bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization and evaluation of olive germplasm in southern Italy
Authors: Di Vaio Claudio , Nocerino Sabrina , Paduano Antonello , Sacchi Raffaele 
Published: January 2013

AbstractBackgroundThe southern Italian region of Campania has suitable pedo‐climatic conditions and a large varietal heritage able to produce oils with high typicality. The aim of this study was to characterize 20 cultivars belonging to Campania's olive germplasm, evaluating their vegetative and production aspects and their oil quality characteristics. The study was conducted from 2003 to 2009, observing the following aspects in six plants per variety: entry into production, vigour, ripening and drupe oil content. The following analyses were carried out on monovarietal oils, obtained by microextractor: acid composition, polyphenol content and aromatic profile.ResultsThe agronomic results showed early entry into production for the cultivars Racioppella, Ortolana, Biancolilla and Carpellese. However, entry into production was delayed for Ritonnella, Ortice, Cornia and Rotondella. As regards vegetative behaviour, Asprinia, from the province of Caserta and Pisciottana and Carpellese, from the province of Salerno, proved the most vigorous cultivars.ConclusionGroups of similar cultivars emerged from chemical and sensory analysis of their oils, while other accessions were well characterized and separated from each other, showing a high level of diversity and specificity. © 2013 Society of Chemical Industry
Wheat bread biofortification with rootlets, a malting by‐product
Authors: Waters Deborah M , Kingston Wilma , Jacob Fritz , Titze Jean , Arendt Elke K , Zannini Emanuele 
Published: January 2013

AbstractBACKGROUNDBarley rootlets, a malting by‐product, are currently discarded or used as fodder. In this study, milled rootlets and Lactobacillus plantarum FST 1.7‐fermented rootlets were incorporated into wheat bread. The objective was to formulate a high‐nutrition alternative to wholemeal breads with improved technological attributes.RESULTSChemical analyses showed that rootlets contribute nutrients and bioactive compounds, including proteins, amino acids, fatty acids, carbohydrates, dietary fibre, polyphenols and minerals. Rootlets are particularly rich in essential amino acids, especially lysine, the typically limiting essential amino acid of cereals. Additionally, rootlets offer potential dietary fibre health benefits such as protection against cardiovascular disease, cancers and digestive disorders.CONCLUSIONBreads prepared with a (fermented) rootlet inclusion level of up to 10% compared favourably with wholemeal breads from nutritive, technological and textural perspectives. Furthermore, they were well accepted by sensory panellists. Using rootlets as a food ingredient would have the added benefit of increasing this malting by‐product's market value. © 2013 Society of Chemical Industry
Controlled release matrices and micro/nanoparticles of chitosan with antimicrobial potential: development of new strategies for microbial control in agriculture
Authors: Cota‐Arriola Octavio , Onofre Cortez‐Rocha Mario , Burgos‐Hernández Armando , Marina Ezquerra‐Brauer Josafat , Plascencia‐Jatomea Maribel 
Published: January 2013

AbstractThe control of micro‐organisms responsible for pre‐ and postharvest diseases of agricultural products, mainly viruses and fungi, is a problem that remains unresolved, together with the environmental impact of the excessive use of chemicals to tackle this problem. Current efforts are focused on the search for efficient alternatives for microbial control that will not result in damage to the environment or an imbalance in the existing biota. One alternative is the use of natural antimicrobial compounds such as chitosan, a linear cationic biopolymer, which is biodegradable, biocompatible and non‐toxic, has filmogenic properties and is capable of forming matrices for the transport of active substances. The study of chitosan has attracted great interest owing to its ability to form complexes or matrices for the controlled release of active compounds such as micro‐ and nanoparticles, which, together with the biological properties of chitosan, has allowed a major breakthrough in the pharmaceutical and biomedical industries. Another important field of study is the development of chitosan‐based matrices for the controlled release of active compounds in areas such as agriculture and food for the control of viruses, bacteria and fungi, which is one of the least exploited areas and holds much promise for future research. © 2013 Society of Chemical Industry
Determination of degree of methylation of food pectins by chromatography
Authors: Luzio Gary A , Cameron Randall G 
Published: January 2013

