bluuebunny/crossref_metadata_2025_split huggingface dataset:
IL-33-binding HpARI family homologues with divergent effects in suppressing or enhancing type 2 immune responses
Authors: Colomb Florent , Ogunkanbi Adefunke , Jamwal Abhishek , Dong Beverly , Maizels Rick M. , Finney Constance A. M. , Wasmuth James D. , Higgins Matthew K. , McSorley Henry J. 
Published: January 2024

ABSTRACT

HpARI is an immunomodulatory protein secreted by the intestinal nematode
Heligmosomoides polygyrus bakeri
, which binds and blocks IL-33. Here, we find that the
H. polygyrus bakeri
genome contains three HpARI family members and that these have different effects on IL-33-dependent responses
in vitro
and
in vivo
, with HpARI1+2 suppressing and HpARI3 amplifying these responses. All HpARIs have sub-nanomolar affinity for mouse IL-33; however, HpARI3 does not block IL-33-ST2 interactions. Instead, HpARI3 stabilizes IL-33, increasing the half-life of the cytokine and amplifying responses to it
in vivo
. Together, these data show that
H. polygyrus bakeri
secretes a family of HpARI proteins with both overlapping and distinct functions, comprising a complex immunomodulatory arsenal of host-targeted proteins.
CURE on yeast genes of unknown function increases students' bioinformatics proficiency and research confidence
Authors: Miller Mary , Tobin Tammy , Aiello David P. , Hanson Pamela , Strome Erin , Johnston Stephen D. , Issel-Tarver Laurie , Kushner David B. , Keeney Jill B. 
Published: January 2024

ABSTRACT

Course-based undergraduate research experiences (CUREs) can reduce barriers to research opportunities while increasing student knowledge and confidence. However, the number of widely adopted, easily transferable CUREs is relatively small. Here, we describe a CURE aimed at determining the function of poorly characterized
Saccharomyces cerevisiae
genes. More than 20 years after sequencing of the yeast genome, nearly 10% of open reading frames (ORFs) still have at least one uncharacterized Gene Ontology (GO) term. We refer to these genes as “ORFans” and formed a consortium aimed at assigning functions to them. Specifically, over 70 faculty members attended summer workshops to learn the bioinformatics workflow and basic laboratory techniques described herein. Ultimately, this CURE was adapted for implementation at 34 institutions, resulting in over 1,300 students conducting course-based research on ORFans. Pre-/post-tests confirmed that students gained both (i) an understanding of gene ontology and (ii) knowledge regarding the use of bioinformatics to assign gene function. After using these data to craft their own hypotheses, then testing their predictions by constructing and phenotyping deletion strains, students self-reported significant gains in several areas, including computer modeling and exposure to a project where no one knows the outcome. Interestingly, most net gains self-reported by ORFan Gene Project participants were greater than published findings for CUREs assessed with the same survey instrument. The surprisingly strong impact of this CURE may be due to the incoming lack of experience of ORFan Project participants and/or the independent thought required to develop testable hypotheses from complex data sets.
Promoting student interest in plant biology through an inquiry-based module exploring plant circadian rhythm, gene expression, and defense against insects
Authors: Hsu Jeremy L. , Atamian Hagop S. , Avendano-Woodruff Kate 
Published: January 2024

