bluuebunny/crossref_metadata_2025 huggingface dataset:
Cranberry Proanthocyanidins Inhibit MMP Production and Activity
Authors: La V.D. , Howell A.B. , Grenier D.
Published: July 2009

Matrix metalloproteinases (MMPs) produced by resident and inflammatory cells in response to periodontopathogens play a major role in periodontal tissue destruction. Our aim was to investigate the effects of A-type cranberry proanthocyanidins (AC-PACs) on: (i) the production of various MMPs by human monocyte-derived macrophages stimulated with Aggregatibacter actinomycetemcomitans lipopolysaccharide (LPS), and (ii) the catalytic activity of recombinant MMP-1 and MMP-9. The effects of AC-PACs on the expression of 5 protein kinases and the activity of nuclear factor-kappa B (NF-κB) p65 in macrophages stimulated with LPS were also monitored. Our results indicated that AC-PACs inhibited the production of MMPs in a concentration-dependent manner. Furthermore, the catalytic activity of MMP-1 and MMP-9 was also inhibited. The inhibition of MMP production was associated with reduced phosphorylation of key intracellular kinases and the inhibition of NF-κB p65 activity. AC-PACs thus show potential for the development of novel host-modulating strategies to inhibit MMP-mediated tissue destruction during periodontitis.
Race and Support for State Takeovers of Local School Districts
Authors: Burns Peter
Published: July 2009

State takeovers of local school districts represent one of the most recent kinds of education reform. Americans favor both local control over education and state takeovers of failing schools. African American leaders tend to oppose takeovers, but survey data suggest that African American citizens support greater state influence over local education. To explain these paradoxes, this study examines conditions under which jurisdictions support state intervention. It concludes that opposition to this reform emanates from jurisdictions where large percentages of African American voters turn out at high rates. The percentage of a jurisdiction’s schools eligible for takeover because of academic deficiencies exerts a statistically insignificant effect on aggregate-level votes for intervention.
Economics Imperialism and Solution Concepts in Political Science
Authors: Kuorikoski Jaakko , Lehtinen Aki
Published: July 2009

Political science and economic science . . . make use of the same language, the same mode of abstraction, the same instruments of thought and the same method of reasoning. (Black 1998, 354)

Proponents as well as opponents of economics imperialism agree that imperialism is a matter of unification; providing a unified framework for social scientific analysis. Uskali Mäki distinguishes between derivational and ontological unification and argues that the latter should serve as a constraint for the former. We explore whether, in the case of rational-choice political science, self-interested behavior can be seen as a common causal element and solution concepts as the common derivational element, and whether the former constraints the use of the latter. We find that this is not the case. Instead, what is common to economics and rational-choice political science is a set of research heuristics and a focus on institutions with similar structures and forms of organization.
Heat demand and air exchange in a multifamily building — simulation with elements of validation
Authors: Baranowski A. , Ferdyn-Grygierek J.
Published: July 2009

The experiment providing data on the energy demand and air exchange in the flat located in the multifamily building is presented in the paper. The measurement was carried out during 3 weeks in winter. The total energy consumption necessary for flat heating was measured continuously. During the same time air change rate in the flat was measured by means of tracer gas concentration decay methods. After measurements were finished the energy demand and ventilating airflows were calculated assuming the same weather data variation as measured during the experiment, using the ESP-r software. Contam program was used for the air infiltration simulation, giving more detailed results about the ventilation airflows within the tested object. Comparison was made between numerical results and measured data over the given cycle and a good correlation of results has been achieved.

Practical applications: Simulation methods can be an alternative to the assessment of energy consumption or heat demand in buildings when the direct measurement is impossible or difficult. A good agreement of simulation and measurement results is reached when the average values of the results are compared for a longer period of time.
The Impact of Change Process and Context on Change Reactions and Turnover During a Merger
Authors: Rafferty Alannah E. , Restubog Simon Lloyd D.
Published: July 2009

The authors examined relationships among two measures of the change process adopted by a firm and a measure of the change context and employees’ reactions to a merger. A longitudinal study was conducted. An employee’s perception that he or she had a poor change history was negatively associated with affective commitment to change. As the number of formal change information sessions attended increased, anxiety decreased. High quality change information was negatively associated with anxiety and positively related to affective commitment to change. Affective commitment was positively associated with job satisfaction and negatively associated with turnover intentions, which were positively associated with voluntary turnover.
Mapping knowledge controversies: science, democracy and the redistribution of expertise
Authors: Whatmore Sarah J.
Published: July 2009

