bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping periplasmic binding protein oligosaccharide recognition with neutron crystallography
Authors: Shukla Shantanu , Myles Dean A. , Cuneo Matthew J. 
Published: October 2022

AbstractNumerous studies have shown how periplasmic binding proteins (PBPs) bind substrates with exquisite specificity, even distinguishing between sugar epimers and anomers, or structurally similar ions. Yet, marked substrate promiscuity is also a feature encoded in some PBPs. Except for three sub-Ångström crystal structures, there are no reports of hydrogen atom positions in the remaining (> 1000) PBP structures. The previous X-ray crystal structure of the maltodextrin periplasmic-binding protein from Thermotoga maritima (tmMBP) complexed with oligosaccharide showed a large network of interconnected water molecules stretching from one end of the substrate binding pocket to the other. These water molecules are positioned to form multiple hydrogen bonds, as well as forming interactions between the protein and substrate. Here we present the neutron crystal structure of tmMBP to a resolution of 2.1 Å. This is the first neutron crystal structure from the PBP superfamily and here we unambiguously identify the nature and orientation of the hydrogen bonding and water-mediated interactions involved in stabilizing a tetrasaccharide in the binding site. More broadly, these results demonstrate the conserved intricate mechanisms that underlie substrate-specificity and affinity in PBPs.
Bioremediation of copper in sediments from a constructed wetland ex situ with the novel bacterium Cupriavidus basilensis SRS
Authors: Kugler Alex , Brigmon Robin L. , Friedman Abby , Coutelot Fanny M. , Polson Shawn W. , Seaman John C. , Simpson Waltena 
Published: October 2022

AbstractThe H-02 constructed wetland was designed to remove metals (primarily copper and zinc) to treat building process water and storm water runoff from multiple sources associated with the Tritium Facility at the DOE-Savannah River Site, Aiken, SC. The concentration of Cu and Zn in the sediments has increased over the lifetime of the wetland and is a concern. A bioremediation option was investigated at the laboratory scale utilizing a newly isolated bacterium of the copper metabolizing genus Cupriavidus isolated from Tim’s Branch Creek, a second-order stream that eventually serves as a tributary to the Savannah River, contaminated with uranium and other metals including copper, nickel, and mercury. Cupriavidus basilensis SRS is a rod-shaped, gram-negative bacterium which has been shown to have predatory tendencies. The isolate displayed resistance to the antibiotics ofloxacin, tetracycline, ciprofloxacin, select fungi, as well as Cu2+ and Zn2+. Subsequent ribosomal sequencing demonstrated a 100% confidence for placement in the genus Cupriavidus and a 99.014% match to the C. basilensis type strain. When H-02 wetland samples were inoculated with Cupriavidus basilensis SRS samples showed significant (p < 0.05) decrease in Cu2+ concentrations and variability in Zn2+ concentrations. Over the 72-h incubation there were no significant changes in the inoculate densities (106–108 cells/ML) indicating Cupriavidus basilensis SRS resiliency in this environment. This research expands our understanding of the Cupriavidus genus and demonstrates the potential for Cupriavidus basilensis SRS to bioremediate sites impacted with heavy metals, most notably copper.
Optical trapping and fluorescence control with vectorial structured light
Authors: Kritzinger Ané , Forbes Andrew , Forbes Patricia B. C. 
Published: October 2022

AbstractHere we functionalized micro-scaled polymer beads with nano-scaled quantum dots and demonstrate optical trapping and tweezing, with in-situ fluorescence measurement, in an all-digital all-optical configuration. We outline the chemistry required to facilitate this, from deactivating the optical trapping environment to size, adhesion and agglomeration control. We introduce a novel holographic optical trapping set-up that leverages on vectorially structured light, allowing for the delivery of tuneable forms of light from purely scalar to purely vector, including propagation invariant flat-top beams for uniform illumination and tailored intensity gradient landscapes. Finally, we show how this has the potential to quench bleaching in a single wavelength trap by linear (spatial mode) rather than non-linear effects, advancing the nascent field of optics for chemistry.
Modeling the spatio‑temporal spread of COVID‑19 cases, recoveries and deaths and effects of partial and full vaccination coverage in Canada
Authors: Momenyan Somayeh , Torabi Mahmoud 
Published: October 2022

