bluuebunny/crossref_metadata_2025_split huggingface dataset:
Substituent Effects on the Stability of Radical Dianion of 4-R-2-Nitrophenols. Electrochemical and ESR Study.
Authors: Morales Jimmy A. , Frontana Carlos E. , Solano Peralta Alejandro , Bautista Martinez Jose Antonio A. , Cuevas Gonzalez-Bravo Gabriel Eduardo , Gonzalez-Martinez Ignacio , Aguilar-Martinez Martha 
Published: August 2007

Voltammetric and spectroelectrochemical-ESR studies of the electro-reduction of five substituted 4-R-2-nitrophenols (R = - H, -OCH3; -CH3; -CN, -CF3) in acetonitrile were made. The results showed that at potential values near the first reduction peak, no ESR signals was recorded for 2-nitrophenol, indicating a difference in stability for the radical anion compared to the behavior reported in DMSO. However, at potential values corresponding to the second peak, the ESR spectrum of this species was detected.	Since at this potential, the reduction is related to the transformation of the conjugated base of 2-nitrophenol. The ESR results suggest that the electrogenerated radical dianion protonates partially in solution by acetonitrile. The chemical nature of the radical species obtained during the electro-reduction of 4-R-2- nitrophenols can be modulated through substituent effects and the solvent used in the solution.
Synergistic Antiangiogenic Effects of Stathmin Inhibition and Taxol Exposure
Authors: Mistry Sucharita J. , Bank Alexander , Atweh George F. 
Published: August 2007

Abstract
Stathmin is one of the key regulators of the microtubule cytoskeleton and the mitotic spindle in eukaryotic cells. It is expressed at high levels in a wide variety of human cancers and may provide an attractive target for cancer therapy. We had previously shown that stathmin inhibition results in the abrogation of the malignant phenotype. The microtubule-interfering drug, taxol, has both antitumorigenic and antiangiogenic properties. We had also shown that the antitumor activities of taxol and stathmin inhibition are synergistic. We hypothesized that taxol and stathmin inhibition may also have synergistic antiangiogenic activities. A replication-deficient bicistronic adenoviral vector that coexpresses green fluorescent protein and an anti-stathmin ribozyme was used to target stathmin mRNA. Exposure of endothelial cells to anti-stathmin adenovirus alone resulted in a dose-dependent inhibition of proliferation, migration, and differentiation into capillary-like structures. This inhibition was markedly enhanced by exposure of transduced endothelial cells to very low concentrations of taxol, which resulted in a virtually complete loss of proliferation, migration, and differentiation of endothelial cells. In contrast, exposure of nontransduced endothelial cells to taxol alone resulted in a modest inhibition of proliferation, migration, and differentiation. Our detailed analysis showed that the antiangiogenic effects of the combination of stathmin inhibition and taxol exposure are synergistic. Our studies also showed that the mechanism of this synergistic interaction is likely to be mediated through the stabilization of microtubules. Thus, this novel combination may provide an attractive therapeutic strategy that combines a synergistic antitumor activity with a synergistic antiangiogenic activity. (Mol Cancer Res 2007;5(8):773–82)
Aegean Surface Circulation from a Satellite-Tracked Drifter Array
Authors: Olson Donald B. , Kourafalou Vassiliki H. , Johns William E. , Samuels Geoff , Veneziani Milena 
Published: August 2007

