Journal: Scientific Reports

Abbreviation

Sci Rep

Publisher

Nature

Journal Volumes

ISSN

2045-2322

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2011 - 20196212020 - 2026480
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Publications 1 - 10 of 1101
  • Collagen constitutes about 12% in females and 17% in males of the total protein in mice
    Item type: Journal Article
    Tarnutzer, Katharina; Siva Sankar, Devanarayanan; Dengjel, Joern; et al. (2023)
    Scientific Reports
    Collagen has been postulated to be the most abundant protein in our body, making up one-third of the total protein content in mammals. However, a direct assessment of the total collagen levels of an entire mammal to confirm this estimate is missing. Here we measured hydroxyproline levels as a proxy for collagen content together with total protein levels of entire mice or of individual tissues. Collagen content normalized to the total protein is approximately 0.1% in the brain and liver, 1% in the heart and kidney, 4% in the muscle and lung, 6% in the colon, 20-40% in the skin, 25-35% in bones, and 40-50% in tendons of wild-type (CD1 and CB57BL/6) mice, consistent with previous reports. To our surprise, we find that collagen is approximately 12% in females and 17% in males of the total protein content of entire wild-type (CD1 and CB57BL/6) mice. Although collagen type I is the most abundant collagen, the most abundant proteins are albumin, hemoglobulin, histones, actin, serpina, and then collagen type I. Analyzing amino acid compositions of mice revealed glycine as the most abundant amino acid. Thus, we provide reference points for collagen, matrisome, protein, and amino acid composition of healthy wild-type mice.
  • Remyelination promoting therapies in multiple sclerosis animal models: a systematic review and meta-analysis
    Item type: Journal Article
    Hooijmans, Carlijn R.; Hlavica, Martin; Schuler, Florian A.F.; et al. (2019)
    Scientific Reports
    An unmet but urgent medical need is the development of myelin repair promoting therapies for Multiple Sclerosis (MS). Many such therapies have been pre-clinically tested using different models of toxic demyelination such as cuprizone, ethidium bromide, or lysolecithin and some of the therapies already entered clinical trials. However, keeping track on all these possible new therapies and their efficacy has become difficult with the increasing number of studies. In this study, we aimed at summarizing the current evidence on such therapies through a systematic review and at providing an estimate of the effects of tested interventions by a meta-analysis. We show that 88 different therapies have been pre-clinically tested for remyelination. 25 of them (28%) entered clinical trials. Our meta-analysis also identifies 16 promising therapies which did not enter a clinical trial for MS so far, among them Pigment epithelium-derived factor, Plateled derived growth factor, and Tocopherol derivate TFA-12.We also show that failure in bench to bedside translation from certain therapies may in part be attributable to poor study quality. By addressing these problems, clinical translation might be smoother and possibly animal numbers could be reduced.
  • In vitro investigation of the blood flow downstream of a 3D-printed aortic valve
    Item type: Journal Article
    Zeugin, Till; Coulter, Fergal Brian; Gülan, Utku; et al. (2024)
    Scientific Reports
    The hemodynamics in the aorta as well as the durability of aortic valve prostheses vary greatly between different types of devices. Although placement and sizing of surgical aortic valve prostheses are excellent, the valve geometry of common devices cannot be customized to fit the patient’s anatomy perfectly. Similarly, transcatheter aortic valve implantation (TAVI) devices are not customizable and may be orientated unfavorably during implantation. Imperfect fit of an aortic valve prosthesis may result in suboptimal performance and in some cases the need for additional surgery. Leveraging the advent of precision, multi-material 3D-printing, a bioinspired silicone aortic valve was developed. The manufacturing technique makes it fully customizable and significantly cheaper to develop and produce than common prostheses. In this study, we assess the hemodynamic performance of such a 3D-printed aortic valve and compare it to two TAVI devices as well as to a severely stenosed valve. We investigate the blood flow distal to the valve in an anatomically accurate, compliant aorta model via three-dimensional particle tracking velocimetry measurements. Our results demonstrate that the 3D-printed aortic valve induces flow patterns and topology compatible with the TAVI valves and showing similarity to healthy aortic blood flow. Compared to the stenosis, the 3D-printed aortic valve reduces turbulent kinetic energy levels and irreversible energy losses by over 75%, reaching values compatible with healthy subjects and conventional TAVIs. Our study substantiates that the 3D-printed heart valve displays a hemodynamic performance similar to established devices and underscores its potential for driving innovation towards patient specific valve prostheses.
  • Megathrust earthquake drives drastic organic carbon supply to the hadal trench
    Item type: Journal Article
