The magnitude of the AIDS-orphaned children crisis in sub-Saharan Africa has so overstretched the resource of most families that the collapse of fostering in the sub-region seems imminent , fueling the need for a complementary/alternative care. This paper examines the probability of the natural mentoring care to ameliorate distress mental health in children orphaned by AIDS.952 children, mean age about 14 years, from local community schools and child-care centers in Kampala (Uganda) and Mafikeng/Klerksdorp (South Africa) towns participated in the study. The design has AIDS-orphaned group (n = 373) and two control groups: Other-causes orphaned (n = 287) and non-orphaned (n = 290) children. We use measures of child abuse, depression, social discrimination, anxiety, parental/foster care, self-esteem, and social support to estimate mental health. Natural mentoring care is measured with the Ragins and McFarlin (1990) Mentor Role Instrument as adapted.AIDS-orphaned children having a natural mentor showed significant decreased distress mental health factors. Similar evidence was not observed in the control groups. Also being in a natural mentoring relationship inversely related to distress mental health factors in the AIDS-orphaned group, in particular. AIDS-orphaned children who scored high mentoring relationship showed significant lowest distress mental health factors that did those who scored moderate and low mentoring relationship.Natural mentoring care seems more beneficial to ameliorate distress mental health in AIDS-orphaned children  than in children in the control groups. Orphan children tend to manifest more depression , personaChitiyo, Changara, and Chitiyo  suggest "An especially important and distinctive characteristic of HIV/AIDS in regard to orphaning is that AIDS is more likely than other causes of death to create double orphans. With HIV/AIDS, if one parent is infected there is a higher probability that the other parent is or will become infected and that both will eventually die .... Surveys consistently show that double orphans are more disadvantaged than single orphans" (p.11).Subbarao, Mattimore, and Plangemann  identifyThe purpose of the present study is to estimate the association of being in a natural mentoring relationship care with mental health in AIDS-orphaned children. Natural mentorship is different from organizational mentoring  which isNatural mentoring care is different from fostering care, in which the child tends to emigrate from her biological home to the fosterer's. In natural mentorship such dislocation is not required. The dyad relationship may not be conflict-free, but a range of its psychosocial benefits such as risk behavior control , personaUN Convention on the Rights of the Child: its relevance for social scientists [There was a pilot preceding the present study to validate the study instruments in the African countries. In keeping with the ientists , the stuientists .We visited nine community schools, and six NGO child support centers at Mafikeng/Klerksdorp areas  and Kampala district (Uganda) to conduct the survey. The UN definition of orphanhood as the loss of one or both parents  is adoptAIDS-orphaned group: We ask: Is your father/mother living (Yes/No)? If not living, what is the cause of death? Response choices: "1. HIV/AIDS, 2. War, 3. Others, 4. Don't know." Children who check HIV/AIDS are assigned to this group (n = 373). Owing to the shame associated with HIV infection, children may feign ignorance of HIV-related cause of parent's death [essential characteristics of AIDS orphaning [Other-causes orphaned group: Children who check "war/others" are assigned to this group (n = 289). Those whose parents are living form the non-orphan group (n = 290).The study participants are 952 children  in 3 groups: AIDS-, other-causes, and non-orphaned children. 's death ,28. We arphaning . A neglirphaning  accountsMental health is estimated by the combination of anxiety, depression, social discrimination, child abuse, self-esteem, social support, and parental/foster care scales.anxiety. The 6-item subscale  negatively  correlates with Rosenberg's Self Esteem, and positively  with the CES-DC  [The Anxiety subscale of the renowned General Health Questionnaire (GHQ-28 (30)) is utilized to measure hildren)  as adaptDepression is estimated with the CES-DC [e CES-DC . The tese CES-DC . We utilWe adapt 6-items  from the 15-item Schwarzer and Schulz  ReceivedThe Rosenberg Self-Esteem  Scale thcompared to other people around you, do you: Feel differently treated? Feel unfairly treated? Made to feel inferior? Prevented from doing things others are allowed to do? People behave as though they are afraid of you? The measure appreciably correlate with depression , social support  and child abuse .We utilize the modified Detroit Area Study Measure of Discrimination  to estimWe ask 4 questions, each of which estimates the physical, verbal, sexual, and labor dimensions of child abuse : Are youParental/foster care is measured with the Parental Bonding Instrument (PBI) [nt (PBI) . The 25-nt (PBI) . We utilDistress mental health factors  is the summation of child abuse, depression, social discrimination, and anxiety scores. Positive mental health factors  is the sum of parental/foster care, perceived social support, and self-esteem scores.1--3 meeting frequencies are classified as being in a mentoring relationship. These children (n = 714) rate the Ragins' Mentor Role Instrument (MRI) that estimates parental, modeling, counseling, friendship, and support roles by mentors to mentees. Children not in a mentoring relationship form the control group. The 33-item MRI [formal mentor roles , and utilize the 5 informal roles  each of which is estimated with 2 items on a 4-point likert response score of 0 (never) to 3 . The internal stability of the adapted MRI is alpha = .91, which is similar to the value found by Ragins and Cotton [In consonance with the operational definition of natural mentoring ,25, we aitem MRI  measure d Cotton . The inslow (scores 0-10), moderate (11-20), and high (21-30) and examined their performance on mental health in the 3 groups  from those who do not n = 234) to perform the ANOVA of distress mental health between them in each of the 3 groups  of the children are aged 10 to 17 years. Grand mean age is 13.59 years (SD = 2.34). There are no significant difference (F = .259(2), p = .77) of age in the groups: Mean = 13.54 (SD = 2.52), 13.55 (SD = 2.11), and 13.67 (SD = 2.32) for AIDS-, other-causes, and non-orphaned children, respectively. No significant educational level variance (F = 1.96(2), p = .14) in the 3 groups is observed. There is no gender influence on mental health outcomes. Male and female children scored similar levels of distress/positive mental health outcomes in the study and control groups.low mentoring relationship show significant high distress mental health factors than do moderate and high mentoring AIDS-orphaned children  than did their counterparts not in a mentoring relationship. Similar significant association are unobserved in the control groups Figure . Also naen Table . In the en Table . In bothWickrama, Lorenz, and Conger  report thigh impact of mentoring relationship score significant lower distress mental health factors than do AIDS-orphans who score moderate and low mentorship. In the control groups, the variances are weak, suggesting that natural mentoring relationship may be stronger to ameliorate distress mental health factors in AIDS-orphaned children, many of whom have no parents.In most domains of the distress mental health construct, having a natural mentor show significant inverse association with distress mental health factors in the AIDS-orphaned group. Children orphaned by AIDS who score Natural mentoring relationship seems more psychosocially beneficial to orphans than to non-orphans. For example, whereas an inverse association of mentoring and distress health is seen in the two orphan groups, the reverse seems the case for non-orphaned children. In this group, high mentoring shows tendencies to elicit high distress mental health factors Table . The reaAge shows inverse relationship to natural mentorship in all the groups. Younger children significantly engage in higher mentoring relationship than do older children. These younger children significantly regarded their mentors as a father, mother or role model than do older children.Ideally, natural mentors should be biologically unrelated, nonparent others. But in the traditional African social environment, a thin line may exist between natural mentors and extended family kins. Most of the natural mentors in the present study are extended family kins rather than non-family members. Natural mentorship does not require the mentee to live with the mentor as the case in fostering. The scenario may mean greater independence for the protégé and lesser social burden for the mentor. Natural mentors have been used to strengthen psychosocial well-being in child-headed households, who are victims of intra-state genocide . In chilover a time may produce a more meaningful result.Our study design is cross-sectional. Perhaps an anthropological design that participatorily investigates the mentoring behaviors of the mentee and mentor We are unable to absolutely vouch for the AIDS-orphaned category. Death certificates are unreliable medical data  in most The natural mentors in the study are not interviewed. We posit that the omission may not adversely affect the study outcome. If the child rates the social milieu between her and her natural mentor as positive, it seems likely that the natural mentor may so positively perceive the social environment.The authors declare that they have no competing interests.FNO and TM jointly conceptualized and concretized the study. Both authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-244X/10/6/prepub


