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See detailModeling seizures in the Human Phenotype Ontology according to contemporary ILAE concepts makes big phenotypic data tractable
Lewis-Smith, David; Galer, Peter D.; Balagura, Ganna et al

in Epilepsia (2021), n/a(n/a),

Abstract Objective The clinical features of epilepsy determine how it is defined, which in turn guides management. Therefore, consideration of the fundamental clinical entities that comprise an epilepsy ... [more ▼]

Abstract Objective The clinical features of epilepsy determine how it is defined, which in turn guides management. Therefore, consideration of the fundamental clinical entities that comprise an epilepsy is essential in the study of causes, trajectories, and treatment responses. The Human Phenotype Ontology (HPO) is used widely in clinical and research genetics for concise communication and modeling of clinical features, allowing extracted data to be harmonized using logical inference. We sought to redesign the HPO seizure subontology to improve its consistency with current epileptological concepts, supporting the use of large clinical data sets in high-throughput clinical and research genomics. Methods We created a new HPO seizure subontology based on the 2017 International League Against Epilepsy (ILAE) Operational Classification of Seizure Types, and integrated concepts of status epilepticus, febrile, reflex, and neonatal seizures at different levels of detail. We compared the HPO seizure subontology prior to, and following, our revision, according to the information that could be inferred about the seizures of 791 individuals from three independent cohorts: 2 previously published and 150 newly recruited individuals. Each cohort's data were provided in a different format and harmonized using the two versions of the HPO. Results The new seizure subontology increased the number of descriptive concepts for seizures 5-fold. The number of seizure descriptors that could be annotated to the cohort increased by 40 and the total amount of information about individuals' seizures increased by 38\%. The most important qualitative difference was the relationship of focal to bilateral tonic-clonic seizure to generalized-onset and focal-onset seizures. Significance We have generated a detailed contemporary conceptual map for harmonization of clinical seizure data, implemented in the official 2020-12-07 HPO release and freely available at hpo.jax.org. This will help to overcome the phenotypic bottleneck in genomics, facilitate reuse of valuable data, and ultimately improve diagnostics and precision treatment of the epilepsies. [less ▲]

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See detailHSM-based Key Management Solution for Ethereum Blockchain
Shbair, Wazen UL; Gavrilov, Eugene; State, Radu UL

in IEEE International Conference on Blockchain and Cryptocurrency, 3-6 May 2021 (2021, May 03)

The security of distributed applications backed by blockchain technology relies mainly on keeping the associated cryptographic keys (i.e. private keys) in well-protected storage. Since they are the unique ... [more ▼]

The security of distributed applications backed by blockchain technology relies mainly on keeping the associated cryptographic keys (i.e. private keys) in well-protected storage. Since they are the unique proof of ownership of the underlying digital assets. If the keys are stolen or lost, there is no way to recover the assets. The cold wallet is a good candidate for basic use cases, but it has a substantial challenge for more complex applications as it does not scale. Warm and hot wallets are more convenient options for blockchain-based solutions that aim to transact in a cloud environment. In this work, we focus on Hardware Security Module (HSM) based wallet. The HSM is the de-facto standard device designed to manage high-value cryptographic keys and to protect them against hacks. In this demonstration, we present an HSM-based working prototype that secures the entire life cycle of Ethereum public and private keys. [less ▲]

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See detailEvaluation of the Molecular Pathogenesis of Adrenocortical Tumors by Whole-Genome Sequencing
Neininger, Kerstin UL; May, Patrick UL; Altieri, Barbara et al

in Journal of the Endocrine Society (2021, May 03), 5(Issue Supplement_1), 68

Pathogenesis of autonomous steroid secretion and adrenocortical tumorigenesis remains partially obscure. Our aim was to identify novel genetic alterations in adrenocortical adenomas (ACA) without somatic ... [more ▼]

