bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activation and evasion of type I interferon responses by SARS-CoV-2
Authors: Lei Xiaobo , Dong Xiaojing , Ma Ruiyi , Wang Wenjing , Xiao Xia , Tian Zhongqin , Wang Conghui , Wang Ying , Li Li , Ren Lili , Guo Fei , Zhao Zhendong , Zhou Zhuo , Xiang Zichun , Wang Jianwei 
Published: July 2020

AbstractThe pandemic of COVID-19 has posed an unprecedented threat to global public health. However, the interplay between the viral pathogen of COVID-19, SARS-CoV-2, and host innate immunity is poorly understood. Here we show that SARS-CoV-2 induces overt but delayed type-I interferon (IFN) responses. By screening 23 viral proteins, we find that SARS-CoV-2 NSP1, NSP3, NSP12, NSP13, NSP14, ORF3, ORF6 and M protein inhibit Sendai virus-induced IFN-β promoter activation, whereas NSP2 and S protein exert opposite effects. Further analyses suggest that ORF6 inhibits both type I IFN production and downstream signaling, and that the C-terminus region of ORF6 is critical for its antagonistic effect. Finally, we find that IFN-β treatment effectively blocks SARS-CoV-2 replication. In summary, our study shows that SARS-CoV-2 perturbs host innate immune response via both its structural and nonstructural proteins, and thus provides insights into the pathogenesis of SARS-CoV-2.
Abnormal dewetting of Ag layer on three-dimensional ITO branches to form spatial plasmonic nanoparticles for organic solar cells
Authors: Dong Wan Jae , Yu Hak Ki , Lee Jong-Lam 
Published: July 2020

AbstractThree-dimensional (3D) plasmonic structures have attracted great attention because abnormal wetting behavior of plasmonic nanoparticles (NPs) on 3D nanostructure can enhance the localized surface plasmons (LSPs). However, previous 3D plasmonic nanostructures inherently had weak plasmonic light absorption, low electrical conductivity, and optical transmittance. Here, we fabricated a novel 3D plasmonic nanostructure composed of Ag NPs as the metal for strong LSPs and 3D nano-branched indium tin oxide (ITO BRs) as a transparent and conductive framework. The Ag NPs formed on the ITO BRs have a more dewetted behavior than those formed on the ITO films. We experimentally investigated the reasons for the dewetting behavior of Ag NPs concerning the geometry of ITO BRs. The spherical Ag NPs are spatially separated and have high density, thereby resulting in strong LSPs. Finite-domain time-difference simulation evidenced that spatially-separated, high-density and spherical Ag NPs formed on ITO BRs dramatically boost the localized electric field in the active layer of organic solar cells (OSCs). Photocurrent of PTB7:PCBM OSCs with the ITO BRs/Ag NPs increased by 14%.
Molecular and metabolomic changes in the proximal colon of pigs infected with Trichuris suis
Authors: Dawson Harry D. , Chen Celine , Li Robert W. , Bell Lauren Nicole , Shea-Donohue Terez , Kringel Helene , Beshah Ethiopia , Hill Dolores E. , Urban Joseph F. 
Published: July 2020

AbstractThe pig whipwormTrichuris suisis important in swine production because of its negative effects on pig performance and, notably, to some humans with inflammatory bowel disease as a therapeutic agent that modulates inflammation. The proximal colon ofT. suis-infected pigs exhibited general inflammation around day 21 after inoculation with infective eggs that is transcriptionally characterized by markers of type-2 immune activation, inflammation, cellular infiltration, tissue repair enzymes, pathways of oxidative stress, and altered intestinal barrier function. Prominent gene pathways involved the Th2-response, de novo cholesterol synthesis, fructose and glucose metabolism, basic amino acid metabolism, and bile acid transport. Upstream regulatory factor analysis implicated the bile acid/farnesoid X receptor in some of these processes. Metabolic analysis indicated changes in fatty acids, antioxidant capacity, biochemicals related to methylation, protein glycosylation, extracellular matrix structure, sugars, Krebs cycle intermediates, microbe-derived metabolites and altered metabolite transport. Close to 1,200 differentially expressed genes were modulated in the proximal colon of pigs with a persistent adult worm infection that was nearly 90% lower in pigs that had expelled worms. The results support a model to test diets that favorably alter the microbiome and improve host intestinal health in both pigs and humans exposed toTrichuris.
Immune network dysregulation precedes clinical diagnosis of asthma
Authors: Chang Yi-Shin , Turturice Benjamin , Schott Cody , Finn Patricia , Perkins David 
Published: July 2020

