Experimental and Calculated Spectra of π-Stacked Mild Charge-Transfer Complexes: Jet-Cooled Perylene·(Tetrachloroethene) n , n = 1,2

The S0 ↔ S1 spectra of the mild charge-transfer (CT) complexes perylene·tetrachloroethene (P·4ClE) and perylene·(tetrachloroethene)2 (P·(4ClE)2) are investigated by two-color resonant two-photon ionization (2C-R2PI) and dispersed fluorescence spectroscopy in supersonic jets. The S0 → S1 vibrationless transitions of P·4ClE and P·(4ClE)2 are shifted by δν = −451 and −858 cm–1 relative to perylene, translating to excited-state dissociation energy increases of 5.4 and 10.3 kJ/mol, respectively. The red shift is ∼30% larger than that of perylene·trans-1,2-dichloroethene; therefore, the increase in chlorination increases the excited-state stabilization and CT character of the interaction, but the electronic excitation remains largely confined to the perylene moiety. The 2C-R2PI and fluorescence spectra of P·4ClE exhibit strong progressions in the perylene intramolecular twist (1au) vibration (42 cm–1 in S0 and 55 cm–1 in S1), signaling that perylene deforms along its twist coordinate upon electronic excitation. The intermolecular stretching (Tz) and internal rotation (Rc) vibrations are weak; therefore, the P·4ClE intermolecular potential energy surface (IPES) changes little during the S0 ↔ S1 transition. The minimum-energy structures and inter- and intramolecular vibrational frequencies of P·4ClE and P·(4ClE)2 are calculated with the dispersion-corrected density functional theory (DFT) methods B97-D3, ωB97X-D, M06, and M06-2X and the spin-consistent-scaled (SCS) variant of the approximate second-order coupled-cluster method, SCS-CC2. All methods predict the global minima to be π-stacked centered coplanar structures with the long axis of tetrachloroethene rotated by τ ≈ 60° relative to the perylene long axis. The calculated binding energies are in the range of −D0 = 28–35 kJ/mol. A second minimum is predicted with τ ≈ 25°, with ∼1 kJ/mol smaller binding energy. Although both monomers are achiral, both the P·4ClE and P·(4ClE)2 complexes are chiral. The best agreement for adiabatic excitation energies and vibrational frequencies is observed for the ωB97X-D and M06-2X DFT methods.

An automated method for mapping physical soil and water conservation structures on cultivated land using GIS and remote sensing techniques

An efficient and reliable automated model that can map physical Soil and Water Conservation (SWC) structures on cultivated land was developed using very high spatial resolution imagery obtained from Google Earth and ArcGIS, ERDAS IMAGINE, and SDC Morphology Toolbox for MATLAB and statistical techniques. The model was developed using the following procedures: (1) a high-pass spatial filter algorithm was applied to detect linear features, (2) morphological processing was used to remove unwanted linear features, (3) the raster format was vectorized, (4) the vectorized linear features were split per hectare (ha) and each line was then classified according to its compass direction, and (5) the sum of all vector lengths per class of direction per ha was calculated. Finally, the direction class with the greatest length was selected from each ha to predict the physical SWC structures. The model was calibrated and validated on the Ethiopian Highlands. The model correctly mapped 80% of the existing structures. The developed model was then tested at different sites with different topography. The results show that the developed model is feasible for automated mapping of physical SWC structures. Therefore, the model is useful for predicting and mapping physical SWC structures areas across diverse areas.

