Multi-fluorescent silica colloids for encoding large combinatorial libraries

Large chemical libraries can be synthesized on solid-support beads by the combinatorial split-and-mix method. A major challenge associated with this type of library synthesis is distinguishing between the beads and their attached compounds. A new method of encoding these solid-support beads, 'colloidal bar-coding', involves attaching fluorescent silica colloids ('reporters') to the beads as they pass through the compound synthesis, thereby creating a fluorescent bar code on each bead. In order to obtain sufficient reporter varieties to bar code extremely large libraries, many of the reporters must contain multiple fluorescent dyes. We describe here the synthesis and spectroscopic analysis of various mono- and multi-fluorescent silica particles for this purpose. It was found that by increasing the amount of a single dye introduced into the particle reaction mixture, mono- fluorescent silica particles of increasing intensities could be prepared. This increase was highly reproducible and was observed for six different fluorescent dyes. Multi-fluorescent silica particles containing up to six fluorescent dyes were also prepared. The resultant emission intensity of each dye in the multi-fluorescent particles was found to be dependent upon a number of factors; the hydrolysis rate of each silane-dye conjugate, the magnitude of the inherent emission intensity of each dye within the silica matrix, and energy transfer effects between dyes. We show that by varying the relative concentration of each silane-dye conjugate in the synthesis of multi-fluorescent particles, it is possible to change and optimize the resultant emission intensity of each dye to enable viewing in a fluorescence detection instrument.

Recurrent gains and losses of large (84-109 bp) repeats in the rDNA internal transcribed spacer 2 (ITS2) of rhipicephaline ticks

We studied the internal transcribed spacer 2 (ITS2) in twenty-two spp. of ticks from the subfamily Rhipicephalinae. A 104-109 base pair (bp) region was Imperfectly repeated In most ticks studied. Mapping the number of repeat copies on to a phylogeny from the ITS2 showed that there have been many Independent gains and losses of repeats. Comparison of the sequences of the repeat copies Indicated that in most taxa concerted evolution had played little if any role in the evolution of these regions, as the copies clustered by sequence position rather than species, In our putative secondary structure, each repeat copy can fold into a distinct and almost identical stem-loop complex; a gain or loss of a repeat copy apparently does not impair the function of the ITS2 in these ticks.

Effect of restricted feed intake on early reproductive development in Large White gilts

Forty-five Large White gilts were used to study the effect of energy intake from 28 to 176 d of age on body composition and reproductive development. From 28 to 60 d, the gilts were fed ad libitum a 16.6 MJ DE/kg, 24% crude protein and 1.3% total lysine diet. From 61 d of age three dietary treatments were used; 1) ad libitum access to feed (15.6 MJ DE/kg, 21% crude protein and 1.07% total lysine) (H), 2) feed offered at 75% (M) of the previous days intake of H, and 3) feed offered at 60% (L) of the previous days intake of H. ADG from 61 to 176 d of age was (p <0.05) affected by treatment. Although live weight at 176 d of age did not differ (p >0.1) the H gilts had higher (p <0.08) carcass weights than the M or L gilts. Back fat depths were similar (p >0.1) for all treatments at 115 d of age, however by 176 d of age M and H gilts were fatter (p <0.1) than L gilts. The mean lipid deposition (LD) from 115 to 176 d of age for L gilts (78.9 g/d) was less (p <0.05) than for M gilts (143.6 g/d) and H gilts (135.6 g/d). There were no differences between treatments for protein deposition (PD) over the same period. More (p <0.05) H gilts (n=8) attained puberty (first observed estrus) than either M gilts or L gilts (n=4 for both). Follicle numbers were similar (p >0.1) across treatments. For gilts that attained puberty, H gilts had fewer (p <0.05) follicles (13.5) than M gilts (19.7) and L gilts (21.3). For gilts with follicular development, H gilts had the heaviest (458.7 g) reproductive tract weight (RTW). However, for those that attained puberty, L gilts had the heaviest RTW. RTW were lowest for those with no follicular development. Energy restriction had a negative impact on puberty attainment, i.e. it took longer to reach puberty. However, for gilts that attained puberty, the number of follicles was greater for those on lower feed intakes. It would appear that rate of fat deposition, but not necessarily the total amount of fat, plays an important role in puberty attainment.

