bluuebunny/crossref_metadata_2025_split huggingface dataset:
The energetics of micellar solubilization
Authors: Mankowich A. M. 
Published: February 2007

AbstractMicellar solubilization, an action of the detergency mechanism, is considered from the stand‐point of quasi‐thermodynamics. The basis of the approach was suggested by the similarity of micellar solubilization and Freundlich adsorption isotherms. Free energy change (खG), heat of solubilization (खH) and change in entropy (खS) for the micellar solubilization of Orange OT are calculated using two‐phase theory and the Gibbs‐Helmholtz equation. It is postulated that the dye concn in the solution (monomer) phase is that at the critical micelle concn. The dye concn in the solubilized phase is computed for the dye‐penetrated portion of the micellar volume. Calculated values of खG in anionic and nonionic surfactants are of the order of magnitude of a physical adsorption. The positive खH values indicate the process is not an adsorption. The positive खS values point to increased randomness or possibly to decreased energy effects due to iceberg water molecule structure surrounding the hydrophobic dye molecules. The loss of the water structure around the latter in the solubilization process would result in their acquiring increased configu‐rational entropy.
Effect of unusual acids on selected seed oil analyses
Authors: Wolff I. A. , Miwa T. K. 
Published: February 2007

AbstractIn the course of chemical compositional studies on seed oils from more than 2600 species of uncultivated plants, a number of new acids were isolated and structurally characterized at our laboratory. Also included in the studies were many fatty acids previously identified but not widely distributed or readily available. Oils containing unusual functional groups often gave unexpected responses to analytical procedures in frequent use. To exemplify the analytical results, data are presented relative to behavior of oils containing oxygenated fatty acids, cyclopropene rings, unusual types and positions of unsaturation, differing chain length, and sundry combinations of these, in the following procedures: Determinatio of polyunsaturated acids by ultraviolet spectrophotometry; iodine value versus refractive index plot to single out unusual oils; oxirane oxygen by HBr titration; gas‐liquid chromatography; infrared, and nuclear magnetic resonance spectroscopy; and lipoxidase assay. Preliminary experimentation on an automatic analytical hydrogenation apparatus indicates good potential, in its aplication to both usual and unusual oils, for a rapid determination of total unsaturation with acceptable accuracy and precision.
A review of antioxidant analysis in food products
Authors: Stuckey B. N. , Osborne C. E. 
Published: February 2007

AbstractTo permit proper usage of antioxidants by the food processor and permit control under applicable governmental regulations, it is necessary to have adequate analytical methods. Such methods should both positively identify and provide a quantitative assay for the additive. Due to the complex nature of foods, analysis of an antioxidant in the very small quantities used presents a very real problem. Solvent extraction and/or steam distillation techniques are employed to separate the antioxidants from the food. Ultraviolet spectra, gas chromatography and colorimetric techniques are used to identify and determine the quantity of each antioxidant present. Slight variations are necessary for each type of food.
Natural Lifetimes and Hyperfine Structure for K39in the 5p2P3/2and 6p2P3/2Levels of the KI Spectrum by Resonance Scattering of Light
Authors: S Svanberg  
Published: February 2007

The hyperfine coupling constants and the natural radiative lifetimes of the 5p2P3/2and 6p2P3/2levels of K39were determined in a level crossing experiment on an enriched K39sample in a sealed-off resonance cell. The following results were obtained:a(5p2P3/2) = 1.973 (12) MHza(6p2P3/2) = 0.886 (8) MHzb(5p2P3/2) = 0.870 (18) MHzb(6p2P3/2) = 0.370 (15) MHzτ(5p2P3/2) = 133 (3) nsτ(6p2P3/2) = 310 (15) nsConsidering the influence of core polarization on the magnetic hyperfine interaction and applying a Sternheimer correction, fairly consistent values of the electric quadrupole momentQare obtained from the first three levels of thenp2P3/2sequence. We findQ(K39) = +0.059 (6) barn.
Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS data
Authors: Galante Pedro A. F. , Trimarchi Jeff , Cepko Constance L. , de Souza Sandro J. , Ohno-Machado Lucila , Kuo Winston P. 
Published: February 2007

