bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis and extension of a biochemical network model using robust control theory
Authors: Kim J.‐S. , Valeyev N. V. , Postlethwaite I. , Heslop‐Harrison P. , Cho K.‐H. , Bates D. G. 
Published: November 2009

AbstractMathematical models of biological processes which have been observed in vivo to be highly robust to intracellular and environmental variations should themselves display appropriate levels of robustness when analysed in silico. This paper uses techniques from robust control theory to analyse and extend a mathematical model of the interacting proteins underlying adenosine 3′, 5′‐cyclic monophosphate (cAMP) oscillations in aggregating Dictyostelium cells. Starting with a previously proposed ‘minimal’ model, we show how robustness analysis using the structured singular value can identify points of structural fragility in the network. By combining these results with insights from recent results from the experimental literature, we show how the original model can be augmented with some important additional modules, comprising networks involving IP3 and Ca2+. By analysing the robustness of our new extended model, we are able to show that dynamic interactions between the different modules play a pivotal role in generating robust cAMP oscillations; thus, significantly improving our understanding of the design principles underlying this complex biological system. Copyright © 2009 John Wiley & Sons, Ltd.
Consensus problem of high‐order multi‐agent systems with external disturbances: AnH∞analysis approach
Authors: Liu Yang , Jia Yingmin 
Published: November 2009

AbstractThis paper is devoted to the output consensus problem of directed networks of multiple high‐order agents with external disturbances, and proposes a distributed protocol using the neighbors' measured outputs. By defining an appropriate controlled output and conducting a model transformation in two steps, consensus performance analysis of the multi‐agent system under the proposed protocol is transformed into a normalH∞problem. Then usingH∞theory of linear systems, conditions are derived to ensure the consensus performance with a prescribedH∞index for networks with fixed and switching topologies, respectively. A numerical example of the formation control application is included to validate the theoretical results. Copyright © 2009 John Wiley & Sons, Ltd.
Identifying and resolving uncertainty as a mediated action in science: A comparative analysis of the cultural tools used by scientists and elementary science students at work
Authors: Kirch Susan A. 
Published: November 2009

AbstractElementary school children are capable of reproducing sophisticated science process skills such as observing, designing experiments, collecting data, and evaluating evidence. An understanding of the nature of scientific knowledge requires more than teaching and learning the performance of these skills. It also requires an appreciation of how these actions lead to knowledge generation and shape its durable and tentative nature. Our understanding of activities that support the teaching and learning of the nature of scientific knowledge is still growing. This study compares how scientific knowledge is generated in science laboratories and in elementary school classrooms. Discourse analysis, conducted through an activity theoretical perspective, of conversations between biomedical researchers revealed that nearly every aspect of discussions among scientists concerned uncertainty—establishing what was known with confidence and what remained unresolved. Analysis of conversations between teachers and students in an urban elementary school showed that a similar pattern of identifying and resolving uncertainty was evident when students were conducting independent investigations. All participants identified new knowledge through processes of reflexivity concerned with what was observed, conducted, and interpreted in investigations. Implications for science education are discussed. © 2009 Wiley Periodicals, Inc. Sci Ed 94:308–335, 2010
FGF2 Specifies hESC-Derived Definitive Endoderm into Foregut/Midgut Cell Lineages in a Concentration-Dependent Manner
Authors: Ameri Jacqueline , Ståhlberg Anders , Pedersen Jesper , Johansson Jenny K. , Johannesson Martina M. , Artner Isabella , Semb Henrik 
Published: November 2009

