bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting binding sites from unbound versus bound protein structures
Authors: Clark Jordan J. , Orban Zachary J. , Carlson Heather A. 
Published: September 2020

AbstractWe present the application of seven binding-site prediction algorithms to a meticulously curated dataset of ligand-bound and ligand-free crystal structures for 304 unique protein sequences (2528 crystal structures). We probe the influence of starting protein structures on the results of binding-site prediction, so the dataset contains a minimum of two ligand-bound and two ligand-free structures for each protein. We use this dataset in a brief survey of five geometry-based, one energy-based, and one machine-learning-based methods: Surfnet, Ghecom, LIGSITEcsc, Fpocket, Depth, AutoSite, and Kalasanty. Distributions of the F scores and Matthew’s correlation coefficients for ligand-bound versus ligand-free structure performance show no statistically significant difference in structure type versus performance for most methods. Only Fpocket showed a statistically significant but low magnitude enhancement in performance for holo structures. Lastly, we found that most methods will succeed on some crystal structures and fail on others within the same protein family, despite all structures being relatively high-quality structures with low structural variation. We expected better consistency across varying protein conformations of the same sequence. Interestingly, the success or failure of a given structure cannot be predicted by quality metrics such as resolution, Cruickshank Diffraction Precision index, or unresolved residues. Cryptic sites were also examined.
PRMT5-mediated methylation of YBX1 regulates NF-κB activity in colorectal cancer
Authors: Hartley Antja-Voy , Wang Benlian , Mundade Rasika , Jiang Guanglong , Sun Mengyao , Wei Han , Sun Steven , Liu Yunlong , Lu Tao 
Published: September 2020

AbstractThe multifunctional protein Y-box binding protein 1 (YBX1), is a critical regulator of transcription and translation, and is widely recognized as an oncogenic driver in several solid tumors, including colorectal cancer (CRC). However, very little is known about the upstream or downstream factors that underlie YBX1′s regulation and involvement in CRC. Previously, we demonstrated that YBX1 overexpression correlated with potent activation of nuclear factor κB (NF-κB), a well-known transcription factor believed to be crucial in CRC progression. Here, we report a novel interaction between NF-κB, YBX1 and protein arginine methyltransferase 5 (PRMT5). Our findings reveal for the first time that PRMT5 catalyzes methylation of YBX1 at arginine 205 (YBX1-R205me2), an event that is critical for YBX1-mediated NF-κB activation and its downstream target gene expression. Importantly, when WT-YBX1 is overexpressed, this methylation exists under basal (unstimulated) conditions and is further augmented upon interleukin-1β (IL-1β) stimulation. Mechanistically, co-immunoprecipitation studies reveal that the R205 to alanine (A) mutant of YBX1 (YBX1-R205A) interacted less well with the p65 subunit of NF-κB and attenuated the DNA binding ability of p65. Importantly, overexpression of YBX1-R205A significantly reduced cell growth, migration and anchorage-independent growth of CRC cells. Collectively, our findings shed important light on the regulation of a novel PRMT5/YBX1/NF-κB axis through PRMT5-mediated YBX1-R205 methylation. Given the fact that PRMT5, YBX1 and NF-κB are all among top crucial factors in cancer progression, pharmacological disruption of this pivotal axis could serve as the basis for new therapeutics for CRC and other PRMT5/YBX1/NF-κB-associated cancers.
Differential epigenetic regulation between the alternative promoters, PRDM1α and PRDM1β, of the tumour suppressor gene PRDM1 in human multiple myeloma cells
Authors: Romero-García Raquel , Gómez-Jaramillo Laura , Mateos Rosa María , Jiménez-Gómez Gema , Pedreño-Horrillo Nuria , Foncubierta Esther , Rodríguez-Gutiérrez Juan Francisco , Garzón Sebastián , Mora-López Francisco , Rodríguez Carmen , Valor Luis M. , Campos-Caro Antonio 
Published: September 2020

