bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autoantibody binding and unique enzyme-substrate intermediate conformation of human transglutaminase 3
Authors: Heggelund Julie Elisabeth , Das Saykat , Stamnaes Jorunn , Iversen Rasmus , Sollid Ludvig M. 
Published: October 2023

AbstractTransglutaminase 3 (TG3), the autoantigen of dermatitis herpetiformis (DH), is a calcium dependent enzyme that targets glutamine residues in polypeptides for either transamidation or deamidation modifications. To become catalytically active TG3 requires proteolytic cleavage between the core domain and two C-terminal β-barrels (C1C2). Here, we report four X-ray crystal structures representing inactive and active conformations of human TG3 in complex with a TG3-specific Fab fragment of a DH patient derived antibody. We demonstrate that cleaved TG3, upon binding of a substrate-mimicking inhibitor, undergoes a large conformational change as a β-sheet in the catalytic core domain moves and C1C2 detaches. The unique enzyme-substrate conformation of TG3 without C1C2 is recognized by DH autoantibodies. The findings support a model where B-cell receptors of TG3-specific B cells bind and internalize TG3-gluten enzyme-substrate complexes thereby facilitating gluten-antigen presentation, T-cell help and autoantibody production.
Warming indirectly simplifies food webs through effects on apex predators
Authors: O’Gorman Eoin J. , Zhao Lei , Kordas Rebecca L. , Dudgeon Steve , Woodward Guy 
Published: October 2023

AbstractWarming alters ecosystems through direct physiological effects on organisms and indirect effects via biotic interactions, but their relative impacts in the wild are unknown due to the difficulty in warming natural environments. Here we bridge this gap by embedding manipulative field experiments within a natural stream temperature gradient to test whether warming and apex fish predators have interactive effects on freshwater ecosystems. Fish exerted cascading effects on algal production and microbial decomposition via both green and brown pathways in the food web, but only under warming. Neither temperature nor the presence of fish altered food web structure alone, but connectance and mean trophic level declined as consumer species were lost when both drivers acted together. A mechanistic model indicates that this temperature-induced trophic cascade is determined primarily by altered interactions, which cautions against extrapolating the impacts of warming from reductionist approaches that do not consider the wider food web.
Hippocampal neurons code individual episodic memories in humans
Authors: Kolibius Luca D. , Roux Frederic , Parish George , Ter Wal Marije , Van Der Plas Mircea , Chelvarajah Ramesh , Sawlani Vijay , Rollings David T. , Lang Johannes D. , Gollwitzer Stephanie , Walther Katrin , Hopfengärtner Rüdiger , Kreiselmeyer Gernot , Hamer Hajo , Staresina Bernhard P. , Wimber Maria , Bowman Howard , Hanslmayr Simon 
Published: October 2023

AbstractThe hippocampus is an essential hub for episodic memory processing. However, how human hippocampal single neurons code multi-element associations remains unknown. In particular, it is debated whether each hippocampal neuron represents an invariant element within an episode or whether single neurons bind together all the elements of a discrete episodic memory. Here we provide evidence for the latter hypothesis. Using single-neuron recordings from a total of 30 participants, we show that individual neurons, which we term episode-specific neurons, code discrete episodic memories using either a rate code or a temporal firing code. These neurons were observed exclusively in the hippocampus. Importantly, these episode-specific neurons do not reflect the coding of a particular element in the episode (that is, concept or time). Instead, they code for the conjunction of the different elements that make up the episode.
Audience synchronies in live concerts illustrate the embodiment of music experience
Authors: Tschacher Wolfgang , Greenwood Steven , Ramakrishnan Sekhar , Tröndle Martin , Wald-Fuhrmann Melanie , Seibert Christoph , Weining Christian , Meier Deborah 
Published: October 2023

