bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two-Dimensional Modeling of the Influence of Underground Mining Direction on Slope Stability in Coordinated Open-Pit and Underground Mining
Authors: Liu Bowen , Wang Zhenwei , Ding Xinpin , Wang Zhitao , Li Bin 
Published: February 2021

Abstract
Under a background of coordinated open-pit and underground mining engineering practice in the Pingshuo mining area, a combination of numerical simulations and similar-model experiments was used to study the influence of the underground mining direction on slope deformation in two dimensions. The results show that the disturbance caused by inverse-slope mining is more obvious than that caused by along-slope mining. Underground mining presents an asymmetric influence on the open-pit slope; the slope rock mass on the open-off cut side is disturbed more than that on the coal-wall side. Compared with the slope in front of the advancing direction of the underground mining face, the degree of rock-mass damage and stress concentration of the slope of the open-off cut side are more serious. As such, in coordinated open-pit and underground mining practice, an along-slope mining direction is recommended to reduce adverse effects on slope stability and improve the recovery rate of coal resources.
Human transcription factor protein interaction networks
Authors: Göös Helka , Kinnunen Matias , Yadav Leena , Tan Zenglai , Salokas Kari , Zhang Qin , Wei Gong-hong , Varjosalo Markku 
Published: February 2021

Abstract
In participation of transcriptional regulation, transcription factors (TFs) interact with several other proteins. Here, we identified 7233 and 2176 protein-protein interactions for 110 different human TFs through proximity-dependent biotinylation (BioID) and affinity purification mass spectrometry (AP-MS), respectively. The BioID analysis resulted more high-confident interactions, highlighting the transient and dynamic nature of many of the TF interactions.

Using clustering and correlation analyses, we identified subgroups of TFs associated with specific biological functions, such as RNA-splicing, actin signalling or chromatin remodeling. We also observed 203 TF-TF interactions, of which 175 were interactions with Nuclear Factor 1 (NFI) -family members, indicating uncharacterized cross-talk between NFI signalling and numerous other TF signalling. Moreover, TF interactions with basal transcription machinery were mainly observed through TFIID and SAGA complexes.

This study, not only, provides a rich resource of human TF interactions, but also act as starting point directing future studies aimed at understanding TF mediated transcription.
Early and Long-Term Prognosis in Patients With and Without Type 2 Diabetes After Carotid Intervention: A Swedish Nationwide Propensity Score Matched Cohort Study
Authors: Zabala Alexander , Gottsäter Anders , Lind Marcus , Svensson Ann-Marie , Eliasson Björn , Bertilsson Rebecka , Ekelund Jan , Nyström Thomas , Jonsson Magnus 
Published: February 2021

Abstract
ObjectivesTo investigate early and long-term outcomes after treatment of carotid artery stenosis in patients with type 2 diabetes (T2D) compared to patients without T2D.Design/MethodThis observational nationwide population-based cohort study investigated all T2D patients treated for carotid stenosis registered in the National Swedish Vascular Surgery and the National Diabetes Registries. Data was collected prospectively for all patients after carotid intervention, during 2009-2015. We estimated crude early (within 30-days) hazard ratios (HRs) risk of stroke and death, and long-term HRs risk, adjusted for confounders with 95% confidence intervals (Cis), for stroke and death and major adverse cardiovascular events (MACE) by using inverse probability of treatment weighting matching.ResultsA total of 1341 patients with T2D and 4162 patients without T2D were included; 89% treated for symptomatic carotid stenosis, 96% with carotid endarterectomy. There was an increased early risk, HRs (95% CI), for stroke in T2D patients 1.65 (1.17-2.32), whereas risk for early death 1.00 (0.49-2.04) was similar in both groups. During a median follow-up of 4.3 (T2D) and 4.6 (without T2D), with a maximum of 8.0 years; after propensity score matching there was an increased HRs (95% CI) of stroke 1.27 (1.05-1.54) and death 1.27 (1.10-1.47) in T2D patients compared to patients without T2D. Corresponding numbers for MACE were 1.21 (1.08-1.35). ConclusionsPatients with T2D run an increased risk for stroke, death, and MACE after carotid intervention. They also have an increased perioperative risk for stroke, but not for death.
Defining Virus-Carrier Networks That Shape the Composition of the Mosquito Core Virome of an Ecosystem
Authors: Konstantinidis Kostantinos , Dovrolis Nikolas , Kouvela Adamantia , Kassela Katerina , Freitas Maria Goreti Rosa , Nearchou Andreas , Williams Michael de Courcy , Veletza Stavroula , Karakasiliotis Ioannis 
Published: February 2021

