bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cluster Evolution in Thermal Decomposition of CL-20/TNT Co-Crystal in Compressed State:A ReaxFF Reactive Molecular Dynamics Simulation Study
Authors: Li Yan , Yu Wen-li , Huang Huang , Zhu Min 
Published: October 2021

Abstract
The thermal decomposition process of CL-20/TNT co-crystal in different compression states is simulated by ReaxFF reactive molecular dynamics method. Co-crystals models with different degrees of compression are obtained under four pressures of atmospheric pressure, 4.6GPa, 9.2GPa and 18.4GPa. The potential energy evolution, product formation and cluster evolution in the process are analyzed. We find that the formation of clusters is the key to the decomposition process. When the system is compressed, there will be more clusters which can bind the free atoms, resulting in the reaction to be inhibited. Other evolution information conforms this.
Five Genes as Diagnostic Markers of Ischemic Stroke and Their Correlation with Immune Infiltration
Authors: Wang Meng , Zhang Ruijie , Guan Qiongfeng , Yao Yindan , Han Liyuan 
Published: October 2021

Abstract
Background: This study aimed to identify potential diagnostic markers of ischemic stroke (IS) and discuss the function of immune cell infiltration during the pathological process. Methods: We used IS datasets from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified, and functional correlation analysis was performed. We then screened and verified the diagnostic markers of IS. We evaluated the infiltration of immune cells in infarcts using CIBERSORT and analyzed the correlation between diagnostic markers and infiltrating immune cells. Results: A total of 366 DEGs were screened in this study. Genes encoding CTSG, F13A1, PABPC1, ECHDC2, BIRC2 and infiltrating monocytes, M0 macrophages, activated dendritic cells, and neutrophils (area under the curve [AUC] = 0.945) were identified as diagnostic markers of IS. Immune cell infiltration analysis suggested that memory B cells, regulatory T cells, M0 macrophages, CD8 + T cells, γδT cells, activated natural killer cells, monocytes, activated mast cells, and neutrophils were involved in the IS process. Analysis of correlations between expressed genes and infiltrating immune cells found that CTSG was positively associated with M0 macrophages, F13A1 was positively associated with monocytes, PABPC1 was positively associated with activated dendritic cells, eosinophils were negatively associated with neutrophils, ECHDC2 was negatively associated with monocytes, and BIRC2 was positively associated with eosinophils. Conclusion: five genes and four types of immune cells were identified as diagnostic markers of IS, and immune cell infiltration may play an important role in the progression of IS.
The PCSK9 Involves in the Dyslipidemia of Ovariectomized Mice and Its Mechanism
Authors: Zhao Dan , Zhang Xue-qin , Guo Wen-jing , Cui Zhi-hui , Wang Yi-cheng , Ma Yong-dan , Zhang Li-xue , Zhang Jin-hu , Nie Li , Yue Limin 
Published: October 2021

Abstract
Ovarian failure in postmenopausal female leads E2 to dramatic decrease which is an important reason of menopausal dyslipidemia. PCSK9 as a secretory lipid metabolic regulator plays a critical role in the cholesterol metabolism by negatively regulating LDLR in hepatocytes. Clinical data showed PCSK9 was elevated and positively correlated with LDL-C in the blood of postmenopausal women. However, the relationship between E2 and PCSK9 and the role of PCSK9 in postmenopausal dyslipidemia are still unclear. In this research, 10-week-old ovariectomized mice were fed for 4 weeks with normal diet or high-fat diet, then tested the lipid metabolism profiles and PCSK9 in the blood and the expression of LDLR and PCSK9 in the liver. On this basis, PCSK9-/- ovariectomized mice were used to further verify the effect of PCSK9 in dyslipidemia of ovariectomized mice. Finally, the ovariectomized mice with high-fat diet were subcutaneous injected respectively with E2 or PCSK9 inhibitor alone or both together for 2 weeks and were tested as previous experiment. The results showed PCSK9, TC and LDL-c all increased in the blood of in WT ovariectomized mice and their PCSK9 is positively correlated with LDL-c, while there were on obvious lipid metabolism disorder in the PCSK9−/− ovariectomized mice. PCSK9 inhibitor increased the LDLR on the liver and ameliorated the dyslipidemia in WT ovariectomized mice. It suggests that PCSK9 plays an important role in the dyslipidemia of ovariectomized mice, which provides a new strategy for clinical diagnosis and treatment of the dyslipidemia in post-menopause.
Oxidative Stimuli Induce Antioxidant Responses by Affecting Nrf2/are Signal Pathway in Common Carp (Cyprinus Carpio)
Authors: Liu Yi , Li Xueting , Yu Lidong , He Mingyue , Gu Ning , Li Bingsheng , LI LI , Cheng Lei 
Published: October 2021