AbstractSummary: A critical step in any SAGE, MPSS and SBS data analysis is tag-to-gene assignment. Current available tools are limited by a tag-by-tag annotation process and/or do not provide the dataset that is used to produce a complete tag-to-gene mapping. We developed ACTG, a web-based application that allows a large-scale tag-to-gene mapping using several reference datasets. ACTG can annotate SAGE (14 or 21 bp), MPSS (17 or 20 bp) and SBS (16 bp) data for both human and mouse organisms.Availability: http://retina.med.harvard.edu/ACTG/Contact: pgalante@ludwig.org.brSupplementary information: Supplementary data are available at Bioinformatics online.
NetMatch: a Cytoscape plugin for searching biological networks
Authors: Ferro A. , Giugno R. , Pigola G. , Pulvirenti A. , Skripin D. , Bader G. D. , Shasha D. 
Published: February 2007

AbstractSummary: NetMatch is a Cytoscape plugin which allows searching biological networks for subcomponents matching a given query. Queries may be approximate in the sense that certain parts of the subgraph-query may be left unspecified. To make the query creation process easy, a drawing tool is provided. Cytoscape is a bioinformatics software platform for the visualization and analysis of biological networks.Availability: The full package, a tutorial and associated examples are available at the following web sites: http://alpha.dmi.unict.it/~ctnyu/netmatch.html, http://baderlab.org/Software/NetMatchContact: ferro@dmi.unict.it
Disease-specific genomic analysis: identifying the signature of pathologic biology
Authors: Nicolau Monica , Tibshirani Robert , Børresen-Dale Anne-Lise , Jeffrey Stefanie S. 
Published: February 2007

AbstractMotivation: Genomic high-throughput technology generates massive data, providing opportunities to understand countless facets of the functioning genome. It also raises profound issues in identifying data relevant to the biology being studied.Results: We introduce a method for the analysis of pathologic biology that unravels the disease characteristics of high dimensional data. The method, disease-specific genomic analysis (DSGA), is intended to precede standard techniques like clustering or class prediction, and enhance their performance and ability to detect disease. DSGA measures the extent to which the disease deviates from a continuous range of normal phenotypes, and isolates the aberrant component of data. In several microarray cancer datasets, we show that DSGA outperforms standard methods. We then use DSGA to highlight a novel subdivision of an important class of genes in breast cancer, the estrogen receptor (ER) cluster. We also identify new markers distinguishing ductal and lobular breast cancers. Although our examples focus on microarrays, DSGA generalizes to any high dimensional genomic/proteomic data.Contact: ssj@standford.eduSupplementary information: Supplementary data are available at Bioinformatics online.
A Novel Major Facilitator Superfamily Protein at the Tonoplast Influences Zinc Tolerance and Accumulation in Arabidopsis
Authors: Haydon Michael J. , Cobbett Christopher S. 
Published: February 2007

Abstract
Zinc (Zn) is an essential micronutrient required by all cells but is toxic in excess. We have identified three allelic Zn-sensitive mutants of Arabidopsis (Arabidopsis thaliana). The gene, designated ZINC-INDUCED FACILITATOR1 (ZIF1), encodes a member of the major facilitator superfamily of membrane proteins, which are found in all organisms and transport a wide range of small, organic molecules. Shoots of zif1 mutants showed increased accumulation of Zn but not other metal ions. In combination with mutations affecting shoot-to-root Zn translocation, zif1 hma2 hma4 triple mutants accumulated less Zn than the wild type but remained Zn sensitive, suggesting that the zif1 Zn-sensitive phenotype is due to altered Zn distribution. zif1 mutants were also more sensitive to cadmium but less sensitive to nickel. ZIF1 promoter-β-glucuronidase fusions were expressed throughout the plant, with strongest expression in young tissues, and predominantly in the vasculature in older tissues. ZIF1 expression was highly induced by Zn and, to a lesser extent, by manganese. A ZIF1-green fluorescent protein fusion protein localized to the tonoplast in transgenic plants. MTP1 has been identified as a tonoplast Zn transporter and a zif1-1 mtp1-1 double mutant was more sensitive to Zn than either of the single mutants, suggesting ZIF1 influences a distinct mechanism of Zn homeostasis. Overexpression of ZIF1 conferred increased Zn tolerance and interveinal leaf chlorosis in some transgenic lines in which ZIF1 expression was high. We propose that ZIF1 is involved in a novel mechanism of Zn sequestration, possibly by transport of a Zn ligand or a Zn ligand complex into vacuoles.
AGF1, an AT-Hook Protein, Is Necessary for the Negative Feedback ofAtGA3ox1Encoding GA 3-Oxidase
Authors: Matsushita Akane , Furumoto Tsuyoshi , Ishida Sarahmi , Takahashi Yohsuke 
Published: February 2007

