bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heavy Metal Contamination of Urban Mangrove Sediments and Their Environmental Significance in the Zhanjiang Bay
Authors: Zhou Xun , Wang Yao-Ping , Gao Yuan , Xia Jia , Wang Sibo , Song Zhiguang 
Published: December 2021

Abstract
Urban mangroves can be used to measure the impact of human activities on the urban ecological environment because mangroves are sensitive to human activities. However, studies on the evaluation of heavy metal elements in urban mangroves are still limited. Consequently, this study selected the urban mangroves in a central commercial area of Zhanjiang Bay as a case study to investigate the content and distribution of the heavy metal elements in mangrove sediments. Combined with the results of elemental analysis, grain size analysis, risk level, influencing factors, and sources of heavy metal pollution in the surficial sediments of the mangroves in the study area were evaluated based on mathematical models and multivariate statistical analysis. The results show that (1) concentration of heavy metals: V> Pb> Cu> Ni> As> Co> Cd> Hg; (2) the content of the eight heavy metal elements has a significant positive correlation with total organic carbon (TOC) and total nitrogen (TN) values, likely as a result of adsorption, complexation, or precipitation of heavy metals by organic matter in the sediments; (3) the mangrove sediments in the study area are affected by heavy metal pollution, among which Cd pollution is the heaviest, followed by Hg pollution; (4) comprehensive analyses of multiple heavy metals using Potential Ecological Risk Index shows that the risk level of the study area is slight to very strong ecological risk; (5) the heavy metals in the study area are mainly derived from human activities such as urban domestic sewage, transportation, and ship pollution.
The Persistence of Natural SARS-CoV-2 Antibodies 12 Months Post COVID-19, a Prospective Cohort Study.
Authors: Jurgens F. , Hogema B. , Siegerink S. , Samwel L. , Gils R. van , Albers S. , Pettai F. , Laar T. van , Molier M. , Thiesbrummel H. , Bresser P. , Brinkman K. 
Published: December 2021

Abstract
Background: It is unknown how long SARS-CoV-2 antibodies persist after COVID-19. The natural course of anti-SARS-CoV-2 antibodies was analyzed in a large post-COVID-19 cohort, until 12 months post-infection. Methods: The total antibodies SARS-CoV-2 (IgM and IgG) were tested in a cohort of patients with different COVID-19 disease severity sampled at 4 timepoints up to 12 months post COVID-19. In 23 randomly selected patients, the antibody isotypes: anti-spike IgM, IgA and IgG and anti-nucleocapsid IgG were analysed. Results: In total 152/153 patients (99%) tested positive for total anti-SARS-CoV-2 after 12 months of COVID-19; 3 patients tested positive at 8 to 10 months post infection just before vaccination. The SARS-CoV-2 antibody subclasses anti-nucleocapsid IgG, anti-spike IgG and IgA were all still detectable after 12 months. Anti-spike IgM waned after 12 months in the majority of patients.Conclusion: IgG and IgA antibodies against SARS-CoV-2 persisted 12 months post-COVID-19.
A Comparison of mRNA Sequencing (RNA-Seq) Library Preparation Methods for Transcriptome Analysis
Authors: Ura Hiroki , Togi Sumihito , Niida Yo 
Published: December 2021

Abstract
Background
mRNA sequencing is a powerful technique, which is used to investigate the transcriptome status of a gene of interest, such as its transcription level and splicing variants. Presently, several RNA sequencing (RNA-Seq) methods have been developed; however, the relative advantage of each method has remained unknown. Here we used three commercially available RNA-Seq library preparation kits; the traditional method (TruSeq), in addition to full-length double-stranded cDNA methods (SMARTer and TeloPrime) to investigate the advantages and disadvantages of these three approaches in transcriptome analysis.
Results
We observed that the number of expressed genes detected from the TeloPrime sequencing method was fewer than that obtained using the TruSeq and SMARTer. We also observed that the expression patterns between TruSeq and SMARTer correlated strongly. Alternatively, SMARTer and TeloPrime methods underestimated the expression of relatively long transcripts. Moreover, genes having low expression levels were undetected stochastically regardless of any three methods used. Furthermore, although TeloPrime detected a significantly higher proportion at the transcription start site (TSS), its coverage of the gene body was not uniform. SMARTer is proposed to be yielded for nonspecific genomic DNA amplification. In contrast, the detected splicing event number was highest in the TruSeq. The percent spliced in index (PSI) of the three methods was highly correlated.
Conclusions
TruSeq detected transcripts and splicing events better than the other methods and measured expression levels of genes, in addition to splicing events accurately. However, although detected transcripts and splicing events in TeloPrime were fewer, the coverage at TSS was highest. Additionally, SMARTer was better than TeloPrime among the understudied full-length double-stranded cDNA methods. In conclusion, for short-read sequencing, TruSeq has relative advantages for use in transcriptome analysis.
Generation of Dystrophin Short Product-Specific Tag-Insertion Mouse: Distinct Dp71 Glycoprotein Complexes at Inhibitory Postsynapse and Glia Limitans
Authors: Fujimoto Takahiro , Yaoi Takeshi , Nakano Kenta , Arai Tetsuya , Okamura Tadashi , Itoh Kyoko 
Published: December 2021

