bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complexations of the hydrophilic and hydrophobic moieties of benzethonium chloride by cucurbit[7]uril in aqueous solution
Authors: MacGillivray Brendan C. , Macartney Donal H. 
Published: November 2012

The sequential complexations of the hydrophilic and hydrophobic end groups of benzethonium chloride by cucurbit[7]uril (CB[7]) in aqueous solution have been investigated using 1H NMR spectroscopy and electrospray ionization mass spectrometry. The initial binding is to the benzyldimethylammonium group, with a stability constant of (8.7 ± 3.1) × 107 (mol/L)–1. This binding constant and the complexation-induced upfield shifts of the benzyl guest protons are similar to those values observed with other cationic guests containing benzyl moieties. This equilibrium is followed by the binding of a second equivalent of the host to the hydrophobic 2-(2,4,4-trimethylpentyl) group, with a stability constant of (4.0 ± 1.9) × 103 (mol/L)–1. The relatively strong binding of this uncharged hydrophobic end of the guest molecule is consistent with the inclusion of eight heavy (nonhydrogen) atoms within the inner cavity of CB[7], with its low polarizability. The packing coefficient for the 2-(2,4,4-trimethylpentyl) group with the inner cavity is calculated to be 61%, close to Rebek’s ideal value of 55%.
Photochemical conversion of AgCl nanocubes to hybrid AgCl–Ag nanoparticles with high activity and long-term stability towards photocatalytic degradation of organic dyes
Authors: Wang Jizhuang , An Changhua , Zhang Meiyu , Qin Chuan , Ming Xijuan , Zhang Qinhui 
Published: November 2012

The performance of a photocatalytic reaction is mainly determined by the quality of the photocatalyst. For real applications, significantly enhancing the stability and activity of the photocatalysts still remains a challenge for materials scientists and chemists. In this paper, we have achieved a highly efficient plasmonic AgCl–Ag nanophotocatalyst via photochemical conversion of AgCl nanocubes. Compared with reported photocatalysts, the as-achieved nanophotocatalyst exhibits superior activity, long-term stability, and wide applicability in the decomposition of organic dye pollutants. For example, only 30 s is needed to bleach methyl orange molecules assisted by AgCl–Ag nanoparticles. Furthermore, the catalyst can be reused up to 50 times without significant loss of activity. A possible mechanism was discussed and the specified photocatalytic reactions verified that both O2•– and OH• radicals were the main active species in decomposing pollutants. The excellent performance of the present photocatalyst suggests promising applications in environmental remediation, clean energy creation, and solar cells.
Application of the high-speed self-reversal background corrector to the determination of cadmium by chemical vapor generation atomic absorption spectrometry
Authors: Waterlot Christophe , Pelfrêne Aurélie , Douay Francis 
Published: November 2012

Concentrations of cadmium (Cd) in extracting solutions (neutral salts) from contaminated soils are often too low to be determined by conventional flame atomic absorption spectrometry. For this reason, determination of Cd requires sensitive analytical methods free from interference problems generated by samples. In this context, vapor generation atomic absorption spectrometry (HGAAS) was combined with a high-speed self-reversal background corrector. This new approach was successfully applied after optimization of the analytical parameters to obtain a maximal absorbance signal of the volatile Cd species. The optimum condition was achieved with a 3% (m/v) NaBH4 in 1.5% (m/v) NaOH reducing solution and a solution containing 0.3 mol/L HNO3. The detection limit was 1 ng mL–1 under the previous conditions and the relative standard deviation was up to 5% for 10 replicate analyses of Cd at 0.2 and 1 ng mL–1, reflecting a very highly sensitive and reproducible method. Moreover, the results showed that the proposed combination was an efficient method to overcome the interference problems caused by different coexisting cations, As, Al, Ca, Cu, Fe, Mg, Mn, Ni, Pb, Se and Zn, up to 10 µg mL–1. The method was validated with analyses of two standard reference materials and was used for Cd determination in 0.01 mol/L CaCl2 extracts from contaminated kitchen garden soils. The data were compared with those obtained by two other more conventional methods, electrothermal atomic absorption spectrometry (ETAAS) and flame atomic absorption spectrometry (FAAS). The analytical results obtained by the ETAAS and HGAAS were in a good agreement, suggesting the suitability of the method for Cd determination in 0.01 mol/L CaCl2 extracting solution.
Variability of Pennsylvanian–Permian Carbonate Associations and implications for NW Pangea Palaeogeography, east-central British Columbia, Canada
Authors: Zubin-Stathopoulos K. D. , Beauchamp B. , Davydov V. I. , Henderson C. M. 
Published: November 2012

