Development of data integration tools within functional genomics

Doctoral thesis (2022)

Due to technological advances across all scientific domains, data is generated at an extremely fast pace. This is especially true in biology, where advances in computational and sequencing technologies ... [more ▼]

Due to technological advances across all scientific domains, data is generated at an extremely fast pace. This is especially true in biology, where advances in computational and sequencing technologies led to the necessity to develop automated methods for data analysis; thus the field of bioinformatics was born. This thesis focuses on one specific field within bioinformatics - functional genomics. To be precise, in the development of techniques and software for the integration of data to generate novel insights. Indeed, as the amount of knowledge increases, so does the need to integrate it systematically. In this context, the work described herein relates to the integration of multiple resources to improve the functional annotation of proteins, which led to the development of two bioinformatic tools - Mantis and UniFunc. For the downstream integration and analysis of functional predictions, a network annotation tool was developed - UniFuncNet, which, together with the previous tools, enables the efficient functional characterisation of individual organisms or communities. [less ▲]

Verifiable, Secure and Privacy-Preserving Computation

Doctoral thesis (2022)

In this thesis, I present the research I conducted with my co-authors on numerous areas of verifiable, secure, and privacy-preserving computation during my doctoral studies at the University of Luxembourg ... [more ▼]

In this thesis, I present the research I conducted with my co-authors on numerous areas of verifiable, secure, and privacy-preserving computation during my doctoral studies at the University of Luxembourg, where Professor Peter Ryan advised me. In the first part, I study the functional encryption scheme. In the standard setting of functional encryption, it is assumed both the Central Authority (CA) and the encryptors to run their respective algorithms faithfully. However, in the case of dishonest parties, the security of the cryptosystem may be violated. It means that dishonest parties can cause inconsistent results which may not be detected. In the first part, we improve on this situation by considering Inner-Product Encryption (IPE), a special case of functional encryption and a primitive that has attracted wide interest from practitioners and researchers in the last decade. Specifically, we construct the first efficient verifiable Inner Product Encryption (VIPE) scheme according to the inner-product functionality. As the next step, we construct a verifiable IPE that satisfies unconditional verifiability, whereas privacy relies on the standard assumption. The second part of this thesis presents my research on e-voting protocols. I revisit the coercion-resistant e-voting protocol by Juels, Catalano and Jakobsson (JCJ) and, particularly, the attempts to make it usable and practical. In JCJ the user needs to handle cryptographic credentials and fake these in case of coercion. We present a hardware-independent protocol that can be implemented using a combination of a digitally stored cryptographic length key and a PIN only known by the voter. The long credential could be stored in several places or hidden via steganography. At the ballot casting phase, the software will input the digital key and the password to form the credential submitted with the vote. Depending on the level of coercion, the coerced voter can either fake the long credential or, for stronger levels of coercion, the voter can reveal the digitally stored credential to the coercer but fake the PIN. Due to our improved tally, the coercer will not know if he got faked credentials or PINs. On the other hand, since the voter memories the PIN is a high chance of users making a PIN typo error which will invalidate the vote and remain undetected. Note that naively giving feedback on the correctness of the PIN is not possible for coercion-resistance as it would allow the coercer to check whether he got a fake PIN or not. Instead, we will define a set of allowed PIN errors (e.g., chosen by the election administrator). We will consider a ballot valid if it has a correct PIN or an allowed PIN error but invalid for other PINs. At the tally phase, we construct protocols that secretly check whether a given PIN is in the set of allowed PINs and will sort out invalid ballots. We also design another End-to-End verifiable e-voting scheme achieving coercion-resistance via deniable vote updating. We propose a new e-voting system that enables voters with an intuitive mechanism to update their possibly coerced vote in a deniable way. What is more, our e-voting system does not introduce any additional trust assumptions for end-to-end verifiability and vote privacy besides the standards. Moreover, we demonstrate that our e-voting system can be instantiated efficiently for practical elections. With these properties, our e-voting system has the potential to close the gap between theory and practice in coercion-resistant e-voting. [less ▲]

