Miracle-dz/UniFAR-FTUs huggingface dataset:
Selection schemes from evolutionary computing show promise for directed evolution of microbes

Directed microbial evolution harnesses evolutionary processes in the laboratory to construct microorganisms with enhanced or novel functional traits. Directing evolutionary processes for applied goals is fundamental to evolutionary computation, which harnesses the principles of Darwinian evolution as a general purpose search engine for solutions to computational problems. Despite overlapping aims, artificial selection methods from evolutionary computing are not commonly applied to living systems in the laboratory. Here, we summarize recent work wherein we ask if parent selection algorithms from evolutionary computation might be useful for directing the evolution of microbial populations when selecting for multiple functional traits. To do so, we developed an agent-based model of directed microbial evolution, which we used to evaluate how well three selection schemes from evolutionary computing (tournament selection, lexicase selection, and non-dominated elite selection) performed relative to schemes used in the laboratory (elite and top-10% selection). We found that lexicase selection and non-dominated elite selection generally outperformed the commonly used directed evolution approaches. Our results are informing ongoing work to transfer these techniques into the laboratory and motivate future work testing more sophisticated selection schemes from evolutionary computation in a directed evolution context.
A verified application of genetic programming: QoS time series modeling and forecasting for web services

In both academia and industry, Web services (WSs) technology (also called Web APIs in recent years) has been a fervid research target for years. In industry, software developers now often develop their application systems with diverse WSs on the internet (i.e., these developers often use service-oriented software engineering, SOSE). However, many companies and organizations, including most tech giants, such as Google, Meta, and Amazon, expose their services and business functionalities in the form of RESTful WSs (Web APIs) for external access (e.g., Amazon Web Services). As a focus of research in services computing, many topics and subjects regarding WSs have been identified, investigated, and addressed. A practical research issue that receives broad attention is the understanding (modeling) and prediction of the time-aware (time-varying) dynamic quality of service (QoS) of WSs. Based on a comprehensive survey and investigation presented in [1]: Y. Syu and C. M. Wang, "QoS Time Series Modeling and Forecasting for Web Services: A Comprehensive Survey", IEEE Transactions on Network and Service Management (TNSM), Vol. 18, P.P. 926--944, 2021, this abstract paper concisely reports to the GECCO community a justified application of genetic programming (GP) on the modeling and forecasting of WS QoS time series. By introducing this employment of GP and the targeted research problem to the community, the purpose is to encourage and attract people in this field to further revise and improve GP to obtain a better solution to the problem or to try to use other evolutionary techniques to better address the problem.
Experience and Guidelines for Sorting Algorithm Choices and Their Energy Efficiency

Energy efficiency has become a major concern in the IT sector as the energy demand for data centers is projected to reach 1PWh per year by 2030. While hardware designers improve the energy efficiency of their products, software developers often do not consider or are unaware of the impact their design choices can make on the energy consumption caused by the execution of their applications. Energy efficiency improvements in applications can, to a certain extent, be achieved through compiler optimizations. Nonetheless, software developers should still make reasonable design choices to improve energy efficiency further. In this paper, we present the energy efficiency of common sorting algorithms under different pre-sorted conditions. Previous work in this field considered only randomized data. We expand on this previous work and measure the sorting algorithms' energy efficiency when the data is already partially sorted to 20% and 50%. Our presented experience is a case study intended to demonstrate the effect simple design choices, such as the selection of algorithm as well as its implementation, can make on energy efficiency. It is intended for industry practitioners to aid them in selecting a more energy-efficient algorithm for their problems at hand through helpful guidelines. Our results also can function as an incentive to make energy efficiency a non-functional requirement for tenders, and as a motivation for researchers to include energy efficiency as an additional quality criterion when studying the properties of algorithms.
Survivor selection in a crossoverless evolutionary algorithm

The plant propagation algorithm is a crossoverless population based evolutionary algorithm, defaultly deploying the plus-selection method for survivor selection - combining parents and offspring population and then selecting the best popSize individuals. In this study, we explore eight different survivor selection methods (plus and comma selection, tournament selection with and without replacement, elitist tournament selection, linear ranking selection and (elitist) roulette wheel selection) on 59 continuous benchmark test function instances and compare the results. In the results, the tournament selection methods outperform PPA's default selection method on 83% to 88% of the 59 benchmark functions. Results show that the performance of all selection methods diminish as dimensions of benchmark function instances increase. Analysis indicates that the tournament selection methods employ more exploitation by decreasing population diversity. Future research should establish if this also benefits performance on other benchmark functions and industrial problems.
Benchmarking Runtime Scripting Performance in Wasmer

