Lung cancer has a high mortality rate, but an early diagnosis can contribute to a favorable prognosis. A liquid biopsy that captures and detects tumor-related biomarkers in body fluids has great ...potential for early-stage diagnosis. Exosomes, nanosized extracellular vesicles found in blood, have been proposed as promising biomarkers for liquid biopsy. Here, we demonstrate an accurate diagnosis of early-stage lung cancer, using deep learning-based surface-enhanced Raman spectroscopy (SERS) of the exosomes. Our approach was to explore the features of cell exosomes through deep learning and figure out the similarity in human plasma exosomes, without learning insufficient human data. The deep learning model was trained with SERS signals of exosomes derived from normal and lung cancer cell lines and could classify them with an accuracy of 95%. In 43 patients, including stage I and II cancer patients, the deep learning model predicted that plasma exosomes of 90.7% patients had higher similarity to lung cancer cell exosomes than the average of the healthy controls. Such similarity was proportional to the progression of cancer. Notably, the model predicted lung cancer with an area under the curve (AUC) of 0.912 for the whole cohort and stage I patients with an AUC of 0.910. These results suggest the great potential of the combination of exosome analysis and deep learning as a method for early-stage liquid biopsy of lung cancer.
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IJS, KILJ, NUK, PNG, UL, UM
Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and ...evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that is useful for genome wide comparisons and visualization of orthologous clusters. OrthoVenn provides coverage of vertebrates, metazoa, protists, fungi, plants and bacteria for the comparison of orthologous clusters and also supports uploading of customized protein sequences from user-defined species. An interactive Venn diagram, summary counts, and functional summaries of the disjunction and intersection of clusters shared between species are displayed as part of the OrthoVenn result. OrthoVenn also includes in-depth views of the clusters using various sequence analysis tools. Furthermore, OrthoVenn identifies orthologous clusters of single copy genes and allows for a customized search of clusters of specific genes through key words or BLAST. OrthoVenn is an efficient and user-friendly web server freely accessible at http://probes.pw.usda.gov/OrthoVenn or http://aegilops.wheat.ucdavis.edu/OrthoVenn.
OrthoVenn is a powerful web platform for the comparison and analysis of whole-genome orthologous clusters. Here we present an updated version, OrthoVenn2, which provides new features that facilitate ...the comparative analysis of orthologous clusters among up to 12 species. Additionally, this update offers improvements to data visualization and interpretation, including an occurrence pattern table for interrogating the overlap of each orthologous group for the queried species. Within the occurrence table, the functional annotations and summaries of the disjunctions and intersections of clusters between the chosen species can be displayed through an interactive Venn diagram. To facilitate a broader range of comparisons, a larger number of species, including vertebrates, metazoa, protists, fungi, plants and bacteria, have been added in OrthoVenn2. Finally, a stand-alone version is available to perform large dataset comparisons and to visualize results locally without limitation of species number. In summary, OrthoVenn2 is an efficient and user-friendly web server freely accessible at https://orthovenn2.bioinfotoolkits.net.
The objective of this study is to examine the user's adoption aspects of autonomous vehicle, as well as to investigate what factors drive people to trust an autonomous vehicle. A model explaining the ...impact of different factors on autonomous vehicles' intention is developed based on the technology acceptance model and trust theory. A survey of 552 drivers was conducted and the results were analyzed using partial least squares. The results demonstrated that perceived usefulness and trust are major important determinants of intention to use autonomous vehicles. The results also show that three constructs-system transparency, technical competence, and situation management-have a positive effect on trust. The study identified that trust has a negative effect on perceived risk. Among the driving-related personality traits, locus of control has significant effects on behavioral intention, whereas sensation seeking did not. This study investigated that the developed model explains the factors that influence the acceptance of autonomous vehicle. The results of this study provide evidence on the importance of trust in the user's acceptance of an autonomous vehicle.
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BFBNIB, DOBA, GIS, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
5.