AbstractBackgroundIn Florida, 90% of citrus is processed into juice, leaving large amounts of peel waste that could be processed into food ingredients such as pectins for other applications. Pectins of low degree of methylation (DM < 50) have important functional properties for use in foods and pharmaceuticals. Thus determination of DM is important, but DM analyses are difficult to perform and assays can have interference due to the presence of salts or neutral sugars.ResultsA chromatography method has been developed for determination of DM of food pectin using alkaline hydrolysis followed by pectin digestion with a commercial pectinase. Analysis was performed by ion exclusion chromatography (IEC) to obtain methanol (MeOH) concentrations and by anion exchange chromatography (AEC) to obtain galacturonic acid (GalA) concentrations. Data were compared with values obtained using other DM analysis procedures. For example, a 55–75 DM pectin assayed as 55.5, 59.6, 60.1 and 57.0 DM by IEC, AEC, colorimetric and conductivity detection methods respectively.ConclusionThe chromatography procedure described in this paper provides an alternative method for determination of DM of food pectins for accurate and efficient analysis when confronted with limited quantities or large numbers of samples. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.
Measurement of the distribution of non‐structural carbohydrate composition in onion populations by a high‐throughput microplate enzymatic assay
Authors: Revanna Roopashree , Turnbull Matthew H , Shaw Martin L , Wright Kathryn M , Butler Ruth C. , Jameson Paula E , McCallum John A 
Published: January 2013

AbstractBackgroundNon‐structural carbohydrate (NSC; glucose, fructose, sucrose and fructan) composition of onions (Allium cepa L.) varies widely and is a key determinant of market usage. To analyse the physiology and genetics of onion carbohydrate metabolism and to enable selective breeding, an inexpensive, reliable and practicable sugar assay is required to phenotype large numbers of samples.ResultsA rapid, reliable and cost‐effective microplate‐based assay was developed for NSC analysis in onions and used to characterise variation in tissue hexose, sucrose and fructan content in open‐pollinated breeding populations and in mapping populations developed from a wide onion cross. Sucrose measured in microplates employing maltase as a hydrolytic enzyme was in agreement with HPLC‐PAD results. The method revealed significant variation in bulb fructan content within open‐pollinated ‘Pukekohe Longkeeper’ breeding populations over a threefold range. Very wide segregation from 80 to 600 g kg−1 in fructan content was observed in bulbs of F2 genetic mapping populations from the wide onion cross ‘Nasik Red × CUDH2150’.ConclusionThe microplate enzymatic assay is a reliable and practicable method for onion sugar analysis for genetics, breeding and food technology. Open‐pollinated onion populations may harbour extensive within‐population variability in carbohydrate content, which may be quantified and exploited using this method. The phenotypic data obtained from genetic mapping populations show that the method is well suited to detailed genetic and physiological analysis. © 2013 Society of Chemical Industry
Non‐intrusive global/local analysis for the study of fine cracking
Authors: Oliver‐Leblond Cécile , Delaplace Arnaud , Ragueneau Frédéric , Richard Benjamin 
Published: January 2013

SUMMARYThe description of damaged zones in large scale structures can nowadays be assessed by means of a finite element approach using an appropriate damage model. Nevertheless, a fine description of cracking (crack pattern, crack length, crack opening, crack tortuosity) is of primary importance to satisfy new requirements in design codes, especially when dealing with structure durability. In this paper, a computational strategy to quantify cracking at structural case is proposed. A continuous damage model is used to perform a full resolution at the global scale. Then, a reanalysis (implemented as a post‐treatment) of the damaged zones is performed at the local scale with a discrete element model. A non‐intrusive and decoupled numerical scheme allows for a two‐scale analysis using each mechanical model (continuous as well as discrete) within its more efficient level. 2D and 3D test cases will be treated to illustrate the non‐intrusive global/local analysis. Copyright © 2013 John Wiley & Sons, Ltd.
Lipid Lowering and Antioxidant Effect of Miglitol in Triton Treated Hyperlipidemic and High Fat Diet Induced Obese Rats
Authors: Shrivastava Atul , Chaturvedi Upma , Singh Shiv Vardan , Saxena Jitendra Kumar , Bhatia Gitika 
Published: January 2013

