Miracle-dz/UniFAR-FTUs huggingface dataset:
Blocking Pseudomonas Aeruginosa, Chromobacterium Violaceum, and Ralstonia Solanacearum Adhesion by Fruit Glycans

The soil-borne pathogens Pseudomonas aeruginosa, Chromobacterium violaceum, and Ralstonia solanacearum, possess the lectins PA-IL, PA-IIL, CV-IIL, RSL, and RS-IIL, which may mediate their adhesion onto animal and plant target cells, enabling infections. Such infections may be prevented by surrounding the sensitive cells with competing glycans, which act as glycodecoys that block patholectins and capture pathogens that bear them. The abovementioned five lectins have been used by us as probes to reveal progeny-protecting glycodecoys in avian eggs, milk, royal jelly, and seeds. Herein we describe their usage as probes for fruit and onion glycodecoys. They revealed lectin-blocking galactosides, fructose, oligo/polysaccharides, and glycoproteins in most of the examined fruits. Galactose/arabinose- bearing compounds were detected by PA-IL in banana, carob, pineapple, pomegranate, kiwifruit, and dates. Diverse mannose/fucose-bearing compounds were detected by PAIIL in banana, onion, and pomegranate; by CV-IIL in pineapple; by RSL in banana, carob, date, onion, and pineapple, and by RS-IIL in date and fig. The results show the high efficiency of these lectins as probes for natural infection-preventing glycodecoys. Usage of fruit and seed embryo-protecting glycodecoys, unless allergenic, is advantageous for preventing animal intestinal and external and plant wilting infections since they are natural, harmless, inexpensive, and widely available.
Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids

Small RNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), and trans-acting siRNAs (tasiRNAs), control gene expression and epigenetic regulation. Although the roles of miRNAs and siRNAs have been extensively studied, their expression diversity and evolution in closely related species and interspecific hybrids are poorly understood. Here, we show comprehensive analyses of miRNA expression and siRNA distributions in two closely related species Arabidopsis thaliana and Arabidopsis arenosa, a natural allotetraploid Arabidopsis suecica, and two resynthesized allotetraploid lines (F1 and F7) derived from A. thaliana and A. arenosa. We found that repeat- and transposon-associated siRNAs were highly divergent between A. thaliana and A. arenosa. A. thaliana siRNA populations underwent rapid changes in F1 but were stably maintained in F7 and A. suecica. The correlation between siRNAs and nonadditive gene expression in allopolyploids is insignificant. In contrast, miRNA and tasiRNA sequences were conserved between species, but their expression patterns were highly variable between the allotetraploids and their progenitors. Many miRNAs tested were nonadditively expressed (deviating from the mid-parent value, MPV) in the allotetraploids and triggered unequal degradation of A. thaliana or A. arenosa targets. The data suggest that small RNAs produced during interspecific hybridization or polyploidization serve as a buffer against the genomic shock in interspecific hybrids and allopolyploids: Stable inheritance of repeat-associated siRNAs maintains chromatin and genome stability, whereas expression variation of miRNAs leads to changes in gene expression, growth vigor, and adaptation.
Diffuse Traumatic Axonal Injury in the Mouse Induces Atrophy, c-Jun Activation, and Axonal Outgrowth in the Axotomized Neuronal Population

