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See detailStatistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions
Moreno-Indias, Isabel; Lahti, Leo; Nedyalkova, Miroslava et al

in Frontiers in Microbiology (2021), 12

The human microbiome has emerged as a central research topic in human biology and biomedicine. Current microbiome studies generate high-throughput omics data across different body sites, populations, and ... [more ▼]

The human microbiome has emerged as a central research topic in human biology and biomedicine. Current microbiome studies generate high-throughput omics data across different body sites, populations, and life stages. Many of the challenges in microbiome research are similar to other high-throughput studies, the quantitative analyses need to address the heterogeneity of data, specific statistical properties, and the remarkable variation in microbiome composition across individuals and body sites. This has led to a broad spectrum of statistical and machine learning challenges that range from study design, data processing, and standardization to analysis, modeling, cross-study comparison, prediction, data science ecosystems, and reproducible reporting. Nevertheless, although many statistics and machine learning approaches and tools have been developed, new techniques are needed to deal with emerging applications and the vast heterogeneity of microbiome data. We review and discuss emerging applications of statistical and machine learning techniques in human microbiome studies and introduce the COST Action CA18131 “ML4Microbiome” that brings together microbiome researchers and machine learning experts to address current challenges such as standardization of analysis pipelines for reproducibility of data analysis results, benchmarking, improvement, or development of existing and new tools and ontologies. [less ▲]

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See detailPublic Covid-19 X-ray datasets and their impact on model bias - a systematic review of a significant problem
Garcia Santa Cruz, Beatriz UL; Bossa, Matias Nicolas UL; Sölter, Jan UL et al

E-print/Working paper (2021)

Computer-aided-diagnosis for COVID-19 based on chest X-ray suffers from weak bias assessment and limited quality-control. Undetected bias induced by inappropriate use of datasets, and improper ... [more ▼]

Computer-aided-diagnosis for COVID-19 based on chest X-ray suffers from weak bias assessment and limited quality-control. Undetected bias induced by inappropriate use of datasets, and improper consideration of confounders prevents the translation of prediction models into clinical practice. This study provides a systematic evaluation of publicly available COVID-19 chest X-ray datasets, determining their potential use and evaluating potential sources of bias. Only 5 out of 256 identified datasets met at least the criteria for proper assessment of risk of bias and could be analysed in detail. Remarkably almost all of the datasets utilised in 78 papers published in peer-reviewed journals, are not among these 5 datasets, thus leading to models with high risk of bias. This raises concerns about the suitability of such models for clinical use. This systematic review highlights the limited description of datasets employed for modelling and aids researchers to select the most suitable datasets for their task. [less ▲]

Detailed reference viewed: 40 (2 UL)
See detailReusing oral histories: challenges, issues, limits
Schafer, Valerie UL

Presentation (2021, February 18)

This short presentation, which is part of a roundtable, will analyse the reuse in oral history, the way Digital Humanities may provide new ways to apply close and distant reading to interviews and the ... [more ▼]

This short presentation, which is part of a roundtable, will analyse the reuse in oral history, the way Digital Humanities may provide new ways to apply close and distant reading to interviews and the challenges of contextualisation, FAIR Data, etc. [less ▲]

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See detail3D modelling for pre-service primary school teachers in mathematics education
Kreis, Yves UL; Haas, Ben

Scientific Conference (2021, February 17)

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See detailPROBABILISTIC CONTENT POPULARITY LEARNING IN PROACTIVE CACHING SYSTEMS
Mehrizi Rahmat Abadi, Sajad UL

Doctoral thesis (2021)

Recent rapid growth of data traffic in mobile networks has stretched the capability of current network architectures. Proactively caching popular contents close to end-users has been proposed as a ... [more ▼]

