bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combinations of scleroderma hallmark autoantibodies associate with distinct clinical phenotypes
Authors: Clark Kristina E. N. , Campochiaro Corrado , Host Lauren V. , Sari Alper , Harvey Jennifer , Denton Christopher P. , Ong Voon H. 
Published: July 2022

AbstractSystemic sclerosis (SSc) is characterized by the presence of SSc-specific or SSc-associated antibodies (SSc-Abs): anti-topoisomerase I (ATA), anti-centromere (ACA), anti-RNA polymerase III (ARA), anti-U3RNP (U3RNP), anti-U1RNP (U1RNP), anti-PmScl (PmScl), anti-Ku (Ku) and anti-Th/To (Th/To), each being associated with specific clinical features and prognosis. The detection of more than one SSc-Abs in SSc patients is rare and only few data about these patients’ clinical phenotype is available. The aim of our study was to evaluate the frequency and the disease’s features associated with the presence of > 1 SSc-Abs positivity in a large cohort of SSc patients. The autoantibody profiles of 2799 SSc patients from February 2001 to June 2017 were retrospectively reviewed. Patients with > 1 SSc-Abs were identified. Clinical features were collected and compared to a large historical cohort of SSc patients with single SSc-Ab positivity. SSc patients were excluded if previously treated with rituximab, intravenous immunoglobulins or stem cell transplantation. Non-parametric tests were used for statistical analysis. Nearly 5% of SSc patients from our cohort had ≥ 2 autoantibody positivity, and 2.3% (n = 72) had ≥ 2 SSc-Abs positivity. Th
e most common combination was U1RNP and ATA (35%). These patients were younger than patients with single autoantibody positivity and showed more commonly a diffuse cutaneous SSc form. They also had higher rates of overlap features compared to ATA patients. Other combinations included U1RNP and ACA (13%), ATA and ACA (7%) and U1RNP and PmScl (5%). In our study we observed that, while infrequently, SSc patients can present with a combination of two SSc-Abs and that the double positivity can influence their clinical phenotype compared to patients with single SSc-Ab positivity. The importance of re-testing SSc-Abs in patients with changing clinical phenotypes was also highlighted, as this may confer a differing risk stratification.
Multi-scale electronics transport properties in non-ideal CVD graphene sheet
Authors: Bishnoi Bhupesh , Buerkle Marius , Nakamura Hisao 
Published: July 2022

AbstractIn this work, we benchmark non-idealities and variations in the two-dimensional graphene sheet. We have simulated more than two hundred graphene-based devices structure. We have simulated distorted graphene sheets and have included random, inhomogeneous, asymmetric out-of-plane surface corrugation and in-plane deformation corrugation in the sheet through autocorrelation function in the non-equilibrium Green’s function (NEGF) framework to introduce random distortion in flat graphene. These corrugation effects inevitably appear in the graphene sheet due to background substrate roughness or the passivation encapsulation material morphology in the transfer step. We have examined the variation in density of state, propagating density of transmission modes, electronic band structure, electronic density, and hole density in those device structures. We have observed that the surface corrugation increases the electronic and hole density distribution variation across the device and creates electron-hole charge puddles in the sheet. This redistribution of microscopic charge in the sheet is due to the lattice fields’ quantum fluctuation and symmetry breaking. Furthermore, to understand the impact of scattered charge distribution on the sheet, we simulated various impurity effects within the NEGF framework. The study’s objective is to numerically simulate and benchmark numerous device design morphology with different background materials compositions to elucidate the electrical property of the sheet device.
Eco-friendly approach to improve traits of winter wheat by combining cold plasma treatments and carbonization of subtropical biomass waste
Authors: Saberi Mahin , Ghomi Hamid , Andreasen Christian 
Published: July 2022

