Transcriptional coupling of neighbouring genes and gene expression noise: evidence that gene orientation and non-coding transcripts are modulators of noise

For some genes, notably essential genes, expression when expression is needed is vital hence low noise in expression is favourable. For others noise is necessary for coping with stochasticity or for providing dice-like mechanisms to control cell fate. But how is noise in gene expression modulated? We hypothesise that gene orientation may be crucial, as for divergently organized gene pairs expression of one gene could affect chromatin of a neighbour thereby reducing noise. Transcription of antisense non-coding RNA from a shared promoter is similarly argued to be a noise-reduction mechanism. Stochastic simulation models confirm the expectation. The model correctly predicts: that protein coding genes with bi-promoter architecture, including those with a ncRNA partner, have lower noise than other genes; divergent gene pairs uniquely have correlated expression noise; distance between promoters predicts noise; ncRNA divergent transcripts are associated with genes that a priori would be under selection for low noise; essential genes reside in divergent orientation more than expected; bi-promoter pairs are rare subtelomerically, cluster together and are enriched in essential gene clusters. We conclude that gene orientation and transcription of ncRNAs, even if unstable, are candidate modulators of noise levels

Interventions designed to reduce implicit prejudices and implicit stereotypes in real world contexts: a systematic review

Background Implicit biases are present in the general population and among professionals in various domains, where they can lead to discrimination. Many interventions are used to reduce implicit bias. However, uncertainties remain as to their effectiveness. Methods We conducted a systematic review by searching ERIC, PUBMED and PSYCHINFO for peer-reviewed studies conducted on adults between May 2005 and April 2015, testing interventions designed to reduce implicit bias, with results measured using the Implicit Association Test (IAT) or sufficiently similar methods. Results 30 articles were identified as eligible. Some techniques, such as engaging with others’ perspective, appear unfruitful, at least in short term implicit bias reduction, while other techniques, such as exposure to counterstereotypical exemplars, are more promising. Robust data is lacking for many of these interventions. Conclusions Caution is thus advised when it comes to programs aiming at reducing biases. This does not weaken the case for implementing widespread structural and institutional changes that are multiply justified

What is the Connection Between Issues, Bugs, and Enhancements? (Lessons Learned from 800+ Software Projects)

Agile teams juggle multiple tasks so professionals are often assigned to multiple projects, especially in service organizations that monitor and maintain a large suite of software for a large user base. If we could predict changes in project conditions changes, then managers could better adjust the staff allocated to those projects.This paper builds such a predictor using data from 832 open source and proprietary applications. Using a time series analysis of the last 4 months of issues, we can forecast how many bug reports and enhancement requests will be generated next month. The forecasts made in this way only require a frequency count of this issue reports (and do not require an historical record of bugs found in the project). That is, this kind of predictive model is very easy to deploy within a project. We hence strongly recommend this method for forecasting future issues, enhancements, and bugs in a project.Comment: Accepted to 2018 International Conference on Software Engineering, at the software engineering in practice track. 10 pages, 10 figure

Designing an Adaptive Web Navigation Interface for Users with Variable Pointing Performance

Many online services and products require users to point and interact with user interface elements. For individuals who experience variable pointing ability due to physical impairments, environmental issues or age, using an input device (e.g., a computer mouse) to select elements on a website can be difficult. Adaptive user interfaces dynamically change their functionality in response to user behavior. They can support individuals with variable pointing abilities by 1) adapting dynamically to make element selection easier when a user is experiencing pointing difficulties, and 2) informing users about these pointing errors. While adaptive interfaces are increasingly prevalent on the Web, little is known about the preferences and expectations of users with variable pointing abilities and how to design systems that dynamically support them given these preferences. We conducted an investigation with 27 individuals who intermittently experience pointing problems to inform the design of an adaptive interface for web navigation. We used a functional high-fidelity prototype as a probe to gather information about user preferences and expectations. Our participants expected the system to recognize and integrate their preferences for how pointing tasks were carried out, preferred to receive information about system functionality and wanted to be in control of the interaction. We used findings from the study to inform the design of an adaptive Web navigation interface, PINATA that tracks user pointing performance over time and provides dynamic notifications and assistance tailored to their specifications. Our work contributes to a better understanding of users' preferences and expectations of the design of an adaptive pointing system