Reflecting on conversations between geography and science and technology studies (STS) over the last 15 years or so, this paper addresses their shared interest in knowledge controversies as generative political events. It explores how such events give rise to new ways of practising relations between science and democracy focusing on the case of environmental knowledge claims and technologies. This exploration interrogates three mobilizations of environmental knowledge controversies that have different implications for redistributing expertise, including that of (social) scientists, in the composition of knowledge polities. The first version sets out to map the language commitments of contributors to a controversy with the aim of enabling interested citizens to trace the ‘partisanship’ of scientific knowledge claims. The second is also a cartographic exercise designed to teach students how to account for the political force of technoscientific controversies by mapping the intense entanglements of scientific knowledge claims with legal, moral, economic and social concerns on the web. The third is concerned less with mapping knowledge controversies from an analytical distance than with an experimental research methodology that sets out to intervene in extant controversies in ways that map researchers’ own knowledge claims into what is at stake.
Experimental Study on the Interaction of a Water Drop Impacting on Hot Liquid Surfaces
Authors: Wang Xi-Shi , Zhao Xiang-Di , Zhang YI , Cai Xin , Gu Rui , Xu Hong-Li
Published: July 2009

This article presents the results of experimental investigation of water drop impacting on surfaces of different fuel liquids, such as alcohol, kerosene, and molten-ghee, which are typical fuels for liquid pool fire study or typical fire source in historical buildings. Each of the liquids was heated to simulate the temperature conditions as it burns, although the temperature is still a little lower than the real one. The impacting processes were recorded using a high-speed digital camera with 1000fps. The results show that the liquid physical properties, such as surface tension, viscosity, and miscibility, have primary influences on the drop impact behavior except for drop Weber number, and liquid temperature mainly influences the size of the splashed drops and bouncing height of the jet. The drop liquid is ejected for water—alcohol impact, while the bulk liquid is ejected for water—kerosene impact. The drop immersed into the liquid when it impacts on molten-ghee surface, no splashing and drop rebounding occur in this case.
A New Type of BTP/Zeolites Nanocomposites as Mixed-phase Fire Suppressant: Preparation, Characterization, and Extinguishing Mechanism Discussion
Authors: Xiaomin Ni  , Kaiqian Kuang  , Xishi Wang  , Guangxuah Liao
Published: July 2009

A new type of nanocomposites consisting of solid 4A zeolites and gaseous fire extinguishing agent of 2-bromo-3,3,3-trifluoropropene (BTP) was fabricated in large scale, in which BTP anchored in the porous zeolites. Laboratory-scale fire extinguishment tests showed that the nanocomposites as additives can greatly improve the performance of conventional sodium bicarbonate (NaHCO 3) dry powder for relatively shorter extinguishing time and smaller amount of agents required. Such an improvement could be ascribed to the simultaneous effect of solid NaHCO3, gaseous BTP desorbed from the zeolite when presented to higher temperature and the porous zeolite as heterogeneous inhibition of flame free radicals.
Ternary Semiconductor Nanoparticles Embedded in PEO—Polymer Electrolyte Matrix
Authors: Singh Pramod K. , Rhee Hee-Woo , Tomar S.K. , Nagarale R.K.
Published: July 2009

Formation of nanosized mixed semiconductor PbxCd1 —xS in situ into PEO—polymer electrolyte matrix at room temperature is reported. The disperse phase was identified by X-ray diffraction analysis. Optical microscopy shows the increase in amorphicity with dispersal of semiconductor while scanning electron microscope/ transmission electron microscope affirmed the formation of nanoparticulates with various sizes. The size distribution was further supported by Ultraviolet/Visible absorption of the colloid. The detailed electrical characterizations show that the dispersed PbxCd1—xS introduced a small (≤13%) electronic conductivity into pure ion conducting PEO:NH4I polymer electrolyte matrix.
Effect of Light Intensity on Ultraviolet Irradiated Polypropylene and its Compatibilization with CaCO3
Authors: Wu Shi-Shan , Ran Qian-Ping , Jian Shen
Published: July 2009

Some oxygen-containing groups such as C—O and C=O were introduced onto the molecular chains of polypropylene (PP) by ultraviolet irradiation at different light intensities in air. The rate of introducing oxygen-containing groups was increased with increasing light intensity. After irradiating at different light intensities, there was no gel formation in PP. The crystal shape of irradiated PP at different light intensities kept unchanged, which was still monoclinic crystal, but its melting temperature decreased and the crystallinity increased, and meanwhile their variation extent was increased with increasing light intensity. The melt flow rate and hydrophilicity of irradiated PP at higher light intensity were higher than those of PP irradiated at lower light intensity. A little of irradiated PP at different light intensities was added into PP/CaCO3 composite and the PP/CaCO3 composite compatibilized by the irradiated PP was obtained. Compared with those of PP/CaCO3 composite, the dispersion, interfacial interaction, and mechanical properties of the compatibilized PP/CaCO3 composite were improved. The mechanical properties of PP/CaCO3 composite added with PP irradiated for 40 min at lower light intensity and PP irradiated for 30 min at higher light intensity reached a maximum value.
Maximization of the Mechanical Properties of Birch-Polypropylene Composites with Additives by Statistical Experimental Design
Authors: Ruijun Gu  , Kokta Bohuslav V.
Published: July 2009

