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Article: The Hypothesis of a "Living Pulse" in Cells.

Walther-Antonio, Marina / Schulze-Makuch, Dirk

2023 Volume 13, Issue 7

Abstract: Motility is a great biosignature and its pattern is characteristic for specific microbes. However, motion does also occur within the cell by the myriads of ongoing processes within the cell and the exchange of gases and nutrients with the outside ... ...

Abstract	Motility is a great biosignature and its pattern is characteristic for specific microbes. However, motion does also occur within the cell by the myriads of ongoing processes within the cell and the exchange of gases and nutrients with the outside environment. Here, we propose that the sum of these processes in a microbial cell is equivalent to a pulse in complex organisms and suggest a first approach to measure the "living pulse" in microorganisms. We emphasize that if a "living pulse" can be shown to exist, it would have far-reaching applications, such as for finding life in extreme environments on Earth and in extraterrestrial locations, as well as making sure that life is not present where it should not be, such as during medical procedures and in the food processing industry.
Language	English
Publishing date	2023-07-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662250-6
ISSN	2075-1729
ISSN	2075-1729
DOI	10.3390/life13071506
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Article ; Online: Memorability of line drawings of scenes: the role of contour properties.

Han, Seohee / Rezanejad, Morteza / Walther, Dirk B

Memory & cognition

2023

Abstract: Why are some images more likely to be remembered than others? Previous work focused on the influence of global, low-level visual features as well as image content on memorability. To better understand the role of local, shape-based contours, we here ... ...

Abstract	Why are some images more likely to be remembered than others? Previous work focused on the influence of global, low-level visual features as well as image content on memorability. To better understand the role of local, shape-based contours, we here investigate the memorability of photographs and line drawings of scenes. We find that the memorability of photographs and line drawings of the same scenes is correlated. We quantitatively measure the role of contour properties and their spatial relationships for scene memorability using a Random Forest analysis. To determine whether this relationship is merely correlational or if manipulating these contour properties causes images to be remembered better or worse, we split each line drawing into two half-images, one with high and the other with low predicted memorability according to the trained Random Forest model. In a new memorability experiment, we find that the half-images predicted to be more memorable were indeed remembered better, confirming a causal role of shape-based contour features, and, in particular, T junctions in scene memorability. We performed a categorization experiment on half-images to test for differential access to scene content. We found that half-images predicted to be more memorable were categorized more accurately. However, categorization accuracy for individual images was not correlated with their memorability. These results demonstrate that we can measure the contributions of individual contour properties to scene memorability and verify their causal involvement with targeted image manipulations, thereby bridging the gap between low-level features and scene semantics in our understanding of memorability.
Language	English
Publishing date	2023-10-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	185691-1
ISSN	1532-5946 ; 0090-502X
ISSN (online)	1532-5946
ISSN	0090-502X
DOI	10.3758/s13421-023-01478-4
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Article ; Online: Functional in vitro diversity of an intrinsically disordered plant protein during freeze-thawing is encoded by its structural plasticity.

Hernández-Sánchez, Itzell / Rindfleisch, Tobias / Alpers, Jessica / Dulle, Martin / Garvey, Christopher J / Knox-Brown, Patrick / Miettinen, Markus S / Nagy, Gergely / Pusterla, Julio M / Rekas, Agata / Shou, Keyun / Stadler, Andreas M / Walther, Dirk / Wolff, Martin / Zuther, Ellen / Thalhammer, Anja

Protein science : a publication of the Protein Society

2024 Volume 33, Issue 5, Page(s) e4989

Abstract: Intrinsically disordered late embryogenesis abundant (LEA) proteins play a central role in the tolerance of plants and other organisms to dehydration brought upon, for example, by freezing temperatures, high salt concentration, drought or desiccation, ... ...

