An Improved Prediction Model for Ovarian Cancer Using Urinary Biomarkers and a Novel Validation Strategy.

This study was designed to analyze urinary proteins associated with ovarian cancer (OC) and investigate the potential urinary biomarker panel to predict malignancy in women with pelvic masses. We analyzed 23 biomarkers in urine samples obtained from 295 patients with pelvic masses scheduled for surgery. The concentration of urinary biomarkers was quantitatively assessed by the xMAP bead-based multiplexed immunoassay. To identify the performance of each biomarker in predicting cancer over benign tumors, we used a repeated leave-group-out cross-validation strategy. The prediction models using multimarkers were evaluated to develop a urinary ovarian cancer panel. After the exclusion of 12 borderline tumors, the urinary concentration of 17 biomarkers exhibited significant differences between 158 OCs and 125 benign tumors. Human epididymis protein 4 (HE4), vascular cell adhesion molecule (VCAM), and transthyretin (TTR) were the top three biomarkers representing a higher concentration in OC. HE4 demonstrated the highest performance in all samples withOC(mean area under the receiver operating characteristic curve (AUC) 0.822, 95% CI: 0.772-0.869), whereas TTR showed the highest efficacy in early-stage OC (AUC 0.789, 95% CI: 0.714-0.856). Overall, HE4 was the most informative biomarker, followed by creatinine, carcinoembryonic antigen (CEA), neural cell adhesion molecule (NCAM), and TTR using the least absolute shrinkage and selection operator (LASSO) regression models. A multimarker panel consisting of HE4, creatinine, CEA, and TTR presented the best performance with 93.7% sensitivity (SN) at 70.6% specificity (SP) to predict OC over the benign tumor. This panel performed well regardless of disease status and demonstrated an improved performance by including menopausal status. In conclusion, the urinary biomarker panel with HE4, creatinine, CEA, and TTR provided promising efficacy in predicting OC over benign tumors in women with pelvic masses. It was also a non-invasive and easily available diagnostic tool.

Comparison of named entity recognition methodologies in biomedical documents.

BACKGROUND: Biomedical named entity recognition (Bio-NER) is a fundamental task in handling biomedical text terms, such as RNA, protein, cell type, cell line, and DNA. Bio-NER is one of the most elementary and core tasks in biomedical knowledge discovery from texts. The system described here is developed by using the BioNLP/NLPBA 2004 shared task. Experiments are conducted on a training and evaluation set provided by the task organizers. RESULTS: Our results show that, compared with a baseline having a 70.09% F1 score, the RNN Jordan- and Elman-type algorithms have F1 scores of approximately 60.53% and 58.80%, respectively. When we use CRF as a machine learning algorithm, CCA, GloVe, and Word2Vec have F1 scores of 72.73%, 72.74%, and 72.82%, respectively. CONCLUSIONS: By using the word embedding constructed through the unsupervised learning, the time and cost required to construct the learning data can be saved.

Best serum biomarker combination for ovarian cancer classification.

BACKGROUND: Screening test using CA-125 is the most common test for detecting ovarian cancer. However, the level of CA-125 is diverse by variable condition other than ovarian cancer. It has led to misdiagnosis of ovarian cancer. METHODS: In this paper, we explore the 16 serum biomarker for finding alternative biomarker combination to reduce misdiagnosis. For experiment, we use the serum samples that contain 101 cancer and 92 healthy samples. We perform two major tasks: Marker selection and Classification. For optimal marker selection, we use genetic algorithm, random forest, T-test and logistic regression. For classification, we compare linear discriminative analysis, K-nearest neighbor and logistic regression. RESULTS: The final results show that the logistic regression gives high performance for both tasks, and HE4-ELISA, PDGF-AA, Prolactin, TTR is the best biomarker combination for detecting ovarian cancer. CONCLUSIONS: We find the combination which contains TTR and Prolactin gives high performance for cancer detection. Early detection of ovarian cancer can reduce high mortality rates. Finding a combination of multiple biomarkers for diagnostic tests with high sensitivity and specificity is very important.

