bluuebunny/crossref_metadata_2025_split huggingface dataset:
New-onset IgG autoantibodies in hospitalized patients with COVID-19
Authors: Chang Sarah Esther , Feng Allan , Meng Wenzhao , Apostolidis Sokratis A. , Mack Elisabeth , Artandi Maja , Barman Linda , Bennett Kate , Chakraborty Saborni , Chang Iris , Cheung Peggie , Chinthrajah Sharon , Dhingra Shaurya , Do Evan , Finck Amanda , Gaano Andrew , Geßner Reinhard , Giannini Heather M. , Gonzalez Joyce , Greib Sarah , Gündisch Margrit , Hsu Alex Ren , Kuo Alex , Manohar Monali , Mao Rong , Neeli Indira , Neubauer Andreas , Oniyide Oluwatosin , Powell Abigail E. , Puri Rajan , Renz Harald , Schapiro Jeffrey , Weidenbacher Payton A. , Wittman Richard , Ahuja Neera , Chung Ho-Ryun , Jagannathan Prasanna , James Judith A. , Kim Peter S. , Meyer Nuala J. , Nadeau Kari C. , Radic Marko , Robinson William H. , Singh Upinder , Wang Taia T. , Wherry E. John , Skevaki Chrysanthi , Luning Prak Eline T. , Utz Paul J. 
Published: September 2021

AbstractCOVID-19 is associated with a wide range of clinical manifestations, including autoimmune features and autoantibody production. Here we develop three protein arrays to measure IgG autoantibodies associated with connective tissue diseases, anti-cytokine antibodies, and anti-viral antibody responses in serum from 147 hospitalized COVID-19 patients. Autoantibodies are identified in approximately 50% of patients but in less than 15% of healthy controls. When present, autoantibodies largely target autoantigens associated with rare disorders such as myositis, systemic sclerosis and overlap syndromes. A subset of autoantibodies targeting traditional autoantigens or cytokines develop de novo following SARS-CoV-2 infection. Autoantibodies track with longitudinal development of IgG antibodies recognizing SARS-CoV-2 structural proteins and a subset of non-structural proteins, but not proteins from influenza, seasonal coronaviruses or other pathogenic viruses. We conclude that SARS-CoV-2 causes development of new-onset IgG autoantibodies in a significant proportion of hospitalized COVID-19 patients and are positively correlated with immune responses to SARS-CoV-2 proteins.
Phylogenetic conservatism drives nutrient dynamics of coral reef fishes
Authors: Allgeier Jacob E. , Weeks Brian C. , Munsterman Katrina S. , Wale Nina , Wenger Seth J. , Parravicini Valeriano , Schiettekatte Nina M. D. , Villéger Sébastien , Burkepile Deron E. 
Published: September 2021

AbstractThe relative importance of evolutionary history and ecology for traits that drive ecosystem processes is poorly understood. Consumers are essential drivers of nutrient cycling on coral reefs, and thus ecosystem productivity. We use nine consumer “chemical traits” associated with nutrient cycling, collected from 1,572 individual coral reef fishes (178 species spanning 41 families) in two biogeographic regions, the Caribbean and Polynesia, to quantify the relative importance of phylogenetic history and ecological context as drivers of chemical trait variation on coral reefs. We find: (1) phylogenetic relatedness is the best predictor of all chemical traits, substantially outweighing the importance of ecological factors thought to be key drivers of these traits, (2) phylogenetic conservatism in chemical traits is greater in the Caribbean than Polynesia, where our data suggests that ecological forces have a greater influence on chemical trait variation, and (3) differences in chemical traits between regions can be explained by differences in nutrient limitation associated with the geologic context of our study locations. Our study provides multiple lines of evidence that phylogeny is a critical determinant of contemporary nutrient dynamics on coral reefs. More broadly our findings highlight the utility of evolutionary history to improve prediction in ecosystem ecology.
Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights
Authors: Stork Devon A. , Squyres Georgia R. , Kuru Erkin , Gromek Katarzyna A. , Rittichier Jonathan , Jog Aditya , Burton Briana M. , Church George M. , Garner Ethan C. , Kunjapur Aditya M. 
Published: September 2021

