Abstract:
:Protein phosphorylation is one of the most widespread regulatory mechanisms in eukaryotes. Over the past decade, phosphorylation site prediction has emerged as an important problem in the field of bioinformatics. Here, we report a new method, termed Random Forest-based Phosphosite predictor 2.0 (RF-Phos 2.0), to predict phosphorylation sites given only the primary amino acid sequence of a protein as input. RF-Phos 2.0, which uses random forest with sequence and structural features, is able to identify putative sites of phosphorylation across many protein families. In side-by-side comparisons based on 10-fold cross validation and an independent dataset, RF-Phos 2.0 compares favorably to other popular mammalian phosphosite prediction methods, such as PhosphoSVM, GPS2.1, and Musite.
journal_name
Biomed Res Intjournal_title
BioMed research internationalauthors
Ismail HD,Jones A,Kim JH,Newman RH,Kc DBdoi
10.1155/2016/3281590subject
Has Abstractpub_date
2016-01-01 00:00:00pages
3281590eissn
2314-6133issn
2314-6141journal_volume
2016pub_type
杂志文章abstract:Background:The purpose of this study was to evaluate the association between the non-high-density lipoprotein cholesterol (non-HDL-C) to high-density lipoprotein cholesterol (HDL-C) ratio and the risk of coronary artery disease (CAD). We also explored the potential role of non-HDL-C/HDL-C in the prognosis of CAD. Meth...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2020/7146028
更新日期:2020-03-07 00:00:00
abstract::In our study, we evaluated the feasibility of a new sampling method for splenic stiffness (SS) measurement by Quantitative Acoustic Radiation Force Impulse Elastography (Virtual Touch Tissue Quantification (VTTQ)).We measured SS in 54 patients with HCV-related cirrhosis of whom 28 with esophageal varices (EV), 27 with...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/365982
更新日期:2014-01-01 00:00:00
abstract::Human dental pulp stem cells (DPSCs) hold great promise in bone regeneration. However, the exact mechanism of osteogenic differentiation of DPSCs remains unknown, especially the role of exosomes played in. The DPSCs were cultured and received osteogenic induction; then, exosomes from osteogenic-induced DPSCs (OI-DPSC-...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2020/6319395
更新日期:2020-09-28 00:00:00
abstract::Spinal cord injured (SCI) individuals show an altered hemodynamic response to metaboreflex activation due to a reduced capacity to vasoconstrict the venous and arterial vessels below the level of the lesion. Exercise training was found to enhance circulating catecholamines and to improve cardiac preload and venous ton...
journal_title:BioMed research international
pub_type: 临床试验,杂志文章
doi:10.1155/2014/893468
更新日期:2014-01-01 00:00:00
abstract:Background:The aim of this article is to present a short review of noninvasive, nonpharmacological treatment methods used in somatic illnesses that fall under the umbrella of approach called behavioral medicine. Methods:The narrative review method was applied in the study. Science paper databases, including PubMed, ha...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2020/5076516
更新日期:2020-11-03 00:00:00
abstract::This study evaluated the potential relationship between exosomal miRNAs and clinical symptoms in patients with multiple myeloma (MM). Forty-eight newly diagnosed myeloma patients and sixteen normal donors were enrolled in the study. The results showed that the relative expression levels of let-7c-5p, let-7d-5p, miR-14...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2019/1575468
更新日期:2019-12-14 00:00:00
abstract:BACKGROUND:Noninvasive tools to diagnose nonalcoholic fatty liver disease (NAFLD), including transient elastography (TE) and enhanced liver fibrosis panel (ELF), have only been evaluated in children with biopsy-proven NAFLD. We evaluated the prevalence of ELF and TE abnormalities in obese children without clinical live...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/457473
更新日期:2015-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/473419
更新日期:2014-01-01 00:00:00
abstract::The release of ATP from the urothelium in response to stretch during filling demonstrates the importance of the purinergic system for the physiological functioning of the bladder. This study examined the effect of P2 receptor agonists on ATP release from two urothelial cell lines (RT4 and UROtsa cells). Hypotonic Kreb...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/830374
更新日期:2014-01-01 00:00:00
abstract::Hepatocellular carcinoma (HCC) is the second leading cause of cancer deaths in Taiwan. CD44, one of the well-known tumor markers, plays an essential role in tumor cell differentiation, invasion, and metastasis. We investigated the CD44 single-nucleotide polymorphisms (SNPs) with environmental risk factors related to H...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/231474
更新日期:2014-01-01 00:00:00
abstract::Aerobic granulation of activated sludge was successfully achieved in a full-scale sequencing batch reactor (SBR) with 50,000 m(3) d(-1) for treating a town's wastewater. After operation for 337 days, in this full-scale SBR, aerobic granules with an average SVI30 of 47.1 mL g(-1), diameter of 0.5 mm, and settling veloc...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/268789
更新日期:2014-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章,随机对照试验
doi:10.1155/2014/673682
更新日期:2014-01-01 00:00:00
abstract::We demonstrate the potential of differentiating embryonic and induced pluripotent stem cells by the regularized linear and decision tree machine learning classification algorithms, based on a number of intragene methylation measures. The resulting average accuracy of classification has been proven to be above 95%, whi...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/976362
更新日期:2015-01-01 00:00:00
abstract::Gender affirmation surgery remains one of the greatest challenges in transgender medicine. In recent years, there have been continuous discussions on bioethical aspects in the treatment of persons with gender dysphoria. Gender reassignment is a difficult process, including not only hormonal treatment with possible sur...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2018/9652305