In this paper, we explore the use of Wasmer and WebAssembly (WASM) as a sandboxed environment for general-purpose runtime scripting. Our work differs from prior research focusing on browser-based performance or SPEC benchmarks. In particular, we use micro-benchmarks and a macro-benchmark (both written in Rust) to compare execution times between WASM and native mode. We first measure which elements of script execution have the largest performance impact, using simple micro-benchmarks. Then we consider a Web proxy caching simulator, with different cache replacement policies, as a macro-benchmark. Using this simulator, we demonstrate a 5-10x performance penalty for WASM compared to native execution.
Learning to balance exploration and exploitation in pareto local search for multi-objective combinatorial optimization

As a natural extension of local search, Pareto local search (PLS) is a basic building block in many state-of-the-art metaheuristics for multi-objective combinatorial optimization problems (MCOPs). However, the basic PLS suffers from a low convergence rate, since it always fully explores the neighborhood of each unexplored solution, which is unnecessary. Some studies tried to introduce heuristic design in PLS to balance exploration and exploitation. In this paper, we handle this issue by a learning based framework. In the framework, PLS applies the firstK strategy, namely it stops exploring a solution's neighborhood when it obtains K non-dominated solutions, where K is adaptively controlled by a neural network based on observations collected during the search. Training the neural network is modeled as a reinforcement learning problem. Thus the proposed PLS variant is called PLSNN. In the experiments, we compared the performance of PLS, PLSNN and several PLS variants with heuristic design on the multi-objective unconstrained binary quadratic programming problem (mUBQP). The experimental results show that PLSNN performed significantly better than its counterparts on all test instances.
The Lower and Middle Ordovician Cephalopod Faunas of England and Wales

ABSTRACT The cephalopods of the Lower and Middle Ordovician of England and Wales are described and referred to twenty-four taxa across sixteen genera, of which six (Castelloceras, Cyclorangeroceras, Moridunoceras, Saloceras, Sacerdosoceras and Semiannuloceras) are new. Twelve named species are described, five of which (Castelloceras arennigense, Cyclorangeroceras blakei, Moridunoceras castelli, Sacerdosoceras promus and Semiannuloceras abbeyense) are new. As a consequence of small sample sizes and poor preservation, the remaining species are treated in open nomenclature. Two new families (Polymeridae and Rangeroceratidae) are proposed. The fauna contains members of the Orthoceratoidea that are earlier than those described from other parts of the world and throw light on the early development of this group.
Examinations of the unprofitability of authentic Blackness: insights from Black media professionals

ABSTRACT Current research describes how the history of Black representation in the United States’ mainstream media – both on screen and behind the scenes – impacts Black media professionals and complicates the reproduction of authentic Blackness in the twenty-first century. Coupling Hall’s model of encoding and decoding with media production studies, we analyze 22 interviews with self-identified Black media professionals at a Black-owned full-service communications company that targets Black consumers for mainstream brands. Findings suggest that mediated representations of Black people, which are inescapable and influential, are also narrow because white audiences’ perceptions of authentic Blackness determine which depictions of Blackness are profitable. By contrast, Black media producers argue that profitable Blackness is not authentic because it does not include the diversity of the Black experience. We leverage participants’ understandings of Blackness and the role of media to provide practical insights into how media industries can incorporate notions of diversity and inclusion to create authentic mediated Blackness.
Calorific measurement of the inward-flowing fraction of absorbed solar radiation in venetian blinds

This paper presents the calorimetric measurement of the inward-flowing fraction of absorbed solar radiation for a venetian blind at various blind slat angles. The general methodology used for this study followed that originally used by Klems and Kelley (1996). By conducting controlled experiments with an electrically heated blind (to simulate the effects of absorbed solar radiation), the magnitude of the inward-flowing fraction can be directly determined, and environmental effects can be evaluated (i.e., irradiance, interior/exterior temperature difference, and exterior air-film coefficient). For these tests, a calibration transfer standard was used rather than a commercial sealed-glazing unit. Furthermore, because irradiation of the specimen was unnecessary, the entire test was performed indoors. Results indicate that the inward-flowing fraction is dependent on the interior/exterior temperature difference, and only slightly dependent on the absorbed irradiance and exterior air film coefficient. The blind slat angle was also found to have an effect under certain circumstances. Specifically, an open blind combined with an interior/exterior temperature difference had higher inward-flowing fraction values than all other cases. Finally, a proposed test method for determining the inward-flowing fraction is presented and examined. The application of these data is discussed.
Noise correlations in the owl optic tectum are differentially impacted by unimodal vs crossmodal competitors

