bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Human Virome in Children and its Relationship to Febrile Illness
Authors: Jaffe David , Muenzer Jared , Storch Gregory , Weinstock George , Sodergren Erica , Wylie Kristine , Arens Max , Buller Richard 
Published: November 2010

AbstractThis study investigates the relationship of viruses to febrile illness in children. Subjects are normal children 2-36 months of age with fever along with normal children of the same age without fever, plus immunocompromised children with fever along with immunocompromised children without fever. Specimens obtained include blood, nasopharyngeal secretions, and feces. Specimens are analyzed using a panel of virus-specific PCR assays and also by high throughput sequencing using 454 and Illumina platforms.
Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires
Authors: Reddy Govardhan , Straub John E. , Thirumalai D. 
Published: November 2010

Amyloid-like fibrils from a number of small peptides that are unrelated by sequence adopt a cross-β-spine in which the two sheets fully interdigitate to create a dry interface. Formation of such a dry interface is usually associated with self-assembly of extended hydrophobic surfaces. Here we investigate how a dry interface is created in the process of protofilament formation in vastly different sequences using two amyloidogenic peptides, one a polar sequence from the N terminus of the yeast prion Sup35 and the other a predominantly hydrophobic sequence from the C terminus of Aβ-peptide. Using molecular dynamics simulations with three force fields we show that spontaneous formation of two ordered one-dimensional water wires in the pore between the two sheets of the Sup35 protofilaments results in long-lived structures, which are stabilized by a network of hydrogen bonds between the water molecules in the wires and the polar side chains in the β-sheet. Upon decreasing the stability of the metastable structures, water molecules are expelled resulting in a helically twisted protofilament in which side chains from a pair of β-strands in each sheet pack perfectly resulting in a dry interface. Although drying in hydrophobically dominated interfaces is abrupt, resembling a liquid to vapor transition, we find that discrete transitions between the liquid to one-dimensional ordered water in the nanopore enclosed by the two β-sheets to dry interface formation characterizes protofilament assembly in the yeast prions. Indeed, as the two sheets of the hydrophobic Aβ-sequence approach each other, fibril formation and expulsion of water molecules occur rapidly and nearly simultaneously.
Contribution of isoprene-derived organosulfates to free tropospheric aerosol mass
Authors: Froyd K. D. , Murphy S. M. , Murphy D. M. , de Gouw J. A. , Eddingsaas N. C. , Wennberg P. O. 
Published: November 2010

Recent laboratory studies have demonstrated that isoprene oxidation products can partition to atmospheric aerosols by reacting with condensed phase sulfuric acid, forming low-volatility organosulfate compounds. We have identified organosulfate compounds in free tropospheric aerosols by single particle mass spectrometry during several airborne field campaigns. One of these organosulfates is identified as the sulfate ester of IEPOX, a second generation oxidation product of isoprene. The patterns of IEPOX sulfate ester in ambient data generally followed the aerosol acidity and NO
x
dependence established by laboratory studies. Detection of the IEPOX sulfate ester was most sensitive using reduced ionization laser power, when it was observed in up to 80% of particles in the tropical free troposphere. Based on laboratory mass calibrations, IEPOX added > 0.4% to tropospheric aerosol mass in the remote tropics and up to 20% in regions downwind of isoprene sources. In the southeastern United States, when acidic aerosol was exposed to fresh isoprene emissions, accumulation of IEPOX increased aerosol mass by up to 3%. The IEPOX sulfate ester is therefore one of the most abundant single organic compounds measured in atmospheric aerosol. Our data show that acidity-dependent IEPOX uptake is a mechanism by which anthropogenic SO
2
and marine dimethyl sulfide emissions generate secondary biogenic aerosol mass throughout the troposphere.
Structure of the 26S proteasome from
Schizosaccharomyces pombe
at subnanometer resolution
Authors: Bohn Stefan , Beck Florian , Sakata Eri , Walzthoeni Thomas , Beck Martin , Aebersold Ruedi , Förster Friedrich , Baumeister Wolfgang , Nickell Stephan 
Published: November 2010

