bluuebunny/crossref_metadata_2025_split huggingface dataset:
Graphane sheets and crystals under pressure
Authors: Wen Xiao-Dong , Hand Louis , Labet Vanessa , Yang Tao , Hoffmann Roald , Ashcroft N. W. , Oganov Artem R. , Lyakhov Andriy O. 
Published: April 2011

Eight isomeric two-dimensional graphane sheets are found in a theoretical study. Four of these nets—two built on chair cyclohexanes, two on boat—are more stable thermodynamically than the isomeric benzene, or polyacetylene. Three-dimensional crystals are built up from the two-dimensional sheets, and their hypothetical behavior under pressure (up to 300 GPa) is explored. While the three-dimensional graphanes remain, as expected, insulating or semiconducting in this pressure range, there is a remarkable inversion in stability of the five crystals studied. Two stacking polytypes that are not the most stable at ambient pressure (one based on an unusual chair cyclohexane net, the other on a boat) are significantly stabilized with increasing pressure relative to stackings of simple chair sheets. The explanation may lie in the balance on intra and intersheet contacts in the extended arrays.
Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds
Authors: Mu Fangping , Unkefer Clifford J. , Unkefer Pat J. , Hlavacek William S. 
Published: April 2011

Abstract
Motivation: Our knowledge of the metabolites in cells and their reactions is far from complete as revealed by metabolomic measurements that detect many more small molecules than are documented in metabolic databases. Here, we develop an approach for predicting the reactivity of small-molecule metabolites in enzyme-catalyzed reactions that combines expert knowledge, computational chemistry and machine learning.
Results: We classified 4843 reactions documented in the KEGG database, from all six Enzyme Commission classes (EC 1–6), into 80 reaction classes, each of which is marked by a characteristic functional group transformation. Reaction centers and surrounding local structures in substrates and products of these reactions were represented using SMARTS. We found that each of the SMARTS-defined chemical substructures is widely distributed among metabolites, but only a fraction of the functional groups in these substructures are reactive. Using atomic properties of atoms in a putative reaction center and molecular properties as features, we trained support vector machine (SVM) classifiers to discriminate between functional groups that are reactive and non-reactive. Classifier accuracy was assessed by cross-validation analysis. A typical sensitivity [TP/(TP+FN)] or specificity [TN/(TN+FP)] is ≈0.8. Our results suggest that metabolic reactivity of small-molecule compounds can be predicted with reasonable accuracy based on the presence of a potentially reactive functional group and the chemical features of its local environment.
Availability: The classifiers presented here can be used to predict reactions via a web site (http://cellsignaling.lanl.gov/Reactivity/). The web site is freely available.
Contact: fmu@lanl.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks
Authors: Audenaert Pieter , Van Parys Thomas , Brondel Florian , Pickavet Mario , Demeester Piet , Van de Peer Yves , Michoel Tom 
Published: April 2011

Abstract
Summary: Network motifs in integrated molecular networks represent functional relationships between distinct data types. They aggregate to form dense topological structures corresponding to functional modules which cannot be detected by traditional graph clustering algorithms. We developed CyClus3D, a Cytoscape plugin for clustering composite three-node network motifs using a 3D spectral clustering algorithm.
Availability: Via the Cytoscape plugin manager or http://bioinformatics.psb.ugent.be/software/details/CyClus3D.
Contact: tom.michoel@frias.uni-freiburg.de
Supplementary Information: Supplementary data are available at Bioinformatics online.
Hierarchy and Roles of Pathogen-Associated Molecular Pattern-Induced Responses in Nicotiana benthamiana
Authors: Segonzac Cécile , Feike Doreen , Gimenez-Ibanez Selena , Hann Dagmar R. , Zipfel Cyril , Rathjen John P. 
Published: April 2011

