{ "types" : { "Bookmark" : { "pluralLabel" : "Bookmarks" }, "Publication" : { "pluralLabel" : "Publications" }, "GoldStandardPublication" : { "pluralLabel" : "GoldStandardPublications" }, "GoldStandardBookmark" : { "pluralLabel" : "GoldStandardBookmarks" }, "Tag" : { "pluralLabel" : "Tags" }, "User" : { "pluralLabel" : "Users" }, "Group" : { "pluralLabel" : "Groups" }, "Sphere" : { "pluralLabel" : "Spheres" } }, "properties" : { "count" : { "valueType" : "number" }, "date" : { "valueType" : "date" }, "changeDate" : { "valueType" : "date" }, "url" : { "valueType" : "url" }, "id" : { "valueType" : "url" }, "tags" : { "valueType" : "item" }, "user" : { "valueType" : "item" } }, "items" : [ { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/213d070ca717db4ad910b6f698ff75056/simtechpuma", "tags" : [ "EXC2075","PN2","PN2-1A","selected" ], "intraHash" : "13d070ca717db4ad910b6f698ff75056", "interHash" : "f4e9c4247e6172bfe4a2c1d3d3b1202b", "label" : "Stochasticity contributes to explaining minority and majority MOMP during apoptosis", "user" : "simtechpuma", "description" : "", "date" : "2026-02-16 15:04:58", "changeDate" : "2026-02-16 15:04:58", "count" : 5, "pub-type": "article", "journal": "Cell Death & Disease", "year": "2025", "url": "https://doi.org/10.1038/s41419-025-08258-9", "author": [ "Jenny Geiger","Fabian Klötzer","Nadine Pollak","Gavin Fullstone","Markus Rehm" ], "authors": [ {"first" : "Jenny", "last" : "Geiger"}, {"first" : "Fabian", "last" : "Klötzer"}, {"first" : "Nadine", "last" : "Pollak"}, {"first" : "Gavin", "last" : "Fullstone"}, {"first" : "Markus", "last" : "Rehm"} ], "volume": "16","number": "1","pages": "893--","abstract": "Apoptosis dysfunction is linked to diseases like cancer and neurodegenerative disorders. A key event during apoptosis is mitochondrial outer membrane permeabilization (MOMP), which typically proceeds in a rapid all-or-none fashion. If MOMP occurs only in a subset of mitochondria (minority MOMP), it can be sublethal and contribute to tumorigenesis and cancer progression. Similarly, individual mitochondria escaping widespread MOMP (majority MOMP) can allow cancer cells to recover if apoptosis execution fails. How such heterogeneities in mitochondrial MOMP responsiveness arise within cells is incompletely understood. In particular, whether stochasticity in subcellular protein distributions and interactions across cytosol and mitochondria can realistically contribute to mitochondrial MOMP heterogeneity has not yet been studied. To assess this, we sequentially built and experimentally parameterized a particle-based, cell-sized model including cytosolic and mitochondrial compartments, and that featured a reduced interactome of MCL-1, BAK and tBID. High-performance computing enabled cell-scale simulations of protein distributions and interactions to understand how and under which conditions stochasticity could contribute to heterogeneity in MOMP susceptibility. Our results show that stochastic effects strongly predispose sub-pools of fragmented mitochondria to MOMP under low apoptotic stress. At higher apoptotic stress, fractions of small mitochondria were more likely to escape MOMP than large mitochondria. Retrospective quantification of mitochondrial sizes in experimental scenarios of minority and majority MOMP confirmed these findings. We therefore conclude that stochasticity substantially contributes to enabling small or fragmented mitochondria to undergo MOMP in minority MOMP scenarios and to escape MOMP in majority MOMP scenarios.", "issn" : "20414889", "refid" : "Geiger2025", "doi" : "10.1038/s41419-025-08258-9", "bibtexKey": "geiger2025stochasticity" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/25412e286ad50be992694b6b4887dff31/simtechpuma", "tags" : [ "EXC2075","PN2","PN2-7","PN5","PN5-6(II)","selected" ], "intraHash" : "5412e286ad50be992694b6b4887dff31", "interHash" : "5a4875d858175206d6f85d84a00a0456", "label" : "Uncertainty-Aware Surrogate-based Amortized Bayesian Inference for Computationally Expensive Models", "user" : "simtechpuma", "description" : "", "date" : "2026-02-16 15:04:58", "changeDate" : "2026-02-16 15:04:58", "count" : 6, "pub-type": "article", "journal": "Transactions in Machine Learning Research", "year": "2026", "url": "https://openreview.net/pdf?id=aVSoQXbfy1", "author": [ "Stefania Scheurer","Philipp Reiser","Tim Brünnette","Wolfgang Nowak","Anneli Guthke","Paul-Christian Bürkner" ], "authors": [ {"first" : "Stefania", "last" : "Scheurer"}, {"first" : "Philipp", "last" : "Reiser"}, {"first" : "Tim", "last" : "Brünnette"}, {"first" : "Wolfgang", "last" : "Nowak"}, {"first" : "Anneli", "last" : "Guthke"}, {"first" : "Paul-Christian", "last" : "Bürkner"} ], "issn" : "2835-8856", "bibtexKey": "scheurer2026uncertainty" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/268637f883b4bfc6a7d8dc12397ae0f83/simtechpuma", "tags" : [ "EXC2075","PN2","PN2-7","selected" ], "intraHash" : "68637f883b4bfc6a7d8dc12397ae0f83", "interHash" : "969d1c2fbe22848311d4151d231c2a60", "label" : "Uncertainty Quantification and Propagation in Surrogate-based Bayesian Inference", "user" : "simtechpuma", "description" : "", "date" : "2026-02-09 16:44:25", "changeDate" : "2026-02-09 16:44:25", "count" : 5, "pub-type": "article", "journal": "Statistics and Computing", "year": "2025", "url": "", "author": [ "Philipp Reiser","Javier Enrique Aguilar","Anneli Guthke","Paul-Christian Bürkner" ], "authors": [ {"first" : "Philipp", "last" : "Reiser"}, {"first" : "Javier Enrique", "last" : "Aguilar"}, {"first" : "Anneli", "last" : "Guthke"}, {"first" : "Paul-Christian", "last" : "Bürkner"} ], "volume": "35","number": "(3)","pages": "66", "doi" : "10.1007/s11222-025-10597-8", "bibtexKey": "reiser2023uncertainty" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2a3a618982087663a44ed27ab5b14536a/simtechpuma", "tags" : [ "EXC2075","PN2","PN2-7","PN5","PN5-6(II)","selected" ], "intraHash" : "a3a618982087663a44ed27ab5b14536a", "interHash" : "c9ca80dd7e09b8555174c7411d3b9d9a", "label" : "Uncertainty-Aware Surrogate-based Amortized Bayesian Inference for Computationally Expensive Models", "user" : "simtechpuma", "description" : "", "date" : "2026-02-09 16:44:25", "changeDate" : "2026-02-09 16:44:25", "count" : 1, "pub-type": "article", "journal": "Transactions on Machine Learning Research", "year": "2025", "url": "", "author": [ "Stefania Scheurer","Philipp Reiser","Tim Brünette","Wolfgang Nowak","Anneli Guthke","Paul-Christian Bürkner" ], "authors": [ {"first" : "Stefania", "last" : "Scheurer"}, {"first" : "Philipp", "last" : "Reiser"}, {"first" : "Tim", "last" : "Brünette"}, {"first" : "Wolfgang", "last" : "Nowak"}, {"first" : "Anneli", "last" : "Guthke"}, {"first" : "Paul-Christian", "last" : "Bürkner"} ], "volume": "under review", "bibtexKey": "scheurer2025uncertaintyaware" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/22ea9b17dfb5a097ef392c40fe653019d/simtechpuma", "tags" : [ "EXC2075","PN2","PN2-1A","unclear" ], "intraHash" : "2ea9b17dfb5a097ef392c40fe653019d", "interHash" : "9344d4546a208948b4213b3abcd7c8de", "label" : "A pH-sensitive binding modality allows successful transferrin receptor-mediated transcytosis of a bivalent antibody across brain barriers", "user" : "simtechpuma", "description" : "", "date" : "2025-10-22 10:57:20", "changeDate" : "2025-10-22 10:57:20", "count" : 6, "pub-type": "article", "journal": "mAbs","booktitle": "mAbs","publisher":"Taylor & Francis", "year": "2025", "url": "https://doi.org/10.1080/19420862.2025.2563758", "author": [ "Philipp Kuhn","Sabrina Petralla","Fatemeh Dabbagh","Valentina Pegoretti","Walter Muranyi","Hiroshi Ishikawa","Horst Schroten","Roman Fischer","André Frenzel","Thomas Schirrmann","Markus Rehm","Christian Schwerk","Gert Fricker","Roland Kontermann","Gavin Fullstone" ], "authors": [ {"first" : "Philipp", "last" : "Kuhn"}, {"first" : "Sabrina", "last" : "Petralla"}, {"first" : "Fatemeh", "last" : "Dabbagh"}, {"first" : "Valentina", "last" : "Pegoretti"}, {"first" : "Walter", "last" : "Muranyi"}, {"first" : "Hiroshi", "last" : "Ishikawa"}, {"first" : "Horst", "last" : "Schroten"}, {"first" : "Roman", "last" : "Fischer"}, {"first" : "André", "last" : "Frenzel"}, {"first" : "Thomas", "last" : "Schirrmann"}, {"first" : "Markus", "last" : "Rehm"}, {"first" : "Christian", "last" : "Schwerk"}, {"first" : "Gert", "last" : "Fricker"}, {"first" : "Roland", "last" : "Kontermann"}, {"first" : "Gavin", "last" : "Fullstone"} ], "volume": "17","number": "1","pages": "2563758--", "issn" : "19420862", "comment" : "doi: 10.1080/19420862.2025.2563758", "doi" : "10.1080/19420862.2025.2563758", "bibtexKey": "kuhn2025phsensitive" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2152183f0edd23d3a6b697219f2c6ca41/simtechpuma", "tags" : [ "PN2","selected" ], "intraHash" : "152183f0edd23d3a6b697219f2c6ca41", "interHash" : "3afe397a451bce869962d016312aff6a", "label" : "Quantification of training\u2010induced alterations in body composition via automated machine learning analysis of MRI images in the thigh region: A pilot study in young females", "user" : "simtechpuma", "description" : "", "date" : "2025-02-28 16:06:53", "changeDate" : "2025-02-28 16:06:53", "count" : 5, "pub-type": "article", "journal": "Physiological Reports","publisher":"Wiley", "year": "2025", "url": "http://dx.doi.org/10.14814/phy2.70187", "author": [ "Saied Ramedani","Ebru Kelesoglu","Norman Stutzig","Hendrik Von Tengg\u2010Kobligk","Keivan Daneshvar Ghorbani","Tobias Siebert" ], "authors": [ {"first" : "Saied", "last" : "Ramedani"}, {"first" : "Ebru", "last" : "Kelesoglu"}, {"first" : "Norman", "last" : "Stutzig"}, {"first" : "Hendrik", "last" : "Von Tengg\u2010Kobligk"}, {"first" : "Keivan", "last" : "Daneshvar Ghorbani"}, {"first" : "Tobias", "last" : "Siebert"} ], "editor": [ "Tobias Siebert" ], "editors": [ {"first" : "Tobias", "last" : "Siebert"} ], "volume": "13","number": "3","abstract": "AbstractThe maintenance of an appropriate ratio of body fat to muscle mass is essentialfor the preservation of health and performance, as excessive body fat is associatedwith an increased risk of various diseases. Accurate body composition assessmentrequires precise segmentation of structures. In this study we developed a novelautomatic machine learning approach for volumetric segmentation and quantita-tive assessment of MRI volumes and investigated the efficacy of using a machinelearning algorithm to assess muscle, subcutaneous adipose tissue (SAT), and bonevolume of the thigh before and after a strength training. Eighteen healthy, young,female volunteers were randomly allocated to two groups: intervention group(IG) and control group (CG). The IG group followed an 8-week strength endur-ance training plan that was conducted two times per week. Before and after thetraining, the subjects of both groups underwent MRI scanning. The evaluation ofthe image data was performed by a machine learning system which is based ona 3D U-Net- based Convolutional Neural Network. The volumes of muscle, bone,and SAT were each examined using a 2 (GROUP [IG vs. CG]) × 2 (TIME [pre-intervention vs. post-intervention]) analysis of variance (ANOVA) with repeatedmeasures for the factor TIME. The results of the ANOVA demonstrate significantTIME × GROUP interaction effects for the muscle volume (F1,16 = 12.80, p = 0.003,ηP2 = 0.44) with an increase of 2.93% in the IG group and no change in the CG(−0.62%, p = 0.893). There were no significant changes in bone or SAT volumebetween the groups. This study supports the use of artificial intelligence systemsto analyze MRI images as a reliable tool for monitoring training responses onbody composition.", "issn" : "2051-817X", "doi" : "10.14814/phy2.70187", "bibtexKey": "Ramedani_2025" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2d4c6f9a31ee0320fc3be6307a85d6c4e/simtechpuma", "tags" : [ "EXC2075","PN2","selected" ], "intraHash" : "d4c6f9a31ee0320fc3be6307a85d6c4e", "interHash" : "c1587910394340ebda12596b663f7b66", "label" : "Eccentric muscle contractions : from single muscle fibre to whole muscle mechanics", "user" : "simtechpuma", "description" : "", "date" : "2025-02-28 16:06:53", "changeDate" : "2025-02-28 16:06:53", "count" : 5, "pub-type": "article", "journal": "Pflügers Archiv","publisher":"Springer", "year": "2023", "url": "", "author": [ "André Tomalka" ], "authors": [ {"first" : "André", "last" : "Tomalka"} ], "volume": "475","pages": "421-435", "language" : "eng", "issn" : "1432-2013", "doi" : "10.1007/s00424-023-02794-z", "bibtexKey": "tomalka2023eccentric" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/21ad96e0232adfc011d13023ff6e39376/simtechpuma", "tags" : [ "EXC2075","PN2","PN2-1(II)","PN2-1A","selected" ], "intraHash" : "1ad96e0232adfc011d13023ff6e39376", "interHash" : "11d95a9a5753703baaf16b3b75e3ab6c", "label" : "Why Bax detection in >1400 publications might be flawed", "user" : "simtechpuma", "description" : "Why Bax detection in $>1400$ publications might be flawed | Cell Death \\& Disease", "date" : "2025-02-28 16:06:53", "changeDate" : "2025-02-28 16:06:53", "count" : 6, "pub-type": "article", "journal": "Cell Death & Disease", "year": "2024", "url": "https://doi.org/10.1038/s41419-024-07273-6", "author": [ "Kristin Entrop","Senait Wieske","Markus Rehm" ], "authors": [ {"first" : "Kristin", "last" : "Entrop"}, {"first" : "Senait", "last" : "Wieske"}, {"first" : "Markus", "last" : "Rehm"} ], "volume": "15","number": "12","pages": "880", "issn" : "2041-4889", "doi" : "10.1038/s41419-024-07273-6", "bibtexKey": "Entrop2024" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2c7e68ae5f3894d810752300311254ade/simtechpuma", "tags" : [ "EXC2075","PN2","curated","unclear" ], "intraHash" : "c7e68ae5f3894d810752300311254ade", "interHash" : "f87d2c872f2e6f474113b724ada23083", "label" : "A benchmark of muscle models to length changes great and small", "user" : "simtechpuma", "description" : "linked to Projekt Adires", "date" : "2025-02-28 