bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seven‐year performance evaluation of a permeable reactive barrier
Authors: Richards Peter 
Published: June 2008

AbstractIn June and July 2001, the Massachusetts Department of Environmental Protection (MassDEP) installed a permeable reactive barrier (PRB) to treat a groundwater plume of chlorinated solvents migrating from an electronics manufacturer in Needham, Massachusetts, toward the Town of Wellesley's Rosemary Valley wellfield. The primary contaminant of concern at the site is trichloroethene (TCE), which at the time had a maximum average concentration of approximately 300 micrograms per liter directly upgradient of the PRB. The PRB is composed of a mix of granular zero‐valent iron (ZVI) filings and sand with a pure‐iron thickness design along its length between 0.5 and 1.7 feet. The PRB was designed to intercept the entire overburden plume; a previous study had indicated that the contaminant flux in the bedrock was negligible. Groundwater samples have been collected from monitoring wells upgradient and downgradient of the PRB on a quarterly basis since installation of the PRB. Inorganic parameters, such as oxidation/reduction potential, dissolved oxygen, and pH, are also measured to determine stabilization during the sampling process. Review of the analytical data indicates that the PRB is significantly reducing TCE concentrations along its length. However, in two discrete locations, TCE concentrations show little decrease in the downgradient monitoring wells, particularly in the deep overburden. Data available for review include the organic and inorganic analytical data, slug test results from nearby bedrock and overburden wells, and upgradient and downgradient groundwater‐level information. These data aid in refining the conceptual site model for the PRB, evaluating its performance, and provide clues as to the reasons for the PRB's underperformance in certain locations. © 2008 Wiley Periodicals, Inc.
Citizen board issues and local newspaper coverage of risk, remediation, and environmental management: Six U.S. nuclear weapons facilities
Authors: Greenberg Michael , Lowrie Karen , Hollander Justin , Burger Joanna , Powers Charles , Gochfeld Michael 
Published: June 2008

AbstractWe examined site‐specific advisory board (SSAB) minutes and local newspaper coverage of the Fernald, Hanford, Idaho, Oak Ridge, Rocky Flats, and Savannah River sites of the U.S. Department of Energy (US DOE) in order to determine the importance of risk‐related issues related to remediation and other forms of environmental management. About one‐third of SSAB issues were risk‐related, and these were disproportionately major issues at meetings. The media focused on risks associated with remediation and other forms of waste management. The analysis implies that contractors and government officials need to establish and maintain communications with advisory panels and accentuate these contacts well in advance of contemplated new actions. © 2008 Wiley Periodicals, Inc.
Identification of pyrene‐degradation pathways: Bench‐scale studies using Pseudomonas fluorescens 29L
Authors: Husain Saleha 
Published: June 2008

AbstractThis article summarizes the bench‐scale studies to identify pyrene‐degradation pathways using an environmental microbial isolate, Pseudomonas fluorescens 29L. Strain 29L was grown on 50 mg of pyrene per liter of mineral medium. At a pyrene biodegradation rate of 14.7 mg/L of medium/day, 82.38 percent of pyrene was degraded in six days. Naphthalene and phenanthrene accounted for 1.09 percent and 3.69 percent, respectively, of the carbon mass from pyrene in the late log phase. Substituted benzene compounds accounted for 26.10 percent of the carbon mass from pyrene in the late log phase. In the stationary phase, carboxylic acids accounted for 10.44 percent of the carbon mass from pyrene. Strain 29L mutants were used for enzyme assays. Pyrene is oxidized by monoxygenases and dioxygenases, and the oxidized ring is cleaved. These enzymes were induced in the presence of pyrene and their activities peaked in the late log phase. No gentisate 1,2‐dioxygenase activity was detected in Strain 29L wild type (WT), whereas mutant M15 did not show any catechol 2,3‐dioxygenase activity. This indicates the possibility of multiple branchings in the pyrene‐biodegradation pathways. In conclusion, multiple degradative pathways are operating concurrently in this strain. The study shows the versatility of Pseudomonas fluorescens Strain 29L for pyrene degradation. It also emphasizes the need to study pyrene‐degradation pathways in other microorganisms so as to enhance the bioremediation potential for the in situ treatment of pyrene‐contaminated sites. © 2008 Wiley Periodicals, Inc.
A PARTICIPATORY APPROACH TO INCREASING PRODUCTIVITY OF MAIZE THROUGH STRIGA HERMONTHICA CONTROL IN NORTHEAST NIGERIA
Authors: KAMARA A. Y. , ELLIS-JONES J. , AMAZA P. , OMOIGUI L. O. , HELSEN J. , DUGJE I. Y. , KAMAI N. , MENKIR A. , WHITE R. W. 
Published: June 2008

