bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photoacoustic effect applied on model membranes and living cells: direct observation with multiphoton excitation microscopy and long-term viability analysis
Authors: Galisteo-González Francisco , Monasterio Bingen G. , Gil David , Valle Mikel , Goñi Félix M. 
Published: January 2020

AbstractThe photoacoustic effect is generated when a variable light interacts with a strongly light-absorbing material. In water, it may produce hot bubbles and shock waves that could affect the integrity of nearby cellular membranes, opening transient pores (photoporation). In this study, we have evaluated the effect of pulsed laser-irradiated carbon nanoparticles (cNP) on model membranes and on Chinese hamster ovary (CHO) cells. Fluorescence lifetime measurements of calcein-loaded liposomes support the notion that the photoacoustic effect causes transient openings in membranes, allowing diffusion fluxes driven by gradient concentrations. With CHO cells, we have shown that this effect can induce either intracellular delivery of calcein, or release of cellular compounds. The latter process has been recorded live with multiphoton excitation microscopy during pulsed infrared laser irradiation. Calcein loading and cell viability were assayed by flow cytometry, measuring necrotic cells as well as those in early apoptosis. To further assess long-term cell recovery after the rather harsh treatment, cells were reseeded and their behaviour recorded for 48 h. These extended studies on cell viability show that pulsed laser cNP photoporation may be considered an adequate intracellular delivery technique only if employed with soft irradiation conditions (below 50 mJ/cm2).
Enhancement of thermo-mechanical stability for nanocomposites containing plasma treated carbon nanotubes with an experimental study and molecular dynamics simulations
Authors: Jung Hana , Choi Hoi Kil , Oh Yuna , Hong Hyunkee , Yu Jaesang 
Published: January 2020

AbstractThis study investigated differences in the thermo-mechanical properties of thermosetting polymer EPON 826 nanocomposites reinforced by modified nanofillers. Carbon nanotubes (CNTs) were modified by environmentally friendly plasma treatments. Composites containing various nitrogen doped CNTs were investigated by morphological and structural analysis, which confirmed that they provided better dispersion and stronger interfacial interaction with the epoxy matrix. In addition, the dynamic mechanical behavior and thermal conductivity were analyzed to understand the energy transfer mechanism in the nanocomposites. The thermal and mechanical properties of the Inductively coupled plasma treated CNTs (ICP-CNT) reinforced nanocomposites containing a high concentration of quaternary and pyridinic types were higher than that of mechanical shear force plasma treated CNTs (MSF-CNT). A molecular dynamics (MD) simulation was performed to support the experimental results and confirmed that controlling the type of nitrogen doping groups was important for improving the thermo-mechanical characteristics of CNT/epoxy nanocomposites.
Classification of Interstitial Lung Abnormality Patterns with an Ensemble of Deep Convolutional Neural Networks
Authors: Bermejo-Peláez David , Ash Samuel Y. , Washko George R. , San José Estépar Raúl , Ledesma-Carbayo María J. 
Published: January 2020

AbstractSubtle interstitial changes in the lung parenchyma of smokers, known as Interstitial Lung Abnormalities (ILA), have been associated with clinical outcomes, including mortality, even in the absence of Interstitial Lung Disease (ILD). Although several methods have been proposed for the automatic identification of more advanced Interstitial Lung Disease (ILD) patterns, few have tackled ILA, which likely precedes the development ILD in some cases. In this context, we propose a novel methodology for automated identification and classification of ILA patterns in computed tomography (CT) images. The proposed method is an ensemble of deep convolutional neural networks (CNNs) that detect more discriminative features by incorporating two, two-and-a-half and three- dimensional architectures, thereby enabling more accurate classification. This technique is implemented by first training each individual CNN, and then combining its output responses to form the overall ensemble output. To train and test the system we used 37424 radiographic tissue samples corresponding to eight different parenchymal feature classes from 208 CT scans. The resulting ensemble performance including an average sensitivity of 91,41% and average specificity of 98,18% suggests it is potentially a viable method to identify radiographic patterns that precede the development of ILD.
Morphological and radiative characteristics of soot aggregates: Experimental and numerical research
Authors: Sutcu Ezgi , Doner Nimeti , Liu Fengshan , Ercetin Umran , Sen Fatih , Yon Jérôme , Morán Jose , Fuentes Andrés 
Published: January 2020