AbstractThe purposes of our study are to map high-risk areas in Canada as well as quantifying the effects of vaccination intervention and socio-demographic factors on the transmission rates of infection, recovery, and death related to COVID-19. The data of this research included weekly number of COVID‑19 ﻿cases, recovered, and dead individuals from 2020 through 2021 in Canada at health region and provincial levels. These data were associated with cumulative rates of partial and full vaccination and socio-demographic factors. We applied the spatio-temporal Susceptible-Exposed-Infected-Removed (SEIR), and Susceptible-Exposed-Infected-Removed-Vaccinated (SEIRV) models. The results indicated the partial vaccination rate has a greater effect compared with full vaccination rate on decreasing the rate of infectious cases (risk ratio (RR) = 0.18; 95%CrI: 0.16–0.2; RR = 0.60; 95%CrI: 0.55–0.65, respectively) and increasing the rate of recovered cases (RR = 1.39; 95%CrI: 1.28–1.51; RR = 1.21; 95%CrI: 1.23–1.29, respectively). However, for mortality risk reduction, only increasing full vaccination rate was significantly associated (RR = 0.09; 95%CrI: 0.05–0.14). In addition, our results showed that regions with higher rates of elderly and aboriginal individuals, higher population density, and lower socioeconomic status (SES) contribute more to the risk of infection transmission. Rates of elderly and aboriginal individuals and SES of regions were significantly associated with recovery rate. However, elderly individuals rate of regions was only a significant predictor of mortality risk. Based on the results, protection against mild and severe COVID-19 infection after the primary vaccination series decreased.
Changes in expression of nuclear factor kappa B subunits in the ovine thymus during early pregnancy
Authors: Yang Ling , Cai Chunjiang , Fang Shengya , Hao Shaopeng , Zhang Taipeng , Zhang Leying 
Published: October 2022

AbstractThere is a pregnant maternal immunological tolerance that protects the fetus and promotes its growth, and nuclear factor kappa B (NF-κB) family participates in the regulation of innate immune and adaptive immune responses. The thymus is related to establishing central tolerance, and early pregnancy has effects on expression of a good number of genes and proteins in the maternal thymus in sheep. However, it is unclear whether early pregnancy changes expression of NF-κB subunits in the ovine thymus. In this study, the thymic samples were collected from day 16 of non-pregnant ewes, and days 13, 16 and 25 of pregnant ewes, and the expression of NF-κB members (NF-κB1, NF-κB2, RelA, RelB and c-Rel) was analyzed through real-time quantitative PCR, Western blot and immunohistochemical analysis. The results showed that c-Rel mRNA and protein upregulated at day 25 of pregnancy, and NF-κB1 mRNA and proteins increased at days 16 and 25 of pregnancy, and RelB mRNA and proteins enhanced during early pregnancy. However, expression levels of NF-κB2 and RelA were decreased during early pregnancy, but upregulated from day 13 to 25 of pregnancy. In addition, the RelA protein was located in the epithelial reticular cells, capillaries and thymic corpuscles. This paper reported for the first time that early pregnancy induced expression of NF-κB1, RelB and c-Rel, but inhibited expression of NF-κB2 and RelA in the maternal thymus during early pregnancy, which is involved in the central immune tolerance, and helpful for successful pregnancy in sheep.
Thermohydraulic analysis of covalent and noncovalent functionalized graphene nanoplatelets in circular tube fitted with turbulators
Authors: Tao Hai , Alawi Omer A. , Hussein Omar A. , Ahmed Waqar , Abdelrazek Ali H. , Homod Raad Z. , Eltaweel Mahmoud , Falah Mayadah W. , Al-Ansari Nadhir , Yaseen Zaher Mundher 
Published: October 2022