SUMMARYStriga hermonthica is a parasitic weed that attacks maize, sorghum and other staple cereal crops and has long been considered one of the greatest biotic constraints to cereal production in Africa. Use of resistant or tolerant maize varieties, a maize–legume rotation using trap crops that stimulate suicidal germination of Striga and the application of nitrogen fertilizer are all effective in reducing infestation and damage. This paper reports on the use of a participatory research and extension approach in assessing the performance and scaling-up of integrated Striga control packages in three agro-ecological zones in Borno State, Nigeria. The participatory process which encourages close interaction between research, extension and farmers, involved 30 local communities and 228 farmers representing 193 farmer groups in identifying their own problems and seeking solutions to them. Results showed not only effective Striga control but productivity increases of over 200%. The involvement of local farmers and groups in the evaluation process, firstly, helped to confirm that Striga control can best be achieved using soyabean followed by Striga-resistant maize together with productivity-increasing management practices and, secondly, promoted farmer-to-farmer extension. A participatory adoption assessment exercise indicated widespread adoption of new varieties and management practices, despite the need for increased labour. Great potential exists to scale out the results to similar areas of Guinea and Sudan savannas in the West Africa region.
THE ROLE OF CATTLE MANURE IN ENHANCING ON-FARM PRODUCTIVITY, MACRO- AND MICRO-NUTRIENT UPTAKE, AND PROFITABILITY OF MAIZE IN THE GUINEA SAVANNA
Authors: FRANKE A. C. , SCHULZ S. , OYEWOLE B. D. , DIELS J. , TOBE O. K. 
Published: June 2008

SUMMARYAn on-farm trial was conducted in the northern Guinea savanna of Nigeria, over a period of five years, with the objectives of quantifying the effects on maize of applying cattle manure in combination with synthetic fertilizer with regard to soil characteristics, yield, plant nutrition and profitability. Maize grain yield was significantly increased by the annual application of cattle manure, compared to maize receiving an equal amount of N through synthetic fertilizer, but only from the third year of the experiment. The application of manure resulted in higher soil Kjel N, Bray-I P and exchangeable K values, and an increased N utilization efficiency by maize, suggesting that yield-limiting factors other than N deficiencies were of lesser importance than in the treatment receiving sole inorganic fertilizer. Nutrients other than N applied via the manure, particularly P, K and/or B, may have contributed to the higher grain yields in treatments receiving manure. A partial budgeting analysis revealed that, over a 5-year period, investments in the application of manure, in combination with synthetic fertilizer, resulted in higher margins than the application of fertilizer alone. However, analyses of marginal rates of return of changes from low urea N to high urea N or additional manure applications suggested that it was more profitable to invest in additional urea than in organic manure in the first two years of the experiment. The results suggested that manure applications, even when applied at relatively high rates, did not serve as a quick fix to on-farm soil fertility problems, but over a longer period, manure applied in combination with synthetic fertilizers did provide a significant and profitable contribution to enhanced cereal production.
The use of virtual reality for training in carotid artery stenting: a construct validation study
Authors: Berry M. , Reznick R. , Lystig T. , Lönn L. 
Published: June 2008

