bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep learning-based network pharmacology for exploring the mechanism of licorice for the treatment of COVID-19
Authors: Fu Yu , Fang Yangyue , Gong Shuai , Xue Tao , Wang Peng , She Li , Huang Jianping 
Published: April 2023

AbstractLicorice, a traditional Chinese medicine, has been widely used for the treatment of COVID-19, but all active compounds and corresponding targets are still not clear. Therefore, this study proposed a deep learning-based network pharmacology approach to identify more potential active compounds and targets of licorice. 4 compounds (quercetin, naringenin, liquiritigenin, and licoisoflavanone), 2 targets (SYK and JAK2) and the relevant pathways (P53, cAMP, and NF-kB) were predicted, which were confirmed by previous studies to be associated with SARS-CoV-2-infection. In addition, 2 new active compounds (glabrone and vestitol) and 2 new targets (PTEN and MAP3K8) were further validated by molecular docking and molecular dynamics simulations (simultaneous molecular dynamics), as well as the results showed that these active compounds bound well to COVID-19 related targets, including the main protease (Mpro), the spike protein (S-protein) and the angiotensin-converting enzyme 2 (ACE2). Overall, in this study, glabrone and vestitol from licorice were found to inhibit viral replication by inhibiting the activation of Mpro, S-protein and ACE2; related compounds in licorice may reduce the inflammatory response and inhibit apoptosis by acting on PTEN and MAP3K8. Therefore, licorice has been proposed as an effective candidate for the treatment of COVID-19 through PTEN, MAP3K8, Mpro, S-protein and ACE2.
Visualization of RNA virus infection in a marine protist with a universal biomarker
Authors: Coy Samantha R. , Utama Budi , Spurlin James W. , Kim Julia G. , Deshmukh Harshavardhan , Lwigale Peter , Nagasaki Keizo , Correa Adrienne M. S. 
Published: April 2023

AbstractHalf of the marine virosphere is hypothesized to be RNA viruses (kingdom Orthornavirae) that infect abundant micro-eukaryotic hosts (e.g. protists). To test this, quantitative approaches that broadly track infections in situ are needed. Here, we describe a technique—dsRNA-Immunofluorescence (dsRIF)—that uses a double-stranded RNA (dsRNA) targeting monoclonal antibody to assess host infection status based on the presence of dsRNA, a replicative intermediate of all Orthornavirae infections. We show that the dinoflagellate Heterocapsa circularisquama produces dsRIF signal ~ 1000 times above background autofluorescence when infected by the + ssRNA virus HcRNAV. dsRNA-positive virocells were detected across > 50% of the 48-h infection cycle and accumulated to represent at least 63% of the population. Photosynthetic and chromosomal integrity remained intact during peak replication, indicating HcRNAV infection does not interrupt these processes. This work validates the use of dsRIF on marine RNA viruses and their hosts, setting the stage for quantitative environmental applications that will accelerate understanding of virus-driven ecosystem impacts.
TAF15 promotes cell proliferation, migration and invasion of gastric cancer via activation of the RAF1/MEK/ERK signalling pathway
Authors: Tang Li , Guo Chengming , Li Xu , Zhang Bo , Huang Liuye 
Published: April 2023

AbstractTATA-box-binding protein-associated Factor 15 (TAF15), a member of the FUS/EWS/TAF15 (FET) family, contributes to the progression of various tumours. However, the role and molecular mechanism of TAF15 in gastric cancer (GC) progression are still unknown. In this study, we found that TAF15 was significantly upregulated in GC tumour tissues and cell lines. Overexpression of TAF15 was associated with a larger tumour size, high pathologic stage and high T stage of GC. TAF15 knockdown suppressed the proliferation, migration and invasion of GC cells in vitro and inhibited the tumour growth in vivo. Additionally, TAF15 knockdown led to the significant reductions in the phosphorylation levels of RAF1, MEK and ERK1/2, while total RAF1, MEK and ERK1/2 exhibited no significant change in GC cell lines. In summary, TAF15 is overexpressed in GC tumour tissues and cell lines, and promotes cell proliferation, migration and invasion in GC via the RAF1/MEK/ERK signaling pathway, which suggests that TAF15 might be a potential molecular diagnostic marker or therapeutic target for GC.
The effect of barium and strontium on activity of glucoamylase QsGH97a from Qipengyuania seohaensis SW-135
Authors: Wu Kaijuan , Zhai Xingyu , Chen Hao , Zheng Jinfeng , Yu Zheng , Xu Xuewei , Huang Jing 
Published: April 2023

