Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers

High-quality and high-throughput prediction of enzyme commission (EC) numbers is essential for accurate understanding of enzyme functions, which have many implications in pathologies and industrial biotechnology. Several EC number prediction tools are currently available, but their prediction performance needs to be further improved to precisely and efficiently process an ever-increasing volume of protein sequence data. Here, we report DeepEC, a deep learning-based computational framework that predicts EC numbers for protein sequences with high precision and in a high-throughput manner. DeepEC takes a protein sequence as input and predicts EC numbers as output. DeepEC uses 3 convolutional neural networks (CNNs) as a major engine for the prediction of EC numbers, and also implements homology analysis for EC numbers that cannot be classified by the CNNs. Comparative analyses against 5 representative EC number prediction tools show that DeepEC allows the most precise prediction of EC numbers, and is the fastest and the lightest in terms of the disk space required. Furthermore, DeepEC is the most sensitive in detecting the effects of mutated domains/binding site residues of protein sequences. DeepEC can be used as an independent tool, and also as a third-party software component in combination with other computational platforms that examine metabolic reactions

Association Between Hearing Impairment and Albuminuria With or Without Diabetes Mellitus

Objectives Few studies have evaluated the accurate association between hearing loss (HL) and albuminuria in patients with or without diabetes mellitus (DM). The aim of our study was to identify the clinical effects of albuminuria on HL with or without DM. Methods This study included 9,762 patients from the Korean National Health and Nutrition Examination Survey between 2011 and 2013. Participants were divided into 4 groups based on DM and urine albumin/creatinine ratio levels: group 1 included participants with neither DM nor albuminuria, group 2 included participants without DM and with albuminuria, group 3 included patients with DM and without albuminuria, and group 4 included patients with both DM and albuminuria. The low- or mid-frequency and high-frequency, and average hearing threshold values were obtained. Results There were 7,508, 545, 1,325, and 384 participants in groups 1, 2, 3, and 4, respectively. Univariate and multivariate analyses showed that the 3 hearing thresholds in group 1 were the lowest and those in group 4 were the highest among the 4 groups. No significant differences were observed in those thresholds between groups 2 and 3. Group 4 was associated with HL compared with the other groups, but moderate to severe HL was not associated with DM or albuminuria. Conclusion The presence of albuminuria was associated with a modest effect on hearing thresholds regardless of presence of DM

Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery

Chromosome 1 of Vibrio vulnificus tends to contain larger portion of essential or housekeeping genes on the basis of the genomic analysis and gene knockout experiments performed in this study, while its chromosome 2 seems to have originated and evolved from a plasmid.The genome-scale metabolic network model of V. vulnificus was reconstructed based on databases and literature, and was used to identify 193 essential metabolites.Five essential metabolites finally selected after the filtering process are 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine (AHHMP), D-glutamate (DGLU), 2,3-dihydrodipicolinate (DHDP), 1-deoxy-D-xylulose 5-phosphate (DX5P), and 4-aminobenzoate (PABA), which were predicted to be essential in V. vulnificus, absent in human, and are consumed by multiple reactions.Chemical analogs of the five essential metabolites were screened and a hit compound showing the minimal inhibitory concentration (MIC) of 2 μg/ml and the minimal bactericidal concentration (MBC) of 4 μg/ml against V. vulnificus was identified

Clinical relevance of ground glass opacity in 105 patients with miliary tuberculosis

SummaryBackgroundAfter the application of chest computed tomography (CT), ground glass opacity (GGO) was introduced as one of major accompanying findings of miliary tuberculosis (MT) in addition to miliary nodules. However, little is known about whether GGO is associated with the clinical manifestations and outcomes of MT. Therefore, the present study examined the clinical relevance of GGO in patients with MT.MethodsChest radiographs and CT scans of MT patients were retrospectively reviewed. Clinical manifestations and outcomes were compared in terms of the extent of GGO revealed by chest CT.ResultsConfirmed 105 MT patients were included. GGO was observed in 70 (67%) patients. MT patients with an extent of GGO >50% (n = 21) had symptoms of shorter duration, more frequent dyspnea, and more pronounced changes in the levels of acute phase reactants. Miliary nodules were less discernible on CT in those with an extent of GGO >50%. MT patients with an extent of GGO >50% were significantly associated with a longer hospital stay (p = 0.02) and with acute respiratory failure (p < 0.001) than those with an extent of GGO ≤50%. However, mortality among MT patients was not associated with the extent of GGO.ConclusionMT patients with an extent of GGO >50% had more rapidly progressive manifestations and a greater potential for delayed diagnosis and poorer prognosis. Nevertheless, mortality was not higher in confirmed MT patients with an extent of GGO >50% than in those with an extent of GGO ≤50%

THE POSSIBILITY OF CLASSIFYING V1 AND V2 SUB-TECHNIQUES OF A SINGLE IMU SENSOR THROUGH COMPARISON OF MOTION-SPECIFIC DATA(PITCH, YAW AND ROLL ANGLE VALUES-ORIENTATION ANGLE VALUE) IN XC SKI

The purpose of this study is to confirm whether the single IMU sensor module(LGE developing and providing for the experiments) that attached to the pelvis can distinguish the motion of the sub-techniques (V1, V2, V2A) with the accuracy of commercial XSENS(equipment consisting of 17 sensors) in freestyle(skate) xc skiing. Therefore, one elite male xc skier with eleven years experience was investigated by measuring the three-directional rotation angle for each of the three sub-techniques used in XC ski freestyle. Through this method, we could found not only the difference of motion patterns of each sub-techniques but also the possibility for replacement of multiple sensor system by a single IMU sensor module from LGE. Thus, it is expected that a single LGE IMU sensor module could be applied to repetitive and periodic sports such as XC ski

Renal Artery Embolization of Perirenal Hematoma in Hemorrhagic Fever with Renal Syndrome: A Case Report

Hemorrhagic fever with renal syndrome (HFRS) is an acute viral disease characterized by fever, hemorrhage and renal failure. Among the various hemorrhagic complications of HFRS, spontaneous rupture of the kidney and perirenal hematoma are very rare findings. We report here on a case of HFRS complicated by massive perirenal hematoma, and this was treated with transcatheter arterial embolization

Very Late Stent Thrombosis after Drug-Eluting Stent Implantation in a Patient without Aspirin and Clopidogrel Resistance

Very late stent thrombosis (VLST) after implantation of drug-eluting stent is rare, but very fatal complication after percutaneous coronary intervention. We report a case of VLST of a sirolimus-eluting Cypher™ stent (Cordis, Johnson and Johnson) presenting as acute ST elevation myocardial infarction at 26 months after deployment with continued combined dual antiplatelet medication of aspirin and clopidogrel. The patient did not show anti-platelet resistance