49 research outputs found
yuanhan-wu-kulplab/KonrathYu_CellReports2021: The Kulp Lab Cluster Version
No full textThis version is for running on the Kulp Lab's cluster only. Necessary modification of paths is required for testing on other slurmq cluster systems
Extreme Financial Risks and Asset Allocation | Kulp-Wright Award 2016
No full textThe Kulp-Wright Book Award is presented annually by the American Risk and Insurance Association to the author(s) of a book considered to be the most influential one published on the subjects of risk management and insurance A pedagogical work of updated financial models using Lévy processes. Very well written, very well explained and argued with examples and appropriate simulations. Recommended to academics, researchers and PhD students, slightly less to practitioners. Zentralblatt MATH (he..
Forest liming in the face of climate change: the implications of restorative liming for soil organic carbon in mature German forests
No full textAbstract. Forest liming is a management tool that has and continues to be used extensively across northern Europe to counteract acidification processes from anthropogenic sulfur and nitrogen (N) deposition. In this study, we quantified how liming affects soil organic carbon (SOC) stocks and attempt to disentangle the mechanisms responsible for the often contrasting processes that regulate net soil carbon (C) fluxes. Using a paired plot experimental design we compared SOC stocks in limed plots with adjacent unlimed control plots at 28 experimental sites to 60 cm soil depth in mature broadleaf and coniferous forests across Germany. Historical soil data from a subset of the paired experiment plots were analyzed to assess how SOC stocks in both control and limed plots changed between 1990 and 2019. Overall, we found that forest floor C stocks have been accumulating over time in the control plots. Liming however largely offset organic layer buildup in the L/Of layer, and forest floor C stocks remained unchanged over time in the limed plots. This, in turn, meant that nutrients remained mobile and were not bound in soil organic matter complexes. Results from the paired plot analysis showed that forest floor C stocks were significantly lower in limed plots than the control (−34 %, −8.4 ± 1.7 Mg C ha−1) but did not significantly affect SOC stocks in the mineral soil, when all sites are pooled together. In the forest floor layers, SOC stocks exhibited an exponential decrease with increasing pH, highlighting how lime-induced improvements in the biochemical environment stimulate organic matter (OM) decomposition. Nevertheless, for both forest floor and mineral soils, the magnitude and direction of the belowground C changes hinged directly on the inherent site characteristics, namely, forest type (conifer versus broadleaf), soil pH, soil texture, and the soil SOC stocks. On the other hand, SOC stock decreases were often offset by other processes that fostered C accumulation, such as improved forest productivity or increased carbon stabilization, which correspondingly translated to an overall variable response by SOC stocks, particularly in the mineral soil. Lastly, we measured soil carbon dioxide (CO2) and soil methane (CH4) flux immediately after a re-liming event at three of the experimental sites. Here, we found that (1) liming doubles CH4 uptake in the long-term; (2) soil organic matter mineralization processes respond quickly to liming, even though the duration and size of the CO2 flush varied between sites; and (3) lime-derived CO2 contributed very little to total CO2 emissions over the measurement period (determined using stable isotope approaches)
Using Structural Bioinformatics to Model and Design Membrane Proteins
No full textCells require membrane proteins for a wide spectrum of critical functions. Transmembrane proteins enable cells to communicate with its environment, catalysis, ion transport and scaffolding. The functional roles of membrane proteins are specified by their sequence composition and precise three dimensional folding.
The exact mechanisms driving folding of membrane proteins is still not fully understood. Further, the association between membrane proteins occurs with pinpoint specificity. For example, there exists common sequence features within families of transmembrane receptors, yet there is little cross talk between families. Therefore, we ask how membrane proteins dial in their specificity and what factors are responsible for adoption of native structure.
Advancements in membrane protein structure determination methods has been followed by a sharp increase in three dimensional structures. Structural bioinfomatics has been utilized effectively to study water soluble proteins. The field is now entering an era where structural bioinformatics can be applied to modeling membrane proteins without structure and engineering novel membrane proteins.
The transmembrane domains of membrane proteins were first categorized structurally. From this analysis, we are able to describe the ways in which membrane proteins fold and associate. We further derived sequence profiles for the commonly occurring structural motifs, enabling us to investigate the role of amino acids within the bilayer. Utilizing these tools, a transmembrane structural model was constructed of principle cell surface receptors (integrins). The structural model enabled understanding of possible mechanisms used to signal and to propose a novel membrane protein packing motif.