Traumatic axonal injury (TAI) is a consistent component of traumatic brain injury (TBI) and is associated with much of its morbidity. Little is known regarding the long-term retrograde neuronal consequences of TAI and/or the potential that TAI could lead to anterograde axonal reorganization and repair. To investigate the repertoire of anterograde and retrograde responses triggered by TIA, Thy1-YFP-H mice were subjected to mild central fluid percussion injury and killed at various times between 15 min and 28 d post-injury. Based upon confocal assessment of the endogenous neuronal fluorescence, such injury was found to result in diffuse TAI throughout layer V of the neocortex within yellow fluorescent protein (YFP)-positive axons. When these fluorescent approaches were coupled with various quantitative and immunohistochemical approaches, we found that this TAI did not result in neuronal death over the 28 d period assessed. Rather, it elicited neuronal atrophy. Within these same axotomized neuronal populations, TAI was also found to induce an early and sustained activation of the transcription factors c-Jun and ATF-3 (activating transcription factor 3), known regulators of axon regeneration. Parallel ultrastructural studies confirmed that these reactive changes are consistent with atrophy in the absence of neuronal death. Concurrent with those events ongoing in the neuronal cell bodies, their downstream axonal segments revealed, as early as 1 d post-injury, morphological changes consistent with reactive sprouting that was accompanied by significant axonal elongation over time. Collectively, these TAI-linked events are consistent with sustained neuronal recovery, an activation of a regenerative genetic program, and subsequent axonal reorganization suggestive of some form of regenerative response.
Polynomial Clones on Squarefree Groups

We prove that, on a set of size n, the number of clones that contain a group operation and all constant functions is finite if n is squarefree. This confirms a conjecture by Pawel Idziak from [5] where the converse implication was shown. Our result follows from the observation that the polynomial clone of an expansion of a squarefree group is uniquely determined by its binary functions. We also note that, in general, such a clone is not determined by the congruence lattice and the commutator operation of the corresponding algebra. This refutes a second conjecture from [5].
Computational Distinguishability of Quantum Channels

The computational problem of distinguishing two quantum channels is central to quantum computing. It is a generalization of the well-known satisfiability problem from classical to quantum computation. This problem is shown to be surprisingly hard: it is complete for the class QIP of problems that have quantum interactive proof systems, which implies that it is hard for the class PSPACE of problems solvable by a classical computation in polynomial space. Several restrictions of distinguishability are also shown to be hard. It is no easier when restricted to quantum computations of logarithmic depth, to mixed-unitary channels, to degradable channels, or to antidegradable channels. These hardness results are demonstrated by finding reductions between these classes of quantum channels. These techniques have applications outside the distinguishability problem, as the construction for mixed-unitary channels is used to prove that the additivity problem for the classical capacity of quantum channels can be equivalently restricted to the mixed unitary channels.
Temperature Sensitivity and Basal Rate of Soil Respiration and Their Determinants in Temperate Forests of North China

The basal respiration rate at 10°C (R10) and the temperature sensitivity of soil respiration (Q10) are two premier parameters in predicting the instantaneous rate of soil respiration at a given temperature. However, the mechanisms underlying the spatial variations in R10 and Q10 are not quite clear. R10 and Q10 were calculated using an exponential function with measured soil respiration and soil temperature for 11 mixed conifer-broadleaved forest stands and nine broadleaved forest stands at a catchment scale. The mean values of R10 were 1.83 µmol CO2 m−2 s−1 and 2.01 µmol CO2 m−2 s−1, the mean values of Q10 were 3.40 and 3.79, respectively, for mixed and broadleaved forest types. Forest type did not influence the two model parameters, but determinants of R10 and Q10 varied between the two forest types. In mixed forest stands, R10 decreased greatly with the ratio of coniferous to broadleaved tree species; whereas it sharply increased with the soil temperature range and the variations in soil organic carbon (SOC), and soil total nitrogen (TN). Q10 was positively correlated with the spatial variances of herb-layer carbon stock and soil bulk density, and negatively with soil C/N ratio. In broadleaved forest stands, R10 was markedly affected by basal area and the variations in shrub carbon stock and soil phosphorus (P) content; the value of Q10 largely depended on soil pH and the variations of SOC and TN. 51% of variations in both R10 and Q10 can be accounted for jointly by five biophysical variables, of which the variation in soil bulk density played an overwhelming role in determining the amplitude of variations in soil basal respiration rates in temperate forests. Overall, it was concluded that soil respiration of temperate forests was largely dependent on soil physical properties when temperature kept quite low.
The spatial pattern of atrial cardiomyocyte calcium signalling modulates contraction

