Biomedical subjects

Juhee Kim

Publications and source records attributed to Juhee Kim.

8 recordsLinked to original sources

PubMed2026

SimpleMicrobiome: An integrated web-based platform for streamlined microbiome data analysis and visualization.

Microbiome studies require multiple analytical steps after initial sequence processing. These steps commonly include data harmonization, preprocessing, taxonomic profiling, diversity analysis, differential abundance testing, predictive modeling, network inference, and preparation of publication-ready outputs. Although robust packages are available for many of these tasks, routine use often depends on command-line workflows, repeated data reformatting, and method-specific scripting. These requirements can limit accessibility for experimental researchers and complicate consistent analysis across interdisciplinary teams. We developed SimpleMicrobiome, a web-based R Shiny platform that integrates established microbiome analysis methods into a single interactive downstream workflow. The application accepts standard abundance, taxonomy, and metadata tables, supports interactive preprocessing and sample filtering, and provides modules for taxa profile visualization, alpha and beta diversity analysis, ANCOM-BC2 and MaAsLin2 differential abundance testing, Random Forest modeling with SHAP-based interpretation, microbial association network inference using SparCC and SPIEC-EASI through NetCoMi, correlation heatmaps, and dbRDA/CAP-style association biplots. The platform is implemented as a modular Shiny application so that preprocessing choices are propagated across downstream analyses, results can be exported as figures and tables, and the same application can be run through the public server, source-code installation, or a Docker image. SimpleMicrobiome consolidates major downstream microbiome analysis tasks in an accessible browser-based environment while retaining links to established analytical frameworks. The platform may reduce technical barriers for non-programming users, improve consistency across exploratory and reporting-oriented analyses, and support collaborative microbiome research. The public application is available at https://simplemicrobiome.mglab.org, the source code is available at https://github.com/yjcho2252/SimpleMicrobiome, and a Docker image for local deployment is available at https://hub.docker.com/r/mglab2252/simplemicrobiome.

differential abundance↗

PubMed2006

When children eat what they watch: impact of television viewing on dietary intake in youth.

OBJECTIVES: To test whether increased television viewing is associated with increased total energy intake and with increased consumption of foods commonly advertised on television, and to test whether increased consumption of these foods mediates the relationship between television viewing and total energy intake. DESIGN: Prospective observational study with baseline (fall 1995) and follow-up (spring 1997) measures of youth diet, physical activity, and television viewing. We used food advertising data to identify 6 food groups for study (sweet baked snacks, candy, fried potatoes, main courses commonly served as fast food, salty snacks, and sugar-sweetened beverages). SETTING AND PARTICIPANTS: Five public schools in 4 communities near Boston. The sample included 548 students (mean age at baseline, 11.70 years; 48.4% female; and 63.5% white). MAIN OUTCOME MEASURES: Change in total energy intake and intake of foods commonly advertised on television from baseline to follow-up. RESULTS: After adjusting for baseline covariates, each hour increase in television viewing was associated with an additional 167 kcal/d (95% confidence interval, 136-198 kcal/d; P<.001) and with increases in the consumption of foods commonly advertised on television. Including changes in intakes of these foods in regression models provided evidence of their mediating role, diminishing or rendering nonsignificant the associations between change in television viewing and change in total energy intake. CONCLUSIONS: Increases in television viewing are associated with increased calorie intake among youth. This association is mediated by increasing consumption of calorie-dense low-nutrient foods frequently advertised on television.

Advertising↗

PubMed2006

Trends in overweight from 1980 through 2001 among preschool-aged children enrolled in a health maintenance organization.

OBJECTIVE: To examine overweight trends over a 22-year period among preschool-aged children from primarily middle-income families enrolled in a health maintenance organization. RESEARCH METHODS AND PROCEDURES: From well-child care visits to a Massachusetts health maintenance organization, we randomly selected one visit per child per calendar year, yielding a study sample of 120,680 children seen at 366,109 visits from 1980 through 2001. Using multivariate logistic regression models accounting for repeated observations of individual children across years, we estimated trends in prevalence of overweight (weight-for-length/height > or = 95th percentile) and at-risk-for-overweight (85th to 95th percentile). RESULTS: Over the 22-year study period, the observed prevalence of overweight increased from 6.3% to 10.0% and at-risk-for-overweight increased from 11.1% to 14.4%. These increases were evident among all groups of children including infants < 6 months of age. Overall, the adjusted odds ratios were 1.21 per decade (95% confidence interval, 1.17 to 1.25) for overweight and 1.06 per decade (95% confidence interval, 1.03 to 1.08) for at-risk-for-overweight. DISCUSSION: Rates of overweight are increasing in very young children, even infants, from primarily middle-class families.

