bluuebunny/crossref_metadata_2025_split huggingface dataset:
First report of diazotrophic Brevundimonas spp. as growth enhancer and root colonizer of potato
Authors: Naqqash Tahir , Imran Asma , Hameed Sohail , Shahid Muhammad , Majeed Afshan , Iqbal Javed , Hanif Muhammad Kashif , Ejaz Shaghef , Malik Kauser Abdullah 
Published: July 2020

AbstractRhizobacteria contain various plant-beneficial traits and their inoculation can sustainably increase crop yield and productivity. The present study describes the growth-promoting potential ofBrevundimonasspp. isolated from rhizospheric soil of potato from Sahiwal, Pakistan. Four different putative strains TN37, TN39, TN40, and TN44 were isolated by enrichment on nitrogen-free malate medium and identified asBrevundimonasspp. based on their morphology, 16SrRNAgene sequence, and phylogenetic analyses. All strains containednifH gene except TN39 and exhibited nitrogen fixation potential through acetylene reduction assay (ARA) except TN40. Among all, theBrevundimonassp. TN37 showed maximum ARA and phosphate solubilization potential but none of them exhibited the ability to produce indole acetic acid. Root colonization studies using transmission electron microscopy and confocal laser scanning microscopy showed thatBrevundimonassp. TN37 was resident over the root surface of potato; forming sheets in the grooves in the rhizoplane. TN37, being the best among all was further evaluated in pot experiment using potato cultivar Kuroda in sterilized sand. Results showed thatBrevundimonassp. TN37 increased growth parameters and nitrogen uptake as compared to non-inoculated controls. Based on the results obtained in this study, it can be suggested thatBrevundimonasspp. (especially TN37) possess the potential to improve potato growth and stimulate nitrogen uptake. This study is the first report ofBrevundimonasspp. as an effective PGPR in potato.
Functional fine-mapping of noncoding risk variants in amyotrophic lateral sclerosis utilizing convolutional neural network
Authors: Yousefian-Jazi Ali , Sung Min Kyung , Lee Taeyeop , Hong Yoon-Ho , Choi Jung Kyoon , Choi Jinwook 
Published: July 2020

AbstractRecent large-scale genome-wide association studies have identified common genetic variations that may contribute to the risk of amyotrophic lateral sclerosis (ALS). However, pinpointing the risk variants in noncoding regions and underlying biological mechanisms remains a major challenge. Here, we constructed a convolutional neural network model with a large-scale GWAS meta-analysis dataset to unravel functional noncoding variants associated with ALS based on their epigenetic features. After filtering and prioritizing of candidates, we fine-mapped two new risk variants, rs2370964 and rs3093720, on chromosome 3 and 17, respectively. Further analysis revealed that these polymorphisms are associated with the expression level of CX3CR1 and TNFAIP1, and affect the transcription factor binding sites for CTCF, NFATc1 and NR3C1. Our results may provide new insights for ALS pathogenesis, and the proposed research methodology can be applied for other complex diseases as well.
Autonomous oil flow generated by self-oscillating polymer gels
Authors: Yoshimura Kyosuke , Otsuka Yuji , Mao Zebing , Cacucciolo Vito , Okutaki Takashi , Yamagishi Hideto , Hashimura Shinji , Hosoya Naoki , Sato Tasuku , Yamanishi Yoko , Maeda Shingo 
Published: July 2020

AbstractThe previously reported gel and polymer actuators require external inputs, such as batteries, circuits, electronic circuits, etc., compared with autonomous motions produced by the living organisms. To realize the spontaneous motions, here, we propose to integrate a power supply, actuators, and control into a single-component self-oscillating hydrogel. We demonstrate self-actuating gel pumps driven by the oscillatory Belousov–Zhabotinsky (BZ) reaction without electronic components. We have developed the volume oscillation of gels synchronized with the BZ reaction (BZ gel). Since the self-actuating gel pumps are driven by chemo-mechanical energy from BZ gels, the self-actuating gel pumps don’t require complex wiring designs, energy supply, and assembling. The mechanical work generated by BZ gels is extremely small. We formulated the thermodynamic cycle of BZ gels and maximized mechanical work. We found that pre-stretched BZ gel shows larger mechanical works. We physically separated the BZ gels and working fluid to create practical pumps. By using optimizing mechanical generated by BZ gels, we demonstrated the self-actuating gel pumps that transfer mechanical work through a stretchable elastomer membrane.
Critical risk analysis of metals toxicity in wastewater irrigated soil and crops: a study of a semi-arid developing region
Authors: Mahfooz Yusra , Yasar Abdullah , Guijian Liu , Islam Qamer Ul , Akhtar Amtul Bari Tabinda , Rasheed Rizwan , Irshad Samina , Naeem Urooj 
Published: July 2020