Pathogenesis of autonomous steroid secretion and adrenocortical tumorigenesis remains partially obscure. Our aim was to identify novel genetic alterations in adrenocortical adenomas (ACA) without somatic mutations in known driver genes. Whole-genome sequencing was performed on 26 ACA/blood-derived DNA pairs without driver mutations in PRKACA, GNAS and CTNNB1 genes at previous WES (ENSAT study JCEM 2016). These included 12 cortisol-producing adenomas with Cushing syndrome (CS-CPAs), 7 with mild autonomous cortisol secretion (MACS-CPAs), and 7 endocrine-inactive ACAs (EIAs). Seven adrenocortical carcinomas (ACC) were added to the cohort. We developed a bioinformatics pipeline for a comprehensive genome analysis and to reveal differences in variant distribution. Strelka, VarScan2 and ANNOVAR software and an in-house confidence score were used for variant calling and functional annotation. Combined Annotation-Dependent-Depletion (CADD) values were used to prioritize pathogenic variants. Additional focus relied on variants in pathogenically known pathways (Wnt/β-catenin, cAMP/PKA pathway). NovoBreak algorithm was applied to discover structural variations. Two hypermutated CS-CPA samples were excluded from further analysis. Using different filters, we detected variants in driver genes not observed at WES (one p.S45P in CTNNB1 and one p.R206L in PRKACA in two different CS-CPAs). In total, we report 179,830 variations (179,598 SNVs; 232 indels) throughout all samples, being more abundant in ACC (88,954) compared to ACA (CS-CPAs: 31,821; MACS-CPAs: 35,008; EIAs: 29,963). Most alterations were in intergenic (>50%), followed by intronic and ncRNA intronic regions. A total of 32 predicted pathogenic variants were found in both coding (CADD values ≥ 15) and non-coding (CADD values ≥ 5) regions. We found 3,301 possibly damaging and recurrent variants (intergenic mutations removed) (CS-CPAs: 1,463; MACS-CPAs: 1,549; EIAs: 1,268; ACC: 1,660), mostly accumulated in intronic regions. Some of these were detected in members of the Wnt/β-catenin (CS-CPAs: 6; MACS-CPAs: 2; EIA: 1) and cAMP/PKA (CS-CPAs: 6; MACS-CPAs: 7; EIA: 4) pathways (e.g. ADCY1, ADCY2, GNA13, PDE11A). We also found a slightly higher number of structural variations in EIA (3,620) and ACC (3,486) compared to CS-CPAs (977) and MACS-CPAs (2,119). In conclusion, still unrevealed genetic alterations, especially in intronic regions, may accompany early adrenal tumorigenesis and/or autonomous cortisol secretion. [less ▲]

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See detailSense of Belonging: Predictors for Host Country Attachment Among Emigrants
Décieux, Jean; Murdock, Elke UL

in Erlinghagen, Marcel; Ette, Andreas; Schneider, Norbert (Eds.) et al The Global Lives of German Migrants: Consequences of International Migration Across the Life Course (2021)

German citizens usually leave their home country voluntarily and face fewer barriers, e.g. in terms of freedom of travel or labour market integration. However, when arriving in their host country, they ... [more ▼]

German citizens usually leave their home country voluntarily and face fewer barriers, e.g. in terms of freedom of travel or labour market integration. However, when arriving in their host country, they are confronted with the need to adapt to life in a new society. Analysing data from the German Emigration and Remigration Panel Study, we found that half of the emigrants developed a sense of belonging to their new host society. Moreover, we set out to examine this development of host country attachment. Guided by findings from acculturation and expatriate attachment research, we identified factors potentially contributing to host country attachment and tested these in a series of regression models. Permanence of the intended stay is the strongest predictor, and social integration also plays an important role. Host country language competence is also important for the identification processes. Regarding cultural distance, our findings suggest an inverted U-shaped relationship with certain cultural novelty facilitating the development of host country belonging. Moreover, the data point to a complex relationship between cultural characteristics of the target country and factors related to an emotional settlement. [less ▲]