AbstractCovalent and non-covalent nanofluids were tested inside a circular tube fitted with twisted tape inserts with 45° and 90° helix angles. Reynolds number was 7000 ≤ Re ≤ 17,000, and thermophysical properties were assessed at 308 K. The physical model was solved numerically via a two-equation eddy-viscosity model (SST k-omega turbulence). GNPs-SDBS@DW and GNPs-COOH@DW nanofluids with concentrations (0.025 wt.%, 0.05 wt.% and 0.1 wt.%) were considered in this study. The twisted pipes' walls were heated under a constant temperature of 330 K. The current study considered six parameters: outlet temperature, heat transfer coefficient, average Nusselt number, friction factor, pressure loss, and performance evaluation criterion. In both cases (45° and 90° helix angles), GNPs-SDBS@DW nanofluids presented higher thermohydraulic performance than GNPs-COOH@DW and increased by increasing the mass fractions such as 1.17 for 0.025 wt.%, 1.19 for 0.05 wt.% and 1.26 for 0.1 wt.%. Meanwhile, in both cases (45° and 90° helix angles), the value of thermohydraulic performance using GNPs-COOH@DW was 1.02 for 0.025 wt.%, 1.05 for 0.05 wt.% and 1.02 for 0.1 wt.%.
Disfluency-Affirming Therapy for Young People Who Stutter: Unpacking Ableism in the Therapy Room
Authors: Sisskin Vivian 
Published: October 2022

Purpose:
Ableist messages are conveyed early in the life of a stutterer and are amplified throughout the school-age years. Increased recognition of the benefits of acceptance-based therapies for positive long-term outcomes has changed the narrative about stuttering and stutterers. Speech-language therapists are resonating with the ideas that “it is okay to stutter,” socioemotional aspects of stuttering must be considered, and support and community are valuable. Despite the shift in understanding, messages conveyed to students and parents commonly encourage suppression of stuttering and masking of one's stuttering identity. The purpose of this article was to (a) expose unintentional ableist messages that perpetuate stigma and feeling “othered” in the therapy relationship and (b) offer suggestions for congruent messaging in stuttering therapy.

Conclusions:
Ableism in stuttering therapy contributes to the physical struggle and socioemotional challenges experienced by stutterers. The author offers ideas for revisioning therapy outcomes, language, and messaging to students to encourage a congruent, disfluency-affirming culture in schools and community. Introspection and advocacy by both therapists and the broader professional community, in collaboration with young people who stutter, will serve to reduce the stigma that fuels many of the daily challenges faced by school-age children who stutter.
Adaptive neural network control of a non‐linear two‐degree‐of‐freedom helicopter system with prescribed performance
Authors: Ma Ge , Wu Huiyuan , Zhao Zhijia , Zou Tao , Hong Keum‐Shik 
Published: October 2022

AbstractThis study develops a neural network control for a non‐linear two‐degree‐of‐freedom unmanned helicopter system satisfying prescribed performance constraints is developed. By introducing a prescribed performance function to express the system constraints, a constrained tracking control problem is transformed into an equivalent unconstrained stability problem through error transformations. The neural network controller is designed to ensure that the tracking error converges to a small neighborhood of zero and that the prescribed performance constraints are satisfied. Furthermore, the stability and error convergence of the system are analysed through the Lyapunov direct approach. The effectiveness of the proposed control scheme is verified by simulation and experimental results.
Fast electrothermal coupling calculation method for supporting digital twin construction of electrical equipment
Authors: Zhu Xiaosong , Wang Youyuan , Meng Ruixiao , Long Shi , Wu Shaowen 
Published: October 2022

AbstractThe failure of electrical equipment directly or indirectly caused by overheating has become one of the main reasons for equipment accidents. The real‐time condition monitoring method of electrical equipment based on digital twin (DT) has received extensive attention and is considered as a technology with great engineering values and excellent application prospects. However, the current calculation of DT mostly relies on the traditional finite element method (CFEM). This method becomes less computationally efficient as the size of the DT increases, especially for electrical equipment with high complexity. It is difficult to meet the requirements real‐time calculation in DT. Therefore, starting from the algorithm optimization and parallel architecture, based on the weighted residual method and stabilised conforming nodal integration, a novel discrete method of electrothermal coupling equation is proposed and the data storage structure of the algorithm from the bottom layer is redesigned, and the corresponding GPU and multi‐core CPU parallel framework are proposed. Finally, taking the high voltage bushing as an example, the correctness of the method in this paper is verified by the CFEM code and commercial software ABAQUS. Under the same grid and accuracy requirement, the calculation time is shortened by at least five times than ABAQUS. And the method is easy to extend to other types of multi‐physics calculations.
Insulation degradation and fracture cracks of mechanical impacted thermal‐ageing oil‐impregnated papers
Authors: Chi Minghe , Xia Ruochun , Guan Yi , Sun Weifeng , Liu Ji , Chen Qingguo 
Published: October 2022