16:06:53", "changeDate" : "2025-02-28 16:06:53", "count" : 16, "pub-type": "article", "journal": "ScienceDirect Elsevier", "year": "2024", "url": "https://www.sciencedirect.com/science/article/pii/S1751616124003722?via%3Dihub", "author": [ "Matthew Millard","Norman Stutzig","Jörg Fehr","Tobias Siebert" ], "authors": [ {"first" : "Matthew", "last" : "Millard"}, {"first" : "Norman", "last" : "Stutzig"}, {"first" : "Jörg", "last" : "Fehr"}, {"first" : "Tobias", "last" : "Siebert"} ], "abstract": "Digital human body models are used to simulate injuries that occur as a result of vehicle collisions, vibration, sports, and falls. Given enough time the body\u2019s musculature can generate force, affect the body\u2019s movements, and change the risk of some injuries. The finite-element code LS-DYNA is often used to simulate the movements and injuries sustained by the digital human body models as a result of an accident. In this work, we evaluate the accuracy of the three muscle models in LS-DYNA (MAT_156, EHTM, and the VEXAT) when simulating a range of experiments performed on isolated muscle: force-length-velocity experiments on maximally and sub-maximally stimulated muscle, active-lengthening experiments, and vibration experiments. The force-length-velocity experiments are included because these conditions are typical of the muscle activity that precedes an accident, while the active-lengthening and vibration experiments mimic conditions that can cause injury. The three models perform similarly during the maximally and sub-maximally activated force-length-velocity experiments, but noticeably differ in response to the active-lengthening and vibration experiments. The VEXAT model is able to generate the enhanced forces of biological muscle during active lengthening, while both the MAT_156 and EHTM produce too little force. In response to vibration, the stiffness and damping of the VEXAT model closely follows the experimental data while the MAT_156 and EHTM models differ substantially. The accuracy of the VEXAT model comes from two additional mechanical structures that are missing in the MAT_156 and EHTM models: viscoelastic cross-bridges, and an active titin filament. To help others build on our work we have made our simulation code publicly available.", "language" : "English", "bemerkung" : "elementare Daten, z.B. Journal fehlen", "doi" : "10.1016/j.jmbbm.2024.106740", "bibtexKey": "millard2024benchmark" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2508330b0e707cab72cde85d5372b57b3/simtechpuma", "tags" : [ "EXC2075","PN2","PN2-6","PN2-6(II)","selected" ], "intraHash" : "508330b0e707cab72cde85d5372b57b3", "interHash" : "ad7bfdc8362fd60c6ac228ce98e15c8c", "label" : "Digitalization of biocatalysis: Best practices to research data management", "user" : "simtechpuma", "description" : "", "date" : "2025-02-28 16:06:53", "changeDate" : "2025-02-28 16:06:53", "count" : 3, "pub-type": "incollection", "series": "Methods in Enzymology","publisher":"Academic Press", "year": "2025", "url": "https://www.sciencedirect.com/science/article/pii/S0076687925000606", "author": [ "Torsten Giess","Jürgen Pleiss" ], "authors": [ {"first" : "Torsten", "last" : "Giess"}, {"first" : "Jürgen", "last" : "Pleiss"} ], "abstract": "The digitalization of biocatalysis presents significant opportunities for advancing research by improving data management, fostering transparency, and enabling more efficient, reproducible experiments. However, this transformation brings challenges, particularly in standardizing and sharing data across diverse platforms and laboratory settings. Managing experimental data and metadata in structured, machine-readable formats is fundamental for integrating automation, while mechanistic modeling and artificial intelligence applications further benefit from well-curated datasets. Creating sustainable, reusable software is also key to the long-term success of biocatalysis projects. Yet, efficient data acquisition remains limited by the lack of universally accepted data formats for analytical instruments. To address these barriers, the best practices presented here focus on optimizing biocatalysis workflows for the FAIR (Findable, Accessible, Interoperable, Reusable) data principles. This includes adopting standardized data exchange formats and sharing reproducible datasets in public repositories, thus enhancing interoperability and reusability. By following these guidelines, researchers can contribute to the digitalization of biocatalysis, facilitating the knowledge sharing and data reuse necessary to support the transition of biocatalysis into a more data-driven