Fluorophotometry is a sensitive method/technique to evaluate epithelial permeability in murine experimental dry eye

Purpose. Fluorophotometry is a well validated method for assessing corneal permeability in human subjects. However, with the growing importance of basic science animal research in ophthalmology, fluorophotometry’s use in animals must be further evaluated. The purpose of this study was to evaluate corneal epithelial permeability following desiccating stress using the modified Fluorotron Master™. ^ Methods. Corneal permeability was evaluated prior to and after subjecting 6-8 week old C57BL/6 mice to experimental dry eye (EDE) for 2 and 5 days (n=9/time point). Untreated mice served as controls. Ten microliters of 0.001% sodium fluorescein (NaF) were instilled topically into each mouse’s left eye to create an eye bath, and left to permeate for 3 minutes. The eye bath was followed by a generous wash with Buffered Saline Solution (BSS) and alignment with the Fluorotron Master™. Seven corneal scans using the Fluorotron Master were performed during 15 minutes (1 st post-wash scans), followed by a second wash using BSS and another set of five corneal scans (2nd post-wash scans) during the next 15 minutes. Corneal permeability was calculated using data calculated with the FM™ Mouse software. ^ Results. When comparing the difference between the Post wash #1 scans within the group and the Post wash #2 scans within the group using a repeated measurement design, there was a statistical difference in the corneal fluorescein permeability of the Post-wash #1 scans after 5 days (1160.21±108.26 vs. 1000.47±75.56 ng/mL, P<0.016 for UT-5 day comparison 8 [0.008]), but not after only 2 days of EDE compared to Untreated mice (1115.64±118.94 vs. 1000.47±75.56 ng/mL, P>0.016 for UT-2 day comparison [0.050]). There was no statistical difference between the 2 day and 5 day Post wash #1 scans (P=.299). The Post-wash #2 scans demonstrated that EDE caused a significant NaF retention at both 2 and 5 days of EDE compared to baseline, untreated controls (1017.92±116.25, 1015.40±120.68 vs. 528.22±127.85 ng/mL, P<0.05 [0.0001 for both]). There was no statistical difference between the 2 day and 5 day Post wash #2 scans (P=.503). The comparison between the Untreated post wash #1 with untreated post wash #2 scans using a Paired T-test showed a significant difference between the two sets of scans (P=0.000). There is also a significant difference between the 2 day comparison and the 5 day comparison (P values = 0.010 and 0.002, respectively). ^ Conclusion. Desiccating stress increases permeability of the corneal epithelium to NaF, and increases NaF retention in the corneal stroma. The Fluorotron Master is a useful and sensitive tool to evaluate corneal permeability in murine dry eye, and will be a useful tool to evaluate the effectiveness of dry eye treatments in animal-model drug trials.^

The relationship between supermarket nutrient movements and the mortality rates from fat-associated and non-fat-associated cardiovascular disease: Development of an ecologic method for determining community food patterns

Supermarket nutrient movement, a community food consumption measure, aggregated 1,023 high-fat foods, representing 100% of visible fats and approximately 44% of hidden fats in the food supply (FAO, 1980). Fatty acid and cholesterol content of foods shipped from the warehouse to 47 supermarkets located in the Houston area were calculated over a 6 month period. These stores were located in census tracts with over 50% of a given ethnicity: Hispanic, black non-Hispanic, or white non-Hispanic. Categorizing the supermarket census tracts by predominant ethnicity, significant differences were found by ANOVA in the proportion of specific fatty acids and cholesterol content of the foods examined. Using ecological regression, ethnicity, income, and median age predicted supermarket lipid movements while residential stability did not. No associations were found between lipid movements and cardiovascular disease mortality, making further validation necessary for epidemiological application of this method. However, it has been shown to be a non-reactive and cost-effective method appropriate for tracking target foods in populations of groups, and for assessing the impact of mass media nutrition education, legislation, and fortification on community food and nutrient purchase patterns. ^

Instrumental variable method for the causal relationship between soluble receptor for advanced glycation end-products (sRAGE) and risk of pancreatic cancer