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See detailOffice Agents: Personal Office Vitality Sensors with Intent
Stamhuis, Sjoerd; Brombacher, Hans; Vos, Steven et al

Scientific Conference (2021, May)

In smart office buildings, almost every aspect of the environment can be assessed and adjusted by sensors. Yet employees rarely have access to the data collected to act upon it. It is also unclear what ... [more ▼]

In smart office buildings, almost every aspect of the environment can be assessed and adjusted by sensors. Yet employees rarely have access to the data collected to act upon it. It is also unclear what they would find meaningful to follow the recommendations on healthy work conditions and behavior, while productivity is the priority. The Office Agents are a set of artefacts placed on the employee’s desk, which capture data about the office environment. Air quality, sound level, light exposure, productivity, and physical activity level are measured to provide office workers with feedback on the ‘best’ working conditions. Using speculative design and Objects with Intent, the employee engages in a negotiation with the Office Agents based on the office ecosystem. Through this project and interactivity session, we open a debate on the use of sensors in office environments and the stakes around office vitality from the viewpoint of the employees. [less ▲]

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See detailAge of Information in IEEE 802.11p
Baiocchi, Andrea; Turcanu, Ion UL; Lyamin, Nikita et al

in 17th IFIP/IEEE International Symposium on Integrated Network Management (IM): ITAVT Workshop (2021, May)

Vehicle-to-Everything (V2X) communication is essential for facilitating connected and automated driving, where vehicles and other road traffic participants share data instantaneously and cooperate to ... [more ▼]

Vehicle-to-Everything (V2X) communication is essential for facilitating connected and automated driving, where vehicles and other road traffic participants share data instantaneously and cooperate to solve tricky traffic situations in milliseconds. This paper proposes two stochastic models for the V2X standard IEEE 802.11p to characterize amongst other things the Age of Information (AoI), a recently-proposed metric that measures the freshness of information. The first model is based on renewal process analysis of a tagged station with mean field approximation, while the second one adopts Markov chain approach with network level view. Analytical results show that IEEE 802.11p, given its adaptability to event-triggered and aperiodic messaging, supports advanced cooperative driving scenarios. [less ▲]

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See detailLimitations of plastic bending resistance for composite beams deviated from strain-limitation
Schäfer, Markus UL; Zhang, Qingjie UL; Braun, Matthias et al

in Journal of Constructional Steel Research (2021), 180(106562),

Due to the demand for sustainable constructions, composite structures have become more important and lead to slim and economic solutions with a low structural self-weight. EN 1994-1-1 distinguishes ... [more ▼]

Due to the demand for sustainable constructions, composite structures have become more important and lead to slim and economic solutions with a low structural self-weight. EN 1994-1-1 distinguishes between four different cross-section classes for the determination of moment resistance. For the plastic moment resistance, it is assumed, that each cross-sectional fibre can plastify without any limit on the strain. For standard composite beams with sagging moments and a high plastic neutral axis, plastic resistance and strain-limited resistance give similar results. For sections with a large compression zone height xpl and limited rotation capacity, concrete failure in the compression zone can occur before the plastic moment resistance Mpl,Rd, is reached. The strain limit design becomes critical. This paper points out the impact of the concrete part on the design of composite beams. A parametric study comparing plastic and strain limited moment resistance of a considerable variety of cross-sections has been carried out to develop the beam design methods considering compression zone height for the next generation of Eurocodes. [less ▲]

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See detailA Replication Study on the Usability of Code Vocabulary in Predicting Flaky Tests
Haben, Guillaume UL; Habchi, Sarra UL; Papadakis, Mike UL et al

in 18th International Conference on Mining Software Repositories (2021, May)

Abstract—Industrial reports indicate that flaky tests are one of the primary concerns of software testing mainly due to the false signals they provide. To deal with this issue, researchers have developed ... [more ▼]