AbstractThis study aims to improve the quality and quantity of winter wheat by using the potential of combining the use of cold plasma and waste biorefinery products for improving wheat yield. Plasma was applied by a radio frequency (RF) plasma reactor operated with air for 180 s and 50 W. The waste biorefinery products, including pyroligneous acid, biochar, and azolla compost, were used as plant nutrition. The effects of cold plasma treatment and waste biorefinery products were determined by measuring plant photosynthesis, grain yield, and content of chlorophyll, carotenoids, anthocyanin, protein, and starch. The experiment was conducted during the cropping seasons 2016−18 in a randomized complete block design with four replications. The combination of cold plasma and pyroligneous acid increased the grain yield up to 40.0%. The photosynthesis rate was improved up to 39.3%, and total chlorophyll content up to 48.3% in both years. Seed plasma treatment combined with biochar application increased the starch content by 36.8%. Adding azolla compost increased the protein content by 35.4%. Using seed plasma treatment with biochar increased the microbial biomass carbon by 16.0%. The application of plasma and azolla compost increased the microbial biomass nitrogen by 29.0%.
Transcriptome analysis of human cholangiocytes exposed to carcinogenic 1,2-dichloropropane in the presence of macrophages in vitro
Authors: Ekuban Abigail , Shichino Shigeyuki , Zong Cai , Ekuban Frederick Adams , Kinoshita Kazuo , Ichihara Sahoko , Matsushima Kouji , Ichihara Gaku 
Published: July 2022

Abstract1,2-Dichloropropane (1,2-DCP), a synthetic organic solvent, has been implicated in causality of cholangiocarcinoma (bile duct cancer). 1,2-DCP-induced occupational cholangiocarcinoma show a different carcinogenic process compared to common cholangiocarcinoma, but its mechanism remains elusive. We reported previously that exposure of MMNK-1 cholangiocytes co-cultured with THP-1 macrophages, but not monocultured MMNK-1 cholangiocytes, to 1,2-DCP induced activation-induced cytidine deaminase (AID) expression, DNA damage and ROS production. The aim of this study was to identify relevant biological processes or target genes expressed in response to 1,2-DCP, using an in vitro system where cholangiocytes are co-cultured with macrophages. The co-cultured cells were exposed to 1,2-DCP at 0, 0.1 or 0.4 mM for 24 h, and then the cell lysates were assessed by transcriptome analysis. 1,2-DCP upregulated the expression of base excision repair genes in MMNK-1 cholangiocytes in the co-cultures, whereas it upregulated the expression of cell cycle-related genes in THP-1 macrophages. Activation of the base excision repair pathway might result from the previously observed DNA damage in MMNK-1 cholangiocytes co-cultured with THP-1 macrophages, although involvement of other mechanisms such as DNA replication, cell death or other types of DNA repair was not disproved. Cross talk interactions between cholangiocytes and macrophages leading to DNA damage in the cholangiocytes should be explored.
Variations in seismic parameters for the earthquakes during loading and unloading periods in the Three Gorges Reservoir area
Authors: Zhang Lifen , Liao Wulin , Chen Zhigao , Li Jinggang , Yao Yunsheng , Tong Guangqin , Zhao Yannan , Zhou Ziyan 
Published: July 2022

AbstractAs the largest water conservancy and hydropower project in China, the Three Gorges Reservoir is a weak seismic activity area before impoundment, but the frequency of earthquakes increases significantly after impoundment. The spatial density scanning method was used to obtain the characteristics of spatio-temporal earthquake distribution in the reservoir area during loading and unloading processes. The results show that the frequencies of earthquakes during the loading and unloading processes were higher than that during the low-water-level operation period, which is well explained by the acoustic emission test results. The seismic b-value, fractal dimension D, and spatial correlation length SCL can be used together to indicate stress criticality. To analyze the impacts of reservoir water loading and unloading on seismicity in the reservoir area, time-scan analyses were performed on the b-value, D-value, and SCL of earthquakes near the Zigui segment and the Badong segment. Previous studies argued that the time-varying characteristics of b-values do not hold predictive significance for earthquakes in the M4.0–6.2 range. However, our study found that the time-varying characteristics of b-values are of predictive significance for earthquakes around M4.0. These seismic parameters decrease significantly before moderate earthquakes but at different rates in different regions.
Human enteric adenovirus F40/41 as a major cause of acute gastroenteritis in children in Brazil, 2018 to 2020
Authors: do Nascimento Lilian Gonçalves , Fialho Alexandre Madi , de Andrade Juliana da Silva Ribeiro , de Assis Rosane Maria Santos , Fumian Tulio Machado 
Published: July 2022