AbstractAllergic asthma is a chronic disease beginning in childhood that is characterized by dominant T-helper 2 cell activation without adequate counter-regulation by T-helper 1 cell and regulatory T cell activity. Prior transcriptomic studies of childhood asthma have primarily investigated subjects who already have a disease diagnosis, and have generally taken an approach of differential gene expression as opposed to differential gene interactions. The immune states that predispose towards allergic sensitization and disease development remain ill defined. We thus characterize immune networks of asthmatic predisposition in children at the age of 2, prior to the diagnosis of allergic asthma, who are subsequently diagnosed with asthma at the age of 7. We show extensive differences of gene expression networks and gene regulatory networks in children who develop asthma versus those who do not using transcriptomic data from stimulated peripheral blood mononuclear cells. Moreover, transcription factors that bind proximally to one another share patterns of dysregulation, suggesting that network differences prior to asthma diagnosis result from altered accessibility of gene targets. In summary, we demonstrate non-allergen-specific immune network dysregulation in individuals long before clinical asthma diagnosis.
Cementitious composite materials for thermal energy storage applications: a preliminary characterization and theoretical analysis
Authors: Lavagna Luca , Burlon Davide , Nisticò Roberto , Brancato Vincenza , Frazzica Andrea , Pavese Matteo , Chiavazzo Eliodoro 
Published: July 2020

AbstractThe lack of robust and low-cost sorbent materials still represents a formidable technological barrier for long-term storage of (renewable) thermal energy and more generally for Adsorptive Heat Transformations—AHT. In this work, we introduce a novel approach for synthesizing cement-based composite sorbent materials. In fact, considering the number of available hygrosopic salts that can be accommodated into a cementitious matrix—whose morphological properties can be also fine-tuned—the new proposed in situ synthesis paves the way to the generation of an entire new class of possible sorbents for AHT. Here, solely focusing on magnesium sulfate in a class G cement matrix, we show preliminary morphological, mechanical and calorimetric characterization of sub-optimal material samples. Our analysis enables us to theoretically estimate one of the most important figures of merit for the considered applications, namely the energy density which was found to range within 0.088–0.2 GJ/m3 (for the best tested sample) under reasonable operating conditions for space heating applications and temperate climate. The above estimates are found to be lower than other composite materials in the literature. Nonetheless, although no special material optimization has been implemented, our samples already compare favourably with most of the known materials in terms of specific cost of stored energy. Finally, an interesting aspect is found in the ageing tests under water sorption-desorption cycling, where a negligible variation in the adsorption capability is demonstrated after over one-hundred cycles.
Electric-double-layer p–i–n junctions in WSe2
Authors: Fathipour Sara , Paletti Paolo , Fullerton-Shirey Susan K. , Seabaugh Alan C. 
Published: July 2020

AbstractWhile p–n homojunctions in two-dimensional transition metal dichalcogenide materials have been widely reported, few show an ideality factor that is constant over more than a decade in current. In this paper, electric double layer p–i–n junctions in WSe2 are shown with substantially constant ideality factors (2–3) over more than 3 orders of magnitude in current. These lateral junctions use the solid polymer, polyethylene oxide: cesium perchlorate (PEO:CsClO4), to induce degenerate electron and hole carrier densities at the device contacts to form the junction. These high carrier densities aid in reducing the contact resistance and enable the exponential current dependence on voltage to be measured at higher currents than prior reports. Transport measurements of these WSe2p–i–n homojunctions in combination with COMSOL multiphysics simulations are used to quantify the ion distributions, the semiconductor charge distributions, and the simulated band diagram of these junctions, to allow applications to be more clearly considered.
Genomic evidence of recent hybridization between sea turtles at Abrolhos Archipelago and its association to low reproductive output
Authors: Arantes Larissa Souza , Ferreira Lucas Cabral Lage , Driller Maximilian , Repinaldo Filho Fernando Pedro Marinho , Mazzoni Camila Junqueira , Santos Fabrício Rodrigues 
Published: July 2020

