bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modulatory role of macrophage migration inhibitory factor on cytokines and clinical features of sarcoidosis
Authors: Elahi Morvarid , Talreja Jaya , Steinbauer Brennen , Koth Laura L. , Samavati Lobelia 
Published: October 2022

AbstractSarcoidosis is a systemic granulomatous disease of unknown etiology with significant heterogeneity in organ manifestations and clinical course. Subjects with sarcoidosis share several features such as, non-necrotizing granuloma, hypergammaglobulinemia, increased local and circulating inflammatory cytokines. Macrophage migration inhibitory factor (MIF) is a pluripotent chemokine modulating cellular function. Study included healthy controls (n = 28) and sarcoidosis patients (n = 65). Sera and BAL of sarcoidosis patients were collected and patients were followed longitudinally for 3 years, and demographics, stages, pulmonary function tests, and organ involvements were recorded. We evaluated MIF in the serum and bronchoalveolar lavage (BAL) fluid of sarcoidosis patients in association with clinical features and cytokines, IL-18, IL-10, IL-6, IFN-γ. We found serum MIF had a positive correlation with IL-10 and IFN-γ and % predicted total lung capacity (%TLC). Serum IL-18 had a significant positive correlation with serum lysozyme, but a negative correlation with %TLC and %DLCO. We identified two groups of sarcoidosis subjects with distinct clinical and cytokine features. A group with prominent extrapulmonary involvement, and low serum MIF, IL-10 and IFN-γ and a group with elevated serum MIF, IL-10 and IFN-γ levels. Our work provides understanding of phenotypic diversity in association with heterogeneity in cytokine landscape in sarcoidosis.
Mitigation pilot contamination based on matching technique for uplink cell-free massive MIMO systems
Authors: Al Ayidh Abdulrahman , Sambo Yusuf , Imran Muhammad Ali 
Published: October 2022

AbstractIn this paper, the cell-free massive multiple input multiple output (MIMO) network is affected by the pilot contamination phenomenon when a large number of users and a small number of available pilots exists, the quality of service (QoS) will deteriorate due to the low accuracy of the channel estimation because some of users will use the same pilot. Therefore, we address this problem by presenting two novel schemes of pilot assignment and pilot power control design based on the matching technique for the uplink of cell-free massive MIMO systems to maximize spectral efficiency. We first formulate an assignment optimization problem in order to find the best possible pilot sequence to be used by utilizing genetic algorithm (GA) and then propose a Hungarian matching algorithm to solve this formulated problem. Regarding the power control design, we formulate a minimum-weighted assignment problem to assign pilot power control coefficients to the estimated channel’s minimum mean-squared error by considering the access point (AP) selection. Then, we also propose the Hungarian algorithm to solve this problem. Simulation results show that our proposed schemes outperform the state-of-the-art techniques concerning both the pilot assignment and the pilot power control design by achieving a 15% improvement in the spectral efficiency. Finally, the computational complexity analysis is provided for the proposed schemes compared with the state-of-the-art techniques.
Extracellular DNA concentrations in various aetiologies of acute kidney injury
Authors: Gaál Kovalčíková Alexandra , Janovičová Ľubica , Hodosy Július , Bábíčková Janka , Vavrincová-Yaghi Diana , Vavrinec Peter , Boor Peter , Podracká Ľudmila , Šebeková Katarína , Celec Peter , Tóthová Ľubomíra 
Published: October 2022

AbstractExtracellular DNA (ecDNA) in plasma is a non-specific biomarker of tissue damage. Urinary ecDNA, especially of mitochondrial origin, is a potential non-invasive biomarker of kidney damage. Despite prominent tissue damage, ecDNA has not yet been comprehensively analysed in acute kidney injury (AKI). We analysed different fractions of ecDNA, i.e. total, nuclear and mitochondrial, in plasma and urine of children, and different animal models of AKI. We also analysed the activity of the deoxyribonuclease (DNase), which is contributes to the degradation of ecDNA. Patients with AKI had higher total and nuclear ecDNA in both, plasma and urine (sixfold and 12-fold in plasma, and 800-fold in urine, respectively), with no difference in mitochondrial ecDNA. This was mainly found for patients with AKI due to tubulointerstitial nephritis and atypical haemolytic uremic syndrome. Increased plasma ecDNA was also found in animal models of AKI, including adenine nephropathy (fivefold), haemolytic uremic syndrome (fourfold), and ischemia–reperfusion injury (1.5-fold). Total urinary ecDNA was higher in adenine nephropathy and ischemia–reperfusion injury (1300-fold and twofold, respectively). DNase activity in urine was significantly lower in all animal models of AKI in comparison to controls. In conclusion, plasma total and nuclear ecDNA and urinary total ecDNA is increased in patients and animals with particular entities of AKI, suggesting a mechanism-dependent release of ecDNA during AKI. Further studies should focus on the dynamics of ecDNA and its potential role in the pathogenesis of AKI.
Acoustic emission induced by sand liquefaction during vibration loading
Authors: Frid Vladimir , Shulov Semen 
Published: October 2022

