bluuebunny/crossref_metadata_2025 huggingface dataset:
Regulated globin mRNA decay is a cytoplasmic event proceeding through
3′-to-5′ exosome-dependent decapping
Authors: RODGERS NANCY D. , WANG ZUOREN , KILEDJIAN MEGERDITCH
Published: July 2022

The α-globin mRNA contains a C-rich stability element (CRE) in its 3′
untranslated region (3′ UTR) which is critical for the stability of this
long-lived mRNA. A protein complex, termed the α-complex, forms on the CRE
and has been shown to contribute to stabilization of the mRNA by at least
two mechanisms, first by interacting with the poly(A)-binding protein (PABP)
to prevent deadenylation, and second by protecting the mRNA from attack by
an erythroid endoribonuclease. In this report, we demonstrate that the
α-globin 3′ UTR can confer stability on a heterologous mRNA in cells, and
this stability is dependent on the α-complex. Moreover, the stability was
exclusively detected with cytoplasmic mRNA, suggesting that the regulation
of α-globin mRNA stability is a cytoplasmic event. An additional mechanism
by which the α-complex can confer stability on an RNA in vitro was also
identified and shown to involve inhibition of 3′ to 5′ exonucleolytic
degradation. Furthermore, using an in vitro mRNA decay system, we were able
to follow the demise of the α-globin RNA and demonstrate that the decay was
initiated by deadenylation followed by 3′-to-5′ decay carried out by the
exosome and ultimately hydrolysis of the residual cap structure.
High gain and circularly polarized beam-switching 8 × 8 Vivaldi antenna array for X-band application
Authors: Aribi Tohid , Sedghi Tohid , Khajeh Mohammad Lou Reza
Published: July 2022

An 8 × 8 butler Vivaldi beam-steering antenna array is introduced for X-band application. Circularly polarized array is made of eight Vivaldi elements with 1×8 platform and an 8×8 beam feeding network. Vivaldi radiating element is used in array form to enhance impedance bandwidth and overall efficiency such as gain. Using microwave passive components, for instance, 3 dB branch line couplers and crossover help to have orthogonal modes for feeding each of the elements, hence circular polarization property is achieved. Extracted results show that the array has an impedance bandwidth over 7–12.7 GHz (~58%) for VSWR≤2 and an axial-ratio bandwidth of 3.15 GHz that is between 8.15 and 11.3 GHz (~33%). The peak gain of antenna array is 18 dBi at 10 GHz. The proposed beam-steering antenna with compact size and good operation is capable to cover an angle range from −42 to 55 degree in whole operation frequency.
Comparative characterization of antibody responses induced by Ad5-vectored spike proteins of emerging SARS-CoV-2 VOCs
Authors: Wang Busen , Xu Jinghan , Wu Shipo , Zhang Zhe , Zhao Zhenghao , Zhang Jun , Fu Ling , Zai Xiaodong , Wang Yudong , Zhang Guanying , Chen ZhengShan , Chen Yi , Sun Hancong , Song Xiaohong , Zhang Jinlong , Zhu Lianhui , Hou Lihua , Chen Wei
Published: July 2022

Highly divergent SARS-CoV-2 variants have continuously emerged and spread around the world, and updated vaccines and innovative vaccination strategies are urgently needed to address the global SARS-COV2 pandemic. Here, we established a series of Ad5-vectored SARS-CoV-2 variant vaccines encoding multiple spike proteins derived from the Alpha, Beta, Gamma, Epsilon, Kappa, Delta and Omicron lineages and analyzed the antibody immune responses induced by single-dose and prime-boost vaccination strategies against emerging SARS-CoV-2 variants of concern (VOCs). Single-dose vaccination with SARS-CoV-2 variant vaccines tended to elicit the optimal self-matched neutralizing effects, and Ad5-B.1.351 produced more broad-spectrum cross-neutralizing antibodies against diverse variants. In contrast, prime-boost vaccination further strengthened and broadened the neutralizing antibody responses against highly divergent SARS-CoV-2 variants. The heterologous administration of Ad5-B.1.617.2 and Ad5-B.1.429 to Ad5-WT-primed mice resulted in superior antibody responses against most VOCs. In particular, the Omicron spike could only stimulate self-matched neutralizing antibodies with infrequent cross-reactivities to other variants used in single-dose vaccination strategies; moreover, with prime-boost regimens, this vaccine elicited an optimal specific neutralizing antibody response to Omicron, and prompted cross-antibody responses against other VOCs that were very similar to those obtained with Ad5-WT booster. Overall, this study delineated the unique characteristics of antibody responses to the SARS-CoV-2 VOC spikes with the single-dose or prime-boost vaccination strategies and provided insight into the vaccine development of next SARS-CoV-2 VOCs.
Whispering-gallery-mode full-color laser textiles and their anticounterfeiting applications
Authors: Ruan Jun , Guo Dan , Niu Ben , Ge Kun , Zhai Tianrui
Published: July 2022

Light-emitting fabric can facilitate the innovation of wearable display applications. Electronic and luminescent textiles capable of communicating, sensing, and supplying energy have been achieved. However, a facile strategy for fabricating large-area flexible lasing textiles has not yet been reported. In this work, we propose a gravity-assisted rotatory drawing method for fabricating flexible lasing microfibers, which can be woven into multicolor lasing textiles. By regulating the doped dyes and solution viscosity, we achieve the mass manufacturing of lasing microfibers with different emission colors and modes and further weave them into full-color textiles with a wide color gamut, approximately 79.1% larger than that of standard RGB space. For application, we print nanoparticle patterns on the lasing textile and encode it with programmable lasing signal distribution, which can supply an anticounterfeiting label for efficient authentication. This work unifies the fabrication and application of lasing textiles, and we expect that this will provide a new platform for flexible lasing devices.
A heterozygous GRID2 mutation in autosomal dominant cerebellar ataxia
Authors: Koh Kishin , Shimazaki Haruo , Ogawa Matsuo , Takiyama Yoshihisa
Published: July 2022

