The role of a class III gibberellin 2-oxidase in tomato internode elongation

[EN] A network of environmental inputs and internal signaling controls plant growth, development and organ elongation. In particular, the growth-promoting hormone gibberellin (GA) has been shown to play a significant role in organ elongation. The use of tomato as a model organism to study elongation presents an opportunity to study the genetic control of internode-specific elongation in a eudicot species with a sympodial growth habit and substantial internodes that can and do respond to external stimuli. To investigate internode elongation, a mutant with an elongated hypocotyl and internodes but wild-type petioles was identified through a forward genetic screen. In addition to stem-specific elongation, this mutant, named tomato internode elongated -1 (tie-1) is more sensitive to the GA biosynthetic inhibitor paclobutrazol and has altered levels of intermediate and bioactive GAs compared with wild-type plants. The mutation responsible for the internode elongation phenotype was mapped to GA2oxidase 7, a class III GA 2-oxidase in the GA biosynthetic pathway, through a bulked segregant analysis and bioinformatic pipeline, and confirmed by transgenic complementation. Furthermore, bacterially expressed recombinant TIE protein was shown to have bona fide GA 2-oxidase activity. These results define a critical role for this gene in internode elongation and are significant because they further the understanding of the role of GA biosynthetic genes in organ-specific elongation.This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 Instrumentation Grants S10RR029668 and S10RR027303. We thank the Tomato Genetics Resource Center for providing seed of the M82 and Heinz cultivars. The material was developed by and/or obtained from the UC Davis/C M Rick Tomato Genetics Resource Center and maintained by the Department of Plant Sciences, University of California, Davis, CA 95616, USA. We thank Anthony Bolger, Alisdair Fernie and Bjorn Usadel for providing us with access to pre-publication genomic reads of the S. lycopersicum cultivar M82, and Cristina Urbez and Noel Blanco-Tourinan (IBMCP, Spain) for technical help with in vitro production of TIE1. This work was supported in part by the Elsie Taylor Stocking Memorial Fellowship awarded to ASL in 2013, by NSF grant IOS-0820854, by USDA National Institute of Food and Agriculture project CA-D-PLB-2465-H, by internal UC Davis funds, and by Spanish Ministry of Economy and Competitiveness grant BFU2016-80621-P.Lavelle, A.; Gath, N.; Devisetty, U.; Carrera Bergua, E.; Lopez Diaz, I.; Blazquez Rodriguez, MA.; Maloof, J. (2018). The role of a class III gibberellin 2-oxidase in tomato internode elongation. 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Universal scaling properties of extremal cohesive holographic phases

We show that strongly-coupled, translation-invariant holographic IR phases at finite density can be classified according to the scaling behaviour of the metric, the electric potential and the electric flux introducing four critical exponents, independently of the details of the setup. Solutions fall into two classes, depending on whether they break relativistic symmetry or not. The critical exponents determine key properties of these phases, like thermodynamic stability, the (ir)relevant deformations around them, the low-frequency scaling of the optical conductivity and the nature of the spectrum for electric perturbations. We also study the scaling behaviour of the electric flux through bulk minimal surfaces using the Hartnoll-Radicevic order parameter, and characterize the deviation from the Ryu-Takayanagi prescription in terms of the critical exponents.Comment: v4: corrected a typo in eqn (3.29), now (3.28). Conclusions unchange

Quantization of fields over de Sitter space by the method of generalized coherent states

A system of generalized coherent states for the de Sitter group obeying the Klein-Gordon equation and corresponding to the massive spin zero particles over the de Sitter space is considered. This allows us to construct the quantized scalar field by the resolution over these coherent states; the corresponding propagator is computed by the method of analytic continuation to the complex de Sitter space and coincides with expressions obtained previously by other methods. Considering the case of spin 1/2 we establish the connection of the invariant Dirac equation over the de Sitter space with irreducible representations of the de Sitter group. The set of solutions of this equation is obtained in the form of the product of two different systems of generalized coherent states for the de Sitter group. Using these solutions the quantized Dirac field over de Sitter space is constructed and its propagator is found. It is a result of action of some de Sitter invariant spinor operator onto the spin zero propagator with an imaginary shift of a mass. We show that the constructed propagators possess the de Sitter-invariance and causality properties.Comment: 19 pages, LATEX, using ioplppt.sty and iopfts.st

Observational study of the development and evaluation of a fertility preservation patient decision aid for teenage and adult women diagnosed with cancer: The Cancer, Fertility and Me research protocol

Introduction: Women diagnosed with cancer and facing potentially sterilising cancer treatment have to make time-pressured decisions regarding fertility preservation with specialist fertility services whilst undergoing treatment of their cancer with oncology services. Oncologists identify a need for resources enabling them to support women’s fertility preservation decisions more effectively; women report wanting more specialist information to make these decisions. The overall aim of the ‘Cancer, Fertility and Me’ study is to develop and evaluate a new evidence-based patient decision aid (ptDA) for women with any cancer considering fertility preservation to address this unmet need. Methods and analysis: This is a prospective mixed-method observational study including women of reproductive age (16 years +) with a new diagnosis of any cancer across two regional cancer and fertility centres in Yorkshire, UK. The research involves three stages. In Stage 1 the aim is to develop the ptDA using a systematic method of evidence synthesis and multidisciplinary expert review of current clinical practice and patient information. In Stage 2, the aim is to assess the face validity of the ptDA. Feedback on its content and format will be ascertained using both questionnaires and interviews with patients, user groups and key stakeholders. Finally, in Stage 3 the acceptability of using this resource when integrated into usual cancer care pathways at the point of cancer diagnosis and treatment planning will be evaluated. This will involve a quantitative and qualitative evaluation of the ptDA in clinical practice. Measures chosen include using count data of the ptDAs administered in clinics and accessed online, decisional and patient-reported outcome measures and qualitative feedback. Quantitative data will be analysed using descriptive statistics, paired sample t tests and confidence intervals; interviews will be analysed using thematic analysis. Ethics and dissemination: Research Ethics Committee approval (Ref: 16/EM/0122) and Health Research Authority approval (Ref: 194751) has been granted. Findings will be published in open access peer-reviewed journals, presented at conferences for academic and health professional audiences, with feedback to health professionals and program managers. The Cancer, Fertility and Me ptDA will be disseminated via a diverse range of open-access media, study and charity websites, professional organisations and academic sources. External endorsement will be sought from the International Patient Decision Aid Standards (IPDAS) Collaboration inventory of ptDAs and other relevant professional organisations e.g. the British Fertility Society. Trial registration number: NCT02753296 (www.clinicaltrials.gov); pre-results