Background: Given that carotid artery stenosis (CAS) intervention is procedurally difficult, possesses an extensive learning curve, and involves a grave list of potential complications, construct validation of new non-clinical training devices is of increasing importance. Purpose: To evaluate the construct validity of the Procedicus-Virtual Interventional Simulator Trainer (Procedicus-VIST) and its use as a training tool. Material and Methods: Sixteen interventionalists (15 males, one female; mean interventional radiology [IR] experience >11 years) and 16 medical students (15 males, one female; no IR experience) received 1 hour of didactic instruction followed by an hour of familiarization training. Subjects then attempted to complete a carotid artery stenting procedure within 1 hour while their performance metrics were recorded. All participants completed a qualitative exit survey of subjective parameters using a visual analog scale. Results: Procedure and fluoroscopic time was 8.7 and 8.7 min greater in the novice group ( P=0.0066 and P=0.0031), respectively. There were no significant differences in performances between the two groups in the remaining metrics of cine loops (number recorded), tool/vessel ratio, coverage percentage, and placement accuracy or residual stenosis. Contrast measurement metrics were found to be too imprecise for statistical analysis. Experienced and novice opinions differed significantly for six of 10 subjective parameters. No statistically significant difference in video-gaming habits was demonstrated. Conclusion: With the exception of the metrics of performance time and fluoroscopic use, construct validity of the Procedicus-VIST carotid metrics were not confirmed. Virtual reality simulation as a training method was valued more by novices than by experienced interventionalists.
Underdiagnosis of vertebral collapse on routine multidetector computed tomography scan of the abdomen
Authors: Obaid H. , Husamaldin Z. , Bhatt R. 
Published: June 2008

Background: Vertebral fractures are commonly associated with osteoporosis and have significant morbidity and mortality rates. Osteoporotic vertebral fractures are presently considered as a treatable and preventable condition, and early detection is vital for further management. The evaluation of vertebral compression on multidetector computed tomography (MDCT) scans of the abdomen has, to our knowledge, not been reported before. Purpose: To assess the prevalence of vertebral collapse on routine abdominal CT scans, and to evaluate the usefulness of the multiplanar reconstruction (MPR) capability of MDCT scans in accurately identifying vertebral abnormalities such as vertebral collapse, spondylolisthesis, and retrolisthesis. Material and Methods: A retrospective review of 307 MDCT scans of the abdomen was carried out at a university teaching hospital. Identifiable patient information was anonymized for data protection. All images were reviewed on a picture archiving and communications system (PACS) using sagittal MPR and bone window for the assessment of the vertebrae. Data were collected from the Computerized Radiology Information System (CRIS). Results: Vertebral collapse was seen in 42 (13.6%) of the 307 patients undergoing routine MDCT of the abdomen. Multilevel and single-level collapses were seen in 24 and 18 patients, respectively. Spondylolisthesis was identified in 5.5% ( n=17), and retrolisthesis was seen in 0.6% ( n=2). All patients with vertebral fracture were older than 50 years. Women were more commonly affected than men. Conclusion: A significant number of patients with vertebral collapse were diagnosed using MPR on MDCT routine scans of the abdomen.
Prevalence of coronary artery intramyocardial course in a large population of clinical patients detected by multislice computed tomography coronary angiography
Authors: De Rosa R. , Sacco M. , Tedeschi C. , Pepe R. , Capogrosso P. , Montemarano E. , Rotondo A. , Runza G. , Midiri M. , Cademartiri F. 
Published: June 2008

