bluuebunny/crossref_metadata_2025_split huggingface dataset:
A joint FTIR, FT‐Raman and scaled quantum mechanical study of 1,3‐dibromo‐2,4,5,6‐tetra‐fluoro benzene (DTB) and 1,2,3,4,5‐pentafluoro benzene (PB)
Authors: Krishnakumar V. , Mathammal R. 
Published: March 2009

AbstractThe liquid phase FTIR and FT‐Raman spectra of 1,3‐dibromo‐2,4,5,6‐tetrafluoro benzene (DTB) and 1,2,3,4,5‐pentafluoro benzene (PB) were recorded in the regions 4000–400 cm−1 and 4000–50 cm−1, respectively. The spectra were interpreted with the aid of normal coordinate analysis following full structure opti1mization and force field calculations based on the density functional theory using the standard B3LYP/6‐31G* method and basis set combination. The scaled force field reproduced the experimental wavenumbers of the molecule for DTFB and PFB, respectively. The effects of halogen substituents on the structure and vibrational wavenumbers have been investigated. Assignments of fundamental modes were made based on the comparison between calculated and experimental results. Copyright © 2009 John Wiley & Sons, Ltd.
Effects of soil‐protecting agricultural practices on soil organic carbon and productivity in fruit tree orchards
Authors: Montanaro G. , Celano G. , Dichio B. , Xiloyannis C. 
Published: March 2009

AbstractThis 4‐year on‐farm study reports the effects of different agricultural practices on yield and soil organic carbon (SOC) in kiwifruit and apricot orchards grown in a Mediterranean area. Groups of plants under local orchard management (LOM,§Correction made here after initial publication.
) practices (i.e. soil tillage, removing of pruning residues and mineral fertilisers) were compared with plots under soil‐protecting orchard management (SPOM) actions (i.e. cover crop, no‐tillage, compost application and mulching of pruning residues). In the SPOM blocks fertilisation rate was based on plant demand and irrigation volumes calculated on the evapotranspiration values, while they were empirically calculated in the LOM plots. Results show that yield was 28–50 per cent enhanced by SPOM practices while SOC remained close to the initial values. In comparison with LOM plots, changed practices increased up to 28–90 per cent the amount of P and K, and 13 per cent that of N annually incorporated into soil increasing their reservoir in the soil. The study demonstrates that appropriate land management can increase the mean annual carbon soil inputs from about 1·5 to 9·0 t ha−1 per year. Copyright © 2009 John Wiley & Sons, Ltd.
Proteomic identification of differentially expressed plasma membrane proteins in renal cell carcinoma by stable isotope labelling of a von Hippel‐Lindau transfectant cell line model
Authors: Aggelis Vassilis , Craven Rachel A. , Peng Jianhe , Harnden Patricia , Cairns David A. , Maher Eamonn R. , Tonge Robert , Selby Peter J. , Banks Rosamonde E. 
Published: March 2009

AbstractThe von Hippel‐Lindau (VHL) tumour suppressor gene plays a central role in development of clear cell renal cell carcinoma (RCC). Using a cell line pair generated from the VHL‐defective RCC cell line UMRC2 by transfection with vector control or VHL (−/+VHL) and stable isotope labelling with amino acids in cell culture (SILAC) followed by enrichment of plasma membrane proteins by cell surface biotinylation/avidin‐affinity chromatography and analysis by GeLC‐MS/MS, VHL‐associated changes in plasma membrane proteins were analysed. Comparative analysis of ‐/+VHL cells identified 19 differentially expressed proteins which were confirmed by reciprocal SILAC labelling. These included several proteins previously reported to be VHL targets, such as transferrin receptor 1 and the α3 and β1 integrin subunits and novel findings including upregulation of CD166 and CD147 in VHL‐defective cells. Western blotting confirmed these changes and also revealed VHL‐dependent alterations in protein form for CD147 and CD166, which in the case of CD166 was shown to be due to differential glycosylation. Analysis of patient‐matched normal and malignant renal tissues confirmed these differences were also present in vivo in a subset of clear cell RCCs. These results illustrate the potential of this approach for identifying VHL‐dependent proteins that may be important in tumorigenesis.
Proteomic analysis of human papillomavirus‐related oral squamous cell carcinoma: Identification of thioredoxin and epidermal‐fatty acid binding protein as upregulated protein markers in microdissected tumor tissue
Authors: Melle Christian , Ernst Günther , Winkler Robert , Schimmel Bettina , Klussmann Jens Peter , Wittekindt Claus , Guntinas‐Lichius Orlando , von Eggeling Ferdinand 
Published: March 2009