A method of inferring the relationship between Biomedical entities through correlation analysis on text.

BACKGROUND: One of the most important processes in a machine learning-based natural language processing is to represent words. The one-hot representation that has been commonly used has a large size of vector and assumes that the features that make up the vector are independent of each other. On the other hand, it is known that word embedding has a great effect in estimating the similarity between words because it expresses the meaning of the word well. In this study, we try to clarify the correlation between various terms in the biomedical texts based on the excellent ability of estimating similarity between words shown by word embedding. Therefore, we used word embedding to find new biomarkers and microorganisms related to a specific diseases. METHODS: In this study, we try to analyze the correlation between diseases-markers and diseases-microorganisms. First, we need to construct a corpus that seems to be related to them. To do this, we extract the titles and abstracts from the biomedical texts on the PubMed site. Second, we express diseases, markers, and microorganisms' terms in word embedding using Canonical Correlation Analysis (CCA). CCA is a statistical based methodology that has a very good performance on vector dimension reduction. Finally, we tried to estimate the relationship between diseases-markers pairs and diseases-microorganisms pairs by measuring their similarity. RESULTS: In the experiment, we tried to confirm the correlation derived through word embedding using Google Scholar search results. Of the top 20 highly correlated disease-marker pairs, about 85% of the pairs have actually undergone a lot of research as a result of Google Scholars search. Conversely, for 85% of the 20 pairs with the lowest correlation, we could not actually find any other study to determine the relationship between the disease and the marker. This trend was similar for disease-microbe pairs. CONCLUSIONS: The correlation between diseases and markers and diseases and microorganisms calculated through word embedding reflects actual research trends. If the word-embedding correlation is high, but there are not many published actual studies, additional research can be proposed for the pair.

Permanent magnet actuation for magnetic bead-based DNA extraction.

BACKGROUND: Recently, automatic molecular diagnostic devices to extract DNA have been extensively developed using magnetic beads. While various methods can be applied to the control of the beads, the efficiency of the control when incorporated in automatic devices has not been studied. This paper proposes a compact magnet actuation method for the control of magnetic beads for DNA extraction, and compares the efficiency to the already available magnetic bead-based DNA extraction device. A permanent magnet was preferred for its compactness, while an electro-magnet provides easy operation. After investigating various methods to actuate the magnet with perspective to the size, circuit complexity, and power requirement, we determined the solenoid actuation method to be most efficient. To further reduce the dimension of the overall actuation device, direct actuation of the permanent magnet to control the hold/release of the beads was employed in this paper. The proposed method was compared with the conventional solenoid actuator with a metal plunger. An experimental fluidics device was set up with a fluidic channel and a syringe pump. The bead holding performance against the fluid speed was tested while a fixed amount of beads was loaded into the center of the channel. The group velocity of the beads was analyzed via image processing to determine whether the magnet was sufficient to hold the beads. The required power and space was analyzed and compared qualitatively and quantitatively. RESULT: The proposed direct actuation method was capable of holding the beads at faster fluidic speed than the conventional solenoid actuator. The required power was comparable contemplating the high initial power of the solenoid actuator, and required much smaller space since no plunger was needed. CONCLUSIONS: The direct actuation of the permanent magnet using a solenoid coil showed enhanced performance in holding the beads via permanent magnet, with less complexity of the actuation circuit and space. The proposed method therefore can efficiently improve the overall performance of the bead-based DNA extraction.

Performance evaluation of optimal real-time polymerase chain reaction achieved with reduced voltage.