Abstract
The Nrf2/ARE signal pathway is a key pathway for antioxidant stress responses and resistance to external stimuli in most organisms. It plays an important role in anti-inflammatory, immune and antioxidant responses. In this paper, the expression of Nrf2/ARE signal pathway related genes in the larval and adult zebrafish were analyzed, including the degree of conservation of the key sites of Nrf2 and Keap1 in carp. And the stress status of the Nrf2/ARE signal pathway was investigated in response to external environment change. The result showed that nrf2 and keap1 binding sites were highly conserved in carp. The expression of nrf2a and keap1a was highest at 48 hpf, keap1b at 8 hpf and varied in adults, suggesting that these genes play different functional roles in different stages of zebrafish. Stimulation by oxidant can induce upregulation of genes related to the Nrf2/ARE signalling pathway, playing an important role in the protection of the organism. This paper not only lays the foundation for studying the role of Nrf2/ARE signaling pathway in the embryonic and adult stages of carp, but also provides a direction for the development of antioxidant drugs and feeds for carp.
Vaccinations or Non-Pharmaceutical Interventions: Safe Reopening of Schools in England
Authors: Cuesta-Lazaro Carolina , Quera-Bofarull Arnau , Aylett-Bullock Joseph , Lawrence Bryan N. , Fong Kevin , Icaza-Lizaola Miguel , Sedgewick Aidan , Truong Henry , Vernon Ian , Williams Julian , Pagel Christina , Krauss Frank 
Published: October 2021

Abstract
With high levels of the Delta variant of COVID-19 circulating in England during September 2021, schools are set to reopen with few school-based non-pharmaceutical interventions (NPIs). In this paper, we present simulation results obtained from the individual-based model, JUNE, for English school opening after a prior vaccination campaign using an optimistic set of assumptions about vaccine efficacy and the likelihood of prior-reinfection. We take a scenario-based approach to modelling potential interventions to assess relative changes rather than real-world forecasts. Specifically, we assess the effects of vaccinating those aged 16-17, those aged 12-17, and not vaccinating children at all relative to only vaccinating the adult population, addressing what might have happened had the UK began teenage vaccinations earlier. Vaccinating children in the 12-15 age group would have had a significant impact on the course of the epidemic, saving thousands of lives overall in these simulations. In the absence of such a vaccination campaign our simulations show there could still be a significant positive impact on the epidemic (fewer cases, fewer deaths) by continuing NPI strategies in schools. Our analysis suggests that the best results in terms of lives saved are likely derived from a combination of the now planned vaccination campaign and NPIs in schools.
Commensal Bacillus From Cow Milk Inhibits Staphylococcus Aureus Biofilm Formation and Mastitis in Mice
Authors: Qiu Min , Zhao Caijun , Feng Lianjun , Gao Siyuan , Hu Xiaoyu , Fu Yunhe , Zhang Naisheng 
Published: October 2021

