bluuebunny/crossref_metadata_2025_split huggingface dataset:
LTR retroelements in the genome of Daphnia pulex
Authors: Rho Mina , Schaack Sarah , Gao Xiang , Kim Sun , Lynch Michael , Tang Haixu 
Published: July 2010

Abstract

Background
Long terminal repeat (LTR) retroelements represent a successful group of transposable elements (TEs) that have played an important role in shaping the structure of many eukaryotic genomes. Here, we present a genome-wide analysis of LTR retroelements in Daphnia pulex, a cyclical parthenogen and the first crustacean for which the whole genomic sequence is available. In addition, we analyze transcriptional data and perform transposon display assays of lab-reared lineages and natural isolates to identify potential influences on TE mobility and differences in LTR retroelements loads among individuals reproducing with and without sex.

Results
We conducted a comprehensive de novo search for LTR retroelements and identified 333 intact LTR retroelements representing 142 families in the D. pulex genome. While nearly half of the identified LTR retroelements belong to the gypsy group, we also found copia (95), BEL/Pao (66) and DIRS (19) retroelements. Phylogenetic analysis of reverse transcriptase sequences showed that LTR retroelements in the D. pulex genome form many lineages distinct from known families, suggesting that the majority are novel. Our investigation of transcriptional activity of LTR retroelements using tiling array data obtained from three different experimental conditions found that 71 LTR retroelements are actively transcribed. Transposon display assays of mutation-accumulation lines showed evidence for putative somatic insertions for two DIRS retroelement families. Losses of presumably heterozygous insertions were observed in lineages in which selfing occurred, but never in asexuals, highlighting the potential impact of reproductive mode on TE abundance and distribution over time. The same two families were also assayed across natural isolates (both cyclical parthenogens and obligate asexuals) and there were more retroelements in populations capable of reproducing sexually for one of the two families assayed.

Conclusions
Given the importance of LTR retroelements activity in the evolution of other genomes, this comprehensive survey provides insight into the potential impact of LTR retroelements on the genome of D. pulex, a cyclically parthenogenetic microcrustacean that has served as an ecological model for over a century.
Motivations and reasons for women attending a Breast Self-Examination training program: A qualitative study
Authors: Yang Rea-Jeng , Huang Lian-Hua , Hsieh Yeu-Sheng , Chung Ue-Lin , Huang Chiun-Sheng , Bih Herng-Dar 
Published: July 2010

AbstractBackgroundBreast cancer is a major threat to Taiwanese women's health. Despite the controversy surrounding the effectiveness of breast self-examination (BSE) in reducing mortality, BSE is still advocated by some health departments. The aim of the study is to provide information about how women decide to practice BSE and their experiences through the training process. Sixty-six women aged 27-50 were recruited.MethodsA descriptive study was conducted using small group and individual in-depth interviews to collect data, and using thematic analysis and constant comparison techniques for data analysis.ResultsIt was found that a sense of self-security became an important motivator for entering BSE training. The satisfaction in obtaining a sense of self-security emerged as the central theme. Furthermore, a ladder motivation model was developed to explain the participants' motivations for entering BSE training. The patterns of motivation include opportunity taking, clarifying confusion, maintaining health, and illness monitoring, which were connected with the risk perception for breast cancer.ConclusionsWe recognize that the way women decide to attend BSE training is influenced by personal and social factors. Understanding the different risk assessments women rely on in making their health decisions is essential. This study will assist researchers and health professionals to gain a better understanding of alternative ways to deal with breast health, and not to be limited by the recommendations of the health authorities.
Analysis of innate defences against Plasmodium falciparum in immunodeficient mice
Authors: Arnold Ludovic , Tyagi Rajeev Kumar , Mejia Pedro , Van Rooijen Nico , Pérignon Jean-Louis , Druilhe Pierre 
Published: July 2010

