Nutrition Commons^™

Commentary: Impact Of Resistance Training Intensity On Body Composition And Nutritional Intake Among College Women With Overweight And Obesity: A Cluster Randomized Controlled Trial, Joshua L Keller, Sarah E Deemer, Gian Luca Di Tanna, Sherri L Pals, Kevin R Fontaine, David B Allison

Children’s Nutrition Research Center Staff Publications

No abstract provided.

Impacts Of Ramadan Fasting During Pregnancy On Pregnancy And Birth Outcomes: An Umbrella Review, Abdullah Al-Taiar, Md Estiar Rahman, May Salama, Ali H. Ziyab, Wilfried Karmaus

Epidemiology, Biostatistics, & Environmental Health Faculty Publications

Background

Despite a large number of primary research studies, and systematic and narrative reviews, there is no consensus on the impact of fasting during Ramadan while pregnant on pregnancy and birth outcomes. Currently, there is no evidence-based guideline for Muslim women regarding Ramadan fasting during pregnancy and clinicians cannot provide firm recommendations.

Objectives

To review the current evidence regarding the impact of Ramadan fasting during pregnancy on pregnancy and birth outcomes.

Search Strategy

We conducted an umbrella review of all systematic and narrative reviews examining the impacts of fasting during Ramadan while pregnant on pregnancy and birth outcomes by searching …

Food For Thought: A Qualitative Assessment Of Medical Trainee And Faculty Perceptions Of Nutrition Education, Olivia Kunitsky, Mahdi Taye, Karla Feeley, Hugh Johnson, Abigail Glynn, Avery Stivale, Matthew Hamers, Alexis Notarianni, Sireesha Mamillapalli, Gabi Waite, Sonia Lobo

Department of Neurology Faculty Papers

BACKGROUND: The American Society of Clinical Nutrition recommends 37 to 44 h of undergraduate medical nutrition education. The Total Health Curriculum at Geisinger Commonwealth School of Medicine (GCSOM) contains 14 h of objective-based nutritional instruction. This study aimed to examine the perceptions of key stakeholders regarding the role of nutrition in medicine and to identify barriers, opportunities for improvement, and roles/responsibilities for innovative implementation of nutrition education.

METHODS: This exploratory, qualitative study employed a phenomenological approach and inductive coding process. Purposive sampling recruited medical students, undergraduate medical education (UME) faculty, physicians, and other healthcare professionals at GCSOM and affiliated clinical …

Improving Food Security To Decrease Hypertension At An Urban Community Clinic, Christine S. Villalta

Master's Projects and Capstones

Diet and lifestyle changes have been proven to reduce blood pressure in patients with hypertension, and a key dietary approach aligned with this recommendation is the DASH diet, which includes consuming fruits and vegetables. Food insecurity, defined as lacking enough safe, nutritious food to maintain an active and healthy life, is a growing crisis in the United States, affecting 13.5% of U.S. households in 2023. This is especially significant for those whose chronic disease management depends on the accessibility of healthy food. An urban community clinic implemented a Food Security Program to decrease food insecurity and reduce hypertension among their …

Ai-Enabled Wearable Cameras For Assisting Dietary Assessment In African Populations, Frank P-W Lo, Jianing Qiu, Modou L Jobarteh, Yingnan Sun, Zeyu Wang, Shuo Jiang, Tom Baranowski, Alex K Anderson, Megan A Mccrory, Edward Sazonov, Wenyan Jia, Mingui Sun, Matilda Steiner-Asiedu, Gary Frost, Benny Lo

Children’s Nutrition Research Center Staff Publications

We have developed a population-level method for dietary assessment using low-cost wearable cameras. Our approach, EgoDiet, employs an egocentric vision-based pipeline to learn portion sizes, addressing the shortcomings of traditional self-reported dietary methods. To evaluate the functionality of this method, field studies were conducted in London (Study A) and Ghana (Study B) among populations of Ghanaian and Kenyan origin. In Study A, EgoDiet's estimations were contrasted with dietitians' assessments, revealing a performance with a Mean Absolute Percentage Error (MAPE) of 31.9% for portion size estimation, compared to 40.1% for estimates made by dietitians. We further evaluated our approach in Study …

Teaching Matters In Formula Preparation-A Measure Of Equity And Nutritional Safety, Matthew D. Di Guglielmo

Department of Pediatrics Faculty Papers

No abstract provided.

