bluuebunny/crossref_metadata_2025 huggingface dataset:
Beyond the screen: visualizing visits to a website as an experience in physical space
Authors: Hohl Michael
Published: August 2009

This article describes an applied investigation into a concept of information visualization where data are not rendered as graphs, charts or diagrams on the screen but as a sensual experience beyond the screen in physical space. It introduces predecessors such as calm technologies and ambient displays among a number of poetic and applied examples from related backgrounds to establish the context and relevance for communication design and graphic design, and presents a current research undertaking in which the social activity of visiting a website is visualized in multiple sensorial modalities in real-time in the form of a kinetic and sensual display.
Information design and the world that comes before us
Authors: McLaughlin Sally
Published: August 2009

Technology or art? The practice of information design occupies an ambiguous position in relation to these very different approaches to making. Heidegger's critique of the metaphysical concepts of being, spatiality and mood provides fertile ground for developing an understanding of the way in which `information design as technology' conceals. The ethical imperative for an alternative conception of information design is explored.
Moving Beyond Scholar-Practitioner Binaries: Exploring the Liminal Possibilities of the Borderlands
Authors: Tyler Jo A.
Published: August 2009

The recent discourse connected to the notion of scholar-practitioner in human resource development commonly uses the metaphor of a “gap” between these two binaries that must somehow be bridged or that otherwise requires linking. This article examines the contemporary expression of this gap in the AHRD literature and the nature of the duality it implies.An alternative metaphor based on Anzaldúa’s borderlands and the mestiza consciousness that emerges there is suggested. This reframing and its implications are explored with an eye toward the possibilities of prompting new dialogue and creative responses across the many types of work, interests, and personas that comprise and enrich HRD as a field.
Marked Inhibition of Growth and Invasive Parameters of Head and Neck Squamous Carcinoma FaDu by a Nutrient Mixture
Authors: Roomi M.W. , Roomi N.W. , Kalinovsky T. , Rath M. , Niedzwiecki A.
Published: August 2009

Head and neck squamous cell carcinomas (HNSCCs) are known for their aggressive growth and propensity to metastasize. The authors investigated the effect of a novel nutrient mixture (NM) containing ascorbic acid, lysine, proline, and green tea extract on human HNSCC cell line FaDu in vivo and in vitro. Athymic male nude mice (n = 12) were inoculated with 3 × 106 FaDu cells subcutaneously and randomly divided into 2 groups: group A was fed a regular diet and group B a regular diet supplemented with 0.5% NM. Four weeks later, the mice were sacrificed and their tumors were excised, weighted, and processed for histology. In vitro, FaDu cells were cultured in Dulbecco's modified Eagle's medium and exposed to NM at 0 to 1000 µg/mL in triplicate. Cell proliferation was assessed by MTT assay, matrix metalloproteinase (MMP) secretion by gelatinase zymography, invasion through Matrigel, apoptosis by live-green caspases, and cell morphology by hematoxylin—eosin staining. NM inhibited the growth of tumors by 55% ( P = .0002) and exhibited dose-dependent toxicity on FaDu cells in vitro, with 53% ( P = .0003) at 1000 µg/mL NM. Zymography revealed MMP-2 and phorbol 12-myristate 13-acetate—induced MMP-9 secretion. NM inhibited secretion of both MMPs in a dose-dependent manner, with virtual total inhibition at 1000 µg/mL. NM significantly inhibited FaDu invasion through Matrigel with total block at 1000 µg/mL. NM induced dose-dependent apoptosis. In conclusion, NM has therapeutic potential in the treatment of HNSCC by significantly suppressing tumor growth and significantly inhibiting MMP secretion and invasion of HNSCC cells in vitro.
The Effects of an Exercise Program in Leukemia Patients
Authors: Battaglini Claudio L. , Hackney A.C. , Garcia Rey , Groff Diane , Evans Elizabeth , Shea Thomas
Published: August 2009

Purpose. To examine the feasibility of administering an in-hospital exercise program to acute leukemia patients undergoing chemotherapy. A secondary purpose explored the impact of exercise on selected physiological, psychological, and inflammatory markers. Methods. Ten patients, aged 18 to 50 years, diagnosed with acute leukemia or newly relapsed were assessed for body weight, height, body composition (skinfolds), cardiorespiratory endurance (total minutes on bicycle ergometer at 60% heart rate reserve), dynamic muscular endurance (Rocky Mountain Cancer Rehabilitation Institute protocol), fatigue (Revised Piper Fatigue Scale), depression (Center for Epidemiologic Studies Depression scale, National Institute of Mental Health questionnaire), and quality of life (Functional Assessment of Cancer Therapy—General) at baseline (within 3 days of diagnosis) and at the end of induction phase of treatment. Blood draws were taken at baseline, midpoint, and at the end of induction for analyses of inflammatory markers (Linco Luminex assay). Combined aerobic and strength training exercises were administered 3 times per week, twice daily, for 30 minutes. Paired-samples t-tests were used for the analyses of physiological and psychological parameters. One-way repeated measures analysis of variance was used for the analyses of inflammatory markers. Results. Significant improvements in cardiorespiratory endurance ( P = .009, baseline 8.9 ± 8.8 minutes, postexercise intervention 17 ± 14.3 minutes) with significant reductions in total fatigue scores ( P = .009, baseline 4.6 ± 1.7, postexercise intervention 1.8 ± 1.6) and depression scores ( P = .023, baseline 19 ± 11.5, postexercise intervention 12 ± 8.2) were observed. Marginally significant decrease in interleukin-6 (IL-6; P = .059) with no significant changes in IL-10 ( P = .223) or interferon-γ ( P = .882) were observed. Conclusion. Administration of exercise to acute leukemia patients undergoing treatment is feasible. The exercise protocol used increased cardiovascular endurance, reduced fatigue and depression scores, and maintained quality of life. Although no significant change in inflammation was observed, a trend demonstrating a reduction in IL-6 and an increase in IL-10 warrants further investigation.
An Alternative Treatment for Cervical Intraepithelial Neoplasia II, III
Authors: Swanick Summer , Windstar-Hamlin Kimberly , Zwickey Heather
Published: August 2009

