Miracle-dz/UniFAR-FTUs huggingface dataset:
DEMO: Self-Preserving Genetic Algorithms vs. Safe Reinforcement Learning in Discrete Action Spaces

Safe learning techniques are learning frameworks that take safety into consideration during the training process. Safe reinforcement learning (SRL) combines reinforcement learning (RL) with safety mechanisms such as action masking and run time assurance to protect an agent during the exploration of its environment. This protection, though, can severely hinder an agent's ability to learn optimal policies as the safety systems exacerbate an already difficult exploration challenge for RL agents. An alternative to RL is an optimization approach known as genetic algorithms (GA), which utilize operators that mimic biological evolution to evolve better policies. By combining safety mechanisms with genetic algorithms, this work demonstrates a novel approach to safe learning called Self-Preserving Genetic Algorithms. To highlight the training benefits of SPGA compared to SRL in discrete action spaces, this demonstration trains and deploys an SPGA agent with action masking (SPGA-AM) and an SRL agent with action masking (SRL-AM) in real-time in the CartPole-v0 environment with a safety boundary condition b = 0.75. After training, each of the learned policies are tested in a CartPole-v0 environment with an extended max timesteps value (T = 200 → T = 1000). After the demo, users will have a better understanding of SPGA and SRL training, as well as the benefits of using SPGA to train in discrete action spaces.
A computational hyperspectral imaging technique

A novel spectral imaging technique is introduced based on a highly dispersive imaging lens system. The chromatic aberration of the lens system is utilized to spread the spectral content of the object over a focal distance. Two three-dimensional surface reconstruction algorithms, depth from focus and depth from defocus, are applied to images captured by dispersive lens system. Using these algorithms, the spectral imager is able to relate either the location of focused image or the amount of defocus at the imaging detector to the spectral content of the object. A spectral imager with ~5 nm spectral resolution is designed based on this technique. The spectral and spatial resolutions of the introduced technique are independent and can be improved simultaneously. Simulation and experimental results are presented.
Direct Speech Quote Attribution for Dutch Literature

We present a dataset and system for quote attribution in Dutch literature. The system is implemented as a neural module in an existing NLP pipeline for Dutch literature (dutchcoref; van Cranenburgh, 2019). Our contributions are as follows. First, we provide guidelines for Dutch quote attribution and annotate 3,056 quotes in fragments of 42 Dutch literary novels, both contemporary and classic. Second, we present three neural quote attribution classifiers, optimizing for precision, recall, and F1. Third, we perform an evaluation and analysis of quote attribution performance, showing that in particular, quotes with an implicit speaker are challenging, and that such quotes are prevalent in contemporary fiction (57%, compared to 32% for classic novels). On the task of quote attribution, we achieve an improvement of 8.0% F1 points on contemporary fiction and 1.9% F1 points on classic novels. Code, data, and models are available at https://github.com/anonymized/repository.
Effects of index angle on flow ripple of a tandem axial piston pump

A high noise level is one of the prominent shortcomings of an axial piston pump which is widely used in industrial and mobile applications. In this paper, a simulation model of an axial piston pump is developed based on a single piston chamber model, for capturing the dynamic characteristics of the discharge flow rate. The compressibility of fluid and main leakages across different friction pairs are considered. The simulation model is validated by a comparison of discharge flow ripple with the measured results using the secondary source method. The main cause of flow ripple is identified by a comparison of the frequency spectrums of actual and kinematic flow ripples. Flow rates with different index angles are analyzed in time and frequency domains. The findings show that an index angle of 20° is the most effective in reducing the flow ripple of a tandem axial piston pump, because the frequency contents at odd harmonics can be cancelled out. A sensitivity analysis is conducted at different pressure levels, speeds, and displacement angles, which reveals that with an index angle of 20°, the sensitivity of flow ripple can be reduced by almost 50% over a wide variety of working conditions. 摘要目的探索转位角对串联泵出口流量脉动的影响, 揭示转位角对流量脉动的影响机理, 获得最佳转位角以减小流量脉动, 以及探索转位角对工况的敏感性。 方法1. 建立基于单柱塞腔模型的单柱塞泵模型, 求解其出口流量脉动特性; 2. 研究不同转位角下串联泵的出口流量脉动, 优选转位角; 3. 对比不同转位角下出口流量脉动对工况的敏感性。 结论1. 对于单个转子使用九柱塞的串联式轴向柱塞泵, 最佳转位角是 20°, 因该角度可消除流量脉动在奇数阶次下的幅值; 2. 在大范围工况下, 转位角为 20° 时可减小约 50% 的流量脉动。
Named Entity Annotation Projection Applied to Classical Languages