AbstractGlycoside hydrolases (GHs), the enzymes that break glycosidic bonds, are ubiquitous in the ecosystem, where they perform a range of biological functions. As an interesting glycosidase family, Glycoside hydrolase family 97 (GH97) contains α-glucosidase, α-galactosidase, and glucoamylase. Only ten members of GH97 have been characterized so far. It is critical to explore novel members to elucidate the catalytic mechanism and application potential of GH97 family. In this study, a novel glucoamylase QsGH97a from Qipengyuania seohaensis SW-135 was cloned and expressed in E. coli. Sequence analysis and NMR results show that QsGH97a is classified into GH97a, and adopts inverting mechanism. The biochemical characterization indicates that QsGH97a shows the optimal activity at 50 °C and pH 8.0. Ca2+ has little effect on the catalytic activity; however, the activity can be substantially increased by 8–13 folds in the presence of Ba2+ or Sr2+. Additionally, the metal content of QsGH97a assay showed a high proportion of Sr2+. The specific metal activity was initially revealed in glucoamylases, which is not found in other members. These results imply that QsGH97a not only is a new member of GH97, but also has potential for industrial applications. Our study reveals that Ba2+ or Sr2+ may be involved in the catalytic mechanism of glucoamylase, laying the groundwork for a more complete knowledge of GH97 and its possible industrial application.
The spatiotemporal prediction method of urban population density distribution through behaviour environment interaction agent model
Authors: Yang Junyan , Shi Yi , Zheng Yi , Zhang Zhonghu 
Published: April 2023

AbstractBased on the interrelationship between the built environment and spatial–temporal distribution of population density, this paper proposes a method to predict the spatial–temporal distribution of urban population density using the depth residual network model (ResNet) of neural network. This study used the time-sharing data of mobile phone users provided by the China Mobile Communications Corporation to predict the time–space sequence of the steady-state distribution of population density. Firstly, 40 prediction databases were constructed according to the characteristics of built environment and the spatial–temporal distribution of population density. Thereafter, the depth residual model ResNet was used as the basic framework to construct the behaviour–environment agent model (BEM) for model training and prediction. Finally, the average percentage error index was used to evaluate the prediction results. The results revealed that the accuracy rate of prediction results reached 76.92% in the central urban area of the verification case. The proposed method can be applied to prevent urban public safety incidents and alleviate pandemics. Moreover, this method can be practically applied to enable the construction of a “smart city” for improving the efficient allocation of urban resources and traffic mobility.
Shaping farmers’ beliefs, risk perception and adaptation response through Construct Level Theory in the southwest Iran
Authors: Yazdanpanah Masoud , Zobeidi Tahereh , Warner Laura A. , Löhr Katharina , Lamm Alexa , Sieber Stefan 
Published: April 2023

AbstractDue to the severe effects of climate change on the agricultural sector, urgent action is required on the part of farmers and is, indeed, critical to reducing climate change impacts. However, reports globally revealed farmers’ engagement in climate change adaptation is still insufficient, ambivalent, and inconsistent and farmers do not consider adaptation to be urgent. Researchers have argued that this issue is rooted in psychological biases beside other factors. Therefore, the aim of this study is to evaluate how psychological distance determines climate change beliefs, risk perception and adaptation strategies among Iranian farmers. A cross-sectional paper-based survey was conducted in theDasht-e Azadegancounty of Khuzestan province in southwest Iran. The study sample consisted of 250 farmers selected through a multi-stage random sampling process. An expert panel review and a pilot study were conducted to confirm convergent validity and reliability of the scales. The results confirm that all four dimensions of psychological distance influence water management adaptation strategies and non-farm activities. Moreover, all psychological dimensions, except the temporal dimension, affect adaptation in farming management. Thus, making climate change more proximal to decision makers could be a strategic way of encouraging individuals to take adaptive actions. This study emphasizes that concepts of psychological distance can be applied to help organizations (e.g., agriculture extension services) to understand farmers’ risk perceptions and responses to climate change impacts and improve risk communication to better engage farmers in climate action.
Potential role of LPAR5 gene in prognosis and immunity of thyroid papillary carcinoma and pan-cancer
Authors: Zhang Ben , Zhang Lixi , Qi Peng , Pang Renzhu , Wang Ziming , Liu Xuyao , Shi Qi , Zhang Qiang 
Published: April 2023

