bluuebunny/crossref_metadata_2025_split huggingface dataset:
The existence of cognitive plateaus in Alzheimer's disease
Authors: Bozoki Andrea C. , An Hyonggin , Bozoki Eva S. , Little Roderick J. 
Published: November 2009

BackgroundThe objective of this study was to evaluate the existence of cognitive plateaus in some individuals during the course of Alzheimer's disease (AD).MethodsData came from the historical patient group collected via the Consortium to Establish a Registry for Alzheimer's Disease (CERAD, Duke University, 1988–1996). Data reduction was performed by using principal components analysis to derive a single cognitive measure (F1), followed by application of a novel plateau‐searching algorithm to individual patient data, looking for stable periods of 3 years or longer. To evaluate the time dependence of F1, we fitted a linear mixed model to the group and to individual data points.ResultsTwenty‐two percent of AD subjects (54/243) and 98% of healthy control subjects (253/258) exhibited a plateau. Within the AD plateau group, the most common pattern was a single plateau (mean, 3.6 years; range, 3 to 7 years) that extended for the entire measurement period (28/54 subjects). Briefer plateau durations were seen at the beginning or end of the measurement period. Initial cognitive function (F1) was slightly higher in the plateau group, which was also slightly older and less well‐educated. Men and women were equally represented.ConclusionsIn a patient sample predating the widespread use of cholinesterase inhibitors, we found that approximately one fifth of individuals with AD demonstrated periods of prolonged cognitive stability. This significant interindividual variability must be considered when providing prognostic information to families and when assessing individual patient responses to pharmacotherapy. We advise caution when assessing results of potentially disease‐modifying agents at the individual patient level.
Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments
Authors: McGuffin Liam J. , Roche Daniel B. 
Published: November 2009

Abstract
Motivation: The accurate prediction of the quality of 3D models is a key component of successful protein tertiary structure prediction methods. Currently, clustering- or consensus-based Model Quality Assessment Programs (MQAPs) are the most accurate methods for predicting 3D model quality; however, they are often CPU intensive as they carry out multiple structural alignments in order to compare numerous models. In this study, we describe ModFOLDclustQ—a novel MQAP that compares 3D models of proteins without the need for CPU intensive structural alignments by utilizing the Q measure for model comparisons. The ModFOLDclustQ method is benchmarked against the top established methods in terms of both accuracy and speed. In addition, the ModFOLDclustQ scores are combined with those from our older ModFOLDclust method to form a new method, ModFOLDclust2, that aims to provide increased prediction accuracy with negligible computational overhead.
Results: The ModFOLDclustQ method is competitive with leading clustering-based MQAPs for the prediction of global model quality, yet it is up to 150 times faster than the previous version of the ModFOLDclust method at comparing models of small proteins (&lt;60 residues) and over five times faster at comparing models of large proteins (&gt;800 residues). Furthermore, a significant improvement in accuracy can be gained over the previous clustering-based MQAPs by combining the scores from ModFOLDclustQ and ModFOLDclust to form the new ModFOLDclust2 method, with little impact on the overall time taken for each prediction.
Availability: The ModFOLDclustQ and ModFOLDclust2 methods are available to download from http://www.reading.ac.uk/bioinf/downloads/
Contact: l.j.mcguffin@reading.ac.uk
The predation of farmed salmon by South American sea lions (Otaria flavescens) in southern Chile
Authors: Vilata Juan , Oliva Doris , Sepúlveda Maritza 
Published: November 2009

