bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrating Text Mining into the MGI Biocuration Workflow
Authors: Dowell Karen , McAndrews-Hill Monica , Hill David , Drabkin Harold , Blake Judith
Published: May 2009

A major challenge for the development of resources for functional and comparative genomics is the extraction of data from the biomedical literature. Although text retrieval and extraction for biological data is an active research field, few applications have been integrated into production literature curation systems such as those of the model organism databases.In September 2008, Mouse Genome Informatics (MGI) at The Jackson Lab initiated a search for dictionary-based text mining tools that we could integrate into our curation workflow. MGI has rigorous document triage and annotation procedures designed to identify articles about mouse genome biology and determine whether those articles should be curated. We currently screens approximately 1000 journal articles a month for Gene Ontology terms, gene mapping, gene expression, phenotype data and other key biological information. Although we don’t foresee that human curation tasks can be fully automated in the near future, we are eager to implement entity name recognition and gene tagging tools that can help streamline our curation workflow and simplify gene indexing tasks in the MGI system. In this presentation, we discuss our search process and the steps we took to identify a short list of potential tools for further evaluation. We present our performance metrics and success criteria, and pilot projects in progress. The primary applications under current review are Fraunhofer SCAI’s ProMiner and NCBO’s Open-Biomedical Annotator.
Production of reactive oxygen species, impairment of photosynthetic function and dynamic changes in mitochondria are early events in cadmium‐induced cell death in Arabidopsis thaliana
Authors: Bi YuHua , Chen WenLi , Zhang WeiNa , Zhou Quan , Yun LiJuan , Xing Da
Published: May 2009

Background information. Cadmium (Cd) is a highly toxic heavy metal that causes changes in plant metabolism through inhibiting photosynthesis and respiration. The effects of Cd on the morphology and function of the chloroplast and mitochondria, as well as on the production and localization of ROS (reactive oxygen species), were studied at the single‐cell level in Arabidopsis.

Results. The present study showed that the morphology of chloroplasts changed after Cd treatment, and the photochemical efficiency dramatically declined prior to obvious morphological distortion in the chloroplasts. A quick burst of ROS was detected after Cd treatment. The ROS appeared first in the mitochondria and subsequently in the chloroplast. Simultaneously, the mitochondria clumped irregularly around the chloroplasts or aggregated in the cytoplasm, and the movement of mitochondria was concomitantly blocked. Furthermore, the production of ROS was decreased after pre‐treatment with ascorbic acid or catalase, which prevented inhibition of photosynthesis, organelle changes and subsequent protoplast death. Our results suggest that the distribution and mobility of mitochondria, the morphology of chloroplasts and the accumulation of ROS play important roles in Cd‐induced cell death. The results are in good agreement with previous reports of many types of apoptotic‐like cell death.

Conclusion. The changes in the distribution and mobility of mitochondria, and morphology of chloroplasts, as well as the accumulation of ROS, play important roles in Cd‐induced cell death.
Artificial β-defensin based on a minimal defensin template
Authors: Antcheva Nikolinka , Morgera Francesca , Creatti Luisa , Vaccari Lisa , Pag Ulrike , Pacor Sabrina , Shai Yechiel , Sahl Hans-Georg , Tossi Alessandro
Published: May 2009

We have designed and chemically synthesized an artificial β-defensin based on a minimal template derived from the comparative analysis of over 80 naturally occurring sequences. This molecule has the disulfide-bridged β-sheet core structure of natural β-defensins and shows a robust salt-sensitive antimicrobial activity against bacteria and yeast, as well as a chemotactic activity against immature dendritic cells. An SAR (structure–activity relationship) study using two truncated fragments or a Cys→Ser point-mutated analogue, from which one or two of the three disulfide bridges were absent, indicated that altering the structure resulted in a different type of membrane interaction and a switch to different modes of action towards both microbial and host cells, and that covalent dimerization could favour antimicrobial activity. Comparison of the structural, aggregational and biological activities of the artificial defensin with those of three human β-defensins and their primate orthologues provided useful information on how their mode of action may relate to specific structural features.
Copper(I)-mediated protein–protein interactions result from suboptimal interaction surfaces
Authors: Banci Lucia , Bertini Ivano , Calderone Vito , Della-Malva Nunzia , Felli Isabella C. , Neri Sara , Pavelkova Anna , Rosato Antonio
Published: May 2009

The homoeostasis of metal ions in cells is the result of the contribution of several cellular pathways that involve transient, often weak, protein–protein interactions. Metal transfer typically implies the formation of adducts where the metal itself acts as a bridge between proteins, by co-ordinating residues of both interacting partners. In the present study we address the interaction between the human copper(I)-chaperone HAH1 (human ATX1 homologue) and a metal-binding domain in one of its partners, namely the P-type copper-transporting ATPase, ATP7A (ATPase, Cu+ transporting, α polypeptide). The adduct was structurally characterized in solution, in the presence of copper(I), and through X-ray crystallography, upon replacing copper(I) with cadmium(II). Further insight was obtained through molecular modelling techniques and site-directed mutagenesis. It was found that the interaction involves a relatively small interface (less than 1000 Å2, 1 Å=0.1 nm) with a low fraction of non-polar atoms. These observations provide a possible explanation for the low affinity of the two apoproteins. It appears that electrostatics is important in selecting which domain of the ATPase is able to form detectable amounts of the metal-mediated adduct with HAH1.
DNA Damage: from Causes to Cures
Authors: Bowater Richard P. , Borts Rhona H. , White Malcolm F.
Published: May 2009