ABSTRACT

We present a weeklong curricular module for high school biology students that promotes knowledge of phytohormones, the circadian clock, and the Central Dogma. The module, which relies on easily accessible items and requires minimal space, integrates a hands-on experiment that guides students through replicating research examining circadian entrainment in postharvest cabbage from groceries. This work found that plants have cyclical, circadian expression of genes that produce phytohormones, and that such cyclical expression influences herbivory by caterpillars. Such cyclical patterns were found in plants both
in situ
and in postharvest cabbage. This work thus provides an ideal platform to shape student conceptions of circadian rhythms, gene expression, and plant herbivory by having students use light timers to entrain postharvest cabbage to alternating light and dark cycles and then measuring herbivory in these plants. The results should replicate previous work and demonstrate less herbivory when both plant and caterpillar are entrained to the same light and dark cycles since the expression of phytohormones involved in plant defense will be greatest when caterpillars are active. The module then concludes with a discussion of gene regulation and how this influences phytohormones. This module was field tested at four public schools, reaching over 600 students, and we present data demonstrating that the module led to learning gains and likely increases in interest in plant biology and self-efficacy.
Draft genomes of four
Kluyveromyces marxianus
isolates retrieved from the elaboration process of henequen (
Agave fourcroydes
) mezcal
Authors: Lozano-Aguirre Luis , Avitia Morena , Lappe-Oliveras Patricia , Licona-Cassani Cuauhtémoc , Cevallos Miguel A. , Le Borgne Sylvie 
Published: January 2024

ABSTRACT

We report the draft genomes of four
Kluyveromyces marxianus
isolates obtained from the elaboration process of henequen (
Agave fourcroydes
) mezcal, a Mexican alcoholic beverage. The average nucleotide identity analysis revealed that isolates derived from agave plants are distinct from those from other environments, including agave fermentations.
Screening and characterization of thermostable enzyme-producing bacteria from selected hot springs of Ethiopia
Authors: Guta Meseret , Abebe Genet , Bacha Ketema , Cools Piet 
Published: January 2024

ABSTRACT

Hot springs are potential sources of diverse arrays of microbes and their thermostable hydrolytic enzymes. Water and sediment samples were collected from three hot springs of Ethiopia and enriched on nutrient and thermus agar media to isolate pure cultures of potential microbes. A total of 252 bacterial isolates were screened and evaluated for the production of amylase, protease, cellulase, and lipase. About 95.23%, 84.12%, 76.58%, and 65.07% of the isolates displayed promising amylase, proteases, cellulase, and lipase activities, respectively. Based on the diameter of the clear zone formed, 45 isolates were further screened and identified to species level using matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry analysis and 16S rRNA gene sequencing. Five of the 45 isolates showed significantly high (
P
< 0.05) clear zone ratios as compared to others. The identified isolates were categorized under five bacterial species, namely,
Bacillus licheniformis
,
Bacillus cereus
,
Paenibacillus thiaminolyticus
,
Paenibacillus dendritiformis
, and
Brevibacillus borstelensis
. The most dominant species (66.7%) was
B. licheniformis
. It could be concluded that hot springs of Ethiopia are potential sources of thermostable extracellular hydrolytic enzymes for various industrial applications. Further optimization of the growth conditions and evaluation for better productivity of the desired products is recommended before attempting for large-scale production of the hydrolytic enzymes.

IMPORTANCE
Thermostable microbial enzymes play an important role in industries due to their stability under harsh environmental conditions, including extreme temperatures. Despite their huge application in different industries, however, the thermostable enzymes of thermophilic microorganism origin have not yet been fully explored in Ethiopia. Here, we explored thermophilic bacteria and their enzymes from selected hot spring water and sediment samples. Accordingly, thermophilic bacteria were isolated and screened for the production of extracellular hydrolytic enzymes. Promising numbers of isolates were found as producers of the enzymes. The potent enzyme producers were further identified using matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry analysis and 16S rRNA gene sequencing. The findings revealed the presence of potential hydrolytic enzyme-producing thermophilic bacteria in hot springs of Ethiopia and necessitate further comprehensive study involving other extreme environments. Our findings also revealed the potential of Ethiopian hot springs in the production of thermostable enzymes of significant application in different industries, including food industries.
A new method to evaluate the power ratio distributions of astronomical signals: A case study from Upper Cretaceous terrestrial sediments
Authors: Huang He , Zhong Hanting , Ma Chao , Sinnesael Matthias , Gao Yuan , Li Yuyin , Hou Mingcai , Wang Chengshan 
Published: January 2024

