bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analysis of wheat spikes in response to Tilletia controversa Kühn which cause wheat dwarf bunt
Authors: Ren Zhaoyu , Liu Jianjian , Din Ghulam Muhae Ud , Zhang Han , Du Zhenzhen , Chen Wanquan , Liu Taiguo , Zhang Jianmin , Zhao Sifeng , Gao Li 
Published: December 2020

AbstractWheat dwarf bunt is caused by Tilletia controversa Kühn, which is one of the most destructive diseases of wheat worldwide. To explore the interaction of T. controversa and wheat, we analysed the transcriptome profile of spikes of the susceptible wheat cultivar Dongxuan 3, which was subjected to a T. controversa infection and a mock infection. The results obtained from a differential expression analysis of T. controversa-infected plants compared with mock-infected ones showed that 10,867 out of 21,354 genes were upregulated, while 10,487 genes were downregulated, and these genes were enriched in 205 different pathways. Our findings demonstrated that the genes associated with defence against diseases, such as PR-related genes, WRKY transcription factors and mitogen-activated protein kinase genes, were more highly expressed in response to T. controversa infection. Additionally, a number of genes related to physiological attributes were expressed during infection. Three pathways were differentiated based on the characteristics of gene ontology classification. KEGG enrichment analysis showed that twenty genes were expressed differentially during the infection of wheat with T. controversa. Notable changes were observed in the transcriptomes of wheat plants after infection. The results of this study may help to elucidate the mechanism governing the interactions between this pathogen and wheat plants and may facilitate the development of new methods to increase the resistance level of wheat against T. controversa, including the overexpression of defence-related genes.
Deep learning reveals 3D atherosclerotic plaque distribution and composition
Authors: Jurtz Vanessa Isabell , Skovbjerg Grethe , Salinas Casper Gravesen , Roostalu Urmas , Pedersen Louise , Hecksher-Sørensen Jacob , Rolin Bidda , Nyberg Michael , van de Bunt Martijn , Ingvorsen Camilla 
Published: December 2020

AbstractComplications of atherosclerosis are the leading cause of morbidity and mortality worldwide. Various genetically modified mouse models are used to investigate disease trajectory with classical histology, currently the preferred methodology to elucidate plaque composition. Here, we show the strength of light-sheet fluorescence microscopy combined with deep learning image analysis for characterising and quantifying plaque burden and composition in whole aorta specimens. 3D imaging is a non-destructive method that requires minimal ex vivo handling and can be up-scaled to large sample sizes. Combined with deep learning, atherosclerotic plaque in mice can be identified without any ex vivo staining due to the autofluorescent nature of the tissue. The aorta and its branches can subsequently be segmented to determine how anatomical position affects plaque composition and progression. Here, we find the highest plaque accumulation in the aortic arch and brachiocephalic artery. Simultaneously, aortas can be stained for markers of interest (for example the pan immune cell marker CD45) and quantified. In ApoE−/− mice we observe that levels of CD45 reach a plateau after which increases in plaque volume no longer correlate to immune cell infiltration. All underlying code is made publicly available to ease adaption of the method.
Age and sex specific target of blood pressure for the prevention of cardiovascular event among the treatment naive hypertensive patients
Authors: Kim Hyoungnae , Lee Seulbi , Ha Eunhee , Kwon Soon Hyo , Jeon Jin Seok , Noh Hyunjin , Han Dong Cheol , Oh Hyung Jung , Ryu Dong-Ryeol 
Published: December 2020

