bluuebunny/crossref_metadata_2025_split huggingface dataset:
The development of finiteness from a lexical to a functional category
Authors: Jordens Peter 
Published: August 2008

Finiteness in adult Dutch is expressed by use of formal means of morpho-syntax, i.e. with both inflectional morphology and word order (verb-second). These formal means are linked to a projection of the functional category FIN as in:
FIN
SpecFIN FIN
FIN VP
SpecVP VP
At the initial stage of acquisition, there is no productive use of functional elements nor do learner languages have verb-second. This is due to the fact that initially learner languages are systems in which the functional category FIN is absent. Properties of validation and anchoring are expressed by lexical means: Expression of illocutionary force occurs with modal predicates, contextual anchoring is expressed with deictic elements. Instantiation of the functional projection FIN is caused by the acquisition of the auxiliary verb heb/heeft (have/has). As a functional category, AUX provides a position for functional elements to express modal or – in the default case – non-modal illocutionary force. With the instantiation of AUX, the initial, i.e. specifier position serves as a position for elements with topic function, i.e. for elements used to establish contextual anchoring of the utterance. The acquisition of AUX is the driving force in the development from the lexical to the functional stage. However, the acquisition of AUX does not come as a deus ex machina. Structures with AUX are learned for reasons of information processing. Utterances with an auxiliary are typically used as a topicalisation device. Due to the fact that structures with AUX are learned as a topicalisation device, it seems possible (1) to provide a functional explanation for why auxiliaries, inversion and subject pronouns are learned simultaneously and (2) to account for the fact that the acquisition process occurs similarly in both L1- and L2-learner languages.
AMIN domains have a predicted role in localization of diverse periplasmic protein complexes
Authors: de Souza Robson Francisco , Anantharaman Vivek , de Souza Sandro José , Aravind L. , Gueiros-Filho Frederico J. 
Published: August 2008

Abstract
We describe AMIN (Amidase N-terminal domain), a novel protein domain found specifically in bacterial periplasmic proteins. AMIN domains are widely distributed among peptidoglycan hydrolases and transporter protein families. Based on experimental data, contextual information and phyletic profiles, we suggest that AMIN domains mediate the targeting of periplasmic or extracellular proteins to specific regions of the bacterial envelope.
Contact: fgueiros@iq.usp.br
Supplementary information: Supplementary data are available at Bioinformatics online.
Optimal design of thermally stable proteins
Authors: Bannen Ryan M. , Suresh Vanitha , Phillips George N. , Wright Stephen J. , Mitchell Julie C. 
Published: August 2008

Abstract
Motivation: For many biotechnological purposes, it is desirable to redesign proteins to be more structurally and functionally stable at higher temperatures. For example, chemical reactions are intrinsically faster at higher temperatures, so using enzymes that are stable at higher temperatures would lead to more efficient industrial processes. We describe an innovative and computationally efficient method called Improved Configurational Entropy (ICE), which can be used to redesign a protein to be more thermally stable (i.e. stable at high temperatures). This can be accomplished by systematically modifying the amino acid sequence via local structural entropy (LSE) minimization. The minimization problem is modeled as a shortest path problem in an acyclic graph with nonnegative weights and is solved efficiently using Dijkstra's method.
Contact: mitchell@biochem.wisc.edu
Improving position-specific predictions of protein functional sites using phylogenetic motifs
Authors: Dukka Bahadur K. C. , Livesay Dennis R. 
Published: August 2008

