bluuebunny/crossref_metadata_2025 huggingface dataset:
Expression of thrombin-activatable fibrinolysis inhibitor (TAFI) is up-regulated by increase in intracellular cyclic AMP levels in cultured HepG2 cells
Authors: Kojima Yuka , Masuda Yutaka , Takada Kimihiko , Sugimoto Katsuyoshi , Ikeda Tomohiro , Ishii Hidemi
Published: September 2009

Thrombin-activatable fibrinolysis inhibitor (TAFI), a carboxypeptidase B-like proenzyme, is predominantly biosynthesised in the liver and released into circulating plasma. Activated TAFI has a role in maintaining the balance between blood coagulation and fibrinolysis. We investigated the regulation of TAFI expression in cultured human hepatoma HepG2 cells. Stimulation of the cells with forskolin and dibutyryl cyclic AMP (DBcAMP) increased TAFI antigen levels in the cells in parallel with TAFI mRNA levels and antigen release from the cells into the conditioned medium. The elevated TAFI expression was abolished by pretreatment of the cells with KT5720, a protein kinase A (PKA) inhibitor. The promoter activity of the TAFI gene and the half-life of the TAFI transcript in DBcAMP-stimulated HepG2 cells increased to 1.5-fold and 2.0-fold, respectively, of those in the control cells. The increased promoter activity and the prolonged half-life were abolished by pretreatment of the cells with KT5720.These results suggest that an increase in intracellular cAMP levels upregulates TAFI expression in the cells in accompaniment with an elevation of TAFI mRNA levels, and that the elevated mRNA levels are derived from both transcriptional and post-transcriptional regulations of the TAFI gene mediated by activation of the AMP/PKA signaling pathway.
Activated partial thromboplastin time monitoring in patients receiving unfractionated heparin for venous thromboembolism in relation to clinical outcomes
Authors: Laor Arie , Bitterman Haim , Vardi Moshe
Published: September 2009

Venous thromboembolism (VTE) is a prevalent and serious condition, which requires anticoagulation treatment for prolonged time duration. The use of unfractionated heparin administered intravenously or subcutaneously for acute management of VTE has been studied with favourable clinical results. Most physicians use activated partial thromboplastin time to monitor the treatment effect, in an effort to obtain better efficacy with less bleeding complications. Recent data however does not support this practice. We set to explore the medical literature for the correlation between the level of anticoagulation and the clinical outcomes. Randomised controlled trials comparing subcutaneous unfractionated heparin to any other treatment modality in patients with venous thromboembolism were obtained and a meta-analysis was performed. Seventeen reports from 15 randomised controlled trials were included. Of these, eleven included anticoagulation measurements. Seven and six trials were included in our analysis for subcutaneous and intravenous modes of administration, respectively. No correlation between the anticoagulation level and the major clinical outcomes were found, except for the initial anticoagulation measurement and the total mortality at three months, but not to death related to treatment or disease progression. In conclusion, weight-adjusted subcutaneous unfractionated heparin without anticoagulation monitoring may be feasible for patients with acute venous thromboembolism. No differences exist between intravenous and subcutaneous modes of administration with regards to the correlation between anticoagulant measures and the clinical outcomes. More research is needed to substantiate this observation.
Mechanism of Decrease in Mitral Regurgitation After Cardiac Resynchronization Therapy
Authors: Solis Jorge , McCarty David , Levine Robert A. , Handschumacher Mark D. , Fernandez-Friera Leticia , Chen-Tournoux Annabel , Mont Luis , Vidal Barbara , Singh Jagmeet P. , Brugada Josep , Picard Michael H. , Sitges Marta , Hung Judy
Published: September 2009

Background—

Cardiac resynchronization therapy (CRT) has been shown to reduce functional mitral regurgitation (MR). It has been proposed that the mechanism of MR reduction relates to geometric change or, alternatively, changes in left ventricular (LV) contractile function. Normal mitral valve (MV) function relies on a balance between tethering and closing forces on the MV leaflets. Functional MR results from a derangement of this force–balance relationship, and CRT may be an important modulator of MV function by its ability to enhance the force–balance relationship on the MV. We hypothesized that CRT improves the comprehensive force balance acting on the valve, including favorable changes in both geometry and LV contractile function.

Methods and Results—

We examined the effect of CRT on 34 patients with functional MR before and after CRT (209�81 days). MR regurgitant volume, closing forces on MV (derived from Doppler transmitral pressure gradients), including dP/dt and a factor (closing pressure ratio) expressing how long the peak closing gradient is maintained over systole (closing pressure ratio=velocity time integral/MR peak velocity�mitral regurgitation time), and dyssynchrony by tissue Doppler were measured. End-diastolic volume, end-systolic volume, mitral valve annular area (MAA) and contraction (percent change in MAA from end-diastole to midsystole), leaflet closing area (leaflet area during valve closure), and tenting volume (volume under leaflets to annular plane) were measured by 3D echocardiography. After CRT, end-diastolic volume (253�111 versus 221�110 mL,
P
<0.001) and end-systolic volume (206�97 versus 167�91 mL,
P
<0.001) decreased and ejection fraction (19�6 versus 27�9%,
P
<0.001) increased. MR regurgitant volume decreased from 35�17 to 23�14 mL (
P
<0.001), MAA from 11.6�3.5 to 10.5�3.1 cm
2
(
P
<0.001), leaflet closing area from 15.4�5 to 13.7�3.8 cm
2
(
P
<0.001), and tenting volume from 5.7�2.6 to 4.6�2.2 mL (
P
<0.001). Peak velocity (and therefore transmitral closing pressure) was more sustained throughout systole, as reflected by the increase in the closing pressure ratio (0.77�0.1 versus 0.84�0.1 before CRT versus after CRT,
P
=0.01); dP/dt also improved after CRT. There was no change in dyssynchrony or MAA contraction.

