Miracle-dz/UniFAR-FTUs huggingface dataset:
GEK1, a gene product of Arabidopsis thaliana involved in ethanol tolerance, is a d-aminoacyl-tRNA deacylase

GEK1, an Arabidopsis thaliana gene product, was recently identified through its involvement in ethanol tolerance. Later, this protein was shown to display 26% strict identity with archaeal d-Tyr-tRNATyr deacylases. To determine whether it actually possessed deacylase activity, the product of the GEK1 open reading frame was expressed in Escherichia coli from a multi-copy plasmid. Purified GEK1 protein contains two zinc ions and proves to be a broad-specific, markedly active d-aminoacyl-tRNA deacylase in vitro. Moreover, GEK1 expression is capable of functionally compensating in E. coli for the absence of endogeneous d-Tyr- tRNATyr deacylase. Possible connections between exposure of plants to ethanol/acetaldehyde and misaminoacylation of tRNA by d-amino acids are considered.
Tail Asymptotics for Discrete Event Systems

In the context of communication networks, the framework of stochastic event graphs allows a modeling of control mechanisms induced by the communication protocol and an analysis of its performances. We concentrate on the logarithmic tail asymptotics of the stationary response time for a class of networks that admit a representation as (max,plus)-linear systems in a random medium. We are able to derive analytic results when the distribution of the holding times are light-tailed. We show that the lack of independence may lead in dimension bigger than one to non-trivial effects in the asymptotics of the sojourn time. We also study in detail a simple queueing network with multipath routing.
Erim Report Series Research in Management How to Normalize Co-occurrence Data? an Analysis of Some Well-known Similarity Measures How to Normalize Co-occurrence Data? an Analysis of Some Well-known Similarity Measures

AND KEYWORDS Abstract In scientometric research, the use of co-occurrence data is very common. In many cases, a similarity measure is employed to normalize the data. However, there is no consensus among researchers on which similarity measure is most appropriate for normalization purposes. In this paper, we theoretically analyze the properties of similarity measures for co-occurrence data, focusing in particular on four well-known measures: the association strength, the cosine, the inclusion index, and the Jaccard index. We also study the behavior of these measures empirically. Our analysis reveals that there exist two fundamentally different types of similarity measures, namely set-theoretic measures and probabilistic measures. The association strength is a probabilistic measure, while the cosine, the inclusion index, and the Jaccard index are set-theoretic measures. Both our theoretical and our empirical results indicate that co-occurrence data can best be normalized using a probabilistic measure. This provides strong support for the use of the association strength in scientometric research. Availability The ERIM Report Series is distributed through the following platforms: Classifications The electronic versions of the papers in the ERIM report Series contain bibliographic metadata by the following classification systems: Abstract In scientometric research, the use of co-occurrence data is very common. In many cases, a similarity measure is employed to normalize the data. However, there is no consensus among researchers on which similarity measure is most appropriate for normalization purposes. In this paper, we theoretically analyze the properties of similarity measures for co-occurrence data, focusing in particular on four well-known measures: the association strength, the cosine, the inclusion index, and the Jaccard index. We also study the behavior of these measures empirically. Our analysis reveals that there exist two fundamentally different types of similarity measures, namely set-theoretic measures and probabilistic measures. The association strength is a probabilistic measure, while the cosine, the inclusion index, and the Jaccard index are set-theoretic measures. Both our theoretical and our empirical results indicate that co-occurrence data can best be normalized using a probabilistic measure. This provides strong support for the use of the association strength in scientomet-ric research.
Intrarenal Oxidative Stress and Augmented Angiotensinogen are Precedent to Renal Injury in Zucker Diabetic Fatty Rats