In this study, we demonstrate how to apply cross-lingual annotation projection to transfer named-entity annotations to classical languages for which limited or no resources and annotated texts are available, aiming to enrich their NER training datasets and train a model to perform NER tagging. Our method uses sentence-level aligned parallel corpora ancient texts and the translation in a modern language, for which high-quality off-the-shelf NER systems are available. We automatically annotate the text of the modern language and employ a state-of-the-art neural word alignment system to find translation equivalents. Finally, we transfer the annotations to the corresponding tokens in the ancient texts using a direct projection heuristic.We applied our method to ancient Greek, Latin, and Arabic using the Bible with the English translation as a parallel corpus. We used the resulting annotations to enhance the performance of an existing NER model for ancient Greek
OdyCy – A general-purpose NLP pipeline for Ancient Greek

This paper presents a general-purpose NLP pipeline that achieves state-of-the-art performance on the Ancient Greek Perseus UD Treebank for several tasks (POS Tagging, Morphological Analysis and Dependency Parsing), and close to state-of-the-art performance on the Proiel UD Treebank. Our aim is to provide a reproducible, open source language processing pipeline for Ancient Greek, capable of handling input texts of varying quality. We measure the performance of our model against other comparable tools and then evaluate lemmatization errors.
Nouvel algorithme de détection des lignes de marquage au sol

We propose in this paper a new lane marking detection algorithm for road safety. This algorithm can extract road marking from a camera mounted on a vehicle. In a first step, we conceived, an original method of edge road lane-marker extraction. This method is based on photometric and temporal criterion. In a second stage, we have used the robust method of RANSAC to adjust edge points detected with a model describing the curvature of the road. The parameters of this algorithm have been adjusted in order to get a good precision of model’s parameters. Some experimental results obtained on real images and prospects of our study are given in the end of this paper.
The impact of soil warming on fine root trait responses of trees, deciduous vs. coniferous: a meta-analysis

Abstract We compiled data from 149 paired observations from 43 publications and performed a meta-analysis to evaluate the variability of trees’ fine root trait responses under various global soil warming experiments. The impacts of warming magnitude, soil depth, and different tree species (deciduous vs. coniferous), on the responses of fine root biomass (FRB), and fine root morphology were assessed in this study. Our results confirmed that soil warming increased FRB while having no significant effect on fine root morphological traits, such as specific root length (SRL), specific root area (SRA), and diameter (D). The effect of warming on FRB decreased significantly at higher warming magnitude. The effect of tree species was also evident in the response of FRB to soil warming magnitude. Furthermore, warming effects on SRA and D increased in deeper soil horizons. The present meta-analysis provides an improved understanding of trees’ fine roots and the tree species-specific adaptive strategy under future soil warming episodes. Our results suggest that trees will resist the altering soil warming conditions by modifications more in fine root biomass allocation rather than morphological adjustments.
You can’t smoke here! Some observations of no-smoking signs in Bangkok, Thailand

ABSTRACT No-smoking signs communicate smoke-free rules to eliminate second-hand smoke and tobacco consumption. In this essay, I critically reflect on the presence, meanings, and context of no-smoking signs in public places in Bangkok, illustrated with photos of signs and accompanying commentary. Impressively, no-smoking signs were omnipresent in the city. However, unattractive designs, condescending messages, lack of language diversity and technological application, and smoking violations observed by the author all raise questions about whether they were noticed and acted upon. I call for an overhaul of no-smoking signs to curb the global tobacco epidemic and its devastating impact in cities.
A unique C-terminal domain contributes to the molecular function of restorer-of-fertility proteins in plant mitochondria

Restorer-of-fertility (Rf) genes have practical applications in hybrid seed production as a means to control self-pollination. They encode pentatricopeptide repeat (PPR) proteins that are targeted to mitochondria where they specifically bind to transcripts that induce cytoplasmic male sterility and repress their expression. In searching for a molecular signature unique to this class of proteins, we found that a majority of known Rf proteins have a unique domain, which we called RfCTD (Restorer-of-fertility C-terminal domain), and its presence correlates with the ability to induce cleavage of the mitochondrial RNA target. We constructed a sequence profile that can quickly and accurately identify RfCTD sequences in plant genomes or transcriptomes. We screened 219 angiosperm genomes from 123 genera and found that each diploid genome encodes, on average, 25 Rf-like (RFL) proteins, of which approximately 55% contain the C-terminal signature domain. This screen also revealed considerable variation in RFL gene numbers across flowering plants. We observed that plant genera with bisexual flowers have significantly higher numbers of RFL genes compared to those with unisexual flowers, consistent with a role of these proteins in restoration of male fertility. Finally, we show that removing the RfCTD from the RFL protein RNA PROCESSING FACTOR 2-nad6 prevented cleavage of its RNA target, the nad6 transcript, in Arabidopsis thaliana mitochondria. This research provides a simple way of identifying putative Rf candidates in genome sequences, new insights into the molecular mode of action of Rf proteins in plant mitochondria and expands our understanding of the evolution of fertility restoration in flowering plants.
DNA Combing versus DNA Spreading and the Separation of Sister Chromatids