Background. This report describes a case of a woman with progressive and recurrent cervical dysplasia 4 years after cervical conization for severe dysplasia. Patient and methods. A 20-year-old female was referred for colposcopy and biopsy following results of moderate to severe atypia of cervical cells on her Papanicolaou (Pap) test. Her colposcopy was satisfactory and her biopsy revealed cervical intraepithelial neoplasia (CIN) II, III. She refused the conventional recommendation of loop electrosurgical excision procedure (LEEP) and, as an alternative, elected to receive escharotic treatment at a frequency of 2 treatments per week for 5 weeks. In addition to the escharotic treatment she followed an oral vitamin and botanical protocol. She was followed for 5 years. Results. The patient's 4-month and 10-month follow-up Pap smears revealed negative cervical cytology for intraepithelial lesion or malignancy. Her 10-month colposcopy was satisfactory and no lesions were noted on the colposcopic exam. Liquid based Pap results continued to remain normal for 5 years after the initiation of treatment. Discussion. Escharotic treatment of high-grade cervical neoplasias with satisfactory colposcopy holds promise as an effective and low-risk alternative therapy to LEEP and other excisional procedures.
Aging and Cancer: Converging Routes to Disease Prevention
Authors: Chobotova Katya
Published: August 2009

An integrative approach to the combined challenges of aging, cancer and stress is a necessary part of a global vision of wellness. Recent research into the mechanisms of aging, cancer and stress has established the biological links between these processes. Understanding these links is an important stepping-stone for developing approaches and therapies that ensure wellness throughout all stages of aging. This paper will consider the most recent developments in research into the molecular mechanisms common to aging and cancer and will discuss the effectiveness of natural approaches for preventing disease. Metabolic regulators as well as nutrient and energy sensors are involved in the processes of aging and cancer, and these are open to external manipulation and control. It is now becoming possible to demonstrate how nutrition, physical activity and stress control can lead to disease-free aging.
Aerobic Exercise Intensity in Breast Cancer Patients: A Preliminary Investigation
Authors: Evans Elizabeth S. , Battaglini Claudio L. , Groff Diane G. , Hackney A.C.
Published: August 2009

Purpose: This study compared the heart rate (HR), rate of perceived exertion (RPE), and blood lactate (BL) responses to aerobic exercise between posttreated breast cancer patients and apparently healthy, age-matched controls. Methods: Seven patients and 7 control subjects underwent a submaximal treadmill test for the estimation of Vo2max. Exercise intensities of 40%, 60%, and 70% of Vo2max were calculated from the treadmill test and randomly examined between groups during three 9-minute exercise bouts on 3 different days. Independent samples t tests were used to examine the HR, RPE, and BL responses at each intensity between groups. Results: No significant differences were observed between the control and patient groups for HR, RPE, and BL at 40% (101 ± 9 vs 101 ± 11 bpm, P = .979; 8 ± 1 vs 9 ± 3, P = .237; and 1.11 ± 0.73 vs 1.26 ± 0.64 mmol/L, P = .188, respectively) and 60% (127 ± 17 vs 117 ± 13 bpm, P = .523; 12 ± 2 vs 11 ± 3, P = .267, and 3.83 ± 2.48 vs 2.23 ± 1.65 mmol/L, P = .237, respectively) of Vo2max . At 70% of Vo2max, no significant differences were found for HR (151 ± 27 vs 135 ± 13 bpm, P = .704) and RPE (14 ± 1 vs 13 ± 3, P = .181), but lower BL responses were observed in the patient group (7.70 ± 1.62 vs 3.29 ± 1.08 mmol/L, P < .0005). Conclusions: The results suggest similar HR, RPE, and BL responses between patients and control subjects at 40%, 60%, and 70% of Vo2max , except for BL at 70% of Vo2max. The lower BL response in the patient group at 70% of Vo2max was somewhat unexpected. Further research is needed to confirm or refute the results of this study to allow for a clearer understanding of the physiological responses of breast cancer patients to aerobic exercise at moderate or higher intensities so that safer aerobic exercise prescriptions can be developed for this population.
What Is an Exceptional Cancer Trajectory?: Multiple Stakeholder Perspectives on Cancer Trajectories in Relation to Complementary and Alternative Medicine Use
Authors: Hök Johanna , Forss Anette , Falkenberg Torkel , Tishelman Carol
Published: August 2009

