DOG-SPOT database for comprehensive management of dog genetic research data

Research laboratories studying the genetics of companion animals have no database tools specifically designed to aid in the management of the many kinds of data that are generated, stored and analyzed. We have developed a relational database, "DOG-SPOT," to provide such a tool. Implemented in MS-Access, the database is easy to extend or customize to suit a lab's particular needs. With DOG-SPOT a lab can manage data relating to dogs, breeds, samples, biomaterials, phenotypes, owners, communications, amplicons, sequences, markers, genotypes and personnel. Such an integrated data structure helps ensure high quality data entry and makes it easy to track physical stocks of biomaterials and oligonucleotides

Human agency in disaster planning: a systems approach

This is the final version of the article. Available from Wiley via the DOI in this record.Current approaches to risk management place insufficient emphasis on the system knowledge available to the assessor, particularly in respect of the dynamic behaviour of the system under threat, the role of human agents and the knowledge availability to those agents. In this paper, we address the second of these issues. We are concerned with a class of systems containing human agents playing a variety of roles as significant system elements - as decision makers, cognitive agents or implementers. i.e. Human Activity Systems (Checkland, 1999). Within this family of HASs we focus upon safety and mission critical systems, referring to this sub-class as critical human activity systems or CHASs. Identification of the role and contribution of these human elements to a system is a nontrivial problem whether in an engineering context, or, as is the case here, in a wider social and public context. Frequently they are treated as standing apart from the system in design or policy terms. Regardless of the process of policy definition followed, analysis of the risk and threats to such a CHAS requires a holistic approach, since the effect of undesirable, uninformed or erroneous actions on the part of the human elements is both potentially significant to the system output and inextricably bound together with the non-human elements of the system. We present a procedure for identifying the potential threats and risks emerging from the role(s) and activity of those human agents, using the 2014 flooding in SW England and the Thames Valley as a contemporary example.The project was partially supported the EU-CIRCLE (A pan-European framework for strengthening critical infrastructure resilience) project, funded by the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 653824)

Concentration and localization of zinc during seed development and germination in wheat

In a field experiment, the effect of foliar Zn applications on the concentration of Zn in seeds of a bread wheat cultivar (Triticum aestivum L. cv. Balatilla) was studied during different stages of seed development. In addition, a staining method using dithizone (DTZ: diphenyl thiocarbazone) was applied to (1) study the localization of Zn in seeds, (2) follow the remobilization of Zn during germination, and (3) develop a rapid visual Zn screening method for seed and flour samples. In all seed development stages, foliar Zn treatments were effective in increasing seed Zn concentration. The highest Zn concentration in the seeds was found in the first stage of seed development (around the early milk stage); after this, seed Zn concentration gradually decreased until maturity. When reacting with Zn, DTZ forms a redcolored complex. The DTZ staining of seed samples revealed that Zn is predominantly located in the embryo and aleurone parts of the seeds. After 36 h of germination, the coleoptile and roots that emerged from seeds showed very intensive red color formation and had Zn concentrations up to 200 mg kg1, indicating a substantial remobilization of Zn from seed pools into the developing roots (radicle) and coleoptile. The DTZ staining method seems to be useful in ranking flour samples for their Zn concentrations. There was a close relationship between the seed Zn concentrations and spectral absorbance of the methanol extracts of the flour samples stained with DTZ. The results suggest that (1) accumulation of Zn in seeds is particularly high during early seed development, (2) Zn is concentrated in the embryo and aleurone parts, and (3) the DTZ staining method can be used as a rapid, semiquantitative method to estimate Zn concentrations of flour and seed samples and to screen genotypes for their Zn concentrations in seeds

An Approximate Dynamic Programming Approach to Urban Freight Distribution with Batch Arrivals

We study an extension of the delivery dispatching problem (DDP) with time windows, applied on LTL orders arriving at an urban consolidation center. Order properties (e.g., destination, size, dispatch window) may be highly varying, and directly distributing an incoming order batch may yield high costs. Instead, the hub operator may wait to consolidate with future arrivals. A consolidation policy is required to decide which orders to ship and which orders to hold. We model the dispatching problem as a Markov decision problem. Dynamic Programming (DP) is applied to solve toy-sized instances to optimality. For larger instances, we propose an Approximate Dynamic Programming (ADP) approach. Through numerical experiments, we show that ADP closely approximates the optimal values for small instances, and outperforms two myopic benchmark policies for larger instances. We contribute to literature by (i) formulating a DDP with dispatch windows and (ii) proposing an approach to solve this DDP

