bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and evaluation ofLeishmania infantumrK26 ELISA for serodiagnosis of visceral leishmaniasis in Iran
Authors: FARAJNIA S. , DARBANI B. , BABAEI H. , ALIMOHAMMADIAN M. H. , MAHBOUDI F. , GAVGANI A. M. 
Published: June 2008

SUMMARYThe purpose of this study was to prepare recombinant K26 antigen fromLeishmania infantumand evaluate its performance by enzyme-linked immunosorbent assay (ELISA) test for serodiagnosis of visceral leishmaniasis (VL) in endemic regions of Iran. The results were compared with those obtained by direct agglutination test (DAT) and whole cell ELISA using crude parasite antigen. Of 93 sera from patients with confirmed VL, 90 sera were positive with rK26 ELISA (sensitivity=96·8%), whereas 85 sera were positive with DAT (sensitivity=91·4%) and 89 sera were positive with whole cell ELISA (sensitivity=95·7%). Of 130 subjects who either had other infectious diseases (n=30) or were healthy (n=100), rK26 ELISA were negative in all cases (specificity=100%), whereas DAT were negative in 116 cases (specificity=89·2%) and whole cell ELISA was negative in 114 cases (specificity=87·7%). The results of this study indicate that the rK26 ELISA is more sensitive and specific than conventional methods and could be used for reliable diagnosis of VL caused byLeishmania infantum.
Sex ratio in flea infrapopulations: number of fleas, host gender and host age do not have an effect
Authors: KRASNOV B. R. , SHENBROT G. I. , KHOKHLOVA I. S. , HAWLENA H. , DEGEN A. A. 
Published: June 2008

SUMMARYThis study set out to determine whether the sex ratio of fleas collected from host bodies is a reliable indicator of sex ratio in the entire flea population. To answer this question, previously published data on 18 flea species was used and it was tested to see whether a correlation exists between the sex ratio of fleas collected from host bodies and the sex ratio of fleas collected from host burrows. Across species, the female:male ratio of fleas on hosts correlated strongly with the female:male ratio of fleas in their burrows, with the slope of the regression overlapping 1. Controlling for flea phylogeny by independent contrasts produced similar results. It was also ascertained whether a host individual is a proportional random sampler of male and female fleas and whether the sex ratio in flea infrapopulations depends on the size of infrapopulations and on the gender and age of a host. Using field data, the sex ratio in infrapopulations of 7 flea species parasitic on 4 rodent species was analysed. Populations of 3 species (Nosopsyllus iranus,Parapulex chephrenisandXenopsylla conformis) were significantly female-biased, whereas male bias was found in 1 species (Synosternus cleopatrae). In general, the sex ratio of fleas collected from an individual rodent did not differ significantly from the sex ratio in the entire flea population. Neither host gender, and age nor number of fleas co-occurring on a host affected (a) the sex ratio in flea infrapopulations and (b) the probability of an infrapopulation to be either female- or male-biased.
The struggle between the ‘image of God’ and Satan in theGreek Life of Adam and Eve
Authors: Nir Rivka 
Published: June 2008

AbstractAccording to a tradition in theGreek Life of Adam and Eve(GLAE), Seth and his mother Eve were confronted by a wild beast that attacked Seth. This article asserts that Seth's battle with the beast should be understood as a struggle between the ‘image of God’ and Satan, and viewed in a Christian context. The claim is based on three aspects of the story: how the beast is described, why it attacked Seth and onlyhecould control it, and why the beast was confined to its dwelling place until the Day of Judgement. The struggle between Seth and the beast/Satan should be seen as a link in the chain of struggle between the image of God and Satan. It begins in Paradise between Adam, the image of God, and Satan, as recounted in the story of Satan's fall from heaven, continues on earth between Seth, Adam's descendant, and Satan, and will culminate with the final victory of Jesus, the ultimate image of God, over Satan at the end of times.
Torture and the Christian conscience: a response to Jeremy Waldron
Authors: Porter Jean 
Published: June 2008