Streptococcus pneumoniae pneumonia.Disturbed alveolar fibrin turnover is a cardinal feature of severe pneumonia. Clinical studies suggest that natural inhibitors of coagulation exert lung-protective effects via anticoagulant and possibly also anti-inflammatory pathways. Intravenous infusion of the natural anticoagulants increases the risk of bleeding. Local administration may allow for higher treatment dosages and increased local efficacy while at the same time reducing the risk of bleeding. We evaluated the effect of nebulized anticoagulants on pulmonary coagulopathy and inflammation in a rat model of in vivo laboratory study rats were challenged intratracheally with S. pneumoniae, inducing pneumonia, and randomized to treatment with normal saline (placebo), recombinant human activated protein C (rh-APC), plasma-derived antithrombin (AT), heparin or danaparoid, by means of nebulization.In this randomized controlled S. pneumoniae infection increased pulmonary levels of thrombin-antithrombin complexes and fibrin degradation products. All nebulized anticoagulants significantly limited pulmonary coagulopathy. None of the agents except danaparoid resulted in changes in systemic coagulopathy. Treatment with plasma-derived AT reduced outgrowth of S. pneumoniae and histopathologic damage in lungs. In vitro experiments confirmed outgrowth was reduced in bronchoalveolar lavage fluid (BALF) from rats treated with plasma-derived AT compared with placebo. Neutralizing of cationic components in BALF diminished the inhibitory effects on bacterial outgrowth of BALF, suggesting a role for cationic antimicrobial proteins.S. pneumoniae pneumonia in rats while only danaparoid affects systemic coagulation. Nebulized plasma-derived AT reduces bacterial outgrowth and exerts significant lung-protective effects.Nebulization of anticoagulants attenuates pulmonary coagulopathy during  Pulmonary coagulopathy is a hallmark of pneumonia -4 and otStreptococcus pneumoniae in rats [We recently demonstrated that systemic anticoagulant treatment attenuates pulmonary coagulopathy in pneumonia caused by  in rats . IntraveThe Institutional Animal Care and Use Committee of the Academic Medical Center approved all experiments. All animals were handled in accordance with the guidelines prescribed by the Dutch legislation and the International Guidelines on protection, care, and handling of laboratory animals.6 colony-forming units (CFU) of S. pneumoniae  as described previously [Pneumonia was induced in male Sprague-Dawley rats  by intratracheal instillation of 5 × 10Rats were randomized to placebo  or treatment with 5000 μg/kg rh-aPC , Eli Lilly, Indianapolis, IN, USA), 500 units/kg plasma-derived AT , 1000 IU/kg heparin  or 250 anti-Xa E/kg danaparoid . Healthy animals without pneumonia served as controls (n = 4). Dosages and timing of study medication were determined using data from previous studies -19; the For local administration of saline or study medication we used an exposure system which allows direct exposure of nebulized agents to the noses of the animals. This system consisted of a concentric manifold connected to the necks of bottle-like restraint tubes  in which the animals were confined with their noses adjacent to the bottle necks. The bottles were detachable and the device could be disassembled  by removing the bottles and removing the manifold. The inhalation chamber was suitable to accommodate several rats at once. One extra outlet was available for measuring the pressure and atmosphere sampling inside the inhalation chamber. The aerosolized agent was supplied to the upper end of the manifold, flows adjacent to the noses of the individual animals, and then was drawn out through the bottom of the manifold. The aerosol atmosphere was generated using the AeronebPro Micropump Nebulizer . The aerosols were directed to the inhalation chamber by a constant oxygen flow (2 L/min).S. pneumoniae, rats were sacrificed and blood samples, bronchoalveolar lavage fluid (BALF) and lung tissue were obtained and analyzed as described previously [At 40 hours after challenge with eviously . For baceviously . Levels Histopathology was analyzed and scored by two investigators who were blinded for group identity. Four micrometer sections were stained with hematoxylin and eosin, and analyzed by two researchers blinded for group identity. To score lung inflammation and damage, the entire lung surface was analyzed with respect to the following variables: interstitial inflammation, endothelialitis, bronchitis, edema, pleuritis, and thrombus formation, as described previously . Each vaFor further analysis of the potential antimicrobial effect of plasma-derived AT we compared cell-free supernatants from BALF of infected animals which were treated with AT (BALF-AT) with BALF from infected placebo-treated rats (BALF-none).To assess the antimicrobial effect of BALF-AT and BALF-none samples, these samples were added to inoculum suspension and incubated. To assess direct antibacterial activity of plasma-derived AT, inoculum suspension was added to dilutions of plasma-derived AT in phosphate-buffered tryptic soy broth (TSB) medium and incubated.Innate host immune responses can lead to the expression of cationic antimicrobial peptides  . Such pein vivo data are expressed as mean ± standard deviation or median with interquartile ranges, as appropriate. Comparisons between the experimental groups and the saline-treated placebo group were performed using one-way analysis of variance (ANOVA) or Kruskal-Wallis test, followed by post-hoc Dunnett's or Dunn's tests, depending on data distribution. A P value less than 0.05 was considered statistically significant. The in vitro data was log-transformed. Then a one-way ANOVA was performed for separate time points to determine the significance of the difference in growth followed by Bonferroni post-testing. Statistical analyses were performed with SPSS 16.0  and Prism 4.0 .All S. pneumoniae, typical clinical symptoms of illness  did not occur until about 20 hours later. The animals lost an average of 9% of their bodyweight mainly due to dehydration. Two rats (one in the placebo group and one in the heparin group) died shortly after intratracheal manipulation due to laryngeal edema caused by the procedure. Rats sacrificed 40 hours after the bacterial challenge had evident bilateral macroscopic lung infiltrates.After instillation of P < 0.01 versus placebo). FDP generation was attenuated significantly by all anticoagulants (P < 0.01 versus placebo) except for heparin (P = 0.26). AT activity seemed to be increased after nebulization of rh-aPC, heparin or danaparoid, although the results were not statistically significant. Administration of AT resulted in supranormal levels of AT (P < 0.01 versus placebo and P < 0.01 versus control). Pulmonary PAA was significantly reduced with infection, with concurrently enhanced PAI-1 activity in lungs. Both rh-aPC and AT attenuated enhanced PAI-1 activity (P < 0.01 versus placebo) and AT treatment significantly increased bronchoalveolar PAA (P < 0.01 versus placebo).Bronchoalveolar levels of TATc were increased by pulmonary infection Figure . Rh-aPC,S. pneumoniae caused increased plasma levels of TATc . Compared with controls, plasma PAA was significantly decreased after intratracheal challenge with bacteria. None of the treatments altered plasma PAA.Compared with healthy controls, challenge with c Figure . This waS. pneumoniae CFU were cultured  placebo rats had bacteremia. The proportion of bacteremia was not different in rats treated with rh-aPC or plasma-derived AT, in which two of seven rats (28%) and one of seven rats (14%) developed bacteremia, respectively. The incidence of bacteremia seemed higher, although not statistically significant, in the heparin and danaparoid treated groups (three of seven rats (43%) and five of seven rats (71%), respectively).From BALF of rats treated with plasma-derived AT fewer P < 0.01; Figure P < 0.001 versus placebo; Figure S. pneumoniae, mostly attributed to neutrophil influx .At 40 hours after induction of a Figure . InterstS. pneumoniae was grown in BALF-AT samples compared with BALF-none samples after five hours  similar bacterial outgrowth curves were observed).A decrease in bacterial outgrowth was observed when s Figure . Adding S. pneumoniae. Adding SPS to the BALF-AT samples rescued the bacteria, because no decrease in CFU relative to the start of the experiment was seen after six hours.Bacterial numbers in BALF-AT in TSB medium were strongly reduced after six hours compared with the start of the experiment, which confirmed that BALF-AT had an antimicrobial effect on S. pneumoniae pneumonia in rats. Reduction of pulmonary coagulopathy with nebulized rh-aPC, heparin or danaparoid did not affect the course of pneumonia and ALI. However, reduction of pulmonary coagulopathy with treatment plasma-derived AT was associated with reduced bacterial outgrowth and pulmonary inflammation in this model. Although local administration of rh-aPC, plasma-derived AT or heparin did not affect systemic thrombin generation, nebulized danaparoid reduced systemic thrombin generation.In this series of experiments we show local anticoagulant treatment through nebulization of rh-aPC, plasma-derived AT, heparin or danaparoid to attenuate pulmonary coagulopathy in Of the investigated nebulized anticoagulant agents only plasma-derived AT treatment resulted in significant lung-protective effects, with less bacterial outgrowth and less histopathological changes. This finding confirms earlier results with systemically administered plasma-derived AT in the same model . AT is oAT may exert its protective effects through increased prostacyclin-mediated inhibition of cytokines, decreased nuclear factor-kB activation , and conS. pneumoniae pneumonia, but additional pre-clinical studies are needed to examine this hypothesis before this therapy is to be tested in patients. The coagulation system plays an important role in containing infections and certain microorganisms even induce profibrinolytic mechanisms to escape from being contained in a fibrin clot [Pseudomonas aeruginosa pneumonia in rats and mice is potentially dangerous [Our data suggest that therapy with plasma-derived AT might benefit patients with rin clot . Coagulaangerous ,35.Systemic administration of anticoagulant compounds substantially increases the risk of bleeding. In the clinical trial with rh-aPC in patients with severe sepsis, the incidence of serious bleeding was higher in the treatment group than in the placebo group (3.5% versus 2.0%) . In a raThe systemic effects on coagulation of nebulized danaparoid suggest that this agent is leaking from the pulmonary compartment into the circulation after local administration. Danaparoid is a relatively small molecule of 5.5 kDa which is more likely to leak into the circulation as compared with rh-aPC (56 kDa) or plasma-derived AT (58 kDa). Heparin is also a small molecule (8 