bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictive modeling of plant messenger RNA polyadenylation sites
Authors: Ji Guoli , Zheng Jianti , Shen Yingjia , Wu Xiaohui , Jiang Ronghan , Lin Yun , Loke Johnny C , Davis Kimberly M , Reese Greg J , Li Qingshun Quinn 
Published: February 2007

Abstract

Background
One of the essential processing events during pre-mRNA maturation is the post-transcriptional addition of a polyadenine [poly(A)] tail. The 3'-end poly(A) track protects mRNA from unregulated degradation, and indicates the integrity of mRNA through recognition by mRNA export and translation machinery. The position of a poly(A) site is predetermined by signals in the pre-mRNA sequence that are recognized by a complex of polyadenylation factors. These signals are generally tri-part sequence patterns around the cleavage site that serves as the future poly(A) site. In plants, there is little sequence conservation among these signal elements, which makes it difficult to develop an accurate algorithm to predict the poly(A) site of a given gene. We attempted to solve this problem.

Results
Based on our current working model and the profile of nucleotide sequence distribution of the poly(A) signals and around poly(A) sites in Arabidopsis, we have devised a Generalized Hidden Markov Model based algorithm to predict potential poly(A) sites. The high specificity and sensitivity of the algorithm were demonstrated by testing several datasets, and at the best combinations, both reach 97%. The accuracy of the program, called p oly(A) s ite s leuth or PASS, has been demonstrated by the prediction of many validated poly(A) sites. PASS also predicted the changes of poly(A) site efficiency in poly(A) signal mutants that were constructed and characterized by traditional genetic experiments. The efficacy of PASS was demonstrated by predicting poly(A) sites within long genomic sequences.

Conclusion
Based on the features of plant poly(A) signals, a computational model was built to effectively predict the poly(A) sites in Arabidopsis genes. The algorithm will be useful in gene annotation because a poly(A) site signifies the end of the transcript. This algorithm can also be used to predict alternative poly(A) sites in known genes, and will be useful in the design of transgenes for crop genetic engineering by predicting and eliminating undesirable poly(A) sites.
Respiratory Effect of Prolonged Electrical Weapon Application on Human Volunteers
Authors: Ho Jeffrey D. , Dawes Donald M. , Bultman Laura L. , Thacker Jenny L. , Skinner Lisa D. , Bahr Jennifer M. , Johnson Mark A. , Miner James R. 
Published: February 2007

Background: Conducted electrical weapons (CEWs) are used by law enforcement to subdue combative subjects. Occasionally, subjects will die after a CEW has been used on them. It is theorized that CEWs may contribute to these deaths by impairing respiration. Objectives: To examine the respiratory effects of CEWs. Methods: Human volunteers received a 15‐second application of electrical current from a CEW while wearing a respiratory measurement device. Common respiratory parameters were collected before, during, and after exposure. Health histories and demographic information were also collected. Results: Fifty‐two subjects were analyzed. Thirty‐four underwent a 15‐second continuous exposure, and 18 underwent three 5‐second burst exposures. In the continuous application group, the baseline mean tidal volume of 1.1 L increased to 1.8 L during application, the baseline end‐tidal CO2 level went from 40.5 mm Hg to 37.3 mm Hg after exposure, the baseline end‐tidal oxygen level went from 118.7 mm Hg to 121.3 mm Hg after exposure, and the baseline respiratory rate went from 15.9 breaths/min to 16.4 breaths/min after exposure. In the 5‐second burst group, the baseline mean tidal volume increased to 1.85 L during application, the baseline end‐tidal CO2 level went from 40.9 mm Hg to 39.1 mm Hg after exposure, the baseline end‐tidal oxygen level went from 123.1 mm Hg to 127.0 mm Hg after exposure, and the baseline respiratory rate went from 13.8 breaths/min to 14.6 breaths/min after exposure. Conclusions: Prolonged CEW application did not impair respiratory parameters in this population of volunteers. Further study is recommended to validate these findings in other populations.
Absence of Stabilizing Mutations of β-Catenin Encoded by CTNNB1 Exon 3 in a Large Series of Sporadic Parathyroid Adenomas
Authors: Costa-Guda Jessica , Arnold Andrew 
Published: February 2007

