bluuebunny/crossref_metadata_2025_split huggingface dataset:
Statistical geometry based prediction of nonsynonymous SNP functional effects using random forest and neuro‐fuzzy classifiers
Authors: Barenboim Maxim , Masso Majid , Vaisman Iosif I. , Jamison D. Curtis 
Published: January 2008

AbstractThere is substantial interest in methods designed to predict the effect of nonsynonymous single nucleotide polymorphisms (nsSNPs) on protein function, given their potential relationship to heritable diseases. Current state‐of‐the‐art supervised machine learning algorithms, such as random forest (RF), train models that classify single amino acid mutations in proteins as either neutral or deleterious to function. However, it is frequently the case that the functional effect of a polymorphism on a protein resides between these two extremes. The utilization of classifiers that incorporate fuzzy logic provides a natural extension in order to account for the spectrum of possible functional consequences. We generated a dataset of single amino acid substitutions in human proteins having known three‐dimensional structures. Each variant was uniquely represented as a feature vector that included computational geometry and knowledge‐based statistical potential predictors obtained though application of Delaunay tessellation of protein structures. Additional attributes consisted of physicochemical properties of the native and replacement amino acids as well as topological location of the mutated residue position in the solved structure. Classification performance of the RF algorithm was evaluated on a training set consisting of the disease‐associated and neutral nsSNPs taken from our dataset, and attributes were ranked according to their relative importance. Similarly, we evaluated the performance of adaptive neuro‐fuzzy inference system (ANFIS). The utility of statistical geometry predictors was compared with that of traditional structural and evolutionary attributes employed by other researchers, revealing an equally effective yet complementary methodology. Among all attributes in our feature set, the statistical geometry predictors were found to be the most highly ranked. On the basis of the AUC (area under the ROC curve) measure of performance, the ANFIS and RF models were equally effective when only statistical geometry features were utilized. Tenfold cross‐validation studies evaluating AUC, balanced error rate (BER), and Matthew's correlation coefficient (MCC) showed that our RF model was at least comparable with the well‐established methods of SIFT and PolyPhen. The trained RF and ANFIS models were each subsequently used to predict the disease potential of human nsSNPs in our dataset that are currently unclassified (http://rna.gmu.edu/FuzzySnps/). Proteins 2008. © 2008 Wiley‐Liss, Inc.
The temporal pattern of captan residues on apple leaves and fruit under field conditions in relation to weather and canopy structure
Authors: Xu Xiang‐Ming , Murray Roy A , Salazar Jose D , Hyder Kieran 
Published: January 2008

AbstractBACKGROUND: Captan is an important fungicide for controlling diseases in horticultural crops. Understanding its dissipation is important for estimating dietary risks and optimising pesticide application. Field experiments were conducted on apple leaves and fruit to investigate (1) the temporal variability of captan residues, (2) the contribution of several factors to the variability in residues and (3) the relationship between residues and climatic conditions.RESULTS: Initial captan deposits and subsequent residues on fruit and leaves were closer to a lognormal than to a normal distribution. The unit‐to‐unit variation contributed most to the observed variability in the initial deposit and subsequent residues. Variability due to orchards or trees or tree–zone interactions was also frequently important, but there was no discernable trend in the effects. The variability in residues did not appear to decrease over time. Canopy structure affected greatly the initial deposition but had little direct effect on subsequent captan loss. Fruit and leaves on the outside of the tree canopy received more deposit than those on the inside, but these differences gradually decreased over time. Captan loss resulted mainly from the first rainfall after an application.CONCLUSIONS: Captan loss is mainly due to rain, and the loss is negligible under dry conditions. Copyright © 2008 Society of Chemical Industry
Kissper, a kiwi fruit peptide with channel‐like activity: Structural and functional features
Authors: Ciardiello M. Antonietta , Meleleo Daniela , Saviano Gabriella , Crescenzo Roberta , Carratore Vito , Camardella Laura , Gallucci Enrico , Micelli Silvia , Tancredi Teodorico , Picone Delia , Tamburrini Maurizio 
Published: January 2008