Background: Although links between exceptional cancer trajectories (ECTs) and complementary and alternative medicines (CAMs) have been suggested, most research on ECT uses predefined criteria for ECTs without necessarily including CAM use. Little knowledge can be found about subjective perspectives of ECTs in relation to CAM. Objectives: This Swedish study explores how patients, significant others, and CAM and biomedical health care (BHC) providers reason about ECT, including the role of CAM. Methods: Using a case study approach, open interviews were conducted with multiple stakeholders about cancer trajectories reported as exceptional. Results: In-depth analysis of 5 cases indicated that although all stakeholders agreed that the reported cases were positive, in no case was the same trajectory considered exceptional by all stakeholders. Different stakeholders shared neither conceptualizations of what constituted an ECT nor attributions for positive trajectories. Patients, significant others, and CAM providers emphasized unexpectedly long survival and well-being in ECTs, whereas BHC providers only referred to survival. CAM and BHC providers normalized reported trajectories, although the forms for this differed between provider groups. Concluding discussion: Stakeholders' accounts are discussed relative to different health care domains, legitimization processes, and legal constraints, which have led to the lack of a public sphere for CAM use in cancer.
Impact of Standardized Rhus verniciflua Stokes Extract as Complementary Therapy on Metastatic Colorectal Cancer: A Korean Single-Center Experience
Authors: Lee Sang-hun , Choi Won-cheol , Yoon Seong-woo
Published: August 2009

Background. To investigate the clinical feasibility of the standardized Rhus verniciflua Stokes (RVS) extract for the metastatic colorectal cancer (mCRC), experimentally proven to have anticancer activities. Patients and Methods. From July 2006 to November 2007, patients with conventional chemotherapy refractory mCRC were checked. After fulfilling inclusion/exclusion criteria, 36 patients were eligible for the final analysis. Overall survival and adverse events of patients treated with RVS in the aftercare period were determined. Results. On October 21, 2008, a total of 26 patients died while the remaining 10 patients were alive with evidence of disease. The median RVS administration period was 2.7 months (95% confidence interval, 1.9-3.5). The median overall survival for the entire population was 10.9 months (95% confidence interval, 5.6-16.1) and 1-year survival rate was 44.4%, which is compatible with external controls. By survival analysis using Cox proportional hazards model, the performance status and the prior chemotherapy regimen number significantly affected overall survival. Adverse reactions to the RVS treatment were mostly mild and self-limiting. Conclusion. Complementary treatment with the standardized RVS extract might be beneficial for patients with mCRC, since it positively affected overall survival without significant side effects. This study suggests that RVS could be a natural anticancer agent candidate for the treatment of colorectal adenocarcinoma.
Falls in Persons With Spinal Cord Injury: Validity and Reliability of the Berg Balance Scale
Authors: Wirz Markus , Müller Roland , Bastiaenen Caroline
Published: August 2009

Background. Persons with spinal cord injury who are able to walk are at risk for falls. Objective . The objectives were to investigate if the Berg Balance Scale (BBS) can discriminate those with a propensity to fall; to determine whether the BBS is associated with mobility measures, fear of falling, and muscle strength; and to assess interobserver reliability. Methods. The measurement tools used were the BBS, the Spinal Cord Independence Measure, the Falls Efficacy Scale (FES-I), the Walking Index for Spinal Cord Injury, the 10-m walk test, and the standard neurological classification including motor scores (MS). Falls were recorded retrospectively for the previous month and prospectively for the subsequent 4 months. To determine interobserver reliability, BBS performance was videotaped and analyzed by additional physical therapists. Associations between BBS and the number of falls, measures of mobility, FES-I, and MS were calculated using Spearman correlations. The interobserver reliability was quantified using Kendall’s coefficient of concordance and intraclass correlation coefficients (ICCs). Results. Forty-two participants were included of whom 26 sustained 1 or more falls. BBS performance correlated with measures of mobility, FES-I, and MS ( rs = -.83 to .93; P < .001) but not with the number of falls ( rs = -.17; P = .28). The interobserver reliability was excellent, both for single items (.84-.98, P < .001) and for the total score (ICC = .95; 95% confidence interval = 0.910-0.975). Conclusions. The BBS proved to be reliable and to relate well with other mobility measures, fear of falling, and muscle strength. However, it was unable discriminate between people who did fall and people who did not fall.
Subculture, style, chavs and consumer capitalism: Towards a critical cultural criminology of youth
Authors: Martin Greg
Published: August 2009

This article examines current controversies in youth culture studies and relates them to recent developments in ‘cultural criminology’. On the one hand, post-subcultural theorists argue the concept of ‘subculture’ is redundant and obsolete and should be replaced by less bounded or rigid concepts, such as ‘neo-tribe’, which supposedly better capture the essence of identity formation and lifestyle choices in postmodern consumer culture. On the other hand, critics argue postmodern subcultural theory is an apology for consumerism and posit the continuing relevance of social class as an analytical category. In the last decade or so, and unbeknownst to those working in youth culture studies, cultural criminologists have attempted to adapt ‘traditional’ subcultural theory to new experiences of ‘transgression’ which now emerge in the transition to late modernity. Cultural criminology nevertheless has poststructural tendencies. By examining the ‘chav’ phenomenon in Britain as well as research in youth transitions under ‘consumer capitalism’, this article argues that ‘old’ theories and concepts, such as subculture, ought not be so readily disregarded and discarded, and that the notion of ‘style’ remains applicable to some young people who are marginalized and disadvantaged. The article thus proposes a ‘critical cultural criminology’ of youth.
Modern serial killers
Authors: Haggerty Kevin D.
Published: August 2009