Abstract—Industrial reports indicate that flaky tests are one of the primary concerns of software testing mainly due to the false signals they provide. To deal with this issue, researchers have developed tools and techniques aiming at (automatically) identifying flaky tests with encouraging results. However, to reach industrial adoption and practice, these techniques need to be replicated and evaluated extensively on multiple datasets, occasions and settings. In view of this, we perform a replication study of a recently proposed method that predicts flaky tests based on their vocabulary. We thus replicate the original study on three different dimensions. First we replicate the approach on the same subjects as in the original study but using a different evaluation methodology, i.e., we adopt a time-sensitive selection of training and test sets to better reflect the envisioned use case. Second, we consolidate the findings of the initial study by building a new dataset of 837 flaky tests from 9 projects in a different programming language, i.e., Python while the original study was in Java, which comforts the generalisability of the results. Third, we propose an extension to the original approach by experimenting with different features extracted from the Code Under Test. Our results demonstrate that a more robust validation has a consistent negative impact on the reported results of the original study, but, fortunately, these do not invalidate the key conclusions of the study. We also find re-assuring results that the vocabulary-based models can also be used to predict test flakiness in Python and that the information lying in the Code Under Test has a limited impact in the performance of the vocabulary-based models [less ▲]

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See detailThEodorE: a Trace Checker for CPS Properties
Menghi, Claudio UL; Vigano, Enrico UL; Bianculli, Domenico UL et al

in Companion Proceedings of the 43rd International Conference on Software Engineering (2021, May)

ThEodorE is a trace checker for Cyber-Physical systems (CPS). It provides users with (i) a GUI editor for writing CPS requirements; (ii) an automatic procedure to check whether the requirements hold on ... [more ▼]

ThEodorE is a trace checker for Cyber-Physical systems (CPS). It provides users with (i) a GUI editor for writing CPS requirements; (ii) an automatic procedure to check whether the requirements hold on execution traces of a CPS. ThEodorE enables writing requirements using the Hybrid Logic of Signals (HLS), a novel, logic-based specification language to express CPS requirements. The trace checking procedure of ThEodorE reduces the problem of checking if a requirement holds on an execution trace to a satisfiability problem, which can be solved using off-the-shelf Satisfiability Modulo Theories (SMT) solvers. This artifact paper presents the tool support provided by ThEodorE. [less ▲]

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See detailYou should never be alone. Social work crossing borders and cultures in child protection and disability rights. Experiences from a current multinational research project.
Limbach-Reich, Arthur UL; Schulze-Kruedener, Joergen

Presentation (2021, May)

Social service providers in the Greater Region report that many children in need of special care and social assistance find themselves in cross-border situations. The legal regulations and practices for ... [more ▼]

Social service providers in the Greater Region report that many children in need of special care and social assistance find themselves in cross-border situations. The legal regulations and practices for the care of children and adolescents can vary considerably from country to country. This can cause delays, breaks or deterioration in the quality of support and sometimes irreversibly worsen the child's situation. Depending on the situation, diagnoses and access to social, medical-social or legal services can change considerably. The EURQUA project deals with cross-border child protection and disability rights within a multinational perspective. [less ▲]

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See detailQuantum moment map and obstructions to the existence of closed Fedosov star products
Futaki, Akito; La Fuente-Gravy, Laurent UL

in Journal of Geometry and Physics (2021), 163

It is shown that the normalized trace of Fedosov star product for quantum moment map depends only on the path component in the cohomology class of the symplectic form and the cohomology class of the ... [more ▼]

It is shown that the normalized trace of Fedosov star product for quantum moment map depends only on the path component in the cohomology class of the symplectic form and the cohomology class of the closed formal 2-form required to define Fedosov connections (Theorem 1.3). As an application we obtain a family of obstructions to the existence of closed Fedosov star products naturally attached to symplectic manifolds (Theorem 1.5) and Kähler manifolds (Theorem 1.6). These obstructions are integral invariants depending only on the path component of the cohomology class of the symplectic form. Restricted to compact Kähler manifolds we re-discover an obstruction found earlier in La Fuente-Gravy (2019). [less ▲]