Are Prediction Models Moving Closer To Clinical Application In The Diagnosis Of Type Of Diabetes In Youth?, Fida Bacha

Children’s Nutrition Research Center Staff Publications

No abstract provided.

Relative Uptake Of Tomato Carotenoids By In Vitro Intestinal And Prostate Cancer Cells, Nancy E Moran, Brianna Alexander, Shivi Garg, Nathan Marchant, Noor A Hason

Children’s Nutrition Research Center Staff Publications

Background: Consumption of tomatoes and tomato carotenoids is associated with a reduced risk of prostate cancer. Prostate tissue accumulates tomato carotenoids, including lycopene, β-carotene, and phytoene. Phytoene accumulation is relatively greater in the prostate than that of lycopene, but the metabolic determinants of tissue carotenoid profiles are poorly understood.

Objectives: The purpose of this study was to determine if differences in stability, cellular uptake, and clearance of phytoene compared with lycopene or β-carotene by prostate and intestinal cells may explain differences in observed tissue carotenoid profiles.

Methods: Gene and protein expression for carotenoid metabolism in prostate cell lines were analyzed …

Random C-Peptide And Islet Antibodies At Onset Predict Β Cell Function Trajectory And Insulin Dependence In Pediatric Diabetes, Mustafa Tosur, Saima Deen, Xiaofan Huang, Serife Uysal, Marcela Astudillo, Richard A Oram, Maria J Redondo, Farook Jahoor, Ashok Balasubramanyam

Children’s Nutrition Research Center Staff Publications

Objective: Identification of prognostic biomarkers in pediatric diabetes is important for precision medicine. We assessed whether C-peptide and islet autoantibodies are useful to predict the natural history of children with new-onset diabetes.

Methods: We prospectively studied 72 children with new-onset diabetes (median follow-up: 8 months) by applying the Aβ classification system ("A+": islet autoantibody positive, "β+": random serum C-peptide ≥1.3 ng/mL at diagnosis). Beta-cell function was assessed longitudinally with 2 hours postprandial/stimulated urinary C-peptide-to-creatinine ratio (UCPCR) 3-12 weeks (V1) and 6 to 12 months after diagnosis (V2). We obtained a type 1 diabetes genetic risk score for each participant, and …

Validation Studies Of The Flash-Tv System To Passively Measure Children’S Tv Viewing, Anil Kumar Vadathya, Tatyana Garza, Uzair Alam, Alex Ho, Salma M A Musaad, Alicia Beltran, Jennette P Moreno, Tom Baranowski, Nimah Haidar, Sheryl O Hughes, Jason A Mendoza, Ashok Veeraraghavan, Joseph Young, Akane Sano, Teresia M O'Connor

Children’s Nutrition Research Center Staff Publications

TV viewing is associated with health risks, but existing measures of TV viewing are imprecise due to relying on self-report. We developed the Family Level Assessment of Screen use in the Home (FLASH)-TV, a machine learning pipeline with state-of-the-art computer vision methods to measure children's TV viewing. In three studies, lab pilot (n = 10), lab validation (n = 30), and home validation (n = 20), we tested the validity of FLASH-TV 3.0 in task-based protocols which included video observations of children for 60 min. To establish a gold-standard to compare FLASH-TV output, the videos were labeled by trained staff …

Nourishing Skin Health: The Impact Of A Balanced Diet On Chronic Inflammatory Skin Conditions, Archana Banda

HCA-NSU MD Research Day

Objective: This study was conducted to determine the influence a balanced diet has on the outcome of specific dermatologic conditions notably psoriasis, atopic dermatitis, and rosacea. Background: Nutritional status is pivotal in shaping holistic wellness, which extends to skin health. Adequate nutrition can prevent the worsening of inflammatory conditions. Methods: A literature review was conducted to analyze how specific dietary habits for selected chronic inflammatory cutaneous conditions influence the presentation and overall clinical outcome. Results: The analysis indicates a higher incidence of flare-ups with diets heavily consisting of carbohydrates, red meat, alcohol, and fats. Specific diets, such as the Western …

Fetal Sex Effects On Maternal Health Can Now Be Tested Via Randomization: A First-In-Class Illustration In Cows On Glucoregulatory Outcomes, Aridany Suarez-Trujillo, Colby J Vorland, Griffin T Nicholls, Daniella E Chusyd, Chelsie Parker, Lilian Golzarri-Arroyo, Sophia Swann, Bethany J Funnell, Kara R Stewart, David B Allison

Children’s Nutrition Research Center Staff Publications

Background: The maternal-offspring relationship, such as whether fetal sex influences maternal health, is essential to explore to advance prenatal and maternal health. While associations exist between fetal sex and maternal health outcomes, it is unclear whether these reflect a causal relationship.

