bluuebunny/crossref_metadata_2025 huggingface dataset:
Hybrid Vibration Control of a Circular Cylindrical Shell Using Electromagnetic Constrained Layer Damping Treatment
Authors: Hongpan Niu  , Shilin Xie  , Xinong Zhang
Published: June 2009

This paper investigates hybrid vibration control of a circular cylindrical shell through electromagnetic constrained layer damping (EMCLD) treatment, which consists of an electromagnet layer, a permanent magnet layer and a sandwiched viscoelastic damping layer. A mathematical model is developed based on the equivalent current method to calculate the electromagnetic control force produced by EMCLD. The governing equations of the shell system are established using Hamilton’s principle and then reduced with the assumed-mode method. The vibration control of a clamped-free circular cylindrical shell is simulated with velocity-proportional feedback to demonstrate the energy dissipation capability of EMCLD. Also, parametric studies are performed to examine the influences of geometry and physical properties of EMCLD on control performance. The results show the distinct energy consumption function of EMCLD in the passive way. The hybrid way provides much better control performance than the passive way in the concerned frequency range. It is also indicated from parametric studies that increasing the value of any one of the physical parameters, such as the loss factor of the viscoelastic material, the thickness of the permanent magnet and the area of EMCLD, has a contribution to the improvement of hybrid control performance. In contrast, increasing the thickness of the viscoelastic layer deteriorates both passive and hybrid control effects.
Discrete Time Sliding Mode Flow Controller for Multi-source Single-bottleneck Connection-oriented Communication Networks
Authors: Bartoszewicz Andrzej , Żuk Justyna
Published: June 2009

In this paper, we propose a sliding mode flow controller for connection-oriented, multi-source, single-bottleneck communication networks. For that purpose, we model the networks as discrete time systems with the available bandwidth acting as the disturbance. The proposed control algorithm is designed in such a way that the closed-loop system stability and finite time error convergence are ensured. Moreover, we demonstrate that the proposed controller guarantees no bottleneck link buffer overflow and full utilization of its available bandwidth. Furthermore, transmission rates generated by the controller are always bounded and nonnegative.
Simple Approaches to Improve the Performance of Noise Cancellation
Authors: Chang Cheng-Yuan
Published: June 2009

In this paper we present a neural-based algorithm to cancel the nonlinear narrowband and broadband noise in an active noise control (ANC) system. The improved method, including the ways to decide the learning rate and optimal initial weighting values of the neural network (NN), are presented to enhance the noise reduction performance. The proposed approach does not need mathematical transfer functions of the duct plant and a method of avoiding the premature saturation problem of NNs is also provided. A comparison with conventional neural methods by simulation shows that the proposed method can effectively cancel the undesired noise very well. The proposed improved method is also versatile to the other applications in NN filter design.
Replacement rate of filament lamps in an organisation: A rule of thumb
Authors: Agrawal DC , Menon VJ
Published: June 2009

We address the issue of renewal rate of fused filament lamps in an organisation and modify the description given in an old edition of the IESNA Lighting Handbook (1968). This is achieved by applying the standard mortality curve to formulate an exact algebraic relation for the renewal fraction at successive stages. Finally, for the benefit of illuminating engineers a rule of thumb is developed, which estimates the saturation number of lamps to be replaced as a function of burning time, half-life and the total number of lamps installed.
Geographic Information Systems (GIS) for Health Promotion and Public Health: A Review
Authors: Nykiforuk Candace I. J. , Flaman Laura M.
Published: June 2009

The purpose of this literature review is to identify how geographic information system (GIS) applications have been used in health-related research and to critically examine the issues, strengths, and challenges inherent to those approaches from the lenses of health promotion and public health. Through the review process, conducted in 2007, it is evident that health promotion and public health applications of GIS can be generally categorized into four predominant themes: disease surveillance (n = 227), risk analysis (n = 189), health access and planning (n = 138), and community health profiling (n = 115). This review explores how GIS approaches have been used to inform decision making and discusses the extent to which GIS can be applied to address health promotion and public health questions. The contribution of this literature review will be to generate a broader understanding of how GIS-related methodological techniques and tools developed in other disciplines can be meaningfully applied to applications in public health policy, promotion, and practice.
Cerebrospinal Immunoglobulin Level Changes and Clinical Response to Treatment of Hashimoto’s Encephalopathy
Authors: Gliebus Gediminas , Lippa Carol F.
Published: June 2009

We describe a 64-year-old male who presented with a 2-year history of behavioral and cognitive decline. Brain imaging showed nonenhancing hemispheric white matter lesions. Blood work revealed elevated thyroglobulin and thyroperoxidase antibody levels. Cerebrospinal fluid (CSF) analysis was largely negative, except for an elevated protein and immunoglobulin G (IgG) level. Because of the absence of stroke, central nervous system (CNS) tumor, or infection, this patient fits into criteria of Hashimoto’s encephalopathy. His Mini-Mental State Examination score improved from 10 to 29 after initial immunotherapy. The patient remained stable over 6 months with monthly outpatient total plasma exchange, but symptoms recurred within 3 months when the outpatient therapy was discontinued. A follow-up CSF IgG level was found to be increased and the treatment was repeated with partial clinical improvement and decline in CSF IgG level. He then underwent high dose steroid treatment after which patients’ clinical condition stabilized and CSF analysis showed even further IgG decline.
I Play Therefore I Am
Authors: Voorhees Gerald A.
Published: June 2009

