bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimizing Performance of a Microwave Salinity Mapper: STARRS L-Band Radiometer Enhancements*
Authors: Burrage Derek M. , Wesson Joel C. , Goodberlet Mark A. , Miller Jerry L. 
Published: May 2008

AbstractAirborne microwave radiometers for salinity remote sensing have advanced to a point where operational surveys can be conducted over the inner continental shelf to observe the evolution of freshwater plumes emanating from rivers and estuaries. To determine seawater microwave emissivity, and hence conductivity and salinity, precisely and accurately demands high instrument sensitivity, stability, and sampling rates; such requirements involve significant design trade-offs. The Salinity, Temperature, and Roughness Remote Scanner (STARRS) was developed to enhance these features relative to existing instruments. The authors describe here key elements of the STARRS design and the results of early performance assessments and deployments. During early deployments, the instrument performed well in areas of moderate to high salinity signal-to-noise ratio, but more homogenous areas revealed band-limited random signal fluctuations on the order of a 6-min period and ∼1-K amplitude that were of internal origin. Detailed analyses of laboratory and field tests revealed that internal “flicker,” or 1/f noise (having spectral roll-off proportional to the reciprocal of frequency f ), was the main source of these fluctuations. The instrument was modified to eliminate the random fluctuations and to further enhance sensitivity and stability. Laboratory tests and recent field deployments show that the upgrade improved instrument performance dramatically, to the extent that continental shelf scale areas with relatively homogenous salinity distributions can now be surveyed reliably using STARRS.
Potential Vorticity Diagnosis of the Severe Convective Regime. Part II: The Impact of Idealized PV Anomalies
Authors: Nielsen-Gammon John W. , Gold David A. 
Published: May 2008

Abstract
Idealized numerical experiments are conducted to understand the effect of upper-tropospheric potential vorticity (PV) anomalies on an environment conducive to severe weather. Anomalies are specified as a single isolated vortex, a string of vortices analogous to a negatively tilted trough, and a pair of string vortices analogous to a position error in a negatively tilted trough. The anomalies are placed adjacent to the tropopause along a strong upper-level jet at a time just prior to a major tornado outbreak and inverted using the nonlinear balance equations.
In addition to the expected destabilization beneath and adjacent to a cyclonic PV anomaly, the spatial pattern of the inverted balanced streamfunction and height fields is distorted by the presence of the horizontal PV gradient along the upper-tropospheric jet stream. Streamfunction anomalies are elongated in the cross-jet direction, while height and temperature anomalies are elongated in the along-jet direction. The amplitude of the inverted fields, as well as the changes in CAPE associated with the inverted temperature perturbations, are linearly proportional to the amplitudes of the PV anomalies themselves, and the responses to complex PV perturbation structures are approximated by the sum of the responses to individual simple PV anomalies. This is true for the range of PV amplitudes tested, which was designed to mimic typical 6-h forecast or analysis errors and produced changes in CAPE beneath the trough of well over 100 J kg−1. Impacts on inverted fields are largest when the PV anomaly is on the anticyclonic shear side of the jet, where background PV is small, compared with the cyclonic shear side of the jet, where background PV is large.
Potential Vorticity Diagnosis of the Severe Convective Regime. Part IV: Comparison with Modeling Simulations of the Moore Tornado Outbreak
Authors: Gold David A. , Nielsen-Gammon John W. 
Published: May 2008

Abstract
A potential vorticity (PV) diagnostic framework is used to explore the sensitivity of the 3 May 1999 Oklahoma City tornado outbreak to the strength of a particular PV anomaly proximate to the geographical region experiencing the tornado outbreak. The results derived from the balanced PV diagnosis agree broadly with those obtained previously in a numerical simulation of the same event, while offering additional insight into the nature of the sensitivity. Similar to the findings of other cases, the balanced diagnosis demonstrates that intensifying (removing) the PV anomaly of interest increases (decreases) the balanced CAPE over the southwestern portion of the outbreak region, reduces (increases) the storm-relative helicity, and increases (reduces) ascent. The latter finding, coupled with the results of the modeling study, demonstrates that intensifying a PV anomaly proximate to an outbreak environment can increase the likelihood that more widespread and possibly less tornadic convection will ensue. The overall results of the balanced diagnosis complement those of other case studies, leading to the formulation of a conceptual model that broadly anticipates how the convective regime will respond to changes in intensity of upper-tropospheric weather features.
Low-Frequency Modulation of Intraseasonal Equatorial Kelvin Wave Activity in the Pacific from SODA: 1958–2001
Authors: Dewitte Boris , Purca Sara , Illig Serena , Renault Lionel , Giese Benjamin S. 
Published: May 2008

