bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice (Oryza sativa L.)
Authors: Najeeb S. , Ali J. , Mahender A. , Pang Y.L. , Zilhas J. , Murugaiyan V. , Vemireddy Lakshminarayana R. , Li Z. 
Published: January 2020

AbstractAn attempt was made in the current study to identify the main-effect and co-localized quantitative trait loci (QTLs) for germination and early seedling growth traits under low-temperature stress (LTS) conditions in rice. The plant material used in this study was an early backcross population of 230 introgression lines (ILs) in BCIF7generation derived from the Weed Tolerant Rice-1 (WTR-1) (as the recipient) and Haoannong (HNG) (as the donor). Genetic analyses of LTS tolerance revealed a total of 27 main-effect quantitative trait loci (M-QTLs) mapped on 12 chromosomes. These QTLs explained more than 10% of phenotypic variance (PV), and average PV of 12.71% while employing 704 high-quality SNP markers. Of these 27 QTLs distributed on 12 chromosomes, 11 were associated with low-temperature germination (LTG), nine with low-temperature germination stress index (LTGS), five with root length stress index (RLSI), and two with biomass stress index (BMSI) QTLs, shoot length stress index (SLSI) and root length stress index (RLSI), seven with seed vigor index (SVI), and single QTL with root length (RL). Among them, five significant major QTLs (qLTG(I)1,qLTGS(I)1–2,qLTG(I)5,qLTGS(I)5, andqLTG(I)7) mapped on chromosomes 1, 5, and 7 were associated with LTG and LTGS traits and the PV explained ranged from 16 to 23.3%. The genomic regions of these QTLs were co-localized with two to six QTLs. Most of the QTLs were growth stage-specific and found to harbor QTLs governing multiple traits. Eight chromosomes had more than four QTLs and were clustered together and designated as promising LTS tolerance QTLs (qLTTs), asqLTT1,qLTT2,qLTT3,qLTT5,qLTT6,qLTT8,qLTT9, andqLTT11. A total of 16 putative candidate genes were identified in the major M-QTLs and co-localized QTL regions distributed on different chromosomes. Overall, these significant genomic regions of M-QTLs are responsible for multiple traits and this suggested that these could serve as the best predictors of LTS tolerance at germination and early seedling growth stages. Furthermore, it is necessary to fine-map these regions and to find functional markers for marker-assisted selection in rice breeding programs for cold tolerance.
A new stable collocation method for solving a class of nonlinear fractional delay differential equations
Authors: Shi Lei , Chen Zhong , Ding Xiaohua , Ma Qiang 
Published: January 2020

AbstractIn this paper, a stable collocation method for solving the nonlinear fractional delay differential equations is proposed by constructing a new set of multiscale orthonormal bases of$W^{1}_{2,0}$W2,01. Error estimations of approximate solutions are given and the highest convergence order can reach four in the sense of the norm of$W_{2,0}^{1}$W2,01. To overcome the nonlinear condition, we make use of Newton’s method to transform the nonlinear equation into a sequence of linear equations. For the linear equations, a rigorous theory is given for obtaining theirε-approximate solutions by solving a system of equations or searching the minimum value. Stability analysis is also obtained. Some examples are discussed to illustrate the efficiency of the proposed method.
Accessibility in the regional CGE framework: the effects of major transport infrastructure investments in Poland
Authors: Rokicki Bartlomiej , Haddad Eduardo A. , Horridge Jonathan M. , Stępniak Marcin 
Published: January 2020

AbstractSince its EU accession, Poland has invested strongly in the development of fast road transport network. As a result, the total length of modern, high-speed roads has increased from around 500 km in 2005 to over 3000 km in 2015. Yet, while the positive impact of transport infrastructure investment on overall accessibility is unquestionable there are no studies that assess its influence on economic development of particular regions. This paper applies a regional dynamic CGE model to measure the effects of big transport infrastructure investments in Polish NUTS2 regions. We use data on both investment spending and accessibility improvement (expressed as a reduction in transport margins) in order to distinguish between possible short and long term impacts. We find that there exist significant disparities in the impact between regions with high share of major road infrastructure investment undertaken by private investors and the ones that relied fully on public funding. In the case of the former, the lack of analyzed investment would lead to relatively significant decrease in real GDP or average employment. In the case of the latter, the impact of major road infrastructure investment is almost negligible.
Construction of an SNP-based high-density genetic map for Japanese plum in a Chinese population using specific length fragment sequencing
Authors: Zhang Qiu-ping , Wei Xiao , Liu Ning , Zhang Yu-ping , Xu Ming , Zhang Yu-jun , Ma Xiao-xue , Liu Wei-sheng 
Published: January 2020