In order to maintain genome integrity, it is essential that any DNA damage is repaired. This is achieved in diverse ways in all cells to ensure cellular survival. There is a large repertoire of proteins that remove and repair DNA damage. However, sometimes these processes do not function correctly, leading to genome instability. Studies of DNA repair and genome instability and their causes and cures were showcased in the 2008 Biochemical Society Annual Symposium. The present article provides a summary of the talks given and the subsequent papers in this issue of Biochemical Society Transactions.
Functions of p53 in metabolism and invasion
Authors: Vousden Karen H.
Published: May 2009

The p53 protein is an important tumour suppressor that is inactivated in many human cancers. Understanding how p53 is regulated and the downstream consequences of p53 function is helping us to devise novel therapies based on the reactivation of p53. Such approaches may be useful in the treatment of cancer, but a growing understanding of a role for p53 in other conditions suggests that modulation of p53 may have broader applications.
The associations of sequence variants in DNA-repair and cell-cycle genes with cancer risk: genotype–phenotype correlations
Authors: Hall Janet , Marcel Virginie , Bolin Celeste , Fernet Marie , Tartier Laurence , Vaslin Laurence , Hainaut Pierre
Published: May 2009

DNA-repair systems maintain the integrity of the human genome, and cell-cycle checkpoints are a critical component of the cellular response to DNA damage. Thus the presence of sequence variants in genes involved in these pathways that modulate their activity might have an impact on cancer risk. Many molecular epidemiological studies have investigated the association between sequence variants, particularly SNPs (single nucleotide polymorphisms), and cancer risk. For instance, ATM (ataxia telangiectasia mutated) SNPs have been associated with increased risk of breast, prostate, leukaemia, colon and early-onset lung cancer, and the intron 3 16-bp repeat in TP53 (tumour protein 53) is associated with an increased risk of lung cancer. In contrast, the variant allele of the rare CHEK2 (checkpoint kinase 2 checkpoint homologue) missense variant (accession number rs17879961) was significantly associated with a lower incidence of lung and upper aerodigestive cancers. For some sequence variants, a strong gene–environment interaction has also been noted. For instance, a greater absolute risk reduction of lung and upper aerodigestive cancers in smokers than in non-smokers carrying the I157T CHEK2 variant has been observed, as has an interaction between TP53 intron 3 16-bp repeats and multiple X-ray exposures on lung cancer risk. The challenge now is to understand the molecular mechanisms underlying these associations.
Biochemical properties of mammalian TREX1 and its association with DNA replication and inherited inflammatory disease
Authors: Lindahl Tomas , Barnes Deborah E. , Yang Yun-Gui , Robins Peter
Published: May 2009

The major DNA-specific 3′–5′ exonuclease of mammalian cells is TREX1 (3′ repair exonuclease 1; previously called DNase III). The human enzyme is encoded by a single exon and, like many 3′ exonucleases, exists as a homodimer. TREX1 degrades ssDNA (single-stranded DNA) more efficiently than dsDNA (double-stranded DNA), and its catalytic properties are similar to those of Escherichia coli exonuclease X. However, TREX1 is only found in mammals and has an extended C-terminal domain containing a leucine-rich sequence required for its association with the endoplasmic reticulum. In normal S-phase and also in response to genotoxic stress, TREX1 at least partly redistributes to the cell nucleus. In a collaborative project, we have demonstrated TREX1 enzyme deficiency in Aicardi–Goutières syndrome. Subsequently, we have shown that AGS1 cells exhibit chronic ATM (ataxia telangiectasia mutated)-dependent checkpoint activation, and these TREX1-deficient cells accumulate ssDNA fragments of a distinct size generated during DNA replication. Other groups have shown that the syndromes of familial chilblain lupus as well as systemic lupus erythematosus, and the distinct neurovascular disorder retinal vasculopathy with cerebral leukodystrophy, can be caused by dominant mutations at different sites within the TREX1 gene.
Short-patch single-strand break repair in ataxia oculomotor apraxia-1
Authors: Reynolds John J. , El-Khamisy Sherif F. , Caldecott Keith W.
Published: May 2009

AOA1 (ataxia oculomotor apraxia-1) results from mutations in aprataxin, a component of DNA strand break repair that removes AMP from 5′-termini. In the present article, we provide an overview of this disease and review recent experiments demonstrating that short-patch repair of oxidative single-strand breaks in AOA1 cell extracts bypasses the point of aprataxin action and stalls at the final step of DNA ligation, resulting in accumulation of adenylated DNA nicks. Strikingly, this defect results from insufficient levels of non-adenylated DNA ligase and short-patch single-strand break repair can be restored in AOA1 extracts, independently of aprataxin, by addition of recombinant DNA ligase.
A molecular model for drug binding to tandem repeats of telomeric G-quadruplexes
Authors: Haider Shozeb M. , Neidle Stephen
Published: May 2009

