bluuebunny/crossref_metadata_2025 huggingface dataset:
The intricate relationship of G-Quadruplexes and bacterial pathogenicity islands
Authors: Lyu Bo , Song Qisheng
Published: February 2024

The dynamic interplay between guanine-quadruplex (G4) structures and pathogenicity islands (PAIs) represents a captivating area of research with implications for understanding the molecular mechanisms underlying pathogenicity. This study conducted a comprehensive analysis of a large-scale dataset from reported 89 pathogenic strains of bacteria to investigate the potential interactions between G4 structures and PAIs. G4 structures exhibited an uneven and non-random distribution within the PAIs and were consistently conserved within the same pathogenic strains. Additionally, this investigation identified positive correlations between the number and frequency of G4 structures and the GC content across different genomic features, including the genome, promoters, genes, tRNA, and rRNA regions, indicating a potential relationship between G4 structures and the GC-associated regions of the genome. The observed differences in GC content between PAIs and the core genome further highlight the unique nature of PAIs and underlying factors, such as DNA topology. High-confidence G4 structures within regulatory regions of Escherichia coli were identified, modulating the efficiency or specificity of DNA integration events within PAIs. Collectively, these findings pave the way for future research to unravel the intricate molecular mechanisms and functional implications of G4-PAI interactions, thereby advancing our understanding of bacterial pathogenicity and the role of G4 structures in pathogenic diseases.
Effects of BRD4 inhibitor JQ1 on the expression profile of super-enhancer related lncRNAs and mRNAs in cervical cancer HeLa cells
Authors: Zheng Jianqing , Huang Bifen , Xiao Lihua , Wu Min
Published: February 2024

Objective

To investigate the effects of bromine domain protein 4 (BRD4) inhibitor JQ1 on the expression profile of super-enhancer-related lncRNAs (SE-lncRNAs) and mRNAs in cervical cancer (CC) HeLa-cells.

Methods

The CCK8 method was implemented to detect the inhibitory effect of JQ1 on HeLa cells and explore the best inhibitory concentration. Whole transcriptome sequencing was performed to detect the changes of lncRNAs and mRNAs expression profiles in cells of the JQ1 treatment group and control group, respectively. The differentially expressed SE-lncRNAs were obtained by matching, while the co-expressed mRNAs were obtained by Pearson correlation analysis.

Results

The inhibitory effect of JQ1 on HeLa cell proliferation increased significantly with increasing concentration and treatment time (P < 0.05). Under the experimental conditions of three concentrations of 0.01, 0.1 and 1 μmol/L of JQ1 on HeLa cells at 24, 48, 72 and 120 h, 1 μmol/L of JQ1 at 72 and 120 h had the same cell viability and the strongest cell proliferation inhibition. In order to understand the inhibitory mechanism of JQ1 on HeLa cells, this study analyzed the expression profile differences from the perspective of SE-lncRNAs and mRNAs. A total of 162 SE-lncRNAs were identified, of which 8 SE-lncRNAs were down-regulated and seven SE-lncRNAs were up-regulated. A total of 418 differentially expressed mRNAs related to SE-lncRNAs were identified, of which 395 mRNAs had positive correlation with 12 SE-lncRNAs and 408 mRNAs had negative correlation with 15 SE-lncRNAs.

Conclusion

JQ1 can significantly inhibit the proliferation of HeLa cells and affect the expression profile of SE-lncRNAs and mRNAs.
Assessment of Groundwater Quality around Amaenyi and State Secretariat Dumpsites in Awka, Southeastern Nigeria
Authors: Okolo, C. M.  , Okonkwo, O. S.  , Madu, F. M.  , Ifeanyichukwu, K. A.
Published: February 2024

The effects of two dumpsites located at Amaenyi and State Secretariat Awka on groundwater resources was investigated using hydrochemical parameters. A total of eighteen (18) groundwater samples were collected from areas in the vicinity of the dumpsites and analysed for various hydrochemical and biological parameters using standard methods. The results of the analysis were subjected to interpretations using various methods such as spatial distribution maps, water quality indices (WQI, HPI, Cd and MEI), comparing with international and local standards and statistical analysis. The results indicate that parameters such as Ec, TDS, Na+, K+, Ca2+, Cl-, NO3- and SO42- were in compliance with the acceptable limits of World Health Organization and Nigerian Drinking Water Standard. However, HCO3-, total hardness, COD, BOD, DO1, DO5, Pb, Fe, Cd and Hg exceeded the permissible guidelines in some samples. WQI rated 20% of the samples in Amaenyi as excellent, 30% (good), 10% (poor), 20% (very poor) and the remaining 20% is unfit for consumption while in State Secretariat area, 37.5% was very poor and the remaining 62.5% was unfit for consumption. HPI rated groundwater as highly contaminated while Cd classified most of the water samples to indicate low contamination except for sample A1 which was highly contaminated.  Also, MEI indicated that groundwater has low heavy metal pollution. The correlation analysis indicates strong positive relationship between BOD, COD, DO1, DO5, total hardness, bicarbonate, calcium and sulphate, lead, magnesium and chloride. It was concluded that groundwater in the study area is mostly contaminated and the contaminants is attributed to be from the waste dumpsites and other anthropogenic activities.
Morpho-physiological Alteration of Mangifera indica L. in Response to Sea Water Induced Salt Stress
Authors: Mou Rashida Rocksana , Riyadh Zabid Al , Mia Md. Giashuddin , Mohi-Ud-Din Mohammed , Hoque Abu Hasnath Mohammad Shohidul , Rahman Md. Abiar
Published: February 2024

