Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal Inductive Path Neural Network for Temporal Knowledge Graph Reasoning

Temporal Knowledge Graph (TKG) is an extension of traditional Knowledge Graph (KG) that incorporates the dimension of time. Reasoning on TKGs is a crucial task that aims to predict future facts based on historical occurrences. The key challenge lies in uncovering structural dependencies within historical subgraphs and temporal patterns. Most existing approaches model TKGs relying on entity modeling, as nodes in the graph play a crucial role in knowledge representation. However, the real-world scenario often involves an extensive number of entities, with new entities emerging over time. This makes it challenging for entity-dependent methods to cope with extensive volumes of entities, and effectively handling newly emerging entities also becomes a significant challenge. Therefore, we propose Temporal Inductive Path Neural Network (TiPNN), which models historical information in an entity-independent perspective. Specifically, TiPNN adopts a unified graph, namely history temporal graph, to comprehensively capture and encapsulate information from history. Subsequently, we utilize the defined query-aware temporal paths on a history temporal graph to model historical path information related to queries for reasoning. Extensive experiments illustrate that the proposed model not only attains significant performance enhancements but also handles inductive settings, while additionally facilitating the provision of reasoning evidence through history temporal graphs.
Phase Transition and Subshifts of Finite Type

The aim of this article is to establish freezing phase transition of the pressure function, considering the generalized Hofbauer potential {\phi}, which is connected to the distance from subshift of finite type {\Sigma}F in the full shift {\Sigma} over finite alphabets. Our objective is to prove that the pressure function exhibits phase transition with the dominating measure is highly concentrated on {\Sigma}F after the transition. Moreover, the pressure function attains C1-smoothness when the transition occurs at 2.
Dataset Generation and Bonobo Classification from Weakly Labelled Videos

This paper presents a bonobo detection and classification pipeline built from the commonly used machine learning methods. Such application is motivated by the need to test bonobos in their enclosure using touch screen devices without human assistance. This work introduces a newly acquired dataset based on bonobo recordings generated semi-automatically. The recordings are weakly labelled and fed to a macaque detector in order to spatially detect the individual present in the video. Handcrafted features coupled with different classification algorithms and deep-learning methods using a ResNet architecture are investigated for bonobo identification. Performance is compared in terms of classification accuracy on the splits of the database using different data separation methods. We demonstrate the importance of data preparation and how a wrong data separation can lead to false good results. Finally, after a meaningful separation of the data, the best classification performance is obtained using a fine-tuned ResNet model and reaches 75% of accuracy.
Large-Scale Asymmetry in the Distribution of Galaxy Spin Directions - Analysis and Reproduction

Recent independent observations using several different telescope systems and analysis methods have provided evidence of parity violation between the numbers of galaxies that spin in opposite directions. On the other hand, other studies argue that no parity violation can be identified. This paper provides detailed analysis, statistical inference, and reproduction of previous reports that show no preferred spin direction. Code and data used for the reproduction are publicly available. The results show that the data used in all of these studies agree with the observation of a preferred direction as observed from Earth. In some of these studies, the datasets were too small, or the statistical analysis was incomplete. In other papers, the results were impacted by experimental design decisions that led directly to showing nonpreferred direction. In some of these cases, these decisions were not stated in the papers but were revealed after further investigation in cases where the reproduction of the work did not match the results reported in the papers. These results show that the data used in all of these previous studies, in fact, agree with the contention that galaxies as observed from Earth have a preferred spin direction, and the distribution of galaxy spin directions as observed from Earth forms a cosmological-scale dipole axis. This study also shows that the reason for the observations is not necessarily an anomaly in the large-scale structure, and can also be related to internal structure of galaxies.
Entropy solutions to macroscopic IPM

We investigate maximal potential energy dissipation as a selection criterion for subsolutions (coarse grained solutions) in the setting of the unstable Muskat problem. We show that both, imposing this criterion on the level of convex integration subsolutions, and the strategy of Otto based on a relaxation via minimizing movements, lead to the same nonlocal conservation law. Our main result shows that this equation admits an entropy solution for unstable initial data with an analytic interface.
Revisiting the $I$-Love-$Q$ relations for superfluid neutron stars