AbstractAstronomical cycles reliably identified in the sedimentary record are useful for their paleoclimatic interpretations and construction of astrochronology. However, the depositional response and burial-diagenesis processes play a crucial role in distorting the time scales of geological records and introducing noise to orbital signals. How to evaluate the response of varied depositional environments to astronomical forcing remains a challenge. We developed the random-length average orbital power ratio calculation (RAOPR) method to evaluate average orbital power ratio distributions within a specific time interval and applied this new method to the theoretical eccentricity–tilt–precession (ETP) plus noise series and an astronomically tuned Cretaceous terrestrial stratigraphic record spanning ~24 m.y. (92–65 Ma, except for an ~3.8 m.y. gap from ca. 79.9 Ma to 76.1 Ma). Using the merged ETP plus noise series, we observed different orbital power ratio distributions for different background noise intervals. For the Cretaceous terrestrial Songliao Basin, we retrieved long-term orbital variations and used the RAOPR method to calculate the average orbital power ratios in different depositional environment intervals. Our results suggest that unusually high precession power in the Yaojia Formation resulted, in part, from autogenic processes, and unusually low precession power in the Nenjiang Formation can be attributed to marine incursion events. The eccentricity power of the meandering river facies was much higher than observed in other facies intervals. Conversely, the lowest precession power in the meandering facies may be attributed, in part, to the erosion “clipping” effect, which decreases the high-frequency precession band power and increases low-frequency eccentricity band power.
Neurodevelopment at age 5.5 years according to Ages & Stages Questionnaire at 2 years’ corrected age in children born preterm: the EPIPAGE-2 cohort study
Authors: Charkaluk Marie-Laure , Kana Gildas Delavoix , Benhammou Valérie , Guellec Isabelle , Letouzey Mathilde , Morgan Andrei Scott , Nuytten Alexandra , Torchin Héloïse , Twilhaar Sabrina , Cambonie Gilles , Marret Stéphane , Ancel Pierre Yves , Pierrat Véronique 
Published: January 2024

ObjectiveTo report neurodevelopment at age 5.5 years according to developmental delay screening with the Ages & Stages Questionnaire (ASQ) in late infancy in preterm-born children.DesignPopulation-based cohort study, EPIPAGE-2.SettingFrance, 2011–2017.Participants2504 children born at 24–26, 27–31 and 32–34 weeks, free of cerebral palsy, deafness or blindness at 2 years’ corrected age.Main outcome measuresModerate/severe, mild or no disability at age 5.5 years using gross and fine motor, sensory, cognitive and behavioural evaluations. Results of the ASQ completed between 22 and 26 months’ corrected age described as positive screening or not.ResultsAmong 2504 participants, 38.3% had ASQ positive screening. The probability of having moderate/severe or mild disability was higher for children with ASQ positive versus negative screening: 14.2% vs 7.0%, adjusted OR 2.5 (95% CI 1.8 to 3.4), and 37.6% vs 29.7%, adjusted OR 1.5 (1.2 to 1.9). For children with ASQ positive screening, the probability of having neurodevelopmental disabilities at age 5.5 years was associated with the number of domain scores below threshold, very low gestational age and severe neonatal morbidities. For children with ASQ negative screening, this probability was increased for boys and children born small-for-gestational age. For both groups, maternal level of education was strongly associated with outcomes.ConclusionIn preterm-born children, ASQ screening at 2 years’ corrected age was associated with neurodevelopmental disabilities at age 5.5 years. However, other factors should be considered when interpreting the ASQ data to draw further follow-up.Trial registration number2016-A00333-48.
Unfavorable social determinants of health and risk of mortality in adults with diabetes: findings from the National Health Interview Survey
Authors: Chang Ryan , Philip Jerrin , Javed Umair , Titus Anoop , Gardezi Syed Karam , Kundi Harun , Yousefzai Raman , Hyder Adnan A , Mossialos Elias , Nasir Khurram , Javed Zulqarnain 
Published: January 2024