AbstractA study of 132 audience members of three classical public concerts (all three staged the same chamber music pieces by Ludwig van Beethoven, Brett Dean, and Johannes Brahms) had the goal of analyzing the physiological and motor responses of audiences. It was assumed that the music would induce synchronous physiology and movement in listeners (induction synchrony). In addition to hypothesizing that such synchronies would be present, we expected that they were linked to participants’ aesthetic experiences, their affect and personality traits, which were assessed by questionnaires before and after the concerts. Clear evidence was found of physiological synchrony (heart rate, respiration rate, skin conductance response) as well as movement synchrony of the audiences, whereas breathing behavior was not synchronized. Thus the audiences of the three concerts resonated with the music, their music perception was embodied. There were links between the bodily synchrony and aesthetic experiences: synchrony, especially heart-rate synchrony, was higher when listeners felt moved emotionally and inspired by a piece, and were immersed in the music. Personality traits were also associated with the individual contributions to induction synchrony.
Environmental influences on induction of itching and scratching using immersive virtual reality
Authors: van de Burgt Emmy W. T. , van der Mijn Robbert , Fabbri Sara , Lorist Monicque M. 
Published: October 2023

AbstractChronic itching is a serious and uncomfortable condition. The scratch response might result in a vicious cycle of alternating itching and scratching. To develop psychological interventions for people suffering from chronic itching and to break the vicious itch-scratching-itch cycle, it is important to elucidate which environmental factors trigger itch sensations. Virtual reality (VR) techniques provide a useful tool to examine specific content characteristics in a three-dimensional (3D VR) environment and their influences on itch sensations and scratching behaviour. This article describes two experiments in which we focused on the effects of environmental information on itching and scratching behaviour. Additionally, in the second experiment, we examined the influence of having a chronic skin condition on sensitivity to itch induction. We found evidence for the importance of the content of audio–visual materials for the effectiveness in inducing feelings of itch in the observers. In both experiments, we observed significantly higher levels of perceived itch in the itch-inducing conditions than in the control condition. Moreover, the results showed that elevated levels of perceived itch were associated with an increase in scratching behaviours, which was especially salient in the contagious itch condition, in which perceived itch was accompanied by a significant increase in the number of scratches. Experiment 2 additionally showed increased perceived itch levels in participants who reported having a chronic skin condition, reflecting higher sensitivity to itch-inducing audio–visual stimuli in this group than in participants without a chronic skin condition. Based on the results we concluded that directing attention towards itch- or scratch aspects of related information in the environment and to the consequences for one’s own skin are effective tools to induce itch sensations and scratching behaviour. This knowledge provides tools for developing novel strategies in advising and treating people suffering from chronic itching and breaking the vicious itch-scratching-itch cycle.
Modeling the space-time correlation of pulsed twin beams
Authors: Gatti Alessandra , Jedrkiewicz Ottavia , Brambilla Enrico 
Published: October 2023

AbstractEntangled twin-beams generated by parametric down-conversion are among the favorite sources for imaging-oriented applications, due their multimodal nature in space and time. However, a satisfactory theoretical description is still lacking. In this work we propose a semi-analytic model which aims to bridge the gap between time-consuming numerical simulations and the unrealistic plane-wave pump theory. The model is used to study the quantum correlation and the coherence in the angle-frequency domain of the parametric emission, and demonstrates a $$g^{{1/2}}$$

g

1
/
2

growth of their size as the gain g increases, with a corresponding contraction of the space-time distribution. These predictions are systematically compared with the results of stochastic numerical simulations, performed in the Wigner representation, of the full model equations: an excellent agreement is shown even for parameters well outside the expected limit of validity of the model.
Game-theoretical description of the go-or-grow dichotomy in tumor development for various settings and parameter constellations
Authors: Dwivedi Shalu , Glock Christina , Germerodt Sebastian , Stark Heiko , Schuster Stefan 
Published: October 2023

AbstractA medically important feature of several types of tumors is their ability to “decide” between staying at a primary site in the body or leaving it and forming metastases. The present theoretical study aims to provide a better understanding of the ultimate reasons for this so-called “go-or-grow” dichotomy. To that end, we use game theory, which has proven to be useful in analyzing the competition between tumors and healthy tissues or among different tumor cells. We begin by determining the game types in the Basanta–Hatzikirou–Deutsch model, depending on the parameter values. Thereafter, we suggest and analyze five modified variants of the model. For example, in the basic model, the deadlock game, Prisoner’s Dilemma, and hawk-dove game can occur. The modified versions lead to several additional game types, such as battle of the sexes, route-choice, and stag-hunt games. For some game types, all cells are predicted to stay on their original site (“grow phenotype”), while for other types, only a certain fraction stay and the other cells migrate away (“go phenotype”). If the nutrient supply at a distant site is high, all the cells are predicted to go. We discuss our predictions in terms of the pros and cons of caloric restriction and limitations of the supply of vitamins or methionine. Our results may help devise treatments to prevent metastasis.
Enhanced spectral resolution for correlated spectroscopic imaging using inner-product and covariance transform: a pilot analysis of metabolites and lipids in breast cancer in vivo
Authors: Joy Ajin , Thomas M. Albert 
Published: October 2023

