bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep Learning Approach for Classifying the Aggressive Comments on Social Media: Machine Translated Data Vs Real Life Data
Authors: akter shapna , Ahmed Nova 
Published: April 2022

Abstract
Aggressive comments on social media negatively impact human life. Such offensive contents are responsible for depression and suicidal-related activities. Since online social networking is increasing day by day, the hate content is also increasing. Several investigations have been done on the domain of cyberbullying, cyberaggression, hate speech, etc. The majority of the inquiry has been done in the English language. Some languages (Hindi and Bangla) still lack proper investigations due to the lack of a dataset. This paper particularly worked on the Hindi, Bangla, and English datasets to detect aggressive comments and have shown a novel way of generating machine-translated data to resolve data unavailability issues. A fully machine-translated English dataset has been analyzed with the models such as Long Short term memory model (LSTM), Bidirectional Long-short term memory model (BiLSTM), LSTM-Autoencoder, word2vec, Bidirectional Encoder Representations from Transformers (BERT), and generative pre-trained transformer (GPT-2) to make an observation on how the models perform on a machine-translated noisy dataset. We have compared the performance of using the noisy data with two more datasets, such as raw data, which does not contain any noises, and semi-noisy data, which contains a certain amount of noisy data. We have classified both the raw and semi-noisy data using the aforementioned models. To evaluate the performance of the models, we have used evaluation metrics such as F1-score, accuracy, precision, and recall. We have achieved the highest accuracy on raw data using the gpt2 model, semi-noisy data using the BERT model, and fully machine-translated data using the BERT model. Since many languages do not have proper data availability, our approach will help researchers create machine-translated datasets for several analysis purposes.
Necdin inhibits the proliferation of osteosarcoma cells by regulating the expression of VEGFA
Authors: Wu Zhuangzhuang , Chen Shiwei , Jin Wenxuan , Feng Yi , Li Pengcui , Guo Li , Bai Junjun , Qiao Xiaochen , Yang Meiju , Lv Zhi 
Published: April 2022

Abstract
Necdin (NDN) acts as a tumor suppressor gene in some malignant tumors, but it is unclear about the role of NDN in osteosarcoma (Osteosarcoma, OS). The results show that the expression level of NDN is low, while that of vascular endothelial growth factor A (VEGFA) is significantly up-regulated in OS cells and tissues. Overexpression of NDN can accelerate apoptosis of OS cells making them less invasiveness, and reduce the tubular shape of human umbilical vein endothelial cells. Meanwhile, the overexpression of NDN can inhibit the expression of VEGFA. Bioinformatics analysis demonstrates that there is no noticeable relationship between NDN and VEGFA and no statistical significance. The studies in vivo further confirmed that NDN could inhibit tumor growth and angiogenesis in xenograft nude mice. Our results show that NDN is a potential tumor suppressor in OS, and it can inhibit tumor angiogenesis by regulating VEGFA. Therefore, NDN may be a new biomarker for the prognosis and a new target for treatment of OS.
Amyotrophic Lateral Sclerosis and Cerebellum
Authors: Kabiljo Renata , Iacoangeli Alfredo , Al-Chalabi Ammar , Rosenzweig Ivana 
Published: April 2022

Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating, heterogeneous neurodegenerative neuromuscular disease that leads to a fatal outcome within two to five years, and yet, a precise nature of the association between its major phenotypes and the cerebellar role in ALS pathology remains unknown. Recently, repeat expansions in several genes in which variants appreciably contribute to cerebellar pathology, including C9orf72, NIPA1, ATXN2 and ATXN1, have been found to confer a significant risk for ALS. To better define this relationship, we performed MAGMA gene-based analysis and tissue enrichment analysis using genome-wide association study (GWAS) summary statistics based on a study of 27205 people with ALS and 110881 controls. Our preliminary results imply a striking cerebellar tissue specificity and further support increasing calls for re-evaluation of the cerebellar role in the ALS pathology.
Redox-dependent Structural Origin of the Temperature Threshold and Sensitivity in the TRPV3 Thermometer
Authors: Wang Guangyu 
Published: April 2022