IntroductionUnderstanding the role of social determinants of health as predictors of mortality in adults with diabetes may help improve health outcomes in this high-risk population. Using population-based, nationally representative data, this study investigated the cumulative effect of unfavorable social determinants on all-cause mortality in adults with diabetes.Research design and methodsWe used data from the 2013–2018 National Health Interview Survey, linked to the National Death Index through 2019, for mortality ascertainment. A total of 47 individual social determinants of health were used to categorize participants in quartiles denoting increasing levels of social disadvantage. Poisson regression was used to report age-adjusted mortality rates across increasing social burden. Multivariable Cox proportional hazards models were used to assess the association between cumulative social disadvantage and all-cause mortality in adults with diabetes, adjusting for traditional risk factors.ResultsThe final sample comprised 182 445 adults, of whom 20 079 had diabetes. In the diabetes population, mortality rate increased from 1052.7 per 100 000 person-years in the first quartile (Q1) to 2073.1 in the fourth quartile (Q4). In multivariable models, individuals in Q4 experienced up to twofold higher mortality risk relative to those in Q1. This effect was observed similarly across gender and racial/ethnic subgroups, although with a relatively stronger association for non-Hispanic white participants compared with non-Hispanic black and Hispanic subpopulations.ConclusionsCumulative social disadvantage in individuals with diabetes is associated with over twofold higher risk of mortality, independent of established risk factors. Our findings call for action to screen for unfavorable social determinants and design novel interventions to mitigate the risk of mortality in this high-risk population.
Rapid ethnographic appraisal of community concepts of and responses to joint pain in Kilimanjaro, Tanzania
Authors: Msoka Elizabeth F , Bunn Christopher , Msoka Perry , Yongolo Nateiya M , Laurie Emma , Wyke Sally , McIntosh Emma , Mmbaga Blandina T 
Published: January 2024

IntroductionMusculoskeletal disorders, experienced as joint pain, are a significant global health problem, but little is known about how joint pain is categorised and understood in Tanzania. Understanding existing conceptualisations of and responses to joint pain is important to ensure both research and interventions are equitable and avoid biomedical imposition.MethodsRapid ethnographic appraisal was conducted in a periurban and rural community in Kilimanjaro, documenting language used to describe joint pain, ideas about causes, understandings of who experiences such pain, the impacts pain has and how people respond to it. We conducted 66 interviews with community leaders, traditional healers, community members and pharmacists.Photographs were taken and included in fieldnotes to supplement the interview data and develop thick descriptions. Data were analysed by constant comparison using QDA Miner software.ResultsAcross the sample, dominant concepts of joint pain were namedugonjwa wa baridi, cold disease;ugonjwa wa uzee, old age disease;rimatizim, disease of the joints; and gauti, gout. Causes mentioned included exposure to the cold, old age, alcohol and red meat consumption, witchcraft, demons and injuries/falls. Age, gender and occupation were seen as important factors for developing joint pain. Perceived impacts of joint pain included loss of mobility, economic and family problems, developing new health conditions, death, reduction in sexual functioning and negative self-perceptions. Responses to joint pain blended biomedical treatments, herbal remedies, consultations with traditional healers and religious rituals.ConclusionsConceptualisations of and responses to joint pain in the two communities were syncretic, mixing folk and biomedical practices. Narratives about who is affected by joint pain mirror emerging epidemiological findings, suggesting a strong ‘lay epidemiology’ in these communities. Anthropological methods can support the decolonisation of global health by decentring the imposition of English language biomedicine and pursuing synthetic, dignified languages of care.
Prevalence of anaemia among married women with recent birth history and high-risk fertility behaviour: secondary data analysis of the National Family Health Survey-India (2019–21)
Authors: Das Milan , Verma Madhur , Barman Papai , Behera Deepak Kumar 
Published: January 2024

