Gutenberg Open Science

The Open Science Repository of Johannes Gutenberg University Mainz.

Visible. Citable. Open.

Recent Submissions

ZeitschriftenaufsatzAccess status: Open Access ,
Accelign : a GPU-based library for accelerating pairwise sequence alignment
(2026)
Kallenborn, Felix
;
Dabbaghie, Fawaz
;
Steinegger, Martin
;
Schmidt, Bertil
Background The continually increasing volume of sequence data results in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments based on dynamic programming is an important part in many bioinformatics pipelines and a major contributor to overall runtime due to the associated quadratic time complexity. This motivates the need for a library of efficient implementations on modern GPUs for a variety of alignment algorithms for different types of sequence data including DNA, RNA, and proteins. Results Accelign is a library of accelerated pairwise sequence alignment algorithms for CUDA-enabled GPUs. Its parallelization strategy is based on a common wavefront design that can be adapted to support a variety of dynamic programming algorithms: local, global, and semi-global alignment of genomic and protein sequences with a variety of commonly used scoring schemes supporting one-to-one, one-to-many or all-to-all pairwise sequence alignments. This leads to a peak performance between 16.1 TCUPS and 9.1 TCUPS for computing optimal global alignment scores with linear gaps and affine gap penalties on a single RTX PRO 6000 Blackwell GPU, respectively. In addition, our library demonstrates significant speedups in several real-world case studies over prior CPU-based (SeqAn, Parasail, BSalign, EdLib, KSW2, WFA2, A*PA2) and GPU-based libraries (ADEPT, GASAL2), and can even outperform highly customized algorithms (WFA-GPU, CUDASW++4.0). Furthermore, the performance of our approach scales linearly with the number of employed GPUs, which makes it feasible to exploit multi-GPU nodes for increased processing speeds. Conclusion Accelign provides significant speedups for commonly used pairwise alignment algorithms compared to prior implementations. It is freely available at https://github.com/fkallen/Accelign.
ZeitschriftenaufsatzAccess status: Open Access ,
Cross-cultural adaptation and validation of the Arabic Rating-of-Fatigue scale
(2026)
Ali Baccouche, Mohamed
;
Trabelsi, Khaled
;
Masmoudi, Liwa
;
Jahrami, Haitham
;
Ammar, Achraf
Background The Rating-of-Fatigue (ROF) scale is increasingly used to quantify subjective sensations of fatigue in exercise science. However, despite its growing international use, its psychometric properties have not yet been examined in Arabic-speaking populations. This study aimed to translate the ROF into Arabic and evaluate its content validity, face validity, and construct validity relative to perceived exertion and heart rate (HR) responses during graded exercise and subsequent passive recovery. Methods The study was conducted in Tunisia and followed established international best-practice guidelines for cross-cultural adaptation. The ROF and its instructions were forward-translated, synthesized, and back-translated using blinded translators, with linguistic and conceptual equivalence evaluated using Sperber’s framework and expert committee review. Face validity was assessed in 68 Arabic-speaking adults. Construct validity was examined in 43 adult participants during a modified Bruce treadmill test followed by 10 min of seated recovery, with the Arabic Rating-of-Fatigue scale (ROF-Ar), Borg CR10, and HR recorded at each exercise stage and during recovery. Within-participant correlations were pooled using Fisher’s r-to-z transformation. Results Sperber-based ratings indicated high linguistic and conceptual equivalence between the ROF-Ar and the original scale, with no item exceeding the predefined revision threshold. Face validity findings showed that participants predominantly interpreted the ROF-Ar as a measure of fatigue rather than exertion and that standardized instructions improved descriptor-related comprehensibility and reduced perceived difficulty. During graded exercise, ROF-Ar demonstrated very strong pooled correlations with Borg CR10 (r = 0.94; 95% CI 0.92–0.95; p < 0.001) and HR (r = 0.95; 95% CI 0.93–0.96; p < 0.001). During recovery, the association between ROF-Ar and Borg CR10 attenuated substantially (r = 0.35; 95% CI 0.15–0.52; p < 0.001), whereas the association with HR remained moderate (r = 0.63; 95% CI 0.49–0.74; p < 0.001). Conclusions The Arabic version of the ROF demonstrated high linguistic and conceptual equivalence, adequate face validity, and strong construct validity. The recovery-phase dissociation between perceived fatigue and perceived exertion supports the intended conceptual distinction of the ROF and justifies the use of ROF-Ar for assessing subjective fatigue during exercise and recovery in Arabic-speaking research and applied settings.
ZeitschriftenaufsatzAccess status: Open Access ,
Prospective memory and executive functions in adults across the wider autistic spectrum
(2026)
Nürnberg, Daniela
;
Altgassen, Mareike
Prospective memory (PM) refers to the cognitive ability of remembering to execute an intended action in the future. Empirical evidence indicates reduced PM performance in autistic individuals. This study aimed to explore PM performance across the wider autistic spectrum, including individuals with diverse cognitive profiles, and to investigate the impact of executive functions on PM. Thirty autistic and 30 non-autistic adults (18–65 years), matched for age, gender and non-verbal abilities, took part in the study. Participants completed an event-based PM task, and three executive function tasks measuring planning, inhibition and generativity abilities. Overall, non-autistic adults performed better in the event-based PM task in comparison to autistic participants. Better executive functioning was associated with better event-based PM performance in both groups; the completion time of the planning task significantly predicted PM performance. Results confirm earlier findings of lower PM performance in autistic individuals and close links of executive functions and PM. Considering the significant impact of PM on day-to-day life, future studies should develop practical interventions to support PM (e.g., targeted training in planning abilities, the use of agendas, to-do lists or assistive technologies), especially for autistic individuals who are dependent on external aid.