Chapter 1 : nucleobases with designed patterns of hydrogen bonding

The chemistry used in key bond-forming steps to prepare nucleobases with designed patterns of hydrogen bonding is surveyed. Incorporation of the nucleobases into DNA and RNA oligomers is achieved either chemically using building blocks such as nucleoside phosphoramidites or enzymatically using nucleotide triphosphates. By varying the hydrogen bonding pattern within nucleobases, and by incorporating additional substituents, new structures have been designed that "reach over" so that contacts with both strands in targeted duplex DNA can be made in antigene strategies to control gene expression. Various new base-pairing systems have been evaluated that expand the genetic alphabet beyond Watson-Crick base pairs A.T and G.C. For example, benzo-homologated analogs of the natural DNA bases represent a new genetic set of orthogonal, size-expanded derivatives that have been shown to encode amino acids of a protein in a living organism.

Managing the dynamic configuration of enterprises

Due to environmental changes and business trends such as globalisation, outsourcing and virtualisation, more and more companies get involved in business activities that are outside their direct control. This typically occurs by entering into collaborative relationships and joint ventures with specialised companies in order to fulfil the demands of customers quickly (DiMaggio, 2001). Organisational structures that results from such collaborative relationships and joint ventures are referred to in this paper as enterprises and the management of them known as enterprise management. The authors use the definition of the European Commission (2003) that defines an enterprise as “… an entity, regardless of its legal form … including partnerships or associations regularly engaged in economic activities.” Therefore in its most simple form an enterprise could be a single integrated company. However, findings from this research show that enterprises can also be made up of parts of different companies and the structure of the enterprise is contingent upon a variety of different factors. The success of the enterprise as a collaborative venture depends on the ability of companies to intermediate their internal core competencies into other participating companies’ value streams and simultaneously outsource their own peripheral activities to companies that can perform them quicker, cheaper, and more effectively (Lal et al., 1995). In other words, the peripheral activities of one member-company must be complemented by a core competence of another member-company within an overall enterprise.

Textbook (non-)adoption motives, legitimizing strategies and academic field configuration

Textbooks are an integral part of structured syllabus coverage in higher education. The argument advanced in this article is that textbooks are not simply products of inscription and embodied scholarly labour for pedagogical purposes, but embedded institutional artefacts that configure entire academic subject fields. Empirically, this article shows the various ways that motives of the (non-) adoption of textbooks have field institutional configuration effects. The research contribution of our study is threefold. First, we re-theorise the textbook as an artefact that is part of the institutional work and epistemic culture of academia. Second, we empirically show that the vocabularies of motive of textbook (non-) adoption and rhetorical strategies form the basis for social action and configuration across micro, meso and macro field levels. Our final contribution is a conceptualization of the ways that textbook (non-) adoption motives ascribe meaning to the legitimating processes in the configuration of whole subject fields.

Studies on the hydrogen bonding of organic chemicals

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Simultaneous demultiplexing and clock recovery using a single electroabsorption modulator in a novel bi-directional configuration

A single electroabsorption modulator was used to demultiplex a 10 Gbit/s channel from a 40 Gbit/s OTDM data stream, whilst simultaneously recovering the 10 GHz electrical clock. This was achieved using a new bi-directional operation of the EA modulator, combined with a simple phase-locked loop feedback circuit. Excellent system performance was achieved, indicating that operation up to and beyond 100 Gbit/s is possible using current technology.

Optimization of erbium-doped actively Q-switched fiber laser implemented in symmetric configuration

We report the results of an experimental study aimed at improving the performance of actively Q-switched fiber lasers. Unlike generic design schemes employing photonic crystal fibers, largemodal diameter fibers or double-clad fibers, we demonstrate a high-power, actively Q-switched laser based on standard com- munication erbium doped fibers with peak irradiance beyond the state-of-the-art at 3.1 GW/cm2 . The laser had 2.2 kW peak power, 15.5 ns pulse duration and 36.8 µJ pulse energy. We have also investigated the dynamics of pulse generation and have success- fully suppressed pulse instabilities caused by backscattered laser emission reaching the pump laser diodes.

Resource-aware configuration in smart camera networks

A recent trend in smart camera networks is that they are able to modify the functionality during runtime to better reflect changes in the observed scenes and in the specified monitoring tasks. In this paper we focus on different configuration methods for such networks. A configuration is given by three components: (i) a description of the camera nodes, (ii) a specification of the area of interest by means of observation points and the associated monitoring activities, and (iii) a description of the analysis tasks. We introduce centralized, distributed and proprioceptive configuration methods and compare their properties and performance. © 2012 IEEE.

