bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activation or exhaustion of CD8+ T cells in patients with COVID-19
Authors: Rha Min-Seok , Shin Eui-Cheol 
Published: August 2021

AbstractIn addition to CD4+T cells and neutralizing antibodies, CD8+T cells contribute to protective immune responses against SARS-CoV-2 in patients with coronavirus disease 2019 (COVID-19), an ongoing pandemic disease. In patients with COVID-19, CD8+T cells exhibiting activated phenotypes are commonly observed, although the absolute number of CD8+T cells is decreased. In addition, several studies have reported an upregulation of inhibitory immune checkpoint receptors, such as PD-1, and the expression of exhaustion-associated gene signatures in CD8+T cells from patients with COVID-19. However, whether CD8+T cells are truly exhausted during COVID-19 has been a controversial issue. In the present review, we summarize the current understanding of CD8+T-cell exhaustion and describe the available knowledge on the phenotypes and functions of CD8+T cells in the context of activation and exhaustion. We also summarize recent reports regarding phenotypical and functional analyses of SARS-CoV-2-specific CD8+T cells and discuss long-term SARS-CoV-2-specific CD8+T-cell memory.
Myopia prevalence and ocular biometry: a cross-sectional study among minority versus Han schoolchildren in Xinjiang Uygur autonomous region, China
Authors: Shi Yumeng , Wang Yan , Cui Aizhi , Liu Sen , He Xiaolan , Qiu Huijuan , Cui Hanwen , Gao Yunxian , Yang Jin 
Published: August 2021

Abstract
Objectives
To describe and compare the prevalence of refractive error and its associated ocular biometric parameters in a large multi-racial sample of schoolchildren from Xinjiang.

Methods
A total of 67,102 school children of five ethnicity groups aged 6–23 years from 46 schools in Xinjiang participated in this study. The children underwent a comprehensive eye examination for vision screening, including uncorrected visual acuity and standardized refraction. Refractive error was determined by autorefractors and subjective refraction. Refraction was recorded in spherical equivalent (SE). The age- and sex- adjusted prevalence of myopia (SE ≤ −0.5 D), low myopia (−6 D < SE ≤ −0.5 D), high myopia (SE ≤ −6.0 D), astigmatism (cylinder < −0.5 D), and anisometropia (difference in SE between two eyes of 1.0 D) in the five ethnic groups were calculated. Ocular biometric parameters including axial length (AL) and corneal radius of curvature (CR) were measured by AL-scan optical biometer.

Results
The age- and sex- adjusted prevalence of myopia in the Han, Hui, Uyghur, Kyrgyz and Kazakh were 65.8% (95% confidence interval [CI] 65.4, 66.3); 59.1% (95% CI 57.8, 60.4); 30.1% (95% CI 29.2, 30.9); 30.2 (95% CI 28.9, 31.4); and 30.0% (95% CI 27.6, 32.3), respectively. The Han and Hui children also had longer ALs (Han, 23.8; Hui, 23.6, Uyghur, 23.1; Kyrgyz, 23.1; Kazakh, 23.3 mm) and larger AL/CR (Han, 3.04; Hui, 3.00; Uyghur, 2.95; Kyrgyz, 2.96; Kazakh, 2.97) values than the other three minorities (P < 0.01). Overall, girls had shorter ALs, steeper corneas, and smaller AL/CR values than boys (P < 0.01).

Conclusions
Significant ethnic difference in the prevalence of myopia was observed in this study on school-aged children in Xinjiang (Han > Hui > Kyrgyz > Uyghur > Kazakh). This study among different ethnic groups in a multiethnic population is valuable for enriching the ethnical information resources for refractive errors and ocular biometry parameters, as well as facilitating further research on myopia-related diseases and risks.
Quantum theory of the nonlinear Hall effect
Authors: Du Z. Z. , Wang C. M. , Sun Hai-Peng , Lu Hai-Zhou , Xie X. C. 
Published: August 2021

