bluuebunny/crossref_metadata_2025_split huggingface dataset:
Introducing metallocene into a triazole peptide conjugate reduces its off‐rate and enhances its affinity and antiviral potency for HIV‐1 gp120
Authors: Gopi Hosahudya , Cocklin Simon , Pirrone Vanessa , McFadden Karyn , Tuzer Ferit , Zentner Isaac , Ajith Sandya , Baxter Sabine , Jawanda Navneet , Krebs Fred C. , Chaiken Irwin M. 
Published: May 2008

AbstractIn this work, we identified a high affinity and potency metallocene‐containing triazole peptide conjugate that suppresses the interactions of HIV‐1 envelope gp120 at both its CD4 and co‐receptor binding sites. The ferrocene‐peptide conjugate, HNG‐156, was formed by an on‐resin copper‐catalysed [2 + 3] cycloaddition reaction. Surface plasmon resonance interaction analysis revealed that, compared to a previously reported phenyl‐containing triazole conjugate HNG‐105 (105), peptide 156 had a higher direct binding affinity for several subtypes of HIV‐1 gp120 due mainly to the decreased dissociation rate of the conjugate‐gp120 complex. The ferrocene triazole conjugate bound to gp120 of both clade A (92UG037‐08) and clade B (YU‐2 and SF162) virus subtypes with nanomolar KD in direct binding and inhibited the binding of gp120 to soluble CD4 and to antibodies that bind to HIV‐1YU‐2 gp120 at both the CD4 binding site and CD4‐induced binding sites. HNG‐156 showed a close‐to nanomolar IC50 for inhibiting cell infection by HIV‐1BaL whole virus. The dual receptor site antagonist activity and potency of HNG‐156 make it a promising viral envelope inhibitor lead for developing anti‐HIV‐1 treatments. Copyright © 2008 John Wiley & Sons, Ltd.
Predicting linear B‐cell epitopes using string kernels
Authors: EL‐Manzalawy Yasser , Dobbs Drena , Honavar Vasant 
Published: May 2008

AbstractThe identification and characterization of B‐cell epitopes play an important role in vaccine design, immunodiagnostic tests, and antibody production. Therefore, computational tools for reliably predicting linear B‐cell epitopes are highly desirable. We evaluated Support Vector Machine (SVM) classifiers trained utilizing five different kernel methods using fivefold cross‐validation on a homology‐reduced data set of 701 linear B‐cell epitopes, extracted from Bcipep database, and 701 non‐epitopes, randomly extracted from SwissProt sequences. Based on the results of our computational experiments, we propose BCPred, a novel method for predicting linear B‐cell epitopes using the subsequence kernel. We show that the predictive performance of BCPred (AUC = 0.758) outperforms 11 SVM‐based classifiers developed and evaluated in our experiments as well as our implementation of AAP (AUC = 0.7), a recently proposed method for predicting linear B‐cell epitopes using amino acid pair antigenicity. Furthermore, we compared BCPred with AAP and ABCPred, a method that uses recurrent neural networks, using two data sets of unique B‐cell epitopes that had been previously used to evaluate ABCPred. Analysis of the data sets used and the results of this comparison show that conclusions about the relative performance of different B‐cell epitope prediction methods drawn on the basis of experiments using data sets of unique B‐cell epitopes are likely to yield overly optimistic estimates of performance of evaluated methods. This argues for the use of carefully homology‐reduced data sets in comparing B‐cell epitope prediction methods to avoid misleading conclusions about how different methods compare to each other. Our homology‐reduced data set and implementations of BCPred as well as the APP method are publicly available through our web‐based server, BCPREDS, at: http://ailab.cs.iastate.edu/bcpreds/. Copyright © 2008 John Wiley & Sons, Ltd.
Determination of apparent decomposition threshold energies of lithium adducts of acylglycerols using tandem mass spectrometry and a novel derived effective reaction path length approach
Authors: Ham Bryan M. , Cole Richard B. 
Published: May 2008

