Miracle-dz/UniFAR-FTUs huggingface dataset:
Clark Kent at SemEval-2023 Task 5: SVMs, Transformers, and Pixels for Clickbait Spoiling

In this paper we present an analysis of our approaches for the 2023 SemEval-2023 Clickbait Challenge. We only participated in the sub-task aiming at identifying different clikcbait spoiling types comparing several machine learning and deep learning approaches.Our analysis confirms previous results on this task and show that automatic methods are able to reach approximately 70\% accuracy at predicting what type of additional content is needed to mitigate sensationalistic posts on social media. Furthermore, we provide a qualitative analysis of the results, showing that the models may do better in practice than the metric indicates since the evaluate does not depend only on the predictor, but also on the typology we choose to define clickbait spoiling.
ALEXSIS+: Improving Substitute Generation and Selection for Lexical Simplification with Information Retrieval

Lexical simplification (LS) automatically replaces words that are deemed difficult to understand for a given target population with simpler alternatives, whilst preserving the meaning of the original sentence. The TSAR-2022 shared task on LS provided participants with a multilingual lexical simplification test set. It contained nearly 1,200 complex words in English, Portuguese, and Spanish and presented multiple candidate substitutions for each complex word. The competition did not make training data available; therefore, teams had to use either off-the-shelf pre-trained large language models (LLMs) or out-domain data to develop their LS systems. As such, participants were unable to fully explore the capabilities of LLMs by re-training and/or fine-tuning them on in-domain data. To address this important limitation, we present ALEXSIS+, a multilingual dataset in the aforementioned three languages, and ALEXSIS++, an English monolingual dataset that together contains more than 50,000 unique sentences retrieved from news corpora and annotated with cosine similarities to the original complex word and sentence. Using these additional contexts, we are able to generate new high-quality candidate substitutions that improve LS performance on the TSAR-2022 test set regardless of the language or model.
An end-to-end neural model based on cliques and scopes for frame extraction in long breast radiology reports

We consider the task of automatically extracting various overlapping frames, i.e, structured entities composed of multiple labels and mentions, from long clinical breast radiology documents. While many methods exist for related topics such as event extraction, slot filling, or discontinuous entity recognition, a challenge in our study resides in the fact that clinical reports typically contain overlapping frames that span multiple sentences or paragraphs.We propose a new method that addresses these difficulties and evaluate it on a new annotated corpus.Despite the small number of documents, we show that the hybridization between knowledge injection and a learning-based system allows us to quickly obtain proper results.We will also introduce the concept of scope relations and show that it both improves the performance of our system, and provides a visual explanation of the predictions.
UIRISC at SemEval-2023 Task 10: Explainable Detection of Online Sexism by Ensembling Fine-tuning Language Models

Under the umbrella of anonymous social networks, many women have suffered from abuse, discrimination, and other sexist expressions online. However, exsiting methods based on keyword filtering and matching performed poorly on online sexism detection, which lacked the capability to identify implicit stereotypes and discrimination. Therefore, this paper proposes a System of Ensembling Fine-tuning Models (SEFM) at SemEval-2023 Task 10: Explainable Detection of Online Sexism. We firstly use four task-adaptive pre-trained language models to flag all texts. Secondly, we alleviate the data imbalance from two perspectives: over-sampling the labelled data and adjusting the loss function. Thirdly, we add indicators and feedback modules to enhance the overall performance. Our system attained macro F1 scores of 0.8538, 0.6619, and 0.4641 for Subtask A, B, and C, respectively. Our system exhibited strong performance across multiple tasks, with particularly noteworthy performance in Subtask B. Comparison experiments and ablation studies demonstrate the effectiveness of our system.
An ancient split of germline and somatic stem cell lineages in Hydra

In many animals, germ cell segregation occurs during early embryogenesis to protect the genome, but its origin in basal metazoans is controversial. Here, we show in the freshwater polyp Hydra by clonal analysis and transgenic animals that interstitial stem cells comprise two separate stem cell populations, i.e., germline and multipotent somatic stem cells. We isolated genetically labelled stem cells for a global transcriptome study and discovered a broad set of germline-specific/enriched genes including Prdm9, Pax5, Dmrt1. In an alternative splicing analysis, we identified many genes with germline-specific isoforms; among them, male-specific isoforms of Dmrt1 and Snf5. The somatic interstitial stem cell lineage was characterized by numerous neuronal control genes like Neurog. But all stem cells in Hydra also share a core of stemness genes that has its roots in unicellular eukaryotes. This suggests an evolutionary scenario in which, at the emergence of animal multicellularity, there was an early split into a stable germline and different somatic stem cell lineages.
A matrisome atlas of germ cell development