Conclusions—

Reduction in MR after CRT is associated with favorable changes in MV geometry and closing forces on the MV. It does so by favorably affecting the force balance acting on the MV in 2 ways: reducing tethering through reversal of LV remodeling and increasing the systolic duration of peak transmitral closing pressures.
The Effects of Explicit and Implicit Interaction on User Experiences in a Mixed Reality Installation: The Synthetic Oracle
Authors: Badia Sergi Bermúdez i , Valjamae Aleksander , Manzi Fabio , Bernardet Ulysses , Mura Anna , Manzolli Jônatas , Verschure Paul F. M. J
Published: September 2009

Virtual and mixed reality environments (VMRE) often imply full-body human-computer interaction scenarios. We used a public multimodal mixed reality installation, the Synthetic Oracle, and a between-groups design to study the effects of implicit (e.g., passively walking) or explicit (e.g., pointing) interaction modes on the users' emotional and engagement experiences, and we assessed it using questionnaires. Additionally, real-time arm motion data was used to categorize the user behavior and to provide interaction possibilities for the explicit interaction group. The results show that the online behavior classification corresponded well to the users' interaction mode. In addition, contrary to the explicit interaction, the engagement ratings from implicit users were positively correlated with a valence but were uncorrelated with arousal ratings. Interestingly, arousal levels were correlated with different behaviors displayed by the visitors depending on the interaction mode. Hence, this study confirms that the activity level and behavior of users modulates their experience, and that in turn, the interaction mode modulates their behavior. Thus, these results show the importance of the selected interaction mode when designing users' experiences in VMRE.
A Case Study: The Indirect Aerosol Effects of Mineral Dust on Warm Clouds
Authors: Li R. , Min Q-L. , Harrison L. C.
Published: September 2009

The indirect aerosol effect (Twomey effect) is studied during a Saharan dust-transport event that presented an unusually favorable combination of a dust-loading gradient across clouds with warm cloud-top temperatures. Standard retrievals from the Moderate Resolution Imaging Spectroradiometer (MODIS), the Advanced Microwave Scanning Radiometer for Earth Observing System (AMSR-E), and the Clouds and the Earth’s Radiant Energy System (CERES) provide cloud-top temperature (a surrogate for height), liquid water path (LWP), classification of precipitation regime, and radiation flux. The authors correlate a retrieved mean effective droplet radius (re) versus the number concentration of cloud condensation nuclei (NCCN), using the regressed slope d lnre/d lnNCCN as the estimator of the aerosol indirect effect (AIE). Results demonstrate statistically significant AIE for only some of the segregated cloud classes. For nonprecipitating clouds (the most direct test of Twomey effect), the estimated AIE is effectively −0.07 over all wider temperature bands and is statistically significant from 1.1 to 1.9 σ. Further classification by LWP strengthens both the AIE (for all LWP > 150 g m−2) to approximately −0.16, and substantially increases the statistical significance, to better than 5σ.

Shortwave radiation forcing of dust aerosols is also estimated directly from satellite measurements. The direct shortwave (SW) radiation effect of Saharan dusts at solar zenith angle 21.6° is 53.48 ± 8.56 W m−2 per unit aerosol optical depth, with a correlation coefficient of 0.92. The indirect SW forcing of Saharan dust is 29.88 ± 2.42 W m−2 per unit AOD for clouds with LWP of 100 g m−2.
On the Variability of the Global Net Radiative Energy Balance of the Nonequilibrium Earth
Authors: Harries John E. , Belotti Claudio
Published: September 2009

Recent observations and model studies of the earth’s radiative energy balance have focused attention on the earth’s top of atmosphere (TOA) energy balance. This is the balance between the shortwave energy absorbed by the earth, which is represented by a spatially and temporally averaged absorbed flux , and the emitted longwave energy, which is represented by the corresponding averaged emitted flux . The TOA average net flux FN is defined as the difference between the two over the averaged area and time, which may be a local, regional, or global average. A global nonzero net flux represents a measure of imbalance between the energy being absorbed and emitted by the earth for the time interval in question. It is of interest to ask what the natural variability of the net flux might be and whether, during times of climate change, signals of important climate change processes might be detected against this natural background variation; examples of these signals include evidence of ocean heat storage, the effects of El Niño, and the radiative effects of volcanic eruptions. In this paper, the authors review the significance of the net flux, survey the observational evidence from a range of satellite instruments over several decades, and analyze some of the most recent observations from the Clouds and the Earth’s Radiant Energy System (CERES) program to determine what signals and what natural variability might be expected in the TOA net flux. Based on this analysis, the use of broadband radiation measurements for global climate change studies can be assessed.
China Challenges Secularization Theory
Authors: Dobbelaere Karel
Published: September 2009