Child, Preschool↗

PubMed2006

The role of parents in preventing childhood obesity.

As researchers continue to analyze the role of parenting both in the development of childhood overweight and in obesity prevention, studies of child nutrition and growth are detailing the ways in which parents affect their children's development of food- and activity-related behaviors. Ana Lindsay, Katarina Sussner, Juhee Kim, and Steven Gortmaker argue that interventions aimed at preventing childhood overweight and obesity should involve parents as important forces for change in their children's behaviors. The authors begin by reviewing evidence on how parents can help their children develop and maintain healthful eating and physical activity habits, thereby ultimately helping prevent childhood overweight and obesity. They show how important it is for parents to understand how their roles in preventing obesity change as their children move through critical developmental periods, from before birth and through adolescence. They point out that researchers, policymakers, and practitioners should also make use of such information to develop more effective interventions and educational programs that address childhood obesity right where it starts-at home. The authors review research evaluating school-based obesity-prevention interventions that include components targeted at parents. Although much research has been done on how parents shape their children's eating and physical activity habits, surprisingly few high-quality data exist on the effectiveness of such programs. The authors call for more programs and cost-effectiveness studies aimed at improving parents' ability to shape healthful eating and physical activity behaviors in their children. The authors conclude that preventing and controlling childhood obesity will require multifaceted and community-wide programs and policies, with parents having a critical role to play. Successful intervention efforts, they argue, must involve and work directly with parents from the earliest stages of child development to support healthful practices both in and outside of the home.

Adolescent↗

PubMed2005

Incidence and remission rates of overweight among children aged 5 to 13 years in a district-wide school surveillance system.

OBJECTIVES: To monitor annual changes in weight status, we determined incidence and remission rates of overweight among school-aged children with longitudinal school-based surveillance. METHODS: We estimated 1-year changes in weight status among students enrolled in public schools in Cambridge, Mass. Physical education teachers measured height and weight annually. Adjusted odds ratios (ORs) were estimated via multivariate logistic regression, accounting for repeated observations of individual children across years. RESULTS: The 1-year incidence of overweight was 4%, and the remission rate was 15%. Among overweight children, 85% remained overweight at a 1-year follow-up, while 18% of children at risk for overweight became overweight. Overweight incidence rates were higher among children aged 7 and 8 years than among those aged 11 to 13 years (boys: OR=1.68; 95% confidence interval [CI]=1.14, 2.47; girls: OR=1.86; 95% CI=1.25, 2.77). CONCLUSIONS: Both incidence and remission rates were higher among younger children. Children who were at risk for overweight were more likely to change their weight status than those who were already overweight. Our results support targeting overweight prevention efforts toward younger children and children at risk for overweight.

Adolescent↗

PubMed2005

Relationship of physical fitness to prevalence and incidence of overweight among schoolchildren.

OBJECTIVES: We examined the relationship between comprehensive fitness tests and overweight using a school surveillance system in a racially diverse city in the United States. RESEARCH METHODS AND PROCEDURES: Trained physical education teachers measured weight, height, and fitness annually from 2001 to 2003. We compiled data for a cross-sectional analysis (11,845 measurements on 6297 students, 5 to 14 years of age) and a 1-year prospective analysis (4215 measurements on 2927 students not overweight at baseline, 5 to 13 years of age). Overweight was defined as a BMI > or =95th percentile (Centers for Disease Control and Prevention 2000 growth charts), and underfit was defined as failing at least one of five fitness tests: endurance run, abdominal strength, flexibility, upper body strength, and agility (Amateur Athletic Union and Fitnessgram). Associations between fitness and overweight were examined using multivariate logistic regression models, adjusting for sociodemographic status and repeated measurements over time. RESULTS: The mean number of fitness tests passed was lower among students with a BMI above the 80th percentile. Overweight incidence over 1 year was 7% and 2% for underfit and fit girls, respectively (odds ratio, 3.3; 95% confidence interval, 2.0 to 5.6). Not passing either the endurance run or upper body strength test was associated with overweight incidence in both boys and girls. After adjusting for baseline BMI, the endurance run remained a significant predictor of incident overweight among girls (odds ratio, 2.0; 95% confidence interval, 1.1 to 3.5). DISCUSSION: Findings support a cross-sectional inverse relationship between physical fitness and overweight among school-aged children. The direction of causation between fitness and overweight is not clearly established and merits further study.

