bluuebunny/crossref_metadata_2025_split huggingface dataset:
International Financial Volatility and Commodity Exports: Evidence from the Thai Agricultural Sector
Authors: May Justin B. 
Published: January 2010

AbstractUsing 1981–2006 data from the Bank of Thailand, I estimate the effect of four measures of real exchange rate volatility on Thai exports of five key agricultural commodities, controlling for both the level of the real exchange rate and foreign incomes. Estimates of the effect of volatility on export volume are generally negative and often significant, lending support to a range of theoretical models that predict such an effect. No such relationship exists between lagged values of exchange rate volatility and agricultural production. The range of results obtained using various measures of volatility suggests caution in comparing studies using different measures.
Profit Margin Hedging
Authors: Kim Hyun Seok , Brorsen B. Wade , Anderson Kim B. 
Published: January 2010

AbstractSome extension economists and others recommend profit margin hedging as a way to choose the timing of crop sales. However, the theory behind this strategy recommendation is not well developed. This article determines the producer's utility function and price processes where profit margin hedging is optimal. Profit margin hedging is shown to be an optimal strategy under a highly restricted target utility function even in an efficient market. Profit margin hedging is profitable if prices are mean reverting.
A fast and automated solution for accurately resolving protein domain architectures
Authors: Yeats Corin , Redfern Oliver C. , Orengo Christine 
Published: January 2010

Abstract
Motivation: Accurate prediction of the domain content and arrangement in multi-domain proteins (which make up &gt;65% of the large-scale protein databases) provides a valuable tool for function prediction, comparative genomics and studies of molecular evolution. However, scanning a multi-domain protein against a database of domain sequence profiles can often produce conflicting and overlapping matches. We have developed a novel method that employs heaviest weighted clique-finding (HCF), which we show significantly outperforms standard published approaches based on successively assigning the best non-overlapping match (Best Match Cascade, BMC).
Results: We created benchmark data set of structural domain assignments in the CATH database and a corresponding set of Hidden Markov Model-based domain predictions. Using these, we demonstrate that by considering all possible combinations of matches using the HCF approach, we achieve much higher prediction accuracy than the standard BMC method. We also show that it is essential to allow overlapping domain matches to a query in order to identify correct domain assignments. Furthermore, we introduce a straightforward and effective protocol for resolving any overlapping assignments, and producing a single set of non-overlapping predicted domains.
Availability and implementation: The new approach will be used to determine MDAs for UniProt and Ensembl, and made available via the Gene3D website: http://gene3d.biochem.ucl.ac.uk/Gene3D/. The software has been implemented in C++ and compiled for Linux: source code and binaries can be found at: ftp://ftp.biochem.ucl.ac.uk/pub/gene3d_data/DomainFinder3/
Contact: yeats@biochem.ucl.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Gene selection in microarray survival studies under possibly non-proportional hazards
Authors: Dunkler Daniela , Schemper Michael , Heinze Georg 
Published: January 2010

AbstractMotivation: Univariate Cox regression (COX) is often used to select genes possibly linked to survival. With non-proportional hazards (NPH), COX could lead to under- or over-estimation of effects.The effect size measure c=P(T1&lt;T0), i.e. the probability that a person randomly chosen from group G1 dies earlier than a person from G0, is independent of the proportional hazards (PH) assumption. Here we consider its generalization to continuous data c′ and investigate the suitability of c′ for gene selection.Results: Under PH, c′ is most efficiently estimated by COX. Under NPH, c′ can be obtained by weighted Cox regression (WHE) or a novel method, concordance regression (CON). The least biased and most stable estimates were obtained by CON. We propose to use c′ as summary measure of effect size to rank genes irrespective of different types of NPH and censoring patterns.Availability: WHE and CON are available as R packages.Contact: georg.heinze@meduniwien.ac.atSupplementary Information: Supplementary Data are available at Bioinformatics online.
The enigma of optical momentum in a medium
Authors: Barnett Stephen M. , Loudon Rodney 
Published: February 2010