The author proposes a reflection on challenges that the three anthropological articles in this issue present for secularization theory. The first two discuss “performances” of religion in two different Chinese cultural periods: welfare services offered by recognized religious associations in the People’s Republic of China and the judicial rituals in colonial settings. The author suggests similarities with such “performances” in western culture. The second part of the article discusses some issues raised by Szonyi in his comparison of recent social research literature on Chinese religion and sociological literature on secularization: a critique of the concept of “modernity” in relation to secularization; a reflection on the possibility of establishing a secularization theory with universal validity; how to integrate rational choice theory and secularization theory; the validity of secularization in view of individual religious sensitivity; and secularization as an ideology and a discussion of the so-called “privatization of religion” in secularized settings.
Ritual? What Ritual? Secularization in the Study of Chinese Legal History, from Colonial Encounters to Modern Scholarship
Authors: Katz Paul R.
Published: September 2009

The author explores the reasons why scholars have overlooked the importance of judicial rituals in Chinese legal culture and considers this neglect in the light of scholarship on secularization. He explores the issue by analysing the interaction between Chinese and western judicial practices in the colonial histories of the Straits Settlements (now Malaysia and Singapore) and Hong Kong. The concept of secularization appears to be of relevance to the study of Chinese legal culture, given that secularized societies tend to become differentiated into autonomous sub-systems, religion being restricted in influence to its own sub-system. In fact, however, religion has continuously interacted with a range of other sub-systems in China, including legal ones, which indicates that, in modern Chinese legal culture, religion and the law have not evolved into separate sub-systems.
Secularization Theories and the Study of Chinese Religions
Authors: Szonyi Michael
Published: September 2009

The author proposes a dialogue between recent literature on the history of Chinese popular religion and recent sociological debates about secularization theory, asking whether a better understanding of concepts, theories and evidence from one field may be productive in interpreting those of the other. The author suggests on the one hand that certain elements of secularization theory can be useful tools in understanding the modern history of religions in China and on the other that thinking about what secularization has meant in China is crucial to a comparative global history of religion and modernity. He also argues that attention to secularization both as a historical process and as a political ideology may help us to better understand the religious policies of the People’s Republic of China today.
Collective Development in Open-Source Communities: An Activity Theoretical Perspective on Successful Online Collaboration
Authors: Hemetsberger Andrea , Reinhardt Christian
Published: September 2009

Online collaboration is often organized without strong predetermined rules or central authority, which is why coordination and ways of organizing cooperation become crucial elements of collaboration. This article investigates how online projects can overcome problems of dispersed work, solve inherent contradictions and utilize tensions in the activity system to develop collaborative artefacts and practices. Empirical evidence is based on a detailed observation of a successful open-source project — the K Desktop Environment (KDE). Our findings show that successful collaboration is based on coat-tailing systems. Coat-tailing means to inextricably bind together individual action and collective activity through careful design of complexes of technological, mental and cultural artefacts.
Trends and New Developments in Automatic Enrollment for Defined Contribution Plans
Authors: Morgenthaler Diane M. , Weyeneth Jamie A.
Published: September 2009

Automatic enrollment can boost employee participation in a Section 401(k) plan, making it easier for the plan to satisfy nondiscrimination requirements that often prevent highly compensated employees from maximizing deferral contributions. The Pension Protection Act (PPA) and recent IRS regulations expand the automatic enrollment design options available to employers and provide additional incentives to adopt automatic enrollment arrangements. Employers with automatic enrollment arrangements should be aware of these new developments and should review their plan documents and administrative procedures to ensure compliance with current requirements. Employers considering automatic enrollment should be aware of the three types of automatic enrollment now available under PPA. This article summarizes the evolution of automatic enrollment, the three types of automatic enrollment authorized by the PPA, the IRS guidance that governs qualified automatic contribution arrangements (QACAa) and eligible automatic contribution arrangements (EACAs), and the planning considerations for employers.
Adherence to National Asthma Education and Prevention Program’s “How Asthma-Friendly Is Your School?” Recommendations
Authors: Jones Sherry Everett , Wheeler Lani S. , Smith Alisa M. , McManus Tim
Published: September 2009

School health policies and programs provide the framework for a safe and supportive environment for students with asthma. School Health Policies and Programs Study 2006 data were examined to assess whether schools nationwide have policies and programs consistent with the “How Asthma-Friendly Is Your School?” checklist from the National Asthma Education and Prevention Program. Adherence to some of the recommendations on the checklist was high. For example, 80% or more of schools allowed students to carry and self-administer asthma medications, and obtained and kept asthma action plans. For other recommendations, however, far fewer schools had the recommended polices or programs; most notably, less than one third of schools had a full-time Registered Nurse. Improvements in many school policies and programs are needed so that students have a safe and supportive school environment to help them control their asthma while away from home.
Hadrian’s Wall
Authors: Nesbitt Claire , Tolia-Kelly Divya
Published: September 2009

