Transfer-matrix theory of surface spin-echo experiments with molecules

${}^3$He beam spin-echo experiments have been used to study surface morphology, molecular and atomic surface diffusion, phonon dispersions, phason dispersions and phase transitions of ionic liquids. However, the interactions between ${}^3$He atoms and surfaces or their adsorbates are typically isotropic and weak. To overcome these limitations, one can use molecules instead of ${}^3$He in surface spin-echo experiments. The molecular degrees of freedom, such as rotation, may be exploited to provide additional insight into surfaces and the behaviour of their adsorbates. Indeed, a recent experiment has shown that $\textit{ortho}$-hydrogen can be used as a probe that is sensitive to the orientation of a Cu(115) surface [Godsi et al., Nat. Comm. $\textbf{8}$, 15357 (2017)]. However, the additional degrees of freedom offered by molecules also pose a theoretical challenge: a large manifold of molecular states and magnetic field-induced couplings between internal states. Here, we present a fully quantum mechanical approach to model molecular surface spin-echo experiments and connect the experimental signal to the elements of the time-independent molecule-surface scattering matrix. We present a one-dimensional transfer matrix method that includes the molecular hyperfine degrees of freedom and accounts for the spatial separation of the molecular wavepackets due to the magnetic control fields. We apply the method to the case of $\textit{ortho}$-hydrogen, show that the calculated experimental signal is sensitive to the scattering matrix elements, and perform a preliminary comparison to experiment. This work sets the stage for Bayesian optimization to determine the scattering matrix elements from experimental measurements and for a framework that describes molecular surface spin-echo experiments to study dynamic surfaces.Comment: 32 pages, 9 figures. Generalized discussion on rotation matrices and updated Figures 3-7. Accepted in Physical Review A (https://journals.aps.org/pra/

Pheromone-Dependent Destruction of the Tec1 Transcription Factor Is Required for MAP Kinase Signaling Specificity in Yeast

AbstractThe yeast MAPK pathways required for mating versus filamentous growth share multiple components yet specify distinct programs. The mating-specific MAPK, Fus3, prevents crosstalk between the two pathways by unknown mechanisms. Here we show that pheromone signaling induces Fus3-dependent degradation of Tec1, the transcription factor specific to the filamentation pathway. Degradation requires Fus3 kinase activity and a MAPK phosphorylation site in Tec1 at threonine 273. Fus3 associates with Tec1 in unstimulated cells, and active Fus3 phosphorylates Tec1 on T273 in vitro. Destruction of Tec1 requires the F box protein Dia2 (Digs-into-agar-2), and Cdc53, the Cullin of SCF (Skp1-Cdc53-F box) ubiquitin ligases. Notably, mutation of the phosphoacceptor site in Tec1, deletion of FUS3, or deletion of DIA2 results in a loss of signaling specificity such that pheromone pathway signaling erroneously activates filamentation pathway gene expression and invasive growth. Signal-induced destruction of a transcription factor for a competing pathway provides a mechanism for signaling specificity

Identification d'un réseau hydrométrique pour le suivi des modifications climatiques dans la province de Québec

Depuis une dizaine d'années, la communauté scientifique s'est beaucoup intéressée à l'hypothèse d'un réchauffement à l'échelle planétaire. De nombreuses études ont porté sur l'analyse de ces modifications climatiques éventuelles ainsi que sur la modélisation de leurs impacts sur les ressources en eau. Cependant, malgré l'attention croissante que reçoit le sujet des modifications climatiques, très peu de travail a été accompli pour mettre en place des réseaux de mesure spécialement conçus pour l'étude des modifications climatiques et leurs impacts sur les ressources en eau, et pour créer des bases de données adaptées à cet objectif. Cette tâche est encore plus nécessaire dans le cadre des réductions budgétaires auxquelles sont soumis les réseaux hydrométriques dans certains pays développés. Cet article présente les bases d'une étude dont l'objectif est la conception d'un réseau hydrométrique pour le suivi des modifications climatiques dans la province de Québec, Canada. Le but est d'identifier, afin de les conserver, les stations de jaugeage les plus adéquates pour accomplir cette tâche. L'article présente aussi une brève revue des types de modifications climatiques qui peuvent être observés et de certains tests qui existent pour leur détection et leur quantification. Une procédure bayésienne de détection des sauts de la moyenne a été sélectionnée sur la base de ses avantages théoriques, et appliquée aux séries de données des stations retenues au Québec.The 1980s and 1990s contained most of the warmest years since the beginning of worldwide temperature recording nearly 140 years ago. Widely accepted estimates project that the earth's average temperature might increase by about 2°C over the next 100 years. It is also expected that, as a result of global warming, the frequency and intensity of floods and droughts may change. However, despite the increasing attention that the issue of climate change receives, there has been little effort to develop a systematic approach for the collection of relevant data, and to establish observational networks specifically designed for the analysis of climate variability and change and their impact on hydrologic regimes and water resources in general. This task is particularly important given the major network reductions that result from recent cutbacks in the funding of monitoring programs in Canada and other countries. This paper presents the results of a rigorous study that was carried out recently, and aimed at establishing a hydrometric network for the study of the attributes of climate change and variability across the province of Quebec (Canada) and their impact on water resources. The approach is based on identifying and maintaining stations that can help provide an understanding of the physical processes within the hydrological cycle and account for climate variations across the province. This network will be of fundamental importance in establishing scientific evidence of the magnitude and direction of possible shifts in climate patterns across the province. These aspects are of global significance and must be considered during the rationalization of monitoring networks. The results of the application of this procedure to the hydrometric network of the province of Quebec are presented. The paper presents also a brief review of the various types of non-stationarities that can be observed in hydrologic data series, and some of the current approaches that can be used for the detection of these non-stationarities. Several statistical tests and procedures have been proposed in the literature for the analysis of the characteristics of data samples and for hypothesis testing, for various types of non-stationarity. A Bayesian procedure, proposed by Lee and Heghinian (1977) and generalized by Bernier (1994), for the detection of shifts in the mean of hydrological and meteorological time-series is selected based on its theoretical advantages (Faucher et al., 1997). The procedure is then applied for the analysis of all streamflow series of selected stations in the province of Quebec with the objective of extracting information on possible climatic changes. Results indicate the presence of significant non-stationarities for a number of the series analyzed. For five stations, the most probable date for the shift in the mean level falls in the period 1983-1985. Recommandations are made for future research activities