Abstract
Intraseasonal equatorial Kelvin wave activity (IEKW) at a low frequency in the Pacific is investigated using the Simple Ocean Data Assimilation (SODA) oceanic reanalyses. A vertical and horizontal mode decomposition of SODA variability allows estimation of the Kelvin wave amplitude according to the most energetic baroclinic modes. A wavenumber–frequency analysis is then performed on the time series to derive indices of modulation of the IEKW at various frequency bands. The results indicate that the IEKW activity undergoes a significant modulation that projects onto baroclinic modes and is not related in a straightforward manner to the low-frequency climate variability in the Pacific. Linear model experiments corroborate that part of the modulation of the IEKW is tightly linked to change in oceanic mean state rather than to the low-frequency change of atmospheric equatorial variability.
Effects of Multiple Scattering on Attenuation-Based Retrievals of Stratiform Rainfall from CloudSat
Authors: Matrosov Sergey Y. , Battaglia Alessandro , Rodriguez Peter 
Published: May 2008

Abstract
An attenuation-based method to retrieve vertical profiles of rainfall rates from height derivatives/gradients of CloudSat nadir-pointing W-band reflectivity measurements is discussed. This method takes advantage of the high attenuation of W-band frequency signals in rain and the low variability of nonattenuated reflectivity due to strong non-Rayleigh scattering from rain drops. The retrieval uncertainties could reach 40%–50%. The suggested method is generally applicable to rainfall rates (R) in an approximate range from about 2–3 to about 20–25 mm h−1. Multiple scattering noticeably affects the gradients of CloudSat measurements for R values greater than about 5 mm h−1. To avoid a retrieval bias caused by multiple-scattering effects, a special correction for retrievals is introduced. For rainfall rates greater than about 25 mm h−1, the influence of multiple scattering gets overwhelming, and the retrievals become problematic, especially for rainfalls with higher freezing-level altitudes. The attenuation-based retrieval method was applied to experimental data from CloudSat covering the range of rainfall rates. CloudSat retrievals were compared to the rainfall estimates available from a National Weather Service ground-based scanning precipitation radar operating at S band. Comparisons between spaceborne and conventional radar rainfall retrievals were generally in good agreement and indicated the mutual consistency of both quantitative precipitation estimate types. The suggested CloudSat rainfall retrieval method is immune to the absolute calibration of the radar and to attenuation caused by the melting layer and snow regions. Since it does not require surface returns, it is applicable to measurements above both land and water surfaces.
Scale-Selective Digital-Filtering Initialization
Authors: Termonia Piet 
Published: May 2008

Abstract
Digital-filtering initialization (DFI) of atmospheric models relies on the fact that the gravity–inertia waves have higher frequencies than the meteorologically relevant rotational modes and assumes that a frequency exists that separates them. This note shows that a Doppler effect of fast-propagating storms may “shift” the frequencies of the small-scale rotational modes into the frequency categories that are deemed to be the ones of the gravity–inertia waves. A forecast is presented in which the impact of this on DFI manifests itself to a substantial extent (i.e., a reduction the depth of the eye of the storm by about 6–7 hPa). As a cure it is proposed to make the filtering scale selective (i.e., filtering the large spatial scales more than the small ones). It is shown that, not only does this leave the storm almost intact, but it also leads to a more balanced initial state. The implementation of such a filter is straightforward in a spectral limited-area model.
Analyses of murine GBP homology clusters based on in silico, in vitro and in vivo studies
Authors: Kresse Alexandra , Konermann Carolin , Degrandi Daniel , Beuter-Gunia Cornelia , Wuerthner Jan , Pfeffer Klaus , Beer Sandra 
Published: May 2008