Abstract
Context: The molecular mechanisms underlying the pathogenesis of sporadic parathyroid adenomas are incompletely understood. Dysfunction of the Wnt signaling pathway is an established pathogenetic contributor to human tumorigenesis and, recently, the role of stabilizing mutations in β-catenin, a cause of abnormal Wnt signaling, has been examined in parathyroid tumors with conflicting results.
Objective: The objective of the present study was to determine the frequency of stabilizing mutations in exon 3 of CTNNB1, encoding β-catenin, in a large series of parathyroid adenomas.
Patients and Design: Ninety-seven sporadic parathyroid adenomas were examined for mutations in exon 3 of CTNNB1 by direct DNA sequencing.
Results: No mutations were identified in any of the adenomas.
Conclusions: The absence of stabilizing mutations of β-catenin, including the previously reported S37A, encoded in CTNNB1 exon 3 among 97 tumors suggests that such mutations contribute rarely if at all to the development of sporadic parathyroid adenomas. A primary role for abnormal Wnt signaling in parathyroid tumor formation remains to be established.
Linezolid for the Treatment of Patients with Central Nervous System Infection
Authors: Ntziora Fotinie , Falagas Matthew E 
Published: February 2007

Objective: To review the available evidence regarding the use of linezolid for the treatment of patients with central nervous system (CNS) infections. Data Sources: Relevant studies were identified through searches of the PubMed, Current Contents, and Cochrane databases (publications archived until October 2006). Study Selection and Data Extraction: Case reports, case series, prospective and retrospective studies, and randomized controlled trials were eligible for inclusion in our review if they evaluated the effectiveness and safety of linezolid for the treatment of patients with CNS infections. Data Synthesis: In 18 (42.9%) of the 42 relevant cases identified, patients had undergone neurosurgical operations and/or had prosthetic devices. Meningitis was the most common CNS infection, accounting for 20 (47.6%) cases. Other CNS infections included brain abscesses (14; 33.3%), ventriculitis (5; 11.9%), and ventriculo-peritoneal shunt infection (3; 7.1%). In the 39 patients in whom the responsible pathogen was isolated, those predominantly responsible for the CNS infections were: penicillin–nonsusceptible Streptococcus pneumoniae (7; 17.9%), vancomycin-resistant enterococci (6; 15.4%), Nocardia spp. (5; 12.8%), methicillin-resistant Staphylococcus epidermidis (4; 10.3%), and methicillin-resistant Staphylococcus aureus (3; 7.7%). Of the 42 patients who received linezolid for the treatment of CNS infections, 38 (90.5%) were either cured or showed clinical improvement of the infection. The mean duration of follow-up was 7.2 months; no recurrent CNS infection was reported. Conclusions: The limited published data suggest that linezolid may be considered for the treatment of patients with CNS infections in cases of failure of previously administered treatment or limited available options.
Absence of Effect of Oral Rifaximin on the Pharmacokinetics of Ethinyl Estradiol/Norgestimate in Healthy Females
Authors: Trapnell Carol Braun , Connolly Margaret , Pentikis Helen , Forbes William P , Bettenhausen Doug K 
Published: February 2007

Background: Rifaximin is an oral rifampin analog, and its activity is targeted within the gastrointestinal tract. Some analogs induce the cytochrome P450 family of oxidative enzymes. Ethinyl estradiol (EE), commonly found in oral contraceptives (OCs), is a known CYP3A4 substrate. Objective: To determine the potential effect of rifaximin on EE and norgestimate pharmacokinetics. Methods: In an open-label, crossover study, healthy females received a single dose of OC (EE 0.07 mg/norgestimate 0.50 mg). Following a 1 week washout period, individuals received rifaximin 200 mg every 8 hours for 3 days, with a single dose of OC administered with the ninth rifaximin dose. During both treatment periods, blood samples were collected periodically for up to 96 hours after each OC dose. Plasma concentration–time profiles and pharmacokinetic parameters were characterized for EE and 2 major metabolites of norgestimate, norgestrel (NG) and 17-deacetyl norgestimate (17-DNGM). A drug–drug interaction was confirmed if the 90% CI for the 2 treatment period comparison was outside the 80–125% limit. Results: Twenty-six of 28 women completed the study. No differences in pharmacokinetic parameters were observed for EE, NG, or 17-DNGM when a single dose of the OC was administered alone or with rifaximin. In addition, the 90% CI for the bioavailability contrasts (OC alone vs OC with rifaximin) for the maximum plasma concentration, area under the plasma concentration–time curve from zero to the last measurable plasma concentration or to infinity for EE, NG. and 17-DNGM all ranged from 86–118%. These intervals were within the predefined range for equivalence; therefore, no interaction was observed between OC and rifaximin. Rifaximin was well tolerated. Conclusions: Administration of a 3 day dosing regimen of oral rifaximin was well tolerated and did not alter the pharmacokinetics of a commonly used combination OC containing EE and norgestimate.
Laboratory Evaluation of Potassium and Creatinine Among Ambulatory Patients Prescribed Spironolactone: Are We Monitoring for Hyperkalemia?
Authors: Raebel Marsha A , McClure David L , Chan K Arnold , Simon Steven R , Feldstein Adrianne C , Lafata Jennifer Elston , Andrade Susan E , Gunter Margaret J , Nelson Winnie W , Roblin Douglas , Platt Richard 
Published: February 2007

