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A comprehensive ML-based Respiratory Monitoring System for Physiological Monitoring & Resource Planning in the ICU
(2024)medRxivRespiratory failure (RF) is a frequent occurrence in critically ill patients and is associated with significant morbidity and mortality as well as resource use. To improve the monitoring and management of RF in intensive care unit (ICU) patients, we used machine learning to develop a monitoring system covering the entire management cycle of RF, from early detection and monitoring, to assessment of readiness for extubation and prediction ...Working Paper -
High-resolution bulked segregant analysis enables candidate gene identification for bacterial wilt resistance in Italian ryegrass
(2023)bioRxivBacterial wilt, caused by Xanthomonas translucens pv. graminis (Xtg), is a serious disease of economically important forage grasses, including Italian ryegrass (Lolium multiflorum Lam.). A major QTL for resistance to Xtg was previously identified, but the precise location as well as the genetic factors underlying the resistance are yet to be determined. To this end, we applied a bulked segregant analysis (BSA) approach, using whole-genome ...Working Paper -
An improved chromosome-level genome assembly of perennial ryegrass (Lolium perenne L.)
(2023)bioRxivThis work is an update and extension of the previously published article “Ultralong Oxford Nanopore Reads Enable the Development of a Reference-Grade Perennial Ryegrass Genome Assembly”, by Frei et al.. The published genome assembly of the doubled haploid perennial ryegrass (Lolium perenne L.) genotype Kyuss marked a milestone for forage grass research and breeding. However, order and orientation errors may exist in the pseudo-chromosomes ...Working Paper -
Higher seed yield through selection for reduced seed shattering in Italian ryegrass (Lolium multiflorum Lam.)
(2023)bioRxivSeed shattering, i.e., the loss of seeds at ripening stage shortly before or during seed harvest, is strongly reducing seed yield in Italian ryegrass (Lolium multiflorum Lam.). The aim of this study was to evaluate the possibility to reduce seed shattering within breeding germplasm via recurrent phenotypic selection on spaced plants. Starting from a founder population of 300 plants serving as F0 population, two cycles of phenotypic selection ...Working Paper -
A nuclear architecture screen in Drosophila identifies Stonewall as a link between chromatin position at the nuclear periphery and germline stem cell fate
(2023)bioRxivThe association of genomic loci to the nuclear periphery is proposed to facilitate cell-type specific gene repression and influence cell fate decisions. However, the interplay between gene position and expression remains incompletely understood, in part because the proteins that position genomic loci at the nuclear periphery remain unidentified. Here, we used an Oligopaint-based HiDRO screen targeting ∼1000 genes to discover novel regulators ...Working Paper -
SimReadUntil for Benchmarking Selective Sequencing Algorithms on ONT Devices
(2023)bioRxivMotivation The Oxford Nanopore Technologies (ONT) ReadUntil API enables selective sequencing, which aims to reduce time spent on sequencing uninteresting reads in favor of more interesting reads, e.g., to deplete or enrich certain genomic regions. The performance gain depends on the selective sequencing decision-making algorithm (SSDA) which decides whether to reject a read, stop receiving a read or wait for more data. Since real runs are ...Working Paper -
On the pH-dependence of α-synuclein amyloid polymorphism and the role of secondary nucleation in seed-based amyloid propagation
(2023)bioRxivThe aggregation of the protein α-synuclein is closely associated with several neurodegenerative disorders and as such the structures of the amyloid fibril aggregates have high scientific and medical significance. However, it seems that there are about as many unique atomic-resolution structures of these aggregates as there are publications describing them. Obviously, this highly polymorphic nature of α-synuclein fibrils hampers efforts ...Working Paper -
An integrated transcriptomic cell atlas of human neural organoids
(2023)bioRxivNeural tissues generated from human pluripotent stem cells in vitro (known as neural organoids) are becoming useful tools to study human brain development, evolution and disease. The characterization of neural organoids using single-cell genomic methods has revealed a large diversity of neural cell types with molecular signatures similar to those observed in primary human brain tissue. However, it is unclear which domains of the human ...Working Paper -
Inferring context-dependent computations through linear approximations of prefrontal cortex dynamics
(2023)bioRxivThe complex neural population activity of prefrontal cortex (PFC) is a hallmark of cognitive processes. How these rich dynamics emerge and support neural computations is largely unknown. Here, we infer mechanisms underlying the context-dependent selection and integration of sensory inputs by fitting dynamical models to PFC population responses of behaving monkeys. A class of models implementing linear dynamics driven by external inputs ...Working Paper -
Morphogen gradients can convey position and time in growing tissues
(2023)bioRxivDuring development, cells need to make fate decisions according to their position and the developmental timepoint. Morphogen gradients provide positional information, but how timing is controlled has remained elusive. Here, we show that in morphogen gradients with constant decay length, cells experience transient, hump-shaped concentration profiles if the morphogen source expands in parallel with the uniformly growing tissue. This transient ...Working Paper