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390 citation(s) found for "Fan, C".

A Simulator-Based Comparison of a Novel 3D and a Conventional 3D Vision System-Surgical Performance and Subjective Ratings
Svenner, Annika, Fan, Xuelong , Forsman, Mikael , Shabo, Ivan , Kjellman, Magnus , Hallbeck, M. Susan

Inventions | September 27, 2019 | Volume: 4 | Issue: 4 | Pages: 58

10.3390/inventions4040058 Get It

In laparoscopy, novel three-dimensional laparoscopic vision systems (3D LVS) without glasses (3D−) have been invented. While standard 3D LVS with glasses (3D+) have shown advantages over original two-dimensional systems, quantitative comparisons of surgical performance between 3D− and 3D+ systems are still lacking. The aim is to compare the systems in simulated robotic surgery tasks. In a crossover study, 18 medical students performed four basic laparoscopic tasks in the validated Simball Box simulator with authentic surgical instruments by using the 3D+ and 3D− systems. Performance was measured by the number of errors and the task’s duration. Subjective ratings of perceptions and preference were assessed after each test. There were significant, but still minor, advantages for the conventional 3D+ system regarding spatial orientation and sense of depth. Overall, ten and eight subjects preferred 3D+ and 3D− systems, respectively. No significant differences were found in performance, post-operative physicals or eye symptoms. The novel 3D− system was similar to the conventional 3D+ system regarding performance and overall preference, while there were minor advantages for the 3D+ system in the subjective ratings. Since the 3D− system is a new invention, it should have a higher potential of usability improvements.
Multimorbidity, functional limitations, and outcomes: Interactions in a population-based cohort of older adults
Chamberlain, Alanna M. , Jacobson, Debra J., Fan, Chun , Wilson, Patrick M. , Rocca, Walter A. , Roger, Véronique L. , St Sauver, Jennifer L, Chamberlain, Alanna M , Rutten, Lila J. Finney , Sauver, Jennifer L. St.

Journal of Comorbidity | September 9, 2019 | Volume: 9 | Issue: No issue available | Pages: No page available

10.1177/2235042x19873486 | PMID 31523633 Get It

Objective: To understand the interaction of multimorbidity and functional limitations in determining health-care utilization and survival in older adults. Methods: Olmsted County, Minnesota, residents aged 60–89 years in 2005 were categorized into four cohorts based on the presence or absence of multimorbidity (≥3 chronic conditions from a list of 18) and functional limitations (≥1 limitation in an activity of daily living from a list of 9), and were followed through December 31, 2016. Andersen–Gill and Cox regression estimated hazard ratios (HRs) for emergency department (ED) visits, hospitalizations, and death using persons with neither multimorbidity nor functional limitations as the reference (interaction analyses). Results: Among 13,145 persons, 34% had neither multimorbidity nor functional limitations, 44% had multimorbidity only, 4% had functional limitations only, and 18% had both. Over a median follow-up of 11 years, 5906 ED visits, 2654 hospitalizations, and 4559 deaths occurred. Synergistic interactions on an additive scale of multimorbidity and functional limitations were observed for all outcomes; however, the magnitude of the interactions decreased with advancing age. The HR (95% confidence interval) for death among persons with both multimorbidity and functional limitations was 5.34 (4.40–6.47) at age 60–69, 4.16 (3.59–4.83) at age 70–79, and 2.86 (2.45–3.35) at age 80–89 years. Conclusion: The risk of ED visits, hospitalizations, and death among persons with both multimorbidity and functional limitations is greater than additive. The magnitude of the interaction was strongest for the youngest age group, highlighting the importance of interventions to prevent and effectively manage multimorbidity and functional limitations early in life.
Performance evaluation of computed tomography systems: Summary of AAPM Task Group 233
Bakalyar, Donovan, Boedeker, Kirsten , Fan, Jiahua , Myers, Kyle J. , Popescu, Lucreţiu M. , Giraldo, Juan Carlos Ramírez, Ranallo, Frank N. , Solomon, Justin , Vaishnav, J. Y., Wang, Jia , Samei, Ehsan , Brady, Samuel L. , Leng, Shuai , Vaishnav, Jay

Medical Physics | August 13, 2019 | Volume: 46 | Issue: 11 | Pages: No page available