A subset-oriented algorithm for minimizing the number of steps required for synthesis of cyclic-peptide libraries

Libraries of cyclic peptides are being synthesized using combinatorial chemistry for high throughput screening in the drug discovery process. This paper describes the min_syn_steps.cpp program (available at http://www.imb.uq.edu.au/groups/smythe/tran), which after inputting a list of cyclic peptides to be synthesized, removes cyclic redundant sequences and calculates synthetic strategies which minimize the synthetic steps as well as the reagent requirements. The synthetic steps and reagent requirements could be minimized by finding common subsets within the sequences for block synthesis. Since a brute-force approach to search for optimum synthetic strategies is impractically large, a subset-orientated approach is utilized here to limit the size of the search. (C) 2002 Elsevier Science Ltd. All rights reserved.

Effect of changing data collection parameters on statistical motor unit number estimates

The effect of number of samples and selection of data for analysis on the calculation of surface motor unit potential (SMUP) size in the statistical method of motor unit number estimates (MUNE) was determined in 10 normal subjects and 10 with amyotrophic lateral sclerosis (ALS). We recorded 500 sequential compound muscle action potentials (CMAPs) at three different stable stimulus intensities (10–50% of maximal CMAP). Estimated mean SMUP sizes were calculated using Poisson statistical assumptions from the variance of 500 sequential CMAP obtained at each stimulus intensity. The results with the 500 data points were compared with smaller subsets from the same data set. The results using a range of 50–80% of the 500 data points were compared with the full 500. The effect of restricting analysis to data between 5–20% of the CMAP and to standard deviation limits was also assessed. No differences in mean SMUP size were found with stimulus intensity or use of different ranges of data. Consistency was improved with a greater sample number. Data within 5% of CMAP size gave both increased consistency and reduced mean SMUP size in many subjects, but excluded valid responses present at that stimulus intensity. These changes were more prominent in ALS patients in whom the presence of isolated SMUP responses was a striking difference from normal subjects. Noise, spurious data, and large SMUP limited the Poisson assumptions. When these factors are considered, consistent statistical MUNE can be calculated from a continuous sequence of data points. A 2 to 2.5 SD or 10% window are reasonable methods of limiting data for analysis. Muscle Nerve 27: 320–331, 2003

Effect of pore-network connectivity on multicomponent adsorption of large molecules

The effect of pore-network connectivity on binary liquid-phase adsorption equilibria using the ideal adsorbed solution theory (LAST) was studied. The liquid-phase binary adsorption experiments used ethyl propionate, ethyl butyrate, and ethyl isovalerate as the adsorbates and commercial activated carbons Filtrasorb-400 and Norit ROW 0.8 as adsorbents. As the single-component isotherm, a modified Dubinin-Radushkevich equation was used. A comparison with experimental data shows that incorporating the connectivity of the pore network and considering percolation processes associated with different molecular sizes of the adsorptives in the mixture, as well as their different corresponding accessibility, can improve the prediction of binary adsorption equilibria using the LAST Selectivity of adsorption for the larger molecule in binary systems increases with an increase in the pore-network coordination number, as well with an increase in the mean pore width and in the spread of the pore-size distribution.

