Modeling contact formation between atomic-sized gold tips via molecular dynamics

The formation and rupture of atomic-sized contacts is modelled by means of molecular dynamics simulations. Such nano-contacts are realized in scanning tunnelling microscope and mechanically controlled break junction experiments. These instruments routinely measure the conductance across the nano-sized electrodes as they are brought into contact and separated, permitting conductance traces to be recorded that are plots of conductance versus the distance between the electrodes. One interesting feature of the conductance traces is that for some metals and geometric configurations a jump in the value of the conductance is observed right before contact between the electrodes, a phenomenon known as jump-to-contact. This paper considers, from a computational point of view, the dynamics of contact between two gold nano-electrodes. Repeated indentation of the two surfaces on each other is performed in two crystallographic orientations of face-centred cubic gold, namely (001) and (111). Ultimately, the intention is to identify the structures at the atomic level at the moment of first contact between the surfaces, since the value of the conductance is related to the minimum cross-section in the contact region. Conductance values obtained in this way are determined using first principles electronic transport calculations, with atomic configurations taken from the molecular dynamics simulations serving as input structures.

The effects of sympatry on patterns of bill morphology between closely related species of birds, worldwide

When closely related species co-occur in sympatry, they face a significant challenge. They must adapt to the same local conditions in their shared environment, which favours the convergent evolution of traits, while simultaneously minimizing the costs of competition for shared resources that typically favours the divergent evolution of traits. Here, we use a comparative sister lineage approach to test how most species have responded to these conflicting selection pressures in sympatry, focusing on a key ecological trait: the bill morphology of birds. If similar bill morphologies incur fitness costs due to species interactions, then we predicted that the bill morphologies of closely related species would differ more in sympatry compared with allopatry. Alternatively, if similar bill morphologies incur fitness benefits due to local adaptation, then we predicted that the bill morphologies would be more similar in sympatry compared with allopatry. We used museum specimens to measure five aspects of bill (maxilla) morphology – depth, length, width, side shape, and bottom shape – in diverse bird species from around the world to test our alternative hypotheses. We found support for both divergent evolution and convergent evolution (or trait retention) in one ecological trait: closely related sympatric species diverged in bill depth, but converged in side shape. These patterns of bill evolution were influenced by the genetic distance between closely related sister taxa and the geographic distance between allopatric lineages. Overall, our results highlight species interactions as an important mechanism for the evolution of some (bill depth), but not all (bill shape), aspects of bill morphology in closely related species in sympatry, and provide strong support for the bill as a key ecological trait that can adapt in different ways to the conflicting challenges of sympatry.

Chronic hepatitis B: A critical appraisal of current approaches to therapy

Background & Aims: Treatment of chronic hepatitis B (CHB) involves a number of complex and controversial issues. Expert opinions may differ from those of practicing hepatologists and gastroenterologists. We aimed to explore this issue further after a critical review of the literature. Methods: A panel of 14 international experts graded the strength of evidence for 16 statements addressing 3 content areas: patient selection, therapeutic end points, and treatment options. Available data relating to the statements were reviewed critically in 3 small work groups. After discussion of each statement with the entire panel, the experts voted anonymously to accept or reject statements based on the strength of evidence and their experience. A total of 241 members of the American Association for the Study of Liver Diseases (AASLD) responded to the same statements and their responses were compared with those of the experts. A discordant response was defined as a difference of more than 20% in any of the 5 graded levels of response (accept or reject) between the 2 groups. Results: With the exception of 2 statements, the experts’ responses were relatively uniform. However, the responses of the AASLD members were discordant from the experts in 12 statements, spanning all 3 content areas. Conclusions: Several areas of disagreement on the management of CHB exist between experts and AASLD members. Our results indicate a potential knowledge gap among practicing hepatologists. Better educational efforts are needed to meet the challenge of managing this complex disorder in which even expert opinion occasionally may disagree.

