bluuebunny/crossref_metadata_2025 huggingface dataset:
Authoritarian science curriculum standards as barriers to teaching and learning: An interpretation of personal experience
Authors: Wallace Carolyn S.
Published: September 2011

This is a critical time for the science education community as we embark on the creation and implementation of new national science standards. The purpose of this essay is to offer insight into how the language of curriculum standards, including that found in state science standards in the United States over the past 15 years, has posed barriers to meaningful science teaching and learning. I synthesize research from educational policy, science education, curriculum theory, critical inquiry, and my own experiential learning from a particular case in the state of Georgia to analyze the effects of authoritarian standards language on science classroom teaching. I argue that curriculum standards based on a content and product model of education (A. V. Kelly, 1999), have been incongruent with research from cognitive psychology, science identity formation, language use, and science as inquiry. The final portion of the essay considers how a process‐oriented set of curriculum standards, for example that found in New Zealand, could provide a more empowering epistemological foundation for classroom teaching. © 2011 Wiley Periodicals, Inc. Sci Ed 96:291–310, 2012
Process warehouses in practice: a goal‐driven method for business process analysis
Authors: Shahzad Khurram , Zdravkovic Jelena
Published: September 2011

Process analysis and improvement, one of the core phases in the business process management life cycle, is reaching the top of the agenda for many enterprises and organizations. An emerging approach to analyzing business processes involves the use of process‐oriented data warehouses to collect information about executed processes to enable their detailed analysis and thereby provide bases for possible improvements. However, very little work has been carried out on employing business orientation in the design and utilization of a process warehouse. The approach presented in this study addresses that limitation by proposing a method that relates business goals to the information from the warehouse. To do so, we start by defining a desired goal structure that concerns an existing business process. The obtained goal model is firstly utilized for scoping and designing a corresponding data model for a process warehouse, and further for retrieving the information from the warehouse to examine the fulfillment of the goals of interest. The key benefits of the proposed method are the provision of the relevant and accurate business process information as well as tracing the process‐related goals to the process execution data and further to the analysis of the process. As validation of the proposed method, we develop a prototype, and a healthcare process is used as an illustrative example. Also, to demonstrate the method quality, we perform an experiment on the effectiveness of the information access and retrieval. Copyright © 2011 John Wiley & Sons, Ltd.
A microRNA-Based System for Selecting and Maintaining the Pluripotent State in Human Induced Pluripotent Stem Cells
Authors: Di Stefano Bruno , Maffioletti Sara Martina , Gentner Bernhard , Ungaro Federica , Schira Giulia , Naldini Luigi , Broccoli Vania
Published: September 2011

Induced pluripotent stem cell (iPSC) technology has provided researchers with a unique tool to derive disease-specific stem cells for the study and possible treatment of degenerative disorders with autologous cells. The low efficiency and heterogeneous nature of reprogramming is a major impediment to the generation of personalized iPSC lines. Here, we report the generation of a lentiviral system based on a microRNA-regulated transgene that enables for the efficient selection of mouse and human pluripotent cells. This system relies on the differential expression pattern of the mature form of microRNA let7a in pluripotent versus committed or differentiated cells. We generated microRNA responsive green fluorescent protein and Neo reporters for specific labeling and active selection of the pluripotent cells in any culture condition. We used this system to establish Rett syndrome and Parkinson's disease human iPSCs. The presented selection procedure represents a straightforward and powerful tool for facilitating the derivation of patient-specific iPSCs.
Molecular catalysis for fullerene functionalization
Authors: Itami Kenichiro
Published: September 2011

This account highlights elements of our efforts to explore new functionalization chemistry of fullerenes using molecular catalysts since 2006. These endeavors have led to the development of new reactions such as (i) organoboron addition to fullerenes, (ii) CH bond allylation and arylation of organo(hydro)fullerenes, (iii) CH/CC bond cleavage of alkynyl(hydro)fullerenes, (iv) regioselective tetraallylation of fullerenes, (v) double nucleophilic substitution of aziridinofullerene, and (vi) [2 + 2] cycloaddition of aziridinofullerene with alkynes. These works not only highlight the potential of molecular catalysis for fullerene functionalization, but also unlock opportunities for markedly different strategies in nanocarbon synthesis. DOI 10.1002/tcr.201100022
Transition to the Clinical Doctorate: Attitudes of the Genetic Counseling Training Program Directors in North America
Authors: Stuenkel Aaron J. , Campion MaryAnn , Allain Dawn , Hampel Heather
Published: September 2011

