bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pick A Color, Any Color: An Inquiry‐Based Laboratory Course Based On Fluorescent Protein Mutagenesis, Expression, Purification And Characterization
Authors: Kraut Daniel Adam 
Published: November 2023

A major problem in science education is the disconnect between a typical laboratory class and the experience of doing research. In most laboratory classes, students are given background reading and a protocol to follow, follow the procedure, and then analyze and report their results in a lab report. They then move on to another experiment, typically unrelated to the previous one. Contrast this to the typical research experience in which students work towards a goal, using whatever techniques are needed, often troubleshooting experiments that fail or have outcomes different from those expected. Undergraduate researchers become intellectually and emotionally invested in their projects, and as a result can get more out of a research experience than a lab class. Unfortunately, the resources to give every undergraduate experience in a research lab are unlikely to become available. A potential solution is the growth of project‐based laboratory classes, which convert laboratory classes into more research‐like experiences where students pursue one project throughout the semester.I implemented such a class for second‐semester junior biochemistry majors. Students were given the DNA sequence for a plasmid encoding a fusion protein derived from my research lab. Students first used bioinformatic tools to determine what these domains were, then, after doing some research, designed mutations to change the fluorescent properties of the Green Fluorescent Protein (GFP) portion (to create a blue, cyan or yellow variant). Students designed oligonucleotide primers for their chosen mutations, and then went on to use molecular biology techniques to make the mutations and determine if the mutations had been successfully made. In some cases this required troubleshooting and repetition of experiments (with variations), something that enhanced the “research‐like” aspect of the project. After successfully making their mutant plasmid, students over‐expressed the protein in bacteria, and purified the resulting fusion protein, visually determining if the mutation had the desired effect. More biochemical characterization (SDS‐PAGE, western blotting, absorbance, fluorescence) followed, including experiments to determine how the mutation changed both the fluorescence properties and the folding properties of the GFP domain. Finally, students were able to use their protein in a pull‐down assay to test a literature hypothesis. The semester culminated in a poster presentation designed to integrate the entire research experience, and ensure that students connected the dots between the weeks of the lab, rather than taking each lab as an isolated event. In the initial iteration of this class, students reported higher levels of learning than in the previous semester's more traditional biochemistry lab.
Development of course‐based undergraduate research experiences using a design‐based approach
Authors: Lo Stanley M. , Drane Denise L. , Swarat Su L. , Mordacq John C. 
Published: November 2023

Laboratory experience is central to undergraduate biology education. In recent years, commissions and reports (such as Vision and Change and Engage to Excel) have called for the revision of traditional laboratory courses to provide authentic research experiences for all students, especially in the first two years of college. Many existing examples of course‐based undergraduate research experiences (CUREs) are designed for advanced undergraduates (Butler 2014, Caspers 2003, Murthy 2014, Taylor 2010), and some are limited to a small number of students (Kloser 2011, Kloser 2013). Here, we present an iterative, design‐based approach for developing CUREs for large introductory biology courses (over 300 students) that helps students develop scientific inquiry skills and expert‐like perceptions about biology.This study involves the design, implementation, evaluation, and revision of a sequence of introductory biology laboratory courses, where students work collaboratively on research projects developed from faculty laboratories on campus. We define authentic research as students performing the same tasks as scientists would in the same setting (legitimate), even though students’ level of competence may not be as sophisticated (peripheral). This idea of legitimate peripheral participation emerges from the theoretical framework of situated learning, which posits that learning takes place in the same context in which it is applied (Lave 1991). Students in these courses learn scientific inquiry in research projects that can result in novel data and conclusions. Research projects include studying protein‐folding diseases using transgenic C. elegans (Brignull 2006) and examining the role of macrophage phagocytosis of apoptotic cells in atherosclerosis (Thorp 2011).Quantitative surveys (Denofrio 2007, Semsar 2011) and qualitative focus groups are used to evaluate these courses and to provide continuing feedback for improvement over three implementation cycles. Pre‐ vs. post‐survey data indicate that students gain self‐efficacy in scientific inquiry skills (statistically significant gains in 13 out of 14 items) and develop more expert‐like perceptions of biology (statistically significant gains in 5 out of 7 categories). These gains are more significant and have larger effect sizes in the second and third implementation years, a trend also supported by qualitative data. Together, these data indicate a progression of improvement of the effectiveness of these CUREs over three design cycles. Our design‐based approach and our experience with the design process provide valuable suggestions for other practitioners who plan to develop CUREs at their own institutions.Support or Funding InformationThis project was supported in part by an institutional award for undergraduate education from the Howard Hughes Medical Institute to Northwestern University.
Simulating the Influence of Changes in Macronutrient Composition and Amounts in the American Diet From 1971–2008 on Body Composition Changes and Their Contribution to the Obesity Epidemic
Authors: Davidson Robert T , Hippard Michelle 
Published: November 2023

