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1.  MaPLE: A MapReduce Pipeline for Lattice-based Evaluation and Its Application to SNOMED CT 
Non-lattice fragments are often indicative of structural anomalies in ontological systems and, as such, represent possible areas of focus for subsequent quality assurance work. However, extracting the non-lattice fragments in large ontological systems is computationally expensive if not prohibitive, using a traditional sequential approach. In this paper we present a general MapReduce pipeline, called MaPLE (MapReduce Pipeline for Lattice-based Evaluation), for extracting non-lattice fragments in large partially ordered sets and demonstrate its applicability in ontology quality assurance. Using MaPLE in a 30-node Hadoop local cloud, we systematically extracted non-lattice fragments in 8 SNOMED CT versions from 2009 to 2014 (each containing over 300k concepts), with an average total computing time of less than 3 hours per version. With dramatically reduced time, MaPLE makes it feasible not only to perform exhaustive structural analysis of large ontological hierarchies, but also to systematically track structural changes between versions. Our change analysis showed that the average change rates on the non-lattice pairs are up to 38.6 times higher than the change rates of the background structure (concept nodes). This demonstrates that fragments around non-lattice pairs exhibit significantly higher rates of change in the process of ontological evolution.
doi:10.1109/BigData.2014.7004301
PMCID: PMC4334137
2.  Using SPARQL to Test for Lattices: application to quality assurance in biomedical ontologies 
We present a scalable, SPARQL-based computational pipeline for testing the lattice-theoretic properties of partial orders represented as RDF triples. The use case for this work is quality assurance in biomedical ontologies, one desirable property of which is conformance to lattice structures. At the core of our pipeline is the algorithm called NuMi, for detecting the Number of Minimal upper bounds of any pair of elements in a given finite partial order. Our technical contribution is the coding of NuMi completely in SPARQL. To show its scalability, we applied NuMi to the entirety of SNOMED CT, the largest clinical ontology (over 300,000 conepts). Our experimental results have been groundbreaking: for the first time, all non-lattice pairs in SNOMED CT have been identified exhaustively from 34 million candidate pairs using over 2.5 billion queries issued to Virtuoso. The percentage of non-lattice pairs ranges from 0 to 1.66 among the 19 SNOMED CT hierarchies. These non-lattice pairs represent target areas for focused curation by domain experts. RDF, SPARQL and related tooling provide an e cient platform for implementing lattice algorithms on large data structures.
doi:10.1007/978-3-642-17749-1_18
PMCID: PMC4330995
3.  Learning curve for hand-assisted laparoscopic D2 radical gastrectomy 
AIM: To describe the learning curves of hand-assisted laparoscopic D2 radical gastrectomy (HALG) for the treatment of gastric cancer.
METHODS: The HALG surgical procedure consists of three stages: surgery under direct vision via the port for hand assistance, hand-assisted laparoscopic surgery, and gastrointestinal tract reconstruction. According to the order of the date of surgery, patients were divided into 6 groups (A-F) with 20 cases in each group. All surgeries were performed by the same group of surgeons. We performed a comprehensive and in-depth retrospective comparative analysis of the clinical data of all patients, with the clinical data including general patient information and intraoperative and postoperative observation indicators.
RESULTS: There were no differences in the basic information among the patient groups (P > 0.05). The operative time of the hand-assisted surgery stage in group A was 8-10 min longer than the other groups, with the difference being statistically significant (P = 0.01). There were no differences in total operative time between the groups (P = 0.30). Postoperative intestinal function recovery time in group A was longer than that of other groups (P = 0.02). Lengths of hospital stay and surgical quality indicators (such as intraoperative blood loss, numbers of detected lymph nodes, intraoperative side injury, postoperative complications, reoperation rate, and readmission rate 30 d after surgery) were not significantly different among the groups.
CONCLUSION: HALG is a surgical procedure that can be easily mastered, with a learning curve closely related to the operative time of the hand-assisted laparoscopic surgery stage.
doi:10.3748/wjg.v21.i5.1606
PMCID: PMC4316103  PMID: 25663780
Learning curve; Gastric cancer; Hand-assisted laparoscopic D2 radical gastrectomy; Operative time; Surgical quality indicators
4.  An outbreak following importation of wild poliovirus in Xinjiang Uyghur Autonomous Region, China, 2011 
Background
After more than 10 years without a case of wild poliovirus (WPV) in China, an outbreak occurred in 2011 in Xinjiang Uyghur Autonomous Region.