Heuristic algorithm for computing reversal distance with multigene families via binary integer programming

Hannenhalli and Pevzner developed the first polynomial-time algorithm for the combinatorial problem of sorting of signed genomic data. Their algorithm solves the minimum number of reversals required for rearranging a genome to another when gene duplication is nonexisting. In this paper, we show how to extend the Hannenhalli-Pevzner approach to genomes with multigene families. We propose a new heuristic algorithm to compute the reversal distance between two genomes with multigene families via the concept of binary integer programming without removing gene duplicates. The experimental results on simulated and real biological data demonstrate that the proposed algorithm is able to find the reversal distance accurately. ©2005 IEEE

The roles of inducer size and distance in the Ebbinghaus illusion (Titchener circles)

Although the Ebbinghaus illusion is commonly used as an example of a simple size-contrast effect, previous studies have emphasised its complexity by identifying many factors that potentially influence the magnitude of the illusion. Here, in a series of three experiments, we attempt to simplify this complexity. In each trial, subjects saw a display comprising, on one side, a target stimulus surrounded by inducers and, on the other, an isolated probe stimulus. Their task was to indicate whether the probe appeared larger or smaller than the target. Probe size was adjusted with a one-up, one-down staircase procedure to find the point of subjective equality between probe and target. From these experiments, we argue that the apparent effects of inducer size are often confounded by the relative completeness of the inducing surround and that factors such as the similarity of the inducers and target are secondary. We suggest a simple model that can explain most of the data in terms of just two primary and independent factors: the relative size of the inducers and target, and the distance between the inducers and the target. The balance between these two factors determines whether the size of the target is underestimated or overestimated. © 2005 a Pion publication.

Applying A Normalized Compression Metric To The Measurement Of Dialect Distance

The paper discusses the application of a similarity metric based on compression to the measurement of the distance among Bulgarian dia- lects. The similarity metric is de ned on the basis of the notion of Kolmo- gorov complexity of a le (or binary string). The application of Kolmogorov complexity in practice is not possible because its calculation over a le is an undecidable problem. Thus, the actual similarity metric is based on a real life compressor which only approximates the Kolmogorov complexity. To use the metric for distance measurement of Bulgarian dialects we rst represent the dialectological data in such a way that the metric is applicable. We propose two such representations which are compared to a baseline distance between dialects. Then we conclude the paper with an outline of our future work.

Distances between Predicates in By-Analogy Reasoning Systems

The purpose is to develop expert systems where by-analogy reasoning is used. Knowledge “closeness” problems are known to frequently emerge in such systems if knowledge is represented by different production rules. To determine a degree of closeness for production rules a distance between predicates is introduced. Different types of distances between two predicate value distribution functions are considered when predicates are “true”. Asymptotic features and interrelations of distances are studied. Predicate value distribution functions are found by empirical distribution functions, and a procedure is proposed for this purpose. An adequacy of obtained distribution functions is tested on the basis of the statistical 2 χ –criterion and a testing mechanism is discussed. A theorem, by which a simple procedure of measurement of Euclidean distances between distribution function parameters is substituted for a predicate closeness determination one, is proved for parametric distribution function families. The proposed distance measurement apparatus may be applied in expert systems when reasoning is created by analogy.

On Coordination of Experts’ Estimations of Quantitative Variable

* The work was supported by the RFBR under Grants N07-01-00331a, 08-07-00136a

The mediating effect of innovation on the relationship between corporate reputation and performance in U.S. firms

In recent years, corporate reputation has gained the attention of many scholars in the strategic management and related fields. There is a general consensus that higher corporate reputation is positively related to firm success or performance. However, the link is not always straightforward; as a result, it calls for researchers to dedicate their efforts to investigate the causes and effects of firm reputation and how it is related to performance. In this doctoral dissertation, innovation is suggested as a mediating variable in this relationship. Innovation is a critical factor for firm success and survival. Highly reputed firms are in a more advantageous position to attract critical resources for innovation such as human and financial capital. These firms face constant pressure from external stakeholders, e.g. the general public, or customers, to achieve and remain at high levels of innovativeness. As a result, firms are in constant search, internally or externally, for new technologies expanding their knowledge base. Consequently, these firms engage in firms acquisitions. In the dissertation, the author assesses the effects of domestic versus international acquisitions as well as related versus unrelated acquisitions on the level of innovativeness and performance. Building upon an established measure of firm-level degree of internationalization (DOI), the dissertation proposes a more detailed and enhanced measure for the firm's DOI. It is modeled as an interaction effect between corporate reputation and resources for innovation. More specifically, firms with higher levels of internationalization will have access to resources for innovation, i.e. human and financial capital, at a global scale. Additionally, the distance between firms and higher education institutions, i.e. universities, is considered as another interaction effect for the human capital attraction. The dissertation is built on two theoretical frameworks, the resource-based view of the firm and institutional theory. It studies 211 U.S. firms using a longitudinal panel data structure from 2006 to 2012. It utilizes a linear dynamic panel data estimation methodology for its hypotheses analyses. Results confirm the hypotheses proposed in the study.