AbstractThe article deals with the study of poorly graded sand samples of different grain content subjected to liquefaction. The research results show the V-shaped behavior of the AE parameters that correspond to the three-stage sand behavior: Phase A is associated with microfractures/displacements between sand grains caused by an increase in pore pressure before the liquefaction point. Phase B (the stage of AE silence just before the liquefaction point) reflects the equality between pore pressure and stress in the confining chamber. Phase C (the stage of increase in AE parameters’ values) is explained by intense friction between sand grains during their movement caused by liquefaction. Our results show that the AE behavior before, at, and after the liquefaction point is significantly affected by the sand grain content. The change in the sand composition from the poorly graded dune sand to "extremely poorly graded sand" significantly increases the time for the creation of the liquefaction state while the coarser the sand grains become, the longer duration of vibration loading is required to reach the liquefaction state.
Integrating graphene oxide into layers of PVDF/PVDF@cross-linked sodium alginate/polyamide membrane for efficiently enhancing desalination performances
Authors: Mohammadi Zohreh , Seyed Dorraji Mir Saeed , Ahmadi Arsalan , Tarighati Sareshkeh Abdolreza , Rasoulifard Mohammad Hossein 
Published: October 2022

AbstractThe membrane modules of the water treatment system are faced costly damages; thereby executing pre-desalination units based on Nanofiltration (NF) could prevent these suffers, and improve the permeated water flux (PWF) and salt rejection (SR). Hence, we focused on the construction of a novel ternary-layer NF membrane through “electrospinning Polyvinylidene Fluoride (PVDF) (as bottom layer)”, “generating middle layer by electrospinning PVDF along with, the implementation cross-linking after electrospraying Sodium Alginate”, and “synthesizing Polyamide (as top layer) through interfacial polymerization”. More importantly, it anticipated that the Taguchi statistical method can expeditiously optimize the effects of Graphene Oxide nano-sheets (GOns) on water-dependent properties, such as PWF and SR. Astonishingly, the desalination capabilities significantly improved, when the top, middle, and bottom layers simultaneously had 1, 0.1, and 0.1 wt.% of GOns, respectively. Overall, comparing the performances between the optimized sample containing low-dosage and without GOns demonstrated the PWF ameliorated from 6.68 to 20.36 L/m2 h; also, the SR ability remained on an incremental basis as NaCl < MgCl2 < MgSO4 under 6 bar pressure. Manifestly, these authentic results denoted promising, innovative, and large-scaling insights when effectual PWF and SR be necessary.
Design optimization of a linkage-based 2-DOF wheel mechanism for stable step climbing
Authors: Won Jeeho , Ryu Sijun , Kim Sangkyun , Yoo Kwan Yeong , Kim Hwa Soo , Seo Taewon 
Published: October 2022

AbstractThis paper presents the design optimization of a linkage-based wheel mechanism with two degrees of freedom, for stable step climbing. The mechanism has seven rotational joints and one prismatic joint. Kinematic and dynamic analyses of the mechanism were performed. The design was optimized in terms of linkage length and architecture to better manipulate the mechanism in its workspace, which was defined here by the targeted step size, as well as to ensure stability while climbing stairs. Optimization by genetic algorithm was performed using MATLAB. The optimized mechanism exhibited enhanced torque transmission from the input torque to the exerted for at the lobe of the wheel. Compliance control of the transformation will be addressed in the future.
Multi-omics disease module detection with an explainable Greedy Decision Forest
Authors: Pfeifer Bastian , Baniecki Hubert , Saranti Anna , Biecek Przemyslaw , Holzinger Andreas 
Published: October 2022

