The zero-inflated negative binomial regression model with correction for misclassification: an example in caries research

Zero-inflated models for count data are becoming quite popular nowadays and are found in many application areas, such as medicine, economics, biology, sociology and so on. However, in practice these counts are often prone to measurement error which in this case boils down to misclassification. Methods to deal with misclassification of counts have been suggested recently, but only for the binomial model and the Poisson model. Here we look at a more complex model, that is, the zero-inflated negative binomial, and illustrate how correction for misclassification can be achieved. Our approach is illustrated on the dmft-index which is a popular measure for caries experience in caries research. An extra problem was the fact that several dental examiners were involved in scoring caries experience. Using our example, we illustrate how a non-differential misclassification process for each examiner can lead to differential misclassification overall.     

One-dimensional extended lines of divacancy defects in graphene

Since the outstanding transport properties of graphene originate from its specific structure, modification at the atomic level of the graphene lattice is needed in order to change its electronic properties. Thus, topological defects play an important role in graphene and related structures. In this work, one-dimensional (1D) arrangement of topological defects in graphene are investigated within a density functional theory framework. These 1D extended lines of pentagons, heptagons and octagons are found to arise either from the reconstruction of divacancies, or from the epitaxial growth of graphene. The energetic stability and the electronic structure of different ideal extended lines of defects are calculated using a first-principles approach. Ab initio scanning tunneling microscopy (STM) images are predicted and compared to recent experiments on epitaxial graphene. Finally, local density of states and quantum transport calculations reveal that these extended lines of defects behave as quasi-1D metallic wires, suggesting their possible role as reactive tracks to anchor molecules or atoms for chemical or sensing applications.     

Compromise approach for predictive control of Timed Event Graphs with specifications defined by P-time Event Graphs

In this paper, the aim is to make the predictive control of a plant described by a Timed Event Graph which follows the specifications defined by a P-time Event Graph. We propose a compromise approach between the ideal optimality of the solution and the on-line application of the computed solution when the relevant optimal control cannot be applied for a given computer. The technique is based on a reduction of the number of iterations of the fixed point algorithm such that the computed control remains causal. The analysis of the partial satisfaction of the specifications at each iteration of the algorithm defined in the (max, + ) algebra shows that a subset of constraints is guaranteed by the control computed at each iteration while another one is possibly satisfied.     

A fully integrated CMOS PM radio receiver for wristwatchcalibration

In this paper, a fully integrated phase modulation radio receiver ASIC is presented. The ASIC is a mixed analog and digital circuit, implemented in a 1.5-μm CMOS technology. The only required external components are the reception antenna and a 32-kHz crystal. The radio receiver is dedicated to the 162-kHz “Allouis” radio transmitter. In addition to the audio information, 40-bit/s digital data are transmitted as phase modulation of the main carrier. These digital data may contain “live” information, such as the exact time. The presented ASIC demodulates and decodes these digital data. The principal features of this radio receiver are a low voltage supply (2.2-4.5 V), low power consumption (less than 150 μA), a large sensitivity range (10 μV-100 mV), and a reduced number of external components. Thanks to all of these performances, the circuit can be built in a wristwatch     

Activation of Bacillus licheniformis alpha-amylase through a disorder-->order transition of the substrate-binding site mediated by a calcium-sodium-calcium metal triad

The use of Rh immune globulin (RhIG) has dramatically decreased the incidence of hemolytic disease of the fetus and newborn resulting from the production of anti-D by an Rh-negative woman. However, despite the widespread use of RhIG, instances of Rh immunization continue to occur, most likely through failure to administer RhIG when indicated or in the appropriate dose. This utilization gap can be closed only through continued active surveillance by health care providers. The following report summarizes recommendations for the administration of RhIG, the dose required in various circumstances, prenatal and postnatal serologic testing of the obstetric patient, and the methods used to determine the degree of fetomaternal hemorrhage or the amount of Rh-positive RBCs in the circulation.     

