpA and AlpB by a simple purification protocol. Production of recombinant lytic enzymes should contribute to the development of new-generation antimicrobial drugs whose application will not be accompanied by selection of resistant microorganisms.
Definability and compression

A compression algorithm takes a finite structure of a class K as input and produces a finite structure of a different class K' as output. Given a property P on the class K defined in a logic /spl Lscr/, we study the definability of property P on the class K'. We consider two compression schemas on unary ordered structures (words), compression by runlength encoding and the classical Lempel-Ziv. First-order properties of strings are first-order on runlength compressed strings, but this fails for images, i.e. 2-dimensional strings. We present simple first-order properties of strings which are not first-order definable on strings compressed with the Lempel-Ziv compression schema. We show that all properties of strings that are first-order definable on strings are definable on Lempel-Ziv compressed strings in FO(TC), the extension of first-order logic with the transitive closure operator. We define a subclass /spl Fscr/ of the first-order properties of strings such that if L is defined by a property in /spl Fscr/, it is also first-order definable on the Lempel-Ziv compressed strings. Monadic second-order properties of strings are dyadic second order definable on Lempel-Ziv compressed strings.
Gelatinomyces siamensis gen. sp. nov. (Ascomycota, Leotiomycetes, incertae sedis) on bamboo in Thailand

Gelatinomyces siamensis gen. sp. nov., incertae sedis within Leotiomycetes, the Siamese jelly-ball, is described. The fungus was collected from bamboo culms and branches in Nam Nao National Park, Phetchabun, Thailand. It presents as a ping-pong ball-sized and golf ball-like gelatinous ascostroma. The asci have numerous ascospores, are thick-walled, and arise on discoid apothecia which are aggregated and clustered to form the spherical gelatinous structures. An hyphomycete asexual morph is morphologically somewhat phialophora-like, and produces red pigments. On the basis of phylogenetic analysis based on rRNA, SSU, and LSU gene sequences, the lineage is closest to Collophora rubra. However, ITS sequences place the fungus on a well-separated branch from that fungus, and the morphological and ecological differences exclude it from Collophora.
Recovery of Seismic Events by Time-Frequency Peak Filtering

The time-frequency peak filtering (TFPF) technology is applied for recovering seismic events without loss of valid information. By using frequency modulation signal encoding and taking peak of Wigner-Ville distribution (WVD) of encoded analytic signal, valid reflect signals constructing seismic events are estimated. To reduce the deterministic bias of TFPF resulted from nonlinearity of seismic reflect signal, the pseudo WVD (PWVD) TFPF is utilized. The reduced bias window length is derived by analyzing bias from experimental resulting. Testing of this method on synthetic seismic data and common shot point recordings indicates that TFPF technique significantly enhances signals from noisy seismic data and improves the continuity of seismic events by filtering out most of the additive noise. The resulting shows the clean recovery of seismic events in noise level down to a signal-to-noise ratio of-2.4dB.
Learning from Observation Paradigm: Leg Task Models for Enabling a Biped Humanoid Robot to Imitate Human Dances

This paper proposes a framework that achieves the Learning from Observation paradigm for learning dance motions. The framework enables a humanoid robot to imitate dance motions captured from human demonstrations. This study especially focuses on leg motions to achieve a novel attempt in which a biped-type robot imitates not only upper body motions but also leg motions including steps. Body differences between the robot and the original dancer make the problem difficult because the differences prevent the robot from straightforwardly following the original motions and they also change dynamic body balance. We propose leg task models, which play a key role in solving the problem. Low-level tasks in leg motion are modelled so that they clearly provide essential information required for keeping dynamic stability and important motion characteristics. The models divide the problem of adapting motions into the problem of recognizing a sequence of the tasks and the problem of executing the task sequence. We have developed a method for recognizing the tasks from captured motion data and a method for generating the motions of the tasks that can be executed by existing robots including HRP-2. HRP-2 successfully performed the generated motions, which imitated a traditional folk dance performed by human dancers.
Flood hazard and management: a UK perspective