Spectrum of Phenotypic, Genetic, and Functional Characteristics in Epilepsy Patients With KCNC2 Pathogenic Variants 10.1212/WNL.0000000000200660

in Neurology (2022)

Background: KCNC2 encodes Kv3.2, a member of the Shaw-related (Kv3) voltage-gated potassium channel subfamily, which is important for sustained high-frequency firing and optimized energy efficiency of ... [more ▼]

Background: KCNC2 encodes Kv3.2, a member of the Shaw-related (Kv3) voltage-gated potassium channel subfamily, which is important for sustained high-frequency firing and optimized energy efficiency of action potentials in the brain. The objective of this study was to analyse the clinical phenotype, genetic background, and biophysical function of disease-associated Kv3.2 variants.Methods: Individuals with KCNC2 variants detected by exome sequencing were selected for clinical, further genetic, and functional analysis. Cases were referred through clinical and research collaborations. Selected de novo variants were examined electrophysiologically in Xenopus laevis oocytes.Results: We identified novel KCNC2 variants in 18 patients with various forms of epilepsy including genetic generalized epilepsy (GGE), developmental and epileptic encephalopathy (DEE) including early-onset absence epilepsy (EOAE), focal epilepsy (FE), and myoclonic-atonic epilepsy (MAE). 10/18 variants were de novo and 8/18 variants were classified as modifying variants. 8 drug responsive cases became seizure-free using valproic acid as monotherapy or in combination including severe DEE cases. Functional analysis of four variants demonstrated gain-of-function in three severely affected DEE cases and loss-of-function in one case with a milder phenotype (GGE) as the underlying pathomechanisms.Conclusion: These findings implicate KCNC2 as a novel causative gene for epilepsy and emphasize the critical role of KV3.2 in the regulation of brain excitability. [less ▲]

Resolving the Complex Spin Structure in Fe-Based Soft Magnetic Nanocrystalline Material by Magnetic Small-Angle Neutron Scattering

in Neutron News (2022), 33(2), 15-17

"But you know you won't be back"

Article for general public (2022)

To Kill or Not to Kill – An experimental test of moral Decision-Making in gaming

in Entertainment Computing (2022)

Commercial video game titles with meaningful and morally relevant storylines are becoming increasingly popular and an intensely researched topic for entertainment scholars. In line with this research, the ... [more ▼]

Commercial video game titles with meaningful and morally relevant storylines are becoming increasingly popular and an intensely researched topic for entertainment scholars. In line with this research, the current study investigates behavioral, emotional, and personality patterns of moral decision-making in gaming with a special emphasis on selected contextual factors. In the current laboratory experiment, a total of N = 101 participants played four chapters of Detroit: Become Human for approx. 55 min. A maximum of 13 moral decisions had to be made either under time pressure or not. Before playing, participants were assigned to one of three conditions (i.e., playing morally vs. immorally framed character vs. no framing/control condition). As expected, players generally preferred to act morally regardless of character framing. Time pressure further increased the proportion of moral (vs. immoral) decision-making. Our results underline that moral decision-making is dependent on specific contexts and that morality theories can be applied to virtual gaming scenarios. [less ▲]

Exploring the use of self-sovereign identity for event ticketing systems

in Electronic Markets (2022), 32

This position paper discusses the challenges of blockchain applications in businesses and the public sector related to an excessive degree of transparency. We first point out the types of sensitive data ... [more ▼]

This position paper discusses the challenges of blockchain applications in businesses and the public sector related to an excessive degree of transparency. We first point out the types of sensitive data involved in different patterns of blockchain use cases. We then argue that the implications of blockchains’ information exposure caused by replicated transaction storage and execution go well beyond the often-mentioned conflicts with the GDPR’s “right to be forgotten” and may be more problematic than anticipated. In particular, we illustrate the trade-off between protecting sensitive information and increasing process efficiency through smart contracts. We also explore to which extent permissioned blockchains and novel applications of cryptographic technologies such as self-sovereign identities and zero-knowledge proofs can help overcome the transparency challenge and thus act as catalysts for blockchain adoption and diffusion in organizations. [less ▲]