AbstractThe Japanese plum (Prunus salicinaLindl.) is one of the most important stone fruit crops in China. High-density linkage map is valuable resources which enhance functional genomics and genetic breeding studies. So far several Japanese plum linkage maps have been reported using different kinds of molecular markers; however, the marker numbers and chromosome coverage are limited. Recently, a newly developed strategy which genome sequencing towards specific-locus amplified fragments (SLAF) markers, has been proven to be powerful for rapid genotyping of genome-wide markers and for high-density genetic map construction. In this study, SLAF was used to genotype markers with 114 F1 seedlings from the ‘09–16’ × ‘Fortune’ cross. Suitable SLAF markers (160,344 out of 343,436,902 pair-end reads) were chosen to conduct genetic map construction, 16.31% of which were polymorphic. The overall integrated map contained 3,341 high quality SLAFs and 720 loci that were grouped in eight genetic linkage groups with a total length of 869.9 cM and an average distance of 1.21 cM, and only five gaps with a genetic distance > 5 cM between adjacent markers occurred in linkage group (LG) 3 and LG6. The number of markers with each LG ranged from 82.3 cM (LG3) to 138.3 cM (LG1). Aligning the map against the peach reference genome sequence (Prunus persica L.) indicated a strictly co-linear relationship between the LGs and peach genome, demonstrating the markers on ours LGs were well ordered. Overall, our studies identified large-scale of genetic markers and constructed high-density linkage maps for Japanese plum, which will obviously provide a solid foundation for marker-assisted selection and sequence assembly of the Japanese plum reference genome.
Conventional versus genomic selection for white spruce improvement: a comparison of costs and benefits of plantations on Quebec public lands
Authors: Chamberland Vincent , Robichaud François , Perron Martin , Gélinas Nancy , Bousquet Jean , Beaulieu Jean 
Published: January 2020

AbstractIntensive plantation forestry is a potent strategy for forest managers to increase wood production on a smaller forest land acreage, especially with the use of genetically improved reforestation stock. The main drawback with conventional conifer improvement is the several decades it takes before stock deployment, which is particularly acute in the context of climate change and evolving wood markets. Use of genomic selection allows to drastically shorten breeding cycles, resulting in more flexibility and potentially increasing benefits. This study compares the financial performance of five white spruce (Picea glauca) breeding and deployment scenarios, from conventional breeding to genomic selection in conjunction with top-grafting or the use of somatic embryogenesis, in the context of plantations established by the Quebec government on public lands with banned herbicide use. We estimated the land expectation value (LEV) for the five scenarios applied to eight site productivity indices, and considered costs and revenues from breeding, plantation establishment, silviculture, and harvest. LEVs at 4% discount rate were positive for all scenarios on all site indices, and varied from $197 to $2015 ha−1assuming mechanical brushing of the plantations. The scenarios integrating genomic selection resulted in the highest LEVs, which increased with site index. We also conducted sensitivity analyses with 3% and 5% discount rates, with a range of costs and benefits, and with herbicide control of competing vegetation. These results should help orientate public investment decisions regarding the integration of genomic selection at the operational level in tree breeding and reforestation programs on public lands.
A Comprehensive Review of Path Planning Algorithms for Autonomous Underwater Vehicles
Authors: Panda Madhusmita , Das Bikramaditya , Subudhi Bidyadhar , Pati Bibhuti Bhusan 
Published: January 2020