Objective: To demonstrate that fetal sex can be randomly assigned to test the causal effect of fetal sex on maternal outcomes.

Methods: Holstein dairy cows were stratified and randomized using sealed opaque envelopes to be artificially inseminated with either X- or Y-sorted bull semen until 40 cows became pregnant. Monthly body weight measurements were recorded, and an intravenous glucose …

Avulsion Of The Flexor Digitorum Profundus Tendon During The Curettage Of A Recurrent Enchondroma: A Case Report, Shunpei Hama, Masataka Yasuda, Makoto Fukuda, Katsuaki Onishi, Takaaki Chikugo

Children’s Nutrition Research Center Staff Publications

Enchondroma rarely occurs in the distal phalanx, and avulsion of the flexor digitorum profundus (FDP) tendon in this area is also rare. We report a case of recurrent enchondroma in the distal phalanx, which required reconstruction for an accidental FDP avulsion during surgery. A 36-year-old right-handed woman visited our hospital with a suspected recurrence of enchondroma and a planned surgery. Radiographs and computed tomography revealed three translucent lesions in the distal phalanx of her left index finger. We performed curettage and calcium phosphate bone cement (CPC) grafting. During the procedure, an avulsion of the FDP tendon was found. We reattached …

Reproduction Has Immediate Effects On Female Mortality, But No Discernible Lasting Physiological Impacts: A Test Of The Disposable Soma Theory, Sharon E Mitchell, Megan Simpson, Lena Coulet, Solenn Gouedard, Catherine Hambly, Juliano Morimoto, David B Allison, John R Speakman

Children’s Nutrition Research Center Staff Publications

The disposable soma theory (DST) posits that organisms age and die because of a direct trade-off in resource allocation between reproduction and somatic maintenance. DST predicts that investments in reproduction accentuate somatic damage which increase senescence and shortens lifespan. Here, we directly tested DST predictions in breeding and nonbreeding female C57BL/6J mice. We measured reproductive outputs, body composition, daily energy expenditure, and oxidative stress at peak lactation and over lifetime. We found that reproduction had an immediate and negative effect on survival due to problems encountered during parturition for some females. However, there was no statistically significant residual effect on …

Supporting African Communities To Increase Resilience And Mental Health Of Kids With Developmental Disabilities And Their Caregivers Using The World Health Organization’S Caregiver Skills Training Programme (Spark Trial): Study Protocol For A Cluster Randomised Clinical Controlled Trial, Melissa Nortey, Vibian Angweny, Beatrice Mkubwa, Rosa Hoekstra, Andrew Healey, Rahel Birhane, Nadine Seward, Temesgen Azmeraw, Fikite Girma

Institute for Human Development, East Africa

Background: Most children with developmental disabilities (DD) live in low- and middle-income countries, but access to services is limited, impacting their ability to thrive. Pilot study findings of the World Health Organization’s Caregiver Skills Training (WHO CST) intervention, which equips caregivers with strategies to facilitate learning and adaptive behaviours in children with DD, are promising but evidence from an appropriately powered trial delivered by non-specialist facilitators is lacking. This study will investigate the effectiveness and the resource impacts and costs and consequences of the WHO CST intervention in four sites in rural and urban Kenya and Ethiopia.

Methods: …

Benefits Of Calorie Restriction In Mice Are Mediated Via Energy Imbalance, Not Absolute Energy Or Protein Intake, Daniel L Smith, Sharon E Mitchell, Maria S Johnson, Victoria K Gibbs, Stephanie Dickinson, Beate Henschel, Rui Li, Kathryn A Kaiser, Daniella E Chusyd, Andrew W Brown, David B Allison, John R Speakman, Tim R Nagy

Children’s Nutrition Research Center Staff Publications

Caloric restriction (CR) results in reduced energy and protein intake, raising questions about protein restriction's contribution to CR longevity benefits. We kept ad libitum (AL)-fed male C57BL/6J mice at 27°C (AL27) and pair-fed (PF) mice at 22°C (22(PF27)). The 22(PF27) group was fed to match AL27 while restricted for calories due to cold-induced metabolism. The 22(PF27) mice had significantly lower body weight, lean mass, fat mass, leptin, IGF-1, and TNF-α levels than AL27 mice (p< 0.001 for all). Manipulations over ~11 weeks resulted in significant differences in body temperature, physical activity, and expression of key genes linked to hunger in the hypothalamus. Survival was significantly greater in 22(PF27) compared to AL27 overall (p< 0.001). CR in the context of equivalent energy and protein intake resulted in hormonal, metabolic, and physiological benefits and extended longevity. Hence, energy imbalance, rather than low energy or protein intake per se, mediates the benefits of CR.

