bluuebunny/crossref_metadata_2025_split huggingface dataset:
Passage of Tropical Storm Allison (2001) over southeast Texas recorded in δ18O values of Ostracoda
Authors: Lawrence James R. , Hyeong Kiseong , Maddocks Rosalie F. , Lee Kwang-Sik 
Published: June 2008

AbstractFreshwater Ostracoda collected in ephemeral pond-waters derived from Tropical Storm Allison (2001, Texas) recorded the unusually low oxygen-isotope values of that storm. Therefore, the potential clearly exists, in locations where tropical cyclones make landfall, to obtain a long-term record of tropical cyclone activity from fossil ostracode calcite.
Guardians at the gate: quarantine and racialism in two Pacific Rim port cities, 1870–1914
Authors: MAYNE ALAN 
Published: June 2008

ABSTRACTThis article examines the ambivalent relationship that San Francisco and Darwin developed with Asia during the late nineteenth and early twentieth centuries. On the one hand they presented themselves as gateways that facilitated trade with Asia. On the other hand they acted as sentinels that protected Europeans from Asian immigration. This quirky behaviour is encapsulated in the quarantine regulations that were applied in both ports to Asian commodities and people. The two case studies suggest a broader paradox in the history of port cities. Their prosperity and vitality rested upon the free flow of goods and people, but those flows generated enormous frictions.
Mapping, tissue distribution and polymorphism of porcine genes encoding retinol binding proteins (RBP1 and RBP4)
Authors: Wei-Hua Gong , Zhong-Lin Tang , Wen-Tao Cui , Shu-Lin Yang , Kui Li 
Published: June 2008

AbstractUsing the INRA – University of Minnesota porcine 7000 Rad Radiation Hybrid panel (IMpRH) containing 118 clones, porcine cellular retinol binding protein gene 1 (RBP1) and plasma retinol binding protein gene 4 (RBP4) were assigned to porcine chromosomes 13 and 14, respectively. The mRNA distributions of the two genes in adult Wuzhishan pig tissues (lung, skeletal muscle, spleen, heart, stomach, large intestine, lymph node, small intestine, liver, brain, kidney and fat) were examined. One single nucleotide polymorphism (SNP) was identified in Laiwu, Wuzhishan, Guizhou, Bama pig breeds and a Tongcheng experimental population and analysed using a polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) method. Significant associations were found between different genotypes of A/G156 and maximum carcass length (LM), minimum carcass length (LN), haemoglobin (HGB), mean corpuscular volume haemoglobin (MCH), and day to slaughter weight (age) traits in the Tongcheng experimental population. This SNP locus might be used as a genetic marker in pig breeding and production.
Sexual assault centers: Attendance rates, and differences between early and late presenting cases
Authors: NESVOLD HELLE , FRIIS SVEIN , ORMSTAD KARI 
Published: June 2008

AbstractObjective. Sexual assault centers (SACs) aim at assisting victims and to provide forensic medical examination (FME). This study explores the gap between assaults actually occurring and those seen at SAC; and the characteristics of cases presented in time/too late for FME (early and late cohorts). Design. Retrograde descriptive study. Setting and sample. A two‐year series from a self‐referral SAC; characteristics of victims, assaults, use of services. Methods. Chi‐quadrate, uni‐ and multivariate logistic regression analyses. Main outcome measures. Number of female victims seen/female at‐risk population (attendance rates). Case and service profiles in the two cohorts. Adjusted odds for late presentation. Results. Attendance rates for females were 0.12% (14–55 years); an estimated 4–7% of sexually assaulted females in the catchment area. Two hundred and seventy eight victims arrived in time for FME, 76 later; 6% males. Assaults in the early cohort were more often performed by strangers. Two hundred and thirty‐eight victims underwent FME, 55% complied with follow‐up, 55% reported to the police. The late cohort contained more adolescent victims, more acquainted/partner perpetrators, more verbal coercion; 45% medically examined, 80% follow‐up compliance; 34% reported to police. Further referrals occurred equally often in both cohorts; 12% to somatic and 39% to psychiatric services. Among victims seen, 5% died within 7 years of consultation. Conclusion. Cases seen at SAC are strongly selected. The late cohort seems more representative of the commonly occurring assaults; young victims, known assailants. Even late presenters are in need of a multidisciplinary approach.
FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space
Authors: Chen Xiang , He Si-Min , Bu Dongbo , Zhang Fa , Wang Zhiyong , Chen Runsheng , Gao Wen 
Published: June 2008

