Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunoblot reactivity of polyclonal and monoclonal antibodies with periplasmic flagellar proteins FlaA1 and FlaB of porcine Serpulina species

The periplasmic-flagellum (PF) proteins of Triton X-100-soluble and Triton X-100-insoluble sodium dodecyl sulfate-treated fractions from reference and field strains of Serpulina hyodysenteriae, Serpulina innocens, and Serpulina pilosicoli were characterized by Western blotting with a rabbit polyclonal antibody (PAb) specific for the 44-kDa PF sheath protein of S. hyodysenteriae (Z. Li, F. Dumas, D. Dubreuil, and M. Jacques, J. Bacteriol. 175:8000-8007, 1993) and a murine monoclonal antibody (MAb), designated 7G2, specific for the PF core FlaB proteins of S. hyodysenteriae. The MAb 7G2 reacted with a conserved epitope present in the 37-, 34-, and 32-kDa PF core FlaB proteins of all Serpulina species. This suggested that the core FlaB proteins are conserved among porcine Serpulina species. An immunoreactive band of approximately 44 kDa was present with all S. hyodysenteriae, S. innocens, and S. pilosicoli strains that were reacted with the PAb. The specificities of the PAb and the MAb for the FlaA1 and FlaB proteins of Serpulina species were confirmed by N-terminal amino acid sequencing of 44- and 37-kDa proteins, respectively, of S. hyodysenteriae and S. pilosicoli. Results from this study provide further evidence that the 44-kDa protein FlaA1 and the 37-, 34-, and 32-kDa FlaB proteins are conserved among porcine Serpulina species.
Local adaptation and maternal effects in two species of marine gastropod (genus Crepidula) that differ in dispersal potential

Adaptation to local conditions should be less likely in species with wide dispersal since periodic immigration from populations not under selection would counteract the short-term results of local selection. To test this hypothesis, we used 2 species of sympatric marine gastropods of the genus Crepidula that have vastly different early life dispersal stages. Offspring of C. fornicata emerge as long-lived free-swimming larvae, whereas offspring of C. convexa emerge as benthic juveniles. We investigated the local adaptation of each species at 2 locations by assessing their tolerance to the toxic metal copper in the laboratory. We conducted 96 h acute copper toxicity tests with juveniles of C. con- vexa and larvae of C. fornicata released in the laboratory by adults collected from a reference site (Lynn Harbor, Nahant, Massachusetts, USA) or a polluted site (New Bedford Harbor, Fairhaven, Massachusetts). To test for maternal effects, we also raised C. fornicata released in the laboratory (F1 generation) to sexual maturity and tested for differences in copper tolerance of their offspring (F2). As expected, juveniles of C. convexa from the polluted site were significantly more copper tolerant than juveniles from the reference site (p ≤ 0.05), suggesting local adaptation at the polluted site. Con- trary to expectations, F1 larvae of C. fornicata from the polluted site were not equally copper tolerant, but less copper tolerant than F1 larvae from the reference site. However, copper tolerance did not differ for F2 larvae of C. fornicata from the 2 sites. Our results suggest that populations of C. convexa can adapt to locally high metal concentrations, while populations of C. fornicata cannot, probably because of the periodic input of C. fornicata larvae from distant populations that do not experience high metal stress. Also, long-term exposure of C. fornicata adults to pollutants apparently decreased the copper tolerance of their offspring (F1 generation), an effect not seen in the laboratory-propa- gated F2 generation.
Single Port Overlay Cognitive Radio Using Reconfigurable Filtennas

— In this paper cognitive radio is presented and the spectrum overlay cognitive radio antenna system is detailed. A UWB antenna with frequency reconfigurable characteristics is proposed. The reconfigurability is achieved when the filter is integrated to the feeding line of the single port overlay cognitive radio. When activated, the filter can transform the UWB frequency response into a reconfigurable narrowband one, which is suitable for the communication operation of the CR system. Here single port overlay cognitive radio antenna is designed and simulated using Ansoft High Frequency Structure Simulator (HFSS).
Protein-protein interactions that regulate the energy stress activation of sigma(B) in Bacillus subtilis.

