Physics-based analysis of Affymetrix microarray data

We analyze publicly available data on Affymetrix microarrays spike-in experiments on the human HGU133 chipset in which sequences are added in solution at known concentrations. The spike-in set contains sequences of bacterial, human and artificial origin. Our analysis is based on a recently introduced molecular-based model [E. Carlon and T. Heim, Physica A 362, 433 (2006)] which takes into account both probe-target hybridization and target-target partial hybridization in solution. The hybridization free energies are obtained from the nearest-neighbor model with experimentally determined parameters. The molecular-based model suggests a rescaling that should result in a "collapse" of the data at different concentrations into a single universal curve. We indeed find such a collapse, with the same parameters as obtained before for the older HGU95 chip set. The quality of the collapse varies according to the probe set considered. Artificial sequences, chosen by Affymetrix to be as different as possible from any other human genome sequence, generally show a much better collapse and thus a better agreement with the model than all other sequences. This suggests that the observed deviations from the predicted collapse are related to the choice of probes or have a biological origin, rather than being a problem with the proposed model.Comment: 11 pages, 10 figure

Incorporating the Dual Customer Roles in e-Service Design

E-service involves the delivery of useful services through information technology based service delivery channels such as the Internet. A distinguishing feature of e-service is the active and significant participation of customers in the service co-production process. With increasing customer participation in the e-service co-production process, it is important to incorporate customers’ needs both as a co-producer and as a patron into the design of e-service systems. However, these dual customer roles create a complex decision problem during e-service design. In the current paper we present a customer orientation strategy for e-service design, and propose a corresponding two-stage decision model based upon the customer orientation strategy to evaluate the efficiency and effectiveness of e-service design when the focus of the design is to meet customers’ needs as both co-producers and patrons. The decision model is then applied in an empirical study of the design of e-services of Internet food retailers. Key Words: Service Operations, E-Service, Co-production, Efficiency Analysis, Data Envelopment Analysis

Importing Corruption Culture from Overseas: Evidence from Corporate Tax Evasion in the United States

This paper studies how cultural norms and enforcement policies influence illicit corporate activities. Using confidential IRS audit data, we show that corporations with owners from countries with higher corruption norms engage in higher amounts of tax evasion in the U.S. This effect is strong for small corporations and decreases as the size of the corporation increases. In the mid-2000s, the United States implemented several enforcement measures which significantly increased tax compliance. However, we find that these enforcement efforts were less effective in reducing tax evasion by corporations whose owners are from countries with higher corruption norms. This suggests that cultural norms can be a challenge to legal enforcement.

Metric thickenings and group actions

2020 Spring.Includes bibliographical references.Let G be a group acting properly and by isometries on a metric space X; it follows that the quotient or orbit space X/G is also a metric space. We study the Vietoris–Rips and Čech complexes of X/G. Whereas (co)homology theories for metric spaces let the scale parameter of a Vietoris–Rips or Čech complex go to zero, and whereas geometric group theory requires the scale parameter to be sufficiently large, we instead consider intermediate scale parameters (neither tending to zero nor to infinity). As a particular case, we study the Vietoris–Rips and Čech thickenings of projective spaces at the first scale parameter where the homotopy type changes

Dynamics of the Pionium with the Density Matrix Formalism

The evolution of pionium, the $\pi^+ \pi^-$ hydrogen-like atom, while passing through matter is solved within the density matrix formalism in the first Born approximation. We compare the influence on the pionium break-up probability between the standard probabilistic calculations and the more precise picture of the density matrix formalism accounting for interference effects. We focus our general result in the particular conditions of the DIRAC experiment at CERN.Comment: 14 pages, 2 figures, submitted to J. Phys. B: At. Mol. Phy