Abstract
Fibroblast growth factor (FGF) signaling controls axis formation during endoderm development. Studies in lower vertebrates have demonstrated that FGF2 primarily patterns the ventral foregut endoderm into liver and lung, whereas FGF4 exhibits broad anterior-posterior and left-right patterning activities. Furthermore, an inductive role of FGF2 during dorsal pancreas formation has been shown. However, whether FGF2 plays a similar role during human endoderm development remains unknown. Here, we show that FGF2 specifies hESC-derived definitive endoderm (DE) into different foregut lineages in a dosage-dependent manner. Specifically, increasing concentrations of FGF2 inhibits hepatocyte differentiation, whereas intermediate concentration of FGF2 promotes differentiation toward a pancreatic cell fate. At high FGF2 levels specification of midgut endoderm into small intestinal progenitors is increased at the expense of PDX1+ pancreatic progenitors. High FGF2 concentrations also promote differentiation toward an anterior foregut pulmonary cell fate. Finally, by dissecting the FGF receptor intracellular pathway that regulates pancreas specification, we demonstrate for the first time to the best of our knowledge that induction of PDX1+ pancreatic progenitors relies on FGF2-mediated activation of the MAPK signaling pathway. Altogether, these observations suggest a broader gut endodermal patterning activity of FGF2 that corresponds to what has previously been advocated for FGF4, implying a functional switch from FGF4 to FGF2 during evolution. Thus, our results provide new knowledge of how cell fate specification of human DE is controlled—facts that will be of great value for future regenerative cell therapies.
Effects of estrogens and antiestrogens on gene expression of fathead minnow (Pimephales promelas) early life stages
Authors: Johns Sonia M. , Denslow Nancy D. , Kane Michael D. , Watanabe Karen H. , Orlando Edward F. , Sepúlveda Maria S. 
Published: November 2009

AbstractEndocrine disrupting chemicals (EDCs) are known to contaminate aquatic environments and alter the growth and reproduction of organisms. The objective of this study was to evaluate the sensitivity and utility of fathead minnow (Pimephales promelas) early life‐stages as a model to measure effects of estrogenic and antiestrogenic EDCs on physiological and gene expression endpoints relative to growth and reproduction. Embryos (<24‐h postfertilization, hpf) were exposed to a potent estrogen (17α‐ethinyl estradiol, EE2, 2, 10, and 50 ng L−1); a weak estrogen (mycotoxin zearalenone, ZEAR, same concentrations as above); an antiestrogen (ZM 189, 154; 40, 250, and 1000 ng L−1); and to mixtures of EE2 and ZM until swim‐up stage (∼170 hpf). Exposure to all concentrations of ZEAR and to the lowest concentration of ZM resulted in increased body sizes, whereas high concentrations of EE2 decreased body sizes. There was a significant increase in the frequency of abnormalities (mostly edema) in larvae exposed to all concentrations of EE2, and high ZEAR, and EE2 + ZM mixture groups. Expression of growth hormone was upregulated by most of the conditions tested. Exposure to 50 ng L−1 ZEAR caused an induction of insulin‐like growth factor 1, whereas exposure to 40 ng L−1 ZM caused a downregulation of this gene. Expression of steroidogenic acute regulatory protein gene was significantly upregulated after exposure to all concentrations of EE2 and luteinizing hormone expression increased significantly in response to all treatments tested. As expected, EE2 induced vitellogenin expression; however, ZEAR also induced expression of this gene to similar levels compared to EE2. Overall, exposure to EE2 + ZM mixture resulted in a different expression pattern compared to single exposures. The results of this study suggest that an early life stage 7‐day exposure is sufficient to recognize and evaluate effects of estrogenic compounds on gene expression in this fish model. © 2009 Wiley Periodicals, Inc. Environ Toxicol, 2009.
Radionuclide induced energy dispersive X‐ray fluorescence for the determination of La, Ce, Pr and Nd and their content sums in the rare‐earth ores
Authors: Zuzaan P. , Gansukh N. , Bolortuya D. 
Published: November 2009

AbstractIn this paper an analytical procedure for the determination of La, Ce, Pr and Nd in rare‐earth ores is described. More than 5000 of powdered samples were prepared from the ores selected in various places of their deposit. The samples were analyzed by energy‐dispersive X‐ray fluorescence (EDXRF) with an Am‐241 source for the radiation excitation of characteristic K‐lines of the elements mentioned. The results were compared with the data of other methods and reference materials. The correlation of LaCe, LaPr, LaNd, CePr, CeNd and PrNd elements pairs were determined. Copyright © 2009 John Wiley & Sons, Ltd.
An activity-based system of models for student mobility simulation
Authors: Mazzulla Gabriella 
Published: November 2009

Abstract

Purpose
The objective of this paper is to provide a tool for transport system planning. Therefore, a system of models for student mobility simulation on a university campus is proposed.

