A Bias in ML Estimates of Branch Lengths in the Presence of Multiple Signals

Sequence data often have competing signals that are detected by network programs or Lento plots. Such data can be formed by generating sequences on more than one tree, and combining the results, a mixture model. We report that with such mixture models, the estimates of edge (branch) lengths from maximum likelihood (ML) methods that assume a single tree are biased. Based on the observed number of competing signals in real data, such a bias of ML is expected to occur frequently. Because network methods can recover competing signals more accurately, there is a need for ML methods allowing a network. A fundamental problem is that mixture models can have more parameters than can be recovered from the data, so that some mixtures are not, in principle, identifiable. We recommend that network programs be incorporated into best practice analysis, along with ML and Bayesian trees.

From Absence to Presence, from Silence to Voice: Victims in Transitional Justice Since the Nuremberg Trials

As much as victims have been absent in traditional and national criminal justice for a long time, they were invisible in transitional and international criminal justice after World War II. The Nuremberg Trials were dominated by the perpetrators, and documents were mainly used instead of victim testimony. Contemporaries shared the perspective that transitional justice, both international and national procedures should channel revenge by the victims and their families into the more peaceful venues of courts and legal procedures. Since then, victims have gained an ever more important role in transitional, post-conflict and international criminal justice. Non-judicial tribunals, Truth and Reconciliation Commissions, and international criminal courts and tribunals are relying on the testimony of victims and thus provide a prominent role for victims who often take centre stage in such procedures and trials. International criminal law and the human rights regime have provided victims with several routes to make themselves heard and fight against impunity. This paper tracks the road from absence to presence, and from invisibility to the visibility of victims during the second half of the last and the beginning of the present century. It shows in which ways their presence has shaped and changed transitional and international justice, and in particular how their absence or presence is linked to amnesties.

Evidence for a dual function of EphB4 as tumor promoter and suppressor regulated by the absence or presence of the ephrin-B2 ligand

Overexpression of the receptor tyrosine kinase EphB4 is common in epithelial cancers and linked to tumor progression by promoting angiogenesis, increasing survival and facilitating invasion and migration. However, other studies have reported loss of EphB4 suggesting a tumor suppressor function in some cancers. These opposing roles may be regulated by (i) the presence of the primary ligand ephrin-B2 that regulates pathways involved in tumor suppression or (ii) the absence of ephrin-B2 that allows EphB4 signaling via ligand-independent pathways that contribute to tumor promotion. To explore this theory, EphB4 was overexpressed in the prostate cancer cell line 22Rv1 and the mammary epithelial cell line MCF-10A. Overexpressed EphB4 localized to lipid-rich regions of the plasma membrane and confirmed to be ligand-responsive as demonstrated by increased phosphorylation of ERK1/2 and internalization. EphB4 overexpressing cells demonstrated enhanced anchorage-independent growth, migration and invasion, all characteristics associated with an aggressive phenotype, and therefore supporting the hypothesis that overexpressed EphB4 facilitates tumor promotion. Importantly, these effects were reversed in the presence of ephrin-B2 which led to a reduction in EphB4 protein levels, demonstrating that ligand-dependent signaling is tumor suppressive. Furthermore, extended ligand stimulation caused a significant decrease in proliferation that correlated with a rise in caspase-3/7 and -8 activities. Together, these results demonstrate that overexpression of EphB4 confers a transformed phenotype in the case of MCF-10A cells and an increased metastatic phenotype in the case of 22Rv1 cancer cells and that both phenotypes can be restrained by stimulation with ephrin-B2, in part by reducing EphB4 levels.