Comparison between transperineal ultrasound and digital dectection of levator ani trauma : can we improve the odds?

Aims To investigate the predictive ability of four digital assessment parameters to detect levator ani (LA) muscle defects (avulsion injury) and compare these to transperineal tomographic ultrasound images. Methods This was an observational study imbedded in a larger quasi-experimental cohort study for women with urinary incontinence. Seventy-two women, ≥60 years who had attended or were going to attend physiotherapy for treatment of urinary incontinence, were included in the study. Inclusion criteria from the parent study were symptoms of stress, urge or both types of urinary incontinence. The predictive ability of the following digital parameters: direct palpation of a discontinuity of the LA muscle from insertion on the pubic ramus; palpation of the distance between the muscle insertion sites; palpation of LA strength; palpation of LA tone, were analyzed against findings from tomographic transperineal ultrasound images. Correlation between methods was measured using Cohen's kappa for each of the individual parameters. Results Seventeen women (24%) presented with a complete or partial avulsion of the puborectalis muscle as diagnosed with tomographic ultrasound imaging. Nine women (13%) had complete avulsions, one of which was bilateral. The predictive ability of the digital assessment parameters varied from poor (k = 0.187, 95% CI [0.02–0.36]) to moderate (k = 0.569, 95% CI [0.31–0.83]). The new parameter of ‘width between insertion sites’ performed best. Conclusions Adding the parameter of “width between insertion sites” appears to enhance our ability to detect avulsion of the levator ani (LA) muscle by digital examination however it does not distinguish between unilateral or bilateral avulsion.

Comparison between transperineal ultrasound and digital dectection of levator ani trauma : can we improve the odds?

Aims To investigate the predictive ability of four digital assessment parameters to detect levator ani (LA) muscle defects (avulsion injury) and compare these to transperineal tomographic ultrasound images. Methods This was an observational study imbedded in a larger quasi-experimental cohort study for women with urinary incontinence. Seventy-two women, ≥60 years who had attended or were going to attend physiotherapy for treatment of urinary incontinence, were included in the study. Inclusion criteria from the parent study were symptoms of stress, urge or both types of urinary incontinence. The predictive ability of the following digital parameters: direct palpation of a discontinuity of the LA muscle from insertion on the pubic ramus; palpation of the distance between the muscle insertion sites; palpation of LA strength; palpation of LA tone, were analyzed against findings from tomographic transperineal ultrasound images. Correlation between methods was measured using Cohen's kappa for each of the individual parameters. Results Seventeen women (24%) presented with a complete or partial avulsion of the puborectalis muscle as diagnosed with tomographic ultrasound imaging. Nine women (13%) had complete avulsions, one of which was bilateral. The predictive ability of the digital assessment parameters varied from poor (k = 0.187, 95% CI [0.02–0.36]) to moderate (k = 0.569, 95% CI [0.31–0.83]). The new parameter of ‘width between insertion sites’ performed best. Conclusions Adding the parameter of “width between insertion sites” appears to enhance our ability to detect avulsion of the levator ani (LA) muscle by digital examination however it does not distinguish between unilateral or bilateral avulsion.