AbstractThe interactions between pathogens and hosts lead to a massive upregulation of antimicrobial host effector molecules. Among these, the 65 kDa guanylate binding proteins (GBPs) are interesting candidates as intricate components of the host effector molecule repertoire. Members of the GBP family are highly conserved in vertebrates. Previous reports indicate an antiviral activity of human GBP1 (hGBP1) and murine GBP2 (mGBP2). We recently demonstrated that distinct murine GBP (mGBP) family members are highly upregulated uponToxoplasma gondiiinfection and localize around the intracellular protozoaT. gondii. Moreover, we characterised five new mGBP family members within the murine 65 kDa GBP family. Here, we identified a new mGBP locus namedmGbp11. Based on bacterial artificial chromosome (BAC), expressed sequence tag (EST), and RT-PCR analyses this study provides a detailed insight into the genomic localization and organization of the mGBPs. These analyses revealed a 166-kb spanning region on chromosome 3 harboring five transcribed mGBPs (mGbp1, mGbp2, mGbp3, mGbp5, andmGbp7) and one pseudogene (pseudomGbp1), as well as a 332-kb spanning region on chromosome 5 consisting of six transcribed mGBPs (mGbp4, mGbp6, mGbp8, mGbp9, mGbp10, andmGbp11), and one pseudogene (pseudomgbp2). Besides the strikingly high homology of 65% to 98% within the coding sequences, the mGBPs on chromosome 5 cluster also exhibit a highly homologous exon-intron structure whereas the mGBP on chromosome 3 reveals a more divergent exon-intron structure. This study details the comprehensive genomic organization of mGBPs and suggests that a continuously changing microbial environment has exerted evolutionary pressure on this gene family leading to multiple gene amplifications. A list of links for this article can be found in the Availability and requirements section.
Genomic analysis of post-mating changes in the honey bee queen (Apis mellifera)
Authors: Kocher Sarah D , Richard Freddie-Jeanne , Tarpy David R , Grozinger Christina M 
Published: May 2008

Abstract

Background
The molecular mechanisms underlying the post-mating behavioral and physiological transitions undergone by females have not been explored in great detail. Honey bees represent an excellent model system in which to address these questions because they exhibit a range of "mating states," with two extremes (virgins and egg-laying, mated queens) that differ dramatically in their behavior, pheromone profiles, and physiology. We used an incompletely-mated mating-state to understand the molecular processes that underlie the transition from a virgin to a mated, egg-laying queen. We used same-aged virgins, queens that mated once but did not initiate egg-laying, and queens that mated once and initiated egg-laying.

Results
Differences in the behavior and physiology among groups correlated with the underlying variance observed in the top 50 predictive genes in the brains and the ovaries. These changes were correlated with either a behaviorally-associated pattern or a physiologically-associated pattern. Overall, these results suggest that the brains and the ovaries of queens are uncoupled or follow different timescales; the initiation of mating triggers immediate changes in the ovaries, while changes in the brain may require additional stimuli or take a longer time to complete. Comparison of our results to previous studies of post-mating changes in Drosophila melanogaster identified common biological processes affected by mating, including stress response and alternative-splicing pathways. Comparison with microarray data sets related to worker behavior revealed no obvious correlation between genes regulated by mating and genes regulated by behavior/physiology in workers.

Conclusion
Studying the underlying molecular mechanisms of post-mating changes in honey bee queens will not only give us insight into how molecular mechanisms regulate physiological and behavioral changes, but they may also lead to important insights into the evolution of social behavior. Post-mating changes in gene regulation in the brains and ovaries of honey bee queens appear to be triggered by different stimuli and may occur on different timescales, potentially allowing changes in the brains and the ovaries to be uncoupled.
cAMP potentiates InsP3-induced Ca2+ release from the endoplasmic reticulum in blowfly salivary glands
Authors: Schmidt Ruth , Baumann Otto , Walz Bernd 
Published: May 2008

Abstract

Background
Serotonin induces fluid secretion from Calliphora salivary glands by the parallel activation of the InsP3/Ca2+ and cAMP signaling pathways. We investigated whether cAMP affects 5-HT-induced Ca2+ signaling and InsP3-induced Ca2+ release from the endoplasmic reticulum (ER).