kDa); however, it did not seem to leak into the circulation in our experiments. This may be due to binding of heparin to pulmonary endothelial cells and alveolar proteins and metabolism by heparinases . A recenOur results are in line with data from previous animal studies. With the same model we previously showed that systemic administration of rh-aPC, plasma-derived AT or heparin altered bronchoalveolar coagulation . In thatrh-aPC exerts profibrinolytic effects through inactivation of PAI-1 . In our in vitro experiments confirmed, at least in part, the findings of the in vivo animal study. Indeed, bacterial outgrowth in BALF from rats treated with plasma-derived AT was reduced when compared with BALF from placebo-treated animals. Our experiment with TSB medium with different concentrations of plasma-derived AT showed this was not caused by a direct antibacterial effect of AT. During infection, innate host immune responses can lead to the expression of cationic antimicrobial peptides [in vivo experiments might have been due to the fact that plasma-derived AT reduced total protein levels in the BALF by a factor of 10 compared with placebo-treated rats, thereby reducing the nonspecific inhibitory effects on cationic antimicrobial peptides. Neutralizing these cationic antimicrobial peptides with SPS then should attenuate the possible inhibitory effect of BALF-AT on S. pneumoniae. Indeed adding SPS to BALF-AT diminished its inhibitory effect on the outgrowth of S. pneumoniae after six hours. This finding implies that the induction of coagulation by S. pneumoniae serves to protect the bacteria against cationic antimicrobial components, most likely innate host defense peptides, and thus can be considered a novel virulence mechanism. However, because the present study treatment with rh-aPC resulted in quite similar anticoagulant and profibrinolytic effects, while at the same time not affecting bacterial outgrowth or ALI, other mechanisms than anticoagulation may be responsible for the effects of plasma-derived AT found. Details of these mechanisms are presently under investigation.The peptides . Such peOur animal study has some important limitations. First, the chosen dosages for each anticoagulant agent are determined based on data from previous studies and pilot studies combined with the efficacy of our nose-only exposure system, and possibility of dissolving each agent to an acceptable volume for nebulization. Although for all studied agents this approach lead to a significant attenuation of pulmonary coagulopathy, lower dosages may also have been sufficient. However, in order to achieve anti-inflammatory effects higher doses of these agents may be required than required for anticoagulant use.Second, due to differences between the studied drugs aerosol characteristics may differ between the treatment groups. Third, in our study the agents were first administered before induction of pneumonia. Pre-treatment models are useful when exploring novel approaches and mechanisms, post-treatment models more closely resemble the clinical situation.in vitro.The fact that the animals were treated intermittently in 6- or 24-hour intervals is another limitation to our study. Although this limited bronchoalveolar coagulation, continuous administration may have been more effective in order to achieve anti-inflammatory effects. Also, during nebulization the rats may have ingested some of the medication. Plasma-derived AT and rh-aPC are most likely to be inactivated immediately by gastric enzymes. Heparin and danaparoid may be absorbed from the digestive tract in small quantities . During Another limitation of the study is inherent to the fact that our rat model of pneumonia at best mimics the clinical situation. In our model healthy animals of the same sex, age and weight are challenged with a high dose of viable log-phase bacteria inducing pneumonia over a short period of time in a reproducible manner, and clinical factors, such as antimicrobial therapy, mechanical ventilation, fluid management and other supportive interventions are not accounted for. Despite the limitations of our model, our results are in line with previous investigations .Although the incidence of bacteremia was higher in the heparin- and danaparoid-treated groups statistical significance was not reached. Our study, however, may have been underpowered to detect effects on bacterial dissemination.in vitro investigation is that S. pneumoniae has a different behavior in vitro compared with in vivo. For example, bacteria have been observed to reach competence (i.e. obtain the ability to kill their non-competent siblings) in rich medium in vitro in early logarithmic growth, which is not seen in vivo, where nutrients are generally limited [in vitro experiments. This altered or impaired activity of competence stimulating peptide or other cationic signaling molecules might result in a change in the growth curve observed for S. pneumoniae.A limitation of our  limited ,42. As tS. pneumoniae.In conclusion, pulmonary coagulopathy with pneumonia may allow for interventions aimed at local administration of anticoagulant agents. The effects of rh-aPC, plasma-derived AT and heparin were restricted to the pulmonary compartment, nebulized danaparoid also affected systemic coagulation. AT has a lung-protective effect which seems to be related, at least in part, to an indirect role in reduction of bacterial outgrowth of • In experimental pneumococcal pneumonia in rats nebulizing anticoagulants attenuates pulmonary coagulopathy allowing a higher local dose, while reducing systemic effects.S. pneumoniae.• AT has significant lung-protective effect which seems to be related, at least in part, to an indirect role in reduction of bacterial outgrowth of • More research is required to evaluate the safety and efficacy of nebulized anticoagulants in patients.ALI: acute lung injury; ARDS: acute respiratory distress syndrome; ANOVA: analysis of variance; ARDS: acute respiratory distress syndrome; AT: antithrombin; BALF: bronchoalveolar lavage fluid; BALF-AT: BALF of infected animals which were treated with AT; BALF-none: BALF from infected placebo-treated rats; CINC-3: cytokine induced chemo chemoattractant-3; ELISA: enzyme linked immunosorbent assay; FDP: fibrinogen degradation products; IL-6: interleukin-6; MPO: myeloperoxidase; PAA: plasminogen activator activity; PAI-1: plasminogen activator inhibitor-1; rh-APC: recombinant human activated protein C; SPS: sodium polyanetholsulphonate; TATc: thrombin-antithrombin complex; TNF: tumor necrosis factor-α; TSB: tryptic soy broth.The authors declare that they have no competing interests.in vitro bacterial outgrowth studies and collected and analysed the animal data, performed statistical analysis and coordinated the drafting of the manuscript. ADC participated in collecting and analysing the animal data and participated in drafting the manuscript. BFdeR participated in the design of the in vitro bacterial outgrowth studies and performed them and participated in drafting the manuscript. APV participated in collecting and analyzing the animal data, and participated in drafting the manuscript. TvdP participated in the design of the animal study and participated in drafting the manuscript. ML participated in the design of the animal study, coordinated the analysis of coagulation and fibrinolysis markers in the animal samples and participated in drafting the manuscript. SAZ coordinated the design of the in vitro bacterial outgrowth studies and participated in drafting the manuscript. MJS participated in the design of the animal study and the in vitro bacterial outgrowth studies and participated in drafting the manuscript. All authors read and approved the final manuscript.JJH participated in the design of the animal study and the


They are overexpressed in a variety of autoimmune diseases and reportedly exist A proprietary N-terminal trimerization domain was used to produce recombinant BLyS/APRIL heterotrimers. Heterotrimer biologic activity was compared with that of BLyS and APRIL in a 4-hour signaling assay by using transmembrane activator and CAML interactor (TACI)-transfected Jurkat cells and in a 4-day primary human B-cell proliferation assay. A bead-based immunoassay was developed to quantify native heterotrimers in human sera from healthy donors (n = 89) and patients with systemic lupus erythematosus  or rheumatoid arthritis . Heterotrimer levels were compared with BLyS and APRIL homotrimer levels in a subset of these samples.50, nMol/L: BLyS, 0.02; APRIL, 0.17; heterotrimers, 4.06). The soluble receptor fusion proteins atacicept and B-cell maturation antigen (BCMA)-immunoglobulin (Ig) neutralized the activity of BLyS, APRIL, and heterotrimers in both cellular assays, whereas B-cell activating factor belonging to the TNF family receptor (BAFF-R)-Ig neutralized only the activity of BLyS. In human sera, significantly more patients with SLE had detectable BLyS , APRIL , and heterotrimer  levels compared with healthy donors. Significantly more patients with RA had detectable APRIL, but not BLyS or heterotrimer, levels compared with healthy donors . Heterotrimer levels weakly correlated with BLyS, but not APRIL, levels.The recombinant heterotrimers consisted mostly of one BLyS and two APRIL molecules. Heterotrimer signaling did not show any significant difference compared with APRIL in the TACI-Jurkat assay. Heterotrimers were less-potent inducers of B-cell proliferation than were homotrimeric BLyS or APRIL (ECRecombinant BLyS/APRIL heterotrimers have biologic activity and are inhibited by atacicept and BCMA-Ig, but not by BAFF-R-Ig. A novel immunoassay demonstrated that native BLyS/APRIL heterotrimers, as well as BLyS and APRIL homotrimers, are elevated in patients with autoimmune diseases. RosIn the serum samples from patients with SLE and RA used in this study, levels of BLyS, APRIL, and heterotrimer were elevated in patients with SLE, compared with the sera of healthy donors. The detection of a single ligand  in more than one third of the samples may reflect specific control mechanisms for these TNF family members. The available data also suggest a trend toward correlation of BLyS and heterotrimer levels in patients with SLE, although this result is based on a very small number of samples with levels above the assay LOQ for both ligands.et al. [et al. [It should be noted that, although our analysis shows that APRIL