The contribution of small punch testing towards the development of materials for aero-engine applications

This paper, invited for presentation at the 33rd Meeting of the Spanish Group on Fracture and Structural Integrity, March 2016 in San Sebastian, Spain, reviews the recent work carried out in the authors’ laboratory, addressing the elucidation of tensile and creep characteristics of materials for aero engine components. Two specific applications of the Small Punch (SP) test assessment technology were identified, the first of these takes on board the unique potential of the SP test for testing small quantities of materials which are either in development or through their directional structure cannot easily be produced in quantities which would allow conventional mechanical testing. This goal also required the development and procurement of new SP test facilities capable of operation up to 1150 °C. The examples given in this paper are TiAl intermetallic alloys and nickel based single crystals, all studied utilising the Code of Practice for SP Creep Testing. The second application illustrates the use of SP testing to assess both the tensile and creep properties of additive layer manufactured (ALM) alloys such as IN718 and Ti-6Al-4V using the Code of Practice for SP Tensile and Fracture Testing. Due to the unavailability of sufficient material to facilitate conventional testing for comparison of materials property data, SP testing is unable to provide absolute data for all of these applications, nevertheless the ranking capabilities of SP testing are demonstrably proven

Controls on the distribution of cosmogenic 10Be across shore platforms

Quantifying rates of erosion on cliffed coasts across a range of timescales is vital for understanding the drivers and processes of coastal change and for assessing risks posed by future cliff retreat. Historical records cover at best the last 150 years; Cosmogenic radionuclides, such as 10Be could allow us to look further into past to assess coastal change at millenial timescales. CRNs accumulate in-situ near the Earth surface and have been used extensively to quantify erosion rates, burial dates and surface exposure ages in terrestrial landscapes over the last three decades. More recently, applications in rocky coast settings have quantified the timing of mass wasting events, determined long-term-averaged rates of cliff retreat and revealed the exposure history of shore platforms. In this contribution, we developed and explored a numerical model for the accumulation of 10Be on eroding shore platforms. In a series of numerical experiments, we investigated the influence of topographic and water shielding, dynamic platform erosion processes, the presence and variation in beach cover, and heterogeneous distribution of erosion on the distribution of 10Be across shore platforms. Results demonstrate that, taking into account relative sea level change and tides, the concentration of 10Be is sensitive to rates of cliff retreat. Factors such as topographic shielding and beach cover, act to reduce 10Be concentrations on the platform, and may result in overestimation of cliff retreat rates if not accounted for. The shape of the distribution of 10Be across a shore platform can potentially reveal whether cliff retreat rates are declining or accelerating through time. Measurement of 10Be in shore platforms has great potential to allow us to quantify long-term rates of cliff retreat and platform erosion

Stochastic models which separate fractal dimension and Hurst effect

Fractal behavior and long-range dependence have been observed in an astonishing number of physical systems. Either phenomenon has been modeled by self-similar random functions, thereby implying a linear relationship between fractal dimension, a measure of roughness, and Hurst coefficient, a measure of long-memory dependence. This letter introduces simple stochastic models which allow for any combination of fractal dimension and Hurst exponent. We synthesize images from these models, with arbitrary fractal properties and power-law correlations, and propose a test for self-similarity.Comment: 8 pages, 2 figure

Do Biogeographical Patterns in Morphological Traits of Insect Host and Parasitoid Wasp Communities Contribute to Ecological Release of a Range-Expanding Host via Trait Mismatching?