It is 100 years since Minkowski and Abraham first gave rival expressions for the momentum of light in a material medium. At the single-photon level, these correspond, respectively, either to multiplying or dividing the free-space value (

) by the refractive index (
n
). The debate that this work started has continued till the present day, punctuated by the occasional publication of ‘decisive’ experimental demonstrations supporting one or other of these values. We review the compelling arguments made in support of the Minkowski and Abraham forms and are led to the conclusion that
both
momenta are correct. We explain why two distinct momenta are needed to describe light in a medium and why each appears as the natural, and experimentally observed, momentum in appropriate situations.
Purification of Proteins by Chromatofocusing
Authors: Mohammad Jamil 
Published: February 2010

INTRODUCTIONThis protocol describes purification of proteins by chromatofocusing, a technique that separates proteins on the basis of differences in their isoelectric point (pI). The equipment required for chromatofocusing includes a chromatography column, pump, sample valve, UV monitor, pH monitor, and fraction collector. Commercially available liquid chromatography systems or high performance liquid chromatography (HPLC) systems can be used for chromatofocusing experiments. Precise pH control is essential for correct interpretation of chromatofocusing results. With a pH monitor connected to a flowthrough pH electrode, it is easy and convenient to monitor the elution pH values for chromatofocusing. Continuous monitoring of the pH profile throughout an experiment often helps explain the UV peak profiles more fully.
Chromatofocusing
Authors: Mohammad Jamil 
Published: February 2010

INTRODUCTIONChromatofocusing separates proteins on the basis of differences in their isoelectric point (pI). The stationary phase (matrix) is usually a weak anion exchanger in which the functional groups are amines, for example, a polybuffer exchanger (PBE 118 and PBE 94) or Mono P column. The eluent is a buffer containing a large number of buffering species that together give a uniform buffering capacity over a broad pH range.
S-Glycoprotein-Like Protein Regulates Defense Responses in Nicotiana Plants against Ralstonia solanacearum
Authors: Maimbo Milimo , Ohnishi Kouhei , Hikichi Yasufumi , Yoshioka Hirofumi , Kiba Akinori 
Published: January 2010

Abstract
RsRGA4 (for Ralstonia solanacearum-responsive gene A4) encodes a polypeptide similar to S-locus glycoprotein (SGP) from Brassica rapa and SGP-like proteins from Ipomoea trifida and Medicago truncatula. Therefore, we designated RsRGA4 as NtSGLP (for Nicotiana tabacum SGP-like protein) and NbSGLP (its Nicotiana benthamiana ortholog). NbSGLP is expressed in root, leaf, petal, gynoecium, and stamen. Expression of NbSGLP was strongly induced by inoculation with an avirulent strain of R. solanacearum (Rs8107) and slightly enhanced by inoculation with virulent R. solanacearum (RsOE1-1). Expression of NbSGLP was induced by inoculation with an hrpY-deficient mutant of RsOE1-1 and Rs8107. Expression was also induced by aminocyclopropane carboxylic acid and salicylic acid. Virus-induced gene silencing of NbSGLP enhanced the growth of Rs8107. Growth of RsOE1-1 and appearance of wilt symptoms were also accelerated in silenced plants. Expression of PR-1a and EREBP was reduced, and markers for basal defense, such as callose deposition and reduced vascular flow, were compromised in NbSGLP-silenced plants. Moreover, growth of Pseudomonas cichorii, Pseudomonas syringae pv tabaci, and P. syringae pv mellea was also enhanced in the silenced plants. On the other hand, silencing of NbSGLP did not interfere with the appearance of the hypersensitive response. NbSGLP was secreted in a signal peptide-dependent manner. Agrobacterium tumefaciens-mediated expression of NbSGLP induced PR-1a and EREBP expression, callose deposition, and reduced vascular flow. NbSGLP-induced callose deposition and reduced vascular flow were not observed in salicylic acid-deficient N. benthamiana NahG plants. Taken together, SGLP might have a role in the induction of basal defense in Nicotiana plants.
Tricarboxylic Acid Cycle Activity Regulates Tomato Root Growth via Effects on Secondary Cell Wall Production
Authors: van der Merwe Margaretha J. , Osorio Sonia , Araújo Wagner L. , Balbo Ilse , Nunes-Nesi Adriano , Maximova Eugenia , Carrari Fernando , Bunik Victoria I. , Persson Staffan , Fernie Alisdair R. 
Published: January 2010