Sigma(B) is an alternative sigma factor that controls the general stress response in Bacillus subtilis. In the absence of stress, sigma(B) is negatively regulated by anti-sigma factor RsbW. RsbW is also a protein kinase which can phosphorylate RsbV. When cells are stressed, RsbW binds to unphosphorylated RsbV, produced from the phosphorylated form of RsbV by two phosphatases (RsbU and RsbP) which are activated by stress. We now report the values of the K(m) for ATP and the K(i) for ADP of RsbW (0.9 and 0.19 mM, respectively), which reinforce the idea that the kinase activity of RsbW is directly regulated in vivo by the ratio of these nucleotides. RsbW, purified as a dimer, forms complexes with RsbV and sigma(B) with different stoichiometries, i.e., RsbW(2)-RsbV(2) and RsbW(2)-sigma(B)(1). As determined by surface plasmon resonance, the dissociation constants of the RsbW-RsbV and RsbW-sigma(B) interactions were found to be similar (63 and 92 nM, respectively). Nonetheless, an analysis of the complexes by nondenaturing polyacrylamide gel electrophoresis in competition assays suggested that the affinity of RsbW(2) for RsbV is much higher than that for sigma(B). The intracellular concentrations of RsbV, RsbW (as a monomer), and sigma(B) measured before stress were similar (1.5, 2.6, and 0.9 micro M, respectively). After ethanol stress they all increased. The increase was greatest for RsbV, whose concentration reached 13 micro M, while those of RsbW (as a monomer) and sigma(B) reached 11.8 and 4.9 micro M, respectively. We conclude that the higher affinity of RsbW for RsbV than for sigma(B), rather than a difference in the concentrations of RsbV and sigma(B), is the driving force that is responsible for the switch of RsbW to unphosphorylated RsbV.
A model for resolving the plankton paradox : coexistence in open flows

1. Recent developments in the field of chaotic advection in hydrodynamical/environmental flows encourage us to revisit the population dynamics of competing species in open aquatic systems. 2. We assume that these species are in competition for a common limiting resource in open flows with chaotic advection dynamics. As an illustrative example, we consider a time periodic two-dimensional flow of viscous fluid (water) around a cylindrical obstacle. 3. Individuals accumulate along a fractal set in the wake of the cylinder, which acts as a catalyst for the biological reproduction process. While in homogeneous, well mixed environments only one species could survive this competition, coexistence of competitors is typical in our hydrodynamical system. 4. It is shown that a steady state sets in after sufficiently long times. In this state, the relative density of competitors is determined rather by the fractal nature of the spatial distribution of the advected species, and by their initial conditions, than by their competitive abilities. We argue that two factors, the strong chaotic mixing along a fractal set and the boundary layer around the obstacle, are responsible for the coexistence.
Provably secure authentication protocol based on convertible proxy signcryption in cloud computing

Mutual authentication between the user and the public cloud is essential requirement for the user to access the public cloud in cloud computing. In 2011, Juang et al. proposed a first authentication scheme based on proxy signature. The advantage of the scheme is that the user only needs to register on his home service cloud (HSC), and can pass through the authentication of the public cloud with the help of his HSC. However, their scheme has three weaknesses: 1) the user's HSC needs to update the user's public key in each session to protect the user's privacy; 2) HSC may suffer from network jam when many users in the same HSC need to register on different public clouds simultaneously; and 3) a secret key should be shared between HSC and visiting cloud. To overcome these weaknesses, a provably secure convertible proxy signcryption for privacy preserving is proposed. Based on this scheme, a novel one-round authentication protocol is proposed, which the user only needs to register on his HSC, and can pass through the authentication of the visiting cloud without the help of his HSC. On the other hand, the proposed protocol can provide some nice properties, such as user privacy protection, non-repudiation, without updating the user's public key, and secret key does not have to be shared between HSC and visiting cloud. In addition, the proposed scheme is provably secure in the random oracle model, and is more efficient than Juang et al.'s scheme.
Técnicas geoestadísticas aplicadas al análisis de la distribución de capturas de Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) mediante trampas conferomonas sexuales en una plantación de tomate.