AbstractHuman adenovirus (HAdV) types F40/41 have long been recognized as major viral agents of acute gastroenteritis (AGE) in children. Despite this, studies on HAdV molecular epidemiology are sparse, and their real impact is likely under-estimated. Thus, our goal was to investigate HAdV incidence, enteric and non-enteric types circulation, co-detections with rotavirus and norovirus and DNA shedding in stool samples from inpatients and outpatients from eleven Brazilian states. During the three-year study, 1012 AGE stool samples were analysed by TaqMan-based qPCR, to detect and quantify HAdV. Positive samples were genotyped by partial sequencing of the hexon gene followed by phylogenetic analysis. Co-detections were accessed by screening for rotavirus and norovirus. Overall, we detected HAdV in 24.5% of single-detected samples (n = 248), with a prevalence of type F41 (35.8%). We observed a higher incidence in children between 6 to 24 months, without marked seasonality. Additionally, we observed a statistically higher median viral load among single-detections between enteric and non-enteric types and a significantly lower HAdV viral load compared to rotavirus and norovirus in co-detections (p < 0.0001). Our study contributes to the knowledge of HAdV epidemiology and reinforces the need for the inclusion of enteric types F40/41 in molecular surveillance programs.
Gestational age-specific serum creatinine can predict adverse pregnancy outcomes
Authors: Kang Jieun , Hwang Sangwon , Lee Tae Sic , Cho Jooyoung , Seo Dong Min , Choi Seong Jin , Uh Young 
Published: July 2022

AbstractSerum creatinine level (SCr) typically decreases during pregnancy due to physiologic glomerular hyperfiltration. Therefore, the clinical practice of estimated glomerular filtration rate (eGFR) based on SCr concentrations might be inapplicable to pregnant women with kidney disease since it does not take into account of the pregnancy-related biological changes. We integrated the Wonju Severance Christian Hospital (WSCH)-based findings and prior knowledge from big data to reveal the relationship between the abnormal but hidden SCr level and adverse pregnancy outcomes. We analyzed 4004 pregnant women who visited in WSCH. Adverse pregnancy outcomes included preterm birth, preeclampsia, fetal growth retardation, and intrauterine fetal demise. We categorized the pregnant women into four groups based on the gestational age (GA)-unadjusted raw distribution (Q1–4raw), and then GA-specific (Q1–4adj) SCr distribution. Linear regression analysis revealed that Q1-4adj groups had better predictive outcomes than the Q1–4raw groups. In logistic regression model, the Q1–4adj groups exhibited a robust non-linear U-shaped relationship with the risk of adverse pregnancy outcomes, compared to the Q1–4raw groups. The integrative analysis on SCr with respect to GA-specific distribution could be used to screen out pregnant women with a normal SCr coupled with a decreased renal function.
Pattern and rate in the Plio-Pleistocene evolution of modern human brain size
Authors: Gingerich Philip D. 
Published: July 2022

AbstractFourteen studies of brain size evolution in Plio-Pleistocene hominins published over the past fifty years show substantial long-term increase in endocranial volume (ECV) for the broad lineage leading to modern humans. The median generation-to-generation step rate for a consensus time series of ECV values, h0 = 0.15 standard deviations per generation, is almost identical to the median step rate observed in modern biological field studies. When specimens are aggregated in a series of 100 k.y. time bins to reflect the precision of their geological ages, temporal scaling identifies four successive phases of stasis and change that are significantly different from random. Phase I from about 3.2 to 2.0 million years before present is an initial phase of relative stasis. Phase II from 2.0 to 1.5 m.y. is a phase of directional brain size increase. Phase III from 1.5 to 0.7 m.y. is a second phase of stasis. Finally, Phase IV from about 0.7 m.y. to 10 k.y. is a second phase of directional increase. The tempo (rate) and the mode (stasis, random, or directional change) of an evolutionary time series are related to each other, and both are related to the time scale appropriate for analysis.
Protein and functional isoform levels and genetic variants of the BAFF and APRIL pathway components in systemic lupus erythematosus
Authors: Ortiz-Aljaro Pilar , Montes-Cano Marco Antonio , García-Lozano José-Raúl , Aquino Virginia , Carmona Rosario , Perez-Florido Javier , García-Hernández Francisco José , Dopazo Joaquín , González-Escribano María Francisca 
Published: July 2022