AbstractBacillus subtilis is a model gram-positive bacterium, commonly used to explore questions across bacterial cell biology and for industrial uses. To enable greater understanding and control of proteins in B. subtilis, here we report broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins using 3 different families of genetic code expansion systems and two choices of codons. We use these systems to achieve click-labelling, photo-crosslinking, and translational titration. These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression, validate a predicted protein-protein binding interface, and begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo. We expect that the establishment of this simple and easily accessible chemical biology system in B. subtilis will help uncover an abundance of biological insights and aid genetic code expansion in other organisms.
Non-fullerene acceptor organic photovoltaics with intrinsic operational lifetimes over 30 years
Authors: Li Yongxi , Huang Xiaheng , Ding Kan , Sheriff Hafiz K. M. , Ye Long , Liu Haoran , Li Chang-Zhi , Ade Harald , Forrest Stephen R. 
Published: September 2021

AbstractOrganic photovoltaic cells (OPVs) have the potential of becoming a productive renewable energy technology if the requirements of low cost, high efficiency and prolonged lifetime are simultaneously fulfilled. So far, the remaining unfulfilled promise of this technology is its inadequate operational lifetime. Here, we demonstrate that the instability of NFA solar cells arises primarily from chemical changes at organic/inorganic interfaces bounding the bulk heterojunction active region. Encapsulated devices stabilized by additional protective buffer layers as well as the integration of a simple solution processed ultraviolet filtering layer, maintain 94% of their initial efficiency under simulated, 1 sun intensity, AM1.5 G irradiation for 1900 hours at 55 °C. Accelerated aging is also induced by exposure of light illumination intensities up to 27 suns, and operation temperatures as high as 65 °C. An extrapolated intrinsic lifetime of > 5.6 × 104 h is obtained, which is equivalent to 30 years outdoor exposure.
Pressure induced superconductivity in MnSe
Authors: Hung T. L. , Huang C. H. , Deng L. Z. , Ou M. N. , Chen Y. Y. , Wu M. K. , Huyan S. Y. , Chu C. W. , Chen P. J. , Lee T. K. 
Published: September 2021

AbstractThe rich phenomena in the FeSe and related compounds have attracted great interests as it provides fertile material to gain further insight into the mechanism of high temperature superconductivity. A natural follow-up work was to look into the possibility of superconductivity in MnSe. We demonstrated in this work that high pressure can effectively suppress the complex magnetic characters of MnSe, and induce superconductivity with Tc ~ 5 K at pressure ~12 GPa confirmed by both magnetic and resistive measurements. The highest Tc is ~ 9 K (magnetic result) at ~35 GPa. Our observations suggest the observed superconductivity may closely relate to the pressure-induced structural change. However, the interface between the metallic and insulating boundaries may also play an important role to the pressure induced superconductivity in MnSe.
Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells
Authors: Cuevas-Velazquez Cesar L. , Vellosillo Tamara , Guadalupe Karina , Schmidt Hermann Broder , Yu Feng , Moses David , Brophy Jennifer A. N. , Cosio-Acosta Dante , Das Alakananda , Wang Lingxin , Jones Alexander M. , Covarrubias Alejandra A. , Sukenik Shahar , Dinneny José R. 
Published: September 2021

AbstractCell homeostasis is perturbed when dramatic shifts in the external environment cause the physical-chemical properties inside the cell to change. Experimental approaches for dynamically monitoring these intracellular effects are currently lacking. Here, we leverage the environmental sensitivity and structural plasticity of intrinsically disordered protein regions (IDRs) to develop a FRET biosensor capable of monitoring rapid intracellular changes caused by osmotic stress. The biosensor, named SED1, utilizes the Arabidopsis intrinsically disordered AtLEA4-5 protein expressed in plants under water deficit. Computational modeling and in vitro studies reveal that SED1 is highly sensitive to macromolecular crowding. SED1 exhibits large and near-linear osmolarity-dependent changes in FRET inside living bacteria, yeast, plant, and human cells, demonstrating the broad utility of this tool for studying water-associated stress. This study demonstrates the remarkable ability of IDRs to sense the cellular environment across the tree of life and provides a blueprint for their use as environmentally-responsive molecular tools.
One-step construction of circularized nanodiscs using SpyCatcher-SpyTag
Authors: Zhang Shanwen , Ren Qian , Novick Scott J. , Strutzenberg Timothy S. , Griffin Patrick R. , Bao Huan 
Published: September 2021