Methods
An activity-based approach has been adopted. The system of models is sequential, in which each choice dimension is linked to the previous one and involves the choices made at a lower level, and it is made up of multinomial and hierarchical Logit models. Additionally, the Revealed and Stated preferences technique has been adopted for investigating user choice behaviour in the hypothesis that an innovative transport system is realized to access the campus.

Conclusions
The proposed system of models adopt the activity-based travel approach combined with the conjoint use of the RP and SP methodologies, allowing a better understanding and prediction of users responses to travel demand management measures. The model structure is very realistic for student mobility simulation, helping the analyst in evaluating the effects of park pricing policies and the introduction of a new transport system in the travel users choices.
Relationship between yield, growth and spike weight in wheat under phosphorus deficiency and shading
Authors: LÁZARO L. , ABBATE P. E. , COGLIATTI D. H. , ANDRADE F. H. 
Published: November 2009

SUMMARYThe effect of phosphorus deficiency on yield formation in spring wheat (Triticum aestivumcv. Prointa Oasis) was investigated, focusing on crop growth and dry matter partitioning during the spike growth period (SGP), which is critical for grain number determination. Two experiments combining shading and P deficiency were performed at Balcarce, Argentina (37°45′S). The main treatments were two levels of soil P-availability: low P, a naturally low P fertility soil (7·0 and 5·5 mg Bray extractable P/kg soil, in the first and second experiments respectively) and high P, a P dose that does not limit growth. The sub-treatments were two levels of radiation (shaded and control). Phosphorus deficiency affected yield mainly through the number of grains/unit surface (m2). Differences in grain number/m2were related to differences in dry weight of spikes/m2, measured 7 days after anthesis, excluding grain weight. The duration of the SGP did not change much as result of P deficiency: 27 days with high P and only 3 days more with low P. Therefore, changes in spike dry weight were mainly due to differences in spike growth rate. In turn, the spike growth rate of all treatments was linearly related to crop growth rate, with little effect of dry matter partitioning to spikes. Finally, differences in crop growth rate between P treatments were mainly determined by the amount of intercepted radiation. It was concluded that P deficiency resulted in a reduction in intercepted radiation during the SGP, thus causing a reduction in grain number and crop yield.
Reproduction, growth and production of Amiantis umbonella (Bivalvia: Veneridae) on northern coast of the Persian Gulf, Bandar Abbas, Iran
Authors: Saeedi Hanieh , Ardalan Aria A. , Kamrani Ehsan , Kiabi Bahram H. 
Published: November 2009

Amiantis umbonella is distributed throughout the coast of the northern Persian Gulf. This study of 893 clams provides data on reproduction, growth and production for the period April 2007 to March 2008 from two transects along the Bandar Abbas coast. Histological preparations showed six stages of gametogenic development: resting stage (Stage 0), early active (Stage I), late active (Stage II), ripe (Stage III), partially spawned (Stage IV) and spent (Stage V). The specimens were gonochoric and showed synchronized spawning. The reproductive cycle commenced in September and finished in March with one major spawning event in January which correlated with lower sea temperature. Von Bertalanffy growth parameters for the sample were asymptotic length (L∞) = 58–62 mm, growth constant (k) = 0.28–0.29 yr−1 and length zero (t0) = –0.48 –0.47. The mean annual clam abundance, mean biomass and production were 10 individuals. m−2, 5.7 g shell free dry weight (SFDW) m−2 and 0.495 g SFDW m−2 yr−1, respectively.
Two ancient (and modern) motivations for ascribing exhaustively definite foreknowledge to God: a historic overview and critical assessment
Authors: BOYD GREGORY A. 
Published: November 2009

AbstractThe traditional Christian view that God foreknows the future exclusively in terms of what will and will not come to pass is partially rooted in two ancient Hellenistic philosophical assumptions. Hellenistic philosophers universally assumed that propositions asserting ‘x will occur’ contradict propositions asserting ‘x will not occur’ and generally assumed that the gods lose significant providential advantage if they know the future partly as a domain of possibilities rather than exclusively in terms of what will and will not occur. Both assumptions continue to influence people in the direction of the traditional understanding of God's knowledge of the future. In this essay I argue that the first assumption is unnecessary and the second largely misguided.
The ethics of belief and Christian faith as commitment to assumptions
Authors: PEELS RIK 
Published: November 2009

