Evidence for positive selection in phycoerythrin genes of red algae and cyanobacteria Prochlorococcus and Synechococcus

Because of the shortage of phycoerythrin (PE) gene sequences from rhodophytes, peBA encoding beta- and alpha-subunits of PE from three species of red algae (Ceramium boydenn, Halymenia sinensis, and Plocamium telfariae) were cloned and sequenced. Different selection forces have affected the evolution of PE lineages. 8.9 % of the codons were subject to positive selection within the PE lineages (excluding high-irradiance adapted Prochlorococcus). More than 40 % of the sites may be under positive selection, and nearly 20 % sites are weakly constraint sites in high-irradiance adapted Prochlorococcus. Sites most likely undergoing positive selection were found in the chromophore binding domains, suggesting that these sites have played important roles in environmental adaptation during PE diversification. Moreover, the heterogeneous distribution of positively selected sites along the PE gene was revealed from the comparison of low-irradiance adapted Prochlorococcus and marine Synechococcus, which firmly suggests that evolutionary patterns of PEs in these two lineages are significantly different.

A probabilistic index for completely positive maps and an application

Gohm, Rolf, (2003) 'A probabilistic index for completely positive maps and an application', Journal of Operator Theory 54(2) pp.339-361 RAE2008

RinA controls phage-mediated packaging and transfer of virulence genes in gram-positive bacteria

Phage-mediated transfer of microbial genetic elements plays a crucial role in bacterial life style and evolution. In this study, we identify the RinA family of phage-encoded proteins as activators required for transcription of the late operon in a large group of temperate staphylococcal phages. RinA binds to a tightly regulated promoter region, situated upstream of the terS gene, that controls expression of the morphogenetic and lysis modules of the phage, activating their transcription. As expected, rinA deletion eliminated formation of functional phage particles and significantly decreased the transfer of phage and pathogenicity island encoded virulence factors. A genetic analysis of the late promoter region showed that a fragment of 272 bp contains both the promoter and the region necessary for activation by RinA. In addition, we demonstrated that RinA is the only phage-encoded protein required for the activation of this promoter region. This region was shown to be divergent among different phages. Consequently, phages with divergent promoter regions carried allelic variants of the RinA protein, which specifically recognize its own promoter sequence. Finally, most Gram-postive bacteria carry bacteriophages encoding RinA homologue proteins. Characterization of several of these proteins demonstrated that control by RinA of the phage-mediated packaging and transfer of virulence factor is a conserved mechanism regulating horizontal gene transfer.

An exploration of the positive and negative relationships associated with the development of asthma and atopic disorders in primary school children in Cork

Childhood asthma, allergic rhinitis and eczema are complex heterogenic chronic inflammatory allergic disorders which constitute a major burden to children, their families. The prevalence of childhood allergic disorders is increasing worldwide and merely rudimentary understanding exists regarding causality, or the influence of the environment on disease expression. Phase Three of the International Study of Asthma and Allergy in Childhood (ISAAC) reported that Irish adolescents had the 4th highest eczema and rhinoconjunctivitis prevalence and 3rd highest asthma prevalence in the world. There are no ISAAC data pertaining to young Irish children. In 2002, Sturley reported a high prevalence of current asthma in Cork primary school children aged 6-9 years. This thesis comprises of three cross-sectional studies which examined the prevalence of and associations with childhood allergy and a quasi-retrospective cohort study which observed the natural history of allergy from 6-9 until 11-13 years. Although not part of ISAAC, data was attained by parentally completed ISAAC-based questionnaires, using the ISAAC protocol. The prevalence, natural history and risk factors of childhood allergy in Ireland, as described in this thesis, echo those in worldwide allergy research. The variations of prevalence in different populations worldwide and the recurring themes of associations between childhood allergy and microbial exposures, from farming environments and/or gastrointestinal infections, as shown in this thesis, strengthen the mounting evidence that microbial exposure on GALT may hold the key to the mechanisms of allergy development. In this regard, probiotics may be an area of particular interest in allergy modification. Although their effects in relation to allergy, have been investigated now for several years, our knowledge of their diversity, complex functions and interactions with gut microflora, remain rudimentary. Birth cohort studies which include genomic and microbiomic research are recommended in order to examine the underlying mechanisms and the natural course of allergic diseases.