BACKGROUND: Polymerase chain reaction (PCR) is used in nucleic acid tests of infectious diseases in point-of-care testing. Previous studies have demonstrated real-time PCR that uses a micro-PCR chip made of packing tape, double-sided tape, and a plastic cover with polycarbonate or polypropylene on a black matte printed circuit board substrate. Despite the success of DNA amplification and fluorescence detection using an early version of the micro-PCR chip, reaching the target temperature was fairly slow and, as a result, the total running time was getting longer. To reduce this runtime, the micro-PCR chip was modified by reducing the heater pattern size of the PCB substrate to one-quarter of the original size or less, while maintaining the ability of the heating pattern to cover the reservoir area of the microfluidic channel. In subsequent experiments, DNA amplification failed several times. During the analysis of the cause of this failure, it was found that the reagent was boiling with the heating range from 25 to 95 °C. METHODS: As a method of DNA amplification verification, images were captured by digital single-lens reflex camera to detect FAM fluorescence using diagonal illumination from a blue LED light source. The images were automatically captured at 72 °C (the extension step in nucleic acid amplification) and the brightness of the captured images was analyzed to con-firm the success of DNA amplification. RESULTS: Compared to the previous chip with a larger heating pattern size, the current chip appears to generate excess energy as the size of the heating pattern was reduced. To reduce this excess energy, the initial voltage was lowered to 2 V and 2.5 V, which is equivalent to a one-fifth and one-quarter voltage-power reduction in pulse width modulation control, respectively. In both voltage reduction cases, the DNA amplification was successful. CONCLUSIONS: DNA amplification tests may fail due to the excess energy generated by reducing the heater pattern size of the PCB substrate. However, the tests succeeded when the voltage was reduced to 2 V or 2.5 V. The 2.5 V power test was more efficient for reducing the overall running time.

Evaluation-independent system for DNA section amplification.

BACKGROUND: In general, the image analysis of nucleic acid for detecting DNA is dependent on the gel documentation system. These experiments may deal with harmful staining agents and are time consuming. To address these issues, real-time polymerase chain reaction (PCR) devices have been developed. The advantages of real-time PCR are its capabilities for real-time diagnosis, improved sensitivity, and digitization of measurement results. However, real-time PCR equipment is still too bulky and expensive for use in small hospitals and laboratories. METHODS: This paper describes an evaluation-independent real-time PCR system that differs from conventional systems in that it uses a side-illumination optical detection system and a temperature adjustment coefficient for DNA detection. The overall configuration of the evaluation-independent system includes the PCR chip and system hardware and software. The use of the side-illumination method for detection enables the system size to be reduced compared to systems using a typical illumination method. Furthermore, the results of a PCR test are strongly affected by the reaction temperature. Thus, extremely precise control of the temperature of the reaction is needed to obtain accurate results and good reliability. We derived a temperature compensation coefficient that allows us to compensate for the differences between the measured temperature of the negative temperature coefficient (NTC) thermistor sensor and the real temperature of the thermocouple. RESULTS: Applying the temperature compensation coefficient parameter using the NTC thermistor and using the side-illumination method resulted in an increase in the initial sensor value. The occurrence of the DNA section amplification decreased to 22 cycles from 24 cycles. CONCLUSIONS: The proposed system showed comparable performance to that of an existing real-time PCR, even with the use of simpler and smaller optical devices.

A study of polymerase chain reaction device control via cloud using Firebase Cloud Messaging protocol.

BACKGROUND: In this paper, we propose a system for data monitoring and control of polymerase chain reaction (PCR) externally. PCR is a technique for amplifying a desired DNA molecule by repeatedly synthesizing a specific part of DNA sequence. Currently, commercially available systems are standalone systems or operate PCR devices through a computer in the vicinity of devices for control purposes. These systems are limited in the number of devices that the host system can monitor at the same time, and there are limitations in controlling devices or accessing experimental data externally. Therefore, we propose a system to control the PCR device via the cloud for the convenience of the user and to overcome the limitation of the place. METHODS: The cloud system used in this study is Google's Firebase. At this time, we use Firebase Cloud Messaging (FCM) protocol to send and receive data. In this paper, we have experimented on the possibility of data transmission and reception using FCM between device, cloud and user. Since the PCR chips used in the research are generally operated at about 10°/s, and the temperature can be controlled within 0.5°, the processing period of the control process should be made much smaller than 1/20 s (50 ms). RESULTS: As a result of experiments, the time of the data round-trip using FCM was measured at 150 ms on the average. Therefore, the data exchange time using FCM is three times slower than the reference time of 50 ms. CONCLUSIONS: Since the data round-trip time using FCM is measured to be three times slower than the reference time of 50 ms, it is impossible for the user to control the device such as the PCR device used in this study through the cloud. However, it is possible for the user to monitor the status of the PCR device from the outside in real time.

