bluuebunny/crossref_metadata_2025_split huggingface dataset:
Space, Time and Mind-Dependence
Authors: Baiasu Sorin 
Published: June 2011

AbstractThe interpretation of Kant's Critical philosophy as a version of traditional idealism has a long history. In spite of Kant's and his commentators’ various attempts to distinguish between traditional and transcendental idealism, his philosophy continues to be construed as committed (whether explicitly or implicitly and whether consistently or inconsistently) to various features usually associated with the traditional idealist project. As a result, most often, the accusation is that his Critical philosophy makes too strong metaphysical and epistemological claims.In his The Revolutionary Kant, Graham Bird engages in a systematic and thorough evaluation of the traditionalist interpretation, as part of perhaps the most comprehensive and compelling defence of a revolutionary reading of Kant's thought. In the third part of this special issue, the exchanges between, on the one hand, Graham Bird and, on the other, Gary Banham, Gordon Brittan, Manfred Kuehn, Adrian Moore and Kenneth Westphal focus on specific aspects of Bird's interpretation of Kant's first Critique. More exactly, the emphasis is on specific aspects of Bird's interpretation of the Introduction, Analytic of Principles and Transcendental Dialectic of Kant's first Critique.The second part of the special issue is devoted to discussions of particular topics in Bird's construal of the remaining significant parts of the first Critique, namely, of the Transcendental Aesthetic and the Analytic of Concepts. Written by Sorin Baiasu and Michelle Grier, these articles examine specific issues in these two remaining parts of the Critique, from the perspective of the debate between the traditionalist and revolutionary interpretation. The special issue begins with an Introduction by the guest co-editors. This provides a summary of the exchanges between Bird and his critics, with a particular focus on the debates stemming from the differences between traditional and revolutionary interpretations of Kant.
Bird on Kant's Mathematical Antinomies
Authors: Moore A. W. 
Published: June 2011

AbstractThe interpretation of Kant's Critical philosophy as a version of traditional idealism has a long history. In spite of Kant's and his commentators’ various attempts to distinguish between traditional and transcendental idealism, his philosophy continues to be construed as committed (whether explicitly or implicitly and whether consistently or inconsistently) to various features usually associated with the traditional idealist project. As a result, most often, the accusation is that his Critical philosophy makes too strong metaphysical and epistemological claims.In hisThe Revolutionary Kant, Graham Bird engages in a systematic and thorough evaluation of the traditionalist interpretation, as part of perhaps the most comprehensive and compelling defence of a revolutionary reading of Kant's thought. In the third part of this special issue, the exchanges between, on the one hand, Graham Bird and, on the other, Gary Banham, Gordon Brittan, Manfred Kuehn, Adrian Moore and Kenneth Westphal focus on specific aspects of Bird's interpretation of Kant's first Critique. More exactly, the emphasis is on specific aspects of Bird's interpretation of the Introduction, Analytic of Principles and Transcendental Dialectic of Kant's first Critique.The second part of the special issue is devoted to discussions of particular topics in Bird's construal of the remaining significant parts of the first Critique, namely, of the Transcendental Aesthetic and the Analytic of Concepts. Written by Sorin Baiasu and Michelle Grier, these articles examine specific issues in these two remaining parts of the Critique, from the perspective of the debate between the traditionalist and revolutionary interpretation. The special issue begins with an Introduction by the guest co-editors. This provides a summary of the exchanges between Bird and his critics, with a particular focus on the debates stemming from the differences between traditional and revolutionary interpretations of Kant.
Identification and isolation of active N2O reducers in rice paddy soil
Authors: Ishii Satoshi , Ohno Hiroki , Tsuboi Masahiro , Otsuka Shigeto , Senoo Keishi 
Published: June 2011