This paper discusses whether flood hazard in the UK is increasing and considers issues of flood risk management. Urban development is known to increase fluvial flood frequency, hence design measures are routinely implemented to minimize the impact. Studies suggest that historical effects, while potentially large at small scale, are not significant for large river basins. Storm water flooding within the urban environment is an area where flood hazard is inadequately defined; new methods are needed to assess and manage flood risk. Development on flood plains has led to major capital expenditure on flood protection, but government is attempting to strengthen the planning role of the environmental regulator to prevent this. Rural land use management has intensified significantly over the past 30 years, leading to concerns that flood risk has increased, at least at local scale; the implications for catchment-scale flooding are unclear. New research is addressing this issue, and more broadly, the role of land management in reducing flood risk. Climate change impacts on flooding and current guidelines for UK practice are reviewed. Large uncertainties remain, not least for the occurrence of extreme precipitation, but precautionary guidance is in place. Finally, current levels of flood protection are discussed. Reassessment of flood hazard has led to targets for increased flood protection, but despite important developments to communicate flood risk to the public, much remains to be done to increase public awareness of flood hazard.
Visibility Graph from Adaptive Optimal Kernel Time-Frequency Representation for Classification of Epileptiform EEG

Detecting epileptic seizure from EEG signals constitutes a challenging problem of significant importance. Combining adaptive optimal kernel time-frequency representation and visibility graph, we develop a novel method for detecting epileptic seizure from EEG signals. We construct complex networks from EEG signals recorded from healthy subjects and epilepsy patients. Then we employ clustering coefficient, clustering coefficient entropy and average degree to characterize the topological structure of the networks generated from different brain states. In addition, we combine energy deviation and network measures to recognize healthy subjects and epilepsy patients, and further distinguish brain states during seizure free interval and epileptic seizures. Three different experiments are designed to evaluate the performance of our method. The results suggest that our method allows a high-accurate classification of epileptiform EEG signals.
A SMALL GRANULAR COMPONENT OF THE CYTOPLASM OF KERATINIZING EPITHELIA

We have often observed small dense bodies in the cytoplasm of cells of the stratum granulosum during a study of the fine structure of normal and experimentally altered mouse ear epidermis. Odland (10) noted their presence in human epidermis, showed that they have an internal structure, and speculated that they may be degenerating mitochondria. Other authors seem to have overlooked them in their descriptions of the fine structure of skin, although the bodies appear in their micrographs (1, 6, 9, 11, 12). These small bodies appear to be a normal component of the cytoplasm of keratinizing epithelia, and may play some role in keratinization. We suggest that these bodies be referred to as corpuscula.
Vesicular stomatitis virus enables gene transfer and transsynaptic tracing in a wide range of organisms

Current limitations in technology have prevented an extensive analysis of the connections among neurons, particularly within nonmammalian organisms. We developed a transsynaptic viral tracer originally for use in mice, and then tested its utility in a broader range of organisms. By engineering the vesicular stomatitis virus (VSV) to encode a fluorophore and either the rabies virus glycoprotein (RABV‐G) or its own glycoprotein (VSV‐G), we created viruses that can transsynaptically label neuronal circuits in either the retrograde or anterograde direction, respectively. The vectors were investigated for their utility as polysynaptic tracers of chicken and zebrafish visual pathways. They showed patterns of connectivity consistent with previously characterized visual system connections, and revealed several potentially novel connections. Further, these vectors were shown to infect neurons in several other vertebrates, including Old and New World monkeys, seahorses, axolotls, and Xenopus. They were also shown to infect two invertebrates, Drosophila melanogaster, and the box jellyfish, Tripedalia cystophora, a species previously intractable for gene transfer, although no clear evidence of transsynaptic spread was observed in these species. These vectors provide a starting point for transsynaptic tracing in most vertebrates, and are also excellent candidates for gene transfer in organisms that have been refractory to other methods. J. Comp. Neurol. 523:1639–1663, 2015. © 2015 Wiley Periodicals, Inc.
Prefactor Reduction of the Guruswami–Sudan Interpolation Step

The most computationally intensive step of the Guruswami-Sudan list decoder for generalized Reed-Solomon codes is the formation of a bivariate interpolation polynomial. Complexity can be reduced if this polynomial has prefactors, i.e., factors of its univariate constituent polynomials that are independent of the received vector, and hence known a priori. For example, the well-known re-encoding projection due to Koetter et al. leads to one class of prefactors. This paper introduces so-called Sierpínski prefactors that result from the property that many binomial coefficients, which arise in the multiplicity constraints defined in terms of the Hasse derivative, are zero modulo the underlying field characteristic. It is shown that re-encoding prefactors and Sierpínski prefactors can be combined to achieve a significantly reduced Guruswami-Sudan interpolation step. In certain practically relevant cases, the introduction of Sierpínski prefactors reduces the number of unknown polynomial coefficients by an additional 10% or more (beyond the reduction due to re-encoding prefactors alone), without incurring additional computational effort at the decoder.
Nodes with high centrality in protein interaction networks are responsible for driving signaling pathways in diabetic nephropathy