AbstractMultiple myeloma (MM) is a B-cell neoplasm that is characterized by the accumulation of malignant plasma cells in the bone marrow. The transcription factor PRDM1 is a master regulator of plasma cell development and is considered to be an oncosuppressor in several lymphoid neoplasms. The PRDM1β isoform is an alternative promoter of the PRDM1 gene that may interfere with the normal role of the PRDM1α isoform. To explain the induction of the PRDM1β isoform in MM and to offer potential therapeutic strategies to modulate its expression, we characterized the cis regulatory elements and epigenetic status of its promoter. We observed unexpected patterns of hypermethylation and hypomethylation at the PRDM1α and PRDM1β promoters, respectively, and prominent H3K4me1 and H3K9me2 enrichment at the PRDM1β promoter in non-expressing cell lines compared to PRDM1β-expressing cell lines. After treatment with drugs that inhibit DNA methylation, we were able to modify the activity of the PRDM1β promoter but not that of the PRDM1α promoter. Epigenetic drugs may offer the ability to control the expression of the PRDM1α/PRDM1β promoters as components of novel therapeutic approaches.
Atomic, electronic and magnetic structure of an oxygen interstitial in neutron-irradiated Al2O3 single crystals
Authors: Seeman V. , Lushchik A. , Shablonin E. , Prieditis G. , Gryaznov D. , Platonenko A. , Kotomin E. A. , Popov A. I. 
Published: September 2020

AbstractA single radiation-induced superoxide ion $$O_{2}^{ - }$$

O

2

-

has been observed for the first time in metal oxides. This structural defect has been revealed in fast-neutron-irradiated (6.9×1018n/cm2) corundum (α-Al2O3) single crystals using the EPR method. Based on the angular dependence of the EPR lines at the magnetic field rotation in different planes and the determined g tensor components, it is shown that this hole-type $$O_{2}^{ - }$$

O

2

-

center (i) incorporates one regular and one interstitial oxygen atoms being stabilized by a trapped hole (S = 1/2), (ii) occupies one oxygen site in the (0001) plane being oriented along the a axis, and (iii) does not contain any other imperfection/defect in its immediate vicinity. The thermal stepwise annealing (observed via the EPR signal and corresponding optical absorption bands) of the $$O_{2}^{ - }$$

O

2

-

centers, caused by their destruction with release of a mobile ion (tentatively the oxygen ion with the formal charge −1), occurs at 500–750 K, simultaneously with the partial decay of single F-type centers (mostly with the EPR-active F+ centers). The obtained experimental results are in line with the superoxide defect configurations obtained via density functional theory (DFT) calculations employing the hybrid B3PW exchange-correlation functional. In particular, the DFT calculations confirm the $$O_{2}^{ - }$$

O

2

-

center spin S = 1/2, its orientation along the a axis. The $$O_{2}^{ - }$$

O

2

-

center is characterized by a short O–O bond length of 1.34 Å and different atomic charges and magnetic moments of the two oxygens. We emphasize the important role of atomic charges and magnetic moments analysis in order to identify the ground state configuration.
Expanded Chinese hamster organ and cell line proteomics profiling reveals tissue-specific functionalities
Authors: Heffner Kelley , Hizal Deniz Baycin , Majewska Natalia I. , Kumar Swetha , Dhara Venkata Gayatri , Zhu Jie , Bowen Michael , Hatton Diane , Yerganian George , Yerganian Athena , O’Meally Robert , Cole Robert , Betenbaugh Michael 
Published: September 2020

AbstractChinese hamster ovary (CHO) cells are the predominant production vehicle for biotherapeutics. Quantitative proteomics data were obtained from two CHO cell lines (CHO-S and CHO DG44) and compared with seven Chinese hamster (Cricetulus griseus) tissues (brain, heart, kidney, liver, lung, ovary and spleen) by tandem mass tag (TMT) labeling followed by mass spectrometry, providing a comprehensive hamster tissue and cell line proteomics atlas. Of the 8470 unique proteins identified, high similarity was observed between CHO-S and CHO DG44 and included increases in proteins involved in DNA replication, cell cycle, RNA processing, and chromosome processing. Alternatively, gene ontology and pathway analysis in tissues indicated increased protein intensities related to important tissue functionalities. Proteins enriched in the brain included those involved in acidic amino acid metabolism, Golgi apparatus, and ion and phospholipid transport. The lung showed enrichment in proteins involved in BCAA catabolism, ROS metabolism, vesicle trafficking, and lipid synthesis while the ovary exhibited enrichments in extracellular matrix and adhesion proteins. The heart proteome included vasoconstriction, complement activation, and lipoprotein metabolism enrichments. These detailed comparisons of CHO cell lines and hamster tissues will enhance understanding of the relationship between proteins and tissue function and pinpoint potential pathways of biotechnological relevance for future cell engineering.
Genipin inhibits rotavirus-induced diarrhea by suppressing viral replication and regulating inflammatory responses
Authors: Kim Jong-Hwa , Kim Kiyoung , Kim Wonyong 
Published: September 2020