Abstract
Transgenic tomato (Solanum lycopersicum ‘Moneymaker’) plants independently expressing fragments of various genes encoding enzymes of the tricarboxylic acid cycle in antisense orientation have previously been characterized as exhibiting altered root growth. In this study, we evaluate the rates of respiration of roots from these lines in addition to determining their total dry weight accumulation. Given that these features were highly correlated, we decided to carry out an evaluation of the cell wall composition in the transformants that revealed a substantial reduction in cellulose. Since the bulk of cellulose is associated with the secondary cell walls in roots, we reasoned that the transformants most likely were deficient in secondary wall cellulose production. Consistent with these findings, cross-sections of the root collar (approximately 15 mm from the junction between root and stem) displayed reduced lignified secondary cell walls for the transformants. In contrast, cell and cell wall patterning displayed no differences in elongating cells close to the root tip. To further characterize the modified cell wall metabolism, we performed feeding experiments in which we incubated excised root tips in [U-14C]glucose in the presence or absence of phosphonate inhibitors of the reaction catalyzed by 2-oxoglutarate dehydrogenase. Taken together, the combined results suggest that restriction of root respiration leads to a deficit in secondary cell wall synthesis. These data are discussed in the context of current models of biomass partitioning and plant growth.
Systems Analysis of Seed Filling in Arabidopsis: Using General Linear Modeling to Assess Concordance of Transcript and Protein Expression
Authors: Hajduch Martin , Hearne Leonard B. , Miernyk Jan A. , Casteel Jill E. , Joshi Trupti , Agrawal Ganesh K. , Song Zhao , Zhou Mingyi , Xu Dong , Thelen Jay J. 
Published: January 2010

AbstractPrevious systems analyses in plants have focused on a single developmental stage or time point, although it is often important to additionally consider time-index changes. During seed development a cascade of events occurs within a relatively brief time scale. We have collected protein and transcript expression data from five sequential stages of Arabidopsis (Arabidopsis thaliana) seed development encompassing the period of reserve polymer accumulation. Protein expression profiling employed two-dimensional gel electrophoresis coupled with tandem mass spectrometry, while transcript profiling used oligonucleotide microarrays. Analyses in biological triplicate yielded robust expression information for 523 proteins and 22,746 genes across the five developmental stages, and established 319 protein/transcript pairs for subsequent pattern analysis. General linear modeling was used to evaluate the protein/transcript expression patterns. Overall, application of this statistical assessment technique showed concurrence for a slight majority (56%) of expression pairs. Many specific examples of discordant protein/transcript expression patterns were detected, suggesting that this approach will be useful in revealing examples of posttranscriptional regulation.
BLADE-ON-PETIOLE1 Coordinates Organ Determinacy and Axial Polarity inArabidopsisby Directly Activating ASYMMETRIC LEAVES2
Authors: Jun Ji Hyung , Ha Chan Man , Fletcher Jennifer C. 
Published: January 2010

