The early Pliocene Titiokura Formation: stratigraphy of a thick, mixed carbonate-siliciclastic shelf succession in Hawke's Bay Basin, New Zealand

This paper presents a systematic stratigraphic description of the architecture of the early Pliocene Titiokura Formation (emended) in the Te Waka and Maungaharuru Ranges of western Hawke's Bay, and presents a facies, sequence stratigraphic, and paleoenvironmental analysis of the sedimentary succession. The Titiokura Formation is of early Pliocene (Opoitian-Waipipian) age, and unconformably overlies Mokonui Formation, which is a regressive late Miocene and early Pliocene (Kapitean to early Opoitian) succession. In the Te Waka Range and the southern parts of the Maungaharuru Range, the Titiokura Formation comprises a single limestone sheet 20-50 m thick, with calcareous sandstone parts. In the vicinity of Taraponui Trig, and to the northeast, the results of 1:50 000 mapping show that the limestone gradually partitions into five members, which thicken markedly to the northeast to total thicknesses of c. 730 m, and concomitantly become dominated by siliciclastic sandstone. The members (all new) from lower to upper are: Naumai Member, Te Rangi Member, Taraponui Member, Bellbird Bush Member, and Opouahi Member. The lower four members are inferred to each comprise an obliquity-controlled 41 000 yr 6th order sequence, and the Opouahi Member at least two such sequences. The sequences typically have the following architectural elements from bottom to top: disconformable sequence boundary that formed as a transgressive surface of erosion; thin transgressive systems tracts (TSTs) with onlap and backlap shellbeds, or alternatively, a single compound shellbed; downlap surface; and very thick (70-200 m) highstand (HST) and regressive systems tracts (RST) composed of fine sandstone. The sequences in the Opouahi Member have cryptic TSTs, sandy siltstone to silty sandstone HSTs, and cross-bedded, differentially cemented, fine sandstone RSTs; a separate variant is an 11 m thick bioclastic limestone (grainstone and packstone) at the top of the member that crops out in the vicinity of Lake Opouahi. Lithostratigraphic correlations along the crest of the ranges suggest that the Titiokura Formation, and its correlatives to the south around Puketitiri, represent a shoreline-to-shelf linked depositional system. Carbonate production was focused around a rocky seascape as the system onlapped basement in the south, with dispersal and deposition of the comminuted carbonate on an inner shelf to the north, which was devoid of siliciclastic sediment input. The rates of both subsidence and siliciclastic sediment flux increased rapidly to the northeast of the carbonate "platform", with active progradation and offlap of the depositional system into more axial parts of Hawke's Bay Basin

Towards Software Based Optical Communication Methods for the Assistance of Docking Autonomous Underwater Vehicles

The use of optical communications systems is prevalent in underwater robotics when short-range data transmission is required or preferred. This paper proposes a method of producing and testing an optical communications system for use in the assistance of optical docking for autonomous underwater vehicles (AUVs). It describes how the Simulink modelling environment was used to program and simulate a model of a transmitter, which was then implemented on a microcontroller. The transmitter model implemented on hardware was then used to produce an optical signal, which was sampled, logged and used to design a receiver model in Simulink. For signalling purposes, the experiment used a light-emitting diode (LED) with a driver circuit and photodiode based receiver. This simulated approach using real world data enabled the analysis of the system at every point during the process, allowing for a hardware in the loop style approach to be used in the receiver model design. Consequently, the Simulink Coder was used to produce the receiver model’s equivalent in C++ for later deployment. A benchmark was determined through experimentation to compare within future studies; the system was tested and found to operate effectively at distances between 1 m and 12 m in a controlled in air test environment

X-rays and Gamma-rays from Cataclysmic Variables: The example case of Intermediate Polar V1223 Sgr

The accretion of matter onto intermediate polar White Dwarfs (IPWDs) seems to provide attractive conditions for acceleration of particles to high energies in a strongly magnetized turbulent region at the accretion disk inner radius. We consider possible acceleration of electrons and hadrons in such region and investigate their high energy radiation processes. It is concluded that accelerated electrons loose energy mainly on synchrotron process producing non-thermal X-ray emission. On the other hand, accelerated hadrons are convected onto the WD surface and interact with dense matter. As a result, high energy $\gamma$-rays from decay of neutral pions and secondary leptons from decay of charged pions appear. We show that GeV-TeV $\gamma$-rays can escape from the vicinity of the WD. Secondary leptons produce synchrotron radiation in the hard X-rays and soft $\gamma$-rays. As an example, we predict the X-ray and $\gamma$-ray emission from IPWD V1223 Sgr. Depending on the spectral index of injected particles, this high energy emission may be detected by the ${\it Fermi}$-LAT telescope and/or the future Cherenkov Telescope Array (CTA) observatory.Comment: 16 pages, 1 figure, accepted to MNRA