Methods
Acute flaccid paralysis (AFP) case surveillance was strengthened with epidemiological investigations and specimen collection and serological surveys were conducted among hospitalized patients.
Results
There were 21 WPV cases and 23 clinical compatible polio cases reported. WPV was isolated from 14 contacts of AFP cases and 13 in the healthy population. Incidence of WPV and clinical compatible polio cases were both highest among children <1 years, however, 24/44 (54.5%) polio cases were reported among adults aged 15–39 years.
Conclusions
High coverage of routine immunization should be maintained among children until WPV transmission is globally eradicated. Expansion of AFP case surveillance and use of serologic surveys to estimate population immunity should be conducted rapidly to guide preparedness and response planning for future WPV outbreaks.
doi:10.1186/s12879-015-0761-y
PMCID: PMC4336520  PMID: 25636581
Wild poliovirus; Importation; Acute flaccid paralysis; Supplementary immunization activities; Serological survey
5.  The PI3K/Akt Signaling Pathway Mediates the High Glucose-Induced Expression of Extracellular Matrix Molecules in Human Retinal Pigment Epithelial Cells 
Journal of Diabetes Research  2015;2015:920280.
Prolonged hyperglycemia is an important risk factor of the pathogenesis of diabetic retinopathy (DR). Extracellular matrix molecules, such as fibronectin, collagen IV, and laminin, are associated with fibrotic membranes. In this study, we investigated the expression of fibronectin, collagen IV, and laminin in RPE cells under high glucose conditions. Furthermore, we also detected the phosphorylation of protein kinase B (Akt) under high glucose conditions in RPE cells. Our results showed that high glucose upregulated fibronectin, collagen IV, and laminin expression, and activated Akt in RPE cells. We also found that pretreatment with LY294002 (an inhibitor of phosphatidylinositol 3-kinase) abolished high glucose-induced expression of fibronectin, collagen IV, and laminin in RPE cells. Thus, high glucose induced the expression of fibronectin, collagen IV, and laminin through PI3K/Akt signaling pathway in RPE cells, and the PI3K/Akt signaling pathway may contribute to the formation of fibrotic membrane during the development of DR.
doi:10.1155/2015/920280
PMCID: PMC4324947
6.  Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure for clinical research and patient care 
Objective
Epilepsy encompasses an extensive array of clinical and research subdomains, many of which emphasize multi-modal physiological measurements such as electroencephalography and neuroimaging. The integration of structured, unstructured, and signal data into a coherent structure for patient care as well as clinical research requires an effective informatics infrastructure that is underpinned by a formal domain ontology.
Methods
We have developed an epilepsy and seizure ontology (EpSO) using a four-dimensional epilepsy classification system that integrates the latest International League Against Epilepsy terminology recommendations and National Institute of Neurological Disorders and Stroke (NINDS) common data elements. It imports concepts from existing ontologies, including the Neural ElectroMagnetic Ontologies, and uses formal concept analysis to create a taxonomy of epilepsy syndromes based on their seizure semiology and anatomical location.
Results
EpSO is used in a suite of informatics tools for (a) patient data entry, (b) epilepsy focused clinical free text processing, and (c) patient cohort identification as part of the multi-center NINDS-funded study on sudden unexpected death in epilepsy. EpSO is available for download at http://prism.case.edu/prism/index.php/EpilepsyOntology.
Discussion
An epilepsy ontology consortium is being created for community-driven extension, review, and adoption of EpSO. We are in the process of submitting EpSO to the BioPortal repository.
Conclusions
EpSO plays a critical role in informatics tools for epilepsy patient care and multi-center clinical research.
doi:10.1136/amiajnl-2013-001696
PMCID: PMC3912711  PMID: 23686934
Epilepsy and Seizure Ontology; Patient Data Capture; Clinical Free Text Processing; Clinical Data Integration
7.  Inhibition of AMPK expression in skeletal muscle by systemic inflammation in COPD rats 
Respiratory Research  2014;15(1):156.
