bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applications of extensive survey techniques to describe freshwater pearl mussel distribution and macrohabitat in the River Spey, Scotland
Authors: Hastie L. C. , Cooksley S. L. , Scougall F. , Young M. R. , Boon P. J. , Gaywood M. J. 
Published: November 2004

AbstractThe spatial distribution and associated physical habitat of endangered freshwater pearl mussels (Margaritifera margaritifera) in a 145 km stretch of the River Spey, northeast Scotland, were investigated. The overall size of the SpeyM. margaritiferapopulation was estimated to be in the order of 10 million. Mussel distributions were compared with River Corridor Survey (RCS) macrohabitat data and found to be positively associated with coarse riverbed substrata, ‘fast‐flowing’ waters, riparian woodland, and river bends; and negatively associated with shingle bars, flood barriers, ‘slow‐flowing’ waters, eroding cliffs and aquatic macrophytes. Significant positive relationships between mussel density and channel slope, width and bank height, were also observed. Binary logistic regression models (based on four to six features) were used to predict the presence/absence of mussels or the occurrence of ‘optimal’ mussel habitat (i.e. mussel density >1 m−2) at any given site. Overall predictive success rates of 79% and 78% were achieved, respectively. Discriminant function models (based on five variables) were also used, with predictive success rates of 78% and 88%, respectively. Copyright © 2004 John Wiley & Sons, Ltd.
Likelihood‐based modelling of age‐related normal ranges for ordinal measurements: changes in visual acuity through early childhood
Authors: Wade A. M. , Salt A. T. , Proffitt R. V. , Heavens S. J. , Sonksen P. M. 
Published: November 2004

AbstractThis paper investigates the construction of age‐related standards for ordinal outcome data. Asymmetric logistic models are used to describe the age‐related changes in the cumulative probabilities for each ordinal level. Maximum likelihood estimation of model parameters allows the use of likelihood ratio tests to ascertain the appropriate model complexity. In contrast to methodologies for constructing age‐related standards where the outcome is continuous, we show how the methodology leads directly to centile estimation for individuals. The method is illustrated using visual acuity measurements collected from 2968 children between 2 and 9 years of age made on a 30‐point ordinal scale. We show how, in this instance, smoothing of parameters across ordinal categories leads to reduced validity of the centiles, justifying the need for specialized methodology for non‐continuous outcomes. Copyright © 2004 John Wiley & Sons, Ltd.
Evaluation of log‐rank tests for infrequent observations from a multi‐state process, with application to HPV vaccine efficacy
Authors: Kang Minhee , Lagakos Stephen W. 
Published: November 2004

AbstractGenital infection by human papillomavirus (HPV) is a common sexually transmitted disease, with over 25 per cent prevalence among young women in the US. Infections are usually without symptoms and transient (or reversible), but a small proportion of infections persist and are believed to be responsible for nearly all cervical cancers and precursor lesions such as cervical intraepithelial neoplasia (CIN). Therefore, successful vaccines against persistent HPV infections could have a great impact in preventing cervical cancers. In trials being planned, ongoing, and recently completed, a log‐rank or a similar test may be employed to assess a vaccine effect in comparison to placebo, with an infection ‘event’ defined to capture persistent but not transient infections. However, it is not clear how best to define such an event, because (1) diagnostic tests cannot distinguish a persistent from a transient infection, (2) participants are only examined periodically, and (3) there can be misclassification errors in the detection of infections. This paper evaluates several definitions of persistent infection that are based on periodically observed infection statuses by postulating a multi‐state model for persistent and transient infections. The type I error and the power of tests on vaccine efficacy based on these operational definitions are then examined under various scenarios of how a vaccine might affect the infection–disease process. We find that none of the candidates performs satisfactorily, thus raising concerns that clinical trials based only on infection endpoints will not be reliable. Copyright © 2004 John Wiley & Sons, Ltd.
Analysis of clustered and interval censored data from a community‐based study in asthma
Authors: Bellamy Scarlett L. , Li Yi , Ryan Louise M. , Lipsitz Stuart , Canner Marina J. , Wright Rosalind 
Published: November 2004

