Identification of protein functions using a machine-learning approach based on sequence-derived properties

<p>Abstract</p> <p>Background</p> <p>Predicting the function of an unknown protein is an essential goal in bioinformatics. Sequence similarity-based approaches are widely used for function prediction; however, they are often inadequate in the absence of similar sequences or when the sequence similarity among known protein sequences is statistically weak. This study aimed to develop an accurate prediction method for identifying protein function, irrespective of sequence and structural similarities.</p> <p>Results</p> <p>A highly accurate prediction method capable of identifying protein function, based solely on protein sequence properties, is described. This method analyses and identifies specific features of the protein sequence that are highly correlated with certain protein functions and determines the combination of protein sequence features that best characterises protein function. Thirty-three features that represent subtle differences in local regions and full regions of the protein sequences were introduced. On the basis of 484 features extracted solely from the protein sequence, models were built to predict the functions of 11 different proteins from a broad range of cellular components, molecular functions, and biological processes. The accuracy of protein function prediction using random forests with feature selection ranged from 94.23% to 100%. The local sequence information was found to have a broad range of applicability in predicting protein function.</p> <p>Conclusion</p> <p>We present an accurate prediction method using a machine-learning approach based solely on protein sequence properties. The primary contribution of this paper is to propose new <it>PNPRD </it>features representing global and/or local differences in sequences, based on positively and/or negatively charged residues, to assist in predicting protein function. In addition, we identified a compact and useful feature subset for predicting the function of various proteins. Our results indicate that sequence-based classifiers can provide good results among a broad range of proteins, that the proposed features are useful in predicting several functions, and that the combination of our and traditional features may support the creation of a discriminative feature set for specific protein functions.</p

Association between prostate-specific antigen and serum testosterone:A systematic review and meta-analysis

Background Serum testosterone assays are an important tool in the clinical evaluation of a number of endocrine disorders including male hypogonadism. However, serum testosterone has a limited role in real clinical use due to its inaccuracy. We aimed to assess the association between prostate-specific antigen (PSA) and testosterone as well as the effects of various types of testosterone replacement therapy (TRT) for PSA level. Methods Two electronic databases were screened: PubMed (1966 through December 2018) and Cochrane Library (1993 through December 2018). The first strategy compared the overall increase in PSA following testosterone treatment compared with placebo. The second strategy analyzed the overall association between PSA and testosterone among the observational studies. Results In the first strategy, 22 articles were included in the final analysis. In the second strategy, 18 studies were included. Testosterone replacement therapy (TRT) showed a significant change in PSA level compared to that in the placebo group (mean difference [MD]: 0.13, 95% CI: 0.01-0.25, P = .04). Compared to placebo, only intramuscular (IM) TRT shows a significant change in PSA level group (MD: 0.16, 95% CI: 0.01-0.30, P = .04), as neither the oral nor topical type showed a significant change in PSA. In the second strategy analysis, there was no overall correlation found between PSA and testosterone (z = 0.04, 95% CI: -0.04 to 0.12, P = .04; r = 0.039). However, in the subgroup of non-BPH (benign prostate hyperplasia), a significant correlation between PSA and testosterone (z = 0.07, 95% CI: 0.01-0.13, P = .009; r = 0.089) was found. Conclusions We found that TRT, particularly IM TRT, significantly changed the PSA level compared with the placebo group. Furthermore, there was a significant correlation between PSA and testosterone in patients with non-BPH. According to these findings, we suggest the possibility of PSA as a surrogate marker of testosterone

Spontaneous Uterine Rupture in the First Trimester: A Case Report

Uterine rupture is one of the most feared obstetric complications affecting the pregnant woman and fetus. Most of the cases have various risk factors and mainly occur during the second or third trimester. However, spontaneous uterine rupture during the first trimester is extremely rare. We experienced a case of spontaneous uterine rupture in a 36-yr-old multiparous woman without definite risk factors. The initial impression was a hemoperitoneum of an unknown origin with normal early pregnancy. Intensive surgical method would be needed for accurate diagnosis and immediate management in bad situation by hemoperitoneum even though a patient was early pregnancy