AbstractMiglitol, an anti‐diabetic drug, has been shown to reduce plasma lipids and inhibit free radical generation. The anti‐hyperlipidemic and antioxidant effects of miglitol were studied in triton‐induced hyperlipidemic rats and high fat diet‐fed obese rats. Plasma cholesterol and triglycerides levels were significantly lowered by miglitol at 100 mg/kg body weight doses. Miglitol inhibited generation of superoxide anion and hydroxyl free radicals by 14 and 31 % in enzymatic systems and 19 and 25 % in non‐enzymatic systems, respectively. The in‐vitro effect of the drug on adipogenesis using 3T3‐L1 preadipocytes at 2‐, 5‐ and 10‐μM concentrations showed significant inhibition of adipogenesis (34.2 %) at 10‐μM concentration. High fat diet‐fed rat model was used to investigate anti‐hyperlipidemic, anti‐obesity and antioxidant effect of miglitol. Miglitol increased the activities of lecithin‐cholesterol‐acyltransferase (19 %), post heparin lipolytic activity (26 %), lipoprotein lipase (26 %) and triglyceride lipase (31 %) which result in a decrease in plasma lipid levels. The antioxidant enzymes viz., catalase, superoxide dismutase, glutathione peroxidase, glutathione reductase and thioredoxin reductase were increased by the drug in the treated animals. The antihyperlipidemic and antioxidant effect of miglitol can be correlated to its effect on different enzymes and it can be used for inhibiting the development of cardiovascular diseases.
Esterification of Fatty Acids in Greases to Fatty Acid Methyl Esters with Highly Active Diphenylamine Salts
Authors: Ngo Helen L. , Vanselous Heather , Strahan Gary D. , Haas Michael 
Published: January 2013

AbstractDiphenylamine sulfate (DPAS) and diphenylamine hydrochloride (DPACl) salts were found to be highly active catalysts for esterification and substantial transesterification of inexpensive greases to fatty acid methyl esters (FAME). In the presence of catalytic amounts of DPAS or DPACl and excess methanol, the free fatty acids as well as the acylglycerols in waste greases were converted to FAME at 125 °C within 1 h. Although the DPAS and DPACl catalysts were found to have similar catalytic activities to their parent liquid acids (i.e., sulfuric and hydrochloric acids) the diphenylammonium salts are much easier to work with than concentrated liquid acids.
Relationship between dental caries status and anemia in children with severe early childhood caries
Authors: Tang Ru‐Shing , Huang Meng‐Chuan , Huang Shun‐Te 
Published: January 2013

AbstractSevere early childhood caries (SECC) is a public health problem among preschool children. Malnutrition is a condition commonly prevalent in children with SECC. This study investigated the nutritional status among preschool children with SECC. Children with SECC (n = 101) aged 2–5 years from the Division of Pediatric Dentistry in an academic hospital in Southern Taiwan were recruited for our cross‐sectional study. The nutritional status of the children was assessed based on anthropometric measurements and clinical tests. By applying the criteria established by the World Health Organization, we found that 9% and 46% of the children with SECC were diagnosed as being anemic and iron deficient, respectively. Using national standards for the body mass index, 30% of children with SECC were classified as underweight. The relationship between the caries status of the children and anemia was examined using multivariable logistic regression analysis (p < 0.05). Our results show that SECC is strongly associated with anemia (7.25‐fold), indicating that clinicians and dentists should provide treatment to improve both the oral hygiene and the nutritional status of children with SECC.
Suppression of the growth of human colorectal cancer cells by therapeutic stem cells expressing cytosine deaminase and interferon‐β via their tumor‐tropic effect in cellular and xenograft mouse models
Authors: Yi Bo-Rim , Park Min-Ah , Lee Hye-Rim , Kang Nam-Hee , Choi Kelvin J. , Kim Seung U. , Choi Kyung-Chul 
Published: January 2013

