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Simon RUSHTON, 2019, Security and Public Health, Cambridge, Polity Press, 240 p

Anne Rasmussen
2021 Population  
Anne RaSmuSSen pour traiter de la santé publique.  ...  Simon ruSHton, 2019, Security and Public Health, Cambridge, Polity Press, 240 p.  ... 
doi:10.3917/popu.2102.0393 fatcat:cbwalgwllzdqjl2vvymzshtudy

Analysing complex metagenomic data with MicroWineBar [article]

Franziska Klincke, Martin Abel-Kistrup, Sofie Maria Gilberte Saerens, Simon Rasmussen
2019 bioRxiv   pre-print
An important step in metagenomics studies is to identify which species are present in a sample as well as to compare samples from different environments. Here we introduce MicroWineBar, a graphical tool for analyzing and comparing metagenomics samples. MicroWineBar can visualize the abundances of metagenomics samples in line and bar graphs, as well as analyse the richness and diversity. For a PCA as well as a differential abundance analysis, the abundance data is treated as compositional data
more » ... d center log-ratio transformed. We use MicroWineBar to analyse two different years of wine fermentation as well as data from a human microbiome study of colorectal cancer. Importantly, MicroWineBar does not require any programming skills, is intuitive and user friendly. MicroWineBar is available at and as a python package from the Python Package Index.
doi:10.1101/742684 fatcat:phojeinswjcefbhzwk2co2l57a

Genome Sequence of Talaromyces atroroseus , Which Produces Red Colorants for the Food Industry

Ulf Thrane, Kasper Bøwig Rasmussen, Bent Petersen, Simon Rasmussen, Thomas Sicheritz-Pontén, Uffe Hasbro Mortensen
2017 Genome Announcements  
Talaromyces atroroseus is a known producer of Monascus colorants suitable for the food industry. Furthermore, genetic tools have been established that facilitate elucidation and engineering of its biosynthetic pathways. Here, we report the draft genome of a potential fungal cell factory, T. atroroseus IBT 11181 (CBS 123796).
doi:10.1128/genomea.01736-16 pmid:28254987 pmcid:PMC5334594 fatcat:6hj5ptlcqnbcbou44s7bojhdbi

(In-)Approximability Results for Interval, Resource Restricted, and Low Rank Scheduling [article]

Marten Maack, Simon Pukrop, Anna Rodriguez Rasmussen
2022 arXiv   pre-print
We consider variants of the restricted assignment problem where a set of jobs has to be assigned to a set of machines, for each job a size and a set of eligible machines is given, and the jobs may only be assigned to eligible machines with the goal of makespan minimization. For the variant with interval restrictions, where the machines can be arranged on a path such that each job is eligible on a subpath, we present the first better than 2-approximation and an improved inapproximability result.
more » ... In particular, we give a (2-1/24)-approximation and show that no better than 9/8-approximation is possible, unless P=NP. Furthermore, we consider restricted assignment with R resource restrictions and rank D unrelated scheduling. In the former problem, a machine may process a job if it can meet its resource requirements regarding R (renewable) resources. In the latter, the size of a job is dependent on the machine it is assigned to and the corresponding processing time matrix has rank at most D. The problem with interval restrictions includes the 1 resource variant, is encompassed by the 2 resource variant, and regarding approximation the R resource variant is essentially a special case of the rank R+1 problem. We show that no better than 3/2, 8/7, and 3/2-approximation is possible (unless P=NP) for the 3 resource, 2 resource, and rank 3 variant, respectively. Both the approximation result for the interval case and the inapproximability result for the rank 3 variant are solutions to open challenges stated in previous works. Lastly, we also consider the reverse objective, that is, maximizing the minimal load any machine receives, and achieve similar results.
arXiv:2203.06171v1 fatcat:us5b3eetrzf4bfjr3nv3ikibi4