A heterozygous mutation in GRID2 that causes SCAR18 was first reported in an Algerian family with autosomal dominant cerebellar ataxia (ADCA). We identified the second ADCA family with a heterozygous GRID2 mutation. The Algerian family had cognitive impairment and hearing loss associated with cerebellar ataxia. However, the Japanese family presented here showed pure cerebellar ataxia. Therefore, we should also screen for the GRID2 mutation in ADCA families with pure cerebellar ataxia.
Bayesian tomography of high-dimensional on-chip biphoton frequency combs with randomized measurements
Authors: Lu Hsuan-Hao , Myilswamy Karthik V. , Bennink Ryan S. , Seshadri Suparna , Alshaykh Mohammed S. , Liu Junqiu , Kippenberg Tobias J. , Leaird Daniel E. , Weiner Andrew M. , Lukens Joseph M.
Published: July 2022

Owing in large part to the advent of integrated biphoton frequency combs, recent years have witnessed increased attention to quantum information processing in the frequency domain for its inherent high dimensionality and entanglement compatible with fiber-optic networks. Quantum state tomography of such states, however, has required complex and precise engineering of active frequency mixing operations, which are difficult to scale. To address these limitations, we propose a solution that employs a pulse shaper and electro-optic phase modulator to perform random operations instead of mixing in a prescribed manner. We successfully verify the entanglement and reconstruct the full density matrix of biphoton frequency combs generated from an on-chip Si3N4 microring resonator in up to an 8 × 8-dimensional two-qudit Hilbert space, the highest dimension to date for frequency bins. More generally, our employed Bayesian statistical model can be tailored to a variety of quantum systems with restricted measurement capabilities, forming an opportunistic tomographic framework that utilizes all available data in an optimal way.
Decoherence of V$${}_{{{{{{{{\rm{B}}}}}}}}}^{-}$$ spin defects in monoisotopic hexagonal boron nitride
Authors: Haykal A. , Tanos R. , Minotto N. , Durand A. , Fabre F. , Li J. , Edgar J. H. , Ivády V. , Gali A. , Michel T. , Dréau A. , Gil B. , Cassabois G. , Jacques V.
Published: July 2022

Spin defects in hexagonal boron nitride (hBN) are promising quantum systems for the design of flexible two-dimensional quantum sensing platforms. Here we rely on hBN crystals isotopically enriched with either 10B or 11B to investigate the isotope-dependent properties of a spin defect featuring a broadband photoluminescence signal in the near infrared. By analyzing the hyperfine structure of the spin defect while changing the boron isotope, we first confirm that it corresponds to the negatively charged boron-vacancy center ($${{{{{{{{\rm{V}}}}}}}}}_{{{{{{{{\rm{B}}}}}}}}}^{-}$$

V

B

−

). We then show that its spin coherence properties are slightly improved in 10B-enriched samples. This is supported by numerical simulations employing cluster correlation expansion methods, which reveal the importance of the hyperfine Fermi contact term for calculating the coherence time of point defects in hBN. Using cross-relaxation spectroscopy, we finally identify dark electron spin impurities as an additional source of decoherence. This work provides new insights into the properties of $${{{{{{{{\rm{V}}}}}}}}}_{{{{{{{{\rm{B}}}}}}}}}^{-}$$

V

B

−

spin defects, which are valuable for the future development of hBN-based quantum sensing foils.
FLASHIda enables intelligent data acquisition for top–down proteomics to boost proteoform identification counts
Authors: Jeong Kyowon , Babović Maša , Gorshkov Vladimir , Kim Jihyung , Jensen Ole N. , Kohlbacher Oliver
Published: July 2022

The detailed analysis and structural characterization of proteoforms by top-down proteomics (TDP) has gained a lot of interest in biomedical research. Data-dependent acquisition (DDA) of intact proteins is non-trivial due to the diversity and complexity of proteoforms. Dedicated acquisition methods thus have the potential to greatly improve TDP. Here, we present FLASHIda, an intelligent online data acquisition algorithm for TDP that ensures the real-time selection of high-quality precursors of diverse proteoforms. FLASHIda combines fast charge deconvolution algorithms and machine learning-based quality assessment for optimal precursor selection. In an analysis ofE. colilysate, FLASHIda increases the number of unique proteoform level identifications from 800 to 1500 or generates a near-identical number of identifications in one third of the instrument time when compared to standard DDA mode. Furthermore, FLASHIda enables sensitive mapping of post-translational modifications and detection of chemical adducts. As a software extension module to the instrument, FLASHIda can be readily adopted for TDP studies of complex samples to enhance proteoform identification rates.
Sustainable oxygen evolution electrocatalysis in aqueous 1 M H2SO4 with earth abundant nanostructured Co3O4
Authors: Yu Jiahao , Garcés-Pineda Felipe A. , González-Cobos Jesús , Peña-Díaz Marina , Rogero Celia , Giménez Sixto , Spadaro Maria Chiara , Arbiol Jordi , Barja Sara , Galán-Mascarós José Ramón
Published: July 2022