AbstractPapillary carcinomas account for the largest proportion of thyroid cancers, with papillary thyroid carcinoma (PTC) being prone to early lymph node metastasis. Some studies have confirmed that LPAR5 can promote the progression of PTC, but immune-related analyses of LPAR5 and PTC have not been widely discussed. This study aimed to determine the role of LPAR5 in PTC prognosis and immunity. We will further explore the role of LPAR5 in 33 different tumor types. Regarding PTC, we analyzed the effect of LPAR5 expression on overall survival (OS). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. Immune-related analyses of immune checkpoints (ICPs) and immune cell infiltration were also performed. For pan-cancer, R packages were used to analyze prognosis, tumor mutational burden (TMB), microsatellite instability (MSI), and immune cell infiltration. Analysis of tumor microenvironment (TME) and ICPs was performed using Sangerbox (http://vip.sangerbox.com/home.html). The TISIDB database (http://cis.hku.hk/TISIDB/index.php) was used to identify immune and molecular subtypes. LPAR5 expression is associated with PTC prognosis and immunity as well as various human tumors. LPAR5 may be a potential biomarker for multiple malignancies and may provide a new target for cancer immunotherapy.
CaMKII regulates the proteins TPM1 and MYOM2 and promotes diacetylmorphine-induced abnormal cardiac rhythms
Authors: Ji Min , Su Liping , Liu Li , Zhuang Mengjie , Xiao Jinling , Guan Yaling , Zhu Sensen , Ma Lijuan , Pu Hongwei 
Published: April 2023

AbstractAlthough opioids are necessary for the treatment of acute pain, cancer pain, and palliative care, opioid abuse is a serious threat to society. Heroin (Diacetylmorphine) is the most commonly abused opioid, and it can have a variety of effects on the body's tissues and organs, including the well-known gastrointestinal depression and respiratory depression; however, there is little known about the effects of diacetylmorphine on cardiac damage. Here, we demonstrate that diacetylmorphine induces abnormal electrocardiographic changes in rats and causes damage to cardiomyocytes in vitro by an underlying mechanism of increased autophosphorylation of CaMKII and concomitant regulation of myocardial contractile protein TPM1 and MYOM2 protein expression. The CaMKII inhibitor KN-93 was first tested to rescue the toxic effects of heroin on cardiomyocytes in vitro and the abnormal ECG changes caused by heroin in SD rats, followed by the TMT relative quantitative protein technique to analyze the proteome changes. Diacetylmorphine causes increased phosphorylation at the CaMKII Thr287 site in myocardium, resulting in increased autophosphorylation of CaMKII and subsequent alterations in myocardial contractile proteins, leading to myocardial rhythm abnormalities. These findings provide a theoretical basis for the treatment and prevention of patients with arrhythmias caused by diacetylmorphine inhalation and injection.
Bilateral increase in MEG planar gradients prior to saccade onset
Authors: Fabius Jasper H. , Fracasso Alessio , Deodato Michele , Melcher David , Van der Stigchel Stefan 
Published: April 2023

AbstractEvery time we move our eyes, the retinal locations of objects change. To distinguish the changes caused by eye movements from actual external motion of the objects, the visual system is thought to anticipate the consequences of eye movements (saccades). Single neuron recordings have indeed demonstrated changes in receptive fields before saccade onset. Although some EEG studies with human participants have also demonstrated a pre-saccadic increased potential over the hemisphere that will process a stimulus after a saccade, results have been mixed. Here, we used magnetoencephalography to investigate the timing and lateralization of visually evoked planar gradients before saccade onset. We modelled the gradients from trials with both a saccade and a stimulus as the linear combination of the gradients from two conditions with either only a saccade or only a stimulus. We reasoned that any residual gradients in the condition with both a saccade and a stimulus must be uniquely linked to visually-evoked neural activity before a saccade. We observed a widespread increase in residual planar gradients. Interestingly, this increase was bilateral, showing activity both contralateral and ipsilateral to the stimulus, i.e. over the hemisphere that would process the stimulus after saccade offset. This pattern of results is consistent with predictive pre-saccadic changes involving both the current and the future receptive fields involved in processing an attended object, well before the start of the eye movement. The active, sensorimotor coupling of vision and the oculomotor system may underlie the seamless subjective experience of stable and continuous perception.
Long-term trends of pediatric type 1 diabetes incidence in Japan before and after the COVID-19 pandemic
Authors: Matsuda Fumika , Itonaga Tomoyo , Maeda Miwako , Ihara Kenji 
Published: April 2023

