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  1. Article ; Online: Exploring the Protein Sequence Space with Global Generative Models.

    Romero-Romero, Sergio / Lindner, Sebastian / Ferruz, Noelia

    Cold Spring Harbor perspectives in biology

    2023  Volume 15, Issue 11

    Abstract: Recent advancements in specialized large-scale architectures for training images and language have profoundly impacted the field of computer vision and natural language processing (NLP). Language models, such as the recent ChatGPT and GPT-4, have ... ...

    Abstract Recent advancements in specialized large-scale architectures for training images and language have profoundly impacted the field of computer vision and natural language processing (NLP). Language models, such as the recent ChatGPT and GPT-4, have demonstrated exceptional capabilities in processing, translating, and generating human language. These breakthroughs have also been reflected in protein research, leading to the rapid development of numerous new methods in a short time, with unprecedented performance. Several of these models have been developed with the goal of generating sequences in novel regions of the protein space. In this work, we provide an overview of the use of protein generative models, reviewing (1) language models for the design of novel artificial proteins, (2) works that use non-transformer architectures, and (3) applications in directed evolution approaches.
    Language English
    Publishing date 2023-11-01
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 1943-0264
    ISSN (online) 1943-0264
    DOI 10.1101/cshperspect.a041471
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Thoraxdrainage beim Thoraxtrauma – Empfehlungen der interdisziplinären Arbeitsgemeinschaft Thoraxtrauma der Deutschen Gesellschaft für Thoraxchirurgie (DGT) und der Deutschen Gesellschaft für Unfallchirurgie (DGU).

    Becker, Lars / Schulz-Drost, Stefan / Schreyer, Christof / Lindner, Sebastian

    Zentralblatt fur Chirurgie

    2023  Volume 148, Issue 1, Page(s) 57–66

    Abstract: For unstable patients with chest trauma, the chest tube is the method of choice for the treatment of a relevant pneumothorax or haemothorax. In the case of a tension pneumothorax, needle decompression with a cannula of at least 5 cm length should be ... ...

    Title translation Chest Tube in Thoracic Trauma - Recommendations of the Interdisciplinary Thoracic Trauma Task Group of the German Society for Thoracic Surgery (DGT) and the German Trauma Society (DGU).
    Abstract For unstable patients with chest trauma, the chest tube is the method of choice for the treatment of a relevant pneumothorax or haemothorax. In the case of a tension pneumothorax, needle decompression with a cannula of at least 5 cm length should be performed, directly followed by the insertion of a chest tube. The evaluation of the patient should be performed primarily with a clinical examination, a chest X-ray and sonography, but the gold standard of diagnostic testing is computed tomography (CT).A small-bore chest tube (e.g. 14 French) should be used in stable patients, while unstable patients should receive a large-bore drain (24 French or larger). Insertion of chest drains has a high complication rate of between 5% and 25%, and incorrect positioning of the tube is the most common complication. However, incorrect positioning can usually only be reliably detected or ruled out with a CT scan, and chest X-rays proofed to be insufficient to answer this question. Therapy should be carried out with mild suction of approximately 20 cmH
    MeSH term(s) Humans ; Thoracic Surgery ; Chest Tubes ; Thoracic Surgical Procedures ; Thoracic Injuries/diagnostic imaging ; Thoracic Injuries/surgery ; Hemothorax/diagnostic imaging ; Hemothorax/etiology
    Language German
    Publishing date 2023-02-27
    Publishing country Germany
    Document type English Abstract ; Journal Article
    ZDB-ID 200935-3
    ISSN 1438-9592 ; 0044-409X
    ISSN (online) 1438-9592
    ISSN 0044-409X
    DOI 10.1055/a-1975-0243
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Book ; Online: Exploring the Protein Sequence Space with Global Generative Models

    Romero-Romero, Sergio / Lindner, Sebastian / Ferruz, Noelia

    2023  

    Abstract: Recent advancements in specialized large-scale architectures for training image and language have profoundly impacted the field of computer vision and natural language processing (NLP). Language models, such as the recent ChatGPT and GPT4 have ... ...

    Abstract Recent advancements in specialized large-scale architectures for training image and language have profoundly impacted the field of computer vision and natural language processing (NLP). Language models, such as the recent ChatGPT and GPT4 have demonstrated exceptional capabilities in processing, translating, and generating human languages. These breakthroughs have also been reflected in protein research, leading to the rapid development of numerous new methods in a short time, with unprecedented performance. Language models, in particular, have seen widespread use in protein research, as they have been utilized to embed proteins, generate novel ones, and predict tertiary structures. In this book chapter, we provide an overview of the use of protein generative models, reviewing 1) language models for the design of novel artificial proteins, 2) works that use non-Transformer architectures, and 3) applications in directed evolution approaches.