AbstractAcquisition duration of correlated spectroscopy in vivo can be longer due to a large number of t1 increments along the indirect (F1) dimension. Limited number of t1 increments on the other hand leads to poor spectral resolution along F1. Covariance transformation (CT) instead of Fourier transform along t1 is an alternative way of increasing the resolution of the 2D COSY spectrum. Prospectively undersampled five-dimensional echo-planar correlated spectroscopic imaging (EP-COSI) data from ten malignant patients and ten healthy women were acquired and reconstructed using compressed sensing. The COSY spectrum at each voxel location was then generated using FFT, CT and a variant of CT called Inner Product (IP). Metabolite and lipid ratios were computed with respect to water from unsuppressed one-dimensional spectrum. The effects of t1-ridging artifacts commonly seen with FFT were not observed with CT/IP. Statistically significant differences were observed in the fat cross peaks measured with CT/IP/FFT. Spectral resolution was increased ~ 8.5 times (~ 19.53 Hz in FFT, ~ 2.32 Hz in CT/IP) without affecting the spectral width along F1 was possible with CT/IP. CT and IP enabled substantially increased F1 resolution effectively with significant gain in scan time and reliable measure of unsaturation index as a biomarker for malignant breast cancer.
New fossil data reveal evolutionary pathways within the genus Trichoneura Loew, 1850 (Diptera, Limoniidae)
Authors: Kopeć Katarzyna , Kania-Kłosok Iwona , Zhang Qingqing , Krzemiński Wiesław 
Published: October 2023

AbstractNew inclusions of Trichoneura preserved in Upper Cretaceous (Cenomanian) Kachin amber allow the description of a new subgenus, Burmania subgen. nov., and four new species: Trichoneura (Burmania) burmitensis subgen. et sp. nov., Trichoneura (Burmania) chungkuni subgen. et sp. nov., Trichoneura (Burmania) sevciki subgen. et sp. nov. and Trichoneura (Burmania) wangi subgen. et sp. nov. The species differ mainly by the morphology of the hypopygium or wing venation but also the construction of the antenna. Based on a comparison of the wing venation and the morphology of the hypopygium it was possible to describe features which are characteristic of the new subgenus, especially the presence of vein R3+4. Moreover, it was possible to elucidate the evolutionary pattern of Trichoneura with two distinct extant and extinct branches. Trichoneura (Trichoneura) canadensis from Upper Cretaceous Canadian amber is transferred to the new subgenus Burmania.
Climate warming accelerates somatic growth of an Arctic fish species in high-latitude lakes
Authors: Kotowych Nicholas , Smalås Aslak , Amundsen Per-Arne , Primicerio Raul 
Published: October 2023

AbstractHigh-latitude aquatic ecosystems are responding to rapid climate warming. A longer ice-free season with higher water temperatures may accelerate somatic growth in lake ectotherms, leading to widespread ecological implications. In fish, rising temperatures are expected to boost rates of food intake and conversion, and predictions based on empirical relationships between temperature and growth suggest a substantial increase in fish growth rates during the last decades. Fish abundance negatively affects growth by limiting food availability. This field study addresses the effects of climate warming on growth of a subarctic population of Arctic charr (Salvelinus alpinus (L.) over nearly 40 years. Juvenile growth of 680 individuals of Arctic charr, was reconstructed by sclerochronological analysis using sagittal otoliths sampled annually from the early 1980s to 2016. Statistical modelling revealed a positive effect of water temperature, and a negative effect of abundance on somatic growth in juvenile individuals. Temperature dependence in growth was significant for average and fast-growing individuals across all investigated age classes. These findings suggest that, as temperatures rise, somatic growth of Arctic charr will increase in high latitude lakes. Climate warming will thus influence cold water fish life history and size-structured interactions, with important consequences for their populations and ecosystems.
Temporal serum metabolomic and lipidomic analyses distinguish patients with access-related hand disability following arteriovenous fistula creation
Authors: Khattri Ram B. , Louis Lauryn Z. , Kim Kyoungrae , Anderson Erik M. , Fazzone Brian , Harland Kenneth C. , Hu Qiongyao , O’Malley Kerri A. , Berceli Scott A. , Wymer James , Ryan Terence E. , Scali Salvatore T. 
Published: October 2023

