Discovery of active proteins directly from combinatorial randomized protein libraries without display, purification or sequencing:identification of novel zinc finger proteins.

We have successfully linked protein library screening directly with the identification of active proteins, without the need for individual purification, display technologies or physical linkage between the protein and its encoding sequence. By using 'MAX' randomization we have rapidly constructed 60 overlapping gene libraries that encode zinc finger proteins, randomized variously at the three principal DNA-contacting residues. Expression and screening of the libraries against five possible target DNA sequences generated data points covering a potential 40,000 individual interactions. Comparative analysis of the resulting data enabled direct identification of active proteins. Accuracy of this library analysis methodology was confirmed by both in vitro and in vivo analyses of identified proteins to yield novel zinc finger proteins that bind to their target sequences with high affinity, as indicated by low nanomolar apparent dissociation constants.

Evaluating small business performance : a matched pair analysis of African Caribbean owned businesses in the UK

African Caribbean Owned Businesses (ACOBs) have been postulated as having performance-related problems especially when compared with other ethnic minority groups in Britain. This research investigates if ACOBs may be performing less than similar firms in the population and why this maybe so. Therefore the aspiration behind this study is one of ratifying the existence of performance differentials between ACOBs and White Asian Owned Businesses (WAOBs), by using a triangulation of methods and matched pair analysis. Every ACOB was matched along firm specific characteristics of age, size, legal form and industry (sector), with similar WAOBs. Findings show support for the hypothesis that ACOBs are more likely to perform less than the WAOBs; WAOBs out-performed ACOBs in the objective and subjective assessments. Though we found some differentials between both groups in the entrepreneur’s characteristics and various emphases in strategic orientation in overall business strategy. The most likely drivers of performance differentials were found in firm activities and operations. ACOBs tended to have brands that were not as popular in the mainstream with most of their manufactured goods being seen as ‘exotic’ while those by WAOBs were perceived as ‘traditional’. Moreover, ACOBs had a higher proportion of clients constituting of individuals than business organisations while the WAOBs had a higher proportion consisting of business organisations.

A novel concentration dependent amino acid ion pair strategy to mediate drug permeation using indomethacin as a model insoluble drug

Assessment of oral drug bioavailability is an important parameter for new chemical entities (NCEs) in drug development cycle. After evaluating the pharmacological response of these new molecules, the following critical stage is to investigate their in vitro permeability. Despite the great success achieved by prodrugs, covalent linking the drug molecule with a hydrophobic moiety might result in a new entity that might be toxic or ineffective. Therefore, an alternative that would improve the drug uptake without affecting the efficacy of the drug molecule would be advantageous. The aim of the current study is to investigate the effect of ion-pairing on the permeability profile of a model drug: indomethacin (IND) to understand the mechanism behind the permeability improvement across Caco-2 monolayers. Arginine and lysine formed ion-pairs with IND at various molar ratios 1:1, 1:2, 1:4 and 1:8 as reflected by the double reciprocal graphs. The partitioning capacities of the IND were evaluated using octanol/water partitioning studies and the apparent permeabilities (P app) were measured across Caco-2 monolayers for the different formulations. Partitioning studies reflected the high hydrophobicity of IND (Log P = 3) which dropped upon increasing the concentrations of arginine/lysine in the ion pairs. Nevertheless, the prepared ion pairs improved IND permeability especially after 60 min of the start of the experiment. Coupling partitioning and permeability results suggest a decrease in the passive transcellular uptake due to the drop in IND portioning capacities and a possible involvement of active carriers. Future work will investigate which transport gene might be involved in the absorption of the ion paired formulations using molecular biology technologies. © 2014 Elsevier B.V. All rights reserved.

Pair breaking and bound states in disordered superconductors

We study the effects of inhomogeneous pairing interactions and impurities in short-coherence-length superconductors. Within the Born approximation, the effects of pairing disorder and magnetic impurities are identical. The T-matrices for pairing disorder sites with and without an impurity give rise to bound states within the BCS (Bardeen-Cooper-Schrieffer) gap, consistent with scanning tunnelling microscopy results on Bi2Sr2CaCu2O8+δ with Zn or Ni impurities.

