Miracle-dz/UniFAR-FTUs huggingface dataset:
Carotid Stiffness Assessment With Ultrafast Ultrasound Imaging in Case of Bicuspid Aortic Valve

Aims To compare the carotid stiffness and flow parameters by ultrafast ultrasound imaging (UF), in bicuspid aortic valve (BAV) patients to first-degree relatives (controls). Methods BAV patients (n = 92) and controls (n = 48) were consecutively included at a reference center for BAV. Aortic valve and ascending aorta were evaluated by echocardiography. Common carotid arteries were evaluated by UF with a linear probe. A high frame rate (2,000 frames/s) was used to measure the pulse wave velocity (PWV). The arterial diameter change over the cardiac cycle was obtained by UF-Doppler imaging. This allowed us to measure the distensibility and the maximal rate of systolic distension (MRSD). The wall shear stress (WSS) was measured based on the same acquisitions, by analyzing blood flow velocities close to the carotid walls. Results BAV patients had significantly larger aortic diameters (p < 0.001) at the Valsalva sinus and at the tubular ascending aorta but no larger carotid diameters. No significant differences were found in carotid stiffness parameters (distensibility, MRSD, and PWV), even though these patients had a higher aortic stiffness. Carotid stiffness correlated linearly with age and similar slopes were obtained for BAV patients and controls. No difference in carotid WSS was found between BAV patients and controls. Conclusion Our results clearly show that the carotid stiffness and flow parameters are not altered in case of BAV compared with controls.
Collagen IV (COL4A1, COL4A2), a Component of the Viral Biofilm, Is Induced by the HTLV-1 Oncoprotein Tax and Impacts Virus Transmission

Human T-cell leukemia virus type 1 (HTLV-1) is the etiologic agent for Adult T-Cell Leukemia/Lymphoma (ATLL) and HTLV-1-Associated Myelopathy/Tropical Spastic Paraparesis (HAM/TSP). HTLV-1 infects CD4+ T-cells via cell-to-cell transmission requiring reorganization of the cytoskeleton and expression of the viral transactivator and oncoprotein Tax. Viruses spread at the virological synapse (VS), a virus-induced specialized cell-cell contact, by polarized budding into synaptic clefts, and by cell surface transfer of viral biofilms (VBs). Since little is known about Tax’s role in formation of the VB, we asked which component of the VB is regulated by Tax and important for HTLV-1 transmission. Collagens are not only structural proteins of the extracellular matrix and basal membrane but also represent an important component of the VB. Here, we report that among the collagens known to be present in VBs, COL4 is specifically upregulated in the presence of HTLV-1 infection. Further, we found that transient expression of Tax is sufficient to induce COL4A1 and COL4A2 transcripts in Jurkat and CCRF-CEM T-cells, while robust induction of COL4 protein requires continuous Tax expression as shown in Tax-transformed T-cell lines. Repression of Tax led to a significant reduction of COL4A1/A2 transcripts and COL4 protein. Mechanistically, luciferase-based promoter studies indicate that Tax activates the COL4A2 and, to a less extent, the COL4A1 promoter. Imaging showing partial co-localization of COL4 with the viral Gag protein in VBs at the VS and transfer of COL4 and Gag to target cells suggests a role of COL4 in VB formation. Strikingly, in chronically infected C91-PL cells, knockout of COL4A2 impaired Gag transfer between infected T-cells and acceptor T-cells, while release of virus-like particles was unaffected. Taken together, we identified COL4 (COL4A1, COL4A2) as a component of the VB and a novel cellular target of Tax with COL4A2 appearing to impact virus transmission. Thus, this study is the first to provide a link between Tax’s activity and VB formation by hijacking COL4 protein functions.
Meemi: Finding the Middle Ground in Cross-lingual Word Embeddings

Word embeddings have become a standard resource in the toolset of any Natural Language Processing practitioner. While monolingual word embeddings encode information about words in the context of a particular language, cross-lingual embeddings define a multilingual space where word embeddings from two or more languages are integrated together. Current state-of-the-art approaches learn these embeddings by aligning two disjoint monolingual vector spaces through an orthogonal transformation which preserves the structure of the monolingual counterparts. In this work, we propose to apply an additional transformation after this initial alignment step, which aims to bring the vector representations of a given word and its translations closer to their average. Since this additional transformation is non-orthogonal, it also affects the structure of the monolingual spaces. We show that our approach both improves the integration of the monolingual spaces as well as the quality of the monolingual spaces themselves. Furthermore, because our transformation can be applied to an arbitrary number of languages, we are able to effectively obtain a truly multilingual space. The resulting (monolingual and multilingual) spaces show consistent gains over the current state-of-the-art in standard intrinsic tasks, namely dictionary induction and word similarity, as well as in extrinsic tasks such as cross-lingual hypernym discovery and cross-lingual natural language inference.
Interactive Causal Discovery in Knowledge Graphs

