Miracle-dz/UniFAR-FTUs huggingface dataset:
Copiotrophs dominate rhizosphere microbiomes and growth rate potential is a major factor explaining the rhizosphere effect

The structure and function of the root microbial community is shaped by plant root activity, enriching specific microbial taxa and functions from the surrounding soil as the plant root grows. Knowledge of bacterial rhizosphere competence traits are important for predictive microbiome modeling and the development of viable bioinoculants for sustainable agriculture solutions. In this work we compared growth rate potential, a complex trait that recently became predictable from bacterial genome sequences, to functional traits encoded by proteins. We analyzed 84 paired rhizosphere- and soil-derived 16S rRNA metabarcoding datasets from 18 different plants and soil types, performed differential abundance analyses and estimated growth rates for each bacterial genus. This analysis revealed that bacteria with a high growth rate potential consistently dominated the rhizosphere. Next, we analyzed the genome sequences of 3270 bacterial isolates and 6707 MAGs from 1121 plant- and soil-associated metagenomes, confirming this trend in different bacterial phyla. We next investigated which functional traits were enriched in the rhizosphere, expanding the catalog of rhizosphere-associated traits with hundreds of new functions. When we compared the importance of different functional categories to the predicted growth rate potential using a machine learning model, we found that growth rate potential was the main feature for differentiating rhizosphere and soil bacteria, revealing the broad importance of this factor for explaining the rhizosphere effect. Together, we contribute new understanding of the bacterial traits needed for rhizosphere competence. As this trait may be inferred from (meta-) genome data, our work has implications for understanding bacterial community assembly in the rhizosphere, where many uncultivated bacteria reside.
Characterization of spatiotemporal dynamics in EEG data during picture naming with optical flow patterns

We present an analysis of the spatiotemporal dynamics of the oscillations in the electric potential that arises from neural activity. Depending on the frequency and phase of oscillations, these dynamics can be characterized as standing waves or as out-of-phase and modulated waves, which represent a combination of standing and moving waves. We characterize these dynamics as optical flow patterns, in terms of sources, sinks, spirals and saddles. Analytical and numerical solutions are compared with real EEG data acquired during a picture-naming task. Analytical approximation of standing waves allows us to establish some properties of pattern location and number. Namely, sources and sinks have mainly the same location, while saddles are located between them. The number of saddles correlates with the sum of all the other patterns. These properties are confirmed in both the simulated and real EEG data.
Prostaglandin E2 prevents radiotherapy-induced alopecia by attenuating transit amplifying cell apoptosis through promoting G1 arrest

Growing hair follicles (HFs) harbor actively dividing transit amplifying cells (TACs), rendering them highly sensitive to radiotherapy (RT). Clinically, there is still a lack of effective treatment for radiotherapy-induced alopecia (RIA). We aimed to dissect the effect and mechanism of local prostaglandin E2 (PGE2) pretreatment in RIA prevention. We found that PGE2 pretreatment reduced RIA by preventing premature termination of anagen through enhancing HF self-repair. Mechanistically, PGE2 did not activate HF stem cells, but preserved more TACs for regenerative attempts. Pretreatment of PGE2 lessened radiosensitivity of TACs by transiently arresting them in the G1 phase, thereby reducing TAC apoptosis and mitigating HF dystrophy. The preservation of more TACs accelerated HF self-repair and bypassed RT-induced premature catagen entry. Promoting G1 arrest by systemic administration of palbociclib isethionate (PD0332991), a CDK4/6 inhibitor, offered a similar protective effect against RT. Therefore, PGE2 protects HF TACs from RT by transiently inducing G1 arrest, and the regeneration of HF structures lost from RT is accelerated to resume anagen growth, thus bypassing the long downtime of hair loss. PGE2 has the potential to be repurposed as a preventive treatment for RIA.
On the Origin and Evolution of Microbial Mercury Methylation