A Wearable Wrist Band-Type System for Multimodal Biometrics Integrated with Multispectral Skin Photomatrix and Electrocardiogram Sensors

Multimodal biometrics are promising for providing a strong security level for personal authentication, yet the implementation of a multimodal biometric system for practical usage need to meet such criteria that multimodal biometric signals should be easy to acquire but not easily compromised. We developed a wearable wrist band integrated with multispectral skin photomatrix (MSP) and electrocardiogram (ECG) sensors to improve the issues of collectability, performance and circumvention of multimodal biometric authentication. The band was designed to ensure collectability by sensing both MSP and ECG easily and to achieve high authentication performance with low computation, efficient memory usage, and relatively fast response. Acquisition of MSP and ECG using contact-based sensors could also prevent remote access to personal data. Personal authentication with multimodal biometrics using the integrated wearable wrist band was evaluated in 150 subjects and resulted in 0.2% equal error rate ( EER ) and 100% detection probability at 1% FAR (false acceptance rate) ( PD.1 ), which is comparable to other state-of-the-art multimodal biometrics. An additional investigation with a separate MSP sensor, which enhanced contact with the skin, along with ECG reached 0.1% EER and 100% PD.1 , showing a great potential of our in-house wearable band for practical applications. The results of this study demonstrate that our newly developed wearable wrist band may provide a reliable and easy-to-use multimodal biometric solution for personal authentication

Smartphone-Based Endoscope System for Advanced Point-of-Care Diagnostics: Feasibility Study

Background: Endoscopic technique is often applied for the diagnosis of diseases affecting internal organs and image-guidance of surgical procedures. Although the endoscope has become an indispensable tool in the clinic, its utility has been limited to medical offices or operating rooms because of the large size of its ancillary devices. In addition, the basic design and imaging capability of the system have remained relatively unchanged for decades. Objective: The objective of this study was to develop a smartphone-based endoscope system capable of advanced endoscopic functionalities in a compact size and at an affordable cost and to demonstrate its feasibility of point-of-care through human subject imaging. Methods: We developed and designed to set up a smartphone-based endoscope system, incorporating a portable light source, relay-lens, custom adapter, and homebuilt Android app. We attached three different types of existing rigid or flexible endoscopic probes to our system and captured the endoscopic images using the homebuilt app. Both smartphone-based endoscope system and commercialized clinical endoscope system were utilized to compare the imaging quality and performance. Connecting the head-mounted display (HMD) wirelessly, the smartphone-based endoscope system could superimpose an endoscopic image to real-world view. Results: A total of 15 volunteers who were accepted into our study were captured using our smartphone-based endoscope system, as well as the commercialized clinical endoscope system. It was found that the imaging performance of our device had acceptable quality compared with that of the conventional endoscope system in the clinical setting. In addition, images captured from the HMD used in the smartphone-based endoscope system improved eye-hand coordination between the manipulating site and the smartphone screen, which in turn reduced spatial disorientation. Conclusions: The performance of our endoscope system was evaluated against a commercial system in routine otolaryngology examinations. We also demonstrated and evaluated the feasibility of conducting endoscopic procedures through a custom HMD

A Case of Right Sided Aortic Arch Combined with Atrial Septal Defect

Right sided aortic arch is an uncommon congenital anomaly. It can be classified into three types, depending on the left aortic arch's degenerating pattern and the branching pattern of the great vessels. It can be associated with major congenital heart disease, depending on the type of right sided aortic arch. We report a case of an 18-years-old female who has right sided aortic arch with atrial septal defect (ASD). In our case, the patient had a right sided aortic arch and aberrant left subclavian artery, also she had ASD (ostium secundum) and moderate tricuspid regurgitation with pulmonary hypertension. The patient was successfully performed patch closure of ASD and tricuspid valve annuloplasty via midline sternotomy. The patient had uneventful postoperative course