The extracellular matrix (matrisome) provides chemical and mechanical cues to control the structure and function of cells and tissues. Yet, comprehensive understanding of how matrisome factors individually and collectively control cell and tissue behavior in vivo is lacking. Here, we systematically investigate the function of 443 conserved matrisome-coding genes in controlling germ cell behavior within a complex tissue - the Caenorhabditis elegans germline. Using high-content imaging, 3D reconstruction and cell behavior analysis of >3500 germlines and >7 million germ cells, we identify specific matrisome factors that regulate germline structure, protein distribution, germ cell cycle and fate, apoptosis, and oocyte health. These findings reveal matrisome networks acting autonomously and non-autonomously to coordinate germ cell behavior, providing new avenues to study and manipulate cell fates.
Effects of copy number variations on longevity in late-onset Alzheimer’s disease patients: insights from a causality network analysis

Alzheimer’s disease (AD), particularly late-onset Alzheimer’s disease (LOAD), is a prevalent form of dementia that significantly affects patients’ cognitive and behavioral capacities and longevity. Although approximately 70 genetic risk factors linked with AD have been identified, their influence on patient longevity remains unclear. Further, recent studies have associated copy number variations (CNVs) with the longevity of healthy individuals and immune-related pathways in AD patients. This study aims to investigate the role of CNVs on the longevity of AD patients by integrating multi-omics data from the Religious Orders Study/Memory and Aging Project (ROSMAP) cohort through causality network inference. Our comprehensive analysis led to the construction of a CNV-gene-age of death (AOD) causality network. We successfully identified three key CNVs (DEL5006, mCNV14192, and DUP42180) and seven AD-longevity causal genes (PLGRKT, TLR1, PLAU, CALB2, SYTL2, OTOF, and NT5DC1) impacting AD patient longevity, independent of disease severity. This outcome emphasizes the potential role of plasminogen activation and chemotaxis in longevity. We propose several hypotheses regarding the role of identified CNVs and the plasminogen system on patient longevity. However, experimental validation is required to further corroborate these findings and uncover precise mechanisms. Despite these limitations, our study offers promising insights into the genetic influence on AD patient longevity and contributes to paving the way for potential therapeutic interventions.
Alterations in grey matter structure linked to frequency-specific cortico-subcortical connectivity in schizophrenia via multimodal data fusion

Schizophrenia (SZ) is a complex psychiatric disorder that is currently defined by symptomatic and behavioral, rather than biological, criteria. Neuroimaging is an appealing avenue for SZ biomarker development, as several neuroimaging-based studies comparing individuals with SZ to healthy controls (HC) have shown measurable group differences in brain structure, as well as functional brain alterations in both static and dynamic functional network connectivity (sFNC and dFNC, respectively). The recently proposed filter-banked connectivity (FBC) method extends the standard dFNC sliding-window approach to estimate FNC within an arbitrary number of distinct frequency bands. The initial implementation used a set of filters spanning the full connectivity spectral range, providing a unified approach to examine both sFNC and dFNC in a single analysis. Initial FBC results found that individuals with SZ spend more time in a less structured, more disconnected low-frequency (i.e., static) FNC state than HC, as well as preferential SZ occupancy in high-frequency connectivity states, suggesting a frequency-specific component underpinning the functional dysconnectivity observed in SZ. Building on these findings, we sought to link such frequency-specific patterns of FNC to covarying data-driven structural brain networks in the context of SZ. Specifically, we employ a multi-set canonical correlation analysis + joint independent components analysis (mCCA + jICA) data fusion framework to study the connection between grey matter volume (GMV) maps and FBC states across the full connectivity frequency spectrum. Our multimodal analysis identified two joint sources that captured co-varying patterns of frequency-specific functional connectivity and alterations in GMV with significant group differences in loading parameters between the SZ group and HC. The first joint source linked frequency-modulated connections between the subcortical and sensorimotor networks and GMV alterations in the frontal and temporal lobes, while the second joint source identified a relationship between low-frequency cerebellar-sensorimotor connectivity and structural changes in both the cerebellum and motor cortex. Together, these results show a strong connection between cortico-subcortical functional connectivity at both high and low frequencies and alterations in cortical GMV that may be relevant to the pathogenesis and pathophysiology of SZ.
On the Spatial Positioning of Ribosomes around chromosome in E. coli Cytoplasm