Determinants of environmental disclosure in the annual reports of large companies operating in Portugal

Similarly to what has happened in other countries, since the early 1990s Portuguese companies have developed corporate environmental reporting practices in response to internal and external factors. This paper is based on empirical research directed to both the study of environmental reporting practices developed by Portuguese companies and the identification of the factors that explain the extent to which these companies disclose environmental information. This study focuses on the environmental disclosures made in the annual reports by a sample of 109 large firms operating in Portugal during the period 2002-04. Using the content analysis technique we have developed an index in order to assess the presence of the environmental disclosures in companies’ annual reports and their breadth. Based on the extant literature, several characteristics relating to firms’ attributes were selected and their influence on the level of environmental disclosure was tested empirically. The selected explanatory variables were firm size, industry membership, profitability, foreign ownership, quotation on the stock market and environmental certification. The results reveal that, in spite of the fact that the level of environmental information disclosed during the period 2002-04 is low, the extent of environmental disclosure has increased as well as the number of Portuguese companies that disclose environmental information. Moreover, the firm size and the fact that a company is listed on the stock market are positively related to the extent of environmental disclosure. This study adds to the international research on environmental disclosure by providing empirical data from a country, Portugal, where empirical evidence is still relatively unknown, extending the scope of the current understanding of the environmental reporting practices.

Effect of the number of shells on the pressure and energy of two-dimensional free bubble clusters

We have performed Surface Evolver simulations of two-dimensional hexagonal bubble clusters consisting of a central bubble of area lambda surrounded by s shells or layers of bubbles of unit area. Clusters of up to twenty layers have been simulated, with lambda varying between 0.01 and 100. In monodisperse clusters (i.e., for lambda = 1) [M.A. Fortes, F Morgan, M. Fatima Vaz, Philos. Mag. Lett. 87 (2007) 561] both the average pressure of the entire Cluster and the pressure in the central bubble are decreasing functions of s and approach 0.9306 for very large s, which is the pressure in a bubble of an infinite monodisperse honeycomb foam. Here we address the effect of changing the central bubble area lambda. For small lambda the pressure in the central bubble and the average pressure were both found to decrease with s, as in monodisperse clusters. However, for large,, the pressure in the central bubble and the average pressure increase with s. The average pressure of large clusters was found to be independent of lambda and to approach 0.9306 asymptotically. We have also determined the cluster surface energies given by the equation of equilibrium for the total energy in terms of the area and the pressure in each bubble. When the pressures in the bubbles are not available, an approximate equation derived by Vaz et al. [M. Fatima Vaz, M.A. Fortes, F. Graner, Philos. Mag. Lett. 82 (2002) 575] was shown to provide good estimations for the cluster energy provided the bubble area distribution is narrow. This approach does not take cluster topology into account. Using this approximate equation, we find a good correlation between Surface Evolver Simulations and the estimated Values of energies and pressures. (C) 2008 Elsevier B.V. All rights reserved.

Determining the number of clusters in categorical data

Cluster analysis for categorical data has been an active area of research. A well-known problem in this area is the determination of the number of clusters, which is unknown and must be inferred from the data. In order to estimate the number of clusters, one often resorts to information criteria, such as BIC (Bayesian information criterion), MML (minimum message length, proposed by Wallace and Boulton, 1968), and ICL (integrated classification likelihood). In this work, we adopt the approach developed by Figueiredo and Jain (2002) for clustering continuous data. They use an MML criterion to select the number of clusters and a variant of the EM algorithm to estimate the model parameters. This EM variant seamlessly integrates model estimation and selection in a single algorithm. For clustering categorical data, we assume a finite mixture of multinomial distributions and implement a new EM algorithm, following a previous version (Silvestre et al., 2008). Results obtained with synthetic datasets are encouraging. The main advantage of the proposed approach, when compared to the above referred criteria, is the speed of execution, which is especially relevant when dealing with large data sets.

Dynamical behaviour of multi-particle large-scale systems

Collective behaviours can be observed in both natural and man-made systems composed of a large number of elemental subsystems. Typically, each elemental subsystem has its own dynamics but, whenever interaction between individuals occurs, the individual behaviours tend to be relaxed, and collective behaviours emerge. In this paper, the collective behaviour of a large-scale system composed of several coupled elemental particles is analysed. The dynamics of the particles are governed by the same type of equations but having different parameter values and initial conditions. Coupling between particles is based on statistical feedback, which means that each particle is affected by the average behaviour of its neighbours. It is shown that the global system may unveil several types of collective behaviours, corresponding to partial synchronisation, characterised by the existence of several clusters of synchronised subsystems, and global synchronisation between particles, where all the elemental particles synchronise completely.

