bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growth, photosynthesis, and nutrient uptake in wheat are affected by differences in nitrogen levels and forms and potassium supply
Authors: Guo Jiuxin , Jia Yamin , Chen Huanhuan , Zhang Lijun , Yang Jinchang , Zhang Jun , Hu Xiangyu , Ye Xin , Li Yan , Zhou Yi 
Published: February 2019

AbstractNitrogen (N) and potassium (K) are essential macronutrients for plants growth; however, the mechanism by which K mediates negative effects on ammonium-sensitive plants is still poorly understood. We hypothesized that K supplies may enhance antagonistic ammonium stress while improving nitrate nutrition function, which wheat seedlings were grown in sand culture in the presence of two N forms (ammonium; nitrate) supplied at two rates (2, 10 mmol L−1) and three K levels (0.5, 5, 15 mmol L−1). We found that a high N rate increased plant biomass under nitrate nutrition, while it had a negative effect under ammonium nutrition. Compared with nitrate, biomass was depressed by 54% or 85% for low or high N rate under ammonium. This resulted in a reduction in gas exchange parameters and a subsequent decrease in growth variables and nutrient uptake, whereas these parameters increased significantly with increasing K levels. Moreover, in principal components analysis, these variations were highly clustered under nitrate nutrition and highly separated under ammonium nutrition. Our study shows a clear positive interaction between K and N, suggesting that high K supply relieves ammonium stress while improving growth vigor under nitrate nutrition by enhancing nutrient uptake and assimilate production in wheat plants.
Understanding HLA associations from SNP summary association statistics
Authors: Lim Jiwoo , Bae Sang-Cheol , Kim Kwangwoo 
Published: February 2019

AbstractStrong genetic associations in the region containing human leukocyte antigen (HLA) genes have been well-documented in various human immune disorders. Imputation methods to infer HLA variants from single nucleotide polymorphism (SNP) genotypes are currently used to understand HLA associations with a trait of interest. However, it is challenging for some researchers to obtain individual-level SNP genotype data or reference haplotype data. In this study, we developed and evaluated a new method, DISH (direct imputing summary association statistics of HLA variants), for imputing summary association statistics of HLA variants from SNP summary association statistics based on linkage disequilibria in Asian and European populations. Disease association Z scores in DISH were highly correlated with those from imputed HLA genotypes in null model datasets (r = 0.934 in Asians; r = 0.960 in Europeans). We applied DISH to two previous GWAS datasets in Asian systemic lupus erythematosus and European rheumatoid arthritis populations. There was a high correlation between Z scores in the DISH and HLA genotype imputations, showing the same disease-susceptible and protective alleles. This study illustrated the usefulness of the DISH method in understanding and identifying disease-associated HLA variants in human diseases while maintaining individual-level data security.
Acute changes in cardiac structural and tissue characterisation parameters following haemodialysis measured using cardiovascular magnetic resonance
Authors: Kotecha Tushar , Martinez-Naharro Ana , Yoowannakul Suree , Lambe Tabitha , Rezk Tamer , Knight Daniel S. , Hawkins Philip N. , Moon James C. , Muthurangu Vivek , Kellman Peter , Rakhit Roby D. , Gillmore Julian D. , Jeetley Paramjit , Davenport Andrew , Fontana Marianna 
Published: February 2019

AbstractIn patients with chronic kidney disease (CKD), reverse left ventricular (LV) remodelling, including reduction in LV mass, can be observed following long-term haemodialysis (HD) and has been attributed to regression of LV hypertrophy. However, LV mass can vary in response to changes in myocyte volume, edema, or fibrosis. The aims of this study were to investigate the acute changes in structural (myocardial mass and biventricular volumes) and tissue characterization parameters (native T1 and T2) following HD using cardiovascular magnetic resonance (CMR). Twenty-five stable HD patients underwent non-contrast CMR including volumetric assessment and native T1 and T2 mapping immediately pre- and post-HD. The mean time between the first and second scan was 9.1 ± 1.1 hours and mean time from completion of dialysis to the second scan was 3.5 ± 1.3 hours. Post-HD, there was reduction in LV mass (pre-dialysis 98.9 ± 36.9 g/m2 vs post-dialysis 93.3 ± 35.8 g/m2, p = 0.003), which correlated with change in body weight (r = 0.717, p < 0.001). Both native T1 and T2 reduced significantly following HD (Native T1: pre-dialysis 1085 ± 43 ms, post-dialysis 1072 ± 43 ms; T2: pre-dialysis 53.3 ± 3.0 ms, post-dialysis 51.8 ± 3.1 ms, both p < 0.05). These changes presumably reflect acute reduction in myocardial water content rather than regression of LV hypertrophy. CMR with multiparametric mapping is a promising tool to assess the cardiac changes associated with HD.
Mathematical Structures in Group Decision-Making on Resource Allocation Distributions
Authors: Friedkin Noah E. , Proskurnikov Anton V. , Mei Wenjun , Bullo Francesco 
Published: February 2019