Abstract
BackgroundMosquitoes are the most important vectors of emerging infectious diseases. During the past decade, our understanding of the diversity of viruses they carry has greatly expanded. Most of these viruses are considered mosquito-specific, while there is increasing evidence that these viruses may affect mosquito vector potential. Metagenomics approaches have focused on specific mosquito species for the identification of what is called core virome. However, in most ecosystems, multiple species may participate in virus emergence and circulation, while there is lack of understanding on the viruses-carrier/host network for both vector-borne and mosquito-specific viruses. Results Here, we studied the core mosquito virome in a diverse ecosystem comprised of 24 different mosquito species. Analysis of these 24 diverse viromes resulted in the discovery of 35 viruses with known genetic traits and 9 novel viruses. Comparison of the viromes of the 24 individual species revealed novel relationships between mosquito species and virus families, as most of the mosquito species had never been analysed in the past. Groups of related viruses and mosquito species from multiple genera formed a complex network in the ecosystem. Analyses of whole traps of mosquitoes of variable composition not only showed a stable core virome for each species but also a relationship between mosquito population and virome composition.ConclusionsOur study highlighted the importance of a holistic approach regarding mosquito viromes in rich and diverse ecosystems. Our data further supported the idea of a stable core virome, characteristic of each mosquito species. The remarkable stability of the core virome seemed to determine the composition of the total mosquito core virome of a habitat in the ecosystem.
Ferulic Acid Inhibits Topoisomerase I of Mycobacterium Tuberculosis
Authors: Lu Nihong , Li Haiyuan , Bai Jingsong , Yang Yongrui , Ou Yangbing , Chen Yangjun , Du Yingrong 
Published: February 2021

Abstract
IntroductionVarious drugs are first line anti-TB drugs for more than thirty years. Since ferulic acid have shown promising inhibition growth of M. tuberculosis and M. smegmatis cell.ObjectiveIn this study, we have explored the inhibitory effect of ferulic acid against Mycobacterium tuberculosis topoisomerase I. We further investigated the mechanism of ferulic acid by various experiments.MethodsDNA relaxation assays was done for supercoiled pUC18 DNA, oligonucleotide cleavage assay was performed for 5ʹ-end-labeled 32-mer harboring the STS (Strong Topoisomerase Site) annealed to a complimentary sequence. Growth inhibition (MIC) values were calculated by performing resazurin reduction microplate assay (REMA).ResultsIn this study, we describe the growth inhibition of M. tuberculosis and M. smegmatis through Mycobacterium tuberculosis topoisomerase I (MttopoI) by ferulic acid. We have further investigated the mechanism of ferulic acid by analysing the two step of topoisomerase 1 (topoI) reaction cycle. Ferulic acid was able to stimulate cleavage which further leads to cleavage-relegation equilibrium. Moreover, it was shown that ferulic acid inhibited topoI overexpressing cells at low minimum inhibitory concentration (MIC). Ferulic acid affects the activity of DNA relexation in the mutations in DxDxE motif of metal binding mutants which contributes to the reaction of enzyme with the drug.ConclusionIn conclusion, our results indicate that ferulic acid leads to combat microbial infection and act as toxins to MstopoI and MttopoI. Moreover, targeting metal coordination to topoisomerases might be a general strategy to develop new lead molecules.
WITHDRAWN: Establishing and Assessing a Nomogram Based on the Clinical Features of Mucosal Melanoma of the Head and Neck
Authors: Xu Qing-Qing , Li Qing-Jie , Chen Liu , Su Xin-Yi , Song Jing-Xia , Du Juan , Chen Lei , Lu Li-Xia 
Published: February 2021