The effects of sympatry on patterns of bill morphology between closely related species of birds, worldwide

When closely related species co-occur in sympatry, they face a significant challenge. They must adapt to the same local conditions in their shared environment, which favours the convergent evolution of traits, while simultaneously minimizing the costs of competition for shared resources that typically favours the divergent evolution of traits. Here, we use a comparative sister lineage approach to test how most species have responded to these conflicting selection pressures in sympatry, focusing on a key ecological trait: the bill morphology of birds. If similar bill morphologies incur fitness costs due to species interactions, then we predicted that the bill morphologies of closely related species would differ more in sympatry compared with allopatry. Alternatively, if similar bill morphologies incur fitness benefits due to local adaptation, then we predicted that the bill morphologies would be more similar in sympatry compared with allopatry. We used museum specimens to measure five aspects of bill (maxilla) morphology – depth, length, width, side shape, and bottom shape – in diverse bird species from around the world to test our alternative hypotheses. We found support for both divergent evolution and convergent evolution (or trait retention) in one ecological trait: closely related sympatric species diverged in bill depth, but converged in side shape. These patterns of bill evolution were influenced by the genetic distance between closely related sister taxa and the geographic distance between allopatric lineages. Overall, our results highlight species interactions as an important mechanism for the evolution of some (bill depth), but not all (bill shape), aspects of bill morphology in closely related species in sympatry, and provide strong support for the bill as a key ecological trait that can adapt in different ways to the conflicting challenges of sympatry.

Using Kullback-Leibler Distance for Text Categorization

International audience

Étude de la médiane de permutations sous la distance de Kendall-Tau

La distance de Kendall-τ compte le nombre de paires en désaccord entre deux permuta- tions. La distance d’une permutation à un ensemble est simplement la somme des dis- tances entre cette permutation et les permutations de l’ensemble. À partir d’un ensemble donné de permutations, notre but est de trouver la permutation, appelée médiane, qui minimise cette distance à l’ensemble. Le problème de la médiane de permutations sous la distance de Kendall-τ, trouve son application en bio-informatique, en science politique, en télécommunication et en optimisation. Ce problème d’apparence simple est prouvé difficile à résoudre. Dans ce mémoire, nous présentons plusieurs approches pour résoudre le problème, pour trouver une bonne solution approximative, pour le séparer en classes caractéristiques, pour mieux com- prendre sa compléxité, pour réduire l’espace de recheche et pour accélérer les calculs. Nous présentons aussi, vers la fin du mémoire, une généralisation de ce problème et nous l’étudions avec ces mêmes approches. La majorité du travail de ce mémoire se situe dans les trois articles qui le composent et est complémenté par deux chapitres servant à les lier.

Stairway Uniformity Measurement: What Lateral Location Should Be Measured?

BACKGROUND: This project addressed an unresolved issue involving measurement methods for determining step uniformity. Leading experts on stairway safety agree that lack of step uniformity within a flight contributes to risk of missteps. A relatively new method for precisely measuring step dimensions is the nosing-to-nosing method. An issue in applying the method is lack of agreement on the lateral location to make the measurements. That location depends on where stairway users ascend and descend relative to the width of the steps. A prior investigator examined people descending to determine the lateral distance between the handrail center and the mid-line of the person’s body. He found the median was 44 cm. AIM: The two objectives of the experiment were to: (1) determine if a different set of stairway users will have the same median lateral distance from the handrail as those described in the prior observational study, and (2) determine if the lateral distance of participants is affected by their direction of travel and use of a handrail. METHODS: The investigators established visible distance markers on one stairway in a campus building and videotaped volunteer students ascending and descending the flight of stairs. Each of the 16 participant ascended with and without using the handrail, and each descended with and without using the handrail. Images were printed and analyzed to determine their lateral distance between the inner edge of the handrail and a point midway between the participant’s knees. Results were analyzed statistically to test hypotheses corresponding to the two objectives. RESULTS: The previous study found a median lateral distance of 44 cm when measured from the center of the handrail. Using comparable data, the median found in this study was 25 cm. Results of this study indicated that lateral distance from the handrail is significantly affected by the direction of travel and by use of the handrail. The greatest lateral distance was for ascending with the handrail. The shortest lateral distance was for descending without the handrail. VALUE: Committees develop and periodically revise standards for stairways leading to fire exits and workplace facilities. The practical value of this project is providing empirical evidence that standard developing committees may consider when convening to update their requirements and guidelines on how to measure step uniformity.