AbstractOptimal decisions on the distribution of finite resources are explicitly structured by mathematical models that specify relevant variables, constraints, and objectives. Here we report analysis and evidence that implicit mathematical structures are also involved in group decision-making on resource allocation distributions under conditions of uncertainty that disallow formal optimization. A group’s array of initial distribution preferences automatically sets up a geometric decision space of alternative resource distributions. Weighted averaging mechanisms of interpersonal influence reduce the heterogeneity of the group’s initial preferences on a suitable distribution. A model of opinion formation based on weighted averaging predicts a distribution that is a feasible point in the group’s implicit initial decision space.
Improved Configuration and LSPR Response of Platinum Nanoparticles via Enhanced Solid State Dewetting of In-Pt Bilayers
Authors: Kunwar Sundar , Sui Mao , Pandey Puran , Gu Zenan , Pandit Sanchaya , Lee Jihoon 
Published: February 2019

AbstractNoble metallic nanoparticles (NPs) can exhibit valuable properties such as localized surface plasmon resonance (LSPR) and large surface to volume ratio, which can find various optoelectronic and catalytic applications. In this work, the improved configuration and uniformity of platinum (Pt) NPs are demonstrated by using a sacrificial indium (In) layer via the enhanced solid state dewetting of In-Pt bilayers on sapphire (0001). In a sharp contrast to the conventional dewetting of intrinsic Pt film, the introduction of In component can significantly enhance the global dewetting process and thus can result in the fabrication of well-defined Pt NPs with the improved uniformity. This can be due to the fact that In possess high diffusivity, low surface energy and low sublimation temperature. Upon annealing, the intermixing of In and Pt atoms can occur at the interface due to the inter-diffusion, which forms In-Pt alloy system. As a result, the overall diffusivity and dewetting degree of system can be significantly improved and this can produce more isolated, uniform and semispherical Pt NPs at much lower temperatures as compared to the pure Pt film dewetting. Conveniently, the In atoms preferentially can be removed from the NP matrix by the sublimation even at relatively low temperatures. These Pt NPs exhibit dynamic LSPR band in the UV-visible wavelength based on the excitation of dipolar, quadrupolar and higher order resonance modes. Specifically, the LSPR wavelength can be tuned between ~480 and 580 nm by the fabrication of small to large size Pt NPs with the distinct configuration and interparticle spacing. Furthermore, at a constant Pt thickness, the size, spacing and density of Pt NPs can be readily tuned by the control of In layer thickness. The introduction of sacrificial In component can enable an additional flexibility for the control of surface morphologies of metallic NPs with the low diffusivity materials.
High-resolution fingerprinting of Candida parapsilosis isolates suggests persistence and transmission of infections among neonatal intensive care unit patients in Kuwait
Authors: Asadzadeh Mohammad , Ahmad Suhail , Al-Sweih Noura , Hagen Ferry , Meis Jacques F. , Khan Ziauddin 
Published: February 2019

AbstractCandida parapsilosis causes ~35% of all candidemia cases in neonates. High-resolution fingerprinting of C. parapsilosis isolates from neonatal intensive care unit (NICU) patients in Maternity Hospital (MH) was performed to identify epidemiologically related strains. Sixty-eight bloodstream/colonizing strains isolated from 59 NICU patients, two isolates from health care workers (HCWs) from MH and 18 bloodstream isolates from two other hospitals were used. Six microsatellite markers were employed, isolates were assigned a numerical microsatellite genotype (MSG), dendrogram was constructed and similarities between genotypes were visualized by minimum spanning tree. Fifty bloodstream isolates from MH yielded 37 MSGs with 20 isolates clustering in 7 MSGs. Duplicate isolates and colonizing strains yielded same/highly similar MSG as bloodstream isolates. Colonizing strains from two non-candidemia patients yielded unique MSGs while others belonged to a cluster. All isolates from HCWs and from two other hospitals belonged to unique MSGs. Cluster isolates came from patients in NICU-1 or from neonates in NICU-1 and other NICUs. Clonal complexes comprising closely related genotypes indicative of microevolution were also detected. Our data show that some C. parapsilosis strains have persisted in MH environment over several years and these endemic genotypes were transmitted to other patients in NICU-1 and/or other nearby NICUs.
Heterodera glycines utilizes promiscuous spliced leaders and demonstrates a unique preference for a species-specific spliced leader over C. elegans SL1
Authors: Barnes Stacey N. , Masonbrink Rick E. , Maier Thomas R. , Seetharam Arun , Sindhu Anoop S. , Severin Andrew J. , Baum Thomas J. 
Published: February 2019