AbstractThe study is aimed at investigating the radiative properties of soot aggregates at determined morphological features using both experimental and numerical methods. Soot aggregates collected from air monitoring stations in different locations were examined. The locations were divided into three groups. The first group (Case 1) included the coastal and industrial zone; the second group (Case 2) consisted of small and large cities; and the third group (Case 3) included areas in the neighbourhood of thermal power plants. The absorbance measurements of the soot aggregates were conducted in the visible and near-infrared spectra, and in the wavelength range of 2 μm-20 μm. The samples were characterised by scanning electron microscopy (SEM), and their radiative properties were assessed using the discrete dipole approximation (DDA) for numerically generated fractal aggregates with two popular refractive indices of m = 1.60 + 0.60i and m = 1.90 + 0.75i. Calculations were conducted for primary particles in point-contact, with 20% overlapping and with a coating (50% and 80%) in the wavelength range of 0.4–1.064 μm. The largest measured absorbance values in both the winter and summer seasons were found in the cities in Case 1, and the x-ray diffraction (XRD) phases of the samples were also presented. The radiative properties of the aggregates, i.e., Df = 1.78 and kf = 2.0 representing Case 3, were close to those of aggregates with Df = 2.1 and kf = 2.35 representing Case 1 in the investigated wavelength range. The calculated radiative properties and the experimental absorbance measurements for point-contact and overlapping situations showed the same trend in the examined wavelengths. The absorbance properties of the samples of coastal and industrial zones were distinctively higher than others in the wavelength range of 2 μm-20 μm which could be attributed to the PAH effects.
Soluble CD93 in allergic asthma
Authors: Park Hye Jung , Oh Eun-Yi , Han Hee-Jae , Park Kyung Hee , Jeong Kyoung-Yong , Park Jung-Won , Lee Jae-Hyun 
Published: January 2020

AbstractCD93 has been shown critical roles in inflammatory and immune diseases. However, in allergic asthma, the potential roles of soluble CD93 (sCD93) have not been well studied. We conducted house dust mite (HDM) stimulation with Der p 1 in BEAS-2B and U937 cells, followed by treatment with dexamethasone or small interfering RNA against CD93. A HDM-induced murine allergic asthma model was also established. We estimated the power of sCD93 to predict allergic asthma in a retrospective post-hoc analysis containing 96 human samples. HDM-stimulated BEAS-2B cells showed increased mRNA expression levels of IL-6, IL-8, IL-33, TSLP, and CD93. The CD93 level in culture supernatants steadily increased for 24 h after allergen stimulation, which was significantly suppressed by both dexamethasone and CD93 silencing. CD93 silencing increased IL-6 and TSLP, but not IL-33 levels in culture supernatants. HDM-induced asthma mice showed significant airway hyperresponsiveness and inflammation with Th2 cytokine activation, along with decreased CD93 expression in bronchial epithelial cells and lung homogenates but increased serum CD93 levels. The sCD93 level in asthma patients was significantly higher than that in healthy controls and could predict asthma diagnosis with moderate sensitivity (71.4%) and specificity (82.4%) (AUC = 0.787, P < 0.001). The level of sCD93 which has potential role to predict asthma significantly increased after HDM stimulation via IL-6 and TSLP in vitro and in vivo.
Characterization of IgG1 Fc Deamidation at Asparagine 325 and Its Impact on Antibody-dependent Cell-mediated Cytotoxicity and FcγRIIIa Binding
Authors: Lu Xiaojun , Machiesky Lee Ann , De Mel Niluka , Du Qun , Xu Weichen , Washabaugh Michael , Jiang Xu-Rong , Wang Jihong 
Published: January 2020

AbstractAntibody-dependent cell-mediated cytotoxicity (ADCC) is an important mechanism of action for many therapeutic antibodies. A therapeutic immunoglobulin (Ig) G1 monoclonal antibody lost more than half of its ADCC activity after heat stress at 40 °C for 4 months. Size-exclusion and ion-exchange chromatography were used to fractionate various size and charge variants from the stressed IgG1. Physicochemical characterization of these fractions revealed that a rarely seen crystallizable fragment (Fc) modification, N325 deamidation, exhibited a positive correlation with the loss of ADCC activity. A further surface plasmon resonance study showed that this modification disrupted the binding between the IgG1 Fc and Fcγ receptor IIIa, resulting in decreased ADCC activity of the IgG1 antibody. Mutants of N325/D and N325/Q were made to confirm the effect of N325 deamidation on ADCC. We hypothesize that N325 deamidation altered the local three-dimensional structure, which might interfere with the binding and interaction with the effector cell. Because of its impact on biological activity, N325 deamidation is a critical quality attribute for products whose mechanism of action includes ADCC. A thorough understanding of the criticality of N325 deamidation and appropriate monitoring can help ensure the safety and efficacy of IgG1 or Fc-fusion products.
Combined microRNA and mRNA detection in mammalian retinas by in situ hybridization chain reaction
Authors: Zhuang Pei , Zhang Huanqing , Welchko Ryan M. , Thompson Robert C. , Xu Shunbin , Turner David L. 
Published: January 2020