Background: Serum potassium and creatinine evaluation is recommended in patients prescribed spironolactone, yet the proportion of ambulatory patients chronically dispensed spironolactone receiving evaluation is not well understood. Objective: To estimate the rate of potassium and creatinine evaluation and identify factors associated with conducting these tests among ambulatory patients dispensed spironolactone. Methods: A retrospective cohort study was designed to evaluate patients at 10 health maintenance organizations with ongoing spironolactone dispensing for one year (N = 2257). Potassium and creatinine evaluation were determined from administrative data. Associations between patient characteristics and laboratory testing were assessed, using logistic regression modeling. Results: Serum creatinine and potassium were evaluated in 72.3% of patients during a 13 month period. The likelihood of potassium and creatinine monitoring was greater among patients who were older (OR 1.28; 95% CI 1.17 to 1.41 per decade of life); male (OR 1.25; 95% CI 1.01 to 1.54); had diabetes (OR 1.63; 95% CI 1.31 to 2.03); received concomitant therapy with angiotensin-converting enzyme inhibitors/angiotensin receptor blockers (OR 2.23; 95% CI 1.74 to 2.87), potassium supplements (OR 1.96; 95% CI 1.51 to 2.54), or digoxin (OR 2.10 95% CI 1.48 to 2.98); or had more outpatient visits (OR 1.31; 95% CI 1.19 to 1.44). Among patients with heart failure (n = 790), factors associated with the incidence of laboratory testing were diabetes (OR 1.64, 95% CI 1.14 to 2.34), outpatient visits (OR 1.20; 95% CI 1.02 to 1.41), and digoxin therapy (OR 2.26; 95% CI 1.38 to 3.69). Conclusions: Three-fourths of ambulatory patients dispensed spironolactone receive recommended laboratory evaluation, with monitoring more likely to be completed in patients prescribed concomitant therapy with drugs that increase hyperkalemia risk, older patients, and those with diabetes.
Kinetics of citrate-induced selenite desorption from montmorillonite as affected by complexation with hydroxyaluminum and hydroxyaluminosilicate ions
Authors: Saha Uttam Kumar , Kozak L. M. , Huang P. M. 
Published: February 2007

AbstractThe citrate-induced desorption kinetics of pre-adsorbed Se from montmorillonite (Mt) and its complexes with hydroxyaluminum (HyA-Mt) and hydroxyaluminosilicate (HAS-Mt) were studied. The mole fraction of pre-adsorbed Se released in 24 h from different clays followed the trends of Mt>> HAS-Mt> HyA-Mt with a significant increase with elevated citrate concentration in the desorbing solution. In contrast, the amount of Se adsorbed per unit mass of different clays followed a clear-cut opposite trend of HyA-Mt>HAS-Mt>>Mt. The Se desorption kinetics in different systems indicated multiple rate characteristics; where an initial fast reaction (0.25–2 h) was followed by a slow reaction (2–16 h). Of the six different kinetic models tested (zero-, first-, and second-order; power function, Elovich, and parabolic diffusion), the second-order rate equation showed the overall best fit to the fast and slow desorption kinetic data from the clays. Based on second-order rate constants, the rates of the mole fraction of Se desorption by citrate from different clay systems at 298 K followed the order Mt > HAS-Mt >> HyA-Mt. For both fast and slow reaction, the rates of desorption increased proportionally with the level of citrate. Replicate experiments conducted across a range of temperature (288–318 K) yielded Arrhenius parameters that followed the order HyA-Mt > HAS-Mt >> Mt. Considering that a lower mole fraction of Se desorption after a particular reaction period, slower desorption kinetics, and a greater activation energy of desorption are the indices of increased adsorption bond strength, the results clearly indicate that HyA- and HAS-interlayering and coatings on Mt not only augmented its Se adsorption affinity and capacity, but also increased the adsorption bond strength. Silication in HyA not only reduced the Se adsorption capacity, but also weakened the adsorption bond strength. This establishes a significant role of HyA/HAS-interlayering and coating on Mt in influencing the rate of citrate-induced release of Se. Reduction in surface-positive potential following citrate adsorption on the clay surface, a direct ligand exchange between Se and citrate, and structural dissolution are possible mechanisms responsible for citrate-induced Se desorption in the present study.
Nontronite particle aggregation induced by microbial Fe(III) reduction and exopolysaccharide production
Authors: Jaisi Deb P. , Dong Hailiang , Kim Jinwook , He Ziqi , Morton John P. 
Published: February 2007