AbstractSpliced leader trans-splicing (SLTS) plays a part in the maturation of pre-mRNAs in select species across multiple phyla but is particularly prevalent in Nematoda. The role of spliced leaders (SL) within the cell is unclear and an accurate assessment of SL occurrence within an organism is possible only after extensive sequencing data are available, which is not currently the case for many nematode species. SL discovery is further complicated by an absence of SL sequences from high-throughput sequencing results due to incomplete sequencing of the 5’-ends of transcripts during RNA-seq library preparation, known as 5′-bias. Existing datasets and novel methodology were used to identify both conserved SLs and unique hypervariable SLs within Heterodera glycines, the soybean cyst nematode. In H. glycines, twenty-one distinct SL sequences were found on 2,532 unique H. glycines transcripts. The SL sequences identified on the H. glycines transcripts demonstrated a high level of promiscuity, meaning that some transcripts produced as many as nine different individual SL-transcript combinations. Most uniquely, transcriptome analysis revealed that H. glycines is the first nematode to demonstrate a higher SL trans-splicing rate using a species-specific SL over well-conserved Caenorhabditis elegans SL-like sequences.
Tuberculosis-associated anemia is linked to a distinct inflammatory profile that persists after initiation of antitubercular therapy
Authors: Gil-Santana Leonardo , Cruz Luís A. B. , Arriaga María B. , Miranda Pryscila F. C. , Fukutani Kiyoshi F. , Silveira-Mattos Paulo S. , Silva Elisangela C. , Oliveira Marina G. , Mesquita Eliene D. D. , Rauwerdink Anneloek , Cobelens Frank , Oliveira Martha M. , Kritski Afranio , Andrade Bruno B. 
Published: February 2019

AbstractPulmonary tuberculosis (PTB) is associated with chronic inflammation and anemia. How anemia impacts systemic inflammation in PTB patients undergoing antitubercular therapy (ATT) is not fully understood. In the present study, data on several blood biochemical parameters were retrospectively analyzed from 118 PTB patients during the first 60 days of ATT. Multidimensional statistical analyses were employed to perform detailed inflammatory profiling of patients stratified by anemia status prior to treatment. Anemia was defined as hemoglobin levels <12.5 g/dL for female and <13.5 g/dL for male individuals. The findings revealed that most of anemia cases were likely caused by chronic inflammation. A distinct biosignature related to anemia was detected, defined by increased values of uric acid, C-reactive protein, and erythrocyte sedimentation rate. Importantly, anemic patients sustained increased levels of several biochemical markers at day 60 of therapy. Preliminary analysis failed to demonstrate association between persistent inflammation during ATT with frequency of positive sputum cultures at day 60. Thus, TB patients with anemia exhibit a distinct inflammatory profile, which is only partially reverted at day 60 of ATT.
Dust Vortex in the Taklimakan Desert by Himawari-8 High Frequency and Resolution Observation
Authors: Yumimoto Keiya , Kajino Mizuo , Tanaka Taichu Y. , Uno Itsushi 
Published: February 2019

AbstractThe Taklimakan Desert is known to be one of the world’s major sources of aeolian dust particles. Continuous images with 10-min temporal and 2-km spatial resolutions from a new-generation geostationary meteorological satellite captured the lifecycle (generation, evolution and outflow) of a previously unrecognized type of Taklimakan dust storm. The dust storm showed an anti-clockwise spiral structure and a clear core and behaved like a “dust vortex”. From image analysis, the horizontal scale and temporal lifetime of the dust vortex were estimated to be 600 km and 36 hours, respectively. We found that a strong pressure trough (cut-off low), along with a cold air mass located on the northwestern side of the Taklimakan Desert and the high mountains surrounding the Taklimakan Desert, played important roles in the formation and evolution of the dust vortex.
Diagnostic accuracy of low-radiation coronary computed tomography angiography with low tube voltage and knowledge-based model reconstruction
Authors: Lee Joohee , Kim Tae Hoon , Lee Byoung Kwon , Yoon Young Won , Kwon Hyuck Moon , Hong Bum Kee , Min Pil-Ki , Choi Eui-Young , Oh Chi Suk , Park Chul Hwan 
Published: February 2019