AbstractIn order to elucidate mechanical impacts affecting the insulation strength of thermal‐ageing oil‐impregnated pressboards, we perform mechanical degradation experiments of impacting forces that are represented as the winding‐suffered stresses on thermal‐ageing oil‐paper insulation in transient short‐circuit of transformer. Water content, degree of polymerisation (DP), partial discharge inception voltage and AC breakdown field strength are tested and analysed for diverse thermal‐ageing levels. An analytical model of mechanical degradation is established by relating dielectric breakdown strength to mechanical impact. Mechanical impacts result in less water content in thermal‐aging oil‐impregnated pressboards while causing reduction and increment of DP, respectively, in mildly and severely aged oil‐impregnated pressboards. Partial discharge inception voltage and dielectric breakdown strength vary significantly with the numbers of impact cycles, showing a maximum value under low‐intensity impact and decreasing monotonously under high‐intensity impact. High‐intensity mechanical impacts will evidently exacerbate the thermal deterioration process of oil‐impregnated pressboards, which is primarily attributed to cellulose fibre fractures in pressboard cracks produced by equivalent tensile stress of mechanical impacts. It is acceptable for mildly aged oil‐impregnated pressboards to suffer low‐intensity mechanical impacts that will alleviate insulation degradation by restraining partial discharge in smaller oil‐gaps and prolonging breakdown discharge pathways along impact‐caused cracks.
Accretion variability in RU Lup
Authors: Stock C. , McGinnis P. , Caratti o Garatti A. , Natta A. , Ray T. P. 
Published: October 2022

Context. The process of accretion in classical T Tauri stars (CTTSs) has been observed to vary on different timescales. Studying this variability is vital to understanding a star’s evolution and provides insight into the complex processes at work within, including sources of the veiling present. Understanding the dichotomy between continuum veiling and emission line veiling is integral to accurately measuring the amount of veiling present in stellar spectra.
Aims. Here, 15 roughly consecutive nights of optical spectroscopic data from the spectropolarimeter ESPaDOnS are utilised to characterise the short-term accretion activity in the CTTS, RU Lup, and investigate its relationship with the veiling in the Li I 6707 Å absorption line.
Methods. The accretion-tracing H I Balmer series emission lines were studied and used to obtain the accretion luminosity (Lacc) and mass accretion rate (Ṁacc) for each night, which vary by a factor of ∼2 between the brightest and dimmest nights. We also measured the veiling using multiple photospheric absorption lines (Na I 5688 Å, Mn I 6021 Å, and Li I 6707 Å) for each night.
Results. We find the Li I 6707 Å line provides measurements of veiling that produce a strong, positive correlation with Lacc in the star. When corrected for Li depletion, the average veiling measured in the Li I 6707 Å line is rLi I, avg ∼ 3.25 ± 0.20, which is consistent with the other photospheric lines studied (ravg ∼ 3.28 ± 0.65).
Conclusions. We measured short timescale variability in the accretion luminosity and mass accretion rate that are intrinsic and not due to geometric effects. As the forbidden line emission we observe ([O I] 6300 Å and [S II] 6730 Å) remains remarkably constant over our epochs, it is clear that the variations in the mass accretion rate are too short to have an effect on these outflow tracers. Upon comparing the changes in veiling and accretion luminosity, we find a strong, positive correlation. This study provides an example of how this correlation can be used as a tool to determine whether a measured variability is due to extinction or an intrinsic change in accretion. As the determination of veiling is an independent process from measuring Lacc, their relationship allows further exploration of accretion phenomena in young stars.
Volume-limited sample of low-mass red giant stars, the progenitors of hot subdwarf stars
Authors: Uzundag Murat , Jones Matías I. , Vučković Maja , Vos Joris , Bobrick Alexey , Paladini Claudia 
Published: October 2022