AbstractThe underwater path planning problem deals with finding an optimal or sub-optimal route between an origin point and a termination point in marine environments. The underwater environment is still considered as a great challenge for the path planning of autonomous underwater vehicles (AUVs) because of its hostile and dynamic nature. The major constraints for path planning are limited data transmission capability, power and sensing technology available for underwater operations. The sea environment is subjected to a large set of challenging factors classified as atmospheric, coastal and gravitational. Based on whether the impact of these factors can be approximated or not, the underwater environment can be characterized as predictable and unpredictable respectively. The classical path planning algorithms based on artificial intelligence assume that environmental conditions are known apriori to the path planner. But the current path planning algorithms involve continual interaction with the environment considering the environment as dynamic and its effect cannot be predicted. Path planning is necessary for many applications involving AUVs. These are based upon planning safety routes with minimum energy cost and computation overheads. This review is intended to summarize various path planning strategies for AUVs on the basis of characterization of underwater environments as predictable and unpredictable. The algorithms employed in path planning of single AUV and multiple AUVs are reviewed in the light of predictable and unpredictable environments.
A likely increase in fine particulate matter and premature mortality under future climate change
Authors: Park S. , Allen R. J. , Lim C. H. 
Published: January 2020

AbstractClimate change modulates the concentration of fine particulate matter (PM2.5) via modifying atmospheric circulation, temperature, and the hydrological cycle. Furthermore, PM2.5is associated with cardiopulmonary diseases and premature mortality. Here, we use seven models to assess the response of PM2.5to end of the twenty-first century climate change under Representative Concentration Pathway 8.5, and the corresponding impact on premature mortality. The majority of models yield an increase in both PM2.5and premature mortality associated with lung cancer and cardiopulmonary disease in all world regions except Africa. These results are robust across five different future population projections, although the magnitude of premature deaths can vary by up to a factor of two. Much larger uncertainty is related to uncertainty in model physics and the representation of aerosol processes. Although our analysis requires several assumptions related to future population estimates, as well as the concentration-response function, results suggest that future emission reductions are necessary to avoid the likely health risks associated with increasing PM2.5in a warmer world.
Ultrastructural Characteristics of DHA-Induced Pyroptosis
Authors: Herr Deron R. , Yam Ting Yu Amelia , Tan Wan Shun Daniel , Koh Sally Shuxian , Wong Wai Shiu Fred , Ong Wei-Yi , Chayaburakul Kanokporn 
Published: January 2020

AbstractMicroglial cells are resident macrophages of the central nervous system (CNS) that respond to bioactive lipids such as docosahexaenoic acid (DHA). Low micromolar concentrations of DHA typically promote anti-inflammatory functions of microglia, but higher concentrations result in a form of pro-inflammatory programmed cell death known as pyroptosis. This study used scanning electron microscopy (SEM) and transmission electron microscopy (TEM) to investigate the morphological characteristics of pyroptosis in BV-2 microglial cells following exposure to 200 µM DHA. Vehicle-treated cells are characterized by extended processes, spine-like projections or 0.4 to 5.2 µm in length, and numerous extracellular vesicles (EVs) tethered to the surface of the plasma membrane. In contrast to vehicle-treated cells, gross abnormalities are observed after treating cells with 200 µM DHA for 4 h. These include the appearance of numerous pits or pores of varying sizes across the cell surface, structural collapse and flattening of the cell shape. Moreover, EVs and spines were lost following DHA treatment, possibly due to release from the cell surface. The membrane pores appear after DHA treatment initially measured ~ 30 nm, consistent with the previously reported gasdermin D (GSDMD) pore complexes. Complete collapse of cytoplasmic organization and loss of nuclear envelope integrity were also observed in DHA-treated cells. These processes are morphologically distinct from the changes that occur during cisplatin-induced apoptosis, such as the appearance of apoptotic bodies and tightly packed organelles, and the maintenance of EVs and nuclear envelope integrity. Cumulatively, this study provides a systematic description of the ultrastructural characteristics of DHA-induced pyroptosis, including distinguishing features that differentiate this process from apoptosis.
Label-free quantitative identification of abnormally ubiquitinated proteins as useful biomarkers for human lung squamous cell carcinomas
Authors: Lu Miaolong , Chen Wei , Zhuang Wei , Zhan Xianquan 
Published: January 2020

