bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large extracellular vesicle (EV) and neutrophil extracellular trap (NET) interaction captured in vivo during systemic inflammation
Authors: Ortmann Weronika , Such Anna , Cichon Iwona , Baj-Krzyworzeka Monika , Weglarczyk Kazimierz , Kolaczkowska Elzbieta 
Published: February 2024

AbstractExtracellular vesicles (EVs) and neutrophil extracellular traps (NETs) are pivotal bioactive structures involved in various processes including inflammation. Herein we report the interactions between EVs and NETs during murine endotoxemia studied in situ directly in the vasculature (cremaster muscle, liver sinusoids) using intravital microscopy (IVM). We captured NETs and EV release in real time by both non- and polarized neutrophils in liver but not in cremaster vasculature. When comparing numbers of circulating EVs of various origin (nanoparticle tracking analysis—NTA, flow cytometry) with those interacting with endothelium and NETs (IVM) we observed that whereas platelet and monocyte/macrophage-derived EVs dominate in blood and peritoneal lavage, respectively, mostly neutrophil-derived EVs interact with the vascular lining, NETs and leukocytes. Despite the interaction, NETs do not affect EV formation as NET release inhibition did not alter EV release. However, EVs inhibit NETs formation and in particular, erythrocyte-derived EVs downregulate NET release and this effect is mediated via Siglec-E-dependent interactions with neutrophils. Overall, we report that EVs are present in NETs in vivo and they do modulate their release but the process in not bidirectional. Moreover, EVs isolated from body fluids might not reflect their importance in direct endothelial- and leukocyte-related interactions.
Indices of airway resistance and reactance from impulse oscillometry correlate with aerosol particle emission in different age groups
Authors: Schumm Benedikt , Bremer Stephanie , Knödlseder Katharina , Schönfelder Martin , Hain Rainer , Semmler Luisa , Lorenz Elke , Wackerhage Henning , Kähler Christian J. , Jörres Rudolf 
Published: February 2024

AbstractAirborne transmission of pathogens plays a major role in the spread of infectious diseases. Aerosol particle production from the lung is thought to occur in the peripheral airways. In the present study we investigated eighty lung-healthy subjects of two age groups (20–39, 60–76 years) at rest and during exercise whether lung function parameters indicative of peripheral airway function were correlated with individual differences in aerosol particle emission. Lung function comprised spirometry and impulse oscillometry during quiet breathing and an expiratory vital capacity manoeuvre, using resistance (R5) and reactance at 5 Hz (X5) as indicators potentially related to peripheral airway function. The association between emission at different ventilation rates relative to maximum ventilation and lung function was assessed by regression analysis. In multiple regression analyses including age group, only vital capacity manoeuvre R5 at 15% to 50% of end-expiratory vital capacity as well as quiet breathing X5 were independently linked to particle emission at 20% to 50% of maximum ventilation, in addition to age group. The fact that age as predictive factor was still significant, although to a lower degree, points towards further effects of age, potentially involving surface properties not accounted for by impulse oscillometry parameters.
Disease resistance and infectivity of virus susceptible and resistant common carp strains
Authors: Dorfman Batya , Marcos-Hadad Evgeniya , Tadmor-Levi Roni , David Lior 
Published: February 2024

AbstractInfectious diseases challenge health and welfare of humans and animals. Unlike for humans, breeding of genetically resistant animals is a sustainable solution, also providing unique research opportunities. Chances to survive a disease are improved by disease resistance, but depend also on chances to get infected and infect others. Considerable knowledge exists on chances of susceptible and resistant animals to survive a disease, yet, almost none on their infectivity and if and how resistance and infectivity correlate. Common carp (Cyprinus carpio) is widely produced in aquaculture, suffering significantly from a disease caused by cyprinid herpes virus type 3 (CyHV-3). Here, the infectivity of disease-resistant and susceptible fish types was tested by playing roles of shedders (infecting) and cohabitants (infected) in all four type-role combinations. Resistant shedders restricted spleen viral load and survived more than susceptible ones. However, mortality of susceptible cohabitants infected by resistant shedders was lower than that of resistant cohabitants infected by susceptible shedders. Virus levels in water were lower in tanks with resistant shedders leading to lower spleen viral loads in cohabitants. Thus, we empirically demonstrated that disease resistant fish survive better and infect less, with implications to epidemiology in general and to the benefit of aquaculture production.
Tumor location matters, next generation sequencing mutation profiling of left-sided, rectal, and right-sided colorectal tumors in 552 patients
Authors: Ciepiela Izabela , Szczepaniak Magdalena , Ciepiela Przemysław , Hińcza-Nowak Kinga , Kopczyński Janusz , Macek Paweł , Kubicka Kamila , Chrapek Magdalena , Tyka Magdalena , Góźdź Stanisław , Kowalik Artur 
Published: February 2024