    Kioka, Arata; Schwestermann, Tobias; Moernaut, Jasper; et al. (2019)
    Scientific Reports
    The giant 2011 Tohoku-oki earthquake has been inferred to remobilise fine-grained, young surface sediment enriched in organic matter from the slope into the >7 km deep Japan Trench. Yet, this hypothesis and assessment of its significance for the carbon cycle has been hindered by limited data density and resolution in the hadal zone. Here we combine new high-resolution bathymetry data with sub-bottom profiler images and sediment cores taken during 2012–2016 in order to map for the first time the spatial extent of the earthquake-triggered event deposit along the hadal Japan Trench. We quantify a sediment volume of ~0.2 km3 deposited from spatially-widespread remobilisation of young surficial seafloor slope sediments triggered by the 2011 earthquake and its aftershock sequence. The mapped volume and organic carbon content in sediment cores encompassing the 2011 event reveals that this single tectonic event delivered >1 Tg of organic carbon to the hadal trench. This carbon supply is comparable to high carbon fluxes described for other Earth system processes, shedding new light on the impact of large earthquakes on long-term carbon cycling in the deep-sea.
  • Recovery of woody plant species richness in secondary forests in China: a meta-analysis
    Item type: Journal Article
    Liu, Xiaofei; Liu, Xuehua; Skidmore, Andrew; et al. (2017)
    Scientific Reports
    There is considerable uncertainty concerning changes in plant diversity of Chinese secondary forests, particularly with respect to diversity recovery following anthropogenic disturbance. Here we present a meta-analysis of the recovery of woody plant species richness in secondary forests in China, with nearby primary forests as a reference. A total of 125 pairs of secondary-primary forest data reported in 55 publications were identified across China. We analyzed the data by region and logging history to examine their influences on secondary forest recovery. Our results indicated that the woody plant richness of secondary forests in China was close to fully recovered when compared to the primary forest, with the recovery ratio being 85–103%. Higher recovery ratios were observed in central, northeast and southwest China, with lower recovery ratios seen in east, south and northwest China, and the recovery in central China significantly reached the primary forests (reference) level. Concerning logging histories, the recovery ratios showed two peak values, with one at 21–40 years after clear cutting and the other at 61–80 years. We reveal the fundamental recovery patterns of woody plant species richness in secondary forests in China. These patterns provide information for the sustainable management of secondary forest resources.
  • Maximum-Entropy Inference with a Programmable Annealer
    Item type: Journal Article
    Chancellor, Nicholas; Szoke, Szilard; Vinci, Walter; et al. (2016)
    Scientific Reports
    Optimisation problems typically involve finding the ground state (i.e. the minimum energy configuration) of a cost function with respect to many variables. If the variables are corrupted by noise then this maximises the likelihood that the solution is correct. The maximum entropy solution on the other hand takes the form of a Boltzmann distribution over the ground and excited states of the cost function to correct for noise. Here we use a programmable annealer for the information decoding problem which we simulate as a random Ising model in a field. We show experimentally that finite temperature maximum entropy decoding can give slightly better bit-error-rates than the maximum likelihood approach, confirming that useful information can be extracted from the excited states of the annealer. Furthermore we introduce a bit-by-bit analytical method which is agnostic to the specific application and use it to show that the annealer samples from a highly Boltzmann-like distribution. Machines of this kind are therefore candidates for use in a variety of machine learning applications which exploit maximum entropy inference, including language processing and image recognition.
  • The chromatin guardian ATRX is a strong prognostic biomarker in melanoma
    Item type: Journal Article
    Frei, Céline Arlette; Litchfield, Cassandra; Mihic, Alanna; et al. (2025)
    Scientific Reports
    In our study, we investigated the role of the chromatin remodeler ATRX in the progression of cutaneous melanoma. We analyzed ATRX protein expression in over 350 melanomas, correlating findings with clinical data, tumor proliferation rates, and vessel density. Additionally, we examined whole-genome sequencing data from 70 melanoma metastases to assess ATRX genetic alterations and compared these with protein expression patterns. We observed a significant reduction in ATRX protein expression in metastases compared to primary tumors: 51% of primary melanomas showed ATRX positivity in over 50% of tumor cells, versus only 25% of metastases (p = 0.01). ATRX loss was associated with earlier metastasis (median 17 vs. 46 months), reduced overall survival (median 69 vs. 162.5 months), and worse tumor-specific survival (p = 0.01). ATRX expression correlated positively with vessel density (rs = 0.3) and negatively with proliferation (rs = – 0.3), suggesting a role in hypoxia response. Genetically, intronic mutations were most frequent (80%), followed by copy number variations (loss: 29%, gain: 37%). Interestingly, ATRX copy number changes did not correlate with protein levels, pointing to epigenetic regulation. Our findings highlight ATRX loss as an early and prognostically relevant event in melanoma, with potential as a therapeutic target.