AbstractIn this paper I evaluate Brian Zamulinski's recent attempt to rebut an argument to the conclusion that having any kind of religious faith violates a moral duty. I agree with Zamulinski that the argument is unsound, but I disagree on where it goes wrong. I criticize Zamulinski's alternative construal of Christian faith as existential commitment to fundamental assumptions. It does not follow that we should accept the moral argument against religious faith, for at least two reasons. First, Zamulinski's Cliffordian ethics of belief is defective in several regards. Second, the truth of doxastic involuntarism and the possibility of doxastic excuse conditions can be used to demonstrate that the argument is unconvincing.
Binary genomotyping using lipooligosaccharide biosynthesis genes distinguishes betweenCampylobacter jejuniisolates within poultry-associated multilocus sequence types
Authors: HOTTER G. S. , LI I. H. , FRENCH N. P. 
Published: November 2009

SUMMARYCampylobacter jejuniis a leading cause of human bacterial gastroenteritis throughout the industrialized world. We investigated whether or not differences in gene complement at the lipooligosaccharide (LOS) biosynthesis locus can identify epidemiologically useful binary genomotypes in 87C. jejuniisolates from poultry-associated multilocus sequence types (STs) collected during the course of a sentinel surveillance study. Using a PCR-based approach, we correlated assignment of both isolate LOS locus class and binary genomotype with ST. We found that isolates within STs 45, 190, 354 and 474 displayed mosaicism in gene complement at the intra-ST level. For example, based upon their binary genomotypes, we assigned individual ST-45 isolates from human clinical cases as probably originating from either a poultry or wild-bird source. However, intra-ST mosaicism in gene complement was observed alongside broader patterns of congruence in LOS locus class and gene complement that distinguished between isolates from different STs.
Predicting seed dormancy loss and germination timing for Bromus tectorum in a semi-arid environment using hydrothermal time models
Authors: Meyer Susan E. , Allen Phil S. 
Published: November 2009

AbstractA principal goal of seed germination modelling for wild species is to predict germination timing under fluctuating field conditions. We coupled our previously developed hydrothermal time, thermal and hydrothermal afterripening time, and hydration–dehydration models for dormancy loss and germination with field seed zone temperature and water potential measurements from early summer through autumn to develop predictions of germination timing for Bromus tectorum at a semi-arid site in north-central Utah, USA. Model predictions were tested with a validation dataset based on concomitant seed retrieval experiments in 2 years. Predictions were generally in agreement with observed field germination time courses, even though integration across multiple precipitation events was necessary. Success of the modelling effort hinged on two factors. First, we used a soil capacitance sensor that measured seed zone (5 mm soil depth) water content accurately over a wide range. Second, simulations were built using physiologically based threshold models that can incorporate differences in germination timing for multiple germination fractions and for multiple stages of dormancy loss. Our results suggest that simulation models using hydrothermal time concepts can predict field germination phenology accurately. Seeds in this study integrated their experiences in a widely fluctuating environment in a manner consistent with the assumptions of hydrothermal time. Such threshold-based models also have the advantage of generality, as these concepts can be applied to many different species, environments and weather scenarios.
Seed-bank dynamics of the tropical weedSida rhombifolia(Malvaceae): incidence of seedling emergence, predators and pathogens
Authors: Rodríguez Claudia , Garcia Maria Alice 
Published: November 2009

AbstractArrowleaf sida (Sida rhombifolia) is a tropical weed that grows in disturbed areas. Its control by hand pulling and mowing are only partially effective because arrowleaf sida is difficult to pull and quickly sprouts after cutting. We studied the seed-bank dynamics ofS. rhombifoliain the region of Campinas, São Paulo State, Brazil for 2 years, following a known number of seeds placed artificially at five burial depths. Predators and pathogens were responsible for the loss ofc.40% of the seeds during the first year of the experiment. The importance of predation declined with depth. Mortality due to fungal attack did not differ among the burial depths, except for seeds placed at the surface (where it was negligible). Seedling emergence only occurred during the first year, after the beginning of the rainy period and when the study area was still free of a dense vegetation cover. Seedlings did not emerge from depths greater than 5 cm. We conclude that seedling emergence and death are significant causes of seed losses from the seed bank ofS. rhombifoliabut their relative importance is highly dependent on depth of burial.
Sensitivity cycling to physical dormancy break and seed vigour of twoIpomoeaspecies (Convolvulaceae)
Authors: Jayasuriya K.M.G. Gehan , Baskin Jerry M. , Tekrony Dennis M. , Baskin Carol C. 
Published: November 2009