Abstract
Dissolved N2O is occasionally detected in surface and ground water in rice paddy fields, whereas little or no N2O is emitted to the atmosphere above these fields. This indicates the occurrence of N2O reduction in rice paddy fields; however, identity of the N2O reducers is largely unknown. In this study, we employed both culture-dependent and culture-independent approaches to identify N2O reducers in rice paddy soil. In a soil microcosm, N2O and succinate were added as the electron acceptor and donor, respectively, for N2O reduction. For the stable isotope probing (SIP) experiment, 13C-labeled succinate was used to identify succinate-assimilating microbes under N2O-reducing conditions. DNA was extracted 24 h after incubation, and heavy and light DNA fractions were separated by density gradient ultracentrifugation. Denaturing gradient gel electrophoresis and clone library analysis targeting the 16S rRNA and the N2O reductase gene were performed. For culture-dependent analysis, the microbes that elongated under N2O-reducing conditions in the presence of cell-division inhibitors were individually captured by a micromanipulator and transferred to a low-nutrient medium. The N2O-reducing ability of these strains was examined by gas chromatography/mass spectrometry. Results of the SIP analysis suggested that Burkholderiales and Rhodospirillales bacteria dominated the population under N2O-reducing conditions, in contrast to the control sample (soil incubated with only 13C-succinate). Results of the single-cell isolation technique also indicated that the majority of the N2O-reducing strains belonged to the genera Herbaspirillum (Burkholderiales) and Azospirillum (Rhodospirillales). In addition, Herbaspirillum strains reduced N2O faster than Azospirillum strains. These results suggest that Herbaspirillum spp. may have an important role in N2O reduction in rice paddy soils.
Theoretical studies of the tunneling splitting of malonaldehyde using the multiconfiguration time-dependent Hartree approach
Authors: Schröder Markus , Gatti Fabien , Meyer Hans-Dieter 
Published: June 2011

Full dimensional multi-configuration time-dependent Hartree calculations of the zero point energy and the tunneling splitting of malonaldehyde using a recently published potential energy surface [Y. Wang, B. J. Braams, J. M. Bowman, S. Carter, and D. P. Tew, J. Chem. Phys. 128, 224314 (2008)] are reported. The potential energy surface has been approximated by a modified version of the n-mode representation and careful convergence check has been performed to ensure accurate results. The obtained value for the splitting (23.4 cm−1) is in acceptable agreement with the experimental value of 21.583 cm−1. The computed zero-point-energy is 14 670 cm−1 which is lower than previous results of Wang et al., but likely to be about 4 cm−1 too low because of shortcomings of the n-mode representation of the potential. The energies reported in this abstract contain a correction to account for neglected vibrational angular momentum terms.
Single‐Nucleotide Polymorphism (SNP) Loci Correlated with Run Timing in Adult Chinook Salmon from the Columbia River Basin
Authors: Hess Jon E. , Narum Shawn R. 
Published: June 2011

AbstractRun timing in Chinook salmon Oncorhynchus tshawytscha is a life history trait that varies among populations throughout the Columbia River basin and has a demonstrated genetic basis. In this study, we used 92 single‐nucleotide polymorphic (SNP) markers linked to at least 75 different functional genes (including OtsClock1a) to test for correlations with run timing. We obtained samples of adult Chinook salmon on a weekly basis as they passed a fixed point (Bonneville Dam) on the lower Columbia River main stem during the majority of the migratory run from April to October for three sequential years from 2007 to 2009 (n = 2,731, 3,479, and 2,960, respectively). Since these fish represented unknown mixtures of the three major genetic lineages in the Columbia River basin, we used genetic stock identification to assign individuals to their likely stock of origin. We then determined whether allelic variation at the SNP loci was correlated with the date of passage of fish in the context of stock of origin. Nine SNP loci were identified as candidates based on significant correlations with date of passage using the spatial analysis method. A multivariate analysis was then used to rank these eight candidate loci according to the proportion of genetic variation that day of passage explained relative to two other predictor variables: population structure and temperature. The three top‐ranked loci were Ots_TAPBP, Ots_97077–179R, and Ots_myoD‐364, which have known involvement in immunological functioning and muscle differentiation. Future work will test candidate SNPs using run‐timing information from fish of known origin within particular Columbia River subbasins to help validate the role of these genetic linkage groups in this important life history trait.
Place Orientation and Rural–Urban Interdependence
Authors: Castle Emery N. , Wu JunJie , Weber Bruce A. 
Published: June 2011

AbstractAn entire economic system cannot be understood unless there is reliable knowledge about both rural and urban sectors, including their interactions. In particular, there are two anomalies that cannot be rationalized satisfactorily by existing economic theory: the decentralizing economic activities that proceed from the city to the countryside; and the unequal per capita economic rewards between rural and urban people over time. This article presents empirical evidence on the two anomalies, proposes an integrated framework of rural–urban space, discusses the historic interdependence of rural and urban places from the perspective of the integrated framework, and looks at the implications for research and public policy.
Menu-driven cloud computing and resource sharing for R and Bioconductor
Authors: Bolouri Hamid , Dulepet Rajiv , Angerman Michael 
Published: June 2011