10.1002/mp.13763 | PMID 31408540 Get It

Background The rapid development and complexity of new x‐ray computed tomography (CT) technologies and the need for evidence‐based optimization of image quality with respect to radiation and contrast media dose call for an updated approach towards CT performance evaluation. Aims This report offers updated testing guidelines for testing CT systems with an enhanced focus on the operational performance including iterative reconstructions and automatic exposure control (AEC) techniques. Materials and Methods The report was developed based on a comprehensive review of best methods and practices in the scientific literature. The detailed methods include the assessment of 1) CT noise (magnitude, texture, nonuniformity, inhomogeneity), 2) resolution (task transfer function under varying conditions and its scalar reflections), 3) task‐based performance (detectability, estimability), and 4) AEC performance (spatial, noise, and mA concordance of attenuation and exposure modulation). The methods include varying reconstruction and tube current modulation conditions, standardized testing protocols, and standardized quantities and metrology to facilitate tracking, benchmarking, and quantitative comparisons. Results The methods, implemented in cited publications, are robust to provide a representative reflection of CT system performance as used operationally in a clinical facility. The methods include recommendations for phantoms and phantom image analysis. Discussion In line with the current professional trajectory of the field toward quantitation and operational engagement, the stated methods offer quantitation that is more predictive of clinical performance than specification‐based approaches. They can pave the way to approach performance testing of new CT systems not only in terms of acceptance testing (i.e., verifying a device meets predefined specifications), but also system commissioning (i.e., determining how the system can be used most effectively in clinical practice). Conclusion We offer a set of common testing procedures that can be utilized towards the optimal clinical utilization of CT imaging devices, benchmarking across varying systems and times, and a basis to develop future performance‐based criteria for CT imaging.
Abstract 588: Relationship of serum progesterone and progesterone metabolites with mammographic density
Hada, Manila , Fan, Sharon, Geller, Berta M., Vacek, Pamela M. , Weaver, Donald L. , Mahmoudzadeh, Amir Pasha , Herschorn, Sally D. , Brinton, Louise A. , Xu, Xia , Gierach, Gretchen L. , Gierach, Gretchen L , Oh, Hannah , Falk, Roni T. , Shepherd, John , Wang, Jeff , Fan, Bo , Malkov, Serghei , Sherman, Mark E. , Trabert, Britton

Cancer Research | August 7, 2019 | Volume: 79 | Issue: 13_Supplement | Pages: 588-588

10.1158/1538-7445.am2019-588 Get It

Abstract Background: Mammographic breast density (MBD) is a strong breast cancer (BC) risk factor, but its biologic underpinnings are poorly understood. Use of estrogen plus progestin menopausal hormone therapy is linked to increased MBD and BC risk. Experimental data suggest that ratios of tumor promoting (5α-dihydroprogesterone [5αP]) and anti-tumorigenic (3α-dihydroprogesterone [3αP]) progesterone metabolite levels may be related to BC risk. However, relationships of endogenous progesterone and its metabolites with MBD and BC risk have not been established. Accordingly, we assessed levels of circulating progesterone and its metabolites with MBD. Methods: In this cross-sectional study, serum progesterone and its metabolites were quantified using a novel liquid chromatography-tandem mass spectrometry assay in 103 postmenopausal and 52 premenopausal (luteal menstrual cycle phase) women, ages 40-65, undergoing diagnostic image-guided ipsilateral breast biopsy. MBD was measured as percent fibroglandular volume (MBD-V) on pre-biopsy digital mammograms using single X-ray absorptiometry. Square-root transformed MBD-V was examined across tertile categories of progesterone/progesterone metabolites using age and body mass index (BMI)-adjusted linear regression models. Results: Concentrations of the hormones were as follows among postmenopausal women: progesterone [mean: 12.6 pmol/L (range: 5.2-45.8)], 3αP [5.6 pmol/L (1.4-18.8)], 5αP [100 pmol/L (16.7-388)], and 5αP/3αP ratio [26.1 (2.1-150)]; and among luteal phase premenopausal women: progesterone [2063 pmol/L (13.6-7098), 3αP [12.7 pmol/L (2.4-64.4)], 5αP [243 pmol/L (25.3-774)], 5αP/3αP ratio [25.9 (2.3-73.7)]. Among postmenopausal women, progesterone was positively associated with MBD-V (Tertile 3 vs. 1: β=0.68, p-trend=0.02). A similar borderline positive association was observed among premenopausal women (β=0.74, p-trend=0.10). Additional adjustment for circulating estradiol did not substantively alter observed associations. Levels of 3αP, 5αP and the 5αP/3αP ratio were not associated with MBD-V among pre- or postmenopausal women. Conclusions: Concentrations of progesterone and it metabolites show substantial inter-woman variation. We observed a positive association between endogenous progesterone and MBD-V among both postmenopausal and premenopausal luteal phase women. We did not observe an association with the ratio of 5αP to 3αP levels and MBD-V. These findings suggest the need for additional studies to understand the biological basis of the role of progesterone and its metabolites in MBD and BC risk. Citation Format: Manila Hada, Hannah Oh, Sharon Fan, Roni T. Falk, Berta Geller, Pamela Vacek, Donald Weaver, John Shepherd, Jeff Wang, Bo Fan, Amir P. Mahmoudzadeh, Serghei Malkov, Sally Herschorn, Louise A. Brinton, Xia Xu, Mark E. Sherman, Britton Trabert, Gretchen L. Gierach. Relationship of serum progesterone and progesterone metabolites with mammographic density [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 588.
A four‐gene transcript score to predict metastatic‐lethal progression in men treated for localized prostate cancer: Development and validation studies
Cheng, Anqi , Zhao, Shanshan , Wright, Jonathan L. , Kolb, Suzanne , Karnes, R. Jeffrey , Jenkins, Robert B. , Ostrander, Elaine A. , Feng, Ziding , Fan, Jian‐Bing , Dai, James Y. , Stanford, Janet L. , Stanford, Janet L , Dai, James Y , FitzGerald, Liesel M. , Davicioni, Elai

