Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores

Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are sometimes transferred not along lineages but rather across lineages. To the extent that this is so, Darwin's paradigm can apply only imperfectly to genomes, potentially complicating or perhaps undermining attempts to reconstruct historical relationships among genomes (i.e., a genome tree). Whether most genes in a genome have arisen via treelike (vertical) descent or by lateral transfer across lineages can be tested if enough complete genome sequences are used. We define a phylogenetically discordant sequence (PDS) as an open reading frame (ORF) that exhibits patterns of similarity relationships statistically distinguishable from those of most other ORFs in the same genome. PDSs represent between 6.0 and 16.8% (mean, 10.8%) of the analyzable ORFs in the genomes of 28 bacteria, eight archaea, and one eukaryote (Saccharomyces cerevisiae). In this study we developed and assessed a distance-based approach, based on mean pairwise sequence similarity, for generating genome trees. Exclusion of PDSs improved bootstrap support for basal nodes but altered few topological features, indicating that there is little systematic bias among PDSs. Many but not all features of the genome tree from which PDSs were excluded are consistent with the 16S rRNA tree.

Normal values for pelvic organ descent in health nulligravid young caucasian women

Translabial ultrasound is increasingly being used for the assessment of women presenting with pelvic floor dysfunction and incontinence (1,2). However, there is little information on normal values for bladder neck descent, with the two available studies disagreeing widely (3,4). No data has so far been published on mobility of the central and posterior compartment which can now also be assessed by ultrasound (5). This study presents normal values for urethral, bladder, cervical and rectal mobility in a cohort of young, stress continent, nulliparous nonpregnant women. Methods 118 nonpregnant nulliparous Caucasian women between 18 and 23 years of age were recruited for an ongoing twin study of pelvic floor function. Translabial ultrasound assessment of pelvic organ mobility was undertaken supine and after bladder emptying (6,7). The best of at least three effective Valsalva manoeuvres was used for evaluation, with no attempts at standardization of Valsalva pressure. Parameters of anterior compartment mobility were obtained by the use of on-screen calipers; cervical and rectal descent were evaluated on printouts. All examinations were carried out under direct supervision of the first author or by personnel trained by him for at least 100 consecutive assessments. Results The median age of participants in this study was 20 (range 18- 23). Mean body mass index was 23 (range 16.9- 36.7). Of 118 women, 2 were completely unable to perform a Valsalva manoeuvre despite repeated efforts at teaching and were excluded from analysis, as were ten women who complained of urinary stress incontinence, leaving 106 datasets. Average measurements for the parameters ‘retrovesical angle at rest’ (RVA-R) and on Valsalva (RVA-S), urethral rotation, bladder neck mobility, cysto-cele descent, cervical descent and descent of the rectal ampulla are given in Table 1.

A study of the radiation chemistry of poly(chlorotrifluoroethylene) by ESR spectroscopy

The ESR spectra of poly(chlorotrifluoroethylene) were recorded following gamma-radiolysis under vacuum at room temperature and 77 K. The very broad spectrum at 77 K revealed little fine structure with which to identity the radicals formed upon irradiation, but subsequent photobleaching and annealing studies, together with radiolytic studies at higher temperatures, afforded scope for making radical assignments. Both main-chain radicals and a range of chain-end radicals have been identified. The G-values for radical formation were 1.55, 0.36 and 0.32 at 77 K, 273 K and room temperature, respectively. (C) 2003 Elsevier Science Ltd. All rights reserved.