AbstractThe physically dormant seeds ofIpomoea lacunosaand ofI. hederaceaundergo sensitivity cycling (insensitive ↔ sensitive) to dormancy-breaking treatment. Sensitivity cycling is important to seeds with physical dormancy in sensing appropriate environmental conditions for germination. Seed vigour is also important to seedling establishment, but no study has compared changes in vigour (or not) with changes in sensitivity. This study was conducted to determine the relationship between sensitivity cycling and seed vigour inI. lacunosaandI. hederacea. The seed moisture contents of insensitive and sensitive seeds ofI. lacunosaand of sensitive seeds ofI. hederaceawere measured, and several vigour tests were performed. Vigour of sensitive seeds ofI. lacunosadecreased more rapidly than that of insensitive seeds. No significant change in vigour was observed in either permeable or impermeable seeds ofI. hederacea. We conclude that sensitivity cycling to physical dormancy break is important in maintaining vigour ofI. lacunosaseeds in the soil seed-bank.
Darwin and seeds
Authors: Black Michael 
Published: November 2009

AbstractIn 2009, the bicentenary of Charles Darwin's birth on 12 February 1809 is being celebrated. For seed scientists, celebrations of the contributions of the great biologist should also mark his involvement with seeds. Darwin was interested in seeds, particularly in their role in dispersal and distribution of plant species over long distances. His studies of seeds, laid down in several books and articles, contributed to the development of his ideas on evolution and the distribution of living organisms on the planet. In this review, the place of seeds in Darwin's work is surveyed and it is shown how he referred to them to support and illustrate some of his most important ideas.
Categorical spatial memory in patients with mild cognitive impairment and Alzheimer dementia: Positional versus object-location recall
Authors: KESSELS ROY P.C. , RIJKEN STEFAN , JOOSTEN-WEYN BANNINGH LIESBETH W.A. , SCHUYLENBORGH-VAN ES NELLEKE VAN , OLDE RIKKERT MARCEL G.M. 
Published: November 2009

AbstractMemory for object locations, as part of spatial memory function, has rarely been studied in patients with Alzheimer dementia (AD), while studies in patients with Mild Cognitive Impairment (MCI) patients are lacking altogether. The present study examined categorical spatial memory function using the Location Learning Test (LLT) in MCI patients (n = 30), AD patients (n = 30), and healthy controls (n = 40). Two scoring methods were compared, aimed at disentangling positional recall (location irrespective of object identity) and object-location binding. The results showed that AD patients performed worse than the MCI patients on the LLT, both on recall of positional information and on recall of the locations of different objects. In addition, both measures could validly discriminate between AD and MCI patients. These findings are in agreement with the notion that visual cued-recall tests may have better diagnostic value than traditional (verbal) free-recall tests in the assessment of patients with suspected MCI or AD. (JINS, 2010, 16, 200–204.)
RECONSIDERING TRIGONOMETRIC INTEGRATORS
Authors: O’NEALE DION R. J. , MCLACHLAN ROBERT I. 
Published: November 2009

AbstractIn this paper we look at the performance of trigonometric integrators applied to highly oscillatory differential equations. It is widely known that some of the trigonometric integrators suffer from low-order resonances for particular step sizes. We show here that, in general, trigonometric integrators also suffer from higher-order resonances which can lead to loss of nonlinear stability. We illustrate this with the Fermi–Pasta–Ulam problem, a highly oscillatory Hamiltonian system. We also show that in some cases trigonometric integrators preserve invariant or adiabatic quantities but at the wrong values. We use statistical properties such as time averages to further evaluate the performance of the trigonometric methods and compare the performance with that of the mid-point rule.