julilili42/papers huggingface dataset:
Comparative study of flow rate- and material-dependent human plasma protein adsorption on oxygenator membranes and heat exchanger materials
2025-06-17

Artificial lungs support patients with acute or chronic lung diseases. However, complications such as the activation of blood components leading to thrombosis and inflammation limit their long-term applicability. The systematic characterization of protein adhesion events on different material parts of the oxygenators at different flow rates can shed light on the initial reaction of blood to foreign materials. Miniaturized extracorporeal circuit devices with heparin-coated gas (PMP) or heat-exchange (PET) hollow-fiber membranes were exposed to high and low flow rates. Hemocompatibility and adsorption of plasma proteins were measured after one minute to six hours using mass spectroscopy analyses. Approximately 150–200 different proteins were present on the membranes, with almost no variation in the 10 most abundant proteins. Protein adsorption to the membrane types did not vary to a large extent, but a decreased flow rate significantly reduced the differences in protein adsorption between both membrane types and led to the adhesion of significantly higher amounts of inhibitory proteins C1INH and α1-AT. At the higher flow rate, coagulation-associated proteins adsorbed significantly more to PET membranes, whereas complement-activating-related proteins adsorbed more on PMP membranes. Our results highlight the importance of analyzing all circuit components to understand the activation of blood components during ECMO. The primary contributor to increased protein adsorption and activation of blood components was an increased flow rate. Therefore, flow rate adjustments should ideally aim to achieve optimal oxygenation levels of around 80% while minimizing protein adsorption and blood activation during ECMO. Notably, at a low flow rate, PMP HFM exhibited a significant increase in binding of complement and inflammation inhibitors, suggesting a potential benefit of lowering the flow rate apart from the general reduction in protein adsorption.
Self-Other Generalisation Shapes Social Interaction and Is Disrupted in Borderline Personality Disorder
2025-06-17

Abstract Generalising information from ourselves to others, and others to ourselves allows for both a dependable source of navigation and adaptability in interpersonal exchange. Disturbances to social development in sensitive periods can cause enduring and distressing damage to lasting healthy relationships. However, identifying the mechanisms of healthy exchange has been difficult. We introduce a theory of self-other generalisation tested with data from a three-phase social value orientation task – the Intentions Game. We involved individuals with (n=50) and without (n=53) a diagnosis of borderline personality disorder and assessed whether infractions to self-other generalisation may explain prior findings of disrupted social learning and instability. Healthy controls initially used their preferences to predict others and were influenced by their partners, leading to self-other convergence. In contrast, individuals with borderline personality disorder maintained distinct self-other representations when learning about others. This allowed for equal predictive performance compared to controls despite reduced updating sensitivity. Furthermore, we explored theory-driven individual differences underpinning contagion. Overall, the findings provide a clear explanation of how self-other generalisation constrains and assists learning and how childhood adversity is associated with separation of internalised beliefs. Our model makes clear predictions about the mechanisms of social information generalisation concerning both joint and individual reward.
Candidate Key Proteins of Tinnitus in the Auditory and Motor Systems of the Thalamus
2025-06-17

To determine candidate key proteins involved in synaptic transmission in the thalamus in tinnitus, we used bioinformatic methods by analyzing protein–protein interaction networks under different conditions of acoustic activity. The motor system was used to analyze the specificity of the response reaction in the auditory system. The databases GeneCard, STRING-, DAVID-, and Cytoscape version 3.9.1 were applied to identify the top three high-degree proteins, their high-score interaction proteins and the gene ontology—biological processes (GO-BPs) associated in the thalamus with synaptic transmission in tinnitus. Under normal hearing conditions, a balanced state of functional connectivity was observed for both systems, the auditory system and the motor system of the thalamus. Under conditions of acoustic stimulation, the GO-BP-enrichment analyses suggest that in the auditory system, tinnitus-related proteins may be involved in responses typically associated with “xenobiotic stimuli”; in the motor system, the activation of the dopaminergic system was observed. Under conditions of tinnitus in the auditory system, key proteins and the GO-BPs indicate the regulation of different developmental processes and regulation by microRNA transcription; in the motor system, tinnitus is also identified as “xenobiotic” but responded with GO-BPs, corresponding to various signaling systems, e.g., tachykinin. Key proteins and their interactions with neurotransmitter receptors may be useful indicators for tinnitus-associated changes in synaptic transmission in the thalamic auditory system.
3D Culture in Functionalized FN‐Silk Networks Facilitate Proliferation, Differentiation and Phenotypic Stability of Mature Human Primary Cells and Stem Cells
2025-06-17