AbstractKissper is a 39‐residue peptide isolated from kiwi fruit (Actinidia deliciosa). Its primary structure, elucidated by direct protein sequencing, is identical to the N‐terminal region of kiwellin, a recently reported kiwi fruit allergenic protein, suggesting that kissper derives from the in vivo processing of kiwellin. The peptide does not show high sequence identity with any other polypeptide of known function. However, it displays a pattern of cysteines similar, but not identical, to those observed in some plant and animal proteins, including toxins involved in defence mechanisms. A number of these proteins are also active on mammalian cells. Functional characterization of kissper showed pH‐dependent and voltage‐gated pore‐forming activity, together with anion selectivity and channeling in model synthetic PLMs, made up of POPC and of DOPS:DOPE:POPC. A 2DNMR analysis indicates that in aqueous solution kissper has only short regions of regular secondary structure, without any evident similarity with other bioactive peptides. Comparative analysis of the structural and functional features suggests that kissper is a member of a new class of pore‐forming peptides with potential effects on human health. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
Gas chromatography/mass spectrometry of polychlorinated biphenyls using atmospheric pressure chemical ionization and atmospheric pressure photoionization microchips
Authors: Luosujärvi Laura , Karikko Mika‐Matti , Haapala Markus , Saarela Ville , Huhtala Sami , Franssila Sami , Kostiainen Risto , Kotiaho Tapio , Kauppila Tiina J. 
Published: January 2008

AbstractGas chromatography (GC) and ion trap mass spectrometry (MS) were combined with microchip atmospheric pressure chemical ionization (µAPCI) and microchip atmospheric pressure photoionization (µAPPI) sources. Selected polychlorinated biphenyls (PCBs, IUPAC Nos. 28, 52, 101, 118, 138, 153 and 180) were analyzed by GC/µAPCI‐MS and GC/µAPPI‐MS to demonstrate the applicability of the miniaturized ion sources in negative ion mode analysis. The µAPCI and µAPPI methods were evaluated in respect of detection limit, linearity and repeatability. The detection limits for the PCB congeners were somewhat lower with µAPCI than with µAPPI, whereas µAPPI showed slightly wider linear range and better repeatability. With both methods, the best results were obtained for highly chlorinated or non‐ortho‐chlorinated PCBs, which possess the highest electron affinities. Finally, the suitability of the GC/µAPPI‐MS method for the analysis of PCBs in environmental samples was demonstrated by analyzing soil extracts, and by comparing the results with those obtained by gas chromatography with electron capture detection (GC/ECD). Copyright © 2008 John Wiley & Sons, Ltd.
The application of ITTFA and ARXPS to study the ion beam mixing of metal/Si bilayers
Authors: Palacio C. , Arranz A. 
Published: January 2008

AbstractMetal/silicon interfaces produced by metal thin film deposition on Si substrates have been ion beam mixed using either Ar+ or reactive N2+ low‐energy ion beams. The ion beam mixing (IBM) has been studied by means of ultraviolet photoelectron spectroscopy (UPS), X‐ray photoelectron spectroscopy (XPS), angle resolved XPS (ARXPS) and iterative target testing transformation factor analysis (ITTFA). The IBM using Ar+ is characterized by the formation of metal silicide. For the IBM interfaces using N2+, a fast nitrogen incorporation in the near surface region, followed by a steady state, is observed. Once the saturation is reached, the Me/Si ratio can be varied in a broad range with a nearly constant nitrogen concentration, as a consequence of sputtering, nitruration and mixing effects taking place simultaneously. The comparison of the experimental results with those obtained from TRIDYN simulations that uses pure ballistic mechanisms, suggests that additional rate‐controlling mechanisms, as radiation‐enhanced diffusion processes or the chemical reaction with nitrogen, have to be considered to explain the IBM of Me/Si interfaces by low‐energy Ar+ and N2+ bombardment. Copyright © 2008 John Wiley & Sons, Ltd.
Relative fatigue life estimation of cylindrical hollow rollers in general pure rolling contact
Authors: Abu Jadayil Wisam M. 
Published: January 2008

