bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impacts of the Primary School Free Breakfast Initiative on socio-economic inequalities in breakfast consumption among 9–11-year-old schoolchildren in Wales
Authors: Moore Graham F , Murphy Simon , Chaplin Katherine , Lyons Ronan A , Atkinson Mark , Moore Laurence 
Published: December 2013

AbstractObjectivesUniversal interventions may widen or narrow inequalities if disproportionately effective among higher or lower socio-economic groups. The present paper examines impacts of the Primary School Free Breakfast Initiative in Wales on inequalities in children's dietary behaviours and cognitive functioning.DesignCluster-randomised controlled trial. Responses were linked to free school meal (FSM) entitlement via the Secure Anonymised Information Linkage databank. Impacts on inequalities were evaluated using weighted school-level regression models with interaction terms for intervention × whole-school percentage FSM entitlement and intervention × aggregated individual FSM entitlement. Individual-level regression models included interaction terms for intervention × individual FSM entitlement.SettingFifty-five intervention and fifty-six wait-list control primary schools.SubjectsApproximately 4500 children completed measures of dietary behaviours and cognitive tests at baseline and 12-month follow-up.ResultsSchool-level models indicated that children in intervention schools ate a greater number of healthy items for breakfast than children in control schools (b = 0·25; 95 % CI 0·07, 0·44), with larger increases observed in more deprived schools (interaction term b = 1·76; 95 % CI 0·36, 3·16). An interaction between intervention and household-level deprivation was not significant. Despite no main effects on breakfast skipping, a significant interaction was observed, indicating declines in breakfast skipping in more deprived schools (interaction term b = −0·07; 95 % CI −0·15, −0·00) and households (OR = 0·67; 95 % CI 0·46, 0·98). No significant influence on inequality was observed for the remaining outcomes.ConclusionsUniversal breakfast provision may reduce socio-economic inequalities in consumption of healthy breakfast items and breakfast skipping. There was no evidence of intervention-generated inequalities in any outcomes.
Usual dietary fatty acid intakes and red-blood-cell membrane fatty acid composition in Inuit children attending child-care centres in Nunavik, northern Québec, Canada
Authors: Blanchet Rosanne , Lauzière Julie , Gagné Doris , Vézina Carole , Ayotte Pierre , O'Brien Huguette Turgeon 
Published: December 2013

AbstractObjectivesTo assess dietary fatty acid intakes and to examine the relationship between dietary sources ofn-3 andn-6 PUFA and red-blood-cell (RBC)n-3 andn-6 PUFA composition.DesignA cross-sectional study. Dietary intakes were assessed with a 24 h dietary recall. A second recall was performed for 44 % of the children. Usual dietary intakes were estimated with the Software for Intake Distribution Estimation (SIDE). The fatty acid composition was measured in RBC membranes. Multivariate linear regression analyses were performed to explain RBCn-3 andn-6 PUFA concentrations.SettingChild-care centres in Nunavik, northern Québec, Canada.SubjectsOne hundred and sixty-seven Inuit children aged 11–53 months.ResultsA high proportion of the participants had inadequaten-3 andn-6 PUFA intakes (47·9 % and 93·5 %, respectively). Breast-feeding status and consumption of traditional food during the first 24 h dietary recall were significantly associated with RBCn-3 PUFA levels. Older children also tended to have higher RBCn-3 PUFA levels (P= 0·0528), whereas sex, infant formula status andn-3 PUFA dietary intakes were not associated with RBCn-3 PUFA concentrations. RBCn-6 PUFA concentrations were positively associated with breast-feeding status andn-6 PUFA dietary intakes, whereas age, sex and infant formula status were not.ConclusionsThe present findings highlight the fact that Inuit pre-school children are not consuming enoughn-3 andn-6 PUFA for optimum health. These observations call for actions to increase traditional food intake among Inuit children and to help them and their parents make healthier store-bought food choices.
Looking back over 150 years of humanitarian action: the photographic archives of the ICRC
Authors: Gorin Valérie 
Published: December 2013