Sid Meier's Civilization allows players to build empires that span the earth and the ages. Complementing existing scholarship on ideologies, practices, and subject positions inculcated by the game, this article interrogates the very conception of subjectivity Civilization fosters in players. Building upon ludological and cybernetic principles, the author takes a formal approach to analyze the processes of human—computer interaction that emerge in the course of players' engagement with the game. Characteristics of the turn-based genre as well as Civilization's interface mechanics, representations of historical processes, and manual are considered for the ways in which they solicit player input. The author contends that player interaction with Civilization reifies a conception of himself or herself as a sovereign agent constituted of pure internality.
Putting the Gay in Games
Authors: Shaw Adrienne
Published: June 2009

This article addresses gay, lesbian, bisexual, and transgender (GLBT) representation in video games from a cultural production perspective. It addresses how members of the video game industry account for the relative lack of GLBT representation in this medium. Previous studies have shown that certain stakeholders actively invest in GLBT representation in media. Factors in the inclusion of GLBT content include (a) the presence of motivated producers in the industry, those that are personally, politically, or commercially interested in GLBT content; (b) how the audience for a text or medium is constructed; (c) what the public backlash from both the GLBT community and conservative groups will be, as well as industry-based reprisals in the form of censorship or ratings; (d) the structure of the industry and how it is funded; and (e) how homosexuality, bisexuality, or transgender identities can be represented in the medium.
The Independent Production of Culture: A Digital Games Case Study
Authors: Martin Chase Bowen , Deuze Mark
Published: June 2009

Throughout the community of game players, developers, and journalists, the term ``independent'' is used in a number of ways to describe a type of development next to, or juxtaposed with, the mainstream process of creating, marketing, distributing, and playing digital games. Yet, this ``independence'' is something quite different from what the literature on independent, alternative, oppositional, radical, or otherwise nonmainstream media tends to suggest or advocate. The contemporary context of game design and development practices throughout the industry forces us to rethink assumptions about independence and autonomy in creative labor, about the communicative practices between media companies across the entire business spectrum of the global media industry, and about diversity or homogeneity in the production of culture. In this article, we aim to articulate more precisely what it means to create, work in, and give meaning to independent computer and video game production.
A comparison of neurocognitive functioning in children previously randomized to dexamethasone or prednisone in the treatment of childhood acute lymphoblastic leukemia
Authors: Kadan-Lottick Nina S. , Brouwers Pim , Breiger David , Kaleita Thomas , Dziura James , Liu Haibei , Chen Lu , Nicoletti Megan , Stork Linda , Bostrom Bruce , Neglia Joseph P.
Published: June 2009

In previous clinical trials of childhood acute lymphoblastic leukemia (ALL), dexamethasone resulted in higher event-free survival rates than prednisone, presumably due to greater central nervous system penetration. Dexamethasone's association with long-term neurocognitive toxicity is unknown. In this multisite study, we measured neurocognitive functioning in 92 children with standard-risk ALL, 1 to 9.99 years at diagnosis, at a mean of 9.8 years after randomization to prednisone (n = 41) or dexamethasone (n = 51) on Children's Cancer Group (CCG) 1922. No significant overall differences in mean neurocognitive and academic performance scores were found between the prednisone and dexamethasone groups after adjusting for age, sex, and time since diagnosis. The exception was that patients receiving dexamethasone scored one-third of a standard deviation worse on word reading (98.8 ± 1.7 vs 104.9 ± 1.8; P = .02). There were no group differences in the distribution of test scores or the parents' report of neurologic complications, psychotropic drug use, and special education. Further analyses suggested for the dexamethasone group, older age of diagnosis was associated with worse neurocognitive functioning; for the prednisone group, younger age at diagnosis was associated with worse functioning. In conclusion, our study did not demonstrate any meaningful differences in long-term cognitive functioning of childhood ALL patients based on corticosteroid randomization. This study is registered with http://www.clinicaltrials.gov under NCT00085176.
Early epigenetic changes and DNA damage do not predict clinical response in an overlapping schedule of 5-azacytidine and entinostat in patients with myeloid malignancies
Authors: Fandy Tamer E. , Herman James G. , Kerns Patrick , Jiemjit Anchalee , Sugar Elizabeth A. , Choi Si-Ho , Yang Allen S. , Aucott Timothy , Dauses Tianna , Odchimar-Reissig Rosalie , Licht Jonathan , McConnell Melanie J. , Nasrallah Chris , Kim Marianne K. H. , Zhang Weijia , Sun Yezou , Murgo Anthony , Espinoza-Delgado Igor , Oteiza Katharine , Owoeye Ibitayo , Silverman Lewis R. , Gore Steven D. , Carraway Hetty E.
Published: June 2009