AbstractType 1 diabetes incidence has increased worldwide, although the long-term trends on pediatric type 1 diabetes in Japan remain elusive. To investigate the incidence and secular trend of pediatric type 1 diabetes from 1999 to 2021, including the coronavirus disease 2019 (COVID-19) pandemic years, in Oita Prefecture, Japan. We investigated the number of newly diagnosed patients with type 1 diabetes aged < 15 years from 1999 to 2021. We surveyed hospital databases in Oita Prefecture in Japan. The type 1 diabetes incidence in children aged < 15 years increased annually by 5.3% among all children, especially in boys aged 10–14 years by 8.1%, over the past 23 years. The average incidence rate of 3.9/100,000/year was nearly consistent with the previous reports on Asian countries. No significant change was found in the increasing incidence trend of type 1 diabetes before and during the COVID-19 pandemic. The incidence of pediatric type 1 diabetes has significantly increased over the past 23 years in Oita Prefecture, Japan, which is consistent with the worldwide trend.
A cross-sectional study on the relationship between visceral adiposity index and periodontitis in different age groups
Authors: Yang Qinghua , Wang Xuming , Li Chen , Wang Xuanming 
Published: April 2023

AbstractObesity and periodontitis are significantly related, and the visceral adiposity index (VAI) is an important indicator of obesity. This study aimed to investigate the association between VAI and periodontitis. The study included participants from the 2009–2014 cycle of the National Health and Nutrition Examination Survey who received a complete periodontal exam and VAI record. Periodontitis, according to the Centers for Disease Control and Prevention-American Academy of Periodontology periodontitis case definitions, is categorized into the following: no periodontitis, moderate periodontitis, mild periodontitis, and severe periodontitis. Hierarchical analysis, multivariable logistic regression, and restricted cubic spline regression were conducted to investigate the relationship between periodontitis and VAI in adults. There was no significant relationship between VAI and the prevalence of periodontitis in all age groups (P = 0.08). Age-stratified analysis showed a significant association between periodontitis and VAI in adults aged 40–50 years (P < 0.001). After adjusting for all covariates, the association between periodontitis and VAI remained significant in the 40–50-years age group (the trend P value = 0.014). Restricted cubic spline analysis showed a non-linear relationship between VAI and periodontitis (P for non-linear = 0.002). Visceral adiposity index was significantly associated with periodontitis risk in the 40–50-year-old group, and the relationship between VAI and periodontitis risk was found to be non-linear.
Alteration of gut microbiota in wild-borne long-tailed macaques after 1-year being housed in hygienic captivity
Authors: Sawaswong Vorthon , Chanchaem Prangwalai , Kemthong Taratorn , Warit Saradee , Chaiprasert Angkana , Malaivijitnond Suchinda , Payungporn Sunchai 
Published: April 2023

AbstractThe wild-born long-tailed macaques (Macaca fascicularis) were recently recruited and used as breeders for the National Primate Research Center of Thailand, Chulalongkorn University (NPRCT-CU), and changes in their in-depth gut microbiota profiles were investigated. The Oxford Nanopore Technology (ONT) was used to explore full-length 16S rDNA sequences of gut microbiota in animals once captured in their natural habitat and 1-year following translocation and housing in a hygienic environment at NPRCT-CU. Our findings show that the gut microbiota of macaques after 1 year of hygienic housing and programmed diets feeding was altered and reshaped. The prevalent gut bacteria such as Prevotella copri and Faecalibacterium prausnitzii were enriched after translocation, causing the lower alpha diversity. The correlation analysis revealed that Prevotella copri, Phascolarctobacterium succinatutens, and Prevotella stercorea, showed a positive correlation with each other. Significantly enriched pathways in the macaques after translocation included biosynthesis of essential amino acids, fatty acids, polyamine and butanoate. The effects of microbiota change could help macaques to harvest the energy from programmed diets and adapt their gut metabolism. The novel probiotics and microbiota engineering approach could be further developed based on the current findings and should be helpful for captive animal health care management.
Randomized design evidence of the attendance benefits of the EPA School Bus Rebate Program
Authors: Pedde Meredith , Szpiro Adam , Hirth Richard , Adar Sara D. 
Published: April 2023

