Miracle-dz/UniFAR-FTUs huggingface dataset:
The Word-Weaving Clock: Time Constraints in Word Associations

A wise design of time constraints is crucial for the computational realization of several creative tasks. In this paper we focus on live generation of word associations unfolding semantic paths modulated by contextual clues. We present the Word-Weaving Clock , a lexical creative system performing the generation of word associations where both semantic and time constraints are taken in account. The system is meant to be used interactively as part of a live demonstration.
Test for interaction in two-way contingency tables

This paper makes use of some well-known concepts in regression modelling to define two-factor interaction in the transformed and untransformed two-way contingency tables. Asymptotic chi-square test statistics, each with one d.f. , for testing interaction in the table are developed. The asymptotic relative efficiency (ARE) of these statistics is studied.
An embedded method-of-lines approach to solving partial differential equations on surfaces

We introduce a method-of-lines formulation of the closest point method, a numerical technique for solving partial differential equations (PDEs) defined on surfaces. This is an embedding method, which uses an implicit representation of the surface in a band containing the surface. We define a modified equation in the band, obtained in a straightforward way from the original evolution PDE, and show that the solutions of this equation are consistent with those of the surface equation. The resulting system can then be solved with standard implicit or explicit time-stepping schemes, and the solutions in the band can be restricted to the surface. Our derivation generalizes existing formulations of the closest point method and is amenable to standard convergence analysis.
A Corpus for Entity Recognition in COVID-19 Full-text Literature (poster)

To support the development of entity recognition tools, this study manually annotates 99 full-text articles about COVID-19. Each article is annotated by 6 annotators through two rounds. 18 types of entity are involved, including genes, diseases, chemicals, coronaviruses and so on. We also calculate the inter-annotator agreement (IAA) scores in term of multi-κ measure to ensure the quality of the annotations. In the end, 39, 118 entity mentions are manually annotated in total. © Copyright 2022 for this paper by its authors.
Is style reproduction a computational creativity task?

Is style reproduction a valid computational creativity task? Does producing output ‘in the style of’ an existing creator contribute to computational creativity research? Where is the creativity in imitation or replication of an existing style, and where does style reproduction fall into what has been criticised as ‘pastiche’ rather than credible creative activity? This paper tackles these debates, which have been under-addressed in computational creativity literature. We review the presentaiton of past work in style reproduction, and consider the fit of such work into evolving definitions of computational creativity research. As part of this, we consider style reproduction itself as a creative task, both within and outside computational forms. We discuss various points of interest that emerge in the analysis, such as control in the creative process, intentionality and effort. Our work gives a more objective understanding of the level of creativity present in style generation, and specifically what value it brings to computational creativity research.
Analyzing Research Diversity of Scholars Based on Multi-dimensional Calculation of Entities (short paper)

Understanding diversity of research contents is essential for facilitating analysis of scholars’ research characteristics. The multi-dimensional character of research diversity makes its analysis a challenging issue. Based on the three primary attributes of research diversity: variety, evenness and disparity, we apply three multi-dimensional calculation methods to analyze the research diversity of scholars as well as discuss scenarios to which the methods apply by comparing calculation results between them. Three categories of research diversity calculated include: one- dimensional diversity (measuring variety, evenness, disparity), two-dimensional diversity (measuring variety/evenness, variety/disparity), and three-dimensional diversity (measuring variety/evenness/disparity). Preliminary results of the three methods show evident differences. The one-dimensional diversity is feasible and can directly demonstrate research diversity in a certain aspect; the two-dimensional diversity can guarantee a more complicated demonstration of the diversity characteristics; the three-dimensional diversity fully reflects different diversity characteristics and is highly adjustable for highlighting certain aspect of diversity. The approach we apply offers a foundation for further studies on applying diversity calculation to evaluating academic performance of scholars in information science.
A Bootstrapped Chinese Biomedical Named Entity Recognition Model Incorporating Lexicons