The Zucker diabetic fatty (ZDF) rat is a model of type II diabetes and metabolic syndrome based on impaired glucose tolerance caused by the inherited insulin-resistance gene. The ZDF rat exhibits progressive nephropathy; however, the detailed mechanisms have remained unclear. This study was performed to examine the possible involvement of enhanced intrarenal angiotensinogen in the development of renal injury in ZDF rats. Genetic pairs of male ZDF rats and control lean rats (N=6 each) were maintained from 12 to 17 weeks of age. At 17 weeks of age, fasting blood glucose and urinary 8-isoprostane levels were significantly higher in ZDF rats compared with the controls. Systolic blood pressure progressively increased in ZDF rats from 120+/-1 to 137+/-1 mmHg during this period. In contrast, systolic blood pressure did not increase in the controls. Kidney angiotensinogen protein levels were significantly increased in ZDF rats compared with the controls (1.83+/-0.34 vs. 1.00+/-0.17, relative ratio). Expression of angiotensin II type 1a receptor mRNA was similar between these groups. The measured indices of renal damage in the present study (glomerular sclerosis, interstitial expansion, glomerular macrophage infiltration, and renal arterial proliferation) were not significantly increased at this stage in ZDF rats. However, we previously showed that the increased reactive oxygen species-related angiotensinogen enhancement plays an important role in the development of renal injury in a genetic salt-sensitive hypertension. Thus, the present data suggest that elevated reactive oxygen species and reactive oxygen species-associated augmentation of intrarenal angiotensinogen may initiate the development of renal injury in ZDF rats.
Are Frontal Cognitive and Atrophy Patterns Different in PSP and bvFTD? A Comparative Neuropsychological and VBM Study

Progressive supranuclear palsy (PSP) and frontotemporal lobar degeneration (FTD) are two clinicohistological entities that share a severe prefrontal syndrome. To what extent do the cognitive syndrome and the location of the underlying brain atrophy unify or segregate these entities? Here, we examined the clinical and radiological patterns of frontal involvement and the neural bases of the cognitive dysfunctions observed in the Richardson form of PSP and the behavioral variant of FTD (bvFTD). The cognitive profile and grey and white matter volume of PSP (n = 19) and bvFTD (n = 16) patients and control participants (n = 18) were compared using a standard battery of neuropsychological tests and voxel-based morphometry (VBM), respectively. Analyses of correlations between neuropsychological and morphometric data were additionally performed. The severity and qualitative pattern of cognitive dysfunction was globally similar between the two patient groups. Grey matter volume was decreased in widespread frontal areas and in the temporal uncus in bvFTD, while it was decreased in the frontal and temporal lobes as well as in the thalamus in PSP. We also found an unexpected involvement of the frontal rectal gyrus in PSP patients compared to controls. Correlation analyses yielded different results in the two groups, with no area showing significant correlations in PSP patients, while several frontal and some temporal areas did so in bvFTD patients. In spite of minor neuropsychological and morphological differences, this study shows that the patterns of cognitive dysfunction and atrophy are very similar in PSP and bvFTD. However, executive dysfunction in these diseases may stem from partially divergent cortical and subcortical neural circuits.
Prevention of intimal hyperplasia using short-period vascular heating without surrounding tissue injury: in vitro/in vivo experiments and thermal conduction calculation

We have been proposed novel short-term (<10s) heating balloon using the combination of light-heat conversion mechanism and heated contrast medium irrigation in the balloon to improve dilatation characteristics of balloon angioplasty. Our new balloon angioplasty had suppressed intimal hyperplasia in rabbit model. We designed following experiments to understand the mechanism of suppression of intimal hyperplasia in our new thermal balloon angioplasty. We also aimed to obtain the suitable heating condition in our angioplasty to suppress intimal hyperplasia. We studied influence of the short-term heating on smooth muscle cells (SMCs) lethality in vitro. We investigated number of SMCs reduction in media in order to prevent intimal hyperplasia. We applied to our heating balloon dilatation to chronic rabbit model using normal iliac artery to study relation between heating condition and hyperplasia suppression. We estimated temperature history of the rabbit vascular wall by thermal conduction calculation. We related the estimated temperature history to the hyperplasia suppression effect in the chronic rabbit model. Finally, we obtained the relation between number of SMCs decreases and intimal hyperplasia suppression. We obtained that the short-term heating with 10s laser irradiation corresponding to estimated temperature of 50°C in the media and prevented intimal hyperplasia in the rabbit chronic model. In this case, we estimated about 30 percents of SMCs cellular lethality in media.
High hydrostatic pressure-induced inactivation of bacterial spores