AbstractSolid and hollow cylindrical rollers in pure rolling contact have been modelled. The two rollers are subjected to a combined normal and tangential loading. The tangential loading is one‐third of the normal loading value. The finite element package, ABAQUS, is used to study the stress distribution and the resulting deformations in the bodies of the rollers. Then the Ioannides–Harris fatigue life model for rolling bearings is applied on the ABAQUS numerical results to investigate the fatigue life of the solid and hollow rollers. Using the fatigue life of the solid rollers as the reference fatigue life, the relative fatigue lives of hollow rollers are determined. Four main different hollowness percentages are been studied: 20, 40, 60 and 80%. The hollowness percentage is the ratio of the diameter of the hole to the outer diameter of the cylinder. For each of those hollowness percentages, two cases are studied – when the two rollers in contact are hollow and when one hollow roller is in contact with a solid roller. This study includes two main models: Model 1, where the two cylindrical rollers in contact are of the same size, and Model 2, where the two rollers in contact are not of the same size. The estimated relative fatigue lives of hollow rollers showed a great improvement of the fatigue life compared with solid rollers under the same loading conditions. This was a result of the redistribution of stresses in the contact zone in the case of hollow rollers. Redistribution of stresses over a larger volume of the roller body decreased the peak stress and reduced the volume under risk. Increasing the hollowness percentage from 20 to 60% increased the flexibility of the roller, and better stress distribution was achieved, which resulted in improving the fatigue life. Although 80% of hollowness rollers have more flexibility than 60% of hollowness rollers, the bending stresses (σb) on the inner surface of the rollers tend to decrease the fatigue life. Copyright © 2007 John Wiley & Sons, Ltd.
Nutrient digestibility and fecal characteristics are different among captive exotic felids fed a beef‐based raw diet
Authors: Vester Brittany M. , Burke Sarah L. , Dikeman Cheryl L. , Simmons Lee G. , Swanson Kelly S. 
Published: January 2008

AbstractNutrient digestibility has not been well characterized in exotic felids. The objective of this experiment was to evaluate differences in nutrient digestibility and fecal characteristics in five large exotic captive felid species, including bobcats, jaguars, cheetahs, Indochinese tigers, and Siberian tigers. All animals were individually housed and adapted to a beef‐based raw diet (Nebraska Brand® Special Beef Feline, North Platte, NE) for 16 d. Total fecal collections were conducted from days 17 to 20. Fecal samples were weighed and scored on collection. Diet and fecal samples were evaluated for dry matter, organic matter, protein, fat, and energy to determine total tract digestibility. Fresh fecal samples were collected to determine fecal pH, ammonia, phenol, indole, short‐chain fatty acid, and branched‐chain fatty acid concentrations. Fecal scores were greater (P<0.01) in Indochinese tigers when compared with all other species, and cheetahs had greater (P<0.01) fecal scores than jaguars and bobcats. Fat digestibility was greater (P<0.01) in Siberian tigers, Indochinese tigers, and bobcats (96%) compared with cheetahs and jaguars (94%). Digestible energy was greater (P<0.05) in bobcats and Indochinese tigers at 93.5 and 92.9%, respectively, compared with cheetahs and jaguars, 91.6%. Fecal pH was greater (P<0.01) in bobcats compared with all other species evaluated. Indole concentrations were greater (P<0.05) in cheetahs and jaguars compared with bobcats and Indochinese tigers. Fecal ammonia concentrations were increased (P<0.05) in cheetahs compared with all other species. The beef‐based raw diet was highly digestible; however, differences in fat and digestible energy suggest that species should be considered when determining caloric needs of exotic felids. Zoo Biol 27:126–136, 2008. © 2008 Wiley‐Liss, Inc.
Alpha‐1 antitrypsin deficiency: A conformational disease associated with lung and liver manifestations
Authors: Greene C. M. , Miller S. D. W. , Carroll T. , McLean C. , O'Mahony M. , Lawless M. W. , O'Neill S. J. , Taggart C. C. , McElvaney N. G. 
Published: January 2008

SummaryAlpha‐1 antitrypsin (A1AT) is a serine anti‐protease produced chiefly by the liver. A1AT deficiency is a genetic disorder characterized by serum levels of less than 11 μmol/L and is associated with liver and lung manifestations. The liver disease, which occurs in up to 15% of A1AT‐deficient individuals, is a result of toxic gain‐of‐function mutations in the A1AT gene, which cause the A1AT protein to fold aberrantly and accumulate in the endoplasmic reticulum of hepatocytes. The lung disease is associated with loss‐of‐function, specifically decreased anti‐protease protection on the airway epithelial surface. The so‐called ‘Z’ mutation in A1AT deficiency encodes a glutamic acid‐to‐lysine substitution at position 342 in A1AT and is the most common A1AT allele associated with disease. Here we review the current understanding of the molecular pathogenesis of A1AT deficiency and the best clinical management protocols.
Male parentage and queen mating frequency in the bumblebee Bombus ignitus (Hymenoptera: bombinae)
Authors: Takahashi Jun‐ichi , Itoh Mitsuru , Shimizu Isamu , Ono Masato 
Published: January 2008