En una plantacion de tomates se aplican metodos geoestadisticos, para obtener unos mapas de la distribucion de capturas de Helicoverpa armigera (Hubner) a partir de 112 trampas con feromonas sexuales. Durante el periodo del 10 al 31de julio, justo antes de la recoleccion del tomate y del 14 al 17 de agosto, unos dias despues de la recoleccion, se estudio diariamente la variacion espacial de las capturas, respuesta conjunta a la emision de feromonas y a la poblacion de mariposas. La feromona empleada fue (Z)-11-hexadecenol y (Z)-9-hexadecenol en proporcion 97/3. Con el uso de tecnicas de estimacion geoestadistica "krigeado", se consiguio representar diariamente las distribuciones espaciales de las capturas, lo que permitio analizar su evolucion temporal. La modelizacion mediante variogramas teoricos de tipo esferico o exponencial, con un importante efecto pepita, denotan la notable oscilacion de las densidades de capturas en la parcela. Se realizaron estimaciones en una gran cantidad de puntos no muestrales, lo cual sirvio de base para la elaboracion de mapas de distribucion de las capturas, para los dias considerados. Con esta informacion se hace una propuesta de reparto de feromonas en la plantacion ya sea con vistas al seguimiento de la plaga o a un posible desarrollo de metodos biotecnicos de control (confusion sexual, trampeo masivo).
AMBIENT NOISE HORIZONTAL-TO-VERTICAL SPECTRAL RATIO FOR ASSESSING SITE EFFECTS IN URBAN ENVIRONMENTS: THE CASE OF THESSALONIKI CITY (NORTHERN GREECE)

ambient noise measurements were performed in a dense grid (about 150mX150m) cover- ing the historical center of the city of Thessaloniki (Northern Greece), that was strongly affected by the 20/6/1978 (M=6.5) damaging earthquake. The data were processed using the method of hori- zontal-to-vertical (H/V) spectral ratio (Nogoshi and Igarashi, 1971; Nakamura, 1989). In order to evaluate diurnal and seasonal variation (summer - winter) of the ambient noise H/V spectral ratio, systematic measurements were performed in eight sites. The fundamental frequency (fo) and the corresponding H/V amplitude level (Ao) from the ambient noise H/V spectral ratio for each site were calculated. Spatial interpolation of the fundamental frequency (fo) and the corresponding H/V ampli- tude level (Ao) was attempted between all points and respective contour maps were produced. Diurnal variation of the ambient noise H/V spectral ratio showed that it is preferable to perform measurements during the calm hours of a day, when manmade noise is relatively low. However, no systematic seasonal fluctuation effect on the ambient noise H/V spectral ratio was identified for the city of Thessaloniki. Contour maps of both fundamental frequency (fo) and corresponding H/V am- plitude level (Ao) were compared versus the macroseismic data of the 1978 earthquake (Leven- takis, 2003), as well as with related geological (IGME, 1978) and geotechnical (Anastasiadis et al., 2001) studies for the same area. Damage distribution due to 20/6/1978 earthquake (Penelis et al., 1985) was also converted to EMS_98 (European Macroseismic Scale, 1998). For seventy build- ings, made of reinforced concrete, we have also compared the obtained results with the dynamic amplification of the buildings (Ubuilding) at the fundamental soil frequency (fo). The results encour- age the use of ambient noise measurements along with the (H/V) spectral ratio technique as a non- expensive and fast tool in microzonation studies to be carried out in urban environments.
The Regulatory β Subunit of Protein Kinase CK2 Mediates Formation of Tetrameric CK2 Complexes*

Protein kinase CK2 is a tetrameric enzyme composed of two catalytic (α and/or α′) subunits and two regulatory (β) subunits. Because CK2β is synthesized in excess of CK2α, we hypothesized that formation of CK2β homodimers precedes the incorporation of the catalytic subunits of CK2 into complexes. To test this hypothesis, we cotransfected cells with two epitope-tagged variants of CK2β. The results of these cotransfection studies demonstrate that interactions between two CK2β subunits take place in the absence of CK2α. Together with results from previous biosynthetic labeling studies, these results suggest that formation of CK2β homodimers occurs before incorporation of catalytic subunits of CK2 into CK2 complexes. We also cotransfected Cos-7 cells with a deletion fragment of CK2β (i.e. Myc-β1–166) together with full-length hemagglutinin (HA)-tagged CK2β and/or CK2α′. Although complexes between Myc-β1–166 and HA-β were readily detected, we obtained no evidence of direct interactions between Myc-β1–166 and HA-CK2α′. These results suggest that residues within the N-terminal 166 amino acids of CK2β are sufficient for interactions between CK2β subunits, whereas the C-terminal domain of CK2β is required for complex formation with the catalytic subunits of CK2. Finally, we observed that expression of full-length HA-β promotes phosphorylation of Myc-β1–166 by HA-CK2α′.
P is a proper subset of NP

