Biosynthesis of neocarazostatin A reveals the sequential carbazole prenylation and hydroxylation in the tailoring steps

Acknowledgments Y.Y. acknowledges the financial support from “973” Program (2012CB721006) and National Natural Science Foundation of China (31570033). R.E., K.K., H.D., and M.J. acknowledge the financial support of the Leverhulme Trust-Royal Society Africa Award (AA090088).

Model updating using genetic algorithms with sequential niche technique

The authors would like to express their gratitude to organizations and people that supported this research. Piotr Omenzetter’s work within the Lloyd’s Register Foundation Centre for Safety and Reliability Engineering at the University of Aberdeen is supported by Lloyd’s Register Foundation. The Foundation helps to protect life and property by supporting engineering-related education, public engagement and the application of research. Ben Ryder of Aurecon and Graeme Cummings of HEB Construction assisted in obtaining access to the bridge and information for modelling. Luke Williams and Graham Bougen, undergraduate research students, assisted with testing.

Bayesian Emulation for Sequential Modeling, Inference and Decision Analysis

The advances in three related areas of state-space modeling, sequential Bayesian learning, and decision analysis are addressed, with the statistical challenges of scalability and associated dynamic sparsity. The key theme that ties the three areas is Bayesian model emulation: solving challenging analysis/computational problems using creative model emulators. This idea defines theoretical and applied advances in non-linear, non-Gaussian state-space modeling, dynamic sparsity, decision analysis and statistical computation, across linked contexts of multivariate time series and dynamic networks studies. Examples and applications in financial time series and portfolio analysis, macroeconomics and internet studies from computational advertising demonstrate the utility of the core methodological innovations.

Chapter 1 summarizes the three areas/problems and the key idea of emulating in those areas. Chapter 2 discusses the sequential analysis of latent threshold models with use of emulating models that allows for analytical filtering to enhance the efficiency of posterior sampling. Chapter 3 examines the emulator model in decision analysis, or the synthetic model, that is equivalent to the loss function in the original minimization problem, and shows its performance in the context of sequential portfolio optimization. Chapter 4 describes the method for modeling the steaming data of counts observed on a large network that relies on emulating the whole, dependent network model by independent, conjugate sub-models customized to each set of flow. Chapter 5 reviews those advances and makes the concluding remarks.

The geographies of encounter: investigating the spatiality and construction of 'meaningful' encounters with difference through the experiences of international students at University College Cork, Ireland

The purpose of this research is to investigate how international students negotiate encounters with Irish students and construct ‘meaning’ from those encounters in the spaces of the university and city. As cities are increasingly characterised by a multiplexity of diversity, the issue of living with difference is becoming more and more pertinent. In the wake of escalating socio-spatial polarisation, inter-cultural tension, racism, and xenophobia, the geographies of encounter seek to untangle the interactions that occur in the quotidian activities and spaces of everyday life to determine whether such encounters might reduce prejudice, antipathy and indifference and establish common social bonds (Amin 2002; Valentine 2008). Thus far, the literature has investigated a number of sites of encounter; public space, the home, neighbourhoods, schools, sports clubs, public transport, cafes and libraries (Wilson 2011; Schuermans 2013; Hemming 2011; Neal and Vincent 2011; Mayblin, Valentine and Anderrson 2015; Laurier and Philo 2006; Valentine and Sadgrove 2013; Harris, Valentine and Piekut 2014; Fincher and Iveson 2008). While these spaces produce a range of outcomes, the literature remains frustrated by a lack of clarity of what constitutes a ‘meaningful’ encounter and how such encounters might be planned for. Drawing on survey and interview data with full-time international students at University College Cork, Ireland, this study contributes to understanding how encounters are shaped by the construction and reproduction of particular identities in particular spaces, imbuing spaces with uneven power frameworks that produce diverse outcomes. Rather than identifying a singular ‘meaningful’ outcome of encounter as a potential panacea to the issues of exclusion and oppression, the contention here is to recognise a range of outcomes that are created by individuals in a range of ways. To define one outcome of encounter as ‘meaningful’ is to overlook the scale of intensity of diverse interactions and the multiplicity of ways in which people learn to live with difference.