The aim of this article is to consider the value of an embodied account of Hadrian’s Wall. This heritage site has often been understood in predominantly imperial and military terms. While this is a crucial aspect of the historical meanings of the monument, there has been little focus on factors such as changing social role, socialities produced through its presence, and perceptions of the Wall evident in historical accounts. Drawing on theoretical approaches in archaeology, geography and anthropology, this article investigates the potential for enriching archaeological knowledge through these approaches. We focus on accounts of some early visitors to the Wall to consider movement on, and encounter with, the Wall through an embodied account. This account seeks to enrich our archaeological history by being attentive to the power of the material landscape on the senses of being and feeling of those that encounter it. The experience of the Wall is made intelligible through a body-centred account.
Platelet factor 4 (CXCL4) facilitates human macrophage infection with HIV-1 and potentiates virus replication
Authors: Schwartzkopff Franziska , Grimm Tobias A. , Lankford Carla S.R. , Fields Karen , Wang Jiun , Brandt Ernst , Clouse Kathleen A.
Published: September 2009

Platelet factor 4 (CXCL4), a member of the CXC chemokine subfamily released in high amounts by activated platelets, has been identified as a monocyte survival factor that induces monocyte differentiation into macrophages. Although CXCL4 has been shown to have biological effects unique to chemokines, nothing is known about the role of CXCL4-derived human macrophages or CXCL4 in human immunodeficiency virus (HIV) disease. In this study, CXCL4-derived macrophages are compared with macrophage-colony stimulating factor (M-CSF)-derived macrophages for their ability to support HIV-1 replication. We show that CXCL4-derived macrophages can be infected with macrophage-tropic HIV-1 that uses either CC-chemokine receptor 5 (CCR5) or CXC-chemokine receptor 4 (CXCR4) as a co-receptor for viral entry. We also find that M-CSF and the chemokines, monocyte chemoattractant protein 1 (MCP-1; CCL2) and macrophage-inflammatory-protein-1-alpha (MIP-1α; CCL3) are produced upon R5- and X4-tropic HIV-1 replication in both M-CSF- and CXCL4-derived human macrophages. In addition, CXCL4 added to M-CSF-derived macrophages after virus adsorption and maintained throughout the infection enhances HIV-1 replication. We thus propose a novel role for CXCL4 in HIV disease.
Structural evolution during the dehydration of gypsum materials
Authors: Jacques S. D. M. , González-Saborido A. , Leynaud O. , Bensted J. , Tyrer M. , Greaves R. I. W. , Barnes P.
Published: September 2009

The dehydration of pure and waste gypsums has been examined using in situ synchrotron angledispersive X-ray diffraction. Pure gypsum was studied under a number of defined environments; various industrial waste gypsums were also studied under a common standard environment. It is found that the dehydration of gypsum to anhydrite proceeds via the hemihydrate and γ-anhydrite phases and the interplay and behaviour of these phases has been determined by full structural ‘Rietveld’ refinement. In the study of the pure gypsum system, the hemihydrate structure is shown to be preserved as water is lost. A ‘zero-water hemihydrate’ is observed before refinement in the higher symmetry γ-anhydrite cell is possible. The waste gypsum materials studied showed significant differences in the temperatures at which key transformation events occurred; these observations raise implications concerning the re-use of by-product gypsum materials. Finally, high temperature data are re-examined in the search for a variation of the anhydrite structure.
Necdin restricts proliferation of hematopoietic stem cells during hematopoietic regeneration
Authors: Kubota Yasushi , Osawa Masatake , Jakt Lars Martin , Yoshikawa Kazuaki , Nishikawa Shin-Ichi
Published: September 2009

Hematopoietic stem cell (HSC) proliferation is tightly regulated by a poorly understood complex of positive and negative cell-cycle regulatory mechanisms. Necdin (Ndn) is an evolutionally conserved multifunctional protein that has been implicated in cell-cycle regulation of neuronal cells. Here, we provide evidence that necdin plays an important role in restricting excessive HSC proliferation during hematopoietic regeneration. We identify Ndn as being preferentially expressed in the HSC population on the basis of gene expression profiling and demonstrate that mice deficient in Ndn show accelerated recovery of the hematopoietic system after myelosuppressive injury, whereas no overt abnormality is seen in steady-state hematopoiesis. In parallel, after myelosuppression, Ndn-deficient mice exhibit an enhanced number of proliferating HSCs. Based on these findings, we propose that necdin functions in a negative feedback loop that prevents excessive proliferation of HSCs during hematopoietic regeneration. These data suggest that the inhibition of necdin after clinical myelosuppressive treatment (eg, chemotherapy, HSC transplantation) may provide therapeutic benefits by accelerating hematologic recovery.
Anti-proliferative activity of silver nanoparticles
Authors: AshaRani PV , Hande M Prakash , Valiyaveettil Suresh
Published: September 2009

Background

Nanoparticles possess exceptional physical and chemical properties which led to rapid commercialisation. Silver nanoparticles (Ag-np) are among the most commercialised nanoparticles due to their antimicrobial potential. Ag-np based cosmetics, therapeutic agents and household products are in wide use, which raised a public concern regarding their safety associated with human and environmental use. No safety regulations are in practice for the use of these nanomaterials. The interactions of nanomaterials with cells, uptake mechanisms, distribution, excretion, toxicological endpoints and mechanism of action remain unanswered.