Abstract
A pilot experiment using an array of 45 drifters to explore the circulation in the north and central Aegean Sea is described. The global positioning system drifters with holey-sock drogues provide positions every hour with data recovery through the Argos system. The drifters were launched in four separate deployments over a 1-yr period. The resulting trajectories confirm the existence of a current around the rim of the basin consistent with a buoyancy plume created by the outflow of Black Sea waters through the Dardanelles (Strait of Çanakkale in Turkish). The degree to which this is augmented by an Ekman response to the dominant northerly winds is not obvious in the dataset owing to mesoscale dynamics that obscure the existence of any westward Ekman flow. The mesoscale eddy field involves anticylonic eddies in the current around the rim of the basin consistent with eddies with low-salinity-water cores. Cyclones are also seen, with the most prominent forming over deep regions in the basin topography. The array also documents the interaction of the currents with the straits through the Sporades and Cyclades island groups. These interactions are complicated by the nature of the mesoscale flow and in some trajectories suggest a Bernouilli acceleration in straits; in others the flow through the island groups appears to be more diffusive and involves deceleration and eddy motions. The rapid sampling by the drifters reveals an extremely nonlinear submesoscale eddy field in the basin with length scales less than 4 km and Rossby numbers of order 1. A better understanding of the dynamics of these features is of importance for understanding the circulation of the basin.
Global Patterns of Low-Mode Internal-Wave Propagation. Part II: Group Velocity
Authors: Alford Matthew H. , Zhao Zhongxiang 
Published: August 2007

Abstract
Using a set of 80 globally distributed time series of near-inertial and semidiurnal energy E and energy flux F computed from historical moorings, the group velocity ĉg ≡ FE−1 is estimated. For a single free wave, observed group speed |ĉg| should equal that expected from linear wave theory. For comparison, the latitude dependence of perceived group speed for perfectly standing waves is also derived. The latitudinal dependence of observed semidiurnal |ĉg| closely follows that expected for free waves at all latitudes, implying that 1) low-mode internal tides obey linear theory and 2) standing internal-tidal waves are rare in the deep ocean for latitudes equatorward of about 35°. At higher latitudes, standing waves cannot be easily distinguished from free waves using this method because their expected group speeds are similar. Near-inertial waves exhibit scattered |ĉg| values consistent with the passage of events generated at various latitudes, with implied frequencies ω ≈ 1.05–1.25 × f, as typically observed in frequency spectra.
Estuarine Boundary Layer Mixing Processes: Insights from Dye Experiments*
Authors: Chant Robert J. , Geyer Wayne R. , Houghton Robert , Hunter Elias , Lerczak James 
Published: August 2007

Abstract
A series of dye releases in the Hudson River estuary elucidated diapycnal mixing rates and temporal variability over tidal and fortnightly time scales. Dye was injected in the bottom boundary layer for each of four releases during different phases of the tide and of the spring–neap cycle. Diapycnal mixing occurs primarily through entrainment that is driven by shear production in the bottom boundary layer. On flood the dye extended vertically through the bottom mixed layer, and its concentration decreased abruptly near the base of the pycnocline, usually at a height corresponding to a velocity maximum. Boundary layer growth is consistent with a one-dimensional, stress-driven entrainment model. A model was developed for the vertical structure of the vertical eddy viscosity in the flood tide boundary layer that is proportional to u2*/N∞, where u* and N∞ are the bottom friction velocity and buoyancy frequency above the boundary layer. The model also predicts that the buoyancy flux averaged over the bottom boundary layer is equal to 0.06N∞u2* or, based on the structure of the boundary layer equal to 0.1NBLu2*, where NBL is the buoyancy frequency across the flood-tide boundary layer. Estimates of shear production and buoyancy flux indicate that the flux Richardson number in the flood-tide boundary layer is 0.1–0.18, consistent with the model indicating that the flux Richardson number is between 0.1 and 0.14. During ebb, the boundary layer was more stratified, and its vertical extent was not as sharply delineated as in the flood. During neap tide the rate of mixing during ebb was significantly weaker than on flood, owing to reduced bottom stress and stabilization by stratification. As tidal amplitude increased ebb mixing increased and more closely resembled the boundary layer entrainment process observed during the flood. Tidal straining modestly increased the entrainment rate during the flood, and it restratified the boundary layer and inhibited mixing during the ebb.
AffyMAPSDetector: a software tool to characterize Affymetrix GeneChip™ expression arrays with respect to SNPs
Authors: Kumari Sunita , Verma Lalit K , Weller Jennifer W 
Published: August 2007

Abstract

Background
Affymetrix gene expression arrays incorporate paired perfect match (PM) and mismatch (MM) probes to distinguish true signals from those arising from cross-hybridization events. A MM signal often shows greater intensity than a PM signal; we propose that one underlying cause is the presence of allelic variants arising from single nucleotide polymorphisms (SNPs). To annotate and characterize SNP contributions to anomalous probe binding behavior we have developed a software tool called AffyMAPSDetector.