In North America, genetic counseling is an allied health profession where entry level practitioners currently must hold a master's degree earned from a graduate program accredited by the American Board of Genetic Counseling. This is one of many health care professions that could transition to an entry level clinical doctorate degree. This study explored the attitudes of genetic counseling training program directors toward such a transition. Thirty‐one North American program directors were invited to complete an online survey and a follow‐up telephone interview. Twenty‐one program directors completed the survey and ten directors also completed a follow up phone interview. There was disagreement among the respondents on the issue of transitioning to a clinical doctorate degree (nine in favor, six against and six undecided). Respondents disagreed about whether the transition would lead to higher salaries (six yes, eight no, and seven unsure) or increased professional recognition (eight yes, eight no, and four unsure). Approximately half (n = 10) of directors were not sure if the transition to a clinical doctorate would help or hurt minority recruitment; six thought it would help and four thought it would hurt. However, the majority (n = 13) thought a clinical doctorate would help genetic counselors to obtain faculty positions. If the field transitions to a clinical doctorate, 11 of the directors thought their program would convert, seven were unsure and one thought their program would shut down. Themes identified in interview data included 1) implications for the profession 2) institution‐specific considerations and 3) perception of the unknown. Opinions are quite varied at this time regarding the possible transition to the clinical doctorate among genetic counseling training program directors.
Stable carbon isotope characteristics of desert plants in the Junggar Basin, China
Authors: Ma Jian‐Ying , Sun Wei , Sun Hui‐Ling , Wang Shao‐Ming
Published: September 2011

Desert plants have unique strategies for survival and growth to cope with the limited water availability in arid regions. The stable carbon isotope (δ13C) provides an integrated measurement of internal plant physiological and external environmental properties affecting photosynthetic gas exchange and water use efficiency. The δ13C values of 84 species in the Junggar Basin were categorized into two groups (ranged from −30.1 to −23.3‰ for C3 and −14.9 to −9.9‰ for C4 species, respectively). No life form differences in δ13C values were detected in C3 (p = 0.78) and C4 plants (p = 0.63). Small differences among life forms were observed in δ13C values in C4 species with shrubs slightly depleted (−13.3‰) relative to perennials (−13.1‰) and annuals (−12.5‰). These differences suggested that δ13C value could not represent a plant functional group classification based on life forms in C4 plants in extremely arid regions. Ephemerals are all using C3 photosynthetic pathway and no significant differences (p = 0.92) in δ13C values were observed between annuals (−26.5‰) and perennials (−26.4‰). The δ13C values of Tulipa iliensis (an important ephemeral species distributed widely in the Junggar Basin) among nine natural populations were positively correlated with leaf (r2 = 0.46, p = 0.046) and soil (r2 = 0.67, p = 0.007) total nitrogen content, and negatively correlated with leaf (r2 = 0.48, p = 0.039) and soil (r2 = 0.79, p = 0.001) water content. This indicated that the variation in δ13C values of T. iliensis was probably caused by both water availability associated stomatal openness and nitrogen availability associated photosynthetic capacity. T. iliensis is very sensitive to water and nitrogen availability in soil.
Transillumination of Hand Tumors: A Cadaver Study to Evaluate Accuracy and Intraobserver Reliability
Authors: Erne Holger C. , Gardner Thomas R. , Strauch Robert J.
Published: September 2011

Background

The aim of this study was to assess the accuracy and intraobserver reliability of the technique of penlight transillumination of simulated hand tumors as well as the rationale for the technique.

Methods

Eight observers examined small (9.5 mm) plastic spheres in a fresh frozen cadaveric human hand 3 weeks apart in a blinded manner. The observers were divided into two overall groups based on their level of training. Four spheres simulating hand tumors (two dorsal and two palmar) were placed subcutaneously. The spheres were known to either transilluminate or to be opaque. The observers noted their impression as to whether the spheres either did or did not transilluminate. Accuracy and multi-rater-kappa-statistical analysis were performed.

Results

The overall accuracy was 87.5%: 95% for senior group, 81% for junior group ( P=.388, not significant). The average kappa of the intraobserver reliability overall was 0.46. The senior group had a kappa value of 0.67 (substantial agreement), the “junior” group: 0.25 (fair agreement).

Conclusions

Accuracy at correctly determining whether or not a small hand tumor transilluminated was high. The senior group was more accurate overall in correctly determining transillumination, though not with statistical significance. Intraobserver reliability was high for the senior group and less robust for the junior group.
Properties of Canola Protein‐based Plastics and Protein Isolates Modified Using SDS and SDBS
Authors: Manamperi Wajira A. R. , Pryor Scott W.
Published: September 2011

Canola protein isolates were prepared from canola meal flour using alkaline solubilization and acid precipitation. The isolates were treated with sodium dodecyl sulfate (SDS) and sodium dodecyl benzene sulfonate (SDBS) with concentrations between 1 and 5%. Functional property analysis of modified isolates revealed that water absorption and fat absorption increased by up to 115 and 78%, respectively, with increasing SDBS concentrations. Fat absorption of SDS‐modified isolates showed a similar trend to that of SDBS‐modified isolates (86% increase), but water absorption decreased (by 77%) in the 5% SDS treatment. SDS and SDBS treatments reduced the emulsifying activity of protein isolates by 34 and 30%, respectively. The denaturation effect of SDS and SDBS treatments increased the surface hydrophobicity of proteins and resulted in increased tensile strength (by 14 and 41%), tensile modulus (by 31 and 52%), and toughness (by 44 and 64%) of plastic specimens prepared using modified isolates. Only the 3% treatments of SDS and SDBS increased the elongation of plastics (by 22 and 11%, respectively) while other treatments did not show significant differences from the plastics that used non‐modified isolates. The water absorption of plastics increased by 33% with the 5% SDS treatment; the SDBS treatments showed a 9% decrease in water absorption for the 1% treatment but no significant differences at higher concentrations. Denaturation by SDS and SDBS can be employed to alter functional properties of canola protein isolates as well as the mechanical properties of canola protein‐based plastics.
Upper limb motion analysis in children with hemiplegic cerebral palsy: Proximal kinematic changes after distal botulinum toxin or surgical treatments
Authors: Fitoussi Frank , Diop Amadou , Maurel Nathalie , Laasel El Mostefa , Ilharreborde Brice , Penneçot Georges François
Published: September 2011

Purpose

The purpose of this study is to describe the kinematic changes in children with cerebral palsy (CP) after treatments performed on the forearm, wrist or thumb, with specific attention to the changes around the trunk, shoulder and elbow kinematics.