Earth-abundant electrocatalysts for the oxygen evolution reaction (OER) able to work in acidic working conditions are elusive. While many first-row transition metal oxides are competitive in alkaline media, most of them just dissolve or become inactive at high proton concentrations where hydrogen evolution is preferred. Only noble-metal catalysts, such as IrO2, are fast and stable enough in acidic media. Herein, we report the excellent activity and long-term stability of Co3O4-based anodes in 1 M H2SO4 (pH 0.1) when processed in a partially hydrophobic carbon-based protecting matrix. These Co3O4@C composites reliably drive O2 evolution a 10 mA cm–2 current density for >40 h without appearance of performance fatigue, successfully passing benchmarking protocols without incorporating noble metals. Our strategy opens an alternative venue towards fast, energy efficient acid-media water oxidation electrodes.
A reconfigurable and magnetically responsive assembly for dynamic solar steam generation
Authors: Hu Yajie , Ma Hongyun , Wu Mingmao , Lin Tengyu , Yao Houze , Liu Feng , Cheng Huhu , Qu Liangti
Published: July 2022

Interfacial solar vapor generation is a promising technique to efficiently get fresh water from seawater or effluent. However, for the traditional static evaporation models, further performance improvement has encountered bottlenecks due to the lack of dynamic management and self-regulation on the evolving water movement and phase change in the evaporation process. Here, a reconfigurable and magnetically responsive evaporator with conic arrays is developed through the controllable and reversible assembly of graphene wrapped Fe3O4nanoparticles. Different from the traditional structure-rigid evaporation architecture, the deformable and dynamic assemblies could reconfigure themselves both at macroscopic and microscopic scales in response to the variable magnetic field. Thus, the internal water transportation and external vapor diffusion are greatly promoted simultaneously, leading to a 23% higher evaporation rate than that of static counterparts. Further, well-designed hierarchical assembly and dynamic evaporation system can boost the evaporation rate to a record high level of 5.9 kg m−2h−1. This proof-of-concept work demonstrates a new direction for development of high performance water evaporation system with the ability of dynamic reconfiguration and reassembly.
Copper-catalyzed Z-selective synthesis of acrylamides and polyacrylamides via alkylidene ketenimines
Authors: Duan Xuelun , Zheng Nan , Li Ming , Liu Gongbo , Sun Xinhao , Wu Qiming , Song Wangze
Published: July 2022

It remains very important to discover and study new fundamental intermediates consisting of carbon and nitrogen as the abundant elements of organic molecules. The unique alkylidene ketenimine could be formed in situ under mild conditions by an unexpected copper-catalyzed three-component reaction of alkyne, azide and water involving a successive cycloaddition, N2 extrusion and carbene-assisted rearrangement. Only Z-α,β-unsaturated amides instead of E-α,β-unsaturated amides or triazoles were acquired from alkylidene ketenimines with excellent selectivities and stereospecificities. In addition, a series of “approximate” alternating copolymers (poly (triazole-alt-Z-acrylamides)) with high Mns and yields were efficiently afforded by multicomponent polymerization through a very simple operation basing on this multicomponent reaction.
T cell receptor β-chain-targeting chimeric antigen receptor T cells against T cell malignancies
Authors: Li Fanlin , Zhang Huihui , Wang Wanting , Yang Puyuan , Huang Yue , Zhang Junshi , Yan Yaping , Wang Yuan , Ding Xizhong , Liang Jie , Qi Xinyue , Li Min , Han Ping , Zhang Xiaoqing , Wang Xin , Cao Jiang , Fu Yang-Xin , Yang Xuanming
Published: July 2022

The success of chimeric antigen receptor (CAR) T cells in treating B cell malignancies comes at the price of eradicating normal B cells. Even though T cell malignancies are aggressive and treatment options are limited, similar strategies for T cell malignancies are constrained by the severe immune suppression arising from bystander T cell aplasia. Here, we show the selective killing of malignant T cells without affecting normal T cell-mediated immune responses in vitro and in a mouse model of disseminated leukemia. Further, we develop a CAR construct that carries the single chain variable fragment of a subtype-specific antibody against the variable TCR β-chain region. We demonstrate that these anti-Vβ8 CAR-T cells are able to recognize and kill all Vβ8+malignant T cells that arise from clonal expansion while sparing malignant or healthy Vβ8−T cells, allowing sufficient T cell-mediated cellular immunity. In summary, we present a proof of concept for a selective CAR-T cell therapy to eradicate T cell malignancies while maintaining functional adaptive immunity, which opens the possibility for clinical development.
An acquired phosphatidylinositol 4-phosphate transport initiates T-cell deterioration and leukemogenesis
Authors: Zhong Wenbin , Lin Weize , Yang Yingjie , Chen Dan , Cao Xiuye , Xu Mengyang , Pan Guoping , Chen Huanzhao , Zheng Jie , Feng Xiaoqin , Yang Li hua , Lai Chaofeng , Olkkonen Vesa M. , Xu Jun , Cui Shuzhong , Yan Daoguang
Published: July 2022