Abstract
Motivation: Accurate computational prediction of protein functional sites is critical to maximizing the utility of recent high-throughput sequencing efforts. Among the available approaches, position-specific conservation scores remain among the most popular due to their accuracy and ease of computation. Unfortunately, high false positive rates remain a limiting factor. Using phylogenetic motifs (PMs), we have developed two combined (conservation + PMs) prediction schemes that significantly improve prediction accuracy.
Results: Our first approach, called position-specific MINER (psMINER), rank orders alignment columns by conservation. Subsequently, positions that are also not identified as PMs are excluded from the prediction set. This approach improves prediction accuracy, in a statistically significant way, compared to the underlying conservation scores. Increased accuracy is a general result, meaning improvement is observed over several different conservation scores that span a continuum of complexity. In addition, a hybrid MINER (hMINER) that quantitatively considers both scoring regimes provides further improvement. More importantly, it provides critical insight into the relative importance of phylogeny versus alignment conservation. Both methods outperform other common prediction algorithms that also utilize phylogenetic concepts. Finally, we demonstrate that the presented results are critically sensitive to functional site definition, thus highlighting the need for more complete benchmarks within the prediction community.
Availability: Our benchmark datasets are available for download at http://www.cs.uncc.edu/~drlivesa/dataset.html.
Contact: drlivesa@uncc.edu
Supplementary information: Supplementary data is available at Bioinformatics online.
Penalties and rewards for over- and underages of catch allocations
Authors: Powers Joseph E. , Brooks Elizabeth N. 
Published: August 2008

Abstract
Powers, J. E., and Brooks, E. N. 2008. Penalties and rewards for over- and underages of catch allocations. – ICES Journal of Marine Science, 65: 1541–1551. Many fisheries are managed using a total allowable catch (TAC) that is subsequently sub-allocated to different fisheries sectors. These allocations are then monitored separately to ensure the adherence of each fishery to its particular allocation quota and to the overall TAC. In some management arenas, there are systems of “payback” where over- and underages are punished or rewarded using particular decision rules. Differences between fishing gear, the sizes and ages of fish being targeted by those gears, and the spatio-temporal distribution of the fishers using those gears can lead to different precision, accuracy, and cost of monitoring the allocation, affecting the probability that an overall management objective is reached. Weaknesses in monitoring may be exploited by user groups in their competition for larger catches and, subsequently, bigger allocations, so differential monitoring precision and accuracy can lead to both short- and long-term reallocations, i.e. a new set of winners and losers. Simulations in a management strategy evaluation framework were used to demonstrate the implications of alternative decision rules regarding payback on conservation and sustainability objectives and rebuilding time frames. The efficacy of the rules under alternative monitoring systems was also examined. Decision rules allowing payback prolong rebuilding (compared with perfect implementation or more precautionary TACs), especially if monitoring is biased (catches misreported) or imprecise. When precision of reported catches was increased and/or bias decreased, better yields and stock abundance resulted. When overages were penalized and underages not rewarded, recovery was achieved earlier. Conversely, policies in which transgressions were ignored and underages rewarded did not perform well. Underreporting by one nation may result in stocks that are well below the stock size conservation standards, yet produce substantial gains in yield for that nation, unless other nations retaliate by underreporting.
DNA base flipping by both members of the PspGI restriction-modification system
Authors: Carpenter Michael A. , Bhagwat Ashok S. 
Published: August 2008

Abstract
The PspGI restriction–modification system recognizes the sequence CCWGG. R.PspGI cuts DNA before the first C in the cognate sequence and M.PspGI is thought to methylate N4 of one of the cytosines in the sequence. M.PspGI enhances fluorescence of 2-aminopurine in DNA if it replaces the second C in the sequence, while R.PspGI enhances fluorescence when the fluorophore replaces ade-nine in the central base pair. This strongly suggests that the methyltransferase flips the second C in the recognition sequence, while the endonuclease flips both bases in the central base pair out of the duplex. M.PspGI is the first N4-cytosine MTase for which biochemical evidence for base flipping has been presented. It is also the first type IIP methyltransferase whose catalytic activity is strongly stimulated by divalent metal ions. However, divalent metal ions are not required for its base-flipping activity. In contrast, these ions are required for both base flipping and catalysis by the endonuclease. The two enzymes have similar temperature profiles for base flipping and optimal flipping occurs at temperatures substantially below the growth temperature of the source organism for PspGI and for the catalytic activity of endonuclease. We discuss the implications of these results for DNA binding by these enzymes and their evolutionary origin.
Abnormal Chloroplast Development and Growth Inhibition in Rice ThioredoxinmKnock-Down Plants
Authors: Chi Yong Hun , Moon Jeong Chan , Park Jin Ho , Kim Ho-Seung , Zulfugarov Ismayil S. , Fanata Wahyu Indra , Jang Ho Hee , Lee Jung Ro , Lee Young Mee , Kim Sun Tae , Chung Yong-Yoon , Lim Chae Oh , Kim Jae-Yean , Yun Dae-Jin , Lee Choon-Hwan , Lee Kyun Oh , Lee Sang Yeol 
Published: August 2008