Background: Intramyocardial course, an inborn coronary anomaly, is defined as a segment of a major epicardial coronary artery that runs intramurally through the myocardium; in particular, we distinguish myocardial bridging, in which the vessel returns to an epicardial position after the muscle bridge, and intramyocardial course, which is described as a vessel running and ending in the myocardium. Purpose: To evaluate the prevalence of myocardial bridging and intramyocardial course of coronary arteries as defined by multidetector computed tomography (MDCT) angiography. Material and Methods: The study population consisted of 242 consecutive patients (211 men, 31 women; mean age 59±6 years) with atypical chest pain admitted to our hospital between December 2004 and September 2006. All MDCT examinations were performed using a 16-detector-row scanner (Aquilion 16 CFX; Toshiba Medical System, Tokyo, Japan). Patients with heart rate above 65 bpm received 50 mg atenolol orally for 3 days prior to the MDCT scan, or they increased their usual therapy with beta-blockers, in order to obtain a prescan heart rate <60 bpm. Curved multiplanar and 3D volume reconstructions were performed to explore coronary anatomy. Results: In 235 patients, the CT scan was successful and images were appropriate for evaluation. The prevalence of myocardial bridging and intramyocardial course of coronary arteries was 18.7% (47 cases) in our patient population. In 30 segments (63.8%), the vessels ran and ended in the myocardium. In the remaining 17 segments (36.2%), the vessels returned to an epicardial position after the muscle bridge. We found no difference in the prevalence of this inborn coronary anomaly when comparing different clinical characteristics of the study population (sex, age, body-mass index [BMI], etc.). The mean length of the subepicardial artery was 7 mm (range 5–12 mm), and the mean depth in the diastolic phase was 1.9 mm (range 1.2–2.3 mm). There was no significant difference of diameter in these segments between the different R–R phases examined. Conclusion: Our study is in agreement with major angiographic literature reporting a prevalence of myocardial bridging and intramyocardial course between 0.5% and 33%. MDCT technology represents a useful, noninvasive imaging method to assess and evaluate the location, depth, and length of this anatomical variation.
Processing Polarity: How the Ungrammatical Intrudes on the Grammatical
Authors: Vasishth Shravan , Brüssow Sven , Lewis Richard L. , Drenhaus Heiner 
Published: June 2008

AbstractA central question in online human sentence comprehension is, “How are linguistic relations established between different parts of a sentence?” Previous work has shown that this dependency resolution process can be computationally expensive, but the underlying reasons for this are still unclear. This article argues that dependency resolution is mediated by cue‐based retrieval, constrained by independently motivated working memory principles defined in a cognitive architecture. To demonstrate this, this article investigates an unusual instance of dependency resolution, the processing of negative and positive polarity items, and confirms a surprising prediction of the cue‐based retrieval model: Partial‐cue matches—which constitute a kind of similarity‐based interference—can give rise to the intrusion of ungrammatical retrieval candidates, leading to both processing slow‐downs and even errors of judgment that take the form of illusions of grammaticality in patently ungrammatical structures. A notable achievement is that good quantitative fits are achieved without adjusting the key model parameters.
Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence
Authors: Saccone Scott F. , Saccone Nancy L. , Swan Gary E. , Madden Pamela A. F. , Goate Alison M. , Rice John P. , Bierut Laura J. 
Published: June 2008

AbstractMotivation: A challenging problem after a genome-wide association study (GWAS) is to balance the statistical evidence of genotype–phenotype correlation with a priori evidence of biological relevance.Results: We introduce a method for systematically prioritizing single nucleotide polymorphisms (SNPs) for further study after a GWAS. The method combines evidence across multiple domains including statistical evidence of genotype–phenotype correlation, known pathways in the pathologic development of disease, SNP/gene functional properties, comparative genomics, prior evidence of genetic linkage, and linkage disequilibrium. We apply this method to a GWAS of nicotine dependence, and use simulated data to test it on several commercial SNP microarrays.Availability: A comprehensive database of biological prioritization scores for all known SNPs is available at http://zork.wustl.edu/gin. This can be used to prioritize nicotine dependence association studies through a straightforward mathematical formula—no special software is necessary.Contact: ssaccone@wustl.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Megafauna community structure and trophic relationships at the recently discovered Concepción Methane Seep Area, Chile, ∼36°S
Authors: Sellanes J. , Quiroga E. , Neira C. 
Published: June 2008