We examined the regulation of calcium signalling in atrial cardiomyocytes during excitation-contraction coupling, and how changes in the distribution of calcium impacts on contractility. Under control conditions, calcium transients originated in subsarcolemmal locations and showed local regeneration through activation of calcium-induced calcium release from ryanodine receptors. Despite functional ryanodine receptors being expressed at regular (∼2 μm) intervals throughout atrial myocytes, the subsarcolemmal calcium signal did not spread in a fully regenerative manner through the interior of a cell. Rather, there was a diminishing centripetal propagation of calcium. The lack of regeneration was due to mitochondria and SERCA pumps preventing the inward movement of calcium. Inhibiting these calcium buffering mechanisms allowed the globalisation of action potential-evoked responses. In addition, physiological positive inotropic agents, such as endothelin-1 and β-adrenergic agonists, as well as enhanced calcium current, calcium store loading and inositol 1,4,5-trisphosphate infusion also led to regenerative global responses. The consequence of globalising calcium signals was a significant increase in cellular contraction. These data indicate how calcium signals and their consequences are determined by the interplay of multiple subcellular calcium management systems.
Fear Modulates Visual Awareness Similarly for Facial and Bodily Expressions

Background: Social interaction depends on a multitude of signals carrying information about the emotional state of others. But the relative importance of facial and bodily signals is still poorly understood. Past research has focused on the perception of facial expressions while perception of whole body signals has only been studied recently. In order to better understand the relative contribution of affective signals from the face only or from the whole body we performed two experiments using binocular rivalry. This method seems to be perfectly suitable to contrast two classes of stimuli to test our processing sensitivity to either stimulus and to address the question how emotion modulates this sensitivity. Method: In the first experiment we directly contrasted fearful, angry, and neutral bodies and faces. We always presented bodies in one eye and faces in the other simultaneously for 60 s and asked participants to report what they perceived. In the second experiment we focused specifically on the role of fearful expressions of faces and bodies. Results: Taken together the two experiments show that there is no clear bias toward either the face or body when the expression of the body and face are neutral or angry. However, the perceptual dominance in favor of either the face of the body is a function of the stimulus class expressing fear.
Kinetics of Gag-specific cytotoxic T lymphocyte responses during the clinical course of HIV-1 infection: a longitudinal analysis of rapid progressors and long-term asymptomatics

To gain more insight into the role of HIV-1-specific cytotoxic T lymphocytes (CTL) in the pathogenesis of AIDS, we investigated temporal relations between HIV-1 Gag-specific precursor CTL (CTLp), HIV-1 viral load, CD4+ T cell counts, and T cell function. Six HIV-1-infected subjects, who were asymptomatic for more than 8 yr with CD4+ counts > 500 cells/mm3, were compared with six subjects who progressed to AIDS within 5 yr after HIV-1 seroconversion. In the long-term asymptomatics, persistent HIV-1 Gag-specific CTL responses and very low numbers of HIV- 1-infected CD4+ T cells coincided with normal and stable CD4+ counts and preserved CD3 mAb-induced T cell reactivity for more than 8 yr. In five out of six rapid progressors Gag-specific CTLp were also detected. However, early in infection the number of circulating HIV-1-infected CD4+ T cells increased despite strong and mounting Gag-specific CTL responses. During subsequent clinical progression to AIDS, loss of Gag- specific CTLp coincided with precipitating CD4+ counts and severe deterioration of T cell function. The possible relationships of HIV-1 Gag-specific CTLp to disease progression are discussed.
The Ultraviolet Spectra of the Weak Emission Line Central Stars of Planetary Nebulae