Salinity is one of the biggest challenges in the southern part of Bangladesh, which is affecting the coastal ecosystem adversely. A pot experiment was conducted to find out the morpho-physiological changes in mango (Mangifera indica L.) seedlings in response to sea water induced salt stress at the Agroforestry and Environment research field of Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU). The experiment was laid out in a Randomized Complete Block Design (RCBD) with five replications, where four treatments, viz 4, 8, 12 dS m-1 salinity level (prepared from sea water), and the tap water (control) were imposed. The results indicated that plant height of mango shortened with the higher level of salinity and the declining magnitude was 28.44% over control at maximum salinity level. Number of leaves per plant of mango were reduced by 27.51% at 12 dS m-1 salinity level compared to that tap water, and the size of mango leaf was also reduced for salinity. Both shoot and root biomass of mango seedlings were significantly reduced due to salinity. The Salt tolerance index in mango was 56.76 only at 12 dS m-1. In case of physiological parameters, the lowest relative water content (RWC) was found in 12 dS m-1, while water saturation deficit (WSD) and water uptake capacity (WUC) were found to be the lowest in control for this plant. Water saturation deficit and water uptake capacity were increased with the increment of salinity level. Total chlorophyll and carotenoid content of mango were decreased by 66.27% and 61.07%, respectively, at the highest salinity level. Proline content of mango increased by 73.07% at 12 dS m-1 salt level in comparison to that of seawater devoid control plants. Considering the overall results, it can be concluded that, although mango seedlings were significantly affected by high salinity (12 dS m-1), but can survive up to moderate salinity (8 dS m-1) at sapling stage.
Bio-efficacy and Phytotoxicity of Gibberellic Acid (GA3) Technical 90% for Improving Yield and Quality in Grapes (Vitis vinifera L.)
Authors: Bhagwat Sharad R , Kalbhor Jeevan N , Wable Tushar U , Gavali Appaso H
Published: February 2024

The experiment was conducted on Thompson Seedless grapevines grafted on dog ridge rootstock to study its response towards the application of gibberellic acid (GA3) Tech. 90% at different time intervals. The experiment was designed in a randomized block design (RBD) having five treatments with four replications were carried out at Maharashtra Rajya Draksha Bagaitdar Sangh, Pune during 2020-2021 & 2021 - 2022. Significant differences were observed with the applications of GA3 at different developmental stages (pre-bloom and fruit set) resulted in to increased bunch weight, berry weight, berry length, berry size, pedicel thickness, rachis length, and quality parameters viz.  total soluble solids along with the highest yield per vine exogenous application of different concentrations of GA3 at different time interval schedules was beneficial for the quality and yield of Thompson Seedless grapevines.
Modeling vital rates improves estimation of population projection matrices
Authors: Gross Kevin , Morris William F. , Wolosin Michael S. , Doak Daniel F.
Published: November 2005

Population projection matrices are commonly used by ecologists and managers to analyze the dynamics of stage‐structured populations. Building projection matrices from data requires estimating transition rates among stages, a task that often entails estimating many parameters with few data. Consequently, large sampling variability in the estimated transition rates increases the uncertainty in the estimated matrix and quantities derived from it, such as the population multiplication rate and sensitivities of matrix elements. Here, we propose a strategy to avoid overparameterized matrix models. This strategy involves fitting models to the vital rates that determine matrix elements, evaluating both these models and ones that estimate matrix elements individually with model selection via information criteria, and averaging competing models with multimodel averaging. We illustrate this idea with data from a population of Silene acaulis (Caryophyllaceae), and conduct a simulation to investigate the statistical properties of the matrices estimated in this way. The simulation shows that compared with estimating matrix elements individually, building population projection matrices by fitting and averaging models of vital‐rate estimates can reduce the statistical error in the population projection matrix and quantities derived from it.
Abiotic mosaics affect seasonal variation of plant resources and influence the performance and mortality of a leaf‐miner in Gambel's oak (Quercus gambelii, Nutt.)
Authors: Yarnes Christopher T. , Boecklen William J.
Published: November 2005

Conceptual models of terrestrial trophic dynamics have emphasized the potential influence of various abiotic factors, though empirical studies have found generalities to be scarce. Progress may result through an increased use of experimental gradients in tandem with existing, natural gradients of abiotic factors that are more difficult to manipulate. Along an elevation/climatic gradient, a fertilization experiment was conducted to examine the impact of environmentally induced variation in foliar nitrogen on tri‐trophic interactions for Phyllonorycter sp., a leaf‐miner (Lepidoptera: Gracillariidae), in Rocky Mountain white oak, Quercus gambelii. Microclimate determined the relative effect of host‐plant and natural‐enemy effects for Phyllonorycter sp. Cooler, more humid microclimates resulted in a higher biomass payoff (total biomass/density). Further, increased seasonal variation in foliar nitrogen content at warmer, drier sites significantly increased parasitism rates. Fertilization treatments increased foliar nitrogen content and resulted in increased early‐instar mortality. Fertilization treatment also acted in a non‐linear fashion with microclimate to influence spatial patterns in parasitism rates. Overall, microclimate was found to affect characteristics of each trophic level, including host‐plant nitrogen dynamics, Phyllonorycter sp. performance, and parasitism rates. Additionally, nutrient availability altered patterns of parasitoid‐related mortality in Phyllonorycter sp. within microclimates. These results suggest that local topographic variation in combinations of abiotic factors, or abiotic mosaics, has important effects for spatial patterns of tri‐trophic interactions.
The effects of understorey dwarf bamboo (Sasa kurilensis) removal on soil fertility in a Betulaermanii forest of northern Japan
Authors: Tripathi Shri Kant , Sumida Akihiro , Ono Kiyomi , Shibata Hideaki , Uemura Shigeru , Takahashi Koichi , Hara Toshihiko
Published: November 2005