The origin of microbial mercury methylation has long been a mystery. Here we employed genome-resolved phylogenetic analyses to decipher the evolution of the mercury methylating gene, hgcAB, constrain the ancestral origin of the hgc operon, and explain the distribution of hgc in Bacteria and Archaea. We infer the extent to which vertical inheritance and horizontal gene transfer have influenced the evolution of mercury methylators and hypothesize that evolution of this trait bestowed the ability to produce an antimicrobial compound (MeHg+) on a potentially resource-limited early Earth. We speculate that, in response, the evolution of MeHg+-detoxifying alkylmercury lyase (encoded by merB) reduced a selective advantage for mercury methylators and resulted in widespread loss of hgc in Bacteria and Archaea. Significance Neurotoxic methylmercury (MeHg+(aq)) is synthesized from HgII(aq) in the environment by microorganisms possessing the gene pair hgcAB. Our phylogenetic analyses elucidate the origin and evolution of the hgc operon, and support a hypothesis that mercury methylation evolved as an antimicrobial production mechanism, possibly from competition for limited resources on the early Earth. We infer from our analyses that hgc has been primarily vertically inherited in Bacteria and Archaea, with extensive parallel loss, and note that few taxa possessing hgc also possess the gene encoding for MeHg+ demethylation, merB. Our findings support the interpretation that merB evolved as a defense mechanism against the evolution of microbial HgII(aq) methylation.
Strategy-Aware Contextual Bandits

Algorithmic tools are often used to make decisions about people in high-stakes domains. In the presence of such automated decision making, there is incentive for strategic agents to modify their input to the algorithm in order to receive a more desirable outcome. While previous work on strategic classification attempts to capture this phenomenon, these models fail to take into account the multiple actions a decision maker usually has at their disposal, and the fact that they often have access only to bandit feedback . In contrast, we capture this setting as a contextual bandit problem, in which a decision maker must take actions based on a sequence of strategically modified contexts. We provide a low-strategic-regret algorithm for the two action setting, and prove that sublinear strategic regret is generally not possible for settings in which the number of actions is greater than two. Along the way, we obtain impossibility results for multi-class strategic classification which may be of independent interest.
Development of a handheld widefield hyperspectral imaging (HSI) sensor for standoff detection of explosive, chemical, and narcotic residues

The utility of Hyper Spectral Imaging (HSI) passive chemical detection employing wide field, standoff imaging continues to be advanced in detection applications. With a drive for reduced SWaP (Size, Weight, and Power), increased speed of detection and sensitivity, developing a handheld platform that is robust and user-friendly increases the detection capabilities of the end user. In addition, easy to use handheld detectors could improve the effectiveness of locating and identifying threats while reducing risks to the individual. ChemImage Sensor Systems (CISS) has developed the HSI Aperio™ sensor for real time, wide area surveillance and standoff detection of explosives, chemical threats, and narcotics for use in both government and commercial contexts. Employing liquid crystal tunable filter technology, the HSI system has an intuitive user interface that produces automated detections and real-time display of threats with an end user created library of threat signatures that is easily updated allowing for new hazardous materials. Unlike existing detection technologies that often require close proximity for sensing and so endanger operators and costly equipment, the handheld sensor allows the individual operator to detect threats from a safe distance. Uses of the sensor include locating production facilities of illegal drugs or IEDs by identification of materials on surfaces such as walls, floors, doors, deposits on production tools and residue on individuals. In addition, the sensor can be used for longer-range standoff applications such as hasty checkpoint or vehicle inspection of residue materials on surfaces or bulk material identification. The CISS Aperio™ sensor has faster data collection, faster image processing, and increased detection capability compared to previous sensors.
Modelling of superelements in mechanism analysis