Response to Keller et al on Justinianic Plague

Simon Rasmussen, Martin Sikora, Peter De Barros Damgaard, Rasmus Nielsen, Eske Willerslev
2019 Figshare  
A manuscript recently posted by Keller et al. proposes that the finding of two individuals with evidence of plague infection from our study of "137 ancient human genomes from across the Eurasian steppes" does not inform about the Justinianic Plague. We are puzzled by their conclusion, as no where in our paper we claim that the Y. pestis strains we discovered were direct ancestors of the Justinianic Plague outbreak. Their criticism appears to be based on simple mis- reading, and do not
more » ... our findings. Rather, we emphasize that the results in another manuscript from the same group confirm and strengthen our finding of a most recent common ancestor between DA101 and the Justinianic plague strains.
doi:10.6084/m9.figshare.10290275.v1 fatcat:keqzhrs72zc3xdgh3mwdyinwnu

EyeLoop: An open-source, high-speed eye-tracker designed for dynamic experiments [article]

Simon Arvin, Rune Rasmussen, Keisuke Yonehara
2020 bioRxiv   pre-print
Eye-tracking is a method for tracking the position of the eye and size of the pupil, often employed in neuroscience laboratories and clinics. Eye-trackers are widely used, from studying brain dynamics to investigating neuropathology and disease models. Despite this broad utility, eye-trackers are expensive, hardware-intensive, and proprietary, which have limited this approach to high-resource facilities. Besides, experiments have largely been confined to static open-loop designs and post hoc
more » ... lysis due to the inflexibility of current systems. Here, we developed an open-source eye-tracking system, named EyeLoop, tailored to dynamic experiments. This Python-based software easily integrates custom functions via a modular logic, tracks a multitude of eyes, including rodent, human, and non-human primate eyes, and it operates well on inexpensive consumer-grade hardware. One of the most appealing applications of EyeLoop is closed-loop experiments, in which the eyes evoke stimulus feedback, such as rapid neuronal optogenetic stimulation. By using EyeLoop, we demonstrate its utility in an open-loop, a closed-loop, and a biomedical experiment. With a remarkably low minimal hardware cost amounting to 29 USD, EyeLoop makes dynamic eye-tracking accessible to low-resource facilities, such as high schools, small laboratories, and small clinics.
doi:10.1101/2020.07.03.186387 fatcat:3ibpylkirngo3l6slu6ggh7nre

cWords - systematic microRNA regulatory motif discovery from mRNA expression data

Simon H Rasmussen, Anders Jacobsen, Anders Krogh
2013 Silence  
Post-transcriptional regulation of gene expression by small RNAs and RNA binding proteins is of fundamental importance in development of complex organisms, and dysregulation of regulatory RNAs can influence onset, progression and potentially be target for treatment of many diseases. Post-transcriptional regulation by small RNAs is mediated through partial complementary binding to messenger RNAs leaving nucleotide signatures or motifs throughout the entire transcriptome. Computational methods
more » ... discovery and analysis of sequence motifs in high-throughput mRNA expression profiling experiments are becoming increasingly important tools for the identification of post-transcriptional regulatory motifs and the inference of the regulators and their targets. Results: cWords is a method designed for regulatory motif discovery in differential case-control mRNA expression datasets. We have improved the algorithms and statistical methods of cWords, resulting in at least a factor 100 speed gain over the previous implementation. On a benchmark dataset of 19 microRNA (miRNA) perturbation experiments cWords showed equal or better performance than two comparable methods, miReduce and Sylamer. We have developed rigorous motif clustering and visualization that accompany the cWords analysis for more intuitive and effective data interpretation. To demonstrate the versatility of cWords we show that it can also be used for identification of potential siRNA off-target binding. Moreover, cWords analysis of an experiment profiling mRNAs bound by Argonaute ribonucleoprotein particles discovered endogenous miRNA binding motifs. Conclusions: cWords is an unbiased, flexible and easy-to-use tool designed for regulatory motif discovery in differential case-control mRNA expression datasets. cWords is based on rigorous statistical methods that demonstrate comparable or better performance than other existing methods. Rich visualization of results promotes intuitive and efficient interpretation of data. cWords is available as a stand-alone Open Source program at Github https://github. com/simras/cWords and as a web-service at:
doi:10.1186/1758-907x-4-2 pmid:23688306 pmcid:PMC3682869 fatcat:5ozlntc6i5cxnajc3z4oasumvm