Lipid remodeling is crucial for malignant cell transformation and tumorigenesis, but the precise molecular processes involved and direct evidences for these in vivo remain elusive. Here, we report that oxysterol-binding protein (OSBP)-related protein 4 L (ORP4L) is expressed in adult T-cell leukemia (ATL) cells but not normal T-cells. In ORP4L knock-in T-cells, ORP4L dimerizes with OSBP to control the shuttling of OSBP between the Golgi apparatus and the plasma membrane (PM) as an exchanger of phosphatidylinositol 4-phosphate [PI(4)P]/cholesterol. The PI(4)P arriving at the PM via this transport machinery replenishes phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] and phosphatidylinositol (3,4,5) trisphosphate [PI(3,4,5)P3] biosynthesis, thus contributing to PI3K/AKT hyperactivation and T-cell deterioration in vitro and in vivo. Disruption of ORP4L and OSBP dimerization disables PI(4)P transport and T-cell leukemogenesis. In summary, we identify a non-vesicular lipid transport machinery between Golgi and PM maintaining the oncogenic signaling competence initiating T-cell deterioration and leukemogenesis.
Proteotoxicity caused by perturbed protein complexes underlies hybrid incompatibility in yeast
Authors: Swamy Krishna B. S. , Lee Hsin-Yi , Ladra Carmina , Liu Chien-Fu Jeff , Chao Jung-Chi , Chen Yi-Yun , Leu Jun-Yi
Published: July 2022

Dobzhansky–Muller incompatibilities represent a major driver of reproductive isolation between species. They are caused when interacting components encoded by alleles from different species cannot function properly when mixed. At incipient stages of speciation, complex incompatibilities involving multiple genetic loci with weak effects are frequently observed, but the underlying mechanisms remain elusive. Here we show perturbed proteostasis leading to compromised mitosis and meiosis inSaccharomyces cerevisiaehybrid lines carrying one or two chromosomes fromSaccharomyces bayanusvar.uvarum. Levels of proteotoxicity are correlated with the number of protein complexes on replaced chromosomes. Proteomic approaches reveal that multi-protein complexes with subunits encoded by replaced chromosomes tend to be unstable. Furthermore, hybrid defects can be alleviated or aggravated, respectively, by up- or down-regulating the ubiquitin-proteasomal degradation machinery, suggesting that destabilized complex subunits overburden the proteostasis machinery and compromise hybrid fitness. Our findings reveal the general role of impaired protein complex assembly in complex incompatibilities.
Functional neuronal circuitry and oscillatory dynamics in human brain organoids
Authors: Sharf Tal , van der Molen Tjitse , Glasauer Stella M. K. , Guzman Elmer , Buccino Alessio P. , Luna Gabriel , Cheng Zhuowei , Audouard Morgane , Ranasinghe Kamalini G. , Kudo Kiwamu , Nagarajan Srikantan S. , Tovar Kenneth R. , Petzold Linda R. , Hierlemann Andreas , Hansma Paul K. , Kosik Kenneth S.
Published: July 2022

Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiology of neuronal circuits within organoids remains under-explored. With high-density CMOS microelectrode arrays and shank electrodes, we captured spontaneous extracellular activity from brain organoids derived from human induced pluripotent stem cells. We inferred functional connectivity from spike timing, revealing a large number of weak connections within a skeleton of significantly fewer strong connections. A benzodiazepine increased the uniformity of firing patterns and decreased the relative fraction of weakly connected edges. Our analysis of the local field potential demonstrate that brain organoids contain neuronal assemblies of sufficient size and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug action, and the effects of external stimuli upon neuronal networks.
Fatigue-free artificial ionic skin toughened by self-healable elastic nanomesh
Authors: Wang Jiqiang , Wu Baohu , Wei Peng , Sun Shengtong , Wu Peiyi
Published: July 2022

Robust ionic sensing materials that are both fatigue-resistant and self-healable like human skin are essential for soft electronics and robotics with extended service life. However, most existing self-healable artificial ionic skins produced on the basis of network reconfiguration suffer from a low fatigue threshold due to the easy fracture of low-energy amorphous polymer chains with susceptible crack propagation. Here we engineer a fatigue-free yet fully healable hybrid ionic skin toughened by a high-energy, self-healable elastic nanomesh, resembling the repairable nanofibrous interwoven structure of human skin. Such a design affords a superhigh fatigue threshold of 2950 J m−2 while maintaining skin-like compliance, stretchability, and strain-adaptive stiffening response. Moreover, nanofiber tension-induced moisture breathing of ionic matrix leads to a record-high strain-sensing gauge factor of 66.8, far exceeding previous intrinsically stretchable ionic conductors. This concept creates opportunities for designing durable ion-conducting materials that replicate the unparalleled combinatory properties of natural skins more precisely.
Cascaded dissipative DNAzyme-driven layered networks guide transient replication of coded-strands as gene models
Authors: Wang Jianbang , Li Zhenzhen , Willner Itamar
Published: July 2022

Dynamic, transient, out-of-equilibrium networks guide cellular genetic, metabolic or signaling processes. Designing synthetic networks emulating natural processes imposes important challenges including the ordered connectivity of transient reaction modules, engineering of the appropriate balance between production and depletion of reaction constituents, and coupling of the reaction modules with emerging chemical functions dictated by the networks. Here we introduce the assembly of three coupled reaction modules executing a cascaded dynamic process leading to the transient formation and depletion of three different Mg2+-ion-dependent DNAzymes. The transient operation of the DNAzyme in one layer triggers the dynamic activation of the DNAzyme in the subsequent layer, leading to a three-layer transient catalytic cascade. The kinetics of the transient cascade is computationally simulated. The cascaded network is coupled to a polymerization/nicking DNA machinery guiding transient synthesis of three coded strands acting as “gene models”, and to the rolling circle polymerization machinery leading to the transient synthesis of fluorescent Zn(II)-PPIX/G-quadruplex chains or hemin/G-quadruplex catalytic wires.
Electronic and magnetic properties of the RuX3 (X = Cl, Br, I) family: two siblings—and a cousin?
Authors: Kaib David A. S. , Riedl Kira , Razpopov Aleksandar , Li Ying , Backes Steffen , Mazin Igor I. , Valentí Roser
Published: July 2022