AbstractMany authors in recent years have proposed extensions of familiar survival analysis methodologies to apply in dependent data settings, for example, when data are clustered or subject to repeated measures. However, these extensions have been considered largely in the context of right censored data. In this paper, we discuss a parametric frailty model for the analysis of clustered and interval censored failure time data. Details are presented for the specific case where the underlying time to event data follow a Weibull distribution. Maximum likelihood estimates will be obtained using commercially available software and the empirical efficiency of these estimators will be explored via a simulation study. We also discuss a score test to make inferences about the magnitude and significance of over‐dispersion in clustered data settings. These methods will be illustrated using data from the East Boston Asthma Study. Copyright © 2004 John Wiley & Sons, Ltd.
Viscoamylographic Studies on Zea Mays [Mexican White Tuxpeño Maize] Partial Gelatinization with Calcium Hydroxide
Authors: Sánchez‐Tovar Salvador A. , Salazar‐Zazueta Alfredo , Mena‐Iniesta Baltasar , Durán‐de‐Bazúa Carmen 
Published: November 2004

AbstractMexicans staple food is maize “tortilla”, prepared by thermal‐alkaline processes. The sensory properties of “masa” and “tortilla” depend on the reactions occuring between lime and chemical compounds in maize. In the present study, the effect of different calcium hydroxide, Ca(OH)2, concentrations (0.0, 0.10, 0.30, 0.50 %, dry basis, d.b.) on the apparent viscosity and maximum gelatinization temperature of a cornstarch water slurry was assessed. This Mexican traditional thermal‐alkaline gelatinization reaction (TAGR) was evaluated in a Brabender Viscoamylograph. This small well‐mixed reactor was homogeneously heated, and apparent viscosity data from corn starch were recorded in Brabender Units BU). It was found that an increase in Ca(OH)2 concentrations considerably increases the apparent viscosity, thus reducing the time needed to reach the maximum gelatinization temperature. A mathematical model that represents the phenomena, that occur in the Viscoamylograph, was developed. In the model the Viscoamylograph was considered as a batch reactor and the apparent kinetic coefficients for the TAGR were obtained, including mass balances and thermal‐alkaline gelatinization rates, considering a spherical cornstarch granule formed by a starchy matrix. Activation energy found for this reaction was 1241 kJ.
Drops of water and of soap solution: Students' constraining mental models of the nature of matter
Authors: Eilam Billie 
Published: November 2004

AbstractThis study investigates how 25 junior high school students employed their bodies of knowledge and responded to problem cues while individually performing a science experiment and reasoning about a drops phenomenon. Line‐by‐line content analysis conducted on students' written ad hoc explanations aimed to reveal students' concepts and their relations within their explanations, and to construe students' mental models for the science phenomenon based on level of specification, models' correspondence with scientific claims, macro versus micro view of matter, and type of evidence used. We then inferred four types of knowledge representations for the nature of matter. Findings are discussed in terms of implications for science teaching. © 2004 Wiley Periodicals, Inc. J Res Sci Teach 41: 970–993, 2004
Enhancing the quality of argumentation in school science
Authors: Osborne Jonathan , Erduran Sibel , Simon Shirley 
Published: November 2004