Being able to provide explanations about a domain is a hard task that requires from a probabilistic reasoning's viewpoint a causal knowledge about the domain variables, allowing one to predict how they can influence each others. However, causal discovery from data alone remains a challenging question. In this article, we introduce a way to tackle this question by presenting an interactive method to build a probabilistic relational model from any given relevant domain represented by a knowledge graph. Combining both ontological and expert knowledge, we define a set of constraints translated into a so-called relational schema. Such a relational schema can then be used to learn a probabilistic relational model, which allows causal discovery.
Exploring the Concept of "Tiers-Lieu" for Information Services: The Value of Conceptual Modeling

To be successful, Digital Transformation cannot be considered as a matter of a single department or a single organization, regardless of whether the organization is private or public. Its mission consists in providing new inter-disciplinary or even trans-disciplinary information services. Therefore, collective intelligence is a key for its success. A collaborative approach enabling innovation and co-creation is necessary to develop sustainable and democratic information services. As a potential solution, we propose a novel approach called Tiers-Lieu for Services (TLS), that we introduce in this paper. In addition, we consider conceptual modeling as the central underpinning technique for co-designing information services and succeeding in a TLS. In the paper we report on two experimental TLS conducted in the context of our continuing education program. Based on these explorations we will further study the concept of TLS and progress towards defining a method for conducting TLS.
Let's Automate! Making Use of a Learning Ontology for Conceptual Data Modelling

Conceptual modelling education remains a challenging pedagogical task, where time investment in the development of materials, as well as providing feedback and assessing the student works is particularly high due to the ill-structured nature of the problems typical for the discipline. A growing number of students in software and enterprise engineering courses and the general digitalization of the higher education, including the shift to blended and distance learning, require an update of the existing methods and tools for conceptual modelling education. One of the possible solutions to these issues could be systematization and automation of various aspects of conceptual modelling courses, depending on the needs of a particular educator and the target audience. In this paper, we describe the steps of development of a learning ontology for conceptual data modelling, define its structure and elements and provide examples of its possible use for systematization and automation of conceptual modelling pedagogy. The learning ontology is aimed at facilitating the structuring of learning materials and provision of feedback to students for university-level and industry-level educators, both in the traditional and in blended/online learning settings.
New Product Development in Media Firms in the Face of Technological Change: The Role of Strategy and Identity Ambiguity

The purpose of this study was to investigate the role of identity change and ambiguity in relation to strategy and product innovation that is largely overlooked in product innovation research. Combining product innovation theory on organization-related determinants of product innovation and theory on organizational identity dynamics we developed a framework that served as a basis for our exploratory empirical investigation. Our case study interview data suggest how internal identity ambiguity becomes dysfunctional for (radical) product innovation and how it was evoked by inconsistencies in strategy and in its intersection with HRM and culture. This implies for managers that they not only guard the internal identity and control ambiguity damage, but also try to prevent inconsistencies in the realm of strategy.
Software Conception for Semantic Interpretation of Spreadsheet Data

Spreadsheet data are a valuable source of knowledge in data science and business intelligence applications. However, most commonly, spreadsheets are not accompanied by explicit semantics which are necessary for a machine interpretation of their contents. Information accumulated in spreadsheets is often poorly structured and not standardized. Analysis of this tabular data requires its preliminary extraction and transformation to a structured representation with the subsequent recovering of the implicit semantics. In this paper, we consider a conception of software for semantic interpretation of spreadsheet data in XLSX format and the linked data generation in the form of RDF triplets. We suggest to use DBpedia as a global taxonomy of concepts for understanding and conceptualizing the content of tables. A list of the main functions of this software is also provided. Issues of the further software development are discussed.
COLIEE-2016: Evaluation of the Competition on Legal Information Extraction and Entailment

We present the evaluation of legal question answering of the Competition on Legal Information Extraction/Entailment (COLIEE)-2016. The COLIEE-2016 task consists of three sub-tasks: legal information retrieval (sub-task 1), recognizing entailment between articles and queries (sub-task 2), and combination of the previous two sub-tasks (sub-task 3). Participation was open to any group based on any approach, and the task attracted 11 teams. We received 7 submissions to the sub-task 1 (for a total of 14 runs), 6 submissions to the subtask 2 (for a total of 13 runs), and 5 submissions to the subtask 3 (for a total of 10 runs).
Forest-type specialization strongly predicts avian responses to tropical agriculture