AbstractDespite the introduction of new molecular classifications, advanced colorectal cancer (CRC) is treated with chemotherapy supplemented with anti-EGFR and anti-VEGF targeted therapy. In this study, 552 CRC cases with different primary tumor locations (250 left side, 190 rectum, and 112 right side) were retrospectively analyzed by next generation sequencing for mutations in 50 genes. The most frequently mutated genes were TP53 in left-sided tumors compared to right-sided tumors and BRAF in right-sided tumors compared to left-sided tumors. Mutations in KRAS, NRAS, and BRAF were not detected in 45% of patients with left-sided tumors and in 28.6% of patients with right-sided tumors. Liver metastases were more common in patients with left-sided tumors. Tumors on the right side were larger at diagnosis and had a higher grade (G3) than tumors on the left. Rectal tumors exhibit distinctive biological characteristics when compared to left-sided tumors, including a higher absence rate of KRAS, NRAS, and BRAF mutations (47.4% in rectal versus 42.8% in left-sided tumors). These rectal tumors are also unique in their primary metastasis site, which is predominantly the lungs, and they have varying mutation rates, particularly in genes such as BRAF, FBXW7, and TP53, that distinguish them from tumors found in other locations. Primary tumor location has implications for the potential treatment of CRC with anti-EGFR therapy.
Community detection with Greedy Modularity disassembly strategy
Authors: Rustamaji Heru Cahya , Kusuma Wisnu Ananta , Nurdiati Sri , Batubara Irmanida 
Published: February 2024

AbstractCommunity detection recognizes groups of densely connected nodes across networks, one of the fundamental procedures in network analysis. This research boosts the standard but locally optimized Greedy Modularity algorithm for community detection. We introduce innovative exploration techniques that include a variety of node and community disassembly strategies. These strategies include methods like non-triad creating, feeble, random as well as inadequate embeddedness for nodes, as well as low internal edge density, low triad participation ratio, weak, low conductance as well as random tactics for communities. We present a methodology that showcases the improvement in modularity across the wide variety of real-world and synthetic networks over the standard approaches. A detailed comparison against other well-known community detection algorithms further illustrates the better performance of our improved method. This study not only optimizes the process of community detection but also broadens the scope for a more nuanced and effective network analysis that may pave the way for more insights as to the dynamism and structures of its functioning by effectively addressing and overcoming the limitations that are inherently attached with the existing community detection algorithms.
Optimal cutoff value of the dry eye-related quality-of-life score for diagnosing dry eye disease
Authors: Zou Xinrong , Nagino Ken , Okumura Yuichi , Midorikawa-Inomata Akie , Eguchi Atsuko , Yee Alan , Fujimoto Keiichi , Miura Maria , Sung Jaemyoung , Huang Tianxiang , Fujio Kenta , Akasaki Yasutsugu , Nakao Shintaro , Kobayashi Hiroyuki , Inomata Takenori 
Published: February 2024

AbstractThis retrospective study aimed to determine the optimal cutoff values of the Dry Eye-Related Quality-of-Life Score (DEQS) questionnaire for diagnosing dry eye disease (DED) and classifying DED severities. Participants completed the DEQS questionnaire, the Japanese version of the Ocular Surface Disease Index (J-OSDI) questionnaire, and DED examinations. DED was diagnosed according to the 2016 Asia Dry Eye Society diagnostic criteria based on DED symptoms (J-OSDI ≥ 13 points) and tear film breakup time ≤ 5 s. Receiver operating characteristic (ROC) analysis was used to calculate the optimal cutoff values of the DEQS summary score for detecting DED and grading its severity. Among 427 patients, 296 (69.3%) and 131 (30.7%) were diagnosed with DED and non-DED, respectively. ROC analysis determined an optimal cutoff value of 15.0 points for DED diagnosis, with 83.5% sensitivity, 87.0% specificity, and an area under the curve of 0.915. The positive and negative predictive values for DEQS ≥ 15.0 points were 93.6% and 69.9%, respectively. DEQS cutoff values of 15.0, 20.0, and 26.8 points could be accepted for severity classification of DED subjective symptoms in clinical use and represent mild, moderate, and severe DED, respectively. Conclusively, the optimal cutoff values of DEQS enable DED detection and subjective symptom severity classification.
Molecular guidelines for promising antimicrobial agents
Authors: Rzycki Mateusz , Gładysiewicz-Kudrawiec Marta , Kraszewski Sebastian 
Published: February 2024