AbstractBackgroundMice with genetic deficiencies in adaptive immunity are used for the grafting of human cells or pathogens, to study human diseases, however, the innate immune responses to xenografts in these mice has received little attention. Using the NOD/SCIDPlasmodium falciparummouse model an analysis of innate defences responsible for the substantial control ofP. falciparumwhich remains in such mice, was performed.MethodsNOD/SCID mice undergoing an immunomodulatory protocol that includes, clodronate-loaded liposomes to deplete macrophages and an anti-polymorphonuclear leukocytes antibody, were grafted with human red blood cells andP. falciparum. The systematic and kinetic analysis of the remaining innate immune responses included the number and phenotype of peripheral blood leukocytes as well as inflammatory cytokines/chemokines released in periphery. The innate responses towards the murine parasitePlasmodium yoeliiwere used as a control.ResultsResults show that 1)P. falciparuminduces a strong inflammation characterized by an increase in circulating leukocytes and the release of inflammatory cytokines; 2) in contrast, the rodent parasiteP. yoelii, induces a far more moderate inflammation; 3) human red blood cells and the anti-inflammatory agents employed induce low-grade inflammation; and 4) macrophages seem to bear the most critical function in controllingP. falciparumsurvival in those mice, whereas polymorphonuclear and NK cells have only a minor role.ConclusionsDespite the use of an immunomodulatory treatment, immunodeficient NOD/SCID mice are still able to mount substantial innate responses that seem to be correlated with parasite clearance. Those results bring new insights on the ability of innate immunity from immunodeficient mice to control xenografts of cells of human origin and human pathogens.
What can global health institutions do to help strengthen health systems in low income countries?
Authors: Balabanova Dina , McKee Martin , Mills Anne , Walt Gill , Haines Andy 
Published: July 2010

Abstract
Weaknesses in health systems contribute to a failure to improve health outcomes in developing countries, despite increased official development assistance. Changes in the demands on health systems, as well as their scope to respond, mean that the situation is likely to become more problematic in the future. Diverse global initiatives seek to strengthen health systems, but progress will require better coordination between them, use of strategies based on the best available evidence obtained especially from evaluation of large scale programs, and improved global aid architecture that supports these processes. This paper sets out the case for global leadership to support health systems investments and help ensure the synergies between vertical and horizontal programs that are essential for effective functioning of health systems. At national level, it is essential to increase capacity to manage and deliver services, situate interventions firmly within national strategies, ensure effective implementation, and co-ordinate external support with local resources. Health systems performance should be monitored, with clear lines of accountability, and reforms should build on evidence of what works in what circumstances.
Adaphostin toxicity in a sensitive non-small cell lung cancer model is mediated through Nrf2 signaling and heme oxygenase 1
Authors: Fer Nicole D , Shoemaker Robert H , Monks Anne 
Published: July 2010

Abstract

Background
Preclinical toxicity of adaphostin has been related to oxidative stress. This study investigated the regulatory mechanism underlying adaphostin induction of heme oxygenase 1 (HMOX1) which plays a significant role in modulation of drug-induced toxicity in the non-small cell lung cancer cell line model, NCI-H522.

Methods
The transcriptional response of NCI-H522 to adaphostin prominently involved oxidative stress genes, particularly HMOX1. Reactive oxygen species (ROS) involvement was additionally established by generation of ROS prior to modulation of adaphostin-toxicity with antioxidants. To identify up-stream regulatory elements of HMOX1, immunofluorescence was used to evaluate nuclear translocation of the transcription factor, NF-E2-related factor 2 (Nrf2), in the presence of adaphostin. The PI3-kinase inhibitor, wortmannin, was employed as a pharmacological inhibitor of this process.

Results
Generation of ROS provided a substantial foundation for the sensitivity of NCI-H522 to adaphostin. However, in contrast to leukemia cell lines, transcriptional response to oxidative stress was associated with induction of HMOX1, which was dependent on nuclear translocation of the transcription factor, Nrf2. Pretreatment of cells with wortmannin inhibited translocation of Nrf2 and induction of HMOX1. Wortmannin pretreatment was also able to diminish adaphostin induction of HMOX1, and as a consequence, enhance the toxicity of adaphostin to NCI-H522.