AbstractKin selection theory predicts conflict between queens and workers in the social insect colony with respect to male production. This conflict arises from the haplodiploid system of sex determination in Hymenoptera that creates relatedness asymmetries in which workers are more closely related to the sons of other workers than to those of the queen. In annual hymenopteran societies that are headed by a single queen, the mating frequency of the queen is the only factor that affects the colony kin structure. Therefore, we examined the mating structure of queens and the parentage of males in a monogynous bumblebee, Bombus ignitus, using DNA microsatellites. In the seven colonies that were studied, B. ignitus queens mated once, thereby leading to the prediction of conflict between the queen and workers regarding male production. In each of the five queen‐right colonies, the majority of the males (95%) were produced by the colony's queen. In contrast, workers produced approximately 47% of all the males in two queenless colonies. These results suggest that male production in B. ignitus is a conflict between queen and workers.
Mesenchymal stem cells from human bone marrow or adipose tissue differently modulate mitogen‐stimulated B‐cell immunoglobulin production in vitro
Authors: Bochev Ivan , Elmadjian Gabriel , Kyurkchiev Dobroslav , Tzvetanov Liubomir , Altankova Iskra , Tivchev Peter , Kyurkchiev Stanimir 
Published: January 2008

AbstractMesenchymal stem cells (MSC) have been characterized as multipotent cells which are able to differentiate into several mesodermal and nonmesodermal lineage cells and this feature along with their extensive growth and comprehensive immunomodulatory properties establish them as a promising tool for therapeutic applications, including cell‐based tissue engineering and treatment of immune‐mediated disorders. Although bone marrow (BM) is the most common MSC source, cells with similar characteristics have been shown to be present in several other adult tissues. Adipose tissue (AT), large quantities of which can be easily obtained, represents an attractive alternative to BM in isolating adipose tissue‐derived MSC (AT‐MSC). BM‐MSCs and AT‐MSCs share some immunomodulatory properties as they are both not inherently immunogenic and suppress the proliferation of alloantigen‐ or mitogen‐stimulated T‐cells. Our purpose was to comparatively examine under appropriate in vitro conditions, phenotypes, morphology and some functional properties of BM‐MSCs and AT‐MSCs, such as differentiation potential and especially the ability to suppress the immunoglobulin production by mitogen‐stimulated B‐cells. While the morphological, immunophenotypical, colony‐forming and adipogenic characteristics of both types of cells were almost identical, AT‐MSCs showed less potential for osteogenic differentiation than BM‐MSCs. We found that AT‐MSCs not only inhibited the Ig‐production but also suppressed this B‐cell function to a much greater extent compared to BM‐MSC. This finding supports the potential role of AT‐MSCs as an alternative to BM‐MSCs for clinical purposes.
Chemical detection of the proteins and lipids in the fat body cells from workers of Attini ants (Hymenoptera: Formicidae)
Authors: Roma Gislaine Cristina , Bueno Odair Corrêa , Camargo‐Mathias Maria Izabel 
Published: January 2008

AbstractThe ultrastructural cytochemistry study and the chemical analysis carried out to examine the fat body of workers of the basal Attini Cyphomyrmex rimosus and Mycetarotes parallelus and the derived Acromyrmex disciger and Atta laevigata revealed very electrondense protein granules of varied sizes and shapes distributed throughout the cytoplasm of parietal and perivisceral trophocytes and oenocytes. Lipids were present in the cytoplasm of trophocytes as very electrondense granules. In M. parallelus, A. disciger, and A. laevigata, lipids were present as droplets. In parietal as well as perivisceral oenocytes, lipid granules were very electrondense. In A. laevigata, lipids were present as droplets. The chemical analysis using gas chromatography showed that the main lipid compounds present in trophocytes and oenocytes were saturated (myristic, palmitic, and stearic) and unsaturated fatty acids (oleic and linoleic). Also, in basal species, lipid compounds consisted of mainly saturated fatty acids, while in derived species saturated as well as unsaturated fatty acids were observed.
Effect of small interfering RNAs of cytochrome P450 17α‐hydroxylase/17,20‐lyase (CYP17) on androgen biosynthesis in theca cells
Authors: Du Jing , Liang Xiaoyan , Zeng Haitao , Shu Yimin , Yao Shuzhong , Zhu Bo , Zhuang Guanglun 
Published: January 2008