field.", "issn" : "0076-6879", "doi" : "https://doi.org/10.1016/bs.mie.2025.01.040", "bibtexKey": "GIESS2025" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/24386f56655faa9b7cc13322ef28d8a24/simtechpuma", "tags" : [ "EXC2075","PN2","PN2-1(II)","PN2-1A","PN3","PN3-11","selected" ], "intraHash" : "4386f56655faa9b7cc13322ef28d8a24", "interHash" : "ab21830497642ce8fdb93068c809c733", "label" : "BCL-2 and BOK regulate apoptosis by interaction of their C-terminal transmembrane domains", "user" : "simtechpuma", "description" : "", "date" : "2025-02-28 16:06:53", "changeDate" : "2025-02-28 16:06:53", "count" : 7, "pub-type": "article", "journal": "EMBO Reports","publisher":"Springer Science and Business Media LLC", "year": "2024", "url": "http://dx.doi.org/10.1038/s44319-024-00206-6", "author": [ "Tobias B Beigl","Alexander Paul","Thomas P Fellmeth","Dang Nguyen","Lynn Barber","Sandra Weller","Benjamin Schäfer","Bernhard F Gillissen","Walter E Aulitzky","Hans-Georg Kopp","Markus Rehm","David W Andrews","Kristyna Pluhackova","Frank Essmann" ], "authors": [ {"first" : "Tobias B", "last" : "Beigl"}, {"first" : "Alexander", "last" : "Paul"}, {"first" : "Thomas P", "last" : "Fellmeth"}, {"first" : "Dang", "last" : "Nguyen"}, {"first" : "Lynn", "last" : "Barber"}, {"first" : "Sandra", "last" : "Weller"}, {"first" : "Benjamin", "last" : "Schäfer"}, {"first" : "Bernhard F", "last" : "Gillissen"}, {"first" : "Walter E", "last" : "Aulitzky"}, {"first" : "Hans-Georg", "last" : "Kopp"}, {"first" : "Markus", "last" : "Rehm"}, {"first" : "David W", "last" : "Andrews"}, {"first" : "Kristyna", "last" : "Pluhackova"}, {"first" : "Frank", "last" : "Essmann"} ], "volume": "25","number": "9","pages": "3896\u20133924", "issn" : "1469-3178", "doi" : "10.1038/s44319-024-00206-6", "bibtexKey": "Beigl_2024" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2a3694399a83c9346ae66fe151dce7e94/simtechpuma", "tags" : [ "EXC2075","PN2","PN2-6","PN2-6(II)","selected" ], "intraHash" : "a3694399a83c9346ae66fe151dce7e94", "interHash" : "975d837ae55dd9dd3eb9e564fd6913c5", "label" : "Influence of water content on thermophysical properties of aqueous glyceline solutions predicted by molecular dynamics simulations", "user" : "simtechpuma", "description" : "", "date" : "2025-02-14 11:17:09", "changeDate" : "2025-02-14 11:17:09", "count" : 6, "pub-type": "article", "journal": "Fluid Phase Equilibria", "year": "2025", "url": "https://www.sciencedirect.com/science/article/pii/S0378381224002991", "author": [ "Marcelle B.M. Spera","Samir Darouich","Jürgen Pleiss","Niels Hansen" ], "authors": [ {"first" : "Marcelle B.M.", "last" : "Spera"}, {"first" : "Samir", "last" : "Darouich"}, {"first" : "Jürgen", "last" : "Pleiss"}, {"first" : "Niels", "last" : "Hansen"} ], "volume": "592","pages": "114324","abstract": "Molecular simulations allow the prediction of a large variety of thermophysical properties for complex mixtures based on one underlying model, i.e. the force field. In the present work static and dynamic properties of aqueous 1:2 choline chloride:glycerol mixtures are computed by molecular dynamics simulations with the aim to report robust simulation protocols that allow for a thorough evaluation of the molecular model with regard to experimental data. In particular for the shear viscosity a rather strong dependence of the results on the simulation method can be found. The simulations do not only provide quantitative data but also insight into the effect of water on the microscopic structure of the fluid. The isobaric thermal expansivity shows a transition from DES-like to water-like behavior beyond a water mole fraction of 0.75. Moreover, inconsistencies in experimental datasets are identified. Molecular dynamics simulations serve as a powerful tool to support the decision for one or the other data set in case of contradictory experimental data.", "orcid" : "0000-0003-1045-8202", "issn" : "0378-3812", "doi" : "https://doi.org/10.1016/j.fluid.2024.114324", "bibtexKey": "SPERA2025114324" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2b962af03d0e70e2009b457665c691400/simtechpuma", "tags" : [ "PN2","PN2-6(II)","selected" ], "intraHash" : "b962af03d0e70e2009b457665c691400", "interHash" : "43db653083278be6b42b11b2642d61c9", "label" : "The STRENDA Biocatalysis Guidelines for cataloguing metadata", "user" : "simtechpuma", "description" : "", "date" : "2025-02-14 11:17:09", "changeDate" : "2025-02-14 11:17:09", "count" : 5, "pub-type": "article", "journal": "Nature Catalysis", "year": "2024", "url": "https://doi.org/10.1038/s41929-024-01261-x", "author": [ "Stephan Malzacher","Dominik Meißner","Jan Range","Zvjezdana Findrik Blažević","Katrin