Semantic Modelling of Citation Contexts for Context-Aware Citation Recommendation

Contents The four CSV files are the data used for the evaluation in: Saier T., Färber M. (2020) Semantic Modelling of Citation Contexts for Context-Aware Citation Recommendation. In: Advances in Information Retrieval. ECIR 2020. Lecture Notes in Computer Science, vol 12035. DOI: 10.1007/978-3-030-45439-5_15 Code: github.com/IllDepence/ecir2020 The evaluation was conducted in a citation re-prediction setting. CSV Format 7 columns divided by \u241E cited document ID for *_nomarker.csv: citation marker position ambiguous for *_withmarker.csv: citation marker position at 'MAINCIT' in citation context adjacent cited document IDs only given in citrec_unarxive_*.csv divided by \u241F order matches 'CIT' markers in citation context citing document ID citation context MAG field of study IDs divided by \u241F predicate:argument tuples generated based on PredPatt JSON noun phrases for *_nomarker.csv: divided by \u241F for *_withmarker.csv: divided by \u241D into noun phrases noun phrase directly preceding citation marker Data Sources citrec_unarxive_cs_withmarker.csv data set unarXive Paper DOI: 10.1007/s11192-020-03382-z Data DOI: 10.5281/zenodo.2553522 filter citing doc from computer science cited doc is cited at least 5 times citrec_mag_cs_en.csv data set Microsoft Academic Graph (MAG) Paper DOI: 10.1145/2740908.2742839 filter citing doc from computer science and in English citing doc abstract in MAG given cited doc is cited at least 50 times citrec_refseer.csv data set RefSeer Paper URL: ojs.aaai.org/index.php/AAAI/article/view/9528 Data URL: psu.app.box.com/v/refseer filter for citing and cited docs title, venue, venuetype, abstract, and year not NULL citrec_acl-arc_withmarker.csv data set ACL ARC Paper URL: aclanthology.org/L08-1005 Data URL: acl-arc.comp.nus.edu.sg/ filter cited doc has a DBLP ID Paper Citation @inproceedings{Saier2020ECIR, author = {Tarek Saier and Michael F{\"{a}}rber}, title = {{Semantic Modelling of Citation Contexts for Context-aware Citation Recommendation}}, booktitle = {Proceedings of the 42nd European Conference on Information Retrieval}, pages = {220--233}, year = {2020}, month = apr, doi = {10.1007/978-3-030-45439-5_15},

Tackling Labour Market Injustice and Organising Workers: The View from a Northern Heartland

This report, based on 42 interviews with workers, trade unionists and other stakeholders, examines the phenomena of low-paid and precarious work in Sheffield. It focuses on the factors driving the prevalence of such work (including the links with welfare reform), the experiences of workers in seven distinct employment sectors, as well as trade union responses to the challenges of organising in these areas. The report also includes a major addition of a postscript focused on the impacts of the Coronavirus pandemic and how this relates to the wider findings of the study

INCHEM-Py v1.2: a community box model for indoor air chemistry

The Indoor CHEMical model in Python, INCHEM-Py, is an open-source and accessible box model for the simulation of the indoor atmosphere, and is a refactor and significant development of the INdoor Detailed Chemical Model (INDCM). INCHEM-Py creates and solves a system of coupled ordinary differential equations that include gas-phase chemistry, surface deposition, indoor/outdoor air change, indoor photolysis processes and gas-to-particle partitioning for three common terpenes. It is optimised for ease of installation and simple modification for inexperienced users, while also providing unfettered access to customise the physical and chemical processes for more advanced users. A detailed user manual is included with the model and updated with each version release. In this paper, INCHEM-Py v1.2 is introduced, the modelled processes are described in detail, with benchmarking between simulated data and published experimental results presented, alongside discussion of the parameters and assumptions used. It is shown that INCHEM-Py achieves excellent agreement with measurements from two experimental campaigns which investigate the effects of people and different surfaces on the concentrations of different indoor air pollutants. In addition, INCHEM-Py shows closer agreement to experimental data than INDCM. This is due to the increased functionality of INCHEM-Py to model additional processes, such as deposition-induced surface emissions. Published community use-cases of INCHEM-Py are also presented to show the variety of applications for which this model is valuable to further our understanding of indoor air chemistry

Requirements Analysis for an Open Research Knowledge Graph

Current science communication has a number of drawbacks and bottlenecks which have been subject of discussion lately: Among others, the rising number of published articles makes it nearly impossible to get an overview of the state of the art in a certain field, or reproducibility is hampered by fixed-length, document-based publications which normally cannot cover all details of a research work. Recently, several initiatives have proposed knowledge graphs (KGs) for organising scientific information as a solution to many of the current issues. The focus of these proposals is, however, usually restricted to very specific use cases. In this paper, we aim to transcend this limited perspective by presenting a comprehensive analysis of requirements for an Open Research Knowledge Graph (ORKG) by (a) collecting daily core tasks of a scientist, (b) establishing their consequential requirements for a KG-based system, (c) identifying overlaps and specificities, and their coverage in current solutions. As a result, we map necessary and desirable requirements for successful KG-based science communication, derive implications and outline possible solutions.Comment: Accepted for publishing in 24th International Conference on Theory and Practice of Digital Libraries, TPDL 202