Abstract
Vilata, J., Oliva, D., and Sepúlveda, M. 2010. The predation of farmed salmon by South American sea lions (Otaria flavescens) in southern Chile. – ICES Journal of Marine Science, 67: 475–482. The South American sea lion Otaria flavescens is abundant off southern Chile. Because Chilean salmon farming has experienced an explosive growth in the past two decades, interactions between O. flavescens and this industry have increased. Fieldwork, including in situ behavioural observations, was carried out at three salmon farms off southern Chile from May to July 2008. The aim was to analyse possible patterns in the interactions and to evaluate whether they were influenced by the endogenous circa-rhythms of the species, prey size, tidal flux, and the use of an acoustic harassment device (AHD). The results showed that the attacks by O. flavescens followed seasonal patterns, with salmon predated more in autumn and winter, and daily patterns, with more interactions at night. In addition, attacks were more frequent on larger salmon, suggesting the existence of a prey-size preference. More sea lions were sighted at the ebb and flow tide peaks, when currents are stronger, suggesting that currents linked to tidal flux might facilitate the access of the sea lions to the farmed salmon. Although the use of AHDs appeared positive at one site, there is a strong suspicion that their efficacy may be site-specific.
The Arabidopsis Tandem Zinc Finger Protein AtTZF1 Traffics between the Nucleus and Cytoplasmic Foci and Binds Both DNA and RNA
Authors: Pomeranz Marcelo C. , Hah Cyrus , Lin Pei-Chi , Kang Shin Gene , Finer John J. , Blackshear Perry J. , Jang Jyan-Chyun 
Published: November 2009

AbstractProcessing bodies (PBs) are specialized cytoplasmic foci where mRNA turnover and translational repression can take place. Stress granules are related cytoplasmic foci. The CCCH tandem zinc finger proteins (TZFs) play pivotal roles in gene expression, cell fate specification, and various developmental processes. Human TZF binds AU-rich elements at the 3′ untranslated region and recruits decapping, deadenylation, and exonucleolytic enzymes to PBs for RNA turnover. Recent genetic studies indicate that plant TZFs are involved in gene regulation and hormone-mediated environmental responses. It is unknown if plant TZFs can bind RNA and be localized to PBs or stress granules. The Arabidopsis (Arabidopsis thaliana) AtTZF1/AtCTH/AtC3H23 was identified as a sugar-sensitive gene in a previous microarray study. It is characterized by a TZF motif that is distinct from the human TZF. Higher plants such as Arabidopsis and rice (Oryza sativa) each have a gene family containing this unique TZF motif. Here, we show that AtTZF1 can traffic between the nucleus and cytoplasmic foci. AtTZF1 colocalizes with markers of PBs, and the morphology of these cytoplasmic foci resembles that of mammalian PBs and stress granules. AtTZF1-associated cytoplasmic foci are dynamic and tissue specific. They can be induced by dark and wound stresses and are preferentially present in actively growing tissues and stomatal precursor cells. Since AtTZF1 can bind both DNA and RNA in vitro, it raises the possibility that AtTZF1 might be involved in DNA and/or RNA regulation.
Functional Analyses of the CLAVATA2-Like Proteins and Their Domains That Contribute to CLAVATA2 Specificity
Authors: Wang Guodong , Long Yuchen , Thomma Bart P.H.J. , de Wit Pierre J.G.M. , Angenent Gerco C. , Fiers Martijn 
Published: November 2009

AbstractThe Arabidopsis (Arabidopsis thaliana) CLAVATA2 (CLV2) gene encodes a leucine-rich repeat receptor-like protein (RLP) that is involved in controlling the stem cell population size in the shoot apical meristem. Our previous genome-wide functional analysis of 57 AtRLP genes revealed only a few phenotypes for mutant alleles, despite screening a wide range of growth and developmental stages and assaying sensitivity to various stress responses, including susceptibility toward pathogens. To gain further insight into the biological role of AtRLPs, in particular CLV2-related AtRLP genes, we tested their ability to complement the clv2 mutant phenotype. We found that out of four close CLV2 homologs tested, AtRLP2 and AtRLP12 could functionally complement the clv2 mutant when expressed under the control of the CLV2 promoter. This indicates that the functional specificity of these three genes is determined at the level of their transcriptional regulation. Single and double mutant combinations with impaired AtRLP2 and/or AtRLP12 did not show an aberrant phenotype, suggesting that other genes are redundant with these CLV2-like genes. To understand which protein domains are essential for CLV2 function and which parts are interchangeable between related CLV2-like proteins, we performed domain-deletion and domain-swap experiments. These experiments revealed that CLV2 remains functional without the island domain, whereas the C1 and C3 regions of the leucine-rich repeat domain are essential for functionality. Analysis of domain-swap constructs showed that the C3-G region of CLV2 can be replaced by that of AtRLP38, although it could not complement the clv2 mutant under control of the CLV2 promoter. This suggests that the C3-G region is conserved among related AtRLP members, whereas the C1 domain may determine the functional specificity of CLV2.
Nicotiana attenuataSIPK, WIPK, NPR1, and Fatty Acid-Amino Acid Conjugates Participate in the Induction of Jasmonic Acid Biosynthesis by Affecting Early Enzymatic Steps in the Pathway
Authors: Kallenbach Mario , Alagna Fiammetta , Baldwin Ian Thomas , Bonaventure Gustavo 
Published: November 2009

