bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-genome phylogenetic analysis of
Mycobacterium avium
complex from clinical respiratory samples
Authors: Ka Lip Chew , Go Joelle , Binte Abu Bakar Nur Aisyah , Octavia Sophie , Pin Lin Raymond Tzer , Teo Jeanette W. P. 
Published: January 2025

ABSTRACT

The
Mycobacterium avium
complex (MAC) is a common causative agent causing nontuberculous mycobacterial (NTM) pulmonary disease worldwide. Whole-genome sequencing was performed on a total of 203 retrospective MAC isolates from respiratory specimens. Phylogenomic analysis identified eight subspecies and species.
M. avium
subspecies
hominissuis
(MAH) was the overwhelmingly dominant species (148/203, 72.9%). The other seven identified species were
M. intracellulare
subsp.
yongonense
(18/203, 8.9%),
M. intracellulare
subsp.
chimaera
(10/203, 4.9%),
M. colombiense
(11/203, 5.4%),
M. paraintracellulare
(6/203, 3%),
M. marseillense
(5/203, 2.5%),
M. intracellulare
(3/203, 1.5%), and
M. avium
subspecies
paratuberculosis
(2/203, 1%). Significant genetic clustering was observed among MAH isolates. Notably, a large cluster (<12 SNPs) of 76 MAH isolates bearing the same sequence type was observed. The presence of closely related isolates within hospital settings raises concerns about transmission routes with environmental sources potentially playing a significant role. Based on susceptibility breakpoints that are available for clarithromycin, amikacin, linezolid, and moxifloxacin, low rates of clarithromycin (0.5%, 1/203) and amikacin (1.5%, 3/203) phenotypic resistance were observed. While linezolid and moxifloxacin resistance were 25.6% (52/2030) and 46.3% (94/203), respectively. Drug resistance-associated loci were searched for mutations linked to phenotypic drug resistance. Of the entire cohort, only one isolate was found to have a A2059G 23S rRNA (
rrl
) gene mutation responsible for macrolide resistance.

IMPORTANCE

Mycobacterium avium
complex (MAC) infections are increasingly challenging to manage due to their complex species diversity and varied resistance patterns. This study underscores the genetic diversity within MAC, identifying at least eight species and subspecies among 203 clinical isolates, with
M. avium
subsp.
hominissuis
(MAH) being most prevalent at 72.9%. Notably, genetic clustering was observed within MAH and
M. intracellulare
subsp.
chimaera
, suggesting potential transmission routes within healthcare settings. Clarithromycin and amikacin resistance was found to be uncommon, aligning with the rarity of resistance-associated genetic mutations. These findings emphasize the need for enhanced infection control measures and routine susceptibility testing to tailor antibiotic therapies effectively.
Appearance of green tea compounds in plasma following acute green tea consumption is modulated by the gut microbiome in mice
Authors: Sterrett John D. , Quinn Kevin D. , Doenges Katrina A. , Nusbacher Nichole M. , Levens Cassandra L. , Armstrong Mike L. , Reisdorph Richard M. , Smith Harry , Saba Laura M. , Kuhn Kristine A. , Lozupone Catherine A. , Reisdorph Nichole A. 
Published: January 2025

ABSTRACT

Studies have suggested that phytochemicals in green tea have systemic anti-inflammatory and neuroprotective effects. However, the mechanisms behind these effects are poorly understood, possibly due to the differential metabolism of phytochemicals resulting from variations in gut microbiome composition. To unravel this complex relationship, our team utilized a novel combined microbiome analysis and metabolomics approach applied to low complexity microbiome (LCM) and human colonized (HU) gnotobiotic mice treated with an acute dose of powdered matcha green tea. A total of 20 LCM mice received 10 distinct human fecal slurries for an
n
= 2 mice per human gut microbiome; 9 LCM mice remained un-colonized with human slurries throughout the experiment. We performed untargeted metabolomics on green tea and plasma to identify green tea compounds that were found in the plasma of LCM and HU mice that had consumed green tea. 16S ribosomal RNA gene sequencing was performed on feces of all mice at study end to assess microbiome composition. We found multiple green tea compounds in plasma associated with microbiome presence and diversity (including acetylagmatine, lactiflorin, and aspartic acid negatively associated with diversity). Additionally, we detected strong associations between bioactive green tea compounds in plasma and specific gut bacteria, including associations between spiramycin and
Gemmiger
and between wildforlide and
Anaerorhabdus
. Notably, some of the physiologically relevant green tea compounds are likely derived from plant-associated microbes, highlighting the importance of considering foods and food products as meta-organisms. Overall, we describe a novel workflow for discovering relationships between individual food compounds and the composition of the gut microbiome.