BackgroundThe obesity epidemic in the US has many suggested causes. We investigated the role that changes in diet macronutrient composition (carbohydrate, protein and fat) and amounts had in contributing to the observed changes in body weight and composition between 1971 and 2008.MethodsUsing a previously validated physiologically‐based mathematical model that simulates the effect of dietary macronutrient composition and amounts on body weight and composition changes in sedentary men and women, we simulated body weight changes from 1971 through 2008 based on dietary macronutrient composition and amounts reported from NHANES and the Centers for Disease Control and Prevention (CDC).ResultsSimulated body weight change patterns for both men and women were similar to those actually observed, though body weight values for men were generally over‐predicted and for women were under‐predicted. Final simulated body weights for men and women were +9.3% and −10.4% actual reported values, respectively.ConclusionsWe conclude that the obesity epidemic has been predominantly driven by the amounts and types of consumed macronutrients in food, and that if the American diet were to return to pre‐epidemic macronutrient levels and composition the obesity epidemic would likely reverse and disappear.
Differences in Plasma Metabolites in Insulin Resistant and Insulin Sensitive Obese Individuals during a Hyperinsulinemic/Euglycemic Clamp
Authors: Casey James L. , Van Pelt Douglas W. , Burant Charles , Horowitz Jeffery , Evans Charles 
Published: November 2023

Although the vast majority of obese adults are insulin resistant (IR), some obese individuals remain relatively insulin sensitive (IS), though the underlying mechanisms for this difference are unclear. The hyperinsulimemic‐euglycemic clamp (HEC) is the gold standard test for insulin sensitivity. However, it is not clear if the differences in insulin‐mediated changes in glucose metabolism between IS and IR obese individuals extend to other key metabolites.In this study, we monitored the dynamics of 49 metabolites in obese IR vs. IS during a HEC. From an original screening of 28 obese adults, twelve non‐diabetic subjects, matched for age, sex, BMI, fat mass and fat‐free mass were divided into the 6 most IS and 6 most IR women based on glucose uptake during a HEC clamp. Mean glucose uptake during the clamp was 7.4±1.2 vs 15.6±2.47 mg/kg FFM/min for IR and IS, respectively (p <0.0001).Serum metabolite levels were measured at 8 time points during the clamp using liquid chromatography‐mass spectrometry (LC‐MS): 2 samples at baseline, immediately prior to insulin infusion, every 20 minutes during the insulin infusion (4 samples), and 2 samples at steady state glucose levels (after ~2h of insulin infusion).Metabolite levels were quantitated by peak area, with stable‐isotope internal standards used to allow absolute quantitation of select metabolites. Statistical differences between IS and IR groups were assessed using t‐tests.Compared with IS, IR individuals had higher baseline levels of valine (p=0.023) and leucine and isoleucine (LI) (combined peak area) (p=0.006). However, the rate of decline in LI in response to insulin was greater in IS compared with IR. At steady‐state glucose infusion (~2 hr of HEC) most metabolites were either unchanged or fell from baseline levels. LI and valine concentrations fell about 50% in response to insulin in both groups, but LI and valine continued to be 40–100% greater in IR compared with IS (p=0.022 and 0.007, respectively). Likewise, threonine, lysine and glutamate levels were greater in IR than IS (all p<0.019) when glucose reached steady‐state during the HEC. No significant differences between IR and IS were found in various fatty acid, TCA cycle intermediates, or lactate levels at baseline or at steady‐state of the HEC.These findings indicate that obese adults, who are seemingly “protected” against a decline in insulin‐mediated glucose uptake, also demonstrate improved response of insulin to lower BCAA and other amino acids that have been associated with and increase risk of development of type 2 diabetes. These results suggest that changes in the plasma level of metabolites associated with risk of type 2 diabetes is driven by insulin resistance and not obesity per se.
In Search of Novel Genes in Branchio‐oto‐renal Spectrum Disorders
Authors: Moody Sally A. 
Published: November 2023