AbstractThe nonlinear Hall effect is an unconventional response, in which a voltage can be driven by two perpendicular currents in the Hall-bar measurement. Unprecedented in the family of the Hall effects, it can survive time-reversal symmetry but is sensitive to the breaking of discrete and crystal symmetries. It is a quantum transport phenomenon that has deep connection with the Berry curvature. However, a full quantum description is still absent. Here we construct a quantum theory of the nonlinear Hall effect by using the diagrammatic technique. Quite different from nonlinear optics, nearly all the diagrams account for the disorder effects, which play decisive role in the electronic transport. After including the disorder contributions in terms of the Feynman diagrams, the total nonlinear Hall conductivity is enhanced but its sign remains unchanged for the 2D tilted Dirac model, compared to the one with only the Berry curvature contribution. We discuss the symmetry of the nonlinear conductivity tensor and predict a pure disorder-induced nonlinear Hall effect for point groups C3, C3h, C3v, D3h, D3 in 2D, and T, Td, C3h, D3h in 3D. This work will be helpful for explorations of the topological physics beyond the linear regime.
Creating synthetic spaces for higher-order topological sound transport
Authors: Chen Hui , Zhang Hongkuan , Wu Qian , Huang Yu , Nguyen Huy , Prodan Emil , Zhou Xiaoming , Huang Guoliang 
Published: August 2021

AbstractModern technological advances allow for the study of systems with additional synthetic dimensions. Higher-order topological insulators in topological states of matters have been pursued in lower physical dimensions by exploiting synthetic dimensions with phase transitions. While synthetic dimensions can be rendered in the photonics and cold atomic gases, little to no work has been succeeded in acoustics because acoustic wave-guides cannot be weakly coupled in a continuous fashion. Here, we formulate the theoretical principles and manufacture acoustic crystals composed of arrays of acoustic cavities strongly coupled through modulated channels to evidence one-dimensional (1D) and two-dimensional (2D) dynamic topological pumpings. In particular, the higher-order topological edge-bulk-edge and corner-bulk-corner transport are physically illustrated in finite-sized acoustic structures. We delineate the generated 2D and four-dimensional (4D) quantum Hall effects by calculating first and second Chern numbers and physically demonstrate robustness against the geometrical imperfections. Synthetic dimensions could provide a powerful way for acoustic topological wave steering and open up a platform to explore any continuous orbit in higher-order topological matter in dimensions four and higher.
Integration of FRET and sequencing to engineer kinase biosensors from mammalian cell libraries
Authors: Liu Longwei , Limsakul Praopim , Meng Xianhui , Huang Yan , Harrison Reed E. S. , Huang Tse-Shun , Shi Yiwen , Yu Yiyan , Charupanit Krit , Zhong Sheng , Lu Shaoying , Zhang Jin , Chien Shu , Sun Jie , Wang Yingxiao 
Published: August 2021

AbstractThe limited sensitivity of Förster Resonance Energy Transfer (FRET) biosensors hinders their broader applications. Here, we develop an approach integrating high-throughput FRET sorting and next-generation sequencing (FRET-Seq) to identify sensitive biosensors with varying substrate sequences from large-scale libraries directly in mammalian cells, utilizing the design of self-activating FRET (saFRET) biosensor. The resulting biosensors of Fyn and ZAP70 kinases exhibit enhanced performance and enable the dynamic imaging of T-cell activation mediated by T cell receptor (TCR) or chimeric antigen receptor (CAR), revealing a highly organized ZAP70 subcellular activity pattern upon TCR but not CAR engagement. The ZAP70 biosensor elucidates the role of immunoreceptor tyrosine-based activation motif (ITAM) in affecting ZAP70 activation to regulate CAR functions. A saFRET biosensor-based high-throughput drug screening (saFRET-HTDS) assay further enables the identification of an FDA-approved cancer drug, Sunitinib, that can be repurposed to inhibit ZAP70 activity and autoimmune-disease-related T-cell activation.
A simple pressure-assisted method for MicroED specimen preparation
Authors: Zhao Jingjing , Xu Hongyi , Lebrette Hugo , Carroni Marta , Taberman Helena , Högbom Martin , Zou Xiaodong 
Published: August 2021

AbstractMicro-crystal electron diffraction (MicroED) has shown great potential for structure determination of macromolecular crystals too small for X-ray diffraction. However, specimen preparation remains a major bottleneck. Here, we report a simple method for preparing MicroED specimens, named Preassis, in which excess liquid is removed through an EM grid with the assistance of pressure. We show the ice thicknesses can be controlled by tuning the pressure in combination with EM grids with appropriate carbon hole sizes. Importantly, Preassis can handle a wide range of protein crystals grown in various buffer conditions including those with high viscosity, as well as samples with low crystal concentrations. Preassis is a simple and universal method for MicroED specimen preparation, and will significantly broaden the applications of MicroED.
Bacterial cellulose spheroids as building blocks for 3D and patterned living materials and for regeneration
Authors: Caro-Astorga Joaquin , Walker Kenneth T. , Herrera Natalia , Lee Koon-Yang , Ellis Tom 
Published: August 2021