(Figure 1 and 2) Phosphorus pools in the investigated sediments quantified by SEDEX sequential extraction and distribution of recovered 33P spike between sedimentary P pools after incubation

Phosphorus is an essential nutrient for life. In the ocean, phosphorus burial regulates marine primary production**1, 2. Phosphorus is removed from the ocean by sedimentation of organic matter, and the subsequent conversion of organic phosphorus to phosphate minerals such as apatite, and ultimately phosphorite deposits**3, 4. Bacteria are thought to mediate these processes**5, but the mechanism of sequestration has remained unclear. Here, we present results from laboratory incubations in which we labelled organic-rich sediments from the Benguela upwelling system, Namibia, with a 33P-radiotracer, and tracked the fate of the phosphorus. We show that under both anoxic and oxic conditions, large sulphide-oxidizing bacteria accumulate 33P in their cells, and catalyse the nearly instantaneous conversion of phosphate to apatite. Apatite formation was greatest under anoxic conditions. Nutrient analyses of Namibian upwelling waters and sediments suggest that the rate of phosphate-to-apatite conversion beneath anoxic bottom waters exceeds the rate of phosphorus release during organic matter mineralization in the upper sediment layers. We suggest that bacterial apatite formation is a significant phosphorus sink under anoxic bottom-water conditions. Expanding oxygen minimum zones are projected in simulations of future climate change**6, potentially increasing sequestration of marine phosphate, and restricting marine productivity.

Communication-efficient decentralized sequential detection

The problem of decentralized sequential detection is studied in this thesis, where local sensors are memoryless, receive independent observations, and no feedback from the fusion center. In addition to traditional criteria of detection delay and error probability, we introduce a new constraint: the number of communications between local sensors and the fusion center. This metric is able to reflect both the cost of establishing communication links as well as overall energy consumption over time. A new formulation for communication-efficient decentralized sequential detection is proposed where the overall detection delay is minimized with constraints on both error probabilities and the communication cost. Two types of problems are investigated based on the communication-efficient formulation: decentralized hypothesis testing and decentralized change detection. In the former case, an asymptotically person-by-person optimum detection framework is developed, where the fusion center performs a sequential probability ratio test based on dependent observations. The proposed algorithm utilizes not only reported statistics from local sensors, but also the reporting times. The asymptotically relative efficiency of proposed algorithm with respect to the centralized strategy is expressed in closed form. When the probabilities of false alarm and missed detection are close to one another, a reduced-complexity algorithm is proposed based on a Poisson arrival approximation. In addition, decentralized change detection with a communication cost constraint is also investigated. A person-by-person optimum change detection algorithm is proposed, where transmissions of sensing reports are modeled as a Poisson process. The optimum threshold value is obtained through dynamic programming. An alternative method with a simpler fusion rule is also proposed, where the threshold values in the algorithm are determined by a combination of sequential detection analysis and constrained optimization. In both decentralized hypothesis testing and change detection problems, tradeoffs in parameter choices are investigated through Monte Carlo simulations.

Traditional Korean islanders encounters with the British navy in the 1880s: The Port Hamilton Affair of 1885-1887

This article deals with the encounters between a traditional Korean rural and island population and western military forces when the British navy occupied Geomundo, an archipelago known to them as Port Hamilton, for 22 months between 1885 and 1887. The paper first outlines the sometimes painful process of East Asian countries being opened up to trade and outside influences in the 19th century, a process sometimes urged upon them by naval weapons in this era of gunboat diplomacy. This provides the setting for the Port Hamilton Affair itself when in preparation for possible war with Russia, a British naval squadron steamed into Port Hamilton and took it without reference to the local people or their national government. After brief reference to the political consequences of this action, the focus is then on what the records from the occupation and earlier investigations by the British, who had long coveted the islands’ strategic harbour, reveal about the life of the islanders. The article considers both their traditional life, from a time rather before western travel accounts were written about the Korean mainland, and how the islanders fared under the British.

No discrimination shock avoidance with sequential presentation of stimuli but shore crabs still reduce shock exposure

Insights into the potential for pain may be obtained from examination of behavioural responses to noxious stimuli. In particular, prolonged responses coupled with long-term motivational change and avoidance learning cannot be explained by nociceptive reflex but are consistent with the idea of pain. Here, we placed shore crabs alternately in two halves of a test area divided by an opaque partition. Each area had a dark shelter and in one repeated small electric shocks were delivered in an experimental but not in a control group. Crabs showed no specific avoidance of the shock shelter either during these trials or in a subsequent test in which both were offered simultaneously; however they often emerged from the shock shelter during a trial and thus avoided further shock. More crabs emerged in later trials and took less time to emerge than in early trials. Thus, despite the lack of discrimination learning between the two shelters they used other tactics to markedly reduce the amount of shock received. We note that a previous experiment using simultaneous presentation of two shelters demonstrated rapid discrimination and avoidance learning but the paradigm of sequential presentation appears to prevent this. Nevertheless, the data show clearly that the shock is aversive and tactics, other than discrimination learning, are used to avoid it. Thus, the behaviour is only partially consistent with the idea of pain.