AbstractFor end-stage kidney disease (ESKD) patients, hemodialysis requires durable vascular access which is often surgically created using an arteriovenous fistula (AVF). However, some ESKD patients that undergo AVF placement develop access-related hand dysfunction (ARHD) through unknown mechanisms. In this study, we sought to determine if changes in the serum metabolome could distinguish ESKD patients that develop ARHD from those that have normal hand function following AVF creation. Forty-five ESKD patients that underwent first-time AVF creation were included in this study. Blood samples were obtained pre-operatively and 6-weeks post-operatively and metabolites were extracted and analyzed using nuclear magnetic resonance spectroscopy. Patients underwent thorough examination of hand function at both timepoints using the following assessments: grip strength manometry, dexterity, sensation, motor and sensory nerve conduction testing, hemodynamics, and the Disabilities of the Arm, Shoulder, and Hand (DASH) questionnaire. Nineteen of the forty-five patients displayed overt weakness using grip strength manometry (P < 0.0001). Unfortunately, the serum metabolome was indistinguishable between patients with and without weakness following AVF surgery. However, a significant correlation was found between the change in tryptophan levels and the change in grip strength suggesting a possible role of tryptophan-derived uremic metabolites in post-AVF hand-associated weakness. Compared to grip strength, changes in dexterity and sensation were smaller than those observed in grip strength, however, post-operative decreases in phenylalanine, glycine, and alanine were unique to patients that developed signs of motor or sensory disability following AVF creation.
The potential of UAV and very high-resolution satellite imagery for yellow and stem rust detection and phenotyping in Ethiopia
Authors: Blasch Gerald , Anberbir Tadesse , Negash Tamirat , Tilahun Lidiya , Belayineh Fikrte Yirga , Alemayehu Yoseph , Mamo Girma , Hodson David P. , Rodrigues Francelino A. 
Published: October 2023

AbstractVery high (spatial and temporal) resolution satellite (VHRS) and high-resolution unmanned aerial vehicle (UAV) imagery provides the opportunity to develop new crop disease detection methods at early growth stages with utility for early warning systems. The capability of multispectral UAV, SkySat and Pleiades imagery as a high throughput phenotyping (HTP) and rapid disease detection tool for wheat rusts is assessed. In a randomized trial with and without fungicide control, six bread wheat varieties with differing rust resistance were monitored using UAV and VHRS. In total, 18 spectral features served as predictors for stem and yellow rust disease progression and associated yield loss. Several spectral features demonstrated strong predictive power for the detection of combined wheat rust diseases and the estimation of varieties’ response to disease stress and grain yield. Visible spectral (VIS) bands (Green, Red) were more useful at booting, shifting to VIS–NIR (near-infrared) vegetation indices (e.g., NDVI, RVI) at heading. The top-performing spectral features for disease progression and grain yield were the Red band and UAV-derived RVI and NDVI. Our findings provide valuable insight into the upscaling capability of multispectral sensors for disease detection, demonstrating the possibility of upscaling disease detection from plot to regional scales at early growth stages.
Risk of incident autoimmune diseases in patients with newly diagnosed psoriatic disease: a nationwide population-based study
Authors: Jung Joon Min , Kim Ye-Jee , Lee Woo Jin , Won Chong Hyun , Lee Mi Woo , Chang Sung Eun 
Published: October 2023