AbstractEngineered living materials (ELMs) based on bacterial cellulose (BC) offer a promising avenue for cheap-to-produce materials that can be programmed with genetically encoded functionalities. Here we explore how ELMs can be fabricated in a modular fashion from millimetre-scale biofilm spheroids grown from shaking cultures of Komagataeibacter rhaeticus. Here we define a reproducible protocol to produce BC spheroids with the high yield bacterial cellulose producer K. rhaeticus and demonstrate for the first time their potential for their use as building blocks to grow ELMs in 3D shapes. Using genetically engineered K. rhaeticus, we produce functionalized BC spheroids and use these to make and grow patterned BC-based ELMs that signal within a material and can sense and report on chemical inputs. We also investigate the use of BC spheroids as a method to regenerate damaged BC materials and as a way to fuse together smaller material sections of cellulose and synthetic materials into a larger piece. This work improves our understanding of BC spheroid formation and showcases their great potential for fabricating, patterning and repairing ELMs based on the promising biomaterial of bacterial cellulose.
Predicting carbon nanotube forest attributes and mechanical properties using simulated images and deep learning
Authors: Hajilounezhad Taher , Bao Rina , Palaniappan Kannappan , Bunyak Filiz , Calyam Prasad , Maschmann Matthew R. 
Published: August 2021

AbstractUnderstanding and controlling the self-assembly of vertically oriented carbon nanotube (CNT) forests is essential for realizing their potential in myriad applications. The governing process–structure–property mechanisms are poorly understood, and the processing parameter space is far too vast to exhaustively explore experimentally. We overcome these limitations by using a physics-based simulation as a high-throughput virtual laboratory and image-based machine learning to relate CNT forest synthesis attributes to their mechanical performance. Using CNTNet, our image-based deep learning classifier module trained with synthetic imagery, combinations of CNT diameter, density, and population growth rate classes were labeled with an accuracy of >91%. The CNTNet regression module predicted CNT forest stiffness and buckling load properties with a lower root-mean-square error than that of a regression predictor based on CNT physical parameters. These results demonstrate that image-based machine learning trained using only simulated imagery can distinguish subtle CNT forest morphological features to predict physical material properties with high accuracy. CNTNet paves the way to incorporate scanning electron microscope imagery for high-throughput material discovery.
Personalized medicine for reconstruction of critical-size bone defects – a translational approach with customizable vascularized bone tissue
Authors: Kengelbach-Weigand Annika , Thielen Carolina , Bäuerle Tobias , Götzl Rebekka , Gerber Thomas , Körner Carolin , Beier Justus P. , Horch Raymund E. , Boos Anja M. 
Published: August 2021

AbstractTissue engineering principles allow the generation of functional tissues for biomedical applications. Reconstruction of large-scale bone defects with tissue-engineered bone has still not entered the clinical routine. In the present study, a bone substitute in combination with mesenchymal stem cells (MSC) and endothelial progenitor cells (EPC) with or without growth factors BMP-2 and VEGF-A was prevascularized by an arteriovenous (AV) loop and transplanted into a critical-size tibia defect in the sheep model. With 3D imaging and immunohistochemistry, we could show that this approach is a feasible and simple alternative to the current clinical therapeutic option. This study serves as proof of concept for using large-scale transplantable, vascularized, and customizable bone, generated in a living organism for the reconstruction of load-bearing bone defects, individually tailored to the patient’s needs. With this approach in personalized medicine for the reconstruction of critical-size bone defects, regeneration of parts of the human body will become possible in the near future.
Poplar-based thermochromic composites that change colour at 38 °C to 46 °C
Authors: Zou Weihua , Li Zimu , Wang Zhangheng , Sun Delin , Zhang Pingfang 
Published: August 2021