ABSTRACT The recombinant functionalized silk protein FN‐silk, including a cell adhesion motif from fibronectin, can form networks suitable for 3D culture of adherent cells. Such FN‐silk networks have previously been shown to support the growth and differentiation of a wide array of cell types. Herein, we have developed a user‐friendly methodology for the creation of free‐floating FN‐silk networks in 96‐well plates with both mature human primary cells and stem cells. We show that human mesenchymal stem cells (hMSC) cultured in FN‐silk networks form both cell‐cell and cell‐matrix contacts, resulting in tissue‐mimicking 3D cultures. Viability and expression analysis revealed that hMSC in FN‐silk networks have an initial proliferative phase with high cell viability and significantly lower hypoxia and apoptosis, compared to when cultured as scaffold‐free spheroids. The FN‐silk networks were shown to support differentiation of hMSC into adipocyte‐like cells with well‐maintained viability during the 3‐week‐long differentiation period, in contrast to the very poor long‐term viability of scaffold‐free 3D cultures. Improved adipogenesis was confirmed by lipid droplet staining, quantification of intracellular triglycerides, and secreted adiponectin levels, as well as expression analysis of multiple bona fide adipose markers. Lastly, we show that primary human hepatocytes maintain important functions and phenotypic markers when cultured in FN‐silk networks, features that are lost rapidly during conventional 2D culture. We therefore propose FN‐silk networks as a valuable scaffold for 3D human cell cultures, providing support for cell proliferation, differentiation, and the maintenance of critical tissue‐specific functionality.
Comparison of ADMIRE, SAFIRE, and Filtered Back Projection in Standard and Low-Dose Non-Enhanced Head CT
2025-06-17

Background/Objectives: Iterative reconstruction (IR) techniques were developed to address the shortcomings of filtered back projection (FBP), yet research comparing different types of IR is still missing. This work investigates how reducing radiation dose influences both image quality and noise profiles when using two iterative reconstruction techniques—Sinogram-Affirmed Iterative Reconstruction (SAFIRE) and Advanced Modeled Iterative Reconstruction (ADMIRE)—in comparison to filtered back projection (FBP) in non-enhanced head CT (NECT). Methods: In this retrospective single-center study, 21 consecutive patients underwent standard NECT on a 128-slice CT scanner. Raw data simulated dose reductions to 90% and 70% of the original dose via ReconCT software. For each dose level, images were reconstructed with FBP, SAFIRE 3, and ADMIRE 3. Image noise power spectra quantified objective image noise. Two blinded neuroradiologists scored overall image quality, image noise, image contrast, detail, and artifacts on a 10-point Likert scale in a consensus reading. Quantitative Hounsfield unit (HU) measurements were obtained in white and gray matter regions. Statistical analyses included the Wilcoxon signed-rank test, mixed-effects modeling, ANOVA, and post hoc pairwise comparisons with Bonferroni correction. Results: Both iterative reconstructions significantly reduced image noise compared to FBP across all dose levels (p &lt; 0.001). ADMIRE exhibited superior image noise suppression at low (&lt;0.51 1/mm) and high (&gt;1.31 1/mm) spatial frequencies, whereas SAFIRE performed better in the mid-frequency range (0.51–1.31 1/mm). Subjective scores for overall quality, image noise, image contrast, and detail were higher for ADMIRE and SAFIRE versus FBP at the original dose and simulated doses of 90% and 70% (all p &lt; 0.001). ADMIRE outperformed SAFIRE in artifact reduction (p &lt; 0.001), while SAFIRE achieved slightly higher image contrast scores (p &lt; 0.001). Objective HU values remained stable across reconstruction methods, although SAFIRE yielded marginally higher gray and white matter (WM) attenuations (p &lt; 0.01). Conclusions: Both IR techniques—ADMIRE and SAFIRE—achieved substantial noise reduction and improved image quality relative to FBP in non-enhanced head CT at standard and reduced dose levels on the specific CT system and reconstruction strength tested. ADMIRE showed enhanced suppression of low- and high-frequency image noise and fewer artifacts, while SAFIRE preserved image contrast and reduced mid-frequency noise. These findings support the potential of iterative reconstruction to optimize radiation dose in NECT protocols in line with the ALARA principle, although broader validation in multi-vendor, multi-center settings is warranted.
What do you mean by “social media”? Introducing the Reporting Items for Social Media Research (RISoMeR)
2025-06-17

