bluuebunny/crossref_metadata_2025_split huggingface dataset:
A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants
Authors: Yang Zhenlin , Wang Yulu , Jin Yujia , Zhu Yuanfei , Wu Yanling , Li Cheng , Kong Yu , Song Wenping , Tian Xiaolong , Zhan Wuqiang , Huang Ailing , Zhou Shanshan , Xia Shuai , Tian Xiaoxu , Peng Chao , Chen Cuicui , Shi Yibing , Hu Gaowei , Du Shujuan , Wang Yuyan , Xie Youhua , Jiang Shibo , Lu Lu , Sun Lei , Song Yuanlin , Ying Tianlei 
Published: November 2021

AbstractThe current COVID-19 pandemic has heavily burdened the global public health system and may keep simmering for years. The frequent emergence of immune escape variants have spurred the search for prophylactic vaccines and therapeutic antibodies that confer broad protection against SARS-CoV-2 variants. Here we show that the bivalency of an affinity maturated fully human single-domain antibody (n3113.1-Fc) exhibits exquisite neutralizing potency against SARS-CoV-2 pseudovirus, and confers effective prophylactic and therapeutic protection against authentic SARS-CoV-2 in the host cell receptor angiotensin-converting enzyme 2 (ACE2) humanized mice. The crystal structure of n3113 in complex with the receptor-binding domain (RBD) of SARS-CoV-2, combined with the cryo-EM structures of n3113 and spike ecto-domain, reveals that n3113 binds to the side surface of up-state RBD with no competition with ACE2. The binding of n3113 to this novel epitope stabilizes spike in up-state conformations but inhibits SARS-CoV-2 S mediated membrane fusion, expanding our recognition of neutralization by antibodies against SARS-CoV-2. Binding assay and pseudovirus neutralization assay show no evasion of recently prevalent SARS-CoV-2 lineages, including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2) for n3113.1-Fc with Y58L mutation, demonstrating the potential of n3113.1-Fc (Y58L) as a promising candidate for clinical development to treat COVID-19.
Mechanisms underlying interactions between two abundant oral commensal bacteria
Authors: Perera Dasith , McLean Anthony , Morillo-López Viviana , Cloutier-Leblanc Kaileigh , Almeida Eric , Cabana Kiana , Mark Welch Jessica , Ramsey Matthew 
Published: November 2021

Abstract
Complex polymicrobial biofilm communities are abundant in nature particularly in the human oral cavity where their composition and fitness can affect health. While the study of these communities during disease is essential and prevalent, little is known about interactions within the healthy plaque community. Here we describe interactions between two of the most abundant species in this healthy microbiome, Haemophilus parainfluenzae and Streptococcus mitis. We discovered that H. parainfluenzae typically exists adjacent to mitis group streptococci in vivo with which it is also positively correlated based on microbiome data. By comparing in vitro coculture data to ex vivo microscopy we revealed that this co-occurrence is density dependent and further influenced by H2O2 production. We discovered that H. parainfluenzae utilizes a more redundant, multifactorial response to H2O2 than related microorganisms and that this system’s integrity enhances streptococcal fitness. Our results indicate that mitis group streptococci are likely the in vivo source of NAD for H. parainfluenzae and also evoke patterns of carbon utilization in vitro for H. parainfluenzae similar to those observed in vivo. Our findings describe mechanistic interactions between two of the most abundant and prevalent members of healthy supragingival plaque that contribute to their in vivo survival.
Carbon ion radiotherapy boosts anti-tumour immune responses by inhibiting myeloid-derived suppressor cells in melanoma-bearing mice
Authors: Zhou Heng , Yang Pengfei , Li Haining , Zhang Liying , Li Jin , Zhang Tianyi , Sheng Chengyan , Wang Jufang 
Published: November 2021