A systematic study of effects of concentrations of maleated polypropylene (MAPP), dicumyl peroxide (DCP), Nanoblend concentrate (MB1001) and birch fibers on the mechanical properties of birch-polypropylene (PP) composite was undertaken with the objective to protect or increase the impact strength without losing tensile strength. Using Stagraphic Plus, the Central Composite Design made it possible to determine the optimum concentrations of additives and to maximize both the impact as well as tensile properties to reach values well above that of virgin PP.
Melt Rheology during Extrusion of Polypropylene Composites Filled with Diatomite Particles
Authors: Liang J.Z.
Published: July 2009

The melt volume flow rate (MVR) is an important parameter for characterization of flow properties of polymer. The MVR of the polypropylene composites filled with diatomite particles was measured by means of a MVR instrument to investigate the effects of the filler content, particle size and extrusion conditions (temperature 210—230°C, load 5.0—12.5 kg) on the melt flow properties of the composite systems. The results showed that the MVR of the composites increased as a quadratic function with the increase of load, while decreased nonlinearly with the increase of filler particle diameter. The MVR was a linear function of temperature. The MVR decreased quickly when the filler volume fraction (φf) was <5%, and then reduced slightly with an increase of φf. In addition, the melt shear flow obeyed roughly power law under the experimental conditions, and the influence of particle size on the temperature sensitivity of the melt shear viscosity is insignificant at low filler concentration.
Revisiting Black Incorporation and Local Political Participation
Authors: Spence Lester K. , McClerking Harwood K. , Brown Robert
Published: July 2009

Testing the proposition that electing black mayors has a positive effect on black political participation, scholars found that black incorporation historically lead to increased black political engagement. However, the research that examines whether length of mayoral tenure influences black political participation is limited. We test this proposition using the 1993—1994 National Black Politics Study. Our findings suggest long-term political incorporation decreases local black political participation while it increases voting for President. However, as the black population percentage of a city rises, local black political participation increases. These findings extend the research on the effect of political incorporation on participation by considering political and demographic context and by engaging in intraracial rather than interracial comparisons.
Gender Differences in Willingness to Pay for Urban Public Services
Authors: Alozie Nicholas O. , McNamara Catherine
Published: July 2009

The “vote” urban residents cast when they make decisions about public services has implications for service delivery in local government. We utilize probability data from one of the nation’s largest municipalities to explore potential gender disparities in willingness to pay for local public services: whether men and women differ in their general orientation toward paying for services; whether any gender gaps are exacerbated in particular service areas; and whether any gender disparities have implications for community governance. Men and women report strong predisposition to paying generally, although glaring gender gaps exist that are both theoretically and practically insightful.
Barriers to participation in a hospital-based falls assessment clinic programme: an interview study with older people
Authors: Evron Lotte , Schultz-Larsen Kirsten , Fristrup Tine
Published: July 2009

Aims: To gain new knowledge about barriers to participation in hospital-based falls assessment. Methods: Semi-structured interviews with 20 older people referred to falls assessment at a hospital-based clinic were conducted. A convenience sample of 10 refusers and 10 accepters was collected. Those who refused referral were recruited in relation to a systematic falls screening programme performed by preventive home visitors. Accepters were selected among 72 participants successively completing the falls assessment clinic programme. The time between the interviews was 12 months; different levels of knowledge were expected, owing to accepters’ participation in the programme. Interview transcriptions were thematically analysed. The analysis was directed towards identification of barriers to falls assessment. Results: Barriers to participation were categorized as being either within or outside the falls clinic, and included administration, time, communication, attitudes to fall prevention, and expected future costs. Accepters completing the programme expressed a feeling of being ‘‘met’’ in the system and maintaining authority over their own life, while the refusers expressed concern about the healthcare system taking over their life. Conclusions: This study indicates that older at-risk patients acknowledge their falls problem, but refuse to participate in hospital-based assessment programmes because they expect to lose their authority and to be caught up in the healthcare system. In order to transform the findings of this study to a public health message, we have to consider moving the focus of falls prevention strategies from disease control to the domain of health promotion in order to engage older adults in preventive healthcare.
Towards hybrid lighting systems: A review
Authors: Mayhoub MS , Carter DJ
Published: July 2009

This paper reviews developments in hybrid light guidance systems. In these daylight and electric light are simultaneously delivered into a building where they are combined and distributed via luminaires. The technology used in hybrid systems, both conceptual and realised, is discussed. The review speculates as to their likely performance in terms of daylight delivery; capital and running costs; user reaction to the systems; potential impact of the systems on the building which they light; and suitable design methods. It is noted that a substantial amount of work remains before the potential of hybrid systems may be realised, notably on their long-term economics and feasibility in different geographic locations.
Intimate Partner Violence and Barriers To Mental Health Care for Ethnically Diverse Populations of Women
Authors: Rodríguez Michael , Valentine Jeanette M. , Son John B. , Muhammad Marjani
Published: July 2009

