bluuebunny/crossref_metadata_2025 huggingface dataset:
Thrombosis and thrombocytopenia after vaccination against and infection with SARS-CoV-2 in Catalonia, Spain
Authors: Burn Edward , Roel Elena , Pistillo Andrea , Fernández-Bertolín Sergio , Aragón Maria , Raventós Berta , Reyes Carlen , Verhamme Katia , Rijnbeek Peter , Li Xintong , Strauss Victoria Y. , Prieto-Alhambra Daniel , Duarte-Salles Talita
Published: November 2022

Population-based studies can provide important evidence on the safety of COVID-19 vaccines. Here we compare rates of thrombosis and thrombocytopenia following vaccination against SARS-CoV-2 with the background (expected) rates in the general population. In addition, we compare the rates of the same adverse events among persons infected with SARS-CoV-2 with background rates. Primary care and linked hospital data from Catalonia, Spain informed the study, with participants vaccinated with BNT162b2 or ChAdOx1 (27/12/2020-23/06/2021), COVID-19 cases (01/09/2020-23/06/2021) or present in the database as of 01/01/2017. We included 2,021,366 BNT162b2 (1,327,031 with 2 doses), 592,408 ChAdOx1, 174,556 COVID-19 cases, and 4,573,494 background participants. Standardised incidence ratios for venous thromboembolism were 1.18 (95% CI 1.06-1.32) and 0.92 (0.81-1.05) after first- and second dose BNT162b2, and 0.92 (0.71-1.18) after first dose ChAdOx1. The standardised incidence ratio for venous thromboembolism in COVID-19 was 10.19 (9.43-11.02). Standardised incidence ratios for arterial thromboembolism were 1.02 (0.95-1.09) and 1.04 (0.97-1.12) after first- and second dose BNT162b2, 1.06 (0.91-1.23) after first-dose ChAdOx1 and 4.13 (3.83-4.45) for COVID-19. Standardised incidence ratios for thrombocytopenia were 1.49 (1.43-1.54) and 1.40 (1.35-1.45) after first- and second dose BNT162b2, 1.28 (1.19-1.38) after first-dose ChAdOx1 and 4.59 (4.41- 4.77) for COVID-19. While rates of thrombosis with thrombocytopenia were generally similar to background rates, the standardised incidence ratio for pulmonary embolism with thrombocytopenia after first-dose BNT162b2 was 1.70 (1.11-2.61). These findings suggest that the safety profiles of BNT162b2 and ChAdOx1 are similar, with rates of adverse events seen after vaccination typically similar to background rates. Meanwhile, rates of adverse events are much increased for COVID-19 cases further underlining the importance of vaccination.
Deglacial release of petrogenic and permafrost carbon from the Canadian Arctic impacting the carbon cycle
Authors: Wu Junjie , Mollenhauer Gesine , Stein Ruediger , Köhler Peter , Hefter Jens , Fahl Kirsten , Grotheer Hendrik , Wei Bingbing , Nam Seung-Il
Published: November 2022

The changes in atmospheric pCO2 provide evidence for the release of large amounts of ancient carbon during the last deglaciation. However, the sources and mechanisms that contributed to this process remain unresolved. Here, we present evidence for substantial ancient terrestrial carbon remobilization in the Canadian Arctic following the Laurentide Ice Sheet retreat. Glacial-retreat-induced physical erosion of bedrock has mobilized petrogenic carbon, as revealed by sedimentary records of radiocarbon dates and thermal maturity of organic carbon from the Canadian Beaufort Sea. Additionally, coastal erosion during the meltwater pulses 1a and 1b has remobilized pre-aged carbon from permafrost. Assuming extensive petrogenic organic carbon oxidation during the glacial retreat, a model-based assessment suggests that the combined processes have contributed 12 ppm to the deglacial CO2 rise. Our findings suggest potentially positive climate feedback of ice-sheet retreat by accelerating terrestrial organic carbon remobilization and subsequent oxidation during the glacial-interglacial transition.
CRISPR-Cas12a induced DNA double-strand breaks are repaired by multiple pathways with different mutation profiles in Magnaporthe oryzae
Authors: Huang Jun , Rowe David , Subedi Pratima , Zhang Wei , Suelter Tyler , Valent Barbara , Cook David E.
Published: November 2022

CRISPR-Cas mediated genome engineering has revolutionized functional genomics. However, understanding of DNA repair following Cas-mediated DNA cleavage remains incomplete. Using Cas12a ribonucleoprotein genome editing in the fungal pathogen, Magnaporthe oryzae, we detail non-canonical DNA repair outcomes from hundreds of transformants. Sanger and nanopore sequencing analysis reveals significant variation in DNA repair profiles, ranging from small INDELs to kilobase size deletions and insertions. Furthermore, we find the frequency of DNA repair outcomes varies between loci. The results are not specific to the Cas-nuclease or selection procedure. Through Ku80 deletion analysis, a key protein required for canonical non-homologous end joining, we demonstrate activity of an alternative end joining mechanism that creates larger DNA deletions, and uses longer microhomology compared to C-NHEJ. Together, our results suggest preferential DNA repair pathway activity in the genome that can create different mutation profiles following repair, which could create biased genome variation and impact genome engineering and genome evolution.
Quantum bath engineering of a high impedance microwave mode through quasiparticle tunneling
Authors: Aiello Gianluca , Féchant Mathieu , Morvan Alexis , Basset Julien , Aprili Marco , Gabelli Julien , Estève Jérôme
Published: November 2022