AbstractWe aimed to evaluate the accuracy of coronary computed tomography angiography (CCTA) with a low-radiation protocol and iterative model reconstruction (IMR), in comparison with invasive coronary angiography (ICA). Sixty-one patients (45 males; mean age, 61.9 ± 9.2 years) with suspected coronary artery disease who underwent CCTA and ICA were retrospectively enrolled. CCTA was performed with low tube voltage (80 or 100 kVp), low tube current (100–200 mAs), prospective ECG triggering, and IMR using a 64-slice computed tomography scanner. Coronary artery disease was defined as luminal narrowing of >50%, as assessed using CCTA and ICA. The sensitivity, specificity, positive (PPV) and negative (NPV) predictive value, and accuracy of CCTA were examined. The mean radiation dose of CCTA was 1.05 ± 0.36 mSv. No non-diagnostic segment was noted. The sensitivity, specificity, PPV, NPV, and accuracy of CCTA were 86.4%, 96.1%, 80.3%, 97.5%, and 94.6% on a per segment basis, 93.1%, 94.7%, 88.3%, 97.0%, and 94.2% on a per vessel basis, and 100%, 83.3%, 93.5%, 100%, and 95.1% on a per patient basis, respectively. In conclusion, a low-radiation CCTA protocol with IMR may be useful for diagnosing coronary artery disease, as it reduces the radiation dose while maintaining diagnostic accuracy.
Experimental and simulation results of the adsorption of Mo and V onto ferrihydrite
Authors: Brinza Loredana , Vu Hong Phuc , Neamtu Mariana , Benning Liane G. 
Published: February 2019

AbstractThis study aims to highlight discrepancies between experimental and simulation linked to the mechanisms of Mo and V adsorption onto ferrihydrite (FHY) nanoparticles. We have measured adsorption capacities and uptake efficiencies and then fitted and compared these with outputs from various geochemical and adsorption models that were run as a function of pH, surface area (SA) and ferrihydrite particles size distributions. Our results revealed that the experimental data for the Mo system could be fitted very well, but this was not the case for the V system, when a model default value for the SA of FHY of 600 m2 g−1 was used. The discrepancy in the results for the V system can be explained by the lack of specific V species and/or associated constants in databases and variation in software versions, which change the outputted chemical species. Our comparative results also confirm that any experimental variables used as modelling inputs need to be checked carefully prior to any modelling exercises.
Population structure and genetic differentiation of tea green leafhopper, Empoasca (Matsumurasca) onukii, in China based on microsatellite markers
Authors: Zhang Li , Wang Fuping , Qiao Li , Dietrich Christopher H. , Matsumura Masaya , Qin Daozheng 
Published: February 2019

AbstractThe tea green leafhopper, Empoasca (Matsumurasca) onukii Matsuda, is one of the dominant pests in major tea production regions of East Asia. Recent morphological studies have revealed variation in the male genitalic structures within and among populations. However, the genetic structure of this pest remains poorly understood. This study explores the genetic diversity and population structure of this pest in nineteen populations from the four main Chinese tea production areas using microsatellite markers, with one Japanese population also examined. The results show low to moderate levels of genetic differentiation with populations grouped into four clusters, i.e. the Jiangbei group, the Southwest group 1, the Southwest group 2 and the South China group. Populations from China have a close phylogenetic relationship but show significant isolation by distance. Lower genetic diversity and genetic differentiation of E. (M.) onukii were found in the Kagoshima population of Japan. Evidence for genetic bottlenecks was detected in the South China and Jiangnan populations. Population expansion was found in the Southwest, Jiangbei and Kagoshima populations. This is the most extensive study of the population genetics of this species and contributes to our understanding of its origin and evolutionary history.
Differential expression and regulation of the non-integrin 37/67-kDa laminin receptor on peripheral blood leukocytes of healthy individuals and patients with rheumatoid arthritis
Authors: Kane Barry A. , An Hongyan , Rajasekariah Poornima , McNeil H. Patrick , Bryant Katherine , Tedla Nicodemus 
Published: February 2019