The study of serial killing has been dominated by an individualized focus on the aetiology and biography of particular offenders. As such, it has tended to downplay the broader social, historical and cultural context of such acts. This article addresses this lacuna by arguing that serial killers are distinctively modern. It highlights six modern phenomena related to serial killing: (a) the mass media and the attendant rise of a celebrity culture; (b) a society of strangers; (c) a type of mean/ends rationality that is largely divorced from value considerations; (d) cultural frameworks of denigration which tend to implicitly single out some groups for greater predation; (e) particular opportunity structures for victimization; and finally (f) the notion that society can be engineered. Combined, these factors help to pattern serial killing in modernity’s own self-image, with modernity setting the parameters of what it means to be a serial killer, and establishing the preconditions for serial murder to emerge in its distinctive contemporary guise.
Physicians’ participatory decision-making and quality of diabetes care processes and outcomes: results from the triad study
Authors: Heisler M. , Tierney E. , Ackermann R.T. , Tseng C. , Venkat Narayan K.M. , Crosson J. , Waitzfelder B. , Safford M.M. , Duru K. , Herman W.H. , Kim C.
Published: August 2009

Objectives: In participatory decision-making (PDM), physicians actively engage patients in treatment and other care decisions. Patients who report that their physicians engage in PDM have better disease self-management and health outcomes. We examined whether physicians’ diabetes-specific treatment PDM preferences as well as their self-reported practices are associated with the quality of diabetes care their patients receive.

Methods: 2003 cross-sectional survey and medical record review of a random sample of diabetes patients (n = 4198) in 10 US health plans across the country and their physicians (n = 1217). We characterized physicians’ diabetes care PDM preferences and practices as ‘no patient involvement,’ ‘physician-dominant,’ ‘shared,’ or ‘patient-dominant’ and conducted multivariate analyses examining their effects on the following: (1) three diabetes care processes (annual hemoglobin A1c test; lipid test; and dilated retinal exam); (2) patients’satisfaction with physician communication; and (3) whether patients’ A1c, systolic blood pressure (SBP), and low-density lipoprotein cholesterol (LDL) were in control.

Results: Most physicians preferred ‘shared’ PDM (58%) rather than ‘no patient involvement’ (9%), ‘physiciandominant’ (28%) or ‘patient dominant’ PDM (5%). However, most reported practicing ‘physician-dominant’ PDM (43%) with most of their patients, rather than ‘no patient involvement’ (13%), ‘shared’ (37%) or ‘patient-dominant’ PDM (7%). After adjusting for patient and physician-level characteristics and clustering by health plan, patients of physicians who preferred ‘shared’ PDM were more likely to receive A1c tests [90% vs. 82%, AOR: 2.05, 95% CI: 1.03—3.07] and patients of physicians who preferred ‘patient-dominant’ treatment decision-making were more likely to receive lipid tests [60% vs. 50%, AOR: 1.58, 95% CI: 1.04—2.39] than those of providers who preferred ‘no patient involvement’ in treatment decision-making. There were no differences in patients’ satisfaction with their doctor’s communication or control of A1c, SBP or LDL depending on their physicians’ PDM preferences. Physicians’ self-reported PDM practices were not associated with any of the examined aspects of diabetes care in multivariate analyses.

Conclusions: Patients whose physicians prefer more patient involvement in decision-making are more likely than patients whose physicians prefer more physician-directed styles to receive some recommended risk factor screening tests, an important first step toward improved diabetes outcomes. Involving patients in treatment decision-making alone, however, appears not to be sufficient to improve biomedical outcomes.
Differential modulation of human β-defensins expression in human gingival epithelia by Porphyromonas gingivalis lipopolysaccharide with tetra- and penta-acylated lipid A structures
Authors: Lu Qian , Darveau Richard P. , Samaranayake Lakshman P. , Wang Cun-Yu , Jin Lijian
Published: August 2009

Porphyromonas gingivalis lipopolysaccharide (LPS) is a crucial virulence factor strongly involved in the development of chronic periodontitis. It displays a significant amount of lipid A structural heterogeneity, containing both tetra- (LPS1435/1449 ) and penta-acylated (LPS 1690) lipid A structures with opposing effects on E-selectin expression in human endothelial cells. Little is known about how these two isoforms of P. gingivalis LPS could differentially affect host innate immune responses in human gingival epithelia. The present study compares the modulatory effects of P. gingivalis LPS1435/1449 and LPS1690 on the expression of human β-defensins (hBDs) in the reconstituted human gingival epithelium, and examines the involvements of a panel of pattern recognition receptors in the modulatory effects concerned. It is shown that hBD-1, hBD-2 and hBD-3 mRNAs are significantly up-regulated by P. gingivalis LPS1690, but down-regulated by P. gingivalis LPS 1435/1449. Toll-like receptor (TLR) 2 and CD14 mRNAs are also differentially regulated, and the modulation of hBD-2 expression may be through the co-operation of both TLR2 and TLR4. This study suggests that P. gingivalis LPS with different lipid A structures could differentially modulate host innate immune responses in human gingival epithelia, which may be a hitherto undescribed novel pathogenic mechanism of P. gingivalis in periodontal pathogenesis.
Loss of matKRNA editing in seed plant chloroplasts
Authors: Tillich Michael , Le Sy Vinh , Schulerowitz Katrin , von Haeseler Arndt , Maier Uwe G , Schmitz-Linneweber Christian
Published: August 2009

Background

RNA editing in chloroplasts of angiosperms proceeds by C-to-U conversions at specific sites. Nuclear-encoded factors are required for the recognition of cis-elements located immediately upstream of editing sites. The ensemble of editing sites in a chloroplast genome differs widely between species, and editing sites are thought to evolve rapidly. However, large-scale analyses of the evolution of individual editing sites have not yet been undertaken.