Several members of the Six family of transcription factors play important roles in vertebrate craniofacial development. Six1 is particularly important for the development of the cranial sensory organs including the inner ear. Mutations in either Six1 and one co‐factor gene, Eya1, result in human Branchiootorenal spectrum disorders that have mild craniofacial defects and hearing loss. However, these mutations only account for about half of the patients, indicating that other mutations underlie this spectrum. To discover potential new causative genes, we identified over 30 Xenopus genes with high sequence identity to proteins previously shown to interact with Drosophila Six, and we determined that many of these genes are expressed in the otocyst, the precursor of the inner ear. We now show that 4 of the novel candidate co‐factors biochemically interact with Six1 and thus may modify its transcriptional activity. When the endogenous expression level of each of these candidate co‐factors is reduced, there is a loss of otic placode genes and expansion of neural plate genes. When the endogenous expression level of each of these candidate co‐factors in increased, Six1 expression is reduced. These results suggest that these previously uncharacterized Six‐interacting partners have potential important roles in vertebrate craniofacial development and congenital syndromes.Support or Funding InformationNIH R01 DE022065
Cranial Nerve Dysmorphogenesis in 22Q11 Deletion (DiGeorge) Syndrome
Authors: LaMantia Anthony‐Samuel , Karpinski Beverly A. , Maynard Thomas M. , Moody Sally A. , Mendelowitz David , Wang Xin , Popratiloff Anastas , Zohn Irene , Lee Norman H 
Published: November 2023

Pediatricdysphagia—feeding and swallowing difficulties that begin at birth, last throughout childhood, and continue into maturity—is one of the most common, least understood complications in children with developmental disorders. Weargue that a major cause of pediatric dysphagia is altered hindbrain patterning during pre‐natal development. Such changes can compromise craniofacial structures including oropharyngeal muscles and skeletal elements as well as motor and sensory circuits necessary for normal feeding and swallowing. Animal models of developmental disorders that include pediatric dysphagia in their phenotypicspectrum can provide mechanistic insight into pathogenesis of feeding and swallowing difficulties. A fairly common human genetic developmental disorder, DiGeorge/22q11.2 Deletion Syndrome(22q11DS) includes a substantial incidence of pediatric dysphagia in its phenotypic spectrum. Children with 22q11DS from birth onward gain weight slower than their typically developing counterparts, struggle with nursing, and aspirate liquid and solid food into the nasal sinuses, middle ear and lungs. This results in frequent infections that require constant clinical intervention. Infant mice carrying a parallel deletion to 22q11DSpatients have feeding and swallowing difficulties that approximate those seen in pediatric dysphagia. We have devised several assays to evaluate the behavioral as well as cellular consequences of disrupted feeding and swallowing in the mouse model of 22q11DS. Altered hindbrain patterning, craniofacial malformations, and changes in cranial nerve growth prefigure these difficulties. Thus, in addition to craniofacial and pharyngeal anomalies that arise independently of altered neural development, pediatric dysphagia may result from disrupted hindbrain patterning and its impact on peripheral and central neural circuit development critical for feeding and swallowing. The mechanisms that disrupt hindbrain patterning and circuitry may provide a foundation to develop novel therapeutic approaches for improved clinical management of pediatric dysphagia.Support or Funding InformationNIH R01 DE022065 (SAM)HD 042182, DC011534 (A‐S.L.), HD083157 (A‐S.L. and SAM)
Validity of photographic imaging for assessing standing height of preschoolers
Authors: Beintema Joni Jade Serena , Solomons Noel W. , Orozco Mónica N. , García‐Meza Rosario , Gwaltney Rebecca , Rolker Heike B. , Doak Colleen M. 
Published: November 2023

