bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non‐Profit Patient Research Services from Rare Genomics Institute Enable Insight into Rare Diseases through Genome Sequencing and Cloud Collaboration
Authors: Tucker Brady , Aguilar Elizabeth , Gurnon Daniel 
Published: November 2023

The non‐profit Rare Genomics Institute (RG) helps provide rare disease patients with access to cutting‐edge molecular biotechnology and analytical expertise with the potential to uncover new directions for research, treatment, and support. As volunteer analysts for RG, we analyzed the exome sequence data of patients with as‐yet undiagnosed diseases with a suspected underlying genetic cause. Data analysis is performed with Omicia Opal, a web‐based genome interpretation and reporting software platform integrating the machine learning algorithms VAAST and Phevor. We summarize our use of the Omicia Opal platform in three cases that represent the range of outcomes that can result from exome analysis; in one case we identified a likely pathogenic variant in the RDH12, associated with Leber's congenital amourosis; in a second case we identified a possibly pathogenic variant in IFT140, associated with Jeune syndrome; and in a third case we identified variants of uncertain significance in genes associated with Sotos and Weaver syndrome. We also outline the additional work RG analysts do to prepare an informative report for the family and their physician, and to connect the family and clinicians to experts who may be able to move their case forward.While definitive answers are still uncommon in exome analysis, the research of RG analysts can provide new leads in a difficult case. Moreover, undergraduate students can make meaningful contributions to patient‐centered rare disease research provided that expert guidance and oversight are in place.Support or Funding InformationFunding provided by DePauw University
Molecular Visualization in the Classroom: Learning Goals and Competencies
Authors: Dries Daniel R. , Craig Paul A. , Dean Diane M. , Listenberger Laura , Novak Walter R.P. , Franzen Margaret A 
Published: November 2023

Biochemical educators agree that visual literacy is an essential tool for learning and as such should be explicitly taught and assessed. However, few resources exist for educators to examine and improve teaching or assessing visual literacy. We have utilized our collective expertise in teaching biomolecular science courses to expand the framework for 3D literacy initially presented by Craig and Bateman. We identify visual literacy skills to be mastered by novices (first year life science students), amateurs (upper division undergraduates) and experts (graduate students or professionals in the field). Moreover, we have begun work to unpack these skills with the goal of facilitating the development of both formative and summative assessments. We encourage the BMB community to use the document presented here to facilitate the inclusion of visualization skills in curriculum development in line with Vision & Change and the ASBMB recommendations. Furthermore, we seek to identify other scientists and educators with an interest in participating in online resource development of 3D literacy materials.Support or Funding InformationThis material is based upon work supported by the National Science Foundation under award number DUE‐1323414. Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
Overweight and obesity among women in a predominantly rural district of Ghana
Authors: Marquis Grace S , Colecraft Esi K , Bannerman Boat , Thompson‐Colón Theresa 
Published: November 2023

The double burden of malnutrition is evident among women of reproductive age (WRA) in Ghana where micronutrient deficiencies commonly occur concurrent with an increasing prevalence of overweight and obesity (OW/OB). However, overnutrition among Ghanaian women has been rarely characterized. We assessed sociodemographic determinants of OW/OB among women in a predominantly rural district of Ghana. Cross‐sectional data were collected from WRA (n=1095) who lived in the Upper Manya Krobo District of the Eastern Region and who participated in the Nutrition Links Infant Household baseline survey between November 2013 and May 2014. The women were interviewed about their personal and household characteristics and weight and height measurements were taken. Body mass index (BMI) was calculated and a dichotomous variable was used to represent non‐OW/OB (BMI<25 kg/m2) and OW/OB (BMI ≥ 25 kg/m2). The mean age of the women was 27.4 ± 7.6 y. Over one‐quarter of them were either overweight (21%) or obese (6.4%); the prevalence of underweight (7.2%) was similar to that of obesity. OW/OB was significantly associated with being 30 y or older, married, and having more household assets (at least 4 out of 12 items) (p<0.05). However, those women who owned their home were less likely to be OW/OB (p<0.05). Combined, the prevalence of overweight and obesity was almost four‐fold higher than that of underweight among these predominantly rural women. Concurrent efforts to address both over‐ and undernutrition are needed to enhance women's health and well‐being in this population.Support or Funding InformationFunded by the Department of Foreign Affairs, Trade, and Development (DFATD) of the Government of Canada
Scant interactions of biomarkers of oxidative stress and anti‐oxidation defense with those of the inflammatory response among preschool children form the Western Highlands of Guatemala
Authors: Méndez Maria José Soto , Aguilera Concepción María , Mesa Maria Dolores , Rico María Cruz , Campaña‐Martín Laura , Martín‐Laguna Victoria , Solomons Noel W. , Schuemann Klaus , Gil Angel 
Published: November 2023