Abstract
Duchenne muscular dystrophy (DMD), the most severe form of dystrophinopathies, is a fatal X-linked recessive neuromuscular disorder characterized by progressive muscle degeneration and various extents of intellectual disabilities. Physiological and pathological roles of the responsible gene, dystrophin, in the brain remain elusive due to the presence of multiple dystrophin products, mainly full-length dystrophin, Dp427, and the short product, Dp71. In this study, we generated a Dp71-specific hemagglutinin (HA) peptide tag-insertion mice to enable specific detection of intrinsic Dp71 expression by anti-HA tag antibodies. Immunohistochemical detections in the transgenic mice demonstrated Dp71 expression not only at the blood-brain barrier, where astrocytic endfeet surround the microvessels, but also at the inhibitory postsynapse of hippocampal dentate granule neurons. Interestingly, hippocampal cornu ammonis (CA)1 pyramidal neurons were negative for Dp71 although Dp427 detected by anti-dystrophin antibody was clearly present at the inhibitory postsynapse, suggesting cell-type dependent dystrophin expressions. Precise examination using the primary hippocampal culture validated exclusive localization of Dp71 at the inhibitory postsynaptic compartment but not at the excitatory synapse in neurons. We further performed interactome analysis and found that Dp71 formed distinct molecular complexes, i.e. synapse-associated Dp71 interacted with dystroglycan (Dg) and dystrobrevinb (Dtnb) whereas glia-associated Dp71 did with Dg and dystrobrevina (Dtna). Thus, our data indicates that Dp71 and its binding partners are relevant to the inhibitory postsynaptic function of hippocampal granule neurons and the novel Dp71-transgenic mouse provides a valuable tool to understand precise physiological expressions and functions of Dp71 and its interaction proteins in vivo and in vitro.
Systematic Evaluation of the Safety and Therapeutic Effects of Para-aortic Lymphadenectomy for Advanced Gastric Cancer: a Systematic Review and Meta-analysis
Authors: Ge Jie , Liao Xiaofeng , Tang Mimi , Yang Zhiyun , Zhao Tingyu , Liu Heli 
Published: December 2021

Abstract
Background: At present, there is still no definite conclusion on whether advanced gastric cancer requires additional para-aortic nodes dissection (PAND). The purpose of this study is an attempt to provide significant data to guide clinical decision-making. Methods: The literature was searched using the terms of gastric cancer, para-aortic lymphadenectomy and D2+ lymphadenectomy and D3 lymphadenectomy. The databases searched included PubMed, Embase, Cochrane library, Web of Science, China National Knowledge Infrastructure, Wanfang Data Knowledge Service Platform, VIP Database for Chinese Technical Periodicals, and China Biology Medicine disc. RevMan 5.3 software was used for the meta-analysis.Results: In total, 20 studies were included, consisting of 6 randomized controlled trials (RCT) and 14 non-randomized controlled trials (nRCT). These studies involved 5643 patients. The meta-analysis showed the following results: (1) compared with group D2 (D2 lymphadenectomy), the operating time in group D2+ (D2+ lymphadenectomy) was longer [mean difference (MD)=99.45 min, 95% confidence interval (CI) (48.93, 149.97), P<0.001], with more intra-operative blood loss [MD=262.14 mL, 95%CI (165.21, 359.07), P<0.001]; (2) there were no significant differences in five-year overall survival [HR=1.09, 95%CI (0.95, 1.25), P=0.22] and post-operative mortality [RR=0.96, 95%CI (0.59, 1.57), P=0.88] between the two groups; (3) the rate of post-operative complication in group D2+ was higher than that in group D2 [RR=1.42, 95%CI (1.11, 1.81), P<0.001]. Conclusions: It is noteworthy that the combination of perioperative chemotherapy and D2+ surgery, particularly D2+ PAND, shows some survival advantages for specific patients. Although prophylactic D2+ surgery is not recommended as it increases postoperative complications and does not improve long-term survival in patients with advanced gastric cancer.
Research on Security Risk Assessment Mechanism of Important Event Based on Multi-Source Data
Authors: Wang Qilei 
Published: December 2021