The purpose of this article is to examine and limit the conditions in which the P complexity class could be equivalent to the NP complexity class. Proof is provided by demonstrating that as the number of clauses in a NP-complete problem approaches infinity, the number of input sets processed per computation performed also approaches infinity when solved by a polynomial time solution. It is then possible to determine that the only deterministic optimization of a NP-complete problem that could prove P=NP would be one that examines no more than a polynomial number of input sets for a given problem. It is then shown that subdividing the set of all possible input sets into a polynomial-sized search partition is a problem in the FEXP complexity class. By demonstrating that at least one NP-complete problem exists such that the set of all possible input sets for that problem cannot be partitioned in polynomial time, it then will follow that P = NP.
The Mutational Landscape of Head and Neck Squamous Cell Carcinoma

The mutational profile of head and neck cancer is complex and may pose challenges to the development of targeted therapies. Head and neck squamous cell carcinoma (HNSCC) is a common, morbid, and frequently lethal malignancy. To uncover its mutational spectrum, we analyzed whole-exome sequencing data from 74 tumor-normal pairs. The majority exhibited a mutational profile consistent with tobacco exposure; human papillomavirus was detectable by sequencing DNA from infected tumors. In addition to identifying previously known HNSCC genes (TP53, CDKN2A, PTEN, PIK3CA, and HRAS), our analysis revealed many genes not previously implicated in this malignancy. At least 30% of cases harbored mutations in genes that regulate squamous differentiation (for example, NOTCH1, IRF6, and TP63), implicating its dysregulation as a major driver of HNSCC carcinogenesis. More generally, the results indicate the ability of large-scale sequencing to reveal fundamental tumorigenic mechanisms.
17th International Conference on Harmonisation within Atmospheric Dispersion Modelling for Regulatory Purposes

The model chain is aimed to simulate high buoyant plume and can be applied in case of risk assessment and emergency response. It consists of the WRF mesoscale meteorological model and the SPRAYWEB dispersion model. The novelty lies in the new interface linking the two models. We use the Bull-Run data-set from the model evaluation kit in order to compare our results.
Consommation d'eau de la vigne en conditions hydriques non limitantes. Formulation simplifiée de la transpiration

La modelisation geometrique de la vigne, utilisee pour l'interception du rayonnement solaire (RIOU et al. 1989) est d'abord reprise pour evaluer les bilans radiatifs de la vigne et du sol intercalaire. La verification experimentale est satisfaisante. Apres une periode pluvieuse, les differents flux du bilan d'energie du vignoble sont ensuite mesures, notamment grâce a la methode des correlations tourbillonnaires tandis que la transpiration de la vigne seule est obtenue par une mesure de flux de seve (VALANCOGNE et NASR 1993). Trois grandeurs concernant la vigne elle-meme restent proches: le taux de transpiration par rapport a l'evaporation totale , le taux d' absorption du rayonnement net par rapport au bilan radiatif total et le taux d'absorption du rayonnement solaire par rapport au rayonnement global absorbe par le vignoble; une simulation montre que ces deux derniers taux restent voisins quand la distance entre rangs varie. L'evapotranspiration maximum etant finalement exprimee correctement par la formule de PENMAN (1948), ces resultats conduisent a proposer une formulation simple de la transpiration de la vigne en conditions hydriques non limitantes. Water use of grapevines well supplied with water. Simplified expression of transpiration A model of solar radiation interception by a vineyard canopy from simple geometrical assumptions (Riou et al. 1989) is first extended into a model of the whole radiative balance of the vine rows and of the intervening soil surface; experimental validation is excellent. After a rainy period, the various fluxes taking part in the energy balance of a vineyard canopy were measured, among which total evaportranspiration by an eddy correlation technique, and vine transpiration from a sap-flow estimation (Valancogne et Nasr 1993). Three partition rates quantifying the exchanges of the vines alone remain noticeably close to each other: those of transpiration over total evaportranspiration, of absorbed net radiation over overall radiative balance, and of intercepted global radiation over global radiation intercepted by the whole canopy. From a simulation, evidence is provided these two latter rates are still hardly distinguishable when the row spacing is changed. As maximum evapotranspiration is quite correctly expressed by the Penman formula, these results lead to the proposal of a simple method for estimating transpiration of grapevines well supplied with water.
Inter-hemispheric Decadal Variations in SST, Surface Wind, Heat Flux and Cloud Cover over the Atlantic Ocean