Sequential administration of DNA methyltransferase (DNMT) inhibitors and histone deacetylase (HDAC) inhibitors has demonstrated clinical efficacy in patients with hematologic malignancies. However, the mechanism behind their clinical efficacy remains controversial. In this study, the methylation dynamics of 4 TSGs (p15INK4B, CDH-1, DAPK-1, and SOCS-1) were studied in sequential bone marrow samples from 30 patients with myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML) who completed a minimum of 4 cycles of therapy with 5-azacytidine and entinostat. Reversal of promoter methylation after therapy was observed in both clinical responders and nonresponders across all genes. There was no association between clinical response and either baseline methylation or methylation reversal in the bone marrow or purified CD34+ population, nor was there an association with change in gene expression. Transient global hypomethylation was observed in samples after treatment but was not associated with clinical response. Induction of histone H3/H4 acetylation and the DNA damage–associated variant histone γ-H2AX was observed in peripheral blood samples across all dose cohorts. In conclusion, methylation reversal of candidate TSGs during cycle 1 of therapy was not predictive of clinical response to combination “epigenetic” therapy. This trial is registered with http://www.clinicaltrials.gov under NCT00101179.
Reintroduction of CEBPA in MN1-overexpressing hematopoietic cells prevents their hyperproliferation and restores myeloid differentiation
Authors: Kandilci Ayten , Grosveld Gerard C.
Published: June 2009

Forced expression of MN1 in primitive mouse hematopoietic cells causes acute myeloid leukemia and impairs all-trans retinoic acid-induced granulocytic differentiation. Here, we studied the effects of MN1 on myeloid differentiation and proliferation using primary human CD34+ hematopoietic cells, lineage-depleted mouse bone marrow cells, and bipotential (granulocytic/monocytic) human acute myeloid leukemia cell lines. We show that exogenous MN1 stimulated the growth of CD34+ cells, which was accompanied by enhanced survival and increased cell cycle traverse in cultures supporting progenitor cell growth. Forced MN1 expression impaired both granulocytic and monocytic differentiation in vitro in primary hematopoietic cells and acute myeloid leukemia cell lines. Endogenous MN1 expression was higher in human CD34+ cells compared with both primary and in vitro–differentiated monocytes and granulocytes. Microarray and real-time reverse-transcribed polymerase chain reaction analysis of MN1-overexpressing CD34+ cells showed down-regulation of CEBPA and its downstream target genes. Reintroduction of conditional and constitutive CEBPA overcame the effects of MN1 on myeloid differentiation and inhibited MN1-induced proliferation in vitro. These results indicate that down-regulation of CEBPA activity contributes to MN1-modulated proliferation and impaired myeloid differentiation of hematopoietic cells.
Editorial
Authors: Bodin Loys
Published: June 2009

The Institut National de la Recherche Agronomique (INRA) was honoured to welcome scientists from all over the world who attended the International Workshop on major Genes and QTL in Sheep and Goats. Approximately 100 participants from 16 countries were registered, contributing 52 oral or poster presentations.

A first session was dedicated to the tools available for identifying and localising major genes or QTL in these two species. Molecular techniques, marker panels, radiation hybrids, genome physical maps, and BAC libraries were presented along with genetic, comparative and cytogenetic maps. A second and largest session concerned different traits for which major genes or QTL have been found, i.e., ovulation and other reproduction traits, milk and meat characters, and resistance to disease and wool production. For each group, a guest's paper focused on one sub-trait gave the state of the art: the history, identification and localisation of sources of monogenic and oligogenic variability, genetic determinism (dominance, imprinting, ...), effects on the phenotype, physiological mechanisms implied, use in populations, etc. The third session was devoted to the strategies for the use of major genes and QTL in populations, while the last session covered future prospects.

A CD (available on request to bodin@toulouse.inra.fr) of the full proceedings was available, and participants invited to give a main paper also had the opportunity to submit it for publication in this special issue of GSE. Nine articles were jointly selected by the Editorial Board of the journal and by the Guest Editor.
Alveolar hypoxia, alveolar macrophages, and systemic inflammation
Authors: Chao Jie , Wood John G , Gonzalez Norberto C
Published: June 2009

Diseases featuring abnormally low alveolar PO2 are frequently accompanied by systemic effects. The common presence of an underlying inflammatory component suggests that inflammation may contribute to the pathogenesis of the systemic effects of alveolar hypoxia. While the role of alveolar macrophages in the immune and defense functions of the lung has been long known, recent evidence indicates that activation of alveolar macrophages causes inflammatory disturbances in the systemic microcirculation. The purpose of this review is to describe observations in experimental animals showing that alveolar macrophages initiate a systemic inflammatory response to alveolar hypoxia. Evidence obtained in intact animals and in primary cell cultures indicate that alveolar macrophages activated by hypoxia release a mediator(s) into the circulation. This mediator activates perivascular mast cells and initiates a widespread systemic inflammation. The inflammatory cascade includes activation of the local renin-angiotensin system and results in increased leukocyte-endothelial interactions in post-capillary venules, increased microvascular levels of reactive O2 species; and extravasation of albumin. Given the known extrapulmonary responses elicited by activation of alveolar macrophages, this novel phenomenon could contribute to some of the systemic effects of conditions featuring low alveolar PO2.
Modeling the role of p53 pulses in DNA damage- induced cell death decision
Authors: Sun Tingzhe , Chen Chun , Wu Yuanyuan , Zhang Shuai , Cui Jun , Shen Pingping
Published: June 2009

Background

The tumor suppressor p53 plays pivotal roles in tumorigenesis suppression. Although oscillations of p53 have been extensively studied, the mechanism of p53 pulses and their physiological roles in DNA damage response remain unclear.