is detectable in a higher fraction of patients with SLE than in healthy controls, some controversy exists with regard to the role of APRIL in SLE. Several studies ,14,24 ha [et al. . The use [et al. ,23,35-37The present analysis of our limited RA patient cohort shows that APRIL may be specifically elevated in RA, whereas BLyS or heterotrimer levels do not appear to be increased. Others have previously reported that levels of both BLyS and APRIL in patients with RA are higher in synovial fluid than in serum, suggesting that these ligands play an important role in the inflamed synovial compartment ,16,38. IOur analysis of the subset of serum samples from patients with SLE for which corresponding disease-activity data were available  indicates that elevated heterotrimer levels may be associated with increasing SLE disease activity  for the serum samples they provided. MD declares that she has no competing interests.SRD coordinated the data collection, helped design and interpret the study, and co-wrote the manuscript. BH developed the heterotrimer assay, measured heterotrimer and BLyS levels in serum samples, and ran the heterotrimer signaling assays. KBL designed the Biacore studies, co-developed the trypsin cleavage method, and contributed to data analysis. MDM designed the heterotrimer expression vectors and co-invented the zz trimerization domain. HL performed early-stage heterotrimer purity assessment. TRB co-developed the heterotrimer purification process and strategy. NBH co-developed and implemented the heterotrimer purification process and the trypsin cleavage method. MML designed and performed the SEC-MALS analyses of the heterotrimer. MM ran the human B cell-proliferation assays. CMK performed the statistical analyses and correlation studies for the BLyS, APRIL, and heterotrimer serum levels in patients with SLE and RA, and co-wrote the manuscript. JLE helped design the heterotrimer assay and assisted with data analysis. SP coordinated the measurement of APRIL levels in serum samples and helped analyze data. KBE, MHW, and MD provided serum samples for analysis. JAG helped design the study and assisted with data analysis. All authors read and approved the final manuscript.Supplemental methods. Additional methodologic details.Click here for fileSupplemental tables. Supplemental Tables 1 and 2 show serum heterotrimer levels and disease-activity markers in a subset of samples from patients with SLE.Click here for file


Quantitative proteomics holds great promise for identifying proteins that are differentially abundant between populations representing different physiological or disease states. A range of computational tools is now available for both isotopically labeled and label-free liquid chromatography mass spectrometry (LC-MS) based quantitative proteomics. However, they are generally not comparable to each other in terms of functionality, user interfaces, information input/output, and do not readily facilitate appropriate statistical data analysis. These limitations, along with the array of choices, present a daunting prospect for biologists, and other researchers not trained in bioinformatics, who wish to use LC-MS-based quantitative proteomics.in vivo targets of the protein kinase Ark1 via phosphopeptide profiling.We have developed Corra, a computational framework and tools for discovery-based LC-MS proteomics. Corra extends and adapts existing algorithms used for LC-MS-based proteomics, and statistical algorithms, originally developed for microarray data analyses, appropriate for LC-MS data analysis. Corra also adapts software engineering technologies  so that computationally intense data processing and statistical analyses can run on a remote server, while the user controls and manages the process from their own computer via a simple web interface. Corra also allows the user to output significantly differentially abundant LC-MS-detected peptide features in a form compatible with subsequent sequence identification via tandem mass spectrometry (MS/MS). We present two case studies to illustrate the application of Corra to commonly performed LC-MS-based biological workflows: a pilot biomarker discovery study of glycoproteins isolated from human plasma samples relevant to type 2 diabetes, and a study in yeast to identify The Corra computational framework leverages computational innovation to enable biologists or other researchers to process, analyze and visualize LC-MS data with what would otherwise be a complex and not user-friendly suite of tools. Corra enables appropriate statistical analyses, with controlled false-discovery rates, ultimately to inform subsequent targeted identification of differentially abundant peptides by MS/MS. For the user not trained in bioinformatics, Corra represents a complete, customizable, free and open source computational platform enabling LC-MS-based proteomic workflows, and as such, addresses an unmet need in the LC-MS proteomics field. One area of particular interest to the proteomics community is the application of proteomics to the determination of proteins that are differentially expressed or abundant between samples representing different physiological or disease states -3. Typicin vivo) include the use of SILAC 3+, confirming it's detection in all 3 replicate analyses of the control strain, and its absence in all 3 replicate analyses of the Ark1 knockout strain.From these data analyses, as with the diabetes study above, we next made an inclusion list for targeted MS/MS, to try and identify some of the phosphopeptides lost in the Ark1 knockout yeast Here we present Corra, a complete, free and open source computational platform that enables LC-MS-based proteomic workflows, and as such, addresses an unmet need in the LC-MS proteomics field. The Corra framework extends and adapts existing algorithms used for LC-MS-based proteomics, as well as existing statistical algorithms from the microarray community suitable for the analysis of high-dimensional LC-MS data, with a view to controlling false-discovery rates. Corra also adapts additional software engineering technologies, such as distributed processing and Google Web Toolkit. Corra enables the use of an array of LC-MS data alignment tools, integrating them with various forms of statistical analyses via Bioconductor, for the generation of statistically validated lists of differentially abundant peptide features for subsequent targeted LC-MS/MS identification, all within a single computational platform. Corra is not intended as an alternative to pre-existing LC-MS analytical tools, such as SpecArray , SuperHiIn the version of Corra presented here, two of the aforementioned LC-MS tools, SpecArray and SuperHirn were implemented, as were the Bioconductor packages LIMMA and maSigPro for statistical analysis. However, with the description of the a common file format for LC-MS data, APML, and with the parsers and documentation also provided with Corra, the ability to incorporate additional software tools and statistical algorithms for additional workflows is fully supported. This allows for a user with appropriate bioinformatics training to set up Corra on any Linux server, either as is, or customized for their own personal or groups workflows. Finally, Corra is provided as open source (Apache 2.0), and may be downloaded, along with all relevant documentation . Corra iN-glycosidase F; SD: synthetic defined; TOF: time of flight; XML: extensible markup language.APML: annotated putative peptide markup language; DB: type 2 diabetes; ESI: electrospray ionization; FT: Fourier transform; Glufib: glu1-fibrinopeptide B; GUI: graphical user interface; LC-MS: liquid chromatography mass spectrometry; LIMMA: linear models for microarray data; MS/MS: tandem mass spectrometry; NGT: normal glucose tolerance; OGTT: oral glucose tolerance test; PNGaseF: protein MB, DC, JE, AG, OV and NZ conceived the original Corra framework, and MB subsequently oversaw Corra framework design, including APML and data analysis tools, and their implementation. MB amended and revised the SpecArray tool for implementation within Corra. LM wrote the SuperHirn software tool and collaborated with MB for modifications required for Corra implementation. VS assisted with Corra data analyses and designed and implemented the Corra GUI. OV did the initial design for the statistical analytical methods. BB performed the yeast phosphopeptide experiments and preliminary data analyses. KC performed glycopeptide isolations for the human diabetes plasma study. HL performed the LC-MS analyses for the human diabetes plasma study. SL oversaw all mass spectrometry experiments at ISB and performed targeted MS/MS experiments for the human diabetes plasma study. RA oversaw the research contributed by ETH and designed the yeast phosphopeptide study with BB. JW oversaw the research contributed by ISB and designed the human diabetes plasma study. JW and MB wrote the manuscript.


British Journal of Cancer (2002) 87, 1337–1338. doi:10.1038/sj.bjc.6600670www.bjcancer.com© 2002 Cancer Research UK SirWe read with interest the excellent paper by PSTs are found throughout the body, but the bowel, liver and platelets are known to contain particularly high activities of this enzyme. PSTs are cytosolic and exist in two forms: (i) P-PST, which selectively sulphates micromolar concentrations of phenols; and (ii) M-PST, which is similarly selective for aromatic amines.The main function of this sulphation is to scavenge low concentrations of endogenous and exogenous toxins from the body, but the lability of the phenolic sulphate-ester bond means it is liable to cause the formation of electrophilic free radicals. These react chemically with DNA which may cause mutations leading to neoplasia .Food cooking can result in a wide variety of mutagenic compounds, including polyaromatic hydrocarbons and heterocyclic amines, especially if the food becomes charred when grilled or barbequed. Certainly, several polyaromatic hydrocarbons have been shown to be activated by hydroxylation to phenols followed by sulphation via P-PST to the final mutagenic form . P-PST hThus, inhibition of P-PST would block one route of activation for both main groups of carcinogen found in food. Indeed, We would therefore suggest that the action of salicylic acid on P-PST, by preventing the excessive activation of carcinogens, may represent another possible pathway by which aspirin may reduce cancer risk.


