BAM: Benchmarking Argument Mining on Scientific Documents

In this paper, we present BAM, a unified Benchmark for Argument Mining (AM). We propose a method to homogenize both the evaluation process and the data to provide a common view in order to ultimately produce comparable results. Built as a four stage and end-to-end pipeline, the benchmark allows for the direct inclusion of additional argument miners to be evaluated. First, our system pre-processes a ground truth set used both for training and testing. Then, the benchmark calculates a total of four measures to assess different aspects of the mining process. To showcase an initial implementation of our approach, we apply our procedure and evaluate a set of systems on a corpus of scientific publications. With the obtained comparable results we can homogeneously assess the current state of AM in this domain

NLQxform: A Language Model-based Question to SPARQL Transformer

In recent years, scholarly data has grown dramatically in terms of both scale and complexity. It becomes increasingly challenging to retrieve information from scholarly knowledge graphs that include large-scale heterogeneous relationships, such as authorship, affiliation, and citation, between various types of entities, e.g., scholars, papers, and organizations. As part of the Scholarly QALD Challenge, this paper presents a question-answering (QA) system called NLQxform, which provides an easy-to-use natural language interface to facilitate accessing scholarly knowledge graphs. NLQxform allows users to express their complex query intentions in natural language questions. A transformer-based language model, i.e., BART, is employed to translate questions into standard SPARQL queries, which can be evaluated to retrieve the required information. According to the public leaderboard of the Scholarly QALD Challenge at ISWC 2023 (Task 1: DBLP-QUAD - Knowledge Graph Question Answering over DBLP), NLQxform achieved an F1 score of 0.85 and ranked first on the QA task, demonstrating the competitiveness of the system

Universal Polynomials for Severi Degrees of Toric Surfaces

The Severi variety parameterizes plane curves of degree d with delta nodes. Its degree is called the Severi degree. For large enough d, the Severi degrees coincide with the Gromov-Witten invariants of P^2. Fomin and Mikhalkin (2009) proved the 1995 conjecture that, for fixed delta, Severi degrees are eventually polynomial in d. In this paper, we study the Severi varieties corresponding to a large family of toric surfaces. We prove the analogous result that the Severi degrees are eventually polynomial as a function of the multidegree. More surprisingly, we show that the Severi degrees are also eventually polynomial "as a function of the surface". We illustrate our theorems by explicit computing, for a small number of nodes, the Severi degree of any large enough Hirzebruch surface and of a singular surface. Our strategy is to use tropical geometry to express Severi degrees in terms of Brugalle and Mikhalkin's floor diagrams, and study those combinatorial objects in detail. An important ingredient in the proof is the polynomiality of the discrete volume of a variable facet-unimodular polytope.Comment: 30 pages, 10 figures; minor modifications, included an explicit computation for some singular toric surfaces in Section 6.

The classification of irreducible admissible mod p representations of a p-adic GL_n

Let F be a finite extension of Q_p. Using the mod p Satake transform, we define what it means for an irreducible admissible smooth representation of an F-split p-adic reductive group over \bar F_p to be supersingular. We then give the classification of irreducible admissible smooth GL_n(F)-representations over \bar F_p in terms of supersingular representations. As a consequence we deduce that supersingular is the same as supercuspidal. These results generalise the work of Barthel-Livne for n = 2. For general split reductive groups we obtain similar results under stronger hypotheses.Comment: 55 pages, to appear in Inventiones Mathematica

S-COL: A Copernican turn for the development of flexibly reusable collaboration scripts

Collaboration scripts are usually implemented as parts of a particular collaborative-learning platform. Therefore, scripts of demonstrated effectiveness are hardly used with learning platforms at other sites, and replication studies are rare. The approach of a platform-independent description language for scripts that allows for easy implementation of the same script on different platforms has not succeeded yet in making the transfer of scripts feasible. We present an alternative solution that treats the problem as a special case of providing support on top of diverse Web pages: In this case, the challenge is to trigger support based on the recognition of a Web page as belonging to a specific type of functionally equivalent pages such as the search query form or the results page of a search engine. The solution suggested has been implemented by means of a tool called S-COL (Scripting for Collaborative Online Learning) and allows for the sustainable development of scripts and scaffolds that can be used with a broad variety of content and platforms. The tool’s functions are described. In order to demonstrate the feasibility and ease of script reuse with S-COL, we describe the flexible re-implementation of a collaboration script for argumentation in S-COL and its adaptation to different learning platforms. To demonstrate that a collaboration script implemented in S-COL can actually foster learning, an empirical study about the effects of a specific script for collaborative online search on learning activities is presented. The further potentials and the limitations of the S-COL approach are discussed

Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-depleted Murine Embryonic Stem Cells

Embryonic stem cells (ESC) have the potential to self-renew indefinitely and to differentiate into any of the three germ layers. The molecular mechanisms for self-renewal, maintenance of pluripotency and lineage specification are poorly understood, but recent results point to a key role for epigenetic mechanisms. In this study, we focus on quantifying the impact of histone 3 acetylation (H3K9,14ac) on gene expression in murine embryonic stem cells. We analyze genome-wide histone acetylation patterns and gene expression profiles measured over the first five days of cell differentiation triggered by silencing Nanog, a key transcription factor in ESC regulation. We explore the temporal and spatial dynamics of histone acetylation data and its correlation with gene expression using supervised and unsupervised statistical models. On a genome-wide scale, changes in acetylation are significantly correlated to changes in mRNA expression and, surprisingly, this coherence increases over time. We quantify the predictive power of histone acetylation for gene expression changes in a balanced cross-validation procedure. In an in-depth study we focus on genes central to the regulatory network of Mouse ESC, including those identified in a recent genome-wide RNAi screen and in the PluriNet, a computationally derived stem cell signature. We find that compared to the rest of the genome, ESC-specific genes show significantly more acetylation signal and a much stronger decrease in acetylation over time, which is often not reflected in an concordant expression change. These results shed light on the complexity of the relationship between histone acetylation and gene expression and are a step forward to dissect the multilayer regulatory mechanisms that determine stem cell fate.Comment: accepted at PLoS Computational Biolog