Results

To address these questions we presented an integrated model in which Ataxia-Telangiectasia Mutated (ATM) activation and p53 oscillation were incorporated with downstream apoptotic events, particularly the interplays between Bcl-2 family proteins. We first reproduced digital oscillation of p53 as the response of normal cells to DNA damage. Subsequent modeling in mutant cells showed that high basal DNA damage is a plausible cause for sustained p53 pulses observed in tumor cells. Further computational analyses indicated that p53-dependent PUMA accumulation and the PUMA-controlled Bax activation switch might play pivotal roles to count p53 pulses and thus decide the cell fate.

Conclusion

The high levels of basal DNA damage are responsible for generating sustained pulses of p53 in the tumor cells. Meanwhile, the Bax activation switch can count p53 pulses through PUMA accumulation and transfer it into death signal. Our modeling provides a plausible mechanism about how cells generate and orchestrate p53 pulses to tip the balance between survival and death.
OrthoClusterDB: an online platform for synteny blocks
Authors: Ng Man-Ping , Vergara Ismael A , Frech Christian , Chen Qingkang , Zeng Xinghuo , Pei Jian , Chen Nansheng
Published: June 2009

Background

The recent availability of an expanding collection of genome sequences driven by technological advances has facilitated comparative genomics and in particular the identification of synteny among multiple genomes. However, the development of effective and easy-to-use methods for identifying such conserved gene clusters among multiple genomes–synteny blocks–as well as databases, which host synteny blocks from various groups of species (especially eukaryotes) and also allow users to run synteny-identification programs, lags behind.

Descriptions

OrthoClusterDB is a new online platform for the identification and visualization of synteny blocks. OrthoClusterDB consists of two key web pages: Run OrthoCluster and View Synteny. The Run OrthoCluster page serves as web front-end to OrthoCluster, a recently developed program for synteny block detection. Run OrthoCluster offers full control over the functionalities of OrthoCluster, such as specifying synteny block size, considering order and strandedness of genes within synteny blocks, including or excluding nested synteny blocks, handling one-to-many orthologous relationships, and comparing multiple genomes. In contrast, the View Synteny page gives access to perfect and imperfect synteny blocks precomputed for a large number of genomes, without the need for users to retrieve and format input data. Additionally, genes are cross-linked with public databases for effective browsing. For both Run OrthoCluster and View Synteny, identified synteny blocks can be browsed at the whole genome, chromosome, and individual gene level. OrthoClusterDB is freely accessible.

Conclusion

We have developed an online system for the identification and visualization of synteny blocks among multiple genomes. The system is freely available at http://genome.sfu.ca/orthoclusterdb/.
Generation and characterization of human insulin-releasing cell lines
Authors: Labriola Leticia , Peters Maria G , Krogh Karin , Stigliano Iván , Terra Letícia F , Buchanan Cecilia , Machado Marcel CC , Joffé Elisa Bal de Kier , Puricelli Lydia , Sogayar Mari C
Published: June 2009

Background

The in vitro culture of insulinomas provides an attractive tool to study cell proliferation and insulin synthesis and secretion. However, only a few human beta cell lines have been described, with long-term passage resulting in loss of insulin secretion. Therefore, we set out to establish and characterize human insulin-releasing cell lines.

Results

We generated ex-vivo primary cultures from two independent human insulinomas and from a human nesidioblastosis, all of which were cultured up to passage number 20. All cell lines secreted human insulin and C-peptide. These cell lines expressed neuroendocrine and islets markers, confirming the expression profile found in the biopsies. Although all beta cell lineages survived an anchorage independent culture, none of them were able to invade an extracellular matrix substrate.

Conclusion

We have established three human insulin-releasing cell lines which maintain antigenic characteristics and insulin secretion profiles of the original tumors. These cell lines represent valuable tools for the study of molecular events underlying beta cell function and dysfunction.
Parallelization and optimization of genetic analyses in isolation by distance web service
Authors: Turner Julia L , Kelley Scott T , Otto James S , Valafar Faramarz , Bohonak Andrew J
Published: June 2009

Background

The Isolation by Distance Web Service (IBDWS) is a user-friendly web interface for analyzing patterns of isolation by distance in population genetic data. IBDWS enables researchers to perform a variety of statistical tests such as Mantel tests and reduced major axis regression (RMA), and returns vector based graphs. The more than 60 citations since 2005 confirm the popularity and utility of this website. Despite its usefulness, the data sets with over 65 populations can take hours or days to complete due to the computational intensity of the statistical tests. This is especially troublesome for web-based software analysis, since users tend to expect real-time results on the order of seconds, or at most, minutes. Moreover, as genetic data continue to increase and diversify, so does the demand for more processing power. In order to increase the speed and efficiency of IBDWS, we first determined which aspects of the code were most time consuming and whether they might be amenable to improvements by parallelization or algorithmic optimization.