In microwave quantum optics, dissipation usually corresponds to quantum jumps, where photons are lost one by one. Here we demonstrate a new approach to dissipation engineering. By coupling a high impedance microwave resonator to a tunnel junction, we use the photoassisted tunneling of quasiparticles as a tunable dissipative process. We are able to adjust the minimum number of lost photons per tunneling event to be one, two or more, through a dc voltage. Consequently, different Fock states of the resonator experience different loss processes. Causality then implies that each state experiences a different energy (Lamb) shift, as confirmed experimentally. This photoassisted tunneling process is analogous to a photoelectric effect, which requires a quantum description of light to be quantitatively understood. This work opens up new possibilities for quantum state manipulation in superconducting circuits, which do not rely on the Josephson effect.
Measuring exposure to misinformation from political elites on Twitter
Authors: Mosleh Mohsen , Rand David G.
Published: November 2022

Misinformation can come directly from public figures and organizations (referred to here as “elites”). Here, we develop a tool for measuring Twitter users’ exposure to misinformation from elites based on the public figures and organizations they choose to follow. Using a database of professional fact-checks by PolitiFact, we calculate falsity scores for 816 elites based on the veracity of their statements. We then assign users an elite misinformation-exposure score based on the falsity scores of the elites they follow on Twitter. Users’ misinformation-exposure scores are negatively correlated with the quality of news they share themselves, and positively correlated with estimated conservative ideology. Additionally, we analyze the co-follower, co-share, and co-retweet networks of 5000 Twitter users and observe an association between conservative ideology and misinformation exposure. Finally, we find that estimated ideological extremity is associated with more misinformation exposure to a greater extent for users estimated to be conservative than for users estimated to be liberal. Finally, we create an open-source R library and an Application Programming Interface (API) making our elite misinformation-exposure estimation tool openly available to the community.
Expanding cross-presenting dendritic cells enhances oncolytic virotherapy and is critical for long-term anti-tumor immunity
Authors: Svensson-Arvelund Judit , Cuadrado-Castano Sara , Pantsulaia Gvantsa , Kim Kristy , Aleynick Mark , Hammerich Linda , Upadhyay Ranjan , Yellin Michael , Marsh Henry , Oreper Daniel , Jhunjhunwala Suchit , Moussion Christine , Merad Miriam , Brown Brian D. , García-Sastre Adolfo , Brody Joshua D.
Published: November 2022

Immunotherapies directly enhancing anti-tumor CD8+ T cell responses have yielded measurable but limited success, highlighting the need for alternatives. Anti-tumor T cell responses critically depend on antigen presenting dendritic cells (DC), and enhancing mobilization, antigen loading and activation of these cells represent an attractive possibility to potentiate T cell based therapies. Here we show that expansion of DCs by Flt3L administration impacts in situ vaccination with oncolytic Newcastle Disease Virus (NDV). Mechanistically, NDV activates DCs and sensitizes them to dying tumor cells through upregulation of dead-cell receptors and synergizes with Flt3L to promote anti-tumor CD8+ T cell cross-priming. In vivo, Flt3L-NDV in situ vaccination induces parallel amplification of virus- and tumor-specific T cells, including CD8+ T cells reactive to newly-described neoepitopes, promoting long-term tumor control. Cross-presenting conventional Type 1 DCs are indispensable for the anti-tumor, but not anti-viral, T cell response, and type I IFN-dependent CD4+ Th1 effector cells contribute to optimal anti-tumor immunity. These data demonstrate that mobilizing DCs to increase tumor antigen cross-presentation improves oncolytic virotherapy and that neoepitope-specific T cells can be induced without individualized, ex vivo manufactured vaccines.
Primate-specific transposable elements shape transcriptional networks during human development
Authors: Pontis Julien , Pulver Cyril , Playfoot Christopher J. , Planet Evarist , Grun Delphine , Offner Sandra , Duc Julien , Manfrin Andrea , Lutolf Matthias P. , Trono Didier
Published: November 2022

The human genome contains more than 4.5 million inserts derived from transposable elements (TEs), the result of recurrent waves of invasion and internal propagation throughout evolution. For new TE copies to be inherited, they must become integrated in the genome of the germline or pre-implantation embryo, which requires that their source TE be expressed at these stages. Accordingly, many TEs harbor DNA binding sites for the pluripotency factors OCT4, NANOG, SOX2, and KLFs and are transiently expressed during embryonic genome activation. Here, we describe how many primate-restricted TEs have additional binding sites for lineage-specific transcription factors driving their expression during human gastrulation and later steps of fetal development. These TE integrants serve as lineage-specific enhancers fostering the transcription, amongst other targets, of KRAB-zinc finger proteins (KZFPs) of comparable evolutionary age, which in turn corral the activity of TE-embedded regulatory sequences in a similarly lineage-restricted fashion. Thus, TEs and their KZFP controllers play broad roles in shaping transcriptional networks during early human development.
Biomimetic electrodynamic nanoparticles comprising ginger-derived extracellular vesicles for synergistic anti-infective therapy
Authors: Qiao Zhuangzhuang , Zhang Kai , Liu Jin , Cheng Daojian , Yu Bingran , Zhao Nana , Xu Fu-Jian
Published: November 2022

