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Article: The Road Less Traveled: Uncovering the Convergence Toward Specific Pleiotropic Phenotypes in Aging.

Stoeger, Thomas

bioRxiv : the preprint server for biology

2023

Abstract: Aging is a complex process influenced by a wide range of environmental and molecular factors. Despite this complexity, individuals tend to age in highly similar ways, leading to the question of what drives this convergence. Recent research, including my ... ...

Abstract	Aging is a complex process influenced by a wide range of environmental and molecular factors. Despite this complexity, individuals tend to age in highly similar ways, leading to the question of what drives this convergence. Recent research, including my own discoveries, suggests that the length of transcript molecules plays a crucial role in age-dependent changes to the transcriptome. Drawing inspiration from the road trip analogy of cellular transcription, I propose that a non-linear scaling law drives convergence towards specific pleiotropic phenotypes in biological aging. This scaling law is based on the notion that molecular changes observed during aging may reflect unspecific damage to cellular physiology. By validating this hypothesis, I can improve our understanding of biological aging and identify new candidate compounds for anti-aging interventions, as well as re-identify one known intervention. This work has actionable implications for improving human health and extending lifespans.
Language	English
Publishing date	2023-03-29
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.03.28.534472
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Article ; Online: Meta-Research: Understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results.

Richardson, Reese / Tejedor Navarro, Heliodoro / Amaral, Luis A Nunes / Stoeger, Thomas

eLife

2024 Volume 12

Abstract: Present-day publications on human genes primarily feature genes that already appeared in many publications prior to completion of the Human Genome Project in 2003. These patterns persist despite the subsequent adoption of high-throughput technologies, ... ...

Abstract	Present-day publications on human genes primarily feature genes that already appeared in many publications prior to completion of the Human Genome Project in 2003. These patterns persist despite the subsequent adoption of high-throughput technologies, which routinely identify novel genes associated with biological processes and disease. Although several hypotheses for bias in the selection of genes as research targets have been proposed, their explanatory powers have not yet been compared. Our analysis suggests that understudied genes are systematically abandoned in favor of better-studied genes between the completion of -omics experiments and the reporting of results. Understudied genes remain abandoned by studies that cite these -omics experiments. Conversely, we find that publications on understudied genes may even accrue a greater number of citations. Among 45 biological and experimental factors previously proposed to affect which genes are being studied, we find that 33 are significantly associated with the choice of hit genes presented in titles and abstracts of -omics studies. To promote the investigation of understudied genes, we condense our insights into a tool,
MeSH term(s)	Humans ; Aging ; Biological Assay ; Physicians
Language	English
Publishing date	2024-03-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.93429
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Time is ticking faster for long genes in aging.

Soheili-Nezhad, Sourena / Ibáñez-Solé, Olga / Izeta, Ander / Hoeijmakers, Jan H J / Stoeger, Thomas

Trends in genetics : TIG

2024 Volume 40, Issue 4, Page(s) 299–312

Abstract: Recent studies of aging organisms have identified a systematic phenomenon, characterized by a negative correlation between gene length and their expression in various cell types, species, and diseases. We term this phenomenon gene-length-dependent ... ...

Abstract	Recent studies of aging organisms have identified a systematic phenomenon, characterized by a negative correlation between gene length and their expression in various cell types, species, and diseases. We term this phenomenon gene-length-dependent transcription decline (GLTD) and suggest that it may represent a bottleneck in the transcription machinery and thereby significantly contribute to aging as an etiological factor. We review potential links between GLTD and key aging processes such as DNA damage and explore their potential in identifying disease modification targets. Notably, in Alzheimer's disease, GLTD spotlights extremely long synaptic genes at chromosomal fragile sites (CFSs) and their vulnerability to postmitotic DNA damage. We suggest that GLTD is an integral element of biological aging.
MeSH term(s)	Humans ; Alzheimer Disease/genetics ; DNA Damage/genetics
Language	English
Publishing date	2024-03-21
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	619240-3
ISSN	1362-4555 ; 0168-9525 ; 0168-9479
ISSN (online)	1362-4555
ISSN	0168-9525 ; 0168-9479
DOI	10.1016/j.tig.2024.01.009
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Article: Meta-Research: understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results.