Multisensory integration in mammalian superior colliculus and its avian homolog, the optic tectum, is essential for rapid orienting towards salient stimuli. The benefits of combining across modalities is expected to depend in part on interneuronal noise correlations (NCs) and trial-to-trial response variance (Fano factor; FF), yet there is scant data on these topics. Here we used multielectrode arrays (MEAs) to record simultaneously from cohorts of single units in the deep layers of the owl optic tectum (OTd). Stimuli were presented individually or simultaneously as spatially aligned or non-aligned competitors. NC values varied from -0.35 to 0.94, an unexpectedly large range, and decreased only modestly as receptive fields diverged. Spatially aligned bimodal stimuli summed in a largely additive fashion over a wide range of response magnitudes. Most of the observed variance in bimodal NCs and FFs could be accounted for by an additive rule without accounting for internal noise. For non-aligned stimuli, crossmodal competitors decreased FFs, whereas unimodal competitors did not. Most striking, visual competitors decreased NCs for auditory drivers but increased NCs for visual drivers, indicating that the OTd network is differentially wired to process bimodal competitors. In total, these data provide novel descriptive information regarding the correlational structure of OTd neurons underlying multisensory processing. SIGNIFICANCE STATEMENT In the owl auditory midbrain and its mammalian homologs, little is known regarding the ensemble response properties during multisensory integration. Using microelectrode arrays we found that noise correlations between pairs of neurons evoked by auditory, visual and bimodal stimuli were large and variable. When two non-aligned (competitor) stimuli were presented simultaneously, response reliability and noise correlations were driven down for crossmodal but not unimodal competitors, which suggests distinct processing strategies. This novel finding predicts that visual competitors drive an increase in localization accuracy for auditory targets.
RAV1 mediates cytokinin signalling for regulating primary root growth in Arabidopsis

Root growth dynamics is an outcome of complex hormonal crosstalk. The primary root meristem size for example, is determined by antagonizing actions of cytokinin and auxin. Here we show that RAV1, a member of the AP2/ERF family of transcription factors, mediates cytokinin signalling in roots to regulate meristem size. The rav1 mutants have prominently longer primary roots, with a meristem that is significantly enlarged and contain higher cell numbers, compared to wild type. The mutant phenotype could be restored on exogenous cytokinin application or by inhibiting auxin transport. At the transcript level, primary cytokinin-responsive genes like ARR1, ARR12 were significantly downregulated in the mutant root, indicating impaired cytokinin signalling. In concurrence, cytokinin induced regulation of SHY2, an Aux/IAA gene, and auxin efflux carrier PIN1 was hindered in rav1, leading to altered auxin transport and distribution. This effectively altered root meristem size in the mutant. Notably, CRF1 another member of the AP2/ERF family implicated in cytokinin signalling, is transcriptionally repressed by RAV1 to promote cytokinin response in roots. Further correlating RAV1 to cytokinin signalling, our results demonstrate that cytokinin upregulate RAV1 expression through ARR1, during post-embryonic root development. Regulation of RAV1 expression is a part of secondary cytokinin response that eventually represses CRF1 to augment cytokinin signalling. To conclude, in Arabidopsis, RAV1 functions in a branch pathway downstream to ARR1 that regulates CRF1 expression to enhance cytokinin action during primary root development.
Drivers of genomic landscapes of differentiation across Populus divergence gradient

Speciation, the continuous process by which new species form, is often investigated by looking at the variation of nucleotide diversity and differentiation across the genome (hereafter genomic landscapes). A key challenge lies in how to determine the main evolutionary forces at play shaping these patterns. One promising strategy, albeit little used to date, is to comparatively investigate these genomic landscapes as a progression through time by using a series of species pairs along a divergence gradient. Here, we resequenced 201 whole-genomes from eight closely related Populus species, with pairs of species at different stages along the divergence gradient to learn more about speciation processes. Using population structure and ancestry analyses, we document extensive introgression between some species pairs, especially those with parapatric distributions. We further investigate genomic landscapes, focusing on within-species (nucleotide diversity and recombination rate) and among-species (relative and absolute divergence) summary statistics of diversity and divergence. We observe highly conserved patterns of genomic divergence across species pairs. Independent of the stage across the divergence gradient, we find support for signatures of linked selection (i.e., the interaction between natural selection and genetic linkage) in shaping these genomic landscapes, along with gene flow and standing genetic variation. We highlight the importance of investigating genomic patterns on multiple species across a divergence gradient and discuss prospects to better understand the evolutionary forces shaping the genomic landscapes of diversity and differentiation.
β-bursts over frontal cortex track the surprise of unexpected events in auditory, visual, and tactile modalities