AbstractToxic elemental exposure through consumption of contaminated crops is becoming a serious concern for human health. Present study is based on the environment and health risk assessment of wastewater irrigated soil and crops in a semi-arid region Faisalabad, Pakistan. The concentrations of potentially toxic elements (Cu, Cr, Mn, Fe, Pb, Zn, Ni) were analysed by atomic absorption spectrometer in five different crops (Corn, rice, wheat, sugarcane and millet), while, their topsoil’s and multi targeted risks analysis were assessed. Results showed, the mean values of Pb and Zn were higher in crop than Food and Agriculture Organization guidelines for food additives and contaminants. A strong positive correlation was found among wastewater and crop’s toxic metals (r2values in Cu, Zn, Pb, Ni and Cr were 0.913, 0.804, 0.752, 0.694, 0.587 respectively). Whereas, a strong correlation was also found among soil and wastewater lead (r2 = 0.639). The calculations of Nemerow Integrated Pollution Index (NIPI) showed the soil samples maximum pollution limit (NIPI > 3) and Potential Ecological Risk Index (PERI) was found to be higher than maximum limit (PERI > 600) for all samples. While, for non-carcinogenic risk, Hazard Index (HI) values in adult were near threshold (HI > 1) for all crop samples. In children, the HI values for Corn, Rice and Wheat were above threshold limit and for Sugarcane and Millet, these were near to threshold. Cancer risk values for Cr found higher than safe limit (1 × 10–6) in adult and children for crop samples. Crop irrigation by wastewater irrigation is a prominent alternative option for water scarce countries, however prior testing and treatment of such wastewater streams must be employed to minimize the adverse impacts on human health and environment.
Volumetric lung nodule segmentation using adaptive ROI with multi-view residual learning
Authors: Usman Muhammad , Lee Byoung-Dai , Byon Shi-Sub , Kim Sung-Hyun , Lee Byung-il , Shin Yeong-Gil 
Published: July 2020

AbstractAccurate quantification of pulmonary nodules can greatly assist the early diagnosis of lung cancer, enhancing patient survival possibilities. A number of nodule segmentation techniques, which either rely on a radiologist-provided 3-D volume of interest (VOI) or use the constant region of interests (ROIs) for all the slices, are proposed; however, these techniques can only investigate the presence of nodule voxels within the given VOI. Such approaches restrain the solutions to freely investigate the nodule presence outside the given VOI and also include the redundant structures (non-nodule) into VOI, which limits the segmentation accuracy. In this work, a novel semi-automated approach for 3-D segmentation of lung nodule in computerized tomography scans, has been proposed. The technique is segregated into two stages. In the first stage, a 2-D ROI containing the nodule is provided as an input to perform a patch-wise exploration along the axial axis using a novel adaptive ROI algorithm. This strategy enables the dynamic selection of the ROI in the surrounding slices to investigate the presence of nodules using a Deep Residual U-Net architecture. This stage provides the initial estimation of the nodule utilized to extract the VOI. In the second stage, the extracted VOI is further explored along the coronal and sagittal axes, in patchwise fashion, with Residual U-Nets. All the estimated masks are then fed into a consensus module to produce a final volumetric segmentation of the nodule. The algorithm is rigorously evaluated on LIDC–IDRI dataset, which is the largest publicly available dataset. The proposed approach achieved the average dice score of 87.5%, which is significantly higher than the existing state-of-the-art techniques.
A FRET-based screening method to detect potential inhibitors of the binding of CNNM3 to PRL2
Authors: Cai Faji , Huang Yichen , Wang Mengqi , Sun Minxuan , Zhao Yimeng , Hattori Motoyuki 
Published: July 2020

