Vincent Chen | Fgjyju - Academia.edu (original) (raw)

Papers by Vincent Chen

Epilepsy & Behavior, 2010

We compared the scores on self-management and associated psychosocial scales of patients with epi... more We compared the scores on self-management and associated psychosocial scales of patients with epilepsy at two clinics in Houston, TX, USA, to determine if there were systematic differences associated with socioeconomic status (SES). Patients of low SES reported higher scores on overall, information, and safety management (P<0.03) and no differences on medication, seizure, and lifestyle management. The two groups were

Source code for biology and medicine, 2009

In molecular applications, virtual reality (VR) and immersive virtual environments have generally... more In molecular applications, virtual reality (VR) and immersive virtual environments have generally been used and valued for the visual and interactive experience - to enhance intuition and communicate excitement - rather than as part of the actual research process. In contrast, this work develops a software infrastructure for research use and illustrates such use on a specific case. The Syzygy open-source toolkit for VR software was used to write the KinImmerse program, which translates the molecular capabilities of the kinemage graphics format into software for display and manipulation in the DiVE (Duke immersive Virtual Environment) or other VR system. KinImmerse is supported by the flexible display construction and editing features in the KiNG kinemage viewer and it implements new forms of user interaction in the DiVE. In addition to molecular visualizations and navigation, KinImmerse provides a set of research tools for manipulation, identification, co-centering of multiple model...

Preventing chronic disease, 2009

The purpose of this study is to 1) examine the variability in the prevalence of adolescent smokin... more The purpose of this study is to 1) examine the variability in the prevalence of adolescent smoking in 60 geographic areas of Minnesota and 2) assess how variability in area-level smoking prevalence is associated with area-level sociodemographic characteristics. Smoking data were collected from 3,636 adolescents residing in 60 areas of the state of Minnesota. Area-level characteristics were obtained from the 2000 US Census. Coefficient of variation was calculated to assess variability in smoking prevalence across areas, and mean smoking prevalence was compared above and below the median for each area-level characteristic. Substantial variation was found in adolescent smoking prevalence rates. Across the 60 areas, the percentage of adolescents that ever smoked varied from 13% to 53%, and the percentage of adolescents that smoked in the past 30 days ranged from 3% to 19%. Mean lifetime smoking prevalence was higher in areas with a higher percentage of residents with less than a high sc...

Substance Use & Misuse, 2009

To examine young adult smoking patterns, we interviewed 732 smokers (from five U.S. upper Midwest... more To examine young adult smoking patterns, we interviewed 732 smokers (from five U.S. upper Midwestern states) via telephone in 2006. We first defined two groups of intermittent smokers-low (smoked 1-14 days in past 30) and high (smoked 15-29 days in past 30), and then analyzed differences between these two groups and daily smokers. Low intermittent smokers were much less likely than high intermittent smokers to consider themselves smokers, feel addicted, or smoke with friends. Daily smokers were more likely than high intermittent smokers to feel addicted and have trouble quitting. Implications, limitations and ideas for future studies are discussed.

Psychological Assessment, 2010

Proteins: Structure, Function, and Bioinformatics, 2009

Protein Science, 2009

Proper visualization of scientific data is important for understanding spatial relationships. Par... more Proper visualization of scientific data is important for understanding spatial relationships. Particularly in the field of structural biology, where researchers seek to gain an understanding of the structure and function of biological macromolecules, it is important to have access to visualization programs which are fast, flexible, and customizable. We present KiNG, a Java program for visualizing scientific data, with a focus on macromolecular visualization. KiNG uses the kinemage graphics format, which is tuned for macromolecular structures, but is also ideal for many other kinds of spatially embedded information. KiNG is written in cross-platform, opensource Java code, and can be extended by end users through simple or elaborate ''plug-in'' modules. Here, we present three such applications of KiNG to problems in structural biology (protein backbone rebuilding), bioinformatics of high-dimensional data (e.g., protein sidechain chi angles), and classroom education (molecular illustration). KiNG is a mature platform for rapidly creating and capitalizing on scientific visualizations. As a research tool, it is invaluable as a test bed for new methods of visualizing scientific data and information. It is also a powerful presentation tool, whether for structure browsing, teaching, direct 3D display on the web, or as a method for creating pictures and videos for publications. KiNG is freely available for download at