AbstractApproximately 25 million children ride buses to school in the United States. While school buses are the safest school transport from an accident perspective, older buses often expose students to high levels of diesel exhaust. Because these exposures can adversely impact health, which may lead to more missed school, the US Environmental Protection Agency (EPA) has spent millions of dollars to hasten the transition of school bus fleets to cleaner vehicles. Here, we leveraged the randomized allocation of the EPA’s 2012–2017 School Bus Rebate Program funding to causally assess the district attendance impacts of upgrading buses. Districts randomly selected for funding had greater attendance improvements after the lottery than unselected districts, resulting in over 350,000 estimated additional student days of attendance each year (95% confidence interval = −70,678 to 772,865) due to the use of EPA funds. Attendance improvements were greatest when the oldest buses were replaced and for districts with high ridership on applicant buses. Extrapolating our results nationwide, we expect that the replacement of all pre-2000 model year school buses would lead to more than 1.3 million additional student days of attendance per year (95% confidence interval = 247,443 to 2,406,511). Given the importance of attendance to educational success, we conclude that increasing the pace at which older, highly polluting buses are replaced positively impacts student attendance.
Topography of associations between cardiovascular risk factors and myelin loss in the ageing human brain
Authors: Trofimova Olga , Latypova Adeliya , DiDomenicantonio Giulia , Lutti Antoine , de Lange Ann-Marie G. , Kliegel Matthias , Stringhini Silvia , Marques-Vidal Pedro , Vaucher Julien , Vollenweider Peter , Strippoli Marie-Pierre F. , Preisig Martin , Kherif Ferath , Draganski Bogdan 
Published: April 2023

AbstractOur knowledge of the mechanisms underlying the vulnerability of the brain’s white matter microstructure to cardiovascular risk factors (CVRFs) is still limited. We used a quantitative magnetic resonance imaging (MRI) protocol in a single centre setting to investigate the cross-sectional association between CVRFs and brain tissue properties of white matter tracts in a large community-dwelling cohort (n = 1104, age range 46–87 years). Arterial hypertension was associated with lower myelin and axonal density MRI indices, paralleled by higher extracellular water content. Obesity showed similar associations, though with myelin difference only in male participants. Associations between CVRFs and white matter microstructure were observed predominantly in limbic and prefrontal tracts. Additional genetic, lifestyle and psychiatric factors did not modulate these results, but moderate-to-vigorous physical activity was linked to higher myelin content independently of CVRFs. Our findings complement previously described CVRF-related changes in brain water diffusion properties pointing towards myelin loss and neuroinflammation rather than neurodegeneration.
A proteo-transcriptomic map of non-alcoholic fatty liver disease signatures
Authors: Govaere Olivier , Hasoon Megan , Alexander Leigh , Cockell Simon , Tiniakos Dina , Ekstedt Mattias , Schattenberg Jörn M. , Boursier Jerome , Bugianesi Elisabetta , Ratziu Vlad ,   LITMUS Investigators, Daly Ann K. , Anstee Quentin M. 
Published: April 2023

AbstractNon-alcoholic fatty liver disease (NAFLD) is a common, progressive liver disease strongly associated with the metabolic syndrome. It is unclear how progression of NAFLD towards cirrhosis translates into systematic changes in circulating proteins. Here, we provide a detailed proteo-transcriptomic map of steatohepatitis and fibrosis during progressive NAFLD. In this multicentre proteomic study, we characterize 4,730 circulating proteins in 306 patients with histologically characterized NAFLD and integrate this with transcriptomic analysis in paired liver tissue. We identify circulating proteomic signatures for active steatohepatitis and advanced fibrosis, and correlate these with hepatic transcriptomics to develop a proteo-transcriptomic signature of 31 markers. Deconvolution of this signature by single-cell RNA sequencing reveals the hepatic cell types likely to contribute to proteomic changes with disease progression. As an exemplar of use as a non-invasive diagnostic, logistic regression establishes a composite model comprising four proteins (ADAMTSL2, AKR1B10, CFHR4 and TREM2), body mass index and type 2 diabetes mellitus status, to identify at-risk steatohepatitis.