Analysing the Protein-DNA Binding Sites in Arabidopsis thaliana from ChIP-seq Experiments

Computational genomics aim at supporting the discovery of how the functionality of the genome of the organism under study is affected both by its own sequence and structure, and by the network of interaction between this genome and different biological or physical factors. In this work, we focus on the analysis of ChIP-seq data, for which many methods have been proposed in the recent years. However, to the best of our knowledge, those methods lack an appropriate mathematical formalism. We have developed a method based on multivariate models for the analysis of the set of peaks obtained from a ChIP-seq experiment. This method can be used to characterize an individual experiment and to compare different experiments regardless of where and when they were conducted. The method is based on a multivariate hypergeometric distribution, which fits the complexity of the biological data and is better suited to deal with the uncertainty generated in this type of experiments than the dichotomous models used by the state of the art methods. We have validated this method with Arabidopsis thaliana datasets obtained from the Remap2020 database, obtaining results in accordance with the original study of these samples. Our work shows a novel way for analyzing ChIP-seq data.

The dry aged beef paradox: Why dry aging is sometimes not better than wet aging

An increasing consumer demand for a higher quality and eating experience has led to a revisit to the dry aging process. Therefore, research also focuses on the effects of different dry aging methods and aims to improve the dry aging process. However, an optimal process cannot be defined and, unfortunately, most of the dry aging results only hold true for the individual experiment. If one repeats a dry aging process in a different facility, the result might differ. The paradox is that the same dry aging process in two different ripening chambers does not inevitably contribute to equal tenderness and flavor. Since this paradox has still not been understood well, this review presents results of the most relevant dry aging studies by illustrating different process parameters and cuts. Some conclusions which may be useful to explain the paradox are derived from the literature in order to understand the crucial factors and commonalities in the dry aging process.

Mini Managers: Children strategically divide cognitive labor among collaborators, but with a self-serving bias

Strategic collaboration according to the law of comparative advantage involves dividing tasks based on the relative capabilities of group members. Three experiments (N = 405, primarily White and Asian, 45% female) examined how this strategy develops in children when dividing cognitive labor. Children divided questions about numbers between two partners. By 7 years, children allocated difficult questions to the skilled partner (Experiment 1, d = 1.42; Experiment 2, d = 0.87). However, younger children demonstrated a self-serving bias, choosing the easiest questions for themselves. Only when engaging in a third-party collaborative task did 5-year-olds assign harder questions to the more skilled individual (Experiment 3, d = 0.55). These findings demonstrate an early understanding of strategic collaboration subject to a self-serving bias.

WoZ4U: An Open-Source Wizard-of-Oz Interface for Easy, Efficient and Robust HRI Experiments

Wizard-of-Oz experiments play a vital role in Human-Robot Interaction (HRI), as they allow for quick and simple hypothesis testing. Still, a publicly available general tool to conduct such experiments is currently not available in the research community, and researchers often develop and implement their own tools, customized for each individual experiment. Besides being inefficient in terms of programming efforts, this also makes it harder for non-technical researchers to conduct Wizard-of-Oz experiments. In this paper, we present a general and easy-to-use tool for the Pepper robot, one of the most commonly used robots in this context. While we provide the concrete interface for Pepper robots only, the system architecture is independent of the type of robot and can be adapted for other robots. A configuration file, which saves experiment-specific parameters, enables a quick setup for reproducible and repeatable Wizard-of-Oz experiments. A central server provides a graphical interface via a browser while handling the mapping of user input to actions on the robot. In our interface, keyboard shortcuts may be assigned to phrases, gestures, and composite behaviors to simplify and speed up control of the robot. The interface is lightweight and independent of the operating system. Our initial tests confirm that the system is functional, flexible, and easy to use. The interface, including source code, is made commonly available, and we hope that it will be useful for researchers with any background who want to conduct HRI experiments.

Analyzing a series of experiments.

In many plant science experiments, normally there are certain factors that can't be control which may influence the outcome of the work. Such factors include weather and pest pressure. In order to get an accurate and reliable measure of crop performance, the experiment is repeated over time, location or both. These repeated experiments should be analyzed in such a fashion that the data from each individual experiment are combined into one grand analysis. This chapter will cover these types of experiments and their analysis. The influence of nitrogen fertilization on broccoli productivity during two seasons, spring and fall, was used as an example.