    Comment: 16 pages, 4 figures, 2 tables
    Keywords Quantitative Biology - Biomolecules ; Computer Science - Machine Learning
    Subject code 004
    Publishing date 2023-05-03
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  4. Article ; Online: Okkulter und residueller Hämatothorax nach Thoraxtrauma – Empfehlungen der interdisziplinären Arbeitsgruppe Thoraxtrauma der Sektion NIS der Deutschen Gesellschaft für Unfallchirurgie (DGU) und der Deutschen Gesellschaft für Thoraxchirurgie (DGT).

    Krämer, Sebastian / Graeff, Pascal / Lindner, Sebastian / Walles, Thorsten / Becker, Lars

    Zentralblatt fur Chirurgie

    2022  Volume 148, Issue 1, Page(s) 67–73

    Abstract: The management of occult and retained haemothorax is challenging for all involved in the care of polytrauma patients in terms of diagnosis and treatment. The focus of decision making is preventing sequelae such as pleural empyema and avoiding a trapped ... ...

    Title translation Occult and Retained Haemothorax - Recommendations of the Interdisciplinary Thoracic Trauma Task Group of the German Trauma Society (DGU - Section NIS) and the German Society for Thoracic Surgery (DGT).
    Abstract The management of occult and retained haemothorax is challenging for all involved in the care of polytrauma patients in terms of diagnosis and treatment. The focus of decision making is preventing sequelae such as pleural empyema and avoiding a trapped lung. An interdisciplinary task force of the German Society for Thoracic Surgery (DGT) and the German Trauma Society (DGU) on thoracic trauma offers recommendations for post-trauma care of patients with occult and/or retained haemothorax, as based on a comprehensive literature review.
    MeSH term(s) Humans ; Thoracic Surgery ; Hemothorax/surgery ; Thoracic Injuries/surgery ; Multiple Trauma/diagnosis ; Thoracic Surgical Procedures ; Germany
    Language German
    Publishing date 2022-12-05
    Publishing country Germany
    Document type Review ; English Abstract ; Journal Article
    ZDB-ID 200935-3
    ISSN 1438-9592 ; 0044-409X
    ISSN (online) 1438-9592
    ISSN 0044-409X
    DOI 10.1055/a-1972-3352
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: [No title information]

    Becker, Lars / Schulz-Drost, Stefan / Schreyer, Christof / Lindner, Sebastian

    Zentralblatt für Chirurgie - Zeitschrift für Allgemeine, Viszeral-, Thorax- und Gefäßchirurgie

    2023  Volume 148, Issue 01, Page(s) 57–66

    Abstract: Die Anlage einer Thoraxdrainage ist zwar grundsätzlich eine einfache, aber oft lebensrettende Notfallmaßnahme. Trotz der Häufigkeit der Prozedur zeigen sich jedoch Unsicherheiten im Umgang mit daraus resultierend hoher Komplikationsrate. Für ... ...

    Abstract Die Anlage einer Thoraxdrainage ist zwar grundsätzlich eine einfache, aber oft lebensrettende Notfallmaßnahme. Trotz der Häufigkeit der Prozedur zeigen sich jedoch Unsicherheiten im Umgang mit daraus resultierend hoher Komplikationsrate. Für alle Beteiligten stellt sowohl die Diagnostik, die Indikationsstellung und die Anlage selbst, wie auch das nachfolgende Management der Drainage eine wiederkehrende Herausforderung dar. Die Unter-AG Lungenverletzung der interdisziplinären AG (Arbeitsgemeinschaft) Thoraxtrauma der Deutschen Gesellschaft für Thoraxchirurgie (DGT) und Deutschen Gesellschaft für Unfallchirurgie (DGU) erarbeitete konsensuelle Behandlungsempfehlungen basierend auf einer Systematic-Review-like Literaturrecherche (MEDLINE via PubMed von 1997 bis 2022). Mit der aktuell vorliegenden Recherche konnten 60 repräsentative Arbeiten identifiziert werden, die Empfehlungen zulassen, jedoch meist nur einen niedrigen Evidenzgrad aufweisen. Die Empfehlungen sind nicht mit Evidenzgraden hinterlegt, sondern haben zunächst Konsenscharakter. Für den instabilen Patienten mit Thoraxtrauma stellt die Thoraxdrainage das Mittel der Wahl zur Entlastung eines Pneumothorax oder Hämatothorax dar. Beim Spannungspneumothorax sollte eine initiale Entlastungspunktion mit einer mindestens 5 cm langen Kanüle, gefolgt von der Anlage einer Thoraxdrainage erfolgen. Diagnostik und Beurteilung des Patienten sollten primär und im Verlauf durch die klinische Untersuchung, eine Röntgenuntersuchung des Thorax sowie eine Thoraxsonografie erfolgen, Goldstandard der Diagnostik ist jedoch die Computertomografie (CT). Beim kreislaufstabilen Patienten soll eine kleinlumige Drainage (z. B. 14 Charrière [Charr]) verwendet werden, instabile Patienten sollten eine großlumige Drainage erhalten. Thoraxdrainagen besitzen eine hohe Komplikationsrate zwischen 5% und 25%. Häufig sind insbesondere Fehlpositionierungen im Rahmen der Anlage. Eine Fehllage kann jedoch meist nur im CT sicher erkannt oder ausgeschlossen werden. Eine Therapie sollte mit mildem Sog erfolgen, ein Abklemmen vor Entfernung ist nicht zielführend. Der Drainagenzug kann sowohl am Ende der Inspiration oder Exspiration sicher erfolgen. Zur Verringerung der hohen Komplikationsrate sollte vermehrt der Fokus auf die Ausbildung und das Training der Anwender gelegt werden.
    Keywords Thoraxdrainage ; Thoraxchirurgie ; Thoraxtrauma ; chest tube ; thoracic surgery ; thoracic trauma ; chest drain
    Language German
    Publishing date 2023-02-01
    Publisher Georg Thieme Verlag KG
    Publishing place Stuttgart ; New York
    Document type Article
    ZDB-ID 200935-3
    ISSN 1438-9592 ; 0044-409X
    ISSN (online) 1438-9592
    ISSN 0044-409X
    DOI 10.1055/a-1975-0243
    Database Thieme publisher's database