Abstract
Our current understanding of pathogen-associated molecular pattern (PAMP)-triggered immunity signaling pathways in plants is limited due to the redundancy of several components or the lethality of mutants in Arabidopsis (Arabidopsis thaliana). To overcome this, we used a virus-induced gene silencing-based approach in combination with pharmacological studies to decipher links between early PAMP-triggered immunity events and their roles in immunity following PAMP perception in Nicotiana benthamiana. Two different calcium influx inhibitors suppressed the reactive oxygen species (ROS) burst: activation of the mitogen-activated protein kinases (MAPKs) and PAMP-induced gene expression. The calcium burst was unaffected in plants specifically silenced for components involved in ROS generation or for MAPKs activated by PAMP treatment. Importantly, the ROS burst still occurred in plants silenced for the two major defense-associated MAPK genes NbSIPK (for salicylic acid-induced protein kinase) and NbWIPK (for wound-induced protein kinase) or for both genes simultaneously, demonstrating that these MAPKs are dispensable for ROS production. We further show that NbSIPK silencing is sufficient to prevent PAMP-induced gene expression but that both MAPKs are required for bacterial immunity against two virulent strains of Pseudomonas syringae and their respective nonpathogenic mutants. These results suggest that the PAMP-triggered calcium burst is upstream of separate signaling branches, one leading to MAPK activation and then gene expression and the other to ROS production. In addition, this study highlights the essential roles of NbSIPK and NbWIPK in antibacterial immunity. Unexpectedly, negative regulatory mechanisms controlling the intensity of the PAMP-triggered calcium and ROS bursts were also revealed by this work.
The Arabidopsis RING Finger E3 Ligase RHA2b Acts Additively with RHA2a in Regulating Abscisic Acid Signaling and Drought Response
Authors: Li Hongmei , Jiang Hongling , Bu Qingyun , Zhao Qingzhen , Sun Jiaqiang , Xie Qi , Li Chuanyou 
Published: April 2011

AbstractWe have previously shown that the Arabidopsis (Arabidopsis thaliana) RING-H2 E3 ligase RHA2a positively regulates abscisic acid (ABA) signaling during seed germination and postgerminative growth. Here, we report that RHA2b, the closest homolog of RHA2a, is also an active E3 ligase and plays an important role in ABA signaling. We show that RHA2b expression is induced by ABA and that overexpression of RHA2b leads to ABA-associated phenotypes such as ABA hypersensitivity in seed germination and seedling growth, enhanced stomatal closure, reduced water loss, and, therefore, increased drought tolerance. On the contrary, the rha2b-1 mutant shows ABA-insensitive phenotypes and reduced drought tolerance. We provide evidence showing that a rha2a rha2b-1 double mutant generally enhances ABA insensitivity of rha2b-1 in seed germination, seedling growth, and stomatal closure, suggesting that RHA2b and RHA2a act redundantly in regulating ABA responses. Genetic analyses support that, like RHA2a, the RHA2b action in ABA signaling is downstream of a protein phosphatase 2C, ABA-INSENSITIVE2 (ABI2), and in parallel with that of the ABI transcription factors ABI3/4/5. We speculate that RHA2b and RHA2a may have redundant yet distinguishable functions in the regulation of ABA responses.
The DNA Damage Response Signaling Cascade Regulates Proliferation of the Phytopathogenic FungusUstilago maydisin Planta
Authors: de Sena-Tomás Carmen , Fernández-Álvarez Alfonso , Holloman William K. , Pérez-Martín José 
Published: April 2011

AbstractIn the phytopathogenic fungus Ustilago maydis, the dikaryotic state dominates the period of growth occurring during the infectious phase. Dikaryons are cells in which two nuclei, one from each parent cell, share a single cytoplasm for a period of time without undergoing nuclear fusion. In fungal cells, maintenance of the dikaryotic state requires an intricate cell division process that often involves the formation of a structure known as the clamp connection as well as the sorting of one of the nuclei to this structure to ensure that each daughter dikaryon inherits a balance of each parental genome. Here, we describe an atypical role of the DNA damage checkpoint kinases Chk1 and Atr1 during pathogenic growth of U. maydis. We found that Chk1 and Atr1 collaborate to control cell cycle arrest during the induction of the virulence program in U. maydis and that Chk1 and Atr1 work together to control the dikaryon formation. These findings uncover a link between a widely conserved signaling cascade and the virulence program in a phytopathogen. We propose a model in which adjustment of the cell cycle by the Atr1-Chk1 axis controls fidelity in dikaryon formation. Therefore, Chk1 and Atr1 emerge as critical cell type regulators in addition to their roles in the DNA damage response.
A DELLA in Disguise: SPATULA Restrains the Growth of the DevelopingArabidopsisSeedling
Authors: Josse Eve-Marie , Gan Yinbo , Bou-Torrent Jordi , Stewart Kelly L. , Gilday Alison D. , Jeffree Christopher E. , Vaistij Fabián E. , Martínez-García Jaime F. , Nagy Ferenc , Graham Ian A. , Halliday Karen J. 
Published: April 2011