AbstractNumerous studies have shown that carbon ion radiotherapy (CIRT) induces anti-cancer immune responses in melanoma patients, yet the mechanism remains elusive. The abundance of myeloid-derived suppressor cells (MDSC) in the tumour microenvironment is associated with therapeutic efficacy and disease outcome. This study analysed the changes in the immune contexture in response to the carbon ion treatment. The murine melanoma B16, MelanA, and S91 tumour models were established in syngeneic immunocompetent mice. Then, the tumours were irradiated with carbon ion beams, and flow cytometry was utilised to observe the immune contexture changes in the bone marrow, peripheral blood, spleen, and tumours. The immune infiltrates in the tumour tissues were further assessed using haematoxylin/eosin staining and immunohistochemistry. The immunoblot detected the expression of proteins associated with the JAK/STAT signalling pathway. The secretion of immune-related cytokines was examined using ELISA. Compared to conventional radiotherapy, particle beams have distinct advantages in cancer therapy. Here, the use of carbon ion beams (5 GyE) for melanoma-bearing mice was found to reduce the population of MDSC in the bone marrow, peripheral blood, and spleen of the animals via a JAK2/STAT3-dependent mechanism. The percentage of CD3+, CD4+, CD8+ T cells, macrophages, and natural killer cells increased after radiation, resulting in reduced tumour growth and prolonged overall survival in the three different mouse models of melanoma. This study, therefore, substantiated that CIRT boosts anti-tumour immune responses via the inhibition of MDSC.
The associations of previous influenza/upper respiratory infection with COVID-19 susceptibility/morbidity/mortality: a nationwide cohort study in South Korea
Authors: Kim So Young , Kim Joo-Hee , Kim Miyoung , Wee Jee Hye , Jung Younghee , Min Chanyang , Yoo Dae Myoung , Sim Songyong , Choi Hyo Geun 
Published: November 2021

AbstractWe aimed to investigate the associations of previous influenza/URI with the susceptibility of COVID-19 patients compared to that of non-COVID-19 participants. A nationwide COVID-19 cohort database was collected by the Korea National Health Insurance Corporation. A total of 8,070 COVID-19 patients (1 January 2020 through 4 June 2020) were matched with 32,280 control participants. Severe COVID-19 morbidity was defined based on the treatment histories of the intensive care unit, invasive ventilation, and extracorporeal membrane oxygenation and death. The susceptibility/morbidity/mortality associated with prior histories of 1–14, 1–30, 1–90, 15–45, 15–90, and 31–90 days before COVID-19 onset were analyzed using conditional/unconditional logistic regression. Prior influenza infection was related to increased susceptibility to COVID-19 (adjusted odds ratio [95% confidence interval] = 3.07 [1.61–5.85] for 1–14 days and 1.91 [1.54–2.37] for 1–90 days). Prior URI was also associated with increased susceptibility to COVID-19 (6.95 [6.38–7.58] for 1–14 days, 4.99 [4.64–5.37] for 1–30 days, and 2.70 [2.55–2.86] for 1–90 days). COVID-19 morbidity was positively associated with influenza (3.64 [1.55–9.21] and 3.59 [1.42–9.05]) and URI (1.40 [1.11–1.78] and 1.28 [1.02–1.61]) at 1–14 days and 1–30 days, respectively. Overall, previous influenza/URI did not show an association with COVID-19 mortality. Previous influenza/URI histories were associated with increased COVID-19 susceptibility and morbidity. Our findings indicate why controlling influenza/URI is important during the COVID-19 pandemic.
Spousal associations of serum metabolomic profiles by nuclear magnetic resonance spectroscopy
Authors: Al Rashid Karema , Goulding Neil , Taylor Amy , Lumsden Mary Ann , Lawlor Deborah A. , Nelson Scott M. 
Published: November 2021