Nanotechnology enlightens promising antibacterial strategies while the complex in vivo infection environment poses a great challenge to the rational design of nanoplatforms for safe and effective anti-infective therapy. Herein, a biomimetic nanoplatform (EV-Pd-Pt) integrating electrodynamic Pd-Pt nanosheets and natural ginger-derived extracellular vesicles (EVs) is proposed. The introduction of ginger-derived EVs greatly endows EV-Pd-Pt with prolonged blood circulation without immune clearance, as well as accumulation at infection sites. More interestingly, EV-Pd-Pt can enter the interior of bacteria in an EV lipid-dependent manner. At the same time, reactive oxygen species are sustainably generated in situ to overcome the limitations of their short lifetime and diffusion distance. Notably, EV-Pd-Pt nanoparticle-mediated electrodynamic and photothermal therapy exhibit synergistic effects. Furthermore, the desirable biocompatibility and biosafety of the proposed nanoplatform guarantee the feasibility of in vivo applications. This proof-of-concept work holds significant promise for developing biomimetic nanoparticles by exploiting their intrinsic properties for synergistic anti-infective therapy.
Chromosome segregation fidelity requires microtubule polyglutamylation by the cancer downregulated enzyme TTLL11
Authors: Zadra Ivan , Jimenez-Delgado Senda , Anglada-Girotto Miquel , Segura-Morales Carolina , Compton Zachary J. , Janke Carsten , Serrano Luis , Ruprecht Verena , Vernos Isabelle
Published: November 2022

Regulation of microtubule (MT) dynamics is key for mitotic spindle assembly and faithful chromosome segregation. Here we show that polyglutamylation, a still understudied post-translational modification of spindle MTs, is essential to define their dynamics within the range required for error-free chromosome segregation. We identify TTLL11 as an enzyme driving MT polyglutamylation in mitosis and show that reducing TTLL11 levels in human cells or zebrafish embryos compromises chromosome segregation fidelity and impairs early embryonic development. Our data reveal a mechanism to ensure genome stability in normal cells that is compromised in cancer cells that systematically downregulate TTLL11. Our data suggest a direct link between MT dynamics regulation, MT polyglutamylation and two salient features of tumour cells, aneuploidy and chromosome instability (CIN).
A non-coding GWAS variant impacts anthracycline-induced cardiotoxic phenotypes in human iPSC-derived cardiomyocytes
Authors: Wu Xi , Shen Fei , Jiang Guanglong , Xue Gloria , Philips Santosh , Gardner Laura , Cunningham Geneva , Bales Casey , Cantor Erica , Schneider Bryan Paul
Published: November 2022

Anthracyclines, widely used to treat breast cancer, have the potential for cardiotoxicity. We have previously identified and validated a germline single nucleotide polymorphism, rs28714259, associated with an increased risk of anthracycline-induced heart failure. We now provide insights into the mechanism by which rs28714259 might confer increased risk of cardiac damage. Using hiPSC-derived cardiomyocyte cell lines with either intrinsic polymorphism or CRISPR-Cas9-mediated deletion of rs28714259 locus, we demonstrate that glucocorticoid receptor signaling activated by dexamethasone pretreatment prior to doxorubicin exposure preserves cardiomyocyte viability and contractility in cardiomyocytes containing the major allele. Homozygous loss of the rs28714259 major allele diminishes dexamethasone’s protective effect. We further demonstrate that the risk allele of rs28714259 disrupts glucocorticoid receptor and rs28714259 binding affinity. Finally, we highlight the activation of genes and pathways involved in cardiac hypertrophy signaling that are blocked by the risk allele, suggesting a decreased adaptive survival response to doxorubicin-related stress.
Sphingosine 1-phosphate mediates adiponectin receptor signaling essential for lipid homeostasis and embryogenesis
Authors: Ruiz Mario , Devkota Ranjan , Panagaki Dimitra , Bergh Per-Olof , Kaper Delaney , Henricsson Marcus , Nik Ali , Petkevicius Kasparas , Höög Johanna L. , Bohlooly-Y Mohammad , Carlsson Peter , Borén Jan , Pilon Marc
Published: November 2022

Cells and organisms require proper membrane composition to function and develop. Phospholipids are the major component of membranes and are primarily acquired through the diet. Given great variability in diet composition, cells must be able to deploy mechanisms that correct deviations from optimal membrane composition and properties. Here, using lipidomics and unbiased proteomics, we found that the embryonic lethality in mice lacking the fluidity regulators Adiponectin Receptors 1 and 2 (AdipoR1/2) is associated with aberrant high saturation of the membrane phospholipids. Using mouse embryonic fibroblasts (MEFs) derived from AdipoR1/2-KO embryos, human cell lines and the model organism C. elegans we found that, mechanistically, AdipoR1/2-derived sphingosine 1-phosphate (S1P) signals in parallel through S1PR3-SREBP1 and PPARγ to sustain the expression of the fatty acid desaturase SCD and maintain membrane properties. Thus, our work identifies an evolutionary conserved pathway by which cells and organisms achieve membrane homeostasis and adapt to a variable environment.
Wildflower phenological escape differs by continent and spring temperature
Authors: Lee Benjamin R. , Miller Tara K. , Rosche Christoph , Yang Yong , Heberling J. Mason , Kuebbing Sara E. , Primack Richard B.
Published: November 2022

Temperate understory plant species are at risk from climate change and anthropogenic threats that include increased deer herbivory, habitat loss, pollinator declines and mismatch, and nutrient pollution. Recent work suggests that spring ephemeral wildflowers may be at additional risk due to phenological mismatch with deciduous canopy trees. The study of this dynamic, commonly referred to as “phenological escape”, and its sensitivity to spring temperature is limited to eastern North America. Here, we use herbarium specimens to show that phenological sensitivity to spring temperature is remarkably conserved for understory wildflowers across North America, Europe, and Asia, but that canopy trees in North America are significantly more sensitive to spring temperature compared to in Asia and Europe. We predict that advancing tree phenology will lead to decreasing spring light windows in North America while spring light windows will be maintained or even increase in Asia and Europe in response to projected climate warming.
Unraveling sulfur chemistry in interstellar carbon oxide ices
Authors: Li Xiaolong , Lu Bo , Wang Lina , Xue Junfei , Zhu Bifeng , Trabelsi Tarek , Francisco Joseph S. , Zeng Xiaoqing
Published: November 2022