Culture, politics and identity: critical readings on gender in southeast Asia

Indian Journal of Gender Studies October 2012 vol. 19 no. 3 437-467

Symbolic Knowledge Extraction from Trained Neural Networks Governed by Lukasiewicz Logics

This work describes a methodology to extract symbolic rules from trained neural networks. In our approach, patterns on the network are codified using formulas on a Lukasiewicz logic. For this we take advantage of the fact that every connective in this multi-valued logic can be evaluated by a neuron in an artificial network having, by activation function the identity truncated to zero and one. This fact simplifies symbolic rule extraction and allows the easy injection of formulas into a network architecture. We trained this type of neural network using a back-propagation algorithm based on Levenderg-Marquardt algorithm, where in each learning iteration, we restricted the knowledge dissemination in the network structure. This makes the descriptive power of produced neural networks similar to the descriptive power of Lukasiewicz logic language, minimizing the information loss on the translation between connectionist and symbolic structures. To avoid redundance on the generated network, the method simplifies them in a pruning phase, using the "Optimal Brain Surgeon" algorithm. We tested this method on the task of finding the formula used on the generation of a given truth table. For real data tests, we selected the Mushrooms data set, available on the UCI Machine Learning Repository.

Identity – towards a conceptualization

The development of economical relations increases the interaction between organizations and stakeholders. It is no more acceptable to manage an organization under a transactional perspective where suppliers had a fundamental role. Nowadays organizations are being managed under a relational perspective where relations and relationship management in general have consequences in identity management (Hakansson e Snehota, 1989, 1995). A correct perception and management of identity is necessary to achieve distinctiveness in the competitive environment. This way, identity is influenced by relations with stakeholders in general and particularly with competitors. The ICIG concept states that identity is related with the values of the organization and it helps creating distinctiveness in the competitive environment (Van Riel, Balmer, 1997); Baker and Balmer (1997) state that identity is what the organization is; Suvatjis and de Chernatony (2005) refer that expressing identity is a dynamic process that evolves the use of a management model to face context changes; Kapferer (1991) states that brand identity is the project, the self conception of the brand. After reviewing and confronting literature under the plethora of identities’ concepts and perspectives (He, Balmer, 2007) one can’t find an integrative answer with all the elements that contribute to identity of organizations. The authors are strongly interested to contribute to the elimination of this limitation and to answer to strategic management needs. In a marketing context one can find: - the corporate identity approach that is focused in the distinctive attributes of an organization (Abratt, Balmer, Marwick e Fill, Stuart, Balmer and Gray, Alessandri, Suvatjis and de Chernatony) - the brand identity approach (related with the application of corporate identity studies to brands) - Kapferer, Semprini, Aaker, de Chernatony). Kapferer (1991), one of the most prolific authors in this field was the first author to integrate identity in a brand concept. In his view, identity is an emission concept. This idea is shared also by Aaker (1996). Yet, identity has to be managed in a competitive environment which is constantly changing. After reviewing and confronting literature, authors select concepts that are generally accepted by the investigators in order to design a model to analyze and manage identity: - corporate identity models: personality, image/reputation, culture, philosophy, mission, strategy, structure, communication - some of these concepts derive from identity models and others from identity management models; - brand identity models – Kapferer (1991, 2008) identity prism, witch is basis of literature in this field: culture, physical facet, personality, relationship (between brand and consumer), reflected consumer, consumers` self-concept. After discussion authors decide to include other concept in line with other authors` view: country of origin (Aaker, 1996). A discussion eliminates the twin concepts and the final selection is as follows: personality, image/reputation, culture (including philosophy and mission), strategy, structure, communication, culture, physical facet, relationship (between brand and consumer), reflected consumer, consumers` self-concept and according to authors` reflections “relationships” deriving from competitors` actions in competitive environment. Competitors’ actions and decisions have a stronger influence in the organizations` positioning than any other stakeholder as stated before. This is a work in progress towards a new model in identity analysis and management so an exploratory study will follow inquiring experts on identity in order to evaluate these concepts and correct the theoretical perspectives.