Conclusions
Adaphostin-induced oxidative stress in NCI-H522 was mediated through nuclear translocation of Nrf2 leading to upregulation of HMOX1. Inhibition of Nrf2 translocation by wortmannin inhibited this cytoprotective response, and enhanced the toxicity of adaphostin, suggesting that inhibitors of the PI3K pathway, such as wortmannin, might augment the antiproliferative effects of adaphostin in solid tumors that depend on the Nrf2/ARE pathway for protection against oxidative stress.
Abnormalities in circulating plasmacytoid dendritic cells in patients with systemic lupus erythematosus
Authors: Jin Ou , Kavikondala Sushma , Mok Mo-Yin , Sun Lingyun , Gu Jieruo , Fu Rong , Chan Albert , Yeung Joseph , Nie Yingjie , Lau Chak-Sing 
Published: July 2010

Abstract
Introduction
Dendritic cells (DCs) are capable of inducing immunity or tolerance. Previous studies have suggested plasmacytoid DCs (pDCs) are pathogenic in systemic lupus erythematosus (SLE). However, the functional characteristics of directly isolated peripheral circulating blood pDCs in SLE have not been evaluated previously.

Methods
Peripheral blood pDCs from 62 healthy subjects and 58 SLE patients were treated with apoptotic cells derived from polymorphonuclear cells (PMNs). Antigen loaded or unloaded pDCs were then co-cultured with autologous or allogenous T cells. Changes in T cell proliferation, cell surface CD25 expression, intracellular Foxp3 expression and cytokine production were evaluated. pDCs that had captured apoptotic PMNs (pDCs + apoPMNs were also studied for their cytokine production (interferon (IFN)-alpha, interleukin (IL)-6, IL-10, IL-18) and toll like receptor (TLR) expression.

Results
Circulating pDCs from SLE patients had an increased ability to stimulate T cells when compared with control pDCs. Using allogenous T cells as responder cells, SLE pDCs induced T cell proliferation even in the absence of apoptotic PMNs. In addition, healthy pDCs + apoPMNs induced suppressive T regulatory cell features with increased Foxp3 expression in CD4 + CD25 + cells while SLE pDCs + apoPMNs did not. There were differences in the cytokine profile of pDCs that had captured apoptotic PMNs between healthy subjects and patients with SLE. Healthy pDCs + apoPMNs showed decreased production of IL-6 but no significant changes in IL-10 and IL-18. These pDCs + apoPMNs also showed increased mRNA transcription of TLR9. On the other hand, while SLE pDCs + apoPMNs also had decreased IL-6, there was decreased IL-18 mRNA expression and persistent IL-10 protein synthesis. In addition, SLE pDCs lacked TLR9 recruitment.

Conclusions
We have demonstrated that peripheral circulating pDCs in patients with SLE were functionally abnormal. They lacked TLR9 expression, were less capable of inducing regulatory T cell differentiation and had persistent IL-10 mRNA expression following the capture of apoptotic PMNs. We suggest circulating pDCs may be pathogenically relevant in SLE.
Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays
Authors: Sellam Adnane , Hogues Hervé , Askew Christopher , Tebbji Faiza , van het Hoog Marco , Lavoie Hugo , Kumamoto Carol A , Whiteway Malcolm , Nantel André 
Published: July 2010

Abstract
Background
Compared to other model organisms and despite the clinical relevance of the pathogenic yeast Candida albicans, no comprehensive analysis has been done to provide experimental support of its in silico-based genome annotation.

Results
We have undertaken a genome-wide experimental annotation to accurately uncover the transcriptional landscape of the pathogenic yeast C. albicans using strand-specific high-density tiling arrays. RNAs were purified from cells growing under conditions relevant to C. albicans pathogenicity, including biofilm, lab-grown yeast and serum-induced hyphae, as well as cells isolated from the mouse caecum. This work provides a genome-wide experimental validation for a large number of predicted ORFs for which transcription had not been detected by other approaches. Additionally, we identified more than 2,000 novel transcriptional segments, including new ORFs and exons, non-coding RNAs (ncRNAs) as well as convincing cases of antisense gene transcription. We also characterized the 5' and 3' UTRs of expressed ORFs, and established that genes with long 5' UTRs are significantly enriched in regulatory functions controlling filamentous growth. Furthermore, we found that genomic regions adjacent to telomeres harbor a cluster of expressed ncRNAs. To validate and confirm new ncRNA candidates, we adapted an iterative strategy combining both genome-wide occupancy of the different subunits of RNA polymerases I, II and III and expression data. This comprehensive approach allowed the identification of different families of ncRNAs.