AbstractPlant cells contain several thioredoxin isoforms that are characterized by subcellular localization and substrate specificity. Here, we describe the functional characterization of a rice (Oryza sativa) thioredoxin m isoform (Ostrxm) using a reverse genetics technique. Ostrxm showed green tissue-specific and light-responsive mRNA expression. Ostrxm was localized in chloroplasts of rice mesophyll cells, and the recombinant protein showed dithiothreitol-dependent insulin β-chain reduction activity in vitro. RNA interference (RNAi) of Ostrxm resulted in rice plants with developmental defects, including semidwarfism, pale-green leaves, abnormal chloroplast structure, and reduced carotenoid and chlorophyll content. Ostrxm RNAi plants showed remarkably decreased F v/F m values under high irradiance conditions (1,000 μmol m−2 s−1) with delayed recovery. Two-dimensional electrophoresis and matrix-assisted laser-desorption/ionization time-of-flight analysis showed that the levels of several chloroplast proteins critical for photosynthesis and biogenesis were significantly decreased in Ostrxm RNAi plants. Furthermore, 2-Cys peroxiredoxin, a known target of thioredoxin, was present in oxidized forms, and hydrogen peroxide levels were increased in Ostrxm RNAi plants. The pleiotropic effects of Ostrxm RNAi suggest that Ostrxm plays an important role in the redox regulation of chloroplast target proteins involved in diverse physiological functions.
Independently Silencing Two Photosynthetic Proteins inNicotiana attenuataHas Different Effects on Herbivore Resistance
Authors: Mitra Sirsha , Baldwin Ian T. 
Published: August 2008

AbstractInsect attack frequently down-regulates photosynthetic proteins. To understand how this influences the plant-insect interaction, we transformed Nicotiana attenuata to independently silence ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPCase) activase (RCA) and RuBPCase and selected lines whose photosynthetic capacity was similarly reduced. Decreases in plant growth mirrored the decreases in photosynthesis, but the effects on herbivore performance differed. Both generalist (Spodoptera littoralis) and specialist (Manduca sexta) larvae grew larger on RCA-silenced plants, which was consistent with decreased levels of trypsin protease inhibitors and diterpene glycosides and increased levels of RuBPCase, the larvae's main dietary protein. RCA-silenced plants were impaired in their attack-elicited jasmonate (JA)-isoleucine (Ile)/leucine levels, but RuBPCase-silenced plants were not, a deficiency that could not be restored by supplementation with Ile or attributed to lower transcript levels of JAR4/6, the key enzyme for JA-Ile conjugation. From these results, we infer that JA-Ile/leucine signaling and the herbivore resistance traits elicited by JA-Ile are influenced by adenylate charge, or more generally, carbon availability in RCA- but not RuBPCase-silenced plants. Growth of generalist larvae on RuBPCase-silenced plants did not differ from growth on empty vector controls, but the specialist larvae grew faster on RuBPCase-silenced plants, which suggests that the specialist can better tolerate the protein deficiency resulting from RuBPCase silencing than the generalist can. We conclude that the plant-herbivore interaction is more influenced by the particular mechanisms that reduce photosynthetic capacity after herbivore attack than by the magnitude of the decrease, which highlights the value of understanding defense mechanisms in evaluating growth-defense tradeoffs.
RACK1 Functions in Rice Innate Immunity by Interacting with the Rac1 Immune Complex
Authors: Nakashima Ayako , Chen Letian , Thao Nguyen Phuong , Fujiwara Masayuki , Wong Hann Ling , Kuwano Masayoshi , Umemura Kenji , Shirasu Ken , Kawasaki Tsutomu , Shimamoto Ko 
Published: August 2008

