bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coexistence of critical phenomena: the concept of manifold multi-spectral criticality
Authors: Chorowski Michał , Kutner Ryszard , Struzik Zbigniew R. 
Published: March 2024

AbstractPrompted by the ubiquity of empirical observations of critical phenomena, often in non-equilibrium macrostates, we developed a modelling approach in which several critical phenomena coexist. Instead of a single critical point, many coexisting critical points in the system are identified, forming a one-dimensional critical manifold. Identified within our game-of-life-like heterogeneous agent-based simulation model, where agents can be created and annihilated in the presence of a catalyst, each critical point belonging to the critical manifold is associated with a multi-spectrum of critical exponents. We find this situation in non-equilibrium mixed percolation-like macrostates obeying continuous phase transitions. These macrostates are quasi-stationary, where some system characteristics are time-independent while others are not. This novel look at universality signals the existance of complexity of critical phenomena richer than described to date.
Diet replacement with whole insect larvae affects intestinal morphology and microbiota of broiler chickens
Authors: Vasilopoulos Stylianos , Giannenas Ilias , Mellidou Ifigeneia , Stylianaki Ioanna , Antonopoulou Efthimia , Tzora Athina , Skoufos Ioannis , Athanassiou Christos G. , Papadopoulos Elias , Fortomaris Paschalis 
Published: March 2024

AbstractInsect-based diets are gaining interest as potential ingredients in improving poultry gut health. This study assessed the dietary treatment with whole dried Tenebrio molitor larvae (TM) on broiler chickens’ gut microbiota and morphology. 120 Ross-308 broilers received treated diets with 5% (TM5) and 10% (TM10) replacement ratio in a 35-day trial. Intestinal histomorphometry was assessed, as well as claudin-3 expression pattern and ileal and caecal digesta for microbial community diversity. Null hypothesis was tested with two-way ANOVA considering the intestinal segment and diet as main factors. The TM5 group presented higher villi in the duodenum and ileum compared to the other two (P < 0.001), while treated groups showed shallower crypts in the duodenum (P < 0.001) and deeper in the jejunum and ileum than the control (P < 0.001). Treatments increased the caecal Firmicutes/Bacteroidetes ratio and led to significant changes at the genus level. While Lactobacilli survived in the caecum, a significant reduction was evident in the ileum of both groups, mainly owed to L. aviarius. Staphylococci and Methanobrevibacter significantly increased in the ileum of the TM5 group. Results suggest that dietary supplementation with whole dried TM larvae has no adverse effect on the intestinal epithelium formation and positively affects bacterial population richness and diversity.
BSI-MVS: multi-view stereo network with bidirectional semantic information
Authors: Jia Ruiming , Yu Jun , Hu Zhenghui , Yuan Fei 
Published: March 2024

AbstractThe basic principle of multi-view stereo (MVS) is to perform 3D reconstruction by extracting depth information from multiple views. Most current SOTA MVS networks are based on Vision Transformer, which usually means expensive computational complexity. To reduce computational complexity and improve depth map accuracy, we propose a MVS network with Bidirectional Semantic Information (BSI-MVS). Firstly, we design a Multi-Level Spatial Pyramid module to generate multiple layers of feature map for extracting multi-scale information. Then we propose a 2D Bidirectional-LSTM module to capture bidirectional semantic information at different time steps in the horizontal and vertical directions, which contains abundant depth information. Finally, cost volumes are built based on various levels of feature maps to optimize the final depth map. We experiment on the DTU and BlendedMVS datasets. The result shows that our network, in terms of overall metrics, surpasses TransMVSNet, CasMVSNet, CVP-MVSNet, and AACVP-MVSNet respectively by 17.84%, 36.42%, 14.96%, and 4.86%, which also shows a noticeable performance enhancement in objective metrics and visualizations.
Identification of extracellular vesicles from their Raman spectra via self-supervised learning
Authors: Jensen Mathias N. , Guerreiro Eduarda M. , Enciso-Martinez Agustin , Kruglik Sergei G. , Otto Cees , Snir Omri , Ricaud Benjamin , Hellesø Olav Gaute 
Published: March 2024