Abstract
Objectives: The rarity of mucosal melanoma of the head and neck (MMHN) and the lack of prospective clinical trials has resulted in the limited knowledge of its clinical features and prognosis. We aimed to understand the clinical characteristics and developed a nomogram to better predict the prognosis of patients with MMHN.Methods: Based on a total of 300 patients with nonmetastatic MMHN, multivariable Cox regression was performed to analyze independent prognostic factors. The overall survival (OS), disease-free survival (DFS), distant metastasis-free survival (DMFS), and locoregional relapse-free survival (LRRFS) of MMHN patients could be monitored using the nomogram. To facilitate clinical application, an online dynamic nomogram was established.Results: Multivariate analysis identified primary tumor site, T stage and N stage as independent risk factors for survival. This factor-based nomogram had prognostic value for OS, DFS, DMFS, and LRRFS. Receiver operating characteristic analysis indicated the high diagnostic accuracy of the nomogram (AUC > 0.7). Kaplan–Meier survival curves indicated that the risk score of the nomogram effectively stratified MMHN patients with poor survival into a high-risk group (all P<0.001). Conclusions: The nomogram is conducive to stratifying MMHN patients into clinically meaningful taxonomies and subsequently providing individualized treatment.
Mapping Thematic Trends and Analysing Hotspots Concerning the Use of Stem Cells for Cartilage Regeneration: a Bibliometric Analysis From 2010 to 2020
Authors: Xia Demeng , Wu Jianghong , Wu Kaiwen , Wang Sheng , Zhang Zhentao , Zhou Panyu , Xu Shuogui 
Published: February 2021

Abstract
Background: Defects of articular cartilage are a common condition that usually progresses to osteoarthritis with pain and dysfunction of the joint. Current treatment strategies have had limited success in these patients. Stem cells are emerging as a promising option for cartilage regeneration. We aim to summarize the developmental history of stem cells for cartilage regeneration and to analyse the trends and hotspots.Methods: We screened all relevant literature on stem cells for cartilage regeneration from Web of Science during 2010-2020 and analysed the research trends in this field by VOSviewer and CiteSpace. We also summarized previous clinical trials.Results: We screened 1,011 publications. China contributed the largest number of publications (317, 31.36%) and citations (81,376, 48.61%). The United States has the highest H-index (39). Shanghai Jiao Tong University had the largest number of publications (34) among all full-time institutions. The Journal of Biomaterials and Stem Cell Research & Therapy published the largest number of studies on stem cells for cartilage regeneration (35). SEKIYA I and YANG F published the majority of articles in this field (14), while TOH WS was cited most frequently (740). Regarding clinical research on stem cells for cartilage regeneration, the keyword “double-blind” emerged in recent years, with an average year of 2018.75. In tissue engineering, the keyword “3D printing” appeared latest, with an average year of 2019.625. In biological studies, the key word “extracellular vesicles” appeared latest, with an average year of 2018.9091. The current research trend indicates that basic research is gradually transforming into tissue engineering. Clinical trials have confirmed the safety and feasibility of stem cells for cartilage regeneration.Conclusions: Multiple scientific methods were employed to reveal productivity, collaborations, and research hotspots related to the use of stem cells for cartilage regeneration. 3D printing, extracellular vesicles, and double-blind clinical trials are research hotspots and are likely to be promising in the near future. Further studies are needed for to improve our understanding of this field, and clinical trials with larger sample sizes and longer follow-up periods are needed for clinical transformation.
D-shaped Photonic Crystal Fiber Based on Surface Plasmon Resonance Sensor with Metal Nanodimers Array
Authors: Jiao Shengxi , Li Xinzhi , Yang Hanrui , Fang Hairui , Xu Shibo 
Published: February 2021

Abstract
A D-shaped photonic crystal fiber (PCF) sensor with metal nanodimers array is presented and demonstrated for analyte detection with refractive index (RI) ranging from 1.28 to 1.37. In contrast to previous D-shaped PCF sensors, the coupling system is composed of Au-Ag nanodimers array, Silver (Ag) nanowires are arranged under the Gold (Au) array on the D-shaped surface, which cause the electric field within a confined volume is strongly enhanced, and the sensitivity of the surface plasmon resonance to dielectric environment of this volume to be promoted by near-field coupling. The finite element method (FEM) is adopted to numerical investigate the coupling characteristics and sensing performance of the PCF sensor in the near-infrared region. An average wavelength sensitivity (WS) of 14021 nm/RIU is attained,and a maximum WS of 16380 nm/RIU is acquired with a supernal RI resolution of 6.11×10 -6 RIU, which has an excellent application prospect in the fields of biological, biochemical and environmental detection.
The Predictive Value of the Peripheral Blood Lymphocyte-to-Monocyte Ratio in Patients with Anaplastic Large Cell Lymphoma
Authors: Zhang Shengnan , Chen Yuqing , Wang Qian , Yuan Fangfang , Ai Hao , Chen Lin , Mi Ruihua , Wei Xudong , Song Yongping , Yin Qingsong 
Published: February 2021