AbstractCircularized nandiscs (cNDs) exhibit superb monodispersity and have the potential to transform functional and structural studies of membrane proteins. In particular, cNDs can stabilize large patches of lipid bilayers for the reconstitution of complex membrane biochemical reactions, enabling the capture of crucial intermediates involved in synaptic transmission and viral entry. However, previous methods for building cNDs require multiple steps and suffer from low yields. We herein introduce a simple, one-step approach to ease the construction of cNDs using the SpyCatcher-SpyTag technology. This approach increases the yield of cNDs by over 10-fold and is able to rapidly generates cNDs with diameters ranging from 11 to over 100 nm. We demonstrate the utility of these cNDs for mechanistic interrogations of vesicle fusion and protein-lipid interactions that are unattainable using small nanodiscs. Together, the remarkable performance of SpyCatcher-SpyTag in nanodisc circularization paves the way for the use of cNDs in membrane biochemistry and structural biology.
Allosteric modulation of LRRC8 channels by targeting their cytoplasmic domains
Authors: Deneka Dawid , Rutz Sonja , Hutter Cedric A. J. , Seeger Markus A. , Sawicka Marta , Dutzler Raimund 
Published: September 2021

AbstractMembers of the LRRC8 family form heteromeric assemblies, which function as volume-regulated anion channels. These modular proteins consist of a transmembrane pore and cytoplasmic leucine-rich repeat (LRR) domains. Despite their known molecular architecture, the mechanism of activation and the role of the LRR domains in this process has remained elusive. Here we address this question by generating synthetic nanobodies, termed sybodies, which target the LRR domain of the obligatory subunit LRRC8A. We use these binders to investigate their interaction with homomeric LRRC8A channels by cryo-electron microscopy and the consequent effect on channel activation by electrophysiology. The five identified sybodies either inhibit or enhance activity by binding to distinct epitopes of the LRR domain, thereby altering channel conformations. In combination, our work provides a set of specific modulators of LRRC8 proteins and reveals the role of their cytoplasmic domains as regulators of channel activity by allosteric mechanisms.
Single-cell RNA sequencing of peripheral blood mononuclear cells from acute Kawasaki disease patients
Authors: Wang Zhen , Xie Lijian , Ding Guohui , Song Sirui , Chen Liqin , Li Guang , Xia Min , Han Dingding , Zheng Yue , Liu Jia , Xiao Tingting , Zhang Hong , Huang Yujuan , Li Yixue , Huang Min 
Published: September 2021

AbstractKawasaki disease (KD) is the most common cause of acquired heart disease in children in developed countries. Although functional and phenotypic changes of immune cells have been reported, a global understanding of immune responses underlying acute KD is unclear. Here, using single-cell RNA sequencing, we profile peripheral blood mononuclear cells from seven patients with acute KD before and after intravenous immunoglobulin therapy and from three age-matched healthy controls. The most differentially expressed genes are identified in monocytes, with high expression of pro-inflammatory mediators, immunoglobulin receptors and low expression of MHC class II genes in acute KD. Single-cell RNA sequencing and flow cytometry analyses, of cells from an additional 16 KD patients, show that although the percentage of total B cells is substantially decreased after therapy, the percentage of plasma cells among the B cells is significantly increased. The percentage of CD8+T cells is decreased in acute KD, notably effector memory CD8+T cells compared with healthy controls. Oligoclonal expansions of both B cell receptors and T cell receptors are observed after therapy. We identify biological processes potentially underlying the changes of each cell type. The single-cell landscape of both innate and adaptive immune responses provides insights into pathogenesis and therapy of KD.
Mechanosensitive recruitment of stator units promotes binding of the response regulator CheY-P to the flagellar motor
Authors: Antani Jyot D. , Gupta Rachit , Lee Annie H. , Rhee Kathy Y. , Manson Michael D. , Lele Pushkar P. 
Published: September 2021