June Sutor and the C-H…O hydrogen bonding controversy

In 1962, D. June Sutor published the first crystallographic analysis of C–H…O hydrogen bonding based on a selection of structures then known. Her follow-up paper the next year cited more structures and provided more details, but her ideas met with formidable opposition. This review begins by describing knowledge of C-H…O hydrogen bonding available at the time from physico-chemical and spectroscopic studies. By comparison of structures cited by Sutor with modern redeterminations, the soundness of her basic data set is assessed. The plausibility of the counter-arguments against her is evaluated. Finally, her biographical details are presented along with consideration of factors that might have impeded the acceptance of her work. © 2012 Taylor & Francis.

Histidine hydrogen bonding in MHC at pH 5 and pH 7 modeled by molecular docking and molecular dynamics simulations

Hydrogen bonds play important roles in maintaining the structure of proteins and in the formation of most biomolecular protein-ligand complexes. All amino acids can act as hydrogen bond donors and acceptors. Among amino acids, Histidine is unique, as it can exist in neutral or positively charged forms within the physiological pH range of 5.0 to 7.0. Histidine can thus interact with other aromatic residues as well as forming hydrogen bonds with polar and charged residues. The ability of His to exchange a proton lies at the heart of many important functional biomolecular interactions, including immunological ones. By using molecular docking and molecular dynamics simulation, we examine the influence of His protonation/deprotonation on peptide binding affinity to MHC class II proteins from locus HLA-DP. Peptide-MHC interaction underlies the adaptive cellular immune response, upon which the next generation of commercially-important vaccines will depend. Consistent with experiment, we find that peptides containing protonated His residues bind better to HLA-DP proteins than those with unprotonated His. Enhanced binding at pH 5.0 is due, in part, to additional hydrogen bonds formed between peptide His+ and DP proteins. In acidic endosomes, protein His79β is predominantly protonated. As a result, the peptide binding cleft narrows in the vicinity of His79β, which stabilizes the peptide - HLA-DP protein complex. © 2014 Bentham Science Publishers.

Dynamic decision-making based on NFR for managing software variability and configuration selection

Due to dynamic variability, identifying the specific conditions under which non-functional requirements (NFRs) are satisfied may be only possible at runtime. Therefore, it is necessary to consider the dynamic treatment of relevant information during the requirements specifications. The associated data can be gathered by monitoring the execution of the application and its underlying environment to support reasoning about how the current application configuration is fulfilling the established requirements. This paper presents a dynamic decision-making infrastructure to support both NFRs representation and monitoring, and to reason about the degree of satisfaction of NFRs during runtime. The infrastructure is composed of: (i) an extended feature model aligned with a domain-specific language for representing NFRs to be monitored at runtime; (ii) a monitoring infrastructure to continuously assess NFRs at runtime; and (iii) a exible decision-making process to select the best available configuration based on the satisfaction degree of the NRFs. The evaluation of the approach has shown that it is able to choose application configurations that well fit user NFRs based on runtime information. The evaluation also revealed that the proposed infrastructure provided consistent indicators regarding the best application configurations that fit user NFRs. Finally, a benefit of our approach is that it allows us to quantify the level of satisfaction with respect to NFRs specification.

Reach extension of high-capacity LR-PONs in chain configuration of distributed amplifier structure

We show 100-Gb/s single-channel transmission in LR-PONs with at least 512 way split and up to 160 km total distance is feasible by means of "chained" cable with amplifier solutions, and appropriate FIR filter designs. © 2015 OSA.

In situ diagnostics and prognostics of wire bonding faults in IGBT modules for electric vehicle drives

This paper presents a diagnostic and prognostic condition monitoring method for insulated-gate bipolar transistor (IGBT) power modules for use primarily in electric vehicle applications. The wire-bond-related failure, one of the most commonly observed packaging failures, is investigated by analytical and experimental methods using the on-state voltage drop as a failure indicator. A sophisticated test bench is developed to generate and apply the required current/power pulses to the device under test. The proposed method is capable of detecting small changes in the failure indicators of the IGBTs and freewheeling diodes and its effectiveness is validated experimentally. The novelty of the work lies in the accurate online testing capacity for diagnostics and prognostics of the power module with a focus on the wire bonding faults, by injecting external currents into the power unit during the idle time. Test results show that the IGBT may sustain a loss of half the bond wires before the impending fault becomes catastrophic. The measurement circuitry can be embedded in the IGBT drive circuits and the measurements can be performed in situ when the electric vehicle stops in stop-and-go, red light traffic conditions, or during routine servicing.