Results

Here, we analyzed the evolution of two chloroplast editing sites, matK-2 and matK-3, for which DNA sequences from thousands of angiosperm species are available. Both sites are found in most major taxa, including deep-branching families such as the nymphaeaceae. However, 36 isolated taxa scattered across the entire tree lack a C at one of the two matK editing sites. Tests of several exemplary species from this in silico analysis of matK processing unexpectedly revealed that one of the two sites remain unedited in almost half of all species examined. A comparison of sequences between editors and non-editors showed that specific nucleotides co-evolve with the C at the matK editing sites, suggesting that these nucleotides are critical for editing-site recognition.

Conclusion

(i) Both matK editing sites were present in the common ancestor of all angiosperms and have been independently lost multiple times during angiosperm evolution.

(ii) The editing activities corresponding to matK-2 and matK-3 are unstable.

(iii) A small number of third-codon positions in the vicinity of editing sites are selectively constrained independent of the presence of the editing site, most likely because of interacting RNA-binding proteins.
Persistence of colicinogenic Escherichia coli in the mouse gastrointestinal tract
Authors: Gillor Osnat , Giladi Itamar , Riley Margaret A
Published: August 2009

Background

The ability of a bacterial strain to competitively exclude or displace other strains can be attributed to the production of narrow spectrum antimicrobials, the bacteriocins. In an attempt to evaluate the importance of bacteriocin production for Escherichia coli strain residence in the gastrointestinal tract, a murine model experimental evolution study was undertaken.

Results

Six colicin-producing, yet otherwise isogenic, E. coli strains were administered and established in the large intestine of streptomycin-treated mice. The strains' persistence, population density, and doubling time were monitored over a period of 112 days. Early in the experiment only minor differences in population density between the various colicin-producing and the non-producing control strains were detected. However, over time, the density of the control strains plummeted, while that of the colicin-producing strains remained significantly higher (F(7,66) = 2.317; P < 0.0008).

Conclusion

The data presented here support prior claims that bacteriocin production may play a significant role in the colonization of E. coli in the gastrointestinal tract. Further, this study suggests that the ability to produce bacteriocins may prove to be a critical factor in determining the success of establishing probiotic E. coli in the gastrointestinal tract of humans and animals.
A single amino acid change (Y318F) in the L-arabitol dehydrogenase (LadA) from Aspergillus niger results in a significant increase in affinity for D-sorbitol
Authors: Rutten Lucy , Ribot Cecile , Trejo-Aguilar Blanca , Wösten Han AB , de Vries Ronald P
Published: August 2009

Background

L-arabitol dehydrogenase (LAD) and xylitol dehydrogenase (XDH) are involved in the degradation of L-arabinose and D-xylose, which are among the most abundant monosaccharides on earth. Previous data demonstrated that LAD and XDH not only differ in the activity on their biological substrate, but also that only XDH has significant activity on D-sorbitol and may therefore be more closely related to D-sorbitol dehydrogenases (SDH). In this study we aimed to identify residues involved in the difference in substrate specificity.

Results

Phylogenetic analysis demonstrated that LAD, XDH and SDH form 3 distinct groups of the family of dehydrogenases containing an Alcohol dehydrogenase GroES-like domain (pfam08240) and likely have evolved from a common ancestor. Modelling of LadA and XdhA of the saprobic fungus Aspergillus niger on human SDH identified two residues in LadA (M70 and Y318), that may explain the absence of activity on D-sorbitol. While introduction of the mutation M70F in LadA of A. niger resulted in a nearly complete enzyme inactivation, the Y318F resulted in increased activity for L-arabitol and xylitol. Moreover, the affinity for D-sorbitol was increased in this mutant.

Conclusion

These data demonstrates that Y318 of LadA contributes significantly to the substrate specificity difference between LAD and XDH/SDH.
Comparative gene expression profiles between heterotic and non-heterotic hybrids of tetraploid Medicago sativa
Authors: Li Xuehui , Wei Yanling , Nettleton Dan , Brummer E Charles
Published: August 2009

Background

Heterosis, the superior performance of hybrids relative to parents, has clear agricultural value, but its genetic control is unknown. Our objective was to test the hypotheses that hybrids expressing heterosis for biomass yield would show more gene expression levels that were different from midparental values and outside the range of parental values than hybrids that do not exhibit heterosis.

Results

We tested these hypotheses in threeMedicago sativa(alfalfa) genotypes and their three hybrids, two of which expressed heterosis for biomass yield and a third that did not, using AffymetrixM. truncatulaGeneChip arrays. Alfalfa hybridized to approximately 47% of theM. truncatulaprobe sets. Probe set signal intensities were analyzed using MicroArray Suite v.5.0 (MAS) and robust multi-array average (RMA) algorithms. Based on MAS analysis, the two heterotic hybrids performed similarly, with about 27% of genes showing differential expression among the parents and their hybrid compared to 12.5% for the non-heterotic hybrid. At a false discovery rate of 0.15, 4.7% of differentially expressed genes in hybrids (~300 genes) showed nonadditive expression compared to only 0.5% (16 genes) in the non-heterotic hybrid. Of the nonadditively expressed genes, approximately 50% showed expression levels that fell outside the parental range in heterotic hybrids, but only one of 16 showed a similar profile in the non-heterotic hybrid. Genes whose expression differed in the parents were three times more likely to show nonadditive expression than genes whose parental transcript levels were equal.