Abstract
Motivation: RNA secondary structures with pseudoknots are often predicted by minimizing free energy, which is proved to be NP-hard. Due to kinetic reasons the real RNA secondary structure often has local instead of global minimum free energy. This implies that we may improve the performance of RNA secondary structure prediction by taking kinetics into account and minimize free energy in a local area.
Result: we propose a novel algorithm named FlexStem to predict RNA secondary structures with pseudoknots. Still based on MFE criterion, FlexStem adopts comprehensive energy models that allow complex pseudoknots. Unlike classical thermodynamic methods, our approach aims to simulate the RNA folding process by successive addition of maximal stems, reducing the search space while maintaining or even improving the prediction accuracy. This reduced space is constructed by our maximal stem strategy and stem-adding rule induced from elaborate statistical experiments on real RNA secondary structures. The strategy and the rule also reflect the folding characteristic of RNA from a new angle and help compensate for the deficiency of merely relying on MFE in RNA structure prediction. We validate FlexStem by applying it to tRNAs, 5SrRNAs and a large number of pseudoknotted structures and compare it with the well-known algorithms such as RNAfold, PKNOTS, PknotsRG, HotKnots and ILM according to their overall sensitivities and specificities, as well as positive and negative controls on pseudoknots. The results show that FlexStem significantly increases the prediction accuracy through its local search strategy.
Availability: Software is available at http://pfind.ict.ac.cn/FlexStem/
Contact: xchen@jdl.ac.cn; wgao@pku.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors
Authors: Liu Jiajian , Stormo Gary D. 
Published: June 2008

Abstract
Motivation: Modeling and identifying the DNA-protein recognition code is one of the most challenging problems in computational biology. Several quantitative methods have been developed to model DNA-protein interactions with specific focus on the C2H2 zinc-finger proteins, the largest transcription factor family in eukaryotic genomes. In many cases, they performed well. But the overall the predictive accuracy of these methods is still limited. One of the major reasons is all these methods used weight matrix models to represent DNA-protein interactions, assuming all base-amino acid contacts contribute independently to the total free energy of binding.
Results: We present a context-dependent model for DNA–zinc-finger protein interactions that allows us to identify inter-positional dependencies in the DNA recognition code for C2H2 zinc-finger proteins. The degree of non-independence was detected by comparing the linear perceptron model with the non-linear neural net (NN) model for their predictions of DNA–zinc-finger protein interactions. This dependency is supported by the complex base-amino acid contacts observed in DNA–zinc-finger interactions from structural analyses. Using extensive published qualitative and quantitative experimental data, we demonstrated that the context-dependent model developed in this study can significantly improves predictions of DNA binding profiles and free energies of binding for both individual zinc fingers and proteins with multiple zinc fingers when comparing to previous positional-independent models. This approach can be extended to other protein families with complex base-amino acid residue interactions that would help to further understand the transcriptional regulation in eukaryotic genomes.
Availability:The software implemented as c programs and are available by request. http://ural.wustl.edu/softwares.html
Contact: stormo@ural.wustl.edu
Unraveling transcriptional regulatory programs by integrative analysis of microarray and transcription factor binding data
Authors: Li Huai , Zhan Ming 
Published: June 2008

Abstract
Motivation: Unraveling the transcriptional regulatory program mediated by transcription factors (TFs) is a fundamental objective of computational biology, yet still remains a challenge.
Method: Here, we present a new methodology that integrates microarray and TF binding data for unraveling transcriptional regulatory networks. The algorithm is based on a two-stage constrained matrix decomposition model. The model takes into account the non-linear structure in gene expression data, particularly in the TF-target gene interactions and the combinatorial nature of gene regulation by TFs. The gene expression profile is modeled as a linear weighted combination of the activity profiles of a set of TFs. The TF activity profiles are deduced from the expression levels of TF target genes, instead directly from TFs themselves. The TF-target gene relationships are derived from ChIP-chip and other TF binding data. The proposed algorithm can not only identify transcriptional modules, but also reveal regulatory programs of which TFs control which target genes in which specific ways (either activating or inhibiting).
Results: In comparison with other methods, our algorithm identifies biologically more meaningful transcriptional modules relating to specific TFs. We applied the new algorithm on yeast cell cycle and stress response data. While known transcriptional regulations were confirmed, novel TF-gene interactions were predicted and provide new insights into the regulatory mechanisms of the cell.
Contact: zhanmi@mail.nih.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
The distribution of chondrichthyans along the northern coast of Norway
Authors: Williams Tom , Helle Kristin , Aschan Michaela 
Published: June 2008