In spite of huge efforts, chronic diseases remain an unresolved problem in medicine. Systems biology could assist to develop more efficient therapies through providing quantitative holistic sights to these complex disorders. In this study, we have re-analyzed a microarray dataset to identify critical signaling pathways related to diabetic nephropathy. GSE1009 dataset was downloaded from Gene Expression Omnibus database and the gene expression profile of glomeruli from diabetic nephropathy patients and those from healthy individuals were compared. The protein-protein interaction network for differentially expressed genes was constructed and enriched. In addition, topology of the network was analyzed to identify the genes with high centrality parameters and then pathway enrichment analysis was performed. We found 49 genes to be variably expressed between the two groups. The network of these genes had few interactions so it was enriched and a network with 137 nodes was constructed. Based on different parameters, 34 nodes were considered to have high centrality in this network. Pathway enrichment analysis with these central genes identified 62 inter-connected signaling pathways related to diabetic nephropathy. Interestingly, the central nodes were more informative for pathway enrichment analysis compared to all network nodes and also 49 differentially expressed genes. In conclusion, we here show that central nodes in protein interaction networks tend to be present in pathways that co-occur in a biological state. Also, this study suggests a computational method for inferring underlying mechanisms of complex disorders from raw high-throughput data.
Viscous Permeability of Random Fiber Structures: Comparison of Electrical and Diffusional Estimates with Experimental and Analytical Results

An investigation of the permeability for viscous flow through random fiber structures used as preforms in composite fabrication processes is presented. A method derived from the electrical conduction principles is employed to predict the viscous permeability of the fiber structures directly from their formation factor, specific surface area, and porosity. The recent Brownian diffusion random-walk simulation results on the molecular survival time are used to derive an upper bound and an approximation to the viscous permeability of these structures. The results are compared to experimental data and theoretical models of the literature. It is found that the conduction-based method provides very good permeability estimates in most cases, resulting in an overall ratio of the theoretical prediction to experimental measurement in the proximity of 1 for the over 500 experimental points utilized. This is one of the most comprehensive experimental validations of the conduction-based method to date and its first validation for anisotropic particle beds. A tortuosity analysis indicates a stronger pore-geometry effect on viscous flow relative to any type of diffusional flow, enhancing the understanding of the differences between pressure-driven and diffusion-driven composite manufacturing techniques.
Force Platform Feedback for Standing Balance Training After Stroke

BACKGROUND Standing balance deficits are common in individuals after stroke. One way to address these deficits is to provide the individual with feedback from a force platform while balance activities are performed. The feedback can take visual and/or auditory form. OBJECTIVES To determine if visual or auditory force platform feedback improves the clinical and force platform standing balance outcomes in clients with stroke. SEARCH STRATEGY We searched the Cochrane Stroke Group trials register (last searched December 2003), and the following electronic bibliographic databases: the Cochrane Central Register of Controlled Trials (The Cochrane Library Issue 3, 2003), MEDLINE (1966 to May 2003), EMBASE (1974 to May 2003), CINAHL (1982 to May 2003), PEDro (May 2003), CIRRIE (May 2003) and REHABDATA (May 2003). Reference lists of articles were reviewed and manufacturers of equipment were contacted. SELECTION CRITERIA Randomized controlled trials comparing force platform with visual feedback and/or auditory feedback to other balance treatments. DATA COLLECTION AND ANALYSIS Two reviewers independently assessed trials for inclusion, methodological quality, and data extraction. Trials were combined for meta-analysis according to outcome and type of feedback. MAIN RESULTS We included seven trials (246 participants). Force platform feedback did not improve clinical measures of balance when moving or walking (Berg Balance Scale and Timed Up and Go). Significant improvements in laboratory force platform indicators of stance symmetry were found for regimens using visual feedback (standardised mean difference (SMD) -0.68, 95% confidence interval (CI) -1.31 to -0.04, p = 0.04) and the concurrent visual and auditory feedback (weighted mean difference (WMD) -4.02, 95% CI -5.99 to -2.04, p = 0.00007). There were no significant effects on laboratory postural sway indicators, clinical outcomes or measures of function at follow-up assessment. REVIEWERS' CONCLUSIONS Force platform feedback (visual or auditory) improved stance symmetry but not sway in standing, clinical balance outcomes or measures of independence.
Dopamine induces platelet production from megakaryocytes via oxidative stress-mediated signaling pathways