Background
Chronic obstructive pulmonary disease (COPD) is a disease characterized by airflow limitation and inflammation. Meanwhile, COPD also is associated with metabolic disorders, such as skeletal muscle weakness. Strikingly, activation of AMP-activated protein kinase (AMPK) exerts critical roles in energy metabolism. However, it remains unclear whether and how the expression levels of AMPK are affected in the COPD model rats which may lead to the dysfunction of the skeletal muscle in these rats.
Methods
Here we developed a rat model of COPD, and we investigated the morphological changes of peripheral skeletal muscle and measured the levels of tumor necrosis factor -α (TNF-α) and AMPK in skeletal muscle by using approaches that include immunohistochemistry and polymerase chain reaction (PCR).
Results
We found that the expression levels of both AMPK mRNA and protein in skeletal muscles were significantly reduced in the COPD model rats, in comparison to those from the control rats, the COPD model rats that received treatments with AICAR and resveratrol, whereas the expression levels of TNF-α were elevated in COPD rats.
Conclusion
Such findings indicate that AMPK may serve as a target for therapeutic intervention in the treatment of muscle weakness in COPD patients.
doi:10.1186/s12931-014-0156-4
PMCID: PMC4265440  PMID: 25481457
8.  Trial Prospector: Matching Patients with Cancer Research Studies Using an Automated and Scalable Approach 
Cancer Informatics  2014;13:157-166.
Cancer is responsible for approximately 7.6 million deaths per year worldwide. A 2012 survey in the United Kingdom found dramatic improvement in survival rates for childhood cancer because of increased participation in clinical trials. Unfortunately, overall patient participation in cancer clinical studies is low. A key logistical barrier to patient and physician participation is the time required for identification of appropriate clinical trials for individual patients. We introduce the Trial Prospector tool that supports end-to-end management of cancer clinical trial recruitment workflow with (a) structured entry of trial eligibility criteria, (b) automated extraction of patient data from multiple sources, (c) a scalable matching algorithm, and (d) interactive user interface (UI) for physicians with both matching results and a detailed explanation of causes for ineligibility of available trials. We report the results from deployment of Trial Prospector at the National Cancer Institute (NCI)-designated Case Comprehensive Cancer Center (Case CCC) with 1,367 clinical trial eligibility evaluations performed with 100% accuracy.
doi:10.4137/CIN.S19454
PMCID: PMC4259509  PMID: 25506198
clinical trial; gastrointestinal cancer; clinical oncology; patient recruitment; clinical decision support system
9.  Interaction between fatty acid synthase and human epidermal growth receptor 2 (HER2) in osteosarcoma cells 
Elevated expression of fatty acid synthase (FASN) and human epidermal growth factor receptor-2 (HER2) are observed in human osteosarcoma (OS). The aim in this study is to investigate a possible connection between FASN expression and the activity of HER2. The immunohistochemistry staining was conducted on 24 OS specimens from patients, which revealed a significant positive correlation between FASN and HER2 as well as p-HER2 protein expression. Furthermore, the human OS cell lines MG-63 and U2-OS were treated with FASN-specific RNAi Plasmid or Lapatinib (an inhibitor of HER2). The mRNA of HER2 and FASN was measured using RT-PCR. Western blot was performed to detect the protein expression of HER2, p-HER2 and FASN. The results demonstrated that HER2 modulates FASN expression, inhibition of FASN resulted in down-regulation of HER2 and p-HER2 protein in OS cells. Our findings suggested that there was positive feedback regulation between FASN and HER2 expression and phosphorylation in OS cells.
PMCID: PMC4313995
Osteosarcoma; FASN; HER2; positive feedback regulation
10.  RMS: a platform for managing cross-disciplinary and multi-institutional research project collaboration 
Background
Cross-institutional cross-disciplinary collaboration has become a trend as researchers move toward building more productive and innovative teams for scientific research. Research collaboration is significantly changing the organizational structure and strategies used in the clinical and translational science domain. However, due to the obstacles of diverse administrative structures, differences in area of expertise, and communication barriers, establishing and managing a cross-institutional research project is still a challenging task. We address these challenges by creating an integrated informatics platform to reduce the barriers to biomedical research collaboration.