The paper deals with substructuring for dynamic analysis of flexible multibody systems. Three different techniques based on component synthesis are discussed, corresponding respectively to fully consistent mass discretization, lumped mass discretization and corotational approximation of inertia forces. To simplify the computer implementation, only the lumped mass and corotational approximations have been considered in detail and programmed. Both approaches are validated on simple examples of rotating beams for which a full elastic model is available using a fully non-linear beam element. The computational efficiency of the corotational inertia approach is also demonstrated on the deployment of a large flexible satellite antenna.
AN ANALYSIS OF IRAS-IDENTIFIED H II REGIONS AND THEIR RADIO PROPERTIES

To try and confirm the types of object in the list of 2298 potential HII regions identified by Hughes \& MacLeod from the IRAS Point Source Catalog, we selected a sample of 82 for observing at the VLA. We selected half with values of Y = log(F$_{25}$/F$_{12}$) $\geq$ 0.8, and for control purposes, half with values of 0.3 $\leq$ log(F$_{25}$/F$_{12}$) $\leq$ 0.5. 78 radio sources were detected, and of all the objects, 72\% had at least one associated radio source. Most of the radio sources had diameters of $<$ 3\arcsec, which was the limit to the angular resolving power of the survey. Those with larger values of Y had significantly larger values of peak radio, integrated radio, and 100$\mu$m flux densities than those with smaller Y. Also, they generally had associated masers, and thus were most likely young compact HII regions containing star forming regions. Those with smaller Y tended not to have associated maser activity and are probably older HII regions, or stars with high IR and ionizing radiation, such as T-Tauri type stars. However, all 2298 objects appear to have a strong galactic concentration. Some comparison is made with the selection of 1717 objects identified by Wood \& Churchwell as HII regions, but their selection criteria were somewhat different, and they actually form a subset of ours.
Toward a better understanding of the attitude – behavior gap in organic food conative loyalty: a moderation and moderated mediation analysis behavior gap in organic food

Purpose – Previous research has found mixed evidence of an attitude – behavior gap in organic food consumption. However, the complex mechanisms underlying this gap warrant further investigation. The purposeofthisstudyistoexaminetheroleofword-of-mouth(WOM),trust,andinvolvementintherelationshipbetweenconsumerorganicfoodattitudesandconativeloyalty.TheTheoryofPlannedBehavior(TPB)wasusedasunderlyingframeworkformodelingourconceptualizedarguments. Design/methodology/approach – A moderation and moderated mediation analysis was performed on a cross-sectional sample of 1,011 Australian organic food consumers. Findings – The resultssupport the TPB-inspired moderated-mediation model. Specifically, the authors found moderatedmediationeffectsofWOM,trust,andinvolvementonconativeloyaltyviaattitudestowardorganics. Research limitations/implications – The cross-sectional research design and the focus solely on Australian consumers constitute limitations of this study. Practical implications – The authors ’ findings imply that an analysis of the attitude – behavior gap should go beyond the testing of contingent consistency hypotheses and instead combine moderation and mediation mechanisms to better model consumer decision-making leading to conative loyalty. Practitioners would face a resource challenge when targeting low-trust, low-involvement, and low-WOM consumers as developing conative loyalty of these segments would require a longer-term approach through building favorable attitudes toward organic foods. Originality/value – This study is one of the first to demonstrate the potential of examining the attitude – behavior gap in the organic food context through a moderated mediation lens in explaining the dynamics of conative loyalty. loyalty as then moderated mediation hypotheses involving WOM, trust, and involvement be postulated.
Designing a Framework for Attracting Public Participation in the Iranian Health System: A Comparative and Mixed-Method Study