Formyl radical (HCO•) and hydroxycarbonyl radical (HOCO•) are versatile building blocks in the formation of biorelevant complex organic molecules (COMs) in interstellar medium. Understanding the chemical pathways for the formation of HCO• and HOCO• starting with primordial substances (e.g., CO and CO2) is of vital importance in building the complex network of prebiotic chemistry. Here, we report the efficient formation of HCO• and HOCO• in the photochemistry of hydroxidooxidosulfur radical (HOSO•)–a key intermediate in SO2photochemistry–in interstellar analogous ices of CO and CO2at 16 K through hydrogen atom transfer (HAT) reactions. Specifically, 266 nm laser photolysis of HOSO• embedded in solid CO ice yields the elusive hydrogen‑bonded complexes HCO•···SO2and HOCO•···SO, and the latter undergoes subsequent HAT to furnish CO2···HOS• under the irradiation conditions. Similar photo-induced HAT of HOSO• in solid CO2ice leads to the formation of HOCO•···SO2. The HAT reactions of HOSO• in astronomical CO and CO2ices by forming reactive acyl radicals may contribute to understanding the interplay between the sulfur and carbon ice-grain chemistry in cold molecular clouds and also in the planetary atmospheric chemistry.
Spatially nanoconfined N-type polymer semiconductors for stretchable ultrasensitive X-ray detection
Authors: Bian Yangshuang , Liu Kai , Ran Yang , Li Yi , Gao Yuanhong , Zhao Zhiyuan , Shao Mingchao , Liu Yanwei , Kuang Junhua , Zhu Zhiheng , Qin Mingcong , Pan Zhichao , Zhu Mingliang , Wang Chenyu , Chen Hu , Li Jia , Li Xifeng , Liu Yunqi , Guo Yunlong
Published: November 2022

Polymer semiconductors are promising candidates for wearable and skin-like X-ray detectors due to their scalable manufacturing, adjustable molecular structures and intrinsic flexibility. Herein, we fabricated an intrinsically stretchable n-type polymer semiconductor through spatial nanoconfinement effect for ultrasensitive X-ray detectors. The design of high-orientation nanofiber structures and dense interpenetrating polymer networks enhanced the electron-transporting efficiency and stability of the polymer semiconductors. The resultant polymer semiconductors exhibited an ultrahigh sensitivity of 1.52 × 104 μC Gyair−1 cm−2, an ultralow detection limit of 37.7 nGyair s−1 (comparable to the record-low value of perovskite single crystals), and polymer film X-ray imaging was achieved at a low dose rate of 3.65 μGyair s−1 (about 1/12 dose rate of the commercial medical chest X-ray diagnosis). Meanwhile, the hybrid semiconductor films could sustain 100% biaxial stretching strain with minimal degeneracy in photoelectrical performances. These results provide insights into future high-performance, low-cost e-skin photoelectronic detectors and imaging.
A distinct ripple-formation regime on Mars revealed by the morphometrics of barchan dunes
Authors: Rubanenko Lior , Lapôtre Mathieu G. A. , Ewing Ryan C. , Fenton Lori K. , Gunn Andrew
Published: November 2022

Sand mobilized by wind forms decimeter-scale impact ripples and decameter-scale or larger dunes on Earth and Mars. In addition to those two bedform scales, orbital and in situ images revealed a third distinct class of larger meter-scale ripples on Mars. Since their discovery, two main hypotheses have been proposed to explain the formation of large martian ripples—that they originate from the growth in wavelength and height of decimeter-scale ripples or that they arise from the same hydrodynamic instability as windblown dunes or subaqueous bedforms instead. Here we provide evidence that large martian ripples form from the same hydrodynamic instability as windblown dunes and subaqueous ripples. Using an artificial neural network, we characterize the morphometrics of over a million isolated barchan dunes on Mars and analyze how their size and shape vary across Mars’ surface. We find that the size of Mars’ smallest dunes decreases with increasing atmospheric density with a power-law exponent predicted by hydrodynamic theory, similarly to meter-size ripples, tightly bounding a forbidden range in bedform sizes. Our results provide key evidence for a unifying model for the formation of subaqueous and windblown bedforms on planetary surfaces, offering a new quantitative tool to decipher Mars’ atmospheric evolution.
The BDSF quorum sensing receptor RpfR regulates Bep exopolysaccharide synthesis in Burkholderia cenocepacia via interaction with the transcriptional regulator BerB
Authors: Steiner Elisabeth , Shilling Rebecca E. , Richter Anja M. , Schmid Nadine , Fazli Mustafa , Kaever Volkhard , Jenal Urs , Tolker-Nielsen Tim , Eberl Leo
Published: November 2022

The polysaccharide Bep is essential for in vitro biofilm formation of the opportunistic pathogen Burkholderia cenocepacia. We found that the Burkholderia diffusible signaling factor (BDSF) quorum sensing receptor RpfR is a negative regulator of the bep gene cluster in B. cenocepacia. An rpfR mutant formed wrinkled colonies, whereas additional mutations in the bep genes or known bep regulators like berA and berB restored the wild-type smooth colony morphology. We found that there is a good correlation between intracellular c-di-GMP levels and bep expression when the c-di-GMP level is increased or decreased through ectopic expression of a diguanylate cyclase or a c-di-GMP phosphodiesterase, respectively. However, when the intracellular c-di-GMP level is changed by site directed mutagenesis of the EAL or GGDEF domain of RpfR there is no correlation between intracellular c-di-GMP levels and bep expression. Except for rpfR, deletion mutants of all 25 c-di-GMP phosphodiesterase and diguanylate cyclase genes encoded by B. cenocepacia showed no change to berA and bep gene expression. Moreover, bacterial two-hybrid assays provided evidence that RpfR and BerB physically interact and give specificity to the regulation of the bep genes. We suggest a model where RpfR binds BerB at low c-di-GMP levels to sequester this RpoN-dependent activator to an RpfR/RpfF complex. If the c-di-GMP levels rise, possibly by the enzymatic action of RpfR, BerB binds c-di-GMP and is released from the RpfR/RpfF complex and associates with RpoN to activate transcription of berA, and the BerA protein subsequently activates transcription of the bep genes.
Oxidative stability and sensory evaluation of sodium caseinate-based yak butter powder
Authors: Agyare Anita N. , Liang Qi , Song Xuemei , Zhang Yan , Yang Jing , Shi Yongqi
Published: November 2022