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  6. Book ; Thesis: Zwischen Öffnung und Abgrenzung

    Lindner, Sebastian

    die Geschichte des innerdeutschen Kulturabkommens 1973-1986

    (Forschungen zur DDR-Gesellschaft)

    2015  

    Institution Christoph Links Verlag
    Author's details Sebastian Lindner
    Series title Forschungen zur DDR-Gesellschaft
    Keywords Kulturpolitik ; Kulturbeziehungen ; Kulturabkommen ; Deutschland
    Language German
    Size 248 S., 210 mm x 148 mm
    Publisher Links
    Publishing place Berlin
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Univ., Diss.--Leipzig, 2012
    Note Literaturverz. S. 238-244
    ISBN 3861538601 ; 9783861538608
    Database Former special subject collection: coastal and deep sea fishing

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  7. Book ; Online ; Thesis: An information system for predicting the influx of spontaneous volunteers at operating sites in natural disasters

    Lindner, Sebastian [Verfasser] / Sackmann, Stefan [Gutachter] / Peters, Ralf [Gutachter]

    2022  

    Author's details Sebastian Lindner ; Gutachter: Stefan Sackmann, Ralf Peters
    Keywords Soziale Probleme, Sozialarbeit ; Social problems, Social work
    Subject code sg360
    Language English
    Publisher Universitäts- und Landesbibliothek Sachsen-Anhalt
    Publishing place Halle (Saale)
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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  8. Article: [No title information]

    Krämer, Sebastian / Graeff, Pascal / Lindner, Sebastian / Walles, Thorsten / Becker, Lars

    Zentralblatt für Chirurgie - Zeitschrift für Allgemeine, Viszeral-, Thorax- und Gefäßchirurgie

    2022  Volume 148, Issue 01, Page(s) 67–73

    Abstract: Der Versorgung okkulter und residueller Hämatothoraces (synonym retinierte/residuale Hämothoraces) stellt für die an der Polytraumaversorgung Beteiligten sowohl in Aspekten der Diagnostik als auch der Therapie eine wiederkehrende ... ...

    Abstract Der Versorgung okkulter und residueller Hämatothoraces (synonym retinierte/residuale Hämothoraces) stellt für die an der Polytraumaversorgung Beteiligten sowohl in Aspekten der Diagnostik als auch der Therapie eine wiederkehrende Herausforderung dar. Diese ergibt sich selten aus einer unmittelbaren Notfallsituation, sondern vielmehr daraus, wie mögliche Folgeerscheinungen eines Pleuraempyems und einer fixierten Lunge vermieden werden können. Die interdisziplinäre Arbeitsgruppe der Deutschen Gesellschaft für Thoraxchirurgie (DGT) und Deutschen Gesellschaft für Unfallchirurgie (DGU) zur Thoraxtraumaversorgung unterstützt die Ausarbeitung einer Empfehlung basierend auf einer umfassenden Literaturrecherche.
    Keywords Hämatothorax ; Thoraxtrauma ; Polytrauma ; Pleuraempyem ; Thoraxdrainage ; hemothorax ; thoracic trauma ; pleural empyema ; chest tube ; retained hemothorax
    Language German
    Publishing date 2022-12-05
    Publisher Georg Thieme Verlag KG
    Publishing place Stuttgart ; New York
    Document type Article
    ZDB-ID 200935-3
    ISSN 1438-9592 ; 0044-409X
    ISSN (online) 1438-9592
    ISSN 0044-409X
    DOI 10.1055/a-1972-3352
    Database Thieme publisher's database