This thesis project is motivated by the potential problem of using observational data to draw inferences about a causal relationship in observational epidemiology research when controlled randomization is not applicable. Instrumental variable (IV) method is one of the statistical tools to overcome this problem. Mendelian randomization study uses genetic variants as IVs in genetic association study. In this thesis, the IV method, as well as standard logistic and linear regression models, is used to investigate the causal association between risk of pancreatic cancer and the circulating levels of soluble receptor for advanced glycation end-products (sRAGE). Higher levels of serum sRAGE were found to be associated with a lower risk of pancreatic cancer in a previous observational study (255 cases and 485 controls). However, such a novel association may be biased by unknown confounding factors. In a case-control study, we aimed to use the IV approach to confirm or refute this observation in a subset of study subjects for whom the genotyping data were available (178 cases and 177 controls). Two-stage IV method using generalized method of moments-structural mean models (GMM-SMM) was conducted and the relative risk (RR) was calculated. In the first stage analysis, we found that the single nucleotide polymorphism (SNP) rs2070600 of the receptor for advanced glycation end-products (AGER) gene meets all three general assumptions for a genetic IV in examining the causal association between sRAGE and risk of pancreatic cancer. The variant allele of SNP rs2070600 of the AGER gene was associated with lower levels of sRAGE, and it was neither associated with risk of pancreatic cancer, nor with the confounding factors. It was a potential strong IV (F statistic = 29.2). However, in the second stage analysis, the GMM-SMM model failed to converge due to non- concaveness probably because of the small sample size. Therefore, the IV analysis could not support the causality of the association between serum sRAGE levels and risk of pancreatic cancer. Nevertheless, these analyses suggest that rs2070600 was a potentially good genetic IV for testing the causality between the risk of pancreatic cancer and sRAGE levels. A larger sample size is required to conduct a credible IV analysis.^

Mean dynamic topography and oceanographic parameters estimated from an inverse model and satellite geodesy, with link to model result in one single NetCDF file (392 MB), including the inverse data error covariance

Geostrophic surface velocities can be derived from the gradients of the mean dynamic topography-the difference between the mean sea surface and the geoid. Therefore, independently observed mean dynamic topography data are valuable input parameters and constraints for ocean circulation models. For a successful fit to observational dynamic topography data, not only the mean dynamic topography on the particular ocean model grid is required, but also information about its inverse covariance matrix. The calculation of the mean dynamic topography from satellite-based gravity field models and altimetric sea surface height measurements, however, is not straightforward. For this purpose, we previously developed an integrated approach to combining these two different observation groups in a consistent way without using the common filter approaches (Becker et al. in J Geodyn 59(60):99-110, 2012, doi:10.1016/j.jog.2011.07.0069; Becker in Konsistente Kombination von Schwerefeld, Altimetrie und hydrographischen Daten zur Modellierung der dynamischen Ozeantopographie, 2012, http://nbn-resolving.de/nbn:de:hbz:5n-29199). Within this combination method, the full spectral range of the observations is considered. Further, it allows the direct determination of the normal equations (i.e., the inverse of the error covariance matrix) of the mean dynamic topography on arbitrary grids, which is one of the requirements for ocean data assimilation. In this paper, we report progress through selection and improved processing of altimetric data sets. We focus on the preprocessing steps of along-track altimetry data from Jason-1 and Envisat to obtain a mean sea surface profile. During this procedure, a rigorous variance propagation is accomplished, so that, for the first time, the full covariance matrix of the mean sea surface is available. The combination of the mean profile and a combined GRACE/GOCE gravity field model yields a mean dynamic topography model for the North Atlantic Ocean that is characterized by a defined set of assumptions. We show that including the geodetically derived mean dynamic topography with the full error structure in a 3D stationary inverse ocean model improves modeled oceanographic features over previous estimates.

Pollen record and calculated holocene vegetation and climate dynamics from Sihailongwan Maar Lake, NE China