Abstract High hydrostatic pressure (HHP) is the most-widely adopted novel non-thermal technology for the commercial pasteurization of foods. However, HHP-induced inactivation of bacterial spores remains a challenge due to spore resistance to the treatment limits of currently available industrial HHP units (i.e. ∼650 MPa and 50 °C). Several reports have demonstrated that high pressure can modulate the germination machinery of bacterial spores, rendering them susceptible to subsequent inactivation treatments. Unfortunately, high pressure-induced germination is a unique phenomenon for spores of the genus Bacillus but not of Clostridium. Alternative strategies to inactivate bacterial spores at commercially available pressure and temperature levels include promoting the germination step by inclusion of known germinants into the food formulation to increase the lethality of HHP treatments on bacterial spores. The aim of this review is to provide an overview of the molecular basis involved in pressure-triggered germination of bacterial spores and of novel strategies to inactivate bacterial spores with HHP treatments.
Elevating crop disease resistance with cloned genes

Essentially all plant species exhibit heritable genetic variation for resistance to a variety of plant diseases caused by fungi, bacteria, oomycetes or viruses. Disease losses in crop monocultures are already significant, and would be greater but for applications of disease-controlling agrichemicals. For sustainable intensification of crop production, we argue that disease control should as far as possible be achieved using genetics rather than using costly recurrent chemical sprays. The latter imply CO2 emissions from diesel fuel and potential soil compaction from tractor journeys. Great progress has been made in the past 25 years in our understanding of the molecular basis of plant disease resistance mechanisms, and of how pathogens circumvent them. These insights can inform more sophisticated approaches to elevating disease resistance in crops that help us tip the evolutionary balance in favour of the crop and away from the pathogen. We illustrate this theme with an account of a genetically modified (GM) blight-resistant potato trial in Norwich, using the Rpi-vnt1.1 gene isolated from a wild relative of potato, Solanum venturii, and introduced by GM methods into the potato variety Desiree.
EXACT SOLVABILITY OF THE CALOGERO AND SUTHERLAND MODELS

Translationally invariant symmetric polynomials as coordinates for N-body problems with identical particles are proposed. It is shown that in those coordinates the Calogero and Sutherland N-body Hamiltonians, after appropriate gauge transformations, can be presented as a quadratic polynomial in the generators of the algebra slN in finitedimensional degenerate representation. The exact solvability of these models follows from the existence of the infinite flag of such representation spaces, preserved by the above Hamiltonians. A connection with Jack polynomials is discussed.
Cross-Genre and Cross-Domain Detection of Semantic Uncertainty

Uncertainty is an important linguistic phenomenon that is relevant in various Natural Language Processing applications, in diverse genres from medical to community generated, newswire or scientific discourse, and domains from science to humanities. The semantic uncertainty of a proposition can be identified in most cases by using a finite dictionary (i.e., lexical cues) and the key steps of uncertainty detection in an application include the steps of locating the (genre- and domain-specific) lexical cues, disambiguating them, and linking them with the units of interest for the particular application (e.g., identified events in information extraction). In this study, we focus on the genre and domain differences of the context-dependent semantic uncertainty cue recognition task.We introduce a unified subcategorization of semantic uncertainty as different domain applications can apply different uncertainty categories. Based on this categorization, we normalized the annotation of three corpora and present results with a state-of-the-art uncertainty cue recognition model for four fine-grained categories of semantic uncertainty.Our results reveal the domain and genre dependence of the problem; nevertheless, we also show that even a distant source domain data set can contribute to the recognition and disambiguation of uncertainty cues, efficiently reducing the annotation costs needed to cover a new domain. Thus, the unified subcategorization and domain adaptation for training the models offer an efficient solution for cross-domain and cross-genre semantic uncertainty recognition.
Predefined-time stability of dynamical systems with sliding modes