Optimal routing with failure-independent path protection

Thomas Stidsen, Bjørn Petersen, Simon Spoorendonk, Martin Zachariasen, Kasper Bonne Rasmussen
2009 Networks  
Reliable communication has become crucial in today's information society. Modern communication networks are required to deliver reliable communication to their customers. Unfortunately, protection against network failures significantly hampers efficient utilization of network investments, because the associated routing problems become much harder. In this article we present a rigorous mathematical analysis of one of the most promising protection methods: Failure independent path protection. We
more » ... resent an LP model which is solved by column generation. The subproblem is proven to be strongly NP -hard, but still solvable for medium sized networks through the use of specialized dynamic programming algorithms. This enables us to evaluate the performance of failure independent path protection for eight networks with up to 37 nodes and 57 links. The results indicate that only between 3% and 8% extra network capacity is necessary when compared with the capacity required by complete rerouting (which is the absolute lower bound for single link failure protection). Most of the backbone networks which today carry long distance communication traffic use path based routing, i.e., a communication connection between two points in the network is established along one or more fixed paths. Despite the huge success of the packet switched Internet, path-based routed network technology will continue to be the dominant technique of backbone networks, because traffic engineering can be performed much more efficiently than in packet switched networks. Examples of such path switched network technologies are SDH/SONET or DWDM networks or circuit switched network technologies like PSTN/ISDN. Furthermore, the new Multi Path Label Switching (MPLS) [34] protocol enables packets to be routed on fixed paths. The standard model of a path switched communication network is a directed graph G = (V , A) consisting of a set of nodes V and a set of arcs A. The nodes correspond to telecommunication switches. The telecommunication switches route
doi:10.1002/net.20323 fatcat:x7vg2tslajcbtdb4g6pcb7fd6y

Deep integrative models for large-scale human genomics [article]

Arnor Ingi Sigurdsson, David Westergaard, Ole Winther, Ole Lund, Søren Brunak, Bjarni J Vilhjalmsson, Simon Rasmussen
2021 bioRxiv   pre-print
Polygenic risk scores (PRSs) are expected to play a critical role in achieving precision medicine. PRS predictors are generally based on linear models using summary statistics, and more recently individual- level data. However, these predictors generally only capture additive relationships and are limited when it comes to what type of data they use. Here, we develop a deep learning framework (EIR) for PRS prediction which includes a model, genome-local-net (GLN), we specifically designed for
more » ... ge scale genomics data. The framework supports multi-task (MT) learning, automatic integration of clinical and biochemical data and model explainability. GLN outperforms LASSO for a wide range of diseases, particularly autoimmune disease which have been researched for interaction effects. We showcase the flexibility of the framework by training one MT model to predict 338 diseases simultaneously. Furthermore, we find that incorporating measurement data for PRSs improves performance for virtually all (93%) diseases considered (ROC-AUC improvement up to 0.36) and that including genotype data provides better model calibration compared to measurements alone. We use the framework to analyse what our models learn and find that they learn both relevant disease variants and clinical measurements. EIR is open source and available at
doi:10.1101/2021.06.11.447883 fatcat:qjcf6qwo7zdirhj647kz4detaa

Persisting effect of community approaches to resuscitation

Anne Møller Nielsen, Dan Lou Isbye, Freddy Knudsen Lippert, Lars Simon Rasmussen
2014 Resuscitation  
Rasmussen have received unrestricted research grants from the private foundation TrygFonden (Denmark,  ... 
doi:10.1016/j.resuscitation.2014.08.019 pmid:25193797 fatcat:7hqbuepcuvgzdialu5dymvth5e

Fidelity, tolerability and safety of acute high-intensity interval training after hospitalisation for COVID-19: a randomised cross-over trial

