Transport in Transitory, Three-Dimensional, Liouville Flows

We derive an action-flux formula to compute the volumes of lobes quantifying transport between past- and future-invariant Lagrangian coherent structures of n-dimensional, transitory, globally Liouville flows. A transitory system is one that is nonautonomous only on a compact time interval. This method requires relatively little Lagrangian information about the codimension-one surfaces bounding the lobes, relying only on the generalized actions of loops on the lobe boundaries. These are easily computed since the vector fields are autonomous before and after the time-dependent transition. Two examples in three-dimensions are studied: a transitory ABC flow and a model of a microdroplet moving through a microfluidic channel mixer. In both cases the action-flux computations of transport are compared to those obtained using Monte Carlo methods.Comment: 30 pages, 16 figures, 1 table, submitted to SIAM J. Appl. Dyn. Sy

On the exactness of the Semi-Classical Approximation for Non-Relativistic One Dimensional Propagators

For one dimensional non-relativistic quantum mechanical problems, we investigate the conditions for all the position dependence of the propagator to be in its phase, that is, the semi-classical approximation to be exact. For velocity independent potentials we find that: (i) the potential must be quadratic in space, but can have arbitrary time dependence. (ii) the phase may be made proportional to the classical action, and the magnitude (``fluctuation factor'') can also be found from the classical solution. (iii) for the driven harmonic oscillator the fluctuation factor is independent of the driving term.Comment: 7 pages, latex, no figures, published in journal of physics

Unusual polyphosphate inclusions observed in a marine Beggiatoa strain

Sulfide-oxidizing bacteria of the genus Beggiatoa are known to accumulate phosphate intracellularly as polyphosphate but little is known about the structure and properties of these inclusions. Application of different staining techniques revealed the presence of unusually large polyphosphate inclusions in the marine Beggiatoa strain 35Flor. The inclusions showed a co-occurrence of polyphosphate, calcium and magnesium when analyzed by scanning electron microscopy and energy dispersive X-ray analysis. Similar to polyphosphate-enriched acidocalcisomes of prokaryotes and eukaryotes, the polyphosphate inclusions in Beggiatoa strain 35Flor are enclosed by a lipid layer and store cations. However, they are not notably acidic. 16S rRNA gene sequence-based phylogenetic reconstruction showed an affiliation of Beggiatoa strain 35Flor to a monophyletic branch, comprising other narrow vacuolated and non-vacuolated Beggiatoa species. The polyphosphate inclusions represent a new type of membrane surrounded storage compartment within the genus Beggiatoa, distinct from the mostly nitrate-storing vacuoles known from other marine sulfide-oxidizing bacteria of the family Beggiatoaceae

Methane Production Pathway Regulated Proximally by Substrate Availability and Distally by Temperature in a High-Latitude Mire Complex

Projected 21st century changes in high-latitude climate are expected to have significant impacts on permafrost thaw, which could cause substantial increases in emissions to the atmosphere of carbon dioxide (CO2) and methane (CH4, which has a global warming potential 28 times larger than CO2 over a 100-year horizon). However, predicted CH4 emission rates are very uncertain due to difficulties in modeling complex interactions among hydrological, thermal, biogeochemical, and plant processes. Methanogenic production pathways (i.e., acetoclastic [AM] and hydrogenotrophic [HM]) and the magnitude of CH4 emissions may both change as permafrost thaws, but a mechanistic analysis of controls on such shifts in CH4 dynamics is lacking. In this study, we reproduced observed shifts in CH4 emissions and production pathways with a comprehensive biogeochemical model (ecosys) at the Stordalen Mire in subarctic Sweden. Our results demonstrate that soil temperature changes differently affect AM and HM substrate availability, which regulates magnitudes of AM, HM, and thereby net CH4 emissions. We predict very large landscape-scale, vertical, and temporal variations in the modeled HM fraction, highlighting that measurement strategies for metrics that compare CH4 production pathways could benefit from model informed scale of temporal and spatial variance. Finally, our findings suggest that the warming and wetting trends projected in northern peatlands could enhance peatland AM fraction and CH4 emissions even without further permafrost degradation

Topotecan-vincristine-doxorubicin in stage 4 high risk neuroblastoma patients failing to achieve a complete metastatic response to rapid COJEC : a SIOPEN study