AbstractReversible switching of the bacterial flagellar motor between clockwise (CW) and counterclockwise (CCW) rotation is necessary for chemotaxis, which enables cells to swim towards favorable chemical habitats. Increase in the viscous resistance to the rotation of the motor (mechanical load) inhibits switching. However, cells must maintain homeostasis in switching to navigate within environments of different viscosities. The mechanism by which the cell maintains optimal chemotactic function under varying loads is not understood. Here, we show that the flagellar motor allosterically controls the binding affinity of the chemotaxis response regulator, CheY-P, to the flagellar switch complex by modulating the mechanical forces acting on the rotor. Mechanosensitive CheY-P binding compensates for the load-induced loss of switching by precisely adapting the switch response to a mechanical stimulus. The interplay between mechanical forces and CheY-P binding tunes the chemotactic function to match the load. This adaptive response of the chemotaxis output to mechanical stimuli resembles the proprioceptive feedback in the neuromuscular systems of insects and vertebrates.
Liquid state properties and solidification features of the pseudo binary BaS-La2S3
Authors: Boury Charles , Allanore Antoine 
Published: September 2021

AbstractThe high temperature thermodynamic properties of chalcogenides materials based on BaS remain elusive. Herein the pseudo binary BaS-La2S3 is investigated above 1573 K. The liquid properties of BaS-La2S3 are measured by means of high resolution in-situ visualization coupled with thermal arrest measurements in a thermal imaging furnace. This enables to report the first observation of such melts in a container-less setting. The melting points of BaS and La2S3 are revisited at 2454 K and 2004 K respectively. La2S3 demonstrates a high stability in its liquid state, in strike difference with the sublimation observed for BaS. BaS is however partially stabilized with the addition of few percents of La2S3. The remarkable chemical and thermal stability of La2S3-rich samples contrasts with the partial decomposition and high vapor pressure observed for BaS-rich samples. Observations and analysis of the solidified samples suggest three different solid solutions. Solid and liquid densities are investigated along the different compositions, supporting a first estimate of the volumetric thermal expansion coefficient for La2S3.
Assessment of flow within developing chicken vasculature and biofabricated vascularized tissues using multimodal imaging techniques
Authors: Padmanaban Prasanna , Chizari Ata , Knop Tom , Zhang Jiena , Trikalitis Vasileios D. , Koopman Bart , Steenbergen Wiendelt , Rouwkema Jeroen 
Published: September 2021

AbstractFluid flow shear stresses are strong regulators for directing the organization of vascular networks. Knowledge of structural and flow dynamics information within complex vasculature is essential for tuning the vascular organization within engineered tissues, by manipulating flows. However, reported investigations of vascular organization and their associated flow dynamics within complex vasculature over time are limited, due to limitations in the available physiological pre-clinical models, and the optical inaccessibility and aseptic nature of these models. Here, we developed laser speckle contrast imaging (LSCI) and side-stream dark field microscopy (SDF) systems to map the vascular organization, spatio-temporal blood flow fluctuations as well as erythrocytes movements within individual blood vessels of developing chick embryo, cultured within an artificial eggshell system. By combining imaging data and computational simulations, we estimated fluid flow shear stresses within multiscale vasculature of varying complexity. Furthermore, we demonstrated the LSCI compatibility with bioengineered perfusable muscle tissue constructs, fabricated via molding techniques. The presented application of LSCI and SDF on perfusable tissues enables us to study the flow perfusion effects in a non-invasive fashion. The gained knowledge can help to use fluid perfusion in order to tune and control multiscale vascular organization within engineered tissues.
Analysis of complex trophic networks reveals the signature of land-use intensification on soil communities in agroecosystems
Authors: Bloor Juliette M. G. , Si-Moussi Sara , Taberlet Pierre , Carrère Pascal , Hedde Mickaël 
Published: September 2021