Results

Runtime tests uncovered two areas of IBDWS that consumed significant amounts of time: randomizations within the Mantel test and the RMA calculations. We found that these sections of code could be restructured and parallelized to improve efficiency. The code was first optimized by combining two similar randomization routines, implementing a Fisher-Yates shuffling algorithm, and then parallelizing those routines. Tests of the parallelization and Fisher-Yates algorithmic improvements were performed on a variety of data sets ranging from 10 to 150 populations. All tested algorithms showed runtime reductions and a very close fit to the predicted speedups based on time-complexity calculations. In the case of 150 populations with 10,000 randomizations, data were analyzed 23 times faster.

Conclusion

Since the implementation of the new algorithms in late 2007, datasets have continued to increase substantially in size and many exceed the largest population sizes we used in our test sets. The fact that the website has continued to work well in "real-world" tests, and receives a considerable number of new citations provides the strongest testimony to the effectiveness of our improvements. However, we soon expect the need to upgrade the number of nodes in our cluster significantly as dataset sizes continue to expand. The parallel implementation can be found at http://ibdws.sdsu.edu/.
Improved resolution in the position of drought-related QTLs in a single mapping population of rice by meta-analysis
Authors: Khowaja Farkhanda S , Norton Gareth J , Courtois Brigitte , Price Adam H
Published: June 2009

Background

Meta-analysis of QTLs combines the results of several QTL detection studies and provides narrow confidence intervals for meta-QTLs, permitting easier positional candidate gene identification. It is usually applied to multiple mapping populations, but can be applied to one. Here, a meta-analysis of drought related QTLs in the Bala × Azucena mapping population compiles data from 13 experiments and 25 independent screens providing 1,650 individual QTLs separated into 5 trait categories; drought avoidance, plant height, plant biomass, leaf morphology and root traits. A heat map of the overlapping 1 LOD confidence intervals provides an overview of the distribution of QTLs. The programme BioMercator is then used to conduct a formal meta-analysis at example QTL clusters to illustrate the value of meta-analysis of QTLs in this population.

Results

The heat map graphically illustrates the genetic complexity of drought related traits in rice. QTLs can be linked to their physical position on the rice genome using Additional file 1 provided. Formal meta-analysis on chromosome 1, where clusters of QTLs for all trait categories appear close, established that the sd1 semi-dwarfing gene coincided with a plant height meta-QTL, that the drought avoidance meta-QTL was not likely to be associated with this gene, and that this meta-QTL was not pleiotropic with close meta-QTLs for leaf morphology and root traits. On chromosome 5, evidence suggests that a drought avoidance meta-QTL was pleiotropic with leaf morphology and plant biomass meta-QTLs, but not with meta-QTLs for root traits and plant height 10 cM lower down. A region of dense root QTL activity graphically visible on chromosome 9 was dissected into three meta-QTLs within a space of 35 cM. The confidence intervals for meta-QTLs obtained ranged from 5.1 to 14.5 cM with an average of 9.4 cM, which is approximately 180 genes in rice.

Conclusion

The meta-analysis is valuable in providing improved ability to dissect the complex genetic structure of traits, and distinguish between pleiotropy and close linkage. It also provides relatively small target regions for the identification of positional candidate genes.
Carbon and arsenic metabolism in Thiomonas strains: differences revealed diverse adaptation processes
Authors: Bryan Christopher G , Marchal Marie , Battaglia-Brunet Fabienne , Kugler Valérie , Lemaitre-Guillier Christelle , Lièvremont Didier , Bertin Philippe N , Arsène-Ploetze Florence
Published: June 2009

Background

Thiomonasstrains are ubiquitous in arsenic-contaminated environments. Differences betweenThiomonasstrains in the way they have adapted and respond to arsenic have never been studied in detail. For this purpose, fiveThiomonasstrains, that are interesting in terms of arsenic metabolism were selected:T. arsenivorans,Thiomonasspp. WJ68 and 3As are able to oxidise As(III), whileThiomonassp. Ynys1 andT. perometabolisare not. Moreover,T. arsenivoransand 3As present interesting physiological traits, in particular that these strains are able to use As(III) as an electron donor.

Results

The metabolism of carbon and arsenic was compared in the fiveThiomonasstrains belonging to two distinct phylogenetic groups. Greater physiological differences were found between these strains than might have been suggested by 16S rRNA/rpoAgene phylogeny, especially regarding arsenic metabolism. Physiologically,T. perometabolisand Ynys1 were unable to oxidise As(III) and were less arsenic-resistant than the other strains. Genetically, they appeared to lack theaoxarsenic-oxidising genes and carried only a singlearsarsenic resistance operon.Thiomonas arsenivoransbelonged to a distinct phylogenetic group and increased its autotrophic metabolism when arsenic concentration increased. Differential proteomic analysis revealed that inT. arsenivorans, therbc/cbbgenes involved in the assimilation of inorganic carbon were induced in the presence of arsenic, whereas these genes were repressed inThiomonassp. 3As.