Conclusion

The higher proportions of probe sets with expression level that differed from the parental midparent value and that were more extreme than either parental value in the heterotic hybrids compared to a non-heterotic hybrid were also found using RMA. We conclude that nonadditive expression of transcript levels may contribute to heterosis for biomass yield in alfalfa.
Profile of hematological abnormalities of Indian HIV infected individuals
Authors: Dikshit Byomakesh , Wanchu Ajay , Sachdeva Ravinder Kaur , Sharma Aman , Das Reena
Published: August 2009

Background

Hematological abnormalities are a common complication of HIV infection. These abnormalities increase as the disease advances. Bone marrow abnormalities occur in all stages of HIV infection.

Methods

Two hundred HIV infected individual were screened for hematological abnormalities from March 2007–March 2008. Absolute CD4 cell count analysis was carried out by flowcytometry. Depending on the results of the primary screening further investigations were performed, like iron studies, hemolytic work up, PNH work up and bone marrow evaluation. Other investigations included coagulation profile, urine analysis, blood culture (bacterial, fungal, mycobacterial), serology for Epstein Barr virus (EBV), Cytomegalovirus (CMV), Hepatitis B and C, and Parvo B19 infection.

Results

The most common hematological abnormality was anemia, seen in 65.5% (131/200) patients. Iron deficiency anemia was seen in 49.2% (/200) cases while anemia of chronic disease occurred in 50.7% (/200) cases. Bone marrow evaluation was carried out in 14 patients out of which staging marrow was performed in 2 cases of non-Hodgkin's lymphoma (NHL) and did not show any bone marrow infiltration. In remaining12 cases bone marrow was done for evaluation of pancytopenia. Among patients with pancytopenia 50% (6/12) showed granulomas (4 were positive for AFB, 2 were positive for fungal cryptococci), 25% (3/12) showed hemophagocytosis. There was a strong negative correlation between anemia and CD4 counts in this study. Thrombocytopenia was seen in 7% (14/200) cases and had no significant correlation with CD4 counts. No patient had absolute neutrophil count (ANC) < 800 cells/μL. No case of coagulation abnormalities was found.

Conclusion

Anemia in HIV patients can be a good clinical indicator to predict and access the underlying immune status. Patients should be investigated for hematological manifestations and appropriate steps should be taken to identify and treat the reversible factors.
Impact of cigarette smoking on the relationship between body mass index and coronary heart disease: a pooled analysis of 3264 stroke and 2706 CHD events in 378579 individuals in the Asia Pacific region
Authors:   The Asia Pacific Cohort Studies Collaboration
Published: August 2009

Background

Elevated levels of body mass index (BMI) and smoking are well established lifestyle risk factors for coronary heart disease (CHD) and stroke. If these two risk factors have a synergistic relationship, rigorous lifestyle modification may contribute to greater reduction in cardiovascular burden than previously expected.

Methods

A pooled analysis of individual participant data from 38 cohorts, involving 378,579 participants. Hazards ratios (HRs) and 95% confidence intervals (CIs) for BMI by cigarette smoking status were estimated using Cox proportional hazard models.

Results

During a mean follow-up of 3.8 years, 2706 CHD and 3264 strokes were recorded. There was a log-linear, positive relationship of BMI with CHD and stroke in both smokers and non-smokers with evidence of a synergistic effect of smoking on the association between BMI and CHD only: HRs (95% CIs) associated with a 2 kg/m2higher BMI were 1.13 (1.10 – 1.17) in current smokers and 1.09 (1.06 – 1.11) in non-smokers (p-value for interaction = 0.04).

Conclusion

Smoking amplifies the positive association between BMI and CHD but not stroke. If confirmed, these results suggest that effective strategies that target smoking cessation and weight loss are likely to have a greater impact than anticipated on reducing the burden of CHD.
Archaeosomes made of Halorubrum tebenquichensetotal polar lipids: a new source of adjuvancy
Authors: Gonzalez Raul O , Higa Leticia H , Cutrullis Romina A , Bilen Marcos , Morelli Irma , Roncaglia Diana I , Corral Ricardo S , Morilla Maria Jose , Petray Patricia B , Romero Eder L
Published: August 2009

Background

Archaeosomes (ARC), vesicles prepared from total polar lipids (TPL) extracted from selected genera and species from the Archaea domain, elicit both antibody and cell-mediated immunity to the entrapped antigen, as well as efficient cross priming of exogenous antigens, evoking a profound memory response. Screening for unexplored Archaea genus as new sources of adjuvancy, here we report the presence of two new Halorubrum tebenquichense strains isolated from grey crystals (GC) and black mood (BM) strata from a littoral Argentinean Patagonia salt flat. Cytotoxicity, intracellular transit and immune response induced by two subcutaneous (sc) administrations (days 0 and 21) with BSA entrapped in ARC made of TPL either form BM (ARC-BM) and from GC (ARC-GC) at 2% w/w (BSA/lipids), to C3H/HeN mice (25 μg BSA, 1.3 mg of archaeal lipids per mouse) and boosted on day 180 with 25 μg of bare BSA, were determined.