The UV spectra of all "weak emission line central stars of planetary nebulae" (WELSs) with available IUE data are presented and discussed. We performed line identifications and equivalent-width and flux measurements for several features in the spectra. We found that the WELSs can be divided into three different groups regarding their UV spectra: (1) strong P Cygni profiles (mainly in C IV λ1549), (2) weak P Cygni features, and (3) absence of P Cygni profiles. The last group encompasses stars with a featureless UV spectrum or with intense emission lines and a weak continuum, which are most likely of nebular origin. We have measured wind terminal velocities for all objects presenting P Cygni profiles in N V λ1238 and/or C IV λ1549. The results obtained were compared to the UV data of the two prototype stars of the [WC]-PG 1159 class, namely, A30 and A78. For WELSs presenting P Cygni features, most of the terminal velocities fall in the range of ∼1000-1500 km s-1, while [WC]-PG 1159 stars possess much higher values, of ∼3000 km s-1. The [WC]-PG 1159 stars are characterized by intense, simultaneous P Cygni emissions in the ∼1150-2000 Å interval of N V λ1238, O V λ1371, and C IV λ1549. In contrast, we found that O V λ1371 is very weak or absent in the WELS spectra. On the basis of the UV spectra alone, our findings indicate that [WC]-PG 1159 stars are distinct from the WELSs, contrary to previous claims in the literature.
Using generative design patterns to generate parallel code for a distributed memory environment

A design pattern is a mechanism for encapsulating the knowledge of experienced designers into a re-usable artifact. Parallel design patterns reflect commonly occurring parallel communication and synchronization structures. Our tools, CO2P3S (Correct Object-Oriented Pattern-based Parallel Programming System) and MetaCO2P3S, use generative design patterns. A programmer selects the parallel design patterns that are appropriate for an application, and then adapts the patterns for that specific application by selecting from a small set of code-configuration options. CO2P3S then generates a custom framework for the application that includes all of the structural code necessary for the application to run in parallel. The programmer is only required to write simple code that launches the application and to fill in some application-specific sequential hook routines. We use generative design patterns to take an application specification (parallel design patterns + sequential user code) and use it to generate parallel application code that achieves good performance in shared memory and distributed memory environments. Although our implementations are for Java, the approach we describe is tool and language independent. This paper describes generalizing CO2P3S to generate distributed-memory parallel solutions.
Minimizing collateral damage by proactive surge protection

Existing mechanisms for defending against distributed denial-of-service (DDoS) attacks are generally reactive in nature. However, the onset of large-scale bandwidth-based attacks can occur suddenly, potentially knocking out substantial parts of a network before reactive defenses can respond. Even for traffic flows that are not under direct attack, significant collateral damage will result if these flows pass through links that are common to attack routes. This paper presents a proactive-surge-protection (PSP) mechanism that aims to provide a broad first line of defense against DDoS attacks. Our solution aims to minimize collateral damage by providing bandwidth isolation between traffic flows. This isolation is achieved through a combination of traffic forecasting, proportional allocation of network capacity, metering and tagging of packets at the network perimeter, and preferential dropping of packets inside the network. Our solution is readily deployable using existing router mechanisms. Simulations across three large backbone networks show that up to 95.5% of the network could suffer collateral damage without protection, but our solution was able to reduce the amount of collateral damage by 60.5-97.8%, even with a coarse-grained forecasting scheme.
Oleuropein Attenuates Deltamethrin-induced Apoptosis in Rat Cerebellar Purkinje Neurons

Corresponding Author: Ali Reza khalatbary Molecular and Cell Biology Research Center, Department of Anatomy, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran. Phone: +98 1133200894 E-mail: khalat90@yahoo.com Abstract Background: Deltamethrin (DM) is a synthetic pyrethroid insecticide that can elicit neurotoxicity, and lead to apoptosis. There is accumulating evidence that oleuropein (OE) has anti-apoptotic effect. This study aimed at determining the DM toxicity and anti-apoptotic effect of OE pretreatment in cerebellar Purkinje neurons. Materials and Methods: Rats were randomly divided into four groups as follow: DM treated group (12.5 mg/kg; single dose), OE treated group (20 mg/kg per day), DM plus OE treated group, and vehicle group. Sections of cerebellum were taken 24 hours after deltamethrin injection and studied for histopathological and immunohistochemistry assessments. Results: Further characteristics of degeneration in Purkinje neurons were observed in DM group compared with DM plus OE group. Compared with DM group (9.56±1.69), the positive staining for Bax in Purkinje neurones decreased in DM plus OE group (2.99±0.50) but upper than OE (0.72±0.15) and vehicle (0.57±0.03) groups. Compared with DM group (0.50±0.05), the positive staining for Bcl-2 in Purkinje neurons increased in DM plus OE group (3.29±0.18) but lower than OE (4.38±0.80) and vehicle (5.87±1.93) groups. Conclusions: Our results suggest that DM induces apoptosis in Purkinje cells which is subsided by oleuropein.
Habitat requirements of Cardaminopsis petraea — Rare and relict species of the Czech Republic