One of the fundamental ways in which the brain regulates and monitors behavior is by making predictions about the sensory environment and adjusting behavior when those expectations are violated. As such, surprise is one of the fundamental computations performed by the human brain. In recent years, it has been well-established that one key aspect by which behavior is adjusted during surprise is inhibitory control of the motor system. Moreover, since surprise automatically triggers inhibitory control without much proactive influence, it can provide unique insights into largely reactive control processes. Recent years have seen tremendous interest in burst-like β frequency events in the human (and non-human) local field potential – especially over (pre)frontal cortex) – as a potential signature of inhibitory control. To date, β-bursts have only been studied in paradigms involving a substantial amount of proactive control (such as the stop-signal task). Here, we used two cross-modal oddball tasks to investigate whether surprise processing is accompanied by increases in scalp-recorded β-bursts. Indeed, we found that unexpected events in all tested sensory domains (haptic, auditory, visual) were followed by low-latency increases in β-bursting over frontal cortex. Across experiments, β-burst rates were positively correlated with estimates of surprise derived from Shannon’s information theory, a type of surprise that represents the degree to which a given stimulus violates prior expectations. As such, the current work clearly implicates frontal β-bursts as a signature of surprise processing. We discuss these findings in the context of common frameworks of inhibitory and cognitive control after unexpected events.
Modeling the genetic footprint of fluctuating balancing selection: From the local to the genomic scale

Natural selection not only affects the actual loci under selection but also leaves “footprints” in patterns of genetic variation in linked genetic regions. This offers exciting opportunities for inferring selection and for understanding the processes shaping levels of genetic variation in natural populations. Here we develop analytical approximations based on coalescent theory to characterize the genetic footprint of a complex, but potentially common type of natural selection: balancing selection with seasonally fluctuating allele frequencies. We show that seasonal allele frequency fluctuations can have important (and partly unexpected) consequences for the genetic footprint of balancing selection. As also confirmed by stochastic simulations, fluctuating balancing selection generally leads to an increase in genetic diversity close to the selected site, the effect of balancing selection, but reduces diversity further away from the selected site, which is a consequence of the allele-frequency fluctuations effectively producing recurrent bottlenecks of allelic backgrounds. This negative effect usually outweighs the positive effect when averaging diversity levels across the entire chromosome. Strong fluctuating balancing selection even induces a loss of genetic variation in unlinked regions, e.g. on different chromosomes. If many loci in the genome are simultaneously under fluctuating balancing selection this could lead to substantial genome-wide reductions in genetic diversity. This may be the case, even if allele-frequency fluctuations are so small that individual footprints are hard to detect. Thus, together with genetic drift, selective sweeps and background selection, fluctuating selection could be one of the major forces shaping levels of genetic diversity in natural populations. Article summary In some species with multiple generations per year, many loci in the genome experience strong seasonally fluctuating selection, in some cases with stable maintenance of polymorphism. Here we investigate the consequences for levels of genetic diversity at linked neutral sites. Using analytical approximations and stochastic simulations, we find a characteristic local genetic footprint with a diversity peak around the selected site and a diversity valley further away and a substantial reduction in diversity levels chromosome-wide and even genome-wide.
Cervical Spinal Cord Modulation with Repeated Epidural Stimulation in Healthy Adult Rats

The effects of spinal epidural stimulation (ES) in regaining various physiological functions after a spinal cord injury (SCI) are well documented. Spinal evoked motor responses (SEMR) are commonly utilized experimental outcomes in longitudinal pre-clinical and human studies to reflect the in-vivo physiological changes in neural networks secondary to a neurological insult or neuro-rehabilitative treatments utilizing ES. However, it remains unknown if the repeated exposure to ES during SEMRs testing itself modulates the spinal cord physiology and hence the SEMRs characteristics. To address this issue, cervical ES was delivered to the healthy adult rat’s cervical cord using standard stimulation paradigms during multiple sessions (~17 hours that spanned across 100 days). Cervical SEMR and electromyography (EMG) activity from forelimb muscles during a reaching & grasping task were collected before and after 100 days. We noted persistent increase in the cervical SEMR and forelimb muscle activity during reaching & grasping task relative to baseline at the end of the stimulation period indicating increased spinal and cortical excitability. Findings from the present work suggests that cervical SEMRs are amenable to modulation by routine ES testing protocols, with prominent changes in the mono and poly synaptic component of evoked responses. Additionally, since multiple testing sessions of cervical ES alone increases the excitability of the intact spinal cord, we suggest that SEMR data be used with caution to infer the physiological status of the spinal circuitry in longitudinal studies involving multiple SEMR testing sessions. Our findings also recommend involving appropriate control groups, motor behavior correlates, and practicing caution while utilizing normalization methods to allow meaningful functional interpretation of SEMR profiles following a SCI.