Biomedical named entity recognition (BioNER) is a sub-task of named entity recognition, aiming at recognizing named entities in medical text to boost the knowledge discovery. In this paper, we propose a bootstrapped model incorporating lexicons, which takes advantage of pretrained language model, semi-supervised learning and external lexicon features to apply BioNER to Chinese medical abstracts. Extensive evaluation shows that our system is competitive on limited annotated training data, which surpasses the baselines including HMM, CRF, BiLSTM, BiLSTM-CRF and BERT for 54.60%, 37.92%, 55.46%, 48.67%, 7.99% respectively. The experimental results demonstrate that unsupervised pretraining makes pretrained language model acquire the ability that only a few annotated data can achieve great performance for downstream tasks. In addition, semi-supervised learning and external lexicon features can further compensate for the problem of insufficient annotated data.
The (Artificial) Physicality of Creativity: How Embodiment Influences Perceptions of Creativity

The generation of artifacts through computational creativity (CC) systems is hitting the headlines with increasing frequency. Although impressive, this paper will not focus on the outcomes achieved by these systems, but rather on a specific dimension of artistic processes: embodiment. I discuss the results of a recent factorial survey study aimed at testing the influence that embodiment has on the evaluation of creativity. These findings show that the physical dimension of artificial systems interacting with human artists contributes to the perception of the interplay between artificial and human agents as a creative collaboration. I propose that a closer study of the dynamics of interaction between embodied machines, human artists, and the public can facilitate progress in both the artistic and the technology sector.
Towards Educating Artificial Neural Systems

In the context of text-to-image generators, we discuss how a neural system could be enhanced to follow a knowledge base expressing certain moral considerations, in order to address some looming concerns. We also propose self-educating procedures that enable the system to produce rule-based approximations of its functioning, and illustrate this with an application to the creative interpretation of images.
CHASING THE WHITE RABBIT - A case study of predicting design phases of architects by training a deep neural network with sketch recognition through a digital drawing board

Within this paper we propose an interdisciplinary approach at the interface of computer science and architecture to predict design phases using a deep neural network, based on archi-tects’ hand drawings. The overall goal of the metis projects is to provide architects with appropriate design step suggestions using deep learning (DL) and based on semantic information of Building Information Modeling (BIM), inspired by textual autocompletion of digital keyboards on smartphones. We describe the process of our sketch protocol study and open-source software prototype developed for sketch data acquisition with a WACOM tablet and video recordings, as well as the evaluation of the sketch protocol study and the results of the recurrent neural network (RNN) with Long Short-Term Memory (LSTM) architecture, trained with the sketch data quantiﬁed through the prototype tool. The initial prediction results of the current and the consecutive design phase appear promising to predict with high accuracy. Our future plans include tracking the architects design process through the labyrinth of design decision making using different mental layers (e.g. design phases ) as ﬁlters all the way to the bottom to isolate the individual mental process of a singular design step .
Eliminating Genes for a Two Component System Increases PHB Productivity in Cupriavidus basilensis 4G11 Under PHB Suppressing, Non-Stress Conditions

Species of bacteria from the genus Cupriavidus are known, in part, for their ability to produce high amounts of poly-hydroxybutyrate (PHB) making them attractive candidate bioplastic producers. The native production of PHB occurs during periods of metabolic stress, and the process regulating the initiation of PHB accumulation in these organisms is not fully understood. Screening an RB-TnSeq transposon library of Cupriavidus basilensis 4G11 allowed us to identify two genes of an apparent, uncharacterized two component system which, when omitted from the genome, are capable of increased PHB productivity in balanced, non-stress growth conditions. We observe average increases in PHB productivity of 56% and 41% relative to the wildtype parent strain, upon deleting each of two genes individually from the genome. The increased PHB phenotype disappears, however, in nitrogen-free unbalanced growth conditions suggesting the phenotype is specific to fast-growing, replete, non-stress growth. Bioproduction modeling suggests this phenotype could be due to a decreased reliance on metabolic stress induced by nitrogen limitation to initiate PHB production in the mutant strains. Such strains may allow for the use of single stage, continuous bioreactor systems, which are far simpler than PHB bioproduction schemes used previously. Bioproductivity modeling suggests that omitting this regulation in the cells may increase PHB productivity up to 24% relative to the wildtype organism when using single stage continuous systems. This work furthermore expands our understanding of the regulation of PHB accumulation in Cupriavidus, in particular the initiation of this process upon transition into unbalanced growth regimes.
The DNA relaxation-dependent OFF-to-ON biasing of the type 1 fimbrial genetic switch requires the Fis nucleoid-associated protein