Conclusion

Taken together, these results show that these closely related bacteria differ substantially in their response to arsenic, amongst other factors, and suggest different relationships between carbon assimilation and arsenic metabolism.
Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family
Authors: Zylicz-Stachula Agnieszka , Bujnicki Janusz M , Skowron Piotr M
Published: June 2009

Background

Restriction-modification systems are a diverse class of enzymes. They are classified into four major types: I, II, III and IV. We have previously proposed the existence of a Thermus sp. enzyme family, which belongs to type II restriction endonucleases (REases), however, it features also some characteristics of types I and III. Members include related thermophilic endonucleases: TspGWI, TaqII, TspDTI, and Tth111II.

Results

Here we describe cloning, mutagenesis and analysis of the prototype TspGWI enzyme that recognises the 5'-ACGGA-3' site and cleaves 11/9 nt downstream. We cloned, expressed, and mutagenised the tspgwi gene and investigated the properties of its product, the bifunctional TspGWI restriction/modification enzyme. Since TspGWI does not cleave DNA completely, a cloning method was devised, based on amino acid sequencing of internal proteolytic fragments. The deduced amino acid sequence of the enzyme shares significant sequence similarity with another representative of the Thermus sp. family – TaqII. Interestingly, these enzymes recognise similar, yet different sequences in the DNA. Both enzymes cleave DNA at the same distance, but differ in their ability to cleave single sites and in the requirement of S-adenosylmethionine as an allosteric activator for cleavage. Both the restriction endonuclease (REase) and methyltransferase (MTase) activities of wild type (wt) TspGWI (either recombinant or isolated from Thermus sp.) are dependent on the presence of divalent cations.

Conclusion

TspGWI is a bifunctional protein comprising a tandem arrangement of Type I-like domains; particularly noticeable is the central HsdM-like module comprising a helical domain and a highly conserved S-adenosylmethionine-binding/catalytic MTase domain, containing DPAVGTG and NPPY motifs. TspGWI also possesses an N-terminal PD-(D/E)XK nuclease domain related to the corresponding domains in HsdR subunits, but lacks the ATP-dependent translocase module of the HsdR subunit and the additional domains that are involved in subunit-subunit interactions in Type I systems. The MTase and REase activities of TspGWI are autonomous and can be uncoupled. Structurally and functionally, the TspGWI protomer appears to be a streamlined 'half' of a Type I enzyme.
Elongation factor eEF1B modulates functions of the release factors eRF1 and eRF3 and the efficiency of translation termination in yeast
Authors: Valouev Igor A , Fominov Gleb V , Sokolova Elizaveta E , Smirnov Vladimir N , Ter-Avanesyan Michael D
Published: June 2009

Background

Termination of translation in eukaryotes is controlled by two interacting polypeptide chain release factors, eRF1 and eRF3. While eRF1 recognizes nonsense codons, eRF3 facilitates polypeptide chain release from the ribosome in a GTP-dependent manner. Besides termination, both release factors have essential, but poorly characterized functions outside of translation.

Results

To characterize further the functions of yeast eRF1 and eRF3, a genetic screen for their novel partner proteins was performed. As a result, the genes for γ (TEF4 and TEF3/CAM1) and α (TEF5/EFB1) subunits of the translation elongation factor eEF1B, known to catalyze the exchange of bound GDP for GTP on eEF1A, were revealed. These genes act as dosage suppressors of a synthetic growth defect caused by some mutations in the SUP45 and SUP35 genes encoding eRF1 and eRF3, respectively. Extra copies of TEF5 and TEF3 can also suppress the temperature sensitivity of some sup45 and sup35 mutants and reduce nonsense codon readthrough caused by these omnipotent suppressors. Besides, overproduction of eEF1Bα reduces nonsense codon readthrough in the strain carrying suppressor tRNA. Such effects were not shown for extra copies of TEF2, which encodes eEF1A, thus indicating that they were not due to eEF1A activation.

Conclusion

The data obtained demonstrate involvement of the translation elongation factor eEF1B in modulating the functions of translation termination factors and suggest its possible role in GDP for GTP exchange on eRF3.
In vivo proton magnetic resonance spectroscopy reveals region specific metabolic responses to SIV infection in the macaque brain
Authors: Ratai Eva-Maria , Pilkenton Sarah J , Greco Jane B , Lentz Margaret R , Bombardier Jeffrey P , Turk Katherine W , He Julian , Joo Chan-Gyu , Lee Vallent , Westmoreland Susan , Halpern Elkan , Lackner Andrew A , González R Gilberto
Published: June 2009

Background

In vivo proton magnetic resonance spectroscopy (1H-MRS) studies of HIV-infected humans have demonstrated significant metabolic abnormalities that vary by brain region, but the causes are poorly understood. Metabolic changes in the frontal cortex, basal ganglia and white matter in 18 SIV-infected macaques were investigated using MRS during the first month of infection.