Abstract Scholars from various disciplines study social media. However, neither researchers nor users have a unified understanding of social media. Even more problematically, many researchers do not define how social media is understood in their studies reducing the transparency, interpretability, and comparability of research. In this article, we introduce the Reporting Items for Social Media Research (RISoMeR), a flexible and easy-to-use matrix with which researchers can transparently report which understanding of social media they apply in their research. The RISoMeR suggests that on Dimension 1, researchers report if they take a technology-centered, usage-centered, or user-centered perspective. In Dimension 2, researchers should report which features and functionalities they use as defining characteristics of social media. We describe applications of the approach.
Advancing plant biomass measurements: Integrating smartphone‐based 3D scanning techniques for enhanced ecosystem monitoring
2025-06-18

Abstract New technological developments open novel possibilities for widely applicable methods of ecosystem analyses. We investigated a novel approach using smartphone‐based 3D scanning for non‐destructive, high‐resolution monitoring of above‐ground plant biomass. This method leverages Structure from Motion (SfM) techniques with widely accessible smartphone apps and subsequent computing to generate detailed ecological data. By implementing a streamlined pipeline for point cloud processing and voxel‐based analysis, we enable frequent, cost‐effective and accessible monitoring of vegetation structure and plant community biomass. Conducted in long‐term experimental grasslands, our study reveals a high correlation ( R 2 up to 0.9) between traditional biomass harvesting and 3D volume estimates derived from smartphone‐generated point clouds, validating the method's accuracy and reliability. Additionally, results indicate significant effects of plant species richness and fertilization on biomass production and volume estimates, underscoring the potential for high‐resolution temporal and spatial analyses of vegetation dynamics. This method's innovation extends beyond traditional practices with implications for future integration of AI to automate species segmentation, ecological trait extraction and predictive modelling. The simplicity and accessibility of the smartphone‐based approach facilitate broader engagement in ecosystem monitoring, encouraging citizen science participation and enhancing data collection efforts. Future research will make it possible to refine the accuracy of point cloud processing, expand applications across diverse vegetation types and explore new possibilities in ecological monitoring, modelling and its application in ecosystem analyses and biodiversity research.
Genetic Diversity and Expanded Phenotypes in Dystonia: Insights From Large‐Scale Exome Sequencing
2025-06-18