AbstractClay particle aggregation affects a number of environmental processes, such as contaminant sorption/desorption, particle movement/deposition, and sediment structure and stability, yet factors that control clay aggregation are not well understood. This study was designed to investigate how microbial reduction of Fe(III) in clay structure, a common process in soils and sediments, affects clay-particle aggregation. Microbial Fe(III) reduction experiments were conducted with Shewanella putrefaciens CN32 in bicarbonate buffer with structural Fe (III) in nontronite as the sole electron acceptor, lactate as the sole electron donor, and AQDS as an electron shuttle. Four size fractions of nontronite (D5–D95 of 0.12–0.22 µm, 0.41–0.69 µm, 0.73–0.96 µm and 1.42–1.78 µm) were used to evaluate size-dependent aggregation kinetics. The extent of Fe(III) bioreduction and the amount of exopolysaccharide (EPS), a major biopolymer secreted by CN32 cells during Fe(III) bioreduction, were measured with chemical methods. Nontronite particle aggregation was determined by photon correlation spectroscopy and scanning electron microscopy. The maximum extent of Fe(III) bioreduction reached 36% and 24% for the smallest and the largest size fractions, respectively. Within the same time duration, the effective diameter, measured at 95% percentile (D95), increased by a factor of 43.7 and 7.7 for these two fractions, respectively. Because there was production of EPS by CN32 cells during Fe(III) reduction, it was difficult to assess the relative role of Fe(III) bioreduction and EPS bridging in particle aggregation. Thus, additional experiments were performed. Reduction of Fe(III) by dithionite was designed to examine the effect of Fe(III) reduction, and pure EPS isolated from CN32 cells was used to examine the effect of EPS. The data showed that both Fe(III) reduction and EPS were important in promoting clay mineral aggregation. In natural environments, the relative importance of these two factors may be dependent on local conditions. These results have important implications for understanding factors in controlling clay particle aggregation in natural environments.
Phosphate and glyphosate adsorption by hematite and ferrihydrite and comparison with other variable-charge minerals
Authors: Gimsing Anne Louise , Borggaard Ole Kragholm 
Published: February 2007

AbstractAdsorption by synthetic 2-line ferrihydrite and hematite of glyphosate and phosphate, separately and together, was compared with adsorption results for goethite, gibbsite and two kaolinites in order to determine adsorption differences and similarities, in particular competition and phosphate preference, of these variable-charge minerals. Hematite rapidly adsorbed both compounds, while adsorption by ferrihydrite was slow, in particular of glyphosate, probably because of very slow diffusion of the bulky glyphosate molecules into interior sites in ferrihydrite particles. Accordingly, the Langmuir adsorption capacity of glyphosate (GAC) was considerably smaller (1.85 µmol m−2)than GAC for hematite (2.61 µmol m−2). The phosphate adsorption capacities (PAC) for ferrihydrite and hematite were more alike, 2.91 µmol m−2 and 2.85 µmol m−2, respectively. Differences between surface coordination (mono- or bidentate) may also contribute to the observed differences but conflicting information about the nature of the surface complexes makes this a difficult contributary factor to assess. The minerals were found to exhibit great variation in extent of competition and phosphate preference. Little competition and phosphate preference characterized hematite adsorption, while phosphate almost completely outcompeted glyphosate on goethite; ferrihydrite adsorption fell between these extremes. These differences may be attributed to different numbers of common (competitive) and specific (selective) adsorption sites on the three Fe oxides with a decreasing number of common sites in the order: goethite>>ferrihydrite>hematite, i.e. almost all goethite sites are common but with strong phosphate preference, while most hematite sites are specific for either glyphosate or phosphate. Alternatively, the result may be explained by adsorption in more planes, e.g. glyphosate adsorption onto the inner-Helmholtz-plane-adsorbed phosphate. For all six minerals compared, desorption of glyphosate following phosphate addition was found to be significantly correlated with the difference between the amounts of phosphate and glyphosate adsorbed indicating that this difference may be used as a competition index for predicting the influence of phosphate on glyphosate adsorption.
Moral Luck: A Partial Map
Authors: Zimmerman Michael J. 
Published: February 2007