We investigated the changes in soil microbial biomass C (MBC), microbial biomass N (MBN) and N mineralization in Sasa kurilensis‐present (SP) and S. kurilensis‐removed (SR) stands in a Betula ermanii forest. The mean levels of MBC and MBN were significantly higher in the SR stand than in the SP, which may have positively influenced the N‐mineralization rate as depicted by a significant positive correlation between these variables and the N‐mineralization rate. N immobilization and subsequent N release along with decreased use of available soil N due to S. kurilensis removal may have ensured greater N availability in the SR stand.
Sr and Nd isotope evidence for successive crustal contamination of Slieve Gullion ring-dyke magmas, Co. Armagh, Ireland
Authors: TROLL VALENTIN R. , CHADWICK JANE P. , ELLAM ROBERT M. , Mc DONNELL SUSAN , EMELEUS C. HENRY , MEIGHAN IAN G.
Published: November 2005

The Palaeogene Slieve Gullion Igneous Centre in southern Armagh, Northern Ireland, consists of a layered central intrusive complex surrounded by a prominent and slightly older ring-dyke that intrudes both Lower Palaeozoic sedimentary rocks and the Caledonian Newry Granodiorite pluton (452 Ma). The ring-dyke comprises two major rock types: porphyritic felsite and porphyritic granophyre. We analysed both ring-dyke lithologies, both types of country rock, and a local Palaeogene basalt dyke sample for Sr and Nd isotopes. Trace element and whole rock data for this suite suggest that there are two distinct groups of both felsite and granophyre: one Si-rich and one Si-poor, most likely representing two magmas from a zoned chamber and their mushy chamber wall equivalents (McDonnell et al. 2004). Isotope data show the low-Si rocks to be higher in radiogenic Sr than the high-Si rocks, which is inconsistent with a simple AFC-scenario of increasing sediment assimilation with higher degrees of differentiation. However, using MORB-type basalt as a starting composition, the low-Si ring-dyke rocks can be modelled through AFC with Lower Palaeozoic sedimentary rock as the contaminant. The decreasing 87Sr/86Sr trend from low-Si to high-Si dyke rocks, in turn, represents a second stage of contamination. Selective assimilation of the most fusible portions of Newry Granodiorite, which is lower in radiogenic Sr than the local sedimentary rocks, appears to be the most plausible solution. The Sr and Nd data are consistent with (a) at least a two-stage contamination history during upper crustal residence and storage, whereby fractionating magmas of basaltic and intermediate composition are contaminated by local sedimentary rocks, giving rise to rhyolite magmas that experience additional shallow contamination by Newry Granodiorite, and (b) a zoned rhyolite magma chamber where high-Si magma is stored in the upper part of the chamber where crystallization and crustal contamination are most extensive.
North Atlantic and North Sea Climate Change: curl up, shut down, NAO and Ocean Colour
Authors: Pingree Robin
Published: November 2005

The strength of the North Atlantic Current (NAC) (based on sea-surface elevation slopes derived from altimeter data) is correlated with westerly winds (based on North Atlantic Oscillation [NAO] Index data over a nine year period [1992–2002] with 108 monthly values). The data time window includes the major change in climate forcing over the last 100 years (1995 to 1996). It is shown that the NAO Index can be used for early warning of system failure for the NAC. The correlation response or early warning time scale for western Europe and south England is six months. The decay scale for the NAC and Subtropical Gyre circulation is estimated as three years. Longer period altimeter elevation/circulation changes are discussed. The sea-surface temperature (SST) response of the North Sea to negative and positive NAO conditions is examined. The overall temperature response for the central North Sea to NAO index forcing, reflecting wind induced inflow, shelf circulation and local climate forcing, is ∼5 months. In years with strong North Atlantic winter wind induced inflow, under marked NAO positive conditions, mean temperatures (∼10.5°C) are about 1°C warmer than under negative conditions. In 1996 under extreme negative winter NAO conditions, the North Sea circulation stopped, conditions near the Dogger Bank became more continentally influenced and the winter (March) temperature fell to 3.1°C whereas in 1995 under NAO positive winter conditions the minimum temperature was 6.4°C (February). Seasonal advance of North Atlantic and North Sea temperature is derived in relation to temperature change. Temperature change and monthly NAO Index are discussed with respect to phytoplankton blooms, chlorophyll-a measurements, ocean colour data and the anomalous north-eastern Atlantic 2002 spring/summer bloom SeaWiFS chlorophyll concentrations.
Cladorhiza corona sp. nov. (Porifera: Demospongiae: Cladorhizidae) from the Aleutian Islands (Alaska)
Authors: Lehnert Helmut , Watling Les , Stone Robert
Published: November 2005