MMaJIC, an Experimental Chamber for Investigating Soldering and Brazing in Microgravity

An E-1 payload, the Microgravity Materials Joining Investigative Chamber (MMaJIC), was designed and built for use aboard the International Space Station to investigate soldering and brazing phenomena in a microgravity environment. MMaJIC is a self-contained unit employing a microcontroller that runs a pre-programed experiment, monitors safety sensors, and supports temperature and video recording. MMaJIC uses individual experiment trays that can be easily modified for a specific investigation. The trays, which include a temperature/video data acquisition card, can be easily changed out and returned to Earth for evaluation. Simple operation of MMaJIC minimizes astronaut time while ensuring maximum sample throughput. It is expected that the results will shed considerable light on soldering and brazing in low-gravity environments, information that is important for NASA in conducting comprehensive repair and/or fabrication operations during long duration space missions.

The Production of Mozzarella Cheese from Goat Curd

The quality of curd is of crucial importance when it comes to cheese production because it directly affects the quality of the final product. This research paper analyzes the financial benefits of producing curd from non-standardized goat milk with 4.44% fat. The Chemical examinations of the used curds adhered to international standards and methods. A total of three experiments were conducted in which for each individual experiment, 500 L of goat milk was used to produce curd that served as a base for the production of mozzarella cheese. Out of these experiments, 48 samples were taken from the milk that was used and another 48 samples were taken from the curd that was produced in order to further analyze and compare their chemical composition. We concluded that it is more financially profitable to use standardized milk with 3.2% fat for curd and cheese production, than using non-standardized milk with 4.44% fat for the same purpose.

Applying artificial precipitations to mitigate the melting of the Muz Taw Glacier, Sawir Mountains

The Glaciers in the Sawir Mountains, Altai area, are characterized by higher latitudes and lower elevations. Influenced by the westerly circulation and the polar air mass, the precipitation is abundant and evenly distributed over the year in this area. However, a continuing and accelerating mass loss of glaciers has been in presence since 1959. To study the role of precipitation in mitigating the glacier’s melting, we carried out two artificial-precipitation experiments on the Muz Taw Glacier of the Sawir Mountains on 19 and 22 August 2018, respectively. We measured the albedo and MB at different sites along the glacier before and after the individual experiment. According to the records of the automatic weather station (AWS) set up at the equilibrium line (EL, 3400 m), the amount of precipitation was 6.2 mm and 12.4 mm water equivalent in solid form by the two experiments, respectively. Due to the artificial solid precipitations, the glacier’s surface albedo significantly increased in the mid-upper area, and the amounts of the mass loss decreased by 17 %. We also propose a possible mechanism describing the role of precipitation in mitigating the melting of the glacier.

LABORATORY EVALUATION OF THE DEVELOPMENT OF Aedes aegypti IN TWO SEASONS: INFLUENCE OF DIFFERENT PLACES AND DIFFERENT DENSITIES

Aedes aegypti is an important vector in Brazil being the main vector of the dengue-fever. This paper employs survival curves to describe the time in days from larvae to adult forms of Aedes aegypti raised, individually and collectively, and compares it during winter and spring when positioned inside and outside a laboratory. The study was conducted in São Vicente, a coastal city in Southeastern Brazil. The lowest water temperature in winter and in spring was 20 °C and the highest was 26 °C in spring. Higher and more stable temperatures were measured in the intra compared to the peri in both seasons. Consequently, larvae positioned in the intra resulted in the lowest median time to develop in the individual and collective experiment (nine and ten days, respectively). At least 25% of the larvae positioned in the intra in the individual experiment in the spring took only seven days to reach adulthood. Sex ratios and the median time development by sex did not show significant differences. These results indicate that efforts to control Aedes aegypti must be continuous and directed mainly to prevent the intra-domiciliary sites that can be infested in a week in order to reduce the human-vector contact.

Effects of Sunlight Exposure on Grapevine Powdery Mildew Development

Natural and artificially induced shade increased grapevine powdery mildew (Erysiphe necator) severity in the vineyard, with foliar disease severity 49 to 75% higher relative to leaves in full sun, depending on the level of natural shading experienced and the individual experiment. Cluster disease severities increased by 20 to 40% relative to those on check vines when ultraviolet (UV) radiation was filtered from sunlight reaching vines in artificial shading experiments. Surface temperatures of leaves in full sunlight averaged 5 to 8°C higher than those in natural shade, and in one experiment, filtering 80% of all wavelengths of solar radiation, including longer wavelengths responsible for heating irradiated tissues, increased disease more than filtering UV alone. In controlled environment experiments, UV-B radiation reduced germination of E. necator conidia and inhibited both colony establishment (hyphal formation and elongation) and maturity (latent period). Inhibitory effects of UV-B radiation were significantly greater at 30°C than at 20 or 25°C. Thus, sunlight appears to inhibit powdery mildew development through at least two mechanisms, i.e., (i) UV radiation's damaging effects on exposed conidia and thalli of the pathogen; and (ii) elevating temperatures of irradiated tissues to a level supraoptimal or inhibitory for pathogen development. Furthermore, these effects are synergistic at temperatures near the upper threshold for disease development.