Corporate brand identity management – proposal of a new framework

The term “corporate brand” has been widely used in literature since the eighties. According to Balmer (1998) this concept tends to be used as an alternative to the concept of corporate identity. The author argues that the use of branding principles to discuss corporate identity has tended to align the area more closely with marketing. However, the literature on brand management (Aaker, 1991; Kapferer, 1991 and de Chernatony and McDonald, 1992), gives little attention to the corporate brand” (p. 985). Based on the concepts of corporate brand, brand identity and B2B relationship, the authors are interested in eliminating this gap in literature by designing a framework of corporate brand identity management. The aim of this investigation is to investigate the impact of B2B relationships in corporate brand identity management. The methodology used is quantitative analysis of surveys and scale development. The originality of this paper is to investigate the influence of the relationship between brands in corporate brand identity. This investigation is very important to help the decisions of the corporate brand managers and academics. According to literature, namely on corporate brands (Balmer 2002b, Hatch and Schultz, 2001, 2003) and on brand identity (Kapferer, 1991, 2008, Aaker, 1996, de Chernatony, 1999) the authors developed a corporate brand identity management framework considering relationships between brands a context variable with definite impact on identity management as stated by Hakansson and Snehota (1989, 1995). These authors consider that organisations´ identity management is pursued under a relational perspective with impact on identity management. Most researchers on identity and corporate brand emphasise the importance of external influences (Kennedy, 1977; King, 1991; de Chernatony, 1999; Balmer and Gray, 2000; Balmer, 2002a). Those influences concern legislation, concurrence, political issues... and stakeholders’ perceptions and reputations (due to the holistic approach demanded by corporate brands). In this context the authors claim the importance of another influence: B2B relationships. This decision is inspired in sociological studies (Mannheim, 1950; and Tajfel and Turner, 1979) regarding individual identity. These authors claim that individuals form their personality by interacting in the social field. The authors argue that corporate brand identity also develops itself under a relational approach. The relationships selected to pursue this investigation are the ones that are developed by Portuguese universities and investigation centres that cooperate by developing investigation. Those centres are administrative and financially autonomous

Corporate brand identity management in a technological faculty – how brand relationships influence students and companies reputations

Identity is traditionally defined as an emission concept [1]. Yet, some research points out that there are external factors that can influence it [2]; [3]; [4]. This subject is even more relevant if one considers corporate brands. According to Aaker [5] the number, the power and the credibility of corporate associations are bigger in the case of corporate brands. Literature recognizes the influence of relationships between companies in identity management. Yet, given the increasingly important role of corporate brands, it is surprising that to date no attempt to evaluate that influence has been made in the management of corporate brand identity. Also Keller and Lehman [6] highlight relationships and costumer experience as two areas requiring more investigation. In line with this, the authors intend to develop an empirical research in order to evaluate the influence of relationships between brands in the identity of corporate brand from an internal perspective by interviewing internal stakeholders (brand managers and internal clients). This paper is organized by main contents: theoretical background, research methodology, data analysis and conclusions and finally cues to future investigation.

The making of saudade. National identity and ethnic psychology in Portugal

Roots and rituals.The construction of ethnic identities, Ton Dekker, John Helsloot Carla Wijers editors, p. 267-268; Selected papers of the 6TH SIEF conference on 'Roots & rituals', Amsterdam 20-25 April 1998.

Enantiomeric fraction evaluation of pharmaceuticals in environmentalmatrices by liquid chromatography-tandem mass spectrometry

The interest for environmental fate assessment of chiral pharmaceuticals is increasing and enantioselective analytical methods are mandatory. This study presents an enantioselective analytical method for the quantification of seven pairs of enantiomers of pharmaceuticals and a pair of a metabolite. The selected chiral pharmaceuticals belong to three different therapeutic classes, namely selective serotonin reuptake inhibitors (venlafaxine, fluoxetine and its metabolite norfluoxetine), beta-blockers (alprenolol, bisoprolol, metoprolol, propranolol) and a beta2-adrenergic agonist (salbutamol). The analytical method was based on solid phase extraction followed by liquid chromatography tandem mass spectrometry with a triple quadrupole analyser. Briefly, Oasis® MCX cartridges were used to preconcentrate 250 mL of water samples and the reconstituted extracts were analysed with a Chirobiotic™ V under reversed mode. The effluent of a laboratory-scale aerobic granular sludge sequencing batch reactor (AGS-SBR) was used to validate the method. Linearity (r2 > 0.99), selectivity and sensitivity were achieved in the range of 20–400 ng L−1 for all enantiomers, except for norfluoxetine enantiomers which range covered 30–400 ng L−1. The method detection limits were between 0.65 and 11.5 ng L−1 and the method quantification limits were between 1.98 and 19.7 ng L−1. The identity of all enantiomers was confirmed using two MS/MS transitions and its ion ratios, according to European Commission Decision 2002/657/EC. This method was successfully applied to evaluate effluents of wastewater treatment plants (WWTP) in Portugal. Venlafaxine and fluoxetine were quantified as non-racemic mixtures (enantiomeric fraction ≠ 0.5). The enantioselective validated method was able to monitor chiral pharmaceuticals in WWTP effluents and has potential to assess the enantioselective biodegradation in bioreactors. Further application in environmental matrices as surface and estuarine waters can be exploited.