Abstract
Pennsylvanian–Early Permian carbonate sedimentation in east-central British Columbia records a complex history of changing environments influenced by evolving palaeogeography and climate. Newly recognized tectonically controlled features affected the distribution and variability of carbonate associations, providing new interpretations for this portion of the NW coast of Pangea. Both a heterozoan (cool-water) and photozoan (warm-water) association were identified on either side of a palaeogeographical high. Cool-water carbonates were located outboard or to the west of this high, an area influenced by upwelling waters. Inboard of this high, a warm, protected sea developed at about 20°N palaeolatitude during the Asselian and Sakmarian. This configuration and palaeolatitude is similar to that of Baja California, Mexico and the Sea of Cortéz, providing a good modern analogue for these deposits where warm-water carbonates grow at latitudes otherwise dominated by cool-water deposits. The warm sea provided a place for a photozoan association to develop during the Early Permian when the low-latitude NW coast of Pangea was dominated by cool-water carbonates.
Sedimentology and palaeoecology of lonestone-bearing mixed clastic rocks and cold-water carbonates of the Lower Permian Basal Beds at Fossil Cliffs, Maria Island, Tasmania (Australia): Insight into the initial decline of the late Palaeozoic ice age
Authors: Isbell J. L. , Henry L. C. , Reid C. M. , Fraiser M. L. 
Published: November 2012

Abstract

The middle Sakmarian Basal Beds on Maria Island were deposited during the initial decline of the Late Palaeozoic Ice Age following Late Pennsylvanian–Early Sakmarian maximum glaciation. At that time, Tasmania was located within the South Polar Circle between an apparent ice-free pole (Antarctica) and the mid- to high-latitude Sydney-Bowen-Gunnedah glacigenic basins in eastern Australia. The dropstone-bearing Basal Beds consist of: interstratified siltstone, conglomerate and cold-water limestones of the Lower Erratic Zone; siltstone and
Eurydesma-
rich cold-water carbonates of the Darlington Limestone; and siltstone and conglomerate of the Upper Erratic Zone. Interstratification of the coarse-clastic strata, siltstones and limestones within these units were previously attributed to glacial/non-glacial cycles. However, the interfingering of beds within each of these units and the occurrence of large, fossil bryozoans crossing and abutting lithological boundaries indicate that cyclicity was of shorter duration than that of Milankovitch-driven cycles. Within these intertidal and subtidal deposits, the occurrence of rounded dropstones derived from local basement rocks exposed along a rocky coastline and an absence of glacial indicators other than dropstones, along with other evidence, suggest that ice rafting was by sea ice rather than by icebergs. Study results confirm the spatial restriction of Middle Sakmarian to earliest Wuchiapingian glaciation.
Arginase Inhibition Improves Endothelial Function in Patients With Coronary Artery Disease and Type 2 Diabetes Mellitus
Authors: Shemyakin Alexey , Kövamees Oskar , Rafnsson Arnar , Böhm Felix , Svenarud Peter , Settergren Magnus , Jung Christian , Pernow John 
Published: November 2012

Background—

Endothelial dysfunction plays an important role in the early development of atherosclerosis and vascular complications in type 2 diabetes mellitus. Increased expression and activity of arginase, metabolizing the nitric oxide substrate
l
-arginine, may result in reduced production of nitric oxide and thereby endothelial dysfunction. We hypothesized that inhibition of arginase activity improves endothelial function in patients with coronary artery disease (CAD) and type 2 diabetes mellitus.