ObjectivesTo describe the prevalence of anaemia among currently married women with high-risk fertility behaviour (HRFB) based on age, parity and birth spacing indicators.DesignCross-sectional study.Settings and participantsFifth round of the National Family Health Survey (NFHS) was conducted in India (2019–2021) and included a nationally representative sample of 724, 115 women in the reproductive age group (15–49). Our analysis focused exclusively on married women who had given birth in the preceding 5 years.Primary and secondary outcome measuresThe prevalence of anaemia with HRFB was the primary outcome, and the likelihood of having anaemia due to HRFB was the secondary outcome.Data and methodsSecondary data analysis of the NFHS-5 (2019–2021) datasets was done using a weighted analysis to determine anaemia prevalence in different HRFB categories. Bivariate analysis was done using the χ2test, and multiple binary logistic regression analyses were done to estimate the odds of having anaemia due to HRFB after adjusting for known confounders. A p value <0.05 was reported as statistically significant.ResultsThe final analysis comprised 145,468 women, of whom 59.1% had anaemia. About 53.1% of women depicted ‘No risk’ fertility behaviour, and 34.6% and 12.3% had single and multiple HRFB. Women with ‘no-risk,’ single and multiple HRFB had anaemia prevalence rates of 58.1%, 59.4% and 63.1%, respectively. Women with ‘Single risk’ had an 18% higher likelihood (1.18; 1.13–1.22) of having anaemia after controlling for confounding variables, compared with the HRFB category with ‘No risk.’ Women with ‘Multiple risks’ showed a 6% higher likelihood (adjusted OR 1.06; 95% CI 1.03 to 1.08).ConclusionsAnaemia remains a prevalent issue in India, and HRFB is observed as a significant contributing factor. This vulnerable group can be targeted through multiple interventions and further our efforts to realise our anaemia-related goals.
Effects of polyphenol supplementation on hepatic steatosis, intima-media thickness and non-invasive vascular elastography in obese adolescents: a pilot study protocol
Authors: Moretti Jean-Baptiste , Drouin Amélia , Truong Caroline , Youn Elizabeth , Cloutier Anik , Alvarez Fernando , Paganelli Massimiliano , Grzywacz Kelly , Jantchou Prevost , Dubois Josee , Levy Emile , El Jalbout Ramy 
Published: January 2024

IntroductionNon-alcoholic fatty liver disease (NAFLD) is increasingly prevalent in obese adolescents. Increased systemic inflammation and decreased gut microbial diversity linked to obesity affect the liver and are also associated with cardiovascular diseases in adulthood. However, NAFLD and vascular alterations are reversible.Methods and analysisThis pilot study evaluated the feasibility of a prospective open-label randomised controlled trial evaluating the effects of polyphenols on NAFLD and vascular parameters in obese adolescents. Children aged 12–18 years with hepatic steatosis (n=60) will be recruited. The participants will be randomised with a 1:1 allocation ratio to receive polyphenol supplementation one time per day for 8 weeks along with the clinician-prescribed treatment (group B, n=30) or to continue the prescribed treatment without taking any polyphenols (group A, n=30). The outcome measures will be collected from both the groups at day 1 before starting polyphenol supplementation, at day 60 after 8 weeks of supplementation and at day 120, that is, 60 days after supplementation. The changes in hepatic steatosis and vascular parameters will be measured using liver and vascular imaging. Furthermore, anthropometric measures, blood tests and stool samples for gut microbiome analysis will be collected. After evaluating the study’s feasibility, we hypothesise that, as a secondary outcome, compared with group A, the adolescents in group B will have improved NAFLD, vascular parameters, systemic inflammation and gut microbiome.Ethics and disseminationThis study is approved by Health Canada and the hospital ethics. Participants and their parents/tutors will both provide consent. Trial results will be communicated to the collaborating gastroenterologists who follow the enrolled participants. Abstracts and scientific articles will be submitted to high-impact radiological societies and journals. ClinicalTrials.gov ID:NCT03994029. Health Canada authorisation referral number: 250 811. Protocole version 13, 2 June 2023.Trial registration numberNCT03994029.