Abstract：
:A larger amount of sequence data in private and public databases produced by next-generation sequencing put new challenges due to limitation associated with the alignment-based method for sequence comparison. So, there is a high need for faster sequence analysis algorithms. In this study, we developed an alignment-free algorithm for faster sequence analysis. The novelty of our approach is the inclusion of fuzzy integral with Markov chain for sequence analysis in the alignment-free model. The method estimate the parameters of a Markov chain by considering the frequencies of occurrence of all possible nucleotide pairs from each DNA sequence. These estimated Markov chain parameters were used to calculate similarity among all pairwise combinations of DNA sequences based on a fuzzy integral algorithm. This matrix is used as an input for the neighbor program in the PHYLIP package for phylogenetic tree construction. Our method was tested on eight benchmark datasets and on in-house generated datasets (18 s rDNA sequences from 11 arbuscular mycorrhizal fungi (AMF) and 16 s rDNA sequences of 40 bacterial isolates from plant interior). The results indicate that the fuzzy integral algorithm is an efficient and feasible alignment-free method for sequence analysis on the genomic scale.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Saw AK,Raj G,Das M,Talukdar NC,Tripathy BC,Nandi Sdoi
10.1038/s41598-019-40452-6subject
Has Abstractpub_date
2019-03-06 00:00:00pages
3753issue
1issn
2045-2322pii
10.1038/s41598-019-40452-6journal_volume
9pub_type
杂志文章abstract：:Circulation through cerebral collaterals can maintain tissue viability until reperfusion is achieved. However, collateral circulation is time limited, and failure of collaterals is accelerated in the aged. Remote ischemic perconditioning (RIPerC), which involves inducing a series of repetitive, transient peripheral cy...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-69122-8
更新日期：2020-07-24 00:00:00
abstract：:Hydrocarbons fuel our economy. Furthermore, intermediate goods and consumer products are often hydrocarbon-based. Beside all the progress they made possible, hydrogen-containing substances can have severe detrimental effects on materials exposed to them. Hydrogen-assisted failure of iron alloys has been recognised mor...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-60370-2
更新日期：2020-02-27 00:00:00
abstract：:Atropine eye drops and myopic retinal defocus each slow progression of myopia (short-sight). They also cause thickening of the choroid, and it has been suggested that the thickening is a precursor for reduced eye growth and slowed myopia progression. We investigated whether choroidal thickening due to optical defocus ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-75342-9
更新日期：2020-10-27 00:00:00
abstract：:Anatomically realistic organ replicas or phantoms allow for accurate studies and reproducible research. To recreate a human kidney, mimicry of the elastic properties of the human kidney is crucial. However, none of the related work addressed the design and development of a kidney phantom using only silicone as materia...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-68886-3
更新日期：2020-07-16 00:00:00
abstract：:Chemical reagents used in traditional mineral processing can be toxic and hazardous for the environment. Therefore, the use of biotechnological methods is becoming increasingly important. Great hopes are being placed in the use of microorganisms for bio-beneficiation of raw materials. However, assessment of adhesion a...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-49406-4
更新日期：2019-09-10 00:00:00
abstract：:Pyrochar (PC) is always with high pH value, and improper application might increase rice paddy ammonia volatilization (PAV), which is the main nitrogen loss through air during rice production. Differently, hydrochar (HC) takes the advantages of high productive rate and always with lower pH value compared with PC. Howe...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-76213-z
更新日期：2020-11-05 00:00:00
abstract：:In this paper, we investigate the unified bound of quantum speed limit time in open systems based on the modified Bures angle. This bound is applied to the damped Jaynes-Cummings model and the dephasing model, and the analytical quantum speed limit time is obtained for both models. As an example, the maximum coherent ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-62409-w
更新日期：2020-03-26 00:00:00
