bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insulator-to-metal transition in ultrathin rutile VO2/TiO2(001)
Authors: Lahneman D. J. , Slusar Tetiana , Beringer D. B. , Jiang Haoyue , Kim Chang-Yong , Kim Hyun-Tak , Qazilbash M. M. 
Published: July 2022

AbstractAn insulator-to-metal transition (IMT) is an emergent characteristic of quantum materials. When the IMT occurs in materials with interacting electronic and lattice degrees of freedom, it is often difficult to determine if the energy gap in the insulating state is formed by Mott electron–electron correlation or by Peierls charge-density wave (CDW) ordering. To solve this problem, we investigate a representative material, vanadium dioxide (VO2), which exhibits both strong electron–electron interaction and CDW ordering. For this research, VO2 films of different thicknesses on rutile (001) TiO2 substrates have been fabricated. X-ray diffraction (XRD) data show that ultrathin VO2 films with thickness below 7.5 nm undergo the IMT between rutile insulator below Tc and rutile metal above Tc, while an ultrathin VO2 film with a thickness of 8 nm experiences the structural phase transition from the monoclinic structure below Tc to the rutile structure above Tc. Infrared and optical measurements on a film of 7.2 nm thickness, below Tc, reveal the energy gap of 0.6 eV in the rutile insulator phase and the absence of the 2.5 eV bonding-antibonding CDW structure. Above Tc, a Drude feature in the optical conductivity reveals the IMT to a metallic phase. These results suggest that for VO2 films below a critical thickness of about 7.5 nm, the IMT occurs in the rutile structure of VO2 without the Peierls lattice distortion.
Effects of feeding mode on the performance, life span and greenhouse gas emissions of a vertical flow macrophyte assisted vermifilter
Authors: Singh Rajneesh , Ray Chittaranjan , Miller Daniel N. , Durso Lisa M. , Meneses Yulie , Bartelt-Hunt Shannon , D’Alessio Matteo 
Published: July 2022

AbstractThis study was conducted to investigate the impact of intermittent feeding on performance, clogging, and gaseous emission on macrophyte assisted vermifiltration (MAVF) based treatment system. Synthetic slaughterhouse wastewater was applied to two different integrated vertical flow based MAVFs. Triplicates were used throughout the study. Eisenia fetida earthworms were added to MAVFs, and Carex muskingmenis plants were planted. Wastewater was applied to the reactors on 1) intermittent (8 h/day) (IMAVF) and 2) continuous (24 h/day) (CMAVF) basis. The average chemical oxygen demand, total nitrogen, and total phosphorous removals achieved by the IMAVF were 80.2 ± 1.6%, 53.9 ± 1.3% and 66.5 ± 1% respectively, and 68.3 ± 1.3%, 61.2 ± 1.4%, and 60.5 ± 1.4% by the CMAVF, respectively. The diffusion of air to the bedding of IMAVFs during no-flow conditions facilitated higher organics oxidation, adsorption of phosphorous, nitrification, and ammonification. At the end of the study, hydraulic conductivity of IMAVF and CMAVF were found to be 0.036 cm/s and 0.037 cm/s, respectively. CO2, CH4 and N2O emissions from IMAVF were 245.5 ± 38.0 mg C/m2, 5.0 ± 4.6 mg C/m2 and 2513.5 ± 2629.9 μg N/m2 respectively, while CO2, CH4 and N2O emissions from CMAVF were 123.3 ± 14.5 mg C/m2, 74.8±45.2 mg C/m2 and 328.4 ± 93.4 μg N/m2, respectively. Intermittent application of influent could be considered for improving the performance and lifespan of MAVFs, causing lower environmental footprints.
The heterogeneous pharmacological medical biochemical network PharMeBINet
Authors: Königs Cassandra , Friedrichs Marcel , Dietrich Theresa 
Published: July 2022

AbstractHeterogeneous biomedical pharmacological databases are important for multiple fields in bioinformatics. Hetionet is a freely available database combining diverse entities and relationships from 29 public resources. Therefore, it is used as the basis for this project. 19 additional pharmacological medical and biological databases such as CTD, DrugBank, and ClinVar are parsed and integrated into Neo4j. Afterwards, the information is merged into the Hetionet structure. Different mapping methods are used such as external identification systems or name mapping. The resulting open-source Neo4j database PharMeBINet has 2,869,407 different nodes with 66 labels and 15,883,653 relationships with 208 edge types. It is a heterogeneous database containing interconnected information on ADRs, diseases, drugs, genes, gene variations, proteins, and more. Relationships between these entities represent drug-drug interactions or drug-causes-ADR relations, to name a few. It has much potential for developing further data analyses including machine learning applications. A web application for accessing the database is free to use for everyone and available at https://pharmebi.net. Additionally, the database is deposited on Zenodo at https://doi.org/10.5281/zenodo.6578218.
Intratracheal administration of mesenchymal stem cells modulates lung macrophage polarization and exerts anti-asthmatic effects
Authors: Mo Yosep , Kang Hanbit , Bang Ji-Young , Shin Jae Woo , Kim Hye Young , Cho Sang-Heon , Kang Hye-Ryun 
Published: July 2022