Adolescent↗

PubMed2003

Stable expression of the avian retroviral oncoprotein v-Rel in avian, mouse, and dog cell lines.

Overexpression of the retroviral oncoprotein v-Rel can rapidly transform and immortalize a variety of avian cells in culture. However, mammalian models for v-Rel-mediated oncogenesis have been compromised by the fact that high-level expression of v-Rel has been reported to be toxic in many mammalian cell types, including mouse 3T3 cells, Rat-1 cells, and mouse bone marrow cells. In this article, we demonstrate that 3T3 cells can support expression of v-Rel for at least 24 days when infected with a mouse stem cell virus (MSCV) retroviral vector containing v-rel. In retrovirus-infected 3T3 cells, v-Rel is located in the nucleus and can bind to DNA, but does not transform the cells. On the other hand, 3T3 and Rat-2 cells do not express v-Rel after stable transfection with a pcDNA-based v-Rel expression vector. We also show that infection of the IL3-dependent mouse B cell line BaF3 with the MSCV-v-rel vector results in expression of v-Rel, but does not convert these cells to growth factor independence. In contrast to 3T3 cells, the dog osteosarcoma D17 cell line can support a high level of v-Rel expression, after either transfection or infection with a retroviral vector. That is, v-Rel can be stably expressed as a nuclear, DNA-binding protein in D17 cells to approximately the same level as in chicken embryo fibroblasts. These results suggest that the restriction to v-Rel expression in rodent fibroblasts is generally absent in D17 cells and that the type of v-rel expression vector determines whether 3T3 cells can support stable expression of v-Rel. The findings reported here are an essential first step in the development of mammalian systems to study Rel-mediated oncogenesis.

3T3 Cells↗

PubMed2003

Promoting healthy weight among elementary school children via a health report card approach.

BACKGROUND: As overweight continues to rise among children, schools seek effective and sensitive ways to engage parents in promoting healthy weight. OBJECTIVE: To evaluate a school-based health report card on the family awareness of and concern about the child weight status, plans for weight control, and preventive behaviors. DESIGN: Quasi-experimental field trial with a personalized weight and fitness health report card intervention (PI), a general-information intervention (GI), and a control group (CG). Outcomes were assessed using a postintervention telephone survey, including process and outcome measures. PARTICIPANTS: The intervention included 1396 ethnically diverse students at 4 elementary schools in an urban area. Telephone surveys were completed by 399 families from an evaluation sample of 793. Intervention Families were randomly assigned to the PI, GI, or CG and mailed intervention materials. The CG was mailed GI materials after the survey. MAIN OUTCOME MEASURES: Parent awareness of child weight status, concerns, weight-control plans, and preventive behaviors. Group effects were significantly different by the child's weight status, so results were stratified. RESULTS: Among overweight students, intervention parents were more likely to know their child's weight status (PI, 44%; GI, 41%; CG, 23%) (P =.02). The PI parents planned medical help (PI, 25%; GI, 7%; CG, 9%) (P =.004), dieting activities (PI, 19%; GI and CG, <5 cases) (P =.02) and physical activities (PI, 42%; GI, 27%; CG, 13%) (P<.001) for their overweight children. No group effect on concern or preventive behaviors was detected. Most parents of overweight children who read materials requested annual weight and health information on their child (PI, 91%; GI, 67%). CONCLUSIONS: Among overweight children, the PI was associated with increased parental awareness of their child's weight status. Although parents wanted PI for their children, more research is needed to test this approach on children's self-esteem and plans for weight control.

Adolescent↗