AbstractMachine learning methods can detect complex relationships between variables, but usually do not exploit domain knowledge. This is a limitation because in many scientific disciplines, such as systems biology, domain knowledge is available in the form of graphs or networks, and its use can improve model performance. We need network-based algorithms that are versatile and applicable in many research areas. In this work, we demonstrate subnetwork detection based on multi-modal node features using a novel Greedy Decision Forest (GDF) with inherent interpretability. The latter will be a crucial factor to retain experts and gain their trust in such algorithms. To demonstrate a concrete application example, we focus on bioinformatics, systems biology and particularly biomedicine, but the presented methodology is applicable in many other domains as well. Systems biology is a good example of a field in which statistical data-driven machine learning enables the analysis of large amounts of multi-modal biomedical data. This is important to reach the future goal of precision medicine, where the complexity of patients is modeled on a system level to best tailor medical decisions, health practices and therapies to the individual patient. Our proposed explainable approach can help to uncover disease-causing network modules from multi-omics data to better understand complex diseases such as cancer.
Growth, structure, phase transition, thermal properties, and structural dynamics of organic–inorganic hybrid [NH3(CH2)5NH3]ZnCl4 crystal
Authors: Lim Ae Ran , Cho Jiung 
Published: October 2022

AbstractIn this study, the physicochemical properties of [NH3(CH2)5NH3]ZnCl4 crystals were investigated using X-ray diffraction (XRD), Fourier transform infrared spectroscopy, differential scanning calorimetry (DSC), thermogravimetric analysis, and nuclear magnetic resonance (NMR). The crystals at 300 K had a monoclinic structure with C2/c space group and lattice constants are a = 21.4175 Å, b = 7.3574 Å, c = 19.1079 Å, β = 120.5190°, and Z = 8. Three endothermic peaks at 256, 390, and 481 K were observed in the DSC curve. From the single-crystal XRD patterns, powder XRD patterns, and optical microscopy results based on the temperature change, the phase transition and melting temperatures were determined to be 390 and 481 K, respectively. NMR studies indicated no change in 1H chemical shifts, but a change in the chemical shifts for C2, located between C1 and C3 of the cation at 340 K. Increase in molecular motion caused an increase in the spin–lattice relaxation time, T1ρ, at low spinning rates, under magic-angle spinning rate conditions. This crystal showed a minor change in the N−H···Cl hydrogen bond, related to the coordination geometry of the ZnCl4 anion.
Pharmacometabolomics reveals urinary diacetylspermine as a biomarker of doxorubicin effectiveness in triple negative breast cancer
Authors: Velenosi Thomas J. , Krausz Kristopher W. , Hamada Keisuke , Dorsey Tiffany H. , Ambs Stefan , Takahashi Shogo , Gonzalez Frank J. 
Published: October 2022

AbstractTriple-negative breast cancer (TNBC) patients receive chemotherapy treatment, including doxorubicin, due to the lack of targeted therapies. Drug resistance is a major cause of treatment failure in TNBC and therefore, there is a need to identify biomarkers that determine effective drug response. A pharmacometabolomics study was performed using doxorubicin sensitive and resistant TNBC patient-derived xenograft (PDX) models to detect urinary metabolic biomarkers of treatment effectiveness. Evaluation of metabolite production was assessed by directly studying tumor levels in TNBC-PDX mice and human subjects. Metabolic flux leading to biomarker production was determined using stable isotope-labeled tracers in TNBC-PDX ex vivo tissue slices. Findings were validated in 12-h urine samples from control (n = 200), ER+/PR+ (n = 200), ER+/PR+/HER2+ (n = 36), HER2+ (n = 81) and TNBC (n = 200) subjects. Diacetylspermine was identified as a urine metabolite that robustly changed in response to effective doxorubicin treatment, which persisted after the final dose. Urine diacetylspermine was produced by the tumor and correlated with tumor volume. Ex vivo tumor slices revealed that doxorubicin directly increases diacetylspermine production by increasing tumor spermidine/spermine N1-acetyltransferase 1 expression and activity, which was corroborated by elevated polyamine flux. In breast cancer patients, tumor diacetylspermine was elevated compared to matched non-cancerous tissue and increased in HER2+ and TNBC compared to ER+ subtypes. Urine diacetylspermine was associated with breast cancer tumor volume and poor tumor grade. This study describes a pharmacometabolomics strategy for identifying cancer metabolic biomarkers that indicate drug response. Our findings characterize urine diacetylspermine as a non-invasive biomarker of doxorubicin effectiveness in TNBC.
The role of Notch signaling in endometrial mesenchymal stromal/stem-like cells maintenance
Authors: Zhang Sisi , Chan Rachel W. S. , Ng Ernest H. Y. , Yeung William S. B. 
Published: October 2022