Ethnically diverse populations of women, particularly survivors of intimate partner violence (IPV), experience many barriers to mental health care. The search terms ‘‘women’’ and ‘‘domestic violence or IPV’’ and ‘‘mental health care’’ were used as a means to review the literature regarding barriers to mental health care and minority women. Abstracts chosen for further review included research studies with findings on women of one or more ethnic minority groups, potential barriers to accessing mental health care, and a nonexclusive focus on IPV. Fifty-five articles were selected for this review. Identified barriers included a variety of patient, provider, and health system/community factors. Attention to the barriers to mental health care for ethnically diverse survivors of IPV can help inform the development of more effective strategies for health care practice and policy.
'That's life innit'
Authors: Hallsworth Simon , Silverstone Daniel
Published: July 2009

Recent years have witnessed an escalation in the number of young men involved in lethal gun-related violence in the UK. Within the last two years these have resulted in over 80 deaths. Lacking any overarching explanation some have attributed such violence to a burgeoning `gun culture', others to the (alleged) arrival of American style gangs onto the streets of the UK. This article rejects these explanations as inadequate on the basis that the problem of gun-related violence cannot be reduced to the problem of gangs, while terms such as `gun culture' and `gang culture' are too general to explain the differing contexts of gun use. The article makes the case that to understand contemporary gun use we need to locate it within an examination of the life world of gun users. There are, we suggest, two we need to consider. First, the patterned world of `successful' violent career criminals, and second, a far more volatile street-based world termed by the violent young men who inhabit it as `on road'.
Sarcoidosis-associated pulmonary hypertension: a role for endothelin receptor antagonists?
Authors: Pitsiou Georgia G. , Spyratos Dionysis , Kioumis Ioannis , Boutou Afroditi K. , Nakou Chrysanthi , Stanopoulos Ioannis
Published: July 2009

Data on the treatment of sarcoidosis-associated pulmonary hypertension are scarce, while the variety of underlying pathophysiologic mechanisms are a major limitation in the implementation of a universal therapy. We report a 47-year-old male patient who presented with stage II sarcoidosis and associated severe pulmonary hypertension. Corticosteroid treatment resolved parenchymal lesions of the lung while vascular involvement did not respond, with the patient remaining in poor functional status. Addition of bosentan, a dual endothelin receptor antagonist, resulted in marked improvement in functional class and exercise capacity of the patient, allowing gradual tapering of steroids.
Aggressive statin therapy in multicenter and effectiveness for the reduction of intra-myocardial damage caused by non-ST elevation acute coronary syndrome: AMERICA study
Authors: Hara Hidehiko , Nakamura Masato , Yokouchi Itaru , Kimura Keiko , Nemoto Naohiko , Ito Shingo , Ono Tsuyoshi , Itaya Hideki , Shiba Masanori , Wada Masamichi , Iijima Raisuke , Yamamoto Masaya , Yamamoto Masato , Hara Hisao , Takagi Takuro , Asahara Toshiyuki , Mitsuo Kazuhisa , Kobayashi Nobuyuki , Sugi Kaoru
Published: July 2009

Background: While preprocedural statin treatment for acute coronary syndrome (ACS) is widely regarded as beneficial, there has been no prospective randomized multicenter trial of patients with non-ST elevation ACS in the Japanese population to examine the efficacy of preprocedural aggressive statin use. The aim of this study was to confirm this effect by prospective randomized multicenter design.

Methods: Fifty patients who presented with non-ST elevation ACS were enrolled, and randomly assigned to aggressive statin administration before percutaneous coronary intervention (PCI). Troponin-T (TnT), creatine phosphokinase (CK), CK-myocardial band (CK-MB), high-sense C-reactive protein (hs-CRP), and brain natriuretic peptide (BNP) were measured at baseline and/ or after procedure.

Results: Three days after PCI, the statin group had significantly less CK elevation compared with the nonstatin group (84±17 IU/l versus 180±68 IU/l, respectively, p = 0.02). CK-MB elevation also tended to be lower in the statin group than in the nonstatin group (3.2±1.9 versus. 7.0±3.0, respectively, p = 0.07), as was BNP level (3.2±1.9 versus 7.0±3.0 pg/ml, respectively, p = 0.07). The change of serum LDL cholesterol was significantly correlated with CK ( p = 0.01) and TnT ( p = 0.02) at 1 day after PCI.

Conclusions: Aggressive statin usage before PCI to Japanese patients with non-ST elevation ACS appears to reduce myocardial damage after procedure. The degree of serum lipid level reduction may reflect the vulnerability of atheromatous plaques that could cause cardiac damage after PCI.
Update on ureteral stent technology
Authors: Lange Dirk , Chew Ben H.
Published: July 2009

Ureteral stents are commonly used in urology but are frequently associated with patient discomfort, stent encrustation and stent-related infection. New biomaterials, coatings and designs have been designed to attempt to reduce these problems. This article reviews coatings to reduce bacterial adhesion and encrustation. In addition, metal ureteral stents, the triclosan and ketorolac drug eluting ureteral stents, and biodegradable ureteral stents are discussed. In summary there is no perfect ureteral stent that avoids all morbidity but there have been significant advances in the last few years in stent technology.
Concussion in Sports: The Sideline Assessment
Authors: Broglio Steven P. , Guskiewicz Kevin M.
Published: July 2009

Context:

The vast differences between individual athletes makes identifying and evaluating sports-related concussion one of the most complex and perplexing injuries faced by medical personnel.