AbstractMesenchymal stem cells (MSCs) possess immunomodulatory properties that have therapeutic potential for the treatment of inflammatory diseases. This study investigates the effects of direct MSC administration on asthmatic airways. Umbilical cord MSCs (ucMSCs) were intratracheally administered to six-week-old female BALB/c mice sensitized and challenged with ovalbumin; airway hyperresponsiveness (AHR), analyses of airway inflammatory cells, lung histology, flow cytometry, and quantitative real-time PCR were performed. Furthermore, ex vivo and in vitro experiments were performed to assess the effects of ucMSC on M2 activation. Intratracheally administered ucMSCs decreased degree of airway resistance and the number of inflammatory cells such as T helper 2 (Th2) cells, type 2 innate lymphoid cells (ILC2), and macrophages in the murine asthma model. Particularly, MHCII and CD86 expression diminished in dendritic cells and alveolar macrophages (AMs) following ucMSC treatment. SiglecF+CD11c+CD11b- AMs show a negative correlation with type II inflammatory cells including Th2 cells, ILC2, and eosinophils in asthmatic mice and were restored following intratracheal ucMSCs treatment. In addition, ucMSCs decreased the macrophage polarization to M2, particularly M2a. The expression levels of markers associated with M2 polarization and Th2 inflammation were also decreased. ucMSC reduced Il-12 and Tnfa expression as well as that of M2 markers such as Cd206 and Retnla ex vivo. Furthermore, the in vitro study using IL-4 treated macrophages confirmed that both direct and indirect MSC treatment significantly reduced the expression of Il-5 and Il-13. In conclusion, ucMSCs appear to suppress type II inflammation by regulating lung macrophages via soluble mediators.
Clock-hour topography and extent of outer retinal damage in hydroxychloroquine retinopathy
Authors: Kim Ko Eun , Kim Ji Hong , Kim Young Hwan , Ahn Seong Joon 
Published: July 2022

AbstractIn this study, we investigated the clock-hour topographic characteristics and extent of photoreceptor and retinal pigment epithelium (RPE) damage and correlated the extent with functional defects in eyes with hydroxychloroquine retinopathy. A total of 146 eyes of 75 patients diagnosed with hydroxychloroquine retinopathy were included. The clock-hour topographic characteristics (relative to the fovea) and extent of the photoreceptor and RPE defects in the parafoveal and pericentral areas were evaluated by reviewing the radial-scan optical coherence tomography (OCT) and wide-field fundus autofluorescence (FAF) images. The extent of outer retinal damage in the parafoveal and pericentral areas were correlated with the perimetric parameters of the Humphrey 10–2 and 30–2 tests, respectively. Although the photoreceptor damage was most commonly noted at the temporal to inferior locations in both parafoveal and pericentral areas, the RPE damage in the pericentral eyes was most commonly noted in the nasal area and showed topographic discrepancies with photoreceptor damage. The extent of RPE damage was almost identical between OCT and FAF images, whereas photoreceptor defect extent was significantly greater on OCT images. The extent of parafoveal and pericentral photoreceptor damage on OCT images was significantly correlated with perimetric parameters of the 10–2 and 30–2 tests, respectively (all P < 0.05). Our findings on the detailed topographic characteristics using a clock-hour-based system and significant correlation between the structural extent and perimetric parameters suggest that this evaluation may facilitate more comprehensive descriptions of structural damage extent and predictions of visual function.
The CD226/TIGIT axis is involved in T cell hypo-responsiveness appearance in long-term kidney transplant recipients
Authors: Del Bello Arnaud , Gouin Anna , Chaubet Camille , Kamar Nassim , Treiner Emmanuel 
Published: July 2022