BackgroundIn an exercise aimed at assessing trunk‐to‐leg ratio from photographic imaging, a derivative study examined its accuracy to estimate standing height.ObjectiveTo compare photographic imaging procedures to measured standing height in preschool children.MethodsThe photographic images of 200 preschool children, 100 each from Sololá and Quetzaltenango were evaluated for estimation of standing height. Original standing height was measured with a wall‐stadiometer. A photograph was taken from a 3‐m distance with the child standing sideways and looking forward in the Frankfort Plane Gaze while standing in front of a color‐coded metric ruler. An ocular estimation of height, at the intersection with the ruler was made from print outs, enlarge don a computer screen and from the zoomed camera screen.ResultsThe mean measured standing height was 108.8 cm (median: 109 cm) compared to 109.0 cm (median: 109cm)(p<0.05) determined by a photo‐image. The Pearson correlation coefficient was r=0.988 and the Lin concordance correlation was r=0.987. According to the Bland‐Altman agreement analysis, height derived from a photo‐image overestimates measured height by 0.20 cm. For 34.5% of the photo‐image data, the estimates were identical, and for an additional 50.0% they were ±1 cm of theme asured value.ConclusionThis study shows a high correlation to measured height from photographic imaging, using the same sagittal photograph applied to body‐segment analysis. Equivalent validity was obtained with direct reading from the camera or computer screen as with measurement from a photographic print.
Nutritional Status of Children Under Five Years and Associated Factors in Kalale District, Benin
Authors: Taren Douglas , Alaofe Halimatou , Burney Jennifer , Naylor Rosamond 
Published: November 2023

BackgroundVariations in inter district nutritional status have puzzled both social policy makers and health workers in developing regions worldwide, including in Benin.ObjectiveThis study sought to determine the nutritional status of children under five years and associated factors in Kalalé District in Benin.MethodsA cross‐sectional descriptive study was conducted using a structured questionnaire. A total of 774 households were sampled and the nutritional status of one child from each household was assessed using anthropometric measurements. Multivariate analysis was performed to determine what independent variables were significantly associated with the nutritional status of children.ResultsUp to 40% of the children were stunted; 11% were wasted; and 24% underweight. The prevalence of underweight was significantly greater in boys than in girls (P =0.023). The individual dietary diversity score showed that the most consumed food group was cereals (71%). Eggs and legumes were the least consumed foods. Low food diversity was recorded for 54% of the children (<4 food groups), 33% had medium scores (4–5 food groups); while 13% had high scores (6–8 food groups). Stunting had a significant association with low child dietary diversity scores [OR=2.33; 95% CI (1.21–4.50)], low mother dietary diversity scores [OR=1.96; 95% CI (1.92–3.77)] and poor access to health services [OR=1.84; 95% CI; (1.75–3.54)]. In addition, 6–11 months old children [OR=1.58; 95% CI (1.08–2.53)], male sex [OR=1.53; 95% CI (1.06–2.21)], and large family size [OR=4.14; 95% CI (1.18–15.11)] were found to be associated factors for underweight. Predictors of wasting in this study were low child dietary diversity scores [OR= 1.17; 95%CI (1.07–2.95)] and poor access to health services [OR=2.05; 95% CI; (1.60–4.85)].ConclusionUnder nutrition is an important public health problem among Kalalé children aged 6–59 months of Benin. In addition, dietary diversity, family size and poor access to health services are major challenges to good nutrition. Therefore, future interventions should focus on improving food access and availability for enhanced diet diversification for the rising population.
How should undernutrition be diagnosed in Nigerian hospitalised infants aged under six months?
Authors: Wright Charlotte M , Ezeofor Ifeyinwa , Garcia Ada 
Published: November 2023