Evidence Acquisition:

This review summarizes the existing literature supporting the use of a multifaceted approach to concussion evaluation on the sideline of the athletic field. Information was drawn from a PubMed search (MEDLINE) for the terms sport concussion for the most recent and relevant literature.

Conclusions:

By using a standardized clinical examination that is supported by objective measures of concussion-related symptoms, mental status, and postural control, the medical professional becomes well equipped to make an informed diagnosis.
Syndecan-1 shedding facilitates the resolution of neutrophilic inflammation by removing sequestered CXC chemokines
Authors: Hayashida Kazutaka , Parks William C. , Park Pyong Woo
Published: July 2009

Heparan sulfate binds to and regulates many inflammatory mediators in vitro, suggesting that it serves an important role in directing the progression and outcome of inflammatory responses in vivo. Here, we evaluated the role of syndecan-1, a major heparan sulfate proteoglycan, in modulating multiorgan host injury responses in murine endotoxemia. The extent of systemic inflammation was similar between endotoxemic syndecan-1–null and wild-type mice. However, high levels of CXC chemokines (KC and MIP-2), particularly at later times after LPS, were specifically sustained in multiple organs in syndecan-1–null mice and associated with exaggerated neutrophilic inflammation, organ damage, and lethality. Syndecan-1 shedding was activated in several organs of endotoxemic wild-type mice, and this associated closely with the removal of tissue-bound CXC chemokines and resolution of accumulated neutrophils. Moreover, administration of a shedding inhibitor exacerbated disease by impeding the removal of CXC chemokines and neutrophils, whereas administration of heparan sulfate inhibited the accumulation of CXC chemokines and neutrophils in tissues and attenuated multiorgan injury and lethality. These data show that syndecan-1 shedding is a critical endogenous mechanism that facilitates the resolution of neutrophilic inflammation by aiding the clearance of proinflammatory chemokines in a heparan sulfate–dependent manner.
Combined epigenetic therapy with the histone methyltransferase EZH2 inhibitor 3-deazaneplanocin A and the histone deacetylase inhibitor panobinostat against human AML cells
Authors: Fiskus Warren , Wang Yongchao , Sreekumar Arun , Buckley Kathleen M. , Shi Huidong , Jillella Anand , Ustun Celalettin , Rao Rekha , Fernandez Pravina , Chen Jianguang , Balusu Ramesh , Koul Sanjay , Atadja Peter , Marquez Victor E. , Bhalla Kapil N.
Published: July 2009

The polycomb repressive complex (PRC) 2 contains 3 core proteins, EZH2, SUZ12, and EED, in which the SET (suppressor of variegation–enhancer of zeste-trithorax) domain of EZH2 mediates the histone methyltransferase activity. This induces trimethylation of lysine 27 on histone H3, regulates the expression of HOX genes, and promotes proliferation and aggressiveness of neoplastic cells. In this study, we demonstrate that treatment with the S-adenosylhomocysteine hydrolase inhibitor 3-deazaneplanocin A (DZNep) depletes EZH2 levels, and inhibits trimethylation of lysine 27 on histone H3 in the cultured human acute myeloid leukemia (AML) HL-60 and OCI-AML3 cells and in primary AML cells. DZNep treatment induced p16, p21, p27, and FBXO32 while depleting cyclin E and HOXA9 levels. Similar findings were observed after treatment with small interfering RNA to EZH2. In addition, DZNep treatment induced apoptosis in cultured and primary AML cells. Furthermore, compared with treatment with each agent alone, cotreatment with DZNep and the pan-histone deacetylase inhibitor panobinostat caused more depletion of EZH2, induced more apoptosis of AML, but not normal CD34+ bone marrow progenitor cells, and significantly improved survival of nonobese diabetic/severe combined immunodeficiency mice with HL-60 leukemia. These findings indicate that the combination of DZNep and panobinostat is effective and relatively selective epigenetic therapy against AML cells.
Evolution of a subtilisin-like protease gene family in the grass endophytic fungus Epichloë festucae
Authors: Bryant Michelle K , Schardl Christopher L , Hesse Uljana , Scott Barry
Published: July 2009

Background

Subtilisin-like proteases (SLPs) form a superfamily of enzymes that act to degrade protein substrates. In fungi, SLPs can play either a general nutritive role, or may play specific roles in cell metabolism, or as pathogenicity or virulence factors.

Results

Fifteen different genes encoding SLPs were identified in the genome of the grass endophytic fungus Epichloë festucae. Phylogenetic analysis indicated that these SLPs belong to four different subtilisin families: proteinase K, kexin, pyrolysin and subtilisin. The pattern of intron loss and gain is consistent with this phylogeny. E. festucae is exceptional in that it contains two kexin-like genes. Phylogenetic analysis in Hypocreales fungi revealed an extensive history of gene loss and duplication.