AbstractApparent decomposition threshold energies for the fragmentation pathways of lithiated acylglycerols were experimentally determined by collisional activation in a quadrupole‐hexapole‐quadrupole (QhQ) mass spectrometer. A previously developed ‘derived effective reaction path length’ approach for predicting bond dissociation energies (BDEs) of simple dissociations of electrostatic complexes such as alkali metal adducts (Li+), or halide adducts (Cl−) of acylglycerols, was extended to predict covalent bond apparent decomposition threshold energies of lithium adducts of a mono‐acylglycerol, a 1,2‐diacylglycerol, and a 1,3‐diacylglycerol. The ability of the model to treat relatively large ionic systems (e.g. more than 100 atoms) represents a huge advantage of this approach. The model's calculated apparent decomposition threshold energies (Ea) are used in conjunction with the method of energy‐resolved mass spectrometry, employing breakdown graphs, to give a more complete quantitative description of the fragmentation processes. Calculated Ea values allowed ranking of the 1,2‐diacylglycerol as more reactive than the 1,3‐diacylglycerol; the mono‐acylglycerol was ranked the least reactive. The method was applied to the low molecular weight product ions generally associated with the hydrocarbon series CnH2n+1+, where two separate pathways are deduced as contributing to the production of the abundant m/z 81 fragment ion. The favored ranking of the neutral losses of fatty acyl substituents for the 1,2‐diacylglycerol was determined as: loss of lithium fatty acetate > loss of fatty acid > loss of fatty acyl chain as ketene. For the 1,3‐diacylglycerol, the descending order of ease of neutral loss was: loss of fatty acyl ketene > loss of lithium fatty acetate > loss of fatty acid. The results of this study demonstrate that the newly developed method is general in nature, and it can be used for the measurement of covalent bond decomposition threshold energies, as well as for the previously documented electrostatic (noncovalent) bond energies. Copyright © 2008 John Wiley & Sons, Ltd.
Fragmentation patterns of newly isolated cassane butenolide diterpenes and differentiation of stereoisomer by tandem mass spectrometry
Authors: Kanojiya Sanjeev , Yadav Prem P. 
Published: May 2008

AbstractDifferent stereoisomers of active molecules often cause different physiological responses and hence pose a challenge for their identification. This study involves perceptive fragmentation behavior of newly isolated cassane butenolides, caesalpinolide A [1] and caesalpinolide B [2] (epimeric at the hemiketal position) by tandem MS. The electrospray ionization‐mass spectrometry (ESI‐MS)/collision‐induced dissociation (CID; ESI‐MS2 and ESI‐IT‐MSn) were investigated. The effect of orientations of hemiketal hydroxyl at C‐12 was clearly observed in the mass spectrum. Tandem mass spectra of 1, 1A or 2, 2A show stereospecific fragmentation resulting in significant abundance dissimilarity of [MH − H2O]+ as well as differences in fragmentation pathway. Both of these pathways seem to be influenced by the stereochemistry of the molecule. The differentiation can be clearly visualized from the [M + H − H2O]+/[M + H]+ ratio of the two isomers where β‐isomer 2 was found to be five times higher than that of α‐isomer 1 in full scan liquid chromatography‐electrospray ionization mass spectrometry(LC‐ESI‐MS). In high‐energy CID, the mass fingerprint of 1, 2, 1A, and 2A was found to be different from one anothers. Copyright © 2008 John Wiley & Sons, Ltd.
A Green's function‐based method for the transient analysis of plane waves obliquely incident on lossy and dispersive planar layers
Authors: Antonini Giulio 
Published: May 2008

AbstractThis paper presents a new methodology for the transient analysis of plane waves obliquely incident on a planar lossy and dispersive layer. The proposed model is based on the Sturm–Liouville problem associated with the propagation equations. Green's function is calculated in a series form and the open‐end impedance matrix is obtained as the sum of infinite rational functions. This form permits an easy identification of poles and residues. Furthermore, the knowledge of poles leads to the development of a model order reduction technique by selecting only the dominant poles of the system. The pole–residue representation is converted into a state‐space model that can be easily interfaced with ordinary differential equation solvers. The numerical results confirm the effectiveness of the proposed modeling technique. Copyright © 2008 John Wiley & Sons, Ltd.
Composite versus single sampling of spent irrigation water to assess the microbiological status of sprouting mung bean beds
Authors: McEgan Rachel , Lee Susan , Schumacher Bengt , Warriner Keith 
Published: May 2008