Conclusions
In summary, we provide a comprehensive expression atlas that covers relevant C. albicans pathogenic developmental stages in addition to the discovery of new ORF and non-coding genetic elements.
Observation of Electrochemiluminescence from Indolo[2,3-b]tropone Zinc(II) Complex Using Benzoyl Peroxide as Coreactant
Authors: Jin Jiye , Ito Kunihiro , Takahashi Fumiki , Oda Mitsunori 
Published: July 2010

Abstract
A new luminescent zinc(II) complex with indolo[2,3-b]tropone ligand has been synthesized and studied with respect to its electrochemiluminescence (ECL) properties for the first time. We observed a distinct blue-green ECL emission from this compound during electrochemical reduction in dimethyl sulfoxide (DMSO) at room temperature when benzoyl peroxide (BPO) was used as coreactant. As the ECL emission is almost identical to its photoluminescence spectrum, it suggested that the ECL is from the lowest excited state of the complex.
Monitoring the Oedometric Compression of Sands with Acoustic Emissions
Authors: Fernandes Fabio , Syahrial Afrildo I. , Valdes Julio R. 
Published: July 2010

Abstract
The development and use of a noninvasive technique to monitor the acoustic emissions (AEs) generated during the oedometric compression of coarse-grained soil are documented. Technique implementation is described with the aid of experiments conducted on sands with contrasting grain features. Results indicate that the proposed technique is capable of capturing the onset of characteristic stress-strain behavior regimes exhibited by the soil during loading. The clarity of such capture is, however, dependent on the amplitude of the AE relative to that of the background noise and, as such, dependent on the soil type. The technique is anticipated to aid in enhancing the fundamental study of soil behavior at high stresses and may find potential use in the realm of penetrometer-based stratigraphy characterization.
Experimental and Theoretical Studies of Vertical Piles Reinforced Sand Slopes Loaded with Strip Footing
Authors: Rao S. V. Krishna , Nasr Ahmed. M. A. 
Published: July 2010

AbstractThis paper presents the results of a series of plain strain model tests of strip footing adjacent to sand slopes reinforced with piles. The main objectives of this study are to determine the influence of piles reinforced sand slope on the bearing capacity characteristics of the footing on slope, to suggest an optimum geometry of piles placement, and to understand the failure mechanism of reinforced sand slopes with piles. The investigations were carried out by varying the piles row location relatively to the slope crest, piles head conditions, piles length, piles spacing, row inclination of piles, and the edge distance of the footing relative to the slope crest, as well as by considering the relative density of sand. The test results indicate that this type of reinforcement significantly increases the confinement of the soil and successively raises the ultimate bearing capacity of the strip footing. In addition, critical values of the parameters for maximum reinforcing effects are established. A numerical study using finite element analyses was performed on a prototype scale model slope. A close agreement between experimental and numerical results was observed. The scaling and size effects of the small-scale model tests can be readily evaluated by means of finite element analysis.
Validation Through Finite Element Simulation of the Behaviour of a Polyurethane Shock Absorber Under In-Service and Extreme Conditions
Authors: Ferreño D. , Cicero S. , Carrascal I. , Meng E. 
Published: July 2010

Abstract
The safety rules for the construction and installation of lifts, currently in force in Europe, include several requirements concerning the behaviour of the shock absorbers when stopping an elevator. In this paper, a finite element model simulating the behaviour of a cellular polyurethane shock absorber has been developed. The material mechanical behaviour was simulated by means of an elastomeric foam theoretical model, previously calibrated in a former paper. Several in-service and extreme condition scenarios have been analysed with this numerical model, thus verifying the fulfilment of the requirements of the standard.
Determining Residual Ammonia in Flue Gas Conditioned Fly Ashes and Its Influence on the Pozzolanic Activity
Authors: Shanthakumar S. , Singh D. N. , Phadke R. C. 
Published: July 2010