Pulmonary Vascular Manifestations Of Hereditary Haemorrhagic Telangiectasia, Sarah Cullivan, Barry Kevane, Brian Mccullagh, Terry M O'Connor, Robin Condliffe, Sean Gaine

Children’s Nutrition Research Center Staff Publications

Hereditary haemorrhagic telangiectasia (HHT) is an autosomal dominant, multisystem disorder that manifests with a spectrum of disease including cardiopulmonary complications. HHT is characterised by aberrant signalling via the transforming growth factor β (TGFβ) pathway, with loss of vascular integrity, angiogenesis and vascular dysplasia. The disease has an estimated prevalence of 1 in 5000 persons and the penetrance increases with increasing age. HHT commonly presents with epistaxis and telangiectasia, while visceral arteriovenous malformations are not uncommon. Mutations in the ENG, ACVRL1 and MADH4 genes account for 97% of all HHT cases, and it is recommended that genetic tests are used in …

Corrigendum: Sars-Cov-2 Seroprevalence In Pregnant Women In Kilifi, Kenya From March 2020 To March 2022, Angela Koech, Geoffrey Omuse, Joseph Mutunga, Moses Mukhanya, Onesmus Wanje, Grace Mwashigadi, Geoffrey Katana, Rachel Craik, Alex Mugo, Marleen Temmerman

Pathology, East Africa

Background: Seroprevalence studies are an alternative approach to estimating the extent of transmission of SARS-CoV-2 and the evolution of the pandemic in different geographical settings. We aimed to determine the SARS-CoV-2 seroprevalence from March 2020 to March 2022 in a rural and urban setting in Kilifi County, Kenya.

Methods: We obtained representative random samples of stored serum from a pregnancy cohort study for the period March 2020 to March 2022 and tested for antibodies against the spike protein using a qualitative SARS-CoV-2 ELISA kit (Wantai, total antibodies). All positive samples were retested for anti-SARS-CoV-2 anti-nucleocapsid antibodies (Euroimmun, ELISA kits, NCP, …

Dense And Persistent Odor Representations In The Olfactory Bulb Of Awake Mice, Delaram Pirhayati, Cameron L Smith, Ryan Kroeger, Saket Navlakha, Paul Pfaffinger, Jacob Reimer, Benjamin R Arenkiel, Ankit Patel, Elizabeth H Moss

Children’s Nutrition Research Center Staff Publications

Recording and analysis of neural activity are often biased toward detecting sparse subsets of highly active neurons, masking important signals carried in low-magnitude and variable responses. To investigate the contribution of seemingly noisy activity to odor encoding, we used mesoscale calcium imaging from mice of both sexes to record odor responses from the dorsal surface of bilateral olfactory bulbs (OBs). The outer layer of the mouse OB is comprised of dendrites organized into discrete "glomeruli," which are defined by odor receptor-specific sensory neuron input. We extracted activity from a large population of glomeruli and used logistic regression to classify odors …

A Bayesian Semi-Parametric Scalar-On-Function Regression With Measurement Error Using Instrumental Variables, Roger S Zoh, Yuanyuan Luan, Lan Xue, David B Allison, Carmen D Tekwe

Children’s Nutrition Research Center Staff Publications

Wearable devices such as the ActiGraph are now commonly used in research to monitor or track physical activity. This trend corresponds with the growing need to assess the relationships between physical activity and health outcomes, such as obesity, accurately. Device-based physical activity measures are best treated as functions when assessing their associations with scalar-valued outcomes such as body mass index. Scalar-on-function regression (SoFR) is a suitable regression model in this setting. Most estimation approaches in SoFR assume that the measurement error in functional covariates is white noise. Violating this assumption can lead to underestimating model parameters. There are limited approaches …