Results
The Request Management System (RMS) is an informatics infrastructure designed to transform a patchwork of expertise and resources into an integrated support network. The RMS facilitates investigators’ initiation of new collaborative projects and supports the management of the collaboration process. In RMS, experts and their knowledge areas are categorized and managed structurally to provide consistent service. A role-based collaborative workflow is tightly integrated with domain experts and services to streamline and monitor the life-cycle of a research project. The RMS has so far tracked over 1,500 investigators with over 4,800 tasks. The research network based on the data collected in RMS illustrated that the investigators’ collaborative projects increased close to 3 times from 2009 to 2012. Our experience with RMS indicates that the platform reduces barriers for cross-institutional collaboration of biomedical research projects.
Conclusion
Building a new generation of infrastructure to enhance cross-disciplinary and multi-institutional collaboration has become an important yet challenging task. In this paper, we share the experience of developing and utilizing a collaborative project management system. The results of this study demonstrate that a web-based integrated informatics platform can facilitate and increase research interactions among investigators.
doi:10.1186/s12911-014-0106-6
PMCID: PMC4264263  PMID: 25433526
Biomedical research; Organization & administration; Research collaboration; System design and development; Collaborative research; Communication networks; Systems integration; Data-driven analysis
11.  Ontology-guided organ detection to retrieve web images of disease manifestation: towards the construction of a consumer-based health image library 
Background
Visual information is a crucial aspect of medical knowledge. Building a comprehensive medical image base, in the spirit of the Unified Medical Language System (UMLS), would greatly benefit patient education and self-care. However, collection and annotation of such a large-scale image base is challenging.
Objective
To combine visual object detection techniques with medical ontology to automatically mine web photos and retrieve a large number of disease manifestation images with minimal manual labeling effort.
Methods
As a proof of concept, we first learnt five organ detectors on three detection scales for eyes, ears, lips, hands, and feet. Given a disease, we used information from the UMLS to select affected body parts, ran the pretrained organ detectors on web images, and combined the detection outputs to retrieve disease images.
Results
Compared with a supervised image retrieval approach that requires training images for every disease, our ontology-guided approach exploits shared visual information of body parts across diseases. In retrieving 2220 web images of 32 diseases, we reduced manual labeling effort to 15.6% while improving the average precision by 3.9% from 77.7% to 81.6%. For 40.6% of the diseases, we improved the precision by 10%.
Conclusions
The results confirm the concept that the web is a feasible source for automatic disease image retrieval for health image database construction. Our approach requires a small amount of manual effort to collect complex disease images, and to annotate them by standard medical ontology terms.
doi:10.1136/amiajnl-2012-001380
PMCID: PMC3822108  PMID: 23792805
Image Retrieval; Object Detection; Ontology
12.  Association between Helicobacter pylori infection and migraine: A meta-analysis 
World Journal of Gastroenterology : WJG  2014;20(40):14965-14972.
AIM: To quantify the association between Helicobacter pylori (H. pylori) infection and migraine.
METHODS: A systematic literature search of PubMed and EMBASE was conducted from inception to December 2013. Studies that provided data dealing with H. pylori infection in patients with migraine, as well as healthy controls, were selected. Meta-analysis was carried out using the odds ratio (OR) with a fixed or random effects model, and a 95%CI for the OR was calculated. An unconditional logistic regression model was used to analyze potential parameters related to H. pylori prevalence. Subgroup analyses were conducted as methods of detection and evidence grade.
RESULTS: Five case-control studies published between 2000 and 2013 were finally identified, involving 903 patients, with a total H. pylori infection rate of 39.31%. The prevalence of H. pylori infection was significantly greater in migraineurs than in controls (44.97% vs 33.26%, OR = 1.92, 95%CI: 1.05-3.51, P = 0.001). A sensitivity test indicated that no single study dominated the combined results. Univariate regression analysis found that publication year, geographical distribution and evidence grade were relevant to the results and were the main reason for the heterogeneity. Subgroup analysis found a significantly greater infection rate of H. pylori in Asian patients with migraine, but no statistically significant infection rate in European patients. The ORs were 3.48 (95%CI: 2.09-5.81, P = 0.000) and 1.19 (95%CI: 0.86-1.65, P = 0.288), respectively.