AbstractPhenotype-based assortative mating is well established in humans, with the potential for further convergence through a shared environment. To assess the correlation within infertile couples of physical, social, and behavioural characteristics and 155 circulating metabolic measures. Cross sectional study at a tertiary medical center of 326 couples undertaking IVF. Serum lipids, lipoprotein subclasses, and low-molecular weight metabolites as quantified by NMR spectroscopy (155 metabolic measures). Multivariable and quantile regression correlations within couples of metabolite profiles. Couples exhibited statistical correlations of varying strength for most physical, social, and behavioural characteristics including age, height, alcohol consumption, education, smoking status, physical activity, family history and ethnicity, with correlation coefficients ranging from 0.22 to 0.73. There was no evidence of within couple associations for BMI and weight, where the correlation coefficients were − 0.03 (95% CI − 0.14, 0.08) and 0.01 (95% CI − 0.10, 0.12), respectively. Within spousal associations of the metabolite measurements were all positive but with weak to modest magnitudes, with the median correlation coefficient across all 155 measures being 0.12 (range 0.01–0.37 and interquartile range 0.10–0.18). With just four having associations stronger than 0.3: docosahexaenoic acid (0.37, 95% CI 0.22, 0.52), omega-3 fatty acids (0.32, 95% CI 0.20, 0.43) histidine (0.32, 95% CI 0.23, 0.41) and pyruvate (0.32, 95% CI 0.22, 0.43). Infertile couples exhibit spousal similarities for a range of demographic and serum metabolite measures, supporting initial assortative mating, with diet-derived metabolites suggesting possible subsequent convergence of their individual metabolic profile.
Sperm lacking Bindin are infertile but are otherwise indistinguishable from wildtype sperm
Authors: Wessel Gary M. , Wada Yuuko , Yajima Mamiko , Kiyomoto Masato 
Published: November 2021

AbstractCell–cell fusion is limited to only a few cell types in the body of most organisms and sperm and eggs are paradigmatic in this process. The specialized cellular mechanism of fertilization includes the timely exposure of gamete–specific interaction proteins by the sperm as it approaches the egg. Bindin in sea urchin sperm is one such gamete interaction protein and it enables species–specific interaction with a homotypic egg. We recently showed that Bindin is essential for fertilization by use of Cas9 targeted gene inactivation in the sea urchin, Hemicentrotus pulcherrimus. Here we show phenotypic details of Bindin-minus sperm. Sperm lacking Bindin do not bind to nor fertilize eggs at even high concentrations, yet they otherwise have wildtype morphology and function. These features include head shape, tail length and beating frequency, an acrosomal vesicle, a nuclear fossa, and they undergo an acrosomal reaction. The only phenotypic differences between wildtype and Bindin-minus sperm identified is that Bindin-minus sperm have a slightly shorter head, likely as a result of an acrosome lacking Bindin. These data, and the observation that Bindin-minus embryos develop normally and metamorphose into normal functioning adults, support the contention that Bindin functions are limited to species–specific sperm–egg interactions. We conclude that the evolutionary divergence of Bindin is not constrained by any other biological roles.
The relationship between health-related quality of life and melancholic depressive symptoms is modified by brain insulin receptor gene network
Authors: Selenius Jannica S. , Silveira Patricia P. , Salonen Minna , Kautiainen Hannu , von Bonsdorff Mikaela , Kajantie Eero , Lahti Jari , Eriksson Johan G. , Wasenius Niko S. 
Published: November 2021