AbstractContinuous organ formation is a hallmark of plant development that requires organ-specific gene activity to establish determinacy and axial patterning, yet the molecular mechanisms that coordinate these events remain poorly understood. Here, we show that the organ-specific BTB-POZ domain proteins BLADE-ON-PETIOLE1 (BOP1) and BOP2 function as transcriptional activators during Arabidopsis thaliana leaf formation. We identify as a direct target of BOP1 induction the ASYMMETRIC LEAVES2 (AS2) gene, which promotes leaf cell fate specification and adaxial polarity. We find that BOP1 associates with the AS2 promoter and that BOP1 and BOP2 are required for AS2 activation specifically in the proximal, adaxial region of the leaf, demonstrating a role for the BOP proteins as proximal-distal as well as adaxial-abaxial patterning determinants. Furthermore, repression of BOP1 and BOP2 expression by the indeterminacy-promoting KNOX gene SHOOTMERISTEMLESS is critical to establish a functional embryonic shoot apical meristem. Our data indicate that direct activation of AS2 transcription by BOP1 and BOP2 is vital for generating the conditions for KNOX repression at the leaf base and may represent a conserved mechanism for coordinating leaf morphogenesis with patterning along the adaxial-abaxial and the proximal-distal axes.
The γ -Tubulin Complex Protein GCP4 Is Required for Organizing Functional Microtubule Arrays inArabidopsis thaliana
Authors: Kong Zhaosheng , Hotta Takashi , Lee Yuh-Ru Julie , Horio Tetsuya , Liu Bo 
Published: January 2010

AbstractMicrotubule (MT) nucleation and organization depend on the evolutionarily conserved protein γ -tubulin, which forms a complex with GCP2-GCP6 (GCP for γ -Tubulin Complex Protein). To date, it is still unclear how GCP4-GCP6 (the non-core GCPs) may be involved in acentrosomal MT nucleation in plant cells. We found that GCP4 was associated with γ -tubulin in vivo in Arabidopsis thaliana. When GCP4 expression was repressed by an artificial microRNA, transgenic plants exhibited phenotypes of dwarfism and reduced organ size. In mitotic cells, it was observed that the γ -tubulin signal associated with the mitotic spindle, and the phragmoplast was depleted when GCP4 was downregulated. Consequently, MTs failed to converge at unified spindle poles, and the bipolar phragmoplast MT array frequently had discrete bundles with extended minus ends, resulting in failed cytokinesis as reflected by cell wall stubs in leaf epidermal cells. In addition, cortical MTs in swollen guard cells and pavement cells of the leaf epidermis became hyperparallel and bundled, which was likely caused by frequent MT nucleation with shallow angles on the wall of extant MTs. Therefore, our results support the notion that GCP4 is an indispensable component for the function of γ -tubulin in MT nucleation and organization in plant cells.
The ABORTED MICROSPORES Regulatory Network Is Required for Postmeiotic Male Reproductive Development in Arabidopsis thaliana
Authors: Xu Jie , Yang Caiyun , Yuan Zheng , Zhang Dasheng , Gondwe Martha Y. , Ding Zhiwen , Liang Wanqi , Zhang Dabing , Wilson Zoe A. 
Published: January 2010

Abstract
The Arabidopsis thaliana ABORTED MICROSPORES (AMS) gene encodes a basic helix-loop-helix (bHLH) transcription factor that is required for tapetal cell development and postmeiotic microspore formation. However, the regulatory role of AMS in anther and pollen development has not been fully defined. Here, we show by microarray analysis that the expression of 549 anther-expressed genes was altered in ams buds and that these genes are associated with tapetal function and pollen wall formation. We demonstrate that AMS has the ability to bind in vitro to DNA containing a 6-bp consensus motif, CANNTG. Moreover, 13 genes involved in transportation of lipids, oligopeptides, and ions, fatty acid synthesis and metabolism, flavonol accumulation, substrate oxidation, methyl-modification, and pectin dynamics were identified as direct targets of AMS by chromatin immunoprecipitation. The functional importance of the AMS regulatory pathway was further demonstrated by analysis of an insertional mutant of one of these downstream AMS targets, an ABC transporter, White-Brown Complex homolog, which fails to undergo pollen development and is male sterile. Yeast two-hybrid screens and pull-down assays revealed that AMS has the ability to interact with two bHLH proteins (AtbHLH089 and AtbHLH091) and the ATA20 protein. These results provide insight into the regulatory role of the AMS network during anther development.
Evolutionary Studies Illuminate the Structural-Functional Model of Plant Phytochromes
Authors: Mathews Sarah 
Published: January 2010