AbstractSystemic lupus erythematosus (SLE) is the prototype of an autoimmune disease. Belimumab, a monoclonal antibody targets BAFF, is the only biologic approved for SLE and active lupus nephritis. BAFF is a cytokine with a key-regulatory role in the B cell homeostasis, which acts by binding to three receptors: BAFF-R, TACI and BCMA. TACI and BCMA also bind APRIL. Many studies reported elevated soluble BAFF and APRIL levels in the sera of SLE patients, but other questions about the role of this system in the disease remain open. The study aimed to investigate the utility of the cytokine levels in serum and urine as biomarkers, the role of non-functional isoforms, and the association of gene variants with the disease. This case–control study includes a cohort (women, 18–60 years old) of 100 patients (48% with nephritis) and 100 healthy controls. We used ELISA assays to measure the cytokine concentrations in serum (sBAFF and sAPRIL) and urine (uBAFF and uAPRIL); TaqMan Gene Expression Assays to quantify the relative mRNA expression of ΔBAFF, βAPRIL, and εAPRIL, and next-generation sequencing to genotype the cytokine (TNFSF13 and TNFSF13B) and receptor (TNFRSF13B, TNFRSF17 and TNFRSF13C) genes. The statistical tests used were: Kruskal–Wallis (qualitative variables), the Spearman Rho coefficient (correlations), the Chi-square and SKAT (association of common and rare genetic variants, respectively). As expected, sBAFF and sAPRIL levels were higher in patients than in controls (p ≤ 0.001) but found differences between patient subgroups. sBAFF and sAPRIL significantly correlated only in patients with nephritis (rs = 0.67, p ≤ 0.001) and βAPRIL levels were lower in patients with nephritis (p = 0.04), and ΔBAFF levels were lower in patients with dsDNA antibodies (p = 0.04). Rare variants of TNFSF13 and TNFRSF13B and TNFSF13 p.Gly67Arg and TNFRSF13B p.Val220Ala were associated with SLE. Our study supports differences among SLE patient subgroups with diverse clinical features in the BAFF/APRIL pathway. In addition, it suggests the involvement of genetic variants in the susceptibility to the disease.
Combined inhibition of BADSer99 phosphorylation and PARP ablates models of recurrent ovarian carcinoma
Authors: Zhang Xi , Wang Liqiong , Chen Shu , Huang Peng , Ma Lan , Ding Hui , Basappa Basappa , Zhu Tao , Lobie Peter E. , Pandey Vijay 
Published: July 2022

AbstractBackgroundPoly (ADP-ribose) polymerase inhibitors (PARPis) have been approved for the treatment of recurrent epithelial ovarian cancer (EOC), regardless ofBRCAstatus or homologous recombination repair deficiency. However, the low response of platinum-resistant EOC, the emergence of resistance inBRCA-deficient cancer, and therapy-associated toxicities in patients limit the clinical utility of PARPis in recurrent EOC.MethodsThe association of phosphorylated (p) BADS99 with clinicopathological parameters and survival outcomes in an EOC cohort was assessed by immunohistochemistry. The therapeutic synergy, and mechanisms thereof, between a pBADS99 inhibitor and PARPis in EOC was determined in vitro and in vivo using cell line and patient-derived models.ResultsA positive correlation between pBADS99 in EOC with higher disease stage and poorer survival is observed. Increased pBADS99 in EOC cells is significantly associated withBRCA-deficiency and decreased Cisplatin or Olaparib sensitivity. Pharmacological inhibition of pBADS99 synergizes with PARPis to enhance PARPi IC50and decreases survival, foci formation, and growth in ex vivo culture of EOC cells and patient-derived organoids (PDOs). Combined inhibition of pBADS99 and PARP in EOC cells or PDOs enhances DNA damage but impairs PARPi stimulated DNA repair with a consequent increase in apoptosis. Inhibition of BADS99 phosphorylation synergizes with Olaparib to suppress the xenograft growth of platinum-sensitive and resistant EOC. Combined pBADS99-PARP inhibition produces a complete response in a PDX derived from a patient with metastatic and chemoresistant EOC.ConclusionsA rational and efficacious combination strategy involving combined inhibition of pBADS99 and PARP for the treatment of recurrent EOC is presented.
DRL‐based frequency response of wind turbine generators adapting their variable regulation capabilities
Authors: Ding Zhetong , Wu Jiping , Wang Ying , Shan Shuo , Yuan Kun , Zhang Kaifeng 
Published: July 2022