Results

DNA G+C content (59.5 and 61.7% mol BM and GC, respectively), 16S rDNA sequentiation, DNA-DNA hybridization, arbitrarily primed fingerprint assay and biochemical data confirmed that BM and GC isolates were two non-previously described strains of H. tebenquichense. Both multilamellar ARC mean size were 564 ± 22 nm, with -50 mV zeta-potential, and were not cytotoxic on Vero cells up to 1 mg/ml and up to 0.1 mg/ml of lipids on J-774 macrophages (XTT method). ARC inner aqueous content remained inside the phago-lysosomal system of J-774 cells beyond the first incubation hour at 37°C, as revealed by pyranine loaded in ARC. Upon subcutaneous immunization of C3H/HeN mice, BSA entrapped in ARC-BM or ARC-GC elicited a strong and sustained primary antibody response, as well as improved specific humoral immunity after boosting with the bare antigen. Both IgG1 and IgG2a enhanced antibody titers could be demonstrated in long-term (200 days) recall suggesting induction of a mixed Th1/Th2 response.

Conclusion

We herein report the finding of new H. tebenquichense non alkaliphilic strains in Argentinean Patagonia together with the adjuvant properties of ARC after sc administration in mice. Our results indicate that archaeosomes prepared with TPL from these two strains could be successfully used as vaccine delivery vehicles.
Application of the indirect fluorescent antibody assay in the study of malaria infection in the Yangtze River Three Gorges Reservoir, China
Authors: Duo-Quan Wang , Lin-Hua Tang , Zhen-Cheng Gu , Xiang Zheng , Man-Ni Yang
Published: August 2009

Background

China Yangtze Three Gorges Project (TGP) is one of the biggest construction projects in the world. The areas around the Three Gorge Dam has a history of tertian malaria and subtertian malaria epidemic, but there are no overall data about malaria epidemics before the completion of the project. The objective of this study was to get a reliable baseline on malaria infection in the Yangtze River Three Gorges reservoir area and to provide reference data for future studies about the impact of the project on malaria epidemics.

Methods

Two surveys of malaria infection were carried out in area, at six-month intervals in May and October 2008. About 3,600 dual specimens blood film samples for parasite diagnosis and filter paper blood spots for serology (using the immunofluorescence antibody test) were collected from the general population, including school populations, whenever possible.

Results

The overall percentage of positive response of the same population during post-transmission periods was about twice (1.40/0.72) of that in pre-transmission. Positive individuals under 15 years of age were detected in all the localities.

Conclusion

A certain extent of malaria infection existed in this area. Additional studies are needed to determine the length of malaria experience, and chemotherapeutic intervention as well as the distribution of main vectors for transmission in this area.
Refractoriness of hepatitis C virus internal ribosome entry site to processing by Dicer in vivo
Authors: Ouellet Dominique L , Plante Isabelle , Boissonneault Vincent , Ayari Cherifa , Provost Patrick
Published: August 2009

Background

Hepatitis C virus (HCV) is a positive-strand RNA virus harboring a highly structured internal ribosome entry site (IRES) in the 5' nontranslated region of its genome. Important for initiating translation of viral RNAs into proteins, the HCV IRES is composed of RNA structures reminiscent of microRNA precursors that may be targeted by the host RNA silencing machinery.

Results

We report that HCV IRES can be recognized and processed into small RNAs by the human ribonuclease Dicer in vitro. Furthermore, we identify domains II, III and VI of HCV IRES as potential substrates for Dicer in vitro. However, maintenance of the functional integrity of the HCV IRES in response to Dicer overexpression suggests that the structure of the HCV IRES abrogates its processing by Dicer in vivo.

Conclusion

Our results suggest that the HCV IRES may have evolved to adopt a structure or a cellular context that is refractory to Dicer processing, which may contribute to viral escape of the host RNA silencing machinery.
A Dictyostelium chalone uses G proteins to regulate proliferation
Authors: Bakthavatsalam Deenadayalan , Choe Jonathan M , Hanson Nana E , Gomer Richard H
Published: August 2009

Background

Several studies have shown that organ size, and the proliferation of tumor metastases, may be regulated by negative feedback loops in which autocrine secreted factors called chalones inhibit proliferation. However, very little is known about chalones, and how cells sense them. We previously identified two secreted proteins, AprA and CfaD, which act as chalones in Dictyostelium. Cells lacking AprA or CfaD proliferate faster than wild-type cells, and adding recombinant AprA or CfaD to cells slows their proliferation.

Results

We show here that cells lacking the G protein components Galpha8, Galpha9, and Gbeta proliferate faster than wild-type cells despite secreting normal or high levels of AprA and CfaD. Compared with wild-type cells, the proliferation of galpha8

-
, galpha9

-
and gbeta

-
cells are only weakly inhibited by recombinant AprA (rAprA). Like AprA and CfaD, Galpha8 and Gbeta inhibit cell proliferation but not cell growth (the rate of increase in mass and protein per nucleus), whereas Galpha9 inhibits both proliferation and growth. galpha8

-
cells show normal cell-surface binding of rAprA, whereas galpha9

-
and gbeta

-
cells have fewer cell-surface rAprA binding sites, suggesting that Galpha9 and Gbeta regulate the synthesis or processing of the AprA receptor. Like other ligands that activate G proteins, rAprA induces the binding of [3H]GTP to membranes, and GTPgammaS inhibits the binding of rAprA to membranes. Both AprA-induced [3H]GTP binding and the GTPgammaS inhibition of rAprA binding require Galpha8 and Gbeta but not Galpha9. Like aprA

-
cells, galpha8

-
cells have reduced spore viability.