Climate change is causing species to expand their ranges poleward into new locations. As species move, they will lose interactions with species that fail to follow and gain new interactions with species with which they are not coevolved or coadapted. As a result, one common outcome for range expansions is that species outbreak in their expanded ranges in response to altered antagonistic interactions (“ecological release”). Insect hosts have a suite of morphological adaptations to evade parasitoid enemies, and enemies have adaptations to effectively attack hosts. Here, we study a recent range expansion of an insect host. Neuroterus saltatorius (Hymenoptera: Cynipidae) is a gall-forming wasp specializing on oaks that has undergone a recent range expansion from Washington state to Vancouver Island, British Columbia. In its expanded range, it experiences ecological release, causing foliar damage and impacting oak ecosystems. It interacts with an array of insect host competitors on its host plant Quercus garryana (other cynipids wasps) that are attacked by a suite of enemies (parasitoid wasps). The aim of this study is to measure morphological traits of cynipid hosts and parasitoids to examine if community traits of interacting hosts and enemies vary along a latitudinal gradient, and in the native and expanded range of N. saltatorius. Specifically, we ask if trait diversity of insect host-parasitoid communities provides biological resistance or facilitates ecological release of N. saltatorius in the native and expanded ranges. We predict that if trait mismatching contributes to ecological release, the degree of trait matching between the range-expanding host and other cynipid hosts and parasitoids will be lower in the expanded range, where it interacts with non-coadapted community members. Understanding factors that lead to ecological release is crucial to predicting outcomes of range expansions and to mitigate negative impacts of range-expanding specieshttps://orb.binghamton.edu/research_days_posters_2021/1061/thumbnail.jp

Implementation of Pesticide Applicator Certification Schools and Continuing Education Workshops

The Oklahoma Department of TransportationÍs (ODOT) herbicide applicator training program consists of initial pesticide applicator training schools followed by independent Certification testing and then on-going yearly continuing education workshops. In support of this on-going effort three pesticide applicator initial certification schools were conducted by Oklahoma State University (OSU) extension staff in fall of 2013 and mid-winter of 2014 to train a total of 103 ODOT participants. One hundred of the attendees at these workshops took the Core as well as Right-of-Way Certification exams administered by the Oklahoma Department of Agriculture, Food & Forestry (ODAFF). Seventy-nine percent (79 participants) passed both the Core and Category 6 (Right-of-Way) examinations to become Oklahoma Certified Pesticide Applicators. Fourteen Pesticide Applicator Continuing Education (CEU) Workshops were conducted by OSU extension staff across a total of eight ODOT Field Divisions in 2014 to provide 637 Certified Applicators with continuing education training. Records of participation in ODAFF approved CEU programs by ODOT personnel were furnished to ODAFF as well as the ODOT Field Divisions, the Maintenance Division Headquarters and the Materials and Research Division. Participation in CEU workshops resulted in granting of CEU credit to ODOT participants in the workshops. The ODOT participants also gained knowledge on various Integrated Pest Management (IPM) and Integrated Vegetation Management (IVM) products, topics and techniques. This increase or maintained operational knowledge of the participants should insure continued effective vegetation management skills.Final report, October 2013-September 2014N

Simulating the mesoscale impacts of sea wall defences on coastal morphology

Solid coastal defences are deployed in many countries to halt or slow coastal erosion. Although the impacts on local sediment fluxes have been studied in detail, the non-local impact of a modified sediment flux regime on mesoscale coastal morphology has received less attention. Morphological changes imparted by defensive structures at these scales (decadal processes over tens of kilometres) can be difficult to quantify or even identify with field data. Difficulties in assessing the impact of these structures arise in the separation of natural and anthropogenic influences, both of which can be highly dynamic and non-linear. Numerical modelling allows these influences to be separated and the impacts of coastal defensive structures to be assessed. We extend previous work (Barkwith et al., 2013) to explore the influences of sea walls on the evolution and morphological sensitivity of a pinned, soft-cliff, sandy coastline under a changing wave climate. The Holderness coast of East Yorkshire, UK, is one of the fastest eroding coastlines in Europe and is used as a case study for this research. Using a mesoscale numerical coastal evolution model, stochastic wave climate data are perturbed gradually to assess the sensitivity of the coastal morphology to changing wave climate for both the defended and natural scenarios. Comparative analysis of the simulated output suggests that sea walls in the south of the region have a greater impact on sediment flux due to the increased sediment availability along this part of the coast. Multiple defended structures, including those separated by several kilometres, were found to interact with each other, producing a complex imprint on coastal morphology under a changing wave climate. Although spatially and temporally heterogeneous, sea walls generally slowed coastal recession and accumulated sediment on their up-drift side