This paper introduces a class of fixed-time stable dynamical systems with settling time as a explicit parameter, namely the inverse the gain. Those systems are defined as predefined-timed stable dynamical systems. Continuous and discontinuous are cases are presented. A detailed Lyapunov characterization of this class of systems is also shown. Finally, the application to the design of a class of first order sliding mode controllers is exposed.
Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes

Three classes of low-G+C Gram-positive bacteria (Firmicutes), Bacilli, Clostridia and Negativicutes, include numerous members that are capable of producing heat-resistant endospores. Spore-forming firmicutes include many environmentally important organisms, such as insect pathogens and cellulose-degrading industrial strains, as well as human pathogens responsible for such diseases as anthrax, botulism, gas gangrene and tetanus. In the best-studied model organism Bacillus subtilis, sporulation involves over 500 genes, many of which are conserved among other bacilli and clostridia. This work aimed to define the genomic requirements for sporulation through an analysis of the presence of sporulation genes in various firmicutes, including those with smaller genomes than B. subtilis. Cultivable spore-formers were found to have genomes larger than 2300 kb and encompass over 2150 protein-coding genes of which 60 are orthologues of genes that are apparently essential for sporulation in B. subtilis. Clostridial spore-formers lack, among others, spoIIB, sda, spoVID and safA genes and have non-orthologous displacements of spoIIQ and spoIVFA, suggesting substantial differences between bacilli and clostridia in the engulfment and spore coat formation steps. Many B. subtilis sporulation genes, particularly those encoding small acid-soluble spore proteins and spore coat proteins, were found only in the family Bacillaceae, or even in a subset of Bacillus spp. Phylogenetic profiles of sporulation genes, compiled in this work, confirm the presence of a common sporulation gene core, but also illuminate the diversity of the sporulation processes within various lineages. These profiles should help further experimental studies of uncharacterized widespread sporulation genes, which would ultimately allow delineation of the minimal set(s) of sporulation-specific genes in Bacilli and Clostridia.
Ca2+ entry following P2X receptor activation induces IP3 receptor‐mediated Ca2+ release in myocytes from small renal arteries

BACKGROUND AND PURPOSE P2X receptors mediate sympathetic control and autoregulation of the renal circulation triggering contraction of renal vascular smooth muscle cells (RVSMCs) via an elevation of intracellular Ca2+ concentration ([Ca2+]i). Although it is well‐appreciated that the myocyte Ca2+ signalling system is composed of microdomains, little is known about the structure of the [Ca2+]i responses induced by P2X receptor stimulation in vascular myocytes.
Extraction of Di-ethylhexyl-phthalate from Perfusion Lines of Various Material, Length and Brand by Lipid Emulsions

Background: The plasticizer di-ethylhexyl-phthalate (DEHP) is extracted especially by lipid emulsions from polyvinylchloride infusion systems. The aim of this study was to systematically examine the extraction from perfusion lines commonly used in our hospital for lipid emulsion infusions. Methods: Perfusion lines made from polyvinylchloride of various lengths and brands, polyethylene, polyvinylchloride/polyethylene (PVC/PE) and polyvinylchloride/polyurethane (PVC/PU), were perfused with lipid emulsions according to the circumstances of newborns on an intensive care unit, i.e. high temperature, 24-hour duration and low quantities. Concentration of di-ethylhexyl-phthalate was determined with gas chromatograph mass spectrometry. Results: The lipid emulsions before perfusion had a contamination with DEHP of 0.82 μg/ml. Pure PVC lines of 1.5 m length leached between 74 μg/ml and 107 μg/ml. Sterilization of the lines did not influence DEHP extraction. After perfusion of DEHP-free PVC lines and PVC-free lines, the emulsions had a contamination with DEHP of 0.23 μg/ml and 0.11 μg/ml, respectively. PVC/PU co-extruded lines leached 73 μg/ml. PVC/PE lines leached 41.6 μg/ml. Conclusions: Lipid emulsions contain a production-inherent load of DEHP. Perfusion through PVC-perfusion lines extracts a varying large amount of DEHP depending on length and brand of the perfusion lines. Co-extruded PVC/PU and PVC/PE lines, intended to avoid DEHP contamination, leach a similar amount of DEHP and thus do not avoid the DEHP toxicity issue. The load accumulated by a baby on an intensive care unit easily reaches several milligrams of DEHP per day. As its effect upon biologic systems has been proven, and alternatives (PE or PU perfusion lines) are available, PVC and PVC co-extruded perfusion lines should be abandoned for infusions, especially in babies.
Activation and Mitochondrial Translocation of Protein Kinase Cδ Are Necessary for Insulin Stimulation of Pyruvate Dehydrogenase Complex Activity in Muscle and Liver Cells*