Methods

With the use of a specific kinematic protocol, we first described the upper limb kinematics in a group of 27 hemiplegic patients during two simple daily tasks. Eight of these children were treated with botulinum toxin (Botox®, Allergan) injection or surgery and were, thereafter, evaluated with another kinematic analysis in order to compare the pre- and post-therapeutic condition. The target muscles were the pronator teres, flexor carpi radialis, flexor carpi ulnaris, flexor digitorum superficialis, flexor pollicis longus and the adductor pollicis.

Results

Significant kinematic changes were found after treatment. Patients increased forearm supination ( P < 0.05) and wrist extension ( P < 0.05) during both tasks. Patients also decreased trunk flexion/extension range of motion (ROM) ( P < 0.05), improved elbow ROM ( P < 0.05) and improved internal shoulder rotation ( P < 0.05).

Conclusions

Dynamic shoulder or elbow limitations in children with mild hemiplegia involvement could be related to a compensatory movement strategy and/or co-contractions. As these proximal kinematics anomalies are improved after treatments performed at the forearm, wrist and thumb, they should not be treated first but should be reconsidered after the treatment of more distal problems.
The stability of developing pipe flow at high Reynolds number and the existence of nonlinear neutral centre modes
Authors: Walton Andrew G.
Published: September 2011

The high-Reynolds-number stability of unsteady pipe flow to axisymmetric disturbances is studied using asymptotic analysis. It is shown that as the disturbance amplitude is increased, nonlinear effects first become significant within the critical layer, which moves away from the pipe wall as a result. It is found that the flow stabilizes once the basic profile has become sufficiently fully developed. By tracing the nonlinear neutral curve back to earlier times, it is found that in addition to the wall mode, which arises from a classical upper branch linear stability analysis, there also exists a nonlinear neutral centre mode, governed primarily by inviscid dynamics. The centre mode problem is solved numerically and the results show the existence of a concentrated region of vorticity centred on or close to the pipe axis and propagating downstream at almost the maximum fluid velocity. The connection between this structure and the puffs and slugs of vorticity observed in experiments is discussed.
The frequency of daily ethanol consumption influences the effect of ethanol on insulin sensitivity in rats fed a high-fat diet
Authors: Feng Li , Han Bo , Wang Ruxia , Li Qiu , Bian Dezhi , Ma Chunyan , Song Guangyao , Gao Ling , Zhao J.
Published: September 2011

The different effects of ethanol on insulin sensitivity may be due to complex reasons. Here, we focus on the various daily ethanol consumption frequencies in rats fed a high-fat (HF) diet and explore the possible mechanism mediated by adiponectin and AMP-activated protein kinase (AMPK). A total of thirty-six male Wistar rats were fed a HF diet and were randomly divided into three groups: those that received tap water (C); those that received ethanol via a gastric tube twice per d (E1); those that received free access to ethanol for drinking (E2). The total daily ethanol dosage in groups E1 and E2 were the same (5 g/kg per d). At the end of 18 weeks, insulin sensitivity was evaluated. Adiponectin AMPK and GLUT4 levels were determined. We found that the different administration frequencies led to markedly different plasma ethanol concentrations and there were intimate relationships between plasma ethanol concentration and insulin sensitivity. Insulin resistance was markedly improved in group E1, whereas only a slight improvement was observed in group E2. Accordingly, adiponectin, phosphorylated AMPK and GLUT4 levels were significantly increased in group E1. Based on these findings, we propose that ethanol concentration might be the major influencing factor mediating the effect of ethanol on insulin sensitivity. At a total daily dosage of 5 g/kg per d, twice daily administration of ethanol was more beneficial than continuous drinking. The protective effect of ethanol might be mediated by increased adiponectin levels, which subsequently improve the activation of AMPKα and GLUT4 expression in adipose tissue.
Laboratory rearing and life history of an emerging grape pest, Xylotrechus arvicola (Coleoptera: Cerambycidae)
Authors: García-Ruiz E. , Marco V. , Pérez-Moreno I.
Published: September 2011