Abstract
Williams, T., Helle, K., and Aschan, M. 2008. The distribution of chondrichthyans along the northern coast of Norway. – ICES Journal of Marine Science, 65: 1161–1174. The relationship between temperature, latitude, and depth and the distribution and relative abundance of chondrichthyans along the northern coast of Norway was examined based on catches made in scientific trawls north of 62°N from 1992 to 2005. It appears that Chimaera monstrosa, Etmopterus spinax, Squalus acanthias, and Galeus melastomus were more abundant in the south, and Amblyraja radiata more common in the north. Between 1992 and 2005, the distribution and relative abundance did not appear to change significantly, although average water temperatures rose during the period. Current fishing levels do not appear to be impacting the populations of the more common species, but the status of species rarely found in the survey catches is unclear.
Antagonistic Interaction between Systemic Acquired Resistance and the Abscisic Acid–Mediated Abiotic Stress Response in Arabidopsis
Authors: Yasuda Michiko , Ishikawa Atsushi , Jikumaru Yusuke , Seki Motoaki , Umezawa Taishi , Asami Tadao , Maruyama-Nakashita Akiko , Kudo Toshiaki , Shinozaki Kazuo , Yoshida Shigeo , Nakashita Hideo 
Published: June 2008

Abstract
Systemic acquired resistance (SAR) is a potent innate immunity system in plants that is effective against a broad range of pathogens. SAR development in dicotyledonous plants, such as tobacco (Nicotiana tabacum) and Arabidopsis thaliana, is mediated by salicylic acid (SA). Here, using two types of SAR-inducing chemicals, 1,2-benzisothiazol-3(2H)-one1,1-dioxide and benzo(1,2,3)thiadiazole-7-carbothioic acid S-methyl ester, which act upstream and downstream of SA in the SAR signaling pathway, respectively, we show that treatment with abscisic acid (ABA) suppresses the induction of SAR in Arabidopsis. In an analysis using several mutants in combination with these chemicals, treatment with ABA suppressed SAR induction by inhibiting the pathway both upstream and downstream of SA, independently of the jasmonic acid/ethylene-mediated signaling pathway. Suppression of SAR induction by the NaCl-activated environmental stress response proved to be ABA dependent. Conversely, the activation of SAR suppressed the expression of ABA biosynthesis–related and ABA-responsive genes, in which the NPR1 protein or signaling downstream of NPR1 appears to contribute. Therefore, our data have revealed that antagonistic crosstalk occurs at multiple steps between the SA-mediated signaling of SAR induction and the ABA-mediated signaling of environmental stress responses.
SPIN1, a K Homology Domain Protein Negatively Regulated and Ubiquitinated by the E3 Ubiquitin Ligase SPL11, Is Involved in Flowering Time Control in Rice
Authors: Vega-Sánchez Miguel E. , Zeng Lirong , Chen Songbiao , Leung Hei , Wang Guo-Liang 
Published: June 2008

Abstract
The rice (Oryza sativa) E3 ligase SPOTTED LEAF11 (SPL11) negatively regulates programmed cell death and disease resistance. We demonstrate here that SPL11 also regulates flowering via interaction with SPIN1 (for SPL11-interacting protein1), a Signal Transduction and Activation of RNA family member. SPIN1 binds RNA and DNA in vitro and interacts with SPL11 in the nucleus. Spl11 mutants have delayed flowering under long-day conditions. Spin1 overexpression causes late flowering independently of daylength; expression analyses of flowering marker genes in these lines suggested that SPIN1 represses flowering by downregulating the flowering promoter gene Heading date3a (Hd3a) via Hd1-dependent mechanisms in short days and by targeting Hd1-independent factors in long days. Both Spin1 and Spl11 are regulated diurnally in opposing phases. SPL11 negatively regulates Spin1 transcript levels, while SPIN1 also affects Spl11 expression. Moreover, we show that coincidence of high accumulation of Spin1 mRNA with the light in the morning and early evening is needed to repress flowering. SPIN1 is monoubiquitinated by SPL11, suggesting that it is not targeted for degradation. Our data are consistent with a model in which SPIN1 acts as a negative regulator of flowering that itself is negatively regulated by SPL11, possibly via ubiquitination.
An integrated research framework to understand consumer attitudes and purchase intentions toward genetically modified foods
Authors: Chen Mei‐Fang 
Published: June 2008

PurposeGiven that the increased marketing of genetically modified (GM) food products and the attitudes of the public have a strong impact on the progress of this emerging gene technology, this study aims to shed light on the antecedents relating to the extent of both the adoption and the purchase intention of GM foods.Design/methodology/approachThis work is done from an integrated research framework based on the Attitude Model and the Theory of Planned Behavior (TPB) by using structural equation modeling (SEM) analysis.FindingsThe results support the use of the construct “attitude toward GM foods” as a bridge to connect the Attitude Model and the Behavioral Intention Model so as to establish an integrated research framework and to shed light on how consumers form their attitudes and make purchase intentions toward GM foods.Practical implicationsGM food marketers should make special efforts to convince the public that this new emerging technology as applied to food production will provide more benefits than ever before, with the consequence that consumers will hold a more positive attitude toward GM foods that leads to their purchase intentions.Originality/valueThis study pioneers in building an integrated research framework to understand how consumers form their attitudes and make purchase intentions toward GM foods.
An analysis of the factors affecting the food places where consumers purchase red meat
Authors: Kizilaslan Halil , Gokalp Goktolga Z. , Kizilaslan Nuray 
Published: June 2008

