bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selenium Alleviated Oxidative Stress-Mediated Complex Poisoning Mechanism in Lead-Treated Chicken Kidneys: Inflammation, Heat Shock Response, and Autophagy
Authors: Miao Zhiying , Yu Weikang , Wang Yueyang , Tang You , Teng Xiaohua 
Published: December 2021

Abstract
Lead (Pb) is a toxic environmental contaminant, and exerts renal toxicity. It is known that selenium (Se) performs antagonistic effect on Pb poisoning. However, biological events during the process were not well understood in chicken kidneys. The purpose of this research was to investigate mitigative mechanism of Se on Pb poisoning from point of view of oxidative stress, inflammation, heat shock response, and autophagy in chicken kidneys. One hundred and eighty male Hyline chickens (7-day-old) were randomly divided into the control group (offering standard diet and potable water), the Se group (offering Na2SeO3-added standard diet and potable water), the Pb group (offering standard diet and (CH3OO)2Pb-added potable water), and the Pb+Se group (offering Na2SeO3-added standard diet and (CH3OO)2Pb-added potable water). On 30th, 60th, and 90th days, kidneys were removed to perform the studies of histological structure, oxidative stress indicators, cytokines, heat shock proteins, and autophagy in the chicken kidneys. The experimental results indicated that Pb poisoning changed renal histological structure; decreased catalase, glutathione-s-transferase, and total antioxidative capacity activities; increased hydrogen peroxide content; induced mRNA and protein expression of heat shock proteins; inhibited interleukin (IL)-2 mRNA expression, and induced IL-4 and IL-12β mRNA expression; inhibited mammalian target of rapamycin mRNA and protein expression, and induced autophagy-related gene mRNA and protein expression in the chicken kidneys. Supplement of Se mitigated the above changes caused by Pb. In conclusion, Pb induced oxidative stress, inflammation, heat shock response, and autophagy and Se administration alleviated Pb poisoning through mitigating oxidative stress in the chicken kidneys.
Effect of Bio-Based Surfactant on Wettability of Low-Rank Coal Surface and Its Mechanism
Authors: Li Lin , Liu Mingpu , Lvu Jianqiao , Li Xiaoteng , Li Zhihao , Lin Mengyu , Ma Chuandong , He Meng , Wang Qingbiao , Yu Hao , you xiaofang 
Published: December 2021

Abstract
In this study, the effect of a bio-based environment-friendly surfactant, cardanol polyoxyethylene ether (BGF), on the wettability of the surface of low-rank coal (LRC) and its mechanism were studied. The adsorption experiment showed that the adsorption of the surfactant conformed to the Langmuir adsorption model and the pseudo-second-order kinetic model. The adsorption was mainly affected by hydrogen bonding, and the adsorption rate was affected by intraparticle diffusion and liquid film diffusion. The wettability experiment showed that the influence of BGF on the wettability of the surface of LRC followed the given order: BGF-7 > BGF-10 > BGF-15. The investigation of adhesion work showed that the adhesion work and the stability of the coal–water system decreased after adsorption. Fourier transform infrared and X-ray photoelectron spectroscopy analyses showed that after adsorption, the peak strength of vinyl ether, the content of elemental carbon, and the content of C-C/C-H groups increased.
Integrative Proteomic Characterization of Trace FFPE Samples in Early-Stage Gastrointestinal Cancer
Authors: Li Lingling , Liu Hui , Li Yan , Guo Chunmei , Wang Bing , Shen Dan , Zhang Qiao , Ding Chen 
Published: December 2021