Recent rapid growth of data traffic in mobile networks has stretched the capability of current network architectures. Proactively caching popular contents close to end-users has been proposed as a promising approach to mitigate the issue. A full-fledged proactive cache management mechanism encompasses two interrelated algorithms which need to be carefully designed: content popularity prediction and caching policy. Abundant research has focused on the performance of various caching policies assuming that the content popularity is perfectly known. Nonetheless, the content popularity is unknown in practice and has to be predicted from users' requests. Due to non-deterministic and time-varying nature of the requests, the prediction is nontrivial. In this thesis, the main focus is to introduce efficient prediction algorithms from Bayesian viewpoint. The Bayesian approach provides a powerful framework to construct statistical models which capture uncertainty and are robust to "over-fitting" issue. Firstly, we consider the prediction problem under stationary scenario. To enhance the accuracy of prediction, content features are leveraged and a Bayesian Poisson regressor based on a Gaussian process is proposed. The model can automatically discover hidden patterns in the feature space among the already-existing or seen contents. It also allows to predict the popularities of newly-added or unseen contents whose statistical data is not available in advance. We show that these capabilities of the model can have significant impact on caching performance. Secondly, we formulate a cooperative content caching in order to optimize the aggregated network cost for delivering contents to users. An efficient caching policy requires an accurate prediction of time varying content popularity. The requests can potentially have interactions over time, among contents, and across locations. To exploit these patterns, a probabilistic dynamical model based on a canonical tensor decomposition is developed. Additionally, an online learning method that works with streaming data where content request arrives sequentially is designed. Numerical results confirm that modeling time-content-location interactions by the proposed model can improve the cooperative caching strategy performance. Last but not least, we take one step further and develop a dynamical model, which besides time-content-location interactions, it can also uncover a non-linear temporal trend structure in content requests through which a more accurate prediction can be attained. Subsequently, a cooperative caching policy is designed which adaptively performs network resource allocation and optimizes content delivery according to the dynamic of content requests. Therefore, the policy provides a more efficient utilization of network resources. Using simulations, we show that the developed caching mechanism outperforms reference methods which ignore the temporal trend information. [less ▲]

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See detailDesign Optimization for Low-Complexity FPGA Implementation of Symbol-Level Multiuser Precoding
Haqiqatnejad, Alireza UL; Krivochiza, Jevgenij UL; Merlano Duncan, Juan Carlos UL et al

in IEEE Access (2021), 9

This paper proposes and validates a low-complexity FPGA design for symbol-level precoding (SLP) in multiuser multiple-input single-output (MISO) downlink communication systems. In the optimal case, the ... [more ▼]

This paper proposes and validates a low-complexity FPGA design for symbol-level precoding (SLP) in multiuser multiple-input single-output (MISO) downlink communication systems. In the optimal case, the symbol-level precoded transmit signal is obtained as the solution to an optimization problem tailored for a given set of users’ data symbols. This symbol-by-symbol design, however, imposes excessive computational complexity on the system. To alleviate this issue, we aim to reduce the per-symbol complexity of the SLP scheme by developing an approximate yet computationally-efficient closed-form solution. The proposed solution allows us to achieve a high symbol throughput in real-time implementations. To develop the FPGA design, we express the proposed solution in an algorithmic way and translate it to hardware description language (HDL). We then optimize the processing to accelerate the performance and generate the corresponding intellectual property (IP) core. We provide the synthesis report for the generated IP core, including performance and resource utilization estimates and interface descriptions. To validate our design, we simulate an uncoded transmission over a downlink multiuser channel using the LabVIEW software, where the SLP IP core is implemented as a clock-driven logic (CDL) unit. Our simulation results show that a throughput of 100 Mega symbols per second per user can be achieved via the proposed SLP design. We further use the MATLAB software to produce numerical results for the conventional zero-forcing (ZF) and the optimal SLP techniques as benchmarks for comparison. Thereby, it is shown that the proposed FPGA implementation of SLP offers an improvement of up to 50 percent in power efficiency compared to the ZF precoding. Remarkably, it enjoys the same per-symbol complexity order as that of the ZF technique. We also evaluate the loss of the real-time SLP design, introduced by the algebraic approximations and arithmetic inaccuracies, with respect to the optimal scheme. [less ▲]