AbstractIn remarks offered in 2006 at a conference at Princeton Theological Seminary, inaugurating a National Religious Campaign against Torture, the legal philosopher Jeremy Waldron observed that Christian leaders have contributed relatively little to the recent debate over the use of torture. This is regrettable, in his view, because secular morality does not have resources sufficient to address the question of torture, and a Christian perspective emphasising the absoluteness and divine character of the relevant moral norms would represent an important contribution to our reflections on this question. This article offers a response to Waldron's timely and important challenge, setting forth a Christian theological argument that the practice of torture is categorically prohibited. The basis for this prohibition does not rest, however, on the absoluteness of moral norms as such – rather, it rests on the distinctive character of torture as an egregious assault on the human person regarded as image of God.
Some reflections on the Contextualist approach to ethico-legal texts of the Quran
Authors: Saeed Abdullah 
Published: June 2008

AbstractA “contextualist” reading of the Quran is becoming increasingly popular, particularly among those Muslims referred to as “progressive-ijtihadis”. One of the primary concerns of this reading is that in order to understand and interpret the ethico-legal content of the Quran and relate that content to the changing needs and circumstances of Muslims today, it is important to approach the text at different levels, giving a high degree of emphasis to the socio-historical context of the text. In the classical tafsīr this emphasis on socio-historical context was not considered important, particularly in the interpretation of the ethico-legal texts, despite the frequent use of asbāb al-nuzūl literature. In this paper, I will explore how progressive-ijtihadis are adopting a contextualist reading of ethico-legal texts of the Quran. To illustrate this, I will use one or two such texts (verses) and their interpretations by the progressive-ijtihadis and will seek to demonstrate the contours of this approach, and highlight some of the challenges this approach is facing.
Fish consumption among young overweight European adults and compliance to varying seafood content in four weight loss intervention diets
Authors: Thorsdottir I , Birgisdottir BE , Kiely M , Martinez JA , Bandarra NM 
Published: June 2008

AbstractBackgroundFish is considered an important part of a healthy diet and is frequently recommended as a main course at least twice a week.ObjectiveTo study the frequency of fish consumption among young overweight European adults and their compliance to varying seafood consumption in weight loss intervention diets.DesignAfter meeting the inclusion criteria, the subject’s seafood intake was evaluated. Subjects were randomly assigned into four groups and were advised energy-restricted diets for 8 weeks, including no seafood (control), cod, salmon or fish oil. A validated FFQ was used to evaluate the consumption of seafood at baseline, midpoint and endpoint, and long-chain n-3 fatty acids in blood erythrocytes were measured.SettingIceland, Ireland and Spain.SubjectsThe sample (n 324); 20–40-year-olds with BMI = 27·5–32·5 kg/m2; 85 % participated.ResultsAt baseline, 34 % of the participants reported eating fish at least twice a week as the main course. During the intervention, six participants reported that they did not finish their fish portions, 15 % of the participants consumed small amount of fish additional to the study protocol in weeks 1–4 and 23 % in weeks 5–8 (P = 0·010). Changes in erythrocyte long-chain n-3 fatty acids confirmed good compliance, with increases in the salmon (P < 0·001) and fish oil (P < 0·001) groups, smaller increase in the cod group (P = 0·037) and decrease in the control group (P = 0·030).ConclusionFrequency of fish consumption among 66 % of young European overweight adults is lower than frequently recommended. Compliance to varying seafood consumption was good. Therefore, including more fish in the diet of this group should be encouraged.
High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil
Authors: Sipilä Timo P , Keskinen Anna-Kaisa , Åkerman Marja-Leena , Fortelius Carola , Haahtela Kielo , Yrjälä Kim 
Published: June 2008