Background: Public participation strengthens the public presence in healthcare. Objectives: This study aimed to determine the dimensions of attracting public participation in the Iranian health system. Methods: A mixed-method research was conducted from May 2019 to July 2020. A comparative study (using the documents of five countries that were selected purposefully), tool design and validation (through holding two expert panels with the participation of 26 people who were selected based on the inclusion criteria), and finalization of the participation framework (field test with the participation of 283 recruited people based on the inclusion criteria) were performed. Exploratory and confirmatory factor analyses (CFA) were applied using SPSS-v26 and AMOS-v26. Results: Forty-eight components on five factors, including citizenship rights and customer orientation, socioeconomic factors, communication with people and non-governmental organizations, research and technology, and managerial and organizational factors with impact factors of 0.967, 0.951, 0.957, 0.944, and 0.955 were loaded, respectively. The CFA denoted the approval of the framework with the five mentioned factors. Conclusions: In this study, a framework was developed and approved during different stages. Using this framework, healthcare policymakers can adopt the best strategies for engaging public participation and improving the effectiveness of decisions through evidence-informed policymaking.
Multibody Modeling of a New Wheel/Track Reconfigurable Locomotion System for a Small Farming Vehicle

Tracks and wheels are the most widely used running gear for the locomotion of agricultural vehicles. The main difference between the two systems is the contact area with the ground and, consequently, the pressure distribution. Evaluating the pressure distribution on the ground is important because soil damage and vehicle performance depend on it. This analysis is especially difficult for tracked vehicles, owing to their complexity compared with wheeled systems. In this paper, we describe a multibody model of a flexible track to evaluate the pressure distribution upon contact with soft terrain. The track considered in this study is part of a reconfigurable locomotion system of a small farming vehicle, which can vary the pressure distribution by switching from a wheeled vehicle to a half-tracked vehicle. The aim of such a vehicle is to minimize soil damage in addition to optimizing its performance. The model is used to characterize this vehicle and evaluate the pressure distribution with varying characteristic parameters, such as track tension, the position of the vehicle’s center of gravity, the weight distribution on the track itself, and the stiffness of the suspension system.
Moodle Gamiﬁcation applied to Higher Education

—Considering that students grow up with digital technology, teachers can use it to solve problems that arise during the long learning process, as such, they can use the Learning Managment System (LMS) platforms to help and streamline the learning method. Gamiﬁcation is the utilization of game design elements in non-game contexts and aims to provide intrinsic and extrinsic motivation to participants. This work aims to apply gamiﬁcation to an LMS, more speciﬁcally on the Moodle platform, to improve students’ engagement and more utilization of interactive features in the curricular unit Independent Studies 1. The evaluation of this work will be supported by surveys and interviews made to students who participated in this demonstration. Based on the results obtained, it was realized that the gamiﬁcation application used did not support the intended objectives, because it presented some bugs that inﬂuenced the attribution of Experience Points (XP). Despite this, the proposal demonstrated positive results in terms of gamiﬁcation, showing to be effective in motivating students carrying out the tasks, improving the interaction between them and the use of Moodle for sharing materials. It was also noticed that gamiﬁcation is a topic to be considered in the educational process.
Assessment of Genetic Diversity among Elite Breeding Lines of Arabica Coffee (Coffea arabica L.) in Ethiopia using Simple Sequence Repeats Markers

: Despite being the center of origin and genetic diversity, there has been limited application of molecular markers in arabica coffee breeding in Ethiopia. In this study, the extent of genetic diversity and relationships of 48 elite breeding lines of arabica coffee from different geographical origins were evaluated using 14 SSR markers. The SSR markers amplified 105 alleles of which 104 are polymorphic with an average of 7.4 polymorphic alleles per locus. The average percent of polymorphism and Polymorphic Information Content (PIC) of the SSR markers were 98.81 and 0.79, respectively. The average genetic similarity coefficient among all possible pairs was 0.37 and ranged from 0.39 to 0.46 within the same geographical origin. The Unweighted Pair Group Method Using Arithmetic averages (UPGMA) cluster analysis placed the studied breeding lines into seven clusters with Jaccard’s similarity coefficient of <0.44. The results of this study demonstrated the powerfulness of the SSR markers and the presence of a high level of genetic diversity and wide genetic dissimilarity within and among elite breeding lines from the same and different geographical origins. The observed diversity could be utilized in the breeding program to improve productivity and maintain the typical quality profile of origin-based landrace coffees. The SSR markers could be used in future genetic analysis of arabica coffee germplasm to increase the efficiency of the breeding program in Ethiopia. The studied breeding lines could also be conserved and managed as an important source of genetic variability to be used in the future coffee improvement program.
THE ROLE OF DAYLIGHT ON USERS’ SEAT PREFERENCES