The effect of positive psychological interventions on psychological and physical well-being during pregnancy

Prenatal well-being can have significant effects on the mother and developing foetus. Positive psychological interventions, including gratitude and mindfulness, consistently demonstrate benefits for well-being in diverse populations. No research has been conducted on gratitude during pregnancy; the few studies of prenatal mindfulness interventions have demonstrated well-being benefits. The current study examined the effects of gratitude and mindfulness interventions on prenatal maternal well-being, cortisol and birth outcomes. Five studies were conducted. Study 1 was a systematic review of mindfulness intervention effects on cortisol; this highlighted potential benefits of mindfulness but the need for rigorous protocols in future research. In Study 2 a gratitude and a mindfulness intervention were developed and evaluated; findings indicate usefulness of two 3 week interventions. Study 3 examined the effects of these interventions in a randomised controlled trial (RCT) of non-pregnant women, before examining a pregnant group. No significant intervention effects were found in this study, potentially due to insufficient power and poor protocol adherence. Changes in expected directions were observed for most outcomes and the potential utility of a combined gratitude and mindfulness intervention was noted. In Study 4 a gratitude during pregnancy (GDP) scale was developed and the reliability of an existing mindfulness measure (MAAS) was examined in a pregnant group. Both scales were found to be suitable and reliable measures in pregnancy. Study 5 incorporated the findings of the previous four studies to examine of the effect of a combined mindfulness and gratitude intervention with a group of pregnant women. Forty-six participants took part in a 5-week RCT that examined intervention effects on prenatal gratitude, mindfulness, happiness, satisfaction with life, social support, prenatal stress, depression and sleep. Findings indicated that the intervention improved sleep quality and that effects for prenatal distress were approaching significance. Issues of attrition and non-compliance to study protocols were problematic and are discussed. In summary, the current thesis highlights the need for robust measurement, and intervention and cortisol sampling protocols in future research, particularly with pregnant groups. Findings also demonstrate tentative benefits of a gratitude and mindfulness intervention during pregnancy.

A feasibility study evaluating docetaxel-based sequential and combination regimens in the adjuvant therapy of node-positive breast cancer

BACKGROUND AND PURPOSE: Docetaxel is an active agent in the treatment of metastatic breast cancer. We evaluated the feasibility of docetaxel-based sequential and combination regimens as adjuvant therapies for patients with node-positive breast cancer. PATIENTS AND METHODS: Three consecutive groups of patients with node-positive breast cancer or locally-advanced disease, aged < or = 70 years, received one of the following regimens: a) sequential A-->T-->CMF: doxorubicin 75 mg/m2 q 3 weeks x 3, followed by docetaxel 100 mg/m2 q 3 weeks x 3, followed by i.v. CMF days 1 + 8 q 4 weeks x 3; b) sequential accelerated A-->T-->CMF: A and T were administered at the same doses q 2 weeks; c) combination therapy: doxorubicin 50 mg/m2 + docetaxel 75 mg/m2 q 3 weeks x 4, followed by CMF x 4. When indicated, radiotherapy was administered during or after CMF, and tamoxifen started after the end of CMF. RESULTS: Seventy-nine patients have been treated. Median age was 48 years. A 30% rate of early treatment discontinuation was observed in patients receiving the sequential accelerated therapy (23% during A-->T), due principally to severe skin toxicity. Median relative dose-intensity was 100% in the three treatment arms. The incidence of G3-G4 major toxicities by treated patients, was as follows: skin toxicity a: 5%; b: 27%; c: 0%; stomatitis a: 20%; b: 20%; c: 3%. The incidence of neutropenic fever was a: 30%; b: 13%; c: 48%. After a median follow-up of 18 months, no late toxicity has been reported. CONCLUSIONS: The accelerated sequential A-->T-->CMF treatment is not feasible due to an excess of skin toxicity. The sequential non accelerated and the combination regimens are feasible and under evaluation in a phase III trial of adjuvant therapy.

3-year results of docetaxel-based sequential and combination regimens in the adjuvant therapy of node-positive breast cancer: a pilot study.