AbstractAntimicrobial resistance presents a pressing challenge to public health, which requires the search for novel antimicrobial agents. Various experimental and theoretical methods are employed to understand drug-target interactions and propose multistep solutions. Nonetheless, efficient screening of drug databases requires rapid and precise numerical analysis to validate antimicrobial efficacy. Diptool addresses this need by predicting free energy barriers and local minima for drug translocation across lipid membranes. In the current study employing Diptool free energy predictions, the thermodynamic commonalities between selected antimicrobial molecules were characterized and investigated. To this end, various clustering methods were used to identify promising groups with antimicrobial activity. Furthermore, the molecular fingerprinting and machine learning approach (ML) revealed common structural elements and physicochemical parameters in these clusters, such as long carbon chains, charged ammonium groups, and low dipole moments. This led to the establishment of guidelines for the selection of effective antimicrobial candidates based on partition coefficients (logP) and molecular mass ranges. These guidelines were implemented within the Reinforcement Learning for Structural Evolution (ReLeaSE) framework, generating new chemicals with desired properties. Interestingly, ReLeaSE produced molecules with structural profiles similar to the antimicrobial agents tested, confirming the importance of the identified features. In conclusion, this study demonstrates the ability of molecular fingerprinting and AI-driven methods to identify promising antimicrobial agents with a broad range of properties. These findings deliver substantial implications for the development of antimicrobial drugs and the ongoing battle against antibiotic-resistant bacteria.
TAS2R38 haplotypes, COVID-19 infection, and symptomatology: a cross-sectional analysis of data from the Canadian Longitudinal Study on Aging
Authors: Meng Tongzhu , Nielsen Daiva E. 
Published: February 2024

AbstractTheTAS2R38gene is well known for its function in bitter taste sensitivity, but evidence also suggests a role in innate immunity.TAS2R38may be relevant in coronavirus disease 2019 (COVID-19), but research findings are inconsistent. The objective of this study was to explore whether commonTAS2R38haplotypes are associated with COVID-19 infection and symptomatology in the Canadian Longitudinal Study on Aging (CLSA). Data from the CLSA COVID-19 Questionnaire and Seroprevalence sub-studies were utilized with CLSA genetic data for commonTAS2R38haplotypes related to bitter taste sensitivity. Haplotypes were categorized into three diplotype groups: [P]AV homozygotes, [P]AV/[A]VI heterozygotes, and [A]VI homozygotes. No significant differences were observed between diplotypes and COVID-19 infection frequency. Among self-reported COVID-19 cases (n = 76), and in uncorrected exploratory analyses, heterozygotes were less likely to report experiencing sinus pain compared to [P]AV homozygotes. Among seroprevalence-confirmed cases (n = 177), [A]VI homozygotes were less likely to report experiencing a sore/scratchy throat compared to [P]AV homozygotes. However, both observations were non-significant upon correction for multiple testing. In this study,TAS2R38haplotypes were not significantly associated with COVID-19 infection or symptomatology. Nevertheless, in light of some exploratory patterns and conflicting evidence, additional research is warranted to evaluate links betweenTAS2R38and innate immunity.
Synergistic potential in spinel ferrite MFe2O4 (M = Co, Ni) nanoparticles-mediated graphene oxide: Structural aspects, photocatalytic, and kinetic studies
Authors: Parastar Gharehlar Mahnaz , Sheshmani Shabnam , Nikmaram Farrokh Roya , Doroudi Zohreh 
Published: February 2024