PurposeThe purpose of this paper is to determine the socio‐economic factors affecting meat sales outlets, as preferred by the consumers of the city of Tokat, Turkey. This paper underlines the social and economic factors leading to healthy meat outlet preferences and focuses the attention of producers, policy makers, sellers and consumers on the issue, which will lead to the creation of a healthier and more aware society.Design/methodology/approachWithin the research, the sample size, preferred as 263, will deviate at a maximum of 6 percent from the main population at 95 percent importance level. The inquiries are proportionally dispersed between the quarters, considering the population, in accordance with the records of 2006. Surveys were carried out by way of direct interviews by the researchers. In the survey, particular attention was paid to ensure that the interviewee was the decision maker in regards to the purchasing of foods. Meat outlets (market places, butchers and hypermarkets) were chosen as the dependent variables of the model. The independent variables were the sex, age and educational background of the consumers, household size, place of residence, the status of the mother, income, price difference, quality difference, hygiene, freshness and the seller's image. The multinomial logit model was used to measure the effect of the independent variables on the dependent variable.FindingsAccording to the results of the research; such factors as age, household size, place of residence, status of the mother, income, price difference, quality difference, hygiene, freshness and the seller's image are deemed to be the variables affecting the consumers' meat outlet preferences.Practical implicationsStudies of this nature will be particularly beneficial for policy makers, producers and consumers in the sector and the researchers in the field. By extension, conducting such studies aimed at determining consumer habits from the perspective of Turkey, will ultimately help form consumer consciousness, protect consumer health and raise the sellers' income. Defining aptitude of consumers' demands, searching reasons for buying choices will be helpful for the food safety, hygiene and quality standards to become a matter of importance.Originality/valueThis paper underlines the social and economic factors leading to healthy meat outlet preferences and focuses the attention of producers, policy makers, sellers and consumers on the issue, which will lead to the creation of a healthier and more aware society.
Intuitive and explicit reactions towards “new” food technologies
Authors: Tenbült Petra , de Vries Nanne K. , Dreezens Ellen , Martijn Carolien 
Published: June 2008

PurposeNew food technologies are of increasing importance but not a lot of research into how people react to these technologies has been conducted. The purpose of this paper is to provide insight into how implicit measurements in addition to explicit measurements give insight into how well an attitude towards a food concept, in relation to its familiarity, is predictive for behaviour.Design/methodology/approachAn implicit measurement (EAST) and an explicit questionnaire were used to investigate people's attitudes and attitude strength towards two food technologies (genetic modification and organic production). Correlations between the two measurements were calculated to determine whether familiar food technologies are more predictive for behaviour than relatively unfamiliar food technologies.FindingsImplicit measurements showed negative associations with genetic modification. Explicit measurements showed neutral associations with genetic modification. In contrast, implicit and explicit measurements showed positive associations with organic production. When a food technology is well known (e.g. organic production), significant correlations between the two measurements were present suggesting that attitudes were predictive for behaviour. In contrast, when a food technology is not well known (e.g. genetic modification), significant correlations were not present suggesting that attitudes were not predictive for behaviour.Originality/valueThis is the first study to examine the relation between intuitive and explicit reactions in relation with the novelty of food technologies.
Who defines ethics in your organization?
Authors: Crosbie Rowena 
Published: June 2008

PurposeThe purpose of this paper is to explore ethics at work and present the inherent challenges facing both leaders and learning professionals in encouraging ethical behavior.Design/methodology/approachSurvey results are presented that reveal large numbers of people who consider themselves ethical also confess to lying, cheating and stealing. Five practical tips are provided to help learning professionals address these contradictions.FindingsPeople often rationalize their bad behavior, after the fact, to preserve their own internal beliefs that their behavior is indeed on high moral ground. This reality presents unique challenges for those charged with defining ethics in organizations.Research limitations/implicationsThe 2006 survey, conducted by the Josephson Institute of Ethics (the CHARACTER COUNTS!SM organization) was extensive in that it involved over 35,000 respondents. While it paints a picture of the future workforce and informs readers of associated challenges, it does not include representatives of the current workforce.Practical implicationsOrganizations seeking to promote ethics must translate their values statements into specific behavioral terms and provide training to help leaders and employees alike clearly understand and demonstrate the desired culture.Originality/valueThis paper provides an analysis of research around (un)ethical behavior of the members of the future workforce, along with useful actionable steps for learning professionals.