Several aspects of the biology of Xylotrechus arvicola (Olivier), an emerging grape pest, were studied under laboratory conditions. Four diets were tested to rear this species in the laboratory. Among them, only one made rearing from larva to adult possible. The highest mortality, in all cases, was recorded during the first days of larval development. Larvae were kept 45 days at 8°C to break diapause in order to reduce the normal field larval developmental time. The species' developmental time was similar between sexes, while pupal developmental time and weight were significantly greater for females than for males. As part of a complementary study, life table parameters of females obtained from the larvae reared on the artificial diet were compared to those of females emerged from field-infested grape root wood. Both laid the majority of eggs in the first two weeks after emergence, and they had a similar pre-laying period. Nevertheless, the females from the diet-reared larvae lived significantly longer, laid eggs over a longer period of time and showed higher fertility than those emerging from infested grape root, suggesting that diet fulfils larval nutritional needs. The species’ laboratory-reared population exhibited a low intrinsic growth rate value (rm=0.01) as a result of its long egg-to-adult developmental time and its high larval mortality.
The contribution of work and non-work stressors to common mental disorders in the 2007 Adult Psychiatric Morbidity Survey
Authors: Clark C. , Pike C. , McManus S. , Harris J. , Bebbington P. , Brugha T. , Jenkins R. , Meltzer H. , Weich S. , Stansfeld S.
Published: September 2011

Background

Evidence for an effect of work stressors on common mental disorders (CMD) has increased over the past decade. However, studies have not considered whether the effects of work stressors on CMD remain after taking co-occurring non-work stressors into account.

Method

Data were from the 2007 Adult Psychiatric Morbidity Survey, a national population survey of participants ⩾16 years living in private households in England. This paper analyses data from employed working age participants (N=3383: 1804 males; 1579 females). ICD-10 diagnoses for depressive episode, generalized anxiety disorder, obsessive compulsive disorder, agoraphobia, social phobia, panic or mixed anxiety and depression in the past week were derived using a structured diagnostic interview. Questionnaires assessed self-reported work stressors and non-work stressors.

Results

The effects of work stressors on CMD were not explained by co-existing non-work stressors. We found independent effects of work and non-work stressors on CMD. Job stress, whether conceptualized as job strain or effort–reward imbalance, together with lower levels of social support at work, recent stressful life events, domestic violence, caring responsibilities, lower levels of non-work social support, debt and poor housing quality were all independently associated with CMD. Social support at home and debt did not influence the effect of work stressors on CMD.

Conclusions

Non-work stressors do not appear to make people more susceptible to work stressors; both contribute to CMD. Tackling workplace stress is likely to benefit employee psychological health even if the employee's home life is stressful but interventions incorporating non-work stressors may also be effective.
Increased risk of mortality associated with social isolation in older men: only when feeling lonely? Results from the Amsterdam Study of the Elderly (AMSTEL)
Authors: Holwerda T. J. , Beekman A. T. F. , Deeg D. J. H. , Stek M. L. , van Tilburg T. G. , Visser P. J. , Schmand B. , Jonker C. , Schoevers R. A.
Published: September 2011

Background

Loneliness has a significant influence on both physical and mental health. Few studies have investigated the possible associations of loneliness with mortality risk, impact on men and women and whether this impact concerns the situation of being alone (social isolation), experiencing loneliness (feeling lonely) or both. The current study investigated whether social isolation and feelings of loneliness in older men and women were associated with increased mortality risk, controlling for depression and other potentially confounding factors.

Method

In our prospective cohort study of 4004 older persons aged 65–84 years with a 10-year follow-up of mortality data a Cox proportional hazard regression analysis was used to test whether social isolation factors and feelings of loneliness predicted an increased risk of mortality, controlling for psychiatric disorders and medical conditions, cognitive functioning, functional status and sociodemographic factors.

Results

At 10 years follow-up, significantly more men than women with feelings of loneliness at baseline had died. After adjustment for explanatory variables including social isolation, the mortality hazard ratio for feelings of loneliness was 1.30 [95% confidence interval (CI) 1.04–1.63] in men and 1.04 (95% CI 0.90–1.24) in women. No higher risk of mortality was found for social isolation.

Conclusions

Feelings of loneliness rather than social isolation factors were found to be a major risk factor for increasing mortality in older men. Developing a better understanding of the nature of this association may help us to improve quality of life and longevity, especially in older men.
Recurrence rates for observations of flows
Authors: ROUSSEAU JÉRÔME
Published: September 2011

We study Poincaré recurrence for flows and observations of flows. For Anosov flow, we prove that the recurrence rates are linked to the local dimension of the invariant measure. More generally, we give for the recurrence rates for the observations an upper bound depending on the push-forward measure. When the flow is metrically isomorphic to a suspension flow for which the dynamic on the base is rapidly mixing, we prove the existence of a lower bound for the recurrence rates for the observations. We apply these results to the geodesic flow and we compute the recurrence rates for a particular observation of the geodesic flow, i.e. the projection on the manifold.
How to measure the onset of babbling reliably?
Authors: MOLEMANS INGE , VAN DEN BERG RENATE , VAN SEVEREN LIEVE , GILLIS STEVEN
Published: September 2011

Various measures for identifying the onset of babbling have been proposed in the literature, but a formal definition of the exact procedure and a thorough validation of the sample size required for reliably establishing babbling onset is lacking. In this paper the reliability of five commonly used measures is assessed using a large longitudinal corpus of spontaneous speech from forty infants (age 0 ; 6−2 ; 0). In a first experiment it is shown that establishing the onset of babbling with reasonable (95%) confidence is impossible when the measures are computed only once, and when the number of vocalizations are not equal for all children at all ages. In addition, each measure requires a different minimal sample size. In the second experiment a robust procedure is proposed and formally defined that permits the identification of the onset of babbling with 95% confidence. The bootstrapping procedure involves extensive resampling and requires relatively few data.
The radial-hedgehog solution in Landau–de Gennes' theory for nematic liquid crystals
Authors: MAJUMDAR APALA
Published: September 2011