Results
AffyMAPSDetector can be used to describe any Affymetrix expression GeneChip™ with respect to SNPs. When AffyMAPSDetector was run on GeneChip™ HG-U95Av2 against dbSNP-build-123, we found 7286 probes (belonging to 2,582 probesets) containing SNPs, out of which 325 probes contained at least one SNP at position 13. Against dbSNP-build-126, 8758 probes (belonging to 3,002 probesets) contained SNPs, of which 409 probes contained at least one SNP at position 13. Therefore, depending on the expressed allele, the MM probe can sometimes be the transcript complement. This information was used to characterize probe measurements reported in a published, well-replicated lung adenocarcinoma study. The total intensity distributions showed that the SNP-containing probes had a larger negative mean intensity difference (PM-MM) and greater range of the difference than did probes without SNPs. In the sample replicates, SNP-containing probes with reproducible intensity ratios were identified, allowing selection of SNP probesets that yielded unique sample signatures. At the gene expression level, use of the (MM-PM) value for SNP-containing probes resulted in different Presence/Absence calls for some genes. Such a change in status of the genes has the clear potential for influencing downstream clustering and classification results.

Conclusion
Output from this tool characterizes SNP-containing probes on GeneChip™ microarrays, thus improving our understanding of factors contributing to expression measurements. The pattern of SNP binding examined so far indicates distinct behavior of the SNP-containing probes and has the potential to help us identify new SNPs. Knowing which probes contain SNPs provides flexibility in determining whether to include or exclude them from gene-expression intensity calculations; selected sets of SNP-containing probes produce sample-unique signatures.
AffyMAPSDetector information is available at http://www.binf.gmu.edu/weller/BMC_bioinformatics/AffyMapsDetector/index.html
Haplotype-based score test for linkage in nuclear families
Authors: Nam Chung Mo , Kang Dae Ryong , Kim Jinheum 
Published: August 2007

Abstract

Background
To look for genetic linkage between angiotensin-I converting enzyme(ACE) gene and hypertension in a Korean adolescent cohort, we developed a powerful test using the covariances between marginal differences and their variances in a transmission/non-transmission table.

Results
We estimated haplotype frequencies using the parental and affected offspring's genotypes and then constructed a transmission/non-transmission table for the parental haplotypes transmitted to the offspring. We then proposed a test for checking the marginal homogeneity in the table. Because the cells in the table were dependent due to the uncertainty of the parental haplotypes, we adopted a randomization procedure to estimate the significance of the observed test statistic. Simulations show that our test performs well on a nominal level and has a monotone power, which increases as the relative risk increases. With our test, there was no evidence of genetic linkage between the ACE gene and hypertension in the Korean adolescent cohort.

Conclusion
We developed a score test for linkage and used simulations to demonstrate that our test performs well at a nominal level. Under some situations where the diversity of haplotypes is low, the proposed test gained a little power over the method based on only variances between marginal differences in a transmission/non-transmission table.
Alterations in transcript abundance of bovine oocytes recovered at growth and dominance phases of the first follicular wave
Authors: Ghanem Nasser , Hölker Michael , Rings Franca , Jennen Danyel , Tholen Ernst , Sirard Marc-André , Torner Helmut , Kanitz Wilhelm , Schellander Karl , Tesfaye Dawit 
Published: August 2007