Absolute configuration and biosynthesis of pahayokolide A from Lyngbya sp. Strain 15-2 of the Florida Everglades

Pahayokolides A-D are cytotoxic cyclic polypeptides produced by the freshwater cyanobacterium Lyngbya sp. strain 15-2 that possess an unusual β-amino acid, 3-amino-2,5,7,8-tetrahydroxy-10-methylundecanoic acid (Athmu). The absolute configuration of pahayokolides A-D was determined using advanced Marfey’s method. It was also confirmed that a pendant N-acetyl- N-methyl leucine moiety in pahayokolide A was absent in pahayokolides B and pahayokolides C-D were conformers of pahayokolide A. Feeding experiments indicated that the biosynthesis of the Athmu sidechain arises from leucine or α-ketoisovalerate, however could not be further extended by three rounds of condensation with malonate units. Putative four peptide and one unique polyketide synthetases in Lyngbya sp. strain 15-2 were identified by using a PCR method and degenerate primers derived from conserved core sequences of known NRPSs and PKSs. Identification of one unique KS domain conflicted with the logic rule that the long side chain of Athmu was assembled by three rounds of ketide extensions if PKSs were involved. A gene cluster (pah) encoding a peptide synthetase putatively producing pahayokolide was cloned, partially sequenced and characterized. Seven modules of the non-ribosomal peptide synthetase (NRPS) were identified. Ten additional opening reading frames (ORFs) were found, responsible for peptide resistance, transport and degradation. Although the predicted substrate specificities of NRPS agreed with the structure of pahayokolide A partially, the disagreement could be explained. However, no PKS gene was found in the pah gene cluster.

Developing a high density platinum/alumina hermetic feedthrough

Typically, hermetic feedthroughs for implantable devices, such as pacemakers, use a alumina ceramic insulator brazed to a platinum wire pin. This combination of material has a long history in implantable devices and has been approved by the FDA for implantable hermetic feedthroughs. The growing demand for increased input/output (I/O) hermetic feedthroughs for implantable neural stimulator applications could be addressed by developing a new, cofired platinum/alumina multilayer ceramic technology in a configuration that supports 300 plus I/Os, which is not commercially available. Seven platinum powders with different particle sizes were used to develop different conductive cofire inks to control the densification mismatch between platinum and alumina. Firing profile (ramp rate, burn- out and holding times) and firing atmosphere and concentrations (hydrogen (wet/dry), air, neutral, vacuum) were also optimized. Platinum and alumina exhibit the alloy formation reaction in a reduced atmosphere. Formation of any compound can increase the bonding of the metal/ceramic interface, resulting in enhanced hermeticity. The feedthrough fabricated in a reduced atmosphere demonstrated significantly superior performance than that of other atmospheres. A composite structure of tungsten/platinum ratios graded thru the via structure (pure W, 50/50 W/Pt, 80/20 Pt/W and pure Pt) exhibited the best performance in comparison to the performance of other materials used for ink metallization. Studies on the high temperature reaction of platinum and alumina, previously unreported, showed that, at low temperatures in reduced atmosphere, Pt 3Al or Pt8Al21 with a tetragonal structure would be formed. Cubic Pt3Al is formed upon heating the sample to temperatures above 1350 °C. This cubic structure is the equilibrium state of Pt-Al alloy at high temperatures. The alumina dissolves into the platinum ink and is redeposited as a surface coating. This was observed on both cofired samples and pure platinum thin films coated on a 99.6 Wt% alumina and fired at 1550 °C. Different mechanisms are proposed to describe this behavior based on the size of the platinum particle

Absolute Configuration and Biosynthesis of Pahayokolide A from Lyngbya sp. Strain 15-2 of the Florida Everglades

Pahayokolides A-D are cytotoxic cyclic polypeptides produced by the freshwater cyanobacterium Lyngbya sp. strain 15-2 that possess an unusual β-amino acid, 3-amino-2,5,7,8-tetrahydroxy-10-methylundecanoic acid (Athmu). The absolute configuration of pahayokolides A-D was determined using advanced Marfey’s method. It was also confirmed that a pendant N-acetyl-N-methyl leucine moiety in pahayokolide A was absent in pahayokolides B and pahayokolides C-D were conformers of pahayokolide A. Feeding experiments indicated that the biosynthesis of the Athmu sidechain arises from leucine or α-ketoisovalerate, however could not be further extended by three rounds of condensation with malonate units. Putative four peptide and one unique polyketide synthetases in Lyngbya sp. strain 15-2 were identified by using a PCR method and degenerate primers derived from conserved core sequences of known NRPSs and PKSs. Identification of one unique KS domain conflicted with the logic rule that the long side chain of Athmu was assembled by three rounds of ketide extensions if PKSs were involved. A gene cluster (pah) encoding a peptide synthetase putatively producing pahayokolide was cloned, partially sequenced and characterized. Seven modules of the non-ribosomal peptide synthetase (NRPS) were identified. Ten additional opening reading frames (ORFs) were found, responsible for peptide resistance, transport and degradation. Although the predicted substrate specificities of NRPS agreed with the structure of pahayokolide A partially, the disagreement could be explained. However, no PKS gene was found in the pah gene cluster.