Identity and belonging in the novels of Dorn Rabinovici

This essay analyses how the different types of memory may influence the process of identity formation. It shall be argued that not only memories formed upon the subject’s experiences play a key role in this process; intermediated, received narratives from the past, memories transmitted either symbolically or by elder members of the group, or, what has been meanwhile termed as “postmemory”, also play an important part in the development of an individual’s identitary map. This theoretical framework will be illustrated with the novelistic work of Austrian Israeli-born historian, writer and political activist Doron Rabinovici (*1961). As a representative of the so-called “second generation” of Holocaust writers, a generation of individuals who did not experience the nazi genocide violence, but who had to form their identities under the shadow of such a brutal past, Rabinovici addresses essential topics such as the intergenerational transmission of memory and guilt within survivor families, identity formation of second generation individuals (Jews and non-Jews) and the question of simultaneously belonging to different social, historical and linguistic contexts.

THE MAKING OF THE IMMIGRANT IDENTITY IN THE PRESS: Constructing the Immigrant Imagined Community

A dissertation submitted in partial fulfilment of the requirements for the degree of Master in Arts

FROM NON-PLACE TO PLACE: A STUDY OF EUROPEAN PUBLIC SPACE AS A SPACE OF IDENTITY

Master Erasmus Mundus Crossways in European Humanities

Ambivalent Islam: the identity construction of Muslims under Portuguese colonial rule

This article wishes to contribute to the study of the historical processes that have been spotting Muslim populations as favourite targets for political analysis and governance. Focusing on the Portuguese archives, civil as well as military, the article tries to uncover the most conspicuous identity representations (mainly negative or ambivalent) that members of Portuguese colonial apparatus built around Muslim communities living in African colonies, particularly in Guinea-Bissau and Mozambique. The paper shows how these culturally and politically constructed images were related to the more general strategies by which Portuguese imagined their own national identity, both as ‘European’ and as ‘coloniser’ or ‘imperial people’. The basic assumption of this article is that policies enforced in a context of inter-ethnic and religious competition are better understood when linked to the identity strategies inherent to them. These are conceived as strategic constructions aimed at the preservation, the protection and the imaginary expansion of the subject, who looks for groups to be included in and out-groups to reject, exclude, aggress or eliminate. We think that most of the inter-ethnic relationships and conflicts, as well as the very experience of ethnicity, are born from this identity matrix.

Ambivalent Islam: the identity construction of Muslims under Portuguese colonial rule

This article wishes to contribute to the study of the historical processes that have been spotting Muslim populations as favourite targets for political analysis and governance. Focusing on the Portuguese archives, civil as well as military, the article tries to uncover the most conspicuous identity representations (mainly negative or ambivalent) that members of Portuguese colonial apparatus built around Muslim communities living in African colonies, particularly in Guinea- Bissau and Mozambique. The paper shows how these culturally and politically constructed images were related to the more general strategies by which Portuguese imagined their own national identity, both as ‘European’ and as ‘coloniser’ or ‘imperial people’. The basic assumption of this article is that policies enforced in a context of interethnic and religious competition are better understood when linked to the identity strategies inherent to them. These are conceived as strategic constructions aimed at the preservation, protection and imaginary expansion of the subject, who looks for groups to be included in and out-groups to reject, exclude, aggress or eliminate. The author argues that most of the inter-ethnic relationships and conflicts, as well as the very experience of ethnicity, are born from this identity matrix.