AbstractExtracellular vesicles (EVs) released from cells attract interest for their possible role in health and diseases. The detection and characterization of EVs is challenging due to the lack of specialized methodologies. Raman spectroscopy, however, has been suggested as a novel approach for biochemical analysis of EVs. To extract information from the spectra, a novel deep learning architecture is explored as a versatile variant of autoencoders. The proposed architecture considers the frequency range separately from the intensity of the spectra. This enables the model to adapt to the frequency range, rather than requiring that all spectra be pre-processed to the same frequency range as it was trained on. It is demonstrated that the proposed architecture accepts Raman spectra of EVs and lipoproteins from 13 biological sources and from two laboratories. High reconstruction accuracy is maintained despite large variances in frequency range and noise level. It is also shown that the architecture is able to cluster the biological nanoparticles by their Raman spectra and differentiate them by their origin without pre-processing of the spectra or supervision during learning. The model performs label-free differentiation, including separating EVs from activated vs. non-activated blood platelets and EVs/lipoproteins from prostate cancer patients versus non-cancer controls. The differentiation is evaluated by creating a neural network classifier that observes the features extracted by the model to classify the spectra according to their sample origin. The classification reveals a test sensitivity of $$92.2\%$$

92.2
%

and selectivity of $$92.3\%$$

92.3
%

over 769 measurements from two labs that have different measurement configurations.
Human dental pulp stem cells derived extracellular matrix promotes mineralization via Hippo and Wnt pathways
Authors: Kornsuthisopon Chatvadee , Nowwarote Nunthawan , Chansaenroj Ajjima , Photichailert Suphalak , Rochanavibhata Sunisa , Klincumhom Nuttha , Petit Stephane , Dingli Florent , Loew Damarys , Fournier Benjamin P. J. , Osathanon Thanaphum 
Published: March 2024

AbstractExtracellular matrix (ECM) is an intricate structure providing the microenvironment niche that influences stem cell differentiation. This study aimed to investigate the efficacy of decellularized ECM derived from human dental pulp stem cells (dECM_DPSCs) and gingival-derived mesenchymal stem cells (dECM_GSCs) as an inductive scaffold for osteogenic differentiation of GSCs. The proteomic analysis demonstrated that common and signature matrisome proteins from dECM_DPSCs and dECM_GSCs were related to osteogenesis/osteogenic differentiation. RNA sequencing data from GSCs reseeded on dECM_DPSCs revealed that dECM_DPSCs upregulated genes related to the Hippo and Wnt signaling pathways in GSCs. In the inhibitor experiments, results revealed that dECM_DPSCs superiorly promoted GSCs osteogenic differentiation, mainly mediated through Hippo and Wnt signaling. The present study emphasizes the promising translational application of dECM_DPSCs as a bio-scaffold rich in favorable regenerative microenvironment for tissue engineering.
Fabrication of date palm kernel biochar-sulfur (DPKB-S) for super adsorption of methylene blue dye from water
Authors: Elkatory Marwa R. , Yılmaz Murat , Hassaan Mohamed A. , El Nemr Ahmed 
Published: March 2024

AbstractA novel form of biochar was created by dehydration of Date palm kernel with 85% sulfuric acid. It was examined how the newly produced biochar (DPKB-S) affected the aqueous solution's capacity to extract Methylene Blue (MB) dye. The prepared DPKB-S was categorized by BET, BJH, FT-IR, SEM, EDX, DSC, and TGA analyses. The ideal pH for the MB dye adsorption by DPKB-S is 8. With 0.75 g L−1 of DPKB-S and an initial concentration of 50 ppm MB dye, Date Palm Kernel Biochar-Sulfur (DPKB-S) had the highest removal percentage of 100%. The Langmuir and Freundlich isotherm models were used to investigate the collected data. Freundlich model is the model that best covers MB dye adsorption in DPKB-S at low concentrations (0.75–1.25 g L−1) and the Langmuir model at high concentrations (1.5–1.75 g L−1). The Langmuir model maximum adsorption capacity (Qm) of the DPKB-S was 1512.30 mg g−1. Furthermore, a variety of error function models were applied to investigate the isotherm models derived data, including Marquardt’s percent standard deviation (MPSD), the sum of absolute errors (EABS), the sum of the errors squared (ERRSQ), root mean square errors (RMS), Chi-square error (X2), the average relative error (ARE), average percent errors (APE), and hybrid error function (HYBRID). Kinetic data were calculated by intraparticle diffusion (IPD), pseudo-second-order (PSO), pseudo-first-order (PFO), and film diffusion (FD) models. A PSO rate model with a strong correlation (R2 = 1.00) largely regulated the adsorption rate. The removal mechanism of MB dye by DPKB-S is based on the principle that these positively charged dyes are attracted by electrostatic attraction forces due to the growth in the number of negatively charged regions at basic pH value. According to the results, DPKB-S shows promise as an affordable and competent adsorbent for the adsorption of MB dye. It can be used frequently without experiencing a discernible decrease in adsorption efficiency.
A GPS assisted translocation experiment to study the homing behavior of red deer
Authors: Silovský Václav , Landler Lukas , Faltusová Monika , Börger Luca , Burda Hynek , Holton Mark , Lagner Ondřej , Malkemper Erich Pascal , Olejarz Astrid , Spießberger Magdalena , Váchal Adam , Ježek Miloš 
Published: March 2024