Second substrate current peak and its relationship to gate-voltage dependent series resistance in submicrometre nMOS LDD transistors

The occurrence of the second substrate current hump (SSCH) has been thoroughly investigated and it is well known that the lateral electric field at the source side (E/sub s/) is responsible for the appearance of the SSCH in submicrometre nMOS LDD transistors. However the fall off of the SSCH after reaching a maximum value, the so called second substrate current peak (SSCP), is not well understood and explained. Here an improved model of the lateral electric field at the source side, which explains the SSCP in terms of the dependence of the source series resistance R/sub is/ on the gate-source voltage, is introduced.<>     

Hyperthermostable mutants of Bacillus licheniformis alpha-amylase: thermodynamic studies and structural interpretation

This paper provides further understanding of the thermodynamic and structural features determining the stability of Bacillus licheniformis alpha-amylase (BLA) at two crucial positions, His133 and Ala209. Results of protein modelling and saturated site-directed mutagenesis at position 133 and 209 have been reported in a previous paper (Declerck et al., 1995, Prot. Engng, 8, 1029-1037). In the first part of the present work, evidence is presented supporting the hypothesis that the stabilizing mutations reduce the rate of initial unfolding of the enzyme during the reversible step of the inactivation reaction and do not modify the irreversible processes undergone subsequently by the unfolded molecules. In the second part, we have examined the three- dimensional structure of BLA which has been determined recently by X- ray analysis (Machius et al., 1995, J. Mol. Biol., 246, 545-559). This analysis showed that our previous predictions made from molecular modelling were partly correct. At position 209, the effect of the stabilizing substitutions can be explained by a groove-filling effect reinforcing the hydrophobic packing between two helices of the central domain, while preserving a well-ordered water structure at the surface. At position 133, the stabilizing substitutions must compensate the loss of the hydrogen bond network in which the original histidine side-chain is involved; this compensation could be achieved through enhanced hydrophobic side-chain interactions within the beta-sheet where residue 133 is located, which correlates with the propensity of the residue to form and maintain a beta-strand conformation of the main chain at this position.      

DART—a High Level Software-Defined Radio Platform Model for Developing the Run-Time Controller

Novel cognitive radio platforms, such as IMEC’s COgnitive Baseband RAdio (COBRA), should ensure the feasibility of multiple streams and their reconfigurability and scalability during run-time. The control over these tasks should be dedicated to a run-time controller that (re)allocates the resources on the platform. E.g., when the channel conditions change requiring a switching to different modulation and coding scheme or a user starts a new stream. Current transaction level models are too detailed for rapid exploration of all run-time options and the high-level data-flow frameworks (such as Kahn process networks) lack the dynamism and reconfigurability that is essential for the exploration. In this paper we propose the DAtaflow for Run-Time (DART), the high-level dynamic data-flow platform model framework, suited for rapid run-time control development. We sketch how to use this framework to develop such a controller in the reactive and more challenging, proactive way. We derive the component timing based on Instruction Set Simulator (ISS) simulation and the reconfiguration timing based on Transaction Level Modeling (TLM) simulation. Finally, we verify results of our DART approach with full TLM simulation of our platform.     

MOS technology for VLSI

The scaling laws for MOS transistors are reviewed and the optimum performance predicted for both n-channel and p-channel devices are discussed. The physical and technological limitations for MOS VLSI are then described and some important technological challenges such as the implementation of new isolation techniques are pointed out. The mobility degragation effect due to velocity saturation is explained and illustrated by experimental data. The various limitations to the maximum operating voltage of scaleg devices are discussed. Finally, some considerations about speed and power consumption of scaled technologies are made.     

Regulation of trypsin activity by Cu2+ chelation of the substrate binding site

Lysine 188 of trypsin was replaced with histidine in order to create a metal chelation site in the substrate binding pocket of this protease, built in a metal binding 'switch,' and to be able to modulate its activity at lower pH. The catalytic properties of wild-type and mutant trypsin were measured with tetrapeptide substrates containing a nitroanilide leaving group and whole native protein substrate: beta- casein. The results obtained reveal that K188H mutation does not affect catalytic efficiency, raising only slightly (from 6 to 8) the arginine/lysine preference of the mutant and increasing 1.8- and 1.2- fold the second-order rate constant k(cat)/Km for arginine- and lysine- containing substrates, respectively. Compared with wild-type trypsin, K188H mutant shows, in the absence of Cu2+, a different catalytic activity pattern as a function of pH. The addition of Cu2+ to trypsin K188H induces a 30-100-fold increase in Km, while k(cat) is scarcely decreased. The hydrolytic activity of this mutant can be fully restored by addition of EDTA. In contrast to a chelating active site, a novel mode of metal-dependent inhibition activity of trypsin with copper is presented. As suggested by molecular modelling studies, the substrate binding pocket of the protease is considerably perturbed by vicinal chelation. More generally, this type of transition metal chelate may present wider possibilities of trypsin activity and specificity modulation than the previously accomplished chelation of a histidine moiety from a catalytic triad.