Genetically engineered stem cells (GESTECs) exhibit a potent therapeutic efficacy via their strong tumor tropism toward cancer cells. In this study, we introduced the human parental neural stem cells, HB1.F3, with the human interferon beta (IFN‐β) gene which is a typical cytokine gene that has an antitumor effect and the cytosine deaminase (CD) gene from Escherichia coli (E. coli) that could convert the non‐toxic prodrug, 5‐fluorocytosine (5‐FC), to a toxic metabolite, 5‐fluorouracil (5‐FU). Two types of stem cells expressing the CD gene (HB1.F3.CD cells) and both the CD and human IFN‐β genes (HB1.F3.CD.IFN‐β) were generated. The present study was performed to examine the migratory and therapeutic effects of these GESTECs against the colorectal cancer cell line, HT‐29. When co‐cultured with colorectal cancer cells in the presence of 5‐FC, HB1.F3.CD and HB1.F3.CD.IFN‐β cells exhibited the cytotoxicity on HT‐29 cells via the bystander effect. In particular, HB1.F3.CD.IFN‐β cells showed the synergistic cytotoxic activity of 5‐FU and IFN‐β. We also confirmed the migration ability of HB1.F3.CD and HB1.F3.CD.IFN‐β cells toward HT‐29 cells by a modified migration assay in vitro, where chemoattractant factors secreted by HT‐29 cells attracted the GESTECs. In a xenograft mouse model, the volume of tumor mass was decreased up to 56% in HB1.F3.CD injected mice while the tumor mass was greatly inhibited about 76% in HB1.F3.CD.IFN‐β injected mice. The therapeutic treatment by these GESTECs is a novel strategy where the combination of the migration capacity of stem cells as a vector for therapeutic genes towards colorectal cancer and a synergistic antitumor effect of CD and IFN‐β genes can selectively target this type of cancer.
Combinatorial exploration of rare-earth-free permanent magnets: Magnetic and microstructural properties of Fe-Co-W thin films
Authors: Gao T. R. , Wu Y. Q. , Fackler S. , Kierzewski I. , Zhang Y. , Mehta A. , Kramer M. J. , Takeuchi I. 
Published: January 2013

We have investigated the magnetic and structural properties of Fe-Co-W films using a composition spread technique. From the magnetometry measurements, large magnetization (900  emu/cm3) and enhanced perpendicular coercive fields (2–3 kOe) of low W concentration films were observed. The synchrotron diffraction results show a structural transition from a crystalline to an amorphous state and the crystallization onset increases with increasing W concentration. The SEM and TEM characterizations show that the films with low W concentrations have vertically standing platelet-like grain structures which is ascribed to the enhanced coercive fields. Magnetometry studies indicate that as the W concentration increases, microstructural change results in evolution of magnetization reversal mechanism.
Improving the reuse of computational models through version control
Authors: Waltemath Dagmar , Henkel Ron , Hälke Robert , Scharm Martin , Wolkenhauer Olaf 
Published: January 2013

Abstract
Motivation: Only models that are accessible to researchers can be reused. As computational models evolve over time, a number of different but related versions of a model exist. Consequently, tools are required to manage not only well-curated models but also their associated versions.
Results: In this work, we discuss conceptual requirements for model version control. Focusing on XML formats such as Systems Biology Markup Language and CellML, we present methods for the identification and explanation of differences and for the justification of changes between model versions. In consequence, researchers can reflect on these changes, which in turn have considerable value for the development of new models. The implementation of model version control will therefore foster the exploration of published models and increase their reusability.
Availability: We have implemented the proposed methods in a software library called Biochemical Model Version Control System. It is freely available at http://sems.uni-rostock.de/bives/. Biochemical Model Version Control System is also integrated in the online application BudHat, which is available for testing at http://sems.uni-rostock.de/budhat/ (The version described in this publication is available from http://budhat-demo.sems.uni-rostock.de/).
Contact: dagmar.waltemath@uni-rostock.de
Systematic inference of highways of horizontal gene transfer in prokaryotes
Authors: Bansal Mukul S. , Banay Guy , Harlow Timothy J. , Gogarten J. Peter , Shamir Ron 
Published: January 2013