AbstractMany animals return to their home areas (i.e., ‘homing’) after translocation to sites further away. Such translocations have traditionally been used in behavioral ecology to understand the orientation and migration behavior of animals. The movement itself can then be followed by marking and recapturing animals or by tracking, for example, using GPS systems. Most detailed studies investigating this behavior have been conducted in smaller vertebrates (e.g., birds, amphibians, and mice), whereas information on larger mammals, such as red deer, is sparse. We conducted GPS-assisted translocation experiments with red deer at two sites in the Czech Republic. Individuals were translocated over a distance of approximately 11 km and their home journey was tracked. Circular statistics were used to test for significant homeward orientation at distances of 100, 500, 1000, and 5000 m from the release site. In addition, we applied Lavielle trajectory segmentation to identify the different phases of homing behavior. Thirty-one out of 35 translocations resulted in successful homing, with a median time of 4.75 days (range 1.23–100 days). Animals were significantly oriented towards home immediately after release and again when they came closer to home; however, they did not show a significant orientation at the distances in between. We were able to identify three homing phases, an initial ‘exploratory phase’, followed by a ‘homing phase’ which sometimes was again followed by an ‘arrival phase’. The ‘homing phase’ was characterized by the straightest paths and fastest movements. However, the variation between translocation events was considerable. We showed good homing abilities of red deer after translocation. Our results demonstrate the feasibility of conducting experiments with environmental manipulations (e.g., to impede the use of sensory cues) close to the release site. The homing behavior of red deer is comparable to that of other species, and might represent general homing behavior patterns in animals. Follow-up studies should further dissect and investigate the drivers of the individual variations observed and try to identify the sensory cues used during homing.
Prediction uncertainty estimates elucidate the limitation of current NSCLC subtype classification in representing mutational heterogeneity
Authors: Puiu Andrei , Gómez Tapia Carlos , Weiss Maximilian E. R. , Singh Vivek , Kamen Ali , Siebert Matthias 
Published: March 2024

AbstractThe heterogeneous pathogenesis and treatment response of non-small cell lung cancer (NSCLC) has led clinical treatment decisions to be guided by NSCLC subtypes, with lung adenocarcinoma and lung squamous cell carcinoma being the most common subtypes. While histology-based subtyping remains challenging, NSCLC subtypes were found to be distinct at the transcriptomic level. However, unlike genomic alterations, gene expression is generally not assessed in clinical routine. Since subtyping of NSCLC has remained elusive using mutational data, we aimed at developing a neural network model that simultaneously learns from adenocarcinoma and squamous cell carcinoma samples of other tissue types and is regularized using a neural network model trained from gene expression data. While substructures of the expression-based manifold were captured in the mutation-based manifold, NSCLC classification accuracy did not significantly improve. However, performance was increased when rejecting inconclusive samples using an ensemble-based approach capturing prediction uncertainty. Importantly, SHAP analysis of misclassified samples identified co-occurring mutations indicative of both NSCLC subtypes, questioning the current NSCLC subtype classification to adequately represent inherent mutational heterogeneity. Since our model captures mutational patterns linked to clinical heterogeneity, we anticipate it to be suited as foundational model of genomic data for clinically relevant prognostic or predictive downstream tasks.
Role of compliant mechanics and motor control in hopping - from human to robot
Authors: Mohammadi Nejad Rashty Aida , Sharbafi Maziar A. , Mohseni Omid , Seyfarth André 
Published: March 2024