IMPORTANCE
Foods contain thousands of unique and biologically important compounds beyond the macro- and micro-nutrients listed on nutrition facts labels. In mammals, many of these compounds are metabolized or co-metabolized by the community of microbes in the colon. These microbes may impact the thousands of biologically important compounds we consume; therefore, understanding microbial metabolism of food compounds will be important for understanding how foods impact health. We used metabolomics to track green tea compounds in plasma of mice with and without complex microbiomes. From this, we can start to recognize certain groups of green tea-derived compounds that are impacted by mammalian microbiomes. This research presents a novel technique for understanding microbial metabolism of food-derived compounds in the gut, which can be applied to other foods.
Evolution of Pressure Waves in Liquid Containing a Porous Partition Saturated with a Bubble Fluid
Authors: Gimaltdinov I. K. , Rodionov A. S. , Valiakhmetova O. Yu. 
Published: January 2025

Abstract
The distinctive features of pressure wave dynamics in the presence of a porous partition (layer) saturated with a bubbly fluid are considered. It is shown that, depending on the parameters of the gas mixture and the porous medium (volume gas content, bubble dispersion, and porosity), reflection of a wave pulse from the porous partition saturated with a bubbly mixture is similar to reflection from the free boundary or from the rigid wall.
Do coping mechanisms moderate the effect of stressful life events on depression and anxiety in young people? A case–control study from Latin America
Authors: Hudson Georgie , Fung Catherine , Sureshkumar Diliniya Stanislaus , Gómez-Restrepo Carlos , Uribe-Restrepo José Miguel , Ariza-Salazar Karen , Diez-Canseco Francisco , Hidalgo-Padilla Liliana , Toyama Mauricio , Brusco Luis Ignacio , Olivar Natividad , Lucchetti Santiago , Priebe Stefan , Kirkbride James B 
Published: January 2025

BackgroundStressful life events (SLEs) are associated with increased risk of depression or anxiety. Coping mechanisms may moderate this relationship but little is known on this topic in young people or in Latin America.AimTo investigate whether coping strategies predict odds of depression and/or anxiety and moderate the relationship between SLEs and depression and/or anxiety in young people in Peru, Lima and Bogotá.MethodUsing case–control data from people aged 15–24, we used logistic regression to examine associations between coping mechanism, SLEs and caseness for depression or anxiety, adjusting for sociodemographic and socioeconomic factors. We included interaction terms to model whether this association varied depending on coping mechanisms (positive cognitive restructuring, problem focused, support seeking, distraction, avoidant).ResultsWe included 1437 cases and 965 controls. Cases reported less use of positive cognitive restructuring (OR 0.66; 95% CI 0.57 to 0.75) and problem-focused coping (OR 0.82; 95% CI 0.73 to 0.93), and more use of avoidance than controls (OR 1.33; 95% CI 1.19 to 1.50) in adjusted models. They had greater odds of reporting lifetime (OR 1.07; 95% CI 1.04 to 1.10) and past-year (OR 1.05; 95% CI 1.01 to 1.10) SLEs than controls. We found weak but consistent evidence of effect modification; the association between lifetime SLEs and case–control status was stronger in those who used less support seeking (p=0.09), problem-focused coping (p=0.08) or positive cognitive restructuring (p=0.09).ConclusionsRelationships between SLEs, coping mechanisms and depression/anxiety appear similar in these Latin American cities to other contexts. Active coping strategies may ameliorate the impact of SLEs on mental health of young people.
Childhood family income and medication use in youth
Authors: Moustgaard Heta , Moore Elina , Malmberg Satu , Tarkiainen Lasse , Martikainen Pekka 
Published: January 2025