AbstractA small GTPase, Rac1, plays a key role in rice (Oryza sativa) innate immunity as part of a complex of regulatory proteins. Here, we used affinity column chromatography to identify rice RACK1 (for Receptor for Activated C-Kinase 1) as an interactor with Rac1. RACK1 functions in various mammalian signaling pathways and is involved in hormone signaling and development in plants. Rice contains two RACK1 genes, RACK1A and RACK1B, and the RACK1A protein interacts with the GTP form of Rac1. Rac1 positively regulates RACK1A at both the transcriptional and posttranscriptional levels. RACK1A transcription was also induced by a fungal elicitor and by abscisic acid, jasmonate, and auxin. Analysis of transgenic rice plants and cell cultures indicates that RACK1A plays a role in the production of reactive oxygen species (ROS) and in resistance against rice blast infection. Overexpression of RACK1A enhances ROS production in rice seedlings. RACK1A was shown to interact with the N terminus of NADPH oxidase, RAR1, and SGT1, key regulators of plant disease resistance. These results suggest that RACK1A functions in rice innate immunity by interacting with multiple proteins in the Rac1 immune complex.
Type B Response Regulators of Arabidopsis Play Key Roles in Cytokinin Signaling and Plant Development
Authors: Argyros Rebecca D. , Mathews Dennis E. , Chiang Yi-Hsuan , Palmer Christine M. , Thibault Derek M. , Etheridge Naomi , Argyros D. Aaron , Mason Michael G. , Kieber Joseph J. , Schaller G. Eric 
Published: August 2008

Abstract
The type B Arabidopsis Response Regulators (ARRs) of Arabidopsis thaliana are transcription factors that act as positive regulators in the two-component cytokinin signaling pathway. We employed a mutant-based approach to perform a detailed characterization of the roles of ARR1, ARR10, and ARR12 in plant growth and development. The most pronounced phenotype was found in the arr1-3 arr10-5 arr12-1 triple loss-of-function mutant, which showed almost complete insensitivity to high levels of exogenously applied cytokinins. The triple mutant exhibited reduced stature due to decreased cell division in the shoot, enhanced seed size, increased sensitivity to light, altered chlorophyll and anthocyanin concentrations, and an aborted primary root with protoxylem but no metaxylem. Microarray analysis revealed that expression of the majority of cytokinin-regulated genes requires the function of ARR1, ARR10, and ARR12. Characterization of double mutants revealed differing contributions of the type B ARRs to mutant phenotypes. Our results support a model in which cytokinin regulates a wide array of downstream responses through the action of a multistep phosphorelay that culminates in transcriptional regulation by ARR1, ARR10, and ARR12.
Effective adoption of agri‐food assurance systems
Authors: Soderlund Russell , Williams Richard , Mulligan Cathy 
Published: August 2008

PurposeThe purpose of this article is to identify the drivers for, and barriers to, the adoption of assurance systems in a range of agri‐food value chains that will allow the design of better, more appropriate‐for‐the‐task assurance systems that are more likely to be fully utilised by value chain members.Design/methodology/approachSemi‐structured interviews were used to collect a snapshot of the knowledge, attitudes, skills and aspirations (KASA) of value‐chain members with regard to assurance systems in fruit (cherries), seafood (mussels) and red meat (lamb). Responses were grouped by KASA characteristic for qualitative analysis. The nature of the dairy industry necessitated the use of a desktop review of the food‐safety assurance system.FindingsThe actual drivers for, and barriers to, adoption varied with the industry studied but included the requirements of domestic and export market customers, realistic appreciation of risk, mandatory schemes, the influence of other value chain members, financial incentives and external influences. The major barrier to the adoption of assurance systems was the perception that the costs of such an assurance system outweigh its benefits.Research limitations/implicationsThis study was purely qualitative and covered only one value chain within each of three industries with a desktop review in a fourth industry.Practical implicationsA suite of drivers that includes financial incentives results in more effective adoption of assurance systems than a single driver such as market access.Originality/valueThe observations could lead to a series of design principles for the development and deployment of agri‐food assurance systems.
Food safety practices in milk collection centers in Turkey: a case study
Authors: Demirbaş Nevin , Gölge Evren , Tosun Duygu , Çukur Figen 
Published: August 2008