DNA combing and DNA spreading are two central approaches for studying DNA replication fork dynamics genome-wide at single-molecule resolution by distributing labeled genomic DNA on coverslips or slides for immunodetection. Perturbations in DNA replication fork dynamics can differentially affect either leading or lagging strand synthesis, for example in instances where replication is blocked by a lesion or obstacle on only one of the two strands. Thus, we sought to investigate whether the DNA combing and/or spreading approaches are suitable for resolving adjacent sister chromatids during DNA replication, thereby enabling the detection of DNA replication dynamics within individual nascent strands. To this end, we developed a thymidine labeling scheme that discriminates between these two possibilities. Our data suggests that DNA combing resolves single chromatids, allowing the detection of strand-specific alterations, whereas DNA spreading does not. These findings have important implications when interpreting DNA replication dynamics from data obtained by these two commonly used techniques.
The Logic of Capture-Recapture Estimates

The estimators derived by Jolly and by Seber for the parameters of an open mobile animal population are maximum likelihood estimators if every live animal has the same probability of surviving until the next sample and the same probability of being observed at that time. The logical structure of the estimatinig equations is emphasised here, and is found to throw light on two classes of problem: what biases will occur if the Seber-Jolly estimates are used in situations in which the standard assumptions do not hold, and what new estimates are reasonable in these cases? The logical argument is applied to various situations including those in which survival is heterogeneous, or correlated with age, and others in which catchability is heterogeneous or affected, permanently or temporarily, by marking.
A Narrow Range of Transcript-error Rates Across the Tree of Life

The expression of information encoded in genomes is not error-free. Transcript-error rates are dramatically higher than DNA-level mutation rates, and despite their transient nature, the steady-state load of such errors imposes a burden on cellular performance. However, a broad perspective on the degree to which transcript-error rates are constrained by natural selection and diverge among lineages remains to be developed. Here, we present a genome-wide analysis of transcript-error rates across the Tree of Life, showing that the effects of such errors are most likely at least partially dominant, and possibly synergistic, such that larger cells with more transcripts experience larger error burdens. Despite having a much narrower phylogenetic range of variation than genomic mutation rates, transcript-error rates vary in a manner that is consistent with the drift-barrier hypothesis, previously postulated as an explanatory framework for genome mutation-rate evolution. Thus, the degree to which natural selection is capable of reducing transcript-error rates is a function of both the population-genetic and the cellular environment (effective population size, cell volume, proteome size, and average fitness effects of individual errors). The idea that transcript-error rates are adaptively reduced in genes with high expression finds little support in the data.
Disease resistance gene count increases with rainfall in Silphium integrifolium

Intracellular plant defense against pathogens is mediated by a class of disease resistance genes known as NB-LRRs or NLRs (R genes). Many of the diseases these genes protect against are more prevalent in regions of higher rainfall, which provide better growth conditions for the pathogens. As such, we expect a higher selective pressure for the maintenance and proliferation of R genes in plants adapted to wetter conditions. In this study, we enriched libraries for R genes using RenSeq from baits primarily developed from the common sunflower (Helianthus annuus) reference genome. We sequenced the R gene libraries of Silphium integrifolium Michx, a perennial relative of sunflower, from 12 prairie remnants across a rainfall gradient in the Central Plains of the United States, with both Illumina short-read (n=99) and PacBio long-read (n=10) approaches. We found a positive relationship between the mean effective annual precipitation of a plant’s source prairie remnant and the number of R genes in its genome, consistent with intensity of plant pathogen coevolution increasing with precipitation. We show that RenSeq can be applied to the study of ecological hypotheses in non-model relatives of model organisms.
Simple and efficient auditory-nerve spike generation

This brief paper documents a simple and efficient method to generate auditory-nerve spike trains for the purpose of simulating neural processes of auditory perception. In response to sound, each auditory nerve fiber carries information to the auditory brainstem in the form of a train of spikes (action potentials), the timing and rate of which reflect the sound. The generation process is usually approximated as Poisson process with a time-varying rate, further modified by refractory effects. The purpose, here, is to simulate spike generation as a time- and interval-dependent thinning process applied to a homogenous Poisson process, allowing for fast generation, cheap storage, and unlimited temporal resolution.
Synergistic effects of predation and parasitism on competition between edible and inedible phytoplankton