AbstractTo investigate whether expression-based polygenic risk scores for the insulin receptor gene network (ePRS-IRs) modifiy the association between type of depressive symptoms and health-related quality of life (HRQoL). This cross-sectional study includes 1558 individuals from the Helsinki Birth Cohort Study. Between 2001 and 2004, the Short Form-36 questionnaire was employed to assess mental and physical components of HRQoL and Beck Depression Inventory (BDI) to assess depressive symptoms. Depressive symptoms were categorized into minimal (BDI < 10), non-melancholic and melancholic types of depression. The ePRS-IRs were calculated for the hippocampal (hePRS-IR) and the mesocorticolimbic (mePRS-IR) regions of the brain. General linear regression models adjusted for age, sex, population stratification, lifestyle factors and body mass index were applied to analyze the data. Both types of depressive symptoms were associated with lower HRQoL (p < 0.0001). HePRS-IR modified the association between the types of depression and mental HRQoL (p for interaction = 0.005). Melancholic type of depressive symptoms was associated with higher mental HRQoL compared to the non-melancholic symptoms among individuals with low hePRS-IR (adjusted mean 4.1, 95% CI 0.7–7.4, p = 0.018). However, no such difference was evident in moderate or high hePRS-IR groups as higher hePRS-IR was associated with lower mental HRQoL (B = − 3.4, 95% CI − 5.6 to − 1.2) in individuals with melancholic type of depressive symptoms. No direct associations were detected between the ePRS-IRs and type of depressive symptoms or HRQoL. Variations in the glucose-insulin metabolism can lower HRQoL in individuals with melancholic depressive symptoms.
DeepGreen: deep learning of Green’s functions for nonlinear boundary value problems
Authors: Gin Craig R. , Shea Daniel E. , Brunton Steven L. , Kutz J. Nathan 
Published: November 2021

AbstractBoundary value problems (BVPs) play a central role in the mathematical analysis of constrained physical systems subjected to external forces. Consequently, BVPs frequently emerge in nearly every engineering discipline and span problem domains including fluid mechanics, electromagnetics, quantum mechanics, and elasticity. The fundamental solution, or Green’s function, is a leading method for solving linear BVPs that enables facile computation of new solutions to systems under any external forcing. However, fundamental Green’s function solutions for nonlinear BVPs are not feasible since linear superposition no longer holds. In this work, we propose a flexible deep learning approach to solve nonlinear BVPs using a dual-autoencoder architecture. The autoencoders discover an invertible coordinate transform that linearizes the nonlinear BVP and identifies both a linear operator L and Green’s function G which can be used to solve new nonlinear BVPs. We find that the method succeeds on a variety of nonlinear systems including nonlinear Helmholtz and Sturm–Liouville problems, nonlinear elasticity, and a 2D nonlinear Poisson equation and can solve nonlinear BVPs at orders of magnitude faster than traditional methods without the need for an initial guess. The method merges the strengths of the universal approximation capabilities of deep learning with the physics knowledge of Green’s functions to yield a flexible tool for identifying fundamental solutions to a variety of nonlinear systems.
EEG-based detection of emotional valence towards a reproducible measurement of emotions
Authors: Apicella Andrea , Arpaia Pasquale , Mastrati Giovanna , Moccaldi Nicola 
Published: November 2021

AbstractA methodological contribution to a reproducibleMeasurement of Emotionsfor an EEG-based system is proposed.Emotional Valencedetection is the suggested use case. Valence detection occurs along theinterval scaletheorized by theCircumplex Modelof emotions. The binary choice, positive valence vs negative valence, represents a first step towards the adoption of a metric scale with a finer resolution. EEG signals were acquired through a 8-channel dry electrode cap. An implicit-more controlled EEG paradigm was employed to elicit emotional valence through the passive view of standardized visual stimuli (i.e., Oasis dataset) in 25 volunteers without depressive disorders. Results from theSelf Assessment Manikinquestionnaire confirmed the compatibility of the experimental sample with that ofOasis. Two different strategies for feature extraction were compared: (i) based on a-priory knowledge (i.e., Hemispheric Asymmetry Theories), and (ii) automated (i.e., a pipeline of a custom 12-band Filter Bank and Common Spatial Pattern). An average within-subject accuracy of 96.1 %, was obtained by a shallow Artificial Neural Network, whilek-Nearest Neighbors allowed to obtain a cross-subject accuracy equal to 80.2%.
Bottlenose dolphins (Tursiops truncatus) aggressive behavior towards other cetacean species in the western Mediterranean
Authors: Crespo-Picazo J. L. , Rubio-Guerri C. , Jiménez M. A. , Aznar F. J. , Marco-Cabedo V. , Melero M. , Sánchez-Vizcaíno J. M. , Gozalbes P. , García-Párraga D. 
Published: November 2021