Seating that meets the needs and preferences of students can promote a longer stay in libraries and keep students motivated, which in turn influences their emotions and learning abilities. However, existing knowledge on the interaction between daylighting and seating preferences is limited. This study aims to understand what type of spaces are in more demand and the relationship between seat occupancy and daylight availability. Occupancy data of the UCL Bartlett library acquired from motion sensors located underneath each desk was used to assess occupancy, which was then compared to characteristics of space, including daylight availability. The study revealed that although daylight has a considerable impact on students’ seat selection, the seating preference of the students cannot be explained by daylight alone. The seats with a good combination of daylight, outdoor view and privacy are in more demand compared to seats that provide only a high level of daylight. Future research should involve individual perception in addition to occupancy monitoring data, considering daylight conditions together with other components such as privacy, outdoor views, and quietness.
THE USE OF HEURISTIC METHOD TO ASSESS THE USABILITY OF UNIVERSITY WEBSITE

Websites have many functions such as to sell products and services, inform about company and their business, educate users, entertain users and can be used as a communication tool, a branding tool and can help to improve company’s image. The most important is that web pages are usable. If it is difficult to use a website, visitors leave it. In this article we describe theory of usability, website usability principles and one of the usability testing methods - heuristic evaluation and its theory. We present different heuristic principles by different authors. We use heuristic evaluation to assess the usability of University of Zilina website. We identify many usability problems and prepare the task list for the realization team, who propose the new university web site.
TREE GRAPH METHOD FOR VISUAL REPRESENTATION OF MULTI-DIMENSIONAL DATA

In this paper, a tree graph is proposed as the method representing multidimensional data on a two-dimensional plane. The tree graph represents the respective multi-items by the branches, roots, fruits, leaves, heights and locations of the tree, and is recognized globally the characteristics and profiles of the data given. It seems to us that the tree graph is particularly superior to the other graphs presented heretofore in grasping the global correlation between one objective item and other items, the mutual correlation among the multiitems and time-dependent aspects of the data.
Alteration of the N-Terminus to analyze Enhancer of Rudimentary Homolog, ERH function

The enhancer of rudimentary gene, e(r) , is the gene that encodes the Enhancer of Rudimentary Homolog protein (ERH). The amino acid structure of this protein, especially the first five amino acids which make up the N-terminus and the beginning of the first β-strand in the β-sheet of the protein’s secondary structure, have been found to be highly conserved among a wide variety of organisms, including vertebrates, insects, and protists. This suggests that these amino acids may play a key role in the activity of ERH, and that ERH may have a conserved function across organisms. Mutations in amino acids 2 through 5 were constructed and the mutant e(r) alleles were inserted into the third chromosome of Drosophila melanogaster . The activity of the resulting mutant ERH proteins was assessed by their ability to rescue two mutant phenotypes of e(r) deletions – low viability of the single mutant and the synthetic lethality as a double mutant with a low-activity Notch mutation. Phenotypic observations of eye color show whether any of the mutations give rise to wild-type ratios of females versus males. The results indicate that the N-terminus of ERH is indeed necessary for its proper function, and that this function may be evolutionarily conserved.
An Interactive Modeling System of Japanese Castles with Decorative Objects

We present an interactive modeling system for Japanese castles. We develop an user interface that can generate the fundamental structure of the castle tower consisting of stone walls, turrets, and roofs. By clicking on the screen with a mouse, relevant parameters for the fundamental structure are automatically calculated to generate 3D models of Japanese-style castles. We use characteristic curves that often appear in ancient Japanese architecture for the realistic modeling of the castles.