Motivated by reports of metallic behavior in the recently synthesized RuI3, in contrast to the Mott-insulating nature of the actively discussed α-RuCl3, as well as RuBr3, we present a detailed comparative analysis of the electronic and magnetic properties of this family of trihalides. Using a combination of first-principles calculations and effective-model considerations, we conclude that RuI3, similarly to the other two members, is most probably on the verge of a Mott insulator, but with much smaller magnetic moments and strong magnetic frustration. We predict the ideal pristine crystal of RuI3 to have a nearly vanishing conventional nearest-neighbor Heisenberg interaction and to be a quantum spin liquid candidate of a possibly different kind than the Kitaev spin liquid. In order to understand the apparent contradiction to the reported resistivity ρ, we analyze the experimental evidence for all three compounds and propose a scenario for the observed metallicity in existing samples of RuI3. Furthermore, for the Mott insulator RuBr3, we obtain a magnetic Hamiltonian of a similar form to that in the much-discussed α-RuCl3 and show that this Hamiltonian is in agreement with experimental evidence in RuBr3.
Mucosal administration of a live attenuated recombinant COVID-19 vaccine protects nonhuman primates from SARS-CoV-2
Authors: Tioni Mariana F. , Jordan Robert , Pena Angie Silva , Garg Aditya , Wu Danlu , Phan Shannon I. , Weiss Christopher M. , Cheng Xing , Greenhouse Jack , Orekov Tatyana , Valentin Daniel , Kar Swagata , Pessaint Laurent , Andersen Hanne , Stobart Christopher C. , Bloodworth Melissa H. , Stokes Peebles R. , Liu Yang , Xie Xuping , Shi Pei-Yong , Moore Martin L. , Tang Roderick S.
Published: July 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 global pandemic. SARS-CoV-2 is an enveloped RNA virus that relies on its trimeric surface glycoprotein spike for entry into host cells. Here we describe the COVID-19 vaccine candidate MV-014-212, a live, attenuated, recombinant human respiratory syncytial virus expressing a chimeric SARS-CoV-2 spike as the only viral envelope protein. MV-014-212 was attenuated and immunogenic in African green monkeys (AGMs). One mucosal administration of MV-014-212 in AGMs protected against SARS-CoV-2 challenge, reducing by more than 200-fold the peak shedding of SARS-CoV-2 in the nose. MV-014-212 elicited mucosal immunoglobulin A in the nose and neutralizing antibodies in serum that exhibited cross-neutralization against virus variants of concern Alpha, Beta, and Delta. Intranasally delivered, live attenuated vaccines such as MV-014-212 entail low-cost manufacturing suitable for global deployment. MV-014-212 is currently in Phase 1 clinical trials as an intranasal COVID-19 vaccine.
Vaccination with Mycoplasma pneumoniae membrane lipoproteins induces IL-17A driven neutrophilia that mediates Vaccine-Enhanced Disease
Authors: Mara Arlind B. , Gavitt Tyler D. , Tulman Edan R. , Miller Jeremy M. , He Wu , Reinhardt Emily M. , Ozyck R. Grace , Goodridge Meagan L. , Silbart Lawrence K. , Szczepanek Steven M. , Geary Steven J.
Published: July 2022

Bacterial lipoproteins are an often-underappreciated class of microbe-associated molecular patterns with potent immunomodulatory activity. We previously reported that vaccination of BALB/c mice withMycoplasma pneumoniae(Mp) lipid-associated membrane proteins (LAMPs) resulted in lipoprotein-dependent vaccine enhanced disease after challenge with virulentMp, though the immune responses underpinning this phenomenon remain poorly understood. Herein, we report that lipoprotein-induced VED in a mouse model is associated with elevated inflammatory cytokines TNF-α, IL-1β, IL-6, IL-17A, and KC in lung lavage fluid and with suppurative pneumonia marked by exuberant neutrophilia in the pulmonary parenchyma. Whole-lung-digest flow cytometry and RNAScope analysis identified multiple cellular sources for IL-17A, and the numbers of IL-17A producing cells were increased in LAMPs-vaccinated/Mp-challenged animals compared to controls. Specific IL-17A or neutrophil depletion reduced disease severity in our VED model—indicating thatMplipoproteins induce VED in an IL-17A-dependent manner and through exuberant neutrophil recruitment. IL-17A neutralization reduced levels of TNF-α, IL-1β, IL-6, and KC, indicating that IL-17A preceded other inflammatory cytokines. Surprisingly, we found that IL-17A neutralization impaired bacterial clearance, while neutrophil depletion improved it—indicating that, while IL-17A appears to confer both maladaptive and protective responses, neutrophils play an entirely maladaptive role in VED. Given that lipoproteins are found in virtually all bacteria, the potential for lipoprotein-mediated maladaptive inflammatory responses should be taken into consideration when developing vaccines against bacterial pathogens.
A high spatial resolution land surface phenology dataset for AmeriFlux and NEON sites
Authors: Moon Minkyu , Richardson Andrew D. , Milliman Thomas , Friedl Mark A.
Published: July 2022