The structural genes expressing type 1 fimbriae in Escherichia coli alternate between expressed (phase ON) and non-expressed (phase OFF) states due to inversion of the 314-bp fimS genetic switch. The FimB tyrosine integrase inverts fimS by site-specific recombination, alternately connecting and disconnecting the fim operon, encoding the fimbrial subunit protein and its associated secretion and adhesin factors, to and from its transcriptional promoter within fimS. Site-specific recombination by the FimB recombinase becomes biased towards phase ON as DNA supercoiling is relaxed, a condition that occurs when bacteria approach the stationary phase of the growth cycle. This effect can be mimicked in exponential phase cultures by inhibiting the negative DNA supercoiling activity of DNA gyrase. We report that this bias towards phase ON depends on the presence of the Fis nucleoid-associated protein. We mapped the Fis binding to a site within the invertible fimS switch by DNase I footprinting. Disruption of this binding site by base substitution mutagenesis abolishes both Fis binding and the ability of the mutated switch to sustain its phase ON bias when DNA is relaxed, even in bacteria that produce the Fis protein. In addition, the Fis binding site overlaps one of the sites used by the Lrp protein, a known directionality determinant of fimS inversion that also contributes to phase ON bias. The Fis-Lrp relationship at fimS is reminiscent of that between Fis and Xis when promoting DNA-relaxation-dependent excision of bacteriophage λ from the E. coli chromosome. However, unlike the co-binding mechanism used by Fis and Xis at λ attR, the Fis-Lrp relationship at fimS involves competitive binding. We discuss these findings in the context of the link between fimS inversion biasing and the physiological state of the bacterium.
A Theoretical Model reveals RNA sequestration in Alpha Synuclein Aggregates

The modulating effect of nucleic acids on protein aggregation has recently come into the spotlight, with RNA shown to either prevent or promote protein assembly depending on the molecular context. Here, we computed the biophysical properties of amyloids and observed a trend indicating that regions outside the aggregates core are highly prone to interact with nucleic acids. In the case of alpha synuclein (aS), an intrinsically disordered protein abundantly expressed in the brain, found in the nucleus and involved in Parkinson’s disease, our predictions indicate that regions outside the aggregate are able to contact RNA, but the acidic C-terminal prevents the formation of stable interactions. We performed aggregation assays with both the wild type α-synuclein (aS140) as well as a C-terminally truncated isoform (aS103) and found that while RNA increases the aggregation rate of aS103, it decreases that of aS140, although at higher RNA concentrations the trend is inverted. To further elucidate the effects driving this behavior, we built a general dynamic model that describes the aggregation process of monomers in the presence of RNA. Our predictions indicate that RNA affects aS103 and aS140 aggregation in a non-linear manner and prioritize the interaction between RNA and aggregate as the most relevant. To confirm this, we extracted RNA from aS103 and aS140 aggregates and observed that they indeed acquire distinct RNA-sequestering abilities. Our research demonstrates that binding to transcripts can drastically alter the aggregation of a protein and represents an important gain-of-function mechanism to be further
The homeobox transcription factor DUXBL controls exit from totipotency