AbstractHuman papillomavirus (HPV) infection has been identified as an etiologic agent for a subset of oral squamous cell carcinoma (OSCC) with increasing incidence. HPV DNA‐positivity may confer better prognosis but the related oncogenic mechanisms are unknown. For the identification of HPV relevant proteins, we analyzed microdissected cells from HPV DNA‐positive (n = 17) and HPV DNA‐negative (n = 7) OSCC tissue samples. We identified 18 proteins from tumor tissues by peptide fingerprint mapping and SELDI MS that were separated using 2‐DE. Among a number of signals that were detected as significantly different in the protein profiling analysis, we identified thioredoxin (TRX) and epidermal‐fatty acid binding protein as upregulated in HPV related tumor tissue. This study, investigating for the first time proteomic changes in microdissected HPV infected tumor tissue, provides an indication on the oncogenic potential of viruses.
Template‐free protein structure prediction and quality assessment with an all‐atom free‐energy model
Authors: Gopal Srinivasa Murthy , Klenin Konstantin , Wenzel Wolfgang 
Published: March 2009

AbstractBiophysical forcefields have contributed less than originally anticipated to recent progress in protein structure prediction. Here, we have investigated the selectivity of a recently developed all‐atom free‐energy forcefield for protein structure prediction and quality assessment (QA). Using a heuristic method, but excluding homology, we generated decoy‐sets for all targets of the CASP7 protein structure prediction assessment with <150 amino acids. The decoys in each set were then ranked by energy in short relaxation simulations and the best low‐energy cluster was submitted as a prediction. For four of nine template‐free targets, this approach generated high‐ranking predictions within the top 10 models submitted in CASP7 for the respective targets. For these targets, our de‐novo predictions had an average GDT_S score of 42.81, significantly above the average of all groups. The refinement protocol has difficulty for oligomeric targets and when no near‐native decoys are generated in the decoy library. For targets with high‐quality decoy sets the refinement approach was highly selective. Motivated by this observation, we rescored all server submissions up to 200 amino acids using a similar refinement protocol, but using no clustering, in a QA exercise. We found an excellent correlation between the best server models and those with the lowest energy in the forcefield. The free‐energy refinement protocol may thus be an efficient tool for relative QA and protein structure prediction. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Engineering monomeric streptavidin and its ligands with infinite affinity in binding but reversibility in interaction
Authors: Wu Sau‐Ching , Ng Kenneth K.‐S. , Wong Sui‐Lam 
Published: March 2009

AbstractNatural tetrameric streptavidin captures and immobilizes biotinylated molecules with ultra‐tight binding (Kd ∼ 10−13 to 10−14 M). In contrast, engineered monomeric streptavidin offers reversible binding (Kd ∼ 10−7 M). To develop an ideal engineered streptavidin which possesses both the immobilization capability of the natural streptavidin and the reversible interaction reactivity of the monomeric streptavidin, a pair of engineered biomaterials was designed through molecular modeling. This system consists of two recombinant components: an engineered monomeric streptavidin M6, which has a cysteine residue (C118) near the biotin binding site, and a cysteine containing biotinylation tag. Interactions between M6 and the biotinylated peptide tag go through a two‐stage process (capture and immobilization) to generate a covalently linked complex. Biotinylation is essential in the capture stage. Once the biotin moiety in the biotinylated tag is captured by M6, the biotinylated tag can fold back and rotate on the surface of the complex with the biotinylated lysine in the peptide tag as the axis until the formationof a disulfide bond. Consequently, cysteine residue in different positions flanking the biotin residue in the biotinylation tag can successfully form a disulfide bond with M6. Intermolecular disulfide bond formation between M6 and the tag containing protein offers the immobilization capability to M6. In the presence of reducing agent and biotin, bound ligands can be dissociated. This system has the potential to extend the biotin‐streptavidin technology to develop reusable biosensor/protein chips and bioreactors. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Liquid chromatography coupled to quadruple time‐of‐flight tandem mass spectrometry for microcystin analysis in freshwaters: method performances and characterisation of a novel variant of microcystin‐RR
Authors: Ferranti Pasquale , Fabbrocino Serena , Nasi Antonella , Caira Simonetta , Bruno Milena , Serpe Luigi , Gallo Pasquale 
Published: March 2009