Results

Normal human lung fibroblasts (IMR-90) and human glioblastoma cells (U251) were exposed to different doses of Ag-nps in vitro. Uptake of Ag-nps occurred mainly through endocytosis (clathrin mediated process and macropinocytosis), accompanied by a time dependent increase in exocytosis rate. The electron micrographs revealed a uniform intracellular distribution of Ag-np both in cytoplasm and nucleus. Ag-np treated cells exhibited chromosome instability and mitotic arrest in human cells. There was efficient recovery from arrest in normal human fibroblasts whereas the cancer cells ceased to proliferate. Toxicity of Ag-np is mediated through intracellular calcium (Ca2+) transients along with significant alterations in cell morphology and spreading and surface ruffling. Down regulation of major actin binding protein, filamin was observed after Ag-np exposure. Ag-np induced stress resulted in the up regulation of metallothionein and heme oxygenase -1 genes.

Conclusion

Here, we demonstrate that uptake of Ag-np occurs mainly through clathrin mediated endocytosis and macropinocytosis. Our results suggest that cancer cells are susceptible to damage with lack of recovery from Ag-np-induced stress. Ag-np is found to be acting through intracellular calcium transients and chromosomal aberrations, either directly or through activation of catabolic enzymes. The signalling cascades are believed to play key roles in cytoskeleton deformations and ultimately to inhibit cell proliferation.
Live cell imaging with protein domains capable of recognizing phosphatidylinositol 4,5-bisphosphate; a comparative study
Authors: Szentpetery Zsofia , Balla Andras , Kim Yeun Ju , Lemmon Mark A , Balla Tamas
Published: September 2009

Background

Phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P
2] is a critically important regulatory phospholipid found in the plasma membrane of all eukaryotic cells. In addition to being a precursor of important second messengers, PtdIns(4,5)P
2 also regulates ion channels and transporters and serves the endocytic machinery by recruiting clathrin adaptor proteins. Visualization of the localization and dynamic changes in PtdIns(4,5)P
2 levels in living cells is critical to understanding the biology of PtdIns(4,5)P
2. This has been mostly achieved with the use of the pleckstrin homology (PH) domain of PLCδ1 fused to GFP. Here we report on a comparative analysis of several recently-described yeast PH domains as well as the mammalian Tubby domain to evaluate their usefulness as PtdIns(4,5)P
2 imaging tools.

Results

All of the yeast PH domains that have been previously shown to bind PtdIns(4,5)P
2 showed plasma membrane localization but only a subset responded to manipulations of plasma membrane PtdIns(4,5)P
2. None of these domains showed any advantage over the PLCδ1PH-GFP reporter and were compromised either in their expression levels, nuclear localization or by causing peculiar membrane structures. In contrast, the Tubby domain showed high membrane localization consistent with PtdIns(4,5)P
2 binding and displayed no affinity for the soluble headgroup, Ins(1,4,5)P3. Detailed comparison of the Tubby and PLCδ1PH domains showed that the Tubby domain has a higher affinity for membrane PtdIns(4,5)P
2 and therefore displays a lower sensitivity to report on changes of this lipid during phospholipase C activation.

Conclusion

These results showed that both the PLCδ1PH-GFP and the GFP-Tubby domain are useful reporters of PtdIns(4,5)P
2 changes in the plasma membrane, with distinct advantages and disadvantages. While the PLCδ1PH-GFP is a more sensitive reporter, its Ins(1,4,5)P3 binding may compromise its accuracy to measure PtdIns(4,5)P
2changes. The Tubby domain is more accurate to report on PtdIns(4,5)P
2 but its higher affinity and lower sensitivity may limit its utility when phospholipase C activation is only moderate. These studies also demonstrated that similar changes in PtdIns(4,5)P
2 levels in the plasma membrane can differentially regulate multiple effectors if they display different affinities to PtdIns(4,5)P
2.
Relative power and sample size analysis on gene expression profiling data
Authors: van Iterson M , 't Hoen PAC , Pedotti P , Hooiveld GJEJ , den Dunnen JT , van Ommen GJB , Boer JM , Menezes RX
Published: September 2009

Background

With the increasing number of expression profiling technologies, researchers today are confronted with choosing the technology that has sufficient power with minimal sample size, in order to reduce cost and time. These depend on data variability, partly determined by sample type, preparation and processing. Objective measures that help experimental design, given own pilot data, are thus fundamental.

Results

Relative power and sample size analysis were performed on two distinct data sets. The first set consisted of Affymetrix array data derived from a nutrigenomics experiment in which weak, intermediate and strong PPARαagonists were administered to wild-type and PPARα-null mice. Our analysis confirms the hierarchy of PPARα-activating compounds previously reported and the general idea that larger effect sizes positively contribute to the average power of the experiment. A simulation experiment was performed that mimicked the effect sizes seen in the first data set. The relative power was predicted but the estimates were slightly conservative. The second, more challenging, data set describes a microarray platform comparison study using hippocampalδC-doublecortin-like kinase transgenic mice that were compared to wild-type mice, which was combined with results from Solexa/Illumina deep sequencing runs. As expected, the choice of technology greatly influences the performance of the experiment. Solexa/Illumina deep sequencing has the highest overall power followed by the microarray platforms Agilent and Affymetrix. Interestingly, Solexa/Illumina deep sequencing displays comparable power across all intensity ranges, in contrast with microarray platforms that have decreased power in the low intensity range due to background noise. This means that deep sequencing technology is especially more powerful in detecting differences in the low intensity range, compared to microarray platforms.