AbstractBackgroundUbiquitination is an important molecular event in lung squamous cell carcinoma (LSCC), which currently is mainly studied in nonsmall cell lung carcinoma cell models but lacking of ubiquitination studies on LSCC tissues. Here, we presented the ubiquitinated protein profiles of LSCC tissues to explore ubiquitination-involved molecular network alterations and identify abnormally ubiquitinated proteins as useful biomarkers for predictive, preventive, and personalized medicine (PPPM) in LSCC.MethodsAnti-ubiquitin antibody-based enrichment coupled with LC-MS/MS was used to identify differentially ubiquitinated proteins (DUPs) between LSCC and control tissues, followed by integrative omics analyses to identify abnormally ubiquitinated protein biomarkers for LSCC.ResultsTotally, 400 DUPs with 654 ubiquitination sites were identified,, and motifs A-X (1/2/3)-K* were prone to be ubiquitinated in LSCC tissues. Those DUPs were involved in multiple molecular network systems, including the ubiquitin–proteasome system (UPS), cell metabolism, cell adhesion, and signal transduction. Totally, 44 hub molecules were revealed by protein–protein interaction network analysis, followed by survival analysis in TCGA database (494 LSCC patients and 20,530 genes) to obtain 18 prognosis-related mRNAs, of which the highly expressed mRNAs VIM and IGF1R were correlated with poorer prognosis, while the highly expressed mRNA ABCC1 was correlated with better prognosis. VIM-encoded protein vimentin and ABCC1-encoded protein MRP1 were increased in LSCC, which were all associated with poor prognosis. Proteasome-inhibited experiments demonstrated that vimentin and MRP1 were degraded through UPS. Quantitative ubiquitinomics found ubiquitination level was decreased in vimentin and increased in MRP1 in LSCC. These findings showed that the increased vimentin in LSCC might be derived from its decreased ubiquitination level and that the increased MRP1 in LSCC might be derived from its protein synthesis > degradation. GSEA and co-expression gene analyses revealed that VIM and MRP1 were involved in multiple crucial biological processes and pathways. Further, TRIM2 and NEDD4L were predicted as E3 ligases to regulate ubiquitination of vimentin and MRP1, respectively.ConclusionThese findings revealed ubiquitinomic variations and molecular network alterations in LSCC, which is in combination with multiomics analysis to identify ubiquitination-related biomarkers for in-depth insight into the molecular mechanism and therapeutic targets and for prediction, diagnosis, and prognostic assessment of LSCC.
Application of TiO2 and ZnO nanoparticles immobilized on clay in wastewater treatment: a review
Authors: Mustapha S. , Ndamitso M. M. , Abdulkareem A. S. , Tijani J. O. , Shuaib D. T. , Ajala A. O. , Mohammed A. K. 
Published: January 2020

AbstractIncrease in industrial and anthropogenic activities leads to a decline in water quality. This necessitates the need for the removal of contaminants from industrial and domestic wastewater. Clay minerals are naturally abundant and non-toxic materials that found to be useful for remediation of emerging contaminants from wastewater. This review paper presents an insight into clay, the simplest material (in solgel techniques) for the synthesis of TiO2and ZnO, mechanisms of their reactions, analytical techniques used for characterizations, and their nanocomposites for wastewater treatment. Nanomaterials, such as nanoclay, titanium, and zinc oxide, have offered the opportunities of sequestering variety of pollutants in wastewater. TiO2and ZnO anchored on clay have been found to be good promising sequesters and have been explored for wastewater remediation via nanotechnology. This water treatment method includes adsorption/absorption, photocatalysis, and microbial disinfection. These nanocomposites provide more active surface sites and reduce the agglomeration of the nanoparticles, but leaching has been their shortcomings. To overcome this, the filtration technique may become significant for the removal and avoidance of fouling of wastewater. This can be achieved through the fabrication of nano-based filters using the nanocomposites.
Progressive effects of single-nucleotide polymorphisms on 16 phenotypic traits based on longitudinal data
Authors: Li Donghe , Kang Hahn , Lee Sanghun , Won Sungho 
Published: January 2020

Abstract
Background
There are many research studies have estimated the heritability of phenotypic traits, but few have considered longitudinal changes in several phenotypic traits together.

Objective
To evaluate the progressive effect of single nucleotide polymorphisms (SNPs) on prominent health-related phenotypic traits by determining SNP-based heritability ($$h_{snp}^{2}$$hsnp2) using longitudinal data.