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  9. Book ; Thesis: Die Mühen der Ebene

    Lindner, Sebastian

    die Verhandlungen zum Kulturabkommen zwischen der Bundesrepublik Deutschland und der DDR 1973 - 1986

    2012  

    Author's details vorgelegt von Sebastian Lindner
    Language German
    Size III, 325 Bl.
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Univ., Diss.--Leipzig, 2012
    Database Former special subject collection: coastal and deep sea fishing

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  10. Article ; Online: A deep-learning workflow to predict upper tract urothelial carcinoma protein-based subtypes from H&E slides supporting the prioritization of patients for molecular testing.

    Angeloni, Miriam / van Doeveren, Thomas / Lindner, Sebastian / Volland, Patrick / Schmelmer, Jorina / Foersch, Sebastian / Matek, Christian / Stoehr, Robert / Geppert, Carol I / Heers, Hendrik / Wach, Sven / Taubert, Helge / Sikic, Danijel / Wullich, Bernd / van Leenders, Geert Jlh / Zaburdaev, Vasily / Eckstein, Markus / Hartmann, Arndt / Boormans, Joost L /
    Ferrazzi, Fulvia / Bahlinger, Veronika

    The journal of pathology. Clinical research

    2024  Volume 10, Issue 2, Page(s) e12369

    Abstract: Upper tract urothelial carcinoma (UTUC) is a rare and aggressive, yet understudied, urothelial carcinoma (UC). The more frequent UC of the bladder comprises several molecular subtypes, associated with different targeted therapies and overlapping with ... ...

    Abstract Upper tract urothelial carcinoma (UTUC) is a rare and aggressive, yet understudied, urothelial carcinoma (UC). The more frequent UC of the bladder comprises several molecular subtypes, associated with different targeted therapies and overlapping with protein-based subtypes. However, if and how these findings extend to UTUC remains unclear. Artificial intelligence-based approaches could help elucidate UTUC's biology and extend access to targeted treatments to a wider patient audience. Here, UTUC protein-based subtypes were identified, and a deep-learning (DL) workflow was developed to predict them directly from routine histopathological H&E slides. Protein-based subtypes in a retrospective cohort of 163 invasive tumors were assigned by hierarchical clustering of the immunohistochemical expression of three luminal (FOXA1, GATA3, and CK20) and three basal (CD44, CK5, and CK14) markers. Cluster analysis identified distinctive luminal (N = 80) and basal (N = 42) subtypes. The luminal subtype mostly included pushing, papillary tumors, whereas the basal subtype diffusely infiltrating, non-papillary tumors. DL model building relied on a transfer-learning approach by fine-tuning a pre-trained ResNet50. Classification performance was measured via three-fold repeated cross-validation. A mean area under the receiver operating characteristic curve of 0.83 (95% CI: 0.67-0.99), 0.8 (95% CI: 0.62-0.99), and 0.81 (95% CI: 0.65-0.96) was reached in the three repetitions. High-confidence DL-based predicted subtypes showed significant associations (p < 0.001) with morphological features, i.e. tumor type, histological subtypes, and infiltration type. Furthermore, a significant association was found with programmed cell death ligand 1 (PD-L1) combined positive score (p < 0.001) and FGFR3 mutational status (p = 0.002), with high-confidence basal predictions containing a higher proportion of PD-L1 positive samples and high-confidence luminal predictions a higher proportion of FGFR3-mutated samples. Testing of the DL model on an independent cohort highlighted the importance to accommodate histological subtypes. Taken together, our DL workflow can predict protein-based UTUC subtypes, associated with the presence of targetable alterations, directly from H&E slides.
    MeSH term(s) Humans ; Urinary Bladder Neoplasms/diagnosis ; Urinary Bladder Neoplasms/genetics ; Urinary Bladder Neoplasms/chemistry ; Carcinoma, Transitional Cell/diagnosis ; Carcinoma, Transitional Cell/genetics ; Urologic Neoplasms/diagnosis ; Urologic Neoplasms/genetics ; Retrospective Studies ; B7-H1 Antigen ; Artificial Intelligence ; Deep Learning ; Workflow ; Biomarkers, Tumor/analysis ; Molecular Diagnostic Techniques
    Chemical Substances B7-H1 Antigen ; Biomarkers, Tumor
    Language English
    Publishing date 2024-03-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2814357-7
    ISSN 2056-4538 ; 2056-4538
    ISSN (online) 2056-4538
    ISSN 2056-4538
    DOI 10.1002/2056-4538.12369
    Database MEDical Literature Analysis and Retrieval System OnLINE

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