AbstractRotavirus is the leading cause of acute gastroenteritis among young children worldwide. However, agents specifically designed to treat rotavirus infection have not been developed yet. In this study, the anti-rotavirus and anti-inflammatory effects of genipin, a chemical compound found in the fruit of Gardenia jasminoides, were evaluated. Genipin had an antiviral effect against the human rotavirus Wa and SA-11 strains in vitro, and it inhibited two distinct stages of the viral replication cycle: attachment and penetration (early stage) in pre-treatment and assembly and release (late stage) in post-treatment. Additionally, genipin downregulated nitric oxide synthase and pro-inflammatory cytokines in lipopolysaccharide-stimulated RAW264.7 cells and rotavirus-infected Caco-2 cells. Oral administration of genipin before and after viral infection with the murine rotavirus epidemic diarrhea of infant mice strain led to a reduced duration of diarrhea and faecal viral shedding and to decreased destruction of the enteric epithelium. Genipin could have potential as a natural compound with preventive and therapeutic effects against infection and colitis caused by rotavirus.
Intrinsic functional connectivity of blue and red brains: neurobiological evidence of different stress resilience between political attitudes
Authors: Kim Taekwan , Hur Ji-Won , Kwak Seoyeon , Jang Dayk , Lee Sang-Hun , Kwon Jun Soo 
Published: September 2020

AbstractConservatives are more sensitive to threatening/anxious situations in perceptual and cognitive levels, experiencing emotional responses and stress, while liberals are more responsive to but tolerant of ambiguous and uncertain information. Interestingly, conservatives have greater psychological well-being and are more satisfied with their lives than liberals despite their psychological vulnerability to stress caused by threat and anxiety sensitivities. We investigated whether conservatives have greater resilience and self-regulation capacity, which are suggested to be psychological buffers that enhance psychological well-being, than liberals and moderates. We also explored associations between intrinsic functional brain organization and these psychological resources to expand our neurobiological understanding of self-regulatory processes in neuropolitics. We found that conservatives, compared to liberals and moderates, had greater psychological resilience and self-regulation capacity that were attributable to greater impulse control and causal reasoning. Stronger intrinsic connectivities between the orbitofrontal cortex (OFC) and precuneus and between the insula and frontal pole/OFC in conservatives were correlated with greater resilience and self-regulation capacity. These results suggest the neural underpinnings that may allow conservatives to manage the psychological stress and achieve greater life satisfaction. This study provides neuroscientific evidence for the different responses of liberals and conservatives to politically relevant social issues.
Inoculation of Ensifer fredii strain LP2/20 immobilized in agar results in growth promotion and alteration of bacterial community structure of Chinese kale planted soil
Authors: Pongsilp Neelawan , Nimnoi Pongrawee 
Published: September 2020

AbstractIn our former research, we succeeded in using agar, alginate, and perlite as immobilization materials to maintain long-term survival of the inoculant, Ensifer fredii LP2/20, in a controlled glasshouse. Therefore the information on the establishment and activity of the inoculant to promote plant growth under field conditions, the effects of the inoculant on the soil microbial communities and specific microbial taxa, and the association between the inoculant and soil elements merit further studies. Here, we found that agar was the most suitable material that supported the establishment of the inoculant under field conditions. RNA-based analysis showed that E. fredii LP2/20 immobilized in agar was still metabolically active at day 50 after being introduced into soil. Inoculation of E. fredii LP2/20 immobilized in agar conferred the highest plant dry weight (up to 89.94%) and all plant elements including total N (9.55%), P (17.94%), K (68.42%), Ca (39.77%), Mg (30.76%), Fe (29.85%), and Zn (22.44%). Inoculation of E. fredii LP2/20 immobilized in agar increased soil chemicals including soil organic matter (99.02%), total N (272.48%), P (31.75%), K (52.74%), Fe (51.06%), and Zn (63.10%). High-throughput next-generation sequencing of bacterial 16S rRNA amplicons showed that the Proteobacteria, Acidobacteria, Bacteroidetes, and Firmicutes were dominant phyla in Chinese kale field soil. Inoculation of E. fredii LP2/20 significantly affected the soil bacterial community structure by decreasing total bacterial richness and diversity. The numbers of alpha- and gamma-Proteobacteria were significantly increased while the number of delta-Proteobacteria was significantly decreased due to E. fredii LP2/20 establishment. Soil total P, K, and Ca and soil pH were the important factors that shaped the soil bacterial community composition.
Prevalence of depression among Chinese university students: a systematic review and meta-analysis
Authors: Gao Li , Xie Yuanchen , Jia Chunhua , Wang Wei 
Published: September 2020