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See detailGenome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture
Chia, Ruth; Sabir, Marya S.; Bandres-Ciga, Sara et al

in Nature Genetics (2021)

The genetic basis of Lewy body dementia (LBD) is not well understood. Here, we performed whole-genome sequencing in large cohorts of LBD cases and neurologically healthy controls to study the genetic ... [more ▼]

The genetic basis of Lewy body dementia (LBD) is not well understood. Here, we performed whole-genome sequencing in large cohorts of LBD cases and neurologically healthy controls to study the genetic architecture of this understudied form of dementia, and to generate a resource for the scientific community. Genome-wide association analysis identified five independent risk loci, whereas genome-wide gene-aggregation tests implicated mutations in the gene GBA. Genetic risk scores demonstrate that LBD shares risk profiles and pathways with Alzheimer’s disease and Parkinson’s disease, providing a deeper molecular understanding of the complex genetic architecture of this age-related neurodegenerative condition. [less ▲]

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See detailBenefits, Motivations, and Challenges of International Collaborative Research: A Sociology of Science Case Study
Dusdal, Jennifer UL; Powell, Justin J W UL

in Science and Public Policy (2021)

Contemporary science is marked by expanding, diverse forms of teamwork. Collaboration across organizational and cultural boundaries extends the possibilities of discovery. International collaborative ... [more ▼]

Contemporary science is marked by expanding, diverse forms of teamwork. Collaboration across organizational and cultural boundaries extends the possibilities of discovery. International collaborative research projects can provide findings beyond what one team could achieve alone. Motivated to grow their scientific network and maintain existing relationships, researchers increasingly collaborate, despite often unrecognized costs, since such projects are challenging to manage and carry out. Rarely studied in-depth and longitudinally, researcher perspectives are crucial to better understand the dynamics of durable collaboration networks. Thus, this retrospective, longitudinal case study of a sociology of science project applies the novel method of autoethnography to examine teamwork benefits, motivations, and challenges. Key challenges found include spatial distance and differences of culture, language, and career stage. This study, spanning North America, Europe, the Middle East, and East Asia, focused on collaborators’ characteristics and evolving perceptions of team dynamics over a decade. [less ▲]

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See detailrio: Reasoner for Input/Output Logics
Steen, Alexander UL

Software (2021)

rio provides a TPTP-aligned [3] automated reasoning system for unconstrained and constrained I/O logics basid on the outi operators, 1 ≤ i ≤ 4. It is implemented as a Scala application and based on the ... [more ▼]

rio provides a TPTP-aligned [3] automated reasoning system for unconstrained and constrained I/O logics basid on the outi operators, 1 ≤ i ≤ 4. It is implemented as a Scala application and based on the scala-tptp-parser [4]. In short, the system allows you to specify a set of conditional norms and a number of inputs (each of which describing aspects of the current situational context), and provides automated means for inferring whether given obligations (also encoded as formulas) can be derived. rio can also be used to infer the set of detached obligations instead of checking detachment of given ones. [less ▲]

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See detailNRAS is unique among RAS proteins in requiring ICMT for trafficking to the plasma membrane
Ahearn, Ian M.; Court, Helen R.; Siddiqui, Farid et al

in Life Science Alliance (2021)

Isoprenylcysteine carboxyl methyltransferase (ICMT) is the third of three enzymes that sequentially modify the C-terminus of CaaX proteins, including RAS. Although all four RAS proteins are substrates for ... [more ▼]

Isoprenylcysteine carboxyl methyltransferase (ICMT) is the third of three enzymes that sequentially modify the C-terminus of CaaX proteins, including RAS. Although all four RAS proteins are substrates for ICMT, each traffics to membranes differently by virtue of their hypervariable regions that are differentially palmitoylated. We found that among RAS proteins, NRAS was unique in requiring ICMT for delivery to the PM, a consequence of having only a single palmitoylation site as its secondary affinity module. Although not absolutely required for palmitoylation, acylation was diminished in the absence of ICMT. Photoactivation and FRAP of GFP-NRAS revealed increase flux at the Golgi, independent of palmitoylation, in the absence of ICMT. Association of NRAS with the prenyl-protein chaperone PDE6δ also required ICMT and promoted anterograde trafficking from the Golgi. We conclude that carboxyl methylation of NRAS is required for efficient palmitoylation, PDE6δ binding, and homeostatic flux through the Golgi, processes that direct delivery to the plasma membrane. [less ▲]