Abstract
In order to effectively assess all types of security risks in the important event, the important decision-making basis for security risk warning and emergency management of important event is provided by analyzing the coupling relationship and evolution mechanism between various risks. The criminal causes, management defects, security and emergency system construction are analyzed from the possibility of accidents and risks. The multi-source data risk assessment system based on five subsystems and its index set of human factors, management factors, site factors, event factors and audit factors are proposed. The weight of each index in the assessment system is determined by the method of information entropy, and then the risk grade of important event is determined according to the weight calculation function and the improved fuzzy matter element model. The verification with an example shows that: the risk assessment model is optimized by combining entropy weight with fuzzy matter-element model，the influence of weight data extreme value was weakened，the qualitative description and quantitative analysis of multi-source data could be combined，and the subjective error was reduced. The risk grade of important event is reasonably evaluated, and the assessment effect is basically consistent with the expert inspection analysis, which shows that the method had certain application value.
Integrated Omics Approach to Unveil Antifungal Bacterial Polyynes as acetyl-CoA Acetyltransferase Inhibitors
Authors: Lin Ching-Chih , Hoo Sin Yong , Ma Li-Ting , Lin Chih , Huang Kai-Fa , Ho Ying-Ning , Sun Chi-Hui , Lee Han-Jung , Chen Pi-Yu , Shu Lin-Jie , Wang Bo-Wei , Hsu Wei-Chen , Ko Tzu-Ping , Yang Yu-Liang 
Published: December 2021

Abstract
Bacterial polyynes are highly active natural products with a broad spectrum of antimicrobial activities. However, their detailed mechanism of action remains unclear. By integrating comparative genomics, transcriptomics, functional genetics, and metabolomics analysis, we identified a unique polyyne resistance gene, masL (encoding acetyl-CoA acetyltransferase), in the biosynthesis gene cluster of antifungal polyynes (massilin A 1, massilin B 2, collimonin C 3, and collimonin D 4) of Massilia sp. YMA4. Crystallographic analysis indicated that bacterial polyynes serve as covalent inhibitors of acetyl-CoA acetyltransferase. Moreover, we confirmed that the bacterial polyynes disrupted cell membrane integrity and inhibited cell viability of Candida albicans by targeting ERG10, the homolog of MasL. Thus, this study demonstrated that acetyl-CoA acetyltransferase is a potential target for the development of antifungal agents.
Phylogenetic Analysis of Canonical/non-canonical Dicers and RNase III Containing Proteins in Fungal Kingdom
Authors: Wu Jiayao , Choi Jaeyoung , Asiegbu Fred O. , Lee Yong-Hwan 
Published: December 2021

Abstract
Background: Dicers were member of RNase III containing proteins family with important RNAi function in eukaryotes. In this study, we tried to address the potential distribution of all RNase III containing proteins among the fungal kingdom, as well as their possible evolution paths including canonical Dicers, non-canonical Dicers and non-canonical Dicer-like proteins.Result: RNase III containing proteins were collected from 83 species, and discussed the features and possible evolution pathways of RNase III containing protein family. In general, RNase III containing protein family could be characterized into three different groups as canonical Dicer, non-canonical Dicers and Dicer-like proteins based on their domain structures and functional annotation. Most eukaryotes obtained multiple RNase III protein of different types at the same time, including canonical Dicers and Dicer-like proteins. Phylogenetic analysis showed that the RNase III domains were different between canonical Dicers and Dicer-like proteins, for the first and second RNase III domains had different insertions in different regions with certain extent of conservation. Regardless of the types, RNA-binging domains in RNase III protein family were very similar to each other. Furthermore, short insertions were found in different positions from the first and second RNase III domains in canonical Dicers separately. RNA-binging domains from all types were quite similar to each other.Conclusion: RNase III containing proteins in general widely exist in eukaryotes with minor divergent among different types and groups. Suggested by the RNase III and RDB domains, the canonical/non-canonical Dicers Dicer-like proteins might share the same ancestor and have evolved from separate mild-types through different directions.
Comparative Transcriptome Analysis of Rice Cultivars Resistant and Susceptible to Rhizoctonia Solani AG1-IA
Authors: Wang Yan , Luo Hang , Wang Haining , Xiang Zongjing , Wei Songhong , Zheng Wenjing 
Published: December 2021