Localizing objects in large-scale cyber- physical systems

We use the term Cyber-Physical Systems to refer to large-scale distributed sensor systems. Locating the geographic coordinates of objects of interest is an important problemin such systems. We present a new distributed approach to localize objects and events of interest in time complexity independent of number of nodes.

An efficient scalable RNS architecture for large dynamic ranges

This paper proposes an efficient scalable Residue Number System (RNS) architecture supporting moduli sets with an arbitrary number of channels, allowing to achieve larger dynamic range and a higher level of parallelism. The proposed architecture allows the forward and reverse RNS conversion, by reusing the arithmetic channel units. The arithmetic operations supported at the channel level include addition, subtraction, and multiplication with accumulation capability. For the reverse conversion two algorithms are considered, one based on the Chinese Remainder Theorem and the other one on Mixed-Radix-Conversion, leading to implementations optimized for delay and required circuit area. With the proposed architecture a complete and compact RNS platform is achieved. Experimental results suggest gains of 17 % in the delay in the arithmetic operations, with an area reduction of 23 % regarding the RNS state of the art. When compared with a binary system the proposed architecture allows to perform the same computation 20 times faster alongside with only 10 % of the circuit area resources.

Matching CO2 large point sources and potential geological storage sites in mainland Portugal

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia do Ambiente, Perfil Gestão e Sistemas Ambientais

Using VISIR in a large undergraduate course: preliminary assessment results

The use of remote labs in undergraduate courses has been reported in literature several times since the mid 90's. Nevertheless, very few articles present results about the learning gains obtained by students using them, especially with a large number of students, thus suggesting a lack of data concerning their pedagogical effectiveness. This paper addresses such a gap by presenting some preliminary results concerning the use of a remote laboratory, known as VISIR, in a large undergraduate course on Applied Physics, with over 500 students enrolled.

Aseptic meningitis in a large MMR vaccine campaign (590,609 people) in Curitiba, Paraná, Brazil, 1998

The aseptic meningitis after Measles-Mumps-Rubella vaccine (MMR) is a well recognized complication, and different incidences have been observed in several studies. We retrospectively analyzed forty cases of aseptic meningitis, during a large public immunization campaign (1998) in Curitiba, Southern Brazil (590,609 people), admitted in our Service. The vaccine utilized was Leningrad-3-Zagreb mumps strain, Edmonston-Zagreb measles strain, and RA 27#3 rubella strain. In all county, a total number of 87 cases were reported, resulting in a incidence of 1.7 cases per 10,000 given doses . The mean age was 23.7 ± 12.8 years. The female:male ratio was 1.35:1. Severe headache with meningismus (92.5%), fever (87.5%), nausea/vomiting (82.5%) were the most common clinical findings. Three cases (7.5%) developed mild mumps. All patients underwent cerebrospinal fluid (CSF) tap with the following findings: mononuclear pleocytosis from 100 to 500 cells/mm³ in 17 cases (42.5%; 257.5 ± 260.6 cells/mm³); increased protein 28 cases (67.5%; 92.1 ± 76.9 mg/dL); glucose was normal in all cases (56.8 ± 11.2 mg/dL) except in 4 (10%) cases, which presented less than 44 mg/dL. All serological tests (latex to bacterial meningitis, Cryptococcus, cysticercosis, VDRL) and bacteriological cultures were negative. Virus identification were also negative in 8 samples. None of the patients had neurological deficits or related symptoms after one year of onset. We believe the benefit of vaccination clearly outweights the incidence of benign vaccine-associated meningitis.