AbstractThe research reported in this study focuses on the design and evaluation of learning environments that support the teaching and learning of argumentation in a scientific context. The research took place over 2 years, between 1999 and 2001, in junior high schools in the greater London area. The research was conducted in two phases. In phase 1, working with a group of 12 science teachers, the main emphasis was to develop sets of materials and strategies to support argumentation in the classroom, and to support and assess teachers' development with teaching argumentation. Data were collected by video‐ and audio‐recording the teachers' attempts to implement these lessons at the beginning and end of the year. During this phase, analytical tools for evaluating the quality of argumentation were developed based on Toulmin's argument pattern. Analysis of the data shows that there was significant development in the majority of teachers use of argumentation across the year. Results indicate that the pattern of use of argumentation is teacher‐specific, as is the nature of the change. In phase 2 of the project, the focus of this paper, teachers taught the experimental groups a minimum of nine lessons which involved socioscientific or scientific argumentation. In addition, these teachers taught similar lessons to a comparison group at the beginning and end of the year. The purpose of this research was to assess the progression in student capabilities with argumentation. For this purpose, data were collected from 33 lessons by video‐taping two groups of four students in each class engaging in argumentation. Using a framework for evaluating the nature of the discourse and its quality developed from Toulmin's argument pattern, the findings show that there was improvement in the quality of students' argumentation. This research presents new methodological developments for work in this field. © 2004 Wiley Periodicals, Inc. J Res Sci Teach 41: 994–1020, 2004
Design‐based science and student learning
Authors: Fortus David , Dershimer R. Charles , Krajcik Joseph , Marx Ronald W. , Mamlok‐Naaman Rachel 
Published: November 2004

AbstractDesign‐Based Science (DBS) is a pedagogy in which the goal of designing an artifact contextualizes all curricular activities. Design is viewed as a vehicle through which scientific knowledge and real‐world problem‐solving skills can be constructed. Following Anderson and Hogan's (1999) call to document the design of new science pedagogies, this goal of this article is twofold: (a) to describe DBS, and (b) to evaluate whether significant science knowledge was constructed during consecutive enactments of three DBS units. In this study, 92 students participated in the consecutive enactments of three different DBS units. The development of their scientific knowledge was assessed through posters and models constructed during the curricular enactments and by identical pre‐ and post‐instruction written tests. The posttests showed considerable gains compared with the pretests, while the models and posters show application of this newly constructed knowledge in solving a design problem. These positive results support efforts being made to restructure school science around inquiry‐based curricula in general and design‐based curricula in particular. © 2004 Wiley Periodicals, Inc. J Res Sci Teach 41: 1081–1110, 2004
When sex hurts, anxiety and fear orient attention towards pain
Authors: Payne Kimberley A. , Binik Yitzchak M. , Amsel Rhonda , Khalifé Samir 
Published: November 2004

AbstractHypervigilance for pain‐relevant stimuli has been associated with anxiety, fear of pain and anxiety sensitivity. This attentional bias has been primarily investigated in heterogeneous pain groups or pain‐free controls, but has not been examined in pain conditions where anxiety and fear are likely to play a central role. Due to the intimate and interpersonal nature of genital pain experienced during sexual intercourse, Vulvar Vestibulitis Syndrome (VVS) constitutes an ideal sample in which to investigate the role of cognitive and affective factors in pain perception and maintenance. Seventeen women suffering from VVS and an equal number of age and education matched control women completed an emotional Stroop and memory recall task in addition to a series of questionnaires assessing pain‐hypervigilance, state and trait anxiety, fear of pain, and anxiety sensitivity. VVS sufferers reported hypervigilance for coital pain and also exhibited a selective attentional bias towards pain stimuli on the emotional Stroop task as compared with controls. This effect was predicted by state and trait anxiety and fear of pain. According to these data, treament strategies for VVS should target anxiety and fear in addition to sensory systems.
TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates
Authors: Tusnády Gábor E. , Dosztányi Zsuzsanna , Simon István 
Published: November 2004

Abstract
Summary: The structure of integral membrane proteins is determined in the absence of the lipid bilayer; consequently the membrane localization of the protein is usually not specified in the corresponding PDB file. Recently, we have developed a new method called TMDET which determines the most possible localization of the membrane relative to the protein structure, and gives the annotation of the membrane embedded parts of the sequence. The entire Protein Data Bank has been scanned by the new TMDET algorithm resulting in the database of structurally determined transmembrane proteins (PDB_TM). Here we present the web interface of the TMDET algorithm to allow scientists to determine the membrane localization of structural data prior to deposition or to analyze model structures.
Availability: The TMDET server is available for academic users on http://www.enzim.hu/TMDET
Contact: tusi@enzim.hu
A parallel graph decomposition algorithm for DNA sequencing with nanopores
Authors: Bokhari Shahid H. , Sauer Jon R. 
Published: November 2004