AbstractThe existence of artificial dyes in water is a significant environmental concern, as it can lead to poor water quality. Photodegradation is becoming an increasingly popular method for treating water contaminated with dyes. In this study, the photodegradation of Reactive Red 66 and Reactive Red 120 dyes, as well as textile wastewater, was investigated under UV and visible light irradiation. To enhance the photoresponse of the MFe2O4 (M = Co, Ni) nanoparticles, modifications were made by incorporating graphene oxide. The MFe2O4 nanoparticles and MFe2O4/GO nanocomposite photocatalysts were subjected to several characterization techniques, including FT-IR, Raman spectroscopy, XRD, DRS, zeta potential, VSM, TGA, DSC, BET, SEM, and EDAX analysis. Experiments were conducted to optimize several key parameters involved in the photodegradation process, including pH, photocatalyst dosage, initial dye concentration, and irradiation time. The removal efficiency of Reactive Red 66 and Reactive Red 120 dyes using CoFe2O4 nanoparticles was found to be 86.97 and 82.63%, respectively. Also, the removal percentage of these dyes using CoFe2O4/GO nanocomposite photocatalyst was 95.57 and 90.9% for Reactive Red 66 and Reactive Red 120, respectively. Experiments found that NiFe2O4 nanoparticles removed 90.92% of Reactive Red 66 dye and 84.7% of Reactive Red 120 dye. The NiFe2O4/GO nanocomposite photocatalyst showed even higher removal efficiencies, degrading 97.96% of Reactive Red 66 and 93.44% of Reactive Red 120. After three days of exposure to visible light irradiation, the removal percentage of Reactive Red 66 using MFe2O4 and MFe2O4/GO nanocomposite was investigated.
Silicone-based highly stretchable multifunctional fiber pumps
Authors: Kanno Ryo , Shimizu Keita , Murakami Kazuya , Shibahara Yuya , Ogawa Naoki , Akai Hideko , Shintake Jun 
Published: February 2024

AbstractRecent advancements on electrohydrodynamic (EHD) soft pumps demonstrate their applicability to various fluid-driven systems such as soft robots, wearable devices, and stretchable electronics. In particular, fiber type EHD pumps reported more recently is a promising pumping element thanks to their versatile fibrous structure. Yet existing EHD fiber pumps are less stretchable and require sophisticated, complex fabrication equipment, implying opportunity for technology advancement. This paper presents a simplified method to create highly stretchable multifunctional fiber EHD pumps. The method employs highly compliant silicone elastomers for the fiber structure that is formed by simple dipping fabrication process. The fabricated pumps (length of 100 mm, inner diameter 4 mm, and mass 5.3 g) exhibit a high stretchability (up to 40% strain) and flow rate and pressure of 167.4 ± 7.6 mL/min (31.6 mL/min/g) and 4.1 ± 0.6 kPa (0.8 kPa/g), respectively. These performances are comparable or even higher than those of previously reported EHD pumps including fiber types. The output performance of the fabricated pumps remain constant for repeated strain cycles (0–25%, up to 2000 cycles) and bending angle up to 180° (corresponding to curvature of 0–30/m). Moreover, the pumps demonstrate unprecedented functionality as a sensor to distinguish the type of fluid inside the tube and to detect strains by reading the capacitance between the electrodes. The characterization result reveals the sensing ability of the pumps as high repeatability up to 30% strain with negligible hysteresis, which is consistent for 5000 cycles.
Assessing urban livability in Shanghai through an open source data-driven approach
Authors: Long Yin , Wu Yi , Huang Liqiao , Aleksejeva Jelena , Iossifova Deljana , Dong Nannan , Gasparatos Alexandros 
Published: February 2024

AbstractUrban livability has become a major policy and practice priority in many parts of the world. However, its attainment remains challenging in many cities of developing and emerging economies. The lack of data with appropriate quality, coverage, and spatial and temporal resolution often complicates both the assessment of livability in such cities and the identification of priority areas for improvement. Here we develop a framework to mobilize and synthesize open-source data to analyze spatially urban livability patterns in Shanghai. The framework brings together diverse types of open-source data including housing characteristics, population distribution, transportation networks, and points of interest to identify city areas with low livability, and thus priority areas for improvement. Such findings can provide a comprehensive overview of the residential living conditions in Shanghai, as well as useful information to urban planners and decision-makers. Furthermore, subject to data availability, the proposed method has the potential for application in other cities.
Humoral and cellular immune responses to COVID-19 mRNA vaccines in immunosuppressed liver transplant recipients
Authors: Nogimori Takuto , Nagatsuka Yuta , Kobayashi Shogo , Murakami Hirotomo , Masuta Yuji , Suzuki Koichiro , Tomimaru Yoshito , Noda Takehiro , Akita Hirofumi , Takahama Shokichi , Yoshioka Yasuo , Doki Yuichiro , Eguchi Hidetoshi , Yamamoto Takuya 
Published: February 2024

Abstract
Background
Liver transplant recipients (LTRs) are at a high risk of severe COVID-19 owing to immunosuppression and comorbidities. LTRs are less responsive to mRNA vaccines than healthy donors (HDs) or other immunosuppressed patients. However, the disruption mechanism in humoral and cellular immune memory responses is unclear.