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See detailRAICC: Revealing Atypical Inter-Component Communication in Android Apps
Samhi, Jordan UL; Bartel, Alexandre UL; Bissyande, Tegawendé François D Assise UL et al

in Samhi, Jordan; Bartel, Alexandre; Bissyande, Tegawendé François D Assise (Eds.) et al 43rd International Conference on Software Engineering (ICSE) (2021, May)

Inter-Component Communication (ICC) is a key mechanism in Android. It enables developers to compose rich functionalities and explore reuse within and across apps. Unfortunately, as reported by a large ... [more ▼]

Inter-Component Communication (ICC) is a key mechanism in Android. It enables developers to compose rich functionalities and explore reuse within and across apps. Unfortunately, as reported by a large body of literature, ICC is rather "complex and largely unconstrained", leaving room to a lack of precision in apps modeling. To address the challenge of tracking ICCs within apps, state of the art static approaches such as Epicc, IccTA and Amandroid have focused on the documented framework ICC methods (e.g., startActivity) to build their approaches. In this work we show that ICC models inferred in these state of the art tools may actually be incomplete: the framework provides other atypical ways of performing ICCs. To address this limitation in the state of the art, we propose RAICC a static approach for modeling new ICC links and thus boosting previous analysis tasks such as ICC vulnerability detection, privacy leaks detection, malware detection, etc. We have evaluated RAICC on 20 benchmark apps, demonstrating that it improves the precision and recall of uncovered leaks in state of the art tools. We have also performed a large empirical investigation showing that Atypical ICC methods are largely used in Android apps, although not necessarily for data transfer. We also show that RAICC increases the number of ICC links found by 61.6% on a dataset of real-world malicious apps, and that RAICC enables the detection of new ICC vulnerabilities. [less ▲]

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See detailThe absolute Gravity Network of Haiti - Status Report 2021
Francis, Olivier UL; Sauveur, Renaldo UL; Beker, Neptune et al

Report (2021)

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See detailLes dangers de pastebin
Samhi, Jordan UL; Bissyande, Tegawendé François D Assise UL; Klein, Jacques UL

Article for general public (2021)

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See detailEvaluation of TPMS Signal Propagation in a Heavy Commercial Vehicle Environement
Rida, Ahmad UL; Ridha, Soua; Engel, Thomas UL

E-print/Working paper (2021)

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See detailANN-aided incremental multiscale-remodelling-based finite strain poroelasticity
Dehghani, Hamidreza UL; Zilian, Andreas UL

in Computational Mechanics (2021)

Mechanical modelling of poroelastic media under finite strain is usually carried out via phenomenological models neglecting complex micro-macro scales interdependency. One reason is that the mathematical ... [more ▼]

Mechanical modelling of poroelastic media under finite strain is usually carried out via phenomenological models neglecting complex micro-macro scales interdependency. One reason is that the mathematical two-scale analysis is only straightforward assuming infinitesimal strain theory. Exploiting the potential of ANNs for fast and reliable upscaling and localisation procedures, we propose an incremental numerical approach that considers rearrangement of the cell properties based on its current deformation, which leads to the remodelling of the macroscopic model after each time increment. This computational framework is valid for finite strain and large deformation problems while it ensures infinitesimal strain increments within time steps. The full effects of the interdependency between the properties and response of macro and micro scales are considered for the first time providing a more accurate predictive analysis of fluid-saturated porous media which is studied via a numerical consolidation example. Furthermore, the (nonlinear) deviation from Darcy’s law is captured in fluid filtration numerical analyses. Finally, the brain tissue mechanical response under the uniaxial cyclic test is simulated and studied. [less ▲]