AbstractT cell exhaustion refers to a dysfunctional state in which effector T cells present a decreased ability to proliferate and to produce cytokines, while the co-expression of inhibitory receptors increases. We investigated global and donor-specific T cell responses in a cohort of stable, living-donor kidney transplant patients that received similar immunosuppression. After transplantation, an increase in the ratio of TIGIT + /CD226 + in mCD4 + T cells (r = 0.47, p = 0.01), and a decrease of CD226 + TIGIT-mCD4 + T cells was observed (r = − 0.55, p = 0.001). This leads to an increase of dysfunctional T cells in patients far from transplantation. In mCD8 + T cells, a decrease of IL-2 production after mitogenic stimulation was observed far from transplantation. Phenotypic analyses revealed an increase of mCD8 + T cells co-expressing PD-1 and TIGIT over time (r = 0.51, p = 0.02). After donor-specific stimulation, the ability of CD4 + T cells to proliferate was decreased compared with third parties. CD4 + T cells expressing CD226 and TIGIT were correlated with allospecific CD4 + proliferation (r = 0.68, p = 0.04). Our study suggests that after kidney transplantation a T cell hyporesponsiveness appears over time, driven by a dysregulation of CD226/TIGIT axis in mCD4 + T cells, associated with an increase of PD1 + TIGIT + in mCD8 + T cells.
Lossy and noisy channel simulation in computational ghost imaging by using noise-induced pattern
Authors: Heo Jaesung , Kim Junghyun , Jeong Taek , Lee Sangkyung , Ihn Yong Sup , Kim Zaeill , Jo Yonggi 
Published: July 2022

AbstractWe provide a method to evaluate effects of a lossy and noisy optical channel in computational ghost imaging (CGI) technique. Instead of preparing an external noise source, we simulate the optical channel with a basic CGI experiment using programmatically generated noise-induced patterns. By using our method, we show that CGI can reject a noise of which intensity is similar with an imaging signal intensity at a target. The results with our method are well matched with experimental ones including external noise source. This method would provide useful knowledge to analyze environmental effects in CGI without realization of the environment.
Time series analysis of the air pollution around Ploiesti oil refining complex, one of the most polluted regions in Romania
Authors: Bodor Katalin , Szép Róbert , Bodor Zsolt 
Published: July 2022

AbstractRefineries and petrochemical industries are known to be the principal sources of emissions for a number of air pollutants, such as Volatile Organic Compounds (VOCs), greenhouse gases and particulate matter, which negatively affect the air quality. The primary goal of this research was the time series analysis of PM2.5, PM10, As, Cd, Ni, Pb, benzene, toluene, ethylbenzene, o-xylene, m-xylene, p-xylene, CO, NO, NO2, NOx, SO2 and O3 over an eleven-year period (2009–2019) and the connection between air pollution and meteorological parameters (air temperature, precipitation quantity and relative humidity). Regarding the pollution level of the major pollutants, the minimum pollution levels, except SO2 and O3, were recorded during warmer periods, meanwhile increased levels, were detected during the cold period (in winter). The air pollutants’ concentration and distribution are affected by meteorological parameters, such as wind speed and direction, rainfall or even relative humidity. Therefore, the highest concentrations in the winter season were 1.25 times higher than in autumn, 1.3 times higher than the average annual value, 1.57 times higher than in spring and 1.79 times higher than in summer. Monthly variation of O3 showed lower concentration during winter (27.62 µg/m3) and higher in summer (46.42 µg/m3). Based on the statistical analysis, a significant Spearman correlation was detected between the studied air pollutants and meteorological parameters, and according to the Principal Component Analysis (PCA) and cluster analysis, some common sources were also detected.
Comparison of the efficacies of 1.0 and 1.5 mm silicone tubes for the treatment of nasolacrimal duct obstruction
Authors: Nakamura Jutaro , Kamao Tomoyuki , Mitani Arisa , Mizuki Nobuhisa , Shiraishi Atsushi 
Published: July 2022

AbstractThis retrospective observational study analyzed the postoperative outcomes of bicanalicular intubation using different diameters of tube stents for treating postsaccal nasolacrimal duct obstruction. A total of 130 patients diagnosed with postsaccal obstruction who underwent endoscopic-assisted silicone tube intubation were included in the study. Patients intubated with a 1.5-mm large-diameter tube were designated as the LD group, and those with a 1.0-mm normal-diameter tube were designated as the ND group. The patency rates of the two groups at 1 year after tube removal were compared using the Kaplan–Meier curve and restricted mean survival time (RMST) method with τ = 365 days. Results demonstrated that the recurrence rate after tube removal was significantly lower in the LD group as compared with the ND group (p = 0.001). The patency rates at 1 year after removal in the LD and ND group were 85.7% (95% confidence interval [CI]: 75.4, 91.9) and 73.9% (95% CI: 61.7, 82.8), respectively. When comparing the patency rates by the RMST method at τ = 365 days, the RMST difference, RMST ratio, and RMTL ratio were higher in the LD group at p = 0.045, 0.052, and 0.046, respectively.
O-terminated interface for thickness-insensitive transport properties of aluminum oxide Josephson junctions
Authors: Shan Zheng , Gou Xuelian , Sun Huihui , Wang Shuya , Shang Jiandong , Han Lin 
Published: July 2022