AbstractEstimates of the depression prevalence among Chinese university students vary considerably across studies. This systematic review and meta-analysis aimed to comprehensively analyze the depression prevalence among Chinese university students. We searched four electronic databases with the search terms of depression, China, university student, and questionnaire. Studies reporting depression among Chinese university students were included in the analysis. Two reviewers independently extracted the data and assessed the qualities of the studies. The package of “meta” in R Foundation for Statistical Computing was used to calculate an overall proportion in a random-effects model with 95% confidence intervals. Subgroup analysis was conducted to analyze the influencing factors on the depression prevalence. Any conflict in the data analysis was discussed by all the reviewers. A total of 113 studies were included in the meta-analysis. The overall prevalence of depression among Chinese university students was shown to be 28.4% (n = 185,787), with 95%CI from 25.7 to 31.2%. The overall depression prevalence among Chinese university students was still relatively high. More efforts need to be done to provide better mental healthcare to university students in China.
The superior frontal longitudinal tract: a connection between the dorsal premotor and the dorsolateral prefrontal cortices
Authors: Bakhit Mudathir , Fujii Masazumi , Hiruta Ryo , Yamada Masayuki , Iwami Kenichiro , Sato Taku , Saito Kiyoshi 
Published: September 2020

AbstractA few studies have identified the structural connection between the premotor area and the lateral prefrontal cortex (DLPFC) as the frontal longitudinal system (FLS). This study investigated the existence of a direct segment (none U-fibre) of the superior part of the FLS (sFLS), which connects the dorsal premotor cortex (PMd) and DLPFC and analysed its asymmetry and termination point patterns. A dataset of diffusion-weighted images from 48 subjects was used for generalised q-sampling imaging tractography. Additionally, a white-fibre dissection was conducted in two right hemispheres. An analysis of spatial location, termination points, laterality, and correlation with the subjects’ gender or handedness was performed. The sFLS was found to have a deeper longitudinal bundle directly connecting the PMd and DLPFC. The bundle is referred to hereafter as the superior frontal longitudinal tract (SFLT). The SFLT was reconstructed in 100% of right and 88% of left hemispheres. It exhibited variable patterns in different subjects in their posterior terminations. In addition, it was found to possess a complicated spatial relationship with the adjacent bundles. The SFLT was revealed successfully in two cadaveric right hemispheres, where the posterior terminations were found to originate in the PMd independent of the superior longitudinal fasciculus.
Systematic selection and validation of suitable reference genes for quantitative real-time PCR normalization studies of gene expression in Nitraria tangutorum
Authors: Wang Bo , Duan Huirong , Chong Peifang , Su Shiping , Shan Lishan , Yi Dan , Wang Lirong , Li Yi 
Published: September 2020

AbstractSuitable reference genes can be used to calibrate the error in quantitative real-time PCR (qPCR) experiments, making the results more credible. However, there are no reference genes suitable for multiple species and under different experimental conditions. Nitraria tangutorum Bobr. is a typical plant native to desert areas. It is drought-resistant, saline-alkali resistant, extreme temperatures-resistant, and has strong adaptability. To date, the importance of this germplasm has not been sufficiently understood; therefore, it is still unclear which genes can be used as reference genes to calibrate qPCR data of N. tangutorum. In this study we analyzed the expression levels of 10 candidate reference genes (ACT, GAPDH, TUA, TUB, CYP, UBC, His, PP2A, HSP, and EF1-α) in N. tangutorum seedlings under a series of experimental conditions, including in different organs (root, stem, and leaf) and under abiotic stresses (salt, drought, heat, and cold) and hormone stimuli (abscisic acid) by qPCR. Three software programs (geNorm, NormFinder, and BestKeeper) were used to evaluate the expression stability of the ten genes. Comprehensive analysis showed that EF1-α and His had the best expression stability, whereas HSP was the least suitable as a reference gene. The expression profile of NtCER7, a gene related to the regulation of cuticular wax biosynthesis in N. tangutorum, verified the accuracy of the experimental results. Based on this study, we recommend EF1-α and His as suitable reference genes for N. tangutorum. This paper provides the first data on stable reference genes in N. tangutorum, which will be beneficial to studying the gene expression of N. tangutorum and other Nitraria species in the future.
Coupled changes in soil organic carbon fractions and microbial community composition in urban and suburban forests
Authors: Zhang Xueying , Chen Xiaomei , Liu Muying , Xu Zhanying , Wei Hui 
Published: September 2020