Abstract
Genes encoding key enzymes of catabolic pathways can be targeted by DNA fingerprinting to explore genetic degradation potential in pristine and polluted soils. We performed a greenhouse microcosm experiment to elucidate structural and functional bacterial diversity in polyaromatic hydrocarbon (PAH)-polluted soil and to test the suitability of birch (Betula pendula) for remediation. Degradation of PAHs was analysed by high-performance liquid chromatography, DNA isolated from soil amplified and fingerprinted by restriction fragment length polymorphism (RFLP) and terminal restriction fragment length polymorphism (T-RFLP). Bacterial 16S rRNA T-RFLP fingerprinting revealed a high structural bacterial diversity in soil where PAH amendment altered the general community structure as well as the rhizosphere community. Birch augmented extradiol dioxygenase diversity in rhizosphere showing a rhizosphere effect, and further pyrene was more efficiently degraded in planted pots. Degraders of aromatic compounds upon PAH amendment were shown by the changed extradiol ring-cleavage community structure in soil. The RFLP analysis grouped extradiol dioxygenase marker genes into 17 distinct operational taxonomic units displaying novel phylogenetic clusters of ring-cleavage dioxygenases representing putative catabolic pathways, and the peptide sequences contained conserved amino-acid signatures of extradiol dioxygenases. A branch of major environmental TS cluster was identified as being related to Parvibaculum lavantivorans ring-cleavage dioxygenase. The described structural and functional diversity demonstrated a complex interplay of bacteria in PAH pollution. The findings improve our understanding of rhizoremediation and unveil the extent of uncharacterized enzymes and may benefit bioremediation research by facilitating the development of molecular tools to detect and monitor populations involved in degradative processes.
Risk Factors for Methicillin-Resistant Staphylococcus aureus (MRSA) Acquisition in Roommate Contacts of Patients Colonized or Infected With MRSA in an Acute-Care Hospital
Authors: Moore Christine , Dhaliwal Jastej , Tong Agnes , Eden Sarah , Wigston Cindi , Willey Barbara ,   Mount Sinai Hospital Infection Control Team, McGeer Allison 
Published: June 2008

Objective.To identify risk factors for acquisition of methicillin-resistant Staphylococcus aureus (MRSA) in patients exposed to an MRSA-colonized roommate.Design.Retrospective cohort study.Setting.A 472-bed acute-care teaching hospital in Toronto, Canada.Patients.Inpatients who shared a room between 1996 and 2004 with a patient who had unrecognized MRSA colonization.Methods.Exposed roommates were identified from infection-control logs and from results of screening for MRSA in the microbiology database. Completed follow-up was defined as completion of at least 2 sets of screening cultures (swab samples from the nares, the rectum, and skin lesions), with at least 1 set of samples obtained 7–10 days after the last exposure. Chart reviews were performed to compare those who did and did not become colonized with MRSA.Results.Of 326 roommates, 198 (61.7%) had completed follow-up, and 25 (12.6%) acquired MRSA by day 7–10 after exposure was recognized, all with strains indistinguishable by pulsed-field gel electrophoresis from those of their roommate. Two (2%) of 101 patients were not colonized at day 7–10 but, with subsequent testing, were identified as being colonized with the same strain as their roommate (one at day 16 and one at day 18 after exposure). A history of alcohol abuse (odds ratio [OR], 9.8 [95% confidence limits {CLs}, 1.8, 53]), exposure to a patient with nosocomially acquired MRSA (OR, 20 [95% CLs, 2.4,171]), increasing care dependency (OR per activity of daily living, 1.7 [95% CLs, 1.1, 2.7]), and having received levofloxacin (OR, 3.6 [95% CLs, 1.1,12]) were associated with MRSA acquisition.Conclusions.Roommates of patients with MRSA are at significant risk for becoming colonized. Further study is needed of the impact of hospital antimicrobial formulary decisions on the risk of acquisition of MRSA.
Predicting sub-Golgi localization of type II membrane proteins
Authors: van Dijk A. D. J. , Bosch D. , ter Braak C. J. F. , van der Krol A. R. , van Ham R. C. H. J. 
Published: June 2008

AbstractMotivation: Recent research underlines the importance of finegrained knowledge on protein localization. In particular, subcompartmental localization in the Golgi apparatus is important, for example, for the order of reactions performed in glycosylation pathways or the sorting functions of SNAREs, but is currently poorly understood.Results: We assemble a dataset of type II transmembrane proteins with experimentally determined sub-Golgi localizations and use this information to develop a predictor based on the transmembrane domain of these proteins, making use of a dedicated proteinstructure based kernel in an SVM. Various applications demonstrate the power of our approach. In particular, comparison with a large set of glycan structures illustrates the applicability of our predictions on a ‘glycomic’ scale and demonstrates a significant correlation between sub-Golgi localization and the ordering of different steps in glycan biosynthesis.Contact: roeland.vanham@wur.nlSupplementary information: Supplementary data are available at Bioinformatics online.
Predicting functional regulatory polymorphisms
Authors: Torkamani Ali , Schork Nicholas J. 
Published: June 2008

