Abstract:
:RNA protein interactions (RPI) play a pivotal role in the regulation of various biological processes. Experimental validation of RPI has been time-consuming, paving the way for computational prediction methods. The major limiting factor of these methods has been the accuracy and confidence of the predictions, and our in-house experiments show that they fail to accurately predict RPI involving short RNA sequences such as TERRA RNA. Here, we present a data-driven model for RPI prediction using a gradient boosting classifier. Amino acids and nucleotides are classified based on the high-resolution structural data of RNA protein complexes. The minimum structural unit consisting of five residues is used as the descriptor. Comparative analysis of existing methods shows the consistently higher performance of our method irrespective of the length of RNA present in the RPI. The method has been successfully applied to map RPI networks involving both long noncoding RNA as well as TERRA RNA. The method is also shown to successfully predict RNA and protein hubs present in RPI networks of four different organisms. The robustness of this method will provide a way for predicting RPI networks of yet unknown interactions for both long noncoding RNA and microRNA.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Jain DS,Gupte SR,Aduri Rdoi
10.1038/s41598-018-27814-2subject
Has Abstractpub_date
2018-06-22 00:00:00pages
9552issue
1issn
2045-2322pii
10.1038/s41598-018-27814-2journal_volume
8pub_type
杂志文章abstract::Age of complementary foods introduction is associated with childhood anemia, but the ideal age for the introduction of complementary foods to infants is a continuing topic of debate. We examined the longitudinal association between complementary foods introduction age and risk of anemia in 18,446 children from the Jia...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep44726
更新日期:2017-03-23 00:00:00
abstract::Metallic glass (MG) generally fails in a brittle manner under uniaxial tension loading at room temperature. The lack of plastic strain of MG is due to the severe plastic instability via the easily formed one dominate shear band. There have been several approaches to improve the ductility in MG, but achieving uniform t...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep03319
更新日期:2013-11-25 00:00:00
abstract::We developed a spongy-like porous polymer (spongy monolith) consisting of poly(ethylene-co-glycidyl methacrylate) with continuous macropores that allowed efficient in situ reaction between the epoxy groups and proteins of interest. Immobilization of protein A on the spongy monolith enabled high-yield collection of imm...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-00264-y
更新日期:2017-03-14 00:00:00
abstract::Here, we present a fast mix-and-measure immunoassay for the specific semiquantitative detection of His-tagged proteins, for example in E. coli cell lysate. The assay is based on Förster resonance energy transfer (FRET) between a lanthanide dye-labeled low-affinity His-peptide and an acceptor-labeled anti-His-tag antib...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep05613
更新日期:2014-07-08 00:00:00
abstract::Most Atlantic hurricanes form in the Main Development Region between 9°N to 20°N along the northern edge of the Intertropical Convergence Zone (ITCZ). Previous research has suggested that meridional shifts in the ITCZ position on geologic timescales can modulate hurricane activity, but continuous and long-term storm r...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep21728
更新日期:2016-02-24 00:00:00
abstract::Krüppel-like factor 6 (KLF6) is a transcription factor and tumor suppressor. We previously identified KLF6 as mediator of hepatocyte glucose and lipid homeostasis. The loss or reduction of KLF6 is linked to the progression of hepatocellular carcinoma, but its contribution to liver regeneration and repair in acute live...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-08680-w
更新日期:2017-08-14 00:00:00
abstract::Phenotypic plasticity describes the ability of a given genotype to produce distinct phenotypes in different environments. We use the temperature sensitivity of abdominal pigmentation in Drosophila melanogaster females as a model to analyse the effect of the environment on development. We reported previously that therm...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep43370
更新日期:2017-02-23 00:00:00
abstract::The bacterial flagellar motor is a unique supramolecular complex which converts ion flow into rotational force. Many biological devices mainly use two types of ions, proton and sodium ion. This is probably because of the fact that life originated in seawater, which is rich in protons and sodium ions. The polar flagell...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-46038-6
更新日期:2019-08-02 00:00:00
abstract::The identification of the most influential individuals in structured populations is an important research question, with many applications across the social and natural sciences. Here, we study this problem in evolutionary populations on static networks, where invading cheaters can lead to the collapse of cooperation....