PurposeThe aim of this study was to reveal the role and importance of the milk collection centers in İzmir in assuring food safety in the Turkish dairy sector.Design/methodology/approachA five‐point Likert scale was applied to collect data on the food safety practices and the problems confronted in MCCs. The difference between the groups in the managers' and MCCs' specifications and the food safety applications in the MCCs were determined by one‐way ANOVA for continuous variables. For the continuous variables, a normal distribution test was applied by Jarque‐Bera test. For variables displaying normal distribution, analysis of variance (one‐way ANOVA) was performed. For the variables not displaying normal distribution, Kruskall‐Wallis test. In the evaluation of other data descriptive statistics were applied.FindingsBecause the milk in the MCCs is generally obtained from small‐scale family farms, it is not of the desired quality from a food safety and food quality perspective. The quality control analysis of raw milk cannot be carried out because of the lack of qualified specialists and equipment inadequacies. The most general test applied on milk delivery is based on the monitoring of the sensory properties of the milk.Research limitations/implicationsAll MCCs were covered in the sample size of the research and the questionnaires were applied to all 43 MCC managers in İzmir.Practical implicationsAn effective organizational and educational structure must be established to monitor food safety and related practices in MCCs.Originality/valueThe paper adds to the body of knowledge on procecessors and their attitudes to food safety and suggests implementation of various practices which could improve results.
Consumer perspectives: take‐out packaging and food safety
Authors: Boyce Janice , Broz Charles C. , Binkley Margaret 
Published: August 2008

PurposeA consumer focus group was conducted in West Texas, to discuss consumer opinion about desired features in take‐out containers or packaging, and perceptions related to food safety practices.FindingsThe results of this qualitative case study indicated that the majority of take‐out food was purchased for personal consumption, and that location, convenience and time are the primary factors influencing the decision for purchase. The main features considered desirable in take‐out containers were these: the ability to insulate food, to contain product without spillage, and to keep individual foods separate within the same package.Practical implicationsAs the desirability for take‐out food continues to increase, risks emerge surrounding the lack of handling instructions on most take‐out packaging, and the scarcity of consumer food safety knowledge. Though most participants in this study claimed to return home quickly with take‐out food after purchase, and consume the food as soon as possible, a good number admitted to not being as knowledgeable about food safety and handling as they would like.Research limitations/implicationsThough data were collected from a diverse group of panelists, the small scope of this research could not be said to represent the USA as a whole. Future studies would need to include multiple focus group studies in metropolitan regions across the nation.Originality/valueThe paper adds to the body of knowledge on take‐out food and customer attitudes to food safety.
Marketing aspects of quality assurance systems
Authors: Achilleas Kontogeorgos , Anastasios Semos 
Published: August 2008

PurposeThe purpose of this paper is to describe the effect of quality assurance systems on business performance and subsequently, how a quality assurance system can be utilized as a determinant factor of a firm's marketing strategy, especially for the organic food sector.Design/methodology/approachBased on literature and the quality theory, the following subjects are examined: the types of goods according to their quality attributes, the benefits of participating in a quality award procedure, how a quality assurance system affect on firms' performance, and finally, the factors that determine consumers' willingness to pay a price premium for organic products.FindingsThe findings showed that, better quality conformance is associated with sales growth and better sales margins. Moreover, the most important benefit of a quality certification is its ability to increase market share and provide access to new market. In addition, the key to define quality is consumers and a company's internal definition of quality must reflect consumers' requirements. Finally, factors such as socio‐demographic characteristics, the perceived quality and risks have been found to be important determinants of consumers' willingness to pay a price premium to buy organic food products.Originality/valueThis study presents an outline of how a quality assurance system can be used to provide not only consistent product quality but also different elements that can be used to determine a firm's marketing strategy. The findings can help all the involved bodies to avoid the impediments and develop an appropriate marketing strategy for the effective promotion of certified organic food products.