abstract：:Pseudoxanthoma Elasticum (PXE) is a rare disorder characterized by fragmentation and progressive calcification of elastic fibres in connective tissues. Although arterial hypertension (AHT) has been reported in PXE patients, its impact on pathological manifestations has as yet been unexplored. We investigated the conse...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-52808-z
更新日期：2019-11-08 00:00:00
abstract：:HIV-1 env sequencing enables predictions of viral coreceptor tropism and phylogenetic investigations of transmission events. The aim of the study was to estimate the contribution of non-R5 strains to the viral spread in Poland. Partial proviral env sequences were retrieved from baseline blood samples of patients with ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-41407-7
更新日期：2019-03-21 00:00:00
abstract：:Complex networks characterize the nature of internal/external interactions in real-world systems including social, economic, biological, ecological, and technological networks. Two issues keep as obstacles to fulfilling control of large-scale networks: structural controllability which describes the ability to guide a ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-22655-5
更新日期：2018-03-15 00:00:00
abstract：:A major task of episodic memory is to create unique, distinguishable representations of highly overlapping perceptual inputs. Several studies on this basic function have shown that it is based on the intact functioning of certain subregions of the hippocampus and is among the most sensitive behavioral indicators of mi...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-73374-9
更新日期：2020-10-02 00:00:00
abstract：:We advance the concept that the charge factors of the simple overlap model and the polarizabilities of Judd-Ofelt theory for the luminescence of europium complexes can be effectively and uniquely modeled by perturbation theory on the semiempirical electronic wave function of the complex. With only three adjustable con...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep13695
更新日期：2015-09-02 00:00:00
abstract：:An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...
journal_title：Scientific reports
pub_type： 已发布勘误
doi：10.1038/s41598-020-64153-7
更新日期：2020-04-29 00:00:00
abstract：:In this report, we propose and demonstrate an air-mode photonic crystal ring resonator (PhCRR) on silicon-on-insulator platform. Air mode is utilized to confine the optical field into photonic crystal (PhC) air holes, which is confirmed by the three-dimensional finite-difference time-domain simulation. PhCRR structure...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep19999
更新日期：2016-01-28 00:00:00
abstract：:Weight regain is one of the most common problems in the long-term after bariatric surgery. It is unknown if high-intensity exercise programs applied in late phases of post-surgical follow-up could counteract this trend. After a 3-year follow-up, 21 patients underwent sleeve gastrectomy were randomized into an exercise...
journal_title：Scientific reports
pub_type： 杂志文章,随机对照试验
doi：10.1038/s41598-020-60044-z
更新日期：2020-02-20 00:00:00
abstract：:A new electrically small antenna with size ka = 0.415 is presented, fabricated and measured in this work. This is intrinsically matched to 50 Ω, has omni-directional and linear-polarized radiation pattern in the horizontal plane with maximum directivity of 1.75 dBi and simulated radiation efficiency of 93%. The antenn...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-33388-w
更新日期：2018-10-09 00:00:00
abstract：:Cholecystokinin (CCK) and leptin are satiety-controlling peptides, yet their interactive roles remain unclear. Here, we addressed this issue using in vitro and in vivo models. In rat C6 glioma cells, leptin pre-treatment enhanced Ca2+ mobilization by a CCK agonist (CCK-8s). This leptin action was reduced by Janus kina...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-69035-6
更新日期：2020-07-20 00:00:00
abstract：:The formation of snow-dirt sludge (SDS) via the mixing of snow and surface-deposited sediment by vehicles and pedestrians is one of the least studied sedimentation processes in urban areas. The aim of this study was to analyse the material, mineral, particle size, and chemical compositions of the SDS solid phase. The ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-53793-z
更新日期：2019-11-21 00:00:00
abstract：:Although plants are essentially sessile in nature, these organisms are very much in tune with their environment and are capable of a variety of movements. This may come as a surprise to many non-botanists, but not to Charles Darwin, who reported that plants do produce movements. Following Darwin's specific interest on...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-53118-0