Upon exit from the totipotent 2-cell (2C) embryo stage, the 2C-associated transcriptional program needs to be efficiently silenced. However, the molecular mechanisms involved in this process remain mostly unknown. Here, we demonstrate that the 2C-specific transcription factor DUX directly induces the expression of DUXBL to promote this silencing. Indeed, DUX expression in Duxbl-knockout ESC causes increased induction of the 2C-transcriptional program, whereas DUXBL overexpression impairs 2C-associated transcription. CUT&RUN analyses show that DUXBL gains accessibility to DUX-bound regions in DUX-induced ESC while it is unable to bind those regions in uninduced cells. Mechanistically, we determined that DUXBL interacts with TRIM24 and TRIM33, two members of the tripartite motif superfamily involved in gene silencing and co-localizes with them in nuclear foci upon DUX expression. Furthermore, DUXBL downregulation in mouse zygotes leads to a penetrant 2C-stage arrest. Our data reveals an unexpected role for DUXBL in controlling the exit from totipotency.
Expression of thioredoxin-1 in the ASJ neuron corresponds with and enhances intrinsic regenerative capacity under lesion conditioning in C. elegans

A conditioning lesion of the peripheral sensory axon triggers robust central axon regeneration in mammals. We trigger conditioned regeneration in the C. elegans ASJ neuron by laser surgery or genetic disruption of sensory pathways. Conditioning upregulates trx-1 expression, as indicated by trx-1 promoter-driven green fluorescent protein and fluorescence in situ hybridization, suggesting trx-1 levels and associated fluorescence indicate regenerative capacity. Redox activity of trx-1 functionally enhances conditioned regeneration, but both redox-dependent and –independent activity inhibit non-conditioned regeneration. Six strains isolated in a forward genetic screen for reduced fluorescence, which suggests diminished regenerative potential, also show reduced axon outgrowth. We demonstrate an association between trx-1 expression and the conditioned state that we leverage to rapidly assess regenerative capacity.
A p21‐GFP zebrafish model of senescence for rapid testing of senolytics in vivo

Senescence drives the onset and severity of multiple ageing-associated diseases as well as frailty. As a result, there has been an increased interest in mechanistic studies and in the search for compounds targeting senescent cells, known as senolytics. Mammalian models are commonly used to test senolytics and generate functional and toxicity data at the level of organs and systems, yet this is expensive and time consuming. Zebrafish share high homology in genes associated with human ageing and disease. They can be genetically-modified relatively easily. In larvae, most organs develop within 5 days of fertilisation and are transparent, which allows tracking of fluorescent cells in vivo in real time, testing drug off-target toxicity and assessment of cellular and phenotypic changes. Here, we have generated a transgenic zebrafish line that expresses green fluorescent protein (GFP) under the promoter of a key senescence marker, p21. We show an increase in p21:GFP+ cells in larvae following exposure to ionising radiation and with natural ageing. p21:GFP+ cells display other markers of senescence, including senescence-associated β-galactosidase and IL6. The observed increase in senescent cells following irradiation is associated with a reduction in the thickness of muscle fibres and mobility, two important ageing phenotypes. We also show that quercetin and dasatinib, two senolytics currently in clinical trials, reduce the number of p21:GFP+ cells, in a rapid 5-day assay. This model provides an important tool to study senescence in a living organism, allowing the rapid selection of senolytics before moving to more expensive and time-consuming mammalian systems.
Minimum detection efficiencies for a loophole-free observable-asymmetric Bell-type test

We discuss the problem of finding the most favorable conditions for closing the detection loophole in a test of local realism with a Bell inequality. For a generic nonmaximally entangled two-qubit state and two incompatible bases to be adopted for alternative measurements of two observables a and b on each party, we apply Hardy's proof of nonlocality without inequality and derive an Eberhard-like inequality. For an infinity of nonmaximally entangled states we find that it is possible to refute local realism by requiring perfect detection efficiency for only one of the two observables, say b, to be measured on each party: The test is free from the detection loophole for any value of the detection efficiency corresponding to the other observable a. The maximum tolerable noise in such a loophole-free observable-asymmetric test is also evaluated.
Aortic Shape Space Topology

