Algorithmic computation of knot polynomials of secondary structure elements of proteins

The classification of protein structures is an important and still outstanding problem. The purpose of this paper is threefold. First, we utilize a relation between the Tutte and homfly polynomial to show that the Alexander-Conway polynomial can be algorithmically computed for a given planar graph. Second, as special cases of planar graphs, we use polymer graphs of protein structures. More precisely, we use three building blocks of the three-dimensional protein structure-alpha-helix, antiparallel beta-sheet, and parallel beta-sheet-and calculate, for their corresponding polymer graphs, the Tutte polynomials analytically by providing recurrence equations for all three secondary structure elements. Third, we present numerical results comparing the results from our analytical calculations with the numerical results of our algorithm-not only to test consistency, but also to demonstrate that all assigned polynomials are unique labels of the secondary structure elements. This paves the way for an automatic classification of protein structures.

Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome

Background: Germline mutations or large-scale deletions in the coding region and splice sites of STK11/LKB1 do not account for all cases of Peutz-Jeghers syndrome (PJS). It is conceivable that, on the basis of data from other diseases, inherited variation in promoter elements of STK11/LKB1 may cause PJS.

Behaviour of joints with bonded-in steel bars loaded parallel to the grain of timber elements

Within the sustainability context, this paper is extremely timely and relevant. The research focuses on broadening the use of timber structurally. The insight gained forms the basis for sustainable, fire resistant, economic and aesthetically pleasing moment resistant connections in timber.

Exploring Innovative Methodologies in time and place to analyze child protection documents as elements of practice

This paper aims to demonstrate how a derived approach to case file analysis, influenced by the work of Michel Foucault and Dorothy E.Smith, can offer innovative means by which to study the relations between discourse and practices in child welfare. The article explores text-based forms of organization in histories of child protection in Finland and in Northern Ireland. It is focused on case file records in different organizational child protection contexts in two jurisdictions. Building on a previous article (Author 1 & 2: 2011), we attempt to demonstrate the potential of how the relations between practices and discourses –a majorly important theme for understanding child welfare social work – can be effectively analysed using a combination of two approaches This article is based on three different empirical studies from our two jurisdictions Northern Ireland (UK) and Finland; one study used Foucault; the other Smith and the third study sought to combine the methods. This article seeks to report on ongoing work in developing, for child welfare studies, ‘a history that speaks back’ as we have described it.

Developing students’ ability to engage critically with science in the news: identifying elements of the ‘media awareness’ dimension

Worldwide, science education reform movements are stressing the need to promote ‘scienti?c literacy’ among young people. Increasingly, this is taken to include empowering students to engage critically with science-related news reporting. Despite this requirement now featuring in statutory curricula throughout the UK, there has, to date, been a dearth of research-informed advice to assist science teachers as they identify appropriate instructional objectives in this regard and design relevant learning activities through which these might be achieved. In this study, prominent science communication
scholars, science journalists, science educators and media educators were interviewed to determine what knowledge, skills and habits of mind they judged valuable for individuals reading science-related news stories. Teachers of science and of English from nine secondary schools in Northern Ireland addressed the same issue. A striking – and signi?cant – ?nding of the study was the very substantial number of statements of knowledge, skill and disposition o?ered by participants that relate to ‘media awareness’, an issue largely overlooked in the science education literature. The school-focused phase of the research suggests that cross-curricular approaches involving teachers of science collaborating with those of English/media education or media studies may best serve to address this important curricular goal.

Bioaccessibility of trace elements in soils in Northern Ireland

Assessment of elevated concentrations of potentially toxic elements (PTE) in soils and the association with specific soil parent material have been the focus of research for a number of years. Risk-based assessment of potential exposure scenarios to identified elevated PTE concentrations has led to the derivation of site- and contaminant-specific soil guideline values (SGVs), which represent generic assessment criteria (GACs) to identify exceeded levels that may reflect an unacceptable risk to human health. A better understanding of the ‘bioavailable’ or ‘bioaccessible’ contaminant concentrations offers an opportunity to better refine contaminant exposure assessments. Utilizing a comprehensive soil geochemical dataset for Northern Ireland provided by the Tellus Survey (GSNI) in conjunction with supplementary bioaccessibility testing of selected soil samples following the Unified BARGE Method, this paper uses exploratory data analysis and geostatistical analysis to investigate the spatial variability of pseudo-total and bioaccessible concentrations of As, Cd, Co, Cr. Cu, Ni, Pb, U, V and Zn. The paper investigates variations in individual element concentrations as well as cross-element correlations and observed lithological/pedological associations. The analysis of PTE concentrations highlighted exceeded levels of GAC values for V and Cr and exceeded SGV/GAC values for Cd, Cu, Ni, Pb, and Zn. UBM testing showed that for some soil parent materials associated with elevated PTE concentrations e.g. the Antrim Lava Group with high Ni concentrations, the measured oral bioaccessible fraction was relatively low. For other soil parent materials with relatively moderate PTE concentrations, measured oral bioaccessible fraction was relatively high (e.g. the Gala Sandstone Group of the Southern Uplands-Down Longford Terrain). These findings have implications for regional human health risk assessments for specific PTEs.