AbstractThe purpose of this article is to suggest some historical milestones for a retrospective reflection on the photographic archives of the International Committee of the Red Cross (ICRC). This collection is little used by researchers, although the 120,000 photographs which it contains have helped to forge the symbolism and identity of the institution and to document its operations in accordance with a memory preservation policy which gradually emerged in the course of the 20th century. The photographs shown in this article are divided into three main themes (the ICRC delegate, the context of action, suffering and the victims), in order to make it easier to discuss the key aspects of this tremendous visual heritage which looks at humanitarian action, its protagonists and its beneficiaries from an anthropological and ethnological point of view.
Edge-controlled growth and kinetics of single-crystal graphene domains by chemical vapor deposition
Authors: Ma Teng , Ren Wencai , Zhang Xiuyun , Liu Zhibo , Gao Yang , Yin Li-Chang , Ma Xiu-Liang , Ding Feng , Cheng Hui-Ming 
Published: December 2013

Significance
Controlled synthesis of wafer-sized single crystalline high-quality graphene is a great challenge of graphene growth by chemical vapor deposition because of the complicated kinetics at edges that govern the growth process. Here we report the synthesis of single-crystal graphene domains with tunable edges from zigzag to armchair via a growth–etching–regrowth process. Both growth and etching of graphene are strongly dependent on the edge structure. This growth/etching behavior is well explained at the atomic level, given the concentrations of kinks on various edges, and allows control of graphene edges and morphology according to the classical kinetic Wulff construction theory. This work provides a deep understanding of the fundamental problems that limit graphene growth by chemical vapor deposition.
The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system
Authors: Vonk Freek J. , Casewell Nicholas R. , Henkel Christiaan V. , Heimberg Alysha M. , Jansen Hans J. , McCleary Ryan J. R. , Kerkkamp Harald M. E. , Vos Rutger A. , Guerreiro Isabel , Calvete Juan J. , Wüster Wolfgang , Woods Anthony E. , Logan Jessica M. , Harrison Robert A. , Castoe Todd A. , de Koning A. P. Jason , Pollock David D. , Yandell Mark , Calderon Diego , Renjifo Camila , Currier Rachel B. , Salgado David , Pla Davinia , Sanz Libia , Hyder Asad S. , Ribeiro José M. C. , Arntzen Jan W. , van den Thillart Guido E. E. J. M. , Boetzer Marten , Pirovano Walter , Dirks Ron P. , Spaink Herman P. , Duboule Denis , McGlinn Edwina , Kini R. Manjunatha , Richardson Michael K. 
Published: December 2013

Significance
Snake venoms are toxic protein cocktails used for prey capture. To investigate the evolution of these complex biological weapon systems, we sequenced the genome of a venomous snake, the king cobra, and assessed the composition of venom gland expressed genes, small RNAs, and secreted venom proteins. We show that regulatory components of the venom secretory system may have evolved from a pancreatic origin and that venom toxin genes were co-opted by distinct genomic mechanisms. After co-option, toxin genes important for prey capture have massively expanded by gene duplication and evolved under positive selection, resulting in protein neofunctionalization. This diverse and dramatic venom-related genomic response seemingly occurs in response to a coevolutionary arms race between venomous snakes and their prey.
Diversity and abundance of phosphonate biosynthetic genes in nature
Authors: Yu Xiaomin , Doroghazi James R. , Janga Sarath C. , Zhang Jun Kai , Circello Benjamin , Griffin Benjamin M. , Labeda David P. , Metcalf William W. 
Published: December 2013

Significance
Phosphonic acids are organophosphorus molecules containing direct carbon–phosphorus bonds that are often perceived as biological rarities. The data presented here show that the ability to synthesize diverse phosphonates is both widespread and relatively common among microbes. These findings are consistent with recent evidence suggesting that phosphonates are important intermediates in the global phosphorus cycle. Moreover, they support the idea that these molecules play a significant role in the biology of producing organisms, including a mechanism to sequester scarce phosphorus resources and to compete via chemical warfare using toxic phosphonate mimics of common metabolic intermediates.
Fingerprinting protein structures effectively and efficiently
Authors: Cui Xuefeng , Li Shuai Cheng , He Lin , Li Ming 
Published: December 2013