Abstract Dopamine (DA), a catecholamine neurotransmitter, is known to for its diverse roles on hematopoiesis, yet its function in thrombopoiesis remains poorly understood. This study shows that DA stimulation can directly induce platelet production from megakaryocytes (MKs) in the final stages of thrombopoiesis via a reactive oxygen species (ROS)-dependent pathway. The mechanism was suggested by the results that DA treatment could significantly elevate the ROS levels in MKs, and time-dependently activate oxidative stress-mediated signaling, including p38 mitogen-activated protein kinase, c-Jun NH2-terminal kinase, and caspase-3 signaling pathways, while the antioxidants N-acetylcysteine and L-glutathione could effectively inhibit the activation of these signaling pathways, as well as the ROS increase and platelet production triggered by DA. Therefore, our data revealed that the direct role and mechanism of DA in thrombopoiesis, which provides new insights into the function recognition of DA in hematopoiesis.
INVERSE INTERVAL MATRIX: A SURVEY ∗

Results on the inverse interval matrix, both theoretical and computational, are surveyed. Described are, among others, formulae for the inverse interval matrix, NP-hardness of its computation, various classes of interval matrices for which the inverse can be given explicitly, and closed-form formulae for an enclosure of the inverse. 1. Introduction. In our recent paper (20), we presented a survey of forty nec- essary and sufficient conditions for regularity of interval matrices. It is nowfollowed by a survey of properties of the inverse interval matrix which is closely related to the previous topic because the inverse interval matrix is only defined for regular interval
Detection of antimicrobial activity of banana peel (Musa paradisiaca L.) on Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans: An in vitro study

Introduction and Aim: Banana is used widely because of its nutritional values. In past, there are studies that show banana plant parts, and their fruits can be used to treat the human diseases. Banana peel is a part of banana fruit that also has the antibacterial activity against microorganisms but has not been studied extensively. Since, there are no studies that relate the antibacterial activity of banana peel against periodontal pathogens. Hence, the aim of this study is to determine the antimicrobial activity of banana peel extract on Porphyromonas gingivalis (P. gingivalis) and Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans). Material and Methods: Standard strains of P. gingivalis and A. actinomycetemcomitans were used in this study which was obtained from the in-house bacterial bank of Department of Molecular Biology and Immunology at Maratha Mandal's Nathajirao G. Halgekar Institute of Dental Sciences and Research Centre. The banana peel extract was prepared, and the antibacterial activity was assessed using well agar diffusion method and minimum inhibitory concentration was assessed using serial broth dilution method. Results: In the current study, both the tested microorganisms showed antibacterial activity. In well diffusion method, P. gingivalis and A. actinomycetemcomitans showed 15 mm and 12 mm inhibition zone against an alcoholic extract of banana peel, respectively. In serial broth dilution method P. gingivalis and A. actinomycetemcomitans were sensitive until 31.25 μg/ml dilutions. Conclusion: From results of the study, it is suggested that an alcoholic extract of banana peel has antimicrobial activity against P. gingivalis and A. actinomycetemcomitans.
Direct milling and casting of polymer-based optical waveguides for improved transparency in the visible range

Polymer waveguides fabricated from photoresist have an inherent high propagation loss in the short visible wavelength range caused by absorption due to the added photosensitizers. We have addressed this problem by development of two novel methods for the fabrication of microfluidic systems with integrated optical waveguides. Polymethylmethacrylate (PMMA) is dissolved in anisole and ‘doped’ with styrene-arcylonitrile copolymer to vary the refractive index. The doped PMMA with a higher refractive index is then spin coated onto a PMMA substrate with a lower refractive index to provide waveguide properties. Direct micromilling enabled us to fabricate 100 µm wide optical waveguides. Propagation losses of less than 1 dB cm−1 could be achieved throughout the entire visual range down to a wavelength of 400 nm. A casting process amenable to high number production of such devices was furthermore developed.
Protection Against Osmotic Stress by cGMP-Mediated Myosin Phosphorylation

Conventional myosin functions universally as a generator of motive force in eukaryotic cells. Analysis of mutants of the microorganism Dictyostelium discoideum revealed that myosin also provides resistance against high external osmolarities. An osmo-induced increase of intracellular guanosine 3′,5′-monophosphate was shown to mediate phosphorylation of three threonine residues on the myosin tail, which caused a relocalization of myosin required to resist osmotic stress. This redistribution of myosin allowed cells to adopt a spherical shape and may provide physical strength to withstand extensive cell shrinkage in high osmolarities.