ABSTRACT Objective Dystonia is one of the most prevalent movement disorders, characterized by significant clinical and etiological heterogeneity. Despite considerable heritability (~25%), the etiology in most patients remains elusive. Moreover, understanding correlations between clinical manifestations and genetic variants has become increasingly complex. Methods Exome sequencing was conducted on 1924 genetically unsolved, mainly late‐onset isolated dystonia patients, recruited primarily from two dystonia registries (DysTract and the Dystonia Coalition). Rare variants in genes previously linked to dystonia ( n = 406) were examined, confirmed via Sanger sequencing, and analyzed for segregation when possible. Results We identified 137 distinct likely pathogenic/pathogenic variants (according to ACMG criteria) across 51 genes in 163/1924 patients, including 153/1895 index patients (diagnostic yield 8.1%). The strongest predictors of a genetic diagnosis were generalized dystonia (28.6% yield) and age at onset (20.4% yield in patients with onset &lt; 30 years). Notably, 56.2% of these variants were novel, with recurrent variants in EIF2AK2 , VPS16 , KCNMA1 , and SLC2A1 . Additionally, 321 index patients (16.9%) harbored variants of uncertain significance in 102 genes. The most frequently implicated genes included VPS16 , THAP1 , GCH1 , SGCE , GNAL , and KMT2B. Presumably pathogenic variants in less well‐established dystonia genes were also found, including KCNMA1 , KIF1A , and ZMYND11. At least six variants (in ADCY5 , GNB1 , IR2BPL, KCNN2 , KMT2B , and VPS16 ) occurred de novo, supporting pathogenicity. Interpretation This study provides valuable insights into the genetic landscape of dystonia, underscores the utility of exome sequencing for diagnosis, substantiates several candidate genes, and expands the phenotypic spectrum of some genes to include prominent, sometimes isolated dystonia.
Weathering by mycorrhizal fungi defines a threshold for nutrients in ecosystems along an aridity gradient
2025-06-18

The Earth's surface is in constant change due to biotic and abiotic processes. During the last decades awareness arose that these biotic and abiotic processes might intensely interfere. Biogenic weathering, the acceleration of mineral weathering by autotroph-symbiont couples fuelled by photoassimilates for the sake of an equilibrated nutrient supply of involved biota, potentially drives denudation rates at ecosystem level. Our experiment aimed to examine how aridity affects biogenic weathering. The study was conducted along a gradient in Chile from humid to hyperarid climate (Atacama Desert), where photoassimilate production is increasingly limited by water stress. We hypothesize that biogenic weathering would cease if a threshold between element loss from denudation and energy demand for additional nutrient element mobilization by biogenic weathering is crossed, as competition between life for these elements becomes less intense when water supply limits biomass growth increasingly. We buried mesh bags containing freshly broken minerals, including biotite, muscovite and apatite along the gradient in Chile on granitic bedrock. Unexpectedly and in contrast to our initial hypothesis, we found that mineral weathering rates driven by mycorrhizal fungi under arid conditions were even proportionally higher, indicating a comparatively higher investment of photoassimilates into biogenic weathering by desert plants than by mediterranean, suggesting an adaptive mechanism. Additionally, biogenic weathering occurred at constant rates over a depth of up to 2.3 m, illustrating the constant mining of mycorrhizal fungi, irrespective of overall biological activity along the soil profile. The relative importance of biogenic weathering in arid climates furthermore points towards a fundamental function of biogenic weathering beyond nutrient mobilization by suggesting a regulatory role in overcoming long periods of missing soil water that prevent nutrient exchange from the soil matrix.
Nubian cores along the coast of the central Levantine corridor: exploring technical variability of Levallois points in Lebanon
2025-06-18

<title>Abstract</title> Nubian Levallois technology constitutes a specific variation of the Levallois point production method, its most distinctive feature being the use of the distal platform to create and maintain the medial distal ridge of the core. The geographical spread and chronological range of this technology remain highly contested. Save for the sites addressed in this article, Middle Palaeolithic sites with Nubian technology are found in desert environments. However, the few dated sites from the Southern Levant, North Africa, and Arabia indicate human occupations during heightened precipitation and increased landscape carrying capacity during Marine Isotope Stage 5. Furthermore, known occurrences have been found away from the coast, along now-dried river systems, plateaus and lakes within the interior. Here, we report on the variability of Levallois point production systems used along the Lebanese coast, a highly dynamic setting repeatedly occupied from the Lower Palaeolithic onwards. We present an overview of Middle Palaeolithic Levallois point production systems across the central Levantine corridor, emphasising Nubian Levallois points and cores from Lebanon. Based on our study, we suggest humans' recurrent use of the Mediterranean and coastal areas of Lebanon using different Levallois production methods, including Nubian Levallois reduction systems.
Antineoplastic Activity of a Novel Trispecific Single-Chain Antibody Targeting the hERG1/β1 Integrin Complex and TRAIL Receptors
2025-06-18