Conclusion

Power and sample size analysis based on pilot data give valuable information on the performance of the experiment and can thereby guide further decisions on experimental design. Solexa/Illumina deep sequencing is the technology of choice if interest lies in genes expressed in the low-intensity range. Researchers can get guidance on experimental design using our approach on their own pilot data implemented as a BioConductor package, SSPAhttp://bioconductor.org/packages/release/bioc/html/SSPA.html.
Identification and characterization of miRNAs expressed in the bovine ovary
Authors: Hossain Md Munir , Ghanem Nasser , Hoelker Michael , Rings Franca , Phatsara Chirawath , Tholen Ernst , Schellander Karl , Tesfaye Dawit
Published: September 2009

Background

MicroRNAs are the major class of gene-regulating molecules playing diverse roles through sequence complementarity to target mRNAs at post-transcriptional level. Tightly regulated expression and interaction of a multitude of genes for ovarian folliculogenesis could be regulated by these miRNAs. Identification of them is the first step towards understanding miRNA-guided gene regulation in different biological functions. Despite increasing efforts in miRNAs identification across various species and diverse tissue types, little is known about bovine ovarian miRNAs. Here, we report the identification and characterization of miRNAs expressed in the bovine ovary through cloning, expression analysis and target prediction.

Results

The miRNA library (5'-independent ligation cloning method), which was constructed from bovine ovary in this study, revealed cloning of 50 known and 24 novel miRNAs. Among all identified miRNAs, 38 were found to be new for bovine and were derived from 43 distinct loci showing characteristic secondary structure. While 22 miRNAs precursor loci were found to be well conserved in more than one species, 16 were found to be bovine specific. Most of the miRNAs were cloned multiple times, in which let-7a, let-7b, let-7c, miR-21, miR-23b, miR-24, miR-27a, miR-126 and miR-143 were cloned 10, 28, 13, 4, 11, 7, 6, 4 and 11 times, respectively. Expression analysis of all new and some annotated miRNAs in different intra-ovarian structures and in other multiple tissues showed that some were present ubiquitously while others were differentially expressed among different tissue types. Bta-miR-29a was localized in the follicular cells at different developmental stages in the cyclic ovary. Bio-informatics prediction, screening and Gene Ontology analysis of miRNAs targets identified several biological processes and pathways underlying the ovarian function.

Conclusion

Results of this study suggest the presence of miRNAs in the bovine ovary, thereby elucidate their potential role in regulating diverse molecular and physiological pathways underlying the ovarian functionality. This information will give insights into bovine ovarian miRNAs, which can be further characterized for their role in follicular development and female fertility as well.
Revisiting the Plasmodium falciparum RIFIN family: from comparative genomics to 3D-model prediction
Authors: Bultrini Emanuele , Brick Kevin , Mukherjee Srayanta , Zhang Yang , Silvestrini Francesco , Alano Pietro , Pizzi Elisabetta
Published: September 2009

Background

Subtelomeric RIFIN genes constitute the most abundant multigene family in Plasmodium falciparum. RIFIN products are targets for the human immune response and contribute to the antigenic variability of the parasite. They are transmembrane proteins grouped into two sub-families (RIF_A and RIF_B). Although recent data show that RIF_A and RIF_B have different sub-cellular localisations and possibly different functions, the same structural organisation has been proposed for members of the two sub-families. Despite recent advances, our knowledge of the regulation of RIFIN gene expression is still poor and the biological role of the protein products remain obscure.

Results

Comparative studies on RIFINs in three clones of P. falciparum (3D7, HB3 and Dd2) by Multidimensional scaling (MDS) showed that gene sequences evolve differently in the 5'upstream, coding, and 3'downstream regions, and suggested a possible role of highly conserved 3' downstream sequences. Despite the expected polymorphism, we found that the overall structure of RIFIN repertoires is conserved among clones suggesting a balance between genetic drift and homogenisation mechanisms which guarantees emergence of novel variants but preserves the functionality of genes. Protein sequences from a bona fide set of 3D7 RIFINs were submitted to predictors of secondary structure elements. In contrast with the previously proposed structural organisation, no signal peptide and only one transmembrane helix were predicted for the majority of RIF_As. Finally, we developed a strategy to obtain a reliable 3D-model for RIF_As. We generated 265 possible structures from 53 non-redundant sequences, from which clustering and quality assessments selected two models as the most representative for putative RIFIN protein structures.

Conclusion

First, comparative analyses of RIFIN repertoires in different clones of P. falciparum provide insights on evolutionary mechanisms shaping the multigene family. Secondly, we found that members of the two sub-families RIF_As and RIF_Bs have different structural organization in accordance with recent experimental results. Finally, representative models for RIF_As have an "Armadillo-like" fold which is known to promote protein-protein interactions in diverse contexts.
Early detection of breast cancer: benefits and risks of supplemental breast ultrasound in asymptomatic women with mammographically dense breast tissue. A systematic review
Authors: Nothacker Monika , Duda Volker , Hahn Markus , Warm Mathias , Degenhardt Friedrich , Madjar Helmut , Weinbrenner Susanne , Albert Ute-Susann
Published: September 2009

Background

Mammographic screening alone will miss a certain fraction of malignancies, as evidenced by retrospective reviews of mammograms following a subsequent screening. Mammographic breast density is a marker for increased breast cancer risk and is associated with a higher risk of interval breast cancer, i.e. cancer detected between screening tests. The purpose of this review is to estimate risks and benefits of supplemental breast ultrasound in women with negative mammographic screening with dense breast tissue.