The extreme 3′-ends of human telomeres consist of 150–250 nucleotides of single-stranded DNA sequence together with associated proteins. Small-molecule ligands can compete with these proteins and induce a conformational change in the DNA to a four-stranded quadruplex arrangement, which is also no longer a substrate for the telomerase enzyme. The modified telomere ends provide signals to the DNA-damage-response system and trigger senescence and apoptosis. Experimental structural data are available on such quadruplex complexes comprising up to four telomeric DNA repeats, but not on longer systems that are more directly relevant to the single-stranded overhang in human cells. The present paper reports on a molecular modelling study that uses Molecular Dynamics simulation methods to build dimer and tetramer quadruplex repeats. These incorporate ligand-binding sites and are models for overhang–ligand complexes.
The role of recombination in telomere length maintenance
Authors: Royle Nicola J. , Méndez-Bermúdez Aarón , Gravani Athanasia , Novo Clara , Foxon Jenny , Williams Jonathan , Cotton Victoria , Hidalgo Alberto
Published: May 2009

Human telomeres shorten during each cell division, predominantly because of incomplete DNA replication. This eventually results in short uncapped telomeres that elicit a DNA-damage response, leading to cellular senescence. However, evasion of senescence results in continued cell division and telomere erosion ultimately results in genome instability. In the long term, this genome instability is not sustainable, and cancer cells activate a TMM (telomere maintenance mechanism), either expression of telomerase or activation of the ALT (alternative lengthening of telomeres) pathway. Activation of the ALT mechanism results in deregulation of recombination-based activities at telomeres. Thus ALT+ cells show elevated T-SCE (telomere sister-chromatid exchange), misprocessing of t-loops that cap chromosomes and recombination-based processes between telomeres or between telomeres and ECTRs (extrachromosomal telomeric repeats). Some or all of these processes underlie the chaotic telomere length maintenance that allows cells in ALT+ tumours unlimited replicative capacity. ALT activation is also associated with destabilization of a minisatellite, MS32. The connection between the minisatellite instability and the deregulation of recombination-based activity at telomeres is not understood, but analysis of the minisatellite can be used as a marker for ALT. It is known that telomere length maintenance in ALT+ cells is dependent on the MRN [MRE11 (meiotic recombination 11)–Rad50–NBS1 (Nijmegen breakage syndrome 1)] complex, but knowledge of the role of other genes, including the Werner's (WRN) and Bloom's (BLM) syndrome DNA helicase genes, is still limited.
Understanding the functions of BRCA1 in the DNA-damage response
Authors: Yun Maximina H. , Hiom Kevin
Published: May 2009

Inheritance of a mutation in BRCA1 (breast cancer 1 early-onset) results in predisposition to early-onset breast and ovarian cancer. Tumours in these individuals arise after somatic mutation or loss of the wild-type allele. Loss of BRCA1 function leads to a profound increase in genomic instability involving the accumulation of mutations, DNA breaks and gross chromosomal rearrangements. Accordingly, BRCA1 has been implicated as an important factor involved in both the repair of DNA lesions and in the regulation of cell-cycle checkpoints in response to DNA damage. However, the molecular mechanism through which BRCA1 functions to preserve genome stability remains unclear. In the present article, we examine the different ways in which BRCA1 might influence the repair of DNA damage and the preservation of genome integrity, taking into account what is currently known about its interactions with other proteins, its biochemical activity and its nuclear localization.
p57kip2 is dynamically regulated in experimental autoimmune encephalomyelitis and interferes with oligodendroglial maturation
Authors: Kremer David , Heinen André , Jadasz Janusz , Göttle Peter , Zimmermann Kristin , Zickler Philipp , Jander Sebastian , Hartung Hans-Peter , Küry Patrick
Published: May 2009

The mechanisms preventing efficient remyelination in the adult mammalian central nervous system after demyelinating inflammatory diseases, such as multiple sclerosis, are largely unknown. Partial remyelination occurs in early disease stages, but repair capacity diminishes over time and with disease progression. We describe a potent candidate for the negative regulation of oligodendroglial differentiation that may underlie failure to remyelinate. The p57kip2 gene is dynamically regulated in the spinal cord during MOG-induced experimental autoimmune encephalomyelitis. Transient down-regulation indicated that it is a negative regulator of post-mitotic oligodendroglial differentiation. We then applied short hairpin RNA-mediated gene suppression to cultured oligodendroglial precursor cells and demonstrated that down-regulation of p57kip2 accelerates morphological maturation and promotes myelin expression. We also provide evidence that p57kip2 interacts with LIMK-1, implying that p57kip2 affects cytoskeletal dynamics during oligodendroglial maturation. These data suggest that sustained down-regulation of p57kip2 is important for oligodendroglial maturation and open perspectives for future therapeutic approaches to overcome the endogenous remyelination blockade in multiple sclerosis.
Expression of AA4.1 marks lymphohematopoietic progenitors in early mouse development
Authors: Yamane Toshiyuki , Hosen Naoki , Yamazaki Hidetoshi , Weissman Irving L.
Published: May 2009

The hematopoietic system of mice is established during the early to midgestational stage of development. However, the earliest lymphohematopoietic progenitors that appear during mouse development have been less well characterized compared with the hematopoietic stem cell compartment of fetal liver and bone marrow. We isolated the earliest lymphohematopoietic progenitors by using embryonic stem (ES) cell culture in vitro. Cells with the c-Kit+Lin−cell surface phenotype were present abundantly in ES cells cocultured with stromal cell lines. We further separated the cells into two distinct cell subsets based on AA4.1 expression. Although AA4.1+and AA4.1−cells had equivalent potency to generate myeloid cell lineages, the lymphoid potential in ES-cell-derived cells was largely restricted to the cells expressing AA4.1. The same cell type was present abundantly in the early yolk sac and in fewer numbers (≈5% of that in the yolk sac) in the caudal half of the developing embryos. These data suggest that AA4.1 is a cell surface marker that can identify the earliest lymphohematopoietic progenitors in mouse development.
Grammaticalization in creoles
Authors: Bruyn Adrienne
Published: May 2009