ObjectiveTo explore the presence and magnitude of paired associations between diagnostic biomarkers of oxidation and inflammation from the same or different anatomical compartments.Methods82 children, 38 girls and 44 boys (median age 56 mo), attending 3 daycare centers from a government‐subsidized system in Quetzaltenango, Guatemala, delivered single samples of urine, whole blood, saliva, and feces for one or more of the selected determinations. We were able to make pairing correlations of Among 23 biomarker variables, paired Spearman rank‐order correlations could be made from 12 from the inflammatory domain (White blood cells, plasmatic and salivary IL‐1β, IL‐6, IL‐8, IL‐10 and TNFα, and fecal calprotectin) and 11 from the oxidation domain (urinary markers of oxidation {15‐Isoprostane‐F2t and 8‐hydroxy‐deoxy‐guanosine}; erythrocyte activity of antioxidant enzymes {catalase, superoxide dismutase, glutathione reductase and glutathione peroxidase}; and plasmatic concentrations of antioxidant nutrients {retinol, tocopherols, β‐carotene and Coenzymes Co‐Q9 and Co‐Q10}). The SPSS version 20 software program was used.ResultsWithin the 132‐cell full matrix, 13 statistically‐significant associations were found (9.8% of possible), seven at a p‐value of <0.01 and 6 from <0.05 to 0.01. Superoxide dismutase and β‐carotene were each associated with 5 and 6 inflammatory biomarkers, respectively. Backward‐elimination multiple‐regression analyses with both as dependent variables showed the same two predictors, plasmatic TNF‐α and saliary IL‐8, with an r2‐value of 0.155 for superoxide dismutase and r2 0.136 for β‐carotene.ConclusionSignificant associations in an inter‐class context between paired, oxidation‐vs‐inflammation biomarker variables represent only a 10th of the possible associations and a fraction of the 33–57% association seen with the same data, previously analyzed on an intra‐class hemi‐matrix basis.Support or Funding InformationFunded by: Fundación Iberoamericana de Nutrición (FINUT), Spain and The Hildegard Grunow Foundation (HGF), Germany
The role of dairy in the comparative effectiveness and cost of fortified blended foods versus ready‐to‐use foods in treatment of children with moderate acute malnutrition
Authors: Suri Devika J , Moorthy Denish , Rosenberg Irwin H. 
Published: November 2023

ObjectiveRecent meta‐analyses found treating young children with MAM using ready‐to‐use foods (RUF) versus fortified blended foods (FBF) resulted in higher recovery rates and weight gain. This analysis aimed to compare studies of RUF and FBF with and without dairy to determine whether the addition of dairy to these food supplements modified the comparative effectiveness and cost of treatment.MethodsA review of literature on the comparative effectiveness of FBF and RUF in treatment of MAM was conducted. Outcomes of recovery from MAM, weight gain and length gain were compared among study cohorts, which included FBF with dairy (FBF+), FBF without dairy (FBF−), RUF with dairy (RUF+) and RUF without dairy (RUF−). Data on recovery from MAM was pooled among the 4 supplement categories. The cost per 500 kcal of each category of food supplement was averaged among studies that reported cost data.ResultsAmong the 7 studies included, 9 RUFs were tested, of which 5 contained dairy, and 9 FBFs were tested, of which 3 contained dairy. Children treated with RUF+ had higher recovery rates compared with FBF− in 5 out of 5 study cohorts, higher weight gain in 4 out of 4, and significantly higher length gain in 1 out of 4. Children treated with RUF+ vs FBF+ had higher recovery rates in 1 out of 2 study cohorts, with no differences in weight or length gain. No differences were found in the 2 studies comparing RUF− and FBF+. Finally, children treated with RUF− had higher recovery rates compared with FBF− in 1 of 2 studies, higher weight gain in 2 out of 2, and no differences in length gain. Recovery from MAM among the 7 studies was 65% (FBF−), 79% (FBF+), 82% (RUF−), and 80% (RUF+). Four of the 7 studies included cost data; on average per 500 kcal costs were $0.15 (FBF−), $0.18 (FBF+), $0.17 (RUF−), and $0.35 (RUF+).ConclusionOur results suggest that addition of dairy to FBF make it comparative in effectiveness to both RUF with and without dairy, but does not appear to be a factor between the RUF categories. RUF with dairy was twice the cost per kcal compared with the other food supplement categories. Cost‐effectiveness analysis will be useful to help determine the most appropriate food supplement for treatment of MAM.Support or Funding InformationThis work was supported in part through a grant from the Food For Peace office of USAID
Contribution of School Meals to Nutrient Intakes of School‐age children enrolled in two feeding programs in Ghana
Authors: Owusu Justina Serwaah , Colecraft Esi , Aryeetey Richmond , Vaccaro Joan A. , Huffman Fatma 
Published: November 2023