AbstractThe red thermochromic dye (R-TD) is the tetradecanoic acid tetradecyl ester (C28H56O2) and methyl red (C15H15N3O2) mixture that has better permeability enabling its infiltration into wood and better thermochromic properties changing its colour at above 30 °C after about 0.5 min. Thicker poplar-based thermochromic composite specimens (R-PTC, thickness: 5.0 mm) were prepared by filling the R-TD into pre-treated poplar veneer (thickness: 5.0 mm) thus allowing better penetration after pre-treatment. After R-TD infiltration, the R-PTC samples were covered by polypropylene wax for preventing R-TD from overflowing from R-PTC under the action of phase-change temperature. This R-PTC, whose colour can change from light-red to dark-red at 38 °C to 46 °C, can recover to light-red at below 38 °C after about 14 h, and the peak of colour change is at about 42 °C. R-PTC will be suitable for materials used in thermochromic furniture that can indicate the surface temperature to potential users, thus allowing assessment of likely scalded pain when used the furniture.
Cannabis and tobacco use prior to pregnancy and subsequent offspring birth outcomes: a 20-year intergenerational prospective cohort study
Authors: Hines Lindsey A. , Spry Elizabeth A. , Moreno-Betancur Margarita , Mohamad Husin Hanafi , Becker Denise , Middleton Melissa , Craig Jeffrey M. , Doyle Lex W. , Olsson Craig A. , Patton George 
Published: August 2021

AbstractThere is increasing evidence that the life-course origins of health and development begin before conception. We examined associations between timing and frequency of preconception cannabis and tobacco use and next generation preterm birth (PTB), low birth weight (LBW) and small for gestational age. 665 participants in a general population cohort were repeatedly assessed on tobacco and cannabis use between ages 14–29 years, before pregnancy. Associations were estimated using logistic regression. Preconception parent (either maternal or paternal) daily cannabis use age 15–17 was associated with sixfold increases in the odds of offspring PTB (aOR 6.65, 95% CI 1.92, 23.09), and offspring LBW (aOR 5.84, 95% CI 1.70–20.08), after adjusting for baseline sociodemographic factors, parent sex, offspring sex, family socioeconomic status, parent mental health at baseline, and concurrent tobacco use. There was little evidence of associations with preconception parental cannabis use at other ages or preconception parental tobacco use. Findings support the hypothesis that the early life origins of growth begin before conception and provide a compelling rationale for prevention of frequent use during adolescence. This is pertinent given liberalisation of cannabis policy.
Quantum tunneling and quantum walks as algorithmic resources to solve hard K-SAT instances
Authors: Campos Ernesto , Venegas-Andraca Salvador E. , Lanzagorta Marco 
Published: August 2021

AbstractWe present a new quantum heuristic algorithm aimed at finding satisfying assignments for hard K-SAT instances using a continuous time quantum walk that explicitly exploits the properties of quantum tunneling. Our algorithm uses a Hamiltonian $$H_A(F)$$

H
A

(
F
)

which is specifically constructed to solve a K-SAT instance F. The heuristic algorithm aims at iteratively reducing the Hamming distance between an evolving state $${|{\psi _j}\rangle }$$

|

ψ
j

⟩

and a state that represents a satisfying assignment for F. Each iteration consists on the evolution of $${|{\psi _j}\rangle }$$

|

ψ
j

⟩

(where j is the iteration number) under $$e^{-iH_At}$$

e

-
i

H
A

t

, a measurement that collapses the superposition, a check to see if the post-measurement state satisfies F and in the case it does not, an update to $$H_A$$

H
A

for the next iteration. Operator $$H_A$$

H
A

describes a continuous time quantum walk over a hypercube graph with potential barriers that makes an evolving state to scatter and mostly follow the shortest tunneling paths with the smaller potentials that lead to a state $${|{s}\rangle }$$

|
s
⟩

that represents a satisfying assignment for F. The potential barriers in the Hamiltonian $$H_A$$

H
A

are constructed through a process that does not require any previous knowledge on the satisfying assignments for the instance F. Due to the topology of $$H_A$$

H
A

each iteration is expected to reduce the Hamming distance between each post measurement state and a state $${|{s}\rangle }$$

|
s
⟩

. If the state $${|{s}\rangle }$$

|
s
⟩

is not measured after n iterations (the number n of logical variables in the instance F being solved), the algorithm is restarted. Periodic measurements and quantum tunneling also give the possibility of getting out of local minima. Our numerical simulations show a success rate of 0.66 on measuring $${|{s}\rangle }$$

|
s
⟩

on the first run of the algorithm (i.e., without restarting after n iterations) on thousands of 3-SAT instances of 4, 6, and 10 variables with unique satisfying assignments.
Thermostable adenosine 5′-monophosphate phosphorylase from Thermococcus kodakarensis forms catalytically active inclusion bodies
Authors: Kamel Sarah , Walczak Miriam C. , Kaspar Felix , Westarp Sarah , Neubauer Peter , Kurreck Anke 
Published: August 2021