AbstractThere are limited large population-based cohort studies on the risk of incident autoimmune diseases among patients with newly diagnosed psoriatic disease. The objective of this study was to assess the risk of autoimmune diseases in patients with newly diagnosed psoriatic disease. Using the Korean National Health Insurance Service database, patients with newly diagnosed psoriatic disease between 2007 and 2019 were included. Comparators were randomly selected and matched according to age and sex. A total of 321,354 patients with psoriatic disease and 321,354 matched comparators were included in this study. Patients with psoriatic disease had a significantly higher risk of Crohn’s disease [adjusted hazard ratio (aHR), 1.95; 95% confidence interval (CI) 1.42–2.67], ulcerative colitis (aHR, 1.65; 95% CI 1.39–1.96), systemic lupus erythematosus (aHR, 1.86; 95% CI 1.34–2.57), rheumatoid arthritis (aHR, 1.63; 95% CI 1.52–1.76), ankylosing spondylitis (aHR, 2.32; 95% CI 1.95–2.77), alopecia areata (aHR, 1.41; 95% CI 1.35–1.46), and type 1 diabetes (aHR, 1.23; 95% CI 1.11–1.37). However, the risk of Graves’ disease, Hashimoto’s disease, Sjögren’s syndrome, and systemic sclerosis was not significantly different between the groups. In conclusion, patients with newly diagnosed psoriatic disease may have a significantly increased risk of incident autoimmune diseases.
Evaluation and validation of reference genes for RT-qPCR gene expression in Naegleria gruberi
Authors: Martín-Pérez Tania , Köhsler Martina , Walochnik Julia 
Published: October 2023

AbstractNaegleria gruberi is a free-living amoeboflagellate commonly found in freshwater and in soils around the world. It is a non-pathogenic relative of Naegleria fowleri, which is the etiologic agent of Primary Amoebic Meningoencephalitis (PAM). PAM occurs world-wide and it is considered a rare disease, but its fatality rate is high (96%) mainly because of delay in initiation of treatment due to misdiagnosis and lack of a specific treatment. The analysis of gene expression by quantitative real-time PCR in N. gruberi could be a highly efficient means to understand the pathogenicity of N. fowleri and also to find drug targets. Accurate RT-qPCR analysis requires correct normalization of gene expression data using reference genes (RG), whose expression should be constant under different experimental conditions. In this study, six genes, representing the most frequently used housekeeping genes, were selected for evaluation as reference genes in N. gruberi. The expression and stability of these genes was evaluated employing four algorithms (geNorm, NormFinder, BestKeeper and RefFinder). This work shows significant variations of the stability of RGs depending on the algorithms employed and on the experimental conditions (i.e. logarithmic, stationary, heat-shock and oxidative stress). The geNorm, NormFinder and RefFinder analysis of all the experimental conditions in combination revealed that ACT and G6PD were the most stable RGs. While BestKeeper analysis showed that 18S and TBP were the most stable RGs. Moreover, normalization of HSP90 gene expression with the most stable RGs resulted in an upregulation whereas when the normalization was done with the unstable RGs, the gene expression was not reliable. Hence, the implications of this study are relevant to gene expression studies in N. gruberi.
Elucidation of lipid nanoparticle surface structure in mRNA vaccines
Authors: Wang Mingzhang Maple , Wappelhorst Caitlin N. , Jensen Erika L. , Chi Ying-Chih Thomas , Rouse Jason C. , Zou Qin 
Published: October 2023

AbstractLipid nanoparticles (LNPs) have been used as a carrier for messenger RNA (mRNA) vaccines. Surface properties of LNPs are important to the stability and function of mRNA vaccines. Polyethylene-glycol (PEG) is a functional lipid at the surface of LNPs that improves colloidal stability, increases circulation time, and impacts cellular uptake. In this study, we explore in-depth lipid composition at the surface of mRNA-LNPs using high-field nuclear magnetic resonance (NMR) spectroscopy. Our results provide a unique surface lipid profile of intact LNPs identifying PEG chains and partial ionizable lipids are present with quantification capability. The surface PEG density is determined to reveal the brush-like conformation on the surface of mRNA-LNPs. Furthermore, we implement a diffusion NMR strategy for routine testing of formulated drug products during drug development. Comparative NMR analysis of different vaccine preparations and stability samples provides a global view of the mRNA-LNP surface structure for enhanced product knowledge.