Cases from Sranan are presented in order to illustrate the various processes and mechanisms involved in developments in a creole language that could be interpreted as grammaticalization. While we do find “ordinary” grammaticalization, substrate patterns sometimes provided a model. In the extreme case, where the development consists of a large shortcut, grammaticalization as a usage-based process is no longer at issue, but rather a kind of local relexification variously referred to as “calquing” (Keesing 1991), “apparent grammaticalization” (Bruyn 1996), or “polysemy copying” (Heine and Kuteva 2005). Yet other cases involve reanalysis of a lexifier form without grammaticalization (Detges 2000). Distinguishing between the various types of developments is essential both for understanding the processes shaping creoles, and for delimiting the concept of grammaticalization.
The simultaneous production of educational achievement and popularity: How do some pupils accomplish it?
Authors: Francis Becky , Skelton Christine , Read Barbara
Published: May 2009

In spite of research showing that pupils—particularly boys—tend to experience tension between high academic achievement and popularity with peers at school, some pupils continue to maintain simultaneous production of both. This article focuses on a sample of 12–13 year‐old pupils, identified as high achieving and popular, to examine classroom subjectivities, with attention to their practices around gender and educational achievement. Data are drawn from a qualitative study funded by the Economic and Social Research Council, which involved observation of classes at nine different co‐educational state schools in England, and interviews with 71 high‐achieving pupils, including 22 that were identified as high achieving and popular. The study findings belie the notion that high‐achieving pupils necessarily jeopardise their social standing with classmates. However, it also demonstrates the importance of embodiment and even essential attributes in productions of subjectivity that successfully ‘balance’ popularity and achievement. Nevertheless, high‐achieving and popular pupils are shown to undertake significant identity work, employing particular gendered performances and practices in order to maintain this simultaneous production.
‘The art of democracy’: Young people's democratic learning in gallery contexts
Authors: Lawy Robert , Biesta Gert , McDonnell Jane , Lawy Helen , Reeves Hannah
Published: May 2009

In this article the authors report on research which aimed to explore the opportunities for democratic action and learning in a number of artist‐led gallery education projects in the south‐west of England. The research takes an approach to citizenship learning and democracy that is less focused on citizenship as a specific subject in the formal school curriculum and the achievement of specific citizenship outcomes that can follow from it. Rather, it is more focused upon understanding how democratic practices that are embedded in the day‐to‐day lives of young people contribute to their democratic learning and participation as citizens. Drawing upon conceptual categories and concepts that illuminate the process, the authors demonstrate the nature and character of young people's democratic learning. An implication arising from this is the need for practice‐orientated research in other contexts (e.g. work, leisure and home) to fully understand the nature of democratic learning.
THE INFLUENCE OF SOCIAL CAPITAL ON WILLINGNESS TO PAY FOR THE ENVIRONMENT AMONG EUROPEAN CITIZENS
Authors: Jones Nikoleta , Malesios Chrisovaladis , Botetzagias Iosif
Published: May 2009

Social capital has been recognized as one of the most influential concepts in social and political sciences. It is assumed that it has significant influence on several issues such as health status, educational achievement and environmental attitudes. In the present article we attempt to investigate the influence of social capital on the tendency of European citizens to contribute money for the environment using data from EVS 1999/2000. Firstly, an estimation of individual social capital is calculated for European citizens with the use of Confirmatory Factor Analysis. Secondly, the relation between individual social capital and willingness to pay (WTP) is examined. Thirdly, further evidence is provided by introducing in the analysis the influence of other factors such as income, age, gender and educational level. In addition, the influence of contextual factors on WTP is explored. Through the results of the study it is observed that most European citizens are willing to pay for the environment and their decision is influenced significantly from elements of social capital. Furthermore, on a contextual level only some of the factors investigated explain the tendency to contribute money for the environment.
Defining a Process for Segmenting the General Practitioner Market for Rural Practice Recruitment
Authors: Hemphill Elizabeth , Kulik Carol T.
Published: May 2009

General practitioner (GP) to patient ratios fall below benchmarks, particularly in rural areas. A marketing solution to this significant social problem might be to develop recruitment strategies differentiating medical practices (brands) and targeting different segments of the GP market. This article uses data gathered in Australia from practice managers, GPs, and recruitment advertisements to develop a taxonomy of family, job, and practice attributes that could be used to recruit GPs. Current recruiting strategies emphasize a mix of family, job and practice attributes, but better recruitment outcomes might be achieved by the implementation of branding principles that more clearly differentiate general practices with targeted recruitment advertisements. This research prescribes a path for future research on GP recruitment. The first step is to gather data on the relative and absolute value of different attributes within the taxonomy. These data can then be used to develop targeted marketing strategies for recruiting GPs to rural practices.
Where are All the Products? Are We Really Doing Social Marketing or are We Doing Social Sales?
Authors: Merritt Rowena , Christopoulos Alex , Thorpe Allison
Published: May 2009

In their description of social marketing, Kotler and Zaltman (1971) postulate the difference between marketing and sales. Sales are defined as “finding customers for existing products and convincing them to buy these products,” whereas marketing is described as “discovering the wants of a target audience and then creating the goods and services to satisfy them” (p. 5).