AbstractBACKGROUND: Spent irrigation water testing has been recommended in sprouted seed production to detect the presence of pathogens. However, because of the heterogeneous distribution of contamination within batches of sprouted seed, taking single samples of spent irrigation water may return false‐negative results. The following evaluated whether spent irrigation water collected from multiple points provided a more representative assessment of the microbiological status of the sprouting mung bean bed compared to when single samples were taken.RESULTS: Generic Escherichia coli or Aeromonas was recovered in one and 10 of the 160 sprout samples taken from 32 sprouting mung bean batches, respectively. Composite spent irrigation water samples tested positive for generic E. coli on 19 occasions compared to 12 when single samples were taken. Mesophilic Aeromonas was detected in 13 composite spent irrigation water samples which compared to eight single samples. The prevalence of either target bacterium in composite spent irrigation water samples was not significantly (P > 0.05) different compared to when a single sample was collected.CONCLUSIONS: Sampling spent irrigation water from multiple points under sprouting mung bean beds does not significantly increase the probability of detecting contamination, if present. The findings of the study should be considered when devising sampling plans for spent irrigation water testing in bean sprout production. Copyright © 2008 Society of Chemical Industry
Extrusion cooking of barley flour and process parameter optimization by using response surface methodology
Authors: Altan Aylin , McCarthy Kathryn L , Maskan Medeni 
Published: May 2008

AbstractBACKGROUND: The nutritional profile of barley places it in a prime position for development of a new extruded–expanded snack food with health benefits. It was therefore the aim to investigate the effect of extrusion processing variables on system parameters (specific mechanical energy, die pressure and die melt temperature) and physical properties (expansion, bulk density, texture and color) of barley flour extrudates and to optimize processing conditions for production of extruded snack food from barley flour by response surface methodology.RESULTS: Barley flour with 219.7 g kg−1 moisture content was extruded at different die temperatures (140–160 °C) and screw speeds (150–200 rpm) through a co‐rotating twin‐screw extruder. The system parameters as well as product responses were mainly dependent on temperature, whereas the screw speed imparted a lesser effect. Extrudates produced under extrusion conditions of 160 °C, 150 and 200 rpm and at 164 °C and 150 rpm had higher preference levels of appearance, taste, texture and overall acceptability than that of other selected extrudates for sensory analysis. The optimal conditions for minimum bulk density and desired textural characteristics and color of extrudates correspond to a temperature of 156 °C and screw speed of 166 rpm.CONCLUSION: The results suggested that use of barley flour in extruded snack products offers a desirable variation in diet and can take advantage of the nutritional quality of barley. Copyright © 2008 Society of Chemical Industry
Establishing native plants on newly‐constructed and older‐reclaimed sites along West Virginia highways
Authors: Skousen J.G. , Venable C.L. 
Published: May 2008

AbstractMany state highway departments in the USA must use native plants for revegetating roadsides. We conducted two field studies in West Virginia to assess native plant establishment under two different conditions. On newly‐constructed sites, native species were seeded alone or combined with non‐native species. On older roadsides, native species were seeded in disturbed existing vegetation. In the first study, we used four seed mixtures comprised of seeds of native and non‐native species, and two N‐P‐K fertilizer treatments at three newly‐constructed sites. Native, warm‐season grasses were slow to establish and only contributed 25 per cent cover in some plots after three years. Indiangrass (Sorghastrum nutans [L.] Nash), big bluestem (Andropogon gerardii Vitman), Brown‐Eyed Susan (Rudbeckia triloba L.), and wild senna (Cassia hebecarpa Fernald) were the only seeded native species found. Fertilizer at 150 kg ha−1 of 10‐20‐10 showed little influence on increasing plant cover. In the second study, we disturbed three different‐aged established stands of vegetation composed of tall fescue (Festuca arundinacea Screb.) and crownvetch (Coronilla varia L.) by mowing, herbicide, or tillage, and native plants were seeded with and without fertilizer. Native cover was <10 per cent in all plots during the first year, but greatly increased by the second year to as much as 45 per cent in tilled plots, indicating that disturbance was necessary for natives to become important contributors within 2 years. Only switchgrass (Panicum virgatum L.), little bluestem (Andropogon scoparius Vitman), partridge pea (Chamaecrista fasciculate Michx.), and Brown‐Eyed Susan were observed in plots. Fertilizer at 300 kg ha−1 of 10‐20‐10 did not increase native plant cover on these sites. Based on our results, introducing or increasing the cover of native species along roadsides requires (1) reducing competition from non‐native species, and (2) longer time periods for these slower‐establishing species to be observed. Copyright © 2008 John Wiley & Sons, Ltd.
Impacts of land use/cover change on soil properties in the Mediterranean region of northwestern Jordan
Authors: Khresat Sa'eb , Al‐Bakri Jawad , Al‐Tahhan Ragheb 
Published: May 2008