AbstractBackgroundOocyte developmental competence is highly affected by the phase of ovarian follicular wave. Previous studies have shown that oocytes from subordinate follicles recovered at growth phase (day 3 after estrus) are developmentally more competent than those recovered at dominance phase (day 7 after estrus). However, the molecular mechanisms associated with these differences are not well elucidated. Therefore, the objective of this study was to investigate transcript abundance of bovine oocytes retrieved from small follicles at growth and dominance phases of the first follicular wave and to identify candidate genes related to oocyte developmental competence using cDNA microarray.ResultsComparative gene expression analysis of oocytes from growth and dominance phases and subsequent data analysis using Significant Analysis of Microarray (SAM) revealed a total of 51 differentially regulated genes, including 36 with known function, 6 with unknown function and 9 novel transcripts. Real-time PCR has validated 10 transcripts revealed by microarray analysis and quantified 5 genes in cumulus cells derived from oocytes of both phases. The expression profile of 8 (80%) transcripts (ANAXA2, FL396, S100A10, RPL24, PP, PTTG1, MSX1 and BMP15) was in agreement with microarray data. Transcript abundance of five candidate genes in relation to oocyte developmental competence was validated using Brilliant Cresyl Blue (BCB) staining as an independent model. Furthermore, localization of mRNA and protein product of the candidate gene MSX1 in sections of ovarian follicles at days 0, 1, 3 and 7 of estrous cycle showed a clear fluorescent signal in both oocytes and cumulus cells with higher intensity in the former. Moreover, the protein product was detected in bovine oocytes and early cleavage embryos after fertilization with higher intensity around the nucleus.ConclusionThis study has identified distinct sets of differentially regulated transcripts between bovine oocytes recovered from small follicles at growth and dominance phases of the first follicular wave. The validation with independent model supports our notion that many of the transcripts identified here may represent candidate genes associated with oocyte developmental competence. Further specific functional analysis will provide insights into the exact role of these transcripts in oocyte competence and early embryonic development.
Comparative mitochondrial genomics of snakes: extraordinary substitution rate dynamics and functionality of the duplicate control region
Authors: Jiang Zhi J , Castoe Todd A , Austin Christopher C , Burbrink Frank T , Herron Matthew D , McGuire Jimmy A , Parkinson Christopher L , Pollock David D 
Published: August 2007

Abstract

Background
The mitochondrial genomes of snakes are characterized by an overall evolutionary rate that appears to be one of the most accelerated among vertebrates. They also possess other unusual features, including short tRNAs and other genes, and a duplicated control region that has been stably maintained since it originated more than 70 million years ago. Here, we provide a detailed analysis of evolutionary dynamics in snake mitochondrial genomes to better understand the basis of these extreme characteristics, and to explore the relationship between mitochondrial genome molecular evolution, genome architecture, and molecular function. We sequenced complete mitochondrial genomes from Slowinski's corn snake (Pantherophis slowinskii) and two cottonmouths (Agkistrodon piscivorus) to complement previously existing mitochondrial genomes, and to provide an improved comparative view of how genome architecture affects molecular evolution at contrasting levels of divergence.

Results
We present a Bayesian genetic approach that suggests that the duplicated control region can function as an additional origin of heavy strand replication. The two control regions also appear to have different intra-specific versus inter-specific evolutionary dynamics that may be associated with complex modes of concerted evolution. We find that different genomic regions have experienced substantial accelerated evolution along early branches in snakes, with different genes having experienced dramatic accelerations along specific branches. Some of these accelerations appear to coincide with, or subsequent to, the shortening of various mitochondrial genes and the duplication of the control region and flanking tRNAs.

Conclusion
Fluctuations in the strength and pattern of selection during snake evolution have had widely varying gene-specific effects on substitution rates, and these rate accelerations may have been functionally related to unusual changes in genomic architecture. The among-lineage and among-gene variation in rate dynamics observed in snakes is the most extreme thus far observed in animal genomes, and provides an important study system for further evaluating the biochemical and physiological basis of evolutionary pressures in vertebrate mitochondria.
Evaluation of B-type Natriuretic Peptide for validation of a heart failure register in primary care
Authors: Bhatia Gurbir S , Sosin Michael D , Stubley Jane , Patel Jeetesh V , Hughes Elizabeth A , Gibbs Rebecca , Davis Russell C 
Published: August 2007

Abstract

Background
Diagnosing heart failure and left ventricular systolic dysfunction is difficult on clinical grounds alone. We sought to determine the accuracy of a heart failure register in a single primary care practice, and to examine the usefulness of b-type (or brain) natriuretic peptide (BNP) assay for this purpose.