A new species of Cladorhizidae, from the Aleutian Islands is described and compared with all known species of Cladorhiza worldwide. Cladorhiza corona sp. nov. has a unique growth form with two planes of differently shaped appendages. Appendages are inserted directly at the stalk; a spherical or conical body at the stalk is lacking. It is the only species reported where different spicule types occur in three morphologically different areas of the sponge. The spiculation of the basal plate is characterized by the occurrence of short, thick anisoxeas and the lack of anisochelae. Anisochelae are found in the stalk and the basal appendages only. Flattened sigmancistras and (sub-)tylostyles are restricted to the crown. The arrangement of spicules is different in the basal plate, the stalk with the basal appendages, and in the distal appendages. The dimensions and combination of spicule types separate C. corona sp. nov. from all known members of the genus.
Relationships between benthic diatoms and hydrozoans (Cnidaria)
Authors: Di Camillo C. , Puce S. , Romagnoli T. , Tazioli S. , Totti C. , Bavestrello G.
Published: November 2005

Some examples of relationships between hydroids and epibionthic diatoms from the Mediterranean Sea are described, verifying the kind of interaction existing between the two partners. The athecate Eudendrium racemosum hosts an extremely rich diatom assemblage, mainly comprising Licmophora spp., Amphora spp. and Cocconeis spp. On the contrary, only adnate growth forms (Cocconeis pseudonotata, C. dirupta) were observed in diatom communities growing on the external side of thecate species Campanularia hincksii, Clytia linearis and Synthecium evansi. Some diatom species (Cocconeis notata, Cylindrotheca sp. and Navicula sp.) are able to survive in the intrathecal microenvironment. They live in the narrow space between hydrotheca and polyp, receiving protection and probably using the nutrients produced by hydroid metabolism. Sunlight can penetrate through transparent thecae and reach the diatom layer, making photosynthesis possible.
Planktonic stages of Processa macrodactyla (Decapoda: Caridea: Processidae) reared in the laboratory
Authors: Ortega A. , Queiroga H. , González-Gordillo J.I.
Published: November 2005

Two ovigerous females of the processid shrimp Processa macrodactyla were caught in April 1997 at 13 m depth in coastal waters of Rota, Cádiz Bay, south-western Spain (36°36′N 6°18′W). Rearing was terminated after nine zoeal stages, when larvae moulted to the first juvenile instar. Descriptions of the appendages of every instar have been made so as to: (1) compare the larval morphology with that of other previous described known species in the genus Processa (P. canaliculata, P. edulis, P. elegantula, P. modica, P. nouveli); and (2) with those larvae not ascribed to a certain species in order to facilitate the specific identification of unknown collected planktonic larvae. When describing P. macrodactyla some characters remained, with few exceptions, invariable in their setation form ZI to ZIV or ZV, to then change and maintain until the last zoeal stage. This can be due to intermediate moults, with the result that some larvae unite the characters of Stages ZIV and ZV and others those of ZV and ZVI.
Adaptation of an immunodot assay for multiple prey identification of squid paralarvae in field trials
Authors: Hoving H.J.T. , Venter J.D. , Worst D.E. , Lipinski M.R.
Published: November 2005

An optimized method, using polyclonal antibodies in an immunoassay, for prey detection in the diet of paralarvae of South African Loligo reynaudii is described. The study has increased the specificity of the antisera by determining the optimum antiserum dilutions and the detection limits of the antisera. Unfed laboratory-hatched paralarvae (negative control) were exposed to antisera and showed cross-reactions with polychaete antiserum.
Repopulation of the shallow subtidal zone by green sea urchins (Strongylocentrotus droebachiensis) following mass mortality in Nova Scotia, Canada
Authors: Brady Sheanna M. , Scheibling Robert E.
Published: November 2005

Repopulation by green sea urchins Strongylocentrotus droebachiensis of a steeply sloping rock bottom was monitored at a wave-exposed headland (Chebucto Head) following a disease outbreak that caused mass mortality in September 1999. Density and size of urchins were sampled in four depth strata: at 8–10 m in an urchin grazing aggregation (front) along the lower margin of a kelp bed, at 12 m and 16 m on a bedrock ramp, and at 24 m on a cobble and boulder field where urchins were unaffected by the disease. Shoreward migration of adults along the ramp from the surviving population at 24 m was the primary means of repopulation, which was augmented by recruitment via planktonic larvae. At 16 m, urchin density stabilized (at ∼50 urchins m−2) within six months of the die-off while repopulation at 12 m took more than eight months. A grazing front of large urchins (40–60 mm, test diameter) had formed along the lower edge of a kelp bed by January 2002, which reached densities of up to 284 urchins m−2. Video surveys at Chebucto Head and two adjacent locations of similar bathymetry revealed an extensive urchin population between 25 and 55 m depth, with a mean density on rocky substrata of 73 urchins m−2.
Diet and diel feeding activity of juvenile pompano (Trachinotus ovatus) (Teleostei: Carangidae) from the southern Adriatic, Croatia
Authors: Batistić Mirna , Tutman Pero , Bojanić Dubravka , Skaramuca Bosko , Kŏzul Valter , Glavić Nik̆sa , Bartulović Vlasta
Published: November 2005