BackgroundLow family socioeconomic position is a well-established determinant of poor health in youth. Much less is known about the social patterning of youth medication use, and the current evidence is mixed. Furthermore, previous studies have not assessed important confounders of the associations. We analyse differences in youth medication use by childhood family income and medication type.MethodsAdministrative register data on full Finnish cohorts born in 1979–2003 (n=1 490 666) and survival analysis were used to assess the risk of using common prescription medications between ages 16 and 20 according to mean household income in ages 11–15, accounting for several observed familial characteristics including parental health. We also compared siblings with discordant childhood income exposures to assess whether any differences are explained by unobserved familial confounding.ResultsFor each 10% increase in childhood family income, there was a 0.6%–1.7% increase in the probability of using the most common prescription medications: antibiotics, painkillers, and allergy and asthma medications. In contrast, a 10% increase in childhood income was related to a 2.5% decrease in the probability of psychotropic medication use. In sibling comparisons, childhood income was not associated with any type of medication use.ConclusionApart from psychotropics, the results may indicate medication underuse among youth from low-income families. The sibling comparisons suggest that moderate differences in childhood income are unlikely to cause differences in youth medication use and thus, in contexts of relative income equality, income differences in medication use are likely to reflect other, unobserved, family factors shared by siblings.
Exploring Ambiguity in Social Prescribing: Creating a Typology of Models Based on a Scoping Review of Core Components and Conceptual Elements in Existing Programs
Authors: Bhaskar Le-Tien , Mulvale Gillian , Underdown Vivien , Des Jardins Mike 
Published: January 2025

Introduction: Despite a growing social prescribing (SP) movement, the concept itself remains ambiguous, resulting in considerable variation in practice across different contexts. As discussions of SP emerge at the policy level, this ambiguity may influence program and policy spread. This research explores current literature and practices of SP to understand the different conceptual elements (i.e., goals and motivations) and core components (i.e., structures and behaviors) of SP.Methods: A scoping review of academic literature was conducted. Search terms included “social prescr ∗,” “social medicine,” “link worker,” “social refer ∗,” and “community refer ∗.” From this data, a typology of models based on descriptions of conceptual elements and core components was developed. Following the development of the typology, we applied our findings to existing SP programs, which were found through reference‐checking academic sources and a community consultation conducted by our partner organization.Results: 29 articles informed the scoping review, and 24 program descriptions were compared to the typology. Four models of SP are proposed. The clinical model follows a biomedical approach where the physician refers patients to SP services primarily geared to lifestyle factors. The holistic model addresses social determinants of health, referring to food security, housing, or income programs. The empowerment model considers well‐being through relationship‐building and a deep understanding of the client context. The healthy community’s model focuses on community development, where community members gain the capacity to better support one another.Conclusion: The proposed typology will help implementers design programs that best suit their goals and contexts. At the policy level, this research demonstrates how a “bounded ambiguity” approach may allow SP to demonstrate its fullest potential. For researchers, this work provides a foundation for future exploration of how SP is implemented despite its ambiguity.
Determination of Oxidative Stress Indexes of Follow‐Up Formulas (> 12 Months) and Certain Flavored Milks
Authors: Özenir Çiler , Cemali Özge , Ağagündüz Duygu 
Published: January 2025