AbstractMotivation: With the potential availability of nanopore devices that can sense the bases of translocating single-stranded DNA (ssDNA), it is likely that ‘reads’ of length ∼105 will be available in large numbers and at high speed. We address the problem of complete DNA sequencing using such reads.We assume that ∼102 copies of a DNA sequence are split into single strands that break into randomly sized pieces as they translocate the nanopore in arbitrary orientations. The nanopore senses and reports each individual base that passes through, but all information about orientation and complementarity of the ssDNA subsequences is lost. Random errors (both biological and transduction) in the reads create further complications.Results: We have developed an algorithm that addresses these issues. It can be considered an extreme variation of the well-known Eulerian path approach. It searches over a space of de Bruijn graphs until it finds one in which (a) the impact of errors is eliminated and (b) both possible orientations of the two ssDNA sequences can be identified separately and unambiguously.Our algorithm is able to correctly reconstruct real DNA sequences of the order of 106 bases (e.g. the bacterium Mycoplasma pneumoniae) from simulated erroneous reads on a modest workstation in about 1 h. We describe, and give measured timings of, a parallel implementation of this algorithm on the Cray Multithreaded Architecture (MTA-2) supercomputer, whose architecture is ideally suited to this ‘unstructured’ problem. Our parallel implementation is crucial to the problem of rapidly sequencing long DNA sequences and also to the situation where multiple nanopores are used to obtain a high-bandwidth stream of reads.Contact: shb@acm.org
Circadian Rhythms of Ethylene Emission in Arabidopsis
Authors: Thain Simon C. , Vandenbussche Filip , Laarhoven Lucas J.J. , Dowson-Day Mandy J. , Wang Zhi-Yong , Tobin Elaine M. , Harren Frans J.M. , Millar Andrew J. , Van Der Straeten Dominique 
Published: November 2004

Abstract
Ethylene controls multiple physiological processes in plants, including cell elongation. Consequently, ethylene synthesis is regulated by internal and external signals. We show that a light-entrained circadian clock regulates ethylene release from unstressed, wild-type Arabidopsis (Arabidopsis thaliana) seedlings, with a peak in the mid-subjective day. The circadian clock drives the expression of multiple ACC SYNTHASE genes, resulting in peak RNA levels at the phase of maximal ethylene synthesis. Ethylene production levels are tightly correlated with ACC SYNTHASE 8 steady-state transcript levels. The expression of this gene is controlled by light, by the circadian clock, and by negative feedback regulation through ethylene signaling. In addition, ethylene production is controlled by the TIMING OF CAB EXPRESSION 1 and CIRCADIAN CLOCK ASSOCIATED 1 genes, which are critical for all circadian rhythms yet tested in Arabidopsis. Mutation of ethylene signaling pathways did not alter the phase or period of circadian rhythms. Mutants with altered ethylene production or signaling also retained normal rhythmicity of leaf movement. We conclude that circadian rhythms of ethylene production are not critical for rhythmic growth.
LIN, aMedicago truncatulaGene Required for Nodule Differentiation and Persistence of Rhizobial Infections
Authors: Kuppusamy Kavitha T. , Endre Gabriella , Prabhu Radhika , Penmetsa R. Varma , Veereshlingam Harita , Cook Douglas R. , Dickstein Rebecca , VandenBosch Kathryn A. 
Published: November 2004