Abstract
Background The surveillance and therapy of early-stage cancer would be better for patients’ prognosis. However, the extreme trace amount of tissue samples in different stages have limited in portraying the characterization of early-stage cancer. Therefore, we focused on and presented comprehensive proteomic and phosphoproproteomic profiling of the trace FFPE samples from early-stage gastrointestinal cancer, and then explored the potential biomarkers of early-stage gastrointestinal cancer. Methods In this study, a quantitative proteomic method with chromatography with mass spectrometry (LC-MS/MS) was used to analyse the proteomic difference between the trace early-stage esophageal squamous cell carcinoma (EESCC) and early-stage duodenum adenocarcinoma cancer (EDAC). Results We identified ~6,000 proteins and >10,000 phosphosites in single trace FFPE samples. The distinct separation of EESCC and EDAC illustrated the functions of cell cycle (RB1 T373, EGFR T693) in EESCC, and the positive impacts of apoptosis, metabolic processes (MTOR and MTOR S1261) in EDAC. Furthermore, we deconvoluted the immune infiltration of early-stage gastrointestinal cancer, in which higher immune cell signatures were detected in EDAC, and showed the specific cytokines in EESCC and EDAC. We performed kinases-substates relationship analysis and elucidated the specific proteomic kinase characterization of EESCC and EDAC, and proposed the medicative effects and corresponding drugs for EESCC and EDAC at the clinic.Conclusion We disclosed the specific immune characterization of the early-stage gastrointestinal cancer, and presented potential makers of EESCC (EGFR, PDGFRB, CDK4, WEE1) and EDAC (MTOR, MAP2K1, MAPK3). This study represents a major stepping stone towards investigating the carcinogenesis mechanism of gastrointestinal cancer, and providing a rich resource for medicative strategy in the clinic.
Quantifying Earth system interactions for sustainable food production: an expert elicitation
Authors: Chrysafi Anna , Virkki Vili , Jalava Mika , Sandström Vilma , Piipponen Johannes , Porkka Miina , Lade Steven , Mere Kelsey La , Wang-Erlandsson Lan , Scherer Laura , Andersen Lauren , Bennett Elena , Brauman Kate , Cooper Gregory , De Palma Adriana , Döll Petra , Downing Andrea , DuBois Timothy , Fetzer Ingo , Fulton Elizabeth , Gerten Dieter , Jaafar Hadi , Jaegermeyr Jonas , Jaramillo Fernando , Jung Martin , Kahiluoto Helena , Mackay Anson , Lassaletta Luis , Mason-D'Croz Daniel , Mekonnen Mesfin , Nash Kirsty , Pastor Amandine , Ramankutty Navin , Ridoutt Bradley , Siebert Stefan , Simmons Benno , Staal Arie , Sun Zhongxiao , Tobian Arne , Usubiaga-Liaño Arkaitz , Ent Ruud van der , Soesbergen Arnout van , Verburg Peter , Wada Yoshihide , Zipper Samuel , Kummu Matti 
Published: December 2021

Abstract
Several safe boundaries of critical Earth system processes have already been crossed by human perturbations. Recent research indicates that not accounting for the interactions between these processes may further narrow the safe operating space for humanity. Yet existing work accounts only for transgression of single boundaries and only a few studies take some of the boundary interactions into account. For future sustainability assessments, it is essential to understand boundary transgressions and their interactions more comprehensively. Here, we explore quantitatively how strongly seven variables, representing Earth system processes relevant to food production, interact with each other, using a structured expert knowledge elicitation. We identify Green water and Land system change as crucial interactive processes through their impacts on multiple relevant processes, while Biosphere integrity-land, freshwater and ocean components appear to be most affected by other Earth system processes, most notably Blue water and Biogeochemical flows. The elicitation also enabled us to map the complex network of mechanisms mediating interactions, to support integrated Earth system and planetary boundaries modelling and assessments. Finally, we created a prioritisation scheme for future research according to the interaction strengths and existing knowledge gaps. Our analysis improves our understanding of Earth system interactions, with clear implications for sustainable use of natural resources such as the biophysical limits for food production.
SARS-CoV-2 Cases Reported From Long-Term Residential Facilities (Care Homes) in South Africa: A Retrospective Cohort Study
Authors: Arendse Tracy , Cowper Beverley , Cohen Cheryl , Masha Maureen , Tempia Stefano , Legodu Civil , Singh Sandhya , Ratau Tebogo , Geffen Leon , Heymans Ansie , Coetzer Dane , Blumberg Lucille , Jassat Waasila 
Published: December 2021