AbstractWounding and herbivore attack elicit the rapid (within minutes) accumulation of jasmonic acid (JA) that results from the activation of previously synthesized biosynthetic enzymes. Recently, several regulatory factors that affect JA production have been identified; however, how these regulators affect JA biosynthesis remains at present unknown. Here we demonstrate that Nicotiana attenuata salicylate-induced protein kinase (SIPK), wound-induced protein kinase (WIPK), nonexpressor of PR-1 (NPR1), and the insect elicitor N-linolenoyl-glucose (18:3-Glu) participate in mechanisms affecting early enzymatic steps of the JA biosynthesis pathway. Plants silenced in the expression of SIPK and NPR1 were affected in the initial accumulation of 13-hydroperoxy-linolenic acid (13-OOH-18:3) after wounding and 18:3-Glu elicitation by mechanisms independent of changes in 13-lipoxygenase activity. Moreover, 18:3-Glu elicited an enhanced and rapid accumulation of 13-OOH-18:3 that depended partially on SIPK and NPR1 but was independent of increased 13-lipoxygenase activity. Together, the results suggested that substrate supply for JA production was altered by 18:3-Glu elicitation and SIPK- and NPR1-mediated mechanisms. Consistent with a regulation at the level of substrate supply, we demonstrated by virus-induced gene silencing that a wound-repressed plastidial glycerolipase (NaGLA1) plays an essential role in the induction of de novo JA biosynthesis. In contrast to SIPK and NPR1, mechanisms mediated by WIPK did not affect the production of 13-OOH-18:3 but were critical to control the conversion of this precursor into 12-oxo-phytodienoic acid. These differences could be partially accounted for by reduced allene oxide synthase activity in WIPK-silenced plants.
Novel and Expanded Roles for MAPK Signaling inArabidopsisStomatal Cell Fate Revealed by Cell Type–Specific Manipulations
Authors: Lampard Gregory R. , Lukowitz Wolfgang , Ellis Brian E. , Bergmann Dominique C. 
Published: November 2009

AbstractMitogen-activated protein kinase (MAPK) signaling networks regulate numerous eukaryotic biological processes. In Arabidopsis thaliana, signaling networks that contain MAPK kinases MKK4/5 and MAPKs MPK3/6 function in abiotic and biotic stress responses and regulate embryonic and stomatal development. However, how single MAPK modules direct specific output signals without cross-activating additional downstream processes is largely unknown. Studying relationships between MAPK components and downstream signaling outcomes is difficult because broad experimental manipulation of these networks is often lethal or associated with multiple phenotypes. Stomatal development in Arabidopsis follows a series of discrete, stereotyped divisions and cell state transitions. By expressing a panel of constitutively active MAPK kinase (MAPKK) variants in discrete stomatal lineage cell types, we identified a new inhibitory function of MKK4 and MKK5 in meristemoid self-renewal divisions. Furthermore, we established roles for MKK7 and MKK9 as both negative and (unexpectedly) positive regulators during the major stages of stomatal development. This has expanded the number of known MAPKKs that regulate stomatal development and allowed us to build plausible and testable subnetworks of signals. This in vivo cell type–specific assay can be adapted to study other protein families and thus may reveal insights into other complex signal transduction pathways in plants.
A relaxed lattice option pricing model: implied skewness and kurtosis
Authors: Ji Dasheng , Wade Brorsen B. 
Published: November 2009