AbstractImproved in situ hybridization methods for mRNA detection in tissues have been developed based on the hybridization chain reaction (HCR). We show that in situ HCR methods can be used for the detection of microRNAs in tissue sections from mouse retinas. In situ HCR can be used for the detection of two microRNAs simultaneously or for the combined detection of microRNA and mRNA. In addition, miRNA in situ HCR can be combined with immunodetection of proteins. We use these methods to characterize cells expressing specific microRNAs in the mouse retina. We find that miR-181a is expressed in amacrine cells during development and in adult retinas, and it is present in both GABAergic and glycinergic amacrine cells. The detection of microRNAs with in situ HCR should facilitate studies of microRNA function and gene regulation in the retina and other tissues.
Stable isotope metabolomics of pulmonary artery smooth muscle and endothelial cells in pulmonary hypertension and with TGF-beta treatment
Authors: Hernandez-Saavedra Daniel , Sanders Linda , Freeman Scott , Reisz Julie A. , Lee Michael H. , Mickael Claudia , Kumar Rahul , Kassa Biruk , Gu Sue , D’ Alessandro Angelo , Stenmark Kurt R. , Tuder Rubin M. , Graham Brian B. 
Published: January 2020

AbstractAltered metabolism in pulmonary artery smooth muscle cells (PASMCs) and endothelial cells (PAECs) contributes to the pathology of pulmonary hypertension (PH), but changes in substrate uptake and how substrates are utilized have not been fully characterized. We hypothesized stable isotope metabolomics would identify increased glucose, glutamine and fatty acid uptake and utilization in human PASMCs and PAECs from PH versus control specimens, and that TGF-β treatment would phenocopy these metabolic changes. We used 13C-labeled glucose, glutamine or a long-chain fatty acid mixture added to cell culture media, and mass spectrometry-based metabolomics to detect and quantify 13C-labeled metabolites. We found PH PASMCs had increased glucose uptake and utilization by glycolysis and the pentose shunt, but no changes in glutamine or fatty acid uptake or utilization. Diseased PAECs had increased proximate glycolysis pathway intermediates, less pentose shunt flux, increased anaplerosis from glutamine, and decreased fatty acid β-oxidation. TGF-β treatment increased glycolysis in PASMCs, but did not recapitulate the PAEC disease phenotype. In TGF-β-treated PASMCs, glucose, glutamine and fatty acids all contributed carbons to the TCA cycle. In conclusion, PASMCs and PAECs collected from PH subjects have significant changes in metabolite uptake and utilization, partially recapitulated by TGF-β treatment.
Immunophenotyping monocytes, macrophages and granulocytes in the Pteropodid bat Eonycteris spelaea
Authors: Gamage Akshamal M. , Zhu Feng , Ahn Matae , Foo Randy Jee Hiang , Hey Ying Ying , Low Dolyce H. W. , Mendenhall Ian H. , Dutertre Charles-Antoine , Wang Lin-Fa 
Published: January 2020