Conclusion

This study provides new insights into the evolution of the SLP superfamily in filamentous fungi.
Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4
Authors: Chen Ke , Roberts Elijah , Luthey-Schulten Zaida
Published: July 2009

Background

The universal ribosomal protein S4 is essential for the initiation of small subunit ribosomal assembly and translational accuracy. Being part of the information processing machinery of the cell, the gene for S4 is generally thought of as being inherited vertically and has been used in concatenated gene phylogenies. Here we report the evolution of ribosomal protein S4 in relation to a broad sharing of zinc/non-zinc forms of the gene and study the scope of horizontal gene transfer (HGT) of S4 during bacterial evolution.

Results

In this study we present the complex evolutionary history of ribosomal protein S4 using 660 bacterial genomes from 16 major bacterial phyla. According to conserved characteristics in the sequences, S4 can be classified into C+ (zinc-binding) and C- (zinc-free) variants, with 26 genomes (mainly from the class Clostridia) containing genes for both. A maximum likelihood phylogenetic tree of the S4 sequences was incongruent with the standard bacterial phylogeny, indicating a departure from strict vertical inheritance. Further analysis using the genome content near the S4 genes, which are usually located in a conserved gene cluster, showed not only that HGT of the C- gene had occurred at various stages of bacterial evolution, but also that both the C- and C+ genes were present before the individual phyla diverged. To explain the latter, we theorize that a gene pool existed early in bacterial evolution from which bacteria could sample S4 gene variants, according to environmental conditions. The distribution of the C+/- variants for seven other zinc-binding ribosomal proteins in these 660 bacterial genomes is consistent with that seen for S4 and may shed light on the evolutionary pressures involved.

Conclusion

The complex history presented for "core" protein S4 suggests the existence of a gene pool before the emergence of bacterial lineages and reflects the pervasive nature of HGT in subsequent bacterial evolution. This has implications for both theoretical models of evolution and practical applications of phylogenetic reconstruction as well as the control of zinc economy in bacterial cells.
QTL analyses of temporal and intensity components of home-cage activity in KJR and C57BL/6J strains
Authors: Umemori Juzoh , Nishi Akinori , Lionikas Arimantas , Sakaguchi Takayuki , Kuriki Satoshi , Blizard David A , Koide Tsuyoshi
Published: July 2009

Background

A variety of mouse strains exhibit diversity in spontaneous activity consistent with an important genetic contribution. To date, many studies have defined spontaneous home-cage activity as total distance or total counts of activity within a test period. However, spontaneous activity is, in fact, a composite of elements of 'temporal' and 'intensity' that is similar to 'velocity'. Here, we report on quantitative trait loci for different components of spontaneous activity, an important step towards dissection of the underlying genetic mechanisms.

Results

In the analysis of total home-cage activity (THA) after habituation in female mice, KJR strain exhibit higher activity than C57BL/6J (B6). In this study, THA was partitioned into two components: active time (AT) was an index of the 'temporal element' of THA, average activity during active time (AA) was an index of 'intensity'. Correlation analysis using B6xKJR F2 female mice indicated that AA is a major component of THA, whereas AA and AT were associated to a lesser degree. To explore the genetic basis of the activity differences, we conducted quantitative trait loci (QTL) analysis on data of THA and its components, AT and AA. Three significant QTL affecting variation of different components of home cage activity were identified, two linked QTL Hylaq1 and Hylaq2 on Chr 2, and Hylaq3 on Chr 10. Chromosomal positions of these QTL were previously implicated in locomotor activity (Chr 2) or open-field ambulation (Chr 10). The results indicated that Hylaq1 influences AT, Hylaq2, AA, while Hylaq3 is associated with both AA and AT.

Conclusion

Through this study, we found that variation in total home cage activity over a 3 day period is affected by variation in active time and intensity of activity. The latter two variables are distinct components of home cage activity with only partially overlapping genetic architecture.
Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase
Authors: Fleury Elodie , Huvet Arnaud , Lelong Christophe , de Lorgeril Julien , Boulo Viviane , Gueguen Yannick , Bachère Evelyne , Tanguy Arnaud , Moraga Dario , Fabioux Caroline , Lindeque Penelope , Shaw Jenny , Reinhardt Richard , Prunet Patrick , Davey Grace , Lapègue Sylvie , Sauvage Christopher , Corporeau Charlotte , Moal Jeanne , Gavory Frederick , Wincker Patrick , Moreews François , Klopp Christophe , Mathieu Michel , Boudry Pierre , Favrel Pascal
Published: July 2009

Background

Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available.

Description

In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster.