Yak butter’s high unsaturated fatty acid level predisposes it to oxidation, hence must be converted into more stable forms like powder. This study aimed to spray dry yak butter using 10% yak butter and four sodium caseinate (NaCas) formulations: sample A: 100% NaCas; sample B: 50% NaCas, 50% lactose; sample C: 75% NaCas, 25% lactose; and sample D: 25% NaCas, 75% maltodextrin. The powders were vacuum and hermetically sealed, and evaluated for oxidative stability, physical and sensory properties during storage at 65 ℃ for 30 days. The results showed that samples B and D had similar and most favorable physical properties (such as, moisture, water activity, particle size, bulk density re-dispersion time, and encapsulation efficiency); though sample B, together with sample C, browned the most during storage. The majority of the sensory panelists preferred samples B and D; observed high caking in samples C and B; and the least whiteness loss and caking in samples D and A but high off-flavors in samples A and C. After storage, peroxide and thiobarbituric acid values of powder samples ranged from 34.98 to 69.54 meqO2/kg and 1.85–9.43 mg MD/kg, respectively, in the decreasing order of A, C, B, and D. Sample D, followed by B, showed the highest radical scavenging activity. Therefore, for optimum yak butter powder physical properties and oxidative stability, 50%:50%, NaCas: lactose, and 25%:75%, NaCas: maltodextrin formulations should be used. This study provides essential knowledge for butter powder processors.
Extinction magnitude of animals in the near future
Authors: Kaiho Kunio
Published: November 2022

There have been five major mass extinctions and some minor mass extinctions of animals since early animal diversification 540–520 Myr ago. It is said that a sixth mass extinction is already underway. However, the future extinction magnitude has not been quantitatively estimated. Here, I show that the sixth major mass extinction (defined as > 60% species loss) will be avoided, but a minor mass extinction, 20–50% animal species loss (1% now), will occur when humans cause nuclear war and/or fail to stop increasing greenhouse gas (GHG) emissions, pollution, and deforestation until 2060–2080 CE. When humans decrease GHG emissions, pollution, and deforestation in 40 years and prevent nuclear war in the future, 10–15% animal species loss will occur. Humans should stop not only industrial GHG emissions but also deforestation, environmental pollution, and nuclear war to prevent this mass extinction. When humans fail to stop these processes, significant decreases in biodiversity and the human population and a collapse of ecological balance will occur on Earth.
Plasma metabolomics and gene regulatory networks analysis reveal the role of nonstructural SARS-CoV-2 viral proteins in metabolic dysregulation in COVID-19 patients
Authors: Ivanisenko V. A. , Gaisler E. V. , Basov N. V. , Rogachev A. D. , Cheresiz S. V. , Ivanisenko T. V. , Demenkov P. S. , Mishchenko E. L. , Khripko O. P. , Khripko Yu. I. , Voevoda S. M. , Karpenko T. N. , Velichko A. J. , Voevoda M. I. , Kolchanov N. A. , Pokrovsky A. G.
Published: November 2022

Metabolomic analysis of blood plasma samples from COVID-19 patients is a promising approach allowing for the evaluation of disease progression. We performed the metabolomic analysis of plasma samples of 30 COVID-19 patients and the 19 controls using the high-performance liquid chromatography (HPLC) coupled with tandem mass spectrometric detection (LC–MS/MS). In our analysis, we identified 103 metabolites enriched in KEGG metabolic pathways such as amino acid metabolism and the biosynthesis of aminoacyl-tRNAs, which differed significantly between the COVID-19 patients and the controls. Using ANDSystem software, we performed the reconstruction of gene networks describing the potential genetic regulation of metabolic pathways perturbed in COVID-19 patients by SARS-CoV-2 proteins. The nonstructural proteins of SARS-CoV-2 (orf8 and nsp5) and structural protein E were involved in the greater number of regulatory pathways. The reconstructed gene networks suggest the hypotheses on the molecular mechanisms of virus-host interactions in COVID-19 pathology and provide a basis for the further experimental and computer studies of the regulation of metabolic pathways by SARS-CoV-2 proteins. Our metabolomic analysis suggests the need for nonstructural protein-based vaccines and the control strategy to reduce the disease progression of COVID-19.
Identification of potentially functional modules and diagnostic genes related to amyotrophic lateral sclerosis based on the WGCNA and LASSO algorithms
Authors: Daneshafrooz Narges , Bagherzadeh Cham Masumeh , Majidi Mohammad , Panahi Bahman
Published: November 2022