Prevention Science, 2011

The Minnesota Adolescent Community Cohort (MACC) Study is a population-based, longitudinal study ... more The Minnesota Adolescent Community Cohort (MACC) Study is a population-based, longitudinal study that enrolled 3,636 youth from Minnesota and 605 youth from comparison states ages 12 to 16 years in 2000-2001. Participants have been surveyed by telephone semi-annually about their tobacco-related attitudes and behaviors. The goals of the study are to evaluate the effects of the Minnesota Youth Tobacco Prevention Initiative and its shutdown on youth smoking patterns, and to better define the patterns of development of tobacco use in adolescents. A multilevel sample was constructed representing individuals, local jurisdictions and the entire state, and data are collected to characterize each of these levels. This paper presents the details of the multilevel study design. We also provide baseline information about MACC participants including demographics and tobacco-related attitudes and behaviors. This paper describes variability in smoking prevalence and demographic characteristics for local units, and compares MACC participants to the state as a whole.

Nucleic Acids Research, 2007

MolProbity is a general-purpose web server offering quality validation for 3D structures of prote... more MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedralangle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at

Nicotine & Tobacco Research, 2006

Many adolescent smokers rely significantly on retail tobacco sources to initiate or maintain thei... more Many adolescent smokers rely significantly on retail tobacco sources to initiate or maintain their smoking behavior. Though promising, the results from various interventions aimed at curtailing retail tobacco access have been mixed. In the present study, 14 communities were randomly assigned to intervention and control groups in an attempt to determine the long-term effect of local youth access laws and policies on adolescent smoking. The intervention continued for 32 months. Assessments were conducted at baseline (1991) and at years 3, 5, and 7. The intervention was based on a community-organizing approach that mobilized community members to support adoption and enforcement of local ordinances to restrict minors&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39; access to commercial sources of tobacco. The major outcome measure for the study was cross-sectional prevalence of daily tobacco use among all students in grades 8, 9, and 10 in each community, measured by a self-administered student survey. A short-term significant intervention effect was observed and reported previously. That difference between intervention and control communities was maintained through the year 5 assessment but had dissipated by the year 7 assessment, very likely related to adoption of ordinances by control communities. Restricting commercial access to tobacco through local ordinances is effective in reducing adolescent smoking both immediately after the intervention (year 3) and 2 years later (year 5). Longer-term results are still inconclusive, because control communities adopted ordinances similar to those in the intervention communities.

Methods, 2011

X-ray crystallography is a critical tool in the study of biological systems. It is able to provid... more X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favour of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface.

The Journal of Chemical Physics, 2008

Guided by ab initio calculations, Fourier transform microwave rotational spectra in the 6-22 GHz ... more Guided by ab initio calculations, Fourier transform microwave rotational spectra in the 6-22 GHz region are obtained for the complex formed between 1,1,2-trifluoroethylene and acetylene, including the normal isotopomer, three of four singly substituted (13)C species obtained in natural abundance, and using commercially available isotopic varieties of acetylene, species containing HCCD and H(13)C(13)CH. Although the ab initio calculations suggest two possible low energy planar arrangements for the molecules in the complex, only a single, unique structure is obtained from a combined analysis of the rotational constants derived from the spectra and atomic positions determined using Kraitchman [Am. J. Phys. 21, 17 (1953)] substitution coordinates. This structure is similar to that obtained for the CF(2)CHF[Single Bond]HF complex [H. O. Leung and M. D. Marshall, J. Chem. Phys. 126, 114310 (2007)] in which both the primary and secondary interactions occur between the HCCH molecule and a F atom and a H atom bonded to the same carbon of CF(2)CHF. The 2.748(15) A hydrogen bond has acetylene as the donor and 1,1,2-trifluoroethylene as the acceptor and forms a 104.49(15) degrees C[Single Bond]Fcdots, three dots, centeredH angle. The 2.8694(9) A secondary interaction between the pi bond of acetylene and the H atom geminal to the acceptor F atom causes the hydrogen bond to deviate 69.24(67) degrees from linearity. This large deviation from linearity and the similarity of the two intermolecular bond lengths suggest that the two interactions are becoming comparable in importance.