Luck varies from person to person, for two reasons. First, for something to occur as a matter of luck is for it to occur beyond the control of someone, and what is beyond one person's control may not be beyond another's. Second, luck may be either good or bad (or neutral — but in that case it is not very interesting), and what is good luck for one person may be bad luck for another.Moral philosophers have paid a good deal of attention to luck in an effort to determine its relevance to moral judgments of various sorts. We may distinguish three broad classes of such judgments: aretaic judgments, having to do with moral virtue and vice; deontic judgments, having to do with moral Obligation; and what I will call hypological judgments, having to do with moral responsibility. In the wake of Harry Frankfurt's ground-breaking discussion of the claim that moral responsibility requires control, most of the attention that has been devoted in recent years to moral luck has concerned hypological judgments in particular; deontic judgments and aretaic judgments have been given relatively short shrift.
Maternal employment and time with children: Dramatic change or surprising continuity?
Authors: Bianchi Suzanne M. 
Published: February 2007

AbstractDespite the rapid rise in mothers’ labor force participation, mothers’ time with children has tended to be quite stable over time. In the past, nonemployed mothers’ time with children was reduced by the demands of unpaid family work and domestic chores and by the use of mother substitutes for childcare, especially in large families. Today employed mothers seek ways to maximize time with children: They remain quite likely to work part-time or to exit from the labor force for some years when their children are young; they also differ from nonemployed mothers in other uses of time (housework, volunteer work, leisure). In addition, changes in children’s lives (e.g., smaller families, the increase in preschool enrollment, the extended years of financial dependence on parents as more attend college) are altering the time and money investments that children require from parents. Within marriage, fathers are spending more time with their children than in the past, perhaps increasing the total time children spend with parents even as mothers work more hours away from home.
Demographics of dumping ii: a national environmental equity survey and the distribution of hazardous materials handlers
Authors: Davidson Pamela , Anderton Douglas L. 
Published: February 2007

Abstract
Using a national survey of facilities governed by the Resource Conservation and Recovery Act (RCRA), we examine the sociospatial distribution of a much larger group of hazardous materials handlers than did previous environmental equity studies. Overall we find that RCRA-governed facilities are more likely to be sited in working-class neighborhoods with lower percentages of minority residents. We do not find evidence of stark environmental inequities. RCRA facilities, however, are close to neighborhoods with a higher percentage of minority residents. And in nonmetropolitan areas, they are slightly more likely to be located in neighborhoods with a higher percentage of black residents.
The spatial separation of the poor in Canadian cities
Authors: Fong Eric , Shibuya Kumiko 
Published: February 2007

AbstractWe used the 1991 Canadian census to examine the extent of spatial separation of the poor in Canadian cities. Although there were no extensive areas of blight, decay, or housing abandonment, we found high spatial separation of poor visible minorities in the selected cities. The index of dissimilarity indicates high segregation of poor blacks and moderate separation of poor Asians from the nonpoor population. We tested the effects of three major structural factors—racial and ethnic segregation, income segregation, and urban redevelopment—and found that racial and ethnic residential patterns are related strongly to the spatial separation of poor persons. The relationship between income segregation and spatial separation of the poor is not significant, however. We also found that the relationship between urban redevelopment and spatial separation of the poor pertains only to blacks. These findings suggest that blacks are vulnerable in the process of urban redevelopment.