BACKGROUND: Docetaxel has proven efficacy in metastatic breast cancer. In this pilot study, we explored the efficacy/feasibility of docetaxel-based sequential and combination regimens as adjuvant therapy of node-positive breast cancer. PATIENTS AND METHODS: From March 1996 till March 1998, four consecutive groups of patients with stages II and III breast cancer, aged < or = 70 years, received one of the following regimens: a) sequential Doxorubicin (A) --> Docetaxel (T) --> CMF (Cyclophosphamide+Methotrexate+5-Fluorouracil): A 75 mg/m q 3 wks x 3, followed by T100 mg/m2 q 3 wks x 3, followed by i.v. CMF Days 1+8 q 4 wks x 3; b) sequential accelerated A --> T --> CMF: A and T administered at the same doses q 2 wks with Lenograstin support; c) combination therapy: A 50 mg/m2 + T 75 mg/m2 q 3 wks x 4, followed by CMF x 4; d) sequential T --> A --> CMF: T and A, administered as in group a), with the reverse sequence. When indicated, radiotherapy was administered during or after CMF, and Tamoxifen after CMF. RESULTS: Ninety-three patients were treated. The median age was 48 years (29-66) and the median number of positive axillary nodes was 6 (1-25). Tumors were operable in 94% and locally advanced in 6% of cases. Pathological tumor size was >2 cm in 72% of cases. There were 21 relapses, (18 systemic, 3 locoregional) and 11 patients (12%) have died from disease progression. At median follow-up of 39 months (6-57), overall survival (OS) was 87% (95% CI, 79-94%) and disease-free survival (DFS) was 76% (95% CI, 67%-85%). CONCLUSION: The efficacy of these docetaxel-based regimens, in terms of OS and DFS, appears to be at least as good as standard anthracycline-based adjuvant chemotherapy (CT), in similar high-risk patient populations.

Aging African American Women and the Impact of Positive Psychological Factors on Quality of Life

Aging African-American women are disproportionately affected by negative health outcomes and mortality. Life stress has strong associations with these health outcomes. The purpose of this research was to understand how aging African American women manage stress. Specifically, the effects of coping, optimism, resilience, and religiousness as it relates to quality of life were examined. This cross-sectional exploratory study used a self-administered questionnaire and examined quality of life in 182 African-American women who were 65 years of age or older living in senior residential centers in Baltimore using convenience sampling. The age range for these women was 65 to 94 years with a mean of 71.8 years (SD = 5.6). The majority (53.1%) of participants completed high school, with 23 percent (N = 42) obtaining college degrees and 19 percent (N = 35) holding advanced degrees. Nearly 58 percent of participants were widowed and 81 percent were retired. In addition to demographics, the questionnaire included the following reliable and valid survey instruments: The Brief Cope Scale (Carver, Scheier, & Weintraub, 1989), Optimism Questionnaire (Scheier, Carver, & Bridges, 1994), Resilience Survey (Wagnild & Young, 1987), Religiousness Assessment (Koenig, 1997), and Quality of Life Questionnaire (Cummins, 1996). Results revealed that the positive psychological factors examined were positively associated with and significant predictors of quality of life. The bivariate correlations indicated that of the six coping dimensions measured in this study, planning (r=.68) was the most positively associated with quality of life. Optimism (r=.33), resilience (=.48), and religiousness (r=.30) were also significantly correlated with quality of life. In the linear regression model, again the coping dimension of planning was the best predictor of quality of life (beta = .75, p <.001). Optimism (beta = .31, p <.001), resilience (beta = .34, p, .001) and religiousness (beta = .17, p <.01) were also significant predictors of quality of life. It appears as if positive psychology plays an important role in improving quality of life among aging African-American women.

The impact of shame on health-related quality of life among HIV-positive adults with a history of childhood sexual abuse.

Childhood sexual abuse is prevalent among people living with HIV, and the experience of shame is a common consequence of childhood sexual abuse and HIV infection. This study examined the role of shame in health-related quality of life among HIV-positive adults who have experienced childhood sexual abuse. Data from 247 HIV-infected adults with a history of childhood sexual abuse were analyzed. Hierarchical linear regression was conducted to assess the impact of shame regarding both sexual abuse and HIV infection, while controlling for demographic, clinical, and psychosocial factors. In bivariate analyses, shame regarding sexual abuse and HIV infection were each negatively associated with health-related quality of life and its components (physical well-being, function and global well-being, emotional and social well-being, and cognitive functioning). After controlling for demographic, clinical, and psychosocial factors, HIV-related, but not sexual abuse-related, shame remained a significant predictor of reduced health-related quality of life, explaining up to 10% of the variance in multivariable models for overall health-related quality of life, emotional, function and global, and social well-being and cognitive functioning over and above that of other variables entered into the model. Additionally, HIV symptoms, perceived stress, and perceived availability of social support were associated with health-related quality of life in multivariable models. Shame is an important and modifiable predictor of health-related quality of life in HIV-positive populations, and medical and mental health providers serving HIV-infected populations should be aware of the importance of shame and its impact on the well-being of their patients.