Frederik Foged, Iben Elmerdahl Rasmussen, Josephine Bjørn Budde, Rasmus Syberg Rasmussen, Villads Rasmussen, Mark Lyngbæk, Simon Jønck, Rikke Krogh-Madsen, Birgitte Lindegaard, Mathias Ried-Larsen, Ronan Martin Griffin Berg, Regitse Højgaard Christensen
2021 BMJ Open Sport & Exercise Medicine  
Many patients with COVID-19 suffer from persistent symptoms, many of which may potentially be reversed by high-intensity interval training (HIIT). Yet, the safety and tolerability of HIIT after COVID-19 is controversial. This study aimed to investigate the fidelity, tolerability and safety of three different HIIT protocols in individuals that had recently been hospitalised due to COVID-19. The study was a randomised cross-over trial. We compared three supervised HIIT protocols (4×4, 6×1,
more » ... 0) in 10 individuals recently discharged after hospitalisation for severe COVID-19. Each HIIT protocol had a duration of 38 min and was performed with a 1-week washout between them. Outcomes included adverse events, exercise training intensity and tolerability assessed by the Likert scale (1-10). All 10 participants aged 61 (mean, SD 8) years (5 males) completed all three HIIT protocols with no adverse events. High intensities were achieved in all three protocols, although they differed in terms of time spent with a heart rate ≥85% of maximum (mean (SD); 4×4: 13.7 (6.4) min; 10-20-30: 12.1 (3.8) min; 6×1: 6.1 (5.6) min; p=0.03). The three protocols were all well tolerated with similar Likert scale scores (mean (SD); 4×4: 8 (2), 10-20-30: 8 (2), 6×1: 9 (2), p=0.72). Our findings indicate that recently hospitalised individuals for severe COVID-19 may safely tolerate acute bouts of supervised HIIT as per protocol. This warrants future studies testing the potential of regular HIIT as a rehabilitation strategy in this context.
doi:10.1136/bmjsem-2021-001156 pmid:34493958 pmcid:PMC8413475 fatcat:wjriztnshrhl5p3eawedf7es4i

Binning microbial genomes using deep learning [article]

Jakob Nybo Nissen, Casper Kaae Sønderby, Jose Juan Almagro Armenteros, Christopher Heje Grønbech, Henrik Bjørn Nielsen, Thomas Nordahl Petersen, Ole Winther, Simon Rasmussen
2018 bioRxiv   pre-print
AbstractIdentification and reconstruction of microbial species from metagenomics wide genome sequencing data is an important and challenging task. Current existing approaches rely on gene or contig co-abundance information across multiple samples and k-mer composition information in the sequences. Here we use recent advances in deep learning to develop an algorithm that uses variational autoencoders to encode co-abundance and compositional information prior to clustering. We show that the deep
more » ... etwork is able to integrate these two heterogeneous datasets without any prior knowledge and that our method outperforms existing state-of-the-art by reconstructing 1.8 - 8 times more highly precise and complete genome bins from three different benchmark datasets. Additionally, we apply our method to a gene catalogue of almost 10 million genes and 1,270 samples from the human gut microbiome. Here we are able to cluster 1.3 - 1.8 million extra genes and reconstruct 117 - 246 more highly precise and complete bins of which 70 bins were completely new compared to previous methods. Our method Variational Autoencoders for Metagenomic Binning (VAMB) is freely available at:
doi:10.1101/490078 fatcat:dz32huqzdvggvnxbwlphda7lwi

Binocular integration of retinal motion information underlies optic flow processing by the cortex [article]