AbstractThe cyclin M (CNNM) family of Mg2+ transporters is reported to promote tumour progression by binding to phosphatase of regenerating liver (PRL) proteins. Here, we established an assay for detection of the binding between the cystathionine-beta-synthase (CBS) domain of human CNNM3 (a region responsible for PRL binding) and human PRL2 using fluorescence resonance energy transfer (FRET) techniques. By fusing YPet to the C-terminus of the CNNM3 CBS domain and CyPet to the N-terminus of PRL2, we performed a FRET-based binding assay with purified proteins in multiwell plates and successfully detected the changes in fluorescence intensity derived from FRET with a reasonable Kd. We then confirmed that the addition of non-YPet-tagged CNNM3 and non-CyPet-tagged PRL proteins inhibited the changes in FRET intensity, whereas non-YPet-tagged CNNM3 with a mutation at the PRL2-binding site did not exhibit such inhibition. Furthermore, newly synthesized peptides derived from the CNNM loop region, with the PRL-binding sequences of the CNNM3 CBS domain, inhibited the interactions between CNNM3 and PRL2. Overall, these results showed that this method can be used for screening to identify inhibitors of CNNM-PRL interactions, potentially for novel anticancer therapy.
Polymerization mechanism of natural lacquer sap with special phase structure
Authors: Yang Jianhong , Chen Nan , Zhu Jianfeng , Cai Jun , Deng Jianping , Pan Feifei , Gao Lianghe , Jiang Zhenfei , Shen Fengqin 
Published: July 2020

AbstractLacquer sap is a water-in-oil natural emulsion with high viscosity. In nature, it exudes from the phloem of lacquer tree to repair its wounds in the presence of O2. So far, it is unclear how rapid and smooth polymerization of urushiol is achieved in such a viscous sap. Here, we find that there is a diffuse interface layer with 2.43 nm of thickness between two phases. The interface layer consists of urushiol, urushiol–laccase complex, urushiol–stellacyanin complex and water-insoluble glycoprotein. Polymerization of urushiol is realized by multicomponent synergistic effect. Radicals are first formed by laccase-catalyzed oxidation of urushiol at the interface layer, then are transferred to the urushiol oil phase via wate-insoluble glycoprotein and initiate the polymerization of urushiol there. Stellacyanin inhibits the formation of certain radicals and controls the concentration of phenoxy radicals at the interface layer. Through the inhibition of radicals by stellacyanin and the electron transfer mediated by water-insoluble glycoprotein, the polymerization of urushiol at the interface layer is inhibited. This ensures that O2 can continuously penetrate into the aqueous phase to oxidize the reduced laccase so that the urushiol polymerization can continue smoothly. This polymerization mechanism provides an idea for developing new chemical reaction systems.
Highly improved convergence approach incorporating edge conditions for scattering analysis of graphene gratings
Authors: Hwang Ruey-Bing 
Published: July 2020

AbstractThis research developed an effective and efficient approach for improving the slow convergence in the scattering analysis of a one-dimensional graphene grating, made of a periodic array of parallel graphene strips, illuminated by a TM-polarized plane wave. Specifically, the electric fields over the graphene strips and slit regions in a unit cell are individually expressed as an expansion of local basis functions inherently satisfying edge conditions. Interestingly, convergence rate is highly improved compared to the customary and modified Fourier modal method. Additionally, with the aid of local basis functions, the Gibbs phenomenon occurring at both edges of graphene strip can be removed.
Shifts in the microbiota associated with male mosquitoes (Aedes aegypti) exposed to an obligate gut fungal symbiont (Zancudomyces culisetae)
Authors: Frankel-Bricker Jonas 
Published: July 2020