AbstractAlumina Josephson junction has demonstrated a tremendous potential to realize superconducting qubits. Further progress towards scalable superconducting qubits urgently needs to be guided by novel analysis mechanisms or methods to reduce the thickness sensitivity of the junction critical current to the tunnel barrier. Here, it is first revealed that the termination mode of AlOx interface plays a crucial role in the uniformity of critical current, and we demonstrate that the O-terminated interface has the lowest resistance sensitivity to thickness. More impressively, we developed atomically structured three-dimensional models and calculated their transport properties using a combination of quantum ballistic transport theory with first-principles DFT and NEGF to examine the effects of the Al2O3 termination mode and thickness variations. This work clarifies that O-terminated interface can effectively improve the resistance uniformity of Josephson junction, offering useful guidance for increasing the yield of fixed-frequency multi-qubit quantum chips which require tight control on qubit frequency.
Deep learning accurately classifies elbow joint effusion in adult and pediatric radiographs
Authors: Huhtanen Jarno T. , Nyman Mikko , Doncenco Dorin , Hamedian Maral , Kawalya Davis , Salminen Leena , Sequeiros Roberto Blanco , Koskinen Seppo K. , Pudas Tomi K. , Kajander Sami , Niemi Pekka , Hirvonen Jussi , Aronen Hannu J. , Jafaritadi Mojtaba 
Published: July 2022

AbstractJoint effusion due to elbow fractures are common among adults and children. Radiography is the most commonly used imaging procedure to diagnose elbow injuries. The purpose of the study was to investigate the diagnostic accuracy of deep convolutional neural network algorithms in joint effusion classification in pediatric and adult elbow radiographs. This retrospective study consisted of a total of 4423 radiographs in a 3-year period from 2017 to 2020. Data was randomly separated into training (n = 2672), validation (n = 892) and test set (n = 859). Two models using VGG16 as the base architecture were trained with either only lateral projection or with four projections (AP, LAT and Obliques). Three radiologists evaluated joint effusion separately on the test set. Accuracy, precision, recall, specificity, F1 measure, Cohen’s kappa, and two-sided 95% confidence intervals were calculated. Mean patient age was 34.4 years (1–98) and 47% were male patients. Trained deep learning framework showed an AUC of 0.951 (95% CI 0.946–0.955) and 0.906 (95% CI 0.89–0.91) for the lateral and four projection elbow joint images in the test set, respectively. Adult and pediatric patient groups separately showed an AUC of 0.966 and 0.924, respectively. Radiologists showed an average accuracy, sensitivity, specificity, precision, F1 score, and AUC of 92.8%, 91.7%, 93.6%, 91.07%, 91.4%, and 92.6%. There were no statistically significant differences between AUC's of the deep learning model and the radiologists (p value > 0.05). The model on the lateral dataset resulted in higher AUC compared to the model with four projection datasets. Using deep learning it is possible to achieve expert level diagnostic accuracy in elbow joint effusion classification in pediatric and adult radiographs. Deep learning used in this study can classify joint effusion in radiographs and can be used in image interpretation as an aid for radiologists.
Integrating digital pathology and mathematical modelling to predict spatial biomarker dynamics in cancer immunotherapy
Authors: Hutchinson L. G. , Grimm O. 
Published: July 2022

AbstractIn oncology clinical trials, on-treatment biopsy samples are taken to confirm the mode of action of new molecules, among other reasons. Yet, the time point of sample collection is typically scheduled according to 'Expert Best Guess'. We have developed an approach integrating digital pathology and mathematical modelling to provide clinical teams with quantitative information to support this decision. Using digitised biopsies from an ongoing clinical trial as the input to an agent-based mathematical model, we have quantitatively optimised and validated the model demonstrating that it accurately recapitulates observed biopsy samples. Furthermore, the validated model can be used to predict the dynamics of simulated biopsies, with applications from protocol design for phase 1–2 studies to the conception of combination therapies, to personalised healthcare.
Suppression without inhibition: how retinal computation contributes to saccadic suppression
Authors: Idrees Saad , Baumann Matthias-Philipp , Korympidou Maria M. , Schubert Timm , Kling Alexandra , Franke Katrin , Hafed Ziad M. , Franke Felix , Münch Thomas A. 
Published: July 2022