Methods

A systematic search and review of studies involving mammography and breast ultrasound for screening of breast cancer was conducted. The search was performed for the period 1/2000-8/2008 within the data source of PubMed, DARE, and Cochrane databases. Inclusion and exclusion criteria were determined prospectively, and the Oxford evidence classification system for diagnostic studies was used for evidence level. The parameters biopsy rate, positive predictive value (PPV) for biopsy, cancer yield for breast ultrasound alone, and carcinoma detection rate by breast density were extracted or constructed.

Results

The systematic search identified no randomized controlled trials or systematic reviews, six cohort studies of intermediate level of evidence (3b) were found. Only two of the studies included adequate follow-up of subjects with negative or benign findings. Supplemental breast ultrasound after negative mammographic screening permitted diagnosis of primarily invasive carcinomas in 0.32% of women in breast density type categories 2-4 of the American College of Radiology (ACR); mean tumor size for those identified was 9.9 mm, 90% with negative lymph node status. Most detected cancers occurred in mammographically dense breast ACR types 3 and 4. Biopsy rates were in the range 2.3%-4.7%, with PPV of 8.4-13.7% for those biopsied due to positive ultrasound, or about one third of the PPV of biopsies due to mammography. Limitations: The study populations included wide age ranges, and the application to women age 50-69 years as proposed for mammographic screening could result in less striking benefit. Further validation studies should employ a uniform assessment system such as BI-RADS and report not only PPV, but also negative predictive value, sensitivity and specificity.

Conclusion

Supplemental breast ultrasound in the population of women with mammographically dense breast tissue (ACR 3 and 4) permits detection of small, otherwise occult, breast cancers. Potential adverse impacts for women in this intermediate risk group are associated with an increased biopsy rate.
Using vital statistics to estimate the population-level impact of osteoporotic fractures on mortality based on death certificates, with an application to France (2000-2004)
Authors: Ziadé Nelly , Jougla Eric , Coste Joël
Published: September 2009

Background

We developed a methodology using vital statistics to estimate the impact of osteoporotic fractures on the mortality of an entire population, and applied it to France for the period 2000-2004.

Methods

Current definitions of osteoporotic fractures were reviewed and their components identified. We used the International Classification of Diseases with national vital statistics data for the French adult population and performed cross-classifications between various components: age, sex, I-code (site) and E-code (mechanism of fracture). This methodology allowed identification of appropriate thresholds and categorization for each pertinent component.

Results

2,625,743 death certificates were analyzed, 2.2% of which carried a mention of fracture. Hip fractures represented 55% of all deaths from fracture. Both sexes showed a similar pattern of mortality rates for all fracture sites, the rate increased with age from the age of 70 years. The E-high-energy code (present in 12% of death certificates with fractures) was found to be useful to rule-out non-osteoporotic fractures, and to correct the overestimation of mortality rates. Using this methodology, the crude number of deaths associated with fractures was estimated to be 57,753 and the number associated with osteoporotic fractures 46,849 (1.85% and 1.78% of all deaths, respectively).

Conclusion

Osteoporotic fractures have a significant impact on overall population mortality.
The Sam domain of the lipid phosphatase Ship2 adopts a common model to interact with Arap3-Sam and EphA2-Sam
Authors: Leone Marilisa , Cellitti Jason , Pellecchia Maurizio
Published: September 2009

Background

Sterile alpha motif (Sam) domains are small protein modules that can be involved in homotypic or heterotypic associations and exhibit different functions. Previous studies have demonstrated that the Sam domain of the lipid phosphatase Ship2 can hetero-dimerize with the Sam domain of the PI3K effector protein Arap3.

Results

Here, we determine the NMR solution structure of Arap3-Sam and implement a multidisciplinary approach consisting of NMR spectroscopy, ITC (Isothermal Titration Calorimetry), mutagenesis and molecular modeling studies to analyze the interaction between Ship2-Sam and Arap3-Sam. This work reveals that Arap3-Sam may associate with Ship2-Sam by adopting a binding mode common to other Sam domains. This binding mode is identical to what we have very recently observed for the association between Ship2-Sam and the Sam domain from the Ephrin A2 receptor.

Conclusion

Our studies further clarify the structural features that are relevant for Sam-Sam interactions involving Ship2 and give additional hints that could be used for the identification of new molecules able to selectively inhibit Sam-Sam associations.
Adherence to anti-tuberculosis treatment among pulmonary tuberculosis patients: a qualitative and quantitative study
Authors: Xu Weiguo , Lu Wei , Zhou Yang , Zhu Limei , Shen Hongbing , Wang Jianming
Published: September 2009

Background

Tuberculosis (TB) patients have difficulty following a long-term treatment regimen. Efforts to improve treatment outcomes require better understanding of adherence as a complex behavioral issue and of the particular barriers to and facilitators of patient adherence.

Methods

This study was carried out in Jiangsu Province of China with both quantitative and qualitative approaches. For the quantitative study, 780 sputum-smear positive TB patients consecutively registered since 2006 in 13 counties (districts) were queried with a structured questionnaire. Patients who had missed 10% of their total prescribed doses of TB drugs were deemed as non-adherent. Risks for non-adherence were estimated by computing odds ratios (ORs) and their 95% confidence intervals (95% CIs) using a logistic regression model. We also invited 20 TB patients and 10 local health workers for in-depth interviews. We then used content analysis based on this qualitative study to explore factors associated with non-adherence.