Adenosine-mono-phosphate-activated protein kinase-independent effects of metformin in T cells

The anti-diabetic drug metformin regulates T-cell responses to immune activation and is proposed to function by regulating the energy-stress-sensing adenosine-monophosphate-activated protein kinase (AMPK). However, the molecular details of how metformin controls T cell immune responses have not been studied nor is there any direct evidence that metformin acts on T cells via AMPK. Here, we report that metformin regulates cell growth and proliferation of antigen-activated T cells by modulating the metabolic reprogramming that is required for effector T cell differentiation. Metformin thus inhibits the mammalian target of rapamycin complex I signalling pathway and prevents the expression of the transcription factors c-Myc and hypoxia-inducible factor 1 alpha. However, the inhibitory effects of metformin on T cells did not depend on the expression of AMPK in T cells. Accordingly, experiments with metformin inform about the importance of metabolic reprogramming for T cell immune responses but do not inform about the importance of AMPK

Molecular beam epitaxy as a growth technique for achieving free-standing zinc-blende GaN and wurtzite AlxGa1-xN

Currently there is a high level of interest in the development of ultraviolet (UV) light sources for solid state lighting, optical sensors, surface decontamination and water purification. III-V semiconductor UV LEDs are now successfully manufactured using the AlGaN material system; however, their efficiency is still low. The majority of UV LEDs require AlxGa1-xN layers with compositions in the mid-range between AlN and GaN. Because there is a significant difference in the lattice parameters of GaN and AlN, AlxGa1-xN substrates would be preferable to those of either GaN or AlN for many ultraviolet device applications. However, the growth of AlxGa1-xN bulk crystals by any standard bulk growth techniques has not been developed so far. There are very strong electric polarization fields inside the wurtzite (hexagonal) group III-nitride structures. The charge separation within quantum wells leads to a significant reduction in the efficiency of optoelectronic device structures. Therefore, the growth of non-polar and semi-polar group III-nitride structures has been the subject of considerable interest recently. A direct way to eliminate polarization effects is to use non-polar (001) zinc-blende (cubic) III-nitride layers. However, attempts to grow zinc-blende GaN bulk crystals by anystandard bulk growth techniques were not successful. Molecular beam epitaxy (MBE) is normally regarded as an epitaxial technique for the growth of very thin layers with monolayer control of their thickness. In this study we have used plasma-assisted molecular beam epitaxy (PA MBE) and have produced for the first time free-standing layers of zinc-blende GaN up to 100 μm in thickness and up to 3-inch in diameter. We have shown that our newly developed PA-MBE process for the growth of zinc-blende GaN layers can also be used to achieve free-standing wurtzite AlxGa1-xN wafers. Zinc-blende and wurtzite AlxGa1-xN polytypes can be grown on different orientations of GaAs substrates - (001) and (111)B respectively. We have subsequently removed the GaAs using a chemical etch in order to produce free-standing GaN and AlxGa1-xN wafers. At a thickness of ∼30 μm, free-standing GaN and AlxGa1-xN wafers can easily be handled without cracking. Therefore, free-standing GaN and AlxGa1-xN wafers with thicknesses in the 30–100 μm range may be used as substrates for further growth of GaN and AlxGa1 xN-based structures and devices. We have compared different RF nitrogen plasma sources for the growth of thick nitride AlxGa1-xN films including a standard HD25 source from Oxford Applied Research and a novel high efficiency source from Riber. We have investigated a wide range of the growth rates from 0.2 to 3 μm/h. The use of highly efficient nitrogen RF plasma sources makes PA-MBE a potentially viable commercial process, since free-standing films can be achieved in a single day. Our results have demonstrated that MBE may be competitive with the other group III-nitrides bulk growth techniques in several important areas including production of free-standing zinc-blende (cubic) (Al)GaN and of free-standing wurtzite (hexagonal) AlGaN

The Impact of Global Warming and Anoxia on Marine Benthic Community Dynamics: an Example from the Toarcian (Early Jurassic)