Abstract
The DNA hairpin with a limited size is sensitive to temperature. However, it is unclear if thermosensitive TRP channels also use temperature-dependent hairpin sizes to govern their activation temperature thresholds and sensitivity. Here, graph theory, together with redox- and state-dependent cryo-electron microscopy structures of TRPV3 with or without the Y564A mutation at different temperatures, was to test this hypothesis. The results showed that the largest hairpin topological loop size and a change in total hairpin sizes along the channel gating pathway control the temperature threshold and sensitivity, respectively. This size-dependent hairpin thermodynamics may mediate the thermal activity of biological macromolecules.
Amplification of integrated microscopic motions of high-density [2]rotaxanes in mechanically interlocked networks
Authors: Yang Xue , Cheng Lin , Zhang Zhaoming , Zhao Jun , Bai Ruixue , Guo Zhewen , Yu Wei , Yan Xuzhou 
Published: April 2022

Abstract
Integrating individual microscopic motion to perform tasks in macroscopic sale is common in living organisms. However, developing artificial materials in which molecular-level motions could be amplified to behave macroscopically is still challenging. Herein, we present a class of mechanically interlocked networks (MINs) carrying densely rotaxanated backbones as a model system to understand macroscopic mechanical properties stemmed from the integration and amplification of intramolecular motion of the embedded [2]rotaxane motifs. On the one hand, the motion of mechanical bonds introduces the original dangling chains into the network, and the synergy of numerous such microscopic motions leads to an expansion of entire network, imparting good stretchability and puncture resistance to the MINs. On the other hand, the dissociation of host−guest recognition and subsequent sliding motion represent a peculiar energy dissipation pathway, whose integration and amplification result in the bulk materials with favorable toughness and damping capacity. Thereinto, we develop a continuous stress-relaxation method to elucidate the microscopic motion of [2]rotaxane units, which contributes to the understanding of the relationship between cumulative microscopic motions and amplified macroscopic mechanical performance. The fundamental insights gained from the study of high-density mechanically bonded networks would facilitate the fabrication and application of mechanically interlocked materials.
Two novel Erwinia amylovora bacteriophages Loshitsa2 and Micant, isolated in Belarus
Authors: Besarab Natalya , Letarov Andrey V. , Kulikov Eugene E. , Babenko Vladislav V. , Belalov Ilya S. , Lagonenko Alexander L. , Golomidova Alla K. , Evtushenkov Anatoly N. 
Published: April 2022

Abstract
The complete genomes of new Erwinia amylovora bacteriophages, Loshitsa2 and Micant, are 43092 bp and 43028 bp, respectively, encode 51 putative proteins and have two tRNA genes. Comparative analysis with Caudovirales representatives suggests that Loshitsa2 and Micant bacteriophages are related to LIMElight bacteriophage within the family Autographiviridae, and could be proposed to share novel subfamily.
A de novo assembled high-quality chromosome-scale Trifolium pratense genome and fine-scale phylogenetic analysis
Authors: Yan Zhenfei , Sang Lijun , Ma Yue , He Yong , Sun Juan , Ma Lichao , Li Shuo , Miao Fuhong , Zhang Zixin , Wang Zengyu , Yang Guofeng 
Published: April 2022

Abstract
Background: Red clover (Trifolium pratense L.) is a diploid perennial temperate legume with 14 chromosomes (2n=14) native to Europe and West Asia, with high nutritional and economic value. It is a very important forage grass and is widely grown in marine climates, such as the United States and New Zealand. Genetic research and molecular breeding are limited by the lack of high-quality reference genomes. In this study, we used Illumina, PacBio HiFi, and Hi-C to obtain a high-quality chromosome-scale red clover genome and used genome annotation results to analyze evolutionary relationships among related species. Results: The red clover genome obtained by PacBio HiFi assembly sequencing was 423 M. The assembly quality was the highest among legume genome assemblies published to date. The contig N50 was 13 Mb, scaffold N50 was 55 Mb, and BUSCO completeness was 97.9%, accounting for 92.8% of the predicted genome. Genome annotation revealed 44,588 gene models with high confidence and 52.81% repetitive elements in red clover genome. Based on a comparison of genome annotation results, red clover was closely related to Trifolium medium and distantly related to Glycine max, Vigna radiata, Medicago truncatula, and Cicer arietinum among legumes. Analyses of gene family expansions and contractions and forward gene selection revealed gene families and genes related to environmental stress resistance, protein synthesis, and energy metabolism.Conclusions: We report a high-quality de novo genome assembly for the red clover at the chromosome level, with a substantial improvement in assembly quality over those of previously published red clover genomes. These annotated gene models can provide an important resource for molecular genetic breeding and legume evolution studies. Furthermore, we analyzed the evolutionary relationships among red clover and closely related species, providing a basis for evolutionary studies of clover leaf and legumes, genomics analyses of forage grass, the improvement of agronomic traits.
Strong linkage of carbon and nitrogen mineralization in rhizosphere soils along an altitudinal forest gradient of Changbai Mountain
Authors: Huo changfu , Lu Jiayu , Yin Liming , Wang Peng , Cheng Weixin 
Published: April 2022