The expression of hepatocyte growth factor/scatter factor (HGF/SF) was studied in 12 mesothelioma cell lines characterized by either an epithelioid or a fibroblast-like phenotype. Conditioned media from these lines were analysed by bioassay and ELISA, and HGF/SF was detected in three cell lines, all with a fibroblast-like or mixed morphology. None of eight epithelioid cell lines expressed the factor. Thus, for these cell lines, the ability to secrete HGF/SF correlated with the cell phenotype. Following on from these observations, two cell lines, BR and BT, with a fibroblast-like and an epithelioid phenotype, respectively, were further investigated. Both cell lines expressed the Met receptor but only BR secreted HGF/SF. Both cell lines responded to exogenous HGF/SF treatment by a change of morphology but in different ways: BR became more elongated and bipolar, while BT formed more spread-out cell colonies. HGF/SF acted as a paracrine effector on the epithelioid BT cells and stimulated both cell-spreading and proliferation. Interestingly, BT cells spread but did not scatter in response to exogenous HGF/SF. In contrast BR cells showed only some stimulation of cell motility with HGF/SF and no increase in cell proliferation was observed. Because HGF/SF was previously found in the pleural effusion fluids of patients with malignant mesothelioma and in paraffin-embedded tumour tissues, it is concluded that HGF/SF may well stimulate the growth and spread of malignant mesothelioma in vivo by paracrine and/or autocrine mechanisms.


Although socioeconomic differences in prevalence of obesity are well documented, whether patterns of weight gain during key periods of growth and development differ among youth from different socioeconomic backgrounds is unknown. This study examines socioeconomic disparities in overweight status and 5-year weight gain among adolescents.Project EAT (Eating Among Teens)-II followed a socioeconomically and ethnically diverse sample of 2,516 adolescents from 1999 through 2004. Mixed-model regression analyses examined longitudinal trends in overweight status as a function of socioeconomic status (SES).P = .006) in overweight prevalence between 1999 and 2004, whereas boys in the low- and middle-SES categories showed no significant change. Girls in the low-SES category showed a significant 5-year increase (P = .004) in overweight prevalence compared with a stable prevalence of overweight among girls in the middle- and high-SES categories.Girls and boys in the low-SES category were more likely to be overweight than were those in the high-SES category. Boys in the high-SES category showed a significant decrease  or become overweight (girls). Designing obesity prevention and treatment interventions that reach and address the unique needs of youth and families from less-advantaged socioeconomic backgrounds is a public health priority. Although the prevalence of overweight in adolescents has increased dramatically during the past several decades among all ethnic and socioeconomic status (SES) groups, considerable data suggest that risk for adolescent obesity is higher for certain racial/ethnic groups and is inversely associated with SES . Recent To date, most studies examining SES disparities in weight have focused on secular trends ,3. AlthoThis study examines longitudinal changes in weight status in a large, socioeconomically and ethnically diverse sample of adolescent boys and girls during a 5-year period. Specifically, this study sought to answer whether SES disparities in overweight status and weight gain persist over time among adolescents and whether these patterns are different for boys and girls.Project EAT (Eating Among Teens)-II is a follow-up study of Project EAT-I, a study of the determinants of dietary intake and weight status in adolescents -8. In Prr = .85 for girls, r = .89 for boys). We classified overweight as BMI more than the 85th percentile for sex and age according to the first National Health and Nutrition Examination Survey because it provides values from childhood to adulthood, and in Project EAT-II adolescents are followed through late adolescence/early adulthood  was computed. For EAT-II, self-reported weight and height data were collected in the mail survey. Participants were asked to report, "How tall are you?" in feet and inches and "How much do you weigh?" in pounds. The trend data we report use the self-reported figures from EAT-I, although if self-reported BMI was not available (n = 117), items were imputed based on baseline-measured BMI, age, race, and SES within sex. The measured and self-reported BMI in EAT-I were highly correlated , cohort (younger or older), SES , and an SES-by-year interaction along with a random effect for individuals to account for longitudinal correlation to estimate and test difference of prevalence of overweight across time, both within and across SES categories. Analyses were stratified by sex and adjusted for race/ethnicity and cohort. SAS version 9.1  was used for all analyses.P = .71). However, when change in overweight status over time was broken down by SES, differential change patterns emerged; the prevalence of overweight increased for adolescents in the low-SES group from 29.8% to 33.1% (P < .001) and decreased for adolescents in the high-SES group from 23.1% to 19.2% (P < .01).The sample was relatively evenly distributed across the 3 SES categories . ApproxiP = .02; 2004, P < .001) (P = .007). Although the prevalence of overweight among boys did not show an overall significant longitudinal increase from 1999 to 2004 (P = .33), changes in overweight prevalence during this period varied as a function of SES. In particular, the SES-by-year interaction was significant (P = .03), and boys in the low- and middle-SES categories showed no significant change in overweight prevalence from 1999 to 2004, compared with boys in the high-SES category, who showed a significant decrease (P = .006). No significant interaction with cohort was observed, which suggests that these results did not vary between the younger and older cohorts. Race/ethnicity was not a significant predictor of overweight prevalence among boys after adjusting for SES. Additionally, the interaction between race/ethnicity and time was not significant, which suggests that changes in overweight prevalence over time did not vary by race/ethnicity among boys after accounting for SES.In both 1999 and 2004, a larger proportion of boys in the low-SES category were overweight than were boys in the high-SES category  . In 1999P = .005; 2004, P < .001). As with boys, the overall prevalence of overweight did not change from 1999 to 2004 (P = .22). However, a significant SES-by-year interaction was observed (P = .02). Girls in the low-SES category showed a significant increase (P = .004) in the prevalence of overweight, compared with the relatively stable prevalence of overweight among girls in the middle- and high-SES categories. Race/ethnicity remained a significant predictor of overweight prevalence after adjusting for SES, which suggests that race/ethnicity and SES were independently associated with prevalence of overweight in girls. However, the interaction between race/ethnicity and time was not significant, which suggests that changes in overweight prevalence over time did not vary by race/ethnicity after accounting for the role of SES.In 1999 and 2004, a larger proportion of girls in the low-SES category were overweight than were high-SES girls (1999, Our findings confirm SES disparities in the prevalence of overweight; boys and girls in the low-SES category are at highest risk. Moreover, SES is associated with different patterns of weight change over time for adolescent boys and girls. Although boys of low and middle SES showed a consistent, relatively high prevalence of overweight during the 5-year study period, boys in the high-SES category showed a significant decrease in the prevalence of overweight. Girls in the low-SES category showed a significant increase in the prevalence overweight during the 5-year period, in contrast with the relatively stable prevalence of overweight among girls in the middle- and high-SES categories, further widening the SES disparities in the prevalence of overweight.These data from Project EAT contribute to the growing complex and occasionally contradictory literature on relationships among weight status, SES, race/ethnicity, and sex. Two recent studies have suggested that SES disparities in overweight status have been narrowing. Between 1988-1994 and 1999-2002, the ratio in the prevalence of overweight between high- and low-SES adolescent boys and girls decreased significantly . SimilarThe Add Health Study  also shoOur study has a number of strengths, including a large and diverse sample in terms of SES and race/ethnicity, a multifactorial measure of SES, and the ability to examine 5-year longitudinal trends. However, some limitations also need to be taken into account when interpreting the findings. In spite of multiple attempts to reach the original study participants, attrition was high, but use of a weighted sample reduces this concern. Although Project EAT included a diverse sample, some cell sizes for race/ethnicity were small, which decreased our ability to examine certain racial/ethnic and SES weight trends. Additionally, sexual maturation was not assessed; therefore, relationships between the timing of pubertal and BMI changes and variations in these relationships by sex and race/ethnicity could not be examined. Finally, BMI values were based on self-report, although measured and self-reported BMI were highly correlated in EAT-I.Our findings underscore the need for obesity prevention and treatment for youth in general, given the overall high prevalence rates, but specifically for interventions tailored for low-SES groups. The school environment is an excellent place to reach out to low-SES youth since most children attend school, and barriers to engaging in physical activity and nutrition interventions, such as cost and transportation, are markedly reduced. Designing obesity prevention and treatment interventions that reach and address the unique needs of low-SES youth is a public health priority because of the increased prevalence of overweight and the high likelihood that these adolescents will remain overweight as adults.