AbstractThe time at which hypertension treatment should be initiated for different age groups and sexes remains controversial. We aimed to determine whether the association between blood pressure (BP) and major adverse cardiovascular events (MACE) varies with age and sex. This study enrolled 327,328 subjects who had not taken antihypertensive medication in the Korean National Health Service-National Health Screening Cohort between 2002 and 2003. Participants were categorized into four groups according to 2017 American College of Cardiology/American Heart Association hypertension guideline. Primary outcome was MACE characterized by cardiovascular mortality, myocardial infarction, unstable angina, and stroke. During a 10-year follow-up, a significant increase in MACE risk was observed from the stage 1 hypertension group (hazard ratio [HR], 1.23; 95% CI 1.15–1.32; P < 0.001) in time-varying Cox analysis. This relationship was persistent in subjects aged < 70 years, but increased MACE risk was observed only in the stage 2 hypertension group in ≥ 70 years (HR, 1.52; 95% CI 1.32–1.76, P < 0.001). When categorized as per sex, both men and women showed significant MACE risk from stage 1 hypertension. However, on comparing the sexes after stratifying by age, a significantly increased risk of MACE was shown from stage 1 hypertension in men aged < 50 years, but from stage 2 hypertension in men aged ≥ 50 years. Meanwhile, increased MACE risk was observed from stage 2 hypertension in women aged < 60 years, but from stage 1 hypertension in women aged ≥ 60 years. Thus, young male subjects had higher MACE risk than young female subjects, but this difference gradually decreased with age and there was no difference between sexes in subjects aged ≥ 70 years. Therefore, our results suggest that hypertension treatment initiation may need to be individualized depending on age and sex.
Diet and life history reduce interspecific and intraspecific competition among three sympatric Arctic cephalopods
Authors: Golikov Alexey V. , Ceia Filipe R. , Sabirov Rushan M. , Batalin Georgii A. , Blicher Martin E. , Gareev Bulat I. , Gudmundsson Gudmundur , Jørgensen Lis L. , Mingazov Gazinur Z. , Zakharov Denis V. , Xavier José C. 
Published: December 2020

AbstractTrophic niche and diet comparisons among closely sympatric marine species are important to understand complex food webs, particularly in regions most affected by climate change. Using stable isotope analyses, all ontogenetic stages of three sympatric species of Arctic cephalopods (genusRossia) were studied to assess inter- and intraspecific competition with niche and diet overlap and partitioning in West Greenland and the Barents Sea. Seven traits related to resource and habitat utilization were identified inRossia: no trait was shared by all three species. High borealR. megapteraand Arctic endemicR. moellerishared three traits with each other, while bothR. megapteraandR. moellerishared only two unique traits each with widespread boreal-ArcticR. palpebrosa. Thus all traits formed fully uncrossing pattern with each species having unique strategy of resource and habitat utilization. Predicted climate changes in the Arctic would have an impact on competition amongRossiawith one potential ‘winner’ (R. megapterain the Barents Sea) but no potential ‘losers’.
Structural and biochemical analyses of an aminoglycoside 2′-N-acetyltransferase from Mycolicibacterium smegmatis
Authors: Jeong Chang-Sook , Hwang Jisub , Do Hackwon , Cha Sun-Shin , Oh Tae-Jin , Kim Hak Jun , Park Hyun Ho , Lee Jun Hyuck 
Published: December 2020

AbstractThe expression of aminoglycoside-modifying enzymes represents a survival strategy of antibiotic-resistant bacteria. Aminoglycoside 2′-N-acetyltransferase [AAC(2′)] neutralizes aminoglycoside drugs by acetylation of their 2′ amino groups in an acetyl coenzyme A (CoA)-dependent manner. To understand the structural features and molecular mechanism underlying AAC(2′) activity, we overexpressed, purified, and crystallized AAC(2′) from Mycolicibacterium smegmatis [AAC(2′)-Id] and determined the crystal structures of its apo-form and ternary complexes with CoA and four different aminoglycosides (gentamicin, sisomicin, neomycin, and paromomycin). These AAC(2′)-Id structures unraveled the binding modes of different aminoglycosides, explaining the broad substrate specificity of the enzyme. Comparative structural analysis showed that the α4-helix and β8–β9 loop region undergo major conformational changes upon CoA and substrate binding. Additionally, structural comparison between the present paromomycin-bound AAC(2′)-Id structure and the previously reported paromomycin-bound AAC(6′)-Ib and 30S ribosome structures revealed the structural features of paromomycin that are responsible for its antibiotic activity and AAC binding. Taken together, these results provide useful information for designing AAC(2′) inhibitors and for the chemical modification of aminoglycosides.
Multilayered salt water with high optical transparency for EMI shielding applications
Authors: Phan Duy Tung , Jung Chang Won 
Published: December 2020