Small Gtp-Binding Protein Gdp Dissociation Stimulator Influences Cisplatin-Induced Acute Kidney Injury Via Perk-Dependent Er Stress, Yuxue Yang, Ting Xiong, Ti Wang, Xiwei Chen, Ziwei Ma, Bangyun Zuo, Dong Ning, Ruilong Song, Xuesong Liu, Daxin Wang

Children’s Nutrition Research Center Staff Publications

Cisplatin is a common anticancer drug, but its frequent nephrotoxicity limits its clinical use. Small GTP-binding protein GDP dissociation stimulator (smgGDS), a small GTPase chaperone protein, was considerably downregulated during cisplatin-induced acute kidney injury (CDDP-AKI), especially in renal tubular epithelial cells. SmgGDS-knockdown mice was established and found that smgGDS knockdown promoted CDDP-AKI, as demonstrated by an increase in serum creatine, blood urea nitrogen levels and the appearance of tubular patterns. RNA sequencing suggested that protein kinase RNA-like ER kinase (PERK), which bridges mitochondria-associated ER membranes, was involved in smgGDS knockdown following CDDP-AKI, and then identified that smgGDS knockdown increased phosphorylated-PERK …

Not Feeling The Heat? Effects Of Dietary Protein On Satiation And Satiety In Mice Are Not Due To Its Impact On Body Temperature, Jazmin Osorio M, Sharon E Mitchell, Catherine Hambly, David B Allison, John R Speakman

Children’s Nutrition Research Center Staff Publications

Dietary protein modulates food intake (FI) via unclear mechanism(s). One possibility is that higher protein leads to greater post-ingestive heat production (Specific dynamic action: SDA) leading to earlier meal termination (increased satiation), and inhibition of further intake (increased satiety). The influence of dietary protein on feeding behaviour in C57BL/6J mice was tested using an automated FI monitoring system (BioDAQ), simultaneous to body temperature (Tb). Total FI, inter meal intervals (IMI, satiety) and meal size (MS, satiation) were related to changes in Tb after consuming low (5%, LP), moderate (15%, MP) and high (30%, HP) protein diets. Diets were tested over …

Translational Potential Of Mouse Models Of Human Metabolic Disease, I Sadaf Farooqi, Yong Xu

Children’s Nutrition Research Center Staff Publications

Obesity causes significant morbidity and mortality globally. Research in the last three decades has delivered a step-change in our understanding of the fundamental mechanisms that regulate energy homeostasis, building on foundational discoveries in mouse models of metabolic disease. However, not all findings made in rodents have translated to humans, hampering drug discovery in this field. Here, we review how studies in mice and humans have informed our current framework for understanding energy homeostasis, discuss their challenges and limitations, and offer a perspective on how human studies may play an increasingly important role in the discovery of disease mechanisms and identification …

Enriching The Pcos Lifestyle, Callie Coleman

Electronic Theses and Dissertations

Polycystic Ovary Syndrome (PCOS) is an endocrine disorder affecting approximately 4 – 20% of women worldwide. It is associated with insulin resistance, fertility problems, and an increased susceptibility to chronic conditions through multiple inflammatory pathways. Women with PCOS are also at increased risk for disordered eating. The Mediterranean diet is associated with decreased inflammation and risk of chronic conditions, and intuitive eating principles are associated with decreased disordered eating patterns. The purpose of this study was to determine if a six-week nutrition education workshop incorporating information and skills related to both the Mediterranean lifestyle and intuitive eating principles can improve …

Individually Randomized Trial Mislabeled As A Cluster-Randomized Trial Comment On: “Effectiveness Of Wearable Technology To Optimize Youth Soccer Players’ Off-Training Behaviour And Training Responses: A Cluster-Randomized Trial”, Jean Michel R S Leite, Jasmine Jamshidi-Naeini, Colby J Vorland, Lilian Golzarri-Arroyo, David B Allison

Children’s Nutrition Research Center Staff Publications

No abstract provided.