CONCLUSION: The pooled data suggest a trend of more frequent H. pylori infections in patients with migraine.
doi:10.3748/wjg.v20.i40.14965
PMCID: PMC4209561  PMID: 25356058
Helicobacter pylori; Migraine; Meta-analysis; Odds ratio; Subgroup analysis
14.  Effect of Ethanol Extract of Selaginella Doederleinii Hieron on the Proliferation of Nasopharyngeal Carcinoma CNE-1 AND C666-1 Cells 
This paper mainly studied the effect of ethanol extract of Selaginella doederleinii Hieron on the proliferation of two kinds of nasopharyngeal carcinoma cell lines, CNE-1 and C666-1, and their mechanisms of action. Extract was obtained by heat reflux extraction with ethanol, and the effect of extract on the extracellular matrix adhesion of the cells, on their proliferation process, as well as on their colony-forming ability were tested using MTT assay. The results showed that the yield of dry extract was 36.4%. 2.5 g/ml extract in the high concentration group exhibited inhibitory activity that was directly proportional to the concentration on CNE-1 cells, while not exhibiting obvious proportional trend in respect with C666-1 cells. However, the inhibition rates against two types of cells can both reach between 30%∼50%. Under the effect of ethanol extract of Selaginella doederleinii Hieron, proliferative capacities of C666-1 and CNE-1 cells were affected to some extent.
PMCID: PMC3847390  PMID: 24311875
Selaginella doederleinii Hieron; Ethanol extract; CNE-1; C666-1
15.  Reference Intervals of Total Bilirubin, ALT, AST, and Creatinine in Healthy Elderly Chinese 
Background
The aim of this study was to establish the reference intervals (RIs) of total bilirubin (TBIL), alanine aminotransferase (ALT), aspartate transaminase (AST), and creatinine (CREA) for apparently healthy elderly (Han ethnicity) in Shuyang, China.
Material/Methods
A total of 54 912 blood specimens from elderly residents age 65–104 years were collected by standard procedures in Shuyang county of Jiangsu province. TBIL, ALT, AST, and CREA for each participant were determined by automatic biochemical analyzer. Distribution and differences of TBIL, ALT, AST, and CREA were analyzed and compared between the elderly of the same age of different sexes and different ages of the same sex. RIs of TBIL, ALT, AST, and CREA were compared with the current RIs. The RIs and 95% confidence intervals were calculated using nonparametric method (2.5th–97.5th percentiles) according to the guideline of the Clinical and Laboratory Standards Institute.
Results
RIs established for the healthy elderly include: TBIL 7.8~30.6 μmol/L for males and 7.3~26.1 μmol/L for females; ALT 8.7~47.3 U/L for males and 8.4~45.2 U/L for females; AST 15.7~46.9 U/L for males and 15.1~46.2 U/L for females; and CREA 45.1~100.9 μmol/L for males and 38.7~85.0 μmol/L for females. Reference intervals of TBIL, ALT, AST, and CREA for male elderly were higher than those of females, and values of CREA increased with increasing age.
Conclusions
We have established a panel of locally relevant RIs. It is necessary to establish scientific and reasonable RIs of TBIL, ALT, AST, and CREA for the healthy elderly in our region, which will provide a reference for clinicians and inspection officers.
doi:10.12659/MSM.892148
PMCID: PMC4196892  PMID: 25272068
Alanine Transaminase; Creatinine; Reference Values
16.  Improved 1-Deoxynojirimycin (DNJ) production in mulberry leaves fermented by microorganism 
Brazilian Journal of Microbiology  2014;45(2):721-729.
DNJ, an inhibitor of α-glucosidase, is used to suppress the elevation of postprandial hyperglycemia. In this study, we focus on screening an appropriate microorganism for performing fermentation to improve DNJ content in mulberry leaf. Results showed that Ganoderma lucidum was selected from 8 species and shown to be the most effective in improvement of DNJ production from mulberry leaves through fermentation. Based on single factor and three factor influence level tests by following the Plackett-Burman design, the optimum extraction yield was analyzed by response surface methodology (RSM). The extracted DNJ was determined by reverse-phase high performance liquid chromatograph equipped with fluorescence detector (HPLC-FD). The results of RSM showed that the optimal condition for mulberry fermentation was defined as pH 6.97, potassium nitrate content 0.81% and inoculums volume 2 mL. The extraction efficiency reached to 0.548% in maximum which is 2.74 fold of those in mulberry leaf.
PMCID: PMC4166305  PMID: 25242964
mulberry; DNJ Production; microorganisms; fermentation
17.  Successful surgical strategy in a late case of Boerhaave’s syndrome 
World Journal of Gastroenterology : WJG  2014;20(35):12696-12700.