Economic growth and inequality patterns in the presence of costly technology adoption and uncertainty

We develop a stochastic endogenous growth model to explain the diversity in growth and inequality patterns and the non-convergence of incomes in transitional economies where an underdeveloped financial sector imposes an implicit, fixed cost on the diversification of idiosyncratic risk. In the model endogenous growth occurs through physical and human capital deepening, with the latter being the more dominant element. We interpret the fixed cost as a ‘learning by doing’ cost for entrepreneurs who undertake risk in the absence of well developed financial markets and institutions that help diversify such risk. As such, this cost may be interpreted as the implicit returns foregone due to the lack of diversification opportunities that would otherwise have been available, had such institutions been present. The analytical and numerical results of the model suggest three growth outcomes depending on the productivity differences between the projects and the fixed cost associated with the more productive project. We label these outcomes as poverty trap, dual economy and balanced growth. Further analysis of these three outcomes highlights the existence of a diversity within diversity. Specifically, within the ‘poverty trap’ and ‘dual economy’ scenarios growth and inequality patterns differ, depending on the initial conditions. This additional diversity allows the model to capture a richer range of outcomes that are consistent with the empirical experience of several transitional economies.

A history of heart interventions moderates the relationship between psychological variables and the presence of chest pain in older women with self-reported coronary heart disease

Objectives: This study examines the hypothesis that a past history of heart interventions will moderate the relationship between psychosocial factors (stressful life events, social support, perceived stress, having a current partner, having a past diagnosis of depression or anxiety over the past 3 years, time pressure, education level, and the mental health index) and the presence of chest pain in a sample of older women. Design: Longitudinal survey over a 3-year period. Methods: The sample was taken from a prospective cohort study of 10,432 women initially aged between 70 and 75 years, who were surveyed in 1996 and then again in 1999. Two groups of women were identified: those reporting to have heart disease but no past history of heart interventions (i.e., coronary artery bypass graft/angioplasty) and those reporting to have heart disease with a past history of heart interventions. Results: Binary logistic regression analysis was used to show that for the women with self-reported coronary heart disease but without a past history of heart intervention, feelings of time pressure as well as the number of stressful life events experienced in the 12 months prior to 1996 were independent risk factors for the presence of chest pain, even after accounting for a range of traditional risk factors. In comparison, for the women with self-reported coronary heart disease who did report a past history of heart interventions, a diagnosis of depression in the previous 3 years was the significant independent risk factor for chest pain even after accounting for traditional risk factors. Conclusion: The results indicate that it is important to consider a history of heart interventions as a moderator of the associations between psychosocial variables and the frequency of chest pain in older women. Statement of Contribution: What is already known on this subject? Psychological factors have been shown to be independent predictors of a range of health outcomes in individuals with coronary heart disease, including the presence of chest pain. Most research has been conducted with men or with small samples of women; however, the evidence does suggest that these relationships exist in women as well as in men. What does this study add? Most studies have looked at overall relationships between psychological variables and health outcomes. The few studies that have looked at moderators have mainly examined gender as a moderator. To our knowledge, this is the first published study to examine a history of heart interventions as a moderator of the relationship between psychological variables and the presence of chest pain.

Analysis of heat transfer and fluid flow in a triangular enclosure in presence of an adiabatic fin

Natural convection thermal boundary layer adjacent to the heated inclined wall of a right angled triangle with an adiabatic fin attached to that surface is investigated by numerical simulations. The finite volume based unsteady numerical model is adopted for the simulation. It is revealed from the numerical results that the development of the boundary layer along the inclined surface is characterized by three distinct stages, i.e. a start-up stage, a transitional stage and a steady stage. These three stages can be clearly identified from the numerical simulations. Moreover, in presence of adiabatic fin, the thermal boundary layer adjacent to the inclined wall breaks initially. However, it is reattached with the downstream boundary layer next to the fin. More attention has been given to the boundary layer development near the fin area.