更新日期:2018-06-13 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2016/4626027
更新日期:2016-01-01 00:00:00
abstract::A number of statistical methods for detecting gene-gene interactions have been developed in genetic association studies with binary traits. However, many phenotype measures are intrinsically quantitative and categorizing continuous traits may not always be straightforward and meaningful. Association of gene-gene inter...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/523641
更新日期:2015-01-01 00:00:00
abstract::Circulating cell-free DNA has been recognized as an accurate marker for the diagnosis of prostate cancer, whereas the role of urine cell-free DNA (UCF DNA) has never been evaluated in this setting. It is known that normal apoptotic cells produce highly fragmented DNA while cancer cells release longer DNA. We thus veri...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2013/270457
更新日期:2013-01-01 00:00:00
abstract:Background and Aims:Contrast-induced nephropathy (CIN) is a relatively infrequent complication after percutaneous coronary intervention (PCI) in patients with ST-elevation myocardial infarction (STEMI). However, little is known about the association between cytochrome c (cyt c) and increased risk of CIN. We conducted t...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2019/9357203
更新日期:2019-01-23 00:00:00
abstract:Objective:This study evaluated the bioactivity and physicochemical properties of three commercial calcium silicate-based endodontic materials (MTA, EndoSequence Root Repair Material putty, and Biodentine™). Material and Methods. Horizontal sections of 3 mm thickness from 18 root canals of human teeth were subjected to ...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2020/9576930
更新日期:2020-05-22 00:00:00
abstract::Retinoblastoma protein (pRB) interacts with E2F and other protein factors to play a pivotal role in regulating the expression of target genes that induce cell cycle arrest, apoptosis, and differentiation. pRB controls the local promoter activity and has the ability to change the structure of nucleosomes and/or chromos...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2016/5959721
更新日期:2016-01-01 00:00:00
abstract:INTRODUCTION:Deep vein thrombosis (DVT) is a severe complication after total hip arthroplasty (THA). It leads to acute pulmonary embolism, a life-threatening disease. P-selectin is a 140-kDa transmembrane glycoprotein. Elevated P-selectin was associated with 1.7-fold increase in the risk of venous thrombosis. MATERIAL...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/783967
更新日期:2014-01-01 00:00:00
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journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2015/891390
更新日期:2015-01-01 00:00:00
abstract::Keratinases are proteolytic enzymes predominantly active when keratin substrates are available that attack disulfide bridges in the keratin to convert them from complex to simplified forms. Keratinases are essential in preparation of animal nutrients, protein supplements, leather manufacture, textile processing, deter...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2015/140726
更新日期:2015-01-01 00:00:00
abstract::Mild cognitive impairment (MCI) refers to a transitional state between normal aging and dementia and is a syndrome with cognitive decline greater than expected for an individual's age and educational level. As a subtype of MCI, amnestic mild cognitive impairment (aMCI) most often leads to Alzheimer's disease. This stu...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/920902
更新日期:2014-01-01 00:00:00
abstract:Background:The purpose of this study was to examine the physical activity patterns and health-related fitness levels of adolescents within the Juvenile Justice System. Methods:Participants included 68 adolescents (Mean age = 17.1 ± 1.0 years) in two secure Juvenile Justice correctional facilities in the Western USA. M...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2018/9710714
更新日期:2018-07-15 00:00:00
abstract::In recent years, new prognostic indexes (PIs) for chronic lymphocytic leukemia (CLL), which include clinical, biological, and genetic variables, have been validated, highlighting the MD Anderson Cancer Center prognostic index (MDACC PI), the CLL-international prognostic index (CLL-IPI), and the Barcelona-Brno biomarke...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2018/9506979
更新日期:2018-03-15 00:00:00
abstract::Newcastle disease (ND) is one of the most devastating diseases that considerably cripple the global poultry industry. Because of its enormous socioeconomic importance and potential to rapidly spread to naïve birds in the vicinity, ND is included among the list of avian diseases that must be notified to the OIE immedia...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2018/7278459
更新日期:2018-08-05 00:00:00
abstract::Trichoderma spp. are important biocontrol filamentous fungi and have tremendous potential in soil bioremediation. In our previous studies, a C2H2 type transcription factor coding gene (thmea1) was cloned from a biocontrol agent T. harzianum Th-33; the encoded sequence of thmea1 contained 3 conserved C2H2 domains with ...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2018/8149682
更新日期:2018-07-18 00:00:00
abstract::Non-small-cell lung cancer (NSCLC) patients often develop bone metastases (BM), and the overall survival for these patients is usually perishing. However, a model with high accuracy for predicting the survival of NSCLC with BM is still lacking. Here, we aimed to establish a model based on artificial intelligence for p...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2020/3462363
更新日期:2020-06-27 00:00:00
abstract:Purpose:We aimed to identify prognostic factors for survival and recurrence of hepatocellular carcinoma (HCC) after liver transplantation (LT) for patients with HCC and hepatitis C virus-related cirrhosis (HCV-cirrhosis). Methods:This retrospective cohort study followed all adult patients with HCV-cirrhosis who underw...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2020/1487593
更新日期:2020-10-17 00:00:00