Background: Milk is known to contain some natural antioxidants, but limited literature is available on the antioxidant/oxidant content of flavored milks, which are commonly consumed in children > 12 months of age.Purpose: This study was performed to investigate the total antioxidant status (TAS) and total oxidant status (TOS) and oxidative stress indices of children’s follow‐up formulas (> 12 months) and flavored milks.Materials and Methods: Milk samples (plain milk [n = 3], cocoa milk [n = 9], chocolate milk [n = 4], strawberry milk [n = 12], banana milk [n = 13], honey milk [n = 2], and children’s follow‐up formula [> 12 months] [n = 8]) between January and March 2021 were included in the study. TAS and TOS levels were measured using commercially available kits (Relassay, Turkey) and Mindray BS300 Auto Biochemistry AnalyzerTM (China). All analyses were carried out in duplicate. The OSI value (arbitrary unit) was calculated.Results: In this study, TOS values (μmol/L) of milk samples showed a significant difference between all groups (p < 0.05) and the lowest was in plain milk (14.90 ± 3.66 μmol/L). There was a difference in TOS values between plain milk and cocoa milk (p = 0.007) and between plain milk and chocolate milk (p = 0.035). There was a significant difference in TAS values between the groups (p < 0.001), and the highest TAS values were observed in chocolate milk (2.64 ± 0.02 mmol/L) and cocoa milk (2.35 ± 0.45 mmol/L), respectively. The differences in TAS values were found between banana–cocoa milks (p < 0.001), banana–chocolate milks (p = 0.007), and strawberry–cocoa milks (p = 0.033). There was a difference between the OSI values of the groups (p < 0.001), the lowest values were found in cocoa milk (2.57 ± 0.47) and chocolate milk (2.22 ± 0.46), respectively. The difference in OSI values was found between chocolate–banana milk (p = 0.006) and cocoa–banana milk (p = 0.001). A positive correlation (r = 0.945; p < 0.001) was found between TAS and energy content of follow‐up formulas (> 12 months). Positive correlations were found between TAS and fat content (r = 0.679; p = 0.044) and saturated fat content (r = 0722; 0.028) of cocoa milk. There was no significant correlation between OSI and any macronutrient and energy in milk groups (p > 0.05).Conclusion: Cocoa and chocolate milks have the highest antioxidant and oxidant capacity and the lowest oxidative stress index. However, plain milk had the lowest oxidant capacity. Furthermore, the linear relationship between the energy content of the follow‐up formula and oxidant capacity indicates the importance of adequate‐balanced and functional consumption of these milks.
Corneal Biomechanical Characteristics and Correlation Analysis in Children With Different Refractive States
Authors: Bai Xiao Jing , Wang Yan Hua , Liang Tian Gang , Zhao Qi , Cui Meng Fan , Cheng Jie , Nie Wei Xiang 
Published: January 2025

Purpose: To investigate the correlation between corneal biomechanical characteristics and refractive status in adolescents aged 5–13 years.Methods: A cross‐sectional study involved 339 children aged 5–13 with a spherical equivalent (SE) range from −6.00 to +2.00 diopters. Axial length (AL) was measured by IOL Master, corneal biomechanical parameters by Corvis ST, and anterior segment parameters by Pentacam. According to SE of right eye, the subjects were divided into moderate myopia, mild myopia, and emmetropia group. The correlation between AL and SE and corneal biomechanical parameters was analyzed. The corneal biomechanical parameters of the three groups were also compared.Results: The A2V value in the moderate myopia group was significantly lower than that in both the mild group and emmetropia group (p < 0.001). PD in the moderate group was higher than that in the mild group (p < 0.05), while PD in mild myopia was higher than that in emmetropia (p < 0.05). The SSI in the emmetropia group was significantly higher than that in the other two groups (all p < 0.001), and the SSI in the mild group was higher than that in the moderate group (p < 0.01). The A2V value in the 11–13 years old group was lower than that in the 5–7 years old group (p < 0.001) and 8–10 years old group (p < 0.01). PD in the 11–13 years old group was significantly higher than that in the 8–10 years old group (p < 0.001), and PD in the 8–10 years old group was significantly higher than that in the 5–7 years old group (p < 0.01). The SSI in the 5–7 years old group was significantly higher than that in the 8–10 years old group (p < 0.001), and the SSI in the 8–10 years old group was significantly higher than that in the 11–13 years old group (p < 0.05). AL was positively correlated with PD and negatively correlated with SSI and A2V. SE was positively correlated with A2V and SSI and negatively correlated with PD.Conclusions: Corneal stiffness seems to decrease with the increase of SE. The changes of SSI, PD, and A2V were statistically significant and can be predictors of myopia progression in adolescents aged 5–13 years.
Risk of Atherosclerotic Cardiovascular Disease After Chronic Obstructive Pulmonary Disease Hospitalization among Primary and Secondary Prevention Older Adults
Authors: Mosher Christopher L. , Osazuwa‐Peters Oyomoare L. , Nanna Michael G. , MacIntyre Neil R. , Que Loretta G. , Palmer Scott M. , Jones W. Schuyler , O'Brien Emily C. 
Published: January 2025

Background
Meta‐analyses have suggested that the risk of cardiovascular disease events is significantly higher after a chronic obstructive pulmonary disease (COPD) exacerbation, but the populations at highest risk have not been well characterized to date.