Sequencing Jobs with Uncertain Processing Times and Minimizing the Weighted Total Flow Time

We consider an uncertain version of the scheduling problem to sequence set of jobs J on a single machine with minimizing the weighted total flow time, provided that processing time of a job can take on any real value from the given closed interval. It is assumed that job processing time is unknown random variable before the actual occurrence of this time, where probability distribution of such a variable between the given lower and upper bounds is unknown before scheduling. We develop the dominance relations on a set of jobs J. The necessary and sufficient conditions for a job domination may be tested in polynomial time of the number n = |J| of jobs. If there is no a domination within some subset of set J, heuristic procedure to minimize the weighted total flow time is used for sequencing the jobs from such a subset. The computational experiments for randomly generated single-machine scheduling problems with n ≤ 700 show that the developed dominance relations are quite helpful in minimizing the weighted total flow time of n jobs with uncertain processing times.

Codon-precise, synthetic, antibody fragment libraries built using automated hexamer codon additions and validated through next generation sequencing

We have previously described ProxiMAX, a technology that enables the fabrication of precise, combinatorial gene libraries via codon-by-codon saturation mutagenesis. ProxiMAX was originally performed using manual, enzymatic transfer of codons via blunt-end ligation. Here we present Colibra™: an automated, proprietary version of ProxiMAX used specifically for antibody library generation, in which double-codon hexamers are transferred during the saturation cycling process. The reduction in process complexity, resulting library quality and an unprecedented saturation of up to 24 contiguous codons are described. Utility of the method is demonstrated via fabrication of complementarity determining regions (CDR) in antibody fragment libraries and next generation sequencing (NGS) analysis of their quality and diversity.

Refractive index sensor based on a pair of hybrid 45° and 81° tilted fiber gratings

A hybrid structure comprising of a 45° and an 81° TFG based RI sensor has been demonstrated. The experiment results show a higher RI sensitivity, being around 180nm/RIU at RI=1.345 and 926nm/RIU at RI=1.412 region. © 2014 OSA.

Operation sequencing optimization for five-axis prismatic parts using a particle swarm optimization approach

Operation sequencing is one of the crucial tasks in process planning. However, it is an intractable process to identify an optimized operation sequence with minimal machining cost in a vast search space constrained by manufacturing conditions. Also, the information represented by current process plan models for three-axis machining is not sufficient for five-axis machining owing to the two extra degrees of freedom and the difficulty of set-up planning. In this paper, a representation of process plans for five-axis machining is proposed, and the complicated operation sequencing process is modelled as a combinatorial optimization problem. A modern evolutionary algorithm, i.e. the particle swarm optimization (PSO) algorithm, has been employed and modified to solve it effectively. Initial process plan solutions are formed and encoded into particles of the PSO algorithm. The particles 'fly' intelligently in the search space to achieve the best sequence according to the optimization strategies of the PSO algorithm. Meanwhile, to explore the search space comprehensively and to avoid being trapped into local optima, several new operators have been developed to improve the particle movements to form a modified PSO algorithm. A case study used to verify the performance of the modified PSO algorithm shows that the developed PSO can generate satisfactory results in optimizing the process planning problem. © IMechE 2009.

Selection, staging and sequencing in the recent Chinese privatization

Selection in privatization is a decision-making process of choosing state-owned enterprises (SOEs), prioritizing and sequencing privatizing events, and determining the extent of private ownership in partial privatization. We investigate this process in an important but rarely studied case of China. Based on the SOE population over 1998-2008, we track 49,456 wholly SOEs and identify 9,359 privatization cases over time. Our econometric analysis concludes: (i) The privatization selection is a complex decision-making process in which local governments balance between various economic, financial and political objectives. (ii) In the recent Chinese privatization, firm performance relates to the selection, staging and sequencing in privatization in an inverted-U fashion. The worse and the best performing SOEs are more likely to remain state-owned, maintain higher state holding when privatized, and are less likely to be privatized later in time. These patterns suggest the privatization reform slowdown and the underlying changes in the privatization policy.

Manageable Workflows for Processing Parallel Sequencing Data

ACM Computing Classification System (1998): D.2.11, D.1.3, D.3.1, J.3, C.2.4.

Chemical sensor using Mach-Zehnder interferometer based on a pair of largely tilted fiber gratings

We propose an in-fiber Mach-Zehnder interferometer formed by a pair of largely tilted fiber gratings. The interference spectral characteristics have been investigated. The experimental results using this device as a chemical sensor have a sensitivity as high as 719nm/RIU. © 2012 OSA.