AbstractCompliant leg function found during bouncy gaits in humans and animals can be considered a role model for designing and controlling bioinspired robots and assistive devices. The human musculoskeletal design and control differ from distal to proximal joints in the leg. The specific mechanical properties of different leg parts could simplify motor control, e.g., by taking advantage of passive body dynamics. This control embodiment is complemented by neural reflex circuitries shaping human motor control. This study investigates the contribution of specific passive and active properties at different leg joint levels in human hopping at different hopping frequencies. We analyze the kinematics and kinetics of human leg joints to design and control a bioinspired hopping robot. In addition, this robot is used as a test rig to validate the identified concepts from human hopping. We found that the more distal the joint, the higher the possibility of benefit from passive compliant leg structures. A passive elastic element nicely describes the ankle joint function. In contrast, a more significant contribution to energy management using an active element (e.g., by feedback control) is predicted for the knee and hip joints. The ankle and knee joints are the key contributors to adjusting hopping frequency. Humans can speed up hopping by increasing ankle stiffness and tuning corresponding knee control parameters. We found that the force-modulated compliance (FMC) as an abstract reflex-based control beside a fixed spring can predict human knee torque-angle patterns at different frequencies. These developed bioinspired models for ankle and knee joints were applied to design and control the EPA-hopper-II robot. The experimental results support our biomechanical findings while indicating potential robot improvements. Based on the proposed model and the robot’s experimental results, passive compliant elements (e.g. tendons) have a larger capacity to contribute to the distal joint function compared to proximal joints. With the use of more compliant elements in the distal joint, a larger contribution to managing energy changes is observed in the upper joints.
Improving the estimation of environment parameters via a two-qubit scheme
Authors: Mirza Ali Raza , Chaudhry Adam Zaman 
Published: March 2024

AbstractWe demonstrate how using two qubits can drastically improve the estimation of environment parameters compared to using only a single qubit. The two qubits are coupled to a common harmonic oscillator environment, and the properties of the environment are imprinted upon the dynamics of the two qubits. The reduced density matrix of only one of these qubits contains a decoherence factor and an additional factor taking into account the indirect interaction induced between the qubits due to the interaction with their common environment. This additional factor can drastically improve the estimation of the environment parameters, as quantified by the quantum Fisher information. In particular, we investigate the estimation of the cutoff frequency, the coupling strength, and the temperature using our two-qubit scheme compared to simply using a single qubit. We find that the precision of the estimates can be improved by orders of magnitude.
DNA metabarcoding reveals ecological patterns and driving mechanisms of archaeal, bacterial, and eukaryotic communities in sediments of the Sansha Yongle Blue Hole
Authors: Li Qingxia , Lei Yanli , Li Tiegang 
Published: March 2024

AbstractThe Sansha Yongle Blue Hole (SYBH) is the world’s deepest marine blue hole with unique physicochemical characteristics. However, our knowledge of the biodiversity and community structure in SYBH sediments remains limited, as past studies have mostly focused on microbial communities in the water column. Here, we collected sediment samples from the aerobic zone (3.1 to 38.6 m) and the deep anaerobic zone (150 m, 300 m) of the SYBH and extracted DNA to characterize the archaeal, bacterial, and eukaryotic communities inhabiting these sediments. Our results showed that the archaeal and bacterial communities were dominated by Thaumarchaeota and Proteobacteria, respectively. The dominant taxa of eukaryotes in different sites varied greatly, mainly including Phaeophyceae, Annelida, Diatomea and Arthropoda. All three examined domains showed clear vertical distributions and significant differences in community composition between the aerobic and anaerobic zones. Sulfide played a prominent role in structuring the three domains, followed by salinity, nitrous oxide, pH, temperature and dissolved oxygen, all of which were positively correlated with the turnover component, the main contributor to beta diversity. Neutral community model revealed that stochastic processes contributed to more than half of the community variations across the three domains. Co-occurrence network showed an equal number of positive and negative interactions in the archaeal network, while positive interactions accounted for ~ 80% in the bacterial and eukaryotic networks. Our findings reveal the ecological features of prokaryotes and eukaryotes in SYBH sediments and shed new light on community dynamics and survival strategies in the special environment of marine blue holes.
Validity of annealed approximation in a high-dimensional system
Authors: Um Jaegon , Hong Hyunsuk , Park Hyunggyu 
Published: March 2024