The impact of structured support groups for pregnant South African women recently diagnosed HIV positive.

The authors of this study evaluated a structured 10-session psychosocial support group intervention for newly HIV-diagnosed pregnant South African women. Participants were expected to display increases in HIV disclosure, self-esteem, active coping and positive social support, and decreases in depression, avoidant coping, and negative social support. Three hundred sixty-one pregnant HIV-infected women were recruited from four antenatal clinics in Tshwane townships from April 2005 to September 2006. Using a quasi-experimental design, assessments were conducted at baseline and two and eight months post-intervention. A series of random effects regression analyses were conducted, with the three assessment points treated as a random effect of time. At both follow-ups, the rate of disclosure in the intervention group was significantly higher than that of the comparison group (p<0.001). Compared to the comparison group at the first follow-up, the intervention group displayed higher levels of active coping (t=2.68, p<0.05) and lower levels of avoidant coping (t=-2.02, p<0.05), and those who attended at least half of the intervention sessions exhibited improved self-esteem (t=2.11, p<0.05). Group interventions tailored for newly HIV positive pregnant women, implemented in resource-limited settings, may accelerate the process of adjusting to one's HIV status, but may not have sustainable benefits over time.

Two versions of life: emotionally negative and positive life events have different roles in the organization of life story and identity.

Over 2,000 adults in their sixties completed the Centrality of Event Scale (CES) for the traumatic or negative event that now troubled them the most and for their most positive life event, as well as measures of current PTSD symptoms, depression, well-being, and personality. Consistent with the notion of a positivity bias in old age, the positive events were judged to be markedly more central to life story and identity than were the negative events. The centrality of positive events was unrelated to measures of PTSD symptoms and emotional distress, whereas the centrality of the negative event showed clear positive correlations with these measures. The centrality of the positive events increased with increasing time since the events, whereas the centrality of the negative events decreased. The life distribution of the positive events showed a marked peak in young adulthood whereas the life distribution for the negative events peaked at the participants' present age. The positive events were mostly events from the cultural life script-that is, culturally shared representations of the timing of major transitional events. Overall, our findings show that positive and negative autobiographical events relate markedly differently to life story and identity. Positive events become central to life story and identity primarily through their correspondence with cultural norms. Negative events become central through mechanisms associated with emotional distress.

Life scripts help to maintain autobiographical memories of highly positive, but not highly negative, events.

A representative sample of 1,307 respondents between the ages of 20 and 94 was asked how old they were when they felt most afraid, most proud, most jealous, most in love, and most angry. They were also asked when they had experienced their most important event and whether this event was positive or negative. In general, there was a reminiscence "bump" for positive but not negative events. To provide data on life scripts, 87 psychology students answered the same questions for a hypothetical 70-year-old. The undergraduates were more confident in dating positive than in dating negative events, and when they were confident, the distribution of responses predicted the survey data. The results support the idea of culturally shared life scripts for positive but not negative events, which structure retrieval processes and spaced practice.

FROM THE AETHIOPICA TO THE RENAISSANCE: RECOVERING A STAGE TRADITION OF POSITIVE REPRESENTATION OF AFRICANS IN EARLY MODERN ENGLAND

