Fingerprint Clustering with Bounded Number of Missing Values

The problem of clustering fingerprint vectors with missing values is an interesting problem in Computational Biology that has been proposed in Figueroa et al. (J. Comput. Biol. 11(5):887–901, 2004). In this paper we show some improvements in closing the gaps between the known lower bounds and upper bounds on the approximability of variants of the biological problem. Moreover, we have studied two additional variants of the original problem proposed in Figueroa et al. (Proc. 11th Computing: The Australasian Theory Symposium (CATS), CRPIT, vol. 41, pp. 57–60, 2005). We prove that all such problems are APX-hard even when each fingerprint contains only two unknown positions and we present a greedy algorithm that has constant approximation factors for these variants. Despite the hardness of these restricted versions of the problem, we show that the general clustering problem on an unbounded number of missing values such that they occur for every fixed position of an input vector in at most one fingerprint is polynomial time solvable.     

A 3D moisture-stress FEM analysis for time dependent problems in timber structures

This paper presents a 3D moisture-stress numerical analysis for timber structures under variable humidity and load conditions. An orthotropic viscoelastic-mechanosorptive material model is specialized on the basis of previous models. Both the constitutive model and the equations needed to describe the moisture flow across the structure are implemented into user subroutines of the Abaqus finite element code and a coupled moisture-stress analysis is performed for several types of mechanical loads and moisture changes. The presented computational approach is validated by analyzing some wood tests described in the literature and comparing the computational results with the reported experimental data.     

Photocatalytic behaviour of n-MoSe2 single crystals in contact with the I−, I2 redox couple in solar photo-electrochemical cells

The photocatalytic activity of the surface of n-MoSe₂ crystals for localized oxidation of iodide ions has been examined in a typical photo-electrochemical cell structure by direct microscopic observation and by output performance measurements under spot illumination.The results demonstrate the presence on the semiconductor surface of ‘active’ and ‘non active’ areas. This drastic difference in the catalytic properties of superficial points in the same semiconductor sample may explain the unique role of the I^?, I₂ redox couple in the behaviour of layer-type semiconductor photoelectrochemical solar cells, as well as the different response to selective superficial chemical agents presented by layered semiconductor crystals of apparently comparable surface morphology.     

Minimal models of adapted neuronal response to in vivo-like input currents

Rate models are often used to study the behavior of large networks of spiking neurons. Here we propose a procedure to derive rate models that take into account the fluctuations of the input current and firing-rate adaptation, two ubiquitous features in the central nervous system that have been previously overlooked in constructing rate models. The procedure is general and applies to any model of firing unit. As examples, we apply it to the leaky integrate-and-fire (IF) neuron, the leaky IF neuron with reversal potentials, and to the quadratic IF neuron. Two mechanisms of adaptation are considered, one due to an afterhyperpolarization current and the other to an adapting threshold for spike emission. The parameters of these simple models can be tuned to match experimental data obtained from neocortical pyramidal neurons. Finally, we show how the stationary model can be used to predict the time-varying activity of a large population of adapting neurons.     

A cyclic CCK8 analogue selective for the cholecystokinin type A receptor: design, synthesis, NMR structure and binding measurements

A cyclic CCK8 analogue, cyclo(29,34)[Dpr(29),Lys(34)]-CCK8 (Dpr=L-2,3-diaminopropionic acid), has been designed on the basis of the NMR structure of the bimolecular complex between the N-terminal fragment of the CCK(A) receptor and its natural ligand CCK8. The conformational features of cyclo(29,34)[Dpr(29),Lys(34)]-CCK8 have been determined by NMR spectroscopy in aqueous solution and in water containing DPC-d(38) micelles (DPC=dodecylphosphocholine). The structure of the cyclic peptide in aqueous solution is found to be in a relaxed conformation, with the backbone and Dpr29 side chain atoms making a planar ring and the N-terminal tripeptide extending approximately along the plane of this ring. In DPC/water, the cyclic peptide adopts a "boat-shaped" conformation, which is more compact than that found in aqueous solution. The cyclic constraint between the Dpr29 side chain and the CCK8 carboxyl terminus (Lys34) introduces a restriction in the backbone conformational freedom. However, the interaction of cyclo(29,34)[Dpr(29),Lys(34)]-CCK8 with the micelles still plays an important role in the stabilisation of the bioactive conformation. A careful comparison of the NMR structure of the cyclic peptide in a DPC micelle aqueous solution with the structure of the rationally designed model underlines that the turn-like conformation in the Trp30-Met31 region is preserved, such that the Trp30 and Met31 side chains can adopt the proper spatial orientation to interact with the CCK(A) receptor. The binding properties of cyclo(29,34)[Dpr(29),Lys(34)]-CCK8 to the N-terminal receptor fragment have been investigated by fluorescence spectroscopy in a micellar environment. Estimates of the apparent dissociation constant, K(d), were in the range of 70-150 nM, with a mean value of 120+/-27 nM. Preliminary nuclear medicine studies on cell lines transfected with the CCK(A) receptor indicate that the sulfated-Tyr derivative of cyclo(29,34)[Dpr(29),Lys(34)]-CCK8 displaces the natural ligand with an IC(50) value of 15 microM.     