Abstract
Background: Mastitis, one of the most serious diseases in dairy industry, could cause tremendous economic losses worldwide and is commonly trigged by pathogen invasion. Staphylococcus aureus (S. aureus) -induced mastitis has been reported to play an important role in mastitis etiology characterized by high morbidity, recurrence, and increased antibiotic resistance, which may attribute to the formation of biofilm formation, a form of bacterial aggregation for better growth and resistance to adverse conditions. Probiotics Bacillus has been reported to disrupt bacteria quorum-sensing (QS) system, a central regulator for biofilm formation. However, whether commensal Bacillus affects S. aureus biofilm formation and consequent colonization during mastitis is still unknown. Results：Here, we identified that the Bacillus is associated with reduced colonization of S. aureus in the mammary gland of cows. Interestingly, Bacillus did not affect S. aureus growth but inhibited the biofilm formation of S. aureus by interfering with S. aureus QS signaling. The most obvious anti-biofilm effect was found in Bacillus subtilis H28, so it was selected for further study. We found that bacillus subtilis H28 treatment alleviated S. aureus-induced mastitis in mice, as showed by limiting pro-inflammatory cytokines production, enhancing barrier integrity, and reducing S. aureus burden. Consistently, Bacillus subtilis with the capacity to interfere S. aureus QS ameliorated S. aureus-induced NF-κB activation in mice mammary epithelial cells（MMECs）. Conclusions: Collectively, our results indicate that commensal Bacillus inhibits S. aureus colonization and alleviates S. aureus-induced mastitis by influencing biofilm formation, which suggests a potential strategy for the decolonization of S. aureus and acts as a basis for the prevention and treatment of S. aureus-related disease.
From compartments to gene loops: Functions of the 3D genome in the human brain
Authors: Roussos Panos , Rahman Samir , Dong Pengfei , Apontes Pasha , Fernando Michael , Townsley Kayla , Girdhar Kiran , Bendl Jaroslav , Shao Zhiping , Misir Ruth , Tsankova Nadejda , Kleopoulos Steven , Brennand Kristen , Fullard John 
Published: October 2021

Abstract
The 3D genome plays a key role in the regulation of gene expression. However, little is known about the spatiotemporal organization of chromatin during human brain development. We investigated the 3D genome in human fetal cortical plate and in adult prefrontal cortical neurons and glia. We found that neurons have weaker compartments than glia that emerge during fetal development. Furthermore, neurons form loop domains whereas glia form compartment domains. We show through CRISPRi on CNTNAP2 that transcription is coupled to loop domain insulation. Gene regulation during neural development involves increased use of enhancer-promoter and repressor-promoter loops. Finally, transcription is associated with gene loops. Altogether, we provide novel insights into the relationship between gene expression and different scales of chromatin organization in the human brain.
Formation and function of bacterial outer membrane proteins- incorporated liposomes using an in vitro translation system
Authors: Kamiya Koki 
Published: October 2021

Abstract
Outer membrane proteins (OMPs), located on the outer membrane of gram-negative bacteria, have a β-strand structure and form nanopores, which allow passage of ions, sugars, and small molecules. Recently, OMPs have been used as sensing elements to detect biological molecules. OMPs are normally expressed and purified from E. coli.. Although the cell-free synthesis of OMPs, such as OmpA and OmpG, is achieved in the presence of liposomes and periplasmic chaperones, the amount of OmpA and OmpG incorporated into the nano-sized liposomes is not clear. In this study, after in vitro translation, the incorporation of OmpG into purified nano-sized liposomes, with various lipid compositions, was investigated. Liposomes containing the synthesized OmpG were purified using a stepwise sucrose density gradient. We report that liposomes prepared with the E. coli lipid extract (PE/PG) had the highest amount of OmpG incorporated compared to liposomes with other lipid compositions, as detected by recording the current across the OmpG containing liposomes using the patch clamp technique. This study reveals some of the requirements for the insertion and refolding of OMPs synthesized by the in vitro translation system into lipid membranes, which plays a role in the biological sensing of various molecules.
WITHDRAWN: Evaluation of the Efficacy of Lactogenic Immunity of Sow Induced by Porcine Epidemic Diarrhea Virus (PEDV) Vaccine By Intranasal Immunization
Authors: Deng Shengchao , Wang Juan , Mohiuddin Mudassar , Zhu Lisai , Wang Guiping , Jia Aiqing 
Published: October 2021