AbstractCyanobacteria, also called blue‐green algae, occur worldwide within water blooms in eutrophic lakes and drinking water reservoirs, producing several biotoxins (cyanotoxins). Among these, microcystins (MCs) are a group of cyclic heptapeptides showing potent hepatotoxicity and activity as tumour promoters. So far, at least 89 MCs from different cyanobacteria genera have been characterised. Herein, ion trap, matrix‐assisted laser desorption/ionisation time‐of‐flight (MALDI‐ToF) and quadruple time‐of‐flight (Q‐ToF) mass spectrometry (MS)‐based methods were tested and compared for analysing MCs in freshwaters. Method performances in terms of limit of detection, limit of quantification, mean recoveries, repeatability, and specificity were evaluated. In particular, a liquid chromatography/electrospray ionisation (LC/ESI)‐Q‐ToF‐MS/MS method was firstly described to analyse MCs in freshwaters; this technique is highly selective and sensitive, and allowed us to characterise the molecular structure of an unknown compound. Indeed, the full structural characterisation of a novel microcystin variant from a bloom of Planktothrix rubescens in the Lake Averno, near Naples, was attained by the study of the fragmentation pattern. The new cyanotoxin was identified as the 9‐acetyl‐Adda variant of microcystin‐RR. Copyright © 2009 John Wiley & Sons, Ltd.
Fully automated chip‐based negative mode nanoelectrospray mass spectrometry of fructooligosaccharides produced by heterologously expressed levansucrase from Pseudomonassyringae pv. tomato DC3000
Authors: Visnapuu Triinu , Zamfir Alina D. , Mosoarca Cristina , Stanescu Michaela D. , Alamäe Tiina 
Published: March 2009

AbstractPseudomonas syringae pathovars possess multiple levansucrases with still unclear specific roles for bacteria. We have cloned and expressed three levansucrase genes, lsc1, lsc2 and lsc3, from P. syringae DC3000 in Escherichia coli. Levansucrases synthesize a high molecular weight fructan polymer, levan, from sucrose and in the case of some levansucrases, fructooligosaccharides (FOS) with potential prebiotic effects are also produced. The ability of purified Lsc3 protein of DC3000 to synthesize FOS was tested using prolonged incubation time and varied concentrations of sugar substrates. Thin‐layer chromatography (TLC) analysis of reaction products disclosed formation of FOS from both sucrose and raffinose, revealing a new catalytic property for P. syringae levansucrases. In order to analyze Lsc3‐produced FOS in underivatized form, we optimized a novel method recently introduced in carbohydrate research, based on fully automated chip‐based nanoelectrospray ionization (nanoESI) high‐capacity ion trap mass spectrometry (HCT‐MS). Uding chip‐based nanoESI MS in negative ion mode, FOS, with degrees of polymerization up to five, were detected in reaction mixtures of Lsc3 with sucrose and raffinose. For confirmation, further structural analysis by tandem mass spectrometry (MS/MS) employing collision‐induced dissociation at low energies was performed. To validate the method, commercial inulin‐derived FOS preparations Orafti®P95 and Orafti®Synergy1, which are currently used as prebiotics, were used as controls. By chip‐based nanoESI HCT‐MS, similar FOS distribution was observed in these reference mixtures. Thereby, the obtained data allowed us to postulate that FOS produced by the Lsc3 protein of P. syringae DC3000 may be prebiotic as well. Copyright © 2009 John Wiley & Sons, Ltd.
Ductus venosus Doppler in screening for trisomies 21, 18 and 13 and Turner syndrome at 11–13 weeks of gestation
Authors: Maiz N. , Valencia C. , Kagan K. O. , Wright D. , Nicolaides K. H. 
Published: March 2009