School‐age children are vulnerable to malnutrition which can negatively influence their growth and maturity, health and academic attainment. School feeding programs offer an opportunity to reduce hunger and malnutrition among school age children. However, there is limited information on how school meals contribute to dietary intakes of school children in Ghana. We compared the contribution of meals provided by ‘Ghana School Feeding Programme’ (GSFP) and a ‘Non‐governmental School Feeding Programme’ (NSFP) to total energy and nutrient intake of school‐age children. Two non‐consecutive 24‐hour dietary recalls were completed with 180 school age children. Additionally, the weighed food method was used to obtain weights of 7 dished portions of school meals served daily over a one‐week period at both feeding sites. Program differences were assessed using independent t‐test. The school‐age children in the ‘Ghana School Feeding Programme’ received significantly smaller portions of the school meal than those in the ‘Non‐Governmental School Feeding Programme’ (243 ± 50g vs. 416 ± 96g; p=0.007). Whereas the ‘Ghana School Feeding Programme’ meals consumed by school‐age children contributed from 12% up to 18.1% of the total energy and nutrient intakes of the children, the ‘Non‐governmental School Feeding Programme’ meals contributed from 17% up to 30% of the total energy and nutrient intakes of the children. The ‘Non‐governmental School Feeding Programme’ contributed significantly more energy (28 ± 10% vs. 16.2 ± 7%; p=<0.001), protein (24.6 ± 9% vs. 13.3 ± 7%; p=<0.001) and micronutrients (p≤0.042) to the children's total intakes compared to meals provided through the ‘Ghana School Feeding Programme’. The smaller portion sizes provided by the GSFP contributed to the meals supplying less energy and nutrients to children's daily intakes. The quality of meals served by both programs needs to be reviewed to ensure that they supply the recommended 30% of energy and nutrients to school children's daily requirements.Support or Funding InformationThe project was funded in part by Prembaf Ghana, an affiliate of Prem Rawat Foundation.
The effect of Iron Deficient Diets (with or without LC‐PUFA) on the Offspring Brain Lipid and Eicosanoid Metabolism during Pre‐Postnatal Development
Authors: Rioux France Marie , Jougleux Jean‐Luc , Surette Marc E , Fiset Sylvain 
Published: November 2023

ObjectivesWe previously found that an iron deficient diet (ID) devoid in long chain polyunsaturated fatty acids (LC‐PUFA, n‐6:n‐3=59:1) fed to pregnant and lactating guinea pigs resulted in a large spectrum of auditory alterations in the peripheral neurophysiology in the offspring. Unexpectedly, we found that adding physiological amount of LC‐PUFA (n‐6:n‐3=11:1) to this ID diet induced minor impairments. The aim of the present study was to evaluate the impact of the (ID) diets (with or without LC‐PUFA) on Δ6‐desaturase expression, COX II protein and prostaglandin levels in the brain of these pups.MethodsIn experiment 1, female guinea pigs were fed an iron sufficient (IS) or iron deficient (ID) diet devoid in LC‐PUFA during the gestation and lactation periods. In experiment 2, female guinea pigs were fed the IS or ID diet in the presence of physiological quantities of LC‐PUFA. After weaning, from postnatal day 9 (PNd9) onward, the IS and IS+LC‐PUFA diets were given to pups in experiment 1 and 2, respectively. Brains and other tissues were collected on PNd24.Summary of resultsIn both experiments, the brain COX II protein levels were unaffected in the ID and ID+LC‐PUFA siblings. In experiment 2, however, PGE2 brain concentrations were reduced in ID+LC‐PUFA compared to IS+LC‐PUFA pups. Similarly, the offspring born to dams fed the ID+LC‐PUFA diet also exhibited a trend for a reduced brain Δ6‐desaturase expression.ConclusionThese experiments are showing that the addition of LC‐PUFA to a diet know to induce a mild iron deficiency have an impact on specific markers of brain lipid‐eisosanoid metabolism. However, the physiological outcomes of these central nervous system changes are unknown.Support or Funding InformationFunded by the Canadian Institutes of Health Research
Gastrointestinal Tolerance of Formula Supplemented with Oligosaccharides
Authors: Kajzer Janice , Oliver Jeffery , Marriage Barbara 
Published: November 2023