Abstract	Intrinsically disordered late embryogenesis abundant (LEA) proteins play a central role in the tolerance of plants and other organisms to dehydration brought upon, for example, by freezing temperatures, high salt concentration, drought or desiccation, and many LEA proteins have been found to stabilize dehydration-sensitive cellular structures. Their conformational ensembles are highly sensitive to the environment, allowing them to undergo conformational changes and adopt ordered secondary and quaternary structures and to participate in formation of membraneless organelles. In an interdisciplinary approach, we discovered how the functional diversity of the Arabidopsis thaliana LEA protein COR15A found in vitro is encoded in its structural repertoire, with the stabilization of membranes being achieved at the level of secondary structure and the stabilization of enzymes accomplished by the formation of oligomeric complexes. We provide molecular details on intra- and inter-monomeric helix-helix interactions, demonstrate how oligomerization is driven by an α-helical molecular recognition feature (α-MoRF) and provide a rationale that the formation of noncanonical, loosely packed, right-handed coiled-coils might be a recurring theme for homo- and hetero-oligomerization of LEA proteins.
MeSH term(s)	Arabidopsis Proteins/chemistry ; Arabidopsis Proteins/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis/chemistry ; Arabidopsis/metabolism ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/metabolism ; Intrinsically Disordered Proteins/genetics ; Freezing ; Models, Molecular ; Protein Multimerization ; Protein Structure, Secondary
Chemical Substances	Arabidopsis Proteins ; Intrinsically Disordered Proteins ; COR15 protein, Arabidopsis
Language	English
Publishing date	2024-04-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.4989
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Zs.A 3407: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: The Development of Attention to Objects and Scenes: From Object-Biased to Unbiased.

Darby, Kevin P / Deng, Sophia W / Walther, Dirk B / Sloutsky, Vladimir M

Child development

2020 Volume 92, Issue 3, Page(s) 1173–1186

Abstract: Selective attention is the ability to focus on goal-relevant information while filtering out irrelevant information. This work examined the development of selective attention to natural scenes and objects with a rapid serial visual presentation paradigm. ...

Abstract	Selective attention is the ability to focus on goal-relevant information while filtering out irrelevant information. This work examined the development of selective attention to natural scenes and objects with a rapid serial visual presentation paradigm. Children (N = 69, ages 4-6 years) and adults (N = 80) were asked to attend to either objects or scenes, while ignoring the other type of stimulus. A multinomial processing tree model was used to decompose selective attention into focusing and filtering components. The results suggest that attention is object-biased in children, due to difficulty filtering attention to goal-irrelevant objects, whereas attention in adults is relatively unbiased. The findings suggest important developmental asymmetries in selective attention to scenes and objects.
MeSH term(s)	Adult ; Attention ; Bias ; Child ; Child, Preschool ; Humans ; Visual Perception
Language	English
Publishing date	2020-11-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	215602-7
ISSN	1467-8624 ; 0009-3920
ISSN (online)	1467-8624
ISSN	0009-3920
DOI	10.1111/cdev.13469
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Article ; Online: Shape-Based Measures Improve Scene Categorization.

Rezanejad, Morteza / Wilder, John / Walther, Dirk B / Jepson, Allan D / Dickinson, Sven / Siddiqi, Kaleem

IEEE transactions on pattern analysis and machine intelligence

2024 Volume 46, Issue 4, Page(s) 2041–2053

Abstract: Converging evidence indicates that deep neural network models that are trained on large datasets are biased toward color and texture information. Humans, on the other hand, can easily recognize objects and scenes from images as well as from bounding ... ...

Abstract	Converging evidence indicates that deep neural network models that are trained on large datasets are biased toward color and texture information. Humans, on the other hand, can easily recognize objects and scenes from images as well as from bounding contours. Mid-level vision is characterized by the recombination and organization of simple primary features into more complex ones by a set of so-called Gestalt grouping rules. While described qualitatively in the human literature, a computational implementation of these perceptual grouping rules is so far missing. In this article, we contribute a novel set of algorithms for the detection of contour-based cues in complex scenes. We use the medial axis transform (MAT) to locally score contours according to these grouping rules. We demonstrate the benefit of these cues for scene categorization in two ways: (i) Both human observers and CNN models categorize scenes most accurately when perceptual grouping information is emphasized. (ii) Weighting the contours with these measures boosts performance of a CNN model significantly compared to the use of unweighted contours. Our work suggests that, even though these measures are computed directly from contours in the image, current CNN models do not appear to extract or utilize these grouping cues.
Language	English
Publishing date	2024-03-06
Publishing country	United States
Document type	Journal Article
ISSN	1939-3539
ISSN (online)	1939-3539
DOI	10.1109/TPAMI.2023.3333352
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Article ; Online: Experience transforms crossmodal object representations in the anterior temporal lobes.