Abstract
Background: Globally, long-term care facilities (LTCFs) experienced a large burden of deaths during the COVID-19 pandemic. The study aimed to describe the temporal trends as well as the characteristics and risk factors for mortality among residents and staff who tested positive for SARS-CoV-2 in selected LTCFs across South Africa.Method: We analysed data reported to the DATCOV sentinel surveillance system by 45 LTCFs. Outbreaks in LTCFs were defined as large if more than one-third of residents and staff had been infected or there were more than 20 epidemiologically linked cases. Multivariable logistic regression was used to assess risk factors for mortality amongst LTCF residents.Results: A total of 2,324 SARS-CoV-2 cases were reported from 5 March 2020 through 31 July 2021; 1,504 (65%) were residents and 820 (35%) staff. Among LTCFs, 6 reported sporadic cases and 39 experienced outbreaks. Of those reporting outbreaks, 10 (26%) reported one and 29 (74%) reported more than one outbreak. There were 48 (66.7%) small outbreaks and 24 (33.3%) large outbreaks reported. There were 30 outbreaks reported in the first wave, 21 in the second wave and 15 in the third wave, with 6 outbreaks reporting between waves. There were 1,259 cases during the first COVID-19 wave, 362 during the second wave, and 299 during the current third wave. The case fatality ratio was 9% (138/1,504) among residents and 0.5% (4/820) among staff. On multivariable analysis, factors associated with SARS-CoV-2 mortality among LTCF residents were age 40-59 years, 60-79 years and ≥80 years compared to <40 years and being a resident in a LTCF in Free State or Northern Cape compared to Western Cape. Compared to pre-wave 1, there was a decreased risk of mortality in wave 1, post-wave 1, wave 2, post-wave 2 and wave 3.Conclusion: The analysis of SARS-CoV-2 cases in sentinel LTCFs in South Africa points to an encouraging trend of decreasing numbers of outbreaks, cases and risk for mortality since the first wave. LTCFs are likely to have learnt from international experience and adopted national protocols, which include improved measures to limit transmission and administer early and appropriate clinical care.
Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon.
Authors: Rosenberg Aviv , Marx Ailie , Bronstein Alex 
Published: December 2021

Abstract
Synonymous codons translate into chemically identical amino acids. Once considered inconsequential to the formation of the protein product, there is now significant evidence to suggest that codon usage affects co-translational protein folding and the final structure of the expressed protein. Here we develop a method for computing and comparing codon-specific Ramachandran plots and demonstrate that the backbone dihedral angle distributions of some synonymous codons are distinguishable with statistical significance for some secondary structures. This shows that there exists a dependence between codon identity and backbone torsion of the translated amino acid. Although these findings cannot pinpoint the causal direction of this dependence, we discuss the vast biological implications should coding be shown to directly shape protein conformation and demonstrate the usefulness of this method as a tool for probing associations between codon usage and protein structure. Finally, we urge for the inclusion of exact genetic information into structural databases.
Gamma-Tocotrienol, A Radiation Countermeasure, Reverses Proteomic Changes In Serum Following Total-Body Gamma Irradiation In Mice
Authors: Rosen Elliot , Fatanmi Oluseyi , Wise Stephen Y. , Rao V. Ashutosh , Singh Vijay K. 
Published: December 2021

Abstract
Radiological incidents or terrorist attacks would likely expose civilians and military personnel to high doses of ionizing radiation, leading to the development of acute radiation syndrome (ARS). While the effects and symptoms of high dose radiation exposure have been established, prophylactic treatments and methods for determining the extent of exposure remain limited. We examined the effectiveness of prophylactic administration of a developmental radiation countermeasure, g-tocotrienol (GT3), in a total-body irradiation (TBI) mouse model. CD2F1 mice received GT3 24 h prior to 11 Gy cobalt-60 gamma-irradiation, a supralethal dose for this strain. Two-dimensional differential in-gel electrophoresis was followed by mass spectrometry and Ingenuity Pathway Analysis (IPA). Analysis revealed a change in expression of 18 proteins in response to TBI, and these changes were reversed with prophylactic treatment of GT3. IPA revealed a network of associated proteins involved in cellular movement, immune cell trafficking, and inflammatory response. Of particular interest, significant expression changes in beta-2-glycoprotein 1, alpha-1-acid glycoprotein 1, alpha-2-macroglobulin, complement C3, mannose-binding protein C, and major urinary protein 6 were noted after TBI and reversed with GT3 treatment. This study reports the network and specific serum proteins which could be translated as biomarkers of both radiation injury and protection by radiation countermeasures.
Epigenetic Silencing of OR and TAS2R Genes Expression in Human Orbitofrontal Cortex At Early Stages of Sporadic Alzheimer’s Disease
Authors: Alves Victoria Cunha , Figueiro-Silva Joana , Ferrer Isidre , Carro Eva 
Published: December 2021