Abstract
Motivation: Limited availability of data has hindered the development of algorithms that can identify functionally meaningful regulatory single nucleotide polymorphisms (rSNPs). Given the large number of common polymorphisms known to reside in the human genome, the identification of functional rSNPs via laboratory assays will be costly and time-consuming. Therefore appropriate bioinformatics strategies for predicting functional rSNPs are necessary. Recent data from the Encyclopedia of DNA Elements (ENCODE) Project has significantly expanded the amount of available functional information relevant to non-coding regions of the genome, and, importantly, led to the conclusion that many functional elements in the human genome are not conserved.
Results: In this article we describe how ENCODE data can be leveraged to probabilistically determine the functional and phenotypic significance of non-coding SNPs (ncSNPs). The method achieves excellent sensitivity (∼80%) and specificity (∼99%) based on a set of known phenotypically relevant and non-functional SNPs. In addition, we show that our method is not overtrained through the use of cross-validation analyses.
Availability: The software platforms used in our analyses are freely available (http://www.cs.waikato.ac.nz/ml/weka/). In addition, we provide the training dataset (Supplementary Table 3), and our predictions (Supplementary Table 6), in the Supplementary Material.
Contact: nschork@scripps.edu.
Supplementary information: Supplementary data are available at Bioinformatics online.
Cross-front variations in adult abundance and recruitment of Patagonian scallop (Zygochlamys patagonica) at the SW Atlantic Shelf Break Front
Authors: Mauna A. Cecilia , Franco Bárbara C. , Baldoni Ana , Acha E. Marcelo , Lasta Mario L. , Iribarne Oscar O. 
Published: June 2008

Abstract
Mauna, A. C., Franco, B. C., Baldoni, A., Acha, E. M., Lasta, M. L., and Iribarne, O. O. 2008. Cross-front variations in adult abundance and recruitment of Patagonian scallop (Zygochlamys patagonica) at the SW Atlantic Shelf Break Front. – ICES Journal of Marine Science, 65: 1184–1190. We studied cross-front variations in adult abundance and recruitment of Patagonian scallop (Zygochlamys patagonica) and their relationship with the Shelf Break Front and satellite-derived chlorophyll a in the Southwest Atlantic between 38°S and 39°30′S. Integrated data from commercial fleets (CF, 1996–2005), research cruises (RC, 1998–2005), sea surface temperature (SST; 1985–1997), and satellite-derived chlorophyll a (CSAT; 1998–2004) were included in the analysis. One-way ANOVA was used to assess differences in recruitment and scallop abundance in a cross-front direction. The abundance of scallops was greatest (RC > 200 kg h−1) closer to the onshore side of the front or beneath it, and the East–West extension of scallop beds (∼40 km) matched the seasonal zonal displacement of the front (∼37 km). The highest CSAT gradients were west of or matched the position of the front. The annual mean position of the front correlated with the spatial variability in recruitment within areas where the species recruited successfully (RC > 2000 h−1). The spatial variability in adult abundance and recruitment of scallops is strongly related to the spatial variability in the position of the front and with the high CSAT concentrations associated with it.
The Molecular Basis of Shoot Responses of Maize Seedlings to Trichoderma harzianum T22 Inoculation of the Root: A Proteomic Approach
Authors: Shoresh Michal , Harman Gary E. 
Published: June 2008