Food and feeding activity of juvenile pompano Trachinotus ovatus (25–97 mm) collected in the summer–autumn in 2003 in coastal shallow-water bays in the south-eastern Adriatic were examined. Juvenile pompano were exclusively daytime feeders and fed in the entire water column, from surface to bottom taking not only plankton, but benthic and terrestrial species as well. Of 18 prey taxa identified, crustaceans—particularly copepods—were the major group, followed by benthic foraminiferans and insects. Feeding on benthic species is reported for the first time in this study.
Thin-film modelling of poroviscous free surface flows
Authors: KING J. R. , OLIVER J. M.
Published: November 2005

Thin-film models for the flow of a low reduced-Reynolds-number poroviscous droplet over a planar substrate are developed. One of the formulations is used to develop a minimal model for active animal cell motion in which the microscopic mechanisms of polymerisation and depolymerisation near the outer cell periphery are modelled by specifying the rate of mass transfer between the phases at the contact-line in terms of the velocity of the latter. An asymptotic analysis in the limit corresponding to strong cell-substrate adhesion is shown to lead to a novel class of multi-valued contact-line laws, a qualitative analysis of which leads in two dimensions to some intriguing behaviour, including (i) periodic contraction and expansion (pulsation), (ii) steady propagation at a contant speed, (iii) an unsteady combination of pulsation and propagation, and (iv) a bistable regime in which both non-motile and motile solutions are admissible, each of them being stable to sufficiently small perturbations, but with sufficiently large perturbations being able to ‘prod’ a stationary cell into motion or halt a moving one; these qualitative predictions are where possible compared with experiment. The contact-line behaviour is likely to be highly sensitive to environmental signals; the formulation may, therefore, provide a useful ‘minimal’ modelling framework for investigation of chemotactic effects at the cell scale. The corresponding extensional flow formulations are also noted.
Moving towards culturally competent dementia care: have we been barking up the wrong tree?
Authors: Mackenzie Jenny , Bartlett Ruth , Downs Murna
Published: November 2005

In the UK it is established that health and social care services for people with dementia from black and minority ethnic communities need to move towards providing evidence-based culturally appropriate care. At present, however, the evidence base available to guide professionals working with people with dementia from diverse ethnic and cultural groups is limited, and beliefs about dementia and the type of treatment and support needed have received little attention. Consequently this creates problems for service providers faced with appropriately supporting people with dementia and their families from black and minority ethnic communities.
Crustal and uppermost mantle structure of the Bohemian Massif based on CELEBRATION 2000 data
Authors: Hrubcová P. , Środa P. , Špičák A. , Guterch A. , Grad M. , Keller G. R. , Brueckl E. , Thybo H.
Published: November 2005

The deep structure of the Bohemian Massif (BM), the largest stable outcrop of Variscan rocks in central Europe, was studied using the data of the international seismic refraction experiment Central European Lithospheric Experiment Based on Refraction (CELEBRATION) 2000. The data were interpreted by seismic tomographic inversion and by two‐dimensional (2‐D) trial‐and‐error forward modeling of P and S waves. Additional constraint on crustal structure was given by amplitude modeling using the reflectivity method and gravity modeling. Though consolidated, the BM can be subdivided into several tectonic units separated by faults, shear zones, or thrusts reflecting varying influence of the Cadomian and Variscan orogeneses: the Saxothuringian, Barrandian, Moldanubian, and Moravian. Velocity models determine three types of crust‐mantle transition in the BM reflecting variable crustal thickness and delimiting contacts of tectonic units in depth. The NW area, the Saxothuringian, has a highly reflective lower crustal layer above Moho with a strong velocity contrast at the top of this layer. This reflective laminated lower crust reaches depths of 26–35 km and is characteristic for the Saxothuringian unit, which was subject to eastward subduction. The Moldanubian in the central part is characterized by the deepest (39 km) and the most pronounced Moho within the whole BM with a strong velocity contrast 6.9–8.1 km s−1. A thick crust‐mantle transition zone in the SE, with velocity increase from 6.8 to 7.8 km s−1 over the depth range of 23–40 km, seems to be the characteristic feature of the Moravian overthrusted by the Moldanubian during Variscan collision.
Comparison of constitutive flow resistance equations based on the Manning and Chezy equations applied to natural rivers
Authors: Bjerklie David M. , Dingman S. Lawrence , Bolster Carl H.
Published: November 2005

A set of conceptually derived in‐bank river discharge–estimating equations (models), based on the Manning and Chezy equations, are calibrated and validated using a database of 1037 discharge measurements in 103 rivers in the United States and New Zealand. The models are compared to a multiple regression model derived from the same data. The comparison demonstrates that in natural rivers, using an exponent on the slope variable of 0.33 rather than the traditional value of 0.5 reduces the variance associated with estimating flow resistance. Mean model uncertainty, assuming a constant value for the conductance coefficient, is less than 5% for a large number of estimates, and 67% of the estimates would be accurate within 50%. The models have potential application where site‐specific flow resistance information is not available and can be the basis for (1) a general approach to estimating discharge from remotely sensed hydraulic data, (2) comparison to slope‐area discharge estimates, and (3) large‐scale river modeling.
In situ timing and pointing verification of the ICESat altimeter using a ground‐based system
Authors: Magruder L. , Silverberg E. , Webb C. , Schutz B.
Published: November 2005