Rosenthal","John M. Woodley","Roland Wohlgemuth","Peter Wied","Bernd Nidetzky","Robert T. Giessmann","Kridsadakorn Prakinee","Pimchai Chaiyen","Andreas S. Bommarius","Johann M. Rohwer","Rodrigo O. M. A. de Souza","Peter J. Halling","Jürgen Pleiss","Carsten Kettner","Dörte Rother" ], "authors": [ {"first" : "Stephan", "last" : "Malzacher"}, {"first" : "Dominik", "last" : "Meißner"}, {"first" : "Jan", "last" : "Range"}, {"first" : "Zvjezdana", "last" : "Findrik Blažević"}, {"first" : "Katrin", "last" : "Rosenthal"}, {"first" : "John M.", "last" : "Woodley"}, {"first" : "Roland", "last" : "Wohlgemuth"}, {"first" : "Peter", "last" : "Wied"}, {"first" : "Bernd", "last" : "Nidetzky"}, {"first" : "Robert T.", "last" : "Giessmann"}, {"first" : "Kridsadakorn", "last" : "Prakinee"}, {"first" : "Pimchai", "last" : "Chaiyen"}, {"first" : "Andreas S.", "last" : "Bommarius"}, {"first" : "Johann M.", "last" : "Rohwer"}, {"first" : "Rodrigo O. M. A.", "last" : "de Souza"}, {"first" : "Peter J.", "last" : "Halling"}, {"first" : "Jürgen", "last" : "Pleiss"}, {"first" : "Carsten", "last" : "Kettner"}, {"first" : "Dörte", "last" : "Rother"} ], "volume": "7","number": "12","pages": "1245--1249","abstract": "Biocatalysis needs improved reproducibility and quality of research reporting. Our interdisciplinary team has developed a flexible and extensible metadata catalogue based on STRENDA guidelines, essential for describing complex experimental setups in biocatalysis. The catalogue is available online via GitHub for community use.", "orcid" : "0000-0003-1045-8202", "issn" : "25201158", "refid" : "Malzacher2024", "doi" : "10.1038/s41929-024-01261-x", "bibtexKey": "malzacher2024strenda" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/20c871f621cfa1fab82d48a1fbeea7d5e/simtechpuma", "tags" : [ "EXC2075","PN2","selected" ], "intraHash" : "0c871f621cfa1fab82d48a1fbeea7d5e", "interHash" : "09e034bb54deccb6ae7d294f7f3efca5", "label" : "Mitochondrial genome variations, mitochondrial-nuclear compatibility, and their association with metabolic diseases", "user" : "simtechpuma", "description" : "", "date" : "2025-02-14 11:14:18", "changeDate" : "2025-02-14 11:14:18", "count" : 7, "pub-type": "article", "journal": "Obesity","publisher":"John Wiley & Sons, Ltd", "year": "2022", "url": "https://onlinelibrary.wiley.com/doi/full/10.1002/oby.23424", "author": [ "Agnieszka H. Ludwig-Słomczyńska","Markus Rehm" ], "authors": [ {"first" : "Agnieszka H.", "last" : "Ludwig-Słomczyńska"}, {"first" : "Markus", "last" : "Rehm"} ], "issn" : "1930-739X", "doi" : "10.1002/OBY.23424", "bibtexKey": "Ludwig-Somczynska2022" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/293dbfd71d89a98b4b0b93df76d9f3ec4/simtechpuma", "tags" : [ "EXC2075","PN2","PN2-8Siebert","selected" ], "intraHash" : "93dbfd71d89a98b4b0b93df76d9f3ec4", "interHash" : "f4b756ccc11536a1ccd58f2bb493eb66", "label" : "Active exoskeleton reduces erector spinae muscle activity during lifting", "user" : "simtechpuma", "description" : "", "date" : "2025-02-14 11:14:18", "changeDate" : "2025-02-14 11:14:18", "count" : 6, "pub-type": "article", "journal": "Frontiers in Bioengineering and Biotechnology", "year": "2023", "url": "https://www.frontiersin.org/articles/10.3389/fbioe.2023.1150170/full", "author": [ "Tobias Walter","Norman Stutzig","Tobias Siebert" ], "authors": [ {"first" : "Tobias", "last" : "Walter"}, {"first" : "Norman", "last" : "Stutzig"}, {"first" : "Tobias", "last" : "Siebert"} ], "editor": [ "Tobias Siebert" ], "editors": [ {"first" : "Tobias", "last" : "Siebert"} ], "volume": "11","abstract": "Neuromuscular control loops feature substantial communication delays, but mammals run robustly even in the most adverse conditions. In vivo experiments and computer simulation results suggest that muscles\u2019 preflex\u2014an immediate mechanical response to a perturbation\u2014could be the critical contributor. Muscle preflexes act within a few milliseconds, an order of magnitude faster than neural reflexes. Their short-lasting action makes mechanical preflexes hard to quantify in vivo. Muscle models, on the other hand, require further improvement of their prediction accuracy during the non-standard conditions of perturbed locomotion. Our study aims to quantify the mechanical work done by muscles during the preflex phase (preflex work) and test their mechanical force modulation. We performed in vitro experiments with biological muscle fibers under physiological boundary conditions, which we determined in computer simulations of perturbed hopping. Our findings show that muscles initially resist impacts with a stereotypical stiffness response\u2014identified as