Frequency selective surface using nested split ring slot elements as a lens with mechanically reconfigurable beam steering capability

The design is described of a double layer frequency selective surface which can produce a differential phase shift of 180 ° as the wave propagates through it at normal incidence. The hand of an applied circularly polarized signal is reversed due to the 180° phase shift, and it is demonstrated that the exit circularly polarized output signal can be phase advanced or phase retarded by 180 ° upon rotation of the elements comprising the structure. This feature allows the surface to act as a spatial phase shifter. In this paper the beam steering capabilities of a 10 × 10 array of such elements are demonstrated. Here the individual elements comprising the array are rotated relative to each other in order to generate a progressive phase shift. At normal incidence the 3 dB Axial Ratio Bandwidth for LHCP to RHCP conversion is 5.3% and the insertion loss was found to be -2.3 dB, with minimum axial ratio of 0.05 dB. This array is shown to be able to steer a beam from -40 ° to +40 ° while holding axial ratio at the pointing angle to below 4 dB. The measured radiation patterns match the theoretical calculation and full-wave simulation results. © 2010 IEEE.

SEROTONINERGIC AND PEPTIDERGIC NERVE ELEMENTS IN THE PROTOSCOLEX OF ECHINOCOCCUS-GRANULOSUS (CESTODA, CYCLOPHYLLIDEA)

The localisation and distribution of 5-hydroxytryptamine (5-HT, or serotonin) and neuropeptides in the nervous system of the protoscolex of the hydatid organism Echinococcus granulosus were determined by an indirect immunofluorescence technique. Nerve-cell bodies immunoreactive for 5-HT occurred in the lateral ganglia and in association with the lateral longitudinal nerve cords. 5-HT immunostaining was also evident in the central nerve ring, in the rostellar nerves and in the nerve plexus innervating the suckers. Of the antisera used to screen the protoscolex for neuropeptide immunoreactivity (IR), immunostaining was obtained with those raised against pancreatic polypeptide (PP), peptide YY (PYY), substance P (SP), peptide histidine isoleucine (PI-II) and vasoactive intestinal peptide (VIP). The most extensive pattern of IR occurred with antisera to PP and PYY. Immunoreactive nerve elements were evident in the lateral ganglia, central nerve ring, rostellar nerves, rostellar ganglia, sucker plexus and longitudinal nerve cords. The distribution of SP-, PHI- and VIP-IRs was more restricted: SP-IR occurred in the lateral ganglia and sucker nerves, whilst PHI- and VIP-immunoreactive nerve elements were associated with the lateral longitudinal nerve cords. Protoscoleces cultured in vitro for 29 days were also examined and neuroanatomical changes noted. A greater development of the longitudinal nerve cords and their cross-connectives in the body of the worm was evident, and a group of nerve cells were seen to develop at the posterior end of the main lateral nerve cords.

CYTOCHEMICAL DEMONSTRATION OF CHOLINERGIC, SEROTONINERGIC AND PEPTIDERGIC NERVE ELEMENTS IN GORGODERINA-VITELLILOBA (TREMATODA, DIGENEA)

Standard enzyme cytochemical and indirect immunocytochemical techniques have been used in conjunction with light and confocal scanning laser microscopy (CSLM) to visualize cholinergic, serotoninergic and peptidergic nerve elements in whole-mount preparations of the amphibian urinary-bladder fluke, Gorgoderina vitelliloba. Cholinesterase (ChE) activity was localized in paired anterior ganglia, a connecting dorsal commissure and in the origins of the ventral nerve cords. Cholinergic ganglia were also evident in shelled embryos in the uterus. Serotonin-immunoreactivity (IR) was more extensive than ChE activity and was identified in both the central and peripheral nervous systems. Serotoninergic nerve fibres were associated with the somatic musculature and female reproductive ducts. Antisera to nine mammalian peptides and one invertebrate (FMRFamide) peptide have been used to investigate the peptidergic nervous system in the parasite. Immunoreactivity was obtained to five peptides, namely pancreatic polypeptide (PP), peptide YY (PYY), neuropeptide Y (NPY), substance P (SP) and FMRFamide. Peptidergic nerve fibres were found to be more abundant than demonstrable cholinergic or serotoninergic nerve fibres. NPY-IR was identified only in the main components of the central nervous system. However, PP- and PYY-IR occurred in the anterior ganglia, dorsal commissure, main nerve cords and in numerous small varicose fibres that ramified throughout the worm. Additionally, PP-immunoreactive nerve fibres were found to innervate the musculature of the female reproductive tracts. Six sites of IR were found in the acetabulum, using antisera directed towards the C-terminal end of PP and PYY, and these matched with the distribution of six non-ciliated rosette-like papillae observed by scanning electron microscopy. SP- and FMRFamide-IR were identified in the CNS, and FMRFamide-immunopositive nerve fibres were also evident in association with the gonopore/cirrus region and with the terminal excretory pore. Results are discussed with respect to possible roles for each of the neurochemical types.