AbstractNegative feedback is a fundamental mechanism of organisms to maintain the internal environment within tolerable limits. Gibberellins (GAs) are essential regulators of many aspects of plant development, including seed germination, stem elongation, and flowering. GA biosynthesis is regulated by the feedback mechanism in plants. GA 3-oxidase (GA3ox) catalyzes the final step of the biosynthetic pathway to produce the physiologically active GAs. Here, we found that only the AtGA3ox1 among the AtGA3ox family of Arabidopsis (Arabidopsis thaliana) is under the regulation of GA-negative feedback. We have identified a cis-acting sequence responsible for the GA-negative feedback of AtGA3ox1 using transgenic plants. Furthermore, we have identified an AT-hook protein, AGF1 (for the AT-hook protein of GA feedback regulation), as a DNA-binding protein for the cis-acting sequence of GA-negative feedback. The mutation in the cis-acting sequence abolished both GA-negative feedback and AGF1 binding. In addition, constitutive expression of AGF1 affected GA-negative feedback in Arabidopsis. Our results suggest that AGF1 plays a role in the homeostasis of GAs through binding to the cis-acting sequence of the GA-negative feedback of AtGA3ox1.
The Effect of Electrical Stimulation and Lesioning of the Anterior Thalamic Nucleus on Kainic Acid–Induced Focal Cortical Seizure Status in Rats
Authors: Takebayashi Seiji , Hashizume Kiyotaka , Tanaka Tatsuya , Hodozuka Akira 
Published: February 2007

Summary:  Purpose: The present study aimed to clarify the effect of electrical stimulation and lesioning of the anterior nucleus of the thalamus (ANT) on kainic acid (KA)–induced focal cortical seizures in a rat model. To address the mechanism underlying these anticonvulsant actions, cerebral glucose metabolism after ANT electrical stimulation and lesioning was also examined. Methods: Wistar rats were divided into five major groups: control (n = 9), unilateral (n = 9), and bilateral (n = 9) ANT electrical stimulation, and unilateral (n = 9) and bilateral (n = 9) ANT lesioning. After KA injection, average clinical‐seizure frequencies in each group were measured. Electrical stimulation of ANT was introduced after induction of seizure status epilepticus. Stimulation was on for 30 min and off for 30 min per 60‐min cycle. Local cerebral glucose utilization (LCGU) was also measured by using [14C] 2‐deoxyglucose autoradiography in three groups of rats: control (n = 7), bilateral ANT stimulation (n = 7), and bilateral ANT lesioning (n = 7). Results: Unilateral ANT electrical stimulation and lesioning significantly reduced clinical seizure frequency, compared with control animals. Strikingly, no animals treated with bilateral ANT procedures demonstrated any clinical seizure. LCGU was markedly increased in the sensorimotor cortex, striatum, thalamus, mammillary body, and midbrain tegmentum of control group rats after KA injection, but no increase in LCGU was noted in rats treated with bilateral ANT lesioning or stimulation. Conclusions: The electrical stimulation and lesioning of ANT suppressed focal cortical clinical seizures induced by KA injection. Additionally, an analysis of cerebral metabolic changes indicated that these procedures might suppress the function as amplifier and synchronizer of seizure activity.
Impaired Functional Status and Echocardiographic Abnormalities Signifying Global Dysfunction Enhance the Prognostic Significance of Previously Unrecognized Myocardial Infarction Detected by Electrocardiography
Authors: Ammar Khawaja Afzal , Makwana Ravindrakumar , Jacobsen Steven J. , Kors Jan A. , Burnett John C. , Redfield Margaret M. , Yawn Barbara P. , Rodeheffer Richard J. 
Published: February 2007

Background: The relationship between electrocardiographic unrecognized myocardial infarction (UMI), abnormal functional status, echocardiographic abnormalities, and mortality has not been evaluated. Methods: A population‐based random sample of 2042 Olmsted County residents, age ≥45 years, was studied by self‐administered questionnaire, chart review, ECG and echocardiogram, and 5 year follow‐up for all‐cause mortality. UMI (n = 81) was diagnosed if ECG‐MI criteria were met without previous documented myocardial infarction. Functional Status was assessed by the Goldman Specific Activity Scale. Results: UMI subjects had an increased prevalence of abnormal functional status compared to no MI controls (22% vs 11%, P < 0.05). This association was independent of sex, obesity, smoking, diabetes, and pulmonary disease. It became insignificant after stratifying for echocardiographic abnormalities. Compared to no MI controls, UMI subjects with impaired functional status had a higher mortality hazard ratio (HR 7.2; P<0.0001) than those without impaired functional status (HR 2.7; P = 0.02). In UMI subjects with impaired functional status and any echocardiographic abnormality signifying global ventricular dysfunction (systolic or diastolic dysfunction, left atrial or left ventricular enlargement), the mortality risk was even higher (HR 9.5; P<0.001) and persisted in multivariate analyses. This increased mortality risk was unaffected by adjustment for regional wall motion abnormalities. Conclusions: The assessment of impaired functional status and echocardiographic abnormalities improves the prognostic significance of UMI. Even in the absence of regional wall motion abnormalities, structural abnormalities of global dysfunction may play a role in mediating the increased mortality associated with UMI.
Significance of Lead Strength during Exercise Testing
Authors: Polizos George , Ellestad Myrvin H. 
Published: February 2007