In addition, novel scoring functions for membrane proteins were developed and applied to modeling membrane proteins. We derived the first all-atom membrane statistical potential and introduced the usage of exposed volume. These potentials
allowed modeling of complex interactions in membrane proteins, such as salt bridges.
To understand the geometric preferences of salt bridges, we surveyed a structural database. We learned about large biases in salt bridge orientations that will be useful in modeling and design. Lastly, we combine these structural bioinformatic efforts, enabling us to model membrane proteins in ways which were previously inaccessible
Employment accessibility and rising seas
No full textRecent projections suggest worst-case scenarios of more than six ft (1.8 m) of global mean sea-level rise by end of century, progressively making coastal flood events more frequent and more severe. The impact on transportation systems along coastal regions is likely to be substantial. An analysis of impacts for Atlantic and Cape May counties in southern New Jersey is conducted. The impact on accessibility to employment is analyzed using a dataset of sea-level increases merged with road network (TIGER) data and Census data on population and employment. Using measures of accessibility, it is shown how access will be reduced at the block-group level. An additional analysis of low and high income quartiles suggest that lower-income block groups will have greater reductions in accessibility. The implication is that increasing sea levels will have large impacts on people and the economy, and large populations will have access to employment disrupted well before their own properties or places of employment may begin to flood (assuming no adaptation).Peer reviewe
Consumer Perception of Bread Quality
No full textBread contains a wide range of important nutritional components which provide a positive effect on human health. However, the consumption of bread in Belgium is declining during the last decades. This is due to factors such as changing eating patterns and a increasing choice of substitutes like breakfast cereals and fast foods. The aim of this study is to investigate consumer’s quality perception of bread towards sensory, health and nutrition attributes. Consumer’s quality perception of bread seams to be determined by sensory and health attributes. Three clusters of consumers are identified based on these attributes. In the first cluster, consumers’ quality perception of bread is not dependent on the health attributes it embraces, but to some extent on sensory attributes. For the second cluster, both health and sensory attributes appear to influence quality perception. In the third cluster only sensory attributes appear to be important in determining quality perception, though in a negative direction. The results of this study will possibly help health professionals and policy makers to systematically inform the consumers about the positive effects of bread and its components. Furthermore, firms can use the result to build up a tailor-made marketing strategy.Consumer, Quality perception, Bread, Demand and Price Analysis, Food Consumption/Nutrition/Food Safety,
The topological form is the Pfaffian form
No full textFor a given graph G , Budzik, Gaiotto, Kulp, Wang, Williams, Wu, Yu, and the first author studied a ‘topological’ differential form \alpha_{G} , which expresses violations of BRST-closedness of a quantum field theory along a single topological direction. In a seemingly unrelated context, Brown, Panzer, and the second author studied a ‘Pfaffian’ differential form \phi_{G} , which is used to construct cohomology classes of the odd commutative graph complex and of \mathsf{GL}_{2n}(\Z) . We give an explicit combinatorial proof that \alpha_{G} coincides with \phi_{G} . We also discuss the equivalence of several properties of these forms which had been established independently for both contexts in previous work
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State Modeling and Pass Automation in Spacecraft Control
No full textInternational Telemetering Conference Proceedings / October 28-31, 1996 / Town and Country Hotel and Convention Center, San Diego, CaliforniaThe Integrated Monitoring and Control COTS System (IMACCS) was developed as a proof-of-concept to show that commercial off-the-shelf (COTS) products could be integrated to provide spacecraft ground support faster and cheaper than current practices. A key component of IMACCS is the Altair Mission Control System (AMCS), one of several commercial packages available for satellite command and control. It is distinguished from otherwise similar tools by its implementation of Finite State Modeling as part of its expert system capability. Using the Finite State Modeling and State Transition capabilities of the ALTAIR Mission Control System (AMCS), IMACCS was enhanced to provide automated monitoring, routine pass support, anomaly resolution, and emergency "lights on again" response. Orbit determination and production of typical flight dynamics products, such as acquisition times and vectors, have also been automated.International Foundation for TelemeteringProceedings from the International Telemetering Conference are made available by the International Foundation for Telemetering and the University of Arizona Libraries. Visit http://www.telemetry.org/index.php/contact-us if you have questions about items in this collection