Recent studies have revealed the associations between insulin resistance (IR) and geriatric conditions such as frailty and cognitive impairment. However, little is known about the relation of IR to physical impairment and limitation in the aging process, eg. slow gait speed and poor muscle strength. The aim of this study is to determine the effect of IR in performance-based physical function, specifically gait speed and leg strength, among nondiabetic older adults.Cross-sectional data were from the population-based National Health and Nutrition Examination Survey (1999-2002). A total of 1168 nondiabetic adults (≥ 50 years) with nonmissing values in fasting measures of insulin and glucose, habitual gait speed (HGS), and leg strength were analyzed. IR was assessed by homeostasis model assessment (HOMA-IR), whereas HGS and peak leg strength by the 20-foot timed walk test and an isokinetic dynamometer, respectively. We used multiple linear regression to examine the association between IR and performance-based physical function.IR was inversely associated with gait speed among the men. After adjusting demographics, body mass index, alcohol consumption, smoking status, chronic co-morbidities, and markers of nutrition and cardiovascular risk, each increment of 1 standard deviation in the HOMA-IR level was associated with a 0.04 m/sec decrease (p = 0.003) in the HGS in men. We did not find such association among the women. The IR-HGS association was not changed after further adjustment of leg strength. Last, HOMA-IR was not demonstrated in association with peak leg strength.IR is inversely associated with HGS among older men without diabetes. The results suggest that IR, an important indicator of gait function among men, could be further investigated as an intervenable target to prevent walking limitation. Recently, increasing research effort has been focused on the role of IR in age-related conditions or geriatric syndromes. The Italian InCHIANTI study, by examining community-dwelling elderly population, suggested that IR is associated with cognitive impairment as evidenced by poor performance in Trail Making Test and Mini-Mental State Examination ,2. By foThe NHANES, a population-based survey, used a stratified, multistage, and cluster sampling design to obtain a representative sample of the noninstitutionalized U.S. civilian population. NHANES consists of a detailed home interview and a health examination conducted in a mobile examination center (MEC). Datasets, Survey Operations Manuals, Consent Documents, and Brochures of the NHANES 1999-2002 are available on the NHANES website ,11.12 , folate , total cholesterol , cotinine , as well as body mass index  were used to impute missing values for these variables, all of which were used in the analysis.A subsample of 2052 participants aged 50 years and older were randomly assigned to a morning session and had complete information of fasting plasma glucose and serum insulin. Individuals who had diabetes  or with missing values in the timed walking and isokinetic leg strength tests because of safety concerns  or any administrative, communicative, or technical problems (n = 450) were excluded from the analysis, leaving 1168 participants as the analytic sample. Among the final sample, median values of C-reactive protein , vitamin BA blood sample was collected following an overnight fast (≥ 8 h) in participants who were assigned to a physical examination during a morning session. Plasma glucose level was measured with a hexokinase enzymatic reference method  and serum insulin level by a radio-immunoassay . Homeostasis model assessment of IR (HOMA-IR), an estimate of IR commonly applied in large epidemiological studies, was used to evaluate IR using the following formula: fasting serum insulin (μU/mL) × fasting plasma glucose (mmol/L)/22.5 .Habitual gait speed (HGS) was measured in the MEC according to the NHANES standardized protocol. A 20 feet long test tract area was set up in a corridor of the MEC. The 20-foot walk was timed using a hand-held stopwatch. The 20-foot timed walk test was performed at the participant's usual pace. Use of a walker or cane was allowed if needed. HGS was calculated as walking distance (20 feet = 6.15 m) divided by time (second). Maximal right knee extensor force (Newton) was measured at an angular velocity of 60 degree/second by a Kinetic Communicator isokinetic dynamometer .Age, gender, and race/ethnicity were obtained by self-report. Co-morbidities including heart disease , chronic lung disease (defined as chronic bronchitis or emphysema), and arthritis were ascertained by self-report questionnaires. Alcohol intake was determined by the questionnaire "In any one year, have you had at least 12 drinks of any type of alcohol beverage?" and was dichotomized. Exposure to tobacco smoke increases the concentration of nicotine in the blood, and nicotine is highly specific for such exposure. Cotinine is a major metabolite of nicotine. Using their serum cotinine concentrations (ng/mL), we classified smoking status of participants in four groups: nonsmoker <14), light smoker (14-99), moderate smoker (100-199), and heavy smoker (≥ 200) . Three a, light sData were analyzed using Stata 9.0  specialized for complex survey data. We used stratum and primary sampling unit (PSU) variables required for variance estimation. In order to account for clustering and stratification of the multi-stage NHANES sampling design, we incorporated appropriate sampling weight in all analyses in order to obtain point estimates and standard errors (SEs) applicable to the U.S. population. In the NHANES 1999-2002, separate 4-year fasting weights were created to reflect the additional stage of sampling and the additional nonresponse for the subsample of fasting participants assigned to the morning session. These 4-year fasting weights were used for data analysis.i-Xm) ÷ SD, where Xi was the natural-log-transformed HOMA-IR in the individual male subject, Xm the mean natural-log-transformed HOMA-IR in the male subjects, and SD the standard deviation of the natural-log-transformed HOMA-IR in the male subjects. The standard-deviation scores of HOMA-IR in women were obtained from the same formula. This calculation allowed us to determine the change in the gait speed and leg strength for each increment of 1SD in the natural-log-transformed HOMA-IR. The relations of HOMA-IR to leg strength and gait speed were also evaluated with a quartile-based analysis by dividing HOMA-IR levels into quartiles with subjects in the lowest quartile as the reference group. We used an extended-model approach for covariates adjustments: Model 1 = age, race, BMI, smoking status, alcohol consumption, and use of walking device; Model 2 = Model 1 + chronic diseases ; Model 3 = Model 2 + markers of nutrition and cardiovascular risk . Given the fact that muscle strength has been shown to be an important correlate for walking speed among community-dwelling older adults [Characteristics of the study population, including means and SEs values for continuous variables and percentages for categorical variables, were calculated with correction for the survey design in both men and women. Stratified by sex, weighted linear regression analysis was used to examine the relation of HOMA-IR to performance-based physical measures, namely leg strength and HGS. The distributions of HOMA-IR in both men and women were right-skewed. Therefore, we used natural-log-transformed values, which provided the best-fitting model for analysis in which the HOMA-IR were treated as a continuous variable. For men, standard-deviation scores of HOMA-IR were obtained from the formula  in HGS Table . AdditioThe cross-sectional relation of IR to muscle strength has been evaluated in two population-based studies of community dwellers that highlighted an inverse association between IR and muscle strength [However, such studies used different confounding variables in their statistical models and one of the studies consisted of a cohort entirely made up of men[which may explain the discrepancies from our findings. To our knowledge, this is the first report to describe the association between IR and performance-based physical function among older men and women by using a large group of geographically dispersed and ethnically diverse national population-based sample. Potential confounders were comprehensively considered and the role of leg strength in the association between IR and gait speed was assessed.Among men without diabetes, there was an inverse association between IR and HGS. The relationship was independent of age, race, BMI, smoking status, alcohol consumption, co-morbidities, markers of nutrition and cardiovascular risk, and peak leg strength. Our findings support and extend previous studies examining the role of metabolic syndrome, a cluster of cardiovascular risk factors strongly associated with IR, in predicting the development of functional impairment. Supporting statements from Blazer and colleagues, by analyzing 1229 older adults from the Duke Established Populations for Epidemiologic Studies of the Elderly (EPESE), demonstrated that metabolic syndrome independently predicted mobility decline, as assessed by the ability to perform heavy housework unaided, walk up and down a flight of stairs unaided, and walk half a mile unaided. Additiostrength . Howeverthus contributing to the development of cerebral micro-angiopathy . The lesions may disrupt the integrity of frontal-subcortical circuits, thus compromising gait function. Cerebrovascular lesions thus provide a conceivable mechanism between IR and slow gait speed. Since the association between IR and gait speed varies across gender, there may be an effect modification of sex in the association. The fact that men had a greater baseline prevalence of cardiovascular risk (such as heart disease and smoking) than women may justify why an inverse association between IR and gait speed is seen in men but not in women. Further research efforts are needed to investigate possible mediating factors, such as differential coordinating processes in brain neural circuiting or sex hormones[additionally improve walking function and prevent functional decline, especially for high-risk subjects.By acting as a cardiovascular risk factor, IR may cause cerebral atherosclerotic changes in the cerebral circulation , thus co hormones, in medi hormones, as well hormones, regular hormones, or weig hormones- may addOur study has potential limitations deserving comments. First, due to the cross-sectional design, causal relationship between IR and gait speed can not be established. The association between IR and gait speed could simply be epiphenomenon of aging and the association should be prospectively explored. Second, although we have comprehensively adjusted for such confounders as chronic co-morbidities, markers of nutrition, inflammation, and cardiovascular risk, as well as leg strength in the association of IR and gait speed, other important measures such as cognitive ability, symptoms of depression, markers of endothelial dysfunction, or evidence of cerebral small vessel disease are absent or incomplete in the NHANES 1999-2002 dataset.In conclusion, a higher level of IR was associated with a slower gait speed among non-diabetic older men. The association does not exist in the women. We provided new information for the association between IR and gait speed among community-dwelling older adults where data currently do not exist.The authors declare that they have no competing interests.All authors critically reviewed the manuscript, read and approved the final manuscript.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2318/9/49/prepub