Abstract
Background: Rice sheath blight, which is caused by Rhizoctonia solani, is the most destructive disease affecting rice production, but the resistance mechanism to this pathogen has not been fully elucidated. Results: In this study, we selected two rice cultivars based on their resistance to the pathogen and analyzed and compared the transcriptomic profiles of two cultivars, the moderately resistant variety Gangyuan8 and the highly susceptible variety Yanfeng47, at different time points after inoculation. The comparative transcriptome profiling showed that the expression of related genes gradually increased after pathogen inoculation. The number of differentially expressed genes (DEGs) in Yanfeng47 was higher than that in Gangyuan8, and this result revealed that Yanfeng47 was more susceptible to fungal attack. At the early stage (24 and 48 h), the accumulation of resistance genes and a resistance metabolism occurred earlier in Ganguan8 than in Yanfeng47, and the resistance enrichment entries were more abundant in Ganguan8 than in Yanfeng47. Conclusions: Based on the GO and KEGG enrichment analyses at five infection stages, we concluded that phenylalanine metabolism and the jasmonic acid pathway play a crucial role in the resistance of rice to sheath blight. Through a comparative transcriptome analysis, we preliminarily analyzed the molecular mechanism responsible for resistance to sheath blight in rice, and the results lay the foundation for the development of gene mining and functional research on rice resistance to sheath blight.
Subglacial sedimentary basins focus key vulnerabilities of the Antarctic ice-sheet
Authors: Li Lu , Aitken Alan , Lindsay Mark , Kulessa Bernd 
Published: December 2021

Abstract
Antarctica preserves Earth’s largest ice sheet which, in response to climate warming, may lose ice mass and raise sea level by several metres. The ice-sheet bed exerts critical controls on dynamic mass loss through feedbacks between water and heat fluxes, topographic forcing and basal sliding. Here we show that through hydrogeological processes, sedimentary basins amplify critical feedbacks that are known to impact ice-sheet retreat dynamics. We create a high-resolution subglacial bedrock classification for Antarctica by applying a supervised machine learning method to geophysical data, revealing the distribution of sedimentary basins. Sedimentary basins are found in the upper reaches of Antarctica’s most rapidly changing ice streams, including Thwaites and Pine Island Glaciers. Hydro-mechanical numerical modelling reveals that where sedimentary basins exist, water discharge rate scales with the rate of ice unloading and the resulting hydrological instabilities are likely to amplify further retreat and unloading. These results indicate that the presence of a sedimentary bed in the catchment focuses instabilities that increase the vulnerability of the ice streams to rapid retreat and enhanced dynamic mass loss.
Real Life Comparison of Afatinib and Erlotinib in Non-small Cell Lung Cancer With Rare EGFR Exon 18 and Exon 20 Mutations: a Turkish Oncology Group (TOG) Study.
Authors: Gürsoy Pınar , Tatlı Ali Murat , Erdem Dilek , Goker Erdem , Çelik Emir , Demirci Nebi Serkan , Sakin Abdullah , Atçı Muhammed Mustafa , Bayram Ertuğrul , Telli Tuğba Akın , Bilgin Burak , Bilici Ahmet , Akagündüz Baran , Ballı Sevinç , Demirkazık Ahmet , Selcukbiricik Fatıh , Menekşe Serkan , Cavdar Eyyup , Öztürk Akın , Bekmez Esma Türkmen , Turhal Serdal , Kılıçkap Saadettin , Yıldırım Hasan Çağrı , Oyan Başak , Aksoy Asude , TURKOZ Fatma Paksoy , Kut Engin , Katgı Nuran , Sakalar Teoman , Akyol Murat , Ellez Halil İbrahim , Topcu Atakan , Erdoğan Atike Pınar , Pilancı Kezban Nur , Hedem Engin , Arak Hacı , Akdeniz Nadiye , Alan Özkan , Yapar Burcu , Nart Deniz , Yumuk Perran Fulden 
Published: December 2021