  • Understanding inter-individual variability of experimental pain habituation and conditioned pain modulation in healthy individuals
    Item type: Journal Article
    De Schoenmacker, Iara; Scheuren, Paulina S.; Sirucek, Laura; et al. (2024)
    Scientific Reports
    Although reduced experimental pain habituation is proposed as a proxy of diminished endogenous pain modulatory capacity in chronic pain, prior studies show contradictory findings. Even across healthy participants, pain habituation varies substantially, which may relate to another measure of endogenous pain modulation, i.e., conditioned pain modulation (CPM). Hence, this study investigated the relationship between pain habituation and CPM. Pain habituation was assessed in 45 healthy participants between two blocks of 15-20 contact-heat stimuli applied to the hand. Habituation of subjective pain ratings and objective neurophysiological readouts (contact-heat evoked potential (CHEP) and palmar sympathetic skin response (SSR)) was investigated. CPM was assessed by comparing heat pain thresholds before and after hand immersion in a noxious cold (9 °C) and lukewarm water bath (32 °C, to control for repeated measures effects). Pain habituation showed a large variability, with subjective but not objective pain habituation correlating with cold-induced CPM effects (r = 0.50; p = 0.025). This correlation was not observed for 'true' CPM effects (corrected for repeated measures effects) nor for CPM effects induced by a lukewarm water bath. These findings suggest that the observed variability in subjective pain habituation may be influenced by both descending endogenous pain modulation and peripheral adaptation processes associated with repeated measures. Objective pain habituation readouts, i.e., CHEPs and SSRs, capture different, complementary aspects of endogenous pain modulation.
  • Longitudinal in vivo evaluation of bone regeneration by combined measurement of multi-pinhole SPECT and micro-CT for tissue engineering
    Item type: Journal Article
    Lienemann, Philipp S.; Metzger, Stéphanie; Kiveliö, Anna-Sofia; et al. (2015)
    Scientific Reports
    Over the last decades, great strides were made in the development of novel implants for the treatment of bone defects. The increasing versatility and complexity of these implant designs request for concurrent advances in means to assess in vivo the course of induced bone formation in preclinical models. Since its discovery, micro-computed tomography (micro-CT) has excelled as powerful high-resolution technique for non-invasive assessment of newly formed bone tissue. However, micro-CT fails to provide spatiotemporal information on biological processes ongoing during bone regeneration. Conversely, due to the versatile applicability and cost-effectiveness, single photon emission computed tomography (SPECT) would be an ideal technique for assessing such biological processes with high sensitivity and for nuclear imaging comparably high resolution (<1 mm). Herein, we employ modular designed poly(ethylene glycol)-based hydrogels that release bone morphogenetic protein to guide the healing of critical sized calvarial bone defects. By combined in vivo longitudinal multi-pinhole SPECT and micro-CT evaluations we determine the spatiotemporal course of bone formation and remodeling within this synthetic hydrogel implant. End point evaluations by high resolution micro-CT and histological evaluation confirm the value of this approach to follow and optimize bone-inducing biomaterials.
  • Two coupled chains are simpler than one: field-induced chirality in a frustrated spin ladder
    Item type: Journal Article
    Pikulski, Marek; Shiroka, Toni; Casola, Francesco; et al. (2020)
    Scientific Reports
    Although the frustrated (zigzag) spin chain is the Drosophila of frustrated magnetism, our understanding of a pair of coupled zigzag chains (frustrated spin ladder) in a magnetic field is still lacking. We address this problem through nuclear magnetic resonance (NMR) experiments on BiCu2PO6 in magnetic fields up to 45 T, revealing a field-induced spiral magnetic structure. Conjointly, we present advanced numerical calculations showing that even a moderate rung coupling dramatically simplifies the phase diagram below half-saturation magnetization by stabilizing a field-induced chiral phase. Surprisingly for a one-dimensional model, this phase and its response to Dzyaloshinskii-Moriya (DM) interactions adhere to classical expectations. While explaining the behavior at the highest accessible magnetic fields, our results imply a different origin for the solitonic phases occurring at lower fields in BiCu2PO6. An exciting possibility is that the known, DM-mediated coupling between chirality and crystal lattice may give rise to a new kind of spin-Peierls instability.
Publications 1 - 10 of 1101