Fungi can affect aquatic ecosystems through syntrophic and parasitic interactions with other organisms and organic matter. In pelagic systems, fungal parasites on phytoplankton can control trophic interactions and food-web dynamics, e.g., zooplankton grazing on fungal parasite zoospores creates an alternative energy pathway (termed “mycoloop”) from otherwise inedible phytoplankton species. We aim to investigate how the mycoloop influences community dynamics in aquatic food-webs combining experimental and modelling approaches. We assembled an experimental system consisting of an inedible (host) phytoplankton species and its parasitic chytrid, an edible (non-host) phytoplankton species, and a zooplankton grazer. Chytrids parasitizing increased edible phytoplankton abundance, while zooplankton grazing decreased edible phytoplankton abundance. In the presence of zooplankton and chytrids, competition effects between edible and inedible phytoplankton species depended on nutrient levels. At high nutrient levels, competition was balanced by an indirect positive chytrid effect and negative zooplankton grazing effects on edible phytoplankton. In contrast, at low nutrient levels, we found chytrid had a negative impact on edible phytoplankton synergistically with zooplankton. Mathematical investigations suggest that the synergistic effect can be caused by the mycoloop. This indicates that the mycoloop substantially affects predator-prey interactions and phytoplankton competition with yet unknown ecological consequences.
Constructing a Credible Estimation for Overreporting of Climate Adaptation Funds in the Creditor Reporting System

Development funds are essential to finance climate change adaptation and are thus an important part of international climate policy. How ever, the absence of a common reporting practice makes it difficult to assess the amount and distribution of such funds. Research has questioned the credibility of reported figures, indicating that adaptation financing is in fact lower than published figures suggest. Projects claiming a greater relevance to climate change adaptation than they target are referred to as “overreported”. To estimate realistic rates of overreporting in large data sets over times, we propose an approach based on state-of-the-art text classification. To date, assessments of credibility have relied on small, manually evaluated samples. We use such a sample data set to train a classifier with an accuracy of 89.81%±0.83% (tenfold cross-validation) and extrapolate to larger data sets to identify overreporting. Additionally, we propose a method that incorporates evidence of smaller, higher-quality data to correct predicted rates using Bayes’ theorem. This enables a comparison of different annotation schemes to estimate the degree of overreporting in climate change adaptation. Our results support findings that indicate extensive overreporting of 32.03% with a credible interval of [19.81%; 48.34%].
Mechanical regulation of substrate adhesion and de-adhesion drives a cell contractile wave during tissue morphogenesis

During morphogenesis tissue-scale forces drive large-scale deformations, yet how these forces arise from the local interplay between cellular contractility and adhesion is poorly understood. In the posterior endoderm of Drosophila embryos, a self-organized tissue-scale wave of actomyosin contractility and cell invagination is coupled with adhesion to the surrounding vitelline membrane to drive the polarized tissue deformation. We report here that this process emerges at the subcellular level from the mechanical coupling between Myosin-II activation and sequential adhesion/de-adhesion to the vitelline membrane. At the wavefront, integrin focal complexes anchor the actin cortex to the vitelline membrane and promote activation of Myosin-II, which in turn enhances adhesion in a positive feedback loop. Subsequently, upon detachment, cortex contraction and advective flow further amplify Myosin-II levels. Prolonged contact with the vitelline membrane increases the duration of the integrin-Myosin-II feedback, integrin adhesion and thus slows down cell detachment and wave propagation of the invagination. Finally, we show that the angle of cell detachment changes as a function of the strength of adhesion and modifies the tensile forces required for detachment to maintain wave propagation. This illustrates how the tissue-scale wave arises from subcellular mechanochemical feedbacks and tissue geometry.
Sperm regulates locomotor activity of C. elegans hermaphrodites

Sex differences in sex-shared behavior are common across various species. During mating, males transfer sperm and seminal fluid to females, which can affect female behavior. Sperm can be stored in the female reproductive tract for extended periods of time. However, its role in regulating female behavior is poorly understood. In the androdioecious nematode C. elegans, hermaphrodites produce both egg cells and sperm, enabling them to self-fertilize or mate with males. Hermaphrodites exhibit less locomotor activity compared to males, indicating sex difference in behavioral regulation. In this study, sperm-deficient mutants were examined to investigate the role of sperm in the regulation of locomotor behavior. The results suggest that sperm plays a significant role in regulating sex-shared behavior in C. elegans, as sperm-deficient mutants exhibited increased locomotor activity. Additionally, females of closely related gonochoristic species, C. remanei and C. brenneri, exhibited reduced locomotor activity after mating. The regulation of locomotion by sperm may be an adaptive mechanism that enables sperm-less hermaphrodites to search for mates and allow females to cease their search for mates after mating.