AbstractThermal power stations employ flue gas conditioning (FGC) technique to reduce the emission of suspended particulate matter in the surrounding atmosphere substantially. This technique involves the treatment of flue gases by adding the chemical agents (viz., ammonia and/or sulfur trioxide) to the flue gas, which in turn increases the collection efficiency of electrostatic precipitators. Since the pozzolanic activity of the fly ash is important for its suitability as a cementitious material in the construction industry, the presence of residual ammonia in fly ash may adversely affect its utilization. Hence, it becomes mandatory to establish the presence of residual ammonia in the fly ash, and its influence on the pozzolanic activity of the fly ash needs to be studied in details. With this in view, fly ash samples from coal based thermal power stations in India, where FGC is being done, were collected, and the residual ammonia as well as pozzolanic activity was determined. Based on these investigations, it has been demonstrated that the influence of residual ammonia from FGC on pozzolanic activity of the fly ash is insignificant.
Pyroxene from martian meteorite NWA856: Structural investigations by X-ray and neutron diffraction
Authors: Frey Friedrich , Weidner Eveline , Pedersen Björn , Boysen Hans , Burghammer Manfred , Hoelzel Markus 
Published: July 2010

Abstract
Despite high mosaicity and complex micro structures in pyroxenes from Mars average occupancies and average atomic positions of pigeonite were determined from X-ray single crystal and neutron and X-ray powder diffraction data. The chemical composition of selected single crystals varied between En39Fs55Wo6 and En60Fs34Wo6. The average composition of the whole sample was determined from powder diffraction to be about En43Fs51Wo6. The ordering of the cations on the M1 and M2 positions, expressed by a partitioning or distribution coefficient K
D, in the pigeonite structure was determined and a closure temperature of about 540 °C was estimated for crystals stemming from the core of our specimen. General trends of the crystal chemistry with K
D are compared with literature data. From in-situ high temperature neutron powder data, however, it is deduced that a simple intra-phase-ordering process is not adequate, since diffusion processes between intimately intergrown augite and pigeonite phases at temperatures above 600 °C also take place. This makes the usual interpretation of structural data towards the prior history of the martian sample material doubtful.
The crystal structure of Sr-hardystonite, Sr2ZnSi2O7
Authors: Ardit Matteo , Cruciani Giuseppe , Dondi Michele 
Published: July 2010

AbstractA synthetic strontium isomorph (Sr2ZnSi2O7) of the hardystonite structure (Ca2ZnSi2O7) was investigated with X-ray powder diffraction. The average structure (S.G.P-421m),a= 8.0007(1) Å,c= 5.1722(1) Å, was refined by Rietveld method and aRF2= 0.0216 was achieved using 394 independent reflections. The results show that Sr-hardystonite has a melilite-type structure with no incommensurate modulations. Its geometrical and bonding features are consistent with trends defined by the other so-called normal and modulated melilite structures.
A user's guide to functional diversity indices
Authors: Schleuter D. , Daufresne M. , Massol F. , Argillier C. 
Published: July 2010

Functional diversity is the diversity of species traits in ecosystems. This concept is increasingly used in ecological research, yet its formal definition and measurements are currently under discussion. As the overall behavior and consistency of functional diversity indices have not been described so far, the novice user risks choosing an inaccurate index or a set of redundant indices to represent functional diversity.In our study we closely examine functional diversity indices to clarify their accuracy, consistency, and independence. Following current theory, we categorize them into functional richness, evenness, or divergence indices. We considered existing indices as well as new indices developed in this study. The new indices aimed at remedying the weaknesses of currently used indices (e.g., by taking into account intraspecific variability). Using virtual data sets, we test (1) whether indices respond to community changes as expected from their category and (2) whether the indices within each category are consistent and independent of indices from other categories. We also test the accuracy of methods proposed for the use of categorical traits.Most classical functional richness indices either failed to describe functional richness or were correlated with functional divergence indices. We therefore recommend using the new functional richness indices that consider intraspecific variability and thus empty space in the functional niche space. In contrast, most functional evenness and divergence indices performed well with respect to all proposed tests. For categorical variables, we do not recommend blending discrete and real‐valued traits (except for indices based on distance measures) since functional evenness and divergence have no transposable meaning for discrete traits. Nonetheless, species diversity indices can be applied to categorical traits (using trait levels instead of species) in order to describe functional richness and equitability.