Abstract
Summary: We report CRdata.org, a cloud-based, free, open-source web server for running analyses and sharing data and R scripts with others. In addition to using the free, public service, CRdata users can launch their own private Amazon Elastic Computing Cloud (EC2) nodes and store private data and scripts on Amazon's Simple Storage Service (S3) with user-controlled access rights. All CRdata services are provided via point-and-click menus.
Availability and Implementation: CRdata is open-source and free under the permissive MIT License (opensource.org/licenses/mit-license.php). The source code is in Ruby (ruby-lang.org/en/) and available at: github.com/seerdata/crdata.
Contact: hbolouri@fhcrc.org
Enhancing the rate of scaffold discovery with diversity-oriented prioritization
Authors: Swamidass S. Joshua , Calhoun Bradley T. , Bittker Joshua A. , Bodycombe Nicole E. , Clemons Paul A. 
Published: June 2011

Abstract
Motivation: In high-throughput screens (HTS) of small molecules for activity in an in vitro assay, it is common to search for active scaffolds, with at least one example successfully confirmed as an active. The number of active scaffolds better reflects the success of the screen than the number of active molecules. Many existing algorithms for deciding which hits should be sent for confirmatory testing neglect this concern.
Results: We derived a new extension of a recently proposed economic framework, diversity-oriented prioritization (DOP), that aims—by changing which hits are sent for confirmatory testing—to maximize the number of scaffolds with at least one confirmed active. In both retrospective and prospective experiments, DOP accurately predicted the number of scaffold discoveries in a batch of confirmatory experiments, improved the rate of scaffold discovery by 8–17%, and was surprisingly robust to the size of the confirmatory test batches. As an extension of our previously reported economic framework, DOP can be used to decide the optimal number of hits to send for confirmatory testing by iteratively computing the cost of discovering an additional scaffold, the marginal cost of discovery.
Contact: swamidass@wustl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Cephalopods in marine predator diet assessments: why identifying upper and lower beaks is important
Authors: Xavier José C. , Phillips Richard A. , Cherel Yves 
Published: June 2011

AbstractXavier, J. C., Phillips, R. A., and Cherel, Y. 2011. Cephalopods in marine predator diet assessments: why identifying upper and lower beaks is important. – ICES Journal of Marine Science, 68: 1857–1864. Cephalopods are components of the diet of many predators worldwide. They are identified mainly using their chitinized upper and lower beaks, but because it has been assumed that the number of upper and lower beaks would be the same in predator diet samples, more effort has been put into creating keys for the lower beaks, which are more easily identifiable from morphology. A test is made of whether the number of upper and lower beaks differs in diet samples collected from a major cephalopod predator, the wandering albatross (Diomedea exulans), potential biases in the estimation of predator diets are assessed, and upper:lower beak ratios in published studies of other seabirds, seals, whales, and fish from different parts of the world reviewed. The ratio of upper to lower beaks in diet samples from wandering albatrosses varied greatly in a single year (from 69.6% more lower beaks to 59% more upper beaks), and between years (from 0.5 to 32.1% more upper beaks), and biases were greater for certain cephalopod species, resulting in underestimation of their relative importance. Future studies need to consider using both upper and lower beaks to improve the assessment of the contribution of different cephalopods to predator diets.
Phosphorylation of GSK-3β Mediates Intralipid-induced Cardioprotection against Ischemia/Reperfusion Injury
Authors: Rahman Siamak , Li Jingyuan , Bopassa Jean Chrisostome , Umar Soban , Iorga Andrea , Partownavid Parisa , Eghbali Mansoureh 
Published: June 2011

Background
Intralipid (Sigma, St. Louis, MO), a brand name for the first safe fat emulsion for human use, has been shown to be cardioprotective. However, the mechanism of this protection is not known. The authors investigated the molecular mechanism(s) of Intralipid-induced cardioprotection against ischemia/reperfusion injury, particularly the role of glycogen synthase kinase-3β (GSK-3β) and mitochondrial permeability transition pore in this protective action.