Purpose : Metastatic response to induction therapy for high-risk neuroblastoma is a prognostic factor. In the International Society of Paediatric Oncology Europe Neuroblastoma (SIOPEN) HR-NBL-1 protocol, only patients with metastatic complete response (CR) or partial response (PR) with <= three abnormal skeletal areas on iodine 123-metaiodobenzylguanidine ([I-123] mIBG) scintigraphy and no bone marrow disease proceed to high dose therapy (HDT). In this study, topotecan-vincristine-doxorubicin (TVD) was evaluated in patients failing to achieve these criteria, with the aim of improving the metastatic response rate. Materials and Methods : Patients with metastatic high-risk neuroblastoma who had not achieved the SIOPEN criteria for HDT after induction received two courses of topotecan 1.5 mg/m(2)/day for 5 days, followed by a 48-hour infusion of vincristine, 2 mg/m(2), and doxorubicin, 45 mg/m(2). Results : Sixty-three patients were eligible and evaluable. Following two courses of TVD, four (6.4%) patients had an overall CR, while 28 (44.4%) had a PR with a combined response rate of 50.8% (95% confidence interval [CI], 37.9 to 63.6). Of these, 23 patients achieved a metastatic CR or a PR with <= 3 mIBG skeletal areas and no bone marrow disease (36.5%; 95% CI, 24.7 to 49.6) and were eligible to receive HDT. Toxicity was mostly haematological, affecting 106 of the 126 courses (84.1%; 95% CI, 76.5 to 90.0), and dose reduction was necessary in six patients. Stomatitis was the second most common nonhematological toxicity, occurring in 20 patients (31.7%). Conclusion : TVD was effective in improving the response rate of high-risk neuroblastoma patients after induction with COJEC enabling them to proceed to HDT. However, the long-term benefits of TVD needs to be determined in randomized clinical trials

Multiple pathways mediate the effects of climate change on maternal reproductive traits in a red deer population

Temporal changes in phenological traits arising as a consequence of recent rapid environmental change have been widely demonstrated in animal populations. Increasingly, studies are seeking to understand the impact of changes in such traits on individual fitness and population dynamics, with the ultimate aim of predicting population persistence or extinction under different climate scenarios. Here, we examined the effects of environmental change on maternal reproductive traits in a wild population of red deer (Cervus elaphus) and sought to explain why, despite a rapid advance in offspring birth dates, we observed no apparent consequences for offspring fitness. By using path analysis, we identified both direct and indirect paths along which changes in environmental conditions affected birth date, birth mass, juvenile survival, and female fecundity. In general, warmer temperatures were associated with earlier birth dates and greater birth mass, and higher rainfall was associated with reduced juvenile survival and reduced female fecundity. We also examined concurrent effects of population density, maternal age, and reproductive history, and found that temporal stasis in average trait values, at least in part, could be explained by antagonistic roles of direct and indirect effects of changing climate and increasing population density. Identification of the many mechanisms that contribute to the dynamics of phenotypic traits is challenging; this study demonstrates the need to consider both climatic and demographic variation in order to understand the fitness consequences of changes in phenological traits

Arctic air pollution: Challenges and opportunities for the next decade

The Arctic is a sentinel of global change. This region is influenced by multiple physical and socio-economic drivers and feedbacks, impacting both the natural and human environment. Air pollution is one such driver that impacts Arctic climate change, ecosystems and health but significant uncertainties still surround quantification of these effects. Arctic air pollution includes harmful trace gases (e.g. tropospheric ozone) and particles (e.g. black carbon, sulphate) and toxic substances (e.g. polycyclic aromatic hydrocarbons) that can be transported to the Arctic from emission sources located far outside the region, or emitted within the Arctic from activities including shipping, power production, and other industrial activities. This paper qualitatively summarizes the complex science issues motivating the creation of a new international initiative, PACES (air Pollution in the Arctic: Climate, Environment and Societies). Approaches for coordinated, international and interdisciplinary research on this topic are described with the goal to improve predictive capability via new understanding about sources, processes, feedbacks and impacts of Arctic air pollution. Overarching research actions are outlined, in which we describe our recommendations for 1) the development of trans-disciplinary approaches combining social and economic research with investigation of the chemical and physical aspects of Arctic air pollution; 2) increasing the quality and quantity of observations in the Arctic using long-term monitoring and intensive field studies, both at the surface and throughout the troposphere; and 3) developing improved predictive capability across a range of spatial and temporal scales