We study the radial-hedgehog solution in a three-dimensional spherical droplet, with homeotropic boundary conditions, within the Landau–de Gennes theory for nematic liquid crystals. The radial-hedgehog solution is a candidate for a global Landau–de Gennes minimiser in this model framework and is also a prototype configuration for studying isolated point defects in condensed matter physics. The static properties of the radial-hedgehog solution are governed by a non-linear singular ordinary differential equation. We study the analogies betweenGinzburg–Landauvortices and the radial-hedgehog solution and demonstrate a Ginzburg–Landau limit for the Landau–de Gennes theory. We prove that the radial-hedgehog solution is not the global Landau–de Gennes minimiser for droplets of finite radius and sufficiently low temperatures and prove the stability of the radial-hedgehog solution in other parameter regimes. These results contain quantitative information about the effect of geometry and temperature on the properties of the radial-hedgehog solution and the associated biaxial instabilities.
Phonological similarity influences word learning in adults learning Spanish as a foreign language
Authors: STAMER MELISSA K. , VITEVITCH MICHAEL S.
Published: September 2011

Neighborhood density – the number of words that sound similar to a given word (Luce & Pisoni, 1998) – influences word learning in native English-speaking children and adults (Storkel, 2004; Storkel, Armbruster & Hogan, 2006): novel words with many similar sounding English words (i.e., dense neighborhood) are learned more quickly than novel words with few similar sounding English words (i.e., sparse neighborhood). The present study examined how neighborhood density influences word learning in native English-speaking adults learning Spanish as a foreign language. Students in their third semester of Spanish-language classes learned advanced Spanish words that sounded similar to many known Spanish words (i.e., dense neighborhood) or sounded similar to few known Spanish words (i.e., sparse neighborhood). In three word-learning tasks, performance was better for Spanish words with dense rather than sparse neighborhoods. These results suggest that a similar mechanism may be used to learn new words in a native and a foreign language.
Immunoglobulin light chain, Blimp‐1 and cytochrome P4501B1 peptides as potential vaccines for AL amyloidosis
Authors: Flies Amanda , Ahmadi Tahamtan , Parks Ashley J , Prokaeva Tatiana , Weng Liangping , Rolfe Sandra Solomon , Seldin David C , Sherr David H
Published: September 2011

Amyloid light chain (AL) amyloidosis is a lethal disorder characterized by the pathologic deposition of clonal plasma cell‐derived, fibrillogenic immunoglobulin light chains in vital organs. Current chemotherapeutic regimens are problematic in patients with compromised organ function and are not effective for all patients. Here, a platform of computer‐based prediction and preclinical mouse modeling was used to begin development of a complementary, immunotherapeutic approach for AL amyloidosis. Three peptide/MHC I‐binding algorithms identified immunogenic peptides from three AL plasma cell‐associated proteins: (1) amyloidogenic λ6 light chains, (2) CYP1B1, a universal tumor antigen hyper‐expressed in AL plasma cells and (3) B lymphocyte‐induced maturation protein 1 (Blimp‐1), a transcription factor required for plasma cell differentiation. The algorithms correctly predicted HLA‐A∗0201‐binding native and heteroclitic peptides. In HLA‐A2 transgenic mice, these peptides, given individually or in combination, induced potent CTL which kill peptide‐loaded human lymphoma cells and/or lymphoma cells producing target protein. Blimp‐1 peptide‐immunized mice exhibited a reduced percentage of splenic, lymph node and bone marrow plasma cells and a decrease in the absolute number of splenic plasma cells demonstrating (1) presentation of target peptide by endogenous plasma cells and (2) appropriate CTL homing to lymphoid organs followed by killing of target plasma cells. These studies suggest that AL amyloidosis, with its relatively low tumor cell burden, may be an attractive target for peptide‐based multivalent vaccines.
Cancer is a side effect of evolution of viruses and bacteria
Authors: Mitin Valentin
Published: September 2011

Any human organism is home to viruses and bacteria. However, viruses (as well as other intracellular parasites) are interested in continuous division of the host cells. Unlimited division of the host cells means unlimited expansion of the living space and possibility for unlimited multiplication of viral particles. For this, human Cell Cycle Regulation System has to be affected in such a way to induce unlimited division of host cells. The present work describes oncogenome`s model of cancer development, according to which, in order to stimulate cell division, viruses affect a gene (or several genes) during transduction of a signal for cell division from growth factor to cyclin/CDK system. At the same time, controlling gene (p53, RB etc.) function and a switch to apoptosis are suppressed. Cell switch to cell division implies inability of the cell to carry out the functions of a differentiated cell. Spreading of viruses (bacteria) to the adjacent cells and forcing them into division, with simultaneous loss of differentiated cell functions, will become evident as the formation of malignant tumor or cancer.
Managing Bio-Models: *Model Storage, Retrieval, Ranking and Versioning
Authors: Henkel Ron , Waltemath Dagmar , Wolkenhauer Olaf
Published: September 2011