AbstractResearch characterizing arthropod-associated microbiota has revealed that microbial dynamics can have an important impact on host phenotypic traits. The influence of fungi on these interactions are emerging as targets for research, especially in organisms associated with global human health. A recent study demonstrated colonization of a widespread gut fungus (Zancudomyces culisetae) in a larval mosquito (Aedes aegypti) digestive tract affected microbiomes in larvae and newly emerged adult females (Frankel-Bricker et al. Appl Environ Microbiol, 2020.https://doi.org/10.1128/AEM.02334-19) but did not investigate these processes in males. The objective of the study presented here was to assess fungal influences on adult male mosquito microbiomes to enable a more complete assessment of fungal–bacterial–host interactions in theA. aegypti–Z. culisetaesystem. Sequencing of 16S rRNA gene amplicons from microbiomes harbored in adult males directly after emerging from pupae revealed larval fungal exposure significantly decreased overall microbial community diversity, altered microbiome composition and structure, and decreased within-group microbiome variation across individuals. Further, bacteria in the familyBurkholderiaceaewere present in high abundance in fungal-exposed males, likely contributing to the disparate microbiota between treatment groups. Comparisons between male and the female microbiomes analyzed in Frankel-Bricker et al. (2020), showed distinct shifts in bacterial communities incurred by larval exposure to fungi, potentially revealing sex-specific fungal–bacterial–host dynamics inA. aegypti. These findings highlight the complex role a gut fungus can play in influencing the microbial communities harbored in an important insect and emphasize the significance of accounting for an organism’s sex when studying fungal–bacterial–host dynamics.
CTLA-4 rs231775 and risk of acute renal graft rejection: an updated meta-analysis with trial sequential analysis
Authors: Cargnin Sarah , Galli Ubaldina , Shin Jae Il , Terrazzino Salvatore 
Published: July 2020

AbstractContrasting results exist on the association between CTLA-4 rs231775 and acute rejection in kidney transplant recipients. We herein conducted an updated systematic review with meta-analysis and trial sequential analysis (TSA) to clarify this relationship and to establish whether the current evidence is sufficient to draw firm conclusions. In addition, noteworthiness of significant pooled odds ratios (ORs) was estimated by false positive report probability (FPRP). A comprehensive search was performed through PubMed, Web of Knowledge, Cochrane Library and Open Grey up to October 2019. Fifteen independent cohorts, including a total of 5,401 kidney transplant recipients, were identified through the systematic review. Overall, no association was detected with the allelic (OR 1.07, 95% CI 0.88–1.30, P = 0.49), dominant (OR 0.94, 95% CI 0.73–1.22, P = 0.66) or the recessive (OR 1.18, 95% CI 0.97–1.43, P = 0.096) model of CTLA-4 rs231775. In each genetic model, the cumulative Z-curve in TSA crossed the futility boundary and entered the futility area. In addition, none of the significant genetic comparisons detected in the subsequent and sensitivity analyses or in previously reported meta-analyses were found to be noteworthy by FPRP. In conclusion, this study provides strong evidence that CTLA-4 rs231775 is not a clinically-relevant genetic risk determinant of acute rejection after renal transplantation.
Congenital abnormalities of the retinal vasculature in neurofibromatosis type I
Authors: Chun Bo Young , Yoon Jung Hyun , Son Byeong Jae , Hwang Su-Kyeong , Lim Hyun Taek 
Published: July 2020

AbstractThe aim of this cross-sectional study was to investigate congenital abnormalities of the retinal vasculature (CARVs) in patients with neurofibromatosis type I (NF-1). Forty-eight patients (96 eyes) with NF-1 diagnosed according to the National Institutes of Health (NIH) criteria and 48 healthy controls were included in this study. Standard fundus photographs were obtained for each subject to evaluate the presence and frequency of CARVs. The sensitivity, specificity, and diagnostic accuracy of different cut-off numbers of CARVs were compared with those of the NIH criteria. Forty-four (91.7%) patients in the NF-1 group demonstrated either supranumeraty optic disc vessels or triple branching of the retinal vasculature, and 22 patients (45.8%) demonstrated both findings. The frequencies of these two CARVs were significantly different between the two groups (p < 0.00001). A cut-off value of either one for supranumerary optic disc vessels or triple branching showed the highest accuracy along with sensitivity and specificity of 91.7% and 87.5%. CARVs such as supranumerary optic disc vessels or triple branching were frequently observed in NF-1 patients, and their occurrence was unrelated to the age of patients. Thus, these CARVs could be added as new ophthalmologic manifestions for NF-1 and may potentially enable early diagnosis of NF-1.
The structure of scleractinian coral skeleton analyzed by neutron diffraction and neutron computed tomography
Authors: Ivankina Tatiana I. , Kichanov Sergey E. , Duliu Octavian G. , Abdo Safa Y. , Sherif Mohamed M. 
Published: July 2020

