Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction.

BackgroundOne of the most powerful methods for the prediction of protein structure from sequence information alone is the iterative construction of profile-type models. Because profiles are built from sequence alignments, the sequences included in the alignment and the method used to align them will be important to the sensitivity of the resulting profile. The inclusion of highly diverse sequences will presumably produce a more powerful profile, but distantly related sequences can be difficult to align accurately using only sequence information. Therefore, it would be expected that the use of protein structure alignments to improve the selection and alignment of diverse sequence homologs might yield improved profiles. However, the actual utility of such an approach has remained unclear.ResultsWe explored several iterative protocols for the generation of profile hidden Markov models. These protocols were tailored to allow the inclusion of protein structure alignments in the process, and were used for large-scale creation and benchmarking of structure alignment-enhanced models. We found that models using structure alignments did not provide an overall improvement over sequence-only models for superfamily-level structure predictions. However, the results also revealed that the structure alignment-enhanced models were complimentary to the sequence-only models, particularly at the edge of the "twilight zone". When the two sets of models were combined, they provided improved results over sequence-only models alone. In addition, we found that the beneficial effects of the structure alignment-enhanced models could not be realized if the structure-based alignments were replaced with sequence-based alignments. Our experiments with different iterative protocols for sequence-only models also suggested that simple protocol modifications were unable to yield equivalent improvements to those provided by the structure alignment-enhanced models. Finally, we found that models using structure alignments provided fold-level structure assignments that were superior to those produced by sequence-only models.ConclusionWhen attempting to predict the structure of remote homologs, we advocate a combined approach in which both traditional models and models incorporating structure alignments are used

Transient and steady-state velocity of domain walls for a complete range of drive fields

Approximate analytic solutions for transient and steady-state 180 deg domain wall motion in bulk magnetic material are obtained from the dynamic torque equations with a Gilbert damping term. The results for the Walker region in which the transient solution approaches the familiar Walker steady-state solution are presented in a slightly new form for completeness. An analytic solution corresponding to larger drive fields predicts an oscillatory motion with an average value which decreases with drive field for reasonable values of the damping parameter. These results agree with those obtained by a computer solution of the torque equation and those obtained with the assumption of a very large anisotropy field

Wall contraction in Bloch wall films

The phenomenon of wall contraction characterized by a peak in the velocity field relationship and a region of negative differential mobility is observed. Uniaxial magnetic thin films of various compositions and magnetic properties are studied in careful interrupted pulse experiments. The observed results agree quite well with the theory for bulk samples

Intra-cavitary uterine pathology in women with abnormal uterine bleeding: a prospective study of 1220 women.

OBJECTIVES: Our primary aim was to assess how patients characteristics, bleeding pattern, sonographic endometrial thickness (ET) and additional features at unenhanced ultrasound examination (UTVS) and at fluid instillation sonography (FIS) contribute to the diagnosis of intracavitary uterine pathology in women presenting with abnormal uterine bleeding (AUB). We further aimed to report the prevalence of pathology in women presenting with AUB. METHODS: 1220 consecutive women presenting with AUB underwent UTVS, colour Doppler imaging (CDI) and FIS. Most women (n = 1042) had histological diagnosis. RESULTS: Mean age was 50 years and 37% were postmenopausal. Of 1220 women 54% were normal, polyps were diagnosed in 26%, intracavitary fibroids in 11%, hyperplasia without atypia in 4% and cancer in 3%. All cancers were diagnosed in postmenopausal (7%) or perimenopausal (1%) women. ET had a low predictive value in premenopausal women (LR+ and LR- of 1.34 and 0.74, respectively), while FIS had a LR+ and LR- of 6.20 and 0.24, respectively. After menopause, ET outperformed all patient characteristics for the prediction of endometrial pathology (LR+ and LR- of 3.13 and 0.24). The corresponding LR+ and LR- were 10.85 and 0.71 for CDI and 8.23 and 0.26 for FIS. CONCLUSION: About half of the women presenting to a bleeding clinic will have pathology. In premenopausal women, benign lesions are often the cause of AUB. For the prediction of intracavitary pathology ET is of little value in premenopausal women. CDI and FIS substantially improve the diagnostic accuracy