To provide validation of the ICESat laser altimeter time of measurement and geolocation, a ground‐based technique was implemented at White Sands Space Harbor (WSSH), during the Laser 2a and 3a operational periods. The activities used an electro‐optical detection system and a passive array of corner cube retro reflectors (CCR). The detectors and the CCRs were designed to provide an independent assessment of the laser footprint location, while the detectors also provide timing verification. This ground‐based system unambiguously validated the elevation product time tag to 3 μsec ± 1 μsec. In addition, the ground equipment provided in situ geolocations of the laser pulse. Comparing the in situ results to the ICESat GLA14 data product the positions differ by 10.6 m ± 4.5 m for Laser 2a (Release 21) operations and 7.5 m ± 6.6 m for Laser 3a (Release 23). These comparisons correlate to pointing validations at this site, for the specific overflight configurations.
High ClO and ozone depletion observed in the plume of Sakurajima volcano, Japan
Authors: Lee Chulkyu , Kim Young J. , Tanimoto Hiroshi , Bobrowski Nicole , Platt Ulrich , Mori Toshiya , Yamamoto Keigo , Hong Chun S.
Published: November 2005

Enhanced BrO and ClO in the boundary layer associated with ozone destruction have been observed over salt lakes, as well as in the polar boundary layer. Volcanic plumes are a major natural source of atmospheric trace gases, influencing the tropospheric and stratospheric trace gas budgets. Though a variety of volcanic gases have been investigated and BrO was found, there is still little information on other halogen oxides (e.g. ClO) in volcanic plumes and the effects on atmospheric ozone. The current belief that volcanic plumes contain ClO has not been quantified to date. Here we report the successful remote measurement of significant amounts of ClO (as well as BrO and SO2) in a volcanic plume from the Sakurajima volcano in Japan, using ground‐based multi‐axis differential optical absorption spectroscopy during May 2004. Additionally halogen‐catalyzed local surface ozone depletion was observed in the vicinity of the volcano.
Shear‐wave splitting beneath the Galápagos archipelago
Authors: Fontaine Fabrice R. , Hooft Emilie E. E. , Burkett Peter G. , Toomey Douglas R. , Solomon Sean C. , Silver Paul G.
Published: November 2005

Shear‐wave splitting measurements in the Galápagos archipelago show a rapid change from consistently oriented anisotropy to no measurable anisotropy. At the western edge of the archipelago delay times are 0.4–0.9 s and fast polarization directions are 81–109°E. These directions are consistent with anisotropy resulting from shear of the asthenosphere by the overlying plate; there is no indication of fossil lithospheric anisotropy in the plate spreading direction. In contrast, beneath the center of the archipelago the upper mantle is isotropic or weakly anisotropic. The isotropic region coincides approximately with a volume of anomalously low upper mantle velocities, suggesting that the presence of melt may weaken the effects of fabric on anisotropy or that melt preferred orientation generates a vertical fast polarization direction. Alternatively, the complex flow field associated with a near‐ridge hotspot may result in apparent isotropy.
Heat flow measurement in shallow seas through long‐term temperature monitoring
Authors: Hamamoto Hideki , Yamano Makoto , Goto Shusaku
Published: November 2005

It is difficult to obtain reliable heat flow values in shallow sea areas where the bottom water temperature is not stable. We attempted to measure heat flow in shallow seas by monitoring temperature profiles in sediments, using pop‐up type instruments with 2 m long temperature probes. Long‐term temperature records for over 200 days were obtained at four stations off southwest Japan. Analysis of the data showed the bottom water temperature variations (BTV) were propagated through sediments by thermal diffusion only. We could then remove the influence of BTV from the temperature records and determine the heat flow, though the effect of longer period components in BTV has possibly remained. The obtained heat flow values are consistent with those estimated from depths of gas hydrate BSRs in the vicinities of the stations. These results indicate that long‐term temperature monitoring is a useful method for heat flow determination in shallow seas.
Fair space weather for solar cycle 24
Authors: Schatten Kenneth
Published: November 2005

We discuss the polar field precursor method of solar activity forecasting, first developed 3 decades ago. Using this method the peak amplitude of the next solar cycle (24) is estimated at 124 ± 30 in terms of smoothed F10.7 Radio Flux and 80 ± 30 in terms of smoothed international or Zurich Sunspot number (Ri or Rz). This may be regarded as a “fair space weather” long term forecast. To support this prediction, direct measurements are obtained from the Wilcox and Mount Wilson Solar Observatories. Additionally, coronal features do not show the characteristics of well‐formed polar coronal holes associated with typical solar minima, but rather resemble stunted polar field levels. The question is raised: why have the Sun's polar fields not strengthened comparably in the 2000–2005 time period, as in the previous few decades? The dramatic field changes seen suggest the importance of field motions associated with photospheric (e.g. meridional) flows for the Sun's dynamo. Flows may also play a role in active region development, e.g., it is possible that field magnification occurs through surface processes, namely active region field strengthening (sunspot growth) through the influx of like photospheric magnetic regions, and even the influx of ERs (ephemeral regions), wherein the same sign (like) flux could be differentially drawn into spots of that sign, leading to field growth.
Ground based VLF observations near L = 2.5 during the Halloween 2003 storm
Authors: Spasojevíc M. , Inan U. S.
Published: November 2005