AbstractPolycystic ovary syndrome (PCOS) is associated with a variety of endocrinologic and metabolic abnormalities, with clinical features of hyperandrogenism and hyperandrogenemia. Cytochrome P450 17α‐hydroxylase/17,20‐lyase (CYP17) is critical in androgen biosynthesis, and CYP17 mRNA expression was proven augmented in PCOS theca cells. To demonstrate whether RNA interference (RNAi) could lower the androgen concentration in theca cells, small interfering RNA (siRNA) targeting the CYP17 gene was co‐cultured with exogenous CYP17 in HeLa cells and endogenous CYP17 of theca cells. CYP17 gene expression was measured by fluorescent microscopy, flow cytometry and real‐time reverse transcription‐polymerase chain reaction analysis. Androstenedione and progesterone concentrations were measured by ELISA. RNAi effectively reduced the expression of exogenous CYP17 in HeLa cells by up to 50%. The CYP17 mRNA and androstenedione production of theca cells were slightly, but not significantly, reduced when compared with non‐specific siRNA.
Reduced thermal hyperalgesia and enhanced peripheral nerve injury after hind paw inflammation in mice lacking the serotonin‐transporter
Authors: Palm Florian , Mössner Rainald , Chen Yong , He Lan , Gerlach Manfred , Bischofs Stefan , Riederer Peter , Lesch Klaus‐Peter , Sommer Claudia 
Published: January 2008

AbstractMice lacking the serotonin‐transporter (5‐HTT‐/‐ mice) develop reduced thermal hyperalgesia after nerve injury, concomitant with reduced serotonin (5‐HT) levels in nervous tissue. Here we investigated pain behaviour in 5‐HTT‐/‐ mice compared to their wild type littermates after hind paw inflammation induced by complete Freund's adjuvant (CFA). We used standard tests for pain behaviour, high performance liquid chromatography for measurement of 5‐HT, and immunohistochemistry of hind paw skin tissue and L5 dorsal root ganglia (DRG) to measure local inflammation and nerve injury. After intraplantar CFA injection, hyperalgesia to heat was attenuated in 5‐HTT‐/‐ mice compared to wild type mice. Their 5‐HT levels in nervous and adrenal tissue were reduced. An intraplantar injection of 5‐HT four days after CFA transiently brought withdrawal latencies of 5‐HTT‐/‐ mice down to the level of wild type mice, thus rescuing the phenotype and supporting the role of 5‐HT in the development of CFA‐induced thermal hyperalgesia. The density of intraepidermal nerve fibres in plantar skin after CFA injection was reduced to a higher degree in 5‐HTT‐/‐ mice than in wild type mice, suggesting greater peripheral nerve injury in the knock‐out mice during hind paw inflammation. Accordingly, a higher number of injured DRG neurons was identified by activating transcription factor 3 (ATF3) staining in 5‐HTT‐/‐ mice after CFA. We conclude that the phenotype of 5‐HTT‐/‐ mice leads to reduced inflammatory pain due to reduced tissue 5‐HT levels and to greater peripheral nerve injury after inflammation. Human variants of the 5‐HTT genotypes might be part of the factors determining the extent of nerve injury and hyperalgesia in inflammation.
Becoming Turk the Rajput Way: Conversion and Identity in an Indian Warrior Narrative
Authors: TALBOT CYNTHIA 
Published: January 2008

AbstractThe Kyamkhanis were a small Indian Muslim community who flourished in northern Rajasthan from c. 1450 to 1730. This article examines memories of the Kyamkhani past recorded in a seventeenth-century history of the ruling lineage, as a case study of both the process of Islamic expansionism in South Asia and the self-identity of rural Muslim gentry. While celebrating the ancestor who had converted to Islam generations earlier, the Kyamkhanis also represented themselves as local warriors of the Rajput class, an affiliation that is considered exclusively Hindu in India today. Their history was written in a local literary language, Braj Bhasa, rather than in the more cosmopolitan Persian that was widely used by Muslim elites at the time. The Kyamkhanis of the early modern era thus negotiated multiple social and cultural spheres, simultaneously participating in the local/vernacular as well as global/cosmopolitan arenas.
In defence of a realist interpretation of theology
Authors: MACDONALD PAUL A. 
Published: January 2008

AbstractIn this essay, I defend theology against a recent argument made by Peter Byrne. According to Byrne, any discipline of thought that can be interpreted realistically shows the accumulation of reliable or widespread belief about the reality it investigates. I challenge this claim, first, by showing how theology, so construed as an exercise of ‘faith seeking understanding’, can and should be interpreted realistically, even if it does not show the accumulation of reliable or widespread belief about divine reality. Second, I give a plausible account of why theology is beset by internal disagreement and division, even if the goal of theological enquiry is to overcome such disagreement and division.