AbstractObjectivesTo investigate the performance of first‐trimester screening for aneuploidies by including assessment of ductus venosus flow in the combined test of maternal age, fetal nuchal translucency thickness, fetal heart rate, and serum free β‐human chorionic gonadotropin and pregnancy‐associated plasma protein‐A.MethodsScreening by the combined test was performed in singleton pregnancies, including 19 614 with euploid fetuses, 122 with trisomy 21, 36 with trisomy 18, 20 with trisomy 13 and eight with Turner syndrome. In all cases the a‐wave in the fetal ductus venosus flow was assessed. We examined the performance of two screening strategies: first, assessment of the a‐wave in all patients and, second, first‐stage screening using the combined test in all patients followed by second‐stage assessment of the a‐wave only in those with an intermediate risk of one in 51 to one in 1000 after the first stageResultsReversed a‐wave was observed in 3.2% of the euploid fetuses, and in 66.4%, 58.3%, 55.0% and 75.0% of fetuses with trisomies 21, 18 and 13 and Turner syndrome, respectively. Inclusion of ductus venosus flow in all pregnancies would detect 96%, 92%, 100% and 100% of trisomies 21, 18 and 13 and Turner syndrome, respectively, at a false‐positive rate of 3%. The same detection rates were achieved with the two‐stage strategy at a false‐positive rate of 2.6%, in which it was necessary to assess the ductus venosus in only 15% of the total population.ConclusionsAssessment of ductus venosus flow improves the performance of first‐trimester screening for aneuploidies. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
Multilevel Community‐Based Culturally Situated Interventions and Community Impact: An Ecological Perspective
Authors: Trickett Edison J. 
Published: March 2009

AbstractThe purpose of this paper is to apply an ecological perspective to the conduct of multilevel community‐based culturally‐situated interventions. After a discussion of the emerging consensus about the value of approaching such interventions ecologically, the paper outlines a series of questions stimulated by an ecological perspective that can guide further theory development in conducting multilevel interventions. These questions all derive from the importance of assessing the local community ecology where the intervention occurs. The paper concludes with a series of topics which, taken together, provide a roadmap for further conceptual development of multilevel interventions as vehicles for long‐range community impact.
A Social Disorganization Perspective on Bullying‐Related Attitudes and Behaviors: The Influence of School Context
Authors: Bradshaw Catherine P. , Sawyer Anne L. , O'Brennan Lindsey M. 
Published: March 2009

AbstractSocial disorganization theory suggests that certain school‐level indictors of disorder may be important predictors of bullying‐related attitudes and behaviors. Multilevel analyses were conducted on bullying‐related attitudes and experiences among 22,178 students in 95 elementary and middle schools. The intraclass correlation coefficients indicated that 0.6–2% of the variance in victimization, 5–10% of the variance in retaliatory attitudes, 5–6% of the variance in perceptions of safety, and 0.9% of the variance in perpetration of bullying was associated with the clustering of students within schools. Although the specific associations varied somewhat for elementary schools as compared to middle schools, the hierarchical linear modeling analyses generally suggested that school‐level indicators of disorder (e.g., student–teacher ratio, concentration of student poverty, suspension rate, and student mobility) were significant predictors of bullying‐related attitudes and experiences. Student‐level characteristics (i.e., sex, ethnicity, status in school) were also relevant to students' retaliatory attitudes, perceptions of safety, and involvement in bullying. Implications for school‐based research and violence prevention are provided.
Optimal waist cutpoint for screening for dysglycaemia and metabolic risk: evidence from a Maori cohort
Authors: Rush Elaine C. , Crook Nic , Simmons David 
Published: March 2009

We sought to identify the sex-specific cut-off in waist circumference which best identifies those with metabolic abnormalities consistent with the metabolic syndrome (MS) among Maori, the indigenous people of New Zealand of Polynesian origin. In 3816 self-identified Maori (2742 women, 1344 men) a 75 g oral glucose tolerance test, fasting lipid, anthropometric and blood pressure measurements were made. MS components were defined by Adult Treatment Panel (ATP) III criteria. Waist cut-off was defined using receiver operating characteristic (ROC) curve analysis to define the presence of at least two of the other MS components ( ≥ 2MS). Prevalence of ≥ 2MS was high (42·1 %). In males and females, waist was as good, or better, a predictor of ≥ 2MS (area under ROC 0·73 women, 0·68 men) as waist:hip ratio (0·66, 0·67), BMI (0·72, 0·68) or percentage body fat (0·70, 0·68). The prediction of dysglycaemia using anthropometric variables followed a similar pattern to ≥ 2MS. Waist circumference to predict ≥ 2MS or dysglycaemia in Maori women and men was 98 cm and 103 cm. Applying this cut-off to the International Diabetes Federation (IDF) criteria would identify 27·8 % (34·0 % males, 25·5 % females) with the MS with an OR for ≥ 2MS (adjusted for sex, smoking and age) of 3·5 (95 % CI 3·1, 4·0). Age >48 years, smoking and being male increased the odds of the MS. These waist cut-offs should be considered in both clinical practice and to optimise the definition of the MS for Maori. The validity of these criteria in other Polynesian groups should be confirmed.
Vitamin D deficiency and insufficiency in pregnant women: a longitudinal study
Authors: Holmes Valerie A. , Barnes Maria S. , Alexander H. Denis , McFaul Peter , Wallace Julie M. W. 
Published: March 2009