Preschool Executive Control And Adolescent Dietary Outcomes: Highlighting The Role Of Context, Marla Lopez

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Research has identified executive control (EC) as an important predictor of dietary outcomes among youth. Executive control in preschool age has been shown to predict important outcomes across development for youth, indicating that good, foundational EC abilities are associated with successful development in later life. Dietary outcomes across adolescence, an important transitional period for establishing healthy eating behaviors, are understudied. Therefore, the current study sought to link two critical developmental periods, examining how preschool EC is associated with dietary trajectories across adolescence. Further, the study aimed to identify how contextual factors, specifically indices of socio-economic status and the home and …

Social Marketing And The Challenges Of Participant Recruitment, Tom Baranowski, Teresia M O'Connor, John A Jimenez-Garcia, Kavita Radhakrishnan, Elva M Arrendondo, Debbe Thompson

Children’s Nutrition Research Center Staff Publications

Recruitment of research participants often has not obtained a desired sample size, thereby becoming a major problem inhibiting investigators' ability to adequately test the specified hypotheses. Social marketing with its four Ps, originally developed by the business world to sell products and adapted for public health initiatives, is proposed as a dynamic comprehensive conceptual framework to apply marketing principles and practices to enhance participant recruitment. Applying a social marketing approach to research recruitment would require initial investigation to understand the motivations of the target audience in regard to research participation, and continued research throughout the main project to adapt the …

Urban-Rural Disparities In Food Insecurity And Weight Status Among Children In The United States, Jayna M Dave, Tzuan A Chen, Alexandra N Castro, Mamie A White, Elizabeth A Onugha, Sloane Zimmerman, Debbe Thompson

Children’s Nutrition Research Center Staff Publications

Place of residence (urban versus rural) is a contextual determinant of health that has received less attention in the food insecurity literature. The purpose of this study was to assess the urban–rural disparity in the prevalence of food insecurity and weight status among US children. Using data from the National Health and Nutrition Examination Survey (NHANES) 2013–2016 with three age groups of children (2–5, 6–11, and 12–17 years old), the associations of weight status and child and household food security status by urban–rural residence were examined using Rao–Scott Chi-square tests. Statistical significance was set at p < 0.05. Children living in urban areas were significantly more likely to experience household food insecurity (29.15%) compared to their rural counterparts (19.10%), among those aged 6–11 years. The associations between children’s weight status and child and household food security status were significant for children living in urban areas overall and different age groups but not for children living in rural areas. These trends were more pronounced in older age groups. Given the link between food insecurity and higher obesity rates, particularly among urban children, this study highlights the importance of incorporating food security interventions into future obesity prevention programs.

Dose-Dependent Effects Of Dnmt3a In An Inducible Murine Model Of Krasg12d-Driven Leukemia, Jason H Rogers, Allison Rosen, Jaime M Reyes, Shamika Ketkar, Shannon E Conneely, Rohit Gupta, Luibin Yang, Matthew B Miller, Geraldo Medrano, Rogelio Aguilar, Nneka Uchenda, Margaret A Goodell, Rachel E Rau

Children’s Nutrition Research Center Staff Publications

DNMT3A mutations are frequently found in clonal hematopoiesis and a variety of hematologic malignancies including acute myeloid leukemia (AML). An assortment of mouse models have been engineered to explore the tumorigenic potential and malignant lineage bias due to loss of function of DNMT3A in consort with commonly co-mutated genes in myeloid malignancies such as Flt3, Nras, Kras, and c-Kit. We employed several tamoxifen-inducible Cre-ER^T2 murine model systems to study the effects of constitutively active Kras^G12D-driven myeloid leukemia (Kras) development together with heterozygous (3aHet) or homozygous Dnmt3a deletion (3aKO). Due to the rapid generation of …

Outcomes Of The Emdataresource Cryo-Em Ligand Modeling Challenge, Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiří Černý, Vincent B Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael G Prisant, Randy J Read, Jane S Richardson, Alexis L Rohou, Bohdan Schneider, Benjamin D Sellers, Chenghua Shao, Elizabeth Sourial, Chris I Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Tom L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, K D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey F Hryc, Carola Hunte, Maxim Igaev, Agnel P Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai R Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel W Moriarty, Andrew Muenks, Garib N Murshudov, Robert A Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar R Pothula, Christopher N Rowley, Daipayan Sarkar, Luisa U Schäfer, Christopher J Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea C Vaiana, Sundeep C Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn D Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen M Berman, Wah Chiu

Children’s Nutrition Research Center Staff Publications

The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein-nucleic acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: Escherichia coli beta-galactosidase with inhibitor, SARS-CoV-2 virus RNA-dependent RNA polymerase with covalently bound nucleotide analog and SARS-CoV-2 virus ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. The quality of submitted ligand models and surrounding atoms were analyzed by visual inspection and quantification of local map quality, model-to-map …