AbstractHybridization between sea turtle species occurs with particularly high frequency at two adjacent nesting areas in northeastern Brazil. To understand the outcomes of hybridization and their consequences for sea turtle conservation, we need to evaluate the extent of hybridization occurrence and possible deleterious effects in the hybrid progeny. Thus, we investigated the hypothesis of the existence of a new hybrid spot offshore of Brazil’s northeastern coast. The Abrolhos Archipelago is surrounded by the largest and richest coral reefs in the South Atlantic and is known to be a nesting site for loggerhead turtles (Carettacaretta). In this study, we performed a multidisciplinary investigation into levels of hybridization in sea turtles and their reproductive output in the Abrolhos beaches. Genetic data from mitochondrial DNA (mtDNA) and six autosomal markers showed that there are first-generation hybrid females nesting in Abrolhos, resulting from crossings between hawksbill males (Eretmochelysimbricata) and loggerhead females, and backcrossed hatchlings from both parental species. The type and extent of hybridization were characterized using genomic data obtained with the 3RAD method, which confirmed backcrossing between F1 hybrids and loggerhead turtles. The reproductive output data of Abrolhos nests suggests a disadvantage of hybrids when compared to loggerheads. For the first time, we have shown the association between hybridization and low reproductive success, which may represent a threat to sea turtle conservation.
Isoform-specific functions of an evolutionarily conserved 3 bp micro-exon alternatively spliced from another exon in Drosophila homothorax gene
Authors: Chang Ling-Wen , Tseng I-Chieh , Wang Lan-Hsin , Sun Y. Henry 
Published: July 2020

AbstractMicro-exons are exons of very small size (usually 3–30 nts). Some micro-exons are alternatively spliced. Their functions, regulation and evolution are largely unknown. Here, we present an example of an alternatively spliced 3 bp micro-exon (micro-Ex8) in the homothorax (hth) gene in Drosophila. Hth is involved in many developmental processes. It contains a MH domain and a TALE-class homeodomain (HD). It binds to another homeodomain Exd via its MH domain to promote the nuclear import of the Hth-Exd complex and serve as a cofactor for Hox proteins. The MH and HD domains in Hth as well as the HTh-Exd interaction are highly conserved in evolution. The alternatively spliced micro-exon lies between the exons encoding the MH and HD domains. We provide clear proof that the micro-Ex8 is produced by alternative splicing from a 48 bp full-length exon 8 (FL-Ex8) and the micro-Ex8 is the first three nt is FL-Ex8. We found that the micro-Ex8 is the ancient form and the 3 + 48 organization of alternatively spliced overlapping exons only emerged in the Schizophora group of Diptera and is absolutely conserved in this group. We then used several strategies to test the in vivo function of the two types of isoforms and found that the micro-Ex8 and FL-Ex8 isoforms have largely overlapping functions but also have non-redundant functions that are tissue-specific, which supports their strong evolutionary conservation. Since the different combinations of protein interaction of Hth with Exd and/or Hox can have different DNA target specificity, our finding of alternatively spliced isoforms adds to the spectrum of structural and functional diversity under developmental regulation.
Estimating survival probability using the terrestrial extinction history for the search for extraterrestrial life
Authors: Tsumura Kohji 
Published: July 2020

AbstractSeveral exoplanets have been discovered to date, and the next step is the search for extraterrestrial life. However, it is difficult to estimate the number of life-bearing exoplanets because our only template is based on life on Earth. In this paper, a new approach is introduced to estimate the probability that life on Earth has survived from birth to the present based on its terrestrial extinction history. A histogram of the extinction intensity during the Phanerozoic Eon is modeled effectively with a log-normal function, supporting the idea that terrestrial extinction is a random multiplicative process. Assuming that the fitted function is a probability density function of extinction intensity per unit time, the estimated survival probability of life on Earth is $$\sim0.15$$∼0.15 from the beginning of life to the present. This value can be a constraint on $$f_i$$fi in the Drake equation, which contributes to estimating the number of life-bearing exoplanets.
A nomogram for predicting cancer-specific survival in patients with osteosarcoma as secondary malignancy
Authors: He Yanqi , Liu Han , Wang Shuai , Zhang Jianjun 
Published: July 2020