Thermochemistry of yavapaiite KFe(SO4)2: Formation and decomposition
No full textYavapaiite, KFe(SO4)2, is a rare mineral in nature, but its structure is considered as a reference for many synthetic compounds in the alum supergroup. Several authors mention the formation of yavapaiite by heating potassium jarosite above ca. 400°C. To understand the thermal decomposition of jarosite, thermodynamic data for phases in the K-Fe-S-O-(H) system, including yavapaiite, are needed. A synthetic sample of yavapaiite was characterized in this work by X-ray diffraction (XRD), scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and thermal analysis. Based on X-ray diffraction pattern refinement, the unit cell dimensions for this sample were found to be a = 8.152 ± 0.001 Å, b = 5.151 ± 0.001 Å, c = 7.875 ± 0.001 Å, and β = 94.80°. Thermal decomposition indicates that the final breakdown of the yavapaiite structure takes place at 700°C (first major endothermic peak), but the decomposition starts earlier, around 500°C. The enthalpy of formation from the elements of yavapaiite, KFe(SO4)2, ΔH°f = −2042.8 ± 6.2 kJ/mol, was determined by high-temperature oxide melt solution calorimetry. Using literature data for hematite, corundum, and Fe/Al sulfates, the standard entropy and Gibbs free energy of formation of yavapaiite at 25°C (298 K) were calculated as S°(yavapaiite) = 224.7 ± 2.0 J.mol−1.K−1 and ΔG°f = −1818.8 ± 6.4 kJ/mol. The equilibrium decomposition curve for the reaction jarosite = yavapaiite + Fe2O3 + H2O has been calculated, at pH2O = 1 atm, the phase boundary lies at 219 ± 2°C
Infrared Studies of Intramolecular Rovibrational Relaxation (Kinetics, Energy Transfer)
No full textInfrared fluorescence data is presented which demonstrates the extent of intramolecular vibrational relaxation from the CH stretching modes of several organic molecules. The molecules are isolated and cooled in a pulsed supersonic expansion. The infrared fluorescence is collected and dispersed using either a cryogenic Michelson interferometer or a circularly variable filter wheel. Resolved fluorescence spectra from dimethyl ether and 1,4 dioxane indicate that the energy distribution within each molecule is dependent upon the CH stretch that is excited. The fluctuations in the relaxed mode energy content with excitation energy can be fit by a statistical model which assumes coupling to all rovibrational states of the correct symmetry within 1 cm('-1) of the excitation frequency. The comparison of the relaxation in beams with rotational temperatures of 2 and 20 K demonstrates the extent of the rotational dependence of the IVR. It is shown that the level of rotational excitation affects both the extent and destination of the vibrational energy flow. Fluorescence spectra from the molecules 1,3 dioxolane and tetrahydropyran are also shown. The fact that each is structurally similar to 1,4 dioxane is used as a basis for comparison of the IVR in each case. It is shown that the presence of the pseudorotor in the five membered ring 1,3 dioxolane enhances the state density such that it is similar to that of the other two molecules. The relaxation in dioxolane and tetrahydropyran is shown to be less state selective than that of dioxane. It is demonstrated that the relaxation in methyl formate can also be fit. Using the laser at higher resolution (.18 cm('-1)), it was possible to take fluorescence excitation spectra which allowed lower limits to be set on the rovibrational lifetimes of some states. In all cases, the linewidths observed were limited by the width of the laser. Lower limits of 15 psec were set on the lifetimes of low (1-2) J states of dimethyl ether and methyl formate, and high (8-12) J states of methyl formate and 1,4 dioxane. Finally, band contour dependences of the dilution factor are presented for three methyl formate CH stretches and one in dimethyl ether. (Abstract shortened with permission of author.)Made available in DSpace on 2014-12-15T23:18:51Z (GMT). No. of bitstreams: 1
8701537.pdf: 4866524 bytes, checksum: 96e64afd24dc04869ac55d769b0d2279 (MD5)
Previous issue date: 1986Embargo set by: Seth Robbins for item 70515
Lift date: Forever
Reason: Restricted to the U of I community idenfinitely during batch ingest of legacy ETDsRestricted to the U of I community idenfinitely during batch ingest of legacy ETDsU of I Only194 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 1986