ObjectiveHuman milk oligosaccharides (HMOs) are the third largest solid component in mature human milk. The objective of this study was to evaluate gastrointestinal tolerance of infants fed infant formula supplemented with short‐chain fructooligosaccharides (scFOS) and 2‐fucosyllactose (2′FL).MethodsWe conducted a prospective, randomized, multi‐center, double‐blinded, controlled 3‐arm tolerance study in full term, singleton infants (birth weight ≥ 2490g) enrolled between 0 and 8 days of age. At enrollment, formula‐fed infants were randomized to one of two experimental milk‐based infant formulas with a caloric density of 643 kcal/L. Experimental Formula 1 (EF1) did not contain oligosaccharides (n=42) and Experimental Formula 2 (EF2) contained 2g/L scFOS and 0.2g/L 2′FL (n=46). The 2 formula groups were compared with a human milk‐fed (HM) reference group (n=43). Infants were exclusively fed formula or human milk from enrollment until 35 days of age. Data related to intake, stool patterns, anthropometrics and parental questionnaires were collected. The primary outcome was average mean rank stool consistency (MRSC) from Study Day 1 to Visit 3. MRSC was calculated from stool records (1=watery, 2=loose/mushy, 3=soft, 4=formed, 5=hard).ResultsThirty‐six (86%) subjects in the EF1 group, 41 (89%) in the EF2 group and 42 (98%) in the HM group completed the study. There were no differences among groups for gender, ethnicity, race, gestational age, birth weight or age at enrollment. Reported results are from the protocol evaluable analysis. From Study Day 1 to Visit 3, there were no differences in MRSC among the three feeding groups. MRSC was 2.37 ± 0.10, 2.15 ± 0.10 and 2.06 ± 0.08 for the EF1, EF2 and HM groups respectively. There were also no differences among groups for predominant stool consistency from Study Day 1 to Visit 3. The average number of stools per day for the HM group was significantly greater than EF1 (p<0.0001) and EF2 (p<0.0001) from Study Day 1 to Visit 3. At Visit 3, there were no differences between groups for average volume of study formula intake, number of study formula feedings per day, anthropometric data or percent feedings with spit‐up/vomit.ConclusionAn experimental formula containing 2′FL and scFOS was well tolerated in young infants as evidenced by stool consistency, formula intake, anthropometric data and percent feedings with spit‐up/vomit similar to that of infants fed formula without oligosaccharides or HM.Support or Funding InformationThis study was funded by Abbott Nutrition, Abbott Laboratories, Columbus, OH.
The Effect of Zinc Supplementation during Pregnancy and Youth on Child Growth up to 5 Years: A Systematic Review and Meta‐Analysis
Authors: Pimpin Laura , Liu Enju , Shulkin Masha , Duggan Christopher , Fawzi Wafaie , Mozaffarian Dariush 
Published: November 2023