Li, Aedan Yue / Ladyka-Wojcik, Natalia / Qazilbash, Heba / Golestani, Ali / Walther, Dirk B / Martin, Chris B / Barense, Morgan

eLife

2024 Volume 13

Abstract: Combining information from multiple senses is essential to object recognition, core to the ability to learn concepts, make new inferences, and generalize across distinct entities. Yet how the mind combines sensory input into coherent crossmodal ... ...

Abstract	Combining information from multiple senses is essential to object recognition, core to the ability to learn concepts, make new inferences, and generalize across distinct entities. Yet how the mind combines sensory input into coherent crossmodal representations - the
Language	English
Publishing date	2024-04-22
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.83382
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Article ; Online: Updated Phylogeny and Protein Structure Predictions Revise the Hypothesis on the Origin of MADS-box Transcription Factors in Land Plants.

Qiu, Yichun / Li, Zhen / Walther, Dirk / Köhler, Claudia

Molecular biology and evolution

2023 Volume 40, Issue 9

Abstract: ... in land plants are categorized into Type I (M-type) and Type II (MIKC-type). Type I and II genes have been ... became MIKC-type before the divergence of Streptophyta. Subsequently in the MRCA of land plants, M-type ...

Abstract	MADS-box transcription factors (TFs), among the first TFs extensively studied, exhibit a wide distribution across eukaryotes and play diverse functional roles. Varying by domain architecture, MADS-box TFs in land plants are categorized into Type I (M-type) and Type II (MIKC-type). Type I and II genes have been considered orthologous to the SRF and MEF2 genes in animals, respectively, presumably originating from a duplication before the divergence of eukaryotes. Here, we exploited the increasing availability of eukaryotic MADS-box sequences and reassessed their evolution. While supporting the ancient duplication giving rise to SRF- and MEF2-types, we found that Type I and II genes originated from the MEF2-type genes through another duplication in the most recent common ancestor (MRCA) of land plants. Protein structures predicted by AlphaFold2 and OmegaFold support our phylogenetic analyses, with plant Type I and II TFs resembling the MEF2-type structure, rather than SRFs. We hypothesize that the ancestral SRF-type TFs were lost in the MRCA of Archaeplastida (the kingdom Plantae sensu lato). The retained MEF2-type TFs acquired a Keratin-like domain and became MIKC-type before the divergence of Streptophyta. Subsequently in the MRCA of land plants, M-type TFs evolved from a duplicated MIKC-type precursor through loss of the Keratin-like domain, leading to the Type I clade. Both Type I and II TFs expanded and functionally differentiated in concert with the increasing complexity of land plant body architecture. The recruitment of these originally stress-responsive TFs into developmental programs, including those underlying reproduction, may have facilitated the adaptation to the terrestrial environment.
MeSH term(s)	Animals ; Transcription Factors ; Phylogeny ; Embryophyta/genetics ; Keratins ; Eukaryota
Chemical Substances	Transcription Factors ; Keratins (68238-35-7)
Language	English
Publishing date	2023-08-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msad194
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Zs.A 2137: Show issues

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Article: Editorial: Metabolome Informatics and Statistics: Current State and Emerging Trends.