The Computational 2D Materials Database: High-Throughput Modeling and Discovery of Atomically Thin Crystals

We introduce the Computational 2D Materials Database (C2DB), which organises a variety of structural, thermodynamic, elastic, electronic, magnetic, and optical properties of around 1500 two-dimensional materials distributed over more than 30 different crystal structures. Material properties are systematically calculated by state-of-the art density functional theory and many-body perturbation theory (G$_0\!$W\!_0 and the Bethe-Salpeter Equation for $\sim$200 materials) following a semi-automated workflow for maximal consistency and transparency. The C2DB is fully open and can be browsed online or downloaded in its entirety. In this paper, we describe the workflow behind the database, present an overview of the properties and materials currently available, and explore trends and correlations in the data. Moreover, we identify a large number of new potentially synthesisable 2D materials with interesting properties targeting applications within spintronics, (opto-)electronics, and plasmonics. The C2DB offers a comprehensive and easily accessible overview of the rapidly expanding family of 2D materials and forms an ideal platform for computational modeling and design of new 2D materials and van der Waals heterostructures.Comment: Add journal reference and DOI; Minor updates to figures and wordin

Spatially modulated instabilities of geometries with hyperscaling violation

We perform a study of possible instabilities of the infrared AdS(2) x R-2 region of solutions to Einstein-Maxwell-dilaton systems which exhibit an intermediate regime of hyperscaling violation and Lifshitz scaling. Focusing on solutions that are magnetically charged, we probe the response of the system to spatially modulated fluctuations, and identify regions of parameter space in which the infrared AdS(2) geometry is unstable to perturbations. The conditions for the existence of instabilities translate to restrictions on the structure of the gauge kinetic function and scalar potential. In turn, these can lead to restrictions on the dynamical critical exponent z and on the amount of hyperscaling violation theta. Our analysis thus provides further evidence for the notion that the true ground state of 'scaling' solutions with hyperscaling violation may be spatially modulated phases

Usability of myfood24 Healthcare and Mathematical Diet Optimisation in Clinical Populations: A Pilot Feasibility Randomised Controlled Trial

Monitoring nutritional intake is of clinical value, but few existing tools offer electronic dietary recording, instant nutritional analysis, and a platform connecting healthcare teams with patients that provides timely, personalised support. This feasibility randomised controlled trial tests the usability of ‘myfood24 Healthcare’, a dietary assessment app and healthcare professional website, in two clinical populations. Patients were recruited from a weight management programme (n21) and from a group of gastroenterology surgery outpatients (n = 27). They were randomised into three groups: standard care, myfood24, or myfood24 + diet optimisation (automated suggestions for dietary improvement). The participants were asked to record their diet at least four times over eight weeks. During the study, healthcare professionals viewed recorded dietary information to facilitate discussions about diet and nutritional targets. The participants provided feedback on usability and acceptability. A total of 48 patients were recruited, and 16 were randomised to each of the three groups. Compliance among app users (n = 32) was reasonable, with 25 (78%) using it at least once and 16 (50%) recording intake for four days or more. Among users, the mean (standard deviation) number of days used was 14.0 (17.5), and the median (interquartile range) was six (2.5–17.0) over 2 months. Feedback questionnaires were completed by only 23 of 46 participants (50%). The mean System Usability Score (n = 16) was 59 (95% confidence interval, 48–70). Patient and healthcare professional feedback indicates a need for more user training and the improvement of some key app features such as the food search function. This feasibility study shows that myfood24 Healthcare is acceptable for patients and healthcare professionals. These data will inform app refinements and its application in a larger clinical effectiveness trial

The value of standards for health datasets in artificial intelligence-based applications

Artificial intelligence as a medical device is increasingly being applied to healthcare for diagnosis, risk stratification and resource allocation. However, a growing body of evidence has highlighted the risk of algorithmic bias, which may perpetuate existing health inequity. This problem arises in part because of systemic inequalities in dataset curation, unequal opportunity to participate in research and inequalities of access. This study aims to explore existing standards, frameworks and best practices for ensuring adequate data diversity in health datasets. Exploring the body of existing literature and expert views is an important step towards the development of consensus-based guidelines. The study comprises two parts: a systematic review of existing standards, frameworks and best practices for healthcare datasets; and a survey and thematic analysis of stakeholder views of bias, health equity and best practices for artificial intelligence as a medical device. We found that the need for dataset diversity was well described in literature, and experts generally favored the development of a robust set of guidelines, but there were mixed views about how these could be implemented practically. The outputs of this study will be used to inform the development of standards for transparency of data diversity in health datasets (the STANDING Together initiative)

The bimodality of the 10k zCOSMOS-bright galaxies up to z ~ 1: a new statistical and portable classification based on the optical galaxy properties

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