AbstractThis study was carried out to evaluate the effects of deforestation on physical and chemical properties of soils under native forest in the Mediterranean region of northwestern Jordan. Land use/cover maps of 1953, 1978 and 2002 were interpreted and analysed within GIS to quantify the shift from forest to rainfed cultivation. Six sites were sampled in a non‐changed forest and in cultivated fields, three for each. Different soil properties of texture, bulk density, organic matter, total nitrogen, pH, cation exchange capacity (CEC), phosphorous and potassium were analysed. Results showed that many forests were changed into cultivated lands at a rate more than the reforestation. Subsequently, adverse effects on the studied physical and chemical properties were observed. The most affected properties were particle size distribution, bulk density of surface soil and subsoil. Organic matter and CEC decreased in cultivated soil as compared to the forest soil. Cultivated soils were found to exhibit a significantly lower status in physical and chemical soil properties as compared to forest soils. This general decline in the soil physical and chemical properties, in turn, contributed to soil erosion, reduction of soil fertility and land degradation.There is an urgent need to improve soil quality by developing sustainable land use practices to reduce the rate of soil degradation and to ensure long‐term sustainability of the farming system in the study area and in similar biophysical settings. Copyright © 2008 John Wiley & Sons, Ltd.
Soil microbiochemical properties as indicators for success of heathland restoration after military disturbance
Authors: Heitkamp F. , Glatzel S. , Michalzik B. , Fischer E. , Gerold G. 
Published: May 2008

AbstractDecline of heathlands in Central Europe raises the question of successful restoration of degraded heathlands. We examined the impact of different restoration techniques on soil microbial biomass carbon (Cmic) and nitrogen (Nmic) and enzyme activity on an abandoned military training site in the Lüneburger Heaths. The aim was to determine which technique resulted in typical heathland soil conditions. The training site was in use for about 50 years. Vegetation and soils were degraded in large areas. Restoration actions were: (1) spreading of heath plaggen (sods, containing the organic layer and a few centimetres mineral soil), (2) spreading of heath plaggen and grass seeds (Festuca filiformis Pourr.), (3) spreading of F. filiformis‐seeds and (4) succession (episodical tree removal). Ten years after restoration, we measured pH, bulk density, abundance of roots, soil organic carbon (SOC), nitrogen (Nt), phosphorus (Pt), Cmic, Nmic and acid phosphatase activity (AcP) in the first 10 cm of the mineral soil. Four restoration treatments were compared with one reference site. The reference site is heathland located near the training site, where no military actions took place.At all disturbed sites, bulk density and pH proved to be higher than on the reference site. Relative to the reference site, SOC storage reached from 37 to 91 per cent, regeneration of Nt was slightly lower. In contrast to the advanced development of SOC and Nt, the regeneration of Cmic and Nmic was much lower (15–44 per cent). The succession site showed a low pool of SOC, Nt, Cmic and Nmic, but microbial ratios indicated a less disturbed C‐ and N‐cycle. AcP pronounced differences in nutrient demand between disturbed sites and reference. On this base, recommendations for restoration management were given. Copyright © 2008 John Wiley & Sons, Ltd.
Social and ecological trade offs in combating land degradation: the case of invasion by a woody shrub (Euryops Floribundus) at Macubeni, South Africa
Authors: Shackleton C. M. , Gambiza J. 
Published: May 2008