AbstractAggressive behavior of bottlenose dolphins (Tursiops truncatus) towards conspecifics is widely described, but they have also often been reported attacking and killing harbour porpoises (Phocoena phocoena) around the world. However, very few reports exist of aggressive interactions between bottlenose dolphins and other cetacean species. Here, we provide the first evidence that bottlenose dolphins in the western Mediterranean exhibit aggressive behavior towards both striped dolphins (Stenella coeruleoalba) and Risso’s dolphins (Grampus griseus). Necropsies and visual examination of stranded striped (14) and Risso’s (2) dolphins showed numerous lesions (external rake marks and different bone fractures or internal organ damage by blunt trauma). Indicatively, these lessons matched the inter-tooth distance and features of bottlenose dolphins. In all instances, these traumatic interactions were presumed to be the leading cause of the death. We discuss how habitat changes, dietary shifts, and/or human colonization of marine areas may be promoting these interactions.
Body mass and geographic distribution determined the evolution of the wing flight-feather molt strategy in the Neornithes lineage
Authors: Kiat Yosef , Slavenko Alex , Sapir Nir 
Published: November 2021

AbstractThe evolutionary history of many organisms is characterized by major changes in morphology and distribution. Specifically, alterations of body mass and geographic distribution may profoundly influence organismal life-history traits. Here, we reconstructed the evolutionary history of flight-feather molt strategy using data from 1,808 Neornithes species. Our analysis suggests that the ancestral molt strategy of first-year birds was partial or entirely absent, and that complete wing flight-feather molt in first-year birds first evolved in the late Eocene and Oligocene (25–40 Ma), at least 30 Myr after birds first evolved. Complete flight-feather molt occurred mainly at equatorial latitudes and in relatively low body mass species, following a diversification of body mass within the lineage. We conclude that both body mass and geographic distribution shaped the evolution of molt strategies and propose that the evolutionary transition towards complete juvenile molt in the Neornithes is a novel, relatively late adaptation.
Persistence and metabolism of the diamide insecticide cyantraniliprole in tomato plants
Authors: Huynh Khang , Leonard Elizabeth , Chong Juang-Horng , Palmer Cristi , Tharayil Nishanth 
Published: November 2021

AbstractPlant uptake and metabolism of pesticides are complex and dynamic processes, which contribute to the overall toxicity of the pesticides. We investigated the metabolic fate of cyantraniliprole, a new diamide class of insecticide, during various growth stages of tomato. Cyantraniliprole was the major residue in leaves, flowers, and fruits, with the relative metabolite-to-parent ratios maintained at < 10% up to 28 days after treatment (DAT). Mature leaves contained consistently higher residues of cyantraniliprole than young leaves throughout the study. Flowers contained the highest cyantraniliprole residues up to 21 DAT, then gradually decreased. Immature green fruits had the highest cyantraniliprole residues (5.3 ± 0.7 ng/g; 42 DAT), and decreased toward red ripening stages (1.4 ± 0.2 ng/g; 84 DAT). Metabolism of cyantraniliprole primarily occurred in the foliage, where 21 metabolites were tentatively identified. Flowers and fruits contained 14 and four of these metabolites, respectively. Major transformation pathways were characterized by ring closure, followed by N-demethylation, and glycosylation. Additionally, plant metabolism of cyantraniliprole was also associated with several minor phase-I, phase-II, and breakdown metabolites. The occurrence of these metabolites in plants varied as a function of tissue types and their developmental stages. Our study highlights a tissue-specific biotransformation and accumulation of metabolites of cyantraniliprole in tomato.
Profiling of ob/ob mice skeletal muscle exosome-like vesicles demonstrates combined action of miRNAs, proteins and lipids to modulate lipid homeostasis in recipient cells
Authors: Jalabert Audrey , Reininger Laura , Berger Emmanuelle , Coute Yohann , Meugnier Emmanuelle , Forterre Alexis , Errazuriz-Cerda Elizabeth , Geloen Alain , Aouadi Myriam , Bouzakri Karim , Rieusset Jennifer , Rome Sophie 
Published: November 2021