Methods
A register validation audit in a single general practice in the UK was carried out. Of 217 patients on the heart failure register, 56 of 61 patients who had not been previously investigated underwent 12-lead electrocardiography and echocardiography within the practice site. Plasma was obtained for BNP assay from 45 subjects, and its performance in identifying echocardiographic abnormalities consistent with heart failure was assessed by analysing area under receiver operator characteristic (ROC) curves.

Results
30/217 were found to have no evidence to suggest heart failure on notes review and were probably incorrectly coded. 70/112 who were previously investigated were confirmed to have heart failure. Of those not previously investigated, 24/56 (42.9%) who attended for the study had echocardiographic left ventricular systolic dysfunction. A further 8 (14.3%) had normal systolic function, but had left ventricular hypertrophy or significant valve disease. Overall, echocardiographic features consistent with heart failure were found in only 102/203 (50.2%). BNP was poor at discriminating those with and without systolic dysfunction (area under ROC curve 0.612), and those with and without any significant echocardiographic abnormality (area under ROC curve 0.723).

Conclusion
In this practice, half of the registered patients did not have significant cardiac dysfunction. On-site echocardiography identifies patients who can be removed from the heart failure register. The use of BNP assay to determine which patients require echocardiography is not supported by these data.
Combined use of Amplified Fragment Length Polymorphism and IS6110 -RFLP in fingerprinting clinical isolates of Mycobacterium tuberculosis from Kerala, South India
Authors: Krishnan Manju Y , Radhakrishnan Indulakshmi , Joseph Biljo V , GK Madhavi Latha , Kumar R Ajay , Mundayoor Sathish 
Published: August 2007

Abstract

Background
DNA fingerprinting by IS6110-RFLP has shown a high incidence of Mycobacterium tuberculosis isolates having no and low copies of the insertion sequence in Kerala, South India. Amplified Fragment Length Polymorphism (AFLP) would scan the entire genome rather than a few repetitive elements, we thought that this technique would help us in differentiating the large reservoir of isolates from an endemic region. Here we evaluate the ability of Amplified Fragment Length Polymorphism (AFLP) to type clinical isolates.

Methods
Fifty clinical isolates of M. tuberculosis were analysed by conventional radioactive AFLP and IS6110- RFLP. M. bovis, M. bovis BCG and two non tuberculous mycobacteria were also analysed to see species specific differences generated by AFLP. Cluster analysis was performed using the AFLP profile that showed the maximum polymorphism within M. tuberculosis and this was compared to the number of copies of IS6110 insertions.

Results
For AFLP, out of ten primer pairs tested, the EO/MC pair generated maximum polymorphism among the clinical isolates of M. tuberculosis. The similarity between the isolates ranged between 88 and 99.5%. Majority (nearly 85%) of the 'low copy' IS6110 isolates clustered together, while the rest clustered irrespective of the copy numbers. AFLP could show rare differences between isolates of M. tuberculosis, M. bovis and M. bovis BCG. The AFLP profiles for non-tuberculous mycobacteria were highly different from those of M. tuberculosis.

Conclusion
Polymorphism generated by AFLP within the M. tuberculosis species is limited and hence AFLP alone seems to have limited use in fingerprinting the isolates in Kerala. The combined use of AFLP and IS6110-RFLP showed relatively better differentiation of 'high copy' IS6110 isolates, but failed to differentiate the 'low copy' isolates. However, the technique may be efficient in inter-species differentiation, and hence potentially useful in identifying and developing species- specific markers.