AbstractWoody plant invasions, either of alien or indigenous species, are deemed to result in loss of ecosystem goods and services in many areas throughout the world, resulting in significant degradation and economic costs. Invasion of Euryops floribundus, a species indigenous to South Africa, is perceived to have reduced the grazing available for domestic livestock. Consequently, a programme of manual eradication has been implemented to improve the grazing resource and provide jobs for poverty alleviation. However, there is potential for a conflict of interest as our study shows that almost all households rely on Euryops for fuel and at times fencing material, whereas only a minority of households own livestock. Moreover, comparison of invaded and non‐invaded sites indicated that the invaded sites harbour greater plant species richness and higher grass culm density per unit area of grass cover, as well as higher forb and litter cover. While invaded sites had lower grass cover, overall plant cover was no different between invaded and non‐invaded sites. Multivariate analysis indicated no obvious differentiation in community composition between invaded and non‐invaded areas, suggesting stronger drivers of community composition other than Euryops invasion presumed to be facilitated by the effects of high livestock densities. Overall, our study suggests that the clearing operation may well benefit from a better understanding of the social needs, perceptions of degradation by the various stakeholders and ecological dynamics of the area, especially local reliance on the resources, and the dynamics of the invasion, particularly its extent, rate of spread and susceptibility for re‐invasion in the cleared areas. Copyright © 2008 John Wiley & Sons, Ltd.
Soil microbial biomass C and N changes in relation to forest conversion in the Northwestern Turkey
Authors: Kara Ö. , Bolat İ. 
Published: May 2008

AbstractTree species differ in their effect on soil development and nutrient cycling. Conversion of beech coppice to pine plantations can alter soil physical and chemical properties, which in turn may have significant impacts on soil microbial biomass C and N (Cmic, Nmic). The major objective of this study was to evaluate soil quality changes associated with the forest conversion in humid NW Turkey. Results from this study showed that levels of soil organic carbon (Corg), total nitrogen (Nt), moisture, Cmic and Nmic under beech coppice were consistently higher but levels of pH, CaCO3 and EC were lower compared to pine plantation. Differences between the forest stands in Cmic and Nmic were mainly related to the size of the Corg stores in soil and to tree species. In addition, high level of CaCO3 is likely to reduce pools of soil organic C and possibly even microbial biomass C and N in pine forests. The average Cmic:Nmic ratios were higher in soils under beech coppice than pine plantation, while Cmic:Corg and Nmic:Nt percentages were similar in both forest types. These results revealed the differences in microbial community structure associated with different tree species and the complex interrelationships between microbial biomass, soil characteristics, litter quantity and quality. Copyright © 2008 John Wiley & Sons, Ltd.
Insights into virus capsid assembly from non‐covalent mass spectrometry
Authors: Morton Victoria L. , Stockley Peter G. , Stonehouse Nicola J. , Ashcroft Alison E. 
Published: May 2008

AbstractThe assembly of viral proteins into a range of macromolecular complexes of strictly defined architecture is one of Nature's wonders. Unraveling the details of these complex structures and the associated self‐assembly pathways that lead to their efficient and precise construction will play an important role in the development of anti‐viral therapeutics. It will also be important in bio‐nanotechnology where there is a plethora of applications for such well‐defined macromolecular complexes, including cell‐specific drug delivery and as substrates for the formation of novel materials with unique electrical and magnetic properties. Mass spectrometry has the ability not only to measure masses accurately but also to provide vital details regarding the composition and stoichiometry of intact, non‐covalently bound macromolecular complexes under near‐physiological conditions. It is thus ideal for exploring the assembly and function of viruses. Over the past decade or so, significant advances have been made in this field, and these advances are summarized in this review, which covers the literature up to the end of 2007. © 2008 Wiley Periodicals, Inc., Mass Spec Rev 27: 575–595, 2008