PurposeThe purpose of this paper is to develop an option pricing model applicable to US options. The lognormality assumption that has typically been imposed with past binomial and trinomial option pricing models is relaxed. The relaxed lattice model is then used to determine skewness and kurtosis of distributions of futures prices implied from option prices.Design/methodology/approachThe relaxed lattice is based on Gaussian quadrature. The markets studied include corn, soybeans, and wheat. Skewness and kurtosis are implied by minimizing the squared deviations of actual option premia from predicted premia.FindingsPositive skewness is the major source of nonnormality, but both skewness and kurtosis are important as the trinomial model that considers kurtosis has greater accuracy than the binomial model. The out‐of‐sample forecasting accuracy of the relaxed lattice models is better than the Black‐Scholes model in most, but not all cases.Research limitations/implicationsThe model might benefit from using option prices from more than one day. The implied skewness and kurtosis were quite variable and using more data might reduce this variability.Practical implicationsEmpirical results mostly show positive implied skewness, which suggests extreme price rises were more likely than extreme price decreases.Originality/valueThe relaxed lattice is a new model and the results about implied higher moments are new for these commodities. There are competing models available that should be able to get similar accuracy, so one key advantage of the new approach is its simplicity and ease of use.
Women farmers' access to credit from rural banks in Ghana
Authors: Akudugu Mamudu A. , Egyir Irene S. , Mensah‐Bonsu Akwasi 
Published: November 2009

PurposeThe purpose of this paper is to examine women farmers' access to credit from rural banks (RBs) in the Upper East region of Ghana. The paper examines the nature of credit supply by the RBs to their customers and the proportion that goes to women over a ten year period. It proposes the modelling of socio‐economic, technical and institutional factors influencing women farmers' access to credit from financial institutions in general and rural banks (RBs) in particular. The paper aims to expand the frontiers of rural and agricultural financing as well as the integration of gender interest in the financial sectors of developing countries.Design/methodology/approachIn total, 200 women farmers were randomly selected and information on socio‐economic, technical and institutional issues solicited from them. Ratio analyses were carried out and the logistic regression used to model the socio‐economic, technical and institutional factors that have influence on access to credit from RBs by women farmers.FindingsThe paper provides empirical evidence of close gender parity in terms of credit supply by RBs in Ghana. About 44 per cent of the credit portfolios of RBs in Ghana go to women and the remaining 56 per cent goes to men. Education, application procedures, access to land, income level, farm size, membership to economic associations, savings, type of crop grown, interest rate and distance to RBs are the socio‐economic, technical and institutional factors that influence women farmers' access to credit.Research limitations/implicationsThe paper is limited to only women farmers. There is the need for further research that considers men and women so as to establish whether or not there is gender insensitivity by financial institutions in Ghana and other developing countries.Practical implicationsThis paper provides empirical implications for the development of a vibrant financial sector in developing countries that provide equal access to men and women, rural and urban dwellers as well as actors in the formal and informal sectors.Originality/valueThis paper brings to light the issues of access to productive resources such as production credit by women in developing countries, particularly Ghana.
Factors affecting precautionary savings of self‐employed farm households
Authors: Mishra Ashok K. , Chang Hung‐Hao 
Published: November 2009