The ice-breaker effect: Singing mediates fast social bonding

It has been proposed that singing evolved to facilitate social cohesion. However, it remains unclear whether bonding arises out of properties intrinsic to singing or whether any social engagement can have a similar effect. Furthermore, previous research has used one-off singing sessions without exploring the emergence of social bonding over time. In this semi-naturalistic study, we followed newly formed singing and non-singing (crafts or creative writing) adult education classes over seven months. Participants rated their closeness to their group and their affect, and were given a proxy measure of endorphin release, before and after their class, at three timepoints (months 1, 3 and 7). We show that although singers and non-singers felt equally connected by timepoint 3, singers experienced much faster bonding: singers demonstrated a significantly greater increase in closeness at timepoint 1, but the more gradual increase shown by non-singers caught up over time. This represents the first evidence for an ‘ice-breaker effect’ of singing in promoting fast cohesion between unfamiliar individuals, which bypasses the need for personal knowledge of group members gained through prolonged interaction. We argue that singing may have evolved to quickly bond large human groups of relative strangers, potentially through encouraging willingness to coordinate by enhancing positive affect

Gated rotation mechanism of site-specific recombination by ϕC31 integrase

Integrases, such as that of the Streptomyces temperate bacteriophage ϕC31, promote site-specific recombination between DNA sequences in the bacteriophage and bacterial genomes to integrate or excise the phage DNA. ϕC31 integrase belongs to the serine recombinase family, a large group of structurally related enzymes with diverse biological functions. It has been proposed that serine integrases use a “subunit rotation” mechanism to exchange DNA strands after double-strand DNA cleavage at the two recombining att sites, and that many rounds of subunit rotation can occur before the strands are religated. We have analyzed the mechanism of ϕC31 integrase-mediated recombination in a topologically constrained experimental system using hybrid “phes” recombination sites, each of which comprises a ϕC31 att site positioned adjacent to a regulatory sequence recognized by Tn3 resolvase. The topologies of reaction products from circular substrates containing two phes sites support a right-handed subunit rotation mechanism for catalysis of both integrative and excisive recombination. Strand exchange usually terminates after a single round of 180° rotation. However, multiple processive “360° rotation” rounds of strand exchange can be observed, if the recombining sites have nonidentical base pairs at their centers. We propose that a regulatory “gating” mechanism normally blocks multiple rounds of strand exchange and triggers product release after a single round

Measuring psychological pain: psychometric analysis of the Orbach and Mikulincer Mental Pain Scale

Background: Suicide is a public health concern, with an estimated 1 million individuals dying each year worldwide. Individual psychological pain is believed to be a contributing motivating factor. Therefore, establishing a psychometrically sound tool to adequately measure psychological pain is important. The Orbach and Mikulincer Mental Pain Scale (OMMP) has been proposed; however, previous psychometric analysis on the OMMP has not yielded a consistent scale structure, and the internal consistency of the subscales has not met recommended values. Therefore, the primary purpose of this study was to assess the psychometric properties of the OMMP in a diverse sample. Methods: A confirmatory factor analysis (CFA) on the 9-factor, 44-item OMMP was conducted on the full sample (n = 1151). Because model fit indices were not met, an exploratory factor analysis (EFA) was conducted on a random subset of the data (n = 576) to identify a more parsimonious structure. The EFA structure was then tested in a covariance model in the remaining subset of participants (n = 575). Multigroup invariance testing was subsequently performed to examine psychometric properties of the refined scale. Results: The CFA of the original 9-factor, 44-item OMMP did not meet recommended model fit recommendations. The EFA analysis results revealed a 3-factor, 9-item scale (i.e., OMMP-9). The covariance model of the OMMP-9 indicated further refinement was necessary. Multigroup invariance testing conducted on the final 3-factor, 8-item scale (i.e., OMMP-8) across mental health diagnoses, sex, injury status, age, activity level, and athlete classification met all criteria for invariance. Conclusions: The 9-factor, 44-item OMMP does not meet recommended measurement criteria and should not be recommended for use in research and clinical practice in its current form. The refined OMMP-8 may be a more viable option to use; however, more research should be completed prior to adoption