Background: The aim of the study was to evaluate the contribution of relative lead strengths to exercise‐induced ECG changes (ST depression) to predict the degree of myocardial ischemia as compared to the angiograms. This was accomplished by comparing the magnitude of ST depression to the ST/R ratio. Studies have shown that the diagnostic strength of a lead is directly related to the R wave amplitude1 and that sensitivity is significantly improved. Methods: Three hundred patients, who underwent treadmill exercise testing and coronary angiography revealing significant coronary narrowing (≥70% luminal diameter narrowing), were studied, along with 150 patients clear of significant coronary artery disease (<70% luminar diameter narrowing). Our goal was to determine the correlation between the relative lead strengths, using a constructed ST/R ratio, to exercise induced ECG changes (ST depression) to predict the presence of myocardial ischemia as compared to angiographic findings. Using a cutoff of 0.1 for the ST/R ratio, our data were compared to the sensitivity and specificity of 1.0 mm ST depression. Results: Overall sensitivity was improved for the ST/R ratio (84% vs 78%), while specificity was slightly decreased (81% vs 92%) in comparison to standard ST depression. When differentiating between R wave amplitudes, those with R wave ≤ 10 mm showed significantly improved sensitivity (88% vs 54%) and a minor decrease in specificity (90% vs 92%). In those with R wave ≥ 20 mm, the sensitivity of ST depression was higher (88% vs 71%) but the ST/R ratio was much more specific (88% vs 46%). No significant difference was observed when differentiating between male and female patients. Conclusion: We found that the correction of ST depression for R wave amplitude results in improved sensitivity in patients with low R waves and specificity in patients with very tall R waves (R ≥ 20 mm).
Variation of the Recirculation Length of Newtonian and Non-Newtonian Power-Law Fluids in Laminar Flow Through a Suddenly Expanded Axisymmetric Geometry
Authors: Nag Debabrata , Datta Amitava 
Published: February 2007

Abstract
A numerical study has been carried out for the laminar flow of Newtonian and non-Newtonian power-law fluids through a suddenly expanded axisymmetric geometry. Mathematical correlations are proposed for the prediction of the length of the recirculating eddy in terms of Reynolds number, expansion ratio and rheological parameters. A wide range of expansion ratios (1.25⩽ER⩽8.0) has been covered for the Newtonian fluid and both the shear-thinning and shear-thickening flow characteristic fluids have been considered for the non-Newtonian fluids.
Flip-Chip Underfill
Packaging Considering Capillary Force, Pressure Difference, and Inertia
Effects
Authors: Lin Chao-Ming , Chang Win-Jin , Fang Te-Hua 
Published: February 2007

Abstract
This study aims to enhance the flow rate and reduce the filling time in flip-chip underfill packaging by combining capillary force, pressure difference, and inertia effects. In the designed underfill apparatus, the capillary force effect is developed by surface tension, the pressure difference between the inlet and the outlet is established using a pump or a vacuum, and the inertia force is achieved via circular rotation. The governing equations containing the three analyzed effects are derived and solved using a dimensionless technique. The analytical results indicate that for the general gap height of approximately 10-1000μm, the pressure difference and inertia effects dominate the driving force and provide a significant reduction in the filling time. However, for a gap height of less than 1μm, the driving force is dominated by the capillary effect. The present results confirm that the productivity of the flip-chip underfill packaging process can be enhanced through the appropriate control of the capillary force, pressure difference, and inertia effects.
Genetic Diversity and Potential Function of Microbial Symbionts Associated with Newly Discovered Species of
Osedax
Polychaete Worms
Authors: Goffredi Shana K. , Johnson Shannon B. , Vrijenhoek Robert C. 
Published: February 2007