Boerhaave’s syndrome refers to the spontaneous transmural rupture of the esophagus. Primary repair may be performed in patients who present within 24 h of perforation, and such cases have the best outcomes as most complications have not yet developed. However, the treatment of late perforations remains controversial. Various approaches and strategies to repair late perforations have been described in the literature, but there is no uniform approach. We present a case of Boerhaave’s syndrome in which the patient underwent surgical repair 48 h after the acute event and was subsequently treated successfully. The initial approach included direct esophageal repair, a drainage series, and nutritional support via a feeding jejunostomy. Although the repair site was subsequently disrupted, the patient showed complete healing of the perforation after three weeks. We consider that our surgical treatment strategy is safe and technically feasible, and appears to be a promising alternative approach for the treatment of patients with late Boerhaave’s perforation.
doi:10.3748/wjg.v20.i35.12696
PMCID: PMC4168112  PMID: 25253979
Boerhaave’s perforation; Surgery; Drainage; Repair; Nutritional support
18.  Successful esophagectomy in a patient with combined esophageal cancer and hemophilia B 
World Journal of Gastroenterology : WJG  2014;20(35):12701-12703.
Patients with esophageal cancer often require esophagectomy with esophagogastrostomy. However, the incidence of complications, such as hemorrhage, during operations for esophageal cancer is high, even with minimally invasive surgery. Without the appropriate interventions, the risk of major intraoperative and postoperative hemorrhage is very high in patients with esophageal cancer and hemophilia. We report the case of a 45-year-old man with esophageal cancer and hemophilia B who underwent a successful hybrid, minimally invasive Ivor-Lewis esophagectomy with appropriate perioperative management.
doi:10.3748/wjg.v20.i35.12701
PMCID: PMC4168113  PMID: 25253980
Esophageal cancer; Esophagectomy; Hemophilia B; Esophagogastrostomy; Hemorrhage
19.  Variation in β-amylase activity and thermostability in Tibetan annual wild and cultivated barley genotypes*  
β-Amylase activity (BAA) and thermostability (BAT) are important traits for malt quality. In this study, 138 Tibetan annual wild barley accessions and 20 cultivated genotypes differing in BAA were planted and analyzed in 2009 and 2012. Significant differences were detected among genotypes in BAA and BAT. The cultivated genotypes had a mean BAA of 1137.6 U/g and a range of from 602.1 to 1407.5 U/g, while the wild accessions had a mean of 1517.9 U/g and a range of from 829.7 to 2310.0 U/g. The cultivated genotypes had a mean relative residual β-amylase activity (RRBAA) of 61.6% and a range of from 22.2% to 82.3%, while the wild barleys had a mean of 57.8% and a range of from 21.9% to 96.1%. Moreover, there was a significant difference among genotypes in the response of RRBAA to the temperature and duration of heat treatment. The wild barleys had wider variation in BAA and BAT than cultivated genotypes.
doi:10.1631/jzus.B1400026
PMCID: PMC4162881  PMID: 25183034
Barley; β-Amylase activity; Thermostability; Tibet
20.  A Novel Laccase with Potent Antiproliferative and HIV-1 Reverse Transcriptase Inhibitory Activities from Mycelia of Mushroom Coprinus comatus 
BioMed Research International  2014;2014:417461.
A novel laccase was isolated and purified from fermentation mycelia of mushroom Coprinus comatus with an isolation procedure including three ion-exchange chromatography steps on DEAE-cellulose, CM-cellulose, and Q-Sepharose and one gel-filtration step by fast protein liquid chromatography on Superdex 75. The purified enzyme was a monomeric protein with a molecular weight of 64 kDa. It possessed a unique N-terminal amino acid sequence of AIGPVADLKV, which has considerably high sequence similarity with that of other fungal laccases, but is different from that of C. comatus laccases reported. The enzyme manifested an optimal pH value of 2.0 and an optimal temperature of 60°C using 2,2′-azinobis(3-ethylbenzothiazolone-6-sulfonic acid) diammonium salt (ABTS) as the substrate. The laccase displayed, at pH 2.0 and 37°C, Km values of 1.59 mM towards ABTS. It potently suppressed proliferation of tumor cell lines HepG2 and MCF7, and inhibited human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) with an IC50 value of 3.46 μM, 4.95 μM, and 5.85 μM, respectively, signifying that it is an antipathogenic protein.