AbstractThis study investigates the suitability of the annealed approximation in high-dimensional systems characterized by dense networks with quenched link disorder, employing models of coupled oscillators. We demonstrate that dynamic equations governing dense-network systems converge to those of the complete-graph version in the thermodynamic limit, where link disorder fluctuations vanish entirely. Consequently, the annealed-network systems, where fluctuations are attenuated, also exhibit the same dynamic behavior in the thermodynamic limit. However, a significant discrepancy arises in the incoherent (disordered) phase wherein the finite-size behavior becomes critical in determining the steady-state pattern. To explicitly elucidate this discrepancy, we focus on identical oscillators subject to competitive attractive and repulsive couplings. In the incoherent phase of dense networks, we observe the manifestation of random irregular states. In contrast, the annealed approximation yields a symmetric (regular) incoherent state where two oppositely coherent clusters of oscillators coexist, accompanied by the vanishing order parameter. Our findings imply that the annealed approximation should be employed with caution even in dense-network systems, particularly in the disordered phase.
Pregnenolone sulfate induces transcriptional and immunoregulatory effects on T cells
Authors: El Hajj Yasmine , Shahin Tala , Dieng Mame Massar , Alshaikh Manar , Khair Mostafa , Manikandan Vinu , Idaghdour Youssef 
Published: March 2024

AbstractPregnenolone sulfate is a steroid metabolite of the steroidogenesis precursor, pregnenolone, with similar functional properties, including immunosuppression. We recently reported an elevation in serum levels of pregnenolone sulfate in children with malaria, contributing to an immunosuppressed state. Yet, the molecular mechanisms in which this steroid exerts its immunoregulatory functions are lacking. In this study, we examined the effects of pregnenolone sulfate on T cell viability, proliferation and transcriptome. We observed a pregnenolone sulfate dose-dependent induction of T cell death and reduction in proliferation. RNA sequencing analysis of pregnenolone sulfate-treated T cells for 2 and 24 h revealed the downregulation of pro-inflammatory genes and the upregulation of the steroid nuclear receptor superfamily, NR4A, as early-response genes. We also report a strong activation of the integrated stress response mediated by the upregulation of EIF2AK3. These results contribute to the knowledge on transcriptional regulation driving the immunoregulatory effects of pregnenolone sulfate on T cells.
Mechanosensitive TRPV4 channel guides maturation and organization of the bilayered mammary epithelium
Authors: Tytti Kärki , Sanna Koskimäki , Carla Guenther , Jonatan Pirhonen , Kaisa Rajakylä , Sari Tojkander 
Published: March 2024

AbstractBiophysical cues from the cell microenvironment are detected by mechanosensitive components at the cell surface. Such machineries convert physical information into biochemical signaling cascades within cells, subsequently leading to various cellular responses in a stimulus-dependent manner. At the surface of extracellular environment and cell cytoplasm exist several ion channel families that are activated by mechanical signals to direct intracellular events. One of such channel is formed by transient receptor potential cation channel subfamily V member, TRPV4 that is known to act as a mechanosensor in wide variaty of tissues and control ion-influx in a spatio-temporal way. Here we report that TRPV4 is prominently expressed in the stem/progenitor cell populations of the mammary epithelium and seems important for the lineage-specific differentiation, consequently affecting mechanical features of the mature mammary epithelium. This was evident by the lack of several markers for mature myoepithelial and luminal epithelial cells in TRPV4-depleted cell lines. Interestingly, TRPV4 expression is controlled in a tension-dependent manner and it also impacts differentation process dependently on the stiffness of the microenvironment. Furthermore, such cells in a 3D compartment were disabled to maintain normal mammosphere structures and displayed abnormal lumen formation, size of the structures and disrupted cellular junctions. Mechanosensitive TRPV4 channel therefore act as critical player in the homeostasis of normal mammary epithelium through sensing the physical environment and guiding accordingly differentiation and structural organization of the bilayered mammary epithelium.