We study the tidal problem and the resulting $I$-Love-$Q$ approximate universal relations for rotating superfluid neutron stars in the Hartle-Thorne formalism. Superfluid stars are described in this work by means of a two-fluid model consisting of superfluid neutrons and all other charged constituents. We employ a stationary and axisymmetric perturbation scheme to second order around a static and spherically symmetric background. Recently, we used this scheme to study isolated rotating superfluid stars. In this paper it is applied to analyze the axially symmetric sector of the tidal problem in a binary system. We show that a consistent use of perturbative matching theory amends the original two-fluid formalism for the tidal problem to account for the possible non-zero value of the energy density at the boundary of the star. This is exemplified by building numerically different stellar models spanning three equations of state. Significant departures from universality are found when the correct matching relations are not taken into account. We also present an augmented set of universal relations for superfluid neutron stars which includes the contribution to the total mass of the star at second order, $\delta M$. Therefore, our results complete the set of universal relations for rotating superfluid stars, generalizing our previous findings in the perfect fluid case.
The Wage Curve, Once More with Feeling: Bayesian Model Averaging of Heckit Models

The sensitivity of the wage curve to sample-selection and model uncertainty was evaluated with Bayesian methods. More than 8000 Heckit wage curves were estimated using data from the 2017 household survey of Bolivia. After averaging the estimates with the posterior probability of each model being true, the wage curve elasticity in Bolivia is close to -0.01. This result suggests that in this country the wage curve is inelastic and does not follow the international statistical regularity of wage curves.
Uncovering Trauma in Genocide Tribunals: An NLP Approach Using the Genocide Transcript Corpus

This paper applies Natural Language Processing (NLP) methods to analyze the exposure to trauma experienced by witnesses in international criminal tribunals when testifying in court. One major contribution of this study is the creation of a substantially extended version of the Genocide Transcript Corpus (GTC) that includes 52,845 text segments of transcripts from three different genocide tribunals. Based on this data, we first examine the prevalence of trauma-related content in witness statements. Second, we are implementing a binary classification algorithm to automatically detect potentially traumatic content. Therefore, in a preparatory step, an Active Learning (AL) approach is applied to establish the ideal size for the training data set. Subsequently, this data is used to train a transformer model. In this case, the two models BERTbase and HateBERT are used for both steps, allowing for a comparison of a base-level model with a model that has already been pre-trained on data more relevant in the context of harmful vocabulary. In a third step, the study employs an Explainable Artificial Intelligence (XAI) model to gain a deeper understanding of the reasoning behind the model's classifications. Our results suggest that both BERTbase and HateBERT perform comparatively well on this classification task, with no model clearly outperforming the other. The classification outcomes further suggest that a reduced data set size can achieve equally high performance metrics and might be a preferable choice in certain use cases. The results can be used to establish more trauma-informed legal procedures in genocide-related tribunals, including the identification of potentially re-traumatizing examination approaches at an early stage. Warning: Due to the overall purpose of the study, this paper contains descriptions of violent events in Section 4.1 (Examples 1 and 2) and in Figure 3 that may be distressing for some readers.
Distinct stem-like cell populations facilitate functional regeneration of the Cladonema medusa tentacle

Blastema formation is a crucial process that provides a cellular source for regenerating tissues and organs. While bilaterians have diversified blastema formation methods, its mechanisms in non-bilaterians remain poorly understood. Cnidarian jellyfish, or medusae, represent early-branching metazoans that exhibit complex morphology and possess defined appendage structures highlighted by tentacles with stinging cells (nematocytes). Here we investigate the mechanisms of tentacle regeneration, using the hydrozoan jellyfish Cladonema pacificum. We show that proliferative cells accumulate at the tentacle amputation site and form a blastema composed of cells with stem cell morphology. Lineage tracing experiments indicate that repair-specific proliferative cells in the blastema are distinct from resident stem cells. We further demonstrate that resident stem cells control nematogenesis and tentacle elongation during both homeostasis and regeneration as homeostatic stem cells, while repair-specific proliferative cells preferentially differentiate into epithelial cells in the newly formed tentacle, analogous to lineage-restricted stem/progenitor cells observed in salamander limbs. Taken together, our findings reveal a regeneration mechanism that utilizes both resident homeostatic stem cells and repair-specific proliferative cells, which in conjunction efficiently enable functional appendage regeneration, and provide novel insight into the diversification of blastema formation across animal evolution.
HLA-B27, axial spondyloarthritis and survival