Results

Changes in the N-acetylaspartate (NAA), choline (Cho), myo-inositol (MI), creatine (Cr) and glutamine/glutamate (Glx) resonances were quantified both in absolute terms and relative to the creatine resonance. Most abnormalities were observed at the time of peak viremia, 2 weeks post infection (wpi). At that time point, significant decreases in NAA and NAA/Cr, reflecting neuronal injury, were observed only in the frontal cortex. Cr was significantly elevated only in the white matter. Changes in Cho and Cho/Cr were similar across the brain regions, increasing at 2 wpi, and falling below baseline levels at 4 wpi. MI and MI/Cr levels were increased across all brain regions.

Conclusion

These data best support the hypothesis that different brain regions have variable intrinsic vulnerabilities to neuronal injury caused by the AIDS virus.
Impairment of mitochondrial calcium handling in a mtSOD1 cell culture model of motoneuron disease
Authors: Jaiswal Manoj Kumar , Zech Wolf-Dieter , Goos Miriam , Leutbecher Christine , Ferri Alberto , Zippelius Annette , Carrì Maria Teresa , Nau Roland , Keller Bernhard U
Published: June 2009

Background

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by the selective loss of motor neurons (MN) in the brain stem and spinal cord. Intracellular disruptions of cytosolic and mitochondrial calcium have been associated with selective MN degeneration, but the underlying mechanisms are not well understood. The present evidence supports a hypothesis that mitochondria are a target of mutant SOD1-mediated toxicity in familial amyotrophic lateral sclerosis (fALS) and intracellular alterations of cytosolic and mitochondrial calcium might aggravate the course of this neurodegenerative disease. In this study, we used a fluorescence charged cool device (CCD) imaging system to separate and simultaneously monitor cytosolic and mitochondrial calcium concentrations in individual cells in an established cellular model of ALS.

Results

To gain insights into the molecular mechanisms of SOD1G93A associated motor neuron disease, we simultaneously monitored cytosolic and mitochondrial calcium concentrations in individual cells. Voltage – dependent cytosolic Ca2+ elevations and mitochondria – controlled calcium release mechanisms were monitored after loading cells with fluorescent dyes fura-2 and rhod-2. Interestingly, comparable voltage-dependent cytosolic Ca2+ elevations in WT (SH-SY5YWT) and G93A (SH-SY5YG93A) expressing cells were observed. In contrast, mitochondrial intracellular Ca2+ release responses evoked by bath application of the mitochondrial toxin FCCP were significantly smaller in G93A expressing cells, suggesting impaired calcium stores. Pharmacological experiments further supported the concept that the presence of G93A severely disrupts mitochondrial Ca2+ regulation.

Conclusion

In this study, by fluorescence measurement of cytosolic calcium and using simultaneous [Ca2+]i and [Ca2+]mito measurements, we are able to separate and simultaneously monitor cytosolic and mitochondrial calcium concentrations in individual cells an established cellular model of ALS. The primary goals of this paper are (1) method development, and (2) screening for deficits in mutant cells on the single cell level. On the technological level, our method promises to serve as a valuable tool to identify mitochondrial and Ca2+-related defects during G93A-mediated MN degeneration. In addition, our experiments support a model where a specialized interplay between cytosolic calcium profiles and mitochondrial mechanisms contribute to the selective degeneration of neurons in ALS.
The HaDREB2 transcription factor enhances basal thermotolerance and longevity of seeds through functional interaction with HaHSFA9
Authors: Almoguera Concepción , Prieto-Dapena Pilar , Díaz-Martín Juan , Espinosa José M , Carranco Raúl , Jordano Juan
Published: June 2009

Background

Transcription factor HaDREB2 was identified in sunflower (Helianthus annuus L.) as a drought-responsive element-binding factor 2 (DREB2) with unique properties. HaDREB2 and the sunflower Heat Shock Factor A9 (HaHSFA9) co-activated the Hahsp17.6G1 promoter in sunflower embryos. Both factors could be involved in transcriptional co-activation of additional small heat stress protein (sHSP) promoters, and thus contribute to the HaHSFA9-mediated enhancement of longevity and basal thermotolerance of seeds.

Results

We found that overexpression of HaDREB2 in seeds did not enhance longevity. This was deduced from assays of basal thermotolerance and controlled seed-deterioration, which were performed with transgenic tobacco. Furthermore, the constitutive overexpression of HaDREB2 did not increase thermotolerance in seedlings or result in the accumulation of HSPs at normal growth temperatures. In contrast, when HaDREB2 and HaHSFA9 were conjointly overexpressed in seeds, we observed positive effects on seed longevity, beyond those observed with overexpression of HaHSFA9 alone. Such additional effects are accompanied by a subtle enhancement of the accumulation of subsets of sHSPs belonging to the CI and CII cytosolic classes.