The spatial organization of ribosomes in the cytoplasm of Escherichia coli (E. coli) bacteria has been a subject of longstanding intrigue. Previous investigations suggested that ribosomes remain completely excluded from the chromosome-rich nucleoid region in a “poor solvent” like cytoplasm. Here, we present an integrated model of the bacterial cytoplasm, informed by experimental data, which updates this prevailing narrative. We demonstrate that ribosomes maintain a delicate balance of both attractive and repulsive interactions with the chromosome, contrary to the conventional notion of it acting as an inert crowder in cytoplasm. The multi-dimensional spatial distribution of free ribosomes (30S and 50S) and bound ribosomes (70S polysome) inside the cytoplasm reveals that the extent of mutual ribosome-chromosome segregation is relatively less pronounced due to the presence of non-negligible amount of ribosomes within the inner core of the cytoplasm. In particular, we identify a central void within the inner-most core of the nucleoid that lacks chromosomal DNA but can accommodate finite proportion of both free (11 %) and bound (18 %) ribosomes. Furthermore, our analysis of the chromosome mesh size and the conformation of bound ribosomes suggests that bound ribosomes remain elongated and would be able to navigate past the chromosome mesh to access the central void. Together by highlighting the dynamic nature of ribosome localization in E. coli, this investigation proposes that this segregation is crucial for maximizing the utilization of synthesized mRNA and facilitating efficient translation into proteins, which are essential for bacterial survival.
Local well-posedness of the full compressible Navier-Stokes-Maxwell system with vacuum

In this paper, we prove the local well-posedness of strong solutions for a compressible Navier-Stokes-Maxwell system, provided the initial data satisfy a natural compatibility condition. We do not assume the positivity of initial density, it may vanish in an open subset (vacuum) of $Ω$.
Least Absolute Deviations Method For Sparse Signal Recovery

We consider a problem in signal processing which deals with the recovery of a highdimensional sparse signal based on a small number of measurements. Our goal is to apply the least absolute deviations (LAD) method in an algorithm that would essentially follow the steps of the orthogonal matching pursuit (OMP) algorithm that has been used mostly in this setting. OMP can recover the signal with high probability in noiseless cases and specic noise distributions such as bounded and Gaussian. In the presence of heavy-tailed distributed noise, OMP algorithm needs a signal to be much larger than the noise in order to recover it (puts too much constraint on a signal). We consider the algorithm using LAD in all the cases above and compare the simulation results using both methods. OMP works better, i.e., recovers a higher percentage of signals in noiseless, bounded and Gaussian noise cases. On the other hand, our new LAD based method recovers a higher percentage of signals in the case when the t(2)-heavy tailed noise is present. This provides an alternative to the standard least-squares based methods especially in the presence of heavy tailed noises. We also provide a sucient condition on the design matrix in order for the LAD
The discovery and characterization of the most distant quasars

Luminous quasars at high redshift (z>5.5) provide direct probes of the growth of supermassive black holes and their host galaxies at the epoch of cosmic reionization, which is one of the current frontiers of astrophysical research. In this thesis, z>5.5 quasars are studied from different angles. (1) The criteria to identify high-redshift quasars using the Panoramic Survey Telescope & Rapid Response System 1 (Pan-STARRS1, PS1) survey are presented. These selection criteria have resulted in 54 newly discovered quasars at z>5.5. These new discoveries almost double the number of known z>5.5 quasars and increase the number of quasars at z>6.5 from four to eight. The quasar sample spans a factor of ~20 in luminosity and shows a diverse range of properties, including a number of weak-line and radio-loud quasars. (2) Using the available data in the literature, the radio-loud fraction (RLF) of quasars at z~6 is constrained to RLF=8.1^{+5.0}_{-3.2}%. This result is consistent with a non-evolving RLF of quasars up to z=6. (3) High-redshift quasars are thought to reside in massive dark matter halos and should therefore be located in regions with an overdensity of galaxies. To find such overdensities, the first search for galaxies using narrow-band imaging in the field of a z=5.7 quasar is performed. No overdensity of galaxies is found around the quasar, with the possible implication that high-redshift quasars may not reside in the center of the most massive dark matter halos. (4) A strong [CII] emission line (an effective cooling line of the interstellar medium) in the host galaxy of a PS1-discovered quasar at z=6.54 is reported. This is the brightest quasar known at z>6.5 and given its high rest-frame UV and [CII] luminosities, it has the potential of becoming an important laboratory for the study of star formation and of the interstellar medium only ~800 Myr after the Big Bang. As a final note, the number of quasars at z>5.5 presented in this thesis marks the transition phase from studies of individual sources to statistical studies of the high-redshift quasar population, which was impossible with earlier, smaller samples.
Estimations d'erreur a posteriori et critères d'arrêt pour des solveurs par décomposition de domaine et avec des pas de temps locaux