The structure of the 26S proteasome from
Schizosaccharomyces pombe
has been determined to a resolution of 9.1 Å by cryoelectron microscopy and single particle analysis. In addition, chemical cross-linking in conjunction with mass spectrometry has been used to identify numerous residue pairs in close proximity to each other, providing an array of spatial restraints. Taken together these data clarify the topology of the AAA-ATPase module in the 19S regulatory particle and its spatial relationship to the α-ring of the 20S core particle. Image classification and variance analysis reveal a belt of high “activity” surrounding the AAA-ATPase module which is tentatively assigned to the reversible association of proteasome interacting proteins and the conformational heterogeneity among the particles. An integrated model is presented which sheds light on the early steps of protein degradation by the 26S complex.
Prognostic transcriptional association networks: a new supervised approach based on regression trees
Authors: Nepomuceno-Chamorro Isabel , Azuaje Francisco , Devaux Yvan , Nazarov Petr V. , Muller Arnaud , Aguilar-Ruiz Jesús S. , Wagner Daniel R. 
Published: November 2010

Abstract
Motivation: The application of information encoded in molecular networks for prognostic purposes is a crucial objective of systems biomedicine. This approach has not been widely investigated in the cardiovascular research area. Within this area, the prediction of clinical outcomes after suffering a heart attack would represent a significant step forward. We developed a new quantitative prediction-based method for this prognostic problem based on the discovery of clinically relevant transcriptional association networks. This method integrates regression trees and clinical class-specific networks, and can be applied to other clinical domains.
Results: Before analyzing our cardiovascular disease dataset, we tested the usefulness of our approach on a benchmark dataset with control and disease patients. We also compared it to several algorithms to infer transcriptional association networks and classification models. Comparative results provided evidence of the prediction power of our approach. Next, we discovered new models for predicting good and bad outcomes after myocardial infarction. Using blood-derived gene expression data, our models reported areas under the receiver operating characteristic curve above 0.70. Our model could also outperform different techniques based on co-expressed gene modules. We also predicted processes that may represent novel therapeutic targets for heart disease, such as the synthesis of leucine and isoleucine.
Availability: The SATuRNo software is freely available at http://www.lsi.us.es/isanepo/toolsSaturno/.
Contact: inepomuceno@us.es
Supplementary information: Supplementary data are available at Bioinformatics online.
Callose Synthase GSL7 Is Necessary for Normal Phloem Transport and Inflorescence Growth in Arabidopsis
Authors: Barratt D.H. Paul , Kölling Katharina , Graf Alexander , Pike Marilyn , Calder Grant , Findlay Kim , Zeeman Samuel C. , Smith Alison M. 
Published: November 2010

Abstract
One isoform of callose synthase, Glucan Synthase-Like7 (GSL7), is tightly coexpressed with two isoforms of sucrose synthase (SUS5 and SUS6) known to be confined to phloem sieve elements in Arabidopsis (Arabidopsis thaliana). Investigation of the phenotype of gsl7 mutants of Arabidopsis revealed that the sieve plate pores of stems and roots lack the callose lining seen in wild-type plants. Callose synthesis in other tissues of the plant appears to be unaffected. Although gsl7 plants show only minor phenotypic alterations during vegetative growth, flowering stems are reduced in height and all floral parts are smaller than those of wild-type plants. Several lines of evidence suggest that the reduced growth of the inflorescence is a result of carbohydrate starvation. Levels of sucrose, hexoses, and starch are lower in the terminal bud clusters of gsl7 than in those of wild-type plants. Transcript levels of “starvation” genes expressed in response to low sugars are elevated in the terminal bud clusters of gsl7 plants, at the end of the night, and during an extended night. Pulse-chase experiments with 14CO2 show that transport of assimilate in the flowering stem is much slower in gsl7 mutants than in wild-type plants. We suggest that the callose lining of sieve plate pores is essential for normal phloem transport because it confers favorable flow characteristics on the pores.
Second to fourth digit ratios, male genital development and reproductive health: a clinical study among fertile men and testis cancer patients
Authors: Auger J. , Eustache F. 
Published: November 2010