AbstractThe period following seedling emergence is a particularly vulnerable stage in the plant life cycle. In Arabidopsis thaliana, the phytochrome-interacting factor (PIF) subgroup of basic-helix-loop-helix transcription factors has a pivotal role in regulating growth during this early phase, integrating environmental and hormonal signals. We previously showed that SPATULA (SPT), a PIF homolog, regulates seed dormancy. In this article, we establish that unlike PIFs, which mainly promote hypocotyl elongation, SPT is a potent regulator of cotyledon expansion. Here, SPT acts in an analogous manner to the gibberellin-dependent DELLAs, REPRESSOR OF GA1-3 and GIBBERELLIC ACID INSENSITIVE, which restrain cotyledon expansion alongside SPT. However, although DELLAs are not required for SPT action, we demonstrate that SPT is subject to negative regulation by DELLAs. Cross-regulation of SPT by DELLAs ensures that SPT protein levels are limited when DELLAs are abundant but rise following DELLA depletion. This regulation provides a means to prevent excessive growth suppression that would result from the dual activity of SPT and DELLAs, yet maintain growth restraint under DELLA-depleted conditions. We present evidence that SPT and DELLAs regulate common gene targets and illustrate that the balance of SPT and DELLA action depends on light quality signals in the natural environment.
RAC/ROP GTPases and Auxin Signaling
Authors: Wu Hen-ming , Hazak Ora , Cheung Alice Y. , Yalovsky Shaul 
Published: April 2011

AbstractAuxin functions as a key morphogen in regulating plant growth and development. Studies on auxin-regulated gene expression and on the mechanism of polar auxin transport and its asymmetric distribution within tissues have provided the basis for realizing the molecular mechanisms underlying auxin function. In eukaryotes, members of the Ras and Rho subfamilies of the Ras superfamily of small GTPases function as molecular switches in many signaling cascades that regulate growth and development. Plants do not have Ras proteins, but they contain Rho-like small G proteins called RACs or ROPs that, like fungal and metazoan Rhos, are regulators of cell polarity and may also undertake some Ras functions. Here, we discuss the advances made over the last decade that implicate RAC/ROPs as mediators for auxin-regulated gene expression, rapid cell surface-located auxin signaling, and directional auxin transport. We also describe experimental data indicating that auxin–RAC/ROP crosstalk may form regulatory feedback loops and theoretical modeling that attempts to connect local auxin gradients with RAC/ROP regulation of cell polarity. We hope that by discussing these experimental and modeling studies, this perspective will stimulate efforts to further refine our understanding of auxin signaling via the RAC/ROP molecular switch.
Effect of germination and probiotic fermentation on nutrient profile of pearl millet based food blends
Authors: Arora Sonia , Jood Sudesh , Khetarpaul N. 
Published: April 2011