PurposeThe purpose of this paper is to empirically investigate the effects of farm income variability, farm size, and other socio‐demographic characteristics on the precautionary saving behavior of farm households and to estimate the influences of the identified factors on the amount of savings by self‐employed farm households.Design/methodology/approachUsing 2003 Agricultural Resource Management Survey (ARMS) data and a Double‐Hurdle procedure, the likelihood and the amount of savings by farm households are estimated.FindingsAn important empirical finding of this study is that variability in income plays an important role in explaining precautionary savings of US farm households. Findings suggest that farm households facing higher income risk save more and accumulate more wealth. It is indicated that several farm, operator, household, and demographic attributes contribute to the precautionary savings of farm households. In particular, results show that educational attainment by operator and spouses have positive impact on the decision to save. In addition, results from this study show that farms that specialize in cash grain are likely to have precautionary savings.Practical implicationsFarm households today are virtually indistinguishable from non‐farm households in their levels of income and diversity of employment. As a result, government policies that influence general economic conditions have much more profound impacts on farm families. Federal support of farm income warrants continued scrutiny. This paper shows that greater income uncertainty increases savings and wealth of farm households. Therefore, farm policies that reduce income variability or uncertainty will have an impact on precautionary savings and wealth of farm households.Originality/valueSeveral studies have investigated savings of households; however, these studies are limited to entire US population, older Americans, or non‐self‐employed individuals in the USA. Little is known about the savings behavior of self‐employed US farm households owing to a lack of household survey data and because of the complex relationship between the farm household and farm business in terms of resource allocation (both capital and labor).
Upper Midwest dairy farm revenue variation and insurance implications
Authors: Wolf Christopher A. , Roy Black J. , Hadrich Joleen C. 
Published: November 2009

PurposeThe purpose of this paper is to examine the sources and magnitude of variation in accrual adjusted gross farm revenue and farm revenue net of feed purchases on Michigan dairy farms representative of Upper Midwest dairy farms. The paper aims to assess whether adjusted gross revenue‐type insurance instruments meet insurability conditions when applied to dairy farms.Design/methodology/approachAccrual adjusted dairy farm revenue and revenue net of feed purchased from Michigan dairy farm panel data from 1995 through 2006 were detrended and summarized. Variance decomposition was used to identify sources of variation in adjusted gross revenue and adjusted gross revenue less feed purchases. In‐sample insurance premiums were estimated and Monte Carlo simulations were used to adjust these premiums for out‐of‐sample considerations.FindingsMilk price variation was the largest source of variation while milk production per cow varied little. Farms with smaller herds and those with larger percentages of farm revenue from crop sales had higher relative revenue variability and would trigger a higher frequency of indemnities under a whole farm revenue insurance contract.Research limitations/implicationsBecause the data analyzed conclude in 2006, the volatility of the past couple of years is not reflected. Therefore, researchers are encouraged to test the proposed insurance feasibility further with more recent data.Practical implicationsThe paper addresses considerations for the development and commercialization of a feasible dairy revenue insurance instrument.Originality/valueThis paper fulfils a need to understand magnitude and source of revenue variation on dairy farms and how insurance might mitigate negative consequences of this variation.
The importance of personal norms for purchasing organic milk
Authors: Klöckner Christian A. , Ohms Silvia 
Published: November 2009

PurposeThe purpose of this paper is to apply a structured approach to understand the importance of personal ecological norms in purchasing organic food. The norm‐activation‐model by Schwartz is used to predict self‐reported and observed purchase behaviour of organic milk.Design/methodology/approachThe paper reports the results of a field study with 63 customers of a German supermarket. A combination of covert observation and in‐store interviews was applied to obtain reliable data on actual shopping behaviour and its predictors.FindingsThe results show that the self‐reported and the observed purchase of organic milk is predicted by personal ecological norms, social norms, and perceived behavioural control. Personal norms are activated by awareness of need, awareness of consequences, perceived behavioural control, and social norms. People with strong personal norms use “organic production”, the “EU‐BIO‐Label” and “ingredients” as additional criteria during their decision process. For people with strong ecological norms the price difference between organic and conventional milk, the lack of knowledge about organic milk, and convenience are less important constraints. Finally, people with strong personal norms react more sensitively to proposed norm‐centred interventions.Practical implicationsThe study offers insight into the processes of motivating behaviour and can therefore be used to design intervention strategies. Suggestions are developed in the closing part of the paper.Originality/valueThe study applies for the first time the norm‐activation‐model to the domain of purchasing organic milk and underlines the importance of normative influences for this decision.