Orthogonally polarized bright–dark pulse pair generation in mode-locked fiber laser with a large-angle tilted fiber grating

We report on the generation of orthogonally polarized bright–dark pulse pair in a passively mode-locked fiber laser with a large-angle tilted fiber grating (LA-TFG). The unique polarization properties of the LA-TFG, i.e., polarization-dependent loss and polarization-mode splitting, enable dual-wavelength mode-locking operation. Besides dual-wavelength bright pulses with uniform polarization at two different wavelengths, the bright–dark pulse pair has also been achieved. It is found that the bright–dark pulse pair is formed due to the nonlinear couplings between lights with two orthogonal polarizations and two different wavelengths. Furthermore, harmonic mode-locking of bright–dark pulse pair has been observed. The obtained bright–dark pulse pair could find potential use in secure communication system. It also paves the way to manipulate the generation of dark pulse in terms of wavelength and polarization, using specially designed fiber grating for mode-locking.

Consistency of the decision-maker in pair-wise comparisons

Most authors assume that the natural behaviour of the decision-maker is being inconsistent. This paper investigates the main sources of inconsistency and analyses methods for reducing or eliminating inconsistency. Decision support systems can contain interactive modules for that purpose. In a system with consistency control, there are three stages. First, consistency should be checked: a consistency measure is needed. Secondly, approval or rejection has to be decided: a threshold value of inconsistency measure is needed. Finally, if inconsistency is ‘high’, corrections have to be made: an inconsistency reducing method is needed. This paper reviews the difficulties in all stages. An entirely different approach is to elaborate a decision support system in order to force the decision-maker to give consistent values in each step of answering pair-wise comparison questions. An interactive questioning procedure resulting in consistent (sub) matrices has been demonstrated.

Comparison of ion pair and buffered mobile phase chromatography of haloacetic acids using direct and indirect UV and fluorescence detection

Reversed-phase high performance liquid chromatographic methods for the analysis of Haloacetic acids have been developed and compared to conventional direct detection methods. Haloacetic acids commonly found in drinking water, including monochloro-, dichloro-, bromo-, iodo- and trichloroacetic acids- have been studied. The ion pairing agent benzyltributylammonium ion was studied in detail using indirect UV and indirect fluorescence detection. Five different competing ions were evaluated to decrease analysis times and lower the detection limit by this new method. The direct detection method utilized an ammonium sulfate buffer and UV detection yielding a detection limit of 100 ppb. The indirect method developed has the advantage of being able to simultaneously analyze UV and non-UV absorbing ions and molecules but requires long equilibration times and demonstrated lower sensitivity than the direct method. ^

Functionalized carbon nanotube nanoelectrodes for biomolecular recognition

The objective of this research is to develop nanoscale ultrasensitive transducers for detection of biological species at molecular level using carbon nanotubes as nanoelectrodes. Rapid detection of ultra low concentration or even single DNA molecules are essential for medical diagnosis and treatment, pharmaceutical applications, gene sequencing as well as forensic analysis. Here the use of functionalized single walled carbon nanotubes (SWNT) as nanoscale detection platform for rapid detection of single DNA molecules is demonstrated. The detection principle is based on obtaining electrical signal from a single amine terminated DNA molecule which is covalently bridged between two ends of an SWNT separated by a nanoscale gap. The synthesis, fabrication, chemical functionalization of nanoelectrodes and DNA attachment were optimized to perform reliable electrical characterization these molecules. Using this detection system fundamental study on charge transport in DNA molecule of both genomic and non genomic sequences is performed. We measured an electrical signal of about 30 pA through a hybridized DNA molecule of 80 base pair in length which encodes a portion of sequence of H5N1 gene of avian Influenza A virus. Due the dynamic nature of the DNA molecules the local environment such as ion concentration, pH and temperature significantly influence its physical properties. We observed a decrease in DNA conductance of about 33% in high vacuum conditions. The counterion variation was analyzed by changing the buffer from sodium acetate to tris(hydroxymethyl) aminomethane, which resulted in a two orders of magnitude increase in the conductivity of the DNA. The fabrication of large array of identical SWNT nanoelectrodes was achieved by using ultralong SWNTs. Using these nanoelectrode array we have investigated the sequence dependent charge transport in DNA. A systematic study performed on PolyG - PolyC sequence with varying number of intervening PolyA - PolyT pairs showed a decrease in electrical signal from 180 pA (PolyG - PolyC) to 30 pA with increasing number of the PolyA - PolyT pairs. This work also led to the development of ultrasensitive nanoelectrodes based on enzyme functionalized vertically aligned high density multiwalled CNTs for electrochemical detection of cholesterol. The nanoelectrodes exhibited selectively detection of cholesterol in the presence of common interferents found in human blood.