SummarySecond‐ to fourth‐digit length ratio, 2D : 4D, is a marker of testosterone level during foetal life that was found associated with sperm concentration or testosterone levels in some studies, but not in others, a difference possibly related to the way the ratio is assessed. In this study, 2D : 4D was assessed in 122 men partners of pregnant women and in 71 testicular cancer patients using a new method based on direct measurements of finger lengths. In addition, we investigated the association between 2D : 4D, birth weight, testicular volume, semen quality and time to pregnancy. A validation study of the method demonstrated high reliability and reproducibility. Neither digit lengths nor 2D : 4D significantly differed in both groups of men. We found a significant negative association between 2D : 4D and birth weight in testicular cancer patients. In fertile men, 2D : 4D was associated with testicular volume (r = −0.36, p < 0.001), total sperm number (r = −0.18, p = 0.04) and time to pregnancy (r = 0.24, p < 0.02). In addition, participants with a history of epididymal cyst had a significantly higher 2D : 4D than those without cysts. In conclusion, all significant findings indicate that the human male reproductive function is negatively related to 2D : 4D. However, 2D : 4D for testicular cancer patients does not point to a hormonal imbalance during foetal life as the common cause for developing germ‐cell cancer. Such results obtained, thanks to an easy, direct and reliable method for measuring finger lengths, suggest the usefulness of this new tool in fertility studies as well as for studying men with developmental disorders of the reproductive tract.
Experimental and parametric study on drying of green peas in spouted bed
Authors: Ghalavand Younes , Hatamipour Mohammad Sadegh , Rahimi Amir 
Published: November 2010

SummaryDrying of Green Peas (Pisum sativum) was studied experimentally in a lab‐scale spouted bed. Experiments were carried out at different operating conditions, and the effect of inlet air temperature and its flow rate, bed height (initial mass of wet particles) and average diameter of particles were examined on performance of dryer and rate of drying. The obtained experimental results were fitted by an exponential form equation to model the drying kinetic behaviour of green peas in a spouted bed. The fitting parameters are presented in the form of mathematical correlations as a function of operating parameters. As expected, it was found that by increasing inlet air temperature and air‐flow rate, the rate of drying increases, but by increasing the bed height and diameter of particles, the rate of drying decreases. The results can help the design engineers to choose the optimum drying conditions for industrial applications.
Non‐digestible carbohydrates in Brazilian soybean seeds [Glycine max (L.) Merril]
Authors: Jiménez‐Escrig Antonio , Serra Myrian‐Thereza , Rupérez Pilar 
Published: November 2010

SummaryNon‐digestible carbohydrate fraction (NDCF) consists of a range of bioactive compounds that escape digestion in the small intestine. NDCF is mainly composed of dietary fibre (DF) and non‐digestible oligosaccharides (NDO). The objective of this work was to analyse directly and compare the NDCF in two Brazilian cultivars of soybean seed with commercial flour. Brazil is the second major soybean producer in the world. The seed cultivars showed on average a NDCF value of 32.80 g per 100 g dry weight (dw). Regarding DF, insoluble DF (IDF) was the main fraction amounting on average to 98%. Uronic acids were significantly higher than neutral sugar (NS) in IDF and soluble DF (SDF) fractions. There was a considerable amount of Klason lignin – on average 84.14% of DF. Regarding NS profile, mannose was the most important sugar in SDF, whereas galactose and arabinose were predominant in IDF. Stachyose was the main oligosaccharide in NDO. DF and NDO were in the same proportion (94.2:5.8) in tested cultivars. No differences in swelling, water retention, or oil retention capacities between seed cultivars were detected. This study on non‐digestible carbohydrate components in soybean seed gives a different approach to the current nutritional knowledge on protein and oil constituents.
Iron deficiency – is there a role for the food industry?
Authors: Derbyshire Emma , Brennan Charles S. , Li Weili , Bokhari Falahat 
Published: November 2010

SummaryIron deficiency is one of the most common nutritional deficiencies worldwide, in both developing and developed regions. Although the aetiology of iron deficiency and resultant anaemia may be multifaceted, inadequate iron intakes, poor iron absorption and disease status may all be underlying causes. Whilst nutrition and supplement interventions may go some way towards improving iron status in ‘at‐risk’ populations, their efficacy can be questioned. New approaches, including food‐based strategies, may be an alternative means of improving the iron status and health of the public sectors. Economically, food‐based approaches may also be more cost‐effective than iron supplements. This paper aims to discuss how the food industry may play an important role in improving the iron status of public sectors, helping to prevent iron deficiency and need for tablet‐based iron supplements.
Effect of ripening on some physicochemical properties of cooking banana (Musa ABB Cardaba) pulp and flour
Authors: Ayo‐Omogie Helen N. , Adeyemi Isaac A. , Otunola Ezekiel T. 
Published: November 2010