In this poster, we present our experience with techniques for the management of bio-models (i.e. XML-encoded computational models of biological systems) in repositories. These techniques support users to find, access, adapt and then re-submit models - tasks which are essential for the reuse of models in systems biology. Here, we focus on model retrieval, the ranking of search results and concepts to track the history of a model through version control. These concepts have so far not been sufficiently addressed in existing systems.To validate our techniques, we have been implemented a framework called Sombi. The underlying database called mDB is tailored towards a fine-grained storage of the model and its annotations. The design is applicable to different representation formats but, to begin with, has been tested with SBML models (Köhn et al., 2009).We furthermore present a retrieval algorithm for bio-model repositories (Henkel et al., 2010). The algorithm has been implemented and validated with mDB and the BioModels Database (www.ebi.ac.uk/biomodels-main/). The ranked retrieval enhances the result set by incorporating expert knowledge in the annotations. In contrast to existing systems, our approach provides a ranked result which is justified and explains the ordering of retrieved models to the users. The mDB design furthermore enables the application of structured queries on the stored model data.Finally, the poster proposes a solution to model version control. We introduce a library called BiVeS for tracking a model’s history in a diff tree; i.e. a tree-like storage of changes between model versions. These changes are additionally classified into modifications to XML structure, biology and mathematics. This information helps to understand existing models.All approaches are independent of the SBML format and can therefore be applied to other XML based exchange formats. All code is freely available on Sourceforge from http://bives.sourceforge.net/ and http://sombi.sourceforge.net/.
Functional Curation: Potential Future Directions for SED-ML
Authors: Cooper Jonathan , Mirams Gary
Published: September 2011

"Functional curation":http://dx.doi.org/10.1016/j.pbiomolbio.2011.06.003 of models is essentially about enabling a set of models to be tested for reproduction of a particular behaviour under some protocol. The idea is to examine which of the models are capable of replicating experimentally observed results, and evaluate their suitability for reuse in particular modelling studies. This requires a description of the protocol being performed on the models, and ideally a community agreed standard for these. Clearly SED-ML is the obvious candidate here, however, in its current form it has a few limitations that preclude this application. This talk discusses the requirements posed by functional curation, and introduces our ideas for extending SED-ML to address them.
Java support for SED-ML
Authors: Adams Richard
Published: September 2011

This presentation describes Java support for the SED-ML simulation experiment description language. Firstly, a Java API library for low-level manipulations of the SED-ML object model, and secondly a SED-ML editor, SED-ED, for visualizing and editing SED-ML workflows
SBML and Synthetic Biology
Authors: Myers Chris
Published: September 2011

This talk describes the synthetic biology open language (SBOL).
PKCβ inhibition with ruboxistaurin reduces oxidative stress and attenuates left ventricular hypertrophy and dysfuntion in rats with streptozotocin-induced diabetes
Authors: Liu Yanan , Lei Shaoqing , Gao Xia , Mao Xiaowen , Wang Tingting , Wong Gordon T. , Vanhoutte Paul M. , Irwin Michael G. , Xia Zhengyuan
Published: September 2011

Oxidative stress plays critical roles in the development of diabetic cardiovascular complications, including myocardial hypertrophy. The β isoform of PKC (protein kinase C) is preferentially overexpressed in the myocardium of diabetic subjects accompanied with increased activation of the pro-oxidant enzyme NADPH oxidase, which may exacerbate oxidative stress. We hypothesized that myocardial PKCβ is a major upstream mediator of oxidative stress in diabetes and that PKCβ inhibition can attenuate myocardial hypertrophy and dysfunction. Control or streptozotocin-induced diabetic rats were treated with the selective PKCβ inhibitor RBX (ruboxistaurin; 1 mg/kg of body weight per day) or the antioxidant NAC (N-acetylcysteine) for 4 weeks. LV (left ventricular) dimensions and functions were detected by echocardiography. 15-F2t-isoprostane (a specific index of oxidative stress) and myocardial activities of superoxide dismutase as well as protein levels of NADPH oxidase were assessed by immunoassay or Western blotting. Echocardiography revealed that the LV mass/body weight ratio was significantly increased in diabetic rats (P<0.01 compared with the control group) in parallel with the impaired LV relaxation. A significant increase in cardiomyocyte cross-sectional area was observed in diabetic rats accompanied by an increased production of O2− (superoxide anion) and 15-F2t-isoprostane (all P<0.05 compared with the control group). RBX normalized these changes with concomitant inhibition of PKCβ2 activation and prevention of NADPH oxidase subunit p67phox membrane translocation and p22phox overexpression. The effects of RBX were comparable with that of NAC, except that NAC was inferior to RBX in attenuating cardiac dysfunction. It is concluded that RBX can ameliorate myocardial hypertrophy and dysfunction in diabetes, which may represent a novel therapy in the prevention of diabetic cardiovascular complications.
Influence of ions on genome packaging and ejection: A molecular dynamics study
Authors: Ali I. , Marenduzzo D.
Published: September 2011