Amyotrophic lateral sclerosis (ALS) is a genetically and phenotypically heterogeneous disease results in the loss of motor neurons. Mounting information points to involvement of other systems including cognitive impairment. However, neither the valid biomarker for diagnosis nor effective therapeutic intervention is available for ALS. The present study is aimed at identifying potentially genetic biomarker that improves the diagnosis and treatment of ALS patients based on the data of the Gene Expression Omnibus. We retrieved datasets and conducted a weighted gene co-expression network analysis (WGCNA) to identify ALS-related co-expression genes. Functional enrichment analysis was performed to determine the features and pathways of the main modules. We then constructed an ALS-related model using the least absolute shrinkage and selection operator (LASSO) regression analysis and verified the model by the receiver operating characteristic (ROC) curve. Besides we screened the non-preserved gene modules in FTD and ALS-mimic disorders to distinct ALS-related genes from disorders with overlapping genes and features. Altogether, 4198 common genes between datasets with the most variation were analyzed and 16 distinct modules were identified through WGCNA. Blue module had the most correlation with ALS and functionally enriched in pathways of neurodegeneration-multiple diseases’, ‘amyotrophic lateral sclerosis’, and ‘endocytosis’ KEGG terms. Further, some of other modules related to ALS were enriched in ‘autophagy’ and ‘amyotrophic lateral sclerosis’. The 30 top of hub genes were recruited to a LASSO regression model and 5 genes (BCLAF1, GNA13, ARL6IP5, ARGLU1, and YPEL5) were identified as potentially diagnostic ALS biomarkers with validating of the ROC curve and AUC value.
Size-dependent bioactivity of electrosprayed core–shell chitosan-alginate particles for protein delivery
Authors: Shamszadeh Sayna , Akrami Mohammad , Asgary Saeed
Published: November 2022

Nano-bio interactions are size-dependent. The present study investigates whether core–shell chitosan-alginate particle size governs biological activities as well as protein release profile. A coaxial electrospraying was used to fabricate bovine serum albumin (BSA)-loaded core–shell micro/nanoparticles and were fully characterized. The bio/hemocompatibility of the particles was assessed using MTT and hemolytic assays, respectively, followed by the uptake assessment using flow cytometry. Finally, protein absorption was investigated using SDS-PAGE. The SEM size of the microparticles, the hydrodynamic, and the actual sizes of the nanoparticles were 1.2 μm, 90.49 nm, and 50 nm, respectively. Interactions among two polymers and BSA were observed using DSC analysis. BET analysis showed a more surface area for nanoparticles. A sustained release trend of BSA was observed after 14- and 10-day for microparticles and nanoparticles, respectively. Microparticles exhibited excellent hemocompatibility (< 5% hemolysis) and cell viability (at least > 70%) in all concentrations. However, acceptable hemolytic activity and cell viability were observed for nanoparticles in concentrations below 250 μg/mL. Furthermore, nanoparticles showed greater cellular uptake (~ 4 folds) and protein absorption (~ 1.61 folds) than microparticles. Overall, the developed core–shell chitosan-alginate particles in the micro/nanoscale can be promising candidates for biomedical application and regenerative medicine regarding their effects on above mentioned biological activities.
A synergistic effect on enriching the Mg–Al–Zn alloy-based hybrid composite properties
Authors: Anbuchezhiyan Gnanasambandam , Mubarak Nabisab Mujawar , Karri Rama Rao , Khalid Mohammad
Published: November 2022

Mg–Al–Zn alloys are widely preferred in many applications by considering their excellent properties of high stiffness-to-weight ratio, lightweight, high strength-to-weight ratio, low density, castability, high-temperature mechanical properties, machinability, high corrosion resistance, and great damping. Improving the properties of such alloys is challenging due to their hexagonal crystal structure and other alloying limitations. This study aims to synthesize Mg–Al–Zn alloy by incorporating the alloying elements 8.3 wt% Al, 0.35 wt% Zn on pure magnesium (Control specimen). Then synthesize Mg–Al–Zn/BN/B4C hybrid composite by reinforcing B4C at three weight proportions (3 wt%, 6 wt%, 9 wt%) along with constant solid lubricant BN (3 wt%) through a stir casting process. The hybrid composite samples were characterized and compared with the performances of the control specimen. The results reveal that 9 wt% B4C reinforced samples outperformed through recording the improvement of tensile strength by 28.94%, compressive strength by 37.89%, yield strength by 74.63%, and hardness by 14.91% than the control specimen. Apart from this, it has reduced the corrosion area (37.81%) and noticed negligible changes in density (increased by 0.03%) and porosity (decreased by 0.01%) than the control specimen. The samples were characterized using SEM, XRD, and EDAX apparatus.
Damage assessment of suspension footbridge using vibration measurement data combined with a hybrid bee-genetic algorithm
Authors: Ngoc-Nguyen Lan , Ngoc-Tran Hoa , Khatir Samir , Le-Xuan Thang , Huu-Nguyen Quyet , De Roeck G. , Bui-Tien Thanh , Abdel Wahab Magd
Published: November 2022

Optimization algorithms (OAs) are a vital tool to deal with complex problems, and the improvement of OA is inseparable from practical strategies and mechanisms. Among the OAs, Bee Algorithm (BA) is an intelligent algorithm with a simple mechanism and easy implementation, in which effectiveness has been proven when handling optimization problems. Nevertheless, BA still has some fundamental drawbacks, which can hinder its effectiveness and accuracy. Therefore, this paper proposes a novel approach to tackle the shortcomings of BA by combining it with Genetic Algorithm (GA). The main intention is to combine the strengths of both optimization techniques, which are the exploitative search ability of BA and the robustness with the crossover and mutation capacity of GA. An investigation of a real-life suspension footbridge is considered to validate the effectiveness of the proposed method. A baseline Finite Element model of the bridge is constructed based on vibration measurement data and model updating, which is used to generate different hypothetical damage scenarios. The proposed HBGA is tested against BA, GA, and PSO to showcase its effectiveness in detecting damage for each scenario. The results show that the proposed algorithm is effective in dealing with the damage assessment problems of SHM.
Wing Interferential Patterns (WIPs) and machine learning, a step toward automatized tsetse (Glossina spp.) identification
Authors: Cannet Arnaud , Simon-Chane Camille , Akhoundi Mohammad , Histace Aymeric , Romain Olivier , Souchaud Marc , Jacob Pierre , Delaunay Pascal , Sereno Darian , Bousses Philippe , Grebaut Pascal , Geiger Anne , de Beer Chantel , Kaba Dramane , Sereno Denis
Published: November 2022