Conclusion

Our results reveal the functional interdependency of HaDREB2 and HaHSFA9 in seeds. HaDREB2 differs from other previously characterized DREB2 factors in plants in terms of its unique functional interaction with the seed-specific HaHSFA9 factor. No functional interaction between HaDREB2 and HaHSFA9 was observed when both factors were conjointly overexpressed in vegetative tissues. We therefore suggest that additional, seed-specific factors, or protein modifications, could be required for the functional interaction between HaDREB2 and HaHSFA9.
Characterization and structural analysis of wild type and a non-abscission mutant at the development funiculus (Def) locus in Pisum sativum L
Authors: Ayeh Kwadwo Owusu , Lee YeonKyeong , Ambrose Mike J , Hvoslef-Eide Anne Kathrine
Published: June 2009

Background

In pea seeds (Pisum sativumL.), theDeflocus defines an abscission event where the seed separates from the funicle through the intervening hilum region at maturity. A spontaneous mutation at this locus results in the seed failing to abscise from the funicle as occurs in wild type peas. In this work, structural differences between wild type peas that developed a distinct abscission zone (AZ) between the funicle and the seed coat and non-abscissiondefmutant were characterized.

Results

A clear abscission event was observed in wild type pea seeds that were associated with a distinct double palisade layers at the junction between the seed coat and funicle. Generally, mature seeds fully developed an AZ, which was not present in young wild type seeds. The AZ was formed exactly below the counter palisade layer. In contrast, the palisade layers at the junction of the seed coat and funicle were completely absent in thedefmutant pea seeds and the cells in this region were seen to be extensions of surrounding parenchymatous cells.

Conclusion

TheDefwild type developed a distinct AZ associated with palisade layer and counterpalisade layer at the junction of the seed coat and funicle while thedefmutant pea seed showed non-abscission and an absence of the double palisade layers in the same region. We conclude that the presence of the double palisade layer in the hilum of the wild type pea seeds plays an important structural role in AZ formation by delimiting the specific region between the seed coat and the funicle and may play a structural role in the AZ formation and subsequent detachment of the seed from the funicle.
Identifying strategies to maximise recruitment and retention of practices and patients in a multicentre randomised controlled trial of an intervention to optimise secondary prevention for coronary heart disease in primary care
Authors: Leathem Claire S , Cupples Margaret E , Byrne Mary C , O'Malley Mary , Houlihan Ailish , Murphy Andrew W , Smith Susan M
Published: June 2009

Background

Recruitment and retention of patients and healthcare providers in randomised controlled trials (RCTs) is important in order to determine the effectiveness of interventions. However, failure to achieve recruitment targets is common and reasons why a particular recruitment strategy works for one study and not another remain unclear. We sought to describe a strategy used in a multicentre RCT in primary care, to report researchers' and participants' experiences of its implementation and to inform future strategies to maximise recruitment and retention.

Methods

In total 48 general practices and 903 patients were recruited from three different areas of Ireland to a RCT of an intervention designed to optimise secondary prevention of coronary heart disease. The recruitment process involved telephoning practices, posting information, visiting practices, identifying potential participants, posting invitations and obtaining consent. Retention involved patients attending reviews and responding to questionnaires and practices facilitating data collection.

Results

We achieved high retention rates for practices (100%) and for patients (85%) over an 18-month intervention period. Pilot work, knowledge of the setting, awareness of change in staff and organisation amongst participant sites, rapid responses to queries and acknowledgement of practitioners' contributions were identified as being important. Minor variations in protocol and research support helped to meet varied, complex and changing individual needs of practitioners and patients and encouraged retention in the trial. A collaborative relationship between researcher and practice staff which required time to develop was perceived as vital for both recruitment and retention.

Conclusion

Recruiting and retaining the numbers of practices and patients estimated as required to provide findings with adequate power contributes to increased confidence in the validity and generalisability of RCT results. A continuous dynamic process of monitoring progress within trials and tailoring strategies to particular circumstances, whilst not compromising trial protocols, should allow maximal recruitment and retention.

Trial registration

ISRCTN24081411
Timing of surgical antibiotic prophylaxis administration: Complexities of analysis
Authors: Cartmill Carrie , Lingard Lorelei , Regehr Glenn , Espin Sherry , Bohnen John , Baker Ross , Rotstein Lorne
Published: June 2009

Background

The timing of prophylactic antibiotic administration is a patient safety outcome that is recurrently tracked and reported. The interpretation of these data has important implications for patient safety practices. However, diverse data collection methods and approaches to analysis impede knowledge building in this field. This paper makes explicit several challenges to quantifying the timing of prophylactic antibiotics that we encountered during a recent study and offers a suggested protocol for resolving these challenges.

Challenges

Two clear challenges manifested during the data extraction process: the actual classification of antibiotic timing, and the additional complication of multiple antibiotic regimens with different timing classifications in a single case. A formalized protocol was developed for dealing with incomplete, ambiguous and unclear documentation. A hierarchical coding system was implemented for managing cases with multiple antibiotic regimens.

Interpretation

Researchers who are tracking prophylactic antibiotic timing as an outcome measure should be aware that documentation of antibiotic timing in the patient chart is frequently incomplete and unclear, and these inconsistencies should be accounted for in analyses. We have developed a systematic method for dealing with specific problematic patterns encountered in the data. We propose that the general adoption of a systematic approach to analysis of this type of data will allow for cross-study comparisons and ensure that interpretation of results is on the basis of timing practices rather than documentation practices.