AbstractCatalytically active inclusion bodies (CatIBs) produced in Escherichia coli are an interesting but currently underexplored strategy for enzyme immobilization. They can be purified easily and used directly as stable and reusable heterogenous catalysts. However, very few examples of CatIBs that are naturally formed during heterologous expression have been reported so far. Previous studies have revealed that the adenosine 5′-monophosphate phosphorylase of Thermococcus kodakarensis (TkAMPpase) forms large soluble multimers with high thermal stability. Herein, we show that heat treatment of soluble protein from crude extract induces aggregation of active protein which phosphorolyse all natural 5′-mononucleotides. Additionally, inclusion bodies formed during the expression in E. coli were found to be similarly active with 2–6 folds higher specific activity compared to these heat-induced aggregates. Interestingly, differences in the substrate preference were observed. These results show that the recombinant thermostable TkAMPpase is one of rare examples of naturally formed CatIBs.
Spatial regression and geostatistics discourse with empirical application to precipitation data in Nigeria
Authors: Okunlola Oluyemi A. , Alobid Mohannad , Olubusoye Olusanya E. , Ayinde Kayode , Lukman Adewale F. , Szűcs István 
Published: August 2021

AbstractIn this study, we propose a robust approach to handling geo-referenced data and discuss its statistical analysis. The linear regression model has been found inappropriate in this type of study. This motivates us to redefine its error structure to incorporate the spatial components inherent in the data into the model. Therefore, four spatial models emanated from the re-definition of the error structure. We fitted the spatial and the non-spatial linear model to the precipitation data and compared their results. All the spatial models outperformed the non-spatial model. The Spatial Autoregressive with additional autoregressive error structure (SARAR) model is the most adequate among the spatial models. Furthermore, we identified the hot and cold spot locations of precipitation and their spatial distribution in the study area.
Regional grey matter microstructural changes and volume loss according to disease duration in multiple sclerosis patients
Authors: Solana Elisabeth , Martinez-Heras Eloy , Montal Victor , Vilaplana Eduard , Lopez-Soley Elisabet , Radua Joaquim , Sola-Valls Nuria , Montejo Carmen , Blanco Yolanda , Pulido-Valdeolivas Irene , Sepúlveda Maria , Andorra Magi , Berenguer Joan , Villoslada Pablo , Martinez-Lapiscina E. H. , Prados Ferran , Saiz Albert , Fortea Juan , Llufriu Sara 
Published: August 2021

AbstractThe spatio-temporal characteristics of grey matter (GM) impairment in multiple sclerosis (MS) are poorly understood. We used a new surface-based diffusion MRI processing tool to investigate regional modifications of microstructure, and we quantified volume loss in GM in a cohort of patients with MS classified into three groups according to disease duration. Additionally, we investigated the relationship between GM changes with disease severity. We studied 54 healthy controls and 247 MS patients classified regarding disease duration: MS1 (less than 5 years, n = 67); MS2 (5–15 years, n = 107); and MS3 (more than15 years, n = 73). We compared GM mean diffusivity (MD), fractional anisotropy (FA) and volume between groups, and estimated their clinical associations. Regional modifications in diffusion measures (MD and FA) and volume did not overlap early in the disease, and became widespread in later phases. We found higher MD in MS1 group, mainly in the temporal cortex, and volume reduction in deep GM and left precuneus. Additional MD changes were evident in cingulate and occipital cortices in the MS2 group, coupled to volume reductions in deep GM and parietal and frontal poles. Changes in MD and volume extended to more than 80% of regions in MS3 group. Conversely, increments in FA, with very low effect size, were observed in the parietal cortex and thalamus in MS1 and MS2 groups, and extended to the frontal lobe in the later group. MD and GM changes were associated with white matter lesion load and with physical and cognitive disability. Microstructural integrity loss and atrophy present differential spatial predominance early in MS and accrual over time, probably due to distinct pathogenic mechanisms that underlie tissue damage.