Abstract Targeted therapies and immunotherapies have largely improved cancer treatment in the last years. One of the most promising approaches is the induction of tumor apoptosis by TRAIL through its binding to apoptosis-inducing receptors DR4 and DR5 on the plasma membrane of target cells. However, some constraints (e.g., the short in vivo half-life and the poor activity on DR5 receptors) hinder the use of naked, soluble forms of TRAIL. Previous studies have shown that fusing TRAIL sequences with antibody-based moieties may represent a novel and efficacious strategy to overcome such hindrances. On these bases, novel TRAIL-related anticancer therapeutic strategies are being developed. In the present article, we describe a novel antibody represented by a single-chain diabody directed against a cancer-specific target, i.e., the hERG1/β1 integrin complex—scDb-hERG1-β1—fused with three TRAIL sequences. The scDb-hERG1-β1-TRAIL antibody combines the specific targeting and downregulation of cancer-specific signaling pathways by scDb-hERG1-β1 with the proapoptotic activity triggered by TRAIL. We provide substantial evidence of the efficacy of the scDb-hERG1-β1-TRAIL antibody to decrease tumor growth triggering apoptotic cell death in vitro in breast cancer cells as well as in vivo in a mouse model of triple-negative breast cancer. Being characterized by a favorable pharmacokinetic and toxicity profile, the scDb-hERG1-β1-TRAIL antibody can be proposed for the treatment of difficult-to-treat cancers, such as triple-negative breast cancer, which express the hERG1/β1 complex and TRAIL receptors.
Two simple ways of making clean nitrogen-doped graphene for TEM studies
2025-06-18

Abstract Graphene is the ideal transmission electron microscopy (TEM) support when it comes to imaging, but often offers poor interaction with samples due to its inert nature, making preparation of the TEM samples difficult. Graphitic nitrogen substitutions in graphene could boost its reactivity while simultaneously bringing minimal disturbance to its periodic structure. Here, two straightforward and easy to implement methods are shown for nitrogen doping of graphene that is already freely suspended on a TEM grid. One procedure utilizes a standard plasma cleaner capable of generating radio frequency plasma, for the other a simple direct current glow discharge plasma chamber was built. Successful implantation of graphitic nitrogen was achieved via both methods and verified by high resolution TEM. A series of experiments allowed to find satisfactory conditions for doping, yielding samples where nitrogen substitutions can be found and imaged within otherwise clean areas of graphene. Interaction of an adsorbate with graphitic nitrogen was observed on an atomic level, demonstrating its capability to bind other materials.
The dynamic course of spontaneous muscular contractions assessed using multiple‐point acquisition in diffusion‐weighted stimulated echo imaging
2025-06-18

Abstract Purpose The temporal course of spontaneous mechanical activities of musculature (SMAMs) is investigated using a novel multiple‐point diffusion‐weighted stimulated echo imaging sequence (MP‐DW‐STE) with adapted spatial and temporal resolution. For this purpose, different sequence settings and measurement parameters are applied. Methods A single‐shot MP‐DW‐STE imaging sequence with multiple signal rephasing by small flip angle RF pulses was developed to acquire image series during spontaneous muscle contractions with duration of several hundred milliseconds. Measurements were conducted on an incoherent motion phantom and in the calf muscles of eight healthy volunteers. The number and cross‐sectional area of SMAM visualizations as well as the contractile behavior in terms of onset and duration of visible SMAMs was analyzed. Results Measurements on the incoherent motion phantom confirmed the ability of the proposed technique to characterize dynamic incoherent motion as signal voids in series of images with a high temporal resolution of approximately 40 ms. All human subjects showed SMAMs with a median duration of 120 ms, therefore, visible in several diffusion‐weighted images in a row. Contraction time of SMAMs was in the range of 80 to 120 ms for the soleus muscle. The MP‐DW‐STE sequence settings have shown to significantly influence the mean frequency and cross‐sectional area of SMAMs. Conclusion MP‐DW‐STE imaging allows for time‐resolved recording of spontaneous muscular contractions and provides new insights into their dynamic course. This new feature can be used for better characterization of physiological SMAMs in healthy subjects and pathological SMAMs in patients suffering from neuromuscular diseases.