Results
Increasing intracellular cAMP level by bath application of forskolin, IBMX or cAMP in the continuous presence of threshold 5-HT concentrations converted oscillatory [Ca2+]i changes into a sustained increase. Intraluminal Ca2+ measurements in the ER of β-escin-permeabilized glands with mag-fura-2 revealed that cAMP augmented InsP3-induced Ca2+ release in a concentration-dependent manner. This indicated that cAMP sensitized the InsP3 receptor Ca2+ channel for InsP3. By using cAMP analogs that activated either protein kinase A (PKA) or Epac and the application of PKA-inhibitors, we found that cAMP-induced augmentation of InsP3-induced Ca2+ release was mediated by PKA not by Epac. Recordings of the transepithelial potential of the glands suggested that cAMP sensitized the InsP3/Ca2+ signaling pathway for 5-HT, because IBMX potentiated Ca2+-dependent Cl- transport activated by a threshold 5-HT concentration.

Conclusion
This report shows, for the first time for an insect system, that cAMP can potentiate InsP3-induced Ca2+ release from the ER in a PKA-dependent manner, and that this crosstalk between cAMP and InsP3/Ca2+ signaling pathways enhances transepithelial electrolyte transport.
Phellodendron and Citrusextracts benefit cardiovascular health in osteoarthritis patients: a double-blind, placebo-controlled pilot study
Authors: Oben Julius , Enonchong Ebangha , Kothari Shil , Chambliss Walter , Garrison Robert , Dolnick Deanne 
Published: May 2008

Abstract

Background
The objective of this clinical study was to assess the potential benefit of a dietary supplement, NP 06-1, on cardiovascular protective properties in overweight and normal weight adults diagnosed with osteoarthritis of the knee.

Methods
An 8-week, placebo-controlled, randomized, double-blind study was conducted with four groups, comparing the effects of NP 06-1 to placebo in overweight and normal weight subjects diagnosed with primary osteoarthritis of the knee. NP 06-1 (a combination of two botanical extracts; Phellodendron amurense bark and Citrus sinensis peel) or matching placebo was given in a dose of two capsules (370 mg each) twice daily. The outcome measures reported are lipid levels, weight, BMI, blood pressure and fasting glucose. Analyses of variance were used to compare changes of physiological measures over the trial period and between groups.

Results
Eighty (80) subjects were enrolled and 45 subjects completed the study. No serious adverse events were reported. NP 06-1 administration was associated with a general improvement in lipid levels. Both the overweight and normal weight treatment groups had significant reductions in triglycerides and LDL-cholesterol, as well as a significant increase in HDL-cholesterol compared to their respective control groups.
Overall there were decreases in blood pressure in both overweight and normal weight treatment groups compared to respective placebo groups. There was also a significant decrease in fasting glucose levels in the overweight treatment group compared to the start of the study and to the overweight placebo group. There was no change in fasting blood sugar for the normal weight groups.
Both overweight and normal weight treatment groups lost a significant amount of weight compared to their respective placebo groups. The overweight treatment group lost an average of 5% body weight after 8 weeks, which was associated with a significant loss in BMI over time.

Conclusion
In this pilot study NP 06-1 had a beneficial effect on cardiovascular risk factors; namely lipid levels, blood pressure and fasting glucose levels. Administration of NP 06-1 was also associated with weight loss.
Anaplastic oligodendrogliomas with 1p19q codeletion have a proneural gene expression profile
Authors: Ducray François , Idbaih Ahmed , de Reyniès Aurélien , Bièche Ivan , Thillet Joëlle , Mokhtari Karima , Lair Séverine , Marie Yannick , Paris Sophie , Vidaud Michel , Hoang-Xuan Khê , Delattre Olivier , Delattre Jean-Yves , Sanson Marc 
Published: May 2008

Abstract

Background
In high grade gliomas, 1p19q codeletion and EGFR amplification are mutually exclusive and predictive of dramatically different outcomes. We performed a microarray gene expression study of four high grade gliomas with 1p19q codeletion and nine with EGFR amplification, identified by CGH-array.