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See detailLes dimensions spatiales et socioprofessionnelles du travail frontalier aux frontières franco-suisse et franco-luxembourgeoise
Pigeron-Piroth, Isabelle UL; Belkacem, Rachid

in Géo-Regards: Revue Neuchâteloise de Géographie (2021), 13(2020), 147-177

This article analyzes the main spatial and socio-professional dimensions of cross-border workers at the different borders of France, particularly within the cross-border employment poles of Geneva, Basel ... [more ▼]

This article analyzes the main spatial and socio-professional dimensions of cross-border workers at the different borders of France, particularly within the cross-border employment poles of Geneva, Basel and Luxembourg. It is based on data from the French population census, supplemented by data from the countries where cross-border workers work. While cross-border workers have socio-demographic characteristics that are relatively common to the different cross-border employment centres (mostly men, relatively young, etc.), the article highlights the territorial specificity of socio-professional profiles according to the different cross-border spaces observed. Cross-border work thus constitutes a modality of territorial management of labor and skills. [less ▲]

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See detailX25, une norme pour le transport de données
Schafer, Valerie UL

in Encyclopédie d'histoire numérique EHNE (2021)

L’avis X25, adopté en 1976 par le Comité consultatif international téléphonique et télégraphique (CCITT) dans le domaine des réseaux de données permet d’explorer des enjeux nationaux et internationaux de ... [more ▼]

L’avis X25, adopté en 1976 par le Comité consultatif international téléphonique et télégraphique (CCITT) dans le domaine des réseaux de données permet d’explorer des enjeux nationaux et internationaux de normalisation. Son histoire témoigne de la convergence entre télécommunications et informatique dans les années 1970, des débats liés au développement des réseaux de données, en particulier autour de la commutation de paquets, mais aussi de choix techniques, industriels et politiques complexes, et ce à plusieurs échelles. En revenant sur le passage du projet de norme à l’avis X25, à valeur non contraignante, son implémentation et développement dans des réseaux, puis sa postérité, cette étude permet d’explorer les acteurs, motivations et choix effectués à plusieurs moments charnières de l’histoire des réseaux de données. [less ▲]

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See detailThe International Legal Framework on Whistle-Blowers: What More Should Be Done?
Kafteranis, Dimitrios UL

in settle journal for social justice (2021), 19(3),

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See detailUsing Domain-specific Corpora for Improved Handling of Ambiguity in Requirements
Ezzini, Saad UL; Abualhaija, Sallam UL; Arora, Chetan et al

in In Proceedings of the 43rd International Conference on Software Engineering (ICSE'21), Madrid 25-28 May 2021 (2021, May)

Ambiguity in natural-language requirements is a pervasive issue that has been studied by the requirements engineering community for more than two decades. A fully manual approach for addressing ambiguity ... [more ▼]

Ambiguity in natural-language requirements is a pervasive issue that has been studied by the requirements engineering community for more than two decades. A fully manual approach for addressing ambiguity in requirements is tedious and time-consuming, and may further overlook unacknowledged ambiguity – the situation where different stakeholders perceive a requirement as unambiguous but, in reality, interpret the requirement differently. In this paper, we propose an automated approach that uses natural language processing for handling ambiguity in requirements. Our approach is based on the automatic generation of a domain-specific corpus from Wikipedia. Integrating domain knowledge, as we show in our evaluation, leads to a significant positive improvement in the accuracy of ambiguity detection and interpretation. We scope our work to coordination ambiguity (CA) and prepositional-phrase attachment ambiguity (PAA) because of the prevalence of these types of ambiguity in natural-language requirements [1]. We evaluate our approach on 20 industrial requirements documents. These documents collectively contain more than 5000 requirements from seven distinct application domains. Over this dataset, our approach detects CA and PAA with an average precision of 80% and an average recall of 89% ( 90% for cases of unacknowledged ambiguity). The automatic interpretations that our approach yields have an average accuracy of 85%. Compared to baselines that use generic corpora, our approach, which uses domain-specific corpora, has 33% better accuracy in ambiguity detection and 16% better accuracy in interpretation. [less ▲]

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