AbstractTwo analytical methods based on the neutrons high penetrability, i.e. neutron diffraction (ND) and neutron computed tomography (NCT) were used to investigate the structure of the aragonitic skeleton of an exemplar/sample of Dipastraea pallida (Dana 1846), a modern hermatypic coral. ND was used to reconstruct the orientation distribution function (ODF) of the crystalline fibrils which compose the coral skeleton. Accordingly, 684 ND spectra were analyzed using the Rietveld method. The result confirmed the aragonite as the sole mineral component of coral skeleton, allowing to recalculate the ODF of aragonite fibrils and to represent it by means of (100), (010) and (001) crystallographic planes pole figures (PF). Experimental PF showed a remarkable similarity with PF recalculated by considering that all aragonite fibrils are oriented either along the growth axis of polyp cups or perpendicular to this direction. This result confirmed the previous observations based on optical microscopy, proving at the same time the availability of ND for such types of investigations. In turn, NCT evidenced the individual polyp cups, their interlocked 3D rigid porous structure as well as a periodic variation of density which could be attributed to a seasonal influence of the marine environment. Different from the classical X-ray computed tomography, the NCT, in view of neutron high cross-section for hydrogen, demonstrated the presence of a small amount of organic matter, otherwise transparent for X- and gamma rays.
The contribution of water extractable forms of plant nutrients to evaluate MSW compost maturity: a case study
Authors: Jamroz Elzbieta , Bekier Jakub , Medynska-Juraszek Agnieszka , Kaluza-Haladyn Andrea , Cwielag-Piasecka Irmina , Bednik Magdalena 
Published: July 2020

AbstractThe object of the experiment was to evaluate municipal solid waste (MSW) compost. Composting was carried out in a pile under aerobic conditions. Total content as well as water-extractable forms of macro and microelements were analysed during composting. Nutrient solubility indices were calculated for samples taken at various stages of maturity. The soluble forms of C, P, K, Ca and Mg decreased relatively to their total forms following maturation phases. For all micronutrients tested, a significant reduction in the proportion of soluble forms in relation to their total content was observed with an increase in composting time. In mature compost, low solubility were found for nitrogen, potassium, sodium and magnesium, which may indicate that the final product is a good source of these nutrients. The solubility index (percentage share of water-extractable forms of macro- and micronutrients in the total content) for iron indicates that the composting process does not affect its degree of solubility. Solubility index instead of the content of water-extractable forms of chosen macro- and microelements could be taken into account in determining the degree of MSW compost maturity.
Uncovering unique plasticity in life history of an endangered centenarian fish
Authors: Hamel Martin J. , Spurgeon Jonathan J. , Steffensen Kirk D. , Pegg Mark A. 
Published: July 2020

AbstractThe ability to adapt to changing environments is fundamental for species persistence. Both plasticity and genetic selection are potential drivers that allow for traits to be advantageous, thus leading to increases in survival or fitness. Identifying phenotypic plasticity in life history traits of long-lived organisms can be difficult owing to high survival, long generation times, and few studies at sufficient spatial and temporal scales to elicit a plastic response within a population. To begin to understand phenotypic plasticity of a long-lived freshwater fish in response to environmental conditions, we used a long-term data set consisting of over 1,200 mark-recapture events to inform our understanding of dynamic rate functions and life history attributes. Furthermore, we used a common garden experimental approach to confirm whether changes in life history traits are in response to plasticity in the reaction norm or are genetically derived. Using these approaches, we demonstrated differences in life history traits among Pallid Sturgeon (Scaphirhynchus albus) occupying river segments of varying physical and hydrological stress. The common garden experiment corroborated plastic phenotypic expression in reaction norms for age at first maturity, longevity, fecundity, and maximum size. These growth-mediated attributes resulted in differences in overall fitness traits, where Pallid Sturgeon fecundity was greater than a tenfold difference and 3–6 times the number of life-time spawning events. Anthropogenic modifications to river form and function are likely responsible for the variation in life history attributes resulting from an increased metabolic demand for maintaining station, foraging, and migration. Collectively, our approach provided surprising insight into the capabilities of a centenarian fish to dramatically respond to a changing environment.
Extraction technique of trap states based on transient photo-voltage measurement
Authors: Lin Zedong 
Published: July 2020

AbstractThis article puts forward a technique for extracting the density of trap states (DOST) distribution based on the transient photo-voltage (TPV) measurement result. We prove that when the TPV result is linear, the DOST distribution is exponential type and vice versa. Compared to the approach based on the space charge limited current measurement, the method given in this paper has the advantage of requiring less calculation. The results obtained by our method provides a guidance for preparing less trap states solar cells.