Conclusion

A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit several filters, such as protein or nucleotide hits, to select and download relevant elements. This database constitutes one of the most developed genomic resources accessible among Lophotrochozoans, an orphan clade of bilateral animals. These data will accelerate the development of both genomics and genetics in a commercially-important species with the highest annual, commercial production of any aquatic organism.
High frequencies of elevated alkaline phosphatase activity and rickets exist in extremely low birth weight infants despite current nutritional support
Authors: Mitchell Shannon M , Rogers Stefanie P , Hicks Penni D , Hawthorne Keli M , Parker Bruce R , Abrams Steven A
Published: July 2009

Background

Osteopenia and rickets are common among extremely low birth weight infants (ELBW, <1000 g birth weight) despite current practices of vitamin and mineral supplementation. Few data are available evaluating the usual course of markers of mineral status in this population. Our objectives in this study were to determine the relationship between birth weight (BW) and peak serum alkaline phosphatase activity (P-APA) in ELBW infants and evaluate our experience with the diagnosis of rickets in these infants.

Methods

We evaluated all ELBW infants admitted to Texas Children's Hospital NICU in 2006 and 2007. Of 211 admissions, we excluded 98 patients who were admitted at >30 days of age or did not survive/stay for >6 weeks. Bone radiographs obtained in 32 infants were reviewed by a radiologist masked to laboratory values.

Results

In this cohort of 113 infants, P-APA was found to have a significant inverse relationship with BW, gestational age and serum phosphorus. In paired comparisons, P-APA of infants <600 g (957 ± 346 IU/L, n = 20) and infants 600–800 g (808 ± 323 IU/L, n = 43) were both significantly higher than P-APA of infants 800–1000 g (615 ± 252 IU/L, n = 50), p < 0.01. Thirty-two patients had radiographic evaluation for evidence of rickets, based on P-APA greater than 800 IU/L, parenteral nutrition greater than 3 to 4 weeks, or clinical suspicion. Of these, 18 showed radiologic rickets and 14 showed osteopenia without rickets. Infants with BW <600 g were more likely to have radiologic rickets (10/20 infants) compared to those with BW 600–800 g (6/43 infants) and BW 800–1000 g (2/50 infants), p < 0.01 for each. P-APA was not significantly higher in infants with radiologic rickets (1078 ± 356 IU/L) compared to those without radiologic evidence of rickets (943 ± 346, p = 0.18).

Conclusion

Elevation of P-APA >600 IU/L was very common in ELBW infants. BW was significantly inversely related to both P-APA and radiologic rickets. No single value of P-APA was related to radiological findings of rickets. Given the very high risk of osteopenia and rickets among ELBW infants, we recommend consideration of early screening and early mineral supplementation, especially among infants <600 g BW.
Treatment of malaria from monotherapy to artemisinin-based combination therapy by health professionals in rural health facilities in southern Cameroon
Authors: Sayang Collins , Gausseres Mathieu , Vernazza-Licht Nicole , Malvy Denis , Bley Daniel , Millet Pascal
Published: July 2009

Background

One year after the adoption of artesunate-amodiaquine (AS/AQ) as first-line therapy for the treatment of uncomplicated malaria, this study was designed to assess the treatment practices regarding anti-malarial drugs at health facilities in four rural areas in southern Cameroon.

Methods

Between April and August 2005, information was collected by interviewing fifty-two health professionals from twelve rural health facilities, using a structured questionnaire.

Results

In 2005, only three anti-malarial drugs were used in rural health facilities, including: amodiaquine, quinine and sulphadoxine-pyrimethamine. Only 2.0% of the health professionals prescribed the recommended AS/AQ combination. After reading the treatment guidelines, 75.0% were in favour of the treatment protocol with the following limitations: lack of paediatric formulations, high cost and large number of tablets per day. Up to 21.0% of professionals did not prescribe AS/AQ because of the level of adverse events attributed to the use of amodiaquine as monotherapy.

Conclusion

The present study indicates that AS/AQ was not available in the public health facilities at the time of the study, and health practitioners were not informed about the new treatment guidelines. Results of qualitative analysis suggest that prescribers should be involved as soon as possible in projects related to the optimization of treatment guidelines and comply with new drugs. Adapted formulations should be made available at the international level and implemented locally before new drugs and treatments are proposed through a national control programme. This baseline information will be useful to monitor progresses in the implementation of artemisinin-based combination therapy in Cameroon.
Fatal Chromobacterium violaceum septicaemia in northern Laos, a modified oxidase test and post-mortem forensic family G6PD analysis
Authors: Slesak Günther , Douangdala Phouvieng , Inthalad Saythong , Silisouk Joy , Vongsouvath Manivanh , Sengduangphachanh Amphonesavanh , Moore Catrin E , Mayxay Mayfong , Matsuoka Hiroyuki , Newton Paul N
Published: July 2009

Background

Chromobacterium violaceum is a Gram negative facultative anaerobic bacillus, found in soil and stagnant water, that usually has a violet pigmented appearance on agar culture. It is rarely described as a human pathogen, mostly from tropical and subtropical areas.

Case presentation

A 53 year-old farmer died with Chromobacterium violaceum septicemia in Laos. A modified oxidase method was used to demonstrate that this violacious organism was oxidase positive. Forensic analysis of the glucose-6-phosphate dehydrogenase genotypes of his family suggest that the deceased patient did not have this possible predisposing condition.