There is an increasing demand to assemble and align large-scale biological sequence data sets. The commonly used multiple sequence alignment programs are still limited in their ability to handle very large amounts of sequences because the system lacks a scalable high-performance computing (HPC) environment with a greatly extended data storage capacity.ClustalXeed, a software system for multiple sequence alignment with incremental improvements over previous versions of the ClustalX and ClustalW-MPI software. The primary advantage of ClustalXeed over other multiple sequence alignment software is its ability to align a large family of protein or nucleic acid sequences. To solve the conventional memory-dependency problem, ClustalXeed uses both physical random access memory (RAM) and a distributed file-allocation system for distance matrix construction and pair-align computation. The computation efficiency of disk-storage system was markedly improved by implementing an efficient load-balancing algorithm, called "idle node-seeking task algorithm" (INSTA). The new editing option and the graphical user interface (GUI) provide ready access to a parallel-computing environment for users who seek fast and easy alignment of large DNA and protein sequence sets.We designed ClustalXeed can now compute a large volume of biological sequence data sets, which were not tractable in any other parallel or single MSA program. The main developments include: 1) the ability to tackle larger sequence alignment problems than possible with previous systems through markedly improved storage-handling capabilities. 2) Implementing an efficient task load-balancing algorithm, INSTA, which improves overall processing times for multiple sequence alignment with input sequences of non-uniform length. 3) Support for both single PC and distributed cluster systems. Genetic and protein sequences are being discovered rapidly, and as a result, the number of sequences entered into biological databases is growing exponentially over time. Most of the work currently being done in computational biology involves searching for inter- and intra-sequence homology in massive volumes of genetic and protein sequence data, which are commonly based on a multiple sequence alignments (MSAs) . HoweverThe oldest and most widely used MSA program that estimates trees as it aligns multiple sequences is ClustalW ,5. ClustUnfortunately, most of the currently available MSA programs are not suitable for large-capacity data storage and massive computation. These programs, including ClustalX (or X 2.0), are still single-PC based, and the storage and computation is entirely dependent on physical random-access memory (RAM). Past MSA performance evaluations focused simply on how compute-intense and sensitive the program was with respect to the longest-common-sequence (LCS)-based exact-string matching algorithm  . DependiClustalXeed, which was designed for a wide range of MSA purposes  mode. The disk-storage system uses an idle node-seeking task algorithm (INSTA), which forces sleeping nodes into active modes during the massive file-swapping and pair-align computation to overcome slow computation speed. The GUI-based parallel-computation system is implemented with Linux and can be classified into two subsystems: the GUI engine  for interactions between users and the parallel-computation system, and the pair-alignment engine for the calculation of pair-align matrices.In this study, we report s Figure . This isClustalXeed assigns two computation platforms incorporating physical RAM addressing, using a modified version of the clustalw-xeed_mem file, which is similar to the original ClustalW or ClustalW-MPI tools [clustalw-xeed file. The new clustalw-xeed file enables large-scale disk memory storage and smart allocation of vast sequence data sets to a disk swap space for construction of temporary pair-align matrices and for accelerated computation. ClustalXeed uses a sequential file writing method that provides a straightforward and efficient way to read and write files. For a large number of sequences, ClustalXeed converts input sequences into individual sequence pairs and stores the pairs using the naming rule/tmp/xxxxx000P, where P = the pair sequence number and the generation number of the file name is always +1.PI tools ,11 and dA distance matrix file, which is a single file with a file name of matrix-file080.tmp, is also generated in a disk storage unit and is based on all-to-all pair sets from the input sequence query. The calculated pair scores generated from each computation node are stored in the master node/tmp directory. Creation of this process involved modification of the three main programming functions in the original ClustalW , as well as the pairalign message-passing-interface (MPI) algorithm in ClustalW-MPI .ClustalXeed uses the distance matrix and the neighbor-joining clustering method to construct a similarity or guided tree. During this step, temporary changes in tree values are recorded sequentially by creating a new similarity tree file that contains the updated records at each computation stage. This technique provides an efficient file handling methodology for analyses involving frequent writing/reading of large data sets, as is required for dynamic programming using the sum of pairs (SP) scoring method. The similarity matrix files generated at each stage are named using the same naming rule as was described for the input file storage system. The final multiple sequence alignment (MSA) results are stored in a {*.aln} file for easy data retrieval.For cluster analysis, Both ClustalW and ClustalX calculate pair-align scores to generate a guided tree for multiple sequence alignment. During this step, a distributed computation strategy may accelerate the computation. This means that the performance of any distributed parallel-computation approach depends on the balance of the workloads among the distributed nodes Figure . In an iDepending both on the volume of the data to be aligned and the accuracy of the comparisons, computation by dynamic programming requires time-consuming iterations to achieve high accuracy. As an example, ClustalX has a parallelized version of ClustalX IRIX that is optimized to run on SGI Origin parallel computers running IRIX 6.5. The main problem of this parallelized version, however, is that the user has to spend extra time pre-sorting the input data to reduce load imbalances.If the overall pair-align computation nodes are well balanced, performance will be greatly improved Figure . The effClustalXeed main.To overcome the slow speed of the file (-disk) memory computation, we designed an efficient load balancer, which uses a fast, intelligent scanning strategy to find sleeping computation nodes. Based on the previous distribution characteristics of ClustalW-MPI, we propose a dynamic scan-load balancing algorithm for efficient job-assignment of non-uniformly  distributed pair-align computation nodes, which is specified to increase the speed of interprocessor (nodes) communications Figure . The oriClustalXeed is the same as that of ClustalX, because ClustalX is very familiar to PC-based MSA users. It provides a consistent interface, except for several new features for parallel computation, but the other functions are very similar to those in ClustalX.Figure ClustalXeed allows the user to change the order of sequences by simply cutting and pasting the sequence names. The sequence block grabber also provides a box-shaded area that enables the user to realign badly aligned sequences in a new window format, and to realign a small box region again. This option provides an independent task for the refinement of aligned sequences. The realignment range can be selected by simply clicking the mouse and dragging on the new sequence area . Easy Sequence finder enables a search for nucleic acids or proteins based on a partial sequence input.ClustalXeed supports standard TrueType and Postscript fonts, which may increase the resulting tree resolution when enlarged, especially in the case of a huge sequence data set.For the convenience of direct tree-drawing, TreeView  open souA real-time in-process dialogue box was built to enable the user to quickly monitor the current status of the computation, the progression of the job, and information on the number of nodes involved in the calculation. Neither ClustalX nor X2.0 gives feedback on the computation status. When the MSA is finished, the user can save all of the computation history to a {result.log} file. The used parameters are also saved in the working directory as a {result.par} file. This allows a user to view and edit tag information about all the individual batch sequence-alignment jobs.ClustalXeed.The GOR IV  and PHD ClustalXeed provides more options for selecting protein-weight matrices. The former version of ClustalX (or 2.0) provides only three different protein-weight matrices: BLOSUM 30, PAM 350, and Gonnet 250. We added more than 34 different types of protein-weight matrices for specifying scoring tables for the easy and accurate adjustment of SP score improvement. This allows the user to reduce or increase the multiple sequence alignment sensitivity.ClustalXeed allows the alignment of large numbers of nucleic acid or protein sequences. Generally, the memory space requirement for the dynamic programming algorithm follows O (m × n). Based on this, for over 400000 sequences, MSA requires at least 1.28 terabytes of memory  just to construct a distance-tree matrix, regardless of sequence length. We evaluated our software using large volumes of real nucleic acid and protein data sets to assess its overall and detailed performance. We set up a typical 100 × CPU AMD Opteron 244 (1.8 GHz) 64-bit cluster system with Linux (Fedora 4 Core). The master node consists of a 10-terabyte HDD (Samsung Electronics): 3ware RAID adapter  and 8 GB DRAM, for a huge-tree matrix construction. Each node is a dual-core Opteron system with 4 GB DRAM and a 1-terabyte HDD.ftp://ftp.ncbi.nih.gov/ blast/FASTA. These DNA sequences were divided into smaller data sets containing 150000 to 280000 sequences. With 200000 sequences as the first test set, which requires a nearly 8-terabyte file-managing environment for the MSA job, the elapsed computation time was 1.5- to 6-times shorter than that without INSTA. The total execution time for the complete alignment of 200,000 nucleic acid sequences by the disk-storage system was about 4700-6100 s with INSTA, and 7500-24000 s without INSTA. Once the INSTA was built, the overall speed-up rate was directly increased with the added computation nodes. The total computation efficiency depends on the pair-align scoring stage . For a given number of sequences, the average speed of ClustalXeed performance increased with the number of computation nodes (up to 50 nodes were tested).To confirm the full sequence-loading and speed-up computation, almost six million sequences (23.08 GB) in an nt.gz file were first downloaded from 9  pair-wise sequence alignments are required to complete each SP score calculation. We randomly mixed all of these sequences and aligned them using the disk-storage system. Figure ClustalXeed was more than four times faster than the usual file-swap mode. The average speed-up for 20 nodes was 11.7 with INSTA and 7.5 without INSTA. The observed speed-up difference was due to the efficient load-balancing of sparsely distributed sequence pairs, and it clearly