Abstract
Background: Porcine epidemic diarrhea virus belongs to family of coronaviruses which are notorious for rapid spread of severe diarrhea among suckling piglets. The virus mainly replicates in the epithelial cells of duodenum, jejunum, ileum and colon and is a life threatening condition in pigs. A highly virulent strain “CHYJ130330” having high mortality rate was isolated from a field outbreak, identified as a new virulent genotype II/G2-b strain and adapted successfully to vero cells was used to prepare inactivated vaccine against PEDV. This newly prepared vaccine was given through intranasal route and is compared with the commercially available bi-combined (PEDV and TGEV) vaccine given by intramuscular injection. In this study milk or mucosal IgA and IgG antibody levels have been used to predict vaccine efficacy and the level of protective immunity against PED virus. Antibody titers in the milk of sows and intestines of suckling piglets were compared by enzyme-linked immunosorbent assay (ELISA). Results: It was shown that CHYJ vaccine induced significantly higher levels of PEDV IgA antibody in milk of sows and intestines of piglets as compared to commercial bi-combined vaccine. Both CHYJ and commercial vaccines were not able to induce detectable IgG levels in the intestines of piglets; the later however induced higher IgG levels when detected in the sow’s milk. Protective efficacy of vaccines was determined against a highly virulent PEDV strain. CHYJ intranasal vaccine gives a better protection 80% (4/5) rate as compared to commercial i.m. vaccine conferring 60% (3/5) immunity in suckling piglets. Conclusions: It is therefore concluded that PEDV inactivated CHYJ vaccine confer better lactogenic immunity and gives more protection to suckling piglets than available bi-combined TGEV and PEDV vaccine through passive immunization.
Tuberculosis Poor Treatment Outcomes and its determinants in Kilifi County, Kenya: A Retrospective Cohort Study
Authors: Katana Geoffrey G. , Ngari Moses , Maina Teresia Wamuyu , Sanga Deche , Abdullahi Osman A 
Published: October 2021

Abstract
Background:Tuberculosis (TB) is one of the leading causes of deaths in Africa, monitoring its treatment outcome is essential to evaluate treatment effectiveness. In this study, we aimed to evaluate proportion of poor TB treatment outcome (PTO) and its determinants during six-months of treatment in Kilifi County, Kenya. Methods:This study was a retrospective analysis of data from the TB surveillance system (TIBU) in Kilifi County, Kenya from 2012 to 2019. The outcome of interest was PTO (lost-to-follow-up (LTFU), death, transferred out, treatment failure, drug resistance) or successful (cured or completed treatment) treatment. We performed time-stratified (at three months follow-up) survival regression analyses accounting for sub-county heterogeneity to determine factors associated with PTO.Results:We included 14706 TB patients, median (IQR) age 37 (28–50) years old and 8791 (60%) males. A total of 13389 (91%) were on first line anti-TB treatment (2RHZE/4RH), 4242 (29%) were HIV infected and 192 (1.3%) had other underlying medical conditions. During 6586 person-years of follow-up, 2408 (16%) patients had PTO: 1074 (45%) deaths, 776 (32%) LTFU, 415 (17%) transferred out, 103 (4.3%) treatment failure and 30 (1.3%) multidrug resistance. The proportion of poor outcome increased from 7.9% in 2012 peaking at 2018 (22.8%) and slightly declining to 20% in 2019 (trend test P=0.03). Over two-thirds 1734(72%), poor outcomes occurred within first three months of follow-up. In the first three months of starting TB treatment, HIV infection (aHR 1.72 (95% CI 1.28–2.30)) and year of starting treatment were positively associated with PTO. However, in the last three months of treatment, elderly age ≥50 years, a retreatment patient, HIV infection, other underlying medical conditions (aHR 2.24 (95%CI 1.41–3.54)) and year of starting treatment were positively associated with PTO while being a female (aHR 0.83 (95%CI 0.70–0.97)) was negatively associated with PTO.ConclusionsOver two-thirds of poor outcomes occur in the first three months of TB treatment, therefore greater efforts are needed during this phase. Intervention targeting the HIV infected and other underlying medical conditions, the elderly and retreated patients provide an opportunity to improve TB treatment outcome.
Monitoring Geological Storage of CO2 – A New Rock Physics Model to Estimate Saturation
Authors: Fawad Manzar , Mondol Nazmul Haque 
Published: October 2021