Polymorphisms of the VDR gene are associated with presence of solar keratoses on the skin

Background Vitamin D has a range of biological effects including antiproliferative functions that are mediated through its receptors, encoded by the VDR gene. Objectives We investigated polymorphisms within the VDR gene for association with solar keratosis (SK), a biomarker for skin cancer, and examined interactions with skin phenotype. Methods Among participants of the community-based Nambour Skin Cancer Study, we genotyped 190 people with SKs and 190 without for ApaI, TaqI and FokI polymorphisms. Results We found a significant difference in genotype frequencies of the TaqI polymorphism between affected and unaffected populations (P = 0Æ008). The TT ⁄tt genotype group was associated with a twofold increase in odds of being affected by one or more SK. Individuals with fair skin and the TT ⁄tt genotype had about a sevenfold increase, whereas fair-skinned people with the Tt genotype had a fourfold increase in odds of being affected by SK. Individuals with the TT ⁄tt genotype who were prone to burn and not tan on acute sun exposure had about a sixfold increase in odds of SK. Fair-skinned people with VDR-Apa AA ⁄aa genotypes had about an eightfold increase in odds of being affected by SK compared with a fivefold increase in individuals with the Aa genotype and fair skin. Conclusions The trend for homozygote genotypes to increase the odds of SK suggests that intermediate VDR activity is important in protection or that the heterodimer formed by a heterozygous genotype may have an altered binding potential. Overall, these analyses indicate that VDR may be important in SK development.

Control of infrastructure inspection aircraft vertical dynamics in the presence of thermal disturbances

The low-altitude aircraft inspection of powerlines, or other linear infrastructure networks, is emerging as an important application requiring specialised control technologies. Despite some recent advances in automated control related to this application, control of the underactuated aircraft vertical dynamics has not been completely achieved, especially in the presence of thermal disturbances. Rejection of thermal disturbances represents a key challenge to the control of inspection aircraft due to the underactuated nature of the dynamics and specified speed, altitude, and pitch constraints. This paper proposes a new vertical controller consisting of a backstepping elevator controller with feedforward-feedback throttle controller. The performance of our proposed approach is evaluated against two existing candidate controllers.

Filter and control performance bounds in the presence of model uncertainties with aerospace applications

This thesis establishes performance properties for approximate filters and controllers that are designed on the basis of approximate dynamic system representations. These performance properties provide a theoretical justification for the widespread application of approximate filters and controllers in the common situation where system models are not known with complete certainty. This research also provides useful tools for approximate filter designs, which are applied to hybrid filtering of uncertain nonlinear systems. As a contribution towards applications, this thesis also investigates air traffic separation control in the presence of measurement uncertainties.

On Presence, Collective Performance and Assumptions of Causality

The ways we assume, observe and model “presence” and its effects are the focus in this paper. Entities with selectively shared presences are the basis of any collective, and of attributions (such as “humorous”, “efficient” or “intelligent”). The subtleties of any joint presence can markedly influence potentials, perceptions and performance of the collective as demonstrated when a humorous tale is counterpoised with disciplined thought. Disciplines build on presences assumed known or knowable while fluid and interpretable presences pervade humor. Explorations in this paper allow considerations of collectives, causality and the philosophy of computing. Economics has long considered issues of collective action in ways circumscribed by assumptions about the presence of economic entities. Such entities are deemed rational but they are clearly not intelligent. To reach its potential, collective intelligence research needs more adequate considerations of alternate presences and their impacts.

Foot massage versus quiet presence on agitation and mood in people with dementia : a randomised controlled trial

Background There is increasing interest in using complementary and alternative treatments to manage behavioural and psychological symptoms of dementia such as agitation, aggression and depressed mood. Objective To compare the effect of foot massage (intervention) and quiet presence (control) on agitation and mood in people with dementia. Design A randomised controlled trial using a within-subjects, crossover design. Settings Five long-term care facilities in Brisbane, Australia. The primary outcome was the Cohen-Mansfield Agitation Inventory (CMAI) and the secondary outcome was the Observed Emotion Rating Scale (OERS). The screening and data collection research assistants, families, and care staff were blinded to participant allocation. Participants Participants of the study were 55 long-term care residents aged 74–103 years (mean age 86.5), with moderate to severe dementia and a history of agitated behaviour according to the Pittsburgh Agitation Scale. A computer-program randomised participants to 10-min foot massage (intervention) or quiet presence (control), every weekday for 3 weeks. Results A carry-over effect was identified in the data, and so the data was treated as a parallel groups RCT. The mean total CMAI increased in both groups (reflecting an increase in agitation) with this increase greater in the quiet presence group than the foot massage group (p=0.03). There was a trend towards a difference on OERS General Alertness, with a positive change in alertness for participants in the foot massage group (indicating reduced alertness) and a negative change for participants in the quiet presence group (indicating increased alertness) (F(1,51)=3.88, p=0.05, partial ή2=0.07). Conclusions The findings highlight the need for further research on the specific conditions under which massage might promote relaxation and improve mood for people with dementia. The unfamiliar research assistants and variations in usual activity may have contributed to the increase in agitation and this needs further research.