Abstract
BackgroundTo assess the value of the peripheral blood lymphocyte-to-monocyte ratio (LMR) in predicting the early treatment response and prognosis in patients with anaplastic large cell lymphoma (ALCL).MethodsThe optimal cut-off value for the LMR was determined using the receiver operating characteristic curve (ROC) method. The LMR was monitored dynamically, and the relationship between the LMR and therapeutic response, and survival was analyzed.Results The cumulative complete remission (CCR) rate was 57.1% in patients with low baseline LMR, remarkably lower than that for patients with high baseline LMR (80.0%) (P = 0.019). The 5-year overall survival (OS) and progression-free survival (PFS) were 51.3% and 32.6%, respectively, in the low baseline LMR group, which were significantly poorer at 90.4% and 70.5% in the high baseline LMR group, respectively (P values were 0.006 and 0.013, respectively). Furthermore, the median OS and PFS of patients with a decreased LMR after treatment were shorter than those with an elevated LMR after treatment (all P values < 0.05). Univariate and multivariate analysis demonstrated that low baseline LMR is an independent indicator for poor prognosis in ALCL patients (P values were 0.006 and 0.020, respectively). Interestingly, the combination of low baseline LMR and ALK positive could strongly predict the good prognosis in patients with ALCL. ConclusionsThe low baseline LMR and a decreased LMR after treatment are prognostic indicator for poor PFS and OS. The combination of LMR and ALK expression can widely risk-stratify patients for treatment and survival in patients with ALCL.
Impact of Diabetes in Patients Waiting for Invasive Cardiac Procedures During COVID-19 Pandemic
Authors: Moreno Raul , Diez Jose Luis , Diarte Jose Antonio , Salinas Pablo , Hernández Jose María de la Torre , Cordon Joan A , Trillo Ramiro , Alonso-Briales Juan , Amat-Santos Ignacio , Romaguera Rafael , Diaz-Fernandez Jose Francisco , Vaquerizo Beatriz , Ojeda Soledad , Cruz-Gonzalez Ignacio , Morena-Salas Daniel , de Prado Armando Perez , Sarnago Fernando , Portero Pilar , Gutierrez-Barrios Alejandro , Alfonso Fernando , Bosch Eduard , Pinar Eduardo , Ruiz-Arroyo Jose Ramon , Ruiz-Quevedo Valeriano , Jiménez-Mazuecos Jesús , Lozano Fernando , Rumoroso Jose Ramón , Novo Enrique , Irazusta Francisco J , Blanco Bruno Garcia del , Moreu José , Ballesteros-Pradas Sara M , Frutos Araceli , Villa Manuel , Alegria-Barrero Eduardo , Lazaro Rosa , Paredes Emilio 
Published: February 2021

Abstract
Background: During COVID-19 pandemic, elective invasive cardiac procedures (ICP) have been frequently cancelled or postponed. Consequences may be more evident in patients with diabetes. Objectives: The objective was to identify the peculiarities of patients with DM among those in whom ICP were cancelled or postponed due to the COVID-19 pandemic, as well as to identify subgroups in which the influence of DM has higher impact on the clinical outcome.Methods: We included 2,158 patients in whom an elective ICP was cancelled or postponed during COVID-19 pandemic in 37 hospitals in Spain. Among them, 700 (32.4%) were diabetics. Patients with and without diabetes were compared.Results: Patients with diabetes were older and had a higher prevalence of other cardiovascular risk factors, previous cardiovascular history and co-morbidities. Diabetics had a higher mortality (3.0% vs. 1.0%; p=0.001) and cardiovascular mortality (1.9% vs. 0.4%; p=0.001). Differences were especially important in patients with valvular heart disease (mortality 6.9% vs 1.7% [p<0.001] and cardiovascular mortality 4.9% vs 0.9% [p=0.002] in patients with and without diabetes, respectively). In the multivariable analysis, diabetes remained as an independent risk factor both for overall and cardiovascular mortality. No significant interaction was found with other clinical variables.Conclusion: Among patients in whom an elective invasive cardiac procedure is cancelled or postponed during COVID-19 pandemic, mortality and cardiovascular mortality is higher in patients with diabetes, irrespectively on other clinical conditions. These procedures should not be cancelled in patients with diabetes.
Fibrinolytic Markers Could Be Useful Predictors of Severity in Patients With Pulmonary Arterial Hypertension: a Retrospective Study
Authors: Shoji Makoto , Matsui Taiju , Tanaka Hideaki , Tsujita Hiroaki , Kodama Yusuke , Koba Shinji , Kobayashi Youichi , Shinke Toshiro 
Published: February 2021