AbstractMotivation: One common task in structural biology is to assess the similarities and differences among protein structures. A variety of structure alignment algorithms and programs has been designed and implemented for this purpose. A major drawback with existing structure alignment programs is that they require a large amount of computational time, rendering them infeasible for pairwise alignments on large collections of structures. To overcome this drawback, a fragment alphabet learned from known structures has been introduced. The method, however, considers local similarity only, and therefore occasionally assigns high scores to structures that are similar only in local fragments.Method: We propose a novel approach that eliminates false positives, through the comparison of both local and remote similarity, with little compromise in speed. Two kinds of contact libraries (ContactLib) are introduced to fingerprint protein structures effectively and efficiently. Each contact group of the contact library consists of one local or two remote fragments and is represented by a concise vector. These vectors are then indexed and used to calculate a new combined hit-rate score to identify similar protein structures effectively and efficiently.Results: We tested our method on the high-quality protein structure subset of SCOP30 containing 3297 protein structures. For each protein structure of the subset, we retrieved its neighbor protein structures from the rest of the subset. The best area under the Receiver-Operating Characteristic curve, archived by ContactLib, is as high as 0.960. This is a significant improvement compared with 0.747, the best result achieved by FragBag. We also demonstrated that incorporating remote contact information is critical to consistently retrieve accurate neighbor protein structures for all- query protein structures.Availability and implementation: https://cs.uwaterloo.ca/∼xfcui/contactlib/.Contact: shuaicli@cityu.edu.hk or mli@uwaterloo.ca
AISAIC: a software suite for accurate identification of significant aberrations in cancers
Authors: Zhang Bai , Hou Xuchu , Yuan Xiguo , Shih Ie-Ming , Zhang Zhen , Clarke Robert , Wang Roger R. , Fu Yi , Madhavan Subha , Wang Yue , Yu Guoqiang 
Published: December 2013

Abstract
Summary: Accurate identification of significant aberrations in cancers (AISAIC) is a systematic effort to discover potential cancer-driving genes such as oncogenes and tumor suppressors. Two major confounding factors against this goal are the normal cell contamination and random background aberrations in tumor samples. We describe a Java AISAIC package that provides comprehensive analytic functions and graphic user interface for integrating two statistically principled in silico approaches to address the aforementioned challenges in DNA copy number analyses. In addition, the package provides a command-line interface for users with scripting and programming needs to incorporate or extend AISAIC to their customized analysis pipelines. This open-source multiplatform software offers several attractive features: (i) it implements a user friendly complete pipeline from processing raw data to reporting analytic results; (ii) it detects deletion types directly from copy number signals using a Bayes hypothesis test; (iii) it estimates the fraction of normal contamination for each sample; (iv) it produces unbiased null distribution of random background alterations by iterative aberration-exclusive permutations; and (v) it identifies significant consensus regions and the percentage of homozygous/hemizygous deletions across multiple samples. AISAIC also provides users with a parallel computing option to leverage ubiquitous multicore machines.
Availability and implementation: AISAIC is available as a Java application, with a user’s guide and source code, at https://code.google.com/p/aisaic/.
Contact: yug@vt.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction
Authors: Dümcke Sebastian , Bräuer Johannes , Anchang Benedict , Spang Rainer , Beerenwinkel Niko , Tresch Achim 
Published: December 2013

Abstract
Motivation: For biological pathways, it is common to measure a gene expression time series after various knockdowns of genes that are putatively involved in the process of interest. These interventional time-resolved data are most suitable for the elucidation of dynamic causal relationships in signaling networks. Even with this kind of data it is still a major and largely unsolved challenge to infer the topology and interaction logic of the underlying regulatory network.
Results: In this work, we present a novel model-based approach involving Boolean networks to reconstruct small to medium-sized regulatory networks. In particular, we solve the problem of exact likelihood computation in Boolean networks with probabilistic exponential time delays. Simulations demonstrate the high accuracy of our approach. We apply our method to data of Ivanova et al. (2006), where RNA interference knockdown experiments were used to build a network of the key regulatory genes governing mouse stem cell maintenance and differentiation. In contrast to previous analyses of that data set, our method can identify feedback loops and provides new insights into the interplay of some master regulators in embryonic stem cell development.
Availability and implementation: The algorithm is implemented in the statistical language R. Code and documentation are available at Bioinformatics online.
Contact: duemcke@mpipz.mpg.de or tresch@mpipz.mpg.de
Supplementary information: Supplementary Materials are available at Bioinfomatics online.
Poly(A) RNA and Paip2 act as allosteric regulators of poly(A)-binding protein
Authors: Lee Seung Hwan , Oh Jungsic , Park Jonghyun , Paek Ki Young , Rho Sangchul , Jang Sung Key , Lee Jong–Bong 
Published: December 2013