Methods and Results—

Three groups of subjects were included: 16 patients with CAD, 16 patients with CAD and type 2 diabetes mellitus (CAD+Diabetes), and 16 age-matched healthy control subjects. Forearm endothelium-dependent and endothelium-independent vasodilatation were assessed with venous occlusion plethysmography before and during intra-arterial infusion of the arginase inhibitor
N
ω
-hydroxy-nor-
l
-arginine (nor-NOHA; 0.1 mg/min). Nor-NOHA was also coinfused with the nitric oxide synthase inhibitor (
N
G
-monomethyl L-arginine). The expression of arginase was determined in the internal mammary artery of patients undergoing bypass surgery. Nor-NOHA markedly increased endothelium-dependent vasodilatation (up to 2-fold) in patients with CAD+Diabetes and CAD (
P
<0.001) but not in the control group.
N
G
-monomethyl L-arginine completely inhibited the increase in endothelium-dependent vasodilatation induced by nor-NOHA. Endothelium-independent vasodilatation was slightly improved by nor-NOHA in the CAD+Diabetes group. Arginase I was expressed in vascular smooth muscle cells and endothelial cells, and arginase II was expressed in endothelial cells of patients with and without diabetes mellitus.

Conclusions—
Arginase inhibition markedly improves endothelial function in patients with CAD and type 2 diabetes mellitus suggesting that increased arginase activity is a key factor in the development of endothelial dysfunction.
The Effectiveness of Airline Pilot Training for Abnormal Events
Authors: Casner Stephen M. , Geven Richard W. , Williams Kent T. 
Published: November 2012

Objective: To evaluate the effectiveness of airline pilot training for abnormal in-flight events. Background: Numerous accident reports describe situations in which pilots responded to abnormal events in ways that were different from what they had practiced many times before. One explanation for these missteps is that training and testing for these skills have become a highly predictable routine for pilots who arrive to the training environment well aware of what to expect. Under these circumstances, pilots get plentiful practice in responding to abnormal events but may get little practice in recognizing them and deciding which responses to offer. Method: We presented 18 airline pilots with three abnormal events that are required during periodic training and testing. Pilots were presented with each event under the familiar circumstances used during training and also under less predictable circumstances as they might occur during flight. Results: When presented in the routine ways seen during training, pilots gave appropriate responses and showed little variability. However, when the abnormal events were presented unexpectedly, pilots’ responses were less appropriate and showed great variability from pilot to pilot. Conclusion: The results suggest that the training and testing practices used in airline training may result in rote-memorized skills that are specific to the training situation and that offer modest generalizability to other situations. We recommend a more complete treatment of abnormal events that allows pilots to practice recognizing the event and choosing and recalling the appropriate response. Application: The results will aid the improvement of existing airline training practices.
Retrospective analysis of fluoroquinolone prophylaxis in patients undergoing allogeneic hematopoietic stem cell transplantation
Authors: Simondsen Katherine A , Reed Michael P , Mably Mary S , Zhang Yang , Longo Walter L 
Published: November 2012

Background: Patients undergoing allogeneic hematopoietic stem cell transplant are at a high risk for infection-related mortality in the immediate post-transplantation phase. Prophylaxis with a fluoroquinolone is now recommended to reduce this risk with the stipulation that surveillance for increased fluoroquinolone resistance Clostridium difficile associated diarrhea be conducted. Methods: We conducted a retrospective chart review of 48 patients who underwent an allogeneic hematopoietic stem cell transplant and received a fluoroquinolone for prophylaxis and 48 patients who underwent an allogeneic hematopoietic stem cell transplant who did not receive a fluoroquinolone for prophylaxis. All patients received the same standard antifungal, antiviral and anti-pneumocystis prophylaxis. Results: Patients receiving fluoroquinolone prophylaxis had a lower incidence of febrile neutropenia than those not receiving prophylaxis, though the difference was not found to be statistically significant (83% vs. 67%, p = 0.098). Similar non-significant improvements in the number of positive cultures recovered during an episode of febrile neutropenia and antimicrobial days were noted. No significant increase in fluoroquinolone resistance, Clostridium difficile associated diarrhea, or in methicillin resistant Staphylococcus aureus infections were noted. Conclusion: Our single institution experience with fluoroquinolone prophylaxis for allogeneic hematopoietic stem cell transplant patients supports continuation of this practice. Expansion to autologous hematopoietic stem cell transplant patients may be appropriate based on guideline recommendations and our institution-specific experience with fluoroquinolone prophylaxis.
A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs
Authors: Seitzer Phillip , Wilbanks Elizabeth G , Larsen David J , Facciotti Marc T 
Published: November 2012