AbstractBats are asymptomatic reservoir hosts for several highly pathogenic viruses. Understanding this enigmatic relationship between bats and emerging zoonotic viruses requires tools and approaches which enable the comparative study of bat immune cell populations and their functions. We show that bat genomes have a conservation of immune marker genes which delineate phagocyte populations in humans, while lacking key mouse surface markers such as Ly6C and Ly6G. Cross-reactive antibodies against CD44, CD11b, CD14, MHC II, and CD206 were multiplexed to characterize circulating monocytes, granulocytes, bone-marrow derived macrophages (BMDMs) and lung alveolar macrophages (AMs) in the cave nectar bat Eonycteris spelaea. Transcriptional profiling of bat monocytes and BMDMs identified additional markers – including MARCO, CD68, CD163, CD172α, and CD88 – which can be used to further characterize bat myeloid populations. Bat cells often resembled their human counterparts when comparing immune parameters that are divergent between humans and mice, such as the expression patterns of certain immune cell markers. A genome-wide comparison of immune-related genes also revealed a much closer phylogenetic relationship between bats and humans compared to rodents. Taken together, this study provides a set of tools and a comparative framework which will be important for unravelling viral disease tolerance mechanisms in bats.
Temporal and spatial variations in the bacterial community composition in Lake Bosten, a large, brackish lake in China
Authors: Zhang Lei , Shen Tingting , Cheng Yu , Zhao Tingting , Li Li , Qi Pengfei 
Published: January 2020

AbstractThe bacteria inhabiting brackish lake environments in arid or semi-arid regions have not been thoroughly identified. In this study, the 454 pyrosequencing method was used to study the sedimentary bacterial community composition (BCC) and diversity in Lake Bosten, which is located in the arid regions of northwestern China. A total of 210,233 high-quality sequence reads and 8,427 operational taxonomic units (OTUs) were successfully obtained from 20 selected sediment samples. The samples were quantitatively dominated by members of Proteobacteria (34.1% ± 11.0%), Firmicutes (21.8% ± 21.9%) and Chloroflexi (13.8% ± 5.2%), which accounted for more than 69% of the bacterial sequences. The results showed that (i) Lake Bosten had significant spatial heterogeneity, and TOC(total organic carbon), TN(total nitrogen) and TP(total phosphorus) were the most important contributors to bacterial diversity; (ii) there was lower taxonomic richness in Lake Bosten, which is located in an arid region, than in reference lakes in eutrophic floodplains and marine systems; and (iii) there was a low percentage of dominant species in the BCC and a high percentage of unidentified bacteria. Our data help to better describe the diversity and distribution of bacterial communities in contaminated brackish lakes in arid regions and how microbes respond to environmental changes in these stable inland waters in arid or semi-arid regions.
Active learning for accuracy enhancement of semantic segmentation with CNN-corrected label curations: Evaluation on kidney segmentation in abdominal CT
Authors: Kim Taehun , Lee Kyung Hwa , Ham Sungwon , Park Beomhee , Lee Sangwook , Hong Dayeong , Kim Guk Bae , Kyung Yoon Soo , Kim Choung-Soo , Kim Namkug 
Published: January 2020

AbstractSegmentation is fundamental to medical image analysis. Recent advances in fully convolutional networks has enabled automatic segmentation; however, high labeling efforts and difficulty in acquiring sufficient and high-quality training data is still a challenge. In this study, a cascaded 3D U-Net with active learning to increase training efficiency with exceedingly limited data and reduce labeling efforts is proposed. Abdominal computed tomography images of 50 kidneys were used for training. In stage I, 20 kidneys with renal cell carcinoma and four substructures were used for training by manually labelling ground truths. In stage II, 20 kidneys from the previous stage and 20 newly added kidneys were used with convolutional neural net (CNN)-corrected labelling for the newly added data. Similarly, in stage III, 50 kidneys were used. The Dice similarity coefficient was increased with the completion of each stage, and shows superior performance when compared with a recent segmentation network based on 3D U-Net. The labeling time for CNN-corrected segmentation was reduced by more than half compared to that in manual segmentation. Active learning was therefore concluded to be capable of reducing labeling efforts through CNN-corrected segmentation and increase training efficiency by iterative learning with limited data.
Sodium pentobarbital dosages for exsanguination affect biochemical, molecular and histological measurements in rats
Authors: Mohamed Ayman S. , Hosney Mohamed , Bassiony Heba , Hassanein Sarah S. , Soliman Amel M. , Fahmy Sohair R. , Gaafar Khadiga 
Published: January 2020