Vegetation phenology is a key control on water, energy, and carbon fluxes in terrestrial ecosystems. Because vegetation canopies are heterogeneous, spatially explicit information related to seasonality in vegetation activity provides valuable information for studies that use eddy covariance measurements to study ecosystem function and land-atmosphere interactions. Here we present a land surface phenology (LSP) dataset derived at 3 m spatial resolution from PlanetScope imagery across a range of plant functional types and climates in North America. The dataset provides spatially explicit information related to the timing of phenophase changes such as the start, peak, and end of vegetation activity, along with vegetation index metrics and associated quality assurance flags for the growing seasons of 2017–2021 for 10 × 10 km windows centred over 104 eddy covariance towers at AmeriFlux and National Ecological Observatory Network (NEON) sites. These LSP data can be used to analyse processes controlling the seasonality of ecosystem-scale carbon, water, and energy fluxes, to evaluate predictions from land surface models, and to assess satellite-based LSP products.
Design, synthesis, in vitro biological assessment and molecular modeling insights for novel 3-(naphthalen-1-yl)-4,5-dihydropyrazoles as anticancer agents with potential EGFR inhibitory activity
Authors: Eldehna Wagdy M. , El Hassab Mahmoud A. , Elsayed Zainab M. , Al-Warhi Tarfah , Elkady Hazem , Abo-Ashour Mahmoud F. , Abourehab Mohammed A. S. , Eissa Ibrahim H. , Abdel-Aziz Hatem A.
Published: July 2022

Currently, the humanity is in a fierce battle against various health-related challenges especially those associated with human malignancies. This created the urge to develop potent and selective inhibitors for tumor cells through targeting specific oncogenic proteins possessing crucial roles in cancer progression and survive. In this respect, new series of pyrazole-thiazol-4-one hybrids (9a–p) were synthesized as potential anticancer agents. All the synthesized molecules exhibited potent antiproliferative actions against breast cancer (BC) T-47D and MDA-MB-231 cell lines with IC50 ranges 3.14–4.92 and 0.62–58.01, respectively. Moreover, the most potent anti-proliferative counterparts 9g and 9k were assessed against EGFR. They displayed nanomolar inhibitory activity, IC50 267 ± 12 and 395 ± 17 nM, respectively. Worth noting, both compounds 9g and 9k induced apoptosis in MDA-MB-231 cells, and resulted in a cell cycle arrest at G2/M phase. Furthermore, an in silico analysis including docking and molecular dynamic simulations was performed.
A deep learning framework for epileptic seizure detection based on neonatal EEG signals
Authors: Gramacki Artur , Gramacki Jarosław
Published: July 2022

Electroencephalogram (EEG) is one of the main diagnostic tests for epilepsy. The detection of epileptic activity is usually performed by a human expert and is based on finding specific patterns in the multi-channel electroencephalogram. This is a difficult and time-consuming task, therefore various attempts are made to automate it using both conventional and Deep Learning (DL) techniques. Unfortunately, authors do not often provide sufficiently detailed and complete information to be able to reproduce their results. Our work is intended to fill this gap. Using a carefully selected 79 neonatal EEG recordings we developed a complete framework for seizure detection using DL approch. We share a ready to use R and Python codes which allow: (a) read raw European Data Format files, (b) read data files containing the seizure annotations made by human experts, (c) extract train, validation and test data, (d) create an appropriate Convolutional Neural Network (CNN) model, (e) train the model, (f) check the quality of the neural classifier, (g) save all learning results.
Freshwater unionid mussels threatened by predation of Round Goby (Neogobius melanostomus)
Authors: Clark Kyle H. , Iwanowicz Deborah D. , Iwanowicz Luke R. , Mueller Sara J. , Wisor Joshua M. , Bradshaw-Wilson Casey , Schill William B. , Stauffer J. R. , Boyer Elizabeth W.
Published: July 2022

Indigenous freshwater mussels (Unionidae) are integral to riverine ecosystems, playing a pivotal role in aquatic food webs and providing ecological services. With populations on the decline worldwide, freshwater mussels are of conservation concern. In this study, we explore the propensity of the invasive Round Goby (Neogobius melanostomus) fish to prey upon indigenous freshwater mussels. First, we conducted lab experiments where Round Gobies were given the opportunity to feed on juvenile unionid mussels and macroinvertebrates, revealing rates and preferences of consumption. Several Round Gobies consumed whole freshwater mussels during these experiments, as confirmed by mussel counts and x-ray images of the fishes. Next, we investigated Round Gobies collected from stream habitats of the French Creek watershed, which is renowned for its unique and rich aquatic biodiversity. We developed a novel DNA metabarcoding method to identify the specific species of mussels consumed by Round Goby and provide a new database of DNA gene sequences for 25 indigenous unionid mussel species. Several of the fishes sampled had consumed indigenous mussels, including the Elktoe (non-endangered), Creeper (non-endangered), Long Solid (state endangered), and Rayed Bean (federally endangered) species. The invasive Round Goby poses a growing threat to unionid mussels, including species of conservation concern. The introduction of the invasive Round Goby to freshwaters of North America is shaping ecosystem transitions within the aquatic critical zone having widespread implications for conservation and management.
Heavy metal removal using an advanced removal method to obtain recyclable paper incineration ash
Authors: Kim Hak-Min , Choi Tae-Yeol , Park Min-Ju , Jeong Dae-Woon
Published: July 2022