PurposeProbiotic fermented foods are fast being recognized as health foods. Most of such foods are based on dairy products but little research work is available on coarse cereals and millets, which constitute the staple foods in developing countries. This paper aims to determine the effect of germination and fementation on nutrient composition of pearl millet based food blends.Design/methodology/approachIndigenously developed pearl millet based food blends containing raw and germinated pearl millet flour, whey powder and tomato pulp (2:1:1w/w) were autoclaved, cooled and fermented with 5 percent Lactobacillus acidophilus curd which supplied 106cells/ml to the slurry at 37°C for 12 h. The unfermented blends, after autoclaving, served as controls. The developed food blends were subjected to nutritional evaluation by using the standard methods of analysis. The data were statistically analysed.FindingsPearl millet based, germinated, autoclaved and fermented, food blend maintained adequate cell viability (8.64 cfu g‐1) as compared to non‐germinated food blend. Germination and probiotic fermentation caused significant improvement in the contents of thiamine, niacin, total lysine, protein fractions, sugars, soluble dietary fibre and in vitro availability of Ca, Fe and Zn of food blends.Practical implicationsResearch is currently aimed at developing probiotic millet based food mixture, which had enhanced nutrient profile. Hence, it can be considered for commercialization after establishing its health/therapeutic implications among the population.Originality/valueDairy foods have preferentially been used as the carrier medium for probiotics. This paper explores the possibility of using staple foods as the carrier medium. The consumption of such food mixtures containing viable probiotic bacteria should be enhanced among consumers in term of their role in health maintenance and disease prevention.
Proximate, amino acid, fatty acid and mineral composition of raw and cooked camel (Camelus dromedarius) meat
Authors: Kadim I.T. , Al‐Ani M.R. , Al‐Maqbaly R.S. , Mansour M.H. , Mahgoub O. , Johnson E.H. 
Published: April 2011

PurposeThe purpose of the paper is to study the effects of cooking on proximate composition, amino acids, fatty acids, minerals and total, heme and non‐heme iron content of camel meat.Design/methodology/approachA total of ten longissimus thoracis muscles (500 grams) were collected between the tenth and twelfth ribs of the left side. Samples were randomly collected from two to three year old camel carcasses chilled (1‐3°C) for 48 hours then stored at −20°C. The first portion was kept fresh while the second one was placed in plastic bags and cooked by immersion in a water bath at 70°C for 90 minutes. Both samples were freeze‐dried, and then ground to a homogeneous mass to be used for chemical analyses.FindingsCooked samples had significantly (p<0.05) higher dry matter by 27.7 per cent, protein by 31.1 per cent and fat by 22.2 per cent, but lower ash content by 8.3 per cent than the raw ones. Cooking had no significant effect on amino acid and fatty acid composition of the meat. The components of camel meat most significantly affected by cooking were macro‐ and micro‐minerals, which ranged between 13.1 and 52.5 per cent, respectively. Cooking resulted in a significant decrease in total, heme and non‐heme iron contents by 4.3, 8.7 and 4.0 per cent, respectively.Research limitations/implicationsThe research is restricted to camel meat but it is an exploratory study. The issue of research outcome as only longissimus thoracic muscle is another limitation. Further investigation is needed to include different muscles, temperatures, durations and cooking methods.Practical implicationsAmino acids and fatty acids of camel meat are not affected by cooking, while heating accelerated total and heme iron oxidation suggest camel meat to be a rich source of heme iron.Originality/valueThe paper is original in its findings and useful for both researchers and academics in the field of meat science.
FT‐NIR spectroscopy: a rapid method for estimation of moisture content in bael pulp
Authors: Bag S.K. , Srivastav P.P. , Mishra H.N. 
Published: April 2011

PurposeThe purpose of this paper is to develop FT‐NIR technique for determination of moisture content in bael pulp.Design/methodology/approachCalibration and validation sets were designed for the conception and evaluation of the method adequacy in the range of moisture content 70 to 95 per cent (wb). The prediction models based on partial least squares (PLS) regression, were developed in the near‐infrared region (4,000‐2,500cm‐1). Conventional criteria such as the R2, the root mean square errors of cross validation (RMSECV), root mean square errors of estimation (RMSEE) as well as the number of PLS factors were considered for the selection of three pre‐processing (vector normalization, minimum‐maximum normalization and multiplicative scatter correction) methods.FindingsThe best calibration model was developed with min‐max normalization (MMN) spectral pre‐processing (R2=99.3). The MMN pre‐processing method was found most suitable and the maximum coefficient of determination (R2) value of 0.993 was obtained for the calibration model developed. The developed results indicated that FTNIR spectroscopy could be used for rapid detection of moisture content in bael pulp samples without any sample destruction.Originality/valueThe research in this paper is useful for the quick detection of moisture content of bael fruit pulp during processing.
Does fish origin matter to European consumers?
Authors: Vanhonacker Filiep , Altintzoglou Themistoklis , Luten Joop , Verbeke Wim 
Published: April 2011