Plant hormones in salt stress tolerance Ryu, Hojin; Cho, Yong-Gu
Journal of plant biology = Singmul Hakhoe chi,
06/2015, Volume:
58, Issue:
3
Journal Article
Peer reviewed
Plants, as a sessile organism, rely on the endogenous regulators for the modulation of growth and development under severe stress conditions for their survival. Plant hormones have long been ...considered as essential endogenous molecules involved in regulating plant development and tolerance or susceptibility of diverse stresses including salinity stress. Plants are frequently exposed to numerous adverse environmental factors such as drought, cold, heat and high salinity. Under high salinity, plants rapidly reduce the growth and developmental programs in response to the stress due to either the effects of specific ions on metabolism, or adverse water relations. Recent investigations on the functional roles of plant hormones in response to unfavorable environmental conditions have eventually unravel their potentials in coffering tolerance to such conditions including salinity stress. In this review, we will present recent progress of our understanding to the important role of plant hormones including abscisic acid (ABA), auxin, cytokinins (CK), brassinosteroids (BRs), jasmonate, gibberellin (GA) and ethylene for alleviation of salt stress in plants.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Summary
Until recently, achieving a reference‐quality genome sequence for bread wheat was long thought beyond the limits of genome sequencing and assembly technology, primarily due to the large ...genome size and > 80% repetitive sequence content. The release of the chromosome scale 14.5‐Gb IWGSC RefSeq v1.0 genome sequence of bread wheat cv. Chinese Spring (CS) was, therefore, a milestone. Here, we used a direct label and stain (DLS) optical map of the CS genome together with a prior nick, label, repair and stain (NLRS) optical map, and sequence contigs assembled with Pacific Biosciences long reads, to refine the v1.0 assembly. Inconsistencies between the sequence and maps were reconciled and gaps were closed. Gap filling and anchoring of 279 unplaced scaffolds increased the total length of pseudomolecules by 168 Mb (excluding Ns). Positions and orientations were corrected for 233 and 354 scaffolds, respectively, representing 10% of the genome sequence. The accuracy of the remaining 90% of the assembly was validated. As a result of the increased contiguity, the numbers of transposable elements (TEs) and intact TEs have increased in IWGSC RefSeq v2.1 compared with v1.0. In total, 98% of the gene models identified in v1.0 were mapped onto this new assembly through development of a dedicated approach implemented in the MAGAAT pipeline. The numbers of high‐confidence genes on pseudomolecules have increased from 105 319 to 105 534. The reconciled assembly enhances the utility of the sequence for genetic mapping, comparative genomics, gene annotation and isolation, and more general studies on the biology of wheat.
Significance Statement
This new release of bread wheat cv. Chinese Spring reference genome sequence, IWGSC RefSeq v2.1, features correction of assembly errors affecting approximately 10% of the prior IWGSC RefSeq v1.0 release using genome‐wide optical maps and filling of gaps with single‐molecule long‐reads as well as incorporating re‐annotation of TEs and re‐computation of gene coordinates. These refinements enhance the sequence utility for breeding and research applications.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Genome-editing technology is a type of genetic engineering in which DNA is inserted into, replaced in, or deleted from the genome using artificially engineered nucleases or genetic scissors ...
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Non-invasive delivery of artificial implants, stents or devices in patients is vital for rapid and successful recovery. Unfortunately, because the delivery passage is often narrower than the size of ...the delivered object, a compromise between the shape that is effective at the targeted location and a thin form that allows smooth unobstructed travel to the destination is needed. We address this problem through two key technologies: 3D printing and shape memory polymers (SMPs). 3D printing can produce patient-customizable objects, and SMPs can change their initially formed shape to the final desired shape through external stimulation. Using these two technologies, we examine the design and fabrication of bifurcated stents. This study presents a mock-up where blood vessels are fabricated using moulded silicon, which supports the effectiveness of the proposed method. The experimental results reveal that a bifurcated stent with a kirigami structure can smoothly travel inside a vessel without being obstructed by branched parts. We believe that this work can improve the success rate of stent insertion operations in medicine.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
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•Alkali modification improves physicochemical properties of pristine SCG biochars.•Chemisorption is responsible for adsorptions of micropolluants by SCG biochars.•Adsorption isotherms ...of micropollutants are highly affected by alkali modification.•Log D values play a critical role in removal of micropollutants by SCG biochars.•Alkali-modified SCG biochars exhibit higher adsorption capacities of micropolluants.