Many-particle interference beyond many-boson and many-fermion statistics

Identical particles exhibit correlations even in the absence of inter-particle interaction, due to the exchange (anti)symmetry of the many-particle wavefunction. Two fermions obey the Pauli principle and anti-bunch, whereas two bosons favor bunched, doubly occupied states. Here, we show that the collective interference of three or more particles leads to a much more diverse behavior than expected from the boson-fermion dichotomy known from quantum statistical mechanics. The emerging complexity of many-particle interference is tamed by a simple law for the strict suppression of events in the Bell multiport beam splitter. The law shows that counting events are governed by widely species-independent interference, such that bosons and fermions can even exhibit identical interference signatures, while their statistical character remains subordinate. Recent progress in the preparation of tailored many-particle states of bosonic and fermionic atoms promises experimental verification and applications in novel many-particle interferometers.Comment: 12 pages, 5 figure

Comparative genomic analysis of the arthropod muscle myosin heavy chain genes allows ancestral gene reconstruction and reveals a new type of 'partially' processed pseudogene

<p>Abstract</p> <p>Background</p> <p>Alternative splicing of mutually exclusive exons is an important mechanism for increasing protein diversity in eukaryotes. The insect <it>Mhc </it>(myosin heavy chain) gene produces all different muscle myosins as a result of alternative splicing in contrast to most other organisms of the Metazoa lineage, that have a family of muscle genes with each gene coding for a protein specialized for a functional niche.</p> <p>Results</p> <p>The muscle myosin heavy chain genes of 22 species of the Arthropoda ranging from the waterflea to wasp and <it>Drosophila </it>have been annotated. The analysis of the gene structures allowed the reconstruction of an ancient muscle myosin heavy chain gene and showed that during evolution of the arthropods introns have mainly been lost in these genes although intron gain might have happened in a few cases. Surprisingly, the genome of <it>Aedes aegypti </it>contains another and that of <it>Culex pipiens quinquefasciatus </it>two further muscle myosin heavy chain genes, called <it>Mhc3 </it>and <it>Mhc4</it>, that contain only one variant of the corresponding alternative exons of the <it>Mhc1 </it>gene. <it>Mhc3 </it>transcription in <it>Aedes aegypti </it>is documented by EST data. <it>Mhc3 </it>and <it>Mhc4 </it>inserted in the <it>Aedes </it>and <it>Culex </it>genomes either by gene duplication followed by the loss of all but one variant of the alternative exons, or by incorporation of a transcript of which all other variants have been spliced out retaining the exon-intron structure. The second and more likely possibility represents a new type of a 'partially' processed pseudogene.</p> <p>Conclusion</p> <p>Based on the comparative genomic analysis of the alternatively spliced arthropod muscle myosin heavy chain genes we propose that the splicing process operates sequentially on the transcript. The process consists of the splicing of the mutually exclusive exons until one exon out of the cluster remains while retaining surrounding intronic sequence. In a second step splicing of introns takes place. A related mechanism could be responsible for the splicing of other genes containing mutually exclusive exons.</p

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.

The QT interval, an electrocardiographic measure reflecting myocardial repolarization, is a heritable trait. QT prolongation is a risk factor for ventricular arrhythmias and sudden cardiac death (SCD) and could indicate the presence of the potentially lethal mendelian long-QT syndrome (LQTS). Using a genome-wide association and replication study in up to 100,000 individuals, we identified 35 common variant loci associated with QT interval that collectively explain ∼8-10% of QT-interval variation and highlight the importance of calcium regulation in myocardial repolarization. Rare variant analysis of 6 new QT interval-associated loci in 298 unrelated probands with LQTS identified coding variants not found in controls but of uncertain causality and therefore requiring validation. Several newly identified loci encode proteins that physically interact with other recognized repolarization proteins. Our integration of common variant association, expression and orthogonal protein-protein interaction screens provides new insights into cardiac electrophysiology and identifies new candidate genes for ventricular arrhythmias, LQTS and SCD

Checklist for a complete chronic urticaria medical history : an easy tool

ABSTARCT: Existing guidelines do not offer a quick, efficient alternative to the patient's recollection of relevant clinical features during anamnesis and physical examination for chronic urticaria (CU). This study aimed to identify specific items reflecting the main characteristics of CU that should be included in a comprehensive medical history for patients with CU. We also aimed to clarify possible eliciting factors for CU to support accurate diagnosis of the disease. METHODS: A panel of postgraduate dermatologists conducted a literature search for relevant studies on CU using Medline, the Cochrane database, and PubMed. RESULTS: We identified82 articles from which we drew a collection of items to inform development of an easy-to-use checklist and collection of items that should be included in a correct medical history. The final version of the checklist included42 items across two areas: essential clues for anamnesis and diagnosis of CU; and typical symptoms/parameters or characteristics according to subtype, etiology, and laboratory findings. Items included time of disease onset; duration, shape, size, color, and distribution of wheals; associated angioedema; atopy; and triggering factors. CONCLUSIONS: Our guide provides an easy-to-use tool to support clinicians to focus, orient themselves, and save time in medical consultations for CU, allowing better diagnosis and management of this disease