The marketing mix and consideration of all its Ps (product, price, place, promotion) is a fundamental contributor to the success of marketing. A successful commercial company would never look to promote a message unless it had a product or service, at the right price, in a convenient location. Despite this knowledge, social marketing projects often focus predominantly, and sometimes solely, on the final P — promotion.

This article looks at a selection of the products and services offered in England, debates whether we are doing marketing or sales, and attempts to answer the question Bill Smith posed at the World Social Marketing Conference held in Brighton, England, in September 2008: “Where's the product?”
GO Men's Health Program
Authors: Burton Amanda , Atherton Matthew , Nygaard Anna
Published: May 2009

In 2008, NHS Halton & St Helens in the United Kingdom launched a Men's Health program pilot focusing on encouraging men to take better care of their health and to make more use of available health services. Targeting men living in the most deprived wards in Halton, the Men's Health program offers a wide variety of activities just for men, all designed to support and enable equal and convenient access to lifestyle and general health services.

The pilot program draws upon best practice by developing a social marketing approach that supports men to choose from a range of tailored activities designed to improve their health and well-being. The Men's Health program is part of the wider Health Improvement Team's program and has demonstrated a range of quantitative and qualitative successes in engaging men living in the most deprived wards. A key element to the design and development of the Men's Health program is the continuous dialogue and refining activities to ensure that men are encouraged to contribute in the shaping of such activities and wider delivery of the program.
Short article: Search guidance is proportional to the categorical specificity of a target cue
Authors: Schmidt Joseph , Zelinsky Gregory J.
Published: May 2009

Visual search studies typically assume the availability of precise target information to guide search, often a picture of the exact target. However, search targets in the real world are often defined categorically and with varying degrees of visual specificity. In five target preview conditions we manipulated the availability of target visual information in a search task for common real-world objects. Previews were: a picture of the target, an abstract textual description of the target, a precise textual description, an abstract + colour textual description, or a precise + colour textual description. Guidance generally increased as information was added to the target preview. We conclude that the information used for search guidance need not be limited to a picture of the target. Although generally less precise, to the extent that visual information can be extracted from a target label and loaded into working memory, this information too can be used to guide search.
Short article: When are moving images remembered better? Study–test congruence and the dynamic superiority effect
Authors: Buratto Luciano G. , Matthews William J. , Lamberts Koen
Published: May 2009

It has previously been shown that moving images are remembered better than static ones. In two experiments, we investigated the basis for this dynamic superiority effect. Participants studied scenes presented as a single static image, a sequence of still images, or a moving video clip, and 3 days later completed a recognition test in which familiar and novel scenes were presented in all three formats. We found a marked congruency effect: For a given study format, accuracy was highest when test items were shown in the same format. Neither the dynamic superiority effect nor the study–test congruency effect was affected by encoding (Experiment 1) or retrieval (Experiment 2) manipulations, suggesting that these effects are relatively impervious to strategic control. The results demonstrate that the spatio-temporal properties of complex, realistic scenes are preserved in long-term memory.
Short article: Does the brain regularize digits and letters to the same extent?
Authors: Perea Manuel , Duñabeitia Jon Andoni , Pollatsek Alexander , Carreiras Manuel
Published: May 2009

The cognitive system does not just act as a mirror from the sensory input; instead, it tends to normalize this information. Given that letter processing seems to be much more specialized than digit processing in the cortex, we examined whether the regularization process occurs differently from digits to letters than from letters to digits: We employed a masked priming same/different experiment (e.g., probe, VESZED; prime, V35Z3D; and target, VESZED). When embedded in letter strings, digits that resemble letters (e.g., 3 and 5 in V35Z3D-VESZED) tend to be encoded in a letter-like manner, whereas when embedded in digit strings, letters that resemble digits (e.g., E and S in 9ES7E2–935732) tend not to be encoded in a digit-like manner.
Parametric decay instability during high harmonic fast wave heating experiments on the TST-2 spherical tokamak
Authors: Oosako T. , Takase Y. , Ejiri A. , Nagashima Y. , Adachi Y. , Kasahara H. , Yamada T. , Watanabe O. , Tojo H. , Kainaga S. , Sugiyama J. , Yamaguchi T. , An B. , Hayashi H. , Kobayashi H. , Kurashina H. , Matsuzawa H. , Yamada K. , Kumazawa R. , Shimpo F. , Ono Y. , Masuda T. , Sasaki M.
Published: May 2009

A degradation of heating efficiency was observed during high harmonic fast wave (HHFW) heating of spherical tokamak plasmas when parametric decay instability (PDI) occurred. Suppression of PDI is necessary to make HHFW a reliable heating and current drive tool in high β plasmas. In order to understand PDI, measurements were made using a radially movable electrostatic probe (ion saturation current and floating potential), arrays of RF magnetic probes distributed both toroidally and poloidally, microwave reflectometry and fast optical diagnostics in TST-2. The frequency spectrum usually exhibits ion-cyclotron harmonic sidebands f
0 ± nf
ci and low-frequency ion-cyclotron quasi-modes (ICQMs) nf
ci. PDI becomes stronger at lower densities, and much weaker when the plasma is far away from the antenna. The lower sideband power was found to increase quadratically with the local pump wave power. The lower sideband power relative to the local pump wave power was larger for reflectometer compared with either electrostatic or magnetic probes. The radial decay of the pump wave amplitude in the SOL was much faster for the ion saturation current than for the floating potential. These results are consistent with the HHFW pump wave decaying into the HHFW or ion Bernstein wave (IBW) sideband and the low-frequency (ICQM). Two additional peaks were discovered between the fundamental lower sideband and the pump wave in hydrogen plasmas. The frequency differences of these peaks from the pump wave increase with the magnetic field. These decay modes may involve molecular ions or partially ionized impurity ions.
One dimensional simulation of diamond DT methane impact fusion
Authors: Liu J. , Wang Z.X. , Chen C. , Lei Y.A.
Published: May 2009