AbstractIncreasing evidence suggests that agricultural intensification is a threat to many groups of soil biota, but how the impacts of land-use intensity on soil organisms translate into changes in comprehensive soil interaction networks remains unclear. Here for the first time, we use environmental DNA to examine total soil multi-trophic diversity and food web structure for temperate agroecosystems along a gradient of land-use intensity. We tested for response patterns in key properties of the soil food webs in sixteen fields ranging from arable crops to grazed permanent grasslands as part of a long-term management experiment. We found that agricultural intensification drives reductions in trophic group diversity, although taxa richness remained unchanged. Intensification generally reduced the complexity and connectance of soil interaction networks and induced consistent changes in energy pathways, but the magnitude of management-induced changes depended on the variable considered. Average path length (an indicator of food web redundancy and resilience) did not respond to our management intensity gradient. Moreover, turnover of network structure showed little response to increasing management intensity. Our data demonstrates the importance of considering different facets of trophic networks for a clearer understanding of agriculture-biodiversity relationships, with implications for nature-based solutions and sustainable agriculture.
Development of a novel self-sanitizing mask prototype to combat the spread of infectious disease and reduce unnecessary waste
Authors: Crawford Matthew J. , Ramezani Sepehr , Jabbari Roghaie , Pathak Pawan , Cho Hyoung J. , Kim Brian N. , Choi Hwan 
Published: September 2021

AbstractWith the spread of COVID-19, significant emphasis has been placed on mitigation techniques such as mask wearing to slow infectious disease transmission. Widespread use of face coverings has revealed challenges such as mask contamination and waste, presenting an opportunity to improve the current technologies. In response, we have developed the Auto-sanitizing Retractable Mask Optimized for Reusability (ARMOR). ARMOR is a novel, reusable face covering that can be quickly disinfected using an array of ultraviolet C lamps contained within a wearable case. A nanomembrane UVC sensor was used to quantify the intensity of germicidal radiation at 18 different locations on the face covering and determine the necessary exposure time to inactivate SARS-CoV-2 in addition to other viruses and bacteria. After experimentation, it was found that ARMOR successfully provided germicidal radiation to all areas of the mask and will inactivate SARS-CoV-2 in approximately 180 s, H1N1 Influenza in 130 s, and Mycobacterium tuberculosis in 113 s, proving that this design is effective at eliminating a variety of pathogens and can serve as an alternative to traditional waste-producing disposable face masks. The accessibility, ease of use, and speed of sanitization supports the wide application of ARMOR in both clinical and public settings.
Having more virtual interaction partners during COVID-19 physical distancing measures may benefit mental health
Authors: Sahi Razia S. , Schwyck Miriam E. , Parkinson Carolyn , Eisenberger Naomi I. 
Published: September 2021

AbstractSocial interactions play an extremely important role in maintaining health and well-being. The COVID-19 pandemic and associated physical distancing measures, however, restricted the number of people one could physically interact with on a regular basis. A large percentage of social interactions moved online, resulting in reports of “Zoom fatigue,” or exhaustion from virtual interactions. These reports focused on how online communication differs from in-person communication, but it is possible that when in-person interactions are restricted, virtual interactions may benefit mental health overall. In a survey conducted near the beginning of the COVID-19 pandemic (N2020 = 230), we found that having a greater number of virtual interaction partners was associated withbettermental health. This relationship was statistically mediated by decreased loneliness and increased perceptions of social support. We replicated these findings during the pandemic 1 year later (N2021 = 256) and found that these effects held even after controlling for the amount of time people spent interacting online. Convergent with previous literature on social interactions, these findings suggest that virtual interactions may benefit overall mental health, particularly during physical distancing and other circumstances where opportunities to interact in-person with different people are limited.Open Science Framework repository:https://osf.io/6jsr2/.