Methods
In vivo rat hearts or isolated Langendorff-perfused mouse hearts were subjected to ischemia followed by reperfusion with Intralipid (1% in ex vivo and one bolus of 20% in in vivo) or vehicle. The hemodynamic function, infarct size, threshold for the opening of mitochondrial permeability transition pore, and phosphorylation levels of protein kinase B (Akt)/extracellular signal regulating kinase (ERK)/GSK-3β were measured.

Results
Administration of Intralipid at the onset of reperfusion resulted in approximately 70% reduction in infarct size in the in vivo rat model. Intralipid also significantly improved functional recovery of isolated Langendorff-perfused mouse hearts as the rate pressure product was increased from 2,999 ± 863 mmHg*beats/min in the control group to 13,676 ± 611 mmHg*beats/min (mean±SEM) and the infarct size was markedly smaller (18.3 ± 2.4% vs. 54.8 ± 2.9% in the control group, P < 0.01). The Intralipid-induced cardioprotection was fully abolished by LY294002, a specific inhibitor of PI3K, but only partially by PD98059, a specific ERK inhibitor. Intralipid also increased the phosphorylation levels of Akt/ERK1/glycogen synthase kinase-3β by eightfold, threefold, and ninefold, respectively. The opening of mitochondrial permeability transition pore was inhibited by Intralipid because calcium retention capacity was higher in the Intralipid group (274.3 ± 8.4 nM/mg vs. 168.6 ± 9.6 nM/mg in the control group).

Conclusions
Postischemic treatment with Intralipid inhibits the opening of mitochondiral permeability transition pore and protects the heart through glycogen synthase kinase-3β via PI3K/Akt/ERK pathways.
Evaluation of Stool Collections to Measure Efficacy of PERT in Subjects With Exocrine Pancreatic Insufficiency
Authors: Caras Steve , Boyd David , Zipfel Lisa , Sander‐Struckmeier Suntje 
Published: June 2011

ABSTRACTObjective:The standard measure of pancreatic enzyme replacement therapy (PERT) efficacy in treating exocrine pancreatic insufficiency (EPI) is the coefficient of fat absorption (CFA). CFA measurement involves 72‐hour stool collection, which presents a logistical challenge because, although the test may be performed on an outpatient basis in clinical practice, hospitalization is needed if assurance of complete collection and 100% compliance is required, for example, in controlled situations such as clinical trials. Our aim was to investigate sparse stool sample collection as an alternative to complete 72‐hour collection for measurement of stool fat in subjects with EPI.Subjects and Methods:Prospective data analysis from a previously published, double‐blind, randomized, placebo‐controlled, 2‐period crossover trial in subjects ages 7 to 11 years with EPI caused by cystic fibrosis. Percentage fat (PF) data from sparse stool samples were compared with 72‐hour CFA values as a dichotomous variable (<80%, ≥80%), with evaluation of sensitivity, specificity, and positive predictive value. Area under the curve values were obtained from receiver operating characteristic plots of sensitivity versus 1–specificity.Results:Twelve subjects provided samples for this analysis. Multiple‐sample PF values ≤30% were greatly predictive for CFA values ≥80%, as shown by positive predictive value, sensitivity, and specificity values ≥0.89, with high accuracy (AUCs ≥0.93).Conclusions:Sparse stool sampling for PF analysis appears to be a valid, practical alternative to 72‐hour CFA determination and has potential as a screening tool in clinical practice to identify both suboptimal dosing in subjects with EPI receiving PERT and substantial fat malabsorption in subjects not receiving PERT.
Novel Characterization of Drug‐associated Pancreatitis in Children
Authors: Bai Harrison X. , Ma Michael H. , Orabi Abrahim I. , Park Alexander , Latif Sahibzada U. , Bhandari Vineet , Husain Sohail Z. 
Published: June 2011