High-resolution palynological analysis on annually laminated sediments of Sihailongwan Maar Lake (SHL) provides new insights into the Holocene vegetation and climate dynamics of NE China. The robust chronology of the presented record is based on varve counting and AMS radiocarbon dates from terrestrial plant macro-remains. In addition to the qualitative interpretation of the pollen data, we provide quantitative reconstructions of vegetation and climate based on the method of biomization and weighted averaging partial least squares regression (WA-PLS) technique, respectively. Power spectra were computed to investigate the frequency domain distribution of proxy signals and potential natural periodicities. Pollen assemblages, pollen-derived biome scores and climate variables as well as the cyclicity pattern indicate that NE China experienced significant changes in temperature and moisture conditions during the Holocene. Within the earliest phase of the Holocene, a large-scale reorganization of vegetation occurred, reflecting the reconstructed shift towards higher temperatures and precipitation values and the initial Holocene strengthening and northward expansion of the East Asian summer monsoon (EASM). Afterwards, summer temperatures remain at a high level, whereas the reconstructed precipitation shows an increasing trend until approximately 4000 cal. yr BP. Since 3500 cal. yr BP, temperature and precipitation values decline, indicating moderate cooling and weakening of the EASM. A distinct periodicity of 550-600 years and evidence of a Mid-Holocene transition from a temperature-triggered to a predominantly moisture-triggered climate regime are derived from the power spectra analysis. The results obtained from SHL are largely consistent with other palaeoenvironmental records from NE China, substantiating the regional nature of the reconstructed vegetation and climate patterns. However, the reconstructed climate changes contrast with the moisture evolution recorded in S China and the mid-latitude (semi-)arid regions of N China. Whereas a clear insolation-related trend of monsoon intensity over the Holocene is lacking from the SHL record, variations in the coupled atmosphere-Pacific Ocean system can largely explain the reconstructed changes in NE China.

Calculated sea surface temperatures of two sediment cores

The reconstruction of ocean history employs a large variety of methods with origins in the biological, chemical, and physical sciences, and uses modern statistical techniques for the interpretation of extensive and complex data sets. Various sediment properties deliver useful information for reconstructing environmental parameters. Those properties that have a close relationship to environmental parameters are called ''proxy variables'' (''proxies'' for short). Proxies are measurable descriptors for desired (but unobservable) variables. Surface water temperature is probably the most important parameter for describing the conditions of past oceans and is crucial for climate modelling. Proxies for temperature are: abundance of microfossils dwelling in surface waters, oxygen isotope composition of planktic foraminifers, the ratio of magnesium or strontium to calcium in calcareous shells or the ratio of certain organic molecules (e.g. alkenones produced by coccolithophorids). Surface water salinity, which is important in modelling of ocean circulation, is much more difficult to reconstruct. At present there is no established method for a direct determination of this parameter. Measurements associated with the paleochemistry of bottom waters to reconstruct bottom water age and flow are made on benthic foraminifers, ostracodes, and deep-sea corals. Important geochemical tracers are d13C and Cd/Ca ratios. When using benthic foraminifers, knowledge of the sediment depth habitat of species is crucial. Reconstructions of productivity patterns are of great interest because of important links to current patterns, mixing of water masses, wind, the global carbon cycle, and biogeography. Productivity is reflected in the flux of carbon into the sediment. There are a number of fluxes other than those of organic carbon that can be useful in assessing productivity fluctuations. Among others, carbonate and opal flux have been used, as well as particulate barite. Furthermore, microfossil assemblages contain clues to the intensity of production as some species occur preferentially in high-productivity regions while others avoid these. One marker for the fertility of sub-surface waters (that is, nutrient availability) is the carbon isotope ratio within that water (13C/12C, expressed as d13C). Carbon isotope ratios in today's ocean are negatively correlated with nitrate and phosphate contents. Another tracer of phosphate content in ocean waters is the Cd/Ca ratio. The correlation between this ratio and phosphate concentrations is quite well documented. A rather new development to obtain clues on ocean fertility (nitrate utilization) is the analysis of the 15N/14N ratio in organic matter. The fractionation dynamics are analogous to those of carbon isotopes. These various ratios are captured within the organisms growing within the tagged water. A number of reconstructions of the partial pressure of CO2 have been attempted using d13C differences between planktic and benthic foraminifers and d13C values of bulk organic material or individual organic components. To define the carbon system in sea water, two elements of the system have to be known in addition to temperature. These can be any combination of total CO2 , alkalinity, or pH. To reconstruct pH, the boron isotope composition of carbonates has been used. Ba patterns have been used to infer the distribution of alkalinity in past oceans. Information relating to atmospheric circulationand climate is transported to the ocean by wind or rivers, in the form of minerals or as plant andanimal remains. The most useful tracers in this respect are silt-sized particles and pollen.