A simple method for accurately identifyingGlossina sppin the field is a challenge to sustain the future elimination of Human African Trypanosomiasis (HAT) as a public health scourge, as well as for the sustainable management of African Animal Trypanosomiasis (AAT). Current methods for Glossina species identification heavily rely on a few well-trained experts. Methodologies that rely on molecular methodologies like DNA barcoding or mass spectrometry protein profiling (MALDI TOFF) haven’t been thoroughly investigated forGlossinasp. Nevertheless, because they are destructive, costly, time-consuming, and expensive in infrastructure and materials, they might not be well adapted for the survey of arthropod vectors involved in the transmission of pathogens responsible for Neglected Tropical Diseases, like HAT. This study demonstrates a new type of methodology to classifyGlossinaspecies. In conjunction with a deep learning architecture, a database of Wing Interference Patterns (WIPs) representative of theGlossinaspecies involved in the transmission of HAT and AAT was used. This database has 1766 pictures representing 23 Glossinaspecies. This cost-effective methodology, which requires mounting wings on slides and using a commercially available microscope, demonstrates that WIPs are an excellent medium to automatically recognize Glossina species with very high accuracy.
SNAL: sensitive non-associative learning network configuration for the automatic driving strategy
Authors: Shi Zhaoning , Zhai Yong , Zhang Youtong , Wei Hongqian
Published: November 2022

Nowadays, there is a huge gap between autonomous vehicles and mankind in terms of the decision response against some dangerous scenarios, which would has stressed the potential users out and even made them nervous. To efficiently identify the possible sensitivity scenarios, a new neural network configuration, named sensitive non-associative learning network (SNAL), is proposed. In such structure, the modulated interneurons, excited by abnormal scene stimulation for scene processing, are well processed and utilized to improve the training structure which refers to the sensitization mechanism in non-associative learning in neurobiology and the neural structure of Aplysia. When encountering the sensitivity scenes that the automatic driving agent is not good at or has not seen, the modulated interneuron facilitates the full connection layer neurons for the decision-making process, so as to change the final automatic driving strategy. In the process of constructing the model, a method to measure the similarity of the convolution feature map is proposed, which provides a new investigation tool for the properties of convolution networks after the feature extraction. Based on the Morris–Lecar equation in neurobiology, the dynamic model of modulating interneurons in the network is constructed. The automatic control optimization of the model is carried out by imitating the biological properties. The optimization method provides a reference for introducing neurobiological mechanism into deep learning and automatic control. To validate the effectiveness of the proposed method, the simulation test are executed and the existing methods are compared accordingly. The results show that the proposed SNAL algorithm can effectively recognize the sensitivity mechanism. Furthermore, compared with the existing algorithms, such as CNN, LSTM, ViT, the proposed algorithm can make better defensive strategies for potentially dangerous scenes rarely seen or not seen in the training stage. This sensitivity mechanism is more in line with the human driving intuition when dealing with abnormal driving scenes, and makes the decision more interpretable, significantly improving the traffic ability of autonomous vehicles under the sensitive scenes. In addition, this configuration can be easily combined with the existing mainstream neural network models and has good expansibility.
Establishment of a finite element model of supination-external rotation ankle joint injury and its mechanical analysis
Authors: Zhang Xin , Xie Pinliang , Shao Weirong , Xu Ming , Xu Xiaoping , Yin Yong , Fei Lan
Published: November 2022

By establishing a three-dimensional finite element model of ankle injury arising from supination and external rotation, the stress characteristics of the posterior malleolar surface can be obtained, and analysis of the corresponding stress on the lateral ankle can be conducted. Thin-layer computed tomography images of normal ankle joint in the supination and external rotation nonweight-bearing states was selected, to construct a three-dimensional data model of each ankle joint. A load was applied to examine different ankle joint stress values and pressure distributions on the surface of the posterior ankle joint. A 600 N vertical compressive and 10 Nm internal rotation load was applied in Stage III (removing the anterior tibiofibular ligament and the posterior tibiofibular ligament) of SER (supination-external rotation). When the lateral malleolar was intact, the maximum stress (132.7 MPa) was located at the point of attachment of the posterior tibiofibular ligament to the fibula, and the maximum pressure of the posterior malleolar surface was lower than 4.505 MPa. When a lateral malleolar fracture was present, the maximum stress (82.72 MPa) was located on the fibular fracture surface, and the maximum pressure of the posterior malleolar surface was 8.022 MPa. This study shows that reconstruction of the lateral malleolus in supination-external rotation ankle injuries significantly affects the stress distribution at the posterior malleolar joint surface. Through this reconstruction, the pressure distribution of the posterior malleolar joint surface can be significantly reduced.
Composition and metabolic potential of microbiomes associated with mesopelagic animals from Monterey Canyon
Authors: Breusing Corinna , Osborn Karen J , Girguis Peter R , Reese Aspen T
Published: November 2022