BACKGROUNDZinc supplementation promotes linear growth in children up to age 5 years. However, there has been no recent review of effects of both maternal and child supplementation trials on multiple anthropometric measure.OBJECTIVETo determine the effect of zinc supplementation during pregnancy, lactation and childhood on height (cm), height‐for‐age z‐score (HAZ) and birth weight (kg) up to age 5 years.METHODSWe searched PubMed, EMBASE, the Cochrane Library, and Web of Science without restriction on publication year, setting, or language for randomized clinical trials examining effects of zinc supplementation lasting at least 3 months in pregnant or lactating women, or children under 5 on our outcomes of interest. Manuscript inclusions and data extractions were performed independently and in duplicate. Study quality was evaluated by the Cochrane Risk of Bias tool. Pooled weighted mean differences (MDs) were calculated by random and fixed effects meta‐analysis, with heterogeneity assessed by the I2 statistic and publication bias by Egger's test.RESULTSWe identified 66 trials including 16 of pregnancy, 0 of lactation, 50 of child supplementation including 24,498 unique participants. Mean (SD) age at supplementation was 24.4 (4.4) years for pregnant women and 9.6 (3.1) months for children. Mean supplementation duration was 6.5 (2.1) and 7.1 (3.1) months, and average dose was 27.1 (8.7) and 8.9 (SD 5.6) mg/day, in maternal and child supplementation, respectively. Control was most often placebo (59% of studies), followed by iron with or without folate (27%) and other micronutrients (14%). In pooled analyses, child zinc supplementation increased child height by 0.69 cm (N=36 trials; MD=0.69, 95%CI=0.14, 1.25, P=0.02) and HAZ by 0.09 units (N=38 trials; MD=0.09, 95%CI=0.07, 0.12, P=0.001). Maternal supplementation did not significantly increase child height (N=3 trials; MD=0.65 cm, 95%CI=0.25, 0.40; P=0.70),HAZ (N=3; MD=−0.151, 95%CI=−0.31, 0.01;P=0.06), or birth weight (N=14 trials; MD=0.07 kg, 95%CI=−0.16,0.29; P=0.554). Heterogeneity in these analyses was generally high (I2: 80 to 100%) and was not explained by differences in population stunting status, zinc dose, control type, duration of supplementation, or rural vs. urban residence (P‐interaction from 0.21 to 0.40). There was a suggestion of a decreasing effect size for studies with a longer follow‐up duration (P=0.09). Quality ratings were moderate to high for most (82%) studies.CONCLUSIONChild but not maternal zinc supplementation increases height and HAZ in children up to 5 years; fewer trials during pregnancy may limit power to detect effects. These novel findings inform the design of evidence‐informed zinc supplementation policies to improve linear growth of children and reduce rates of stunting globally.Support or Funding InformationBill & Melinda Gates Foundation
Effects of Consuming Bifidobacterium longum subspecies infantis on intestinal microbiota in exclusively breastfed term infants
Authors: Smilowitz Jennifer T , Fineberg Annette , Underwood Mark 
Published: November 2023

Universally, for the first six months of life, Bifidobacterium longum subspecies infantis (B. infantis) is the dominant strain of intestinal bacteria in infants delivered vaginally and exclusively breastfed. In developed nations, infants delivered by cesarean section or vaginally have lower levels of intestinal B. infantis than infants born in developing nations. Additionally, the dominance of intestinal B. infantis is found in fewer infants of developed than of developing nations. The objective of the Infant Microbiota and Probiotic Intake (IMPRINT) Study was to determine if the daily consumption of B. infantis for 21 consecutive days by exclusively breastfed infants would increase levels of B. infantis during and one month post‐supplementation. Before Day 6 of life, women and their infants delivered vaginally or by cesarean section, were randomized into a lactation consultation (LC) group or lactation consultation plus B. infantis (LC+Bi) group. Infants in the LC+Bi group were fed daily 1×10^10 colony forming units of B. infantis that was mixed with 5 mL of their mother's breastmilk starting on Day 7 and ending on Day 27 of life. Mothers collected two fecal samples (before Day 6, Day 60), five milk samples (Days 7, 14, 21, 32, 60) and infant fecal samples (before Day 6, Days 10, 14, 21, 25, 29, 32, 40, 50, 60). Mothers filled out in‐depth health questionnaires, weekly health questionnaires and daily logs about their infants’ diet and intestinal symptoms. Fecal samples were analyzed for B. infantis by quantitative polymerase chain reaction. The fecal level of B. infantis was significantly higher in infants in the LC+Bi compared with infants in the LS group. B. infantis was well‐tolerated and did not result in any adverse events. This study is the first to demonstrate increasing intestinal bacteria toward a dominance of B. infantis with an exogenous source of B. infantis in term breastfed infants.Support or Funding InformationEvolve Biosystems Inc.