A new impact fusion concept is presented. Both the projectile (macron) and the fusion fuel are carefully chosen, so that the acceleration of the macron is much easier and the stopping of the fusion alpha particle is much larger. The physics of the impact process is discussed. Other than formerly believed shock compression or global adiabatic compression, we tried a fluidal plus particle diffusion approach to model the impact process. A one-dimensional code is implemented. The simulation shows, with the ion–electron temperature relaxation and bremsstrahlung being considered, that the ignition is much harder than previously believed, 1–2 MJ for a millimetre size diamond macron. Diamond DT methane impact fusion is more similar to volume ignition fusion.
A group bridge approach for variable selection
Authors: Huang Jian , Ma Shuange , Xie Huiliang , Zhang Cun-Hui
Published: May 2009

In multiple regression problems when covariates can be naturally grouped, it is important to carry out feature selection at the group and within-group individual variable levels simultaneously. The existing methods, including the lasso and group lasso, are designed for either variable selection or group selection, but not for both. We propose a group bridge approach that is capable of simultaneous selection at both the group and within-group individual variable levels. The proposed approach is a penalized regularization method that uses a specially designed group bridge penalty. It has the oracle group selection property, in that it can correctly select important groups with probability converging to one. In contrast, the group lasso and group least angle regression methods in general do not possess such an oracle property in group selection. Simulation studies indicate that the group bridge has superior performance in group and individual variable selection relative to several existing methods.
Health‐Beneficial Phenolic Aldehyde in Antigonon leptopus Tea
Authors: Mulabagal Vanisree , Alexander-Lindo Ruby L. , DeWitt David L. , Nair Muraleedharan G.
Published: May 2009

Tea prepared from the aerial parts of Antigonon leptopus is used as a remedy for cold and pain relief in many countries. In this study, A. leptopus tea, prepared from the dried aerial parts, was evaluated for lipid peroxidation (LPO) and cyclooxygenase (COX‐1 and COX‐2) enzyme inhibitory activities. The tea as a dried extract inhibited LPO, COX‐1 and COX‐2 enzymes by 78%, 38% and 89%, respectively, at 100 μg/mL. Bioassay‐guided fractionation of the extract yielded a selective COX‐2 enzyme inhibitory phenolic aldehyde, 2,3,4‐trihydroxy benzaldehyde. Also, it showed LPO inhibitory activity by 68.3% at 6.25 μg/mL. Therefore, we have studied other hydroxy benzaldehydes and their methoxy analogs for LPO, COX‐1 and COX‐2 enzymes inhibitory activities and found that compound 1 gave the highest COX‐2 enzyme inhibitory activity as indicated by a 50% inhibitory concentration (IC50) at 9.7 μg/mL. The analogs showed only marginal LPO activity at 6.25 μg/mL. The hydroxy analogs 6, 7 and 9 showed 55%, 61% and 43% of COX‐2 inhibition at 100 μg/mL. However, hydroxy benzaldehydes 3 and 12 showed selective COX‐1 inhibition while compounds 4 and 10 gave little or no COX‐2 enzyme inhibition at 100 μg/mL. At the same concentration, compounds 14, 21 and 22 inhibited COX‐1 by 83, 85 and 70%, respectively. Similarly, compounds 18, 19 and 23 inhibited COX‐2 by 68%, 72% and 70%, at 100 μg/mL. This is the first report on the isolation of compound 1 from A. leptopus tea with selective COX‐2 enzyme and LPO inhibitory activities.
Classifying fish schools and estimating their species proportions in fishery-acoustic surveys
Authors: Fablet Ronan , Lefort Riwal , Karoui Imen , Berger Laurent , Massé Jacques , Scalabrin Carla , Boucher Jean-Marc
Published: May 2009

Fablet, R., Lefort, R., Karoui, I., Berger, L., Massé, J., Scalabrin, C., and Boucher, J-M. 2009. Classifying fish schools and estimating their species proportions in fishery-acoustic surveys. – ICES Journal of Marine Science, 66: 1136–1142. Automated or computer-assisted tools are needed for estimating the proportion of species and their biomass in echosounder surveys of marine ecosystems. Operational systems rely mainly on school morphologies or the frequency responses of scatterers to identify target species in echograms. This paper presents two complementary methods for classifying schools and estimating their species proportion in a multispecies, pelagic environment. One method relies on the training of probabilistic school classifiers; the other exploits echogram similarities to infer species proportions directly from the proportions known at trawled sites. The methods are demonstrated with empirical and simulated data. School classifications and species-proportion estimates are compared to demonstrate the effectiveness of the proposed methods.
Influence of Amylose Content on Cookie and Sponge Cake Quality and Solvent Retention Capacities in Wheat Flour
Authors: Nishio Zenta , Oikawa Hanaki , Haneda Takanobu , Seki Masako , Ito Miwako , Tabiki Tadashi , Yamauchi Hiroaki , Miura Hideho
Published: May 2009