doi:10.1155/2014/417461
PMCID: PMC4164474  PMID: 25540778
21.  Three-step hand-assisted laparoscopic surgery for radical distal gastrectomy: an effective surgical approach 
Objective: Three-step hand-assisted laparoscopic D2 radical gastrectomy (HALG) is a modified surgical technique based on hand-assisted laparoscopic surgery (HALS) for the treatment of gastric cancer. This surgical approach is particularly easy and convenient for radical distal gastrectomy. In order to thoroughly understand the advantages of applying “three-step HALG” in distal gastrectomy, our center conducted a retrospective study to analyze data from patients who underwent HALG and laparoscopic-assisted D2 radical gastrectomy (LAG) during the corresponding time period. Methods: The HALG procedure is performed in three steps, namely the operation performed through an auxiliary incision under direct vision, hand-assisted laparoscopic operation, and gastrointestinal tract reconstruction through the auxiliary incision under direct vision. This study performed comprehensive, in-depth comparative analyses on the clinical data of two groups of patients who underwent HALG and LAG. Results: The auxiliary incision under the xiphoid was maximally utilized in the HALG procedure. The rate of conversion to open surgery in HALG group patients was significantly lower than in the LAG group (P = 0.03), and the operating time was significantly shorter in the HALG group than in the LAG group (P = 0.00). There was no significant difference in the pain rate score on postoperative day 2 and on the day of discharge between the HALG and LAG groups (P > 0.05). No statistically significant difference was found in the time to recovery of bowel function, postoperative hospital stay, or postoperative complications (P > 0.05), although the values were all lower in the HALG group than in the LAG group. Conclusion: “Three-step HALG” is a highly feasible surgical approach for radical distal gastrectomy.
PMCID: PMC4161561  PMID: 25232401
Hand-assisted laparoscopic surgery; three-step hand-assisted laparoscopic D2 radical gastrectomy; laparoscopic-assisted D2 radical gastrectomy; distal gastrectomy
22.  Value of segmental coronary calcium score on diagnosis and interventional treatment of coronary lesions by 320-slice DVCT 
The global coronary calcium score has been widely used in the evaluation of coronary plaque burden and cardiovascular disease events. In this study, we investigated the value of segmental coronary calcium score (SCCS) on the diagnosis and interventional treatment. We studied 87 patients with coronary angiography (CAG) and coronary CT angiography (CTA) by 320-slice dynamic volume CT (DVCT). SCCS was determined for each segmental separately. All lesions which SCCS was greater than 0 were enrolled, and were divided into three groups, mild calcification group (SCCS were less than 80), Moderate calcification group (SCCS were more than 80 and less than 200) and Severe calcification group (SCCS were more than 200). From above three groups, lesions received the intervention treatment were elected as subgroup. The position of lesions, plaque morphology, calcification proportion and interventional treatment data were analyzed. Severe calcification group were more frequent in the proximal lesions, stenosis with lesser extent, nubbly and nodular types of plaque, and the inconsistency with CAG was higher than the other two groups (P < 0.05). In the subgroup, more pre-dilatation and post-dilatation balloon were used in severe calcification group, with higher expansion pressure of balloon and stent (P < 0.05), but the diameter of stents was no difference between the three groups. Conclusion: SCCS is better than GCCS in the evaluation of coronary calcification, and play an important role in the judgment of stenosis by coronary CT and in the choice of interventional therapeutic devices.