Richardson, Reese Ak / Tejedor Navarro, Heliodoro / Amaral, Luis A Nunes / Stoeger, Thomas

bioRxiv : the preprint server for biology

2024

Abstract	Present-day publications on human genes primarily feature genes that already appeared in many publications prior to completion of the Human Genome Project in 2003. These patterns persist despite the subsequent adoption of high-throughput technologies, which routinely identify novel genes associated with biological processes and disease. Although several hypotheses for bias in the selection of genes as research targets have been proposed, their explanatory powers have not yet been compared. Our analysis suggests that understudied genes are systematically abandoned in favor of better-studied genes between the completion of -omics experiments and the reporting of results. Understudied genes remain abandoned by studies that cite these -omics experiments. Conversely, we find that publications on understudied genes may even accrue a greater number of citations. Among 45 biological and experimental factors previously proposed to affect which genes are being studied, we find that 33 are significantly associated with the choice of hit genes presented in titles and abstracts of - omics studies. To promote the investigation of understudied genes we condense our insights into a tool,
Language	English
Publishing date	2024-02-05
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.02.28.530483
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Article ; Online: The characteristics of early-stage research into human genes are substantially different from subsequent research.

Stoeger, Thomas / Nunes Amaral, Luís A

PLoS biology

2022 Volume 20, Issue 1, Page(s) e3001520

Abstract: Throughout the last 2 decades, several scholars observed that present day research into human genes rarely turns toward genes that had not already been extensively investigated in the past. Guided by hypotheses derived from studies of science and ... ...

Abstract	Throughout the last 2 decades, several scholars observed that present day research into human genes rarely turns toward genes that had not already been extensively investigated in the past. Guided by hypotheses derived from studies of science and innovation, we present here a literature-wide data-driven meta-analysis to identify the specific scientific and organizational contexts that coincided with early-stage research into human genes throughout the past half century. We demonstrate that early-stage research into human genes differs in team size, citation impact, funding mechanisms, and publication outlet, but that generalized insights derived from studies of science and innovation only partially apply to early-stage research into human genes. Further, we demonstrate that, presently, genome biology accounts for most of the initial early-stage research, while subsequent early-stage research can engage other life sciences fields. We therefore anticipate that the specificity of our findings will enable scientists and policymakers to better promote early-stage research into human genes and increase overall innovation within the life sciences.
MeSH term(s)	Genome, Human ; History, 20th Century ; History, 21st Century ; Human Genetics/economics ; Human Genetics/history ; Human Genetics/methods ; Humans
Language	English
Publishing date	2022-01-06
Publishing country	United States
Document type	Historical Article ; Journal Article ; Meta-Analysis ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3001520
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Article: Highly Stable Self-Cleaning Paints Based on Waste-Valorized PNC-Doped TiO

Maqbool, Qaisar / Favoni, Orlando / Wicht, Thomas / Lasemi, Niusha / Sabbatini, Simona / Stöger-Pollach, Michael / Ruello, Maria Letizia / Tittarelli, Francesca / Rupprechter, Günther

ACS catalysis

2024 Volume 14, Issue 7, Page(s) 4820–4834

Abstract: Adding photocatalytically active ... ...

Abstract	Adding photocatalytically active TiO
Language	English
Publishing date	2024-03-15
Publishing country	United States
Document type	Journal Article
ISSN	2155-5435
ISSN	2155-5435
DOI	10.1021/acscatal.3c06203
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Article ; Online: Microalgae-derived Co

Sidorowicz, Agnieszka / Yigit, Nevzat / Wicht, Thomas / Stöger-Pollach, Michael / Concas, Alessandro / Orrù, Roberto / Cao, Giacomo / Rupprechter, Günther

RSC advances

2024 Volume 14, Issue 7, Page(s) 4575–4586

Abstract: Efficient carbon monoxide oxidation is important to reduce its impacts on both human health and the environment. Following a sustainable synthesis route toward new catalysts, nanosized ... ...

Abstract	Efficient carbon monoxide oxidation is important to reduce its impacts on both human health and the environment. Following a sustainable synthesis route toward new catalysts, nanosized Co
Language	English
Publishing date	2024-02-05
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d4ra00343h
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Book ; Online: Upper and lower bounds for the Lipschitz constant of random neural networks

Geuchen, Paul / Heindl, Thomas / Stöger, Dominik / Voigtlaender, Felix

2023

Abstract: Empirical studies have widely demonstrated that neural networks are highly sensitive to small, adversarial perturbations of the input. The worst-case robustness against these so-called adversarial examples can be quantified by the Lipschitz constant of ... ...