Bcl-xL (S49) and (S62) sequential phosphorylation/dephosphorylation during mitosis prevents chromosome instability and aneuploidy

Une caractéristique intéressante de la protéine Bcl-xL est la présence d'un domaine en boucle non-structurée entre les hélices α1 and α2 de la protéine. Ce domaine protéique n'est pas essentiel pour sa fonction anti-apoptotique et absent chez CED-9, la protéine orthologue chez Caenorhabditis elegans. A l'intérieur de ce domaine, Bcl-xL subit une phosphorylation et déphosphorylation dynamique sur les résidus Ser49 et Ser62 en phase G2 du cycle cellulaire et lors de la mitose. Lorsque ces résidus sont mutés et les protéines exprimées dans des cellules cancéreuses, les cellules démontrent plusieurs défauts mitotiques liés à l'instabilité chromosomique. Pour analyser les effets de Bcl-xL Ser49 et Ser62 dans les cellules normales, les présentes études ont été réalisées dans des cellules diploïdes humaines normales, et in vivo chez Caenorhabditis elegans. Dans une première étude, nous avons utilisé la lignée cellulaire de cellules fibroblastiques diploïdes humaines normales BJ, exprimant Bcl-xL (type sauvage), (S49A), (S49D), (S62A), (S62D) et les double (S49/62A) et (S49/62D) mutants. Les cellules exprimant les mutants de phosphorylation ont montré des cinétiques de doublement de la population cellulaire réduites. Ces effets sur la cinétique de doublement de la population cellulaire corrèle avec l'apparition de la sénescence cellulaire, sans impact sur les taux de mort cellulaire. Ces cellules sénescentes affichent des phénotypes typiques de sénescence associés notamment à haut niveau de l'activité β-galactosidase associée à la sénescence, la sécrétion d' interleukine-6, l'activation de p53 et de p21WAF1/ Cip1, un inhibiteur des complexes kinase cycline-dépendant, ainsi que la formation de foyers de chromatine nucléaire associés à γH2A.X. Les analyses de fluorescence par hybridation in situ et des caryotypes par coloration au Giemsa ont révélé que l'expression des mutants de phosphorylation de Bcl-xL provoquent de l'instabilité chromosomique et l'aneuploïdie. Ces résultats suggèrent que les cycles de phosphorylation et déphosphorylation dynamiques de Bcl-xL Ser49 et Ser62 sont importants dans le maintien de l'intégrité des chromosomes lors de la mitose dans les cellules normales. Dans une deuxième étude, nous avons entrepris des expériences chez Caenorhabditis elegans pour comprendre l'importance des résidus Ser49 et Ser62 de Bcl-xL in vivo. Les vers transgéniques portant les mutations de Bcl-xL (S49A, S62A, S49D, S62D et S49/62A) ont été générés et leurs effets ont été analysés sur les cellules germinales des jeunes vers adultes. Les vers portant les mutations de Bcl-xL ont montré une diminution de ponte et d'éclosion des oeufs, des variations de la longueur de leurs régions mitotiques et des zones de transition, des anomalies chromosomiques à leur stade de diplotène, et une augmentation de l'apoptose des cellules germinales. Certaines de ces souches transgéniques, en particulier les variants Ser/Ala, ont également montré des variations de durée de vie par rapport aux vers témoins. Ces observations in vivo ont confirmé l'importance de Ser49 et Ser62 à l'intérieur du domaine à boucle de Bcl-xL pour le maintien de la stabilité chromosomique. Ces études auront une incidence sur les futures stratégies visant à développer et à identifier des composés qui pourraient cibler non seulement le domaine anti-apoptotique de la protéine Bcl-xL, mais aussi son domaine mitotique pour la thérapie du cancer.

Sequential Morphological Changes in the CNV Net after Intravitreal Anti-VEGF Evaluated with OCT Angiography

PURPOSE: To assess and describe sequential morphological changes in the choroidal neovascularization (CNV) net using optical coherence tomography angiography (OCTA) in patients undergoing treatment with intravitreal antivascular endothelial growth factor (VEGF). METHODS: Prospective cohort study. OCTA was performed sequentially: before (t0), 1 h (t1), 1 week (t2) and 1 month after the injection (t3), using Avanti RTVue XR equipped with the AngioVue® software (Optovue, Calif., USA). All images were classified by two independent graders. RESULTS: Ten eyes of 10 patients, with a mean age of 72.4 ± 10.5 years, were included. CNV morphology was described as tree-like in 5 eyes, glomerular in 1 and fragmented in 4. A fibrovascular capsule surrounding the CNV net was found in 4 eyes and a feeder trunk was noticed in 6. No changes were observed at t1. Loss of peripheral capillaries, vessel fragmentation and decreased vessel density were evident in 8 eyes at t2. The CNV capillary density and the peripheral anastomosis increased in all of these at t3. Two eyes remained unchanged through the whole length of follow-up. CONCLUSIONS: Significant changes in the CNV net can be observable in OCTA at least 1 week after intravitreal anti-VEGF. The safety of frequent examinations may provide a method of gauging treatment effects.

Positive Encounters: An Investigative Study on the Effects of Interactions between Cations and Quantum Dots

Thesis (Ph.D.)--University of Washington, 2016-06