SummaryCardaba banana (Musa ABB) pulp and flours were evaluated for changes in some physicochemical properties during ripening. Compositional changes in the pulp showed that ripening significantly (P < 0.05) increased the crude protein (2.48–9.88%), fat (1.33–4.67%), crude fibre (0.80–0.93%), ash (1.66–2.32%) and Vitamin C (12.60–24.28%), while carbohydrate and tannin reduced. Mineral composition varied, following this trend: K > Mg > P > Na > Zn. pH and ‘whiteness’ reduced, while yield, softness index and pulp/peel ratio increased significantly (P < 0.05). Pasting and functional properties of the flours were lowered, however, ripening enhanced better pasting properties. Flours from stages 1–7 could be used as binders, emulsifiers and thickeners, while flours from stages 5–7 may be useful as aerating agents and in preparation of baby formulas and flours from stages 1–2 may be used in bakery products. This investigation proposes the utilisation of the Cardaba banana flour as an industrial raw material and a good substitute to potato, corn or tapioca starches.
Interrelationships among tocopherols of commercial Runner market type peanuts grown in the United States
Authors: Shin Eui‐Cheol , Pegg Ronald B. , Phillips R. Dixon , Eitenmiller Ronald R. 
Published: November 2010

SummaryCommercially grown US Runner peanuts from 10 cultivars comprising 151 samples over two recent crop years contained 10.54 ± 1.50 mg α‐tocopherol (T)/100 g kernel, 0.31 ± 0.12 β‐T, 10.93 ± 2.04 γ‐T and 0.76 ± 0.31 δ‐T. Box plots revealed segregations in tocopherol levels for normal, mid and high oleic cultivars as well as production years among the cultivars. Correlation coefficients indicated positive relationships between β‐ and γ‐T (r = 0.436,P < 0.001) and γ‐ and δ‐T (r = 0.437,P < 0.001) but no relationship between α‐ and γ‐T (r = −0.032). Principal component analysis of tocopherol contents simplified the data set and revealed two significant principal components (PCs) (PC1 and PC2), which together accounted for 72.6% of the total variance in the data. Eigen analysis of the correlation matrix loadings of the PCs revealed that PC1 was mainly contributed to by α‐, β‐ and δ‐T, whereas PC2 was by γ‐T. This study clearly demonstrates that using a chemometric approach to analyse raw data can provide scientists with more information concerning the variation in peanut cultivars than by simply reporting the means and standard deviations of HPLC results.
Influence of different crop management practices on the nutritional properties and benefits of tomato ‐Lycopersicon esculentumcv Perfectpeel‐
Authors: Durazzo Alessandra , Azzini Elena , Foddai Maria Stella , Nobili Fabio , Garaguso Ivana , Raguzzini Anna , Finotti Enrico , Tisselli Vanni , Del Vecchio Stefania , Piazza Cristina , Perenzin Maurizio , Plizzari Luca , Maiani Giuseppe 
Published: November 2010

SummaryIn this study, we have explored the relationship between the cultivation method and the concentration of major flavonoid aglycones, hydroxycinnamic acids, carotenoids and the total antioxidant activity of tomato (Lycopersicon esculentumcv Perfectpeel); in addition, we have investigated the bioactivity of polyphenol extracts from tomato. The main polyphenols in extracts were quercetin (33.90 ± 6.31 mg kg−1and 17.92 ± 1.09 mg kg−1in conventional and organic extracts), chlorogenic acid (3.52 ± 0.74 mg kg−1and 2.82 ± 0.92 mg kg−1in conventional and organic extracts) and caffeic acid (3.61 ± 0.71 mg kg−1and 3.29 ± 0.33  mg kg−1in conventional and organic extracts). Although statistical differences were found between organic and conventional extracts in several target compounds, no difference in biological effect was observed using cell models. The observed Trans Epithelial Electrical Resistance values were not significantly different between organic and conventional tomato extracts, but we have observed, in both samples, a decrease in tight‐junction permeability at 17 μmof polyphenol concentrations. Antioxidant compounds entering within the cell could exert an antioxidant action, nevertheless at concentrations >17 μmcould have a pro‐oxidant effect.
Immunoaffinity removal and immunoassay for rhodamine B in chilli powder
Authors: Song Shanshan , Lin Fei , Liu Liqiang , Kuang Hua , Wang Libing , Xu Chuanlai 
Published: November 2010