We, theoretically, investigate the effect of ions on the packing and ejection dynamics of flexible and semiflexible polymers from spherical viral capsids. We find that when the polymer charge is less screened, or the Debye length increases (corresponding to a buffer with low concentration of a monovalent salt, such as Na+), the packing becomes more difficult and it may stop midway. Ejection, instead, proceeds more easily if the electrostatic screening is small. On the other hand, more screening (corresponding, for example, to the addition of divalent ions such as Mg2 +) results in easier packing and slower ejection. We interpret this as resulting from electrostatic forces among the various polymer sections, which can be tuned with the type of salt present in the solution. We also discuss how the DNA structure inside the capsid changes due to screened electrostatic interactions.
Alternating half-loop shedding in the turbulent wake of a finite surface-mounted square cylinder with a thin boundary layer
Authors: Bourgeois J. A. , Sattari P. , Martinuzzi R. J.
Published: September 2011

The configuration and energetics of the large-scale vortex structure are presented for quasi-periodic shedding in the turbulent wake of a finite (h/d = 4) square-cross-section surface-mounted cylinder protruding from a thin boundary layer (δ/h = 0.18). The three-dimensional large-scale structure is educed from phase averaged x-y and x-z planar data measured with particle image velocimetry (PIV). Simultaneous measurements of the surface pressure difference on either side of the obstacle were used to phase-align the PIV planar measurements. The topology of the educed structures resembles alternating half-loops interconnecting close to the base plate. The time averaging of this unsteady structure gives rise to mean streamwise vortices akin to those presented in the literature for similar geometries. This topological analysis offers a contrasting interpretation of the mean streamwise vorticity, which has, otherwise, been presumed to originate from structures generated at the leading edge of the free-end. The dynamical significance of the resolved large scale structures and unresolved fluctuating kinetic energy in the wake is presented, either part being responsible for roughly half the mean kinetic energy. A discussion of turbulence production in light of the base flow that supplies it with energy is put forward.
Threshold conductivity switching in sulfurized antimony selenide nanowires
Authors: Karthik C. , Mehta Rutvik J. , Jiang Wei , Castillo Eduardo , Borca-Tasciuc Theodorian , Ramanath Ganpati
Published: September 2011

We report reversible switching between Ohmic and negative differential resistance states at a threshold voltage in sub-100-nm diameter sulfurized antimony selenide nanowires. We show that threshold switching in our nanowires arises due to high non-equilibrium free carrier concentrations resulting from impact ionization of carriers from defect states traceable to sulfurization and surface dangling bonds. Threshold switching is suppressed because of inhibited carrier generation at air-passivated defect states or at high temperatures due to thermally induced carrier depletion from deep states which preempts impact ionization. Such non-linear phenomena would be important for designing phase-change memories, thermoelectric devices, and sensors using pnictogen chalcogenide nanowires.
Manipulation of magnetic anisotropy of Co ultrathin films by substrate engineering
Authors: Saisyu Yuki , Hirahara Toru , Hobara Rei , Hasegawa Shuji
Published: September 2011

The magnetic and structural properties of Co films prepared on various substrates were investigated in situ based on the surface-magneto-optical Kerr effect (SMOKE) and using reflection high-energy electron diffraction (RHEED) and scanning tunneling microscopy (STM). The magnetic signals of the Co films were found to change significantly depending on the underlying substrates, the film thickness, and the temperature. Both STM and RHEED observations revealed that the shape and atomic structure of the Co islands were very different, which explains the observed magnetic anisotropy in SMOKE. We also observed a steep increase in coercivity for Co films thicker than 1.5 bi-layers grown on an Ag(111) film. This increase may be interpreted as a fcc-to-hcp structural transformation.
Beyond Zeeman spectroscopy: Magnetic-field diagnostics with Stark-dominated line shapes
Authors: Tessarin S. , Mikitchuk D. , Doron R. , Stambulchik E. , Kroupp E. , Maron Y. , Hammer D. A. , Jacobs V. L. , Seely J. F. , Oliver B. V. , Fisher A.
Published: September 2011

A recently suggested spectroscopic approach for magnetic-field determination in plasma is employed to measure magnetic fields in an expanding laser-produced plasma plume in an externally applied magnetic field. The approach enables the field determination in a diagnostically difficult regime for which the Zeeman-split patterns are not resolvable, as is often encountered under the conditions characteristic of high-energy-density plasmas. Here, such conditions occur in the high-density plasma near the laser target, due to the dominance of Stark broadening. A pulsed-power system is used to generate magnetic fields with a peak magnitude of 25 T at the inner-electrode surface in a coaxial configuration. An aluminum target attached to the inner electrode surface is then irradiated by a laser beam to produce the expanding plasma that interacts with the applied azimuthal magnetic field. A line-shape analysis of the Al III 4s–4p doublet (5696 and 5722 Å) enables the simultaneous determination of the magnetic field and the electron density. The measured magnetic fields are generally found to agree with those expected in a vacuum based on the pulsed-power system current. Examples of other transitions that can be used to diagnose a wide range of plasma and magnetic field parameters are presented.
Structural and magnetic properties of quaternary Co2Mn1-xCrxSi Heusler alloy thin films
Authors: Aftab M. , Hassnain Jaffari G. , Hasanain S. K. , Ismat Shah S.
Published: September 2011