AbstractVisual perception remains stable across saccadic eye movements, despite the concurrent strongly disruptive visual flow. This stability is partially associated with a reduction in visual sensitivity, known as saccadic suppression, which already starts in the retina with reduced ganglion cell sensitivity. However, the retinal circuit mechanisms giving rise to such suppression remain unknown. Here, we describe these mechanisms using electrophysiology in mouse, pig, and macaque retina, 2-photon calcium imaging, computational modeling, and human psychophysics. We find that sequential stimuli, like those that naturally occur during saccades, trigger three independent suppressive mechanisms in the retina. The main mechanism is triggered by contrast-reversing sequential stimuli and originates within the receptive field center of ganglion cells. It does not involve inhibition or other known suppressive mechanisms like saturation or adaptation. Instead, it relies on temporal filtering of the inherently slow response of cone photoreceptors coupled with downstream nonlinearities. Two further mechanisms of suppression are present predominantly in ON ganglion cells and originate in the receptive field surround, highlighting another disparity between ON and OFF ganglion cells. The mechanisms uncovered here likely play a role in shaping the retinal output following eye movements and other natural viewing conditions where sequential stimulation is ubiquitous.
Lymphocyte subsets in Atlantic cod (Gadus morhua) interrogated by single-cell sequencing
Authors: Guslund Naomi Croft , Krabberød Anders K. , Nørstebø Simen F. , Solbakken Monica Hongrø , Jakobsen Kjetill S. , Johansen Finn-Eirik , Qiao Shuo-Wang 
Published: July 2022

AbstractAtlantic Cod (Gadus morhua) has lost themajor histocompatibility complex class IIpresentation pathway. We recently identified CD8-positive T cells, B cells, and plasma cells in cod, but further characterisation of lymphocyte subsets is needed to elucidate immune adaptations triggered by the absence of CD4-positive T lymphocytes. Here, we use single-cell RNA sequencing to examine the lymphocyte heterogeneity in Atlantic cod spleen. We describe five T cell subsets and eight B cell subsets and propose a B cell trajectory of differentiation. Notably, we identify a subpopulation of T cells that are CD8-negative. Most of the CD8-negative T lymphocytes highly express the homologue ofmonocyte chemotactic protein 1b, and another subset of CD8-negative T lymphocytes express the homologue of the scavenger receptorm130. Uncovering the multiple lymphocyte cell sub-clusters reveals the different immune states present within the B and T cell populations, building a foundation for further work.
Mechanisms of resistance to tyrosine kinase inhibitors in liver cancer stem cells and potential therapeutic approaches
Authors: Man Ki-Fong , Ma Stephanie 
Published: July 2022

AbstractThe administration of tyrosine kinase inhibitors (TKIs) for the treatment of advanced-stage patients is common in hepatocellular carcinoma (HCC). However, therapy resistance is often encountered, and its emergence eventually curtails long-term clinical benefits. Cancer stem cells (CSCs) are essential drivers of tumor recurrence and therapy resistance; thus, the elucidation of key hallmarks of resistance mechanisms of liver CSC-driven HCC may help improve patient outcomes and reduce relapse. The present review provides a comprehensive summary of the intrinsic and extrinsic mechanisms of TKI resistance in liver CSCs, which mediate treatment failure, and discusses potential strategies to overcome TKI resistance from a preclinical perspective.
Diagnostics of the dynamics of the Langmuir spectrum based on radio emission during the 12 March 2015 solar radio burst
Authors: Kudryavtsev I. V. , Kaltman T. I. , Karlický M. 
Published: July 2022

Aims.We investigate the dynamics of spectra of Langmuir waves in the plasma radiation of solar radio bursts.Methods.We simulated the radio emission that is formed during the merging of Langmuir waves. The observed frequency spectra of radio bursts were fitted by the model spectrum of Langmuir waves.Results.We determined shapes of the Langmuir wave spectra, consistent with the solar burst observed in the 0.8–2.0 GHz range on 12 March 2015 by the Ondřejov radiospectrograph. We estimated the sizes of the corresponding radio source for different values of the energy density of Langmuir waves. We present the time evolution of the model Langmuir wave spectra at four instants. Finally, we explain a role of the induced scattering of Langmuir waves in the formation of their spectra.