Ground based recordings at Palmer Station, Antarctica (L = 2.44) provide rare observations of VLF waves at low L during and in the aftermath of the Halloween 2003 superstorms. VLF observations in the morning magnetic local time sector for Oct 29 to Nov 5 2003 are compared with daily global average changes in the electron radiation belts near the slot region. Wave activity observed at Palmer was remarkably intense during this period and included discrete chorus emissions, mid‐latitude hiss as well as an unusual form of hiss extending up to ∼15 kHz suggestive of auroral hiss. While the inner edge of the new radiation belt formed near L = 2, analysis of VLF data indicate that chorus was primarily confined outside L ≈ 2.75.
Effect of initial stress on the propagation of plane waves in a general anisotropic poroelastic medium
Authors: Sharma M. D.
Published: November 2005

Biot's theory is used to study the wave propagation in fluid‐saturated porous medium in the presence of initial stress. The medium is a general anisotropic porous frame saturated with a viscous fluid flowing through its pores of anisotropic permeability. Propagation of plane waves in the medium is represented through two systems of equations. One is consisting of modified Christoffel equations that define the existence of the four waves in the medium. The complex phase velocities of the four waves and the corresponding polarizations of solid particles are derived from this system. The effect of initial stress on the propagation is represented through the modifications in a square matrix of order 3. The other system relates the fluid discharge in the medium to the motion of its solid particles. This relation does not involve the components of initial stress, if any, present in the medium. A particular numerical example shows that the attenuation is more sensitive to the presence of initial stress as compared to the propagation velocities. The effect of initial stress on velocities may be little more in high‐frequency regime of Biot's theory. The effect of initial stress on attenuation varies considerably with frequency, but these variations are different for different waves. The symmetries in the anisotropy may reduce the effect of initial stress on velocities and attenuations.
Detection of advected concentration and pH fronts from self‐potential measurements
Authors: Maineult Alexis , Bernabé Yves , Ackerer Philippe
Published: November 2005

In this paper, we report on a series of experiments aimed at testing the possibility of detecting concentration or pH fronts advected through a well‐controlled, laboratory‐scale, artificial aquifer system, using self‐potential monitoring. A rectangular Plexiglas tank was filled up with water‐saturated sand, inside of which an array of unpolarizable electrodes was installed. After a nearly uniform, steady state flow was established by tilting the tank and controlling the water level at both ends, we abruptly changed the salt concentration or pH of the upstream fluid. During the subsequent motion of the concentration or pH front thus generated, the electrical potential differences between each electrode and a reference were recorded. We observed systematic, sharp variations successively occurring at increasing distances in the flow direction. These signals precisely corresponded to the calculated arrival times of the front at the various electrodes. Additional experiments were performed, in which the lateral motion of a transverse concentration or pH front was monitored. In the case of a NaCl front, the self‐potential signal can be modeled as the sum of two terms, (1) a junction potential term produced by the difference in ionic mobility of Na+ and Cl− and (2) an electrokinetic term corresponding to the variations of the electrokinetic coupling coefficient caused by changes in concentration. In the case of a pH front, only the electrokinetic term appears to be present.
Multicomponent fluid flow by discontinuous Galerkin and mixed methods in unfractured and fractured media
Authors: Hoteit H. , Firoozabadi A.
Published: November 2005

A discrete fracture model for the flow of compressible, multicomponent fluids in homogeneous, heterogeneous, and fractured media is presented in single phase. In the numerical model we combine the mixed finite element (MFE) and the discontinuous Galerkin (DG) methods. We use the cross‐flow equilibrium concept to approximate the fractured matrix mass transfer. The discrete fracture model is numerically superior to the single‐porosity model and overcomes limitations of the dual‐porosity models including the use of a shape factor. The MFE method provides a direct and accurate approximation for the velocity field, which is crucial for the convective terms in the flow equations. The DG method associated with a slope limiter is used to approximate the species balance equations. This method can capture the sharp moving fronts. The calculation of the fracture‐fracture flux across three and higher intersecting fracture branches is a challenge. In this work, we provide an accurate approximation of these fluxes by using the MFE formulation. Numerical examples in unfractured and fractured media illustrate the efficiency and robustness of the proposed numerical model.
A quantum yield map for synthetic eumelanin
Authors: Nighswander-Rempel Stephen P. , Riesz Jennifer , Gilmore Joel , Meredith Paul
Published: November 2005

The quantum yield of synthetic eumelanin is known to be extremely low and it has recently been reported to be dependent on excitation wavelength. In this paper, we present quantum yield as a function of excitation wavelength between 250 and 500nm, showing it to be a factor of 4 higher at 250nm than at 500nm. In addition, we present a definitive map of the steady-state fluorescence as a function of excitation and emission wavelengths, and significantly, a three-dimensional map of the “specific quantum yield”: the fraction of photons absorbed at each wavelength that are subsequently radiated at each emission wavelength. This map contains clear features, which we attribute to certain structural models, and shows that radiative emission and specific quantum yield are negligible at emission wavelengths outside the range of 585 and 385nm (2.2 and 3.2eV), regardless of excitation wavelength. This information is important in the context of understanding melanin biofunctionality, and the quantum molecular biophysics therein.
Phase matching for third-harmonic generation in collisional magnetoplasmas
Authors: Sodha Mahendra S. , Verma Mahendra P. , Sharma Ashutosh
Published: November 2005