AbstractThe non-integrin 37/67-kDa laminin receptor (LAMR1) is a complex protein with diverse functions. LAMR1 is widely expressed in epithelial cells and recently it was reported on neutrophils and a subset of activated T cells. Ligation of LAMR1 on peripheral blood mononuclear cells (PBMC) downregulated LPS-induced TNFα production, suggesting immune functions. However, its expression on primary monocytes remain unknown. Interestingly, LAMR1 mRNA is downregulated in PBMC of patients with early rheumatoid arthritis (RA), and low gene expression is an independent predictor of poor response to anti-TNFα treatment, suggesting a role in RA pathogenesis. We found LAMR1 was constitutively expressed on all peripheral blood monocytes and a subset of B cells from healthy individuals and patients with RA and it was abundantly present in synovial tissue of patients with RA. On monocytes and synovial tissue lower levels of LAMR1 expression tended to correlate with increased disease activity scores.In vitrotreatment of monocytes with IFNγ or IL-10 up-regulated surface LAMR1 in healthy individuals and patients with RA with greater effects observed in healthy individuals. Importantly, treatment with IFNγ significantly increased specific binding of monocytes to laminin-1. TNFα and IL-1β caused marginal downregulation of LAMR1 in patients but effects in controls were variable. Taken together, constitutively expressed LAMR1 on monocytes is differentially regulated by pro-inflammatory and immune-regulatory cytokines suggesting LAMR1 may regulate the threshold and amplitude of their activation and migration. Decreased levels in patients with RA may indicate loss of this potentially critical homeostatic regulation thereby contributing to the excessive inflammation.
OptiPharm: An evolutionary algorithm to compare shape similarity
Authors: Puertas-Martín S. , Redondo J. L. , Ortigosa P. M. , Pérez-Sánchez H. 
Published: February 2019

AbstractVirtual Screening (VS) methods can drastically accelerate global drug discovery processes. Among the most widely used VS approaches, Shape Similarity Methods compare in detail the global shape of a query molecule against a large database of potential drug compounds. Even so, the databases are so enormously large that, in order to save time, the current VS methods are not exhaustive, but they are mainly local optimizers that can easily be entrapped in local optima. It means that they discard promising compounds or yield erroneous signals. In this work, we propose the use of efficient global optimization techniques, as a way to increase the quality of the provided solutions. In particular, we introduce OptiPharm, which is a parameterizable metaheuristic that improves prediction accuracy and offers greater computational performance than WEGA, a Gaussian-based shape similarity method. OptiPharm includes mechanisms to balance between exploration and exploitation to quickly identify regions in the search space with high-quality solutions and avoid wasting time in non-promising areas. OptiPharm is available upon request via email.
Pancreatic adenocarcinomas with mature blood vessels have better overall survival
Authors: Katsuta Eriko , Qi Qianya , Peng Xuan , Hochwald Steven N. , Yan Li , Takabe Kazuaki 
Published: February 2019

AbstractPancreatic ductal adenocarcinoma (PDAC) is known for its hypovascularity. Bevacizumab, an anti-angiogenic drug, added to standard chemotherapy demonstrated no improvement in outcome for PDAC. Therefore, we hypothesized that increased vascularity may be associated with improved outcomes in PDAC possibly due to better delivery of tumor specific immune cells. To test this hypothesis, PDAC patients were classified into either high or low CD31 expression groups utilizing mRNA expression from RNA-sequence data in The Cancer Genome Atlas (TCGA) pancreatic cancer cohort. High expression of CD31, which indicates presence of more vascular endothelial cells, was associated with significantly better OS (p = 0.002). Multivariate analysis demonstrated that residual tumor (R1, 2; p = 0.026) and CD31 low expression (p = 0.007) were the only independent predictors that negatively impacted OS. Vascular stability as well as immune response related pathways were significantly upregulated in the CD31 high expressing tumors. Furthermore, there were higher proportions of anti-cancer immune cells infiltration, including activated memory CD4+ T cells (p = 0.038), CD8+ T cells (p = 0.027), gamma-delta T cells (p < 0.001) as well as naïve B cells (p = 0.006), whereas lower proportions of regulatory T cell fractions (p = 0.009), which induce an immune tolerant microenvironment, in the CD31 high expressing tumors. These findings imply that stable vessels supply anti-cancer immune cells, which are at least partially responsible for better OS in the CD31 high expressing tumors. In conclusion, CD31 high expressing PDACs have better OS, which may be due to stable vessels that supply anti-cancer immune cells.