Abstract
When bound to the 3′ poly(A) tail of mRNA, poly(A)-binding protein (PABP) modulates mRNA translation and stability through its association with various proteins. By visualizing individual PABP molecules in real time, we found that PABP, containing four RNA recognition motifs (RRMs), adopts a conformation on poly(A) binding in which RRM1 is in proximity to RRM4. This conformational change is due to the bending of the region between RRM2 and RRM3. PABP-interacting protein 2 actively disrupts the bent structure of PABP to the extended structure, resulting in the inhibition of PABP-poly(A) binding. These results suggest that the changes in the configuration of PABP induced by interactions with various effector molecules, such as poly(A) and PABP-interacting protein 2, play pivotal roles in its function.
ARF induction in response to DNA strand breaks is regulated by PARP1
Authors: Orlando Giulia , Khoronenkova Svetlana V. , Dianova Irina I. , Parsons Jason L. , Dianov Grigory L. 
Published: December 2013

Abstract
The ARF tumour suppressor protein, the gene of which is frequently mutated in many human cancers, plays an important role in the cellular stress response by orchestrating up-regulation of p53 protein and consequently promoting cell-cycle delay. Although p53 protein function has been clearly linked to the cellular DNA damage response, the role of ARF protein in this process is unclear. Here, we report that arf gene transcription is induced by DNA strand breaks (SBs) and that ARF protein accumulates in response to persistent DNA damage. We discovered that poly(ADP-ribose) synthesis catalysed by PARP1 at the sites of unrepaired SBs activates ARF transcription through a protein signalling cascade, including the NAD+-dependent deacetylase SIRT1 and the transcription factor E2F1. Our data suggest that poly(ADP-ribose) synthesis at the sites of SBs initiates DNA damage signal transduction by reducing the cellular concentration of NAD+, thus down-regulating SIRT1 activity and consequently activating E2F1-dependent ARF transcription. Our findings suggest a vital role for ARF in DNA damage signalling, and furthermore explain the critical requirement for ARF inactivation in cancer cells, which are frequently deficient in DNA repair and accumulate DNA damage.
Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling
Authors: Zhang Xiaojun , Dantas Machado Ana Carolina , Ding Yuan , Chen Yongheng , Lu Yan , Duan Yankun , Tham Kenneth W. , Chen Lin , Rohs Remo , Qin Peter Z. 
Published: December 2013

Abstract
The tumor suppressor protein p53 regulates numerous signaling pathways by specifically recognizing diverse p53 response elements (REs). Understanding the mechanisms of p53-DNA interaction requires structural information on p53 REs. However, such information is limited as a 3D structure of any RE in the unbound form is not available yet. Here, site-directed spin labeling was used to probe the solution structures of REs involved in p53 regulation of the p21 and Bax genes. Multiple nanometer distances in the p21-RE and BAX-RE, measured using a nucleotide-independent nitroxide probe and double-electron-electron-resonance spectroscopy, were used to derive molecular models of unbound REs from pools of all-atom structures generated by Monte-Carlo simulations, thus enabling analyses to reveal sequence-dependent DNA shape features of unbound REs in solution. The data revealed distinct RE conformational changes on binding to the p53 core domain, and support the hypothesis that sequence-dependent properties encoded in REs are exploited by p53 to achieve the energetically most favorable mode of deformation, consequently enhancing binding specificity. This work reveals mechanisms of p53-DNA recognition, and establishes a new experimental/computational approach for studying DNA shape in solution that has far-reaching implications for studying protein–DNA interactions.
The output of the tRNA modification pathways controlled by theEscherichia coliMnmEG and MnmC enzymes depends on the growth conditions and the tRNA species
Authors: Moukadiri Ismaïl , Garzón M.-José , Björk Glenn R. , Armengod M.-Eugenia 
Published: December 2013