Various agents, including ethylenediaminetetraacetic acid, oxalic acid, citric acid, and HCl, were applied to remove heavy metals from raw paper incineration ash and render the ash recyclable. Among these prepared agent solutions, ethylenediaminetetraacetic acid showed the highest efficiency for Pb removal, while oxalic acid showed the highest efficiencies for Cu, Cd, and As removal. Additionally, three modes of an advanced removal method, which involved the use of both ethylenediaminetetraacetic acid and oxalic acid, were considered for use at the end of the rendering process. Among these three modes of the advanced removal method, that which involved the simultaneous use of ethylenediaminetetraacetic acid and oxalic acid, i.e., a mixture of both solutions, showed the best heavy metal removal efficiencies. In detail, 11.9% of Cd, 10% of Hg, 28.42% of As, 31.29% of Cu, and 49.19% of Pb were removed when this method was used. Furthermore, the application of these three modes of the advanced removal method resulted in a decrease in the amounts of heavy metals eluted and brought about an increase in the CaO content of the treated incineration ash, while decreasing its Cl content. These combined results enhanced the solidification effect of the treated incineration ash. Thus, it was confirmed that the advanced removal method is a promising strategy by which recyclable paper incineration ash can be obtained.
Comparison of survival between unilocular cystic and purely solid renal cell carcinoma
Authors: Wang Yapeng , Niu Xiaoyu , Wang Lihui , Li Yunlong , Qiao Baoping
Published: July 2022

To evaluate clinicopathological features and survival outcomes of unilocular cystic renal cell carcinoma (ucRCC) compared with purely solid renal cell carcinoma (sRCC), and to evaluate the oncologic aggressiveness of ucRCC. The relevant data of 957 patients with sporadic unilateral renal cell carcinoma (RCC) underwent surgical treatment in 2 institutions from Jan 2014 to Oct 2018 were obtained. We excluded multilocular cystic renal neoplasm of low malignant potential (MCRNLMP), RCC with multilocular cysts and necrotic RCC. 74 ucRCCs were identified by pathology reports. We performed propensity score matching (PSM) and eventually selected 144 sRCCs. The clinicopathological features and survival outcomes were compared properly. After PSM, age, BMI, Charlson Comorbidity Index, and postoperative Chronic Kidney Disease grade were not significantly different. Both overall survival and progression-free survival of ucRCC were significantly better than sRCC by the log-rank test. Twenty-five cases of sRCCs were in the pT3 or pT4 stage, while no pT3 or pT4 tumors were found in ucRCCs. Fuhrman grade and lymphatic metastasis were found to be significant prognostic factors for the overall survival of ucRCC. Unilocular cystic RCC has a lower Fuhrman grade and pathological stage and a better prognosis compared with solid RCC. Patients with ucRCC still probably have lymphatic metastasis at surgery and may have postoperative metastasis, which is different from MCRNLMP. We recommend that the diagnosis of ucRCC should be reflected in pathology report. Different subtype of cystic RCC should be taken into consideration in counseling and management.
A microfluidic diagnostic device with air plug-in valves for the simultaneous genetic detection of various food allergens
Authors: Natsuhara Daigo , Misawa Sae , Saito Ryogo , Shirai Koki , Okamoto Shunya , Nagai Moeto , Kitamura Masashi , Shibata Takayuki
Published: July 2022

The identification of accidental allergen contamination in processed foods is crucial for risk management strategies in the food processing industry to effectively prevent food allergy incidents. Here, we propose a newly designed passive stop valve with high pressure resistance performance termed an “air plug-in valve” to further improve microfluidic devices for the detection of target nucleic acids. By implementing the air plug-in valve as a permanent stop valve, a maximal allowable flow rate of 70 µL/min could be achieved for sequential liquid dispensing into an array of 10 microchambers, which is 14 times higher than that achieved with the previous valve arrangement using single-faced stop valves. Additionally, we demonstrate the simultaneous detection of multiple food allergens (wheat, buckwheat, and peanut) based on the colorimetric loop-mediated isothermal amplification assay using our diagnostic device with 10 microchambers compactly arranged in a 20-mm-diameter circle. After running the assays at 60 °C for 60 min, any combination of the three types of food allergens and tea plant, which were used as positive and negative control samples, respectively, yielded correct test results, without any cross-contamination among the microchambers. Thus, our diagnostic device will provide a rapid and easy sample-to-answer platform for ensuring food safety and security.
A methodology for evaluating digital contact tracing apps based on the COVID-19 experience
Authors: Hernández-Orallo Enrique , Manzoni Pietro , Calafate Carlos T. , Cano Juan-Carlos
Published: July 2022

Controlling the spreading of infectious diseases has been shown crucial in the COVID-19 pandemic. Traditional contact tracing is used to detect newly infected individuals by tracing their previous contacts, and by selectively checking and isolating any individuals likely to have been infected. Digital contact tracing with the utilisation of smartphones was contrived as a technological aid to improve this manual, slow and tedious process. Nevertheless, despite the high hopes raised when smartphone-based contact tracing apps were introduced as a measure to reduce the spread of the COVID-19, their efficiency has been moderately low. In this paper, we propose a methodology for evaluating digital contact tracing apps, based on an epidemic model, which will be used not only to evaluate the deployed Apps against the COVID-19 but also to determine how they can be improved for future pandemics. Firstly, the model confirms the moderate effectiveness of the deployed digital contact tracing, confirming the fact that it could not be used as the unique measure to fight against the COVID-19, and had to be combined with additional measures. Secondly, several improvements are proposed (and evaluated) to increase the efficiency of digital control tracing to become a more useful tool in the future.
Exploring the operational potential of the forest-photovoltaic utilizing the simulated solar tree
Authors: Um Dan-Bi
Published: July 2022