更新日期：2019-11-12 00:00:00
abstract：:ANCA vasculitis encompasses several autoimmune conditions characterised by destruction of small vessels, inflammation of the respiratory tract and glomerulonephritis. Most patients harbour autoantibodies to myeloperoxidase (MPO) or proteinase 3 (PR3). Clinical and experimental data suggest that pathogenesis is driven ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep11888
更新日期：2015-07-07 00:00:00
abstract：:It is well known that supercritical water is a favourable medium for biomass conversion followed by its hydrodeoxygenation (HDO). Moreover, the actual kinetics and mechanism of reaction occurring in the supercritical water are not yet completely understood, either by experimental or computational approaches. Within th...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-66237-w
更新日期：2020-06-08 00:00:00
abstract：:Plant health is strongly connected with plants´ microbiome. In case of raw-eaten plants, the microbiome can also affect human health. To study potential impacts on health issues of both hosts, the microbiome composition of seven different Brassica vegetables, originating from different food processing pathways, was an...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-17949-z
更新日期：2017-12-15 00:00:00
abstract：:Liver repopulation by transplanted hepatocytes has not been achieved previously in a normal liver microenvironment. Here we report that adult rat hepatocytes transduced ex vivo with a lentivirus expressing a human YapERT2 fusion protein (hYapERT2) under control of the hepatocyte-specific transthyretin (TTR) promoter r...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep19275
更新日期：2016-01-14 00:00:00
abstract：:Antenna systems serve to absorb light and to transmit excitation energy to the reaction center (RC) in photosynthetic organisms. As the emitted (bacterio)chlorophyll fluorescence competes with the photochemical utilization of the excitation, the measured fluorescence yield is informed by the migration of the excitatio...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-70966-3
更新日期：2020-08-19 00:00:00
abstract：:Monitoring one's actions is essential for goal-directed performance. In the event-related potential (ERP), errors are followed by fronto-centrally distributed negativities. These error(-related) negativity (Ne/ERN) amplitudes are often found to be attenuated in patients with Parkinson's disease (PD) compared to health...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep41222
更新日期：2017-01-24 00:00:00
abstract：:Asthma is characterized by airway inflammation, mucus secretion, remodeling and hyperresponsiveness (AHR). Recent research has established the bronchodilatory effect of bitter taste receptor (TAS2R) agonists in various models. Comprehensive pre-clinical studies aimed at establishing effectiveness of TAS2R agonists in ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep46166
更新日期：2017-04-11 00:00:00
abstract：:This study aimed to observe the morphological characteristics of a PGLA [poly(glycolide-co-L-lactide)] nerve conduit and regenerated nerve bundle in the human body using high-frequency ultrasound and examine functional recovery of the regenerated nerve using functional magnetic resonance imaging (fMRI) after neural pr...
journal_title：Scientific reports
pub_type： 临床试验,杂志文章
doi：10.1038/srep46403
更新日期：2017-04-13 00:00:00
abstract：:The IκB kinase (IKK) complex acts as the gatekeeper of canonical NF-κB signaling, thereby regulating immunity, inflammation and cancer. It consists of the catalytic subunits IKKα and IKKβ and the regulatory subunit NEMO/IKKγ. Here, we show that the ubiquitin binding domain (UBAN) in NEMO is essential for IKK/NF-κB act...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep18934
更新日期：2016-01-07 00:00:00
abstract：:In the following article, we present a simple, two-step method of creating spaced, hollow nanopillars, from the titania nanotube arrays via pulsed laser-treatment. Due to the high ordering of the structure, the prepared material exhibits photonic properties, which has been shown to increase the overall photoefficiency...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-77309-2
更新日期：2020-11-19 00:00:00
abstract：:Diagnosis and treatment of vocal fold lesions has been a long-evolving science for the otolaryngologist. Contemporary practice requires biopsy of a glottal lesion in the operating room under general anesthesia for diagnosis. Current in-office technology is limited to visualizing the surface of the vocal folds with fib...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep22792
更新日期：2016-03-10 00:00:00