Species’ traits influence how populations respond to land-use change. However, even in well-characterized groups such as birds, widely studied traits explain only a modest proportion of the variance in response across species. Here, we show that associations with particular forest types strongly predict the sensitivity of forest-dwelling Amazonian birds to agriculture. Incorporating these fine-scale habitat associations into models of population response dramatically improves predictive performance and markedly outperforms the functional traits that commonly appear in similar analyses. Moreover, by identifying habitat features that support assemblages of unusually sensitive habitat-specialist species, our model furnishes straightforward conservation recommendations. In Amazonia, species that specialize on forests along a soil–nutrient gradient (i.e. both rich-soil specialists and poor-soil specialists) are exceptionally sensitive to agriculture, whereas species that specialize on floodplain forests are unusually insensitive. Thus, habitat specialization per se does not predict disturbance sensitivity, but particular habitat associations do. A focus on conserving specific habitats that harbour highly sensitive avifaunas (e.g. poor-soil forest) would protect a critically threatened component of regional biodiversity. We present a conceptual model to explain the divergent responses of habitat specialists in the different habitats, and we suggest that similar patterns and conservation opportunities probably exist for other taxa and regions.
Complex factors shape phenotypic variation in deep-sea limpets

Pectinodontid limpets are important members of deep-sea hot vents and cold seeps as can be seen by their conspicuous presence in both extant and extinct systems. They have traditionally been classified into different genera and species based on shell and radula characteristics; the reliability of these characters has been questioned but not tested thoroughly. Here, for the first time in taxa endemic to deep-sea chemosynthetic ecosystems, we combine substrate translocation with molecular data to assess the plasticity and variability of key phenotypic characters. Molecular data revealed that several ‘species’ of extant vent/seep pectinodontids actually represent intergrading morphotypes of a single, highly plastic, evolutionary lineage, with each morphological trait being possibly influenced differently by environmental and genetic factors. Our results challenge previous interpretations of paleoecology at fossil chemosynthetic ecosystems and highlight the importance of modern analogues in understanding fossil systems.
Accurate and efficient discretizations for stochastic models providing near agent-based spatial resolution at low computational cost

Understanding how cells proliferate, migrate and die in various environments is essential in determining how organisms develop and repair themselves. Continuum mathematical models, such as the logistic equation and the Fisher–Kolmogorov equation, can describe the global characteristics observed in commonly used cell biology assays, such as proliferation and scratch assays. However, these continuum models do not account for single-cell-level mechanics observed in high-throughput experiments. Mathematical modelling frameworks that represent individual cells, often called agent-based models, can successfully describe key single-cell-level features of these assays but are computationally infeasible when dealing with large populations. In this work, we propose an agent-based model with crowding effects that is computationally efficient and matches the logistic and Fisher–Kolmogorov equations in parameter regimes relevant to proliferation and scratch assays, respectively. This stochastic agent-based model allows multiple agents to be contained within compartments on an underlying lattice, thereby reducing the computational storage compared to existing agent-based models that allow one agent per site only. We propose a systematic method to determine a suitable compartment size. Implementing this compartment-based model with this compartment size provides a balance between computational storage, local resolution of agent behaviour and agreement with classical continuum descriptions.
Altered lentiviral infection dynamics follow genetic rescue of the Florida panther

Wildlife translocations are a commonly used strategy in endangered species recovery programmes. Although translocations require detailed assessment of risk, their impact on parasite distribution has not been thoroughly assessed. This is despite the observation that actions that alter host–parasite distributions can drive evolution or introduce new parasites to previously sequestered populations. Here, we use a contemporary approach to amplify viral sequences from archived biological samples to characterize a previously undocumented impact of the successful genetic rescue of the Florida panther (Puma concolor coryi). Our efforts reveal transmission of feline immunodeficiency virus (FIV) during translocation of pumas from Texas to Florida, resulting in extirpation of a historic Florida panther FIV subtype and expansion of a genetically stable subtype that is highly conserved in Texas and Florida. We used coalescent theory to estimate viral demography across time and show an exponential increase in the effective population size of FIV coincident with expansion of the panther population. Additionally, we show that FIV isolates from Texas are basal to isolates from Florida. Interestingly, FIV genomes recovered from Florida and Texas demonstrate exceptionally low interhost divergence. Low host genomic diversity and lack of additional introgressions may underlie the surprising lack of FIV evolution over 2 decades. We conclude that modern FIV in the Florida panther disseminated following genetic rescue and rapid population expansion, and that infectious disease risks should be carefully considered during conservation efforts involving translocations. Further, viral evolutionary dynamics may be significantly altered by ecological niche, host diversity and connectivity between host populations.
Invariance of Spanish version of Sexual Double Standard Scale across sex, age, and education level.