AbstractElectromagnetic interference (EMI) shielding for visual observation applications, such as windows utilized in military or aerospace, is important but difficult to realize due to conventional materials having difficulty in achieving sufficient transparency and EMI shielding simultaneously. In this paper, we present multilayered structures based on salt water for simultaneous highly optical transparency (OT) and EM shielding effectiveness (SE) performance. In the proposed structures, planar acrylic and glass were used as two types of clear substrates to hold salt water. The measured OT of both acrylic/salt water/acrylic and glass/salt water/glass structures was higher than 90% with a nearly uniform light transmission, which introduced a negligible impact on optical observation. Furthermore, both simulations and experimental results demonstrated that the SE of the multilayer structure was higher than 20 dB in the X-band from 7.5 to 8.5 GHz. Moreover, the SE was significantly enhanced by increasing the thickness of the salt water layer. Especially, both OT and SE of the multilayered structures were improved simultaneously by increasing the salinity of the salt water. These proposed structures demonstrate great potential in EMI shielding observation applications.
Molecular phenotypes of circulating tumor cells and efficacy of nivolumab treatment in patients with head and neck squamous cell carcinoma
Authors: Tada Hiroe , Takahashi Hideyuki , Kawabata-Iwakawa Reika , Nagata Yurino , Uchida Miho , Shino Masato , Ida Shota , Mito Ikko , Matsuyama Toshiyuki , Chikamatsu Kazuaki 
Published: December 2020

AbstractThe emergence of immune checkpoint inhibitors (ICIs) has revolutionized the treatment of recurrent/metastatic (R/M) head and neck squamous cell carcinoma (HNSCC). Biomarkers of the therapeutic efficacy of ICIs have been extensively investigated. In this study, we aimed to analyze whether molecular phenotypes of circulating tumor cells (CTCs) are associated with treatment responses and clinical outcomes in patients with R/M HNSCC treated with nivolumab. Peripheral blood samples were collected before treatment initiation and after four infusions of nivolumab. CTCs isolated by depletion of CD45-positive cells were analyzed to determine the expression of EPCAM, MET, KRT19, and EGFR using real-time quantitative polymerase chain reaction. CTC-positive samples were analyzed to determine the expression of PIK3CA, CCND1, SNAI1, VIM, ZEB2, CD44, NANOG, ALDH1A1, CD47, CD274, and PDCD1LG2. Of 30 patients treated with nivolumab, 28 (93.3%) were positive for CTCs. In 20 CTC-positive patients, molecular alterations in CTCs before and after nivolumab treatment were investigated. Patients with MET-positive CTCs had significantly shorter overall survival than those with MET-negative CTCs (p = 0.027). The expression level of CCND1 in CTCs of disease-controlled patients was significantly higher than that of disease-progressed patients (p = 0.034). In disease-controlled patients, the expression level of CCND1 in CTCs significantly decreased after nivolumab treatment (p = 0.043). The NANOG expression in CTCs was significantly increased in disease-controlled patients after nivolumab treatment (p = 0.036). Our findings suggest that the molecular profiling of CTCs is a promising tool to predict the treatment efficacy of nivolumab.
Hyperpolarized 15N-labeled, deuterated tris(2-pyridylmethyl)amine as an MRI sensor of freely available Zn2+
Authors: Suh Eul Hyun , Park Jae Mo , Lumata Lloyd , Sherry A. Dean , Kovacs Zoltan 
Published: December 2020

AbstractDynamic nuclear polarization (DNP) coupled with15N magnetic resonance imaging (MRI) provides an opportunity to image quantitative levels of biologically important metal ions such as Zn2+, Mg2+or Ca2+using appropriately designed15N enriched probes. For example, a Zn-specific probe could prove particularly valuable for imaging the tissue distribution of freely available Zn2+ions, an important known metal ion biomarker in the pancreas, in prostate cancer, and in several neurodegenerative diseases. In the present study, we prepare the cell-permeable,15N-enriched, d6-deuterated version of the well-known Zn2+chelator, tris(2-pyridylmethyl)amine (TPA) and demonstrate that the polarized ligand had favorable T1and linewidth characteristics for15N MRI. Examples of how polarized TPA can be used to quantify freely available Zn2+in homogenized human prostate tissue and intact cells are presented.
Reading mixtures of uniform sequence-defined macromolecules to increase data storage capacity
Authors: Frölich Maximiliane , Hofheinz Dennis , Meier Michael A. R. 
Published: December 2020

AbstractIn recent years, the field of molecular data storage has emerged from a niche to a vibrant research topic. Herein, we describe a simultaneous and automated read-out of data stored in mixtures of sequence-defined oligomers. Therefore, twelve different sequence-defined tetramers and three hexamers with different mass markers and side chains are successfully synthesised via iterative Passerini three-component reactions and subsequent deprotection steps. By programming a straightforward python script for ESI-MS/MS analysis, it is possible to automatically sequence and thus read-out the information stored in these oligomers within one second. Most importantly, we demonstrate that the use of mass-markers as starting compounds eases MS/MS data interpretation and furthermore allows the unambiguous reading of sequences of mixtures of sequence-defined oligomers. Thus, high data storage capacity considering the field of synthetic macromolecules (up to 64.5 bit in our examples) can be obtained without the need of synthesizing long sequences, but by mixing and simultaneously analysing shorter sequence-defined oligomers.
Southward migration of the Southern Hemisphere westerly winds corresponds with warming climate over centennial timescales
Authors: Perren Bianca B. , Hodgson Dominic A. , Roberts Stephen J. , Sime Louise , Van Nieuwenhuyze Wim , Verleyen Elie , Vyverman Wim 
Published: December 2020