Journal of Applied Crystallography, 2010

phenix.model_vs_data is a high-level command-line tool for the computation of crystallographic mo... more phenix.model_vs_data is a high-level command-line tool for the computation of crystallographic model and data statistics, and the evaluation of the fit of the model to data. Analysis of all Protein Data Bank structures that have experimental data available shows that in most cases the reported statistics, in particular R factors, can be reproduced within a few percentage points. However, there are a number of outliers where the recomputed R values are significantly different from those originally reported. The reasons for these discrepancies are discussed.

Ejc Supplements, 2010

Background: In cancer metabolism, cancer cells have higher aerobic glycolysis than that of normal... more Background: In cancer metabolism, cancer cells have higher aerobic glycolysis than that of normal cells even when oxygen is present. Increased glucose uptake and glycolysis in cancer cells have been shown to correlate with poor prognosis, increased invasiveness and metastatic potential in numerous cancers. Recent evidence reported that dietary restriction of carbohydrate and energy supplies may influence various cancer cells metabolism and their growth delay. However, the effect of those nutrient restrictions and their underlying signaling mechanisms are not well understood.

Objective: Evaluate effectiveness of weight-loss interventions in a managed care setting. Methods... more Objective: Evaluate effectiveness of weight-loss interventions in a managed care setting. Methods: Three-arm randomized clinical trial: usual care, mail, and phone intervention. Participants were 1801 overweight managed care organization (MCO) members. Measures included baseline height, weight at baseline and 24 months, selfreported weight at 18 months. Intervention and participation in other weight-related programs was monitored across 24 months. Results: Weight losses were 2.2, 2.4, and 1.9 kg at 18 months in the mail, phone, and usual care groups, respectively. Mail and phone group weight changes were not significantly different from usual care (Po0.35).Weight losses at 24 months did not differ by condition (0.7 kg mail, 1.0 kg phone, and 0.6 kg usual care, P ¼ 0.55). Despite treatment availability over 24 months, participation diminished after 6 months. Participation was a significant predictor of outcomes in the mail and phone groups at 18 months and the mail group at 24 months. Cost-effectiveness of phone counseling was 132per1kgofweightlosswithmailandusualcareachievingsimilarcost−efficiencyof132 per 1 kg of weight loss with mail and usual care achieving similar cost-efficiency of 132per1kgofweightlosswithmailandusualcareachievingsimilarcost−efficiencyof72 per 1 kg of weight loss. Conclusion: Although mail-and phone-based weight-loss programs are a reasonably efficient way to deliver weight-loss services, additional work is needed to enhance their short-and long-term efficacy.

American Journal of Health Promotion, 2011

To determine the prevalence and predictors of the awareness of cigarette price increases followin... more To determine the prevalence and predictors of the awareness of cigarette price increases following a cigarette tax increase, and assess the association of the tax increase and attempts to quit and reduce smoking among adolescents and young adults. We used a prospective cohort design. Surveys were conducted in Minnesota before and after a $0.75 cigarette tax increase. We surveyed 3167 adolescents and young adults, including a subsample of 781 past-30-day smokers. Outcome measures were awareness of cigarette price increases and, among past-30-day smokers, reported changes in smoking behaviors because of the tax increase. Predictors included demographics, social factors, and prior smoking behaviors. We estimated the prevalence of the outcomes and their associations with the predictors using logistic regression. Among all participants, 42% noticed an increase in cigarette prices after the tax increase, including 76% of past-30-day smokers. Being a heavier smoker, living with smokers, having more smoking close friends, and generally being aware of cigarette price changes prospectively predicted the awareness of the price increase after the tax increase. Among past-30-day smokers, 16.7% reported quit attempts and 24.1% reported reducing smoking because of the tax increase. Because fewer than half of the participants noticed the cigarette tax increase, media campaigns to raise awareness of tax changes may increase their effectiveness.