The Pliensbachian-Toarcian (Early Jurassic) fossil record is an archive of natural data of benthic community response to global warming and marine long-term hypoxia and anoxia. In the early Toarcian mean temperatures increased by the same order of magnitude as that predicted for the near future; laminated, organic-rich, black shales were deposited in many shallow water epicontinental basins; and a biotic crisis occurred in the marine realm, with the extinction of approximately 5% of families and 26% of genera. High-resolution quantitative abundance data of benthic invertebrates were collected from the Cleveland Basin (North Yorkshire, UK), and analysed with multivariate statistical methods to detect how the fauna responded to environmental changes during the early Toarcian. Twelve biofacies were identified. Their changes through time closely resemble the pattern of faunal degradation and recovery observed in modern habitats affected by anoxia. All four successional stages of community structure recorded in modern studies are recognised in the fossil data (i.e. Stage III: climax; II: transitional; I: pioneer; 0: highly disturbed). Two main faunal turnover events occurred: (i) at the onset of anoxia, with the extinction of most benthic species and the survival of a few adapted to thrive in low-oxygen conditions (Stages I to 0) and (ii) in the recovery, when newly evolved species colonized the re-oxygenated soft sediments and the path of recovery did not retrace of pattern of ecological degradation (Stages I to II). The ordination of samples coupled with sedimentological and palaeotemperature proxy data indicate that the onset of anoxia and the extinction horizon coincide with both a rise in temperature and sea level. Our study of how faunal associations co-vary with long and short term sea level and temperature changes has implications for predicting the long-term effects of “dead zones” in modern oceans

Daily life stress and the cortisol awakening response : testing the anticipation hypothesis

Acknowledgments We thank Paul Stewart for his contribution to data collection and Dr Matthew Jones for programming the handheld computers. Author Contributions Conceived and designed the experiments: WS DJP. Performed the experiments: DJP. Analyzed the data: WS. Wrote the paper: WS DJP.Peer reviewedPublisher PD

Cis and Trans Effects of Human Genomic Variants on Gene Expression

This work was funded by the Louis-Jeantet Foundation (http://www.jeantet.ch/), the European Research Council (Grant ID: 260927 http://erc.europa.eu/), the Swiss National Foundation (Grant ID: 130342 http://www.snf.ch), NCCR Frontiers In Genetics (http://www.frontiers-in-genetics.org), the UK Medical Research Council (http://www.mrc.ac.uk) and the Wellcome Trust (Grant ID: 092731).

Abacavir, zidovudine, or stavudine as paediatric tablets for African HIV-infected children (CHAPAS-3): an open-label, parallel-group, randomised controlled trial

BACKGROUND: WHO 2013 guidelines recommend universal treatment for HIV-infected children younger than 5 years. No paediatric trials have compared nucleoside reverse-transcriptase inhibitors (NRTIs) in first-line antiretroviral therapy (ART) in Africa, where most HIV-infected children live. We aimed to compare stavudine, zidovudine, or abacavir as dual or triple fixed-dose-combination paediatric tablets with lamivudine and nevirapine or efavirenz. METHODS: In this open-label, parallel-group, randomised trial (CHAPAS-3), we enrolled children from one centre in Zambia and three in Uganda who were previously untreated (ART naive) or on stavudine for more than 2 years with viral load less than 50 copies per mL (ART experienced). Computer-generated randomisation tables were incorporated securely within the database. The primary endpoint was grade 2-4 clinical or grade 3/4 laboratory adverse events. Analysis was intention to treat. This trial is registered with the ISRCTN Registry number, 69078957. FINDINGS: Between Nov 8, 2010, and Dec 28, 2011, 480 children were randomised: 156 to stavudine, 159 to zidovudine, and 165 to abacavir. After two were excluded due to randomisation error, 156 children were analysed in the stavudine group, 158 in the zidovudine group, and 164 in the abacavir group, and followed for median 2·3 years (5% lost to follow-up). 365 (76%) were ART naive (median age 2·6 years vs 6·2 years in ART experienced). 917 grade 2-4 clinical or grade 3/4 laboratory adverse events (835 clinical [634 grade 2]; 40 laboratory) occurred in 104 (67%) children on stavudine, 103 (65%) on zidovudine, and 105 (64%), on abacavir (p=0·63; zidovudine vs stavudine: hazard ratio [HR] 0·99 [95% CI 0·75-1·29]; abacavir vs stavudine: HR 0·88 [0·67-1·15]). At 48 weeks, 98 (85%), 81 (80%) and 95 (81%) ART-naive children in the stavudine, zidovudine, and abacavir groups, respectively, had viral load less than 400 copies per mL (p=0·58); most ART-experienced children maintained suppression (p=1·00). INTERPRETATION: All NRTIs had low toxicity and good clinical, immunological, and virological responses. Clinical and subclinical lipodystrophy was not noted in those younger than 5 years and anaemia was no more frequent with zidovudine than with the other drugs. Absence of hypersensitivity reactions, superior resistance profile and once-daily dosing favours abacavir for African children, supporting WHO 2013 guidelines. FUNDING: European Developing Countries Clinical Trials Partnership