The Prostate | August 3, 2019 | Volume: 79 | Issue: 14 | Pages: 1589-1596

10.1002/pros.23882 | PMID 31376183 Get It

AbstractBackgroundMolecular studies have tried to address the unmet need for prognostic biomarkers in prostate cancer (PCa). Some gene expression tests improve upon clinical factors for prediction of outcomes, but additional tools for accurate prediction of tumor aggressiveness are needed.MethodsBased on a previously published panel of 23 gene transcripts that distinguished patients with metastatic progression, we constructed a prediction model using independent training and testing datasets. Using the validated messenger RNAs and Gleason score (GS), we performed model selection in the training set to define a final locked model to classify patients who developed metastatic‐lethal events from those who remained recurrence‐free. In an independent testing dataset, we compared our locked model to established clinical prognostic factors and utilized Kaplan‐Meier curves and receiver operating characteristic analyses to evaluate the model's performance.ResultsThirteen of 23 previously identified gene transcripts that stratified patients with aggressive PCa were validated in the training dataset. These biomarkers plus GS were used to develop a four‐gene (CST2, FBLN1, TNFRSF19, and ZNF704) transcript (4GT) score that was significantly higher in patients who progressed to metastatic‐lethal events compared to those without recurrence in the testing dataset (P = 5.7 × 10−11). The 4GT score provided higher prediction accuracy (area under the ROC curve [AUC] = 0.76; 95% confidence interval [CI] = 0.69‐0.83; partial area under the ROC curve [pAUC] = 0.008) than GS alone (AUC = 0.63; 95% CI = 0.56‐0.70; pAUC = 0.002), and it improved risk stratification in subgroups defined by a combination of clinicopathological features (ie, Cancer of the Prostate Risk Assessment‐Surgery).ConclusionOur validated 4GT score has prognostic value for metastatic‐lethal progression in men treated for localized PCa and warrants further evaluation for its clinical utility.
P035 Clostridium difficile infection in ulcerative colitis: Data from the tofacitinib clinical program and an insurance claims database
Edward, Loftus, Baumgart, Daniel, Marco, DiBonaventura, Jeffrey, Curtis, Gary, Chan, Eric, Maller, Quirk, Daniel, Fan, Haiyun, Koram, Nana , Salese, Leonardo , Su, Chinyu , Armuzzi, Alessandro , Marco, DiBonaventura, Gary, Chan

American Journal of Gastroenterology | July 21, 2019 | Volume: 114 | Issue: 1 | Pages: S10-S10