Methods
Sixteen phenotypic traits associated with major health indices were observed biennially for 6843 individuals with 10-year follow-up in a Korean community-based cohort. Average SNP heritability and longitudinal changes in the total period were estimated using a two-stage model. Average and periodic differences for each subject were considered responses to estimate SNP heritability. Furthermore, a genome-wide association study (GWAS) was performed for significant SNPs.

Results
Each SNP heritability for the phenotypic mean of all sixteen traits through 6 periods (baseline and five follow-ups) were significant. Gradually, the forced vital capacity in one second (FEV1) reflected the only significant SNP heritability among longitudinal changes at a false discovery rate (FDR)-adjusted 0.05 significance level ($$h_{snp}^{2} = 0.171$$hsnp2=0.171, FDR = 0.0012). On estimating chromosomal heritability, chromosome 2 displayed the highest heritability upon periodic changes in FEV1. SNPs including rs2272402 and rs7209788 displayed a genome-wide significant association with longitudinal changes in FEV1 (P = 1.22 × 10−8 for rs2272402 and P = 3.36 × 10−7 for rs7209788). De novo variants including rs4922117 (near LPL, P = 2.13 × 10−15) of log-transformed high-density lipoprotein (HDL) ratios and rs2335418 (near HMGCR, P = 3.2 $$\times$$× 10−9) of low-density lipoprotein were detected on GWAS.

Conclusion
Significant genetic effects on longitudinal changes in FEV1 among the middle-aged general population and chromosome 2 account for most of the genetic variance.
New triazepine carboxylate derivatives: correlation between corrosion inhibition property and chemical structure
Authors: Alaoui K. , El Kacimi Y. , Galai M. , Serrar H. , Touir R. , Kaya S. , Kaya C. , Ebn Touhami M. 
Published: January 2020

AbstractIn this investigation, attempts have been made to study the corrosion inhibition properties of three new triazepine carboxylate compounds for mild steel in 1.0 M hydrochloric acid medium. The evaluation was carried out using mass loss, electrochemical impedance spectroscopy and polarization curves measurement. Impedance diagrams and Bode plots for uninhibited and inhibited systems were analyzed using Zview program. The fitted data observed trails in nearly the same pattern as the experimental results. It is showed that triazepine carboxylate compounds are very good inhibitors for mild steel corrosion in 1.0 M hydrochloric acid medium which act as mixed-type inhibitors. So, the inhibition efficiency was increased with inhibitor concentration in the order Cl–Me–CN > Me–CN > Cl–Me–CO2Et which depended on their molecular structures. Electrochemical impedance spectroscopy showed that all compounds act by the formation of a protective film at the metal surface. Surface analyses via SEM and Optical 3D profilometry were used to investigate the morphology of the steels before and after immersion in 1.0 M HCl solution containing inhibitors. The correspondence between inhibition property and molecular structure of the triazepine carboxylate compounds was investigated, using density functional theory (DFT). Experimental and DFT study was further supported by molecular dynamic simulations study.
How electrostatic and non-electrostatic interactions play a role in water wettability of possible nanostructure surfaces
Authors: Novin Nima , Shameli Abolghasem , Balali Ebrahim , Zomorodbakhsh Shahab 
Published: January 2020

Abstract
The present paper investigated the effects of the electrostatic and non-electrostatic interactions on the water wettability of a surface. Based on this aim, examinations are performed on the molybdenum disulfide (MoS2) as possible nanostructure surface. The results obtained through calculating the water contact angle on the MoS2 surface indicate which this surface is a weak hydrophobic substrate. The present simulations illustrate that the electrostatic interactions have little impact on the wettability amount of the MoS2 substrate. However, the molybdenum disulfide is composed of two charged parts with significant values. In addition, it is observed that the relation between density, van der Waals and electrostatic interactions is different from each other. It have been observed that the van der Waals interactions have direct relationship with water density while there is not anything between the electrostatic interactions and water density peak. The Obtained results via simulation demonstrate that the effectiveness of electrostatic interactions on the wettability depends on the sigma in the Lennard–Jones equation. In the other words, the role of electrostatic and van der Waals interactions on the wettability are not indissociable from each other and this method is sufficient in nanostructure systems.

Graphic abstract