This paper presents a derivation of the phase-matching conditions for generation of the third-harmonic (3ω1) and combination frequencies (ω1+2ω2), by two fundamental electromagnetic waves of frequencies ω1 and ω2, propagating in the extraordinary mode along a magnetic field in a collisional plasma. Expressions for the corresponding optimum distance of propagation for maximum output and the associated values of the phase functions have been derived. In the case of the third-harmonic generation phase matching occurs when the gyrofrequency of the electrons is twice the wave frequency (for all values of plasma frequency). In the case of the combination frequencies, the phase-matching condition is represented by an expression for plasma frequency ωp in terms of the wave frequencies ω1, ω2 and the gyrofrequency ωc of electrons. Furthermore, it is seen that in the (ωc∕ω1)−(ω2∕ω1) plane, phase matching occurs in a narrow region; for every point in this region, there is a corresponding value of (ωp∕ω1). The dependence of optimum distance of propagation and the corresponding value of the phase function on electron collision frequency νav∕ω1 have been graphically illustrated for a specific case. An estimate of the maximum value of the third-harmonic conversion efficiency has also been made.
Constrained reductions of two-dimensional dispersionless Toda hierarchy, Hamiltonian structure, and interface dynamics
Authors: Harnad J. , Loutsenko I. , Yermolayeva O.
Published: November 2005

Finite-dimensional reductions of the two-dimensional dispersionless Toda hierarchy constrained by the “string equation” are studied. These include solutions determined by polynomial, rational, or logarithmic functions, which are of interest in relation to the “Laplacian growth” or Hele-Shaw problem governing interface dynamics. The consistency of such reductions is proved, and the Hamiltonian structure of the reduced dynamics is derived. The Poisson structure of the rationally reduced dispersionless Toda hierarchies is also derived.
Fundamental limits of the dispersion of the two-photon absorption cross section
Authors: Pérez Moreno Javier , Kuzyk Mark G.
Published: November 2005

We rigorously apply the sum rules to the sum-over-states expression to calculate the fundamental limits of the dispersion of the two-photon absorption cross section. A comparison of the theory with the data suggests that the truncated sum rules in the three-level model give a reasonable fundamental limit. Furthermore, we posit that the two-photon absorption cross section near the limit must have only three dominant states, so by default, the three-level model is appropriate. This ansatz is supported by a rigorous analytical calculation that the resonant term gets smaller as more states are added. We also find that the contributions of the nonexplicitly resonant terms cannot be neglected when analyzing real molecules with many excited states, even near resonance. However, puzzling as it may be, extrapolating an off-resonant result to resonance using only the resonant term of the three-level model is shown to be consistent with the exact result. In addition, the off-resonant approximation is shown to scale logarithmically when compared with the full three-level model. This scaling can be used to simplify the analysis of measurements. We find that existing molecules are still far from the fundamental limit; so, there is room for improvement. But, reaching the fundamental limit would require precise control of the energy-level spacing, independently of the transition dipole moments—a task that does not appear possible using today’s synthetic approaches. So, we present alternative methods that can still lead to substantial improvements which only require the control of the transition moment to the first excited state. While it is best to normalize measured two-photon absorption cross sections to the fundamental limits when comparing molecules, we show that simply dividing by the square of the number of electrons per molecule yields a good metric for comparison.
Theoretical study of the electronic spectra of square-planar platinum (II) complexes based on the two-component relativistic time-dependent density-functional theory
Authors: Wang Fan , Ziegler Tom
Published: November 2005

In the present work the electronic spectra of [PtCl4]2−, [PtBr4]2−, and [Pt(CN)4]2− are studied with a recently proposed relativistic time-dependent density-functional theory (TDDFT) based on the two-component zeroth-order regular approximation and a noncollinear exchange-correlation (XC) functional. The contribution to the double group excited states in terms of singlet and triplet single group excited states is estimated through the inner product of the transition density matrix obtained from two-component and scalar relativistic TDDFT calculations to better understand the double group excited states. Spin-orbital coupling effects are found to be very important in order to simulate the electronic spectra of these complexes. The results show that the two-component TDDFT formalism can afford excitation energies with high accuracy for the transition-metal systems studied here when use is made of a proper XC potential.
Nonlinear response theory with relaxation: The first-order hyperpolarizability
Authors: Norman Patrick , Bishop David M. , Jensen Hans Jørgen Aa. , Oddershede Jens
Published: November 2005

Based on the Ehrenfest theorem, an equation of motion that takes relaxation into account has been presented in wave-function theory, and the resulting response functions are nondivergent in the off-resonant as well as the resonant regions of optical frequencies. The derivation includes single- and multideterminant reference states. When applied to electric dipole properties, the response functions correspond to the phenomenological sum-over-states expressions of Orr and Ward [Mol. Phys. 20, 513 (1971)] for polarizabilities and hyperpolarizabilities of an isolated system. A universal dispersion formula is derived for the complex second-order response function. Response theory calculations are performed on lithium hydride and para-nitroaniline for off-resonant and resonant frequencies in the electro-optical Kerr effect and second-harmonic generation.