Rune N. Rasmussen, Akihiro Matsumoto, Simon Arvin, Keisuke Yonehara
2020 bioRxiv   pre-print
Locomotion creates various patterns of optic flow on the retina, which provide the observer with information about their movement relative to the environment. However, it is unclear how these optic flow patterns are encoded by the cortex. Here we use two-photon calcium imaging in awake mice to systematically map monocular and binocular responses to horizontal motion in four areas of the visual cortex. We find that neurons selective to translational or rotational optic flow are abundant in
more » ... visual areas, whereas neurons suppressed by binocular motion are more common in the primary visual cortex. Disruption of retinal direction selectivity in Frmd7 mutant mice reduces the number of translation-selective neurons in the primary visual cortex, and translation- and rotation-selective neurons as well as binocular direction-selective neurons in the rostrolateral and anterior visual cortex, blurring the functional distinction between primary and higher visual areas. Thus, optic flow representations in specific areas of the visual cortex rely on binocular integration of motion information from the retina.
doi:10.1101/2020.10.16.342402 fatcat:o2sdoz7k4ze2hbfvdegajzqruu

Rectal hodgkin lymphoma in a patient with ulcerative colitis: a case study

Simon Ladefoged Rasmussen, Christian Thomsen
2015 Diagnostic Pathology  
A case of Hodgkin lymphoma located in the rectum of a patient with ulcerative colitis is described. The patient was a 44 year old male treated with thiopurines for ulcerative colitis for ten years. He was admitted with malaise, weight loss and abdominal pain. Endoscopy revealed a large ulcerative lesion involving the rectum and distal part of the sigmoid colon. Although it macroscopically resembled a rectal cancer, repeated biopsies did not reveal any malignancy. In order to resolve the
more » ... of stenosis and to get the final diagnosis a recto-sigmoid resection was performed. Pathologic examination revealed nodular sclerosis classical Hodgkin lymphoma, positive for Epstein Barr Virus. Subsequent examination revealed disseminated disease involving the pelvic wall, liver, and bone marrow. The patient is currently receiving chemotherapeutic treatment, and follow-up shows disease remission. Hodgkin lymphoma associated with immunosuppressive therapy is rare. However, patients with ulcerative colitis receiving such treatment are at increased risk of lymphoproliferative disordes, potentially due to loss of immunosurveillance and presence of oncogenic viruses (i.e. Epstein-Barr virus). Virtual Slides: The virtual slide(s) for this article can be found here: 6156776351558952
doi:10.1186/s13000-015-0271-7 pmid:25890312 pmcid:PMC4427961 fatcat:7gpbb2tc3fe47bwsvfuhamjkb4

Fe Protein-Independent Substrate Reduction by Nitrogenase MoFe Protein Variants

Karamatullah Danyal, Andrew J. Rasmussen, Stephen M. Keable, Boyd S. Inglet, Sudipta Shaw, Oleg A. Zadvornyy, Simon Duval, Dennis R. Dean, Simone Raugei, John W. Peters, Lance C. Seefeldt
2015 Biochemistry  
The reduction of substrates catalyzed by nitrogenase normally requires nucleotide-dependent Fe protein delivery of electrons to the MoFe protein, which contains the active site FeMo cofactor. Here, it is reported that independent substitution of three amino acids (β-98 Tyr→His , α-64 Tyr→His , and β-99 Phe→His ) located between the P cluster and FeMo cofactor within the MoFe protein endows it with the ability to reduce protons to H 2 , azide to ammonia, and hydrazine to ammonia without the need
more » ... for Fe protein or ATP. Instead, electrons can be provided by the low-potential reductant polyaminocarboxylate-ligated Eu(II) (E m values of −1.1 to −0.84 V vs the normal hydrogen electrode). The crystal structure of the β-98 Tyr→His variant MoFe protein was determined, revealing only small changes near the amino acid substitution that affect the solvent structure and the immediate vicinity between the P cluster and the FeMo cofactor, with no global conformational changes observed. Computational normal-mode analysis of the nitrogenase complex reveals coupling in the motions of the Fe protein and the region of the MoFe protein with these three amino acids, which suggests a possible mechanism for how Fe protein might communicate subtle changes deep within the MoFe protein that profoundly affect intramolecular electron transfer and substrate reduction.
doi:10.1021/acs.biochem.5b00140 pmid:25831270 fatcat:ohk5govwvzhprfixdcrs2uuqru
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