Atlantic decadal climate variations are studied using marine meteorological observations. To remove artificial interhemispheric correlation, we perform empirical orthogonal function (EOF) analysis of sea surface temperature (SST) variability separately for the North and South Atlantic. The first EOF for the North (South) Atlantic in the decadal (8‐16 years) band features a meridional tripole (dipole). In the tropics, the northern and southern leading EOFs form a meridional dipole with a center of action at 15 � on either side of the equator. The leading sea level pressure (SLP) EOFs for the North and South Atlantic each feature a center of action that is displaced poleward of the tropical SST extreme, at 30 � latitude. The SLP center of action in the North Atlantic has a barotropic structure and contributes significantly to surface wind variability in the tropics. Despite being derived from statistically independent data samples, the principle components for the leading SST and SLP EOFs (four in total) are significantly correlated with one another, indicative of the existence of an interhemispheric mode spanning the entire Atlantic Ocean. The same analysis for a longer SST record suggests that this pan-Atlantic decadal variability exists throughout the 20th century. In the North Atlantic, composite analysis of wind velocity and heat fluxes based on the PCs of the leading SST modes indicates that wind-induced latent heat flux is the major forcing for decadal SST variability. In the South Atlantic, by contrast, wind anomalies are neither organized in space nor in geostrophic balance with SLP, a problem likely due to poor sampling there as indicated by a comparison with well-sampled satellite measurements. Spatially coherent anomalies of low-level cloud cover are found to be associated with the tropical Atlantic dipole, with increased (decreased) cloudiness over the cold (warm) lobe. These low-level cloud anomalies do not appear to be associated with significant surface wind convergence, unlike the deep convective clouds near the equator. By shielding solar radiation, these low-level cloud anomalies act to reinforce the underlying SST anomalies, reducing the Newtonian cooling rate for SST by as much as 30%.
Using clouds to provide grids with higher levels of abstraction and explicit support for usage modes

Grids in their current form of deployment and implementation have not been as successful as hoped in engendering distributed applications. Among other reasons, the level of detail that needs to be controlled for the successful development and deployment of applications remains too high. We argue that there is a need for higher levels of abstractions for current Grids. By introducing the relevant terminology, we try to understand Grids and Clouds as systems; we find this leads to a natural role for the concept of Affinity, and argue that this is a missing element in current Grids. Providing these affinities and higher‐level abstractions is consistent with the common concepts of Clouds. Thus this paper establishes how Clouds can be viewed as a logical and next higher‐level abstraction from Grids. Copyright © 2009 John Wiley & Sons, Ltd.
Adaptive Continuous Collision Detection for Cloth Models Using a Skipping Frame Session

simulation. The pipeline consists of four components: bounding volume hierarchy (BVH) update, BVH traversal, a skipping frame session, and elementary test processing. The skipping frame session is activated adaptively for skipping both BVH update and BVH traversal during the process of collision detection. The proposed method improves the performance of collision detection in simulating cloth models comparing to some existing feature-based collision detection techniques, as indicated from experimental results.
SATELLITE BASED MULTI-SCALE METHODS TO SUPPORT THE GOVERNANCE OF BRAZIL’S LOW-CARBON AGRICULTURE (ABC PLAN)

Brazil’s Low Carbon Agriculture is one the initiatives that puts the climate in the agricultural agenda towards a more sustainable and adapted agriculture under global changes. Among the several practices listed and supported by the ABC Plan, zero tillage and integrated crop-livestock-forestry systems including the recovery of degraded pasture are the most relevant ones. The objective of this paper is to present the Geo-ABC Project, a procedure to monitor the implementation of the Brazil’s Low Carbon Agriculture (ABC Plan) and aiming at the development of remote sensing methods to monitor agricultural systems listed in the ABC Plan and adopted at local scale.