Abstract
Trichoderma spp. are effective biocontrol agents for several soil-borne plant pathogens, and some are also known for their abilities to enhance systemic resistance to plant diseases and overall plant growth. Root colonization with Trichoderma harzianum Rifai strain 22 (T22) induces large changes in the proteome of shoots of maize (Zea mays) seedlings, even though T22 is present only on roots. We chose a proteomic approach to analyze those changes and identify pathways and genes that are involved in these processes. We used two-dimensional gel electrophoresis to identify proteins that are differentially expressed in response to colonization of maize plants with T22. Up- or down-regulated spots were subjected to tryptic digestion followed by identification using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry and nanospray ion-trap tandem mass spectrometry. We identified 91 out of 114 up-regulated and 30 out of 50 down-regulated proteins in the shoots. Classification of these revealed that a large portion of the up-regulated proteins are involved in carbohydrate metabolism and some were photosynthesis or stress related. Increased photosynthesis should have resulted in increased starch accumulation in seedlings and did indeed occur. In addition, numerous proteins induced in response to Trichoderma were those involved in stress and defense responses. Other processes that were up-regulated were amino acid metabolism, cell wall metabolism, and genetic information processing. Conversely, while the proteins involved in the pathways noted above were generally up-regulated, proteins involved in other processes such as secondary metabolism and protein biosynthesis were generally not affected. Up-regulation of carbohydrate metabolism and resistance responses may correspond to the enhanced growth response and induced resistance, respectively, conferred by the Trichoderma inoculation.
Survey of the vectorial competence of ticks in an endemic area of spotted fever group rickettsioses in Fukui Prefecture, Japan
Authors: Ishiguro Fubito , Takada Nobuhiro , Fujita Hiromi , Noji Yoshihiro , Yano Yasuhiro , Iwasaki Hiromichi 
Published: June 2008

ABSTRACTThe prevalence of SFGR in ixodid ticks in the Mt. Arashima‐dake area in the northern part of Fukui Prefecture was surveyed, because of strong suspicions that the first case identified in this Prefecture had become infected withR. helveticain this region. The ticks identified consisted of three genera and six species;I.ovatus, I. persulcatus, I. monospinosus, H. flava, H. japonicaandD. taiwanensis. Of all 222 ticks collected, onlyI. monospinosusticks (8 of 32 examined) were positive for SFGR isolates, which were genetically identified asR. helvetica. Ticks (157 of all 222) positive for SFGR‐DNA fragments consisted ofI. monospinosus(14 of 32),I. persulcatus(11 of 55),I. ovatus(3 of 38),H. flava(5 of 21) andH. japonica(2 of 9). Of these, thirteenI. monospinosus,eightI. persulcatus, threeI. ovatus, twoH. flavaand oneH. japonicawere identified by nucleotide sequences as positive forR. helvetica. DNA fragments from threeH. flavaand oneH. japonicashowed greater homology toR. japonicathan toR. helveticaorR. asiatica.The present results indicate that it is most likely that the vector tick ofR. helveticainfection in Fukui Prefecture isI. monospinosus.
Nucleotide variability and linkage disequilibrium patterns at the porcine FABP5 gene
Authors: Ojeda A. , Estellé J. , Folch J. M. , Pérez‐Enciso M. 
Published: June 2008

Summary Fatty acid binding protein 5 (FABP5) is a major positional and physiological candidate gene for the porcine FAT1 QTL on SSC4. Here we characterize the nucleotide polymorphism and haplotype variability of FABP5 and we compare it with that of FABP4, given their close physical location and similar metabolic roles. DNA resequencing of the FABP5 gene region in 29 pigs from 14 breeds and in European and Japanese wild boars revealed 36 polymorphisms in 5.2 kb, and a nucleotide diversity of 0.19%, comparable to values reported in other domestic species but sixfold lower than that previously found for FABP4. Remarkably, both the nucleotide variability and the haplotype structure of FABP5 and FABP4 were dramatically different, and the Hudson–Kreitman–Aguadé test was highly significant. Nevertheless, both genes also had similarities. The neighbour‐joining trees of their haplotypes did not show a geographical arrangement for any of the genes. Besides, both genes presented a similar extent and pattern of linkage disequilibrium. Haplotype blocks did not extend for large stretches (∼1 kb in both genes), and the number of tag SNPs required to capture all variability was higher than previously expected. Our findings indicate that FABP4 and FABP5 have undergone different selective or evolutive processes. The fact that haplotype blocks were so small may require us to increase the number of SNPs in prospective whole‐genome association studies in the pig.