AbstractThe prognostic factors for survival among patients with secondary osteosarcoma remain unclear. The aim of this study was to develop a practical nomogram for predicting cancer-specific survival (CSS) in patients with osteosarcoma as a secondary malignancy. The surveillance, epidemiology, and end results database was used for the identification of osteosarcoma cases. The total sample comprised 5860 cases of primary osteosarcoma and 268 cases of secondary osteosarcoma during the period from 1973 to 2015. The CSS and overall survival (OS) of primary and secondary osteosarcomas were analyzed. The predictors of CSS for secondary osteosarcoma were identified and integrated to build a nomogram. Validation of the nomogram was performed using concordance index (C-index) and calibration plots. The results indicated that patients with secondary osteosarcoma had poorer CSS and OS than patients with primary osteosarcoma. The nomogram model exhibited high discriminative accuracy in the training cohort (C-index = 0.826), which was confirmed in the internal validation cohort (C-index = 0.791). In addition, the calibration plots confirmed good concordance for prediction of CSS at 3, 5, and 10 years. In conclusion, we developed a practical nomogram that provided individual predictions of CSS for patients with secondary osteosarcoma. This nomogram may help clinicians with prognostic evaluations and with the development of individualized therapies for this aggressive disease.
Binding of S100A6 to actin and the actin–tropomyosin complex
Authors: Jurewicz Ewelina , Robaszkiewicz Katarzyna , Moraczewska Joanna , Filipek Anna 
Published: July 2020

AbstractS100A6 is a low molecular weight Ca2+-binding protein belonging to the S100 family. Many reports indicate that in the cell S100A6 has an influence on the organization of actin filaments, but so far no direct interaction between S100A6 and actin has been shown. In the present study we investigated binding of S100A6 to actin and the actin–tropomyosin complex. The analyses were performed on G- and F-actin and two tropomyosin isoforms—Tpm1.6 and Tpm1.8. Using purified proteins and a variety of biochemical approaches we have shown that, in a Ca2+-bound form, S100A6 directly interacts with G- and F-actin and with tropomyosin, preferentially with isoform Tpm1.8. S100A6 and tropomyosin bind to the same population of filaments and the presence of tropomyosin on the microfilament facilitates the binding of S100A6. By applying proximity ligation assay we have found that in NIH3T3 fibroblasts S100A6 forms complexes both with actin and with tropomyosin. These results indicate that S100A6, through direct interactions with actin and tropomyosin, might regulate the organization and functional properties of microfilaments.
Optical detection of the magnetophoretic transport of superparamagnetic beads on a micromagnetic array
Authors: Gandhi Dhruv , Li Peng , Rampini Stefano , Parent Charlotte , Lee Gil U. 
Published: July 2020

AbstractMicromagnetic arrays (MMAs) have proven to be powerful tools for controlling the transport and separation of bioanalytes, i.e., they allow bioanalyte-superparamagnetic (SPM) bead complexes of specific size and magnetization to be moved in a synchronized manner that is precisely controlled with the orientation of an external magnetic field. This article presents a laser-photodetector system for the simple detection of individual SPM beads moving on a specific region of an MMA. This system detects the SPM beads through the change in intensity of reflective light as they move from the highly reflective micromagnetics to the supporting substrate. We demonstrate that this opti-MMA system allowed the size, number, and magnetic and optical properties of the SPM beads to be rapidly determined for regions > 49 µm2 in size. The response of the opti-MMA system was characterized in several optical configurations to develop a theoretical description of its sensitivity and dynamic range. The speed, low-cost, and sensitivity of this system promises to allow MMAs to be readily applied in in vitro diagnostics and biosensing.
In vivo imaging of the hyaloid vascular regression and retinal and choroidal vascular development in rat eyes using optical coherence tomography angiography
Authors: Kim Yongjoo , Park Jang Ryul , Hong Hye Kyoung , Han Myounghee , Lee Jingu , Kim Pilhan , Woo Se Joon , Park Kyu Hyung , Oh Wang-Yuhl 
Published: July 2020