Context. Current theory predicts that hot subdwarf binaries are produced from evolved low-mass binaries that have undergone mass transfer and drastic mass loss during either a common-envelope phase or a stable Roche-lobe overflow while on the red giant branch (RGB).
Aims. We perform a spectroscopic survey to find binary systems that include low-mass red giants near the tip of the RGB, which are predicted to be the direct progenitors of subdwarf B (sdB) stars. We aim to obtain a homogeneous sample to search for the observational evidence of correlations between the key parameters governing the formation of sdB stars and constrain the physics of stable mass transfer.
Methods. Based on data from the Gaia mission and several ground-based, multiband photometry surveys, we compiled a sample of low-mass red giant branch (RGB) candidates. The candidates were selected according to their Gaia data release 2 (DR2) color, absolute magnitude, and proper motion cuts. In this work, we concentrated on the southern hemisphere targets and conducted a spectroscopic survey of 88 red giant stars to search for the long-period RGB plus main-sequence binary systems within 200 pc. Combining radial velocity (RV) measurements from ground-based observations with CORALIE and RV measurements from Gaia DR2 and from the early data release 3 (eDR3) as well as the astrometric excess noise and renormalized unit weight error measurements from Gaia DR3, we defined a robust binary classification method. In addition, we searched for known binary systems in the literature and in Gaia DR3.
Results. We select a total of 211 RGB candidates in the southern hemisphere within 200 pc based on the Gaia DR2 color-magnitude diagram. Among them, a total of 33 red giants were reported as binary systems with orbital periods between 100 and 900 days, some of which are expected to be the direct progenitors of wide binary sdB stars. In addition, we classified 37 new main-sequence plus RGB binary candidates, whose orbital parameters will be measured with future spectroscopic follow-up.
Conclusions. Using high-quality astrometric measurements provided by the Gaia mission coupled with high-resolution spectroscopy from the ground, we provide a powerful method for searching for low-mass red giant stars in long-period binary systems.
Effects of solid–liquid interaction and mixture concentration on wettability of nano-droplets: Molecular dynamics simulations
Authors: Xu Jinzhu , Jia Li , Dang Chao , Liu Xinyuan , Ding Yi 
Published: October 2022

The wetting of droplets plays a critical role in engineering applications. Intensive study on nano-droplets is of great significance in revealing the wetting characteristics of droplets. The wetting behavior of ethanol/water mixture nano-droplets on a smooth substrate was investigated through molecular dynamics simulation in this paper. Five nano-droplets of the ethanol/water mixture with different mass fractions placed on a copper surface with different surface energies were simulated to equilibrium at 298.15 K. The contract angle, wetting limit (the minimum and the maximum surface tension of droplets make the surface completely wetted or completely non-wetted by the droplet), and density distribution at the solid–liquid interface of the nano-droplet were analyzed. The effects of ethanol concentration and solid–liquid interaction (corresponding to the droplet’s surface tension and the substrate’s surface energy, respectively) on droplet wettability were intensely discussed. Results revealed that the contact angle of nano-droplets decreased with the increase in ethanol concentration and the interaction between droplets and the substrate. In addition, the critical and ultimate surface tension increased with the increase in the substrate surface energy. The peak density values of the droplets were proportional to the interaction between the droplets and substrate and not related to the droplet concentration. The research also indicated that solid substrates with different surface energies and droplets with various components affected the contact angle of droplets in different ways: the former not only increased the surface tension of droplets at the solid–liquid interface but also increased the separation energy of solids and droplets, while the latter only had a great influence on the surface tension of droplets at the solid–liquid interface.
Human neutrophil development and functionality are enabled in a humanized mouse model
Authors: Zheng Yunjiang , Sefik Esen , Astle John , Karatepe Kutay , Öz Hasan H. , Solis Angel G. , Jackson Ruaidhrí , Luo Hongbo R. , Bruscia Emanuela M. , Halene Stephanie , Shan Liang , Flavell Richard A. 
Published: October 2022

Mice with a functional human immune system serve as an invaluable tool to study the development and function of the human immune system in vivo. A major technological limitation of all current humanized mouse models is the lack of mature and functional human neutrophils in circulation and tissues. To overcome this, we generated a humanized mouse model named MISTRGGR, in which the mouse granulocyte colony-stimulating factor (G-CSF) was replaced with human G-CSF and the mouse G-CSF receptor gene was deleted in existing MISTRG mice. By targeting the G-CSF cytokine-receptor axis, we dramatically improved the reconstitution of mature circulating and tissue-infiltrating human neutrophils in MISTRGGR mice. Moreover, these functional human neutrophils in MISTRGGR are recruited upon inflammatory and infectious challenges and help reduce bacterial burden. MISTRGGR mice represent a unique mouse model that finally permits the study of human neutrophils in health and disease.