The aim of this study was to explore the operational potential of forest-photovoltaic by simulating solar tree installation. The forest-photovoltaic concept is to maintain carbon absorption activities in the lower part while acquiring solar energy by installing a photovoltaic structure on the upper part of forest land. This study was conducted by simulating solar tree installation using Google Earth satellite imagery in a mountainous area where an agrophotovoltaic system was already installed. When the simulation results were evaluated based on the installation guideline of the agrophotovoltaic system, it was confirmed that the operational potential of forest-photovoltaic was very high in almost all items of the guideline. Therefore, forest photovoltaic can be a possible alternative with priority in South Korea, where it is challenging to secure spatial competitiveness with a conventional flat fixed panel due to costly land prices. Although South Korea has been selected here as a case study, this discussion can be applied to other countries facing the disturbance risk to the forestry landscape due to solar power projects. To the best of the author's knowledge, this is the world's first study exploring the possibility of the forest-photovoltaic.
A nationwide study of patients operated for cervical degenerative disorders in public and private hospitals
Authors: Danielsen Elisabet , Mjåset Christer , Ingebrigtsen Tor , Gulati Sasha , Grotle Margreth , Rudolfsen Jan Håkon , Nygaard Øystein P. , Solberg Tore K.
Published: July 2022

During the last decades, there has been an increase in the rate of surgery for degenerative disorders of the cervical spine and in the use of supplementary private health insurance. Still, there is limited knowledge about the differences in characteristics of patients operated in public and private hospitals. Therefore, we aimed at comparing sociodemographic-, clinical- and patient management data on patients operated for degenerative cervical radiculopathy and degenerative cervical myelopathy in public and private hospitals in Norway. This was a cross-sectional study on patients in the Norwegian Registry for Spine Surgery operated for degenerative cervical radiculopathy and degenerative cervical myelopathy between January 2012 and December 2020. At admission for surgery, we assessed disability by the following patient reported outcome measures (PROMs): neck disability index (NDI), EuroQol-5D (EQ-5D) and numerical rating scales for neck pain (NRS-NP) and arm pain (NRS-AP). Among 9161 patients, 7344 (80.2%) procedures were performed in public hospitals and 1817 (19.8%) in private hospitals. Mean age was 52.1 years in public hospitals and 49.7 years in private hospitals (P < 0.001). More women were operated in public hospitals (47.9%) than in private hospitals (31.6%) (P < 0.001). A larger proportion of patients in private hospitals had high education (≥ 4 years of college or university) (42.9% vs 35.6%, P < 0.001). Patients in public hospitals had worse disease-specific health problems than those in private hospitals: unadjusted NDI mean difference was 5.2 (95% CI 4.4 – 6.0; P < 0.001) and adjusted NDI mean difference was 3.4 (95% CI 2.5 – 4.2; P < 0.001), and they also had longer duration of symptoms (P < 0.001). Duration of surgery (mean difference 29 minutes, 95% CI 27.1 – 30.7; P < 0.001) and length of hospital stay (mean difference 2 days, 95% CI 2.3 – 2.4; P < 0.001) were longer in public hospitals. In conclusion, patients operated for degenerative cervical spine in private hospitals were healthier, younger, better educated and more often men. They also had less and shorter duration of symptoms and seemed to be managed more efficiently. Our findings indicate that access to cervical spine surgery in private hospitals could be skewed in favour of patients with higher socioeconomic status.
Selective biofunctionalization of 3D cell-imprinted PDMS with collagen immobilization for targeted cell attachment
Authors: Babaei Mahrokh , Bonakdar Shahin , Nasernejad Bahram
Published: July 2022

Cell-imprinted polydimethylsiloxane substrates, in terms of their ability to mimic the physiological niche, low microfabrication cost, and excellent biocompatibility were widely used in tissue engineering. Cells inside the mature cells' cell-imprinted PDMS pattern have been shown in previous research to be capable of being differentiated into a specific mature cell line. On the other hand, the hydrophobicity of PDMS substrate leads to weak cell adhesion. Moreover, there was no guarantee that the cells would be exactly located in the cavities of the cells' pattern. In many studies, PDMS surface was modified by plasma treatment, chemical modification, and ECM coating. Hence, to increase the efficiency of cell-imprinting method, the concavity region created by the cell-imprinted pattern is conjugated with collagen. A simple and economical method of epoxy silane resin was applied for the selective protein immobilization on the desired regions of the PDMS substrate. This method could be paved to enhance the cell trapping into the cell-imprinted pattern, and it could be helpful for stem cell differentiation studies. The applied method for selective protein attachment, and as a consequence, selective cell integration was assessed on the aligned cell-imprinted PDMS. A microfluidic chip created the aligned cell pattern. After Ar+plasma and APTES treatment of the PDMS substrate, collagen immobilization was performed. The immobilized collagen was removed by epoxy silane resin stamp from the ridge area where the substrate lacked cell pattern and leaving the collagen only within the patterned areas. Coomassie brilliant blue staining was evaluated for selective collagen immobilization, and the collagen-binding stability was assessed by BCA analysis. MTT assay for the evaluation of cell viability on the modified surface was further analyzed. Subsequently, the crystal violet staining has confirmed the selective cell integration to the collagen-immobilized site on the PDMS substrate. The results proved the successfully selective collagen immobilization on the cell-imprinted PDMS and showed that this method increased the affinity of cells to attach inside the cell pattern cavity.