Cross-sectional imaging, such as computed tomography (CTA) scans, provide unparalleled visualization of aortic anatomy. However, despite the immense geometric and anatomic detail provided by CTA imaging, surgeons continue to interact with this data in a linear and dimensionally reduced feature space. Aortic pathologies such as aneurysms and dissections are clinically quantiﬁed using a single scalar: maximum aortic diameter. To date, not feature of aortic shape has reproducibly captured what surgeons often describe qualitatively when look-ing at CT scans or when in the operating room observing the physical anatomy. Shape along with size plays a central role in differentiating normal from diseased aortas. We deﬁned a geometric feature space using tools of modern differential geometry that incorporate shape and size. We show that size can be parameterized by (cid:96) , the radial aortic extent commonly taken as aortic diameter. Size invariant shape is quantiﬁed by perform-ing a Gauss map of local regions on the aortic surface and calculating the variance of the total integrated curvature ( δK ) across each aorta. While we do not inherently study aortic stability as it relates to clinical rupture in this paper, aortas appearing at high δK are clinically classiﬁed by size and qualitative appearance as high risk. It is therefor interesting to conjecture that divergence in the ( δK, ˜ (cid:96) ) -space is a sign of aortic topologic instability. Projection into ( δK, ˜ (cid:96) ) -space provides two independent variables that show a natural division of the data as it transitions from size to shape dominated behavior, an indictor of aortic fragility.
Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis

Saccharomyces cerevisiae is an important model organism and a workhorse in bioproduction. Here, we reconstructed a compact and tractable genome-scale resource balance analysis (RBA) model (i.e., scRBA) to analyze metabolic fluxes and proteome allocation in a computationally efficient manner. Resource capacity models such as scRBA provide the quantitative means to identify bottlenecks in biosynthetic pathways due to enzyme, compartment size, and/or ribosome availability limitations. ATP maintenance rate and in vivo apparent turnover numbers (kapp) were regressed from metabolic flux and protein concentration data to capture observed physiological growth yield and proteome efficiency and allocation, respectively. Estimated parameter values were found to vary with oxygen and nutrient availability. Overall, this work (i) provides condition-specific model parameters to recapitulate phenotypes corresponding to different extracellular environments, (ii) alludes to the enhancing effect of substrate channeling and post-translational activation on in vivo enzyme efficiency in glycolysis and electron transport chain, and (iii) reveals that the Crabtree effect is underpinned by specific limitations in mitochondrial proteome capacity and secondarily ribosome availability rather than overall proteome capacity.
Evolutionary analysis reveals the role of a non-catalytic domain of peptidyl arginine deiminase 2 in transcriptional regulation

Peptidyl arginine deiminases (PADIs) catalyze protein citrullination, a post-translational conversion of arginine to citrulline. The most widely expressed member of this family, PADI2, regulates cellular processes that impact several diseases. We hypothesized that we could gain new insights into PADI2 function through a systematic evolutionary and structural analysis. Here, we identify 20 positively selected PADI2 residues, 16 of which are structurally exposed and maintain PADI2 interactions with cognate proteins. Many of these selected residues reside in non-catalytic regions of PADI2. We validate the importance of a prominent loop in the middle domain that encompasses PADI2 L162, a residue under positive selection. This site is essential for interaction with the transcription elongation factor (P-TEFb) and mediates active transcription of the oncogenes c-MYC, and CCNB1, as well as impacting cellular proliferation. These insights could be key to understanding and addressing the role of the PADI2 c-MYC axis in cancer progression. Significance Statement Here we use a systematic evolutionary analysis to identify positively selected residues in the non-catalytic domain of PADI2 and link the positive selection of key residues to a role in transcription. Specifically, a structurally exposed loop in the PADI2 middle domain encompasses the positively selected residue L162 which is linked to transcription and cellular proliferation. This loop contributes to PADI2 interaction with the P-TEFb complex and cellular proliferation. Our results showcase the utility of combining evolutionary and experimental approaches to dissect the evolution of essential functional processes.