AbstractRodents are widely used for animal research in Egypt. Pentobarbital is the most common anesthetic agent; however overdoses may affect the experimental outcomes and limit the use of tissues. To investigate the effects of sodium pentobarbital overdoses during exsanguination, three groups (6 rats/group) of male and female rats were injected i.p. with 50, 100 and 150 mg/kg of sodium pentobarbital, then carotid exsanguination was performed immediately after loss of consciousness. Hypoxia-inducible factor 1-alpha (Hif1a) and tumor necrosis factor-alpha (Tnfa) mRNA expressions in liver and kidney organs were evaluated. As well as, serum aminotransferase activities (AST&ALT), glucose, urea, creatinine, malondialdehyde (MDA), reduced glutathione (GSH) and catalase (CAT) levels were determined. The histological alterations in liver, kidney and spleen were studied. It was found that Hif1a and Tnfa were significantly overexpressed in the studied organs and serum AST, glucose, creatinine and urea levels were significantly increased after sodium pentobarbital overdoses (100 and 150 mg/kg) compared to 50 mg/kg dose. Similarly, significant increase in MDA and GSH levels of liver, kidney and spleen were noticed. Results showed gender difference where Hif1a and Tnfa levels were significantly overexpressed at high dose of sodium pentobarbital of liver and kidney organs in female more than male rats. Since euthanasia protocol may influence the physiological variables and affect genes’ expression, it is recommended to avoid sodium pentobarbital overdose during euthanasia as it may interfere with the biochemical, molecular and histological measurements.
Impacts of climate change and mitigation policies on malt barley supplies and associated virtual water flows in the UK
Authors: Yawson D. O. , Adu M. O. , Armah F. A. 
Published: January 2020

AbstractBarley is a major ingredient for the malting industry which is highly sensitive and vulnerable to malt barley supply. The United Kingdom (UK) has the second highest malting capacity in the EU and the third largest malting industry in the world, supplying malt to major global breweries. Premium whisky, which has both economic and cultural significance for the UK, also makes sustainable malt barley supply critical for the UK. There is paucity of information on the sustainability of future supplies of malt barley in the UK, as much as it is in the world. This study applied a food balance approach to assess the combined effects of climate change and mitigation policies on UK malt barley balances for the 2030s, 2040 s, and 2050 s. Future yields of spring barley were simulated under the low, medium and high emissions scenarios (or LES, MES, and HES, respectively) for the three time slices. Future areas of land for barley production were obtained via land use change simulation in response to climate mitigation policies and aspirations of the UK. Future yields and land areas were combined to obtain total barley production, which served as a basis of supply. Per capita malt barley consumption was combined with future population to obtain demand. The gaps between demand and supply were then assessed. The results show large deficits in malt barley supplies for all combinations of climate change, land use and population, with adverse implications for the malting industry. Total malt barley supplies under current land area for barley and using the 90th percentile yield, ranged from 1899 (LES, 2030s) to 2,437 thousand tonnes (HES, 2050s). The largest supply under climate mitigation land use scenarios ranged from 1,592 (LES, 2030s) to 2,120 thousand tonnes (HES, 2050s). Deficits in supply were observed for all climate mitigation land use scenarios and time slices, ranging from 128 to 585 thousand tonnes at 90th percentile yield. However, surpluses were observed from the 2040s if current land area for barley remains unchanged. Imports to balance the observed deficits would result in large inflows of blue water to the UK, with adverse implications for global freshwater supply and environmental sustainability. It is concluded that even though spring barley yields in the UK could increase under projected climate change, reductions in croplands (due mainly to climate mitigation policies and aspirations) could combine with population growth to undermine the sustainability of malt barley supplies, both nationally and internationally.
Endpoint stiffness magnitude increases linearly with a stronger power grasp
Authors: Takagi A. , Xiong G. , Kambara H. , Koike Y. 
Published: January 2020

AbstractHumans can increase the endpoint stiffness of their arm to reduce self-generated movement variability and to reject unpredictable perturbations from the environment, like during handheld drilling, thereby increasing movement precision. Existing methods to estimate changes in the endpoint stiffness use robotic interfaces to apply position or force perturbations to measure the arm’s dynamic response. We propose an alternative method of measuring changes in the power grasp force to estimate adaptations in the magnitude of the arm’s endpoint stiffness. To validate our method, we examined how the strength of the power grasp, when holding onto a robotic manipulandum, affected the arm’s endpoint stiffness in three different locations of the workspace. The endpoint stiffness magnitude increased linearly with the grasp force, and this linear relationship did not depend on the arm’s posture or position in the workspace. The endpoint stiffness may have increased as a combination of greater grasp stiffness and greater arm stiffness, since larger co-contraction was observed in the elbow and shoulder with a stronger grasp. Changes in the grasp force could serve as a metric in assessing how humans adapt their endpoint stiffness magnitude.