Methods
We longitudinally collected peripheral blood mononuclear cells and plasma samples from HDs (n = 44) and LTRs (n = 54) who received BNT162b2 or mRNA-1273 vaccines. We measured the levels of anti-receptor-binding domain (RBD) antibodies and spike-specific CD4+ and CD8+ T-cell responses.

Results
Here, we show that the induction of anti-RBD IgG was weaker in LTRs than in HDs. The use of multiple immunosuppressive drugs is associated with lower antibody titers than only calcineurin inhibitor, and limits the induction of CD4+ T-cell responses. However, spike-specific CD4+ T-cell and antibody responses improved with a third vaccination. Furthermore, mRNA vaccine-induced spike-specific CD8+ T cells are quantitatively, but not qualitatively, limited to LTRs. Both CD4+ and CD8+ T cells react to omicron sublineages, regardless of the presence in HDs or LTRs. However, there is no boosting effect of spike-specific memory CD8+ T-cell responses after a third vaccination in HDs or LTRs.

Conclusions
The third mRNA vaccination improves both humoral responses and spike-specific CD4+ T-cell responses in LTRs but provides no booster effect for spike-specific memory CD8+ T-cell responses. A third mRNA vaccination could be helpful in LTRs to prevent severe COVID-19, although further investigation is required to elicit CD8+ T-cell responses in LTRs and HDs.
Stable training via elastic adaptive deep reinforcement learning for autonomous navigation of intelligent vehicles
Authors: Zhao Yujiao , Ma Yong , Zhu Guibing , Hu Songlin , Yan Xinping 
Published: February 2024

AbstractThe uncertain stability of deep reinforcement learning training on complex tasks impedes its development and deployment, especially in intelligent vehicles, such as intelligent surface vessels and self-driving cars. Complex and varied environmental states puzzle training of decision-making networks. Here we propose an elastic adaptive deep reinforcement learning algorithm to address these challenges and achieve autonomous navigation in intelligent vehicles. Our method trains the decision-making network over the function and optimization learning stages, in which the state space and action space of autonomous navigation tasks are pruned by choosing classic states and actions to reduce data similarity, facilitating more stable training. We introduce a task-adaptive observed behaviour classification technique in the function learning stage to divide state and action spaces into subspaces and identify classic states and actions. In which the classic states and actions are accumulated as the training dataset that enhances its training efficiency. In the subsequent optimization learning stage, the decision-making network is refined through meticulous exploration and accumulation of datasets. The proposed elastic adaptive deep reinforcement learning enables the decision-making network to effectively learn from complex state and action spaces, leading to more efficient training compared to traditional deep reinforcement learning approaches. Simulation results demonstrate the remarkable effectiveness of our method in training decision-making networks for intelligent vehicles. The findings validate that our method provides reliable and efficient training for decision-making networks in intelligent vehicles. Moreover, our method exhibits stability in training other tasks characterized by continuous state and action spaces.
Gli1 labels progenitors during chondrogenesis in postnatal mice
Authors: Li Boer , Yang Puying , Shen Fangyuan , You Chengjia , Wu Fanzi , Shi Yu , Ye Ling 
Published: February 2024

AbstractSkeletal growth promoted by endochondral ossification is tightly coordinated by self-renewal and differentiation of chondrogenic progenitors. Emerging evidence has shown that multiple skeletal stem cells (SSCs) participate in cartilage formation. However, as yet, no study has reported the existence of common long-lasting chondrogenic progenitors in various types of cartilage. Here, we identify Gli1+chondrogenic progenitors (Gli1+CPs), which are distinct from PTHrP+or FoxA2+SSCs, are responsible for the lifelong generation of chondrocytes in the growth plate, vertebrae, ribs, and other cartilage. The absence of Gli1+CPs leads to cartilage defects and dwarfishness phenotype in mice. Furthermore, we show that the BMP signal plays an important role in self-renewal and maintenance of Gli1+CPs. Deletion ofBmpr1αtriggers Gli1+CPs quiescence exit and causes the exhaustion of Gli1+CPs, consequently disrupting columnar cartilage. Collectively, our data demonstrate that Gli1+CPs are common long-term chondrogenic progenitors in multiple types of cartilage and are essential to maintain cartilage homeostasis.