This dissertation looks at the connection between Heliodorus's fifth-century prose romance, An Aethiopian History, certain Renaissance texts, and how these texts helped influence an alternate representation of Africans in the early modern world. Through their portrayals of Africans, early modern English playwrights frequently give the impression that Africans, especially black Africans, were people without accomplishments, without culture. Previously, however, this was not the case. Africans were depicted with dignity, as a tradition existed for this kind of representation--and Renaissance Europe had long been acquainted with the achievements of Africans, dating back to antiquity. As the source of several lost plays, the Aethiopica is instrumental in dramatizing Africans favorably, especially on the early modern stage, and helped shape a stage tradition that runs alongside the stereotyping of Africans. This Heliodoran tradition can be seen in works of Greene, Heywood, Jonson, Shakespeare, and others in the motifs of crosscultural and transracial romance, male and female chastity, racial metamorphosis, lost or abandoned babies, wandering heroes, and bold heroines. In Jonson's Masque of Blackness and Masque of Beauty, I establish a connection between these two masques and Heliodorus's Aethiopica and argue for a Heliodoran stage tradition implicit in both masques through the conceit of blanching. In The English Moore, I explore how Richard Brome uses the Heliodoran and Jonsonian materials to create a negative quality of blackness that participates in the dramatic tradition of the degenerate African on the English Renaissance stage. With Othello, I contend that it is a drama that can be seen in the Heliodoran tradition by stressing certain motifs found in the play that derives from the Aethiopica. Reading Othello this way provides us with a more layered and historicized interpretation of Shakespeare's protagonists. Othello's nationality and faith make his exalted position in Venice and the Venetian army credible and logical. His nobility and heroic status become more sharply defined, giving us a fuller understanding of the emphasis he places on chastity--both for himself and for Desdemona. Instead of a traditional, compliant, and submissive Desdemona, a courageous, resourceful, witty, and pure heroine emerges--one who lives by the dictates of her conscience than by the constraints of societal norms. Recovering the tradition of positive portrayal of Africans that originated from the Aethiopica necessitated an examination of eleven plays that I contend helped to frame the dramatic tradition under investigation. Six of these plays are continental dramas, and five are English. Although three of the English plays are lost and the other two are seventeenth-century dramas, their titles and names of their protagonists, like those of the six extant continental plays, share the names of Heliodorus's hero and heroine, making an exploration of the continental plays imperative to facilitate their use as paradigms in reconstructing the three lost English plays. These continental dramas show that plays whose titles derive from the Aethiopica itself or reflect the names of its major characters follow Heliodorus's text closely, enabling an investigation of the Heliodoran tradition on the early modern English stage. Recovering the Heliodoran tradition adds to the exploration of racial politics and the understanding of the dramatic tradition that constrained and enabled Renaissance playwrights' representation of race and gender.

Structured Illumination Microscopy and a Quantitative Image Analysis for the Detection of Positive Margins in a Pre-Clinical Genetically Engineered Mouse Model of Sarcoma.

Intraoperative assessment of surgical margins is critical to ensuring residual tumor does not remain in a patient. Previously, we developed a fluorescence structured illumination microscope (SIM) system with a single-shot field of view (FOV) of 2.1 × 1.6 mm (3.4 mm2) and sub-cellular resolution (4.4 μm). The goal of this study was to test the utility of this technology for the detection of residual disease in a genetically engineered mouse model of sarcoma. Primary soft tissue sarcomas were generated in the hindlimb and after the tumor was surgically removed, the relevant margin was stained with acridine orange (AO), a vital stain that brightly stains cell nuclei and fibrous tissues. The tissues were imaged with the SIM system with the primary goal of visualizing fluorescent features from tumor nuclei. Given the heterogeneity of the background tissue (presence of adipose tissue and muscle), an algorithm known as maximally stable extremal regions (MSER) was optimized and applied to the images to specifically segment nuclear features. A logistic regression model was used to classify a tissue site as positive or negative by calculating area fraction and shape of the segmented features that were present and the resulting receiver operator curve (ROC) was generated by varying the probability threshold. Based on the ROC curves, the model was able to classify tumor and normal tissue with 77% sensitivity and 81% specificity (Youden's index). For an unbiased measure of the model performance, it was applied to a separate validation dataset that resulted in 73% sensitivity and 80% specificity. When this approach was applied to representative whole margins, for a tumor probability threshold of 50%, only 1.2% of all regions from the negative margin exceeded this threshold, while over 14.8% of all regions from the positive margin exceeded this threshold.

Positive regularised solutions in electromagnetic inverse scattering

Fredholm integral equations of the first kind are the mathematical model common to several electromagnetic, optical and acoustical inverse scattering problems. In most of these problems the solution must be positive in order to satisfy physical plausibility. We consider ill-posed deconvolution problems and investigate several linear regularization algorithms which provide positive approximate solutions at least in the absence of errors on the data.