10.14309/01.ajg.0000578212.86577.86 Get It

BACKGROUND: Patients with inflammatory bowel disease (IBD), particularly ulcerative colitis (UC), have a higher risk of Clostridium difficile infection (CDI) than the general population (1). The incidence of CDI is increasing among patients with IBD, and certain UC treatments may be associated with greater risk (1). We report CDI events in the tofacitinib UC clinical program, and the incidence of CDI among patients receiving other treatments for UC. METHODS: For the tofacitinib UC program, rates of CDI (patients with an adverse event [AE] of CDI, Clostridium difficile colitis, or Clostridium test-positive, plus concomitant oral metronidazole or vancomycin, counted once per cohort) are reported for Induction Cohort (patients from an 8-week Phase [P]2 and two 8-week P3 induction studies; placebo or tofacitinib 10 mg twice daily [BID; NCT00787202; NCT01465763; NCT01458951]); Maintenance Cohort (patients from a 52-week maintenance study; placebo or tofacitinib 5 or 10 mg BID [NCT01458574]); and Overall Cohort (all tofacitinib-treated patients in P2/3 induction and maintenance studies and an ongoing, open-label, long-term extension study [as of December 2016; NCT01470612]). Positive Clostridium difficile test at screening was an exclusion criterion for program entry. Overall Cohort incidence rate (IR) was calculated as number of unique patients with events per 100 patient-years (PY). For contextualization, CDI rates among patients receiving other UC medications were obtained from a retrospective cohort study utilizing data from the Truven MarketScan ® Database, an administrative healthcare claims database in the US. Patients with moderately to severely active UC, with either an inpatient or outpatient diagnosis code of CDI, plus a prescription for oral therapy (including metronidazole, vancomycin, and fidaxomicin) within 14 days of CDI diagnosis (observation period: October 1, 2010–September 30, 2015), were included. Truven cohort IRs were calculated as number of patients with events per 100 PY. RESULTS: In the tofacitinib Induction Cohort, CDI occurred in 3 patients (placebo, 1/282 [0.4%]; tofacitinib 10 mg BID, 2/938 [0.2%]). In the Maintenance Cohort, CDI occurred in 3 patients (placebo, 3/198 [1.5%]; tofacitinib 5 or 10 mg BID, 0/394 [0.0%]). In the Overall Cohort of all tofacitinib-treated patients (1,664 PY of follow-up), CDI occurred in 8/1,157 patients (0.7%), with an IR (95% confidence interval [CI]) of 0.48 (0.21, 0.95). Two cases were reported as serious AEs. All were mild (n = 4) or moderate (n = 4) in severity; 6 continued with study treatment, one temporarily discontinued, one permanently discontinued. All CDI cases resolved with treatment. In the Truven Cohort, 160 CDI events occurred during 4,918 PY of follow-up, with an overall CDI IR (95% CI) of 3.25 (2.77, 3.80); of which 116 were CDI-associated hospitalizations (4,936 PY of follow-up). Among patients receiving azathioprine, 6-mercaptopurine, or tumor necrosis factor inhibitors, CDI IRs were 3.23 (2.18, 4.62), 2.31 (1.26, 3.87), and 3.58 (2.95, 4.29), respectively. CONCLUSION(S): In the tofacitinib UC program, CDI rates among patients receiving tofacitinib were similar to or lower than those observed with placebo. The IR among patients receiving tofacitinib was numerically lower than those observed for immunomodulators and tumor necrosis factor inhibitors in the Truven Cohort.
PS1337 IVOSIDENIB (AG‐120) INDUCES DURABLE REMISSIONS AND TRANSFUSION INDEPENDENCE IN PATIENTS WITH IDH1‐MUTANT RELAPSED/REFRACTORY MYELODYSPLASTIC SYNDROME IN A PHASE 1 DOSE ESCALATION AND EXPANSION STUDY
Foran, James M. , Watts, Justin M. , Stein, E.M., Fathi, Amir T. , Prince, Gabrielle T., Stein, A.S., Stone, Richard M. , Patel, Pankaj , Tallman, Martin S. , Wang, Heng-Xiang, Zhang, V., Dai, D. , Fan, Bin , Yen, K.E., Kapsalis, Stephanie M., Hickman, D. , Agresta, Sam, Liu, H., Wu, Bor-Wen, Attar, Eyal C. , Kantarjian, H., DiNardo, Courtney D. , Botton, Stéphane de , Patel, P.A., Choe, Sung