Results
The two groups of gliomas exhibited very different gene expression profiles and were consistently distinguished by unsupervised clustering analysis. One of the most striking differences was the expression of normal brain genes by oligodendrogliomas with 1p19q codeletion. These gliomas harbored a gene expression profile that partially resembled the gene expression of normal brain samples, whereas gliomas with EGFR amplification expressed many genes in common with glioblastoma cancer stem cells. The differences between the two types of gliomas and the expression of neuronal genes in gliomas with 1p19q codeletion were both validated in an independent series of 16 gliomas using real-time RT-PCR with a set of 22 genes differentiating the two groups of gliomas (AKR1C3, ATOH8, BMP2, C20orf42, CCNB1, CDK2, CHI3L1, CTTNBP2, DCX, EGFR, GALNT13, GBP1, IGFBP2, IQGAP1, L1CAM, NCAM1, NOG, OLIG2, PDPN, PLAT, POSTN, RNF135). Immunohistochemical study of the most differentially expressed neuronal gene, alpha-internexin, clearly differentiated the two groups of gliomas, with 1p19q codeletion gliomas showing specific staining in tumor cells.

Conclusion
These findings provide evidence for neuronal differentiation in oligodendrogliomas with 1p19q codeletion and support the hypothesis that the cell of origin for gliomas with 1p19q codeletion could be a bi-potential progenitor cell, able to give rise to both neurons and oligodendrocytes.
Blue shift of CdSe/ZnS nanocrystal-labels upon DNA-hybridization
Authors: Riegler Jürgen , Ditengou Franck , Palme Klaus , Nann Thomas 
Published: May 2008

Abstract
Luminescence color multiplexing is one of the most intriguing benefits, which might occur by using semiconductor Quantum Dots (QDs) as labels for biomolecules. It was found, that the luminescence of QDs can be quenched, and replaced by a luminescence peak at approximately 460 nm on hybridization with certain regions of Arabidopsis thaliana tissue. This effect is site selective, and it is unclear whether it occurs due to an energy transfer process, or due to quenching and scattering of the excitation light. The article describes methods for phase-transfer of differently coloured, hydrophobically ligated QDs, coupling of DNA strands to the QD's surface, and hybridization of the labelled DNA to different cell types of Arabidopsis thaliana. The reason for the luminescence blue-shift was studied systematically, and narrowed down to the above mentioned causes.
Using genetic markers to orient the edges in quantitative trait networks: The NEO software
Authors: Aten Jason E , Fuller Tova F , Lusis Aldons J , Horvath Steve 
Published: May 2008

Abstract

Background
Systems genetic studies have been used to identify genetic loci that affect transcript abundances and clinical traits such as body weight. The pairwise correlations between gene expression traits and/or clinical traits can be used to define undirected trait networks. Several authors have argued that genetic markers (e.g expression quantitative trait loci, eQTLs) can serve as causal anchors for orienting the edges of a trait network. The availability of hundreds of thousands of genetic markers poses new challenges: how to relate (anchor) traits to multiple genetic markers, how to score the genetic evidence in favor of an edge orientation, and how to weigh the information from multiple markers.

Results
We develop and implement Network Edge Orienting (NEO) methods and software that address the challenges of inferring unconfounded and directed gene networks from microarray-derived gene expression data by integrating mRNA levels with genetic marker data and Structural Equation Model (SEM) comparisons. The NEO software implements several manual and automatic methods for incorporating genetic information to anchor traits. The networks are oriented by considering each edge separately, thus reducing error propagation. To summarize the genetic evidence in favor of a given edge orientation, we propose Local SEM-based Edge Orienting (LEO) scores that compare the fit of several competing causal graphs. SEM fitting indices allow the user to assess local and overall model fit. The NEO software allows the user to carry out a robustness analysis with regard to genetic marker selection. We demonstrate the utility of NEO by recovering known causal relationships in the sterol homeostasis pathway using liver gene expression data from an F2 mouse cross. Further, we use NEO to study the relationship between a disease gene and a biologically important gene co-expression module in liver tissue.

Conclusion
The NEO software can be used to orient the edges of gene co-expression networks or quantitative trait networks if the edges can be anchored to genetic marker data. R software tutorials, data, and supplementary material can be downloaded from: http://www.genetics.ucla.edu/labs/horvath/aten/NEO.