Automated pipette failure monitoring using image processing for point-of-care testing devices.

BACKGROUND: The accuracy and precision of liquid handling can be altered by several causes including wearing or failure of parts, and human error. The last cause is crucial since point-of-care testing (POCT) devices can be used by non-experienced users or patients themselves. Therefore it is important to improve the method of informing the users of POCT device malfunctions due to damage of parts or human error. METHODS: In this paper, image-based failure monitoring of the automated pipetting was introduced for POCT devices. An inexpensive, high-performance camera for smartphones was employed in our previous work to resolve various malfunctions such as incorrect insertion of the tip, false positioning of the tip and pump, and improper operation of the pump. The image acquired from the camera was analyzed to detect the malfunctions. In this paper, the reagent volume in the tip was estimated from the image processing to verify the pump operation. First, the color component corresponding to the reagent intrinsic color was extracted to identify the reagent area in the tip before applying the binary image processing. The extracted reagent area was projected horizontally and the support length of the projection image was calculated. As the support length was related to the reagent volume, it was referred to the volume length. The relationship between the measured volume length and the previously measured solution mass was investigated. If we can predict the mass of the solution by the volume length, we will be able to detect the pump malfunction. RESULTS: The cube of the volume length obtained by the proposed image processing method showed a very linear relationship with the reagent mass in the tip injected by the pumping operation (R2 = 0.996), indicating that the volume length could be utilized to estimate the reagent volume to monitor the accuracy and precision of the pumping operation. CONCLUSIONS: An inexpensive smartphone camera was enough to detect various malfunctions of a POCT device with pumping operation. The proposed image processing could monitor the level of inaccuracy of pumping volume in limited range. The simple image processing such as a fixed threshold and projections was employed for the cost optimization and system robustness. However it delivered the promising results because the imaging condition was highly controllable in the devices.

Fluorescence reference plate for UV illumination using quantum dots.

Many image acquisition methods of nucleic acids still depend on UV illumination, especially after the electrophoresis when determining the size of the target DNA. Therefore the quality of the UV illuminator in the gel documentation system, and the comparison of the fluorescence detected are crucial. This paper presents a fluorescence standard reference plate using quantum dots compared to the conventional method where an agarose gel containing ethidium bromide is loaded with standard samples. The fluorescence standard reference plate consists of chambers filled with commercially available quantum dots such as phosphor dots. The chamber is made by thermally attaching nylon and polyester, the former on the inside and the latter on the outside, for increased stability. The images of the proposed reference plate were captured more than 2 months in regular intervals. The intensity analysis of the images shows that the proposed reference plate delivers stable fluorescence over a long term period. The proposed reference plate can be utilized to compare the performance of various UV illuminators, or to set a standard fluorescence point for certain analyses.

Automatic detection of malaria parasite in blood images using two parameters.

Malaria must be diagnosed quickly and accurately at the initial infection stage and treated early to cure it properly. The malaria diagnosis method using a microscope requires much labor and time of a skilled expert and the diagnosis results vary greatly between individual diagnosticians. Therefore, to be able to measure the malaria parasite infection quickly and accurately, studies have been conducted for automated classification techniques using various parameters. In this study, by measuring classification technique performance according to changes of two parameters, the parameter values were determined that best distinguish normal from plasmodium-infected red blood cells. To reduce the stain deviation of the acquired images, a principal component analysis (PCA) grayscale conversion method was used, and as parameters, we used a malaria infected area and a threshold value used in binarization. The parameter values with the best classification performance were determined by selecting the value (72) corresponding to the lowest error rate on the basis of cell threshold value 128 for the malaria threshold value for detecting plasmodium-infected red blood cells.