Maternal vitamin D insufficiency is associated with childhood rickets and longer-term problems including schizophrenia and type 1 diabetes. Whilst maternal vitamin D insufficiency is common in mothers with highly pigmented skin, little is known about vitamin D status of Caucasian pregnant women. The aim was to investigate vitamin D status in healthy Caucasian pregnant women and a group of age-matched non-pregnant controls living at 54–55°N. In a longitudinal study, plasma 25-hydroxyvitamin D (25(OH)D) was assessed in ninety-nine pregnant women at 12, 20 and 35 weeks of gestation, and in thirty-eight non-pregnant women sampled concurrently. Plasma 25(OH)D concentrations were lower in pregnant women compared to non-pregnant women (P < 0·0001). Of the pregnant women, 35, 44 and 16 % were classified as vitamin D deficient (25(OH)D < 25 nmol/l), and 96, 96 and 75 % were classified as vitamin D insufficient (25(OH)D < 50 nmol/l) at 12, 20 and 35 weeks gestation, respectively. Vitamin D status was higher in pregnant women who reported taking multivitamin supplements at 12 (P < 0·0001), 20 (P = 0·001) and 35 (P = 0·001) weeks gestation than in non-supplement users. Vitamin D insufficiency is evident in pregnant women living at 54–55°N. Women reporting use of vitamin D-containing supplements had higher vitamin D status, however, vitamin D insufficiency was still evident even in the face of supplement use. Given the potential consequences of hypovitaminosis D on health outcomes, vitamin D supplementation, perhaps at higher doses than currently available, is needed to improve maternal vitamin D nutriture.
A gluten-free diet score to evaluate dietary compliance in patients with coeliac disease
Authors: Biagi Federico , Andrealli Alida , Bianchi Paola Ilaria , Marchese Alessandra , Klersy Catherine , Corazza Gino Roberto 
Published: March 2009

A dietary interview performed by expert personnel is considered to be the most appropriate tool to check whether patients with coeliac disease follow a strict gluten-free diet. However, we currently have no straightforward and non-subjective method for performing such a dietary interview. We therefore developed a fast questionnaire based on four simple questions with a five-level score (0–IV). To verify whether our questionnaire is an efficient tool, we applied it to 168 coeliac patients (126 females and 42 males; mean age 42·4 (sd 12·9) years) on a gluten-free diet (median 82, 25th–75th percentile 50–108, range 15–389 months). The score we obtained was compared with the persistence of both villous atrophy and endomysial antibodies while on a gluten-free diet. A comparison with survival of the patients was also performed. Patients were interviewed over the phone by non-expert personnel. The questionnaire was completed in less than 1 min. The lowest results were significantly more frequent among the patients with a persistence of both villous atrophy and positive endomysial antibodies. Death risk was also significantly correlated with the lowest score results. We conclude that our questionnaire is a reliable and simple method of verifying compliance with a gluten-free diet.
Shorn and unshorn Awassi sheep II. Pulse rate
Authors: Eyal E. 
Published: March 2009

1. A comparison was made between the pulse rate of shorn and unshorn sheep maintained in the shade and direct sunlight during the various seasons of the year.2. The variability of the pulse rate during the day generally agreed with the daily changes in body temperature and presumed level of metabolism. Fluctuations were greater in unshorn sheep.3. Pulse rate was lower during summer (60–100 for unshorn and 63–100 for shorn sheep) than in winter (90–130 for unshorn and 90–115 for shorn sheep). It tended to increase with a rise in ambient temperature, especially during winter and spring. A lower pulse rate accompanied a rise in environmental temperature, during summer. The slowest pulse rate of 42 per minute was observed during summer in the hot dry area.4. The pulse rate of both groups increased with a rise in rectal temperature, particularly at low ambient temperatures. At comparable rectal temperatures, a higher average pulse rate was observed in shorn sheep during winter and spring. With elevated summer temperatures, equal pulse rates were noted in both groups of equal rectal temperatures. Since the rectal temperatures of the shorn exceeded that of unshorn sheep, in high environmental temperatures, and in the sun, their pulse rate under these conditions was also higher.5. The differences in pulse rate between the two groups appeared to reflect the combined effects of metabolic rate, body temperature and the vasomotor activity, all of which vary with season and environmental temperatures.