Methods and Results

The authors analyzed the risk of atherosclerotic cardiovascular disease (ASCVD) hospitalizations after COPD hospitalization compared with before COPD hospitalization and patient factors associated with ASCVD hospitalizations after COPD hospitalization among 2 high‐risk patient cohorts. The primary outcome was risk of an ASCVD hospitalization composite outcome (myocardial infarction, coronary artery bypass graft, percutaneous coronary intervention, stroke, transient ischemic accident) after COPD hospitalization relative to before COPD hospitalization. Additional analyses evaluated for risk factors associated with the composite ASCVD hospitalization outcome. In the high‐risk primary prevention cohort, the hazard ratio (HR) estimate following adjustment for the composite ASCVD hospitalization outcome after COPD hospitalization versus before COPD hospitalization for 30 days was 0.74 (95% CI, 0.66–0.82;
P
≤0.0001); for 90 days, 0.69 (95% CI, 0.64–0.75;
P
≤0.0001); and for 1 year, 0.78 (95% CI, 0.73–0.82;
P
≤0.0001). In the secondary prevention cohort, the HR for 30‐day hospitalization was 1.15 (95% CI, 1.05–1.26;
P
=0.0036); 90‐day hospitalization, 1.08 (95% CI, 1.01–1.15;
P
=0.0178); and 1‐year hospitalization, 1.07 (95% CI, 1.02–1.11;
P
=0.0026). Among the 19 characteristics evaluated, hyperlipidemia and history of acute ASCVD event were associated with the highest risk of ASCVD events 1 year after COPD hospitalization in the high‐risk primary and secondary prevention cohorts.

Conclusions
The risk of ASCVD hospitalization was higher in patients with established ASCVD and lower among high‐risk patients without established ASCVD after‐COPD hospitalization relative to before hospitalization. We identified multiple risk factors for ASCVD hospitalization after COPD hospitalization.
Health Care Resource Use and Costs of Rivaroxaban Versus Warfarin Among Nonvalvular Atrial Fibrillation Polypharmacy Patients With Obesity
Authors: Alberts Mark , He Jinghua , Kharat Akshay , Pericone Christopher D. , Ashton Veronica 
Published: January 2025

Background
The economic burden of nonvalvular atrial fibrillation (NVAF) is substantial. Many patients with NVAF are obese and manage other health conditions requiring multiple medications. This real‐world study compared health care resource use (HRU) and costs for rivaroxaban and warfarin in patients with NVAF who had polypharmacy and obesity.

Methods and Results
We used health care claims databases (Merative MarketScan commercial and Medicare supplemental claims) to identify patients initiating the direct oral anticoagulant rivaroxaban or warfarin with ≥1 diagnostic claim for atrial fibrillation, presence of polypharmacy (based on 3 categories for the number of concurrent medications: 1–4, 5–9, ≥10), and obesity. Cohorts were balanced for demographic and baseline characteristics using propensity score matching. All‐cause and NVAF‐related HRU rates and costs were compared between treatments using rate ratios and adjusted mean differences per patient per year. Eligible patients totaled 95 875, with 19 990 patients in each treatment cohort following propensity score matching. All‐cause HRU rates were significantly lower with rivaroxaban versus warfarin, and hospital stays were reduced by 3.1 days with rivaroxaban. Mean (95% CI) all‐cause total medical and total health care costs per patient per year were significantly reduced with rivaroxaban versus warfarin (−$4499 [−$5660 to −$3305] and –$1627 [−$2790 to −$438], respectively). NVAF‐related HRU was reduced with rivaroxaban versus warfarin, but total NVAF‐related medical costs were not significantly different between treatment groups ($144 [−$756 to $1079] per patient per year). Subgroup and sensitivity analysis results were generally consistent with the main analysis.

Conclusions
Among patients with NVAF, polypharmacy, and obesity, rivaroxaban was associated with a reduction in HRU and all‐cause costs compared with warfarin.