AbstractA synthesis of insights from functional and evolutionary studies reveals how the phytochrome photoreceptor system has evolved to impart both stability and flexibility. Phytochromes in seed plants diverged into three major forms, phyA, phyB, and phyC, very early in the history of seed plants. Two additional forms, phyE and phyD, are restricted to flowering plants and Brassicaceae, respectively. While phyC, D, and E are absent from at least some taxa, phyA and phyB are present in all sampled seed plants and are the principal mediators of red/far-red–induced responses. Conversely, phyC-E apparently function in concert with phyB and, where present, expand the repertoire of phyB activities. Despite major advances, aspects of the structural-functional models for these photoreceptors remain elusive. Comparative sequence analyses expand the array of locus-specific mutant alleles for analysis by revealing historic mutations that occurred during gene lineage splitting and divergence. With insights from crystallographic data, a subset of these mutants can be chosen for functional studies to test their importance and determine the molecular mechanism by which they might impact light perception and signaling. In the case of gene families, where redundancy hinders isolation of some proportion of the relevant mutants, the approach may be particularly useful.
Buying behaviour of consumers for food products in an emerging economy
Authors: Ali Jabir , Kapoor Sanjeev , Moorthy Janakiraman 
Published: January 2010

PurposeThe purpose of this paper is to develop a marketing strategy for a modern food/grocery market based on consumer preferences and behaviour.Design/methodology/approachA total of 101 households having sufficient purchasing power were personally surveyed with a structured questionnaire. These households are spread across the well‐developed Gomtinagar area of Lucknow city. Simple statistical analysis such as descriptive statistical analysis, frequency distribution, cross tabulation, analysis of variance, and factor analysis to assess the consumers' preferences for food and grocery products and market attributes were carried out.FindingsThe preferences of the consumers clearly indicate their priority for cleanliness/freshness of food products followed by price, quality, variety, packaging, and non‐seasonal availability. The consumers' preference of marketplace largely depends on the convenience in purchasing at the marketplace along with the availability of additional services, attraction for children, basic amenities and affordability. Results suggest that most of the food and grocery items are purchased in loose form from the nearby outlets. Fruits and vegetables are mostly purchased daily or twice a week due to their perishable nature, whereas grocery items are less frequently purchased.Research limitations/implicationsThis paper analyses the buying behaviour of the consumers under survey with respect to food and grocery items. These consumers are in a relatively advantageous position in terms of purchasing power and awareness of health and nutrition.Practical implicationsThe results may help the food processors and outlet owners to understand a diversified set of preferences for products and market attributes, so that they can make better decisions in the emerging organized food and grocery retail environment.Originality/valueThe topic is relatively less researched in emerging markets especially where organized retail is still in its early stages.
Evaluation of food purchasing behaviour of consumers from supermarkets
Authors: Sanlier Nevin , Seren Karakus Suzan 
Published: January 2010

PurposeThis study was conducted with the aim of determining the food purchasing behaviour of consumers from supermarkets.Design/methodology/approachA total of 430 consumers, 194 males and 236 females, with an average age of 29.96 ±10.99 were included in this study, and was conducted to find out the criteria which consumers took into account while purchasing food.FindingsA significant relationship was determined between the scores the consumers received from nutrition, the reliability and all of the shopping criteria, and their level of education (p < 0.05) between the percentage of income spared for nutrition (p < 0.01) and between the cost (p < 0.05) and the total scores received from all of the shopping criteria (p < 0.01). It was also determined that women paid more attention to the nutrition and reliability criteria than men did (p < 0.05).Research limitations/implicationsThe research is restricted in so far as it only considers consumers in the big city and as it is an exploratory study the research is limited in so far as the number of participants is only 430. Further research needs to include other big and small cities.Practical implicationsThe study has concluded that consumers need effective and versatile education in the subjects of label reading and buying the right kind of food for their budgets. It is revealed that consumer education is essential in the process from cradle to grave in creating the awareness of consumers to buy food.Originality/valueThe paper is useful to both practitioners and academics in the fields of relationship consumer and marketing. Informing and training consumers will help increase the awareness of consumers and make them behave more rationally in their shopping. It will lead the studies to be carried out in the future to activate the control of the consumers on their shopping, instead of losing the control of consumers.