AbstractClimate change and rapid urbanization have greatly impacted urban forest ecosystems and the carbon (C) cycle. To assess the effects of urbanization on forest soil C and soil microorganisms, six natural forests in a highly-urbanized region were selected as the research objects. Soil samples were collected to investigate the content and fractions of the soil organic carbon (SOC), as well as the soil microbial community composition. The results showed that the SOC content and fractions were substantially lower in the urban forests than in the suburban forests. Meanwhile, the total amount of phospholipid fatty acids (PLFAs) at suburban sites was twice more than that at urban sites, with shifts in microbial community structure. The potential differences in C inputs and nutrient limitation in urban forests may aggravate the low quantity and quality of SOC and consequently impact microbial community abundance and structure. Variation in microbial community structure was found to explain the loss of soil C pools by affecting the C inputs and promoting the decomposition of SOC. Therefore, the coupled changes in SOC and soil microorganisms induced by urbanization may adversely affect soil C sequestration in subtropical forests.
Effectiveness of nanoscale zero-valent iron for the immobilization of Cu and/or Ni in water and soil samples
Authors: Gil-Díaz M. , Álvarez M. A. , Alonso J. , Lobo M. C. 
Published: September 2020

AbstractIn the last few years, the effectiveness of nanoscale zero-valent iron (nZVI) as a treatment for polluted waters and soils has been widely studied. However, little data are available on its efficacy for metal immobilization at low and moderate doses. In this study, the effectiveness of two doses of commercial nZVI (1 and 5%) to immobilize Cu and/or Ni in water and acidic soil samples was evaluated. The influence of the nanoremediation technology on iron availability, physico-chemical soil properties and soil phytotoxicity was also assessed. The results show that the effectiveness of nZVI to immobilize Cu and Ni in water and soil samples was determined by the dose of the nanomaterial and the presence of both metals. Nickel immobilization was significantly decreased by the presence of Cu but the opposite effect was not observed. nZVI showed better immobilization capacity in water than in soil samples. In water, the dose of 5% completely removed both metals, whereas at a lower dose (1%) the percentage of immobilized metal decreased, especially for Ni in Cu + Ni samples. In soil samples, 5% nZVI was more effective in immobilizing Ni than Cu, with a 54% and 21% reduction of leachability, respectively, in single contaminated samples. In Cu + Ni soil samples, nZVI treatment led to a significant decrease in Ni immobilization, similar to that observed in water samples. The application of nZVI induced a dose-dependent increase in available Fe—a relevant effect in the context of soil rehabilitation. Germination assays of Medicago sativa and Vicia sativa seeds revealed that treatment with nZVI did not induce phytotoxicity under the experimental conditions tested, and that the phytotoxicity induced by Ni decreased significantly after the treatment. Thus, the use of nZVI emerges as an interesting option for Cu and/or Ni immobilization in water samples. The effectiveness of nZVI to remove Cu from acidic soil samples was moderate, while for Ni it was strongly dependent on the presence of Cu. These observations therefore indicate that the results in water samples cannot be extrapolated to soil samples.
Effect of enzymatic treatment of citrus by-products on bacterial growth, adhesion and cytokine production by Caco-2 cells
Authors: de Paula Menezes Barbosa Paula , Roggia Ruviaro Amanda , Mateus Martins Isabela , Alves Macedo Juliana , LaPointe Gisèle , Alves Macedo Gabriela 
Published: September 2020

Enzymatic extracts of citrus by-products presented antibacterial and prebiotic activities, played an important role in the adhesion of probiotics, foodborne pathogens, and in the inflammatory response of Caco-2 cells due to S. Typhimurium infection.