AbstractHuman endometrium undergoes cycles of regeneration in women of reproductive age. The endometrial mesenchymal stromal/stem cells (eMSC) contribute to this process. Notch signaling is essential for homeostasis of somatic stem cells. However, its role in eMSC remains unclear. We show with gain- and loss-of-function experiments that activation of Notch signaling promotes eMSC maintenance, while inhibition induces opposite effect. The activation of Notch signaling better maintains eMSC in a quiescent state. However, these quiescent eMSC can re-enter the cell cycle depending on the Notch and Wnt activities in the microenvironment, suggesting a crosstalk between the two signaling pathways. We further show that the Notch signaling is involved in endometrial remodeling event in a mouse menstrual-like model. Suppression of Notch signaling reduces the proliferation of Notch1+ label-retaining stromal cells and delays endometrial repair. Our data demonstrate the importance of Notch signaling in regulating the endometrial stem/progenitor cells in vitro and in vivo.
Frontal polymerization-triggered simultaneous ring-opening metathesis polymerization and cross metathesis affords anisotropic macroporous dicyclopentadiene cellulose nanocrystal foam
Authors: Park Jinsu , Kwak Seung-Yeop 
Published: October 2022

AbstractMultifunctionality and effectiveness of macroporous solid foams in extreme environments have captivated the attention of both academia and industries. The most recent rapid, energy-efficient strategy to manufacture solid foams with directionality is the frontal polymerization (FP) of dicyclopentadiene (DCPD). However, there still remains the need for a time efficient one-pot approach to induce anisotropic macroporosity in DCPD foams. Here we show a rapid production of cellular solids by frontally polymerizing a mixture of DCPD monomer and allyl-functionalized cellulose nanocrystals (ACs). Our results demonstrate a clear correlation between increasing % allylation and AC wt%, and the formed pore architectures. Especially, we show enhanced front velocity (vf) and reduced reaction initiation time (tinit) by introducing an optimal amount of 2 wt% AC. Conclusively, the small- and wide-angle X-ray scattering (SAXS, WAXS) analyses reveal that the incorporation of 2 wt% AC affects the crystal structure of FP-mediated DCPD/AC foams and enhances their oxidation resistance.
Defect-induced tuning of polarity-dependent adsorption in hydrophobic–hydrophilic UiO-66
Authors: Jajko Gabriela , Calero Sofia , Kozyra Paweł , Makowski Wacław , Sławek Andrzej , Gil Barbara , Gutiérrez-Sevillano Juan José 
Published: October 2022

AbstractStructural defects in metal–organic frameworks can be exploited to tune material properties. In the case of UiO-66 material, they may change its nature from hydrophobic to hydrophilic and therefore affect the mechanism of adsorption of polar and non-polar molecules. In this work, we focused on understanding this mechanism during adsorption of molecules with different dipole moments, using the standard volumetric adsorption measurements, IR spectroscopy, DFT + D calculations, and Monte Carlo calculations. Average occupation profiles showed that polar and nonpolar molecules change their preferences for adsorption sites. Hence, defects in the structure can be used to tune the adsorption properties of the MOF as well as to control the position of the adsorbates within the micropores of UiO-66.
Wide-bandgap GaN-based watt-class photonic-crystal lasers
Authors: Emoto Kei , Koizumi Tomoaki , Hirose Masaki , Jutori Masahiro , Inoue Takuya , Ishizaki Kenji , De Zoysa Menaka , Togawa Hiroyuki , Noda Susumu 
Published: October 2022

AbstractShort-wavelength (blue-violet-to-green) lasers with high power and high beam quality are required for various applications including the machining of difficult-to-process materials and high-brightness illuminations and displays. Promising light sources for such applications are wide-bandgap GaN-based photonic-crystal surface-emitting lasers (PCSELs), which are based on two-dimensional resonance in the photonic crystal. Developments of these devices have lagged behind those of longer-wavelength GaAs-based PCSELs, because device designs for achieving robust two-dimensional resonance and a nanofabrication process that avoids introducing disorders have remained elusive for wide-bandgap GaN-based materials. Here, we address these issues and successfully realize GaN-based PCSELs with high, watt-class (>1 W) output power and a circular, single-lobed beam with a very narrow (~0.2°) divergence angle at blue wavelengths. In addition, we demonstrate continuous-wave operation with a high output power (~320 mW) and a high beam quality (M2~1). Our results will enable the use of GaN-based PCSELs in the above-mentioned applications.
Multi-omic phenotyping reveals host-microbe responses to bariatric surgery, glycaemic control and obesity
Authors: Penney Nicholas C. , Yeung Derek K. T. , Garcia-Perez Isabel , Posma Joram M. , Kopytek Aleksandra , Garratt Bethany , Ashrafian Hutan , Frost Gary , Marchesi Julian R. , Purkayastha Sanjay , Hoyles Lesley , Darzi Ara , Holmes Elaine 
Published: October 2022