Abstract
Background: The severity of pulmonary arterial hypertension (PAH) is classified based on mean pulmonary artery pressure (mPAP) levels. However, other markers have not been elucidated. Fibrinolytic markers, such as total plasminogen activator inhibitor-1 (tPAI-1) and thrombomodulin (TM), are known to reflect arterial endothelial function. However, the relationship between serum tPAI-1, TM and pulmonary circulation has not been completely determined. Methods: This study included 100 consecutive patients (38 men), with a mean age of 68.9±12.0 years, with cardiac diseases who underwent right heart catheterization. Serum coagulation and fibrinolytic marker levels were measured.Results: The average mPAP value was 25.1±13.1 mmHg for all patients. The mPAP levels revealed a significant positive correlation with serum tPAI-1 (ρ=0.24, p=0.042) and uric acid (ρ=0.29, p=0.0031) levels. In the group with mPAP levels less than 25 mmHg (n=58, ave. 17.3±4.3 mmHg), mPAP levels showed a significant positive correlation with serum tPA-1 (ρ=0.34, p=0.034) and TM (ρ=0.34, p=0.043) values. The mean tPAI-1 (29.8±23.3 ng/ml, p=0.047) and uric acid (5.7±1.8 mg/dl, p=0.026) levels were significantly less in those with lower mPAP levels. A multivariate analysis revealed that tPAI-1 alone was a significant independent characteristic marker of PAH (odds ratio 1.02, 95%CI 1.000-1.036, p=0.034).Conclusions: These results indicate that serum tPAI-1 and TM may be useful predictors of severity, similar to mPAP in patients with PAH. They could be beneficial in predicting PAH among patients in the early stage of the disease.
Long-term population trends of the lesser horseshoe bat Rhinolophus hipposideros and the greater mouse-eared bat Myotis myotis in Poland
Authors: Węgiel Andrzej , Grzywiński Witold , Kosicki Jakub Z. , Tryjanowski Piotr , Nowak Jakub , Węgiel Jolanta 
Published: February 2021

Abstract
Bats are particularly susceptible to environmental changes because of their low reproductive rate, longevity, and high metabolic rates, which lead to relatively high food requirements. Thus, bat populations take a relatively long time to recover from increased mortality rates, and monitoring schemes should cover long time periods. In this work we analyzed the population trajectories of two bat species, Rhinolophus hipposideros and Myotis myotis, the most numerous in five caves in southern Poland, which are known as important bat hibernacula on a continental scale. Data were collected by regular counts in 1985–2001, depending on the particular cave; in addition, previous data on the number of hibernating bats in these caves, available since 1951, were taken from existing publications. We analyzed time-series data using average locality indices and TRIM methods, and both produced similar results. Generally, the populations of the two studied bat species showed recent increasing trends, especially visible as an effect of recovery after years of decline. The situation recorded in southern Poland is very similar to that described in other places in Europe, where recoveries of bat populations have also been observed in the last decades. Although it is difficult to present results from formal analyses, because of the lack of good data, at least some factors—less exposure to contaminants (pesticides, heavy metals), improving food availability due to climate change, and a lower predation rate (including human pressure), both in the breeding season and during wintering—positively affected both species.
pmTR database: population matched (PM) germline allelic variants of T-cell receptor (TR) loci
Authors: Dekker Julian , Dongen Jacques J.M. , Reinders Marcel J.T. , Khatri Indu 
Published: February 2021

Abstract
T-cell receptor (TR) germline allele sequences are arranged, organized and made available to the research community by the IMGT database. This state-of-the-art database, however, does not provide information regarding population specificity and allelic frequencies of the four human TR loci (TRA, TRB, TRG and TRD). The specificity of allelic variants to different human populations can, however, be a rich source of information when studying the genetic basis of population-specific immune responses in disease and in vaccination. To make TR germline alleles available for such population-specific studies, we meticulously identified true germline alleles enriched with complete TR allele sequences and their frequencies across 26 different human populations, profiled by “1,000 Genomes data”. We identified 205 TRAV, 249 TRBV, 16 TRGV and 5 TRDV germline alleles supported by at least four haplotypes (= minimum of two unrelated individuals). The diversity of germline allelic variants in the TR loci is highest in Africans, while the majority of the Non-African alleles are specific to the Asian populations, suggesting a diverse profile of TR germline alleles in different human populations. Interestingly, the alleles known in the IMGT database are frequent and common across all five super-populations. We believe that this new set of genuine germline TR sequences represents a valuable new resource which we have made available through the new population-matched TR (pmTR) database, accessible via https://pmtrig.lumc.nl/.