Introduction Ankylosing spondylitis (AS), and carriage of HLA-B27 gene in otherwise healthy individuals, are reportedly associated with increased mortality. We evaluated this hypothesis, using data from both a 35-year AS follow-up study and UK Biobank data. Methods In 1985, 363 members of the Swiss AS Patient Society and 806 relatives were screened clinically and then radiographically for AS/axial spondyloarthritis (axSpA). Life expectancy was analysed in 377 axSpA patients having available pelvic radiographs and HLA-B27 status, comparing with matched Swiss population data. Survival in relation to HLA-B27 status in the general population was studied in UK Biobank European-ancestry participants (n=407 480, n=30 419 deaths). Results AS patients have increased standardised mortality rate (SMR) compared with the general population (1.37, 95% CI 1.11 to 1.62). This increase was significant for HLA-B27-positive AS (SMR 1.38, 95% CI 1.11 to 1.65). Shortened life expectancy was observed among both HLA-B27-positive AS women (SMR 1.77, 95% CI 1.09 to 2.70) and men (SMR 1.31, 95% CI 1.02 to 1.59). Patients with non-radiographic axSpA (nr-axSpA) had significantly lower SMR: 0.44 (95% CI 0.23 to 0.77), compared with the general population. In the UK Biobank European-ancestry population cohort, HLA-B27 carriage was not significantly associated with any change in mortality (HR 1, 95% CI 0.97 to 1.1, p=0.349, adjusted by sex), in either males (HR 1, 95% CI 0.98 to 1.1, p=0.281) or females (HR 0.96, 95% CI 0.9 to 1, p=0.232), and no increase in vascular disease mortality was observed. Discussion AS patients, but not nr-axSpA patients, have a significantly shortened life expectancy. Increased mortality is particularly significant among women with HLA-B27-positive AS. HLA-B27 carriage in the European-ancestry general population does not influence survival, or the risk of death due to vascular disease.
Texture Synthesis and Unsupervised Recognition with Nonparametric Multiscale Markov Random Field Models

In this paper we present noncausal, nonparametric, multiscale, Markov Random Field (MRF) models for synthesising and recognising texture. The models have the ability to capture the characteristics of a wide variety of textures, varying from the structured to the stochastic. For texture synthesis, we use our own novel multiscale approach, incorporating local annealing, allowing us to use large neighbourhood systems to model some complex textures. The new multiscale texture synthesis algorithm also produces synthetic textures with few phase discontinuities. The power of our modelling technique is evident in that only a small training image is required to synthesis representative examples of the training texture. We also show how the high dimensional model of the texture may be modelled with lower dimensional statistics without over compromising the integrity of the representation. We then show how these models can be used for the unsupervised texture segmentation and recognition of images containing previously unseen textures; a technique useful in the practical application of recognising different terrain types from Synthetic Aperture Radar (SAR) images.
Looking for a New Approach to Measuring the Spatial Concentration of the Human Population

Abstract In the article a new approach for measuring the spatial concentration of human population is presented and tested. The new procedure is based on the concept of concentration introduced by Gini and, at the same time, on its spatial extension (i.e., taking into account the concept of spatial autocorrelation, polarization). The proposed indicator, the Spatial Gini Index, is then computed by using two different kind of territorial partitioning methods: MaxMin (MM) and the Constant Step (CS) distance. In this framework an ad hoc extension of the Rey and Smith decomposition method is then introduced. We apply this new approach to the Italian and foreign population resident in almost 7,900 statistical units (Italian municipalities) in 2002, 2010 and 2018. All elaborations are based on a new ad hoc library developed and implemented in Python.
Single-B cell analysis correlates high-lactate secretion with stress and increased apoptosis

While cellular metabolism was proposed to be a driving factor of the activation and differentiation of B cells and the function of the resulting antibody-secreting cells (ASCs), the study of correlations between cellular metabolism and functionalities has been difficult due to the absence of technologies enabling the parallel measurement. Herein, we performed single-cell transcriptomics and introduced a direct concurrent functional and metabolic flux quantitation of individual murine B cells. Our transcriptomic data identified lactate metabolism as dynamic in ASCs, but antibody secretion did not correlate with lactate secretion rates (LSRs). Instead, our study of all splenic B cells during an immune response linked increased lactate metabolism with acidic intracellular pH and the upregulation of apoptosis. T cell-dependent responses increased LSRs, and added TLR4 agonists affected the magnitude and boosted LSRhigh B cells in vivo, while resulting in only a few immunoglobulin-G secreting cells (IgG-SCs). Therefore, our observations indicated that LSRhigh cells were not differentiating into IgG-SCs, and were rather removed due to apoptosis.
Sensitivity of BA.2.86 to prevailing neutralising antibody responses

A new SARS-CoV-2 variant, designated BA.2. 86, has recently emerged with over 30 spike mutations relative to its parental BA.2, raising questions about its degree of resistance to neutralising antibodies. Using a spike-pseudotyped virus model we characterise neutralisation of BA.2. 86 by clinically relevant monoclonal antibodies and by two cohorts of serum sampled from Stockholm, including both a recent cohort, and one sampled prior to the arrival of XBB in Sweden.
Trapping non-cognate nucleotide upon initial binding for replication fidelity control in SARS-CoV-2 RNA dependent RNA polymerase