Cette these developpe des estimations d’erreur a posteriori et criteres d’arret pour les methodes de decomposition de domaine avec des conditions de transmission de Robin optimisees entre les interfaces. Differents problemes sont consideres: l’equation de Darcy stationnaire puis l’equation de la chaleur, discretisees par les elements finis mixtes avec un schema de Galerkin discontinu de plus bas degre en temps pour le second cas. Pour l’equation de la chaleur, une methode de decomposition de domaine globale en temps, avec memes ou differents pas de temps entre les differents sous domaines, est utilisee. Ce travail est finalement etendu a un modele diphasique en utilisant une methode de volumes finis centres par maille en espace. Pour chaque modele, un probleme d’interface est resolu iterativement, ou chaque iteration necessite la resolution d’un probleme local dans chaque sous-domaine, et les informations sont ensuite transmises aux sous-domaines voisins. Pour les modeles instationnaires, les problemes locaux dans les sous-domaines sont instationnaires et les donnees sont transmises par l’interface espace-temps. L’objectif de ce travail est, pour chaque modele, de borner l’erreur entre la solution exacte et la solution approchee a chaque iteration de l’algorithme de decomposition de domaine. Differentes composantes d’erreur en jeu de la methode sont identifiees, dont celle de l’algorithme de decomposition de domaine, de facon a definir un critere d’arret efficace pour cette methode. En particulier, pour l’equation de Darcy stationnaire, on bornera l’erreur par un estimateur de decomposition de domaine ainsi qu’un estimateur de discretisation en espace. On ajoutera a la borne de l’erreur un estimateur de discretisation en temps pour l’equation de la chaleur et pour le modele diphasique. L’estimation a posteriori repose sur des techniques de reconstructions de pressions et de flux conformes respectivement dans les espaces H1 et H(div) et sur la resolution de problemes locaux de Neumann dans des bandes autour des interfaces de chaque sous-domaine pour les flux. Ainsi, des criteres pour arreter les iterations de l’algorithme iteratif de decomposition de domaine sont developpes. Des simulations numeriques pour des problemes academiques ainsi qu’un probleme plus realiste base sur des donnees industrielles sont presentees pour illustrer l’efficacite de ces techniques. En particulier, differents pas de temps entre les sous-domaines sont consideres pour cet exemple.
Fixed points of set-valued F-contractions and its application to non-linear integral equations

We observe that the assumption of set-valued F-contractions (Sgroi and Vetro [13]) is actually very strong for the existence of fixed point and can be weakened. In this connection, we introduce the notion of set-valued α-F-contractions and prove a corresponding fixed point theorem in complete metric spaces. Consequently, we derive several fixed point theorems in metric spaces. Some examples are given to illustrate the new theory. Then we apply our results to establishing the existence and uniqueness of solutions for a certain type of non-linear integral equations. To the memory of Professor Lj. Ćirić (1935–2016)
Interstellar flow longitude from pickup ion cut-off observations at 1 AU with STEREO and ACE

A precision determination of the interstellar neutral (ISN) flow direction is important in several ways. As a cardinal axis of the heliosphere it has strong leverage on the plane subtended by the ISN velocity and interstellar magnetic field vector, which controls the shape of the heliosphere and its interaction with the interstellar medium. Continuing observations of the ISN flow through the heliosphere for several decades allow the search for potential temporal variations of the ISN flow and comparison with astronomical observations. Recent efforts to obtain a consistent ISN vector and temperature with Ulysses and IBEX neutral gas observations point to remaining uncertainties and potential systematic effects. In particular, IBEX measurements provide a very precise relation between ISN flow longitude and speed via the hyperbolic trajectory equation, but they contain larger uncertainties along the parameter tube defined by this relation. The pickup ion (PUI) cut-off variation with ecliptic longitude at 1 AU can provide a complementary determination of the ISN flow longitude with high precision. We compare STEREO PLASTIC and ACE SWICS observations with a simple analytical model of the cut-off. We perform a Pearson correlation analysis of the cut-off as a function of ecliptic longitude with its mirrored function and obtain the symmetry axis with a statistical uncertainty <0.1°. Here we test variations of this value due to Poisson fluctuations in the original data with simulations and due to systematic effects with multi year and location ACE SWICS and STEREO PLASTIC samples.
On the nonexistence of time dependent global weak solutions to the compressible fluid equations

In this paper we derive an integral inequality for a possible global weak solution to the time dependent compressible Euler equations under certain conditions of integrability for the density and the velocity fields. One immediate consequence of this inequality is the nonexistence of global time dependent weak solution to the compressible Euler equations on R , N ≥ 1, which satisfies suitable integrability and certain condition for the initial data. For some class of viscous isothermal fluids the condition for density is satisfied if we assume the energy inequality for the possible global weak solution, and hence the nonexistence of solution is proved under milder conditions. Similar results hold also for the compressible magnetohydrodynamics equations.