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See detailMyths and realities around Open Access before and after 2021
England, Jonathan UL

Learning material (2021)

Presentation given to researchers and research support staff for projects funded by Luxembourg's national funder (FNR) as part of an information session on their pre-2021 and their new post-2021 Open ... [more ▼]

Presentation given to researchers and research support staff for projects funded by Luxembourg's national funder (FNR) as part of an information session on their pre-2021 and their new post-2021 Open Access policy. The idea is to break some of the myths around OA (e.g. OA is a journal, OA is only possible the 'Gold' way), encourage researchers to always self-archive their publications and inform about the new policies coming up due to Plan S. The presentation uploaded was given on 11/02/2021. [less ▲]

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See detailKeynote: Service Oriented Architecture Chances and Challenges
Gonzalez de Oliveira, Ricardo UL; Chirstian, Kerstan; Henkel, Achim

Scientific Conference (2021, February 11)

Service Oriented Architectures are neither new nor very complicated. Quite the opposite. With the introduction of Ethernet into vehicles service based communication became reality. Therefore, the big SOA ... [more ▼]

Service Oriented Architectures are neither new nor very complicated. Quite the opposite. With the introduction of Ethernet into vehicles service based communication became reality. Therefore, the big SOA dream of independent hardware and software deployment seems to be in reach. Not only SOME/IP faces the challenge of service discovery and situation aware communication. However, automotive industry is far from mobilizing the full potential. The presentation will give an overview about the most crucial challenges we have to tackle and provide some – hopefully – helpful approaches how to overcome them. [less ▲]

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See detailThe winner writes it all. Wie erzählen wir Vergangenheit?
Brüll, Christoph UL

Conference given outside the academic context (2021)

Detailed reference viewed: 13 (2 UL)
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See detailCompte rendu de Jakob Müller, Die importierte Nation
Brüll, Christoph UL

in H-Soz-Kult (2021)

Detailed reference viewed: 19 (4 UL)
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See detailQoS-Predictable SOA on TSN: Insights from a Case-Study
Villanueva, Josetxo; Migge, Jörn; Navet, Nicolas UL

Scientific Conference (2021, February 09)

This work is about the design and configuration of service-oriented communication on top of Ethernet TSN. The first objective is to present takeaways from the design and implementation of the Renault E/E ... [more ▼]

This work is about the design and configuration of service-oriented communication on top of Ethernet TSN. The first objective is to present takeaways from the design and implementation of the Renault E/E Service-Oriented Architecture (SOA) called FACE. In particular, we discuss technological, design and configuration choices made for the SOA, such as how to segment messages (UDP with multiple events, TCP, SOME/IP TP), and the technical possibilities to shape the transmission of the packets on the Ethernet network. The second objective is to study how to ensure the Quality of Service (QoS) required by services. Indeed, services introduce specific challenges, be it only the sheer amount of traffic they generate and if there is a growing body of experiences in the use of TSN QoS mechanisms most of what has been learned so far is mostly about meeting the requirements of individual streams. Less is known for services that involve the transmission of several, possibly segmented, messages with more complex transmission patterns. We show on the FACE architecture how SOME/IP messages were mapped to TSN QoS mechanisms in a manual then automated manner so as to meet the individual requirements of the services in terms of timing, and the system’s requirements in terms of memory usage. [less ▲]

Detailed reference viewed: 37 (4 UL)
See detailAssange’s Extradition: Status Pending
Kafteranis, Dimitrios UL; Andreadakis, Stelios

E-print/Working paper (2021)

Detailed reference viewed: 13 (1 UL)