Abstract
Objectives To compare the survival of first- and second-generation tyrosine kinase inhibitors (TKIs) in patients with rare EGFR exon 18 and exon 20 mutation-positive non-small cell lung cancer (NSCLC).Materials and Methods We retrospectively evaluated survival characteristics of 125 patients with EGFR exon 18 and exon 20 mutated NSCLC who received erlotinib or afatinib as first line treatment between 2012 and 2021 from 34 oncology centres. Since exon 20 insertion is associated with TKI resistance, these 18 patients were excluded from the study.Results EGFR exon 18 mutations were seen in 60%, exon 20 mutations in 16%, and complex mutations in 24% of the patients with NSCLC who were evaluated for the study. There were 75 patients in erlotinib treated arm and 50 patients in afatinib arm. Patients treated with erlotinib had progression-free survival time (PFS) of 8.0 months and PFS was 7.0 months in the afatinib arm (p=0.869), while overall survival time (OS) was 20.0 vs 24.8 months, respectively (p=0.190). PFS of exon 18 mutated arm was 7.0 months, exon 20 mutated arm was 4.3 months, and complex mutation positive group was 17.3 months, and this was statistically significant (p=0.036). The longest OS was 32.5 months, seen in the complex mutations group, which was not statistically different than exon 18 and in exon 20 mutated groups (21.0 and 21.2 months, respectively) (p=0.323).Conclusion In this patient group, especially patients with complex mutations are as sensitive to EGFR TKI treatment similar to classical mutations, and in patients with rare exon 18 and exon 20 EGFR mutation both first- and second-generation EGFR-TKIs should be considered, especially as first- and second-line options.
Uterine Factors Modify the Association Between Embryo Transfer Depth and Clinical Pregnancy: A Retrospective Study in 7849 Fresh Transfer In Vitro Fertilization Cycles
Authors: Sun Xiaohua , Cai Jiali , Liu Lanlan , Chen Haixiao , Jiang Xiaoming , Ren Jianzhi 
Published: December 2021

Abstract
The embryo position is supposed to affect implantation following embryo transfer. However, embryo dislodging caused by uterine contraction may occurred after transfer. The retrospective study was to investigated whether the factors associated with uterine contractility, such as endometrial thickness and progesterone elevation, affect the association between embryo position and implantation. A total of 7849 fresh transfer cycles on conventional stimulation in a single IVF centre during the period 2013–2015 was reviewed. Patients were categorized according to quartiles of embryo-fundus distance (≤9, 9.1-11, 11.1-14, ≥1.4 mm, respectively). Adjusted for confounding factors, the odds ratio (OR) (95%CI) for clinical pregnancy was 0.90 (0.79-1.02), 0.86 (0.74-0.99) and 0.70 (0.60-0.82) respectively in quartiles 2 through 4, comparing with quartile 1. However, ORs were significantly increased when endometrial thickness was < 8 mm. The ORs comparing quartiles 2 through 4 with quartile 1 increased 1.96 (95%: 1.33-2.90), 1.20 (95%: 0.78-1.87) and 1.98 (95%: 1.20-3.26) fold respectively in cycles with an endometrial thickness < 8 mm than in cycles with a normal endometrial thickness (8-11 mm). Elevated progesterone on the day of hCG and blastocyst stage transfer reduced the ORs. Our data suggested an interaction between patient characteristics and embryo transfer techniques.
Short-term, Low-Dose Etoposide in Refractory Adult-Onset Still’s Disease-Associated Macrophage Activation Syndrome, a Case Series Study
Authors: Wang Ran , Li Ting , Ye Shuang , Lv Liangjin , Chen Sheng , Wang Xiaodong , Bao Chun-de , Fu Qiong 
Published: December 2021

Abstract
Objectives:In this study, we modified the classical regimen of the hemophagocytic lymphohistiocytosis-04 protocol and evaluated the efficacy and safety of short-term, low-dose etoposide in patients with refractory macrophage activation syndrome (MAS) associated with adult-onset Still’s disease (AOSD).Methods:A total of 17 patients with refractory AOSD-associated MAS were enrolled and received short-term, low-dose etoposide (100 mg twice a week for four times). Another 11 patients, who were not treated with etoposide, were included as historical controls. Patient information, such as clinical manifestations, laboratory results, treatments, and short-term prognosis, were recorded and analyzed.Results:In this case series, 88.24% of the patients with MAS who were treated with short-term, low-dose etoposide had a favorable response in 3 weeks, which was significantly higher (p = 0.017) than that in the patients with MAS who were treated without etoposide (45.45%). The 90-day survival rate after the onset of MAS was significantly higher (p = 0.0029) among the patients in the short-term etoposide group (16/17, 94.12%) than in the control group (5/11, 45.45%). Conclusion:The regimen of short-term (2-week), low-dose etoposide was highly effective in the treatment for patients with refractory AOSD associated MAS with an acceptable safety profile.