AbstractThis study investigates the hyaloid vascular regression and its relationship to the retinal and choroidal vascular developments using optical coherence tomography angiography (OCTA). Normal and oxygen-induced retinopathy (OIR) rat eyes at postnatal day 15, 18, 21, and 24 were longitudinally imaged using OCTA. At each day, two consecutive imaging for visualizing the hyaloid vasculature and the retinal and choroidal vasculatures were conducted. The hyaloid vessel volume and the retinal and choroidal vessel densities were measured. The hyaloid vessel volumes gradually decreased during the regression, although the OIR eyes exhibited large vessel volumes at all time points. A spatial relationship between persistent hyaloid vasculature and retardation of underlying retinal vascular development was observed in the OIR eyes. Furthermore, anti-vascular endothelial growth factor (VEGF) was administered intravitreally to additional OIR eyes to observe its effect on the vascular regression and development. The VEGF injection to OIR eyes showed reduced persistent hyaloid vessels in the injected eyes as well as in the non-injected fellow eyes. This study presents longitudinal imaging of intraocular vasculatures in the developing eye and shows the utility of OCTA that can be widely used in studies of vascular development and regression and preclinical evaluation of new anti-angiogenic drugs.
Antenatal magnesium sulfate treatment and risk of necrotizing enterocolitis in preterm infants born at less than 32 weeks of gestation
Authors: Hong Ji Young , Hong Jee Youn , Choi Yun-Sun , Kim Yoo-Min , Sung Ji-Hee , Choi Suk-Joo , Oh Soo-young , Roh Cheong-Rae , Kim Hye Seon , Sung Se In , Ahn So Yoon , Chang Yun Sil , Park Won Soon 
Published: July 2020

AbstractAntenatal magnesium sulfate (MgSO4) treatment is widely used for fetal neuroprotection in women at risk of preterm delivery. However, some studies have recently suggested that in utero MgSO4 exposure is associated with an increased risk of necrotizing enterocolitis (NEC). This study aimed to investigate the association between antenatal MgSO4 treatment and risk of NEC. This retrospective cohort study included 756 infants born at 24–31 weeks’ gestation. Subjects were classified into three groups: period 1, when MgSO4 treatment protocol for fetal neuroprotection was not adopted (n = 267); period 2, when the protocol was adopted (n = 261); and period 3, when the protocol was withdrawn because of concern of risk of NEC (n = 228). Rates of NEC (≥ stage 2b) were analyzed according to time period and exposure to antenatal MgSO4. Significant difference in the rate of NEC was not found across the three time periods (2.6% vs. 6.5% vs. 4.8% in periods 1, 2 and 3, respectively, p = 0.103). The rate of NEC was comparable between the infants unexposed and exposed to antenatal MgSO4 (5.1% vs. 3.6%, p = 0.369). These results showed that antenatal MgSO4 treatment was not associated with risk of NEC in our study population.
A transcriptome and proteome of the tick Rhipicephalus microplus shaped by the genetic composition of its hosts and developmental stage
Authors: Garcia Gustavo R. , Chaves Ribeiro José Marcos , Maruyama Sandra Regina , Gardinassi Luiz Gustavo , Nelson Kristina , Ferreira Beatriz R. , Andrade Thales Galdino , de Miranda Santos Isabel K. Ferreira 
Published: July 2020

AbstractThe cattle tick, Rhipicephalus microplus, is a monoxenous tick that co-evolved with indicine cattle on the Indian subcontinent. It causes massive damage to livestock worldwide. Cattle breeds present heritable, contrasting phenotypes of tick loads, taurine breeds carrying higher loads of the parasite than indicine breeds. Thus, a useful model is available to analyze mechanisms that determine outcomes of parasitism. We sought to gain insights on these mechanisms and used RNA sequencing and Multidimensional Protein Identification Technology (MudPIT) to generate a transcriptome from whole larvae and salivary glands from nymphs, males and females feeding on genetically susceptible and resistant bovine hosts and their corresponding proteomes. 931,698 reads were annotated into 11,676 coding sequences (CDS), which were manually curated into 116 different protein families. Male ticks presented the most diverse armamentarium of mediators of parasitism. In addition, levels of expression of many genes encoding mediators of parasitism were significantly associated with the level and stage of host immunity and/or were temporally restricted to developmental stages of the tick. These insights should assist in developing novel, sustainable technologies for tick control.