Abstract	Empirical studies have widely demonstrated that neural networks are highly sensitive to small, adversarial perturbations of the input. The worst-case robustness against these so-called adversarial examples can be quantified by the Lipschitz constant of the neural network. In this paper, we study upper and lower bounds for the Lipschitz constant of random ReLU neural networks. Specifically, we assume that the weights and biases follow a generalization of the He initialization, where general symmetric distributions for the biases are permitted. For shallow neural networks, we characterize the Lipschitz constant up to an absolute numerical constant. For deep networks with fixed depth and sufficiently large width, our established upper bound is larger than the lower bound by a factor that is logarithmic in the width.
Keywords	Statistics - Machine Learning ; Computer Science - Machine Learning ; Mathematics - Probability ; 68T07 ; 26A16 ; 60B20 ; 60G15
Subject code	629
Publishing date	2023-11-02
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Criminal and Civil Responsibility of the Donor in a Case of Transmission of Malaria by a Blood Transfusion in a Nonendemic Country.

Wagner, Thomas / Stadlbauer, Vanessa / Stöger, Karl / Schorna, Karin / Zink, Michael

Transfusion medicine and hemotherapy : offizielles Organ der Deutschen Gesellschaft fur Transfusionsmedizin und Immunhamatologie

2022 Volume 49, Issue 4, Page(s) 230–233

Abstract: Introduction: The blood donation process is strictly regulated by law. The process includes the necessity of a medical history taken to determine if a donor is suitable to donate, which shall guarantee both donor and recipient safety. Supplementary ... ...

Abstract	Introduction: The blood donation process is strictly regulated by law. The process includes the necessity of a medical history taken to determine if a donor is suitable to donate, which shall guarantee both donor and recipient safety. Supplementary screening for a limited number of infections is performed by antibody (HIV, HCV, syphilis) or antigen (HBV) tests or NAT (HIV, HCV, HBV). Case presentation: With regard to a possible infection due to (sexual) risk behavior or foreign travel, blood donation facilities are predominantly dependent on information provided by the donor. This is especially true for malaria in nonendemic areas such as Europe. Transmission of malaria by a blood transfusion in a nonendemic country that led to fulminant septic shock and death of the patient happened. Discussion: From a legal perspective, the donor thus assumes a high level of responsibility with regard to the accuracy and completeness of the information provided on the donor questionnaire. Incorrect information may, as in this Austrian case reported, result in civil or criminal responsibility of the donor.
Language	English
Publishing date	2022-06-10
Publishing country	Switzerland
Document type	Case Reports
ZDB-ID	2100848-6
ISSN	1660-3818 ; 1660-3796
ISSN (online)	1660-3818
ISSN	1660-3796
DOI	10.1159/000525103
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Article: The Value of the First Clinical Impression as Assessed by 18 Observations in Patients Presenting to the Emergency Department.

Tschoellitsch, Thomas / Krummenacker, Stefan / Dünser, Martin W / Stöger, Roland / Meier, Jens

Journal of clinical medicine

2023 Volume 12, Issue 2

Abstract: The first clinical impression of emergency patients conveys a myriad of information that has been incompletely elucidated. In this prospective, observational study, the value of the first clinical impression, assessed by 18 observations, to predict the ... ...

Abstract	The first clinical impression of emergency patients conveys a myriad of information that has been incompletely elucidated. In this prospective, observational study, the value of the first clinical impression, assessed by 18 observations, to predict the need for timely medical attention, the need for hospital admission, and in-hospital mortality in 1506 adult patients presenting to the triage desk of an emergency department was determined. Machine learning models were used for statistical analysis. The first clinical impression could predict the need for timely medical attention [area under the receiver operating characteristic curve (AUC ROC), 0.73; p = 0.01] and hospital admission (AUC ROC, 0.8; p = 0.004), but not in-hospital mortality (AUC ROC, 0.72; p = 0.13). The five most important features informing the prediction models were age, ability to walk, admission by emergency medical services, lying on a stretcher, breathing pattern, and bringing a suitcase. The inability to walk at triage presentation was highly predictive of both the need for timely medical attention (p < 0.001) and the need for hospital admission (p < 0.001). In conclusion, the first clinical impression of emergency patients presenting to the triage desk can predict the need for timely medical attention and hospital admission. Important components of the first clinical impression were identified.
Language	English
Publishing date	2023-01-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662592-1
ISSN	2077-0383
ISSN	2077-0383
DOI	10.3390/jcm12020724
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