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-59020-4
更新日期:2020-02-10 00:00:00
abstract::This work reports a facile method for preparing the new photoactive In(2)O(3) films as well as their implementation in photoelectrochemical (PEC) application. We firstly investigated the relationship between oxygen vacancies (V(O)) and PEC performance and revealed a rule between them. We found that the optimized In(2)...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep01021
更新日期:2013-01-01 00:00:00
abstract::The probability of mitochondrial permeability transition (mPT) pore opening is inversely related to the magnitude of the proton electrochemical gradient. The module conferring sensitivity of the pore to this gradient has not been identified. We investigated mPT's voltage-sensing properties elicited by calcimycin or H2...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep26700
更新日期:2016-05-25 00:00:00
abstract::Enterohemorrhagic Escherichia coli (EHEC) are major food-borne pathogens whose survival and virulence in the human digestive tract remain unclear owing to paucity of relevant models. EHEC interact with the follicle-associated epithelium of Peyer's patches of the distal ileum and translocate across the intestinal epith...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep44655
更新日期:2017-03-20 00:00:00
abstract::Visualization of morphological dynamics of live cells with nanometer resolution under physiological conditions is highly desired, but challenging. It has been demonstrated that high-speed atomic force microscopy is a powerful technique for visualizing dynamics of biomolecules under physiological conditions. However, a...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep08724
更新日期:2015-03-04 00:00:00
abstract::Due to the substantial limitation of study population, Spindle cell sarcoma (SCS) was unexplored comprehensively. In this study, we investigated the clinical characteristics and disease specific prognostic factors of SCS. 3299 SCS cases were identified and extracted from Surveillance, Epidemiology, and End Results (SE...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-23145-4
更新日期:2018-03-22 00:00:00
abstract::Lactic acidosis is common in critical care; by contrast, a subtype called alcohol-associated lactic acidosis (AALA) is rarely encountered. The primary purpose of this study was to determine the prognosis of AALA in critically ill patients and the second aim was to determine whether the survival was associated to the p...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep35368
更新日期:2016-10-17 00:00:00
abstract::Emergent phases in the two-dimensional electron gas (2DEG) formed at the interface between two insulating oxides have attracted great attention in the past decade. We present ab-initio electronic structure calculations for the interface between a Mott insulator GdTiO3 (GTO) and a band insulator SrTiO3 (STO) and compar...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep18647
更新日期:2015-12-22 00:00:00
abstract::Urinary tract infections (UTIs) are the third most common types of infection in human medicine worldwide. There is increasing appreciation for the pathogenic role of Gram-positive cocci (GPC) in UTIs, as they have a plethora of virulence factors, maintaining their pathogenicity and high affinity for the epithelial cel...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-74834-y
更新日期:2020-10-19 00:00:00
abstract::Settling due to gravity force is a basic transport mechanism of solid particles in fluids in the Earth. A large portion of particles occurring in nature and used in technical applications are non-spherical. Settling of particles is usually studied in homogeneous ambient conditions, however, stratification is inherent ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-18654-7
更新日期:2018-01-11 00:00:00
abstract::The G protein-coupled receptor opsin is a phospholipid scramblase that facilitates rapid transbilayer phospholipid exchange in liposomes. The mechanism by which opsin scrambles lipids is unknown. It has been proposed that lipid translocation may occur at protein-protein interfaces of opsin dimers. To test this possibi...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-16842-z
更新日期:2017-12-01 00:00:00
abstract::The life-like fidelity of organisms captured in amber is unique among all kinds of fossilization and represents an invaluable source for different fields of palaeontological and biological research. One of the most challenging aspects in amber research is the study of traits related to behaviour. Here, indirect eviden...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep34352
更新日期:2016-10-04 00:00:00
abstract::The transition from unicellular to multicellular organisms poses the question as to when genes that regulate cell-cell interactions emerged during evolution. The receptor and ligand pairing of plexins and semaphorins regulates cellular interactions in a wide range of developmental and physiological contexts. We survey...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-38512-y
更新日期:2019-02-13 00:00:00
abstract::The associations of 18F-THK5351 tau positron emission tomography (PET) findings with core domains of progressive supranuclear palsy (PSP) and its diagnostic certainty have yet to be fully elucidated. The 18F-THK5351 PET patterns of 17 patients with PSP (68.9 ± 6.5 years; 8 women) were compared with those observed in 2...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-76339-0
更新日期:2020-11-10 00:00:00
abstract::Chronic sleep fragmentation (SF) commonly occurs in human populations, and although it does not involve circadian shifts or sleep deprivation, it markedly alters feeding behaviors ultimately promoting obesity and insulin resistance. These symptoms are known to be related to the host gut microbiota. Mice were exposed t...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep35405
更新日期:2016-10-14 00:00:00
abstract::Lysine-specific demethylase 1 (LSD1) is a histone demethylase that participates in transcriptional repression or activation. Recent studies reported that LSD1 is involved in learning and memory. Although LSD1 phosphorylation by PKCα was implicated in circadian rhythmicity, the importance of LSD1 phosphorylation in lea...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-05239-7
更新日期:2017-07-07 00:00:00
abstract::Soil components (e.g., clays, bacteria and humic substances) are known to produce mineral-organic composites in natural systems. Herein, batch sorption isotherms, isothermal titration calorimetry (ITC), and Cd K-edge EXAFS spectroscopy were applied to investigate the binding characteristics of Cd on montmorillonite(Mo...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep19499
更新日期:2016-01-21 00:00:00
abstract::Chromosomal toxin-antitoxin (TA) systems are widespread genetic elements among bacteria, yet, despite extensive studies in the last decade, their biological importance remains ambivalent. The ability of TA-encoded toxins to affect stress tolerance when overexpressed supports the hypothesis of TA systems being associat...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-65504-0
更新日期:2020-06-08 00:00:00
abstract::Ocular involvement in leukemia is considered rare. Ocular symptoms can be the presenting signs of leukemia, they can appear after diagnosis has been established, or they can be the first manifestation of a relapse after remission. We report, to the best of our knowledge for the first time, the ocular manifestation of ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-58654-8
更新日期:2020-02-06 00:00:00
abstract::Candida albicans biofilm formation is governed by a regulatory circuit comprising nine transcription factors which control a network of target genes. However, there are still unknown genes contributing to biofilm features. Thus, the GRACE library was screened to identify genes involved in mature biofilm development. T...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-45624-y
更新日期:2019-06-24 00:00:00
abstract::We investigated the relationship between aqueous cytokine levels, changes in ocular blood flow, and morphological and functional improvements after intravitreal ranibizumab injection (IRI) in treatment-naïve eyes with center-involving diabetic macular edema (DME). Thirty-three eligible patients with DME (33 eyes) were...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-78792-3
更新日期:2020-12-10 00:00:00
abstract::This study aims to prepare, characterize and evaluate the pharmacokinetics of liposomal donepezil HCl (LDH) dispersed into thiolated chitosan hydrogel (TCH) in rabbits. Various hydrogels including TCH were prepared, and after characterization, TCH was selected for subsequent evaluations, due to the promising results. ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-46032-y
更新日期:2019-07-02 00:00:00