Aggregation Prediction in Therapeutic Protein Formulations for Excipient Design

Computational Infrastructure & Informatics Poster SessionA major concern in the development therapeutic protein formulations is protein aggregation. Proteins can interact to form bound groups of protein molecules or aggregates. Aggregates in protein formulations reduce effectiveness and can lead to severe immune responses in patients. Excipients are additive molecules that are not therapeutically active, but can increase the stability of protein formulations. An ideal excipient binds with aggregation prone regions on the protein to limit interaction of that region with another protein molecule. The goal of this project is to predict aggregation prone regions and design excipients to interact with these regions. Several tools exist to predict which regions on a protein will be most likely to initiate aggregation. Aggrescan (http://bioinf.uab.es/aggrescan/) and SAP (Spatial Aggregation Potential) were used to predict aggregation prone regions on proteins and the results were compared. Aggrescan uses experimental data to assign each amino acid an aggregation propensity score. An aggregation prone region is identified by a sequence of amino acids with high propensities. The three-dimensional structure is not used in the aggregation prediction. SAP uses molecular simulation to determine regions that are hydrophobic and solvent accessible. Each residue is scored and the results are mapped to the three-dimensional protein structure. A successful prediction tool must use parameters that correlate with aggregation potential for a folded protein. The aggregation prone regions predicted by Aggrescan and SAP were compared to experimental data on protein aggregation. Proteins with a high number of predicted regions or large predicted regions were found to have higher experimental percent aggregation. With the regions identified, molecular simulations were performed for protein-excipient systems. A protein and small molecule docking algorithm was used to determine which regions of the protein certain excipients interacted with. Trehalose, poly(vinylpyrrolidone), and guanadine hydrochloride were used. For an excipient to successfully stabilize a protein and prevent aggregation, the excipient should interact with the aggregation prone regions predicted by Aggrescan and SAP. The predicted regions were compared to the regions where the excipient docks in the molecular simulation. The simulation results were compared to experimental data on the percent aggregation observed in several protein-excipient formulations. The excipients that were found to interact with the predicted aggregation prone regions in simulations should also experimentally prohibit aggregation, leading to lower percent aggregation. Hydrogen-deuterium swapping along with FTIR analysis will be performed experimentally to determine exposed regions on the protein. Proteins with a high number of exposed regions are less stable. The exposed regions will be compared to the aggregation prone regions predicted by Aggrescan and SAP

Transmission of bovine viral diarrhea virus among white-tailed deer (Odocoileus virginianus)

Cattle persistently infected (PI) with bovine viral diarrhea virus (BVDV), a pestivirus in the family Flaviviridae, are an important source of viral transmission to susceptible hosts. Persistent BVDV infections have been identified in white-tailed deer (Odocoileus virginianus), the most abundant free-ranging ruminant in North America. As PI deer shed BVDV similarly to PI cattle, maintenance of BVDV within white-tailed deer populations may be possible. To date, intraspecific transmission of BVDV in white-tailed deer has not been evaluated, which prompted this study. Six pregnant white-tailed deer were captured in the first trimester of pregnancy and cohabitated with a PI white-tailed deer. Cohabitation with the PI deer resulted in BVDV infection in all does, as indicated by seroconversion. All does gave birth to live fawns and no reproductive losses were observed. At birth, evidence of BVDV infection was identified in two singlet fawns, of which one was determined to be PI by repeated serum reverse transcription nested PCR, whole blood virus isolation and immunohistochemistry. This study demonstrates for the first time that BVDV transmission may occur among white-tailed deer. The birth of a PI fawn through contact to a PI white-tailed deer indicates that under appropriate circumstances, BVDV may be maintained in white-tailed deer by congenital infection

Necessary Optimality Conditions for Higher-Order Infinite Horizon Variational Problems on Time Scales

We obtain Euler-Lagrange and transversality optimality conditions for higher-order infinite horizon variational problems on a time scale. The new necessary optimality conditions improve the classical results both in the continuous and discrete settings: our results seem new and interesting even in the particular cases when the time scale is the set of real numbers or the set of integers.Comment: This is a preprint of a paper whose final and definite form will appear in Journal of Optimization Theory and Applications (JOTA). Paper submitted 17-Nov-2011; revised 24-March-2012 and 10-April-2012; accepted for publication 15-April-201