Turbidity measurements in 96-wells microplates to determine the densities of copiotrophic and oligotrophic bacteria with the Most-Probable-Number-method during POLARSTERN cruise ANT-XI/2

A new microtiter-plate dilution method was applied during the expedition ANTARKTIS-XI/2 with RV Polarstern to determine the distribution of copiotrophic and oligotrophic bacteria in the water columns at polar fronts. Twofold serial dilutions were performed with an eight-channel Electrapette in 96-wells plates by mixing 150 µl of seawater with 150 µl of copiotrophic or olitrophic Trypticase-Broth, three times per well. After incubation of about 6 month at 2 °C, turbidities were measured with an eight-channel photometer at 405 nm and combinations of positive test results for three consecutive dilutions chosen and compared with a Most Probable Number table, calculated for 8 replicates and twofold serial dilutions. Densities of 12 to 661 cells/ml for copiotrophs, and 1 to 39 cells/ml for oligotrophs were found. Colony Forming Units on copiotrophic Trypticase-Agar were between 6 and 847 cells/ml, which is in the same range as determined with the MPN method.

Calculated sea level records and deep ocean temperatures from DSDP and ODP sites

During the mid-Pleistocene transition the dominant 41 ka periodicity of glacial cycles transitioned to a quasi-100 ka periodicity for reasons not yet known. This study investigates the potential role of deep ocean hydrography by examining oxygen isotope ratios in benthic foraminifera. Oxygen isotope records from the Atlantic, Pacific and Indian Ocean basins are separated into their ice volume and local temperature/hydrography components using a piece-wise linear transfer function and a temperature calibration. Although our method has certain limitations, the deep ocean hydrography reconstructions show that glacial deep ocean temperatures approached freezing point as the mid-Pleistocene transition progressed. Further analysis suggests that water mass reorganisation could have been responsible for these temperature changes, leading to such stable conditions in the deep ocean that some obliquity cycles were skipped until precessional forcing triggered deglaciation, creating the apparent quasi-100 ka pattern. This study supports previous work that suggests multiples of obliquity cycles dominate the quasi-100 ka glacial cycles with precession components driving deglaciations.

Carbon uptake rate calculated for melt pond water samples during POLARSTERN cruise ARK-XXVII/3 (IceArc) in 2012

Net Primary Production was measured using the 14**C uptake method with minor modifications. Melt pond samples were spiked with 0.1µCi ml**-1 of 14**C labelled sodium bicarbonate (Moravek Biochemicals, Brea, USA) and distributed in 10 clear bottles (20 ml each). Subsequently they were incubated for 12 h at -1.3°C under different scalar irradiances (0-420 µmol photons m**-2 s**-1) measured with a spherical sensor (Spherical Micro Quantum Sensor US-SQS/L, Heinz Walz, Effeltrich, Germany). At the end of the incubation, samples were filtered onto 0.2 µm nitrocellulose filters and the particulate radioactive carbon uptake was determined by liquid scintillation counting using Filter count scintillation cocktail (Perkin Elmer, Waltham, USA). The carbon uptake values in the dark were subtracted from the carbon uptake values measured in the light incubations. Dissolved inorganic carbon (DIC) was measured for each sample using the flow injection system (Hall and Aller, 1992). The DIC concentration was taken into account to calculate the amount of labeled bicarbonate incorporated into the cell. Carbon fixation rates were normalized volumetrically and by chlorophyll a. Photosynthesis-irradiance curves (PI curves) were fitted using MATLAB® according to the equation proposed by Platt et al. (1980) including a photoinhibition parameter (beta) and providing the main photosynthetic parameters: maximum Chla normalized carbon fixation rate if there were no photoinhibition (Pb) and the initial slope of the saturation curve (alpha). The derived parameters: light intensity at which photosynthesis is maximal (Im), the carbon fixation rate at that maximal irradiance (Pbm) and the adaptation parameter or photoacclimation index (Ik) were calculated according to Platt et al. (1982).