Fluorescence detection test by black printed circuit board based microfluidic channel for polymerase chain reaction.

This paper proposes the optimal structure of a PCB-based micro PCR chip constructed on a PCB substrate using commercial adhesive tapes and plastic covers. The solder mask of the PCB substrate was coated black, and the area where the reaction chamber is attached was legend printed with white silk to minimize the noise during fluorescence detection. The performance of the PCR and fluorescence detection was compared using 6 types of reaction chambers, each made with different double-sided tapes. Three of the chambers were unsuccessful in completing the PCR. The performance of the other three chambers that successfully amplified DNA was compared using Taqman probe for Chlamydia Trachomatis DNA. The amplified product was illuminated diagonally with a blue LED to excite the product just before imaging, and the LED was turned off when the image was captured to prevent quenching of the probe. The images were taken 10 seconds prior to the last extension step for each cycle using a DSLR camera. The experiments were run as a quartet for each three chambers made with different double-sided tape. The results showed that there were significant difference between the three tapes.

Fluorescence reference plate for UV illumination using quantum dots.

Many image acquisition methods of nucleic acids still depend on UV illumination, especially after the electrophoresis when determining the size of the target DNA. Therefore the quality of the UV illuminator in the gel documentation system, and the comparison of the fluorescence detected are crucial. This paper presents a fluorescence standard reference plate using quantum dots compared to the conventional method where an agarose gel containing ethidium bromide is loaded with standard samples. The fluorescence standard reference plate consists of chambers filled with commercially available quantum dots such as phosphor dots. The chamber is made by thermally attaching nylon and polyester, the former on the inside and the latter on the outside, for increased stability. The images of the proposed reference plate were captured more than 2 months in regular intervals. The intensity analysis of the images shows that the proposed reference plate delivers stable fluorescence over a long term period. The proposed reference plate can be utilized to compare the performance of various UV illuminators, or to set a standard fluorescence point for certain analyses.

Looking for optimized weights of CA125 and HE4 in early screening system of ovarian cancer for Korean patients.

We try to find out the best weight values of CA125 and HE4 in a discriminant formula classifying ovarian cancer patients from benign patients. We utilize a logistic regression analysis for the early screening system of the ovarian cancer for Korean patients. We compare our system with ROMA (Risk of Ovarian Malignancy Algorithm) of Abbot corp. In view of AUC (Area under the ROC curve), sensitivity with 95% of specificity and accuracy are considered. We performed experiments based on the logistic regression analysis separated by the case of pre- and post- menopausal stages and by the stages of progression of cancer. In our experiments, we can increase about 15.6% points of sensitivity with 95% of specificity, compared to that of ROMA. In premenopausal cases, ROMA shows 93.32% of AUC value and our system shows 97.48% of AUC, 4.1% points higher than ROMA. AUC of the ROMA for premenopausal women was 93.32%, whereas the AUC of our system was 97.48%. Furthermore, the AUC of the ROMA for early-staged ovarian cancer was 91.35%, whereas the AUC of our system was 97.22%, showing that the diagnostic performance of our system was superior over that of the ROMA in Korean patient cases.

Performance evaluation of cost-optimized thermal cycler.

A polymerase chain reaction is a test method currently used in almost all process steps of a genetic manipulation experiment. It involves the amplification of the given genetic material targeted by the detection test. In consideration of the graphical user interface development environment or user accessibility, if a PC with the windows operating system or its embedded version can be employed as a host, it will contribute significantly to resource saving, including development-related human resources and time, along with enabling a broad use of the product. In this study, we focus on the low cost implementation of a PCR thermal cycler for the personal usage. It is aimed to drastically reduce the product development time and maintenance/repair costs. To achieve this, we implement the functions for biochemical process in a local embedded system, and the functions of data management, including the PCR protocol, and user-interface management are implemented on a PC.