AbstractRecent changes in the strength and location of the Southern Hemisphere westerly winds (SHW) have been linked to continental droughts and wildfires, changes in the Southern Ocean carbon sink, sea ice extent, ocean circulation, and ice shelf stability. Despite their critical role, our ability to predict their impacts under future climates is limited by a lack of data on SHW behaviour over centennial timescales. Here, we present a 700-year record of changes in SHW intensity from sub-Antarctic Marion Island using diatom and geochemical proxies and compare it with paleoclimate records and recent instrumental data. During cool periods, such as the Little Ice Age (c. 1400–1870 CE), the winds weakened and shifted towards the equator, and during warm periods they intensified and migrated poleward. These results imply that changes in the latitudinal temperature gradient drive century-scale SHW migrations, and that intensification of impacts can be anticipated in the coming century.
Mitochondrial tRNA mutations in Chinese children with tic disorders
Authors: Jiang Peifang , Ling Yinjie , Zhu Tao , Luo Xiaoying , Tao Yilin , Meng Feilong , Cheng Weixin , Ji Yanchun 
Published: December 2020

Abstract
Aim: To conduct the clinical, genetic, and molecular characterization of 494 Han Chinese subjects with tic disorders (TD).
Methods: In the present study, we performed the mutational analysis of 22 mitochondrial tRNA genes in a large cohort of 494 Han Chinese subjects with TD via Sanger sequencing. These variants were then assessed for their pathogenic potential via phylogenetic, functional, and structural analyses.
Results: A total of 73 tRNA gene variants (49 known and 24 novel) on 22 tRNA genes were identified. Among these, 18 tRNA variants that were absent or present in &lt;1% of 485 Chinese control patient samples were localized to highly conserved nucleotides, or changed the modified nucleotides, and had the potential structural to alter tRNA structure and function. These variants were thus considered to be TD-associated mutations. In total, 25 subjects carried one of these 18 putative TD-associated tRNA variants with the total prevalence of 4.96%.
Limitations: The phenotypic variability and incomplete penetrance of tic disorders in pedigrees carrying these tRNA mutations suggested the involvement of modifier factors, such as nuclear encoded genes associated mitochondrion, mitochondrial haplotypes, epigenetic, and environmental factors.
Conclusion: Our data provide the evidence that mitochondrial tRNA mutations are the important causes of tic disorders among Chinese population. These findings also advance current understanding regarding the clinical relevance of tRNA mutations, and will guide future studies aimed at elucidating the pathophysiology of maternal tic disorders.
Toxicity profiling of the ethanolic extract of Citrullus lanatus seed in rats: behavioral, biochemical and histopathological aspects
Authors: Belemkar Sateesh , Shendge Parshuram Nivrutti 
Published: December 2020

Abstract
Citrullus lanatus (Cucurbitaceae) is conventionally used for the treatment of urinary tract infection, renal stones, hypertension, diabetes and diarrhoea. Current study evaluates acute and 28 days repeated toxicity ethanolic extract of C. lanatus seed (EECLS) in Wistar rats to measure its safety profile. The single dose (2000 mg/kg BW) of EECLS was administered while in 28 days repeated study 250, 500 and 1000 mg/kg BW were administered orally in rats. Parameters such as biochemical, haematological and histopathological were analysed in subacute toxicity study. During study, no apparent sign of toxicity, behavioural changes and mortality were detected in acutely exposed animals. In 28 days repeated toxicity study, rats did not show significant changes in behaviour, gross pathology, body weight, biochemical and haematological parameters. Abridged serum glucose and cholesterol levels during the study designate their roles in treatment of hyperglycaemic and hyperlipidaemic conditions. No significant difference was observed in histopathology of liver and kidneys of treated rats. The current investigation demonstrated that EECLS is non-toxic below 1000 mg/kg BW and provides protection to some body organs. The data propose that LD50 of EECLS was greater than 2000 mg/kg BW and the no observed adverse effect level (NOAEL) of EECLS was at the dose of 1000 mg/kg in rats. Taken together, our finding suggests that, EECLS is safe and provides some protection to body organs; also, its extract can be used for further preclinical and clinical evaluation for its therapeutic activity.
Association of α-fetoprotein levels with liver stiffness measurement in outpatients with chronic hepatitis B
Authors: Wang Juan , Zhang Pengpeng , Liao Juan , Zhu Yan , Liu Xiaoli , Tang Hong 
Published: December 2020