Reduced amylose wheat (Triticum æstivum L.) produces better quality noodles and bread less prone to going stale, while little is known about the relationships between amylose content and the quality of soft wheat baking products such as sugar snap cookies (SSC) and Japanese sponge cakes (JSC). Near‐isogenic lines developed from wheat cultivar Norin 61, differing in their level of granule‐bound starch synthase (Wx protein) activity, were used to produce wheat grains and ultimately flours of different amylose contents. These were tested with regard to their effect on soft wheat baking quality and solvent retention capacities (SRC). Amylose content was strongly correlated to cookie diameter (r = 0.969, P < 0.001) and cake volume (r = 0.976, P < 0.001), indicating that the soft wheat baking quality associated with SSC diameter and JSC volume were improved by an incremental increases in amylose content. Among the four kinds of SRC tests (water, sodium carbonate, sucrose and lactic acid), the water SRC test showed the highest correlation with amylose content, SSC diameter, and JSC volume. When the regression analysis was conducted between the nonwaxy and partial waxy isogenic lines that are available in commercial markets, only water SRC was significantly correlated to amylose content (r = –0.982, P < 0.001) among of four SRC tests. This suggests that, unlike udon noodle quality, high‐amylose content is indispensable in improving soft wheat baking quality, a process requiring less water retention capacity.
Protease Treatment to Improve Ethanol Fermentation in Modified Dry Grind Corn Processes
Authors: Vidal Bernardo C. , Rausch Kent D. , Tumbleson M. E. , Singh Vijay
Published: May 2009

To improve fractionation efficiency in modified dry grind corn processes, we evaluated the effectiveness of protease treatment in reducing residual starch in endosperm fiber. Three schemes of protease treatment were conducted in three processes: 1) enzymatic milling or E‐Mill, 2) dry fractionation with raw starch fermentation or dry RS, and 3) dry fractionation with conventional fermentation or dry conv. Kinetics of free amino nitrogen production were similar in both dry and wet fractionation (E‐Mill), indicating that proteolysis was effective in all three schemes. At the end of fermentation, endosperm fiber was recovered and its residual starch measured. Using protease treatment, residual starch in the endosperm fiber was reduced by 1.9% w/w (22% relative reduction) in dry conv and 1.7% w/w (8% relative reduction) in dry RS, while no reduction was observed in the E‐Mill process. Protease treatment increased ethanol production rates early in fermentation (≤24 hr) but final ethanol concentrations were unaffected in both dry RS and E‐Mill. In dry conv, the addition of protease resulted in a decline in final ethanol concentration by 0.3% v/v, as well as a higher variability in liquefaction product concentration (higher standard deviations in the glucose and maltose yields). Protease treatment can be used effectively to enhance modified dry grind processes.
Characterization of Water State in Masa with Different Additives
Authors: Lucius Ruth , Gao Yani , Vodovotz Yael
Published: May 2009

Carboxymethyl cellulose (CMC) is added to tortillas to maintain a pliable texture during storage. A need exists to optimize or replace CMC in masa and tortilla manufacturing with cheaper yet adequate alternatives. Change in water distribution upon gum addition may be key to understanding stability of cooked masa. Therefore, the objective of this study was to characterize the state and distribution of water in masa systems containing two types of CMC and guar gum. Masa was mixed with 10% (1% in viscosity measurements) of different gums (either one of two CMCs varying in viscosity or guar) then hydrated to 50% moisture content. Viscosity, water holding capacity (WHC), total moisture content (TGA) as well as “freezable” (FW) and “unfreezable” (UFW) water (DSC) of all samples were obtained and compared. Viscosity measurements indicated guar gum may provide a good substitution for high viscosity CMC. The two water measurements, WHC and UFW, differed as to the effect of viscosity on water entrapment. WHC represented the short‐term imbibing of gums, while UFW indicated how the hydrocolloids responded in masa given full hydration time. UFW in guar gum was lower than in medium viscosity CMC. These initial results indicate that guar gum may prove a good substitute for CMC in masa applications.
Triaqua(2,2′-bipyridineN,N′-dioxide-κ2O,O′)(5-nitrobenzene-1,3-dicarboxylato-κO1)zinc(II)
Authors: Lu Hui-Juan , Wang Fang-Ming
Published: May 2009

In the title compound, [Zn(C8H3NO6)(C10H8N2O2)(H2O)3], the ZnIIion is coordinated in a distorted octahedral geometry by three water molecules, one O atom from a 5-nitrobenzene-1,3-dicarboxylate ligand and two O atoms from a chelating 2,2′-bipyridineN,N′-dioxide ligand. An extensive network of O—H...O hydrogen bonds is formed between the water molecules and the carboxylate groups. C—H...O interactions are also present.
4-(4-Chlorophenyl)-6-hydroxy-5-(2-thienylcarbonyl)-6-(trifluoromethyl)-3,4,5,6-tetrahydropyrimidin-2(1H)-one monohydrate
Authors: Mosslemin Mohammad Hossein , Nateghi Mohammad Reza , Sadoughi Hesamaddin , Lamei Asal
Published: May 2009