HemaSphere | June 17, 2019 | Volume: 3 | Issue: S1 | Pages: 610-611

10.1097/01.hs9.0000563628.38037.c3 Get It

Background:Mutations in isocitrate dehydrogenase 1 (IDH1) occur in ∼4% of patients with myelodysplastic syndrome (MDS) and have been linked with increased transformation to acute myeloid leukemia (AML). Ivosidenib (IVO; AG‐120) is an oral, potent, targeted inhibitor of the mutant IDH1 protein (mIDH1) that is approved for the treatment of adults with mIDH1 relapsed or refractory (R/R) AML. Through inhibition of mIDH1, IVO suppresses production of the oncometabolite 2‐hydroxyglutarate, leading to clinical responses via differentiation of malignant cells.Aims:To report safety and efficacy data from patients with R/R MDS enrolled in the first‐in‐human, phase 1, dose escalation and expansion study of IVO in patients with mIDH1 advanced hematologic malignancies (NCT02074839).Methods:This ongoing study is evaluating the safety, maximum tolerated dose (MTD), pharmacokinetics, pharmacodynamics, and clinical activity of IVO. Enrollment was completed on May 8, 2017. In dose escalation, patients received single‐agent IVO orally (dose range, 200–1200 mg daily) in 28‐day cycles. The MTD was not reached and 500 mg QD was selected as the dose for expansion. The overall response rate (ORR) for MDS was defined as complete remission (CR) + partial remission + marrow CR (mCR) according to International Working Group 2006 criteria for MDS. Exploratory biomarker assessments included baseline co‐occurring mutations (next‐generation sequencing panel for hematologic malignancies) and mIDH1 variant allele frequency (VAF) in bone marrow mononuclear cells (BEAMing Digital PCR; lower limit of detection for mIDH1, 0.02–0.04%).Results:Baseline characteristics of the 12 patients with R/R MDS who received 500 mg IVO once daily were: 9 men/3 women; median age 72.5 years (range 52–78), and 42% were ≥75 years of age; median number of prior therapies 1 (range 1–3). As of Nov 2, 2018, 3 of 12 (25.0%) patients remained on treatment; 9 (75.0%) had discontinued (one for allogeneic stem cell transplantation). Median duration of exposure to IVO was 11.4 months (range 3.3–42.5). Adverse events (AEs) of any grade, irrespective of causality, occurring in ≥20% of the 12 patients were diarrhea, fatigue, back pain, rash (n = 4 each, 33.3%), anemia, urinary tract infection, decreased appetite, hypokalemia, arthralgia, dyspnea, pruritus, and hypotension (n = 3 each, 25.0%). No AEs led to permanent discontinuation of treatment. IDH differentiation syndrome was observed in 1 of 12 (8.3%) patients (grade 2). Electrocardiogram QT prolonged was reported in 2 of 12 patients (17%; grade 1 in 1 patient and grade 2 in 1 patient). Five of 12 patients achieved CR (41.7%; 95% CI 15.2%, 72.3%), 1 achieved PR (8.3%), and 5 achieved mCR (41.7%), resulting in an ORR of 91.7% (95% CI 61.5%, 99.8%). The median duration of CR was not estimable (NE) at the time of datacutoff and the median duration of response was 21.4 months (95% CI 2.3, NE). At 12 months, 60.0% of patients remained in CR. Among 5 patients who were transfusion dependent at baseline, 4 became transfusion independent for ≥56 consecutive days on treatment. Baseline co‐occurring mutations and changes in mIDH1 VAF levels will be presented.Summary/Conclusion:In patients with mIDH1 R/R MDS, IVO monotherapy was well tolerated and induced durable remissions and transfusion independence. These findings support the role of IVO as an effective, oral, targeted treatment for patients with mIDH1 R/R MDS.
Abstract B27: Interaction of mammographic breast density with menopausal status and postmenopausal hormone use in relation to the risk of aggressive breast cancer subtypes
Yaghjyan, Lusine , Jensen, Matthew R. , Pankratz, Shane, Brandt, Kathleen R. , Visscher, Daniel W., Cough, Fergus, Chen, Yunn‐Yi , Beck, Andrew H., Cummings, Steven R. , Vachon, Celine M. , Tamimi, Rulla M. , Bertrand, Kimberly A. , Scott, Christopher G. , Norman, Aaron D. , Shepherd, John , Fan, Bo , Kerlikowske, Karla , Vachon, Celine M.

Cancer Epidemiology, Biomarkers & Prevention | May 9, 2019 | Volume: 26 | Issue: 5_Supplement | Pages: B27-B27