Alzheimer's Disease-Linked Mutations in Presenilin-1 Result in a Drastic Loss of Activity in Purified γ-Secretase Complexes

BACKGROUND: Mutations linked to early onset, familial forms of Alzheimer's disease (FAD) are found most frequently in PSEN1, the gene encoding presenilin-1 (PS1). Together with nicastrin (NCT), anterior pharynx-defective protein 1 (APH1), and presenilin enhancer 2 (PEN2), the catalytic subunit PS1 constitutes the core of the γ-secretase complex and contributes to the proteolysis of the amyloid precursor protein (APP) into amyloid-beta (Aβ) peptides. Although there is a growing consensus that FAD-linked PS1 mutations affect Aβ production by enhancing the Aβ1-42/Aβ1-40 ratio, it remains unclear whether and how they affect the generation of APP intracellular domain (AICD). Moreover, controversy exists as to how PS1 mutations exert their effects in different experimental systems, by either increasing Aβ1-42 production, decreasing Aβ1-40 production, or both. Because it could be explained by the heterogeneity in the composition of γ-secretase, we purified to homogeneity complexes made of human NCT, APH1aL, PEN2, and the pathogenic PS1 mutants L166P, ΔE9, or P436Q. METHODOLOGY/PRINCIPAL FINDINGS: We took advantage of a mouse embryonic fibroblast cell line lacking PS1 and PS2 to generate different stable cell lines overexpressing human γ-secretase complexes with different FAD-linked PS1 mutations. A multi-step affinity purification procedure was used to isolate semi-purified or highly purified γ-secretase complexes. The functional characterization of these complexes revealed that all PS1 FAD-linked mutations caused a loss of γ-secretase activity phenotype, in terms of Aβ1-40, Aβ1-42 and APP intracellular domain productions in vitro. CONCLUSION/SIGNIFICANCE: Our data support the view that PS1 mutations lead to a strong γ-secretase loss-of-function phenotype and an increased Aβ1-42/Aβ1-40 ratio, two mechanisms that are potentially involved in the pathogenesis of Alzheimer's disease

Presenilin Controls CBP Levels in the Adult Drosophila Central Nervous System

Background: Dominant mutations in both human Presenilin (Psn) genes have been correlated with the formation of amyloid plaques and development of familial early-onset Alzheimer’s disease (AD). However, a definitive mechanism whereby plaque formation causes the pathology of familial and sporadic forms of AD has remained elusive. Recent discoveries of several substrates for Psn protease activity have sparked alternative hypotheses for the pathophysiology underlying AD. CBP (CREB-binding protein) is a haplo-insufficient transcriptional co-activator with histone acetly-transferase (HAT) activity that has been proposed to be a downstream target of Psn signaling. Individuals with altered CBP have cognitive deficits that have been linked to several neurological disorders. Methodology/Principal Findings: Using a transgenic RNA-interference strategy to selectively silence CBP, Psn, and Notch in adult Drosophila, we provide evidence for the first time that Psn is required for normal CBP levels and for maintaining specific global acetylations at lysine 8 of histone 4 (H4K8ac) in the central nervous system (CNS). In addition, flies conditionally compromised for the adult-expression of CBP display an altered geotaxis behavior that may reflect a neurological defect. Conclusions/Significance: Our data support a model in which Psn regulates CBP levels in the adult fly brain in a manner that is independent of Notch signaling. Although we do not understand the molecular mechanism underlying th

Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution

BACKGROUND: The functional consequences of whole genome duplications in vertebrate evolution are not fully understood. It remains unclear, for instance, why paralogues were retained in some gene families but extensively lost in others. Cdx homeobox genes encode conserved transcription factors controlling posterior development across diverse bilaterians. These genes are part of the ParaHox gene cluster. Multiple Cdx copies were retained after genome duplication, raising questions about how functional divergence, overlap, and redundancy respectively contributed to their retention and evolutionary fate. RESULTS: We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xenopus tropicalis followed by RNA-seq. We found that one paralogue, Cdx4, has a much stronger effect on gene expression than the others, including a strong regulatory effect on FGF and Wnt genes. Functional annotation revealed distinct and overlapping roles and subtly different temporal windows of action for each gene. The data also reveal a colinear-like effect of Cdx genes on Hox genes, with repression of Hox paralogy groups 1 and 2, and activation increasing from Hox group 5 to 11. We also highlight cases in which duplicated genes regulate distinct paralogous targets revealing pathway elaboration after whole genome duplication. CONCLUSIONS: Despite shared core pathways, Cdx paralogues have acquired distinct regulatory roles during development. This implies that the degree of functional overlap between paralogues is relatively low and that gene expression pattern alone should be used with caution when investigating the functional evolution of duplicated genes. We therefore suggest that developmental programmes were extensively rewired after whole genome duplication in the early evolution of vertebrates