PurposeThis study aims to gain insights into the relevance and market potential of fish origin (farmed or wild) among consumers in Belgium, Norway and Spain.Design/methodology/approachCross‐sectional data were collected through a consumer survey (n=1,319), conducted in November‐December 2007 in three European countries: Belgium, Norway and Spain. The study describes personal and food characteristics, as well as consumer attitudes and knowledge related to fish origin. Further, these characteristics were analysed in terms of their impact on the choice of either farmed or wild fish, using bivariate analyses.FindingsIn general, European consumers have little knowledge or awareness regarding the origin of fish. This results in uncertainty in consumers' perception of farmed fish in particular. The study is in line with previous ones suggesting that perceptions of aquaculture and farmed fish are based more on emotions than on rational considerations. Still, the perception of farmed fish is positive in general. Consumers do not prioritise fish origin as an information cue, although variation is present between different consumer groups. Consumers of predominantly farmed versus wild fish did not have a very distinct profile, which corroborates with the only modest significance of fish origin as a product‐specific information cue during the fish purchase and consumption decision process.Originality/valueThe strength of the paper pertains to its international scope, and to the diversity of countries selected in terms of relevant variables. Also, the growing relevance of aquaculture as a fish production method and farmed fish as a food product makes results and findings of the study topical and of practical relevance.
Logistics outsourcing by Taiwanese and Dutch food processing industries
Authors: Hsiao Hsin‐I , Kemp Ron G.M. , van der Vorst Jack G.A.J. , Omta S.W.F. (Onno) 
Published: April 2011

PurposeThis paper aims to investigate outsourcing of different types of logistics activities in Taiwanese food industry, and benchmark with practices in The Netherlands.Design/methodology/approachThe outsourcing of four levels of logistics activities is investigated: transportation (level 1), packaging (level 2), transportation management (level 3), and distribution network management (level 4). A structured questionnaire was designed and sent to logistics managers in The Netherlands and Taiwan to evaluate the most commonly outsourced activities and identify specific outsourcing firm's characteristics.FindingsAbout 69 per cent of the companies, in both countries outsource level 1 activities, 16 per cent level 2, and 37 per cent level 3 activities. Only few companies (about 10 per cent) outsource the highest level of activities. In particular, The Netherlands has higher percentages for levels 1 and 3. This might be caused by the fact that most Taiwanese companies emphasise low cost whereas the Dutch companies focus on flexibility in order to deal with higher complexities. When intentions for the future are included, Taiwan is planning to outsource level 2 (40 per cent) and level 4 activities (36 per cent) much more than The Netherlands (respectively 13 and 17 per cent). When zooming in, it was found that outsourcing strategies of companies in the subsectors differ. For instance, the dairy sector outsources more frequently than the meat sector on the first three levels. This might be caused by the fact that meat companies emphasise food quality, whereas dairy companies emphasise flexibility and reliability.Research limitations/implicationsThis study investigated only food processors. The paper suggests further research should include other types of food organisations.Originality/valueThe paper provides valuable insights in outsourcing strategies of food processing companies in Taiwan and The Netherlands for advanced logistics service providers who are looking at the market potential of Taiwan.
The brave new world of open innovation
Authors: Sloane Paul 
Published: April 2011

PurposeThe purpose of this paper is to examine the concept of open innovation (OI).Design/methodology/approachThe paper looks at different forms of OI, including suggestive/participative, suggestive/invitational, directed/invitational and directed/participative.FindingsThe paper suggests that in choosing which approach to adopt it is important to first define your strategy and identify what you want to get out of OI. It also suggests that OI needs executive level commitment if it is to succeed, as this is generally the first and most important obstacle that companies face in trying to adopt it.Originality/valueThe paper provides useful information on the concept of OI in corporate strategy.