Abstract

Background
Discovery of functionally significant short, statistically overrepresented subsequence patterns (motifs) in a set of sequences is a challenging problem in bioinformatics. Oftentimes, not all sequences in the set contain a motif. These non-motif-containing sequences complicate the algorithmic discovery of motifs. Filtering the non-motif-containing sequences from the larger set of sequences while simultaneously determining the identity of the motif is, therefore, desirable and a non-trivial problem in motif discovery research.

Results
We describe MotifCatcher, a framework that extends the sensitivity of existing motif-finding tools by employing random sampling to effectively remove non-motif-containing sequences from the motif search. We developed two implementations of our algorithm; each built around a commonly used motif-finding tool, and applied our algorithm to three diverse chromatin immunoprecipitation (ChIP) data sets. In each case, the motif finder with the MotifCatcher extension demonstrated improved sensitivity over the motif finder alone. Our approach organizes candidate functionally significant discovered motifs into a tree, which allowed us to make additional insights. In all cases, we were able to support our findings with experimental work from the literature.

Conclusions
Our framework demonstrates that additional processing at the sequence entry level can significantly improve the performance of existing motif-finding tools. For each biological data set tested, we were able to propose novel biological hypotheses supported by experimental work from the literature. Specifically, in Escherichia coli, we suggested binding site motifs for 6 non-traditional LexA protein binding sites; in Saccharomyces cerevisiae, we hypothesize 2 disparate mechanisms for novel binding sites of the Cse4p protein; and in Halobacterium sp. NRC-1, we discoverd subtle differences in a general transcription factor (GTF) binding site motif across several data sets. We suggest that small differences in our discovered motif could confer specificity for one or more homologous GTF proteins. We offer a free implementation of the MotifCatcher software package athttp://www.bme.ucdavis.edu/facciotti/resources_data/software/.
The evolution of the class A scavenger receptors
Authors: Whelan Fiona J , Meehan Conor J , Golding G Brian , McConkey Brendan J , E Bowdish Dawn M 
Published: November 2012

Abstract

Background
The class A scavenger receptors are a subclass of a diverse family of proteins defined based on their ability to bind modified lipoproteins. The 5 members of this family are strikingly variable in their protein structure and function, raising the question as to whether it is appropriate to group them as a family based on their ligand binding abilities.

Results
To investigate these relationships, we defined the domain architecture of each of the 5 members followed by collecting and annotating class A scavenger receptor mRNA and amino acid sequences from publicly available databases. Phylogenetic analyses, sequence alignments, and permutation tests revealed a common evolutionary ancestry of these proteins, indicating that they form a protein family. We postulate that 4 distinct gene duplication events and subsequent domain fusions, internal repeats, and deletions are responsible for the diverse protein structures and functions of this family. Despite variation in domain structure, there are highly conserved regions across all 5 members, indicating the possibility that these regions may represent key conserved functional motifs.