AbstractFrequency response of wind turbine generators (WTGs) is a crucial technology to ensure safe integration of increasing future wind power into power grids. WTGs' regulation capabilities are variable compared to conventional generations due to uncertain wind speed and dynamic deloading factors, which affects the design of their frequency response strategy. This paper proposes a novel deep reinforcement learning (DRL)‐based frequency response framework of WTGs, combining a deep deterministic policy gradient (DDPG)‐based control and a proportional power sharing (PPS) strategy. The DDPG‐based control dynamically determines the optimal total regulation power of WTGs and the PPS strategy allocates the total regulation power to each WTG. Benefiting from the ability of DDPG algorithm to handle multi‐dimensional continuous system states and actions, the proposed DDPG‐control enables a wind farm to dynamically determine the optimal total frequency regulation power under WTGs' variable regulation capabilities. Besides, the application of deep neural networks (DNN) in DDPG algorithm makes the DDPG‐based control possible to be implemented in complex nonlinear systems. Simulations on an IEEE 39‐bus system demonstrate that effectiveness of the proposed frequency response strategy of WTGs.
Evolution of the flow field in decaying active regions
Authors: Strecker H. , Bello González N. 
Published: July 2022

Context. In a previous work, we investigated the evolution of the flow field around sunspots during sunspot decay and compared it with the flow field of supergranular cells. The decay of a sunspot proceeds as it interacts with its surroundings. This is manifested by the changes observed in the flow field surrounding the decaying spot.
Aims. We now investigate in detail the evolution of the flow field in the direct periphery of the sunspots of the same sample and aim to provide a complete picture of the role of large-scale flows present in sunspot cells.
Methods. We analyse the horizontal velocity profiles of sunspots obtained from observations by the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory (SDO). We follow their evolution across the solar disc from their stable phase to their decay and their final disappearance.
Results. We find two different scenarios for the evolution of the flow region surrounding a spot in the final stage of its decay: (i) either the flow cell implodes and disappears under the action of the surrounding supergranules or (ii) it outlives the spot. In the later case, an inwards flow towards the remaining naked spot develops in the vicinity closest to the spot followed by an outflow further out. These findings provide observational evidence to theoretical predictions by realistic magnetohydrodynamic (MHD) sunspot and moat region simulations.
Conclusions. The Evershed flow and the moat flow, both connected to the presence of fully fledged sunspots in a spot cell, vanish when penumbrae decay. Moat flows decline into supergranular flows. The final fate of a spot cell depends on its interaction with the surrounding supergranular cells. In the case of non-imploding spot cells, the remaining naked spot develops a converging inflow driven by radiative cooling and a geometrical alignment of granules in its periphery which is similar to that observed in pores.
Nano-diamonds in proto-planetary discs
Authors: Jones A. P. 
Published: July 2022

Context.Nano-diamonds remain an intriguing component of the dust in the few sources where they have been observed in emission.Aims.This work focusses on the nano-diamonds observed in circumstellar discs and is an attempt to derive critical information about their possible sizes, compositions, and evolution using a recently derived set of optical constants.Methods.The complex indices of refraction of nano-diamonds and their optical properties (the efficiency factorsQext,Qsca,Qabs, andQpr) were used to determine their temperatures, lifetimes, and drift velocities as a function of their radii (0.5–100 nm), composition (surface hydrogenation and irradiated states), and distance from the central stars in circumstellar regions.Results.The nano-diamond temperature profiles were determined for the stars HR 4049, Elias 1, and HD 97048 in the optically thin limit. The results indicate that large nano-diamonds (a= 30–100 nm) are the hottest and therefore the least resistant in the inner disc regions (~10–50 AU), while small (a< 10 nm) fully hydrogenated nano-diamonds remain significantly cooler in these same regions. We discuss these results within the context of nano-diamond formation in circumstellar discs.Conclusions.Large nano-diamonds, being the hottest, are most affected by the stellar radiation field; however, the effects of radiation pressure appear to be insufficient to move them out of harm’s way. The nano-diamonds that best survive and therefore shine in the inner regions of proto-planetary discs are then seemingly small (a< 10 nm), hydrogenated, and close in size to pre-solar nano-diamonds (〈a〉 ≃ 1.4 nm). Nevertheless, it does not yet appear possible to reconcile their existence with their seemingly short lifetimes in such regions.