There is growing recognition that microbiomes play substantial roles in animal eco-physiology and evolution. To date, microbiome research has largely focused on terrestrial animals, with far fewer studies on aquatic organisms, especially pelagic marine species. Pelagic animals are critical for nutrient cycling, yet are also subject to nutrient limitation and might thus rely strongly on microbiome digestive functions to meet their nutritional requirements. To better understand the composition and metabolic potential of midwater host-associated microbiomes, we applied amplicon and shotgun metagenomic sequencing to eleven mesopelagic animal species. Our analyses reveal that mesopelagic animal microbiomes are typically composed of bacterial taxa from the phyla Proteobacteria, Firmicutes, Bacteroidota and, in some cases, Campylobacterota. Overall, compositional and functional microbiome variation appeared to be primarily governed by host taxon and depth and, to a lesser extent, trophic level and diel vertical migratory behavior, though the impact of host specificity seemed to differ between migrating and non-migrating species. Vertical migrators generally showed lower intra-specific microbiome diversity (i.e., higher host specificity) than their non-migrating counterparts. These patterns were not linked to host phylogeny but may reflect differences in feeding behaviors, microbial transmission mode, environmental adaptations and other ecological traits among groups. The results presented here further our understanding of the factors shaping mesopelagic animal microbiomes and also provide some novel, genetically informed insights into their diets.
Trimetallic Au@Pd@Pt nanozyme-enhanced lateral flow immunoassay for the detection of SARS-CoV-2 nucleocapsid protein
Authors: Sun Yue , Xie Zihao , Pei Fubin , Hu Wei , Feng Shasha , Hao Qingli , Liu Bing , Mu Xihui , Lei Wu , Tong Zhaoyang
Published: November 2022

The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seriously threatened global public health.
A sensitive MnO2 nanosheet sensing platform based on a fluorescence aptamer sensor for the detection of zearalenone
Authors: Qin Guoxin , Wei Yuanwen , Zhou Qifeng , Wang Haijun , Wei Yuning , Lao Shuibing , Luo Lihong , Mo Renfu , Chen Yongxian , Yang Yuxia , He Jie , Li Huiling
Published: November 2022

An aptamer sensor based on manganese dioxide (MnO2) nanosheets was developed for the detection of zearalenone (ZEN).
A signal-on electrochemical DNA biosensor based on exonuclease III-assisted recycling amplification
Authors: Yu Xiongtao , Jiang Bowen , Wang Lishi
Published: November 2022

A signal-on electrochemical DNA biosensor was constructed for MnSOD gene detection by incorporating electrodeposited AuNPs and exonuclease III-assisted target recycling signal amplification strategy.
Regulating the activity of boronate moiety to construct fluorescent probes for the detection of ONOO−in vitroandin vivo
Authors: Ji Xin , Zhou Junliang , Liu Chang , Zhang Jian , Dong Xiaochun , Zhang Fuli , Zhao Weili
Published: November 2022

Abnormal intracellular peroxynitrite (ONOO−) concentration is related to oxidative damage, which is correlated with many pathological consequences.
Rapid determination of 14 odorous compounds in drinking water using gas chromatography-mass spectrometry coupled with headspace solid-phase microextraction pretreatment
Authors: Tong Xuezhi , Zhang Hao , Fan Xiang , Yang Shengyuan , Chen Dongyang , Feng JiaLi , Tan Shan , Zeng Dong
Published: November 2022

A sensitive and effective method was developed to detect 14 odorous compounds in water using GC-MS with headspace solid-phase microextraction.
Ferrocene-based P-chiral amidophosphinate: stereoselective synthesis and X-ray structural study
Authors: Shekurov Ruslan P. , Zagidullin Almaz A. , Khrizanforov Mikhail N. , Islamov Daut R. , Gerasimova Tatiana P. , Akhmatkhanova Farida F. , Miluykov Vasily A.
Published: November 2022

The first example of an asymmetric reaction of ortho-lithiatied Ugi's amine with tetracoordinated phosphorus(v) chloride has been demonstrated.
Pair distribution function analysis of the reassembly step of the assembly-disassembly-organisation-reassembly (ADOR) process
Authors: Russell Samantha E. , Costa Fanny N. , Diaz-Lopez Maria , Morris Russell E.
Published: November 2022

Differences in the ADOR reassembly step were revealed by in situ pair distribution function analysis.
Near-unity electrochemical conversion of nitrate to ammonia on crystalline nickel porphyrin-based covalent organic frameworks
Authors: Lv Fang , Sun Mingzi , Hu Yongpan , Xu Jie , Huang Wei , Han Na , Huang Bolong , Li Yanguang
Published: November 2022

A novel 2D nickel porphyrin-based covalent organic framework is fabricated as an efficient nitrate reduction electrocatalyst that shows a great selectivity of ∼90% under a mild overpotential with a remarkable production rate and turnover frequency.
Chemical composition and anti-inflammatory activities of Castanopsis honey
Authors: Yu Wenjie , Sun Fengjie , Xu Ruixin , Cui Meng , Liu Yongquan , Xie Quanyuan , Guo Limin , Kong Chenxian , Li Xin , Guo Xiali , Luo Liping
Published: November 2022

Castanopsis honey is a high-quality, phenolic acid and flavonoid-rich honey with good antioxidant capacity, and has good anti-inflammatory effects by regulation of NF-κB pathway.
Curcumol inhibits breast cancer growth via NCL/ERα36 and the PI3K/AKT pathway
Authors: Wei Zhou Lu , Juan Wang , Tong Dou , Juan Li Xiao , Sa Liu Yi , Jie Huang Fu Meng , Xiao Guan , Xiang Liu Guo , Jie Han Meng , Xu Chen
Published: November 2022

Schematic representation of the action mechanisms of curcumol.
Green preparation of CoMoO4 nanoparticles through a mechanochemical method for energy storage applications
Authors: Liu Liangyu , Dai Dianfeng , Yang Bin , Li Bing , Liu Xiaoyang
Published: November 2022

α- and β-Phases of CoMoO4 were synthesized by a ball milling-calcination process.