Conclusions
We have shown with significant evidence that the 5 members of the class A scavenger receptors form a protein family. We have indicated that these receptors have a common origin which may provide insight into future functional work with these proteins.
East African cassava mosaic-like viruses from Africa to Indian ocean islands: molecular diversity, evolutionary history and geographical dissemination of a bipartite begomovirus
Authors: De Bruyn Alexandre , Villemot Julie , Lefeuvre Pierre , Villar Emilie , Hoareau Murielle , Harimalala Mireille , Abdoul-Karime Anli L , Abdou-Chakour Chadhouliati , Reynaud Bernard , Harkins Gordon W , Varsani Arvind , Martin Darren P , Lett Jean-Michel 
Published: November 2012

Abstract

Background
Cassava (Manihot esculenta) is a major food source for over 200 million sub-Saharan Africans. Unfortunately, its cultivation is severely hampered by cassava mosaic disease (CMD). Caused by a complex of bipartite cassava mosaic geminiviruses (CMG) species (Family: Geminivirideae; Genus: Begomovirus) CMD has been widely described throughout Africa and it is apparent that CMG's are expanding their geographical distribution. Determining where and when CMG movements have occurred could help curtail its spread and reveal the ecological and anthropic factors associated with similar viral invasions. We applied Bayesian phylogeographic inference and recombination analyses to available and newly described CMG sequences to reconstruct a plausible history of CMG diversification and migration between Africa and South West Indian Ocean (SWIO) islands.

Results
The isolation and analysis of 114 DNA-A and 41 DNA-B sequences demonstrated the presence of three CMG species circulating in the Comoros and Seychelles archipelagos (East African cassava mosaic virus, EACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV). Phylogeographic analyses suggest that CMG’s presence on these SWIO islands is probably the result of at least four independent introduction events from mainland Africa occurring between 1988 and 2009. Amongst the islands of the Comoros archipelago, two major migration pathways were inferred: One from Grande Comore to Mohéli and the second from Mayotte to Anjouan. While only two recombination events characteristic of SWIO islands isolates were identified, numerous re-assortments events were detected between EACMV and EACMKV, which seem to almost freely interchange their genome components.

Conclusions
Rapid and extensive virus spread within the SWIO islands was demonstrated for three CMG complex species. Strong evolutionary or ecological interaction between CMG species may explain both their propensity to exchange components and the absence of recombination with non-CMG begomoviruses. Our results suggest an important role of anthropic factors in CMGs spread as the principal axes of viral migration correspond with major routes of human movement and commercial trade. Finer-scale temporal analyses of CMGs to precisely scale the relative contributions of human and insect transmission to their movement dynamics will require further extensive sampling in the SWIO region.
Analyses of expressed sequence tags in Neurosporareveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi
Authors: Nygren Kristiina , Wallberg Andreas , Samils Nicklas , Stajich Jason E , Townsend Jeffrey P , Karlsson Magnus , Johannesson Hanna 
Published: November 2012

AbstractBackgroundThe broadly accepted pattern of rapid evolution of reproductive genes is primarily based on studies of animal systems, although several examples of rapidly evolving genes involved in reproduction are found in diverse additional taxa. In fungi, genes involved in mate recognition have been found to evolve rapidly. However, the examples are too few to draw conclusions on a genome scale.ResultsIn this study, we performed microarray hybridizations between RNA from sexual and vegetative tissues of two strains of the heterothallic (self-sterile) filamentous ascomyceteNeurospora intermedia, to identify a set of sex-associated genes in this species. We aligned Expressed Sequence Tags (ESTs) from sexual and vegetative tissue ofN. intermediato orthologs from three closely related species:N. crassa,N. discretaandN. tetrasperma. The resulting four-species alignments provided a dataset for molecular evolutionary analyses. Our results confirm a general pattern of rapid evolution of fungal sex-associated genes, compared to control genes with constitutive expression or a high relative expression during vegetative growth. Among the rapidly evolving sex-associated genes, we identified candidates that could be of importance for mating or fruiting-body development. Analyses of five of these candidate genes from additional species of heterothallicNeurosporarevealed that three of them evolve under positive selection.ConclusionsTaken together, our study represents a novel finding of a genome-wide pattern of rapid evolution of sex-associated genes in the fungal kingdom, and provides a list of candidate genes important for reproductive isolation inNeurospora.