We present the structural, magnetic, and transport properties of quaternary Co2Mn1-xCrxSi (0 ≤ x ≤ 1) Heusler alloy thin films prepared by DC magnetron sputtering on commercially available glass substrates without any buffer layer. Recent theoretical calculations have shown the compositions to be half-metallic. XRD patterns show the presence of L21 structure in the films for x = 0, however, the peaks intensities are not in accordance with the literature. High resolution transmission electron microscopy images of films show granular morphologies, crystalline growth, and an ordered L21 structure for x ≤ 0.6. For higher Cr concentrations, secondary phases start to appear in the films. Magnetization measurements as a function of applied magnetic field show that the saturation moments for x ≤ 0.2 follow the Slater-Pauling rule, however, for 0.2 < x ≤ 0.6 the saturation moments fall short of the theoretically predicted values. Transport measurements at room temperature show a monotonic increase in resistivity with increasing Cr concentration. These results are explained in terms of texturing effects, Co-Cr antisite disorder, presence of secondary phases, and the amount of disorder present in the films.
Preferential concentration and rise velocity reduction of bubbles immersed in a homogeneous and isotropic turbulent flow
Authors: Aliseda A. , Lasheras J. C.
Published: September 2011

The behavior of small spherical bubbles immersed in a homogeneous isotropic turbulent carrier flow of a heavier fluid has been experimentally studied. Air bubbles with diameters between 10 and 900 μm were injected in the test section of a horizontal water channel and allowed to interact with the turbulence induced by a grid located at the entrance to the test section. Point measurements of the bubble diameter and convective and rise velocities were taken from light interferometry data, together with flow visualizations that showed the instantaneous concentration field of bubbles in the carrier flow. The effect of the turbulence on the bubbles was found to alter the concentration field of bubbles leading to preferential accumulation at small scales, a phenomenon referred to as clustering, and to a decrease in the rise velocity of bubbles in the flow below the value measured and predicted for bubbles in a stationary fluid. These results are interpreted in terms of the different forces acting on the bubble in an inhomogeneous flow and in particular as the effect of pressure fluctuations that drive the bubbles preferentially to the core of vortices.
Numerical investigation of the subcritical effects at the onset of three-dimensionality in the circular cylinder wake
Authors: Akbar Tanvir , Bouchet Gilles , Dušek Jan
Published: September 2011

The presented numerical simulations focus on the strong non-linear effects at the onset of three-dimensionality in the circular cylinder wake. The obtained numerical results shed light on the link between the linear theory and experimental observations. The latter are represented mainly by the Williamson’s Strouhal vs. Reynolds number experimental curve presenting a double discontinuity at the onset of three-dimensionality. In this paper, we show that the subcritical nature of the secondary bifurcation triggering the three-dimensionality considerably weakens the relevance of linear predictions. We first investigate the bi-stability interval of the subcritical bifurcation as a function of the spanwise periodicity of simulations. This allows us to define a non-linear marginal stability curve and to show that it predicts no preferred wavelength. The large spanwise scales and their effect on the simulated flow are then investigated in simulations with a spanwise periodicity of 31.4d and run for subcritical Reynolds numbers Re = 185, 170, and 160. It is shown that the non-linear state is chaotic and that the bi-stability interval in which it co-exists with the 2D parallel vortex shedding extends at least from Re = 170 to the linear secondary instability threshold lying between Re = 188 and Re = 189. Strouhal numbers obtained in simulations with a spanwise period close to 4d (linear preferred wavelength) tend to overestimate the Strouhal number drop. Simulations with a large spanwise period tend to put the Strouhal number closer to experimental values. Below the bi-stability interval, at Re = 160, the wake is observed to settle from the chaotic state to oblique vortex shedding.
Laser induced electron acceleration in an ion-channel guiding
Authors: Esmaeilzadeh Mahdi , Taghavi Amin , Hanifpour Maryam
Published: September 2011

Direct electron acceleration by a propagating laser pulse of circular polarization in an ion-channel guiding is studied by developing a relativistic three-dimensional single particle code. The electron chaotic dynamic is also studied using time series, power spectrum, and Liapunov exponent. It is found that the electron motion is regular (non-chaotic) for laser pulse with short time duration, while for long enough time duration, the electron motion may be chaotic. In the case of non-chaotic motion, the electron can gain and retain very high energy in the presence of ion-channel before reaching the steady-state, whereas in the case of chaotic motion, the electron gains energy and then loses it very rapidly in an unpredictable manner.
Formation of quasistationary states in a ferromagnetic plate by scattering of ultrasound pulse in the vicinity of magnetoacoustic resonance
Authors: Peisakhovich Yuri G. , Shtygashev Alexander A.
Published: September 2011

We study the scattering of ultrasound wave packet that normally falls on a ferromagnetic plate in the vicinity of the magnetoelastic resonance. The reflection and transmission amplitudes spectra contain zeros and poles, which are connected with the coupling of elastic and spin clockwise polarized waves. Two types of poles determining the wave field evolution and the formation of quasistationary states have been found. The results depend on the surface pinning of the spins, on the magnetic field, and the plate thickness.