AbstractSellanes, J., Quiroga, E., and Neira, C. 2008. Megafauna community structure and trophic relationships at the recently discovered Concepción Methane Seep Area, Chile, ∼36°S. – ICES Journal of Marine Science, 65: 1102–1111. The fauna, community composition, and trophic support of the newly discovered Concepción Methane Seep Area (CMSA) are compared with those at a nearby non-seep control. The assemblage of chemosymbiotic bivalves is defined by eight species, including the families Lucinidae, Thyasiridae, Solemyidae, and Vesicomyidae. Seep polychaetes are represented by Lamellibrachia sp. and two commensal species of the vesicomyid Calyptogena gallardoi. Although taxonomic analysis is still under way, most of the chemosymbiotic species seem to be endemics. The CMSA is a hotspot for non-seep benthic megafauna too; 101 taxa were present, but most of them are colonists or vagrants (i.e. not endemics of methane seeps). Isotope analysis supported the belief that non-symbiont-bearing species utilize photosynthetically fixed carbon, because they were isotopically distinct from the chemosymbiotic bivalve species present. It is our opinion that, at this site, which underlies one of the most productive coastal upwelling regions of the world, spatial heterogeneity and the availability of hard substratum, generated by the presence of authigenic carbonate crusts, are more important factors in attracting non-seep fauna than the availability of locally produced chemosynthetic food.
Enzyme Susceptibility of High‐Amylose Starch Precipitated from Sodium Hydroxide Dispersions
Authors: Evans Annette , Thompson Donald B. 
Published: June 2008

ABSTRACTType III resistant starch (RS) is understood to be due to the ordered structure formation in the process of retrogradation. Most treatments of granular high‐amylose maize starch (HAMS) do not completely eliminate the original ordered structure. We hypothesized that residual ordered structure would constrain subsequent physical reassociation of chains and the formation of RS. The objective was to generate differences in enzyme susceptibility using two means of precipitation of fully dispersed starch and to relate differences in enzyme susceptibility to the structure of the precipitates. Dispersions in sodium hydroxide were precipitated either with ethanol or ammonium sulfate. RS and the timecourse of digestion were determined. Crystallinity and helicity were estimated using wide‐angle X‐ray diffraction and solid‐state 13C CP/MAS NMR, respectively. Precipitation of whole starch with ethanol led to lower RS values (≈24%) than precipitation with ammonium sulfate (≈39%) and also to higher reaction rate constants for an early component of digestion. Ethanol precipitation of a branched starch fraction gave essentially no RS, whereas ammonium sulfate precipitation of the same branched material had >20% RS. Ethanol precipitates contained single helices, in most but not all cases, contributing to V‐type crystallinity. Ammonium sulfate precipitates had double helices contributing to B‐type crystallinity.
Chaste: using agile programming techniques to develop computational biology software
Authors: Pitt-Francis Joe , Bernabeu Miguel O , Cooper Jonathan , Garny Alan , Momtahan Lee , Osborne James , Pathmanathan Pras , Rodriguez Blanca , Whiteley Jonathan P , Gavaghan David J 
Published: June 2008

Cardiac modelling is the area of physiome modelling where the available simulation software is perhaps most mature, and it therefore provides an excellent starting point for considering the software requirements for the wider physiome community. In this paper, we will begin by introducing some of the most advanced existing software packages for simulating cardiac electrical activity. We consider the software development methods used in producing codes of this type, and discuss their use of numerical algorithms, relative computational efficiency, usability, robustness and extensibility.
We then go on to describe a class of software development methodologies known as test-driven agile methods and argue that such methods are more suitable for scientific software development than the traditional academic approaches. A case study is a project of our own, Cancer, Heart and Soft Tissue Environment, which is a library of computational biology software that began as an experiment in the use of agile programming methods. We present our experiences with a review of our progress thus far, focusing on the advantages and disadvantages of this new approach compared with the development methods used in some existing packages.
We conclude by considering whether the likely wider needs of the cardiac modelling community are currently being met and suggest that, in order to respond effectively to changing requirements, it is essential that these codes should be more malleable. Such codes will allow for reliable extensions to include both detailed mathematical models—of the heart and other organs—and more efficient numerical techniques that are currently being developed by many research groups worldwide.