ABSTRACTBackground and Objectives:Medications are a major cause of acute pancreatitis; however, little is known about their influence in children. Our primary aims were to identify common comorbidities and concomitant pancreatitis etiologies in children with drug‐associated pancreatitis. Our secondary aims were to identify the most commonly associated drugs in the different age groups, evaluate management practices, and compare drug‐associated cases with non–drug‐associated cases.Patients and Methods:In the present study, we examined children (ages 0–20 years) admitted to Yale‐New Haven Children's Hospital with pancreatitis between 1994 and 2007.Results:Of a total of 271 pediatric cases, drugs were associated with pancreatitis in 25.6% (55). The 3 most common comorbidities in children with drug‐associated pancreatitis were seizure disorders, acute lymphocytic leukemia, and Crohn disease. One third of drug‐associated cases had an additional pancreatitis etiology. The most commonly associated drugs were valproic acid and corticosteroids. Compared with non–drug‐associated cases, children with drug‐associated cases were more likely to undergo CT scanning (54.5% vs 28.4%; P < 0.001), stay in the hospital longer (10 vs 4 days; P < 0.001), and transition to parenteral nutrition from a nil per os status (37.5% vs 21.2%; P < 0.05). There was a higher frequency of valproic acid–associated cases in children younger than 11 years (29.4% vs 9.5% in the 11‐ to 20‐year‐old age group).Conclusions:Our study underscores the importance of considering drugs as a cause and a contributor to pancreatitis in children, particularly valproic acid in young children.
Critical Role for P‐Glycoprotein Expression in Hematopoietic Cells in the FVB.Mdr1a−/− Model of Colitis
Authors: Staley Elizabeth M. , Dimmitt Reed A. , Schoeb Trenton R. , Tanner Scott M. , Lorenz Robin G. 
Published: June 2011

ABSTRACTObjective:P‐glycoprotein (P‐gp), the functional product of the multidrug resistance gene (MDR), is a transmembrane protein that extrudes substrates from the intracellular environment. P‐gp is expressed on the apical surface of epithelial cells and on cells from the hematopoietic lineage. Human MDR polymorphisms have been associated with the increased risk of inflammatory bowel disease, and FVB/N animals deficient in mdr1a expression develop spontaneous colitis. Previous studies using adult bone marrow chimeras indicated that colitis development in this animal model was contingent on P‐gp deficiency in radiation‐resistant epithelial cells; however, the use of adult animals may mask the role of hematopoietic immune cells in colitis initiation, due to preexisting epithelial abnormalities.Subjects and Methods:To assess the importance of P‐gp expression in intestinal epithelial and hematopoietic‐derived cells on colitis induction in FVB.mdr1a−/− animals, we developed a neonatal model of bone marrow reconstitution. FVB/N and FVB.mdr1a−/− adult and neonatal animals were lethally irradiated and reconstituted with bone marrow from FVB/N or FVB.mdr1a−/− donors. Animals were observed for 20 weeks.Results:Adult FVB/N animals deficient in P‐gp expression in hematopoietically derived immune cells developed colitis similar to adult animals deficient in P‐gp expression in radiation‐resistant epithelial/stromal cells. Neonatal animals deficient in P‐gp expression in hematopoietically derived immune cells developed a more histologically significant colitis than those deficient in P‐gp expression in epithelial tissue.Conclusions:The use of a neonatal model of bone marrow reconstitution has revealed a critical role for P‐gp expression in hematopoietically derived immune cells in colitis development in the FVB.mdr1a−/− model.
Value of Information in Nonfocal Colonic Biopsies
Authors: Badizadegan Kamran , Thompson Kimberly M. 
Published: June 2011

ABSTRACTObjectives:Pediatric gastrointestinal (GI) biopsies represent a disproportionately large fraction of the mucosal biopsies submitted for pathology evaluation relative to the fraction of pediatric endoscopies performed. We sought to explore the rationale for this large sample volume and identify its diagnostic value.Patients and Methods:Conceptual value‐of‐information analysis of 100 sequential colonoscopies, including 770 total biopsy specimens. The diagnostic value of each biopsy was evaluated based on its order of appearance in the model and overall contribution to the pathological classification of the disease.Results:Current practice standards for pediatric GI biopsies provide no guidance on sampling strategy for nonfocal biopsy of suspected inflammatory diseases, resulting in the collection of a nonstandardized number of individual samples and sampling sites that may vary significantly by clinician and institution. We find that this practice adds little to no diagnostic value over more cost‐effective protocols, such as a fewer biopsies overall, or fewer specimens with pooled regional biopsies.Conclusions:In the absence of clear guidance, pediatric GI clinicians and institutions should explore alternative strategies such as the left‐right pooled biopsy protocol (common in adult GI practice), or preferably, a more conservative 4‐region protocol covering major anatomical landmarks in the colon for nonfocal pediatric colonic biopsies. This will allow individual practitioners and clinical centers to test the hypothesis, supported by our analysis, that such a reduction in resource utilization will have no measurable impact on the quality of care.