Effective affinities in microarray data

In the past couple of years several studies have shown that hybridization in Affymetrix DNA microarrays can be rather well understood on the basis of simple models of physical chemistry. In the majority of the cases a Langmuir isotherm was used to fit experimental data. Although there is a general consensus about this approach, some discrepancies between different studies are evident. For instance, some authors have fitted the hybridization affinities from the microarray fluorescent intensities, while others used affinities obtained from melting experiments in solution. The former approach yields fitted affinities that at first sight are only partially consistent with solution values. In this paper we show that this discrepancy exists only superficially: a sufficiently complete model provides effective affinities which are fully consistent with those fitted to experimental data. This link provides new insight on the relevant processes underlying the functioning of DNA microarrays.Comment: 8 pages, 6 figure

Effects of multiple targeted repelling measures on the behaviour of individually tracked birds in an area of increasing human–wildlife conflict

1. Some animal populations are rapidly increasing in numbers and expanding their ranges, leading to intensified human–wildlife conflicts. A wide range of tools has been developed to repel animals from areas where they are suspected to cause damage. For waterfowl, direct comparisons of multiple repelling methods have so far focused only on species´ presence, total numbers, cost effectiveness or subsequent damage assessments, but not on individual behaviour. 2. Here, we investigated the individual responses of free-flying geese to three repelling methods using high-resolution tracking data. In an experimental setup, tracked individuals were repelled by human approach, gunshot sound or handheld lasers. 3. We found that repelling success and return time to the field where the repelling took place increased when individuals were repelled multiple times. Travel distances after the repelling events were longer after human approach and gunshot sound compared to the handheld laser treatments. In spring, the probability to return to the same field was higher after repelling with handheld lasers, but no difference between treatments was evident in autumn. We observed no increase in the probability to visit accommodation fields, where geese were allowed to forage and were not repelled, after the repelling events. 4. Synthesis and applications. We found no strong differences between the three methods regarding the repelling effectiveness and the resulting behaviour of the tracked geese. However, the higher return rates of individuals after repelling with handheld lasers in spring suggest that this method might be less effective in situations with bright sunlight or very large aggregations of geese. Apart from these limitations, we can recommend handheld lasers for repelling as they might reduce energetic losses for the geese and disturbance of non-target wildlife. Since repelling by gunshot sound and handheld lasers was twice as fast as repelling by human approach, those methods will reduce working hours by 50% and therefore be more cost-effective in practice

Dependence of α-synuclein aggregate morphology on solution conditions

α-Synuclein is the major component of Lewy bodies and Lewy neurites, which are granular and filamentous protein inclusions that are the defining pathological features of several neurodegenerative conditions such as Parkinson's disease. Fibrillar aggregates formed from α-synuclein in vitro resemble brain-derived material, but the role of such aggregates in the etiology of Parkinson's disease and their relation to the toxic molecular species remain unclear. In this study, we investigated the effects of pH and salt concentration on the in vitro assembly of human wild-type α-synuclein, particularly with regard to aggregation rate and aggregate morphology. Aggregates formed at pH 7.0 and pH 6.0 in the absence of NaCl and MgCl, were fibrillar; the pH 6.0 fibrils displayed a helical twist, as clearly evident by scanning force and electron microscopy. Incubations at pH 7.0 remained transparent during the process of aggregation and exhibited strong thioflavin-T and weak 8-anilino-1-naphthalene-sulfonate (ANS) binding; furthermore, they were efficient in seeding fibrillization of fresh solutions. In contrast, incubating α-synuclein at low pH (pH 4.0 or pH 5.0) resulted in the rapid formation of turbid suspensions characterized by strong ANS binding, reduced thioflavin-T binding and reduced seeding efficiency. At pH 4.0, fibril formation was abrogated; instead, very large aggregates (dimensions similar to100 mum) of amorphous appearance were visible by light microscopy. As with acidic conditions, addition of 0.2 M NaCl or 10 mM MgCl, to pH 7.0 incubations led to a shorter aggregation lag time and formation of large, amorphous aggregates. These results demonstrate that the morphology of α-synuclein aggregates is highly sensitive to solution conditions, implying that the fibrillar state does not necessarily represent the predominant or most functionally significant aggregated state under physiological conditions. (C) 2002 Elsevier Science Ltd. All rights reserved