ABSTRACT

We investigated the genetic diversity of symbiotic bacteria associated with two newly discovered species of
Osedax
from Monterey Canyon, CA, at 1,017-m (
Osedax
Monterey Bay sp. 3 “rosy” [
Osedax
sp. MB3]) and 381-m (
Osedax
Monterey Bay sp. 4 “yellow collar”) depths. Quantitative PCR and clone libraries of 16S rRNA gene sequences identified differences in the compositions and abundances of bacterial phylotypes associated with the newly discovered host species and permitted comparisons between adult
Osedax frankpressi
and juveniles that had recently colonized whalebones implanted at 2,891 m. The newly discovered
Osedax
species hosted
Oceanospirillales
symbionts that are related to
Gammaproteobacteria
associated with the previously described
O. frankpressi
and
Osedax rubiplumus
(S. K. Goffredi, V. J. Orphan, G. W. Rouse, L. Jahnke, T. Embaye, K. Turk, R. Lee, and R. C. Vrijenhoek, Environ. Microbiol. 7:1369-1378, 2005). In addition,
Osedax
sp. MB3 hosts a diverse and abundant population of additional bacteria dominated by
Epsilonproteobacteria
. Ultrastructural analysis of symbiont-bearing root tissues verified the enhanced microbial diversity of
Osedax
sp. MB3. Root tissues from the newly described host species and
O. frankpressi
all exhibited collagenolytic enzyme activity, which covaried positively with the abundance of symbiont DNA and negatively with mean adult size of the host species. Members of this unusual genus of bone-eating worms may form variable associations with symbiotic bacteria that allow for the observed differences in colonization and success in whale fall environments throughout the world's oceans.
Comparison of Levels of Inactivation of Two Isolates of
Giardia lamblia
Cysts by UV Light
Authors: Li Dong , Craik Stephen A. , Smith Daniel W. , Belosevic Miodrag 
Published: February 2007

ABSTRACT

The effects of 254-nm UV irradiation on two human isolates (WB and H3) of
Giardia lamblia
cysts were assessed using a collimated beam protocol and a Mongolian gerbil model. The levels of infection of cysts in the gerbils were assessed based on the presence of cysts in feces and the presence and activity of trophozoites in the small intestine of inoculated gerbils. The results suggest that there were differences in the infectivities of the WB and H3 isolates, as well as in susceptibilities of the parasites to UV light. Without UV exposure, gerbils were more readily infected by isolate H3 cysts. After UV exposure of the cysts, however, the gerbils were more susceptible to isolate WB cysts.
Plasmid Replicon Typing of Commensal and Pathogenic
Escherichia coli
Isolates
Authors: Johnson Timothy J. , Wannemuehler Yvonne M. , Johnson Sara J. , Logue Catherine M. , White David G. , Doetkott Curt , Nolan Lisa K. 
Published: February 2007

ABSTRACT

Despite the critical role of plasmids in horizontal gene transfer, few studies have characterized plasmid relatedness among different bacterial populations. Recently, a multiplex PCR replicon typing protocol was developed for classification of plasmids occurring in members of the
Enterobacteriaceae
. Here, a simplified version of this replicon typing procedure which requires only three multiplex panels to identify 18 plasmid replicons is described. This method was used to screen 1,015
Escherichia coli
isolates of avian, human, and poultry meat origin for plasmid replicon types. Additionally, the isolates were assessed for their content of several colicin-associated genes. Overall, a high degree of plasmid variability was observed, with 221 different profiles occurring among the 1,015 isolates examined. IncFIB plasmids were the most common type identified, regardless of the source type of
E. coli
. IncFIB plasmids occurred significantly more often in avian pathogenic
E. coli
(APEC) and retail poultry
E. coli
(RPEC) than in uropathogenic
E. coli
(UPEC) and avian and human fecal commensal
E. coli
isolates (AFEC and HFEC, respectively). APEC and RPEC were also significantly more likely than UPEC, HFEC, and AFEC to possess the colicin-associated genes
cvaC
,
cbi
, and/or
cma
in conjunction with one or more plasmid replicons. The results suggest that
E. coli
isolates contaminating retail poultry are notably similar to APEC with regard to plasmid profiles, with both generally containing multiple plasmid replicon types in conjunction with colicin-related genes. In contrast, UPEC and human and avian commensal
E. coli
isolates generally lack the plasmid replicons and colicin-related genes seen in APEC and RPEC, suggesting limited dissemination of such plasmids among these bacterial populations.