Abstract
Modulation of brain olfactory (OR) and taste receptors (TASR) expression was recently reported in neurological diseases. We explored the possible expression and regulation of selected OR and TASR genes in human orbitofrontal cortex of sporadic Alzheimer’s disease (AD) and found that these are expressed and markedly downregulated at early stages. The expression pattern did not follow disease progression suggesting regulation through epigenetic mechanisms. We found an increase of global H3K9me3 levels and substantial enrichment of this repressive signature at ORs and TAS2Rs proximal promoter at early stages, ultimately lost at advanced stages. By mass spectrometry-based proteomic and further validation, we found that H3K9me3 interacts with MeCP2 at early stages and that this protein is increased in sporadic AD. Findings suggest MeCP2 might be implicated in OR and TAS2R genes expression regulation through interaction with H3K9me3, and as an early event, it may uncover a novel etiopathogenetic mechanism of sporadic AD.
CircZNF609 Promotes Bladder Cancer Progression and Inhibits Cisplatin Sensitivity via miR-1200/CDC25B Pathway
Authors: Feng Dexiang , Lv Jiancheng , Li Kai , Cao Qiang , Han Jie , Yu Hao , Cheng Yidong , Zhuang Juntao , Cai Lingkai , Yang Haiwei , Yang Xiao , Lu Qiang 
Published: December 2021

Abstract
Circular RNAs (circRNAs) have been extensively studied in tumor development and treatment. CircZNF609 has been shown to act as an oncogene in a variety of solid tumors and may serve as a novel biomarker for tumor diagnosis and treatment. However, the underlying role and mechanism of circZNF609 in bladder cancer (BCa) development and cisplatin chemosensitivity were unknown. Quantitative real-time PCR (qRT-PCR) was applied to determine the expression of circZNF609, microRNA 1200 (miR-1200) and CDC25B in BCa cells and tissues. Western blot was used to detect the protein level of CDC25B. Functional assays in vitro and in vivo were conducted to investigate the effects of circZNF609 on tumor development and cisplatin chemosensitivity in BCa. RNA sequencing and online databases were used to predict the interactions among circZNF609, miR-1200 and CDC25B. Dual luciferase reporter assay, RNA pull-down assay and RNA fluorescence in situ hybridization (FISH) were applied to confirm the mechanism. CircZNF609 expression was significantly up-regulated in BCa cell lines and tissues. Increased expression of circZNF609 was related to a worse survival in BCa patients. In vitro and in vivo, enforced-expression of circZNF609 enhanced BCa cells proliferation, migration and cisplatin chemoresistance. Mechanistically, circZNF609 alleviated the inhibition effect on target CDC25B expression by sponging miR-1200. CircZNF609 promoted tumor growth through novel circZNF609/miR-1200/CDC25B axis, implying that circZNF609 has significant potential to serve as a new diagnostic biomarker and therapeutic target for BCa patients.
The Pharmacokinetic Study of Progesterone and Allopregnanolone in Refractory Epilepsy : Phase II Study
Authors: Senngam Marisa , Suphanklang Juthathip , santimaleeworagun Wichai , Suwanpakdee Piradee , Mekhasingharrak Pornsawan , Dhapasita Chanittha , Sithinamsuwan Pasiri 
Published: December 2021

Abstract
Background: Progesterone belongs to a class of neurosteroids used for the reduction of seizure frequency in patients with refractory epilepsy. However, the pharmacokinetics of progesterone and its active derivative, allopregnanolone, have never been studied in these patients. Objectives: This study was aim to explore the pharmacokinetic parameters of progesterone 400 mg every 12 h, for 3 months, in patients with refractory epilepsy as an add-on therapy to control seizures. Phoenix® WinNonlin® was used to analyse the pharmacokinetic parameters. Results: Twelve patients were recruited. From a therapeutic drug monitoring, the serum progesterone and allopregnanolone levels after taking the first dose of progesterone were characterised by a time to maximum concentration (Tmax) median of 1 and 2.5 h, a maximum concentration (Cmax) median of 274.97 and 3.81 ng/mL, and a minimum concentration (Cmin) median of 56.93 and 1.06 ng/mL, respectively. The median values of the pharmacokinetic parameters of progesterone and allopregnanolone during the steady state were as follows: t1/2 of 2.4 and 2.0 h, Cmax of 964.35 and 8.92 ng/mL, and Cmin of 64.67 and 1.86 ng/mL, respectively. By examining the relationship between the progesterone or allopregnanolone concentrations with seizure-controlling ability, we could identify a responder patient group with 6- to 7-fold higher serum concentrations of progesterone and allopregnanolone than the non-responders. Conclusions: We could establish higher serum levels of both progesterone and allopregnanolone, which could consequently relate to lowering the seizure frequency in patients with refractory epilepsy. The suggested progesterone dose was 400 mg orally every 12 h against refractory epilepsy Trial registration: This study has been registered on the Thai Clinical Trials Registry (No. TCTR20200710005, 10 July 2020)
Dual-comb Photothermal Spectroscopy
Authors: Wang Qiang , Wang Zhen , Zhang Hui , Jiang Shoulin , Wang Yingying , Jin Wei , Ren Wei 
Published: December 2021