BACKGROUND The Sexual Double Standard Scale (SDSS) is one of the most widely-used scales for evaluating the Sexual Double Standard (SDS) and the Spanish version of the scale displays adequate psychometric properties in the adult Spanish population. The aim of this study is to examine the factorial invariance and differential item functioning (DIF) of the Spanish version according to sex, education level, and age, with the objective of describing and comparing SDS based on these variables. METHOD A sample of 3,838 heterosexual participants was used (1,908 men and 1,930 women) between the ages of 18 and 90. RESULTS The results showed that the factorial structure of the SDSS is invariant in terms of sex and education level; with none of these items displaying DIF. Only items 11 and 14 display DIF in terms of age and, therefore, it is recommended that these items be excluded when making comparisons between age ranges. The association of SDSS with sex, education level, and age follows the expected results. CONCLUSIONS The Spanish version of the SDSS is invariant and, as a consequence, can be used in different types of samples.
Graphene-Based Biosensors for Detection of Composite Vibrational Fingerprints in the Mid-Infrared Region

In this study, a label-free multi-resonant graphene-based biosensor with periodic graphene nanoribbons is proposed for detection of composite vibrational fingerprints in the mid-infrared range. The multiple vibrational signals of biomolecules are simultaneously enhanced and detected by different resonances in the transmission spectrum. Each of the transmission dips can be independently tuned by altering the gating voltage applied on the corresponding graphene nanoribbon. Geometric parameters are investigated and optimized to obtain excellent sensing performance. Limit of detection is also evaluated in an approximation way. Besides, the biosensor can operate in a wide range of incident angles. Electric field intensity distributions are depicted to reveal the physical insight. Moreover, another biosensor based on periodic graphene nanodisks is further proposed, whose performance is insensitive to the polarization of incidence. Our research may have a potential for designing graphene-based biosensor used in many promising bioanalytical and pharmaceutical applications.
Computerized neuropsychological assessment devices in multiple sclerosis: A systematic review

Background: The proliferation of computerized neuropsychological assessment devices (CNADs) for screening and monitoring cognitive impairment is increasing exponentially. Previous reviews of computerized tests for multiple sclerosis (MS) were primarily qualitative and did not rigorously compare CNADs on psychometric properties. Objective: We aimed to systematically review the literature on the use of CNADs in MS and identify test batteries and single tests with good evidence for reliability and validity. Method: A search of four major online databases was conducted for publications related to computerized testing and MS. Test–retest reliability and validity coefficients and effect sizes were recorded for each CNAD test, along with administration characteristics. Results: We identified 11 batteries and 33 individual tests from 120 peer-reviewed articles meeting the inclusion criteria. CNADs with the strongest psychometric support include the CogState Brief Battery, Cognitive Drug Research Battery, NeuroTrax, CNS-Vital Signs, and computer-based administrations of the Symbol Digit Modalities Test. Conclusion: We identified several CNADs that are valid to screen for MS-related cognitive impairment, or to supplement full, conventional neuropsychological assessment. The necessity of testing with a technician, and in a controlled clinic/laboratory environment, remains uncertain.
Lethality of Brucella microti in a murine model of infection depends on the wbkE gene involved in O-polysaccharide synthesis

ABSTRACT Brucella microti was isolated a decade ago from wildlife and soil in Europe. Compared to the classical Brucella species, it exhibits atypical virulence properties such as increased growth in human and murine macrophages and lethality in experimentally infected mice. A spontaneous rough (R) mutant strain, derived from the smooth reference strain CCM4915T, showed increased macrophage colonization and was non-lethal in murine infections. Whole-genome sequencing and construction of an isogenic mutant of B. microti and Brucella suis 1330 revealed that the R-phenotype was due to a deletion in a single gene, namely wbkE (BMI_I539), encoding a putative glycosyltransferase involved in lipopolysaccharide (LPS) O-polysaccharide biosynthesis. Complementation of the R-strains with the wbkE gene restored the smooth phenotype and the ability of B. microti to kill infected mice. LPS with an intact O-polysaccharide is therefore essential for lethal B. microti infections in the murine model, demonstrating its importance in pathogenesis.