Abstract
To mitigate the global warming crisis, one of the effective ways is to capture CO2 at an emitting source and inject it underground in saline aquifers, depleted oil and gas reservoirs, or in coal beds. This process is known as carbon capture and storage (CCS). With CCS, CO2 is considered a waste product that has to be disposed of properly, like sewage and other pollutants. While and after CO2 injection, monitoring of the CO2 storage site is necessary to observe CO2 plume movement and detect potential leakage. For CO2 monitoring, various physical property changes are employed to delineate the plume area and migration pathways with their pros and cons. We introduce a new rock physics model to facilitate the time-lapse estimation of CO2 saturation and possible pressure changes within a CO2 storage reservoir based on physical properties obtained from the prestack seismic inversion. We demonstrate that the CO2 plume delineation, saturation, and pressure changes estimation are possible using a combination of Acoustic Impedance (AI) and P- to S-wave velocity ratio (Vp/Vs) inverted from time-lapse or four-dimensional (4D) seismic. We assumed a scenario over a period of 40 years comprising an initial 25 year injection period. Our results show that monitoring the CO2 plume in terms of extent and saturation can be carried out using our rock physics-derived method. The suggested method without going into the elastic moduli level handles the elastic property cubes which are commonly obtained from the prestack seismic inversion. Pressure changes quantification is also possible within un-cemented sands; however, the stress/cementation coefficient in our proposed model needs further study to relate that with effective stress in various types of sandstones. The three-dimensional (3D) seismic usually covers the area from the reservoir's base to the surface makes it possible to detect the CO2 plume's lateral and vertical migration. However, the comparatively low resolution of seismic, the inversion uncertainties, lateral mineral, and shale property variations are some limitations, which warrant consideration. This method can also be applied for the exploration and monitoring of hydrocarbon production.
Predicting the Metro Scenario-based Spatiotemporal Evolution of Land Use Using CA-Kalman Filter Model: a Case Study of Nanjing City, China
Authors: Dai Jialing , Li Xiaozhao , Zhang Wei , Liao Ke , Liu Tao , Zhao Peng , Xu Wentao 
Published: October 2021

Abstract
The expansion of metro system can bring varying degrees of impact to the surrounding environment. To study this complex system problem, this paper discusses the temporal and spatial impact by metro system from the perspective of land use change simulation and scenario analysis. The traditional cellular automata (CA) model can realize the simulation of land use change under various scenarios through system dynamics or Markov chain to control the long-term demand forecasting. However, this type of model ignores the filtering of noise data from imageries and increases uncertainty of the system. Therefore, based on the Future Land Use Simulation (FLUS) model, this paper integrates Kalman filter to control the stochastic process of the state-space system, and predicts the spatio-temporal evolution of land use change impacted by metro system in Nanjing from 2019 to 2035. The results show that: (1) The proposed CA-Kalman filter model can realize the optimized simulation of land use change with good accuracy; (2) Urban patches impacted by metro system will emerge from the existing urban boundaries at the cost of occupation of cultivated land, although there is still significant expansion of urban land and construction land, it will reach the upper limit in 2050.
Separator-less Amino Acid-powered Biofuel Cell Through an Artificial Multi-enzyme Cascade Reaction
Authors: Satomura T , Horinaga Kousaku , Takamura Eiichiro , Sakamoto Hiroaki , Sakuraba Haruhiko , Ohshima Toshihisa , Suye Shin-ichiro 
Published: October 2021

Abstract
Objective This study was aimed at constructing a highly stable one-compartment enzymatic biofuel cell (EFC) without a separator through a multi-enzyme cascade reaction pathway. Results A separator-less EFC composed of a multi-enzyme cascade anode containing four dehydrogenases from a thermophile and a cathode devised using a multi-copper oxidase mutant with enhanced enzyme activity from a hyperthermophile was developed. To fabricate an EFC without a separator, redox mediators utilized in the enzymatic cascade reaction were also immobilized on the anode. In the presence of the fuel 100 mM L -proline, the separator-less EFC with four thermophilic dehydrogenase-modified anode achieved a maximum power density of 11.3 υW/cm 2 at 37°C, which was 1.6-fold higher than that of a similar EFC fabricated with a one enzyme-modified anode. The separator-less EFC composed of a multi-enzyme modified anode maintained approximately 57% of the load current at 0.3 V measured on the first day of EFC fabrication, even after 4 days.Conclusion Efficient L-proline electric generation utilizing a separator-less EFC composed of a multi-enzyme modified anode through a multi-step fuel oxidation reaction and a highly stable multi-copper oxidase mutant-modified cathode was successfully achieved over a long period. The long-term stability of the separator-less EFC can facilitate its application as an efficient power source for implantable medical devices requiring continuous operation.