SummaryA rapid and simple immunoassay and a sol–gel‐based immunoaffinity chromatography (IAC) purification method for Rhodamine B (RB) were developed using spiked chilli powder. A polyclonal antibody against RB was generated by immunisation of rabbits with an immunogen hapten. An enzyme‐linked immunosorbent assay (ELISA) was developed that achieved a 50% inhibition (IC50) value of 0.94 ± 0.05 ng mL−1. The limit of detection of the ELISA method was 1 ng g−1 in chilli powder. For the IAC, recovery was 68.1–86.2% at 1 ng g−1 and 72.6–89.3% at 5 ng g−1 in spiked chilli powder. Fortified samples were analysed by high performance liquid chromatography–mass spectrometry (HPLC–MS) after IAC purification, and the results showed a good agreement between the two methods. The ELISA could be a convenient tool for screening RB residue in foods, and the IAC cleanup procedure coupled with HPLC–MS could be an effective alternative method for the determination of RB in various substances.
Effect of hydrothermal processing on colour, antioxidant and free radical scavenging capacities of edible Irish brown seaweeds
Authors: Rajauria Gaurav , Jaiswal Amit K. , Abu‐Ghannam Nissreen , Gupta Shilpi 
Published: November 2010

SummaryThe effect of heat processing on change in colour (ΔE), level of bioactive compounds and overall antioxidant capacity in raw and heat‐processed edible Irish brown seaweeds was investigated. Raw seaweeds were heated at 85–121 °C for 15 min in an autoclave and extracted with 60% methanol. In comparison with raw seaweeds for all the species studied, heating increased total phenol (TPC) (1.6‐ to 1.9‐fold) and total tannin (TTC) (1.3‐ to 2.6‐fold) at 95 °C, while total flavonoid (TFC) (1.6‐ to 3.3‐fold) and total sugar (TSC) (1.9‐ to 4.3‐fold) at 85 °C. Similarly, EC50 value reduced in case of DPPH• scavenging (30.7–51.8%), metal chelating ability (FIC) (27–67.8%) and H2O2 scavenging capacity (13.3–16.1%) at 95 °C, while reduction in lipid peroxidation (10.8–31.5%) observed at 85 °C. Results showed that heating affects content of bioactive compounds as well as beneficial biological activity associated with these compounds, which can suggest new processing for application of seaweeds extract as nutraceutical.
Vitality predicts level of guideline‐concordant care in routine treatment of mood, anxiety and somatoform disorders
Authors: van Fenema Esther M. , van der Wee Nic J.A. , Giltay Erik J. , den Hollander‐Gijsman Margien E. , Zitman Frans G. 
Published: November 2010

AbstractObjective  To examine the clinical and psychosocial correlates of adherence to treatment guidelines among outpatients with common mental disorders in a routine clinical setting.Methods  In this retrospective cohort study, we analysed 192 patients who were treated for a mood, anxiety or somatoform disorder with pharmacotherapy, psychotherapy or a combination of both treatment modalities. Guideline adherence was assessed with a disorder independent set of quality indicators during up to 3 years of follow‐up. At baseline, a standardized diagnostic interview, the Brief Symptom Inventory (BSI), the Short Form 36 (SF‐36) and demographic variables were assessed. Using multivariable regression analysis we identified independent predictors associated with guideline adherence.Results  Patients were aged 36.8 years (SD 11.6) on average. The majority of patients were treated with psychotherapy (47.4%), followed by pharmacotherapy (37.5%) and a combination of pharmacotherapy and psychotherapy (15.1%). Three adherence groups were defined: low (29.7%), intermediate (43.2%) and high (27.1%). Univariate predictors of low adherence were low scores on the subscales vitality and social functioning of the SF‐36. In the multivariable model, low adherence was independently predicted by a score lower than 50 on the subscale vitality of the SF‐36 (odds ratio per 10 units increase in vitality = 1.34, 95% confidence interval: 1.06–1.71). No significant differences were found within socio‐demographic variables, co‐morbidity and the scores on the BSI subscales between the adherence groups.Conclusions  We found that patients with low scores on the vitality subscale of the SF‐36 were at the highest risk to receive low guideline‐concordant care. Understanding factors that affect treatment adherence may help to prevent non‐adherence and increase the quality of care as well as cost‐effectiveness.