Conclusion

This study shows that Galpha8 and Gbeta are part of the signal transduction pathway used by AprA to inhibit proliferation but not growth in Dictyostelium, whereas Galpha9 is part of a differealnt pathway that regulates both proliferation and growth, and that a chalone signal transduction pathway uses G proteins.
Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin
Authors: Almén Markus Sällman , Nordström Karl JV , Fredriksson Robert , Schiöth Helgi B
Published: August 2009

Background

Membrane proteins form key nodes in mediating the cell's interaction with the surroundings, which is one of the main reasons why the majority of drug targets are membrane proteins.

Results

Here we mined the human proteome and identified the membrane proteome subset using three prediction tools for alpha-helices: Phobius, TMHMM, and SOSUI. This dataset was reduced to a non-redundant set by aligning it to the human genome and then clustered with our own interactive implementation of the ISODATA algorithm. The genes were classified and each protein group was manually curated, virtually evaluating each sequence of the clusters, applying systematic comparisons with a range of databases and other resources. We identified 6,718 human membrane proteins and classified the majority of them into 234 families of which 151 belong to the three major functional groups: receptors (63 groups, 1,352 members), transporters (89 groups, 817 members) or enzymes (7 groups, 533 members). Also, 74 miscellaneous groups with 697 members were determined. Interestingly, we find that 41% of the membrane proteins are singlets with no apparent affiliation or identity to any human protein family. Our results identify major differences between the human membrane proteome and the ones in unicellular organisms and we also show a strong bias towards certain membrane topologies for different functional classes: 77% of all transporters have more than six helices while 60% of proteins with an enzymatic function and 88% receptors, that are not GPCRs, have only one single membrane spanning α-helix. Further, we have identified and characterized new gene families and novel members of existing families.

Conclusion

Here we present the most detailed roadmap of gene numbers and families to our knowledge, which is an important step towards an overall classification of the entire human proteome. We estimate that 27% of the total human proteome are alpha-helical transmembrane proteins and provide an extended classification together with in-depth investigations of the membrane proteome's functional, structural, and evolutionary features.
Acyl peptide hydrolase degrades monomeric and oligomeric amyloid-beta peptide
Authors: Yamin Rina , Zhao Cheng , O'Connor Peter B , McKee Ann C , Abraham Carmela R
Published: August 2009

Background

The abnormal accumulation of amyloid-beta peptide is believed to cause malfunctioning of neurons in the Alzheimer's disease brain. Amyloid-beta exists in different assembly forms in the aging mammalian brain including monomers, oligomers, and aggregates, and in senile plaques, fibrils. Recent findings suggest that soluble amyloid-beta oligomers may represent the primary pathological species in Alzheimer's disease and the most toxic form that impairs synaptic and thus neuronal function. We previously reported the isolation of a novel amyloid-beta-degrading enzyme, acyl peptide hydrolase, a serine protease that degrades amyloid-beta, and is different in structure and activity from other amyloid-beta-degrading enzymes.

Results

Here we report the further characterization of acyl peptide hydrolase activity using mass spectrometry. Acyl peptide hydrolase cleaves the amyloid-beta peptide at amino acids 13, 14 and 19. In addition, by real-time PCR we found elevated acyl peptide hydrolase expression in brain areas rich in amyloid plaques suggesting that this enzyme's levels are responsive to increases in amyloid-beta levels. Lastly, tissue culture experiments using transfected CHO cells expressing APP751 bearing the V717F mutation indicate that acyl peptide hydrolase preferentially degrades dimeric and trimeric forms of amyloid-beta.

Conclusion

These data suggest that acyl peptide hydrolase is involved in the degradation of oligomeric amyloid-beta, an activity that, if induced, might present a new tool for therapy aimed at reducing neurodegeneration in the Alzheimer's brain.
A gene expression profile for detection of sufficient tumour cells in breast tumour tissue: microarray diagnosis eligibility
Authors: Roepman Paul , Schuurman Arenda , Delahaye Leonie JMJ , Witteveen Anke T , Floore Arno N , Glas Annuska M
Published: August 2009

Background

Microarray diagnostics of tumour samples is based on measurement of prognostic and/or predictive gene expression profiles. Typically, diagnostic profiles have been developed using bulk tumour samples with a sufficient amount of tumour cells (usually >50%). Consequentially, a diagnostic results depends on the minimal percentage of tumour cells within a sample. Currently, tumour cell percentage is assessed by conventional histopathological review. However, even for experienced pathologists, such scoring remains subjective and time consuming and can lead to ambiguous results.

Methods

In this study we investigated whether we could use transcriptional activity of a specific set of genes instead of histopathological review to identify samples with sufficient tumour cell content. Genome-wide gene expression measurements were used to develop a transcriptional gene profile that could accurately assess a sample's tumour cell percentage.

Results

Supervised analysis across 165 breast tumour samples resulted in the identification of a set of 13 genes which expression correlated with presence of tumour cells. The developed gene profile showed a high performance (AUC 0.92) for identification of samples that are suitable for microarray diagnostics. Validation on 238 additional breast tumour samples indicated a robust performance for correct classification with an overall accuracy of 91 percent and a kappa score of 0.63 (95%CI 0.47–0.73).

Conclusion

The developed 13-gene profile provides an objective tool for assessment whether a breast cancer sample contains sufficient tumour cells for microarray diagnostics. It will improve the efficiency and throughput for diagnostic gene expression profiling as it no longer requires histopathological analysis for initial tumour percentage scoring. Such profile will also be very use useful for assessment of tumour cell percentage in biopsies where conventional histopathology is difficult, such as fine needle aspirates.