'Public Relations in the World of Finance'

Public relations in financial markets came into its own after many Western economies liberalised during the 1980s. Public relations became an important means of building credibility in and shaping attitudes toward financial markets. This chapter explores PR activity throughout the world of finance - from wholesale finance (the 'factory floor') to retail finance (the 'shop window'). The chapter examines critiques of PR activity in both areas

Fintech’s transparency-publicity nexus: Value co-creation through transparency discourses in business-to-business digital marketing

This article engages with the critical study of contemporary publicity by examining transparency as a strategic project to platformize financial services. The article contributes to understandings of transparency as value co-creation in business-to-business (B2B) markets. Through field-level discourse analysis, the article shows that transparency is contingent primarily on the nature of the market, in this case, a platformized industry, which valorizes transparency as part of a regime of data-sharing and open access. Transparency is further contingent on the market actor: actors with lesser status and market legitimacy are more likely to seek to co-create transparency with market actors of greater or similar status and legitimacy. The article concludes that in commercial spaces, publicity’s relationship to transparency is not only determined by market logic, but that all market logics are being drawn further toward a technological definition of transparency as “shareveillance,” as more segments of economic life become platformized

Mathematical models in physiology

Computational modelling of biological processes and systems has witnessed a remarkable development in recent years. The search-term (modelling OR modeling) yields over 58000 entries in PubMed, with more than 34000 since the year 2000: thus, almost two-thirds of papers appeared in the last 5–6 years, compared to only about one-third in the preceding 5–6 decades.\ud \ud The development is fuelled both by the continuously improving tools and techniques available for bio-mathematical modelling and by the increasing demand in quantitative assessment of element inter-relations in complex biological systems. This has given rise to a worldwide public domain effort to build a computational framework that provides a comprehensive theoretical representation of integrated biological function—the Physiome.\ud \ud The current and next issues of this journal are devoted to a small sub-set of this initiative and address biocomputation and modelling in physiology, illustrating the breadth and depth of experimental data-based model development in biological research from sub-cellular events to whole organ simulations

AI Hype: Public Relations and AI's doomsday machine

This chapter broadens current professional debates by highlighting a different but vital relationship between the PR profession and AI, one in which PR professionals – acting as AI cheerleaders – are deeply implicated in generating AI hype. My discussion explores recent market studies research on disruption and hype cycles, before delving into the latest, somewhat disturbing phase in AI’s hype cycle, in which end-of-the-world scenarios are invoked to stimulate a climate of fear around AI. The chapter concludes by exploring some ethical concerns with promoting AI and automation as humanity’s inevitable future

How Will the Use of Technology in Translation and Testing Affect Language Learning?

Technology has an ever increasing impact on how we work and live. Article adressed the issue of the impact of technology in two key areas of language learning. On the one side learners increasingly used technology to translate. Given this trend, was there any real need to learn a language. On the other side, educational institutions increasingly used technology to rate language proficiency. Given this trend, would the work of the teacher become less and less important. The survey was conducted by using quantitative method. The respondents' age range was 18-25. There were 53 respondents, 35% were male and 65% were female. The instrument was a questionaire having 9 questions describing the students' reliance on computer in translation. It can be concluded that learners of English indicate that they accept and welcome the role of technology in language learning, but there is a doubt that the role and participation of humans in the learning process will be completely replaced. The human element remains an important ingredient. (EE

Low frequency creep in CoNiFe films

The results of an investigation of domain wall motion excited by slow rise-time, bipolar, hard-axis pulses in vacuum deposited CoNiFe films 1500A to 2000A thick are presented. The results are consistent with those of comparable NiFe films in spite of large differences in film properties. The present low frequency creep data together with previously published results in this and other laboratories can be accounted for by a model which requires that the wall structure change usually associated with low frequency creep be predominately a gyromagnetic process. The correctness of this model is reinforced by the observation that the wall coercive force, the planar wall mobility, and the occurrence of an abrupt wall structure change are the only properties closely correlated to the creep displacement characteristics of a planar wall in low dispersion films