Carbon uptake rate calculated for CTD water samples during POLARSTERN cruise ARK-XXVII/3 (IceArc) in 2012

Net Primary Production was measured using the 14**C uptake method with minor modifications. Seawater samples were spiked with 0.1µCi ml**-1 of 14**C labelled sodium bicarbonate (Moravek Biochemicals, Brea, USA) and distributed in 10 clear bottles (20 ml each). Subsequently they were incubated for 12 h at -1.3°C under different scalar irradiances (0-420 µmol photons m**-2 s**-1) measured with a spherical sensor (Spherical Micro Quantum Sensor US-SQS/L, Heinz Walz, Effeltrich, Germany). At the end of the incubation, samples were filtered onto 0.2 µm nitrocellulose filters and the particulate radioactive carbon uptake was determined by liquid scintillation counting using Filter count scintillation cocktail (Perkin Elmer, Waltham, USA). The carbon uptake values in the dark were subtracted from the carbon uptake values measured in the light incubations. Dissolved inorganic carbon (DIC) was measured for each sample using the flow injection system (Hall and Aller, 1992). The DIC concentration was taken into account to calculate the amount of labeled bicarbonate incorporated into the cell. Carbon fixation rates were normalized volumetrically and by chlorophyll a. Photosynthesis-irradiance curves (PI curves) were fitted using MATLAB® according to the equation proposed by Platt et al. (1980) including a photoinhibition parameter (beta) and providing the main photosynthetic parameters: maximum Chla normalized carbon fixation rate if there were no photoinhibition (Pb) and the initial slope of the saturation curve (alpha). The derived parameters: light intensity at which photosynthesis is maximal (Im), the carbon fixation rate at that maximal irradiance (Pbm) and the adaptation parameter or photoacclimation index (Ik) were calculated according to Platt et al. (1982).

Carbon uptake rate calculated for sea-ice core samples during POLARSTERN cruise ARK-XXVII/3 (IceArc) in 2012

Net Primary Production was measured using the 14**C uptake method with minor modifications. Melted sea ice samples were spiked with 0.1µCi ml**-1 of 14**C labelled sodium bicarbonate (Moravek Biochemicals, Brea, USA) and distributed in 10 clear bottles (20 ml each). Subsequently they were incubated for 12 h at -1.3°C under different scalar irradiances (0-420 µmol photons m**-2 s**-1) measured with a spherical sensor (Spherical Micro Quantum Sensor US-SQS/L, Heinz Walz, Effeltrich, Germany). At the end of the incubation, samples were filtered onto 0.2 µm nitrocellulose filters and the particulate radioactive carbon uptake was determined by liquid scintillation counting using Filter count scintillation cocktail (Perkin Elmer, Waltham, USA). The carbon uptake values in the dark were subtracted from the carbon uptake values measured in the light incubations. Dissolved inorganic carbon (DIC) was measured for each sample using the flow injection system (Hall and Aller, 1992). The DIC concentration was taken into account to calculate the amount of labeled bicarbonate incorporated into the cell. Carbon fixation rates were normalized volumetrically and by chlorophyll a. Photosynthesis-irradiance curves (PI curves) were fitted using MATLAB® according to the equation proposed by Platt et al. (1980) including a photoinhibition parameter (beta) and providing the main photosynthetic parameters: maximum Chla normalized carbon fixation rate if there were no photoinhibition (Pb) and the initial slope of the saturation curve (alpha). The derived parameters: light intensity at which photosynthesis is maximal (Im), the carbon fixation rate at that maximal irradiance (Pbm) and the adaptation parameter or photoacclimation index (Ik) were calculated according to Platt et al. (1982).