In L6 skeletal muscle cells and immortalized hepatocytes, insulin induced a 2-fold increase in the activity of the pyruvate dehydrogenase (PDH) complex. This effect was almost completely blocked by the protein kinase C (PKC) δ inhibitor Rottlerin and by PKCδ antisense oligonucleotides. At variance, overexpression of wild-type PKCδ or of an active PKCδ mutant induced PDH complex activity in both L6 and liver cells. Insulin stimulation of the activity of the PDH complex was accompanied by a 2.5-fold increase in PDH phosphatases 1 and 2 (PDP1/2) activity with no change in the activity of PDH kinase. PKCδ antisense blocked insulin activation of PDP1/2, the same as with PDH. In insulin-exposed cells, PDP1/2 activation was paralleled by activation and mitochondrial translocation of PKCδ, as revealed by cell subfractionation and confocal microscopy studies. The mitochondrial translocation of PKCδ, like its activation, was prevented by Rottlerin. In extracts from insulin-stimulated cells, PKCδ co-precipitated with PDP1/2. PKCδ also bound to PDP1/2 in overlay blots, suggesting that direct PKCδ-PDP interaction may occur in vivo as well. In intact cells, insulin exposure determined PDP1/2 phosphorylation, which was specifically prevented by PKCδ antisense. PKCδ also phosphorylated PDP in vitro, followed by PDP1/2 activation. Thus, in muscle and liver cells, insulin causes activation and mitochondrial translocation of PKCδ, accompanied by PDP phosphorylation and activation. These events are necessary for insulin activation of the PDH complex in these cells.
A numerical approach for simulating the behaviour of timber shear walls

A numerical approach to simulate the behaviour of timber shear walls under both static and dynamic loading is proposed. Because the behaviour of timber shear walls hinges on the behaviour of the nail connections, the force-displacement behaviour of sheathing-to-framing nail connections are first determined and then used to define the hysteretic properties of finite elements representing these connections. The model nails are subsequently implemented into model walls. The model walls are verified using experimental results for both monotonic and cyclic loading. It is demonstrated that the complex hysteretic behaviour of timber shear walls can be reasonably represented using model shear walls in which nonlinear material failure is concentrated only at the sheathing-to-framing nail connections.
HIGH-STRENGTH CONCRETE IN UNIAXIAL TENSION

The behavior of high-strength concrete (HSC) subjected to uniaxial tension was investigated in this paper. The complete tensile stress-deformation response of HSC was acquired through an extensive experimental program. The experimental program comprised of testing concrete with compressive strengths equal to 6 ksi (41 MPa), 12 ksi (83 MPa), and 15 ksi (103 MPa). An analytical expression was proposed for the relationship between the axial stress and crack width in HSC. This relationship was developed for the determination of fracture parameters such as fracture energy and the characteristic length for the three compressive strengths. The higher compressive strength concretes exhibited larger fracture energies and lower characteristic lengths. A relationship between the tensile and compressive strengths of HSC was established. Although HSCs exhibit larger tensile strengths, there is a decrease in the ratio of tensile-to-compressive strength at higher compressive strengths. Accordingly, the uniaxial tensile strength of HSC can be predicted by the expression f't = 6.1 times the square root of f'c, where f't and f'c are the tensile and compressive strengths, respectively. In comparison with the expression developed for normal strength concrete (f't = 6.5 times the square root of f'c), this expression predicts lower tensile strengths at higher strength levels.