Abstract
Aims
Rhizosphere is a hotspot for soil C and N biogeochemical cycling in terrestrial ecosystems. Our understanding of interaction between C and N mineralization mainly comes from the bulk soils, yet it is unknown the interaction in the rhizosphere soils. The study aimed to identify interactions between soil C and N mineralization in paired rhizosphere soils and bulk soils.
Methods
We used the “soil adhering to fine roots after shaking” method to collect paired rhizosphere soils and bulk soils along an altitudinal forest gradient. Soil C mineralization rates (Cmin) and net N mineralization rates (Nmin) were determined with laboratory incubation.
Results
We found a strong positive relationship between Cmin and Nmin in the rhizosphere soils across sites, whereas Cmin was not correlated with Nmin in the bulk soils. Furthermore, soil properties, microbial biomass C (MBC) and extracellular enzyme activities showed substantial paths affecting Cmin and Nmin using structural equation model. The coupling of Cmin and Nmin in rhizosphere soils could be triggered by root-soil interactions, resulting in the higher level of MBC, soil total C, soil total N, extracellular enzyme activities and specific microbial community structure. By contrast, the decoupling of Cmin and Nmin in the bulk soils might be attributed to the lower level of MBC and extracellular enzyme activities.
Conclusions
Our results demonstrated that soil C and N mineralization coupled in the rhizosphere rather than the bulk soils. These results highlight the need to distinguish rhizosphere from bulk soils for simulating soil C and N cycling in terrestrial ecosystems.
Evidence-based analysis of the SARS-CoV-2 furin site origin
Authors: Romeu Antonio R. 
Published: April 2022

Abstract
The origin of the SARS-CoV-2 is still unclear. Simply said, its emergence is due to the acquisition of the polybasic furin cleavage site on the S protein in one of its closest relatives. The recent discovery in Laos of bat Rhinolophus coronaviruses that contain receptor binding domains almost identical to that of SARS-CoV-2, and despite not having the furin site, they can therefore infect human cells (1), is the cornerstone to identify the SARS-CoV-2 progenitor. However, it is not yet known where the insertion of the furin site at the S1/S2 junction in the S protein of the pandemic virus came from. Not only from where, but also how, where and when of such acquisition. The most surprising was: (i) that the polybasic furin cleavage site is unique to SARS-CoV-2 among Sarbecovirus (2), and (ii) that the inserted four amino acid motif has a CGG-CGG encoded arginine pair which is rare in coronaviruses (3). So, my question is if the SARS-CoV-2 insert in the S gene insert would match to human transcripts. Here, I address this issue by using NCBI and GISAID databases, the NCBI Human Genome Resources, sequence analysis tools and in-house developed bioinformatic tools. I found that the 12-nucleotide insert encoding SARS-CoV-2 furin site 100% match to several human transcripts. Taken together the presence of these human transcripts and the expression patterns their genes, results provide insight into human potential recombination link to SARS-CoV-2 furin cleavage site, during undetected human-to-human virus transmission. Other PRRA-like insertions in the SARS-CoV-2 spike protein are shown.
Chemokine CCL5 immune subtypes of human liver cancer with prognostic significance
Authors: Xia Yin , Zhou Linlin , Yang Hung-Chih , Yu Chen-Wei 
Published: April 2022