Vegetation with Cardaminopsis petraea was sampled by phytosociological relevés at almost all the known Czech sites, and characterized by indicator values, influence of potential direct solar irradiation, and bedrock type with the aid of multivariate methods. It has been declared that C. petraea prefers open natural or seminatural drier to mesophilous habitats without some preference to the bedrock. It occupies habitats with various slopes, but it prefers more extreme slants and northerly exposed slopes. The classification and ordination methods showed clear distinction between Moravian and Bohemian habitats. Apart from other types, in Bohemia this species occurs uniquely in acidophilous rock communities, whereas in Moravia it grows uniquely within calcareous grasslands. Relictness of the species was discussed in relation to the specific site conditions (light supply, disturbance regime, and geographical isolation) and to the occurrence of other rare taxa and habitats. Occurrence on some man-made habitats was also observed.
Down syndrome critical region protein 5 regulates membrane localization of Wnt receptors, Dishevelled stability and convergent extension in vertebrate embryos

The Glypican family of heparan sulfate proteoglycans regulates Wnt signaling and convergent extension (CE) in vertebrate embryos. They are predicted to be glycosylphosphatidylinositol (GPI)-tethered membrane-bound proteins, but there is no functional evidence of their regulation by the GPI synthesis complex. Down syndrome critical region protein 5 (Dscr5, also known as Pigp) is a component of the GPI-N-acetylglucosaminyltransferase (GPI-GnT) complex, and is associated with specific features of Down syndrome. Here we report that Dscr5 regulates CE movements through the non-canonical Wnt pathway. Both dscr5 overexpression and knockdown impaired convergence and extension movements. Dscr5 functionally interacted with Knypek/Glypican 4 and was required for its localization at the cell surface. Knockdown of dscr5 disrupted Knypek membrane localization and caused an enhanced Frizzled 7 receptor endocytosis in a Caveolin-dependent manner. Furthermore, dscr5 knockdown promoted specific Dishevelled degradation by the ubiquitin-proteosome pathway. These results reveal a functional link between Knypek/Glypican 4 and the GPI synthesis complex in the non-canonical Wnt pathway, and provide the new mechanistic insight that Dscr5 regulates CE in vertebrate embryos by anchoring different Wnt receptors at the cell surface and maintaining Dishevelled stability.
Time is of the essence: exploring a measles outbreak response vaccination in Niamey, Niger

The current World Health Organization recommendations for response during measles epidemics focus on case management rather than outbreak response vaccination (ORV) campaigns, which may occur too late to impact morbidity and mortality and have a high cost per case prevented. Here, we explore the potential impact of an ORV campaign conducted during the 2003–2004 measles epidemic in Niamey, Niger. We measured the impact of this intervention and also the potential impact of alternative strategies. Using a unique geographical, epidemiologic and demographic dataset collected during the epidemic, we developed an individual-based simulation model. We estimate that a median of 7.6% [4.9–8.9] of cases were potentially averted as a result of the outbreak response, which vaccinated approximately 57% (84 563 of an estimated 148 600) of children in the target age range (6–59 months), 23 weeks after the epidemic started. We found that intervening early (up to 60 days after the start of the epidemic) and expanding the age range to all children aged 6 months to 15 years may lead to a much larger (up to 90%) reduction in the number of cases in a West African urban setting like Niamey. Our results suggest that intervening earlier even with lower target coverage (approx. 60%), but a wider age range, may be more effective than intervening later with high coverage (more than 90%) in similar settings. This has important implications for the implementation of reactive vaccination interventions as they can be highly effective if the response is fast with respect to the spread of the epidemic.