This study investigated the single and competitive adsorption characteristics of micropollutants using the pristine and alkali-modified spent coffee grounds (SCG) biochars. The alkali modification substantially improved the physicochemical characteristics of the SCG biochars (specific surface area and pore volume), which may have led to differences in the adsorption behaviors of the micropollutants. The pseudo second order model (R2 ≥ 0.990) better described the single and competitive adsorption kinetics than the pseudo first order model (R2 ≥ 0.664). It is evident that chemisorption played a key role in the removal of the micropollutants by the pristine and alkali-modified SCG biochars. The single and competitive adsorptions of the micropollutants were highly dependent on the solution pH and ionic strength since the pore-filling effects, electrostatic and hydrophobic interactions governed their removal by the pristine and alkali-modified SCG biochars. The higher removal efficiencies of the micropollutants by the alkali-modified SCG biochars (≥ 44.5%) in the presence of dissolved organic matter compared to the pristine SCG biochars (≤ 18.5%) support the assumption that alkali modification could markedly reinforce the surface structural properties of the SCG biochars related to the adsorption capacities.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
This study investigated the competitive adsorption mechanisms of pharmaceuticals (i.e., naproxen, diclofenac, and ibuprofen) toward the pristine and NaOH-activated biochars from spent coffee wastes ...(SCW) in lake water and wastewater effluent. The kinetic and isotherm studies revealed that the improved physicochemical characteristics and physically homogenized surfaces of the pristine SCW biochar through the chemical activation with NaOH were beneficial to the adsorption of pharmaceuticals (competitive equilibrium adsorption capacity (Qe, exp): NaOH-activated SCW biochar (61.25–192.07 μmol/g) > pristine SCW biochar (14.81–20.65 μmol/g)). The adsorptive removal of naproxen (Qe, exp = 14.81–18.81 μmol/g), diclofenac (Qe, exp = 15.73–20.00 μmol/g), and ibuprofen (Qe, exp = 16.20–20.65 μmol/g) for the pristine SCW biochar showed linear correlations with their hydrophobicity (log D at pH 7.0: ibuprofen (1.71) > diclofenac (1.37) > naproxen (0.25)). However, their Qe, exp values for the NaOH-activated SCW biochar (naproxen (176.39–192.07 μmol/g) > diclofenac (78.44–98.74 μmol/g) > ibuprofen (61.25–80.02 μmol/g)) were inversely correlated to the order of their log D values. These results suggest that the reinforced aromatic structure of the NaOH-activated SCW biochar facilitated the π-π interaction. The calculated thermodynamic parameters demonstrated that the competitive adsorption of pharmaceuticals on the NaOH-activated SCW biochar compared to pristine SCW biochar occurred more spontaneously over the entire pH (5.0–11.0) and ionic strength (NaCl: 0–0.125 M) ranges. These observations imply that the NaOH-activated SCW biochar might be potentially applicable for the removal of pharmaceuticals in lake water and wastewater effluent.
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•Competitive adsorption of pharmaceuticals investigated under real water matrices.•NaOH-activated SCW biochar has high specific surface area and total pore volume.•NaOH-activated SCW biochar eliminates NPX, DCF, and IBU more effectively.•Adsorption of pristine SCW biochar corresponds to Log D values of micropollutants.•Increased aromaticity of NaOH-activated SCW biochar stimulates π-π interaction.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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