Results

The proportion of non-adherence among 670 patients was 12.2%. Univariate analysis showed that patients, who were illiterate, divorced/widowed, lacked health insurance and were migrants, were more likely to be non-adherent. The crude ORs(95%CIs) were 2.38(1.37-4.13), 2.42(1.30-4.52), 1.89(1.07-3.32) and 1.98(1.03-3.83), respectively. The risk of non-adherence was lower among patients whose treatment was given under direct observation by village doctors or regular home visits by health workers, with ORs (95% CIs) of 0.19(0.10-0.36) and 0.23(0.10-0.51), respectively. In multivariate analysis, factors associated with non-adherence included illiteracy (OR: 2.42; 95% CI: 1.25-4.67) and direct observation by village doctors (OR: 0.23; 95% CI: 0.11-0.45). The in-depth interviews indicated that financial burdens and extra medical expenditures, adverse drug reactions, and social stigma were additional potential factors accounted for non-adherence.

Conclusion

More importance should be given to treatment adherence under the current TB control program. Heavy financial burdens, lack of social support, adverse drug reactions and personal factors are associated with non-adherence. Direct observation and regular home visits by health workers appear to reduce the risk of non-adherence. More patient-centered interventions and greater attention to structural barriers are needed to improve treatment adherence.
Visualizing fusion of pseudotyped HIV-1 particles in real time by live cell microscopy
Authors: Koch Peter , Lampe Marko , Godinez William J , Müller Barbara , Rohr Karl , Kräusslich Hans-Georg , Lehmann Maik J
Published: September 2009

Background

Most retroviruses enter their host cells by fusing the viral envelope with the plasma membrane. Although the protein machinery promoting fusion has been characterized extensively, the dynamics of the process are largely unknown.

Results

We generated human immunodeficiency virus-1 (HIV-1) particles pseudotyped with the envelope (Env) protein of ecotropic murine leukemia virus eMLV to study retrovirus entry at the plasma membrane using live-cell microscopy. This Env protein mediates highly efficient pH independent fusion at the cell surface and can be functionally tagged with a fluorescent protein. To detect fusion events, double labeled particles carrying one fluorophor in Env and the other in the matrix (MA) domain of Gag were generated and characterized. Fusion events were defined as loss of Env signal after virus-cell contact. Single particle tracking of >20,000 individual traces in two color channels recorded 28 events of color separation, where particles lost the Env protein, with the MA layer remaining stable at least for a short period. Fourty-five events were detected where both colors were lost simultaneously. Importantly, the first type of event was never observed when particles were pseudotyped with a non-fusogenic Env.

Conclusion

These results reveal rapid retroviral fusion at the plasma membrane and permit studies of the immediate post-fusion events.
Beneficial effect of the oxygen free radical scavenger amifostine (WR-2721) on spinal cord ischemia/reperfusion injury in rabbits
Authors: Chronidou Fany , Apostolakis Efstratios , Papapostolou Ioannis , Grintzalis Konstantinos , Georgiou Christos D , Koletsis Efstratios N , Karanikolas Menelaos , Papathanasopoulos Panagiotis , Dougenis Dimitrios
Published: September 2009

Background

Paraplegia is the most devastating complication of thoracic or thoraco-abdominal aortic surgery. During these operations, an ischemia-reperfusion process is inevitable and the produced radical oxygen species cause severe oxidative stress for the spinal cord. In this study we examined the influence of Amifostine, a triphosphate free oxygen scavenger, on oxidative stress of spinal cord ischemia-reperfusion in rabbits.

Methods

Eighteen male, New Zealand white rabbits were anesthetized and spinal cord ischemia was induced by temporary occlusion of the descending thoracic aorta by a coronary artery balloon catheter, advanced through the femoral artery. The animals were randomly divided in 3 groups. Group I functioned as control. In group II the descending aorta was occluded for 30 minutes and then reperfused for 75 min. In group III, 500 mg Amifostine was infused into the distal aorta during the second half-time of ischemia period. At the end of reperfusion all animals were sacrificed and spinal cord specimens were examined for superoxide radicals by an ultra sensitive fluorescent assay.

Results

Superoxide radical levels ranged, in group I between 1.52 and 1.76 (1.64 ± 0.10), in group II between 1.96 and 2.50 (2.10 ± 0.23), and in group III (amifostine) between 1.21 and 1.60 (1.40 ± 0.19) (p = 0.00), showing a decrease of 43% in the Group of Amifostine. A lipid peroxidation marker measurement ranged, in group I between 0.278 and 0.305 (0.296 ± 0.013), in group II between 0.427 and 0.497 (0.463 ± 0.025), and in group III (amifostine) between 0.343 and 0.357 (0.350 ± 0.007) (p < 0.00), showing a decrease of 38% after Amifostine administration.

Conclusion

By direct and indirect methods of measuring the oxidative stress of spinal cord after ischemia/reperfusion, it is suggested that intra-aortic Amifostine infusion during spinal cord ischemia phase, significantly attenuated the spinal cord oxidative injury in rabbits.