The RNA dependent RNA polymerase (RdRp) in SARS-CoV-2 is a highly conserved enzyme responsible for viral genome replication/transcription. Here we investigate computationally natural non-cognate vs cognate nucleotide addition cycle (NAC) and intrinsic nucleotide selectivity during the viral RdRp elongation, focusing prechemically from initial nucleotide substrate binding (enzyme active site open) to insertion (active site closed) of RdRp in contrast with one-step only substrate binding process. Current studies have been first carried out using microsecond ensemble equilibrium all-atom molecular dynamics (MD) simulations. Due to slow conformational changes (from the open to closed) accompanying nucleotide insertion and selection, enhanced or umbrella sampling methods have been further employed to calculate free energy profiles of the non-cognate NTP insertion. Our studies show notable stability of noncognate dATP and GTP upon initial binding in the active-site open state. The results indicate that while natural cognate ATP and Remdesivir drug analogue (RDV-TP) are biased to be stabilized in the closed or insertion state, the natural non-cognate dATP and GTP can be well trapped in off-path initial binding configurations. Current work thus presents an intrinsic nucleotide selectivity mechanism of SARS-CoV-2 RdRp for natural substrate fidelity control in viral genome replication.
Long-term severe hypoxia adaptation induces non-canonical EMT and a novel Wilms Tumor 1 (WT1) isoform

The majority of cancer deaths are caused by solid tumors, where the four most prevalent cancers (breast, lung, colorectal and prostate) account for more than 60% of all cases (1). Tumor cell heterogeneity driven by variable cancer microenvironments, such as hypoxia, is a key determinant of therapeutic outcome. We developed a novel culture protocol, termed the Long-Term Hypoxia (LTHY) time course, to recapitulate the gradual development of severe hypoxia seen in vivo, to mimic conditions observed in primary tumors. Cells subjected to LTHY underwent a non-canonical epithelial to mesenchymal transition (EMT) based on miRNA and mRNA signatures as well as displayed EMT-like morphological changes. Concomitant to this, we report production of a novel truncated isoform of WT1 transcription factor (tWt1), a non-canonical EMT driver, with expression driven by a yet undescribed intronic promoter through hypoxia-responsive elements (HREs). We further demonstrated that tWt1 initiates translation from an intron-derived start codon, retains proper subcellular localization, DNA binding, and its human ortholog negatively predicts long-term patient survival. Our study demonstrates the importance of culture conditions that better mimic those observed in cancers, especially with regards to hypoxia, and identifies a novel isoform of WT1 which correlates with poor long-term survival in ovarian cancer.
Uncovering the mosaic evolution of the carnivoran skeletal system

The diversity of vertebrate skeletons is often attributed to adaptations to distinct ecological factors such as diet, locomotion, and sensory environment. Although the adaptive evolution of skull, appendicular skeleton, and vertebral column is well studied in vertebrates, comprehensive investigations of all skeletal components simultaneously are rarely performed. Consequently, we know little of how modes of evolution differ among skeletal components. Here, we tested if ecological and phylogenetic effects led to distinct modes of evolution among the cranial, appendicular, and vertebral regions in extant carnivoran skeletons. Using multivariate evolutionary models, we found mosaic evolution in which only the mandible, hindlimb, and posterior (i.e., last thoracic and lumbar) vertebrae showed evidence of adaptation towards ecological regimes whereas the remaining skeletal components reflect clade-specific evolutionary shifts. We hypothesize that the decoupled evolution of individual skeletal components may have led to the origination of distinct adaptive zones and morphologies among extant carnivoran families that reflect phylogenetic hierarchies. Overall, our work highlights the importance of examining multiple skeletal components simultaneously in ecomorphological analyses. Ongoing work integrating the fossil and paleoenvironmental record will further clarify deep-time drivers that govern carnivoran diversity we see today and reveal the complexity of evolutionary processes in multicomponent systems.
Reward expectation selectively boosts the firing of accumbens D1+ neurons during motivated approach

The nucleus accumbens (NAc) helps govern motivation to pursue rewards. Two distinct sets of NAc projection neurons-expressing dopamine D1 versus D2 receptors-are thought to promote and suppress motivated behaviors respectively. However, support for this conceptual framework is limited: in particular the spiking patterns of these distinct cell types during motivated behavior have been largely unknown. We monitored identified D1+ and D2+ neurons in the NAc Core, as unrestrained rats performed an operant task in which motivation to initiate work tracks recent reward rate. D1+ neurons preferentially increased firing as rats initiated trials, and fired more when reward expectation was higher. By contrast, D2+ cells preferentially increased firing later in the trial especially in response to reward delivery - a finding not anticipated from current theoretical models. Our results provide new evidence for the specific contribution of NAc D1+ cells to self-initiated approach behavior, and will spur updated models of how we learn from rewards.