10.1158/1538-7755.carisk16-b27 Get It

Abstract Purpose: The evidence on associations of mammographic breast density with breast cancer risk by combination of tumor aggressiveness features is limited. We examined associations of breast density phenotypes with risk of aggressive breast tumor features by menopausal status, and current postmenopausal hormone therapy. Methods: This study included 2,635 invasive breast cancer cases and 4,059 controls from participants of four nested case-control studies within four established cohorts: the Mayo Mammography Health Study, the Nurses Health Study, Nurses Health Study II, and San Francisco Mammography Registry. Percent breast density, absolute dense and non-dense areas were assessed from digitized film-screen mammograms using a computer-assisted threshold technique and standardized across studies. We used polytomous logistic regression to quantify the associations of breast density measures with risk of breast tumor aggressiveness (defined as presence of 2 or more of the following tumor characteristics: size ≥2cm, grade 2 or 3, or positive nodes), stratified by menopausal status and current hormone therapy (i.e., premenopausal, postmenopausal/estrogen therapy, postmenopausal/combined therapy, and postmenopausal/no hormones). We also evaluated differences in the strength of associations across categories. In a secondary analysis, we examined these associations while excluding cases with mammogram date within 2 years of diagnosis. Results: Positive associations of percent density and dense area and inverse associations of non-dense area with breast cancer risk were stronger in aggressive vs. non-aggressive tumors (OR=2.62, 95%CI 2.08-3.31 vs. OR=1.94, 95%CI 1.62-2.33 for percent density≥51% vs. 11-25%, p-heterogeneity=0.001; OR=1.89, 95%CI 1.54-2.31 vs. OR=1.65, 95%CI 1.41-1.93 for dense area 4th vs. 2nd quartile, p-heterogeneity=0.015; OR=0.56, 95%CI 0.44-0.72 vs. OR=0.71, 95%CI 0.59-0.86 for non-dense area 4th vs 2nd quartile, p-heterogeneity=0.007, respectively). These patterns were similar across all menopausal and hormone therapy groups (P-interactions=0.62, 0.76, and 0.23, for percent density, dense area and non-dense area, respectively). Excluding cases diagnosed within 2 years of mammography resulted in similar findings. Conclusion: Mammographic density phenotypes were more strongly associated with aggressive cancer (having two or more of the following: size ≥2cm, grade 2 or 3, or positive nodes) vs. non-aggressive types of breast cancer across categories of menopause and hormone therapy types. Citation Format: Lusine Yaghjyan, Rulla Tamimi, Kimberly Bertrand, Christopher G. Scott, Matthew R. Jensen, Shane Pankratz, Kathleen Brandt, Daniel Visscher, Aaron Norman, Fergus Cough, John Shepherd, Bo Fan, Yunn-Yi Chen, Lin Ma, Andrew H. Beck, Steven R. Cummings, Karla Kerlikowske, Celine Vachon. Interaction of mammographic breast density with menopausal status and postmenopausal hormone use in relation to the risk of aggressive breast cancer subtypes. [abstract]. In: Proceedings of the AACR Special Conference: Improving Cancer Risk Prediction for Prevention and Early Detection; Nov 16-19, 2016; Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2017;26(5 Suppl):Abstract nr B27.
MENDA: a comprehensive curated resource of metabolic characterization in depression
Pu, Juncai , Yu, Yue , Liu, Yiyun , Tian, Lu , Gui, Siwen , Zhong, Xiaogang , Fan, Chu , Song, Xuemian, Liu, Lanxiang , Yang, Lining , Zheng, Peng , Chen, Jianjun , Cheng, Ke , Zhou, Chanjuan, Wang, Haiyang , Xie, Peng , Xu, Shaohua

Briefings in Bioinformatics | April 18, 2019 | Volume: 21 | Issue: 4 | Pages: 1455-1464

10.1093/bib/bbz055 | PMID 31157825 Get It

Abstract Depression is a seriously disabling psychiatric disorder with a significant burden of disease. Metabolic abnormalities have been widely reported in depressed patients and animal models. However, there are few systematic efforts that integrate meaningful biological insights from these studies. Herein, available metabolic knowledge in the context of depression was integrated to provide a systematic and panoramic view of metabolic characterization. After screening more than 10 000 citations from five electronic literature databases and five metabolomics databases, we manually curated 5675 metabolite entries from 464 studies, including human, rat, mouse and non-human primate, to develop a new metabolite-disease association database, called MENDA (http://menda.cqmu.edu.cn:8080/index.php). The standardized data extraction process was used for data collection, a multi-faceted annotation scheme was developed, and a user-friendly search engine and web interface were integrated for database access. To facilitate data analysis and interpretation based on MENDA, we also proposed a systematic analytical framework, including data integration and biological function analysis. Case studies were provided that identified the consistently altered metabolites using the vote-counting method, and that captured the underlying molecular mechanism using pathway and network analyses. Collectively, we provided a comprehensive curation of metabolic characterization in depression. Our model of a specific psychiatry disorder may be replicated to study other complex diseases.