On-Line Construction of Two-Dimensional Suffix Trees in O(n<Superscript>2</Superscript> log n) Time

The two-dimensional suffix tree of an n × n square matrix A is a compacted trie that represents all square submatrices of A[11]. For the off-line case, i.e., A is given in advance to the algorithm, it is known how to build it in optimal time, for any type of alphabet size [11],[18]. Motivated by applications in Image Compression[22[, Giancarlo and Guaiana [14] considered the on-line version of the two-dimensional suffix tree and presented an O(n² log² n)-time algorithm, which we refer to as GG. That algorithm is a nontrivial generalization of Ukkonen's on-line algorithm for standard suffix trees [23]. The main contribution in this paper is an O(log n) factor improvement in the time complexity of the GG algorithm, making it optimal for unbounded alphabets [9]. Moreover, the ideas presented here also lead to a major simplification of the GG algorithm. Technically, we are able to preserve most of the structure of the original GG algorithm, by reducing a computational bottleneck to a primitive operation, i.e., comparison of Lcharacters, which is here implemented in constant time rather than O(log n) time as in GG. However, preserving that structure comes at a price. Indeed, in order to make everything work, we need a careful reorganization of another fundamental algorithm: Weiner's algorithm for the construction of standard suffix trees [24]. Specifically, here we provide a version of that algorithm which takes linear time and works on-line and concurrently over a set of strings.     

An Optical Thermometer Exploiting Periodically Poled Lithium Niobate for Monitoring the Pantographs of High-Speed Trains

Optical thermometers have been widely investigated. Here, the temperature behavior of second harmonic generation (SHG) in periodically poled lithium niobate (PPLN) substrates is analyzed; indeed, the QPM tuning in PPLN devices and the obtained SHG efficiency depend on the crystal thermal expansion and dispersion, particularly in the case of guided propagation. Therefore, such devices are suitable to realize optical thermometers for demanding applications. This investigation originated with the request of a thermometer to be installed on the pantographs of high-speed trains. Therefore, it must be sturdy and reliable, but it has even to work in an EMD environment. The temperature behavior of the SHG was theoretically modeled and experimentally validated at 1550 nm, in both bulk propagation and APE channel waveguides. In the first case, by using a 10-mW source, which was obtained from a laser diode and a fiber amplifier, an accuracy of 0.3 degC was found. The pump power was about three orders of magnitude smaller in guided propagation. In view of testing on the trains, our investigation resulted in the design of a device without mechanical contacts with the input and output fibers. Since it works in free propagation, there are no serious alignment and packaging problems. The performances, which are expected to be the same of our tests, widely satisfy all the requirements for working effectively in a strongly hostile and EMD environment and for giving accurate measurements on a wide range of temperatures     

A new route to graphene starting from heavily ozonized fullerenes: Part 3 – an electron spin resonance study

It is shown that graphite oxide (GO) and both heavily ozonized C₆₀ and C₇₀ fullerenes, known as “fullerene ozopolymers,” are paramagnetic materials with a very strong electron spin resonance (ESR) signal at room temperature. When thermally annealed, the paramagnetic centers are gradually lost in large part. This occurs at 350°C in the case of GO, while for fullerene ozopolymers, a higher temperature is required, reaching the same results in the end. The half-width of ESR signal is linked to the distribution of paramagnetic centers. Once again, striking analogies were found in the half-width of the ESR signal measured on GO and fullerene ozopolymers, at least in the temperature range of 25–450°C. Similarly, the same g-factor values, which are diagnostic for understanding the chemical nature of paramagnetic centers, were found on both GO and fullerene ozopolymers in all ranges of temperature considered.     

Real-time risk monitoring in business processes: A sensor-based approach

This article proposes an approach for real-time monitoring of risks in executable business process models. The approach considers risks in all phases of the business process management lifecycle, from process design, where risks are defined on top of process models, through to process diagnosis, where risks are detected during process execution. The approach has been realized via a distributed, sensor-based architecture. At design-time, sensors are defined to specify risk conditions which when fulfilled, are a likely indicator of negative process states (faults) to eventuate. Both historical and current process execution data can be used to compose such conditions. At run-time, each sensor independently notifies a sensor manager when a risk is detected. In turn, the sensor manager interacts with the monitoring component of a business process management system to prompt the results to process administrators who may take remedial actions. The proposed architecture has been implemented on top of the YAWL system, and evaluated through performance measurements and usability tests with students. The results show that risk conditions can be computed efficiently and that the approach is perceived as useful by the participants in the tests.