Architecture as media and the war of presence

This essay is a critique of the discourse concerned with a so coiled Crisis of Representation. It examines the role of representational media (text and drawing) in the formation of the notion of an architectural ‘work’ and argues that there is no necessary privilege to any ordering of modes of representation rather particular orderings uncover specific agendas.

Capability presence in the newly internationalizing firm

We investigate the enablers of early internationalization of the firm. We posit that for firms to internationalize early in their lifecycles, sets of capabilities must be present at the firm’s formative stage and that these capabilities build upon routines that the founders bring into the new firm. These capabilities are aligned to establish a platform for internationalization unencumbered by the administrative heritage often observed in well-established firms. We model this phenomenon, testing it in a cross-national setting of early internationalizing firms in Australia and the United States. To do so, we draw upon a dynamic capabilities framing, conceptualizing and measuring the dynamic capabilities that founders apply in their early internationalization activities.

Control, operation and power sharing among parallel converter-interfaced DERs in a microgrid in the presence of unbalanced and harmonic loads

This paper demonstrates power management and control of DERs in an autonomous MG. The paper focuses on the control and performance of converter-interfaced DERs in voltage controlled mode. Several case studies are considered for a MG based on the different types of loads supplied by the MG (i.e. balanced three-phase, unbalanced, single-phase and harmonic loads). DERs are controlled by adjusting the voltage magnitude and angle in their converter output through droop control, in a decentralized concept. Based on this control method, DERs can successfully share the total demand of the MG in the presence of any type of loads. This includes proper total power sharing, unbalanced power sharing as well as harmonic power sharing, depending on the load types. The efficacy of the proposed power control, sharing and management among DERs in a microgrid is validated through extensive simulation studies using PSCAD/EMTDC.

Mass spectrometric study of the dissociation of Group XI metal complexes with fatty acids and glycerolipids : Ag2H+ and Cu2H+ ion formation in the presence of a double bond

Results of mass spectrometric studies are reported for the collisional dissociation of Group XI (Cu, Ag, Au) metal ion complexes with fatty acids (palmitic, oleic, linoleic and a-linolenic) and glycerolipids. Remarkably, the formation of M2H+ ions (M = Cu, Ag) is observed as a dissociation product of the ion complexes containing more than one metal cation and only if the lipid in the complex contains a double bond. Ag2H+ is formed as the main dissociation channel for all three of the fatty acids containing double bonds that were investigated while Cu2H+ is formed with one of the fatty acids and, although abundant, is not the dominant dissociation channel. Also. Cu(I) and Ag(I) ion complexes were observed with glycerolipids (including triacylglycerols and glycerophospholipids) containing either saturated or unsaturated fatty acid substituents. Interestingly. Ag2H+ ion is formed in a major fragmentation channel with the lipids that are able to form the complex with two metal cations (triacylglycerols and glycerophosphoglycerols), while lipids containing a fixed positive charge (glycerophospocholines) complex only with a single metal cation. The formation of Ag2H+ ion is a significant dissociation channel from the complex ion Ag-2(L-H)(+) where L = Glycerophospholipid (GP) (18:1/18:1). Cu(I) also forms complexes of two metal cations with glycerophospholipids but these do not produce Cu2H+ upon dissociation. Rather organic fragments, not containing Cu(I), are formed, perhaps due to different interactions of these metal cations with lipids resulting from the much smaller ionic radius of Cu(I) compared to Ag(I) (C).