The asymmetric unit of the title compound, C16H12ClF3N2O3S·H2O, contains two crystallographically independent organic molecules and two water molecules. The organic species are linked by an intermolecular O—H...O hydrogen bond, while the water molecules are connected to them through intermolecular O—H...N hydrogen bonds. The thiophene and phenyl rings are oriented at dihedral angles of 62.35 (4) in the first independent molecule and 60.74 (5)° in the second, while the pyrimidine rings adopt twisted conformations in both molecules. Intramolecular N—H...F interactions result in the formation of two five-membered rings having envelope conformations. In the crystal structure, further intermolecular O—H...O and N—H...O hydrogen bonds link the molecules into chains.
2-Phenyl-1H-1,3,7,8-tetraazacyclopenta[l]phenanthrene
Authors: Liu Dong-Ming , Li Xiu-Ying , Wang Xiang-Cheng , Li Chun-Xiang , Liu Chun-Bo
Published: May 2009

There are two molecules in the asymmetric unit of the title compound, C19H12N4, with dihedral angles of 2.41 (10) and 10.53 (12)° between the fused ring system and the pendant phenyl ring. In the crystal, molecules are linked into chains by N—H...N hydrogen bonds and aromatic π–π stacking interactions [shortest centroid–centroid distance = 3.6176 (16) Å] complete the structure.
Cyclohexanaminium trichloroacetate
Authors: Shahwar Durre , Tahir M. Nawaz , Ahmad Naeem , Khan Muhammad Akmal , Saeed Afifa
Published: May 2009

In the crystal of the title compound, C6H14N+·C2Cl3O2−, centrosymmetric assemblies of two cyclohexanaminium cations and two trichloroacetate ions are linked by N—H...O hydrogen bonds, thereby formingR44(12) ring motifs. Further N—H...O interactions link the tetramers into chains propagating along theaaxis.
1,3-Bis{(+)-(S)-[1-(1-naphthyl)ethyl]iminomethyl}benzene dichloromethane solvate
Authors: Espinosa Leija Armando , Hernández Guadalupe , Cruz Sandra , Bernès Sylvain , Gutiérrez René
Published: May 2009

In the title compound, C32H28N2·CH2Cl2, the complete Schiff base and solvent molecules are both generated by crystallographic twofold axes, with the two C atoms of the former and the C atom of the latter lying on the rotation axis. The central benzene ring is substituted with two chiral groups including imine functionalities, with the commonEconfiguration. The dihedral angle between the central benzene ring and the terminal naphthalene ring is 45.42 (9)° and that between the two naphthalene rings is 89.16 (8)°. The conformation of the Schiff base allows solvent molecules to fill the voids in the crystal, affording a stable 1:1 solvate, but the solvent interacts poorly with the Schiff base, as reflected by its rather high displacement parameters.
Bis(μ-5-carboxylato-1-carboxylatomethyl-2-oxidopyridinium)-κ2O5:O1;κ2O1:O5-[diaqua(phenanthroline-κ2N,N′)manganese(II)] dihydrate
Authors: Jiang Mei-Xiang , Feng Yun-Long
Published: May 2009

The centrosymmetric binuclear title complex, [Mn2(C8H5NO5)2(C12H8N2)2(H2O)4]·2H2O, was obtained by the reaction of manganese chloride with 5-carboxy-1-carboxymethyl-2-oxidopyridinium and 1,10-phenanthroline. The MnIIatom is coordinated by two N atoms from the 1,10-phenanthroline ligand, two O atoms from two 5-carboxylato-1-carboxylatomethyl-2-oxidopyridinium ligands and two water molecules, leading to a distorted octahedral MnN2O4environment. Intermolecular O—H...O hydrogen bonds link neighbouring molecules into a layer structure parallel to (001).
1,1′,2,2′-Tetramethyl-3,3′-(4-methoxybenzylidene)di-1H-indole
Authors: Zhang Cai-Li , Ye Ping-Ping , Du Zhi-Qiang
Published: May 2009

The title compound, C28H28N2O, was prepared by condensation of 1,2-bimethylindole and 4-methoxybenzaldehyde. In the molecular structure, the plane of the non-fused benzene ring is twisted with respect to the planes of the two indole ring systems, exhibiting dihedral angles of 72.04 (7) and 72.24 (7)°, while the planes of the two indole ring systems are oriented at a dihedral angle of 87.05 (5)°. Neither hydrogen bonding nor π–π stacking is observed in the crystal structure.
Oxonium 2-carboxy-3-(2-furyl)acrylate
Authors: Liang Wen-Xian , Wang Gang , Qu Zhi-Rong
Published: May 2009

In the title compound, H3O+·C8H5O5−, neighbouring cations and anions are linked by O—H...O hydrogen bonds, forming a one-dimensional chain framework along [001]. The crystal structure is further stabilized by π–π interactions, with centroid–centroid distances of 3.734 (3) Å.
Capecitabine from X-ray powder synchrotron data
Authors: Rohlicek Jan , Husak Michal , Gavenda Ales , Jegorov Alexandr , Kratochvil Bohumil , Fitch Andy
Published: May 2009

In the title compound [systematic name 5-deoxy-5-fluoro-N-(pentyloxycarbonyl)cytidine], C15H22FN3O6, the pentyl chain is disordered over two positions with refined occupancies of 0.53 (5) and 0.47 (5). The furan ring assumes an envelope conformation. In the crystal, intermolecular N—H...O hydrogen bonds link the molecules into chains propagating along thebaxis. The crystal packing exhibits electrostatic interactions between the 5-fluoropyrimidin-2(1H)-one fragments of neighbouring molecules as indicated by short O...C [2.875 (3) and 2.961 (3) Å] and F...C [2.886 (3) Å] contacts.