Joint Optical Flow and Temporally Consistent Semantic Segmentation

The importance and demands of visual scene understanding have been steadily increasing along with the active development of autonomous systems. Consequently, there has been a large amount of research dedicated to semantic segmentation and dense motion estimation. In this paper, we propose a method for jointly estimating optical flow and temporally consistent semantic segmentation, which closely connects these two problem domains and leverages each other. Semantic segmentation provides information on plausible physical motion to its associated pixels, and accurate pixel-level temporal correspondences enhance the accuracy of semantic segmentation in the temporal domain. We demonstrate the benefits of our approach on the KITTI benchmark, where we observe performance gains for flow and segmentation. We achieve state-of-the-art optical flow results, and outperform all published algorithms by a large margin on challenging, but crucial dynamic objects.Comment: 14 pages, Accepted for CVRSUAD workshop at ECCV 201

Real-time PCR reveals a high incidence of Symbiodinium clade D at low levels in four scleractinian corals across the Great Barrier Reef:Implications for symbiont shuffling

Reef corals form associations with an array of genetically and physiologically distinct endosymbionts from the genus Symbiodinium. Some corals harbor different clades of symbionts simultaneously, and over time the relative abundances of these clades may change through a process called symbiont shuffling. It is hypothesized that this process provides a mechanism for corals to respond to environmental threats such as global warming. However, only a minority of coral species have been found to harbor more than one symbiont clade simultaneously and the current view is that the potential for symbiont shuffling is limited. Using a newly developed real-time PCR assay, this paper demonstrates that previous studies have underestimated the presence of background symbionts because of the low sensitivity of the techniques used. The assay used here targets the multi-copy rDNA ITS1 region and is able to detect Symbiodinium clades C and D with > 100-fold higher sensitivity compared to conventional techniques. Technical considerations relating to intragenomic variation, estimating copy number and non-symbiotic contamination are discussed. Eighty-two colonies from four common scleractinian species (Acropora millepora, Acropora tenuis, Stylophora pistillata and Turbinaria reniformis) and 11 locations on the Great Barrier Reef were tested for background Symbiodinium clades. Although these colonies had been previously identified as harboring only a single clade based on SSCP analyses, background clades were detected in 78% of the samples, indicating that the potential for symbiont shuffling may be much larger than currently thought

Bayesian Joint Detection-Estimation of cerebral vasoreactivity from ASL fMRI data

International audienceAlthough the study of cerebral vasoreactivity using fMRI is mainly conducted through the BOLD fMRI modality, owing to its relatively high signal-to-noise ratio (SNR), ASL fMRI provides a more interpretable measure of cerebral vasoreactivity than BOLD fMRI. Still, ASL suffers from a low SNR and is hampered by a large amount of physiological noise. The current contribution aims at improving the re- covery of the vasoreactive component from the ASL signal. To this end, a Bayesian hierarchical model is proposed, enabling the recovery of per- fusion levels as well as fitting their dynamics. On a single-subject ASL real data set involving perfusion changes induced by hypercapnia, the approach is compared with a classical GLM-based analysis. A better goodness-of-fit is achieved, especially in the transitions between baseline and hypercapnia periods. Also, perfusion levels are recovered with higher sensitivity and show a better contrast between gray- and white matter

Climate change promotes parasitism in a coral symbiosis.