Temporary Protection in the EU - State of Play

Report (2022)

On 24 February 2022, the armed forces of the Russian Federation launched an unprovoked full-scale invasion of Ukraine. This was an unprecedented act of aggression against a sovereign and independent ... [more ▼]

On 24 February 2022, the armed forces of the Russian Federation launched an unprovoked full-scale invasion of Ukraine. This was an unprecedented act of aggression against a sovereign and independent country and goes against fundamental principles of international law. It has been strongly condemned by the international community, including the European Union. As of mid-March, over three million Ukrainian and international refugees are fleeing the war to neighbouring EU and third countries (including Moldova). This massive inflow of Ukrainian refugees into the EU resulted in the Council adopting the implementing Decision 2022/382 of 4 March 2022, introducing temporary protection as a means of dealing with the crisis. [less ▲]

La relecture entre pairs : un levier de motivation de la pratique de l’écrit

Scientific Conference (2022, March 17)

Les enseignants corrigent et donnent des conseils d’amélioration à leurs apprenants, mais les commentaires des enseignants sont parfois mal compris (Cole, Coats, Lentell 1986 ; Smith 1997), alors que la ... [more ▼]

Les enseignants corrigent et donnent des conseils d’amélioration à leurs apprenants, mais les commentaires des enseignants sont parfois mal compris (Cole, Coats, Lentell 1986 ; Smith 1997), alors que la relecture entre pairs apporte un échange avec moins de pression (Lejot 2017). Cet échange se fait à un niveau de hiérarchie égal et facilite la négociation de sens des éléments du texte. Néanmoins, certains élèves pointent le manque de qualification des pairs pour remplacer les commentaires des professeurs dans l’enseignement supérieur (Rollinson 2005). Cette démarche trouve toute sa force pour les doctorants. Mis en place sur un semestre, ce système fermé de relecture et de commentaires reçus en boucle est bénéfique et motivant pour ces derniers. Dans les ateliers interdisciplinaires sur les compétences transversales et en l'occurrence celle de l'écrit académique, les doctorants soulignent l’énergie, la réflexion commune et le soutien que leur a apporté la relecture de texte d'un pair et d'être eux-mêmes relus (Lejot 2017). Relire est formateur et être compris par des chercheurs pairs fait faire un grand pas en termes de cohérence d'écriture et d'argumentation bien articulée à ces groupes des écoles doctorales. [less ▲]

Retrograde Procedural Memory in Parkinson’s Disease: A Cross-Sectional, Case-Control Study

in Journal of Parkinson's Disease (2022)

Background: The analysis of the procedural memory is particularly relevant in neurodegenerative disorders like Parkinson’s disease, due to the central role of the basal ganglia in procedural memory. It ... [more ▼]

Background: The analysis of the procedural memory is particularly relevant in neurodegenerative disorders like Parkinson’s disease, due to the central role of the basal ganglia in procedural memory. It has been shown that anterograde procedural memory, the ability to learn a new skill, is impaired in Parkinson’s disease. However, retrograde procedural memory, the long-term retention and execution of skills learned in earlier life stages, has not yet been systematically investigated in Parkinson’s disease. Objective: This study aims to investigate retrograde procedural memory in people with Parkinson’s disease.We hypothesized that retrograde procedural memory is impaired in people with Parkinson’s disease compared to an age- and gender-matched control group. Methods: First, we developed the CUPRO evaluation system, an extended evaluation system based on the Cube Copying Test, to distinguish the cube copying procedure, representing functioning of retrograde procedural memory, and the final result, representing the visuo-constructive abilities. Development of the evaluation system included tests of discriminant validity. Results: Comparing people with typical Parkinson’s disease (n = 201) with age- and gender-matched control subjects (n = 201), we identified cube copying performance to be significantly impaired in people with Parkinson’s disease (p = 0.008) No significant correlation was observed between retrograde procedural memory and disease duration. Conclusion: We demonstrated lower cube copying performance in people with Parkinson’s disease compared to control subjects, which suggests an impaired functioning of retrograde procedural memory in Parkinson’s disease. [less ▲]