PMCID: PMC4161572  PMID: 25232412
Segmental coronary calcium score; plaque morphology; calcification; dynamic volume CT; coronary angiography
23.  Transvaginal early fistula debridement and repair plus continuous vacuum aspiration via anal tube for rectovaginal fistula following rectal cancer surgery: report of four cases 
Objective: To investigate the feasibility and superiority of transvaginal early fistula debridement and repair plus continuous vacuum aspiration via anal tube for rectovaginal fistula following rectal cancer surgery. Methods: The clinical data of four cases of rectovaginal fistula following rectal cancer surgery were retrospectively analyzed in our center. After adequate preoperative preparation, the patients underwent transvaginal fistula debridement and repair plus continuous vacuum aspiration via anal tube under continuous epidural anesthesia. After surgery and before discharge, anti-infection and nutritional support was administered for 2 d, and fluid diet and anal tube vacuum aspiration continued for 7 d. Results: All the four cases healed. Three of them healed after one operation, and the other patient had obvious shrinkage of the fistular orifice after the first operation and underwent the same operation for a second time before complete healing. The duration of postoperative follow-up was 2, 7, 8 and 9 months respectively. No recurrence or abnormal sex life was reported. Conclusions: Early transvaginal fistula debridement and repair plus continuous vacuum aspiration via anal tube are feasible for rectovaginal fistula following rectal cancer surgery. This operation has many advantages, such as minimal invasiveness, short durations of operation, short treatment cycles, and easy acceptance by the patient. In addition, it does not necessitate colostomy for feces shunt and a secondary colostomy and reduction.
PMCID: PMC4161576  PMID: 25232416
Fistula; debridement and repair; anal tube; continuous vacuum aspiration; after rectal cancer surgery; rectovaginal fistula
24.  Multi-topic assignment for exploratory navigation of consumer health information in NetWellness using formal concept analysis 
Background
Finding quality consumer health information online can effectively bring important public health benefits to the general population. It can empower people with timely and current knowledge for managing their health and promoting wellbeing. Despite a popular belief that search engines such as Google can solve all information access problems, recent studies show that using search engines and simple search terms is not sufficient. Our objective is to provide an approach to organizing consumer health information for navigational exploration, complementing keyword-based direct search. Multi-topic assignment to health information, such as online questions, is a fundamental step for navigational exploration.
Methods
We introduce a new multi-topic assignment method combining semantic annotation using UMLS concepts (CUIs) and Formal Concept Analysis (FCA). Each question was tagged with CUIs identified by MetaMap. The CUIs were filtered with term-frequency and a new term-strength index to construct a CUI-question context. The CUI-question context and a topic-subject context were used for multi-topic assignment, resulting in a topic-question context. The topic-question context was then directly used for constructing a prototype navigational exploration interface.
Results
Experimental evaluation was performed on the task of automatic multi-topic assignment of 99 predefined topics for about 60,000 consumer health questions from NetWellness. Using example-based metrics, suitable for multi-topic assignment problems, our method achieved a precision of 0.849, recall of 0.774, and F1 measure of 0.782, using a reference standard of 278 questions with manually assigned topics. Compared to NetWellness’ original topic assignment, a 36.5% increase in recall is achieved with virtually no sacrifice in precision.
Conclusion
Enhancing the recall of multi-topic assignment without sacrificing precision is a prerequisite for achieving the benefits of navigational exploration. Our new multi-topic assignment method, combining term-strength, FCA, and information retrieval techniques, significantly improved recall and performed well according to example-based metrics.
doi:10.1186/1472-6947-14-63
PMCID: PMC4131492  PMID: 25086916
Consumer health information; Multi-topic assignment; Formal concept analysis; Navigational exploration
25.  Epilepsy informatics and an ontology-driven infrastructure for large database research and patient care in epilepsy 
Epilepsia  2013;54(8):1335-1341.
Summary
The epilepsy community increasingly recognizes the need for a modern classification system that can also be easily integrated with effective informatics tools. The 2010 reports by the United States President's Council of Advisors on Science and Technology (PCAST) identified informatics as a critical resource to improve quality of patient care, drive clinical research, and reduce the cost of health services. An effective informatics infrastructure for epilepsy, which is underpinned by a formal knowledge model or ontology, can leverage an ever increasing amount of multimodal data to improve (1) clinical decision support, (2) access to information for patients and their families, (3) easier data sharing, and (4) accelerate secondary use of clinical data. Modeling the recommendations of the International League Against Epilepsy (ILAE) classification system in the form of an epilepsy domain ontology is essential for consistent use of terminology in a variety of applications, including electronic health records systems and clinical applications. In this review, we discuss the data management issues in epilepsy and explore the benefits of an ontology-driven informatics infrastructure and its role in adoption of a “data-driven” paradigm in epilepsy research.
doi:10.1111/epi.12211
PMCID: PMC3774789  PMID: 23647220
Informatics; Epilepsy; Large scale data management; Clinical research; Biomedical ontologies

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