Coastal oceans are increasingly eutrophic, warm and acidic through the addition of anthropogenic nitrogen and carbon, respectively. Among the most sensitive taxa to these changes are scleractinian corals, which engineer the most biodiverse ecosystems on Earth. Corals' sensitivity is a consequence of their evolutionary investment in symbiosis with the dinoflagellate alga, Symbiodinium. Together, the coral holobiont has dominated oligotrophic tropical marine habitats. However, warming destabilizes this association and reduces coral fitness. It has been theorized that, when reefs become warm and eutrophic, mutualistic Symbiodinium sequester more resources for their own growth, thus parasitizing their hosts of nutrition. Here, we tested the hypothesis that sub-bleaching temperature and excess nitrogen promotes symbiont parasitism by measuring respiration (costs) and the assimilation and translocation of both carbon (energy) and nitrogen (growth; both benefits) within Orbicella faveolata hosting one of two Symbiodinium phylotypes using a dual stable isotope tracer incubation at ambient (26 °C) and sub-bleaching (31 °C) temperatures under elevated nitrate. Warming to 31 °C reduced holobiont net primary productivity (NPP) by 60% due to increased respiration which decreased host %carbon by 15% with no apparent cost to the symbiont. Concurrently, Symbiodinium carbon and nitrogen assimilation increased by 14 and 32%, respectively while increasing their mitotic index by 15%, whereas hosts did not gain a proportional increase in translocated photosynthates. We conclude that the disparity in benefits and costs to both partners is evidence of symbiont parasitism in the coral symbiosis and has major implications for the resilience of coral reefs under threat of global change

Glutathione-S-transferases in lung and sputum specimens, effects of smoking and COPD severity

<p>Abstract</p> <p>Background</p> <p>Oxidative stress plays a potential role in the pathogenesis and progression of chronic obstructive pulmonary disease (COPD). Glutathione S-transferases (GSTs) detoxify toxic compounds in tobacco smoke via glutathione-dependent mechanisms. Little is known about the regulation and expression of GSTs in COPD lung and their presence in airway secretions.</p> <p>Methods</p> <p>GST alpha, pi and mu were investigated by immunohistochemistry in 72 lung tissue specimens and by Western analysis in total lung homogenates and induced sputum supernatants from non-smokers, smokers and patients with variable stages of COPD severity.</p> <p>Results</p> <p>GST alpha was expressed mainly in the airway epithelium. The percentage of GST alpha positive epithelial cells was lower in the central airways of patients with very severe (Stage IV) COPD compared to mild/moderate COPD (p = 0.02). GST alpha by Western analysis was higher in the total lung homogenates in mild/moderate COPD compared to cases of very severe disease (p < 0.001). GST pi was present in airway and alveolar epithelium as well as in alveolar macrophages. GST mu was expressed mainly in the epithelium. Both GST alpha and pi were detectable in sputum supernatants especially in patients with COPD.</p> <p>Conclusion</p> <p>This study indicates the presence of GST alpha and pi especially in the epithelium and sputum supernatants in mild/moderate COPD and low expression of GST alpha in the epithelium in cases of very severe COPD. The presence of GSTs in the airway secretions points to their potential protective role both as intracellular and extracellular mediators in human lung.</p

Lung glutathione adaptive responses to cigarette smoke exposure

<p>Abstract</p> <p>Background</p> <p>Smoking tobacco is a leading cause of chronic obstructive pulmonary disease (COPD), but although the majority of COPD cases can be directly related to smoking, only a quarter of smokers actually develop the disease. A potential reason for the disparity between smoking and COPD may involve an individual's ability to mount a protective adaptive response to cigarette smoke (CS). Glutathione (GSH) is highly concentrated in the lung epithelial lining fluid (ELF) and protects against many inhaled oxidants. The changes in GSH that occur with CS are not well investigated; therefore the GSH adaptive response that occurs with a commonly utilized CS exposure was examined in mice.</p> <p>Methods</p> <p>Mice were exposed to CS for 5 h after which they were rested in filtered air for up to 16 h. GSH levels were measured in the ELF, bronchoalveolar lavage cells, plasma, and tissues. GSH synthesis was assessed by measuring γ-glutamylcysteine ligase (GCL) activity in lung and liver tissue.</p> <p>Results</p> <p>GSH levels in the ELF, plasma, and liver were decreased by as much as 50% during the 5 h CS exposure period whereas the lung GSH levels were unchanged. Next, the time course of rebound in GSH levels after the CS exposure was examined. CS exposure initially decreased ELF GSH levels by 50% but within 2 h GSH levels rebound to about 3 times basal levels and peaked at 16 h with a 6-fold increase and over repeat exposures were maintained at a 3-fold elevation for up to 2 months. Similar changes were observed in tissue GCL activity which is the rate limiting step in GSH synthesis. Furthermore, elevation in ELF GSH levels was not arbitrary since the CS induced GSH adaptive response after a 3d exposure period prevented GSH levels from dropping below basal levels.</p> <p>Conclusions</p> <p>CS exposures evoke a powerful GSH adaptive response in the lung and systemically. These data suggests there may be a sensor that sets the ELF GSH adaptive response to prevent GSH levels from dipping below basal levels. Factors that disrupt GSH adaptive responses may contribute to the pathophysiology of COPD.</p