Conclusion

C. violaceum infection should be included in the differential diagnosis in patients presenting with community-acquired septicaemia in tropical and subtropical areas. The apparently neglected but simple modified oxidase test may be useful in the oxidase assessment of other violet-pigmented organisms or of those growing on violet coloured agar.
LH pulse frequency and the emergence and growth of ovarian antral follicular waves in the ewe during the luteal phase of the estrous cycle
Authors: Seekallu Srinivas V , Toosi Behzad M , Rawlings Norman C
Published: July 2009

Background

In the ewe, ovarian antral follicles emerge or grow from a pool of 2–3 mm follicles in a wave like pattern, reaching greater than or equal to 5 mm in diameter before regression or ovulation. There are 3 or 4 such follicular waves during each estrous cycle. Each wave is preceded by a peak in serum FSH concentrations. The role of pulsatile LH in ovarian antral follicular emergence and growth is unclear; therefore, the purpose of the present study was to further define this role.

Methods

Ewes (n = 7) were given 200 ng of GnRH (IV) every hour for 96 h from Day 7 of the estrous cycle, to increase LH pulse frequency. Controls (n = 6) received saline. In a second study, ewes (n = 6) received subcutaneous progesterone-releasing implants for 10 days starting on Day 4 of the cycle, to decrease LH pulse frequency. Controls (n = 6) underwent sham surgery. Daily transrectal ovarian ultrasonography and blood sampling was performed on all ewes from the day of estrus to the day of ovulation at the end of the cycle of the study. At appropriate times, additional blood samples were taken every 12 minutes for 6 h and 36 min or 6 h in studies 1 and 2 respectively.

Results

The largest follicle of the follicular wave growing when GnRH treatment started, grew to a larger diameter than the equivalent wave in control ewes (P < 0.05). Mean serum estradiol and progesterone concentrations were higher but mean serum FSH concentrations were lower during GnRH treatment compared to control ewes (P < 0.05). The increased serum concentrations of estradiol and progesterone, in GnRH treated ewes, suppressed a peak in serum concentrations of FSH, causing a follicular wave to be missed. Treatment with progesterone decreased the frequency of LH pulses but did not have any influence on serum FSH concentrations or follicular waves.

Conclusion

We concluded that waves of ovarian follicular growth can occur at LH pulse frequencies lower than those seen in the luteal phase of the estrous cycle but frequencies seen in the follicular phase, when applied during the mid-luteal phase, in the presence of progesterone, do enhance follicular growth to resemble an ovulatory follicle, blocking the emergence of the next wave.
Development of a microarray platform for FFPET profiling: application to the classification of human tumors
Authors: Duenwald Sven , Zhou Mingjie , Wang Yanqun , Lejnine Serguei , Kulkarni Amit , Graves Jaime , Smith Ryan , Castle John , Tokiwa George , Fine Bernard , Dai Hongyue , Fare Thomas , Marton Matthew
Published: July 2009

Background

mRNA profiling has become an important tool for developing and validating prognostic assays predictive of disease treatment response and outcome. Archives of annotated formalin-fixed paraffin-embedded tissues (FFPET) are available as a potential source for retrospective studies. Methods are needed to profile these FFPET samples that are linked to clinical outcomes to generate hypotheses that could lead to classifiers for clinical applications.

Methods

We developed a two-color microarray-based profiling platform by optimizing target amplification, experimental design, quality control, and microarray content and applied it to the profiling of FFPET samples. We profiled a set of 50 fresh frozen (FF) breast cancer samples and assigned class labels according to the signature and method by van 't Veer et al [1] and then profiled 50 matched FFPET samples to test how well the FFPET data predicted the class labels. We also compared the sorting power of classifiers derived from FFPET sample data with classifiers derived from data from matched FF samples.

Results

When a classifier developed with matched FF samples was applied to FFPET data to assign samples to either "good" or "poor" outcome class labels, the classifier was able to assign the FFPET samples to the correct class label with an average error rate = 12% to 16%, respectively, with an Odds Ratio = 36.4 to 60.4, respectively. A classifier derived from FFPET data was able to predict the class label in FFPET samples (leave-one-out cross validation) with an error rate of ~14% (p-value = 3.7 × 10-7). When applied to the matched FF samples, the FFPET-derived classifier was able to assign FF samples to the correct class labels with 96% accuracy. The single misclassification was attributed to poor sample quality, as measured by qPCR on total RNA, which emphasizes the need for sample quality control before profiling.

Conclusion

We have optimized a platform for expression analyses and have shown that our profiling platform is able to accurately sort FFPET samples into class labels derived from FF classifiers. Furthermore, using this platform, a classifier derived from FFPET samples can reliably provide the same sorting power as a classifier derived from matched FF samples. We anticipate that these techniques could be used to generate hypotheses from archives of FFPET samples, and thus may lead to prognostic and predictive classifiers that could be used, for example, to segregate patients for clinical trial enrollment or to guide patient treatment.