AbstractWe have determined the lipid, protein and miRNA composition of skeletal muscle (SkM)-released extracellular vesicles (ELVs) from Ob/ob (OB) vs wild-type (WT) mice. The results showed that atrophic insulin-resistant OB-SkM released less ELVs than WT-SkM, highlighted by a RAB35 decrease and an increase in intramuscular cholesterol content. Proteomic analyses of OB-ELVs revealed a group of 37 proteins functionally connected, involved in lipid oxidation and with catalytic activities. OB-ELVs had modified contents for phosphatidylcholine (PC 34-4, PC 40-3 and PC 34-0), sphingomyelin (Sm d18:1/18:1) and ceramides (Cer d18:1/18:0) and were enriched in cholesterol, likely to alleviated intracellular accumulation. Surprisingly many ELV miRNAs had a nuclear addressing sequence, and targeted genes encoding proteins with nuclear activities. Interestingly, SkM-ELV miRNA did not target mitochondria. The most significant function targeted by the 7 miRNAs altered in OB-ELVs was lipid metabolism. In agreement, OB-ELVs induced lipid storage in recipient adipocytes and increased lipid up-take and fatty acid oxidation in recipient muscle cells. In addition, OB-ELVs altered insulin-sensitivity and induced atrophy in muscle cells, reproducing the phenotype of the releasing OB muscles. These data suggest for the first time, a cross-talk between muscle cells and adipocytes, through the SkM-ELV route, in favor of adipose tissue expansion.
Thioredoxin-1 mediates neuroprotection of Schisanhenol against MPP+-induced apoptosis via suppression of ASK1-P38-NF-κB pathway in SH-SY5Y cells
Authors: Yang Hongyan , Li Libo , Jiao Yu , Zhang Yuanliang , Wang Yuhua , Zhu Kunjie , Sun Chao 
Published: November 2021

AbstractOxidative stress-induced dopaminergic neuronal loss and apoptosis play a crucial role in the pathogenesis of Parkinson’s disease (PD), and as a vital antioxidant protein, thioredoxin (Trx) exerts neuroprotection against PD. In this study, we investigated the effect of Schisanhenol (Sal), an active component from a traditional Chinese herb Schisandra rubriflora (Franch.), on MPP+-induced apoptosis and its association with thioredoxin-1 (Trx1) in SH-SY5Y cells. The protein levels of Trx1 and apoptosis-related proteins were detected by Western blot, the expression of Trx1 mRNA by real time qPCR, and apoptosis was detected by fluorescence microscopy and flow cytometry. Pretreatment with Sal (1 µM, 10 µM, and 50 µM) dose-dependently ameliorated MPP+-induced neuronal injury, confirmed by the improvement of the viability and morphological changes. Sal decreased the apoptosis rate of cells, suppressed the production of DNA ladder and sub-G1 peak, inhibited the Caspase-3 activity and the expression of apoptosis-related proteins. Sal enhanced the expression of Trx1 both in the protein and mRNA levels. However, the Trx1 inhibitor PX-12 suppressed the protective effects of Sal. In addition, Sal inhibited NF-κB translocation and activation. These results suggest that Sal has a protective effect against MPP+-induced apoptosis in SH-SY5Y cells via up-regulation of Trx1 expression and suppression of ASK1-P38-NF-κB pathway.