Carroll, Adam James / Salek, Reza M / Arita, Masanori / Kopka, Joachim / Walther, Dirk

Frontiers in bioengineering and biotechnology

2016 Volume 4, Page(s) 63

Language	English
Publishing date	2016-07-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2719493-0
ISSN	2296-4185
ISSN	2296-4185
DOI	10.3389/fbioe.2016.00063
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Article: Nanobiosensing with graphene and carbon quantum dots: Recent advances.

Walther, Brandon K / Dinu, Cerasela Zoica / Guldi, Dirk M / Sergeyev, Vladimir G / Creager, Stephen E / Cooke, John P / Guiseppi-Elie, Anthony

Materials today (Kidlington, England)

2020 Volume 39, Page(s) 23–46

Abstract: Graphene and carbon quantum dots (GQDs and CQDs) are relatively new nanomaterials that have demonstrated impact in multiple different fields thanks to their unique quantum properties and excellent biocompatibility. Biosensing, analyte detection and ... ...

Abstract	Graphene and carbon quantum dots (GQDs and CQDs) are relatively new nanomaterials that have demonstrated impact in multiple different fields thanks to their unique quantum properties and excellent biocompatibility. Biosensing, analyte detection and monitoring wherein a key feature is coupled molecular recognition and signal transduction, is one such field that is being greatly advanced by the use of GQDs and CQDs. In this review, recent progress on the development of biotransducers and biosensors enabled by the creative use of GQDs and CQDs is reviewed, with special emphasis on how these materials specifically interface with biomolecules to improve overall analyte detection. This review also introduces nano-enabled biotransducers and different biosensing configurations and strategies, as well as highlights key properties of GQDs and CQDs that are pertinent to functional biotransducer design. Following relevant introductory material, the literature is surveyed with emphasis on work performed over the last 5 years. General comments and suggestions to advance the direction and potential of the field are included throughout the review. The strategic purpose is to inspire and guide future investigations into biosensor design for quality and safety, as well as serve as a primer for developing GQD- and CQD-based biosensors.
Language	English
Publishing date	2020-05-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2083513-9
ISSN	1873-4103 ; 1369-7021
ISSN (online)	1873-4103
ISSN	1369-7021
DOI	10.1016/j.mattod.2020.04.008
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Article: Fatigue Assessment of Twin Wire Arc Sprayed and Machine Hammer-Peened ZnAl4 Coatings on S355 JRC+C Substrate.

Milz, Michael P / Wirtz, Andreas / Abdulgader, Mohamed / Biermann, Dirk / Tillmann, Wolfgang / Walther, Frank

Materials (Basel, Switzerland)

2022 Volume 15, Issue 3

Abstract: Structural elements for applications in maritime environments, especially offshore installations, are subjected to various stresses, such as mechanical loads caused by wind or waves and corrosive attacks, e.g., by seawater, mist and weather. Thermally ... ...

Abstract	Structural elements for applications in maritime environments, especially offshore installations, are subjected to various stresses, such as mechanical loads caused by wind or waves and corrosive attacks, e.g., by seawater, mist and weather. Thermally sprayed ZnAl coatings are often used for maritime applications, mainly due to good corrosion protection properties. Machine hammer peening (MHP) has the potential to increase fatigue and corrosion fatigue resistance of ZnAl coatings by adjusting various material properties such as hardness, porosity and roughness. This study investigates the fatigue behavior of twin wire arc sprayed and MHP post-treated ZnAl4 coatings. Unalloyed steel (S355 JRC+C) was selected as substrate material and tested as a reference. MHP achieved the desired improvements in material properties with increased hardness, decreased roughness and uniform coating thickness. Multiple and constant amplitude tests have been carried out to evaluate the fatigue capability of coating systems. In the high cycle fatigue regime, the additional MHP post-treatment led to an improvement of the lifetime in comparison to pure sandblasted specimens. The surface was identified as a crack initiation point. ZnAl coating and MHP post-treatment are suitable to improve the fatigue behavior in the high cycle fatigue regime compared to uncoated specimens.
Language	English
Publishing date	2022-02-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2487261-1
ISSN	1996-1944
ISSN	1996-1944
DOI	10.3390/ma15031182
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