Abstract
Dual-comb spectroscopy (DCS) has revolutionized optical spectroscopy by providing broadband spectral measurements with unprecedent resolution and fast response. Photothermal spectroscopy (PTS) offers an ultrasensitive and background-free gas sensing method, which is normally performed using a single-wavelength pump laser. The merging of PTS with DCS may enable a new spectroscopic method by taking advantage of both technologies, which has never been studied yet. Here, we report dual-comb photothermal spectroscopy (DC-PTS) by passing dual combs and a probe laser through a gas-filled anti-resonant hollow-core fiber, where the generated multi-heterodyne modulation of the refractive index is sensitively detected by an in-line interferometer. As an example, we have measured photothermal spectra of acetylene over 1 THz, showing a good agreement with the spectral database. Our proposed DC-PTS provides new opportunities for broadband gas sensing with super-fine resolution and high sensitivity, as well as with a small sample volume and compact configuration.
Study on Emergency Evacuation and Intervention Behavior of Population with Spatial Knowledge Integrity
Authors: Wang Xuan , Mao Yan , Xiong Jing Jing , He Wu 
Published: December 2021

Abstract
The level of spatial knowledge integrity of a population is crucial for fire escape behavior. The use of appropriate interventions for people with different levels of spatial knowledge can effectively improve evacuation efficiency. However, different emergency situations also have different effects on evacuation behavior. In this paper, we combine spatial knowledge integrity, intervention behavior and emergency situations in a fire evacuation study. To complete this study, 128 participants were recruited using VR technology, classified into spatial knowledge completeness, and studied crowd evacuation through different intervention behaviors in different simulated emergency scenarios. The results of the study showed that participants with complete spatial knowledge had shorter evacuation distances and times. Secondly, leader interventions guided evacuation better for participants with incomplete spatial knowledge in low-hazard emergencies, while range interventions were better for participants with complete spatial knowledge. Thirdly, in high-risk emergencies, leader intervention was better than range intervention for evacuation, regardless of spatial knowledge completeness. Fourth, the interaction between spatial knowledge completeness and intervention behavior was significant, positively influencing the evacuation time and distance of participants.
Structural insight on the mechanism of an electron-bifurcating [FeFe] hydrogenase
Authors: Birrell James , Furlan Chris , Chongdar Nipa , Gupta Pooja , Lubitz Wolfgang , Ogata Hideaki , Blaza James 
Published: December 2021

Abstract
Electron-bifurcation is a fundamental energy conservation mechanism in nature. The electron-bifurcating [FeFe] hydrogenase from Thermotoga maritima (HydABC) requires both NADH and ferredoxin to reduce protons generating hydrogen. The mechanism of electron-bifurcation in HydABC remains enigmatic primarily due to the lack of structural information. Here, we present a 2.3 Å electron cryo-microscopy structure of HydABC. The structure is a heterododecamer composed of two independent ‘halves’ each made of two strongly interacting HydABC heterotrimers electrically connected via a [4Fe-4S] cluster. A central electron transfer pathway connects the active sites for NADH oxidation and proton reduction. Symmetry expansion identified two conformations of a flexible iron-sulfur cluster domain: a “closed bridge” and an “open bridge” conformation, where a Zn2+ site may act as a “hinge” allowing domain movement. Based on these structural revelations, we propose two new mechanisms of electron-bifurcation in HydABC.