An optimized TOPS+ comparison method for enhanced TOPS models

This article has been made available through the Brunel Open Access Publishing Fund.Background Although methods based on highly abstract descriptions of protein structures, such as VAST and TOPS, can perform very fast protein structure comparison, the results can lack a high degree of biological significance. Previously we have discussed the basic mechanisms of our novel method for structure comparison based on our TOPS+ model (Topological descriptions of Protein Structures Enhanced with Ligand Information). In this paper we show how these results can be significantly improved using parameter optimization, and we call the resulting optimised TOPS+ method as advanced TOPS+ comparison method i.e. advTOPS+. Results We have developed a TOPS+ string model as an improvement to the TOPS [1-3] graph model by considering loops as secondary structure elements (SSEs) in addition to helices and strands, representing ligands as first class objects, and describing interactions between SSEs, and SSEs and ligands, by incoming and outgoing arcs, annotating SSEs with the interaction direction and type. Benchmarking results of an all-against-all pairwise comparison using a large dataset of 2,620 non-redundant structures from the PDB40 dataset [4] demonstrate the biological significance, in terms of SCOP classification at the superfamily level, of our TOPS+ comparison method. Conclusions Our advanced TOPS+ comparison shows better performance on the PDB40 dataset [4] compared to our basic TOPS+ method, giving 90 percent accuracy for SCOP alpha+beta; a 6 percent increase in accuracy compared to the TOPS and basic TOPS+ methods. It also outperforms the TOPS, basic TOPS+ and SSAP comparison methods on the Chew-Kedem dataset [5], achieving 98 percent accuracy. Software Availability: The TOPS+ comparison server is available at http://balabio.dcs.gla.ac.uk/mallika/WebTOPS/.This article is available through the Brunel Open Access Publishing Fun

Development of a Halotolerant Community in the St. Lucia Estuary (South Africa) during a Hypersaline Phase

Background: The St. Lucia Estuary, Africa’s largest estuarine lake, is currently experiencing unprecedented freshwater deprivation which has resulted in a northward gradient of drought effects, with hypersaline conditions in its northern lakes. Methodology/Principal Findings: This study documents the changes that occurred in the biotic communities at False Bay from May 2010 to June 2011, in order to better understand ecosystem functioning in hypersaline habitats. Few zooplankton taxa were able to withstand the harsh environmental conditions during 2010. These were the flatworm Macrostomum sp., the harpacticoid copepod Cletocamptus confluens, the cyclopoid copepod Apocyclops cf. dengizicus and the ciliate Fabrea cf. salina. In addition to their exceptional salinity tolerance, they were involved in a remarkably simple food web. In June 2009, a bloom of an orange-pigmented cyanobacterium (Cyanothece sp.) was recorded in False Bay and persisted uninterruptedly for 18 months. Stable isotope analysis suggests that this cyanobacterium was the main prey item of F. cf. salina. This ciliate was then consumed by A. cf. dengizicus, which in turn was presumably consumed by flamingos as they flocked in the area when the copepods attained swarming densities. On the shore, cyanobacteria mats contributed to a population explosion of the staphylinid beetle Bledius pilicollis. Although zooplankton disappeared once salinities exceeded 130, many taxa are capable of producing spores or resting cysts to bridge harsh periods. The hypersaline community was disrupted by heavy summer rains in 2011, which alleviated drought conditions and resulted in a sharp increase in zooplankton stock an

Zinc-finger recombinase activities in vitro

Zinc-finger recombinases (ZFRs) are chimaeric proteins comprising a serine recombinase catalytic domain linked to a zinc-finger DNA binding domain. ZFRs can be tailored to promote site-specific recombination at diverse ‘Z-sites’, which each comprise a central core sequence flanked by zinc-finger domain-binding motifs. Here, we show that purified ZFRs catalyse efficient high-specificity reciprocal recombination between pairs of Z-sites in vitro. No off-site activity was detected. Under different reaction conditions, ZFRs can catalyse Z-site-specific double-strand DNA cleavage. ZFR recombination activity in Escherichia coli and in vitro is highly dependent on the length of the Z-site core sequence. We show that this length effect is manifested at reaction steps prior to formation of recombinants (binding, synapsis and DNA cleavage). The design of the ZFR protein itself is also a crucial variable affecting activity. A ZFR with a very short (2 amino acids) peptide linkage between the catalytic and zinc-finger domains has high activity in vitro, whereas a ZFR with a very long linker was less recombination-proficient and less sensitive to variations in Z-site length. We discuss the causes of these phenomena, and their implications for practical applications of ZFRs

A study of patent thickets

Report analysing whether entry of UK enterprises into patenting in a technology area is affected by patent thickets in the technology area