AbstractIn Escherichia coli, the MnmEG complex modifies transfer RNAs (tRNAs) decoding NNA/NNG codons. MnmEG catalyzes two different modification reactions, which add an aminomethyl (nm) or carboxymethylaminomethyl (cmnm) group to position 5 of the anticodon wobble uridine using ammonium or glycine, respectively. In and , however, cmnm5 appears as the final modification, whereas in the remaining tRNAs, the MnmEG products are converted into 5-methylaminomethyl (mnm5) through the two-domain, bi-functional enzyme MnmC. MnmC(o) transforms cmnm5 into nm5, whereas MnmC(m) converts nm5 into mnm5, thus producing an atypical network of modification pathways. We investigate the activities and tRNA specificity of MnmEG and the MnmC domains, the ability of tRNAs to follow the ammonium or glycine pathway and the effect of mnmC mutations on growth. We demonstrate that the two MnmC domains function independently of each other and that and are substrates for MnmC(m), but not MnmC(o). Synthesis of mnm5s2U by MnmEG-MnmC in vivo avoids build-up of intermediates in . We also show that MnmEG can modify all the tRNAs via the ammonium pathway. Strikingly, the net output of the MnmEG pathways in vivo depends on growth conditions and tRNA species. Loss of any MnmC activity has a biological cost under specific conditions.
Novel method for site-specific induction of oxidative DNA damage reveals differences in recruitment of repair proteins to heterochromatin and euchromatin
Authors: Lan Li , Nakajima Satoshi , Wei Leizhen , Sun Luxi , Hsieh Ching-Lung , Sobol Robert W. , Bruchez Marcel , Van Houten Bennett , Yasui Akira , Levine Arthur S. 
Published: December 2013

Abstract
Reactive oxygen species (ROS)-induced DNA damage is repaired by the base excision repair pathway. However, the effect of chromatin structure on BER protein recruitment to DNA damage sites in living cells is poorly understood. To address this problem, we developed a method to specifically produce ROS-induced DNA damage by fusing KillerRed (KR), a light-stimulated ROS-inducer, to a tet-repressor (tetR-KR) or a transcription activator (TA-KR). TetR-KR or TA-KR, bound to a TRE cassette (∼90 kb) integrated at a defined genomic locus in U2OS cells, was used to induce ROS damage in hetero- or euchromatin, respectively. We found that DNA glycosylases were efficiently recruited to DNA damage in heterochromatin, as well as in euchromatin. PARP1 was recruited to DNA damage within condensed chromatin more efficiently than in active chromatin. In contrast, recruitment of FEN1 was highly enriched at sites of DNA damage within active chromatin in a PCNA- and transcription activation-dependent manner. These results indicate that oxidative DNA damage is differentially processed within hetero or euchromatin.
Impact of e-business on perceived supply chain risks
Authors: Caldwell Nigel , Harland Christine , Powell Philip , Zheng Jurong 
Published: December 2013

Purpose– The purpose of this paper is to understand the risks managers and individual supply chains perceive from e-business.Design/methodology/approach– This research takes a long-term, staged view of the risks managers and individual supply chains perceive from e-business. By taking a two-stage approach, investigating four supply chains at a three year interval, the research considers perceived risks from e-business and the extent to which these risks obtained.Findings– E-business has the potential to deliver substantial benefits, but it also involves new and different risks. This research finds that small firms (SMEs) adopted a “watching brief” rather than implemented e-business. Between the two studies it emerges that e-business can support rather than detract from inter-organisational relationships. Global forces are in evidence in terms of low cost competition, but low cost competitors are not e-enabled.Research limitations/implications– Limitations, pragmatism and opportunism in the sampling is acknowledged. For example, the work and concepts that led to the expectation of e-business dominating and decimating industrial supply chains may have been based in chains more open to external forces than the ones examined here. Further research is required that identifies the minimum critical mass necessary to retain national manufacturing capacity at a chain or sector level, and empirical work is needed on the suggested link between supply chain stability and certainty of payment. The cases here are based on four UK supply chains, so various chain forms are likely to have been excluded.Originality/value– This research, by taking a staged approach and going back to the same chain and reviewing perceived risks, identifies how the build up of numerous – but small – events, for example factory closures, can aggregate over time to be just as significant as high profile, headline-worthy risks. Methods that produce a snapshot such as a one-off survey may be inadequate for fully exploring an area such as risk. Especially if the risks are hard to assess and are biased toward high profile events – catastrophic risks rather than accumulations of smaller, less noticeable risks.