Abstract
The association between α-fetoprotein (AFP) levels with the assessment of liver stiffness (LS) in chronic hepatitis B (CHB) patients were explored. A total of 283 outpatients with CHB were enrolled. Patient age, alanine aminotransferase (ALT), aspartate aminotransferase (AST), AFP, platelet (PLT), total bilirubin (TB), direct bilirubin (DB), alkaline phosphatase (ALP), albumin (ALB), globulin, and albumin/globulin (A/G) levels were associated with LS values in the univariate model (P&lt;0.05). Significant associations between AFP and PLT levels with LS values were observed when both variables were included in the multivariate analysis models. Receiver operation characteristic (ROC) analysis indicated that the combination of AFP and PLT levels could enhance the predictive performance of liver fibrosis (area under the curve (AUC) = 0.819, P&lt;0.001) and that PLT levels (PLT &lt; 100 × 109/l) combined with high AFP levels (AFP &gt; 8 ng/ml) significantly increased the prediction of liver fibrosis (OR = 11.216). More importantly, LS values associated with higher AFP levels (AFP &gt; 8 ng/ml), independently of higher ALT or AST values, were significantly higher than those of low AFP level groups. In conclusion, in Chinese outpatients with CHB, AFP outperformed ALT and/or AST levels in terms of their association with LS. AFP and PLT levels were independently associated with LS, and their combined assessment could enhance the diagnostic and predictive performance of liver fibrosis among CHB patients.
Real‐time fabric defect detection based on multi‐scale convolutional neural network
Authors: Zhao Shuxuan , Yin Li , Zhang Jie , Wang Junliang , Zhong Ray 
Published: December 2020

Fabric defect detection plays an important role in ensuring quality control in the textile manufacturing industry. This study introduces a fabric defect detection method based on a multi‐scale convolutional neural network (MSCNN) to improve accuracy and time efficiency. For detection accuracy, the MSCNN is constructed to obtain different scales of feature maps, which enhance the representation of tiny scale fabric defects. A faster defect locating method is designed with pre‐known size information obtained by clustering analysis to reduce the computation time. An experiment is carried out for illustrating that the accuracy of MSCNN for each defect reaches over 92%, and the frames per second (FPS) is more than 29. Further analysis results demonstrate that the proposed MSCNN can accurately detect the fabric defects with a tiny scale, and the speed of detection can reach 30 m/min to satisfy the industrial requirements.
The hot interstellar medium towards 4U 1820-30: a Bayesian analysis
Authors: Rogantini D. , Costantini E. , Mehdipour M. , Kuiper L. , Ranalli P. , Waters L. B. F. M. 
Published: December 2020

Context. High-ionisation lines in the soft X-ray band are generally associated to either interstellar hot gas along the line of sight or to photoionised gas intrinsic to the source. In the low-mass X-ray binary 4U 1820-30, the nature of these lines is not well understood.
Aims. We aim to characterise the ionised gas present along the line of sight towards 4U 1820-30 producing the X-ray absorption lines of Mg XI, Ne IX, Fe XVII, O VII, and O VIII.
Methods. We analysed all the observations available for this source in the XMM-Newton and Chandra archives that were taken with the RGS, HETG, and LETG spectrometers. We accurately examined the high-resolution grating spectra using a standard X-ray analysis procedure based on the C-statistic and using Bayesian parameter inference. We tested two physical models which describe a plasma in either collisional ionisation or photoionisation equilibrium. We adopted the Bayesian model comparison to statistically compare the different combinations of models used for the analysis.
Results. We find that the lines are consistent with hot gas in the interstellar medium rather than the intrinsic gas of the X-ray binary. Our best-fit model reveals the presence of a collisionally ionised plasma with a temperature of T = (1.98 ± 0.05) × 106 K. The photoionisation model fails to fit the Fe XVII line (which is detected with a significance of 6.5σ) because of the low column density predicted by the model. Moreover, the low inclination of the binary system is likely the reason for the non-detection of ionised gas intrinsic to the source.