short-range stiffness\u2014regardless of the exact perturbation condition. We then observe a velocity adaptation to the force related to the amount of perturbation similar to a damping response. The main contributor to the preflex work modulation is not the change in force due to a change in fiber stretch velocity (fiber damping characteristics) but the change in magnitude of the stretch due to the leg dynamics in the perturbed conditions. Our results confirm previous findings that muscle stiffness is activity-dependent and show that also damping characteristics are activity-dependent. These results indicate that neural control could tune the preflex properties of muscles in expectation of ground conditions leading to previously inexplicable neuromuscular adaptation speeds.", "language" : "English", "doi" : "10.3389/fbioe.2023.1150170", "bibtexKey": "siebert2023active" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2d9f50320acfea6c088804d94af731c83/simtechpuma", "tags" : [ "EXC2075","PN2","PN2-1B","PN2-9","selected" ], "intraHash" : "d9f50320acfea6c088804d94af731c83", "interHash" : "61d8f0a594585ba150702cb0b6fc9537", "label" : "The impossible challenge of estimating non-existent moments of the Chemical Master Equation", "user" : "simtechpuma", "description" : "", "date" : "2025-02-14 11:14:18", "changeDate" : "2025-02-14 11:14:18", "count" : 7, "pub-type": "article", "journal": "Bioinformatics", "year": "2023", "url": "https://doi.org/10.1093/bioinformatics/btad205", "author": [ "Vincent Wagner","Nicole Radde" ], "authors": [ {"first" : "Vincent", "last" : "Wagner"}, {"first" : "Nicole", "last" : "Radde"} ], "volume": "39","number": "Supplement_1","pages": "i440-i447","abstract": "The Chemical Master Equation (CME) is a set of linear differential equations that describes the evolution of the probability distribution on all possible configurations of a (bio-)chemical reaction system. Since the number of configurations and therefore the dimension of the CME rapidly increases with the number of molecules, its applicability is restricted to small systems. A widely applied remedy for this challenge is moment-based approaches which consider the evolution of the first few moments of the distribution as summary statistics for the complete distribution. Here, we investigate the performance of two moment-estimation methods for reaction systems whose equilibrium distributions encounter fat-tailedness and do not possess statistical moments.We show that estimation via stochastic simulation algorithm (SSA) trajectories lose consistency over time and estimated moment values span a wide range of values even for large sample sizes. In comparison, the method of moments returns smooth moment estimates but is not able to indicate the non-existence of the allegedly predicted moments. We furthermore analyze the negative effect of a CME solution\u2019s fat-tailedness on SSA run times and explain inherent difficulties. While moment-estimation techniques are a commonly applied tool in the simulation of (bio-)chemical reaction networks, we conclude that they should be used with care, as neither the system definition nor the moment-estimation techniques themselves reliably indicate the potential fat-tailedness of the CME\u2019s solution.", "eprint" : "https://academic.oup.com/bioinformatics/article-pdf/39/Supplement\\_1/i440/50741574/btad205.pdf", "issn" : "1367-4811", "doi" : "10.1093/bioinformatics/btad205", "bibtexKey": "10.1093/bioinformatics/btad205" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/21c09ad3a57d45986105107c77d0da5cf/simtechpuma", "tags" : [ "EXC2075","PN2","PN2-8Siebert","selected" ], "intraHash" : "1c09ad3a57d45986105107c77d0da5cf", "interHash" : "539e1f9768e937f368f3546f4de55813", "label" : "Determination of muscle shape deformations of the tibialis anterior during dynamic contractions using 3D ultrasound", "user" : "simtechpuma", "description" : "", "date" : "2025-02-14 11:14:18", "changeDate" : "2025-02-14 11:14:18", "count" : 7, "pub-type": "article", "journal": "Frontiers in Bioengineering and Biotechnology", "year": "2024", "url": "https://www.frontiersin.org/articles/10.3389/fbioe.2024.1388907", "author": [ "Annika S. Sahrmann","Lukas Vosse","Tobias Siebert","Geoffrey G. Handsfield","Oliver Röhrle" ], "authors": [ {"first" : "Annika S.", "last" : "Sahrmann"}, {"first" : "Lukas", "last" : "Vosse"}, {"first" : "Tobias", "last" : "Siebert"}, {"first" : "Geoffrey G.", "last" : "Handsfield"}, {"first" : "Oliver", "last" : "Röhrle"} ], "volume": "12", "issn" : "2296-4185", "doi" : "10.3389/fbioe.2024.1388907", "bibtexKey": "Sahrmann2024c" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2fe432bff3e18e905e35e1c6d83224e5f/simtechpuma", "tags" : [ "EXC2075","PN2","PN2-3(1)","PN3","PN6","PN6-6","selected" ], "intraHash" : "fe432bff3e18e905e35e1c6d83224e5f", "interHash" : "6495de6a63a68795adaeec89fea4b0c6", "label" : "Use of the N\u2013O Bonds in N-Mesyloxyamides and N-Mesyloxyimides To Gain Access to 5-Alkoxy-3,4-dialkyloxazol-2-ones and 3-Hetero-Substituted Succinimides: A Combined Experimental and Theoretical Study", "user" : "simtechpuma", "description" : "", "date" : "2025-02-14 11:14:18", "changeDate" : "2025-02-14 11:14:18", "count" : 6, "pub-type": "article", "journal": "Synthesis", "year": "2023", "url": "", "author": [ "Lucca Pfitzer","Juliane Heitkämper","Johannes Kästner","R. Peters" ], "authors": [ {"first" : "Lucca", "last" : "Pfitzer"}, {"first" : "Juliane", "last" : "Heitkämper"}, {"first" : "Johannes", "last" : "Kästner"}, {"first" : "R.", "last" : "Peters"} ], "volume": "55","number": "26","pages": "2460-2472", "doi" : "10.1055/s-0042-1751447", "bibtexKey": "pfi23" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/201a9d22b6f3646d3a3d7210f346db251/simtechpuma", "tags" : [ "EXC2075","PN2","PN2-2A","misc" ], "intraHash" : "01a9d22b6f3646d3a3d7210f346db251", "interHash" : "2767cc050e2473714b929359f37201f6", "label" : "Optimization of the Groundwater Remediation Process Using a Coupled Genetic Algorithm-Finite Difference Method", "user" : "simtechpuma", "description" : "", "date" : "2025-02-14 11:14:18", "changeDate" : "2025-02-14 11:14:18", "count" : 9, "pub-type": "article", "journal": "Water", "year": "2021", "url": "", "author": [ "S. M. Seyedpour","I. Valizadeh","P. Kirmizakis","R. Doherty","T. Ricken" ], "authors": [ {"first" : "S. M.", "last" : "Seyedpour"}, {"first" : "I.", "last" : "Valizadeh"}, {"first" : "P.", "last" : "Kirmizakis"}, {"first" : "R.", "last" : "Doherty"}, {"first" : "T.", "last" : "Ricken"} ], "volume": "13","number": "3","pages": "383", "file" : "Das Attachment konnte nicht verknüpft werden. Die interne Fehlermeldung lautet: Eine Ausnahme vom Typ \"SwissAcademic.Azure.CitaviWebApiException\" wurde ausgelöst.", "doi" : "10.3390/w13030383", "bibtexKey": "Seyedpour.2021" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/272af99c797370695f57647c06fb10429/simtechpuma", "tags" : [ "EXC2075","PN2","PN2-5","selected" ], "intraHash" : "72af99c797370695f57647c06fb10429", "interHash" : "08a87a4b59f0eec9105c21ec6be71ee4", "label" : "Discovery of NSD2 non-histone substrates and design of a super-substrate", "user" : "simtechpuma", "description" : "", "date" : "2025-02-14 11:14:18", "changeDate" : "2025-02-14 11:14:18", "count" : 7, "pub-type": "article", "journal": "Communications Biology", "year": "2024", "url": "https://doi.org/10.1038/s42003-024-06395-z", "author": [ "Sara Weirich","Denis Kusevic","Philipp Schnee","Jessica Reiter","Jürgen Pleiss","Albert Jeltsch" ], "authors": [ {"first" : "Sara", "last" : "Weirich"}, {"first" : "Denis", "last" : "Kusevic"}, {"first" : "Philipp", "last" : "Schnee"}, {"first" : "Jessica", "last" : "Reiter"}, {"first" : "Jürgen", "last" : "Pleiss"}, {"first" : "Albert", "last" : "Jeltsch"} ], "volume": "7","number": "1","pages": "707--","abstract": "The human protein lysine methyltransferase NSD2 catalyzes dimethylation at H3K36. It has very important roles in development and disease but many mechanistic features and its full spectrum of substrate proteins are unclear. Using peptide SPOT array methylation assays, we investigate the substrate sequence specificity of NSD2 and discover strong readout of residues between G33 (-3) and P38 (+2) on H3K36. Unexpectedly, we observe that amino acid residues different from natural ones in H3K36 are preferred at some positions. Combining four preferred residues led to the development of a super-substrate which is methylated much faster by NSD2 at peptide and protein level. Molecular dynamics simulations demonstrate that this activity increase is caused by distinct hyperactive conformations of the enzyme-peptide complex. To investigate the substrate spectrum of NSD2, we conducted a proteome wide search for nuclear proteins matching the specificity profile and discovered 22 peptide substrates of NSD2. In protein methylation studies, we identify K1033 of ATRX and K819 of FANCM as NSD2 methylation sites and also demonstrate their methylation in human cells. Both these proteins have important roles in DNA repair strengthening the connection of NSD2 and H3K36 methylation to DNA repair.", "orcid" : "0000-0003-1045-8202", "issn" : "23993642", "refid" : "Weirich2024", "doi" : "10.1038/s42003-024-06395-z", "bibtexKey": "weirich2024discovery" } ] }