demonstrated the success of the implemented load-balancing algorithm. We showed that there exists an optimal node number to be assigned to jobs for the effective usage of computation resources. It is important to determine what system size will result in the maximum speed-up. The speed-up rate, as a function of participating node numbers, was not linear, because there was implicit waiting time due to communication latency . All pairs of sequences in the ClustalXeed main disk-storage are transferred to compute nodes, and the calculated pair scores are then returned to the master and are saved in the disk-storage distance matrix , with minimal length around 10 aa and maximal length of 11600 aa. In total, 1.39×10ClustalW is the most widely used multiple sequence alignment program. The program uses a profile-based progressive alignment, with the alignment process divided into three steps: (1) distance matrix/pair-wise alignment, (2) guided tree generation, and (3) progressive alignment. However, ClustalW is not capable of estimating phylogenies and alignments for large data sets, because of slow computation times and limited memory usage. Alternatives to ClustalW include ClustalX (or X2.0), a graphical user interface (GUI)-based version of ClustalW, and ClustalW-MPI, a recently developed, parallel implementation version of ClustalW. In the latter tool, all three required computation steps are performed in parallel to reduce the total computation time. For parallel job scheduling, ClustalW-MPI uses a fixed-size chunk scheduler, which divides each job into uniform, fixed sizes. This method of batch job scheduling sometimes reduces the communication overhead required for a small and moderate number of sequences having very short lengths, such as ESTs (expressed sequence tags). However, it is not always effective at balancing the workload required for a large number of sequences having unequal lengths. Under these circumstances, the iteration for the next job scheduling is often delayed, which may result in high processor idle time . MoreoveClustalXeed was designed to simultaneously address the dual needs of fast computation and large sequence data handling. Core changes with significant strides in supporting disk-memory access capabilities and enhanced job scheduling can tackle this bottleneck by enhancing both storage capacity and speed. As mentioned previously, ClustalW-MPI delivers fixed-size chunks to every compute node before the calculation. The batch scheduling mode needs high memory on each node, which may result in processor idling when the sequence lengths are not uniform. In contrast, the ClustalXeed disk storage algorithm does not send all pair sequences to the computation nodes and instead master allocates (distributes) the pair sequences individually to an appropriate node using a load-balancing idle node-seeking task algorithm (INSTA) to reduce the initial file transfer cost and slave node memory requirements. ClustalXeed also provides a fixed size chunk algorithm in the memory-storage mode for alignment of small-to-medium-sized sequences.ClustalXeed was designed to work at the capacity of disk memory space, it has no inherent limitation on input sequence amounts. With a 64-bit compiler version, ClustalXeed works with sequence arrays containing up to 18 terabytes in disk-storage mode. In the disk memory operation, alignment speed was also improved by incorporating INSTA, which allocates or re-allocates tasks to idle nodes during pair alignment without the requirement for prior task information. In this way, INSTA determines from moment to moment which imbalanced nodes can be resolved immediately by allocating a new job. The main advantage of INSTA is its prompt scanning and decision-making without requiring decision complexity of rescheduling or reallocating tasks to resources at runtime, as occurs with static or other general dynamic load-balancing algorithms.Because ClustalXeed menu link individually . Users can follow the progress of their alignment execution from the real-time in-process dialogue box. As indicated previously, the new parameter inputs, the easy-to-use realign option, the fully integrated graphical user interface, and the improved speed-up performance for very large volumes of sequence data may provide optimized computation of biological sequence alignments. ClustalXeed demonstrates that the embedded INSTA is a simple and effective means to meet the high computational demands (speed and memory) for massive biological-sequence alignments.While setting up a new sequence batch job, the user has the option to choose an appropriate alternate computing environment using the graphical menu option. Other precise values of multiple sequence alignment tuning parameters can be set for each ClustalXeed provides a great opportunity for the discovery of large and reliable phylogenetic trees between interesting biological sequence data sets. Based on the combination of 38 new protein-weight matrices, encouraging results show that ClustalXeed is one of most powerful MSA tools available for the rapid construction of huge phylogenies.Moreover, large phylogenetic tree construction is becoming increasingly important, as vast amounts of biological sequences are used in the evolutionary and functional analysis of grouping organisms. Project name: ClustalXeed.Project home page: http://pchm.inje.ac.kr/clustalxeed.Operating System(s): runs both on single and parallel Linux-based clustal systems.Programming Language: C-language, Message Passing Interface (MPI).Other requirements: described in the project home page. More detailed installation instructions and a tutorial manual will also be available for download.License: ClustalXeed is available in source code, without fee, for academic, non-profit uses. The program is distributed in the hope that it will become further improved and put to practical use.HPC: High Performance Computing; GUI: Graphical User Interface; MSA: Multiple Sequence Alignment; MPI: Message Passing Interface; RAM: Random Access Memory; INSTA: Idle Node-Seeking Task Algorithm; CPU: Central Processing Unit; HDD: Hard Disk Drive; I/O: Input/Output; MALIGN: Multiple Alignment; SP: Sum of PairsHJ designed and wrote the software, with support from TK. Both authors contributed to the writing of the manuscript. All authors read and approved the final manuscript.


To examine the effects of a 6 month lifestyle intervention on quality of life, depression, self-efficacy and eating behavior changes in overweight and obese endometrial cancer survivors.Early stage endometrial cancer survivors were randomized to intervention (n = 23) or usual care (n = 22) groups. Chi-square, Student's t-test and repeated measures analysis of variance were used in intent-to-treat analyses. Outcomes were also examined according to weight loss.Morbidly obese patients had significantly lower self-efficacy, specifically when feeling physical discomfort. There was a significant improvement for self-efficacy related to social pressure (p = .03) and restraint (p = .02) in the LI group. There was a significant difference for emotional well-being quality of life (p = .02), self-efficacy related to negative emotions (p < .01), food availability (p = .03), and physical discomfort (p = .01) in women who lost weight as compared to women who gained weight. Improvement in restraint was also reported in women who lost weight (p < .01).This pilot lifestyle intervention had no effect on quality of life or depression but did improve self-efficacy and some eating behaviors.; NCT00420979 Endometrial cancer is the most common gynecologic cancer in the United States and obesity is the most significant risk factor for development of the disease . A recenDifferences in quality of life (QOL) between obese and non-obese endometrial cancer survivors are related to physical health. In a prospective examination of QOL, general health status, and obesity in women with early stage endometrial cancer,  women wiWe have previously reported the effects of a six-month lifestyle intervention on weight loss, exercise behavior, and nutrient intake changes in overweight and obese endometrial cancer survivors . We founThe study was a prospective randomized controlled trial comparing a lifestyle intervention (LI) consisting of exercise and nutritional counseling with cognitive-behavior modification to usual care (UC) in overweight and obese endometrial cancer survivors. An invitation letter was sent to women included in the cancer registry from the Ireland Cancer Center at University Hospitals Case Medical Center diagnosed with stage I-II endometrial cancer from 2001–2004. The 6 month intervention was delivered to the LI group while the UC group received only an informational brochure outlining the benefits of proper nutrition and physical activity. Institutional review board approval was granted and informed consent and authorization to use protected health information (HIPAA) was obtained from all patients prior to study procedures. Feasibility, eligibility criteria, and details of the intervention have been published elsewhere . RandomiThe counseling protocol was administered by the study registered dietitian (RD), primary investigator (PI), and psychologist. It followed a stepwise, phased approach using strategies outlined by social cognitive theory, indicating that the optimal intervention for a major behavior change should focus on establishing short-term goals, and enabling the person to build self-efficacy -16. The Functional Assessment of Cancer Therapy-General (FACT-G), a valid and reliable questionnaire evaluating physical, functional, family-social, and emotional well-being domains , however the difference was consistent with minimally important differences (5–6 points) [Baseline QOL , BDI, WEL and TFEQ scores did not differ between the LI and UC groups. However significant differences were observed when patients were categorized according to BMI Table . Total Q points) . SF-36 pIn regards to eating patterns, morbidly obese patients had significantly lower self-efficacy when feeling physical discomfort and decreased total self-efficacy (WEL) score. Restraint on the TFEQ questionnaire was decreased in patients with BMI > 40 as compared to BMI < 40.Repeated measures ANOVA with baseline measurements as a covariate and 3, 6 and 12 months as outcomes revealed no group (LI versus UC) effects for QOL outcomes  can improve outcome measures. Others have questioned whether improving QOL could be attributable to the increased attention (or increasing self-efficacy) given to cancer patients involved in exercise interventions . QOL mayThis pilot lifestyle intervention had no effect on quality of life, or depression but did improve self-efficacy and restraint. A substantial amount of endometrial cancer survivors are surviving their cancer, however, they are succumbing to other diseases correlated with obesity. The Gynecologic Oncology Group is considering adding QOL measures to their next large prospective endometrial cancer trial with long term follow up. Future directions will also consist of the measurement of 5 year outcomes in this study population . Goals oThe authors declare that they have no competing interests.VVG, HG, MBK, JJ, EL and KC conceived of the study, and participated in its design and coordination. VVG, HG, and MBK implemented the study and were responsible for day to day conduct of the study. VVG, HG, and KC analyzed the data. VVG, HG, and KC drafted the manuscript; MBK, JJ and EL provided critical review. All authors read and approved the final manuscript.