Abstract
Background
Resolution of type 2 diabetes (T2D) is common following bariatric surgery, particularly Roux-en-Y gastric bypass. However, the underlying mechanisms have not been fully elucidated.

Methods
To address this we compare the integrated serum, urine and faecal metabolic profiles of participants with obesity ± T2D (n = 80, T2D = 42) with participants who underwent Roux-en-Y gastric bypass or sleeve gastrectomy (pre and 3-months post-surgery; n = 27), taking diet into account. We co-model these data with shotgun metagenomic profiles of the gut microbiota to provide a comprehensive atlas of host-gut microbe responses to bariatric surgery, weight-loss and glycaemic control at the systems level.

Results
Here we show that bariatric surgery reverses several disrupted pathways characteristic of T2D. The differential metabolite set representative of bariatric surgery overlaps with both diabetes (19.3% commonality) and body mass index (18.6% commonality). However, the percentage overlap between diabetes and body mass index is minimal (4.0% commonality), consistent with weight-independent mechanisms of T2D resolution. The gut microbiota is more strongly correlated to body mass index than T2D, although we identify some pathways such as amino acid metabolism that correlate with changes to the gut microbiota and which influence glycaemic control.

Conclusion
We identify multi-omic signatures associated with responses to surgery, body mass index, and glycaemic control. Improved understanding of gut microbiota - host co-metabolism may lead to novel therapies for weight-loss or diabetes. However, further experiments are required to provide mechanistic insight into the role of the gut microbiota in host metabolism and establish proof of causality.
Interfacial-assembly engineering of asymmetric magnetic-mesoporous organosilica nanocomposites with tunable architectures
Authors: Wu Yue , Sun Yangyi , Zhang Chengyu , He Mengyao , Qi Dongming 
Published: October 2022

Interfacial-assembly engineering for controllable preparation of length-tunable asymmetric nanoarchitectures (i.e., organosilica nano-tails) on magnetic Fe3O4 nanoparticles.
α-Adrenergic blockade prevented environmental temperature reduction-induced transient portal pressure surge in cirrhotic and portal hypertensive rats
Authors: Huang Hui-Chun , Chang Ching-Chih , Pun Chon Kit , Tsai Ming-Hung , Chuang Chiao-Lin , Hsu Shao-Jung , Huang Yi-Hsiang , Hou Ming-Chih , Lee Fa-Yauh 
Published: October 2022

Abstract
Exposure to low temperatures has been associated with increased gastroesophageal variceal bleeding in patients with cirrhosis and portal hypertension; however, the mechanism remains unclear. Therefore, the aim of the present study was to evaluate the impact of environmental temperature reduction on portal hypertension and the role of adrenergic signaling pathways in this phenomenon. Male Sprague-Dawley rats underwent common bile duct ligation or partial portal vein ligation to induce liver cirrhosis and/or portal hypertension. The impacts of acute or chronic changes in environmental temperature were surveyed. The results showed that acute cooling from 25 to 15°C and 5°C increased the portal pressure by 10.6% and 15.5% in cirrhotic rats, and by 22.2% and 36.1% in portal hypertensive rats, respectively. The transient portal pressure surge started shortly after cooling, reached a peak within 5 min and returned to baseline after 10 min. Systemic vascular resistance, mean arterial pressure and splanchnic blood flow increased significantly at the same time. Plasma epinephrine and norepinephrine concentrations, phospholipase C, protein kinase C activity and myosin phosphorylation of peripheral arteries increased significantly in response to cooling. Phentolamine (an α-blocker) but not propranolol (a non-selective β-blocker) dose-dependently inhibited the transient portal pressure surge and aforementioned molecular changes. In conclusion, environmental temperature reduction induced peripheral vasoconstriction via α-adrenergic pathways, and redistribution of blood flow to the splanchnic system led to a surge in transient portal pressure. Treatment with α-adrenergic receptor antagonists may exert additional benefits in controlling portal hypertension, especially on exposure to low temperatures.