Abstract
Motivation: Horizontal gene transfer (HGT) plays a crucial role in the evolution of prokaryotic species. Typically, no more than a few genes are horizontally transferred between any two species. However, several studies identified pairs of species (or linages) between which many different genes were horizontally transferred. Such a pair is said to be linked by a highway of gene sharing. Inferring such highways is crucial to understanding the evolution of prokaryotes and for inferring past symbiotic and ecological associations among different species.
Results: We present a new improved method for systematically detecting highways of gene sharing. As we demonstrate using a variety of simulated datasets, our method is highly accurate and efficient, and robust to noise and high rates of HGT. We further validate our method by applying it to a published dataset of &gt;22 000 gene trees from 144 prokaryotic species. Our method makes it practical, for the first time, to perform accurate highway analysis quickly and easily even on large datasets with high rates of HGT.
Availability and implementation: An implementation of the method can be freely downloaded from: http://acgt.cs.tau.ac.il/hide.
Contact: rshamir@tau.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
APoc: large-scale identification of similar protein pockets
Authors: Gao Mu , Skolnick Jeffrey 
Published: January 2013

Abstract
Motivation: Most proteins interact with small-molecule ligands such as metabolites or drug compounds. Over the past several decades, many of these interactions have been captured in high-resolution atomic structures. From a geometric point of view, most interaction sites for grasping these small-molecule ligands, as revealed in these structures, form concave shapes, or ‘pockets’, on the protein’s surface. An efficient method for comparing these pockets could greatly assist the classification of ligand-binding sites, prediction of protein molecular function and design of novel drug compounds.
Results: We introduce a computational method, APoc (Alignment of Pockets), for the large-scale, sequence order-independent, structural comparison of protein pockets. A scoring function, the Pocket Similarity Score (PS-score), is derived to measure the level of similarity between pockets. Statistical models are used to estimate the significance of the PS-score based on millions of comparisons of randomly related pockets. APoc is a general robust method that may be applied to pockets identified by various approaches, such as ligand-binding sites as observed in experimental complex structures, or predicted pockets identified by a pocket-detection method. Finally, we curate large benchmark datasets to evaluate the performance of APoc and present interesting examples to demonstrate the usefulness of the method. We also demonstrate that APoc has better performance than the geometric hashing-based method SiteEngine.
Availability and implementation: The APoc software package including the source code is freely available at http://cssb.biology.gatech.edu/APoc.
Contact: skolnick@gatech.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction
Authors: Arunapuram Preeti , Edvardsson Ingolfur , Golden Michael , Anderson James W. J. , Novák Ádám , Sükösd Zsuzsanna , Hein Jotun 
Published: January 2013

Abstract
Motivation: Comparative modeling of RNA is known to be important for making accurate secondary structure predictions. RNA structure prediction tools such as PPfold or RNAalifold use an aligned set of sequences in predictions. Obtaining a multiple alignment from a set of sequences is quite a challenging problem itself, and the quality of the alignment can affect the quality of a prediction. By implementing RNA secondary structure prediction in a statistical alignment framework, and predicting structures from multiple alignment samples instead of a single fixed alignment, it may be possible to improve predictions.
Results: We have extended the program StatAlign to make use of RNA-specific features, which include RNA secondary structure prediction from multiple alignments using either a thermodynamic approach (RNAalifold) or a Stochastic Context-Free Grammars (SCFGs) approach (PPfold). We also provide the user with scores relating to the quality of a secondary structure prediction, such as information entropy values for the combined space of secondary structures and sampled alignments, and a reliability score that predicts the expected number of correctly predicted base pairs. Finally, we have created RNA secondary structure visualization plugins and automated the process of setting up Markov Chain Monte Carlo runs for RNA alignments in StatAlign.
Availability and implementation: The software is available from http://statalign.github.com/statalign/.
Contact: novak@stats.ox.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.