AbstractEthyl methanesulfonate mutagenesis of the model legume Medicago truncatula has previously identified several genes required for early steps in nodulation. Here, we describe a new mutant that is defective in intermediate steps of nodule differentiation. The lin (lumpy infections) mutant is characterized by a 4-fold reduction in the number of infections, all of which arrest in the root epidermis, and by nodule primordia that initiate normally but fail to mature. Genetic analyses indicate that the symbiotic phenotype is conferred by a single gene that maps to the lower arm of linkage group 1. Transcriptional markers for early Nod factor responses (RIP1 and ENOD40) are induced in lin, as is another early nodulin, ENOD20, a gene expressed during the differentiation of nodule primordia. By contrast, other markers correlated with primordium differentiation (CCS52A), infection progression (MtN6), or nodule morphogenesis (ENOD2 and ENOD8) show reduced or no induction in homozygous lin individuals. Taken together, these results suggest that LIN functions in maintenance of rhizobial infections and differentiation of nodules from nodule primordia.
Processes Modulating Calcium Distribution in Citrus Leaves. An Investigation Using X-Ray Microanalysis with Strontium as a Tracer
Authors: Storey Richard , Leigh Roger A. 
Published: November 2004

Abstract
Citrus leaves accumulate large amounts of calcium that must be compartmented effectively to prevent stomatal closure by extracellular Ca2+ and interference with Ca2+-based cell signaling pathways. Using x-ray microanalysis, the distribution of calcium between vacuoles in different cell types of leaves of rough lemon (Citrus jambhiri Lush.) was investigated. Calcium was accumulated principally in palisade, spongy mesophyll, and crystal-containing idioblast cells. It was low in epidermal and bundle sheath cells. Potassium showed the reverse distribution. Rubidium and strontium were used as tracers to examine the pathways by which potassium and calcium reached these cells. Comparisons of strontium and calcium distribution indicated that strontium is a good tracer for calcium, but rubidium did not mirror the potassium distribution pattern. The amount of strontium accumulated was highest in palisade cells, lowest in bundle sheath and epidermal cells, and intermediate in the spongy mesophyll. Accumulation of strontium in palisade and spongy mesophyll was accompanied by loss of potassium from these cells and its accumulation in the bundle sheath. Strontium moved apoplastically from the xylem to all cell types, and manipulation of water loss from the adaxial leaf surface suggested that diffusion is responsible for strontium movement to this side of the leaf. The results highlight the importance of palisade and spongy mesophyll as repositories for calcium and suggest that calcium distribution between different cell types is the result of differential rates of uptake. This tracer technique can provide important information about the ion uptake and accumulation properties of cells in intact leaves.
Citrate-Permeable Channels in the Plasma Membrane of Cluster Roots from White Lupin
Authors: Zhang Wen-Hao , Ryan Peter R. , Tyerman Stephen D. 
Published: November 2004

Abstract
White lupin (Lupinus albus) is well adapted to phosphorus deficiency by developing cluster roots that release large amounts of citrate into the rhizosphere to mobilize the sparingly soluble phosphorus. To determine the mechanism underlying citrate release from cluster roots, we isolated protoplasts from different types of roots of white lupin plants grown in phosphorus-replete (+P) and phosphorus-deficient (−P) conditions and used the patch-clamp technique to measure the whole-cell currents flowing across plasma membrane of these protoplasts. Two main types of anion conductance were observed in protoplasts prepared from cluster root tissue: (1) an inwardly rectifying anion conductance (IRAC) activated by membrane hyperpolarization, and (2) an outwardly rectifying anion conductance (ORAC) that became more activated with membrane depolarization. Although ORAC was an outward rectifier, it did allow substantial inward current (anion efflux) to occur. Both conductances showed citrate permeability, with IRAC being more selective for citrate3− than Cl− (PCit/PCl = 26.3), while ORAC was selective for Cl− over citrate (PCl/PCit = 3.7). Both IRAC and ORAC were sensitive to the anion channel blocker anthracene-9-carboxylic acid. These currents were also detected in protoplasts derived from noncluster roots of −P plants, as well as from normal (noncluster) roots of plants grown with 25 μm phosphorus (+P). No differences were observed in the magnitude or frequency of IRAC and ORAC currents between the cluster roots and noncluster roots of −P plants. However, the IRAC current from +P plants occurred less frequently than in the −P plants. IRAC was unaffected by external phosphate, but ORAC had reduced inward current (anion efflux) when phosphate was present in the external medium. Our data suggest that IRAC is the main pathway for citrate efflux from white lupin roots, but ORAC may also contribute to citrate efflux.