It is often assumed that breast fed infants aged under 6 months are at low risk for undernutrition, but where there is non‐exclusivity or underlying medical problems the risk is high. Because of extremely high energy requirements this rapidly impacts on weight gain, causing wasting and weight faltering (WF).Common screening methods for undernutrition have largely not been standardised or validated for very young infants, in particular for skin folds. The WHO growth chart project published standards for subscapular and triceps skin folds in 2007, but only from age 3 months to 5 years.ObjectivesTo assess the prevalence of undernutrition in hospitalised infants aged 0.5–6 months, defined as either WF or low fat stores and then to assess the utility of different screening methods to identify these infants.MethodsNorms for weight gain were established using retrospective weights of 411 healthy infants age < 6 months attending a large well baby clinic in Eunugu, Nigeria; the lower 5th percentile for weight gain conditional on birth weight was defined as WF. Skin folds measured in 195 UK hospitalised infants 0–1 years with very low rates of undernutrition were used to identify the lower 5th percentile for sum of skin folds (10mm) (SSF). A sample of infants age 2 weeks to < 6 months admitted to the teaching hospital in Eunugu were studied. Measures of weight, length, mid‐upper arm circumference (MUAC) and triceps and subscapular skin folds were taken.ResultsOf the 125 hospitalised infants, 86 (69%) were admitted for infectious causes and only 6 (5%) because of undernutrition. Low SSF were found in 41 (33%). Birth weight was known in 105 infants, from these 25 (24%) had WF and a total of 45 (36%) had WF or low SSF, or both. Low MUAC showed high sensitivity to identify WF and/or low fat stores, but at a cost of more children being mislabelled. Low weight for age also showed high sensitivity, particularly for WF, but with a higher positive predictive value (PPV) and thus fewer children being mislabelled. Low WFH showed both low sensitivity and low PPV.ConclusionsIn hospitalised infants under six months a MUAC <11 cm is a reasonably effective screening threshold for identification of undernutrition, but low weight is more specific, while low WFH would miss over half the undernourished infants.Support or Funding InformationIfeyinwa Ezeofor was supported by a Ford Foundation Scholarship

Sensitivity and positive predictive value of different screening measures to predict undernutrition, as defined by WF and/or low fat or measure or low fat or WF individually.

Screening Measure

To predict WF and/or low fat
Low fat (SSF)
Low CWG (WF)

Prevalence
Sensitivity
PPV
Sensitivity
PPV
Sensitivity
PPV

MUAC <11cm
36% (45)
73%
73%
73%
67%
80%
51%

WFHZ <‐2
25% (30)
49%
67%
46%
57%
65%
51%

WAZ <‐2SD
29% (36)
69%
86%
66%
75%
92%
77%
Developing food‐based recommendations to complement distribution of a meat‐based fortified food product for school‐aged children from rural Quetzaltenango, Guatemala using the Optifood linear programming tool
Authors: Vossenaar Marieke , Escobar Marta Lucía , Bonorden Melissa J. L. , Solomons Noel W 
Published: November 2023

BackgroundCurrent diets of school‐aged children in Guatemala are nutritionally inadequate. Spammy®, a meat‐based fortified food product was developed to complement the local diet.ObjectiveTo develop food‐based recommendations (FBRs) using linear programming for children from a low socio‐economic, rural area in the department of Quetzaltenango according to habitual dietary practices and the local food supply, and to examine the effect of this modeling with the addition of Spammy® given as food aid.Methods24‐h dietary recall data for 100 school‐aged children were used to derive linear programing inputs, including foods consumed, their portion sizes and frequency of intake. Optifood was used to develop FBRs based on existing dietary patterns using locally available and acceptable foods, and with the addition of Spammy®. The cost of the most affordable and nutritionally best diet was also modeled.ResultsA total of 5 food‐based recommendations (promoting dairy, fortified grains, eggs, meat/poultry and fruit consumption) can help achieve nutrient adequacy for 7 of 12 nutrients examined. With the additional of a daily portion of Spammy®, 4 food‐based recommendations (promoting dairy, fortified grains, eggs, and tortillas) can help achieve nutrient adequacy for 10 of 12 nutrients examined and the daily cost of the most affordable and nutritionally best diet is reduced from $2.23 to 1.75 (USD).ConclusionContext‐specific FBRs could ensure adequate levels of most nutrients examined. Used alone, however, the proposed FBRs are unlikely to contribute sufficiently to calcium, vitamins C and D, iron and zinc intakes. With the addition of Spammy®, more nutrient requirements are met, but calcium and iron intakes remain problematic.Support or Funding InformationHormel Foods Corporation, Austin, USA