Abstract
Background The immunogenicity of the liver tumor microenvironment is clinically heterogeneous and mysterious. The insight into the role of immune cells including tumor-infiltrating lymphocytes (TILs) and chemokine networks, might enable optimal patient selection for immunotherapy. In this study, we aimed at characterizing the liver cancer immune subtypes linked to chemokines and associating with the patient characteristics and clinical outcomes. Methods We analyzed the immune cells and chemokine signatures of human liver cancer using The Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) database profiling of 110 normal liver tissues and 369 liver tumor patients. We performed hierarchical clustering to the chemokine expression by applying immune cells status to categorize the CCL5-related chemokine in liver tumors. The separation was characterized by dividing the liver tumor patients into CCL5-high and low subtypes. Results Our results showed that the high expression of myeloid-derived suppressor cells (MDSCs) is associated with a decrease in effector T cells expressing PRF1 in liver tumor progression. The chemokines and immune cells in CCL-5-high subtype including CCR5, MDSCs and effector T cells, are significantly associated with CCL5 and a potential predictive clinical benefit. The estimated odds for CCL5-low subtype liver tumors were higher than CCL5-high subtype liver tumors particularly in the stage IV tumors (OR = 3.54; 95 % CI: 0.36, 34.92). Our data demonstrated that the CCL5-high subtype significantly improved OS (p = 0.0379, hazard ratio 0.67; 95% CI 0.43, 0.98), DFI (p = 0.0104, hazard ratio 0.63; 95% CI 0.44, 0.90), PFI (p = 0.0066, hazard ratio 0.64; 95% CI 0.46, 0.89) and working performance status when compared to the CCL5-low subtype. Conclusion Our findings provide a novel perspective of liver cancer chemokine subtypes linked to immune cells. A suitable therapy that can effectively activate effector T cells and inhibit MDSCs targeting chemokines might support the magnitude of lymphocytic infiltration in liver tumors, and should be considered for the design of precision therapies targeting the tumor and its immune microenvironment. The chemokine signatures in the CCL5-subtype are a valuable resource for future research to help identify clinically relevant biomarkers.
Dyslipidemia and its association with early mortality in children with hemophagocytic lymphohistiocytosis：a retrospective cohort study of 353 Chinese patients
Authors: Xiao Li , Xu Ximing , Zhang Zhiling , Dou Ying , Guan Xianmin , Guo Yuxia , Wen Xianhao , Shen Yali , Meng Yan , Liao Meiling , Hu Qinshi , Yu Jie 
Published: April 2022

Abstract
Background
Hemophagocytic lymphohistiocytosis (HLH) is a rapidly progressive and potentially life-threatening disorder. Identifying risk factors and timely adjustment of the given treatment regimens is critical to reducing the early mortality in HLH patients. Hypocholesterolemia has been reported to be associated with poor prognosis in a variety of critical illnesses. However, serum cholesterol is rarely studied in HLH patients, and its prognostic value is unclear.
Methods
We conducted a retrospective cohort study in National Clinical Research Center for Child Health and Disorders (Chongqing), identifying pediatric HLH patients diagnosed with the HLH-2004 protocol and treated with immunochemotherapy between January 2008 and December 2020. The patients’ blood lipid levels at initial diagnosis of HLH, including triglycerides (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein- cholesterol (LDL-C), were reviewed based on electronic medical records. Both Cox and logistic regression models were used to estimate the effects of blood lipid indicators on early death (within 30 days after diagnosis).
Results
The observed 30-day mortality rate of the 353 included patients was 19.05% (64/336, 17 were lost to follow-up). The Kaplan-Meier-estimated 3-year survival rate was 61.67% (95% CI, 56.27%-67.59%). Lipid panel was performed in 349 patients: 91.98% (321/349) had TG ≥ 1.80 mmol/L, 92.84% (324/349) had HDL-C ≤ 1.04 mmol/L, 58.74% (205/349) had LDL-C ≤ 1.30 mmol/L and 24.64% (86/349) had TC ≤ 3.11 mmol/L. TC ≤ 3.11 mmol/L and BUN ≥ 7.14 mmol/L were the independent risk factors for 30-day mortality [HR(95%CI): 2.85(1.46, 5.57) and 2.90(1.48, 5.68), respectively]. Compared with the low-risk group (no risk factors present), the patients had a nearly 10-fold increased risk of early death [HR = 9.98, 95%CI: (4.23, 23.56)] in the high-risk group (two risk factors were present) and a 6-fold increased risk of early death [HR = 6.24, 95%CI: (3.18, 12.22)] in the intermediate-risk group (one risk factor was present).
Conclusion
Severe derangement of lipoproteins is common in children with HLH, and decreased TC is an independent risk factor for early death. More attention needs to be paid to hypocholesterolemia during the diagnosis and management of HLH patients.
Advancing small-animal perfusion models: Normothermic dual-vessel ex vivo rat liver machine perfusion based on a clinical setup
Authors: Strobl Felix , Michelotto Julian , Muth Vanessa , Moosburner Simon , Knaub Kristina , Zimmer Maximilian , Pratschke Johann , Sauer Igor Maximilian , Raschzok Nathanael , Gassner Joseph Maria George Vernon 
Published: April 2022

Abstract
Normothermic ex vivo liver machine perfusion (NEVLP) has been developed to address organ shortage in liver transplantation. To establish new therapeutic concepts for the expansion of the donor pool, standardized animal models are needed, that simulate clinical NEVLP. Rat liver grafts were perfused in a dual-vessel NEVLP system using varying doses of the clinically used vasodilator epoprostenol, with and without the addition of the Kupffer cell inhibitor glycine. Cell culture medium supplemented with rat plasma was compared to SteenTM-based perfusion solution, which is used in clinical NEVLP. Perfusion pressures and bile production were recorded, perfusate transaminases levels were measured and tissue was analyzed for cytokines and 8-Isoprostane. Increasing levels of epoprostenol and the addition of glycine resulted in a stepwise decrease of transaminase secretion and improved bile production. SteenTM significantly decreased transaminase secretion as well as IL-1β production, resulting in lowest levels of oxidative stress and best-preserved liver integrity. In conclusion, high doses of epoprostenol seem to ameliorate liver function and prevent cellular damage, with glycine acting synergistically. SteenTM as perfusion basis seems superior. Our rodent NEVLP system may be used to rapidly test new agents for pharmacologic conditioning of livers and to translate these findings from bench-to-bedside.
Incompatible insect technique mass rearing infrastructure cost calculator for the control of Culex quinquefasciatus in Hawaiʻi
Authors: Vorsino Adam E. , Xi Zhiyong 
Published: April 2022

Abstract
BackgroundHawaiʻi’s native forest avifauna is experiencing drastic declines due to climate change induced increases in temperature encroaching on their upper elevation montane rainforest refugia. Increasing temperature supports higher avian malaria infection rates due to increasing densities of its primary vector, the southern house mosquito C. quinquefasciatus, and an increase in developmental success of the avian malaria parasite Plasmodium relictum. Here we propose the use of the Incompatible Insect Technique (IIT) or the combined IIT/Sterile Insect Technique (SIT) for the landscape scale control of C. quinquefasciatus, and have developed a calculator to estimate the costs of IIT and IIT/SIT applications at various sites in Hawaiʻi.MethodsThe calculator described here links the infrastructure, personnel and space necessary to deploy a larval rearing unit (or units) that can rear ~ 1 million Culicid/week. We assessed the rearing costs and needs for effective control at various elevations in Hawaiʻi using approximations of the overflooding ratio at each elevation. The calculator derives a rate describing the number of Culicid needed to control wild-type mosquitoes at each site/elevation, in relation to the number of larval rearing units. This rate is a constant from which other costs are quantified. With minor modifications, the calculator described here can be applied to other areas, mosquito species, and techniques.ResultsAs a proof of concept, we have used the calculator to estimate rearing infrastructure costs for an application of IIT in the Alakaʻi Wilderness Reserve on the island of Kauaʻi. Our analysis estimates an initial investment of at least $1,338,874.00 with subsequent yearly costs of approximately $751,764.00. We also present supplemental examples of infrastructure costs needed to control C. quinquefasciatus in the home range of ʻiʻiwi Drepanis coccinea